Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold142
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1252394
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.30
Warning! 144568 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:664565 original size:22 final size:22
Alignment explanation
Indices: 664537--664579 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
664527 GCATTACACT
664537 TTGAATATATATCACCTTCACC
1 TTGAATATATATCACCTTCACC
664559 TTGAATATATATCACCTTCAC
1 TTGAATATATATCACCTTCAC
664580 AAGTCAAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.37
Consensus pattern (22 bp):
TTGAATATATATCACCTTCACC
Found at i:668083 original size:2 final size:2
Alignment explanation
Indices: 668078--668153 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
668068 TGATATTTTG
668078 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
668120 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
668154 TTCATCTATG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:674313 original size:21 final size:21
Alignment explanation
Indices: 674287--674427 Score: 106
Period size: 21 Copynumber: 6.7 Consensus size: 21
674277 TACAAGATAA
674287 ACGATAGGATAGGATTCACGC
1 ACGATAGGATAGGATTCACGC
* *
674308 ACGATAGGATAGCATTAACGC
1 ACGATAGGATAGGATTCACGC
* * *
674329 ACGATA-GAGCAGTATACACGC
1 ACGATAGGA-TAGGATTCACGC
* *
674350 ACGAAAGGATAGGATTAACGC
1 ACGATAGGATAGGATTCACGC
* * * *
674371 ACGATAGAACAGTATACACGC
1 ACGATAGGATAGGATTCACGC
* * **
674392 ACAAT-GTGATAGGATTGATAC
1 ACGATAG-GATAGGATTCACGC
*
674413 ACGATAGGAAAGGAT
1 ACGATAGGATAGGAT
674428 AAACGATGTT
Statistics
Matches: 89, Mismatches: 27, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.03
21 83 0.93
22 3 0.03
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.18
Consensus pattern (21 bp):
ACGATAGGATAGGATTCACGC
Found at i:674403 original size:42 final size:42
Alignment explanation
Indices: 674303--674407 Score: 158
Period size: 42 Copynumber: 2.5 Consensus size: 42
674293 GGATAGGATT
* * *
674303 CACGCACGATAGGATAGCATTAACGCACGATAGAGCAGTATA
1 CACGCACGAAAGGATAGGATTAACGCACGATAGAACAGTATA
674345 CACGCACGAAAGGATAGGATTAACGCACGATAGAACAGTATA
1 CACGCACGAAAGGATAGGATTAACGCACGATAGAACAGTATA
*
674387 CACGCAC-AATGTGATAGGATT
1 CACGCACGAAAG-GATAGGATT
674408 GATACACGAT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
41 3 0.05
42 55 0.95
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (42 bp):
CACGCACGAAAGGATAGGATTAACGCACGATAGAACAGTATA
Found at i:674416 original size:42 final size:42
Alignment explanation
Indices: 674303--674419 Score: 146
Period size: 42 Copynumber: 2.8 Consensus size: 42
674293 GGATAGGATT
* * * *
674303 CACGCACGATAGGATAGCATTAACGCACGATAGAGCAGTATA
1 CACGCACGAAAGGATAGGATTAACACACGATAGAACAGTATA
*
674345 CACGCACGAAAGGATAGGATTAACGCACGATAGAACAGTATA
1 CACGCACGAAAGGATAGGATTAACACACGATAGAACAGTATA
* * *
674387 CACGCAC-AATGTGATAGGATTGATACACGATAG
1 CACGCACGAAAG-GATAGGATTAACACACGATAG
674420 GAAAGGATAA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 3 0.04
42 64 0.96
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (42 bp):
CACGCACGAAAGGATAGGATTAACACACGATAGAACAGTATA
Found at i:675450 original size:21 final size:21
Alignment explanation
Indices: 675426--675559 Score: 101
Period size: 21 Copynumber: 6.4 Consensus size: 21
675416 CGATAAACCT
675426 GATAGGATTAACGCACGATAG
1 GATAGGATTAACGCACGATAG
*
675447 GATAGCATTAACGCACGATAG
1 GATAGGATTAACGCACGATAG
* * *
675468 AACAGTA-TACACGCACGATAG
1 GATAGGATTA-ACGCACGATAG
* *
675489 GATAGAAATAACGCACGATAG
1 GATAGGATTAACGCACGATAG
* * * * *
675510 AACAGTA-TACAAGCACGATAC
1 GATAGGATTA-ACGCACGATAG
* ** *
675531 GATAGGATTGATACACGATAC
1 GATAGGATTAACGCACGATAG
675552 GATAGGAT
1 GATAGGAT
675560 AGGATTGTAA
Statistics
Matches: 91, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
20 4 0.04
21 84 0.92
22 3 0.03
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (21 bp):
GATAGGATTAACGCACGATAG
Found at i:675483 original size:42 final size:42
Alignment explanation
Indices: 675436--675535 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
675426 GATAGGATTA
* *
675436 ACGCACGATAGGATAGCATTAACGCACGATAGAACAGTATAC
1 ACGCACGATAGGATAGAAATAACGCACGATAGAACAGTATAC
675478 ACGCACGATAGGATAGAAATAACGCACGATAGAACAGTATAC
1 ACGCACGATAGGATAGAAATAACGCACGATAGAACAGTATAC
* *
675520 AAGCACGATACGATAG
1 ACGCACGATAGGATAG
675536 GATTGATACA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (42 bp):
ACGCACGATAGGATAGAAATAACGCACGATAGAACAGTATAC
Found at i:678273 original size:21 final size:22
Alignment explanation
Indices: 678247--678295 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
678237 GTTTTTCAAC
678247 TTGTACTATAATT-AGTATAAT
1 TTGTACTATAATTAAGTATAAT
*
678268 TTGTACTATAATTAATTATAAT
1 TTGTACTATAATTAAGTATAAT
*
678290 TAGTAC
1 TTGTAC
678296 AGTAATCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (22 bp):
TTGTACTATAATTAAGTATAAT
Found at i:698978 original size:63 final size:63
Alignment explanation
Indices: 698900--699298 Score: 557
Period size: 63 Copynumber: 6.3 Consensus size: 63
698890 CTCAGGTACA
* * *
698900 TTGATATTGGTATAGCTACAAAAGTTACGTATCCTGTTTACTTTACTTACTCTTCAAGCTCCT
1 TTGATATTGTTATAGCTACAGAAGTTACCTATCCTGTTTACTTTACTTACTCTTCAAGCTCCT
698963 TTGATATTGTTATAGCTACAGAAGTTACCTATCCTGTTTACTTTACTTACTCTTCAAGCTCCT
1 TTGATATTGTTATAGCTACAGAAGTTACCTATCCTGTTTACTTTACTTACTCTTCAAGCTCCT
699026 TTGATATTGTTATAGCTACAGAAGTTACCTATCCTGTTTACTTTACTTACTCTTCAAGCTCCT
1 TTGATATTGTTATAGCTACAGAAGTTACCTATCCTGTTTACTTTACTTACTCTTCAAGCTCCT
*
699089 TTGATATTGTTATAGCTACAGAAGTTACCTATCCTGTTTACTTTACTTACTCTTCAAGCTACT
1 TTGATATTGTTATAGCTACAGAAGTTACCTATCCTGTTTACTTTACTTACTCTTCAAGCTCCT
* * * * * * * * * *
699152 TCGATATTGTTATAGCTACAGGAGTTATCTACCCTGTTTACCTGACGTACTCTACAAGCTACA
1 TTGATATTGTTATAGCTACAGAAGTTACCTATCCTGTTTACTTTACTTACTCTTCAAGCTCCT
* * * * *
699215 TTGATATTGTTATAGCTAGCTAGAGGAGTTATCC-ATCCTGTTAACTTGACTTACCCTGCAGGCT
1 TTGATATTGTTATAGCTA-C-AGA--AGTTA-CCTATCCTGTTTACTTTACTTACTCTTCAAGCT
* *
699279 ACA
61 CCT
699282 TTGATATTGTTATAGCT
1 TTGATATTGTTATAGCT
699299 GCCGGGACTA
Statistics
Matches: 308, Mismatches: 23, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
63 256 0.83
64 1 0.00
65 2 0.01
67 48 0.16
68 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (63 bp):
TTGATATTGTTATAGCTACAGAAGTTACCTATCCTGTTTACTTTACTTACTCTTCAAGCTCCT
Found at i:701904 original size:19 final size:19
Alignment explanation
Indices: 701882--701920 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
701872 CGGAAGGTCG
701882 AAGTAACAAAAAAAGGTAC
1 AAGTAACAAAAAAAGGTAC
701901 AAGTAACAAAAAAAGGTAC
1 AAGTAACAAAAAAAGGTAC
701920 A
1 A
701921 TGTAGATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.10, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGTAACAAAAAAAGGTAC
Found at i:703805 original size:21 final size:21
Alignment explanation
Indices: 703779--703966 Score: 112
Period size: 21 Copynumber: 8.8 Consensus size: 21
703769 TTTTTTCGCA
*
703779 AATAAACTCGAAACTTTTGCG
1 AATAAACGCGAAACTTTTGCG
**
703800 AATAAACGCGTTACTTTTGCG
1 AATAAACGCGAAACTTTTGCG
**
703821 AATAAACGCGTTA-TTTTCGCG
1 AATAAACGCGAAACTTTT-GCG
* * **
703842 AATAAATGCAAAACTTACGCG
1 AATAAACGCGAAACTTTTGCG
* *
703863 -ATATAACGCGACACTTTCGCG
1 AATA-AACGCGAAACTTTTGCG
* ** * *
703884 AATAAACGTGTTACTTTCGTG
1 AATAAACGCGAAACTTTTGCG
* * *
703905 ATATATCTATCGCGAATCTTTCGCG
1 A-ATA---AACGCGAAACTTTTGCG
*
703930 -ATAAAACGCGAAACTTTTGCA
1 AAT-AAACGCGAAACTTTTGCG
703951 AATAAACGCGAAACTT
1 AATAAACGCGAAACTT
703967 AAATATAAAT
Statistics
Matches: 130, Mismatches: 27, Indels: 20
0.73 0.15 0.11
Matches are distributed among these distances:
20 7 0.05
21 99 0.76
22 10 0.08
23 2 0.02
24 1 0.01
25 11 0.08
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (21 bp):
AATAAACGCGAAACTTTTGCG
Found at i:703846 original size:63 final size:63
Alignment explanation
Indices: 703771--703902 Score: 151
Period size: 63 Copynumber: 2.1 Consensus size: 63
703761 AAAAATATTT
* ** ** *
703771 TTTTCGCAAATAAACT-CGAAACTTTTGCGA-ATAAACGCGTTACTTTTGCGAATAAACGCGTTA
1 TTTTCGCAAATAAA-TGCAAAACTTACGCGATAT-AACGCGACACTTTCGCGAATAAACGCGTTA
* *
703834 TTTTCGCGAATAAATGCAAAACTTACGCGATATAACGCGACACTTTCGCGAATAAACGTGTTA
1 TTTTCGCAAATAAATGCAAAACTTACGCGATATAACGCGACACTTTCGCGAATAAACGCGTTA
*
703897 CTTTCG
1 TTTTCG
703903 TGATATATCT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
62 1 0.02
63 55 0.95
64 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (63 bp):
TTTTCGCAAATAAATGCAAAACTTACGCGATATAACGCGACACTTTCGCGAATAAACGCGTTA
Found at i:704972 original size:2 final size:2
Alignment explanation
Indices: 704967--704996 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
704957 AGATAGACTC
704967 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
704997 TGTGTGTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:705458 original size:11 final size:11
Alignment explanation
Indices: 705442--705467 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
705432 GACAATCATA
705442 TGTTACATAAG
1 TGTTACATAAG
705453 TGTTACATAAG
1 TGTTACATAAG
705464 TGTT
1 TGTT
705468 TATGACTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (11 bp):
TGTTACATAAG
Found at i:708670 original size:21 final size:21
Alignment explanation
Indices: 708646--708778 Score: 171
Period size: 21 Copynumber: 6.3 Consensus size: 21
708636 ACGCATCATC
**
708646 TCGCGAAAGTTTTGCGTTTAT
1 TCGCGAAAGTTACGCGTTTAT
*
708667 TCGCGAAAGTTACGCGTTAAT
1 TCGCGAAAGTTACGCGTTTAT
708688 TCGCGAAAGTTACGCGTTTAT
1 TCGCGAAAGTTACGCGTTTAT
* *
708709 TCGC-AAATGTTTCGCGTTAAT
1 TCGCGAAA-GTTACGCGTTTAT
*
708730 TCGCGAAAGTTACGCG-TTACA
1 TCGCGAAAGTTACGCGTTTA-T
*
708751 TCGCGAAAGTTACGCGTTTTT
1 TCGCGAAAGTTACGCGTTTAT
708772 TCGCGAA
1 TCGCGAA
708779 TTTTTCTTTT
Statistics
Matches: 97, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
20 5 0.05
21 87 0.90
22 5 0.05
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (21 bp):
TCGCGAAAGTTACGCGTTTAT
Found at i:708738 original size:63 final size:63
Alignment explanation
Indices: 708654--708784 Score: 201
Period size: 63 Copynumber: 2.1 Consensus size: 63
708644 TCTCGCGAAA
* *
708654 GTTTTGCGTTTATTCGCGAAAGTTACGCGTTA-ATTCGCGAAAGTTACGCGTTTATTCGCAAAT
1 GTTTCGCGTTAATTCGCGAAAGTTACGCGTTACA-TCGCGAAAGTTACGCGTTTATTCGCAAAT
* *
708717 GTTTCGCGTTAATTCGCGAAAGTTACGCGTTACATCGCGAAAGTTACGCGTTTTTTCGCGAAT
1 GTTTCGCGTTAATTCGCGAAAGTTACGCGTTACATCGCGAAAGTTACGCGTTTATTCGCAAAT
*
708780 TTTTC
1 GTTTC
708785 TTTTGTTACC
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
63 61 0.98
64 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (63 bp):
GTTTCGCGTTAATTCGCGAAAGTTACGCGTTACATCGCGAAAGTTACGCGTTTATTCGCAAAT
Found at i:713090 original size:14 final size:14
Alignment explanation
Indices: 713066--713193 Score: 76
Period size: 14 Copynumber: 8.5 Consensus size: 14
713056 ATAAAACTTC
*
713066 TATAAGAATAAGGT
1 TATAAGGATAAGGT
* *
713080 TATAAAGATAATGTT
1 TATAAGGATAA-GGT
713095 TATAAGGTTATAAGGAT
1 TATAAGG--ATAAGG-T
****
713112 TATGTTTATAAGGT
1 TATAAGGATAAGGT
*
713126 TAGAAGGATAAGGT
1 TATAAGGATAAGGT
*
713140 TAGAAGGATAAGGAT
1 TATAAGGATAAGG-T
* *
713155 TATAAGGGTCCATATGT
1 TATAAGGAT--A-AGGT
713172 TATAAGGATAAGGAT
1 TATAAGGATAAGG-T
713187 TATAAGG
1 TATAAGG
713194 GTAAATATGA
Statistics
Matches: 86, Mismatches: 19, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
14 34 0.40
15 31 0.36
16 1 0.01
17 18 0.21
18 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.25, T:0.32
Consensus pattern (14 bp):
TATAAGGATAAGGT
Found at i:713101 original size:23 final size:23
Alignment explanation
Indices: 713073--713136 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
713063 TTCTATAAGA
*
713073 ATAAGGTTATAAAGATAATGTTT
1 ATAAGGTTATAAGGATAATGTTT
*
713096 ATAAGGTTATAAGGATTATGTTT
1 ATAAGGTTATAAGGATAATGTTT
*
713119 ATAAGGTTAGAAGGATAA
1 ATAAGGTTATAAGGATAA
713137 GGTTAGAAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (23 bp):
ATAAGGTTATAAGGATAATGTTT
Found at i:713114 original size:9 final size:8
Alignment explanation
Indices: 713073--713161 Score: 50
Period size: 8 Copynumber: 11.8 Consensus size: 8
713063 TTCTATAAGA
713073 ATAAGGTT
1 ATAAGGTT
*
713081 ATAAAG--
1 ATAAGGTT
*
713087 ATAATGTTT
1 ATAA-GGTT
713096 ATAAGGTT
1 ATAAGGTT
713104 ATAAGGATT
1 ATAAGG-TT
*
713113 AT--GTTT
1 ATAAGGTT
713119 ATAAGGTT
1 ATAAGGTT
*
713127 AGAAGG--
1 ATAAGGTT
713133 ATAAGGTT
1 ATAAGGTT
*
713141 AGAAGG--
1 ATAAGGTT
713147 ATAAGGATT
1 ATAAGG-TT
713156 ATAAGG
1 ATAAGG
713162 GTCCATATGT
Statistics
Matches: 60, Mismatches: 10, Indels: 21
0.66 0.11 0.23
Matches are distributed among these distances:
6 18 0.30
7 1 0.02
8 27 0.45
9 14 0.23
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.33
Consensus pattern (8 bp):
ATAAGGTT
Found at i:713202 original size:32 final size:32
Alignment explanation
Indices: 713138--713202 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
713128 GAAGGATAAG
**
713138 GTTAGAAGGATAAGGATTATAAGGGTCCATAT
1 GTTAGAAGGATAAGGATTATAAGGGTAAATAT
*
713170 GTTATAAGGATAAGGATTATAAGGGTAAATAT
1 GTTAGAAGGATAAGGATTATAAGGGTAAATAT
713202 G
1 G
713203 ATGTAACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.40, C:0.03, G:0.28, T:0.29
Consensus pattern (32 bp):
GTTAGAAGGATAAGGATTATAAGGGTAAATAT
Found at i:714135 original size:23 final size:22
Alignment explanation
Indices: 714109--714155 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
714099 ATAAAACTTC
714109 TATAAGGATAAGGTTAATAAGGT
1 TATAAGGATAAGGTT-ATAAGGT
*
714132 TATAAGGATATGGTTATAAGGT
1 TATAAGGATAAGGTTATAAGGT
714154 TA
1 TA
714156 AGGATTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.40, C:0.00, G:0.26, T:0.34
Consensus pattern (22 bp):
TATAAGGATAAGGTTATAAGGT
Found at i:714428 original size:4 final size:4
Alignment explanation
Indices: 714419--714505 Score: 174
Period size: 4 Copynumber: 21.8 Consensus size: 4
714409 TTTACCAAGG
714419 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
714467 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATC
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATC
714506 ATATATCTCG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 83 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.49
Consensus pattern (4 bp):
ATCT
Found at i:716117 original size:20 final size:20
Alignment explanation
Indices: 716092--716130 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
716082 GAATCACCTT
716092 GTCCGTCCGTCCGTCTGTCA
1 GTCCGTCCGTCCGTCTGTCA
716112 GTCCGTCCGTCCGTCTGTC
1 GTCCGTCCGTCCGTCTGTC
716131 TGTGGAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.03, C:0.41, G:0.26, T:0.31
Consensus pattern (20 bp):
GTCCGTCCGTCCGTCTGTCA
Found at i:716133 original size:4 final size:4
Alignment explanation
Indices: 716092--716126 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
716082 GAATCACCTT
* *
716092 GTCC GTCC GTCC GTCT GTCA GTCC GTCC GTCC GTC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
716127 TGTCTGTGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.03, C:0.43, G:0.26, T:0.29
Consensus pattern (4 bp):
GTCC
Found at i:716456 original size:148 final size:146
Alignment explanation
Indices: 716138--716678 Score: 686
Period size: 148 Copynumber: 3.7 Consensus size: 146
716128 GTCTGTGGAA
* * *
716138 TCGTGTCCGGTCCAAATCTTTCTTATGGAAAAACATTGGAAGTTTTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
** *
716203 TTATGACCTAAGGGTGTGGGATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAA-G-----GGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGA
716262 AGAAAAAATGCAAAAT
131 AGAAAAAATGCAAAAT
* * * *
716278 TCGTGTCCGATCTATATCTTTCTTATGGAGAAACATTGGAAGTACTTACTTCACACAAAGA-TCC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
716342 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGA
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGA
716407 AGAAAAAATGCAAACTAAT
131 AGAAAAAATGC-AA--AAT
*
716426 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAGAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* * * * *
716491 TTATGACCCT-AGGGTGTGTCATGACCTTGATCCAAGGTCATTTGGACAAGGTCCAGTTCACTGG
66 TTATGA-CCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGG
*
716555 CAGAAAAAAAATGCAAAAT
130 -A-AGAAAAAATGCAAAAT
* * * * * * * * * *
716574 TTGAGTCCGGTCTATATCTTCCTTATTGAGAAGCATT-GAATGTTCTAAATTCACACAAATATAG
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAA-GTTCTTACTTCACACAAAGATTG
* * *
716638 CTTATGGCCCAAGGATGTGTCATGACCTTGACCCAAGGTCA
65 CTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCA
716679 ATTGAGGAAG
Statistics
Matches: 350, Mismatches: 36, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
139 55 0.16
140 56 0.16
145 13 0.04
146 2 0.01
147 5 0.01
148 146 0.42
149 57 0.16
150 6 0.02
151 10 0.03
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (146 bp):
TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGA
AGAAAAAATGCAAAAT
Found at i:721109 original size:42 final size:42
Alignment explanation
Indices: 721020--721111 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
721010 TAGCTGCCTA
* * *
721020 ATGTGGCTATTTCATGTAAAGATGGTGCTTTATTATATCATG
1 ATGTGGCTATTTCATGGAAAGATGGTGCTTTATAATATAATG
* * *
721062 CTGTGGTTATTTCATGGGAAGATGGTGCTTTATAATATGAAT-
1 ATGTGGCTATTTCATGGAAAGATGGTGCTTTATAATAT-AATG
721104 ATGTGGCT
1 ATGTGGCT
721112 TTATTATATT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
42 39 0.95
43 2 0.05
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (42 bp):
ATGTGGCTATTTCATGGAAAGATGGTGCTTTATAATATAATG
Found at i:721145 original size:63 final size:63
Alignment explanation
Indices: 721046--721183 Score: 249
Period size: 63 Copynumber: 2.2 Consensus size: 63
721036 TAAAGATGGT
*
721046 GCTTTATTATATCATGCTGTGGTTATTTCATGGGAAGATGGTGCTTTATAATATGAATATGTG
1 GCTTTATTATATCATGCTGTGGTTATTTCATGGGAAGATGGTGCTTTATAATATGAAGATGTG
* *
721109 GCTTTATTATATTATGCTGTGGTTATTTCATGGGAAGATGGTGCTTTATAATATGACGATGTG
1 GCTTTATTATATCATGCTGTGGTTATTTCATGGGAAGATGGTGCTTTATAATATGAAGATGTG
721172 GCTTTATTATAT
1 GCTTTATTATAT
721184 GAAGAATTTA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 72 1.00
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (63 bp):
GCTTTATTATATCATGCTGTGGTTATTTCATGGGAAGATGGTGCTTTATAATATGAAGATGTG
Found at i:721188 original size:42 final size:41
Alignment explanation
Indices: 721142--721275 Score: 99
Period size: 42 Copynumber: 3.4 Consensus size: 41
721132 TATTTCATGG
721142 GAAGATGGTGCTTTATAATATGACGATGTGGCTTTATTATAT
1 GAAGATGGTGCTTTATAATATGA-GATGTGGCTTTATTATAT
* *
721184 GAAGAAT-TTAG-TTGA-AA-AT--G--GT-GCTTTATTATAT
1 GAAG-ATGGT-GCTTTATAATATGAGATGTGGCTTTATTATAT
* * *
721218 GAAGATGGTGCTTTTTTATATGAAGATG-GTGCTTTATTATGT
1 GAAGATGGTGCTTTATAATATG-AGATGTG-GCTTTATTATAT
*
721260 GAAGGTGGTGCTTTAT
1 GAAGATGGTGCTTTAT
721276 TAAATGAAGA
Statistics
Matches: 70, Mismatches: 9, Indels: 26
0.67 0.09 0.25
Matches are distributed among these distances:
33 3 0.04
34 19 0.27
35 3 0.04
36 2 0.03
37 1 0.01
39 1 0.01
40 2 0.03
41 3 0.04
42 33 0.47
43 3 0.04
ACGTcount: A:0.28, C:0.05, G:0.25, T:0.42
Consensus pattern (41 bp):
GAAGATGGTGCTTTATAATATGAGATGTGGCTTTATTATAT
Found at i:721220 original size:21 final size:21
Alignment explanation
Indices: 721196--721338 Score: 156
Period size: 21 Copynumber: 7.1 Consensus size: 21
721186 AGAATTTAGT
*
721196 TGAAAATGGTGCTTTATTATA
1 TGAAGATGGTGCTTTATTATA
*
721217 TGAAGATGGTGCTTTTTTATA
1 TGAAGATGGTGCTTTATTATA
*
721238 TGAAGATGGTGCTTTATTATG
1 TGAAGATGGTGCTTTATTATA
* *
721259 TGAAGGTGGTGCTTTATTAAA
1 TGAAGATGGTGCTTTATTATA
721280 TGAAGATGGTGCTTT-TT-TA
1 TGAAGATGGTGCTTTATTATA
*
721299 T--TGATGGTGCTTT-TT-TA
1 TGAAGATGGTGCTTTATTATA
* * *
721316 TG-TGAAGGTGCTTTTTTATA
1 TGAAGATGGTGCTTTATTATA
721336 TGA
1 TGA
721339 TGGTGCTTTT
Statistics
Matches: 107, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
17 16 0.15
18 11 0.10
19 4 0.04
20 6 0.06
21 70 0.65
ACGTcount: A:0.24, C:0.05, G:0.25, T:0.46
Consensus pattern (21 bp):
TGAAGATGGTGCTTTATTATA
Found at i:721266 original size:18 final size:18
Alignment explanation
Indices: 721224--721361 Score: 107
Period size: 21 Copynumber: 7.2 Consensus size: 18
721214 ATATGAAGAT
*
721224 GGTGCTTTTTTATATGAAGA
1 GGTGCTTTTTTATGTG-A-A
*
721244 TGGTGCTTTATTATGTGAA
1 -GGTGCTTTTTTATGTGAA
* **
721263 GGTGGTGCTTTATTAAATGAA
1 ---GGTGCTTTTTTATGTGAA
*
721284 GATGGTGCTTTTTTAT-TGAT
1 G---GTGCTTTTTTATGTGAA
721304 GGTGCTTTTTTATGTGAA
1 GGTGCTTTTTTATGTGAA
* *
721322 GGTGCTTTTTTATATGAT
1 GGTGCTTTTTTATGTGAA
*
721340 GGTGCTTTTTAATGTGAA
1 GGTGCTTTTTTATGTGAA
721358 GGTG
1 GGTG
721362 TTCACTCGGA
Statistics
Matches: 98, Mismatches: 13, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
17 12 0.12
18 39 0.40
19 1 0.01
20 5 0.05
21 41 0.42
ACGTcount: A:0.20, C:0.05, G:0.28, T:0.47
Consensus pattern (18 bp):
GGTGCTTTTTTATGTGAA
Found at i:721340 original size:36 final size:35
Alignment explanation
Indices: 721287--721361 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 35
721277 AAATGAAGAT
*
721287 GGTGCTTTTTTATTGATGGTGCTTTTTTATGTGAA
1 GGTGCTTTTTTATTGATGGTGCTTTTTAATGTGAA
721322 GGTGCTTTTTTATATGATGGTGCTTTTTAATGTGAA
1 GGTGCTTTTTTAT-TGATGGTGCTTTTTAATGTGAA
721358 GGTG
1 GGTG
721362 TTCACTCGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 13 0.34
36 25 0.66
ACGTcount: A:0.16, C:0.05, G:0.28, T:0.51
Consensus pattern (35 bp):
GGTGCTTTTTTATTGATGGTGCTTTTTAATGTGAA
Found at i:722336 original size:21 final size:21
Alignment explanation
Indices: 722282--722515 Score: 244
Period size: 21 Copynumber: 11.1 Consensus size: 21
722272 AAAAGCACCG
722282 TCATATAA-AAAGCACCATCT
1 TCATATAATAAAGCACCATCT
722302 TCATATAA-AAAGCACCATCT
1 TCATATAATAAAGCACCATCT
* **
722322 TCAGATAATAAAGCACCGCCT
1 TCATATAATAAAGCACCATCT
722343 TCATATAATAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
* *
722364 TCATATCA-AAAGCACCATCA
1 TCATATAATAAAGCACCATCT
* *
722384 TCATAAAATAAAGCACCGTCT
1 TCATATAATAAAGCACCATCT
* *
722405 TCACATAATAAAGCAGCACCACCT
1 TCATATAAT-AA--AGCACCATCT
* *
722429 TCATATAAGAAAGCACCACCT
1 TCATATAATAAAGCACCATCT
722450 TCATATAATAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
* * * *
722471 TCACATGAA-ATAACCA-CAGCA
1 TCATAT-AATA-AAGCACCATCT
*
722492 TAATATAATAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
722513 TCA
1 TCA
722516 CATGAAATAG
Statistics
Matches: 175, Mismatches: 30, Indels: 17
0.79 0.14 0.08
Matches are distributed among these distances:
20 50 0.29
21 100 0.57
22 8 0.05
23 2 0.01
24 15 0.09
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.23
Consensus pattern (21 bp):
TCATATAATAAAGCACCATCT
Found at i:722345 original size:41 final size:42
Alignment explanation
Indices: 722282--722473 Score: 228
Period size: 41 Copynumber: 4.6 Consensus size: 42
722272 AAAAGCACCG
*
722282 TCATATAA-AAAGCACCATCTTCATATAA-AAAGCACCATCT
1 TCATATAATAAAGCACCACCTTCATATAATAAAGCACCATCT
* *
722322 TCAGATAATAAAGCACCGCCTTCATATAATAAAGCACCATCT
1 TCATATAATAAAGCACCACCTTCATATAATAAAGCACCATCT
* * * * *
722364 TCATATCA-AAAGCACCATCATCATAAAATAAAGCACCGTCT
1 TCATATAATAAAGCACCACCTTCATATAATAAAGCACCATCT
* * *
722405 TCACATAATAAAGCAGCACCACCTTCATATAAGAAAGCACCACCT
1 TCATATAAT-AA--AGCACCACCTTCATATAATAAAGCACCATCT
*
722450 TCATATAATAAAGCACCATCTTCA
1 TCATATAATAAAGCACCACCTTCA
722474 CATGAAATAA
Statistics
Matches: 126, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
40 7 0.06
41 52 0.41
42 30 0.24
43 2 0.02
44 2 0.02
45 33 0.26
ACGTcount: A:0.43, C:0.27, G:0.07, T:0.23
Consensus pattern (42 bp):
TCATATAATAAAGCACCACCTTCATATAATAAAGCACCATCT
Found at i:722366 original size:62 final size:62
Alignment explanation
Indices: 722282--722466 Score: 255
Period size: 62 Copynumber: 2.9 Consensus size: 62
722272 AAAAGCACCG
*
722282 TCATATAA-AAAGCACCATCTTCATATAAAAAGCACCATCTTCAGATAATAAAGCACCGCCT
1 TCATATAATAAAGCACCATCTTCATATAAAAAGCACCATCTTCATATAATAAAGCACCGCCT
* * * *
722343 TCATATAATAAAGCACCATCTTCATATCAAAAGCACCATCATCATAAAATAAAGCACCGTCT
1 TCATATAATAAAGCACCATCTTCATATAAAAAGCACCATCTTCATATAATAAAGCACCGCCT
* * *
722405 TCACATAATAAAGCAGCACCACCTTCATATAAGAAAGCACCACCTTCATATAATAAAGCACC
1 TCATATAAT-AA--AGCACCATCTTCATATAA-AAAGCACCATCTTCATATAATAAAGCACC
722467 ATCTTCACAT
Statistics
Matches: 108, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
61 8 0.07
62 56 0.52
63 2 0.02
65 16 0.15
66 26 0.24
ACGTcount: A:0.43, C:0.27, G:0.08, T:0.22
Consensus pattern (62 bp):
TCATATAATAAAGCACCATCTTCATATAAAAAGCACCATCTTCATATAATAAAGCACCGCCT
Found at i:722391 original size:17 final size:19
Alignment explanation
Indices: 722272--722386 Score: 63
Period size: 20 Copynumber: 5.8 Consensus size: 19
722262 CCTCACATTA
* *
722272 AAAAGCACCGTCAT--ATA
1 AAAAGCACCATCATCAATC
* *
722289 AAAAGCACCATCTTCATATA
1 AAAAGCACCATCATCA-ATC
* *
722309 AAAAGCACCATCTTCAGATA
1 AAAAGCACCATCATCA-ATC
** * *
722329 ATAAAGCACCGCCTTCATATA
1 A-AAAGCACCATCATCA-ATC
*
722350 ATAAAGCACCATCTTCATATC
1 A-AAAGCACCATCATCA-ATC
722371 AAAAGCACCATCATCA
1 AAAAGCACCATCATCA
722387 TAAAATAAAG
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
17 12 0.14
20 37 0.44
21 35 0.42
ACGTcount: A:0.43, C:0.27, G:0.08, T:0.22
Consensus pattern (19 bp):
AAAAGCACCATCATCAATC
Found at i:722472 original size:107 final size:108
Alignment explanation
Indices: 722290--722518 Score: 299
Period size: 107 Copynumber: 2.2 Consensus size: 108
722280 CGTCATATAA
* * * *
722290 AAAGCACCATCTT--CAT-ATAAA-AAGCACCATCTTCAGATAATAAAGCACCGCCTTCATATAA
1 AAAGCACCATCTTCACATAATAAAGCAGCACCACCTTCAGATAAGAAAGCACCACCTTCATATAA
* * * *
722351 TAAAGCACCATCTTCATATC-AA-AAGCACCATCATCATAAAAT
66 TAAAGCACCATCTTCACATCAAATAACCA-CAGCATAATAAAAT
* *
722393 AAAGCACCGTCTTCACATAATAAAGCAGCACCACCTTCATATAAGAAAGCACCACCTTCATATAA
1 AAAGCACCATCTTCACATAATAAAGCAGCACCACCTTCAGATAAGAAAGCACCACCTTCATATAA
* *
722458 TAAAGCACCATCTTCACATGAAATAACCACAGCATAATATAAT
66 TAAAGCACCATCTTCACATCAAATAACCACAGCATAATAAAAT
722501 AAAGCACCATCTTCACAT
1 AAAGCACCATCTTCACAT
722519 GAAATAGCCA
Statistics
Matches: 107, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
103 12 0.11
105 3 0.03
106 5 0.05
107 53 0.50
108 30 0.28
109 4 0.04
ACGTcount: A:0.43, C:0.27, G:0.07, T:0.22
Consensus pattern (108 bp):
AAAGCACCATCTTCACATAATAAAGCAGCACCACCTTCAGATAAGAAAGCACCACCTTCATATAA
TAAAGCACCATCTTCACATCAAATAACCACAGCATAATAAAAT
Found at i:724584 original size:195 final size:194
Alignment explanation
Indices: 724252--724640 Score: 769
Period size: 195 Copynumber: 2.0 Consensus size: 194
724242 TTTCAGTTTA
724252 TATTTTTCACTCTGCCCGCTCCTCTAAATATTCAACAACGTAGTTTTTTTTTATTTCAATTTTAA
1 TATTTTTCACTCTGCCCGCTCCTCTAAATATTCAACAACGTAGTTTTTTTTTATTTCAATTTTAA
724317 AGAATAAGATAAGGAAAAAAATCTGACATTAAAAAAAATCGGACAAAGAATATGTCAAAAAGTTG
66 AGAATAAGATAAGGAAAAAAATCTGACATTAAAAAAAATCGGACAAAGAATATGTCAAAAAGTTG
724382 CATATAAGTAAAACCATATATTATAACATTTGAGTTTTGGTGAATTAAAAATGTTTTCCTTTGT
131 CATATAAGTAAAACCATATATTATAACATTTGAGTTTTGGTGAATTAAAAATGTTTTCCTTTGT
724446 NTATTTTTCACTCTGCCCGCTCCTCTAAATATTCAACAACGTAGTTTTTTTTTATTTCAATTTTA
1 -TATTTTTCACTCTGCCCGCTCCTCTAAATATTCAACAACGTAGTTTTTTTTTATTTCAATTTTA
724511 AAGAATAAGATAAGGAAAAAAATCTGACATTAAAAAAAATCGGACAAAGAATATGTCAAAAAGTT
65 AAGAATAAGATAAGGAAAAAAATCTGACATTAAAAAAAATCGGACAAAGAATATGTCAAAAAGTT
724576 GCATATAAGTAAAACCATATATTATAACATTTGAGTTTTGGTGAATTAAAAATGTTTTCCTTTGT
130 GCATATAAGTAAAACCATATATTATAACATTTGAGTTTTGGTGAATTAAAAATGTTTTCCTTTGT
724641 AAAATTGGAN
Statistics
Matches: 194, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
195 194 1.00
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (194 bp):
TATTTTTCACTCTGCCCGCTCCTCTAAATATTCAACAACGTAGTTTTTTTTTATTTCAATTTTAA
AGAATAAGATAAGGAAAAAAATCTGACATTAAAAAAAATCGGACAAAGAATATGTCAAAAAGTTG
CATATAAGTAAAACCATATATTATAACATTTGAGTTTTGGTGAATTAAAAATGTTTTCCTTTGT
Found at i:733299 original size:16 final size:15
Alignment explanation
Indices: 733269--733314 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
733259 ATTTAATATG
733269 ATAAAGGTG-GTCTC
1 ATAAAGGTGAGTCTC
733283 ATAAAGGTGAAGTCTC
1 ATAAAGGTG-AGTCTC
*
733299 ATAAGGGTGATGTCTC
1 ATAAAGGTGA-GTCTC
733315 GTCTCGGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 9 0.32
15 1 0.04
16 18 0.64
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.28
Consensus pattern (15 bp):
ATAAAGGTGAGTCTC
Found at i:737009 original size:17 final size:18
Alignment explanation
Indices: 736987--737021 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
736977 AGCACGAACA
736987 CGGATACAGCGAA-TTTT
1 CGGATACAGCGAAGTTTT
*
737004 CGGATATAGCGAAGTTTT
1 CGGATACAGCGAAGTTTT
737022 TTGAGTCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (18 bp):
CGGATACAGCGAAGTTTT
Found at i:737103 original size:17 final size:17
Alignment explanation
Indices: 737062--737104 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
737052 TTTGCAAAAT
*
737062 TTTACGGTTATAACGAA
1 TTTACGGATATAACGAA
737079 -TT-CGGATATAACGAA
1 TTTACGGATATAACGAA
737094 TTTACGGATAT
1 TTTACGGATAT
737105 GATATTTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 12 0.52
16 4 0.17
17 7 0.30
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (17 bp):
TTTACGGATATAACGAA
Found at i:737395 original size:16 final size:16
Alignment explanation
Indices: 737374--737404 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
737364 TCGTTAATTA
737374 TACGGATATAACGAAT
1 TACGGATATAACGAAT
737390 TACGGATATAACGAA
1 TACGGATATAACGAA
737405 GTAAATCCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (16 bp):
TACGGATATAACGAAT
Found at i:747300 original size:2 final size:2
Alignment explanation
Indices: 747293--747361 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
747283 AAACTTATGT
747293 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
747335 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
747362 AAAACAAGCT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:757749 original size:15 final size:15
Alignment explanation
Indices: 757725--757756 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
757715 AATGACTTCA
*
757725 TTTCCTCATCTTAAC
1 TTTCCACATCTTAAC
757740 TTTCCACATCTTAAC
1 TTTCCACATCTTAAC
757755 TT
1 TT
757757 AGAATTAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTCCACATCTTAAC
Found at i:758702 original size:20 final size:22
Alignment explanation
Indices: 758663--758705 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
758653 GGTAACCGTC
758663 TTTGGGGAAAACCACATAGATT
1 TTTGGGGAAAACCACATAGATT
758685 TTTGGGG-AAACC-CATAGATT
1 TTTGGGGAAAACCACATAGATT
758705 T
1 T
758706 CTCACAGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.43
21 5 0.24
22 7 0.33
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (22 bp):
TTTGGGGAAAACCACATAGATT
Found at i:766882 original size:46 final size:47
Alignment explanation
Indices: 766830--766943 Score: 124
Period size: 46 Copynumber: 2.4 Consensus size: 47
766820 CCTGCTTATT
* *
766830 TTTCCAATATACTAGTACAGTGGGAATGCCCGTGTTTT-GGATATCC
1 TTTCCAATACACTAGTACAGTCGGAATGCCCGTGTTTTGGGATATCC
* * * * * * *
766876 TTTCCAATGCACTAGTGCAGTCGGATTGCTCTTGTTTTGGGGTATTC
1 TTTCCAATACACTAGTACAGTCGGAATGCCCGTGTTTTGGGATATCC
766923 TTTCCAGA-ACACTAGTACAGT
1 TTTCCA-ATACACTAGTACAGT
766944 AGGATCGCTA
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
46 31 0.56
47 23 0.42
48 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (47 bp):
TTTCCAATACACTAGTACAGTCGGAATGCCCGTGTTTTGGGATATCC
Found at i:767759 original size:2 final size:2
Alignment explanation
Indices: 767752--767801 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
767742 CTTAATTAAA
767752 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
767794 CT CT CT CT
1 CT CT CT CT
767802 ATATATATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:784159 original size:110 final size:112
Alignment explanation
Indices: 783622--784219 Score: 493
Period size: 115 Copynumber: 5.3 Consensus size: 112
783612 AAAGGGAGAC
* * * * ** * *
783622 TTACATGCGTCAGCAAACCTCGATAGGAAGAGAAAAAGGAACATGTGTCAGCAGACTGCAATAGT
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAAAAGTTACATGTGTCAGCAGACAGC--GA-T
** * * * * * *
783687 AAGAGGAA-CCG-TATCATGTGTCAGCATACCTCAATAGAAAGAGGAAAAG
63 AAGAGGAATAAGTTA-CATATGTCAGCAAACCGCGATAGGAAGAGGAACAG
* * * * *
783736 TTACATGTGTCAGCAGAACGTGAAAGGAAGA-GAAATAGTTACACGTGTCAGCAAACCA-CGATA
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAAA-AGTTACATGTGTCAGCAGA-CAGCGATA
* * * * * * *
783799 GGTAGAGGGA-CAGTTACATGTGTCAGCAAACCGCAATAGTAAAAGGAATAAG
64 ---AGAGGAATAAGTTACATATGTCAGCAAACCGCGATAGGAAGAGGAA-CAG
* * *
783851 TTACAAGTGTCAGCAGACCGCCATAGGAAGAGGAAAAGCTT-CATGTGTCAGCAGACTGCGATAG
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAAAAG-TTACATGTGTCAGCAGACAGCGAT--
*
783915 GAAGAGGAATAAGTTACATATGTCAGCAGAA-TGCGATAGGAAGAGGAACAG
63 -AAGAGGAATAAGTTACATATGTCAGCA-AACCGCGATAGGAAGAGGAACAG
* * * * * *
783966 TTACATTTGTCAGCAGACTGCGATAGTAAAAGGAACAGTTACATGTGTCAGCAAACCA-CG--AA
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAAAAGTTACATGTGTCAGCAGA-CAGCGATAA
* * * *
784028 GAGGAATAATTTCCATGTGTCAGCAGACCGCGATAGGAAGAGGAACAG
65 GAGGAATAAGTTACATATGTCAGCAAACCGCGATAGGAAGAGGAACAG
* *
784076 TT-CA-GTGTCAGTAGACCGCGATAGGAAGAGGAATAAGTTACATGTGTCAGCAGACAGTGATAA
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAA-AAGTTACATGTGTCAGCAGACAGCGATAA
* * * * *
784139 GA-GAATCAGTTACACATGTCAGCAAACCGCGATAGTATGAAGAACAG
65 GAGGAATAAGTTACATATGTCAGCAAACCGCGATAGGAAGAGGAACAG
* *
784186 TTCCATGTGTCAGCAGACCGCGACAGGAAGAGGA
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGA
784220 GCAGTTGCAT
Statistics
Matches: 392, Mismatches: 68, Indels: 50
0.77 0.13 0.10
Matches are distributed among these distances:
108 26 0.07
109 22 0.06
110 83 0.21
111 8 0.02
112 27 0.07
113 3 0.01
114 80 0.20
115 104 0.27
116 36 0.09
117 2 0.01
118 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.18
Consensus pattern (112 bp):
TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAAAAGTTACATGTGTCAGCAGACAGCGATAAG
AGGAATAAGTTACATATGTCAGCAAACCGCGATAGGAAGAGGAACAG
Found at i:784225 original size:38 final size:38
Alignment explanation
Indices: 783622--784225 Score: 505
Period size: 38 Copynumber: 16.1 Consensus size: 38
783612 AAAGGGAGAC
* * * * *
783622 TTACATGCGTCAGCAAACCTCGATAGGAAGAGAAAAAG
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAACAG
** * * * *
783660 GAACATGTGTCAGCAGACTGCAATAGTAAGAGGAACCG
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAACAG
* * * * *
783698 -TATCATGTGTCAGCATACCTCAATAGAAAGAGGAAAAG
1 TTA-CATGTGTCAGCAGACCGCGATAGGAAGAGGAACAG
* * * * *
783736 TTACATGTGTCAGCAGAACGTGAAAGGAAGAGAAATAG
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAACAG
* * * * *
783774 TTACACGTGTCAGCAAACCACGATAGGTAGAGGGACAG
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAACAG
* * * * *
783812 TTACATGTGTCAGCAAACCGCAATAGTAAAAGGAATAAG
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAA-CAG
* * *
783851 TTACAAGTGTCAGCAGACCGCCATAGGAAGAGGAAAAG
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAACAG
* *
783889 CTT-CATGTGTCAGCAGACTGCGATAGGAAGAGGAATAAG
1 -TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAA-CAG
* **
783928 TTACATATGTCAGCAGAATGCGATAGGAAGAGGAACAG
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAACAG
* * * *
783966 TTACATTTGTCAGCAGACTGCGATAGTAAAAGGAACAG
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAACAG
* * * *
784004 TTACATGTGTCAGCA-AAC-C---ACGAAGAGGAATAAT
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAA-CAG
*
784038 TTCCATGTGTCAGCAGACCGCGATAGGAAGAGGAACAG
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAACAG
* *
784076 TT-CA-GTGTCAGTAGACCGCGATAGGAAGAGGAATAAG
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAA-CAG
* *
784113 TTACATGTGTCAGCAGACAGTGAT---AAGA-GAATCAG
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAA-CAG
** * * * *
784148 TTACACATGTCAGCAAACCGCGATAGTATGAAGAACAG
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAACAG
* * *
784186 TTCCATGTGTCAGCAGACCGCGACAGGAAGAGGAGCAG
1 TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAACAG
784224 TT
1 TT
784226 GCATTTGTAG
Statistics
Matches: 453, Mismatches: 94, Indels: 38
0.77 0.16 0.06
Matches are distributed among these distances:
33 8 0.02
34 15 0.03
35 27 0.06
36 34 0.08
37 8 0.02
38 264 0.58
39 97 0.21
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.19
Consensus pattern (38 bp):
TTACATGTGTCAGCAGACCGCGATAGGAAGAGGAACAG
Found at i:786917 original size:16 final size:16
Alignment explanation
Indices: 786892--786922 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
786882 AAAAATCAAT
*
786892 CTAATGTTTACAAAAA
1 CTAATATTTACAAAAA
786908 CTAATATTTACAAAA
1 CTAATATTTACAAAA
786923 TGACCAATAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.32
Consensus pattern (16 bp):
CTAATATTTACAAAAA
Found at i:789769 original size:38 final size:38
Alignment explanation
Indices: 789714--790619 Score: 875
Period size: 38 Copynumber: 23.5 Consensus size: 38
789704 GAATTAAAGA
* * * *
789714 GAAGAGAAACAGTTACATATGTCAGCAAACTTCGATAG
1 GAAGAGGAACAGTTACATGTGTCAGCAGACCTCGATAG
* * * *
789752 GAAAAGAAACATTTACATGTGTCAGCAACACCTCGATAG
1 GAAGAGGAACAGTTACATGTGTCAGC-AGACCTCGATAG
* * ** * *
789791 GAAGAGAAACAGTTCCATGTGTCAAAAGACCGCGATAA
1 GAAGAGGAACAGTTACATGTGTCAGCAGACCTCGATAG
* * * *
789829 AAAGAGAAACAAGTTACATGTGTCAGTAGA-CTATGATA-
1 GAAGAGGAAC-AGTTACATGTGTCAGCAGACCT-CGATAG
* * * *
789867 GAATAAGAAACAGTTACATATGTCAGCAGACCGCGATAG
1 GAA-GAGGAACAGTTACATGTGTCAGCAGACCTCGATAG
* *
789906 G-ATAGGAACAGTTACATGTGTCAGCAGA-CTGCGTTAG
1 GAAGAGGAACAGTTACATGTGTCAGCAGACCT-CGATAG
* * * * * *
789943 AAACAGGAACAGTTACTTGTGTCACCGGACCACGATAG
1 GAAGAGGAACAGTTACATGTGTCAGCAGACCTCGATAG
*
789981 GAAGAGGAACAGTTACATGTGTCAGCAGA-CTGCAATAAAGGGAG
1 GAAGAGGAACAGTTACATGTGTCAGCAGACCT-CGAT------AG
* * * *
790025 GTAACATGTGTAACAAGTAACATGTGTCAGCAGACCGT-TAAAG
1 G-AAGA-G-G-AAC-AGTTACATGTGTCAGCAGACC-TCGATAG
* * * * * *
790068 AAAGAGAAACAGTGACATATGTCAGCGGACTTCGATAG
1 GAAGAGGAACAGTTACATGTGTCAGCAGACCTCGATAG
* * *
790106 GAAGAGGAACAGTTAAATGTGTCAGCAAACCCCGATAG
1 GAAGAGGAACAGTTACATGTGTCAGCAGACCTCGATAG
* * *
790144 GGAGAGGAATAGTTACATGTGTCAGCAGACTTCGATAG
1 GAAGAGGAACAGTTACATGTGTCAGCAGACCTCGATAG
* * * *
790182 GAAGAGGGACAGCTACATGTGT-AGGCGGACCACGATAG
1 GAAGAGGAACAGTTACATGTGTCA-GCAGACCTCGATAG
790220 GAAGAGGAACAGTTACATGTGTCAGCAGACCTCGATAG
1 GAAGAGGAACAGTTACATGTGTCAGCAGACCTCGATAG
* *
790258 GAAGAGGAACAGTTCCATGTGTCAGCAGACCTTGATAG
1 GAAGAGGAACAGTTACATGTGTCAGCAGACCTCGATAG
* * *
790296 AAAGAGG-A-AGTTACATATGTCAGCAGACCGCGATAG
1 GAAGAGGAACAGTTACATGTGTCAGCAGACCTCGATAG
* * *
790332 GAAGAGGAATAGTTACATATGTCAGCAGA-CTGCGATAA
1 GAAGAGGAACAGTTACATGTGTCAGCAGACCT-CGATAG
* * *
790370 TAAGAGGAATAGTTACATGTGTCAGCAGACTTCGATAG
1 GAAGAGGAACAGTTACATGTGTCAGCAGACCTCGATAG
790408 GAAGAGGAACAGTTACATGTGTCAGCAGACCTCGATAG
1 GAAGAGGAACAGTTACATGTGTCAGCAGACCTCGATAG
790446 GAAGAGGAACAGTTACATGTGTCAGCAGACCTCGATAG
1 GAAGAGGAACAGTTACATGTGTCAGCAGACCTCGATAG
790484 GAAGAGGAACAGTTACATGTGTCAGCAGACCTTC-ATAG
1 GAAGAGGAACAGTTACATGTGTCAGCAGACC-TCGATAG
* *
790522 GAAAAGGAACAGTTACATGTGTCAGCAGA-CTGCAATA-
1 GAAGAGGAACAGTTACATGTGTCAGCAGACCT-CGATAG
* * *
790559 AAGAGAGGAACAAGTTACAAGTGTCAGCAGACCTTGATAG
1 GA-AGAGGAAC-AGTTACATGTGTCAGCAGACCTCGATAG
**
790599 GAAGAAAAACAGGTTACATGT
1 GAAGAGGAACA-GTTACATGT
790620 ATTGGTCGAA
Statistics
Matches: 720, Mismatches: 110, Indels: 75
0.80 0.12 0.08
Matches are distributed among these distances:
36 32 0.04
37 37 0.05
38 508 0.71
39 102 0.14
40 3 0.00
41 1 0.00
42 3 0.00
43 2 0.00
44 3 0.00
45 3 0.00
46 1 0.00
47 1 0.00
48 3 0.00
49 19 0.03
50 1 0.00
51 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (38 bp):
GAAGAGGAACAGTTACATGTGTCAGCAGACCTCGATAG
Found at i:791536 original size:16 final size:16
Alignment explanation
Indices: 791511--791541 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
791501 AAAAATCAAT
*
791511 CTAATGTTTACAAAAA
1 CTAATATTTACAAAAA
791527 CTAATATTTACAAAA
1 CTAATATTTACAAAA
791542 TGACCAATAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.32
Consensus pattern (16 bp):
CTAATATTTACAAAAA
Found at i:796179 original size:8 final size:8
Alignment explanation
Indices: 796168--796221 Score: 64
Period size: 8 Copynumber: 7.4 Consensus size: 8
796158 TAAAAAGTTT
796168 ACAGACGG
1 ACAGACGG
*
796176 ACAGACAG
1 ACAGACGG
796184 ACAGACGG
1 ACAGACGG
796192 AC--A--G
1 ACAGACGG
796196 ACAGACGG
1 ACAGACGG
796204 ACAGACGG
1 ACAGACGG
796212 AC-GACGG
1 ACAGACGG
796219 ACA
1 ACA
796222 AAATGTGATC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 3 0.08
6 2 0.05
7 7 0.18
8 27 0.69
ACGTcount: A:0.41, C:0.26, G:0.33, T:0.00
Consensus pattern (8 bp):
ACAGACGG
Found at i:796185 original size:12 final size:12
Alignment explanation
Indices: 796168--796214 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
796158 TAAAAAGTTT
* *
796168 ACAGACGGACAG
1 ACAGACAGACGG
796180 ACAGACAGACGG
1 ACAGACAGACGG
796192 ACAGACAGACGG
1 ACAGACAGACGG
*
796204 ACAGACGGACG
1 ACAGACAGACG
796215 ACGGACAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.40, C:0.26, G:0.34, T:0.00
Consensus pattern (12 bp):
ACAGACAGACGG
Found at i:796214 original size:4 final size:4
Alignment explanation
Indices: 796168--796209 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
796158 TAAAAAGTTT
* * *
796168 ACAG ACGG ACAG ACAG ACAG ACGG ACAG ACAG ACGG ACAG AC
1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG AC
796210 GGACGACGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.43, C:0.26, G:0.31, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:799013 original size:14 final size:14
Alignment explanation
Indices: 798994--799020 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
798984 ATGATTTGAA
798994 ATTCATATCTTAAG
1 ATTCATATCTTAAG
799008 ATTCATATCTTAA
1 ATTCATATCTTAA
799021 AAAGATGTCA
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:0.37, C:0.15, G:0.04, T:0.44
Consensus pattern (14 bp):
ATTCATATCTTAAG
Found at i:825443 original size:21 final size:21
Alignment explanation
Indices: 825419--825518 Score: 98
Period size: 21 Copynumber: 4.8 Consensus size: 21
825409 ATTAAACTAT
825419 AACAAATTAGTAATTTGTTAC
1 AACAAATTAGTAATTTGTTAC
* * *
825440 AACAAATTATTTATTTGTTAT
1 AACAAATTAGTAATTTGTTAC
*
825461 AA-AAGATTA-TCAATTTGTTAT
1 AACAA-ATTAGT-AATTTGTTAC
*
825482 AACAAATTCGTAATTTGTTAC
1 AACAAATTAGTAATTTGTTAC
*
825503 AATAAATT-GATAATTT
1 AACAAATTAG-TAATTT
825519 TTTTTATAAC
Statistics
Matches: 67, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
20 4 0.06
21 60 0.90
22 3 0.04
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (21 bp):
AACAAATTAGTAATTTGTTAC
Found at i:825476 original size:42 final size:42
Alignment explanation
Indices: 825430--825560 Score: 122
Period size: 42 Copynumber: 3.0 Consensus size: 42
825420 ACAAATTAGT
*
825430 AATTTGTTACAACAAATTATTTATTTGTTATAAAAGATTATC
1 AATTTGTTATAACAAATTATTTATTTGTTATAAAAGATTATC
** * *
825472 AATTTGTTATAACAAATTCGTAATTTGTTACAATAA-ATTGAT-
1 AATTTGTTATAACAAATTATTTATTTGTTATAA-AAGATT-ATC
* * *
825514 AATTTTTTTTATAACAAATTATAGTAGTTTGTTATCAAAGATTATC
1 AA--TTTGTTATAACAAATTAT-TTA-TTTGTTATAAAAGATTATC
825560 A
1 A
825561 TAGATTATCA
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
42 33 0.48
43 4 0.06
44 15 0.22
45 5 0.07
46 12 0.17
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (42 bp):
AATTTGTTATAACAAATTATTTATTTGTTATAAAAGATTATC
Found at i:825586 original size:21 final size:21
Alignment explanation
Indices: 825562--825619 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
825552 AGATTATCAT
825562 AGATTATCAATTTGTTATAAC
1 AGATTATCAATTTGTTATAAC
*
825583 AGATTATCAATTTGTTTTAAC
1 AGATTATCAATTTGTTATAAC
*
825604 AAATTATCAATTTGTT
1 AGATTATCAATTTGTT
825620 CAAATGAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (21 bp):
AGATTATCAATTTGTTATAAC
Found at i:831515 original size:15 final size:16
Alignment explanation
Indices: 831476--831519 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
831466 GATATAATAC
831476 CTATGGGAAATTTTTA
1 CTATGGGAAATTTTTA
831492 CTATGGGAAATTTTTA
1 CTATGGGAAATTTTTA
* *
831508 CTTTGGAAAATT
1 CTATGGGAAATT
831520 ACATGGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (16 bp):
CTATGGGAAATTTTTA
Found at i:845409 original size:16 final size:16
Alignment explanation
Indices: 845388--845419 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
845378 CCCCCCCCCC
845388 CCAAAAAAAAAAAAAA
1 CCAAAAAAAAAAAAAA
845404 CCAAAAAAAAAAAAAA
1 CCAAAAAAAAAAAAAA
845420 AAGNNNNNNN
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (16 bp):
CCAAAAAAAAAAAAAA
Found at i:846545 original size:18 final size:18
Alignment explanation
Indices: 846514--846549 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
846504 GGTGGACTTT
846514 GGAGTAAAGATGAACCGC
1 GGAGTAAAGATGAACCGC
* *
846532 GGAGTGAAGCTGAACCGC
1 GGAGTAAAGATGAACCGC
846550 CTCAAGGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.19, G:0.36, T:0.11
Consensus pattern (18 bp):
GGAGTAAAGATGAACCGC
Found at i:850612 original size:9 final size:9
Alignment explanation
Indices: 850590--850620 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
850580 ACCATTTGTC
850590 CGTTGTCTGT
1 CGTTGTC-GT
850600 CGTTGTCGT
1 CGTTGTCGT
850609 CGTTGTCGT
1 CGTTGTCGT
850618 CGT
1 CGT
850621 CGTTGTAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.67
10 7 0.33
ACGTcount: A:0.00, C:0.23, G:0.32, T:0.45
Consensus pattern (9 bp):
CGTTGTCGT
Found at i:851192 original size:156 final size:154
Alignment explanation
Indices: 850973--851254 Score: 359
Period size: 156 Copynumber: 1.8 Consensus size: 154
850963 AACAAAATTC
* * * * **
850973 TTTTAAAAACTATTTGGCCAAGAAAGCTCAAATTGGCGTGTAATTATCCTCAGATAATGTAGATT
1 TTTTAAAAACTATTAGGCCAAGAAAGCCCAAATTGGAGTGGAAGCATCCTCAGATAATGTAGATT
* * * * * *
851038 CAAGTTTATTTAAATCATGGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGGATACATTTTTATA
66 CAAGTTTATTCAAATAATAGT-CC-AGGGGTAGGGCGAGGCCACAATGGGGGATAAATTTTTATA
851103 TAAAAAGAAAATCTTTAAAAATCTTT
129 TAAAAAGAAAATCTTTAAAAATCTTT
* * ** *
851129 TTTTAAAAACTATTAGGCCAGGAAAGCCCAAATTTGAGTGGAAGCATCC-CGAGATCGTTTAGAT
1 TTTTAAAAACTATTAGGCCAAGAAAGCCCAAATTGGAGTGGAAGCATCCTC-AGATAATGTAGAT
* *
851193 TCAAGTTTGTTCAAATAATAGTCCAGGGGTAGGGTGAGGCCACAATGGGGGATAAATTTTTA
65 TCAAGTTTATTCAAATAATAGTCCAGGGGTAGGGCGAGGCCACAATGGGGGATAAATTTTTA
851255 CATGGGAATA
Statistics
Matches: 106, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
154 34 0.32
155 3 0.03
156 69 0.65
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (154 bp):
TTTTAAAAACTATTAGGCCAAGAAAGCCCAAATTGGAGTGGAAGCATCCTCAGATAATGTAGATT
CAAGTTTATTCAAATAATAGTCCAGGGGTAGGGCGAGGCCACAATGGGGGATAAATTTTTATATA
AAAAGAAAATCTTTAAAAATCTTT
Found at i:852660 original size:18 final size:18
Alignment explanation
Indices: 852637--852674 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
852627 AAATACTGAC
852637 ATGCAATACACAATAACA
1 ATGCAATACACAATAACA
852655 ATGCAATACACAATAACA
1 ATGCAATACACAATAACA
852673 AT
1 AT
852675 TTTTTTGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.21, G:0.05, T:0.18
Consensus pattern (18 bp):
ATGCAATACACAATAACA
Found at i:853191 original size:2 final size:2
Alignment explanation
Indices: 853184--853230 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
853174 TCTTGGAGAA
853184 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
853226 TC TC T
1 TC TC T
853231 AAATATATAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:858841 original size:18 final size:18
Alignment explanation
Indices: 858818--858853 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
858808 TATGCATATT
*
858818 CAAACTAAATGTGCATAA
1 CAAACTAAATGTACATAA
858836 CAAACTAAATGTACATAA
1 CAAACTAAATGTACATAA
858854 AGGGAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.17, G:0.08, T:0.22
Consensus pattern (18 bp):
CAAACTAAATGTACATAA
Found at i:863098 original size:2 final size:2
Alignment explanation
Indices: 863091--863136 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
863081 CAACCACTTT
863091 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
863133 TC TC
1 TC TC
863137 AGCTACTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:871629 original size:21 final size:21
Alignment explanation
Indices: 871600--871882 Score: 314
Period size: 21 Copynumber: 13.5 Consensus size: 21
871590 CATAATATGA
871600 TGATACTTCAACATTACATGC
1 TGATACTTCAACATTACATGC
* *
871621 TGATTCTTCAACATTACATGA
1 TGATACTTCAACATTACATGC
* *
871642 TGGTACTTTAACATTACATGC
1 TGATACTTCAACATTACATGC
*
871663 TGATACTTCAACATTACATGA
1 TGATACTTCAACATTACATGC
* * * *
871684 TGGTACTTAAACATAACGTGC
1 TGATACTTCAACATTACATGC
*
871705 TGATACTTCAACATTACATGA
1 TGATACTTCAACATTACATGC
* * *
871726 TGTTACTTTAACATTACGTGC
1 TGATACTTCAACATTACATGC
* *
871747 TGATACTTTAACATTACATGA
1 TGATACTTCAACATTACATGC
* * *
871768 TGGTACTTTAACATTACGTGC
1 TGATACTTCAACATTACATGC
*
871789 TGATACTTCAACATTACATGA
1 TGATACTTCAACATTACATGC
* * *
871810 TGGTACTTTAACATTACGTGC
1 TGATACTTCAACATTACATGC
* * *
871831 TGATACTTTAATATTATATGC
1 TGATACTTCAACATTACATGC
* *
871852 TGATACTTCATCATTACATGA
1 TGATACTTCAACATTACATGC
*
871873 TGGTACTTCA
1 TGATACTTCA
871883 CTATGTGGTG
Statistics
Matches: 215, Mismatches: 47, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 215 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (21 bp):
TGATACTTCAACATTACATGC
Found at i:871839 original size:84 final size:84
Alignment explanation
Indices: 871596--871882 Score: 421
Period size: 84 Copynumber: 3.4 Consensus size: 84
871586 TCTCCATAAT
* *
871596 ATGATGATACTTCAACATTACATGCTGATTCTTCAACATTACATGATGGTACTTTAACATTACAT
1 ATGATGATACTTCAACATTACATGCTGATACTTCAACATTACATGATGGTACTTTAACATTACGT
*
871661 GCTGATACTTCAACATTAC
66 GCTGATACTTTAACATTAC
* * * * *
871680 ATGATGGTACTTAAACATAACGTGCTGATACTTCAACATTACATGATGTTACTTTAACATTACGT
1 ATGATGATACTTCAACATTACATGCTGATACTTCAACATTACATGATGGTACTTTAACATTACGT
871745 GCTGATACTTTAACATTAC
66 GCTGATACTTTAACATTAC
* * *
871764 ATGATGGTACTTTAACATTACGTGCTGATACTTCAACATTACATGATGGTACTTTAACATTACGT
1 ATGATGATACTTCAACATTACATGCTGATACTTCAACATTACATGATGGTACTTTAACATTACGT
* *
871829 GCTGATACTTTAATATTAT
66 GCTGATACTTTAACATTAC
* * * *
871848 ATGCTGATACTTCATCATTACATGATGGTACTTCA
1 ATGATGATACTTCAACATTACATGCTGATACTTCA
871883 CTATGTGGTG
Statistics
Matches: 183, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 183 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (84 bp):
ATGATGATACTTCAACATTACATGCTGATACTTCAACATTACATGATGGTACTTTAACATTACGT
GCTGATACTTTAACATTAC
Found at i:871868 original size:42 final size:42
Alignment explanation
Indices: 871596--871838 Score: 405
Period size: 42 Copynumber: 5.8 Consensus size: 42
871586 TCTCCATAAT
* * * *
871596 ATGATGATACTTCAACATTACATGCTGATTCTTCAACATTAC
1 ATGATGGTACTTTAACATTACGTGCTGATACTTCAACATTAC
*
871638 ATGATGGTACTTTAACATTACATGCTGATACTTCAACATTAC
1 ATGATGGTACTTTAACATTACGTGCTGATACTTCAACATTAC
* *
871680 ATGATGGTACTTAAACATAACGTGCTGATACTTCAACATTAC
1 ATGATGGTACTTTAACATTACGTGCTGATACTTCAACATTAC
* *
871722 ATGATGTTACTTTAACATTACGTGCTGATACTTTAACATTAC
1 ATGATGGTACTTTAACATTACGTGCTGATACTTCAACATTAC
871764 ATGATGGTACTTTAACATTACGTGCTGATACTTCAACATTAC
1 ATGATGGTACTTTAACATTACGTGCTGATACTTCAACATTAC
871806 ATGATGGTACTTTAACATTACGTGCTGATACTT
1 ATGATGGTACTTTAACATTACGTGCTGATACTT
871839 TAATATTATA
Statistics
Matches: 189, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 189 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (42 bp):
ATGATGGTACTTTAACATTACGTGCTGATACTTCAACATTAC
Found at i:873512 original size:21 final size:21
Alignment explanation
Indices: 873486--873550 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
873476 ATACAGTAAG
* *
873486 CATGTAATGTTTAAGGACCAT
1 CATGTAATGTTGAAGTACCAT
873507 CATGTAATGTTGAAGTACCAT
1 CATGTAATGTTGAAGTACCAT
*
873528 AATGTAATGTTGAAGTACCAT
1 CATGTAATGTTGAAGTACCAT
873549 CA
1 CA
873551 CAGGGCGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.32
Consensus pattern (21 bp):
CATGTAATGTTGAAGTACCAT
Found at i:873596 original size:11 final size:11
Alignment explanation
Indices: 873580--873609 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
873570 TAAGCAAGTC
873580 CTTAAAGGTGG
1 CTTAAAGGTGG
873591 CTTAAAGGTGG
1 CTTAAAGGTGG
873602 CTTAAAGG
1 CTTAAAGG
873610 ATATACAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.30, C:0.10, G:0.33, T:0.27
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:873695 original size:11 final size:10
Alignment explanation
Indices: 873679--873728 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 10
873669 GTCCAAACTT
873679 CTTTAAGTCAC
1 CTTTAAG-CAC
*
873690 CTTTAAGCCAT
1 CTTTAAG-CAC
873701 CTTTAAGCTAC
1 CTTTAAGC-AC
*
873712 CTTTAAGCAT
1 CTTTAAGCAC
873722 CTTTAAG
1 CTTTAAG
873729 TGGCATTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.26
11 25 0.74
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (10 bp):
CTTTAAGCAC
Found at i:873724 original size:21 final size:22
Alignment explanation
Indices: 873678--873729 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
873668 TGTCCAAACT
873678 TCTTTAAGTCACCTTTAAGCCA
1 TCTTTAAGTCACCTTTAAGCCA
873700 TCTTTAAG-CTACCTTTAAG-CA
1 TCTTTAAGTC-ACCTTTAAGCCA
873721 TCTTTAAGT
1 TCTTTAAGT
873730 GGCATTTACG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (22 bp):
TCTTTAAGTCACCTTTAAGCCA
Found at i:873782 original size:22 final size:22
Alignment explanation
Indices: 873678--873782 Score: 54
Period size: 22 Copynumber: 4.8 Consensus size: 22
873668 TGTCCAAACT
*
873678 TCTTTAAG-TCACCTTTAAGCCA
1 TCTTTAAGTTC-CCTTTAAACCA
* * *
873700 TCTTTAAGCTACCTTT-AAGCA
1 TCTTTAAGTTCCCTTTAAACCA
** * **
873721 TCTTTAAGTGGCATTTACGCTC-
1 TCTTTAAGTTCCCTTTAAAC-CA
* ** *
873743 CCTTTAAGTTGTCGTTAAACCA
1 TCTTTAAGTTCCCTTTAAACCA
873765 TCTTTAAGTTCCCTTTAA
1 TCTTTAAGTTCCCTTTAA
873783 GTCAAGTTTG
Statistics
Matches: 58, Mismatches: 21, Indels: 8
0.67 0.24 0.09
Matches are distributed among these distances:
21 16 0.28
22 40 0.69
23 2 0.03
ACGTcount: A:0.25, C:0.24, G:0.11, T:0.40
Consensus pattern (22 bp):
TCTTTAAGTTCCCTTTAAACCA
Found at i:874052 original size:2 final size:2
Alignment explanation
Indices: 874045--874123 Score: 131
Period size: 2 Copynumber: 39.5 Consensus size: 2
874035 ATCGGTGAAA
** *
874045 TC TC TC TC AA TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
874087 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
874124 TAGTTCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:874539 original size:112 final size:112
Alignment explanation
Indices: 874342--874565 Score: 394
Period size: 112 Copynumber: 2.0 Consensus size: 112
874332 TAGTTTTGTT
* * * *
874342 CGTTTGTGTATATTTAATTTGAGTCTATTGTTTGTCCAACTTATGAAAACCCCTGGAACTAACAC
1 CGTTTGTGTACATCTAATTAGAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACAC
* *
874407 AGAATATACAAGATATACACAGCAGTTGTGTCGTGTGCCCAGGTGCA
66 AGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
874454 CGTTTGTGTACATCTAATTAGAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACAC
1 CGTTTGTGTACATCTAATTAGAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACAC
874519 AGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
66 AGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
874566 AGTCAGGGTT
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 106 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (112 bp):
CGTTTGTGTACATCTAATTAGAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACAC
AGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
Found at i:875149 original size:6 final size:6
Alignment explanation
Indices: 875140--875168 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
875130 AATGCCTGTG
875140 CCTAAC CCTAAC CCTAAC CCTAAC CCTAA
1 CCTAAC CCTAAC CCTAAC CCTAAC CCTAA
875169 TGAATGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.48, G:0.00, T:0.17
Consensus pattern (6 bp):
CCTAAC
Found at i:886576 original size:24 final size:24
Alignment explanation
Indices: 886549--886597 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
886539 CGTTAATTCT
886549 GCACTGTATGATCACGTGACAGTG
1 GCACTGTATGATCACGTGACAGTG
886573 GCACTGTATGATCACGTGACAGTG
1 GCACTGTATGATCACGTGACAGTG
886597 G
1 G
886598 GTTTAGATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (24 bp):
GCACTGTATGATCACGTGACAGTG
Found at i:888073 original size:2 final size:2
Alignment explanation
Indices: 888066--888126 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
888056 TATCGGATGC
888066 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
888108 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
888127 TGCATGCAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:893889 original size:74 final size:75
Alignment explanation
Indices: 893779--893950 Score: 183
Period size: 74 Copynumber: 2.3 Consensus size: 75
893769 ATACTGACAA
* * ** * * *
893779 AATCAATATTTGGAGTCTCTTG-AATTCTCTTAATATTTGTGATTTT-TTATTGGATTTTCTCAT
1 AATCAATATTTAGAGTGTCTTGCAATTCTCTTAATATTTGCAATTTTGAT-TTGAATTTTCTCAC
893842 TAATCCGAAAT
65 TAATCCGAAAT
* *
893853 GATCAATATTTAGAGTGTCTTGCAATATCT-TT-ATATTTGCAATTTTGATTTGAATTTTCTTAC
1 AATCAATATTTAGAGTGTCTTGCAAT-TCTCTTAATATTTGCAATTTTGATTTGAATTTTCTCAC
* * *
893916 TACTCTGATAT
65 TAATCCGAAAT
893927 AATCAATATTTAGAGTGTC-TGCAA
1 AATCAATATTTAGAGTGTCTTGCAA
893951 ACTTGGATTG
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
73 5 0.06
74 68 0.83
75 6 0.07
76 3 0.04
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (75 bp):
AATCAATATTTAGAGTGTCTTGCAATTCTCTTAATATTTGCAATTTTGATTTGAATTTTCTCACT
AATCCGAAAT
Found at i:900615 original size:1 final size:1
Alignment explanation
Indices: 900609--900633 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
900599 GTGTGTGTGT
900609 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
900634 TGTCCCGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:911049 original size:2 final size:2
Alignment explanation
Indices: 911042--911085 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
911032 AATGATCGTC
911042 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
911084 AG
1 AG
911086 CATACTGGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:911434 original size:2 final size:2
Alignment explanation
Indices: 911427--911467 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
911417 GCTGTAAAAT
*
911427 TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
911468 GTACTTTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:913401 original size:10 final size:10
Alignment explanation
Indices: 913386--913419 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
913376 GTCACACAAC
913386 CATTACATAA
1 CATTACATAA
*
913396 CATTACACAA
1 CATTACATAA
913406 CCATTACATAA
1 -CATTACATAA
913417 CAT
1 CAT
913420 GCTAATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (10 bp):
CATTACATAA
Found at i:913405 original size:21 final size:21
Alignment explanation
Indices: 913379--913419 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
913369 TCCAAATGTC
913379 ACACAACCATTACATAACATT
1 ACACAACCATTACATAACATT
913400 ACACAACCATTACATAACAT
1 ACACAACCATTACATAACAT
913420 GCTAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (21 bp):
ACACAACCATTACATAACATT
Found at i:913412 original size:11 final size:11
Alignment explanation
Indices: 913379--913413 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
913369 TCCAAATGTC
913379 ACACAACCATT
1 ACACAACCATT
*
913390 ACATAA-CATT
1 ACACAACCATT
913400 ACACAACCATT
1 ACACAACCATT
913411 ACA
1 ACA
913414 TAACATGCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (11 bp):
ACACAACCATT
Found at i:914829 original size:21 final size:21
Alignment explanation
Indices: 914804--914845 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
914794 AATAATAGGT
914804 ATGAAAATGAC-AAAAATTACC
1 ATGAAAAT-ACTAAAAATTACC
*
914825 ATGAAAATACTACAAATTACC
1 ATGAAAATACTAAAAATTACC
914846 CTACACGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21
Consensus pattern (21 bp):
ATGAAAATACTAAAAATTACC
Found at i:916170 original size:2 final size:2
Alignment explanation
Indices: 916163--916220 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
916153 ACTTAGAATG
*
916163 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CN
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
916205 CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT
916221 TGCAATACAC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:916790 original size:1 final size:1
Alignment explanation
Indices: 916784--916820 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
916774 TTGCCGCCTA
*
916784 CCCCCCCCCCCCCTCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
916821 TGCACCTCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:917877 original size:159 final size:164
Alignment explanation
Indices: 917577--917902 Score: 493
Period size: 159 Copynumber: 2.0 Consensus size: 164
917567 TAAAGGTAGA
917577 ATTTGGGTTTAGCCTAGTACATTCTTTTAAAATATGCTTATCATTATGCATACATGTATGATATC
1 ATTTGGGTTTAGCCTAGTACATTC-TTT-AAATATGC-TATCATTATGCATACATGTATGATATC
*
917642 AAAATTCAAAGGCAATAGGTGTCCTCCTTGACCACACAAAGGCATATTTTCTTTTCTGTTTTAAA
63 AAAATTCAAAGGCAATAGGTGTCCTCCTTGAACACACAAAGGCATATTTTCTTTTCTGTTTTAAA
917707 ACGCATATGCATTTGAATGGAAATCTTAAAAAGTTTG
128 ACGCATATGCATTTGAATGGAAATCTTAAAAAGTTTG
* * *
917744 ATTTGGGTTTAGCCTTGTACATTC-TT-AATATG-T-TCATTAT-TATGCATGTATGATATCAAA
1 ATTTGGGTTTAGCCTAGTACATTCTTTAAATATGCTATCATTATGCATACATGTATGATATCAAA
* * *
917804 ATTCAAAGGCATTTGGTGTCCTCCTTGAACACACAAAGGCATATTTTCTTTTCTGTTTTAAAATG
66 ATTCAAAGGCAATAGGTGTCCTCCTTGAACACACAAAGGCATATTTTCTTTTCTGTTTTAAAACG
* *
917869 CGA-GTGCATTTGAATGGAAATCTTTAAAAGTTTG
131 C-ATATGCATTTGAATGGAAATCTTAAAAAGTTTG
917903 TTTAAACTCC
Statistics
Matches: 149, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
159 109 0.73
160 8 0.05
161 1 0.01
163 6 0.04
165 2 0.01
167 23 0.15
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.39
Consensus pattern (164 bp):
ATTTGGGTTTAGCCTAGTACATTCTTTAAATATGCTATCATTATGCATACATGTATGATATCAAA
ATTCAAAGGCAATAGGTGTCCTCCTTGAACACACAAAGGCATATTTTCTTTTCTGTTTTAAAACG
CATATGCATTTGAATGGAAATCTTAAAAAGTTTG
Found at i:927336 original size:16 final size:16
Alignment explanation
Indices: 927317--927349 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
927307 GTATTTCTTA
927317 TGTTTTGGTTTTGTTT
1 TGTTTTGGTTTTGTTT
*
927333 TGTTTTGTTTTTGTTT
1 TGTTTTGGTTTTGTTT
927349 T
1 T
927350 TTTGTGAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (16 bp):
TGTTTTGGTTTTGTTT
Found at i:930199 original size:26 final size:26
Alignment explanation
Indices: 930170--930221 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
930160 ATCTTATATG
* *
930170 ATATAGAAGACCTTGTAGATCTATTT
1 ATATAGAAAACCTTGTAGATATATTT
930196 ATATAGAAAACCTTGTAGATATATTT
1 ATATAGAAAACCTTGTAGATATATTT
930222 CAGTATAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (26 bp):
ATATAGAAAACCTTGTAGATATATTT
Found at i:934093 original size:2 final size:2
Alignment explanation
Indices: 934088--934131 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
934078 CCCAAAAAAC
934088 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
934130 CA
1 CA
934132 TAAAAATAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:944746 original size:2 final size:2
Alignment explanation
Indices: 944739--944773 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
944729 ACAGACAAAC
* *
944739 AG AG AG AG AG AG AG AG AG TG AG AG GG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
944774 AGGGGTCTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.51, T:0.03
Consensus pattern (2 bp):
AG
Found at i:947190 original size:2 final size:2
Alignment explanation
Indices: 947183--947213 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
947173 TTGTGCGAAT
*
947183 CA CA CA CA CT CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
947214 TTCAGTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.52, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:948064 original size:2 final size:2
Alignment explanation
Indices: 948057--948171 Score: 230
Period size: 2 Copynumber: 57.5 Consensus size: 2
948047 ATAGTATGTT
948057 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
948099 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
948141 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
948172 ATAAGCGACT
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 113 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:952227 original size:17 final size:17
Alignment explanation
Indices: 952205--952239 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
952195 TGCATTTGCA
952205 TAAGAGATTCCTCTGAC
1 TAAGAGATTCCTCTGAC
952222 TAAGAGATTCCTCTGAC
1 TAAGAGATTCCTCTGAC
952239 T
1 T
952240 CTAATCTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (17 bp):
TAAGAGATTCCTCTGAC
Found at i:966293 original size:15 final size:16
Alignment explanation
Indices: 966273--966307 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
966263 CACTGATAAC
966273 TCATAAAATAAACA-A
1 TCATAAAATAAACACA
966288 TCATAAAATAAACACA
1 TCATAAAATAAACACA
966304 TCAT
1 TCAT
966308 TGGCTAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (16 bp):
TCATAAAATAAACACA
Found at i:966355 original size:21 final size:21
Alignment explanation
Indices: 966329--966417 Score: 126
Period size: 21 Copynumber: 4.2 Consensus size: 21
966319 CAAGTACATG
*
966329 TACTGTAAATGTCAATTGTAA
1 TACTGTAAATGTCAAATGTAA
*
966350 TACTGTAAATGTCAATTGTAA
1 TACTGTAAATGTCAAATGTAA
*
966371 TACTGTAAATGTCAAATCTAA
1 TACTGTAAATGTCAAATGTAA
*
966392 TGCTGTAAATG-CTAAATGTAA
1 TACTGTAAATGTC-AAATGTAA
966413 TACTG
1 TACTG
966418 CATGTAAACA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 1 0.02
21 61 0.98
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (21 bp):
TACTGTAAATGTCAAATGTAA
Found at i:968207 original size:2 final size:2
Alignment explanation
Indices: 968200--968226 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
968190 ATTTGGAAAT
968200 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
968227 CAAGTTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:970138 original size:2 final size:2
Alignment explanation
Indices: 970131--970179 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
970121 GGGCCACACT
970131 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
970173 TC TC TC T
1 TC TC TC T
970180 GATTTTATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:977428 original size:21 final size:21
Alignment explanation
Indices: 977403--977454 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
977393 CTTTAATTGT
*
977403 AACTTCATAAGAAAATTAAAA
1 AACTTCATAACAAAATTAAAA
977424 AACTTCATAACAAAATTAAAA
1 AACTTCATAACAAAATTAAAA
977445 AACTTCATAA
1 AACTTCATAA
977455 TATTTATCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.25
Consensus pattern (21 bp):
AACTTCATAACAAAATTAAAA
Found at i:984413 original size:13 final size:13
Alignment explanation
Indices: 984395--984426 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
984385 TGGGACATCG
984395 CGGGACATATGTC
1 CGGGACATATGTC
984408 CGGGACATATGTC
1 CGGGACATATGTC
*
984421 CCGGAC
1 CGGGAC
984427 TACTTTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.22, C:0.28, G:0.31, T:0.19
Consensus pattern (13 bp):
CGGGACATATGTC
Found at i:996562 original size:27 final size:27
Alignment explanation
Indices: 996524--996583 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
996514 TATAACGCCT
*
996524 AGGAAACGATCTCGTAGTTTGACTCCC-
1 AGGAAACGATCTCGAAGTTTGAC-CCCG
996551 AGGAAACGATCTCGAAGTTTGACCCCG
1 AGGAAACGATCTCGAAGTTTGACCCCG
996578 AGGAAA
1 AGGAAA
996584 AGGTCCTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 3 0.10
27 28 0.90
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (27 bp):
AGGAAACGATCTCGAAGTTTGACCCCG
Found at i:1002398 original size:21 final size:20
Alignment explanation
Indices: 1002363--1002444 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 20
1002353 GAGAGGGAGA
* *
1002363 AGAAGCAGAAGAAGAAGAAG
1 AGAAGCATAAAAAGAAGAAG
* *
1002383 AGCAAGCATAAAAAGAACAAAA
1 AG-AAGCATAAAAAGAA-GAAG
* *
1002405 AGAAGCATAAAAAGCATAAG
1 AGAAGCATAAAAAGAAGAAG
*
1002425 AAAAAGCATAAAAAGCAAGA
1 -AGAAGCATAAAAAG-AAGA
1002445 TGGGGATGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
20 4 0.08
21 38 0.79
22 6 0.12
ACGTcount: A:0.65, C:0.10, G:0.21, T:0.05
Consensus pattern (20 bp):
AGAAGCATAAAAAGAAGAAG
Found at i:1002418 original size:12 final size:12
Alignment explanation
Indices: 1002386--1002439 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 12
1002376 GAAGAAGAGC
1002386 AAGCATAAAAAG
1 AAGCATAAAAAG
1002398 AA-C--AAAAAG
1 AAGCATAAAAAG
1002407 AAGCAT--AAA-
1 AAGCATAAAAAG
1002416 AAGCATAAGAAA-
1 AAGCATAA-AAAG
1002428 AAGCATAAAAAG
1 AAGCATAAAAAG
1002440 CAAGATGGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
9 14 0.40
10 4 0.11
11 4 0.11
12 13 0.37
ACGTcount: A:0.69, C:0.09, G:0.15, T:0.07
Consensus pattern (12 bp):
AAGCATAAAAAG
Found at i:1004942 original size:22 final size:22
Alignment explanation
Indices: 1004912--1004981 Score: 55
Period size: 22 Copynumber: 3.5 Consensus size: 22
1004902 ATATTGTTGC
1004912 TTCTACAGTAGTCACAATGATG
1 TTCTACAGTAGTCACAATGATG
* *
1004934 TTCTGCAGTATGT-----TGCT-
1 TTCTACAGTA-GTCACAATGATG
1004951 -TCTACAGTAGTCACAATGATG
1 TTCTACAGTAGTCACAATGATG
*
1004972 TTCTGCAGTA
1 TTCTACAGTA
1004982 TGAACTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 16
0.62 0.09 0.29
Matches are distributed among these distances:
15 2 0.06
16 8 0.23
18 3 0.09
20 3 0.09
22 17 0.49
23 2 0.06
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (22 bp):
TTCTACAGTAGTCACAATGATG
Found at i:1004957 original size:38 final size:38
Alignment explanation
Indices: 1004906--1004983 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
1004896 TAACGAATAT
1004906 TGTTGCTTCTACAGTAGTCACAATGATGTTCTGCAGTA
1 TGTTGCTTCTACAGTAGTCACAATGATGTTCTGCAGTA
1004944 TGTTGCTTCTACAGTAGTCACAATGATGTTCTGCAGTA
1 TGTTGCTTCTACAGTAGTCACAATGATGTTCTGCAGTA
1004982 TG
1 TG
1004984 AACTATATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (38 bp):
TGTTGCTTCTACAGTAGTCACAATGATGTTCTGCAGTA
Found at i:1008668 original size:2 final size:2
Alignment explanation
Indices: 1008661--1008718 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1008651 GGGAGGATAA
1008661 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1008703 AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG
1008719 CTCTCTTTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1013688 original size:2 final size:2
Alignment explanation
Indices: 1013681--1013722 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1013671 AGAGTAGATA
1013681 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1013723 GTAGGTGGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1016904 original size:7 final size:7
Alignment explanation
Indices: 1016894--1016936 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
1016884 AGTGAAAGCT
1016894 AAATTCA
1 AAATTCA
1016901 AAATTCA
1 AAATTCA
1016908 AAATT--
1 AAATTCA
1016913 AAATTCA
1 AAATTCA
1016920 AAATT--
1 AAATTCA
1016925 AAATTCA
1 AAATTCA
1016932 AAATT
1 AAATT
1016937 ACAGTCATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 10 0.31
7 22 0.69
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (7 bp):
AAATTCA
Found at i:1016918 original size:12 final size:12
Alignment explanation
Indices: 1016901--1016937 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
1016891 GCTAAATTCA
1016901 AAATTCAAAATT
1 AAATTCAAAATT
1016913 AAATTCAAAATT
1 AAATTCAAAATT
1016925 AAATTCAAAATT
1 AAATTCAAAATT
1016937 A
1 A
1016938 CAGTCATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATTCAAAATT
Found at i:1020487 original size:17 final size:17
Alignment explanation
Indices: 1020465--1020498 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1020455 CAGTATTTTT
1020465 TCATTACGGTAATCAAA
1 TCATTACGGTAATCAAA
1020482 TCATTACGGTAATCAAA
1 TCATTACGGTAATCAAA
1020499 ACCATTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (17 bp):
TCATTACGGTAATCAAA
Found at i:1039664 original size:2 final size:2
Alignment explanation
Indices: 1039657--1039694 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1039647 GATGCACATG
1039657 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1039695 TTCTTGAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1042907 original size:2 final size:2
Alignment explanation
Indices: 1042900--1042934 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1042890 CCGGATGAAA
1042900 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1042935 AAAATTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1043134 original size:2 final size:2
Alignment explanation
Indices: 1043129--1043161 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1043119 CCCCCCCCCC
1043129 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1043162 ATGTTGACGC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1043548 original size:2 final size:2
Alignment explanation
Indices: 1043543--1043608 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1043533 GTGTACACAC
1043543 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1043585 AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG
1043609 GGGGGGGGGG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1043692 original size:16 final size:15
Alignment explanation
Indices: 1043656--1043691 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
1043646 CACTGGTTAN
1043656 GGGGGGAGGGGGAGG
1 GGGGGGAGGGGGAGG
1043671 GGGGGGAGTGGGG-GG
1 GGGGGGAG-GGGGAGG
1043686 GGGGGG
1 GGGGGG
1043692 GGACCGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.08, C:0.00, G:0.89, T:0.03
Consensus pattern (15 bp):
GGGGGGAGGGGGAGG
Found at i:1044814 original size:2 final size:2
Alignment explanation
Indices: 1044807--1044857 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
1044797 AAAGCCGCTC
* *
1044807 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT TT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1044849 CT CT CT CT C
1 CT CT CT CT C
1044858 AACCGATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Done.