Array 1 9833-9980 		**** Predicted by CRISPRDetect 2.4 *** 
>NZ_WPGM01000043.1 Shigella flexneri strain 2008BJ19 NODE_43_length_31947_cov_56.5221_ID_53000, whole genome shotgun sequence		Array_Orientation: Forward

  Position	Repeat	   %id	Spacer	Repeat_Sequence             	Spacer_Sequence                 	Insertion/Deletion
==========	======	======	======	============================	================================	==================
      9833	    28	 100.0	    32	............................	TCGACGGGGTGCGGTAAAACCTTTGCGAACGC	
      9893	    28	 100.0	    32	............................	TTCACAGGTAACATACTCCACCCGCCCACCAT	
      9953	    28	  78.6	     0	................A...A.A.A.TG	|                               	
==========	======	======	======	============================	================================	==================
         3	    28	  92.9	    32	GTTCACTGCCGTACAGGCAGCTTAGAAA	                                	       

# Left flank :   TAAATTCATCGTCGAGTTGCAGGTTCAGCTGGATCAGAAAGGTGTTTCTCTGGAAGTGAGCCAGGAAGCGCGTAACTGGCTGGCCGAGAAAGGTTACGACCGGGCAATGGGCGCACGTCCGATGGCGCGTGTCATCCAGGACAACCTGAAAAAACCGCTCGCCAACGAACTGCTGTTTGGTTCGCTGGTGGACGGCGGTCAGGTGACGGTTGCGCTGGATAAAGAGAAAAATGAGCTGACTTACGGATTCCAGAGTGCACAAAAGCACAAGGCGGAAGCAGCGCATTAATCTGATTGTCAGGTAGGTTGGTGAAGTCCGTAATCTCGTCAGGGGTTACGGACTTTTTATTTATGGGGTGGAACGGTGAAAACCCTATTTTTGGAGGTGAAGGTAAGTTGTTGATAATTAGTGCTGCTGGAAGGTAAGGATAAAAAAGGGTGCTGCAGGAGAATGGGATGGTTTTGCTTTATTAACAACGGGCTAAACGTGTAGTATTTGA
# Right flank :  GCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCATGGGTGGCAACGGGGCGCTACTATAGGGAGTTGGAGTAAAACGGTCAAGAAGAATTTTAATGATAATTATTGTTTGCTCATACTGTAAACAACTTGTGCAGTATATCTACATCGAGACAAGTTATGGACTTATACTTCCAAAGTACTTCATACATATCACAAAATAAAAAGGCCGGTTAAACCGACCTTTTACTCGTTCTTTCTCTTCGCCCATCAGGCGGTAAAACAATCAGCGACTACGGAAGACAATGCGGCCTTTGCTCAGGTCGTACGGGGTCAGTTCAACAGTCACTTTGTCGCCCGTCAGGATGCGGATGTAGTTTTTGCGCATTTTACCGGAGATG

# Questionable array : NO	 Score: 5.01
# 	Score Detail : 1:0, 2:3, 3:0, 4:0.65, 5:0, 6:0.25, 7:0.02, 8:0.4, 9:0.69,
# 	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 :     GTTCACTGCCGTACAGGCAGCTTAGAAA
# 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 [Repeat is AT rich:51.72%AT]
# 	Reference repeat match prediction:         F [matched GTTCACTGCCGTACAGGCAGCTTAGAAA with 100% identity] Score: 4.5/4.5
# 	Secondary Structural analysis prediction:  F [-8.00,-7.70] Score: 0.37/0.37
# 	Array degeneracy analysis prediction:      F [0-7] Score: 0.41/0.41
# 	AT richness analysis in flanks prediction: NA [58.3-53.3]%AT Score: 0/0.27
# 	Longer leader analysis prediction:         NA 
# 	----------------------------------------------------------------------------
# 	Final direction:         F [5.28,0   Confidence: HIGH] 

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


Array 1 459-2 		**** Predicted by CRISPRDetect 2.4 *** 
>NZ_WPGM01000668.1 Shigella flexneri strain 2008BJ19 NODE_674_length_507_cov_0.818421_ID_54262, whole genome shotgun sequence		Array_Orientation: Reverse

  Position	Repeat	   %id	Spacer	Repeat_Sequence              	Spacer_Sequence                  	Insertion/Deletion
==========	======	======	======	=============================	=================================	==================
       458	    29	  96.6	    32	...............T.............	AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 	
       397	    29	 100.0	    32	.............................	CAACCAGGCTGGATCGTAACTCCTATCCCCTC 	
       336	    29	 100.0	    32	.............................	AAAATGCAGGTGGGGTAACGAATGCTAGATTG 	
       275	    29	 100.0	    32	.............................	CCATTATTCAACCCTCCAGGCTCGCGCCGGCT 	
       214	    29	 100.0	    33	.............................	CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC	
       152	    29	 100.0	    32	.............................	CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 	
        91	    29	 100.0	    32	.............................	CGTCACTACCGAGACCGAGACCGAGACCGAGA 	
        30	    29	 100.0	     0	.............................	|                                	
==========	======	======	======	=============================	=================================	==================
         8	    29	  99.6	    32	GTGTTCCCCGCGCCAGCGGGGATAAACCG	                                 	       

# Left flank :   CCAGCGGGGATAAACCGTTAGCAACGACAGTAAATAATTTTTCGTGCT
# Right flank :  GC

# Questionable array : NO	 Score: 6.24
# 	Score Detail : 1:0, 2:3, 3:0, 4:0.98, 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:     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 [-12.00,-13.50] Score: 0.37/0.37
# 	Array degeneracy analysis prediction:      F [0-3] Score: 0.41/0.41
# 	AT richness analysis in flanks prediction: R [0.0-45.0]%AT Score: 0.27/0.27
# 	Longer leader analysis prediction:         NA 
# 	----------------------------------------------------------------------------
# 	Final direction:         R [0.41,5.51   Confidence: HIGH] 

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