Array 1 34-490 		**** Predicted by CRISPRDetect 2.4 *** 
>NZ_CTNV01000012.1 Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 strain H28 isolate H28, whole genome shotgun sequence		Array_Orientation: Forward

  Position	Repeat	   %id	Spacer	Repeat_Sequence              	Spacer_Sequence                 	Insertion/Deletion
==========	======	======	======	=============================	================================	==================
        34	    29	  96.6	    32	.............T...............	ATGCCGGAACGCTGATGGCGTTTGACATGAGC	
        95	    29	 100.0	    32	.............................	TCTGGTTATAACATCGCAGCAAAATCAAAAGA	
       156	    29	 100.0	    32	.............................	GAAACCCATTAATTAACTAAGCAGTAATAAAC	
       217	    29	 100.0	    32	.............................	TGACGAGGTGCGAGCGATGGTATCAAGGCCTA	
       278	    29	  96.6	    32	.....T.......................	GGTTAACCAGGGGTTTTTCCCCACTATTTCGC	
       339	    29	 100.0	    32	.............................	AATTATTTCTGTGGCTGGGGTTTCGATTCGAT	
       400	    29	 100.0	    32	.............................	AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA	
       461	    29	  96.6	     0	A............................	|                               	A [487]
==========	======	======	======	=============================	================================	==================
         8	    29	  98.7	    32	GTGTTCCCCGCGCCAGCGGGGATAAACCG	                                	       

# Left flank :   GCGGAGGATGGAATATTTCCGAGGCTGGCGATTG
# Right flank :  GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG

# Questionable array : NO	 Score: 6.20
# 	Score Detail : 1:0, 2:3, 3:0, 4:0.94, 5:0, 6:0.25, 7:0.01, 8:1, 9:1,
# 	Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats),
# Primary repeat :     GTGTTCCCCGCGCCAGCGGGGATAAACCG
# Alternate repeat :   NA

# Directional analysis summary from each method:
# 	Motif ATTGAAA(N) match prediction:         NA Score: 0/4.5
# 	A,T distribution in repeat prediction:     F [5,4] Score: 0.37/0.37
# 	Reference repeat match prediction:         F [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5
# 	Secondary Structural analysis prediction:  F [-13.50,-12.00] Score: 0.37/0.37
# 	Array degeneracy analysis prediction:      F [1-3] Score: 0.41/0.41
# 	AT richness analysis in flanks prediction: R [25.0-48.3]%AT Score: 0.27/0.27
# 	Longer leader analysis prediction:         NA 
# 	----------------------------------------------------------------------------
# 	Final direction:         F [5.65,0.27   Confidence: HIGH] 

# Array family : I-E [Matched known repeat from this family],   
//


Array 1 45-194 		**** Predicted by CRISPRDetect 2.4 *** 
>NZ_CTNV01000044.1 Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 strain H28 isolate H28, whole genome shotgun sequence		Array_Orientation: Forward

  Position	Repeat	   %id	Spacer	Repeat_Sequence              	Spacer_Sequence                 	Insertion/Deletion
==========	======	======	======	=============================	================================	==================
        45	    29	  93.1	    32	.................A........T..	AAACGAAAGAGGCTATGCGGTTGTTTATCGGT	
       106	    29	 100.0	    32	.............................	CGTTCATCGGCAGCGTCACGCAATATGAAGAT	
       167	    28	  82.8	     0	...............A.AA.....G-...	|                               	
==========	======	======	======	=============================	================================	==================
         3	    29	  92.0	    33	GTGTTCCCCGCGCCAGCGGGGATAAACCG	                                	       

# Left flank :   GGGGATAAACCGCCAGCTTACGCTATTTACGACGTTATTGAGCAG
# Right flank :  GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG

# Questionable array : NO	 Score: 5.27
# 	Score Detail : 1:0, 2:3, 3:0, 4:0.60, 5:0, 6:0.25, 7:0.02, 8:0.4, 9:1,
# 	Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats),
# Primary repeat :     GTGTTCCCCGCGCCAGCGGGGATAAACCG
# Alternate repeat :   NA

# Directional analysis summary from each method:
# 	Motif ATTGAAA(N) match prediction:         NA Score: 0/4.5
# 	A,T distribution in repeat prediction:     NA [4,4] Score: 0.37/0.37
# 	Reference repeat match prediction:         F [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 96% identity] Score: 4.5/4.5
# 	Secondary Structural analysis prediction:  R [-1.60,-4.10] Score: 0.37/0.37
# 	Array degeneracy analysis prediction:      F [0-3] Score: 0.41/0.41
# 	AT richness analysis in flanks prediction: R [38.3-61.7]%AT Score: 0.27/0.27
# 	Longer leader analysis prediction:         NA 
# 	----------------------------------------------------------------------------
# 	Final direction:         F [4.91,0.64   Confidence: HIGH] 

# Array family : I-E [Matched known repeat from this family],   
//