Array 1 45-377 		**** Predicted by CRISPRDetect 2.4 *** 
>NZ_CTAN01000055.1 Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 strain V40 isolate V40, whole genome shotgun sequence		Array_Orientation: Forward

  Position	Repeat	   %id	Spacer	Repeat_Sequence              	Spacer_Sequence                 	Insertion/Deletion
==========	======	======	======	=============================	================================	==================
        45	    29	 100.0	    32	.............................	CCAGCTTACGCTATTTACGACGTTATTGAGCA	
       106	    29	  93.1	    32	.................A........T..	AAACGAAAGAGGCTATGCGGTTGTTTATCGGT	
       167	    29	 100.0	    32	.............................	CAGGTTATGCGCAAAAATTAATTCATATTATA	
       228	    29	  96.6	    32	.................A...........	GACGAGTTCTGGAAATGGTTAGCTGATAAAGA	
       289	    29	 100.0	    32	.............................	CGTTCATCGGCAGCGTCACGCAATATGAAGAT	
       350	    28	  82.8	     0	...............A.AA....-.G...	|                               	
==========	======	======	======	=============================	================================	==================
         6	    29	  95.4	    32	GTGTTCCCCGCGCCAGCGGGGATAAACCG	                                	       

# Left flank :   GGGGATAAACCGTTGACGGTGACGTCAGTGCCGAAGGCGAAATAG
# Right flank :  GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG

# Questionable array : NO	 Score: 6.03
# 	Score Detail : 1:0, 2:3, 3:0, 4:0.77, 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 [2-6] Score: 0.41/0.41
# 	AT richness analysis in flanks prediction: R [33.3-63.3]%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 161741-161590 		**** Predicted by CRISPRDetect 2.4 *** 
>NZ_CTAN01000009.1 Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 strain V40 isolate V40, whole genome shotgun sequence		Array_Orientation: Reverse

  Position	Repeat	   %id	Spacer	Repeat_Sequence              	Spacer_Sequence                 	Insertion/Deletion
==========	======	======	======	=============================	================================	==================
    161740	    29	  96.6	    32	.....T.......................	GGTTAACCAGGGGTTTTTCCCCACTATTTCGC	
    161679	    29	 100.0	    32	.............................	AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA	
    161618	    29	  89.7	     0	A..........................AC	|                               	
==========	======	======	======	=============================	================================	==================
         3	    29	  95.4	    32	GTGTTCCCCGCGCCAGCGGGGATAAACCG	                                	       

# Left flank :   GGGGATAAACCGTGACGAGGTGCGAGCGATGGTATCAAGGCCT
# Right flank :  GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG

# Questionable array : NO	 Score: 3.94
# 	Score Detail : 1:0, 2:3, 3:0, 4:0.77, 5:-1.5, 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:     R [4,5] Score: 0.37/0.37
# 	Reference repeat match prediction:         R [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5
# 	Secondary Structural analysis prediction:  R [-8.90,-10.50] Score: 0.37/0.37
# 	Array degeneracy analysis prediction:      F [0-1] Score: 0.41/0.41
# 	AT richness analysis in flanks prediction: F [50.0-31.7]%AT Score: 0.27/0.27
# 	Longer leader analysis prediction:         NA 
# 	----------------------------------------------------------------------------
# 	Final direction:         R [0.68,5.24   Confidence: HIGH] 

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