Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000542.1 Hibiscus syriacus cultivar Beakdansim tig00001052_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 715625
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 2 of 3
Found at i:345005 original size:20 final size:19
Alignment explanation
Indices: 344980--345028 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
344970 AACCCCTTTT
*
344980 AAAATACATGATTTTTGATG
1 AAAATACATGA-TTTTAATG
*
345000 AAAATAAATGATTTTAATG
1 AAAATACATGATTTTAATG
345019 AAAATACATG
1 AAAATACATG
345029 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.35
Consensus pattern (19 bp):
AAAATACATGATTTTAATG
Found at i:345965 original size:30 final size:31
Alignment explanation
Indices: 345926--345985 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
345916 ACATGCTGCC
**
345926 ATGATATCTAAATGATATGCAAACAAAATAA
1 ATGATATCTAAAACATATGCAAACAAAATAA
* *
345957 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACAAAATA
345986 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACAAAATAA
Found at i:351177 original size:623 final size:623
Alignment explanation
Indices: 349991--351236 Score: 2483
Period size: 623 Copynumber: 2.0 Consensus size: 623
349981 GATTCATGAA
349991 ACATCTTTGGAGAATCAAATGAGCTGGAAAATGCATCCCACTTGTCCTTATTATATTTCCACTTA
1 ACATCTTTGGAGAATCAAATGAGCTGGAAAATGCATCCCACTTGTCCTTATTATATTTCCACTTA
350056 CTTGGGCATAGGATAAAGACAAACCACGTGCACTTGCTGATAGAAAACATTCACACAATTGCATT
66 CTTGGGCATAGGATAAAGACAAACCACGTGCACTTGCTGATAGAAAACATTCACACAATTGCATT
350121 TAGAGACATCCCATGTGCGTGAGGGAATAAGGCACTCAAACAGCCCATGTGCTTGGAATATTACT
131 TAGAGACATCCCATGTGCGTGAGGGAATAAGGCACTCAAACAGCCCATGTGCTTGGAATATTACT
350186 TGTCTCCACTACACCACCATTGAAGGAAATTCGGCCAAGGCATTTCACTTCTCCATTTGACCGAA
196 TGTCTCCACTACACCACCATTGAAGGAAATTCGGCCAAGGCATTTCACTTCTCCATTTGACCGAA
350251 TTTAAGCATTATAATTGTGCTTAAAACACTTTTGAATTATATGTTAAAGGTTGCCACATCATCAA
261 TTTAAGCATTATAATTGTGCTTAAAACACTTTTGAATTATATGTTAAAGGTTGCCACATCATCAA
350316 GCACGACTAGGCCATGCATATTATCATTTTCAGCATTGTATTCCAAGTCCTATAAAATGGACTTC
326 GCACGACTAGGCCATGCATATTATCATTTTCAGCATTGTATTCCAAGTCCTATAAAATGGACTTC
350381 ATATTGCATTGTAATGACAGACTTTGTTTTAATGAAATTGTGAGAGTTTTCTCTAATTGAGTCCT
391 ATATTGCATTGTAATGACAGACTTTGTTTTAATGAAATTGTGAGAGTTTTCTCTAATTGAGTCCT
350446 TCGTGACTTTTATCGACTTATCAAGTAACTCGTTACTTGTGGCGTCATTACTATCACCTTGATAC
456 TCGTGACTTTTATCGACTTATCAAGTAACTCGTTACTTGTGGCGTCATTACTATCACCTTGATAC
350511 TTATGGTTCCTAGTTCTTATAACTAGCGGGTCAAAGTCCGATTTACCATCCCTTATCGAAGCAAT
521 TTATGGTTCCTAGTTCTTATAACTAGCGGGTCAAAGTCCGATTTACCATCCCTTATCGAAGCAAT
350576 ATAAATTTGGGTCGTTGTTCTCTAACATCGGTTCTTCT
586 ATAAATTTGGGTCGTTGTTCTCTAACATCGGTTCTTCT
350614 ACATCTTTGGAGAATCAAATGAGCTGGAAAATGCATCCCACTTGTCCTTATTATATTTCCACTTA
1 ACATCTTTGGAGAATCAAATGAGCTGGAAAATGCATCCCACTTGTCCTTATTATATTTCCACTTA
350679 CTTGGGCATAGGATAAAGACAAACCACGTGCACTTGCTGATAGAAAACATTCACACAATTGCATT
66 CTTGGGCATAGGATAAAGACAAACCACGTGCACTTGCTGATAGAAAACATTCACACAATTGCATT
350744 TAGAGACATCCCATGTGCGTGAGGGAATAAGGCACTCAAACAGCCCATGTGCTTGGAATATTACT
131 TAGAGACATCCCATGTGCGTGAGGGAATAAGGCACTCAAACAGCCCATGTGCTTGGAATATTACT
350809 TGTCTCCACTACACCACCATTGAAGGAAATTCGGCCAAGGCATTTCACTTCTCCATTTGACCGAA
196 TGTCTCCACTACACCACCATTGAAGGAAATTCGGCCAAGGCATTTCACTTCTCCATTTGACCGAA
350874 TTTAAGCATTATAATTGTGCTTAAAACACTTTTGAATTATATGTTAAAGGTTGCCACATCATCAA
261 TTTAAGCATTATAATTGTGCTTAAAACACTTTTGAATTATATGTTAAAGGTTGCCACATCATCAA
*
350939 GCACGACTAGGCCATGCATATTATCATTTTCAGCTTTGTATTCCAAGTCCTATAAAATGGACTTC
326 GCACGACTAGGCCATGCATATTATCATTTTCAGCATTGTATTCCAAGTCCTATAAAATGGACTTC
351004 ATATTGCATTGTAATGACAGACTTTGTTTTAATGAAATTGTGAGAGTTTTCTCTAATTGAGTCCT
391 ATATTGCATTGTAATGACAGACTTTGTTTTAATGAAATTGTGAGAGTTTTCTCTAATTGAGTCCT
351069 TCGTGACTTTTATCGACTTATCAAGTAACTCGTTACTTGTGGCGTCATTACTATCACCTTGATAC
456 TCGTGACTTTTATCGACTTATCAAGTAACTCGTTACTTGTGGCGTCATTACTATCACCTTGATAC
351134 TTATGGTTCCTAGTTCTTATAACTAGCGGGTCAAAGTCCGATTTACCATCCCTTATCGAAGCAAT
521 TTATGGTTCCTAGTTCTTATAACTAGCGGGTCAAAGTCCGATTTACCATCCCTTATCGAAGCAAT
351199 ATAAATTTGGGTCGTTGTTCTCTAACATCGGTTCTTCT
586 ATAAATTTGGGTCGTTGTTCTCTAACATCGGTTCTTCT
351237 TTGAGTCTTC
Statistics
Matches: 622, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
623 622 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (623 bp):
ACATCTTTGGAGAATCAAATGAGCTGGAAAATGCATCCCACTTGTCCTTATTATATTTCCACTTA
CTTGGGCATAGGATAAAGACAAACCACGTGCACTTGCTGATAGAAAACATTCACACAATTGCATT
TAGAGACATCCCATGTGCGTGAGGGAATAAGGCACTCAAACAGCCCATGTGCTTGGAATATTACT
TGTCTCCACTACACCACCATTGAAGGAAATTCGGCCAAGGCATTTCACTTCTCCATTTGACCGAA
TTTAAGCATTATAATTGTGCTTAAAACACTTTTGAATTATATGTTAAAGGTTGCCACATCATCAA
GCACGACTAGGCCATGCATATTATCATTTTCAGCATTGTATTCCAAGTCCTATAAAATGGACTTC
ATATTGCATTGTAATGACAGACTTTGTTTTAATGAAATTGTGAGAGTTTTCTCTAATTGAGTCCT
TCGTGACTTTTATCGACTTATCAAGTAACTCGTTACTTGTGGCGTCATTACTATCACCTTGATAC
TTATGGTTCCTAGTTCTTATAACTAGCGGGTCAAAGTCCGATTTACCATCCCTTATCGAAGCAAT
ATAAATTTGGGTCGTTGTTCTCTAACATCGGTTCTTCT
Found at i:351575 original size:12 final size:13
Alignment explanation
Indices: 351552--351576 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
351542 AACGTCAACG
351552 AAAATACAAAAAA
1 AAAATACAAAAAA
351565 AAAATACAAAAA
1 AAAATACAAAAA
351577 GAAGTTCAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAATACAAAAAA
Found at i:355480 original size:623 final size:623
Alignment explanation
Indices: 354294--355539 Score: 2474
Period size: 623 Copynumber: 2.0 Consensus size: 623
354284 GATTCATGAA
354294 ACATCTTTGGAGAATCAAATGAGCTGGAAAATGCATCCCACTTGTCCTTATTATATTTCCACTTA
1 ACATCTTTGGAGAATCAAATGAGCTGGAAAATGCATCCCACTTGTCCTTATTATATTTCCACTTA
354359 CTTGGGCATAGGATAAAGACAAACCACGTGCACTTGCTGATAGAAAACATTCACACAATTGAATT
66 CTTGGGCATAGGATAAAGACAAACCACGTGCACTTGCTGATAGAAAACATTCACACAATTGAATT
354424 TAGAGACATCCCATGTGCGTGAGGGAATAAGGCACTCAAACAGCCCATGTGCTTGGAATATTACT
131 TAGAGACATCCCATGTGCGTGAGGGAATAAGGCACTCAAACAGCCCATGTGCTTGGAATATTACT
354489 TGTCTCCACTACACCACCATTGAAGGAAATTCGGCCAAGGCATTTCACTTCTCCATTTGACCGAA
196 TGTCTCCACTACACCACCATTGAAGGAAATTCGGCCAAGGCATTTCACTTCTCCATTTGACCGAA
354554 TTTAAGCATTATAATTGTGCTTAAAACACTTTTGAATTATATGTTAAAGGTTGCCACATCATCAA
261 TTTAAGCATTATAATTGTGCTTAAAACACTTTTGAATTATATGTTAAAGGTTGCCACATCATCAA
354619 GCACGACTAGGCCATGCATATTATCATTTTCAGCATTGTATTCCAAGTCCTATAAAATGGACTTC
326 GCACGACTAGGCCATGCATATTATCATTTTCAGCATTGTATTCCAAGTCCTATAAAATGGACTTC
354684 ATATTGCATTGTAATGACAGACTTTGTTTTAATGAAATTGTGAGAGTTTTCTCTAATTGAGTCCT
391 ATATTGCATTGTAATGACAGACTTTGTTTTAATGAAATTGTGAGAGTTTTCTCTAATTGAGTCCT
354749 TCGTGACTTTTATCGACTTATCAAGTAACTCGTTACTTGTGGCGTCATTACTATCACCTTGATAC
456 TCGTGACTTTTATCGACTTATCAAGTAACTCGTTACTTGTGGCGTCATTACTATCACCTTGATAC
354814 TTATGGTTCCTAGTTCTTATAACTAGCGGGTCAAAGTCCGATTTACCATCCCTTATCGAAGCAAT
521 TTATGGTTCCTAGTTCTTATAACTAGCGGGTCAAAGTCCGATTTACCATCCCTTATCGAAGCAAT
354879 ATAAATTTGGGTCGTTGTTCTCTAACATCGGTTCTTCT
586 ATAAATTTGGGTCGTTGTTCTCTAACATCGGTTCTTCT
354917 ACATCTTTGGAGAATCAAATGAGCTGGAAAATGCATCCCACTTGTCCTTATTATATTTCCACTTA
1 ACATCTTTGGAGAATCAAATGAGCTGGAAAATGCATCCCACTTGTCCTTATTATATTTCCACTTA
*
354982 CTTGGGCATAGGATAAAGACAAACCACGTGCACTTGCTGATAGAAAACATTCACACAATTGCATT
66 CTTGGGCATAGGATAAAGACAAACCACGTGCACTTGCTGATAGAAAACATTCACACAATTGAATT
355047 TAGAGACATCCCATGTGCGTGAGGGAATAAGGCACTCAAACAGCCCATGTGCTTGGAATATTACT
131 TAGAGACATCCCATGTGCGTGAGGGAATAAGGCACTCAAACAGCCCATGTGCTTGGAATATTACT
355112 TGTCTCCACTACACCACCATTGAAGGAAATTCGGCCAAGGCATTTCACTTCTCCATTTGACCGAA
196 TGTCTCCACTACACCACCATTGAAGGAAATTCGGCCAAGGCATTTCACTTCTCCATTTGACCGAA
355177 TTTAAGCATTATAATTGTGCTTAAAACACTTTTGAATTATATGTTAAAGGTTGCCACATCATCAA
261 TTTAAGCATTATAATTGTGCTTAAAACACTTTTGAATTATATGTTAAAGGTTGCCACATCATCAA
*
355242 GCACGACTAGGCCATGCATATTATCATTTTCAGCTTTGTATTCCAAGTCCTATAAAATGGACTTC
326 GCACGACTAGGCCATGCATATTATCATTTTCAGCATTGTATTCCAAGTCCTATAAAATGGACTTC
355307 ATATTGCATTGTAATGACAGACTTTGTTTTAATGAAATTGTGAGAGTTTTCTCTAATTGAGTCCT
391 ATATTGCATTGTAATGACAGACTTTGTTTTAATGAAATTGTGAGAGTTTTCTCTAATTGAGTCCT
355372 TCGTGACTTTTATCGACTTATCAAGTAACTCGTTACTTGTGGCGTCATTACTATCACCTTGATAC
456 TCGTGACTTTTATCGACTTATCAAGTAACTCGTTACTTGTGGCGTCATTACTATCACCTTGATAC
355437 TTATGGTTCCTAGTTCTTATAACTAGCGGGTCAAAGTCCGATTTACCATCCCTTATCGAAGCAAT
521 TTATGGTTCCTAGTTCTTATAACTAGCGGGTCAAAGTCCGATTTACCATCCCTTATCGAAGCAAT
355502 ATAAATTTGGGTCGTTGTTCTCTAACATCGGTTCTTCT
586 ATAAATTTGGGTCGTTGTTCTCTAACATCGGTTCTTCT
355540 TTGAGTCTTC
Statistics
Matches: 621, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
623 621 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (623 bp):
ACATCTTTGGAGAATCAAATGAGCTGGAAAATGCATCCCACTTGTCCTTATTATATTTCCACTTA
CTTGGGCATAGGATAAAGACAAACCACGTGCACTTGCTGATAGAAAACATTCACACAATTGAATT
TAGAGACATCCCATGTGCGTGAGGGAATAAGGCACTCAAACAGCCCATGTGCTTGGAATATTACT
TGTCTCCACTACACCACCATTGAAGGAAATTCGGCCAAGGCATTTCACTTCTCCATTTGACCGAA
TTTAAGCATTATAATTGTGCTTAAAACACTTTTGAATTATATGTTAAAGGTTGCCACATCATCAA
GCACGACTAGGCCATGCATATTATCATTTTCAGCATTGTATTCCAAGTCCTATAAAATGGACTTC
ATATTGCATTGTAATGACAGACTTTGTTTTAATGAAATTGTGAGAGTTTTCTCTAATTGAGTCCT
TCGTGACTTTTATCGACTTATCAAGTAACTCGTTACTTGTGGCGTCATTACTATCACCTTGATAC
TTATGGTTCCTAGTTCTTATAACTAGCGGGTCAAAGTCCGATTTACCATCCCTTATCGAAGCAAT
ATAAATTTGGGTCGTTGTTCTCTAACATCGGTTCTTCT
Found at i:356091 original size:19 final size:18
Alignment explanation
Indices: 356047--356098 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
356037 TTGAAACCCC
356047 TTTGAAAATACATGATTT
1 TTTGAAAATACATGATTT
*
356065 TTGATGAAAATGCATGATTT
1 TT--TGAAAATACATGATTT
*
356085 TATTGAAGATACAT
1 T-TTGAAAATACAT
356099 TCTCTTGGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 2 0.07
19 9 0.32
20 16 0.57
21 1 0.04
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (18 bp):
TTTGAAAATACATGATTT
Found at i:356900 original size:30 final size:31
Alignment explanation
Indices: 356861--356920 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
356851 ACATGCTGCC
**
356861 ATGATATCTAAATGATATGCAAACAAAATAA
1 ATGATATCTAAAACATATGCAAACAAAATAA
* *
356892 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACAAAATA
356921 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACAAAATAA
Found at i:364750 original size:24 final size:23
Alignment explanation
Indices: 364723--364770 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
364713 GTGCTACAAC
364723 AAAAAAAAAGA-AACAAGAAAGAAG
1 AAAAAAAAAGAGAA-AAGAAA-AAG
*
364747 AAAACAAAAGAGAAAAGAAAAAG
1 AAAAAAAAAGAGAAAAGAAAAAG
364770 A
1 A
364771 CTCCTACATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 16 0.73
25 2 0.09
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAGAGAAAAGAAAAAG
Found at i:374792 original size:120 final size:119
Alignment explanation
Indices: 374580--374819 Score: 455
Period size: 120 Copynumber: 2.0 Consensus size: 119
374570 ATAAGTTATG
374580 TGAAACAGGTGCTCATGAAAAATATTACTAGCATATGGATATCTTTCAGGAAGGGAGGCTTTGTA
1 TGAAACAGGTGCTCATGAAAAATATTACTAGCATATGGATATCTTTCAGGAAGGGAGGCTTTGTA
374645 TCCTATAAGGTTCCATGAGAGAAGTATTAACCAAATAAGCACATG-AGGAGGAC
66 TCCTATAAGGTTCCATGAGAGAAGTATTAACCAAATAAGCACATGAAGGAGGAC
374698 TGAAACAGGTGCTCATGAAAAATATTACTAGCATATGGATATCTTTTCAAGGAAGGGAGGCTTTG
1 TGAAACAGGTGCTCATGAAAAATATTACTAGCATATGGATATC-TTTC-AGGAAGGGAGGCTTTG
374763 TATCCTATAAGGTTCCATGAGAGAAGTATTAACCAAATAAGCACATGAAGGAGGAC
64 TATCCTATAAGGTTCCATGAGAGAAGTATTAACCAAATAAGCACATGAAGGAGGAC
374819 T
1 T
374820 TATGGGACAC
Statistics
Matches: 119, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
118 43 0.36
119 4 0.03
120 63 0.53
121 9 0.08
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (119 bp):
TGAAACAGGTGCTCATGAAAAATATTACTAGCATATGGATATCTTTCAGGAAGGGAGGCTTTGTA
TCCTATAAGGTTCCATGAGAGAAGTATTAACCAAATAAGCACATGAAGGAGGAC
Found at i:381555 original size:275 final size:275
Alignment explanation
Indices: 381058--381615 Score: 999
Period size: 275 Copynumber: 2.0 Consensus size: 275
381048 AAAAGCATAT
*
381058 AAAGGTGGACTTATGGGACATTCTAAAGTTACTAAGACGTTGCACATTCTGAAGGAGCATCTATT
1 AAAGATGGACTTATGGGACATTCTAAAGTTACTAAGACGTTGCACATTCTGAAGGAGCATCTATT
*
381123 ATGGCCTAAGATGCGTAGGGACGTTGAAAGAATATGTGAACGTTGTGTAACATGTAAGAAAGTAA
66 ATGGCCTAAGATGCGTAGGGACGTTGAAAGAATATGTGAACGTTGTGTAACATGTAAGAAAGCAA
*
381188 AATGAAAGGTTCTACCACATGATATGTATTTGCCTTTACCTATTCCTAATTCTCCTTGGCTAGAT
131 AATGAAAGGTTCTACCACATGATATCTATTTGCCTTTACCTATTCCTAATTCTCCTTGGCTAGAT
*
381253 ATCTCGATGAATTTTGTGTTAGGATTGCCTAGAACTAGGACAGGCAGAGATATTATCTTTGTTGT
196 ATCTCGATGAATTTTGTGTTAGGATTGCCTAGAACTAGGACAGGCAGAGATAGTATCTTTGTTGT
*
381318 CGTTGATAGTTTTTC
261 CGTTGATAGGTTTTC
**
381333 AAAGATGGACTTATGGGACATTCTGGAGTTACTAAGACGTTGCACATTCTGAAGGAGCATCTATT
1 AAAGATGGACTTATGGGACATTCTAAAGTTACTAAGACGTTGCACATTCTGAAGGAGCATCTATT
* *
381398 CTTGCCTAAGATGCGTAGGGACGTTGAAAGAATATGTGAACGTTGTGTAACATGTAAGAAAGCAA
66 ATGGCCTAAGATGCGTAGGGACGTTGAAAGAATATGTGAACGTTGTGTAACATGTAAGAAAGCAA
*
381463 AATGAAAGGTTCTACCACATGATATCTATTTGCCTTTACCTATTCCTAATTCTCCTTGGCTGGAT
131 AATGAAAGGTTCTACCACATGATATCTATTTGCCTTTACCTATTCCTAATTCTCCTTGGCTAGAT
* *
381528 ATCTCGATGGATTTTGTGTTGGGATTGCCTAGAACTAGGACAGGCAGAGATAGTATCTTTGTTGT
196 ATCTCGATGAATTTTGTGTTAGGATTGCCTAGAACTAGGACAGGCAGAGATAGTATCTTTGTTGT
*
381593 TGTTGATAGGTTTTC
261 CGTTGATAGGTTTTC
381608 AAAGATGG
1 AAAGATGG
381616 CACATTTCAT
Statistics
Matches: 270, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
275 270 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (275 bp):
AAAGATGGACTTATGGGACATTCTAAAGTTACTAAGACGTTGCACATTCTGAAGGAGCATCTATT
ATGGCCTAAGATGCGTAGGGACGTTGAAAGAATATGTGAACGTTGTGTAACATGTAAGAAAGCAA
AATGAAAGGTTCTACCACATGATATCTATTTGCCTTTACCTATTCCTAATTCTCCTTGGCTAGAT
ATCTCGATGAATTTTGTGTTAGGATTGCCTAGAACTAGGACAGGCAGAGATAGTATCTTTGTTGT
CGTTGATAGGTTTTC
Found at i:386291 original size:11 final size:12
Alignment explanation
Indices: 386261--386307 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
386251 TTTGTACTGG
386261 AAACAAGATAAA
1 AAACAAGATAAA
* *
386273 AAATAAGAT-TA
1 AAACAAGATAAA
386284 AAACAAGATAAA
1 AAACAAGATAAA
*
386296 TAA-AAGATAAA
1 AAACAAGATAAA
386307 A
1 A
386308 GAATTGAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.15
Consensus pattern (12 bp):
AAACAAGATAAA
Found at i:386291 original size:23 final size:21
Alignment explanation
Indices: 386261--386307 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
386251 TTTGTACTGG
386261 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGA-TA
*
386284 AAACAAGATAAATAAAAGATA
1 AAACAAGATAAAAAAAAGATA
386305 AAA
1 AAA
386308 GAATTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.22
22 4 0.17
23 14 0.61
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.15
Consensus pattern (21 bp):
AAACAAGATAAAAAAAAGATA
Found at i:393420 original size:22 final size:22
Alignment explanation
Indices: 393395--393443 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
393385 AAATTTTGGC
*
393395 TTTTTTTGGCTCTTTTTTTGTTT
1 TTTTTTTGGC-CGTTTTTTGTTT
*
393418 TTTTTTTTGCCGTTTTTTGTTT
1 TTTTTTTGGCCGTTTTTTGTTT
393440 TTTT
1 TTTT
393444 GAAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.80
Consensus pattern (22 bp):
TTTTTTTGGCCGTTTTTTGTTT
Found at i:403511 original size:19 final size:20
Alignment explanation
Indices: 403487--403537 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
403477 CGGCCAAGAG
*
403487 CATGTATCTTCA-TTAAAAT
1 CATGTATTTTCATTTAAAAT
403506 CATGTATTTTCATTTAAAAT
1 CATGTATTTTCATTTAAAAT
403526 CATGTATTTTCA
1 CATGTATTTTCA
403538 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTTAAAAT
Found at i:404276 original size:34 final size:31
Alignment explanation
Indices: 404234--404305 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 31
404224 GTACAAAAAG
*
404234 AAAGAAAAGACA-AAAAGAAGAAGAAAATTCAGAA
1 AAAGAAAAGA-AGAAAAGAAAAAG-AAATTC--AA
404268 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
1 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
404299 AAAGAAA
1 AAAGAAA
404306 GCAAGCCAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 9 0.25
33 7 0.19
34 20 0.56
ACGTcount: A:0.74, C:0.04, G:0.17, T:0.06
Consensus pattern (31 bp):
AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
Found at i:407751 original size:19 final size:20
Alignment explanation
Indices: 407727--407777 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
407717 CGGCCAAGAG
*
407727 CATGTATCTTCA-TTAAAAT
1 CATGTATTTTCATTTAAAAT
407746 CATGTATTTTCATTTAAAAT
1 CATGTATTTTCATTTAAAAT
407766 CATGTATTTTCA
1 CATGTATTTTCA
407778 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTTAAAAT
Found at i:411990 original size:19 final size:20
Alignment explanation
Indices: 411966--412016 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
411956 CGGCCAAGAG
*
411966 CATGTATCTTCA-TTAAAAT
1 CATGTATTTTCATTTAAAAT
411985 CATGTATTTTCATTTAAAAT
1 CATGTATTTTCATTTAAAAT
412005 CATGTATTTTCA
1 CATGTATTTTCA
412017 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTTAAAAT
Found at i:412754 original size:34 final size:31
Alignment explanation
Indices: 412712--412783 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 31
412702 GTACAAAAAG
*
412712 AAAGAAAAGACA-AAAAGAAGAAGAAAATTCAGAA
1 AAAGAAAAGA-AGAAAAGAAAAAG-AAATTC--AA
412746 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
1 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
412777 AAAGAAA
1 AAAGAAA
412784 GCAAGCCAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 9 0.25
33 7 0.19
34 20 0.56
ACGTcount: A:0.74, C:0.04, G:0.17, T:0.06
Consensus pattern (31 bp):
AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
Found at i:416229 original size:19 final size:20
Alignment explanation
Indices: 416205--416255 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
416195 CGGCCAAGAG
*
416205 CATGTATCTTCA-TTAAAAT
1 CATGTATTTTCATTTAAAAT
416224 CATGTATTTTCATTTAAAAT
1 CATGTATTTTCATTTAAAAT
416244 CATGTATTTTCA
1 CATGTATTTTCA
416256 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTTAAAAT
Found at i:416994 original size:34 final size:31
Alignment explanation
Indices: 416952--417023 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 31
416942 GTACAAAAAG
*
416952 AAAGAAAAGACA-AAAAGAAGAAGAAAATTCAGAA
1 AAAGAAAAGA-AGAAAAGAAAAAG-AAATTC--AA
416986 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
1 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
417017 AAAGAAA
1 AAAGAAA
417024 GCAAGCCAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 9 0.25
33 7 0.19
34 20 0.56
ACGTcount: A:0.74, C:0.04, G:0.17, T:0.06
Consensus pattern (31 bp):
AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
Found at i:420463 original size:19 final size:20
Alignment explanation
Indices: 420439--420489 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
420429 CGGCCAAGAG
*
420439 CATGTATCTTCA-TTAAAAT
1 CATGTATTTTCATTTAAAAT
420458 CATGTATTTTCATTTAAAAT
1 CATGTATTTTCATTTAAAAT
420478 CATGTATTTTCA
1 CATGTATTTTCA
420490 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTTAAAAT
Found at i:424698 original size:19 final size:20
Alignment explanation
Indices: 424674--424724 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
424664 CAGCCAAGAG
*
424674 CATGTATCTTCA-TTAAAAT
1 CATGTATTTTCATTTAAAAT
424693 CATGTATTTTCATTTAAAAT
1 CATGTATTTTCATTTAAAAT
424713 CATGTATTTTCA
1 CATGTATTTTCA
424725 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTTAAAAT
Found at i:426015 original size:153 final size:153
Alignment explanation
Indices: 425737--426043 Score: 614
Period size: 153 Copynumber: 2.0 Consensus size: 153
425727 AAAGCCTAAG
425737 AGTTAACATGAATGCAAATAAACTAATGAAATGCATTATAAGTATGCTGCCTTGATGTATATATA
1 AGTTAACATGAATGCAAATAAACTAATGAAATGCATTATAAGTATGCTGCCTTGATGTATATATA
425802 ATAATCATGCATAATATGATAATAAAACTATCCTAACATTCTTAACATATTAAAAATAACAATGT
66 ATAATCATGCATAATATGATAATAAAACTATCCTAACATTCTTAACATATTAAAAATAACAATGT
425867 GTAATATGAATTCATACTAAGTT
131 GTAATATGAATTCATACTAAGTT
425890 AGTTAACATGAATGCAAATAAACTAATGAAATGCATTATAAGTATGCTGCCTTGATGTATATATA
1 AGTTAACATGAATGCAAATAAACTAATGAAATGCATTATAAGTATGCTGCCTTGATGTATATATA
425955 ATAATCATGCATAATATGATAATAAAACTATCCTAACATTCTTAACATATTAAAAATAACAATGT
66 ATAATCATGCATAATATGATAATAAAACTATCCTAACATTCTTAACATATTAAAAATAACAATGT
426020 GTAATATGAATTCATACTAAGTT
131 GTAATATGAATTCATACTAAGTT
426043 A
1 A
426044 TTTTAACTAA
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
153 154 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (153 bp):
AGTTAACATGAATGCAAATAAACTAATGAAATGCATTATAAGTATGCTGCCTTGATGTATATATA
ATAATCATGCATAATATGATAATAAAACTATCCTAACATTCTTAACATATTAAAAATAACAATGT
GTAATATGAATTCATACTAAGTT
Found at i:430849 original size:34 final size:31
Alignment explanation
Indices: 430807--430878 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 31
430797 GTACAAAAAG
*
430807 AAAGAAAAGACA-AAAAGAAGAAGAAAATTCAGAA
1 AAAGAAAAGA-AGAAAAGAAAAAG-AAATTC--AA
430841 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
1 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
430872 AAAGAAA
1 AAAGAAA
430879 GCAAGCCAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 9 0.25
33 7 0.19
34 20 0.56
ACGTcount: A:0.74, C:0.04, G:0.17, T:0.06
Consensus pattern (31 bp):
AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
Found at i:434321 original size:19 final size:20
Alignment explanation
Indices: 434297--434347 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
434287 CGGCCAAGAG
*
434297 CATGTATCTTCA-TTAAAAT
1 CATGTATTTTCATTTAAAAT
434316 CATGTATTTTCATTTAAAAT
1 CATGTATTTTCATTTAAAAT
434336 CATGTATTTTCA
1 CATGTATTTTCA
434348 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTTAAAAT
Found at i:435069 original size:19 final size:17
Alignment explanation
Indices: 435036--435120 Score: 59
Period size: 18 Copynumber: 4.9 Consensus size: 17
435026 AAATTAGAGT
435036 ACAAAAAGAAAGAAAAG
1 ACAAAAAGAAAGAAAAG
*
435053 ACAAAAAGAATAAGAAAAT
1 ACAAAAAG-A-AAGAAAAG
* *
435072 TC-AGAA-AAAGAAAAG
1 ACAAAAAGAAAGAAAAG
* *
435087 A-AGAAAAGAAAAAGAAAT
1 ACA-AAAAGAAAGA-AAAG
*
435105 TCAAAAAGAAAGAAAA
1 ACAAAAAGAAAGAAAA
435121 CCAAGGAAAG
Statistics
Matches: 51, Mismatches: 10, Indels: 14
0.68 0.13 0.19
Matches are distributed among these distances:
15 7 0.14
16 4 0.08
17 15 0.29
18 16 0.31
19 9 0.18
ACGTcount: A:0.74, C:0.05, G:0.15, T:0.06
Consensus pattern (17 bp):
ACAAAAAGAAAGAAAAG
Found at i:435086 original size:34 final size:31
Alignment explanation
Indices: 435044--435115 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 31
435034 GTACAAAAAG
*
435044 AAAGAAAAGACA-AAAAGAATAAGAAAATTCAGAA
1 AAAGAAAAGA-AGAAAAGAAAAAG-AAATTC--AA
435078 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
1 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
435109 AAAGAAA
1 AAAGAAA
435116 GAAAACCAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 9 0.25
33 7 0.19
34 20 0.56
ACGTcount: A:0.74, C:0.04, G:0.15, T:0.07
Consensus pattern (31 bp):
AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
Found at i:438470 original size:19 final size:20
Alignment explanation
Indices: 438446--438488 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
438436 CCAAAGACTC
438446 TTCA-TTAAAATCATGTATT
1 TTCATTTAAAATCATGTATT
438465 TTCATTTAAAATCATGTATT
1 TTCATTTAAAATCATGTATT
438485 TTCA
1 TTCA
438489 AAGGGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.49
Consensus pattern (20 bp):
TTCATTTAAAATCATGTATT
Found at i:439537 original size:10 final size:10
Alignment explanation
Indices: 439524--439557 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
439514 TTTTTTAAAA
*
439524 TTTTGGCTTT
1 TTTTGCCTTT
*
439534 TTTTGTCTTT
1 TTTTGCCTTT
439544 TTTTGCCTTT
1 TTTTGCCTTT
439554 TTTT
1 TTTT
439558 TTGTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.76
Consensus pattern (10 bp):
TTTTGCCTTT
Found at i:439547 original size:20 final size:20
Alignment explanation
Indices: 439524--439567 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
439514 TTTTTTAAAA
*
439524 TTTTGGCTTTTTTTGTCTTT
1 TTTTGCCTTTTTTTGTCTTT
* *
439544 TTTTGCCTTTTTTTTTGTTT
1 TTTTGCCTTTTTTTGTCTTT
439564 TTTT
1 TTTT
439568 TTGAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (20 bp):
TTTTGCCTTTTTTTGTCTTT
Found at i:439564 original size:10 final size:10
Alignment explanation
Indices: 439531--439570 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
439521 AAATTTTGGC
*
439531 TTTTTTTGTC
1 TTTTTTTGTT
439541 TTTTTTTGCCTT
1 TTTTTTTG--TT
439553 TTTTTTTGTT
1 TTTTTTTGTT
439563 TTTTTTTG
1 TTTTTTTG
439571 AAAAAAAAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 18 0.67
12 9 0.33
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.82
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:439915 original size:12 final size:12
Alignment explanation
Indices: 439898--439944 Score: 62
Period size: 11 Copynumber: 4.1 Consensus size: 12
439888 TTTGTGCTGG
439898 AAATAAGATAAA
1 AAATAAGATAAA
*
439910 AAATAAGAT-TA
1 AAATAAGATAAA
*
439921 AAACAAGATAAA
1 AAATAAGATAAA
439933 AAA-AAGATAAA
1 AAATAAGATAAA
439944 A
1 A
439945 GAATTGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
11 18 0.58
12 13 0.42
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (12 bp):
AAATAAGATAAA
Found at i:439932 original size:23 final size:21
Alignment explanation
Indices: 439902--439944 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
439892 TGCTGGAAAT
439902 AAGATAAAAAATAAGATTAAAAC
1 AAGATAAAAAA-AAGA-TAAAAC
439925 AAGATAAAAAAAAGATAAAA
1 AAGATAAAAAAAAGATAAAA
439945 GAATTGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.25
22 4 0.20
23 11 0.55
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.14
Consensus pattern (21 bp):
AAGATAAAAAAAAGATAAAAC
Found at i:442044 original size:11 final size:10
Alignment explanation
Indices: 442013--442045 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
442003 ATTTTTTTTC
442013 AAAAAAA-CA
1 AAAAAAAGCA
442022 AAAAAAAGCA
1 AAAAAAAGCA
442032 AAAAAAAGCCA
1 AAAAAAAG-CA
442043 AAA
1 AAA
442046 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 7 0.32
10 10 0.45
11 5 0.23
ACGTcount: A:0.82, C:0.12, G:0.06, T:0.00
Consensus pattern (10 bp):
AAAAAAAGCA
Found at i:448515 original size:8 final size:8
Alignment explanation
Indices: 448502--448540 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
448492 TATGAACCAC
448502 ATATTTAT
1 ATATTTAT
448510 ATATTTAT
1 ATATTTAT
448518 ATATTTAT
1 ATATTTAT
*
448526 AT-CTTAT
1 ATATTTAT
448533 ATTATTTA
1 A-TATTTA
448541 GCTTATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
7 5 0.19
8 19 0.70
9 3 0.11
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (8 bp):
ATATTTAT
Found at i:458210 original size:13 final size:13
Alignment explanation
Indices: 458192--458216 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
458182 TGGCCAAAGA
458192 TGAAAAGGTATGT
1 TGAAAAGGTATGT
458205 TGAAAAGGTATG
1 TGAAAAGGTATG
458217 CGAAAGGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:464026 original size:2 final size:2
Alignment explanation
Indices: 464019--464051 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
464009 ATCACCAACT
464019 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
464052 CGCTTCCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:467753 original size:13 final size:12
Alignment explanation
Indices: 467734--467817 Score: 63
Period size: 11 Copynumber: 7.0 Consensus size: 12
467724 ATATAGGCAT
467734 GATATGGTGATG
1 GATATGGTGATG
467746 GAATATGGTGAT-
1 G-ATATGGTGATG
*
467758 GATATAGGCG-T-
1 GATAT-GGTGATG
467769 GATAATGGTGATG
1 GAT-ATGGTGATG
467782 GACTATGGTGAT-
1 GA-TATGGTGATG
467794 GATATAGGTG-T-
1 GATAT-GGTGATG
467805 GATAATGGTGATG
1 GAT-ATGGTGATG
467818 AATAGATTGT
Statistics
Matches: 60, Mismatches: 2, Indels: 19
0.74 0.02 0.23
Matches are distributed among these distances:
11 22 0.37
12 17 0.28
13 20 0.33
14 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:467789 original size:36 final size:36
Alignment explanation
Indices: 467716--467821 Score: 162
Period size: 36 Copynumber: 3.0 Consensus size: 36
467706 ATTTATAAGT
* *
467716 TGGTGATAATATAGGCATGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
467751 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
467787 TGGTGATGATATAGGTGTGATAATGGTGAT-GAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
467822 GATTGTATCT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 23 0.35
36 42 0.65
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.32
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:470175 original size:2 final size:2
Alignment explanation
Indices: 470168--470200 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
470158 ATCACCAACT
470168 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
470201 TGCTTCCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:476516 original size:19 final size:20
Alignment explanation
Indices: 476492--476537 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
476482 CGGCCAAGAG
**
476492 CATGTATCTTCAT-TTAAAT
1 CATGTATCTTCATCAAAAAT
*
476511 CATGTATTTTCATCAAAAAT
1 CATGTATCTTCATCAAAAAT
476531 CATGTAT
1 CATGTAT
476538 TTTTAAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (20 bp):
CATGTATCTTCATCAAAAAT
Found at i:476949 original size:35 final size:36
Alignment explanation
Indices: 476881--476949 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
476871 GATTGAATCT
* *
476881 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCAACACCATA
*
476917 GTCCATCACCA-TATCACGCCTATATTAACACCA
1 GTCCATCACCATTATCACGCCTATATCAACACCA
476950 ACTTATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.32, C:0.35, G:0.06, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCAACACCATA
Found at i:477434 original size:14 final size:15
Alignment explanation
Indices: 477399--477427 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
477389 AATTTGGAGT
477399 GAAAAAGAAAGAAAA
1 GAAAAAGAAAGAAAA
477414 GAAAAAG-AAGAAAA
1 GAAAAAGAAAGAAAA
477428 TCAAAAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
GAAAAAGAAAGAAAA
Found at i:480547 original size:19 final size:20
Alignment explanation
Indices: 480523--480568 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
480513 CGGCCAAGAG
**
480523 CATGTATCTTCAT-TTAAAT
1 CATGTATCTTCATCAAAAAT
*
480542 CATGTATTTTCATCAAAAAT
1 CATGTATCTTCATCAAAAAT
480562 CATGTAT
1 CATGTAT
480569 TTTTAAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (20 bp):
CATGTATCTTCATCAAAAAT
Found at i:480979 original size:35 final size:36
Alignment explanation
Indices: 480911--480979 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
480901 GATTGAATCT
* *
480911 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCAACACCATA
*
480947 GTCCATCACCA-TATCACGCCTATATTAACACCA
1 GTCCATCACCATTATCACGCCTATATCAACACCA
480980 ACATATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.32, C:0.35, G:0.06, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCAACACCATA
Found at i:481463 original size:14 final size:15
Alignment explanation
Indices: 481429--481475 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
481419 AATTTGGAGT
481429 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
481444 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
481458 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
481475 G
1 G
481476 TGAAACAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:485031 original size:35 final size:36
Alignment explanation
Indices: 484937--485041 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
484927 GATTGAATCT
* * *
484937 GTCCATCGCCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATTATCACCATA
484973 GTCCATCACCATTATCACGCCTATATTATCACCATA
1 GTCCATCACCATTATCACGCCTATATTATCACCATA
*
485009 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATTATCACCA
485042 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 22 0.34
36 43 0.66
ACGTcount: A:0.30, C:0.34, G:0.06, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATTATCACCATA
Found at i:486728 original size:31 final size:31
Alignment explanation
Indices: 486671--486731 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
486661 ACATACTATC
**
486671 ATGATATCTAAATGATATGAAAACATAATAA
1 ATGATATCTAAAACATATGAAAACATAATAA
486702 ATGA-ATCTAAAACATATGTAAAACATAATA
1 ATGATATCTAAAACATATG-AAAACATAATA
486732 TAAAGCTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGAAAACATAATAA
Found at i:508099 original size:15 final size:17
Alignment explanation
Indices: 508057--508102 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
508047 TTTGGGATGC
*
508057 CAAGGGACATGATCATT
1 CAAGAGACATGATCATT
*
508074 CAAAGAAACATG-TC-TT
1 C-AAGAGACATGATCATT
508090 CAAGAGACATGAT
1 CAAGAGACATGAT
508103 TTTTAACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 9 0.38
16 4 0.17
17 3 0.12
18 8 0.33
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (17 bp):
CAAGAGACATGATCATT
Found at i:509584 original size:19 final size:20
Alignment explanation
Indices: 509560--509602 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
509550 AGCATTTATC
*
509560 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATGATGTATT
*
509579 TTCATTAAAAATGATGTGTT
1 TTCATTAAAAATGATGTATT
509599 TTCA
1 TTCA
509603 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATGATGTATT
Found at i:511523 original size:21 final size:21
Alignment explanation
Indices: 511497--511537 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
511487 CAAAACTCAT
**
511497 TGAAGGAACGCATTGAAGAAA
1 TGAAGGAACAAATTGAAGAAA
511518 TGAAGGAACAAATTGAAGAA
1 TGAAGGAACAAATTGAAGAA
511538 GAAAGTTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.07, G:0.27, T:0.15
Consensus pattern (21 bp):
TGAAGGAACAAATTGAAGAAA
Found at i:513979 original size:20 final size:19
Alignment explanation
Indices: 513937--513979 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
513927 AGCATTTATC
* *
513937 TTCATTAAAATTATGTATT
1 TTCATTAAAATCATGTATA
*
513956 TTCATTAAAAATCATGTGTA
1 TTCATT-AAAATCATGTATA
513976 TTCA
1 TTCA
513980 AAGGGGTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (19 bp):
TTCATTAAAATCATGTATA
Found at i:515917 original size:19 final size:20
Alignment explanation
Indices: 515879--515921 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
515869 GAAACCCCTT
*
515879 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
515899 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
515918 TGAA
1 TGAA
515922 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:516666 original size:20 final size:21
Alignment explanation
Indices: 516628--516666 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
516618 GATCATCTAA
* *
516628 AAGCTAAGATAACATGTATAT
1 AAGCTAAGATAAAAGGTATAT
516649 AAGCT-AGATAAAAGGTAT
1 AAGCTAAGATAAAAGGTAT
516667 TGGACGTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.26
Consensus pattern (21 bp):
AAGCTAAGATAAAAGGTATAT
Found at i:518157 original size:21 final size:21
Alignment explanation
Indices: 518131--518171 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
518121 CCAAACTTTC
**
518131 TTCTTCAATTTGTTCCTTCAT
1 TTCTTCAATGCGTTCCTTCAT
518152 TTCTTCAATGCGTTCCTTCA
1 TTCTTCAATGCGTTCCTTCA
518172 ACGAGTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.27, G:0.07, T:0.51
Consensus pattern (21 bp):
TTCTTCAATGCGTTCCTTCAT
Found at i:523486 original size:14 final size:14
Alignment explanation
Indices: 523469--523506 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
523459 CTTGGTTTGC
523469 TTTCTCTTTTTTCT
1 TTTCTCTTTTTTCT
*
523483 TTTCTC-TTCTTCT
1 TTTCTCTTTTTTCT
523496 TTTCTTCTTTT
1 TTTC-TCTTTT
523507 CTGATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 10 0.50
14 8 0.40
15 2 0.10
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTCTCTTTTTTCT
Found at i:523527 original size:13 final size:14
Alignment explanation
Indices: 523469--523528 Score: 59
Period size: 16 Copynumber: 4.0 Consensus size: 14
523459 CTTGGTTTGC
523469 TTTCTCTT-TTTTCT
1 TTTCTCTTCTTTT-T
523483 TTTCTCTTCTTCTTT
1 TTTCTCTTCTT-TTT
*
523498 TCTTCTTTTCTGATTTT
1 T-TTCTCTTCT--TTTT
523515 TTTCTCTTCTTTTT
1 TTTCTCTTCTTTTT
523529 GTCGTTTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 12 0.31
15 4 0.10
16 18 0.46
17 4 0.10
18 1 0.03
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (14 bp):
TTTCTCTTCTTTTT
Found at i:523544 original size:29 final size:30
Alignment explanation
Indices: 523478--523545 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
523468 CTTTCTCTTT
* *
523478 TTTCTTTTCTCTTCTTCTTTTCTTCTTTTC
1 TTTCTTTTTTCTTCTTCTTTTCTTCGTTTC
*
523508 TGAT-TTTTTTC-TCTTCTTTT-TGTCGTTTC
1 T-TTCTTTTTTCTTCTTCTTTTCT-TCGTTTC
523537 TTTCTTTTT
1 TTTCTTTTT
523546 GTACTCCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
28 2 0.06
29 21 0.68
30 7 0.23
31 1 0.03
ACGTcount: A:0.01, C:0.21, G:0.04, T:0.74
Consensus pattern (30 bp):
TTTCTTTTTTCTTCTTCTTTTCTTCGTTTC
Found at i:526293 original size:19 final size:20
Alignment explanation
Indices: 526255--526293 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
526245 GAAACCCCTT
*
526255 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
526275 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
526294 AGAAGATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:529768 original size:16 final size:16
Alignment explanation
Indices: 529736--529783 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
529726 AGGGTAATGA
529736 AATAAGAATAGATGAAAG
1 AATAAGAA-A-ATGAAAG
*
529754 AATAAGAAAATGAAAT
1 AATAAGAAAATGAAAG
* *
529770 AGTAAGAAAGTGAA
1 AATAAGAAAATGAA
529784 GATAACGTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 18 0.67
17 1 0.04
18 8 0.30
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (16 bp):
AATAAGAAAATGAAAG
Found at i:529928 original size:11 final size:11
Alignment explanation
Indices: 529912--529954 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
529902 TGAAAATTGC
529912 TTCTTTTCGTT
1 TTCTTTTCGTT
529923 TTCTTTTCGTT
1 TTCTTTTCGTT
*
529934 TTC--TTCTTT
1 TTCTTTTCGTT
529943 TTCTTTTC-TT
1 TTCTTTTCGTT
529953 TT
1 TT
529955 GCACTCCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 8 0.28
10 4 0.14
11 17 0.59
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.77
Consensus pattern (11 bp):
TTCTTTTCGTT
Found at i:529949 original size:5 final size:5
Alignment explanation
Indices: 529912--529954 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
529902 TGAAAATTGC
*
529912 TTCTT TTCGTT TTCTT TTCGTT TTCTT CT-TT TTCTT TTCTT TT
1 TTCTT TTC-TT TTCTT TTC-TT TTCTT TTCTT TTCTT TTCTT TT
529955 GCACTCCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.09
5 20 0.61
6 10 0.30
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.77
Consensus pattern (5 bp):
TTCTT
Found at i:530007 original size:6 final size:6
Alignment explanation
Indices: 529978--530027 Score: 64
Period size: 6 Copynumber: 8.2 Consensus size: 6
529968 GTTGTAGGAG
* * *
529978 TCTTTT TCTTTC TCTTTC TCTTTT TGTTTT TCTTCTT TCTTTT TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT
530027 T
1 T
530028 GTTGCTTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 33 0.85
7 6 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (6 bp):
TCTTTT
Found at i:530018 original size:25 final size:24
Alignment explanation
Indices: 529980--530030 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
529970 TGTAGGAGTC
529980 TTTTTCTTTCTCTTTCTCTTTTTG
1 TTTTTCTTTCTCTTTCTCTTTTTG
* *
530004 TTTTTCTTCTTTCTTTTTCTTTTTG
1 TTTTTCTT-TCTCTTTCTCTTTTTG
530029 TT
1 TT
530031 GCTTTTGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (24 bp):
TTTTTCTTTCTCTTTCTCTTTTTG
Found at i:532729 original size:30 final size:31
Alignment explanation
Indices: 532677--532736 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
532667 CTTAGCTTTA
**
532677 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
532707 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
532737 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:533669 original size:19 final size:20
Alignment explanation
Indices: 533645--533695 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
533635 CGGCCAAGAG
* *
533645 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
533664 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
533684 CATGTATTTTCA
1 CATGTATTTTCA
533696 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:537504 original size:16 final size:16
Alignment explanation
Indices: 537471--537519 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
537461 TAAGGTAATG
537471 GAATAAGAATAGATGAAA
1 GAATAAGAA-A-ATGAAA
537489 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* * *
537505 TAGTAAGAAAGTGAA
1 GAATAAGAAAATGAA
537520 GATAACTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:537681 original size:14 final size:14
Alignment explanation
Indices: 537662--537688 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
537652 TTTCGTTTTA
537662 TTTTTGTTTTCTTC
1 TTTTTGTTTTCTTC
537676 TTTTTGTTTTCTT
1 TTTTTGTTTTCTT
537689 TTGCACTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.81
Consensus pattern (14 bp):
TTTTTGTTTTCTTC
Found at i:537725 original size:6 final size:6
Alignment explanation
Indices: 537714--537751 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
537704 ATTGCAGGAG
*
537714 TCTTTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT T
537752 GTTGCTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.82
Consensus pattern (6 bp):
TCTTTT
Found at i:537742 original size:19 final size:18
Alignment explanation
Indices: 537714--537751 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
537704 ATTGCAGGAG
*
537714 TCTTTTTCTTTTTGTTTT
1 TCTTTTTCTTTTTCTTTT
537732 TCTTCTTTCTTTTTCTTTT
1 TCTT-TTTCTTTTTCTTTT
537751 T
1 T
537752 GTTGCTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.82
Consensus pattern (18 bp):
TCTTTTTCTTTTTCTTTT
Found at i:538597 original size:19 final size:20
Alignment explanation
Indices: 538559--538601 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
538549 GAAACCCCTT
*
538559 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
538579 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
538598 TGAA
1 TGAA
538602 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:539345 original size:20 final size:21
Alignment explanation
Indices: 539307--539345 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
539297 GATCATCTAG
* *
539307 AAGCTAAGATAACATGTATAT
1 AAGCTAAGATAAAAGGTATAT
539328 AAGCT-AGATAAAAGGTAT
1 AAGCTAAGATAAAAGGTAT
539346 TGGACGTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.26
Consensus pattern (21 bp):
AAGCTAAGATAAAAGGTATAT
Found at i:543411 original size:20 final size:21
Alignment explanation
Indices: 543373--543411 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
543363 TATCATCTAG
* *
543373 AAGCTAAGATAACATGTATAT
1 AAGCTAAGATAAAAGGTATAT
543394 AAGCT-AGATAAAAGGTAT
1 AAGCTAAGATAAAAGGTAT
543412 TAGATGTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.26
Consensus pattern (21 bp):
AAGCTAAGATAAAAGGTATAT
Found at i:544923 original size:21 final size:21
Alignment explanation
Indices: 544891--544942 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
544881 GTTGCCTTTC
*
544891 CTTTCCTT-ATAGCCTCAACA
1 CTTTGCTTCATAGCCTCAACA
544911 CTTTGCTTCATAGCCTCAACA
1 CTTTGCTTCATAGCCTCAACA
544932 CTTTGCTTCAT
1 CTTTGCTTCAT
544943 TTTGGCTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 7 0.23
21 23 0.77
ACGTcount: A:0.21, C:0.33, G:0.08, T:0.38
Consensus pattern (21 bp):
CTTTGCTTCATAGCCTCAACA
Found at i:547028 original size:13 final size:13
Alignment explanation
Indices: 547012--547052 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
547002 GAGAAAAATC
547012 AGAAAAGAAGAAA
1 AGAAAAGAAGAAA
547025 AGAAGAA-AAGAAA
1 AGAA-AAGAAGAAA
547038 AGAAAAGAA-AAA
1 AGAAAAGAAGAAA
547050 AGA
1 AGA
547053 GAAGTTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 8 0.31
13 16 0.62
14 2 0.08
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAGAAA
Found at i:547042 original size:18 final size:17
Alignment explanation
Indices: 547019--547052 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
547009 ATCAGAAAAG
547019 AAGAAAAGAAGAAAAGAA
1 AAGAAAAGAA-AAAAGAA
547037 AAGAAAAGAAAAAAGA
1 AAGAAAAGAAAAAAGA
547053 GAAGTTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAGAAAAGAAAAAAGAA
Found at i:552817 original size:17 final size:17
Alignment explanation
Indices: 552795--552828 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
552785 GGCTTAAAAA
552795 AAATGGTTAGGGTATAG
1 AAATGGTTAGGGTATAG
*
552812 AAATGGTTATGGTATAG
1 AAATGGTTAGGGTATAG
552829 GTATGATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (17 bp):
AAATGGTTAGGGTATAG
Found at i:553160 original size:26 final size:24
Alignment explanation
Indices: 553120--553168 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
553110 TGTAGGGGTC
553120 TTTTTCTTTTCTTTTTCT-TTTTG
1 TTTTTCTTTTCTTTTTCTCTTTTG
553143 TTTTTCTTCTTTCTTTTTTCTCTTTT
1 TTTTTC-T-TTTC-TTTTTCTCTTTT
553169 TGTTGCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.27
24 1 0.05
25 4 0.18
26 7 0.32
27 4 0.18
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (24 bp):
TTTTTCTTTTCTTTTTCTCTTTTG
Found at i:553168 original size:7 final size:6
Alignment explanation
Indices: 553118--553160 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
553108 GATGTAGGGG
*
553118 TCTTTT TC-TTT TCTTTT TCTTTT TGTTTT TCTTCTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT T
553161 TCTCTTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
7 6 0.18
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.81
Consensus pattern (6 bp):
TCTTTT
Found at i:554753 original size:20 final size:21
Alignment explanation
Indices: 554715--554753 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
554705 GATCATCTAG
*
554715 AAGCTATGATAACATGTATAA
1 AAGCTATGATAACAGGTATAA
*
554736 AAGCTA-GATAAGAGGTAT
1 AAGCTATGATAACAGGTAT
554754 TGGACGTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.26
Consensus pattern (21 bp):
AAGCTATGATAACAGGTATAA
Found at i:557080 original size:17 final size:18
Alignment explanation
Indices: 557049--557082 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
557039 ATGGTAATAA
*
557049 AATAAGAAAAGATGAAAG
1 AATAAGAAAAAATGAAAG
557067 AATAA-AAAAAATGAAA
1 AATAAGAAAAAATGAAA
557083 TAGAGAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (18 bp):
AATAAGAAAAAATGAAAG
Found at i:557323 original size:16 final size:14
Alignment explanation
Indices: 557301--557343 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 14
557291 TGTAGGGGTC
557301 TTTTTCTTTTCTCTT
1 TTTTTCTTTT-TCTT
557316 TATTTTCTTCTTTCTT
1 T-TTTTCTT-TTTCTT
557332 TTTTCTCTTTTT
1 TTTT-TCTTTTT
557344 GTTGCTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.28
16 16 0.64
17 2 0.08
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTCTTTTTCTT
Found at i:557351 original size:23 final size:23
Alignment explanation
Indices: 557299--557343 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
557289 GATGTAGGGG
*
557299 TCTT-TTTCTTTTCTCTTTATTT
1 TCTTCTTTCTTTTCTCTCTATTT
*
557321 TCTTCTTTCTTTTTTCTCT-TTT
1 TCTTCTTTCTTTTCTCTCTATTT
557343 T
1 T
557344 GTTGCTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (23 bp):
TCTTCTTTCTTTTCTCTCTATTT
Found at i:558935 original size:20 final size:21
Alignment explanation
Indices: 558897--558935 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
558887 GATCATCTAG
* *
558897 AAGCTAAGATAACATGTATAT
1 AAGCTAAGATAAAAGGTATAT
558918 AAGCT-AGATAAAAGGTAT
1 AAGCTAAGATAAAAGGTAT
558936 TGGACGTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.26
Consensus pattern (21 bp):
AAGCTAAGATAAAAGGTATAT
Found at i:560380 original size:12 final size:12
Alignment explanation
Indices: 560365--560389 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
560355 CATTCCATCA
560365 TTCAAACTTTCT
1 TTCAAACTTTCT
560377 TTCAAACTTTCT
1 TTCAAACTTTCT
560389 T
1 T
560390 CTTCAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (12 bp):
TTCAAACTTTCT
Found at i:561204 original size:26 final size:28
Alignment explanation
Indices: 561152--561214 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 28
561142 TGGTTAGGGT
*
561152 ATAA-AAAATGGTTAAGATAGAGGTATG
1 ATAATAAAATGGTTAAGATAAAGGTATG
561179 AT-ATAAAA-GGTTAAGA-AAAGGATATG
1 ATAATAAAATGGTTAAGATAAAGG-TATG
*
561205 GTAATAAAAT
1 ATAATAAAAT
561215 AAGAAAAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 4 0.13
26 14 0.47
27 12 0.40
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.25
Consensus pattern (28 bp):
ATAATAAAATGGTTAAGATAAAGGTATG
Found at i:561480 original size:12 final size:11
Alignment explanation
Indices: 561463--561506 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 11
561453 GATGTAGGGG
561463 TCTTTTTCTTTT
1 TCTTTTT-TTTT
561475 TCTTTTTTTTCT
1 TCTTTTTTTT-T
561487 TCTTTCTTTTTT
1 TCTTT-TTTTTT
561499 CTCTTTTT
1 -TCTTTTT
561507 GTTGCTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.10
12 16 0.55
13 10 0.34
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:561484 original size:16 final size:16
Alignment explanation
Indices: 561465--561503 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
561455 TGTAGGGGTC
561465 TTTTTCTT-TTTCTTT
1 TTTTTCTTCTTTCTTT
561480 TTTTTCTTCTTTCTTT
1 TTTTTCTTCTTTCTTT
*
561496 TTTCTCTT
1 TTTTTCTT
561504 TTTGTTGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTCTTCTTTCTTT
Found at i:561514 original size:23 final size:22
Alignment explanation
Indices: 561463--561506 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
561453 GATGTAGGGG
*
561463 TCTT-TTTCTTTTTCTTTTTTT
1 TCTTCTTTCTTTTTCTTCTTTT
561484 TCTTCTTTCTTTTT-TCTCTTTT
1 TCTTCTTTCTTTTTCT-TCTTTT
561506 T
1 T
561507 GTTGCTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (22 bp):
TCTTCTTTCTTTTTCTTCTTTT
Found at i:562352 original size:19 final size:20
Alignment explanation
Indices: 562314--562356 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
562304 GAAACCCCTT
*
562314 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
562334 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
562353 TGAA
1 TGAA
562357 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:576250 original size:13 final size:11
Alignment explanation
Indices: 576228--576293 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
576218 TATAACGCCT
576228 ATATCATCACC
1 ATATCATCACC
576239 ATAGTCCATCACC
1 ATA-T-CATCACC
*
576252 ATTATCA-CGCC
1 A-TATCATCACC
576263 TATATCATCACC
1 -ATATCATCACC
576275 ATATTCCATCACC
1 ATA-T-CATCACC
576288 ATATCA
1 ATATCA
576294 CGCCTATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:576253 original size:36 final size:36
Alignment explanation
Indices: 576206--576310 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
576196 GATACAATCT
*
576206 GTCCATCACCATTATAACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
576242 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
576278 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
576311 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:580316 original size:36 final size:36
Alignment explanation
Indices: 580268--580369 Score: 163
Period size: 36 Copynumber: 2.9 Consensus size: 36
580258 ACAATCTGTC
580268 CATCACCATTATCACGCCTATATCATCACCATAGT-
1 CATCACCATTATCACGCCTATATCATCACCATAGTA
*
580303 CTATCACCATTATCACGCCTATATCATCACCATATTA
1 C-ATCACCATTATCACGCCTATATCATCACCATAGTA
*
580340 CATCACCA-TATCACGCCTATATTATCACCA
1 CATCACCATTATCACGCCTATATCATCACCA
580370 ACTTATAAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
35 22 0.35
36 40 0.63
37 1 0.02
ACGTcount: A:0.32, C:0.34, G:0.04, T:0.29
Consensus pattern (36 bp):
CATCACCATTATCACGCCTATATCATCACCATAGTA
Found at i:582898 original size:22 final size:20
Alignment explanation
Indices: 582873--582912 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
582863 ATGTTTGTTT
582873 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
582895 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
582913 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:587162 original size:22 final size:20
Alignment explanation
Indices: 587137--587176 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
587127 ATGTTTGTTT
587137 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
587159 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
587177 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:587410 original size:15 final size:15
Alignment explanation
Indices: 587387--587422 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
587377 ACTAATATTC
* *
587387 TTATCATAATATATA
1 TTATAATAACATATA
587402 TTATAATAACATATA
1 TTATAATAACATATA
587417 TTATAA
1 TTATAA
587423 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:600222 original size:186 final size:186
Alignment explanation
Indices: 599908--600283 Score: 743
Period size: 186 Copynumber: 2.0 Consensus size: 186
599898 CATCTTACAG
599908 ATTGTGGTTTGAAAAAGGTAGCATATGTTGTTTCATATTCTAAGCAAATAAGAGTGTCTAAAACT
1 ATTGTGGTTTGAAAAAGGTAGCATATGTTGTTTCATATTCTAAGCAAATAAGAGTGTCTAAAACT
599973 TCTTTAGTGCTTTTCATTTTATGTGGTATTACATATAGTTCCATTCAAATGCGCATGAAAAAATC
66 TCTTTAGTGCTTTTCATTTTATGTGGTATTACATATAGTTCCATTCAAATGCGCATGAAAAAATC
*
600038 ATCTCAAATTCCTAGGAGGATATTGGTTATTTTTATCTTCTCATTGTGTTTTTGTA
131 ATCTCAAATTCCTAGGAGGATATTGGTTATTTTTATCTTCTCATTGTGTTTCTGTA
600094 ATTGTGGTTTGAAAAAGGTAGCATATGTTGTTTCATATTCTAAGCAAATAAGAGTGTCTAAAACT
1 ATTGTGGTTTGAAAAAGGTAGCATATGTTGTTTCATATTCTAAGCAAATAAGAGTGTCTAAAACT
600159 TCTTTAGTGCTTTTCATTTTATGTGGTATTACATATAGTTCCATTCAAATGCGCATGAAAAAATC
66 TCTTTAGTGCTTTTCATTTTATGTGGTATTACATATAGTTCCATTCAAATGCGCATGAAAAAATC
600224 ATCTCAAATTCCTAGGAGGATATTGGTTATTTTTATCTTCTCATTGTGTTTCTGTA
131 ATCTCAAATTCCTAGGAGGATATTGGTTATTTTTATCTTCTCATTGTGTTTCTGTA
600280 ATTG
1 ATTG
600284 GCAACTCAAT
Statistics
Matches: 189, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
186 189 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (186 bp):
ATTGTGGTTTGAAAAAGGTAGCATATGTTGTTTCATATTCTAAGCAAATAAGAGTGTCTAAAACT
TCTTTAGTGCTTTTCATTTTATGTGGTATTACATATAGTTCCATTCAAATGCGCATGAAAAAATC
ATCTCAAATTCCTAGGAGGATATTGGTTATTTTTATCTTCTCATTGTGTTTCTGTA
Found at i:601219 original size:13 final size:13
Alignment explanation
Indices: 601203--601259 Score: 71
Period size: 13 Copynumber: 4.4 Consensus size: 13
601193 TCAATGCGCT
*
601203 TCATAAATGAGCG
1 TCATAAATGTGCG
*
601216 TCATAAATGTGTG
1 TCATAAATGTGCG
*
601229 TCATAAAT-TCGTG
1 TCATAAATGT-GCG
601242 TCATAAATGTGCG
1 TCATAAATGTGCG
601255 TCATA
1 TCATA
601260 GATTTATGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
12 1 0.03
13 37 0.95
14 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (13 bp):
TCATAAATGTGCG
Found at i:603158 original size:11 final size:11
Alignment explanation
Indices: 603144--603170 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
603134 AAAAAAAAAC
603144 AAAAAAGGCAA
1 AAAAAAGGCAA
603155 AAAAAAGGCAA
1 AAAAAAGGCAA
603166 AAAAA
1 AAAAA
603171 CCAAAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAGGCAA
Found at i:603166 original size:20 final size:20
Alignment explanation
Indices: 603133--603196 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
603123 ATTTTTTTCA
* *
603133 AAAAAAAAAACAAAAAAGGC
1 AAAAAAAAGACAAAAAAGCC
* *
603153 AAAAAAAAGGCAAAAAAACC
1 AAAAAAAAGACAAAAAAGCC
* *
603173 AAAAAAGAGCCAAAAAAGCC
1 AAAAAAAAGACAAAAAAGCC
603193 AAAA
1 AAAA
603197 TTTCAAAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.75, C:0.14, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGACAAAAAAGCC
Found at i:603190 original size:11 final size:11
Alignment explanation
Indices: 603143--603190 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
603133 AAAAAAAAAA
603143 CAAAAAAG-G-
1 CAAAAAAGAGC
* *
603152 CAAAAAAAAGG
1 CAAAAAAGAGC
603163 CAAAAAA-A-C
1 CAAAAAAGAGC
603172 CAAAAAAGAGC
1 CAAAAAAGAGC
603183 CAAAAAAG
1 CAAAAAAG
603191 CCAAAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 14 0.42
10 3 0.09
11 16 0.48
ACGTcount: A:0.71, C:0.15, G:0.15, T:0.00
Consensus pattern (11 bp):
CAAAAAAGAGC
Found at i:606970 original size:22 final size:21
Alignment explanation
Indices: 606931--606981 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
606921 ATATAATTTA
606931 TATTAGGATGATTAATTATCT
1 TATTAGGATGATTAATTATCT
* *
606952 T-TTAGGATCAGATTTATTATTT
1 TATTAGGAT--GATTAATTATCT
606974 TATTAGGA
1 TATTAGGA
606982 ATTAAGGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 7 0.28
21 1 0.04
22 11 0.44
23 6 0.24
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (21 bp):
TATTAGGATGATTAATTATCT
Found at i:622072 original size:14 final size:13
Alignment explanation
Indices: 622037--622084 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
622027 GAAAAAGACA
622037 AAAAGAAGAAAA-
1 AAAAGAAGAAAAG
**
622049 AAAATCAGAAAAGG
1 AAAAGAAGAAAA-G
622063 AAAAGAAGAAAAG
1 AAAAGAAGAAAAG
622076 AAAAAGAAG
1 -AAAAGAAG
622085 TTCAAAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 10 0.34
13 1 0.03
14 18 0.62
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (13 bp):
AAAAGAAGAAAAG
Found at i:626567 original size:22 final size:23
Alignment explanation
Indices: 626541--626593 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
626531 AAAATCAGCT
*
626541 AAGAAATTGAACCACTC-AAAAG
1 AAGAAATTCAACCACTCAAAAAG
*
626563 AAGAAAAATTCAAGCACTCAAAAAG
1 AAG--AAATTCAACCACTCAAAAAG
626588 AAGAAA
1 AAGAAA
626594 AAAAGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 3 0.12
23 3 0.12
24 12 0.46
25 8 0.31
ACGTcount: A:0.60, C:0.15, G:0.13, T:0.11
Consensus pattern (23 bp):
AAGAAATTCAACCACTCAAAAAG
Found at i:626580 original size:24 final size:25
Alignment explanation
Indices: 626544--626595 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
626534 ATCAGCTAAG
*
626544 AAATTGAACCACTC-AAAAGAAGAA
1 AAATTCAACCACTCAAAAAGAAGAA
*
626568 AAATTCAAGCACTCAAAAAGAAGAA
1 AAATTCAACCACTCAAAAAGAAGAA
626593 AAA
1 AAA
626596 AAGAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.62, C:0.15, G:0.12, T:0.12
Consensus pattern (25 bp):
AAATTCAACCACTCAAAAAGAAGAA
Found at i:626611 original size:18 final size:17
Alignment explanation
Indices: 626582--626634 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
626572 TCAAGCACTC
*
626582 AAAAAGAAGAAAAAAAG
1 AAAAAAAAGAAAAAAAG
*
626599 AAAATAAAAGAAAGAAAG
1 AAAA-AAAAGAAAAAAAG
*
626617 AAAAGAAAGAAAGAAAAG
1 AAAAAAAAGAAA-AAAAG
626635 TTGAAGCACT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 11 0.37
18 19 0.63
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (17 bp):
AAAAAAAAGAAAAAAAG
Found at i:626614 original size:4 final size:4
Alignment explanation
Indices: 626584--626632 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
626574 AAGCACTCAA
* *
626584 AAAG -AAG AAAA AAAG AAA- ATA- AAAG AAAG AAAG AAAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG
626630 AAA
1 AAA
626633 AGTTGAAGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
3 7 0.18
4 27 0.71
5 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:626620 original size:13 final size:13
Alignment explanation
Indices: 626584--626634 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
626574 AAGCACTCAA
626584 AAAG-AAGAAAA-
1 AAAGAAAGAAAAG
*
626595 AAAGAAAATAAAAG
1 AAAG-AAAGAAAAG
626609 AAAGAAAGAAAAG
1 AAAGAAAGAAAAG
626622 AAAGAAAGAAAAG
1 AAAGAAAGAAAAG
626635 TTGAAGCACT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 4 0.11
13 27 0.77
14 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (13 bp):
AAAGAAAGAAAAG
Found at i:627717 original size:27 final size:26
Alignment explanation
Indices: 627687--627742 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
627677 TAAGAAAAGA
* *
627687 AAATGATTAATA-AAGGAAGATTAAATG
1 AAATGATAAATATAA-GAA-ATGAAATG
627714 AAATGATAAATATAAGAAATGAAATG
1 AAATGATAAATATAAGAAATGAAATG
627740 AAA
1 AAA
627743 AAAAGAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 10 0.38
27 14 0.54
28 2 0.08
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (26 bp):
AAATGATAAATATAAGAAATGAAATG
Found at i:627735 original size:21 final size:18
Alignment explanation
Indices: 627709--627753 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 18
627699 AAGGAAGATT
627709 AAATGAAATGATAAATATAAG
1 AAATGAAATGA-AAA-A-AAG
627730 AAATGAAATGAAAAAAAG
1 AAATGAAATGAAAAAAAG
627748 AAATGA
1 AAATGA
627754 TAGAGATGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.38
19 1 0.04
20 3 0.12
21 11 0.46
ACGTcount: A:0.67, C:0.00, G:0.16, T:0.18
Consensus pattern (18 bp):
AAATGAAATGAAAAAAAG
Found at i:639925 original size:10 final size:10
Alignment explanation
Indices: 639912--639967 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
639902 TTTTTGGCTC
639912 TTTTTTTTGT
1 TTTTTTTTGT
*
639922 TTTTTTTTCCT
1 TTTTTTTT-GT
639933 TTTTTTTT-T
1 TTTTTTTTGT
**
639942 GCCTTTTTTGT
1 -TTTTTTTTGT
639953 TTTTTTTTGT
1 TTTTTTTTGT
639963 TTTTT
1 TTTTT
639968 GAAGAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 1 0.03
10 27 0.71
11 10 0.26
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:641920 original size:18 final size:19
Alignment explanation
Indices: 641890--641926 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
641880 TGATTAAAAT
641890 GGAATATGGAAG-AAGAAA
1 GGAATATGGAAGAAAGAAA
641908 GGAA-ATGGTAAGAAAGAAA
1 GGAATATGG-AAGAAAGAAA
641927 ATGGATAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.32, T:0.11
Consensus pattern (19 bp):
GGAATATGGAAGAAAGAAA
Found at i:642616 original size:40 final size:40
Alignment explanation
Indices: 642572--642659 Score: 90
Period size: 43 Copynumber: 2.1 Consensus size: 40
642562 GGGCCAAGTT
642572 CTAAAA-GTCCTAA-ATAACTAATGAATAAAATAATAATAAA
1 CTAAAATGTCCTAACATAACTAAT-AATAAAATAATAAT-AA
* * * *
642612 CTAAACATGTCTTAACTCTAATTCATAATAAAATAATAATAA
1 CTAAA-ATGTCCTAAC-ATAACTAATAATAAAATAATAATAA
642654 CTAAAA
1 CTAAAA
642660 ATAATATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
40 5 0.12
41 2 0.05
42 13 0.32
43 14 0.35
44 6 0.15
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.28
Consensus pattern (40 bp):
CTAAAATGTCCTAACATAACTAATAATAAAATAATAATAA
Found at i:642704 original size:25 final size:22
Alignment explanation
Indices: 642675--642721 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
642665 ATTTTAACAT
642675 AACCTTAATTCCTAATAAAATAATA
1 AACC-TAA-TCCTAA-AAAATAATA
*
642700 AACCTAATCCTAAAAGATAATA
1 AACCTAATCCTAAAAAATAATA
642722 CATCATCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 6 0.29
24 3 0.14
25 4 0.19
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (22 bp):
AACCTAATCCTAAAAAATAATA
Found at i:650899 original size:16 final size:15
Alignment explanation
Indices: 650877--650936 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 15
650867 AGGATAAAGT
650877 AATGAAAATAAGAAA
1 AATGAAAATAAGAAA
650892 ATATGAAAGAATAAG-AA
1 A-ATG-AA-AATAAGAAA
650909 AATGAAATAGTAAGAAA
1 AATGAAA-A-TAAGAAA
*
650926 AATGAAGATAA
1 AATGAAAATAA
650937 CTTACAACTC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
14 1 0.03
15 7 0.18
16 11 0.29
17 13 0.34
18 6 0.16
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
AATGAAAATAAGAAA
Found at i:650906 original size:18 final size:17
Alignment explanation
Indices: 650883--650931 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
650873 AAGTAATGAA
650883 AATAAGAAAATATGAAAG
1 AATAAGAAAA-ATGAAAG
*
650901 AATAAG-AAAATGAAAT
1 AATAAGAAAAATGAAAG
*
650917 AGTAAGAAAAATGAA
1 AATAAGAAAAATGAA
650932 GATAACTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.39
17 11 0.39
18 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.16, T:0.16
Consensus pattern (17 bp):
AATAAGAAAAATGAAAG
Found at i:655433 original size:17 final size:17
Alignment explanation
Indices: 655411--655464 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
655401 AATTAAGAGT
655411 TAGTTT-ATTAAATGAAC
1 TAGTTTAATT-AATGAAC
* *
655428 TAGTTTGATGAATGAAC
1 TAGTTTAATTAATGAAC
655445 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
655462 TAG
1 TAG
655465 ATGTATGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 31 0.94
18 2 0.06
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:655459 original size:34 final size:34
Alignment explanation
Indices: 655411--655493 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 34
655401 AATTAAGAGT
*
655411 TAGTTTATTAAATGAACTAG-TTTGATGAATGAAC
1 TAGTTTATTAAATGAACTAGATGT-ATGAATGAAC
*
655445 TAGTTTAATT-AATGAACTAGATGTATGAATGAAG
1 TAGTTT-ATTAAATGAACTAGATGTATGAATGAAC
* *
655479 TAGCTTACTAAATGA
1 TAGTTTATTAAATGA
655494 TCTAAATATG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
33 2 0.05
34 35 0.83
35 5 0.12
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (34 bp):
TAGTTTATTAAATGAACTAGATGTATGAATGAAC
Found at i:655475 original size:17 final size:17
Alignment explanation
Indices: 655411--655477 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
655401 AATTAAGAGT
* *
655411 TAGTTTATTAAATGAAC
1 TAGTTTAATGAATGAAC
*
655428 TAGTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
*
655445 TAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
*
655462 TAGATGT-ATGAATGAA
1 TAG-TTTAATGAATGAA
655478 GTAGCTTACT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
17 40 0.95
18 2 0.05
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.37
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:657877 original size:18 final size:16
Alignment explanation
Indices: 657822--657889 Score: 82
Period size: 17 Copynumber: 3.9 Consensus size: 16
657812 TAAGAGTTAG
*
657822 TTTATTAAATGAACTAG
1 TTTATT-AATGAACTAC
657839 TTTGATTAATGAACTAC
1 TTT-ATTAATGAACTAC
657856 TTTAATTAATGAACTAAC
1 TTT-ATTAATGAACT-AC
657874 TTTATTCAATGAACTA
1 TTTATT-AATGAACTA
657890 GATACGTGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
17 30 0.65
18 16 0.35
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (16 bp):
TTTATTAATGAACTAC
Done.