Array 1 966942-967927 		**** Predicted by CRISPRDetect 2.4 *** 
>NZ_LT571437.1 Salmonella enterica subsp. enterica serovar Java strain NCTC5706 chromosome 1, complete sequence		Array_Orientation: Forward

  Position	Repeat	   %id	Spacer	Repeat_Sequence              	Spacer_Sequence                 	Insertion/Deletion
==========	======	======	======	=============================	================================	==================
    966942	    29	 100.0	    32	.............................	GGGCGTGCTGGTCAAAGGTGACGGCTTTGTCC	
    967003	    29	 100.0	    32	.............................	AATTTCCTTTTTAGAATCCGATAAGTTGCCTA	
    967064	    29	 100.0	    32	.............................	CCTGGCGGCACACTCTACCGCCCGTGGTGACA	
    967125	    29	 100.0	    32	.............................	GCATCGCCTGGCTGAGTCCGTCGCTAACTGCG	
    967186	    28	  96.6	    32	..........-..................	ACATCTGGGAGGCGTGGCTAAAACTTACAGCT	
    967246	    29	 100.0	    32	.............................	GGCGCGCGTGTTGTTGGTGATTCCGCATATCT	
    967307	    29	 100.0	    32	.............................	AATAAGGCGCGGTGCCACCCTCGGCTTTAATT	
    967368	    29	  65.5	    13	..............GA..C.TTCC.G.GC	ACGTTACTCGATC                   	Deletion [967410]
    967410	    29	 100.0	    32	.............................	GCACTATTTCGAATGTCTCGACGCCAGATTTA	
    967471	    29	 100.0	    32	.............................	TAAACACCTCTTCTGGATATCCGTTACCAAAC	
    967532	    29	 100.0	    32	.............................	GAGCTATCTCGTCGGGTCGTTGCAAATATTGT	
    967593	    29	 100.0	    32	.............................	AGTATTGCAACTACGGCTGACGCGCTGATCGA	
    967654	    29	 100.0	    32	.............................	AACGAATTGAGACTATTAGAGATTATTCGCCT	
    967715	    29	 100.0	    32	.............................	GCTAAAACGGCGCTTGAGAACAGTATCAATAT	
    967776	    29	  96.6	    32	..........T..................	CTTCATCTCGCAGTACGTAAACGCCTGCATCA	
    967837	    29	 100.0	    32	.............................	AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA	
    967898	    29	  93.1	     0	A...........T................	|                               	A [967924]
==========	======	======	======	=============================	================================	==================
        17	    29	  97.2	    31	GTGTTCCCCGCGCCAGCGGGGATAAACCG	                                	       

# Left flank :   GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGTTGCGGAAATGCCGTCATGGCTTGGGCGACCAACACGGAGTCGGGATTTGAGTTTCAGACATGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT
# Right flank :  GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG

# Questionable array : NO	 Score: 6.02
# 	Score Detail : 1:0, 2:3, 3:0, 4:0.86, 5:0, 6:0.25, 7:-0.09, 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 [1-4] Score: 0.41/0.41
# 	AT richness analysis in flanks prediction: F [71.7-48.3]%AT Score: 0.27/0.27
# 	Longer leader analysis prediction:         NA 
# 	----------------------------------------------------------------------------
# 	Final direction:         F [5.92,0   Confidence: HIGH] 

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