Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold22
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: 1964558
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.31
Warning! 137786 characters in sequence are not A, C, G, or T
File 5 of 6
Found at i:1112814 original size:32 final size:31
Alignment explanation
Indices: 1112759--1112837 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
1112749 ATTCGGATTT
* *
1112759 TTTTGTTAAGTCGCT-CATGAAATCAAGAAGGG
1 TTTTGTTAAGTCG-TACATAAAATC-AGAAGGA
* ***
1112791 TTTTGTTAAGTCGTACTTAAAATCATTCGGA
1 TTTTGTTAAGTCGTACATAAAATCAGAAGGA
1112822 TTTTGTTAAGTCGTAC
1 TTTTGTTAAGTCGTAC
1112838 CAGGAATAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 20 0.50
32 20 0.50
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (31 bp):
TTTTGTTAAGTCGTACATAAAATCAGAAGGA
Found at i:1112850 original size:31 final size:30
Alignment explanation
Indices: 1112791--1112855 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
1112781 TCAAGAAGGG
* *
1112791 TTTTGTTAAGTCGTACTTAAAATCATTCGGA
1 TTTTGTTAAGTCGTACTCAAAATAATTC-GA
*
1112822 TTTTGTTAAGTCGTAC-CAGGAATAATTCGA
1 TTTTGTTAAGTCGTACTCA-AAATAATTCGA
1112852 TTTT
1 TTTT
1112856 TTCATCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (30 bp):
TTTTGTTAAGTCGTACTCAAAATAATTCGA
Found at i:1114162 original size:437 final size:437
Alignment explanation
Indices: 1113410--1114391 Score: 1883
Period size: 437 Copynumber: 2.2 Consensus size: 437
1113400 ATATTTACAA
1113410 GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACGAAAGTGCTCTAA
1 GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACGAAAGTGCTCTAA
* * *
1113475 AGTCTTTAATATGTAGCCCTTTACTGAGAAATATTTTGTGAAATGTTATAGAAGCAAATATGTTT
66 AGTCTTTAATTTGTAGCCCTTTACTGAGAGATGTTTTGTGAAATGTTATAGAAGCAAATATGTTT
*
1113540 ATCTCACAGTTATGTATCCAAGCAGTGTAAATATTTTGTTATATGTTACGTAATTAAGGGGTTTT
131 ATCTCACAGTTATGTATCCAAGCAGTGTAAATATTTTGTCATATGTTACGTAATTAAGGGGTTTT
*
1113605 AGGGGCCAAAAGTCCAAAATTTTGATCATCCATATCTCAGAAAGGATAAATATTTTGTATTGCAG
196 AGGGGCCAAAAGTCCAAAATTTTGATCATCCATATCTCAGAAAGGAAAAATATTTTGTATTGCAG
1113670 TACAGAAGAAAAGTTGTTCAAAATGATGTTCTTAACAATATGCAACCGTCAAAATTTCGTTAAAC
261 TACAGAAGAAAAGTTGTTCAAAATGATGTTCTTAACAATATGCAACCGTCAAAATTTCGTTAAAC
1113735 GGCCCCTAAAAGGAGATAAGGGACCGGCCCCTAAAACCTACTTTCTCATATATCTCTAGAACGGT
326 GGCCCCTAAAAGGAGATAAGGGACCGGCCCCTAAAACCTACTTTCTCATATATCTCTAGAACGGT
1113800 AACGAATTTTTACACACTTGTAGAACAAAATGTGTTCAGAATTAAAT
391 AACGAATTTTTACACACTTGTAGAACAAAATGTGTTCAGAATTAAAT
* *
1113847 GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACGAAAGTGTTCTAC
1 GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACGAAAGTGCTCTAA
*
1113912 AGTCTTTAATTTGTAGCCCTTTACTGAGAGATGTTTTGTGTAATGTTATAGAAGCAAATATGTTT
66 AGTCTTTAATTTGTAGCCCTTTACTGAGAGATGTTTTGTGAAATGTTATAGAAGCAAATATGTTT
1113977 ATCTCACAGTTATGTATCCAAGCAGTGTAAATATTTTGTCATATGTTACGTAATTAAGGGGTTTT
131 ATCTCACAGTTATGTATCCAAGCAGTGTAAATATTTTGTCATATGTTACGTAATTAAGGGGTTTT
1114042 AGGGGCCAAAAGTCCAAAATTTTGATCATCCATATCTCAGAAAGGAAAAATATTTTGTATTGCAG
196 AGGGGCCAAAAGTCCAAAATTTTGATCATCCATATCTCAGAAAGGAAAAATATTTTGTATTGCAG
1114107 TACAGAAGAAAAGTTGTTCAAAATGATGTTCTTAACAATATGCAACCGTCAAAATTTCGTTAAAC
261 TACAGAAGAAAAGTTGTTCAAAATGATGTTCTTAACAATATGCAACCGTCAAAATTTCGTTAAAC
1114172 GGCCCCTAAAAGGAGATAAGGGACCGGCCCCTAAAACCTACTTTCTCATATATCTCTAGAACGGT
326 GGCCCCTAAAAGGAGATAAGGGACCGGCCCCTAAAACCTACTTTCTCATATATCTCTAGAACGGT
1114237 AACGAATTTTTACACACTTGTAGAACAAAATGTGTTCAGAATTAAAT
391 AACGAATTTTTACACACTTGTAGAACAAAATGTGTTCAGAATTAAAT
*
1114284 GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACGAAAGGGCTCTAA
1 GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACGAAAGTGCTCTAA
1114349 AGTCTTTAATTTGTAGCCCTTTACTGAGAGATGTTTTGTGAAA
66 AGTCTTTAATTTGTAGCCCTTTACTGAGAGATGTTTTGTGAAA
1114392 GGTTGTTAAA
Statistics
Matches: 533, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
437 533 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (437 bp):
GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACGAAAGTGCTCTAA
AGTCTTTAATTTGTAGCCCTTTACTGAGAGATGTTTTGTGAAATGTTATAGAAGCAAATATGTTT
ATCTCACAGTTATGTATCCAAGCAGTGTAAATATTTTGTCATATGTTACGTAATTAAGGGGTTTT
AGGGGCCAAAAGTCCAAAATTTTGATCATCCATATCTCAGAAAGGAAAAATATTTTGTATTGCAG
TACAGAAGAAAAGTTGTTCAAAATGATGTTCTTAACAATATGCAACCGTCAAAATTTCGTTAAAC
GGCCCCTAAAAGGAGATAAGGGACCGGCCCCTAAAACCTACTTTCTCATATATCTCTAGAACGGT
AACGAATTTTTACACACTTGTAGAACAAAATGTGTTCAGAATTAAAT
Found at i:1117690 original size:2 final size:2
Alignment explanation
Indices: 1117683--1117745 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1117673 TCTTTTCAAA
1117683 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
1117725 AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG A
1117746 TCTTATTTGT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1124212 original size:2 final size:2
Alignment explanation
Indices: 1124205--1124260 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1124195 GCCATTGTAT
1124205 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1124247 GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA
1124261 TATGGACAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1130256 original size:33 final size:34
Alignment explanation
Indices: 1130208--1130271 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 34
1130198 AAAAAGGCAG
*
1130208 AGAGAGAGAGAGAATGGCACAGAGCTAGAGAGAA
1 AGAGAGAGAGAGAATGGCACAGAGATAGAGAGAA
1130242 AGAGA-AGAGAGAATGGCACAGAGATAGAGA
1 AGAGAGAGAGAGAATGGCACAGAGATAGAGA
1130272 AAGGCAGAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 24 0.83
34 5 0.17
ACGTcount: A:0.48, C:0.08, G:0.38, T:0.06
Consensus pattern (34 bp):
AGAGAGAGAGAGAATGGCACAGAGATAGAGAGAA
Found at i:1130272 original size:18 final size:18
Alignment explanation
Indices: 1130210--1130290 Score: 62
Period size: 18 Copynumber: 4.7 Consensus size: 18
1130200 AAAGGCAGAG
*
1130210 AGAGAGAGAGAATGGCAC
1 AGAGATAGAGAATGGCAC
* *
1130228 AGAGCTAGAG-A--G-AA
1 AGAGATAGAGAATGGCAC
*
1130242 AGAGAAGAGAGAATGGCAC
1 AGAG-ATAGAGAATGGCAC
* *
1130261 AGAGATAGAGAAAGGCAG
1 AGAGATAGAGAATGGCAC
*
1130279 AGAGATAAAGAA
1 AGAGATAGAGAA
1130291 AGAGAGAGAG
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
14 5 0.10
15 5 0.10
16 1 0.02
17 1 0.02
18 31 0.65
19 5 0.10
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.06
Consensus pattern (18 bp):
AGAGATAGAGAATGGCAC
Found at i:1130291 original size:18 final size:18
Alignment explanation
Indices: 1130251--1130301 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1130241 AAGAGAAGAG
* * *
1130251 AGAATGGCACAGAGATAG
1 AGAAAGGCAGAGAGATAA
1130269 AGAAAGGCAGAGAGATAA
1 AGAAAGGCAGAGAGATAA
1130287 AGAAAGAG-AGAGAGA
1 AGAAAG-GCAGAGAGA
1130302 AACTGTAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 28 0.97
19 1 0.03
ACGTcount: A:0.53, C:0.06, G:0.35, T:0.06
Consensus pattern (18 bp):
AGAAAGGCAGAGAGATAA
Found at i:1132664 original size:2 final size:2
Alignment explanation
Indices: 1132657--1132712 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1132647 GCAGTGAACT
1132657 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1132699 GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA
1132713 TTGCCTTGAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1133228 original size:20 final size:20
Alignment explanation
Indices: 1133203--1133269 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
1133193 TGGAATGATT
1133203 ACATGTAATAATCTATTCTG
1 ACATGTAATAATCTATTCTG
*
1133223 ACATGTAATATTCTATTCTG
1 ACATGTAATAATCTATTCTG
1133243 ACATGTAATAATCTATTCTG
1 ACATGTAATAATCTATTCTG
1133263 ACATGTA
1 ACATGTA
1133270 TGTCTTTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.40
Consensus pattern (20 bp):
ACATGTAATAATCTATTCTG
Found at i:1136441 original size:2 final size:2
Alignment explanation
Indices: 1136434--1136460 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1136424 AACAGAGGTG
1136434 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 C
1136461 ATTTTATCTT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1136556 original size:2 final size:2
Alignment explanation
Indices: 1136546--1136634 Score: 65
Period size: 2 Copynumber: 45.5 Consensus size: 2
1136536 TGCACACACG
* * * *
1136546 CT CT GT CT CT CC CT CT CT CT CT CC CT CT CT CT CT CC 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
* * * * * * *
1136588 CT C- CA CT CT TT CT CT CC CT CT C- CT CT CT TT AT TT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1136628 CT CT CT C
1 CT CT CT C
1136635 ATCTTTCATC
Statistics
Matches: 68, Mismatches: 17, Indels: 4
0.76 0.19 0.04
Matches are distributed among these distances:
1 2 0.03
2 66 0.97
ACGTcount: A:0.02, C:0.49, G:0.01, T:0.47
Consensus pattern (2 bp):
CT
Found at i:1136561 original size:12 final size:12
Alignment explanation
Indices: 1136546--1136614 Score: 97
Period size: 12 Copynumber: 5.9 Consensus size: 12
1136536 TGCACACACG
*
1136546 CTCTGTCTCTCC
1 CTCTCTCTCTCC
1136558 CTCTCTCTCTCC
1 CTCTCTCTCTCC
1136570 CTCTCTCTCTCC
1 CTCTCTCTCTCC
*
1136582 CTCTCTCTC-CA
1 CTCTCTCTCTCC
*
1136593 CTCTTTCTCTCC
1 CTCTCTCTCTCC
1136605 CTCTC-CTCTC
1 CTCTCTCTCTC
1136615 TTTATTTTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
11 14 0.27
12 37 0.73
ACGTcount: A:0.01, C:0.55, G:0.01, T:0.42
Consensus pattern (12 bp):
CTCTCTCTCTCC
Found at i:1141557 original size:16 final size:17
Alignment explanation
Indices: 1141536--1141568 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1141526 GATTTCTCTG
1141536 ATAAAAAATGA-AAAAA
1 ATAAAAAATGAGAAAAA
1141552 ATAAAAAATGAGAAAAA
1 ATAAAAAATGAGAAAAA
1141569 CCCCTGTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (17 bp):
ATAAAAAATGAGAAAAA
Found at i:1160085 original size:48 final size:48
Alignment explanation
Indices: 1160009--1160146 Score: 154
Period size: 48 Copynumber: 2.9 Consensus size: 48
1159999 CACTGTCAGC
*
1160009 AATGTCAGGTATGTTGATGTAAATAGAGGTAACTGCTAGGTGGGTCAA
1 AATGTCAGGTATGTTGATGTAAAAAGAGGTAACTGCTAGGTGGGTCAA
* * * *
1160057 AATGTCAAGTGTGTTGATGTAAAAAGAGGTAACTG-TCAGGTGTGTCGA
1 AATGTCAGGTATGTTGATGTAAAAAGAGGTAACTGCT-AGGTGGGTCAA
* * * **
1160105 AATGTCCGGTTTGTCGATG-AAAATAGATTTAACTGCTAGGTG
1 AATGTCAGGTATGTTGATGTAAAA-AGAGGTAACTGCTAGGTG
1160147 AGTTATTATG
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
47 5 0.07
48 70 0.92
49 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.30
Consensus pattern (48 bp):
AATGTCAGGTATGTTGATGTAAAAAGAGGTAACTGCTAGGTGGGTCAA
Found at i:1162902 original size:32 final size:32
Alignment explanation
Indices: 1162857--1162984 Score: 195
Period size: 32 Copynumber: 4.0 Consensus size: 32
1162847 GAGGAGAAGT
*
1162857 AGTG-TGATTGGCTGAAATGTAGAGCTCAGAG
1 AGTGCTGATTGGCTGAAATGTACAGCTCAGAG
*
1162888 AGTGCTGATTGGCTGAAATGTACAGCTCAGTG
1 AGTGCTGATTGGCTGAAATGTACAGCTCAGAG
* * *
1162920 AGTGCTTATTGGCTGAAATATACAGCTCAGTG
1 AGTGCTGATTGGCTGAAATGTACAGCTCAGAG
*
1162952 AGTGCTGATTGGCTGAAATGTACAGCTAAGAG
1 AGTGCTGATTGGCTGAAATGTACAGCTCAGAG
1162984 A
1 A
1162985 CTGTGAATGA
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
31 4 0.05
32 84 0.95
ACGTcount: A:0.29, C:0.13, G:0.30, T:0.27
Consensus pattern (32 bp):
AGTGCTGATTGGCTGAAATGTACAGCTCAGAG
Found at i:1165338 original size:15 final size:15
Alignment explanation
Indices: 1165318--1165347 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1165308 TGGTGTTTGG
1165318 GTACATACATGTACT
1 GTACATACATGTACT
1165333 GTACATACATGTACT
1 GTACATACATGTACT
1165348 AATTTTCAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (15 bp):
GTACATACATGTACT
Found at i:1171035 original size:12 final size:12
Alignment explanation
Indices: 1171018--1171044 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1171008 GTTGGTGCGC
1171018 CATTACCATCAG
1 CATTACCATCAG
1171030 CATTACCATCAG
1 CATTACCATCAG
1171042 CAT
1 CAT
1171045 CAAGGACGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.07, T:0.26
Consensus pattern (12 bp):
CATTACCATCAG
Found at i:1173507 original size:23 final size:23
Alignment explanation
Indices: 1173477--1173525 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
1173467 CAATGTTTAG
1173477 TGACCTCAATA-TATACTGACATT
1 TGACCTCAATACTA-ACTGACATT
*
1173500 TGACCTCAATACTAATTGACATT
1 TGACCTCAATACTAACTGACATT
1173523 TGA
1 TGA
1173526 ATCCAATACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (23 bp):
TGACCTCAATACTAACTGACATT
Found at i:1177512 original size:31 final size:31
Alignment explanation
Indices: 1177428--1177668 Score: 113
Period size: 31 Copynumber: 7.9 Consensus size: 31
1177418 GTTTCATTGT
* * ** *
1177428 TGATATTGACACTTACATGGCCTGTCTACGC
1 TGATATAGACACTTAAATGGTTTGTCTACAC
* *
1177459 TGATATAGACACATAAAAGGTTTGTCTACAC
1 TGATATAGACACTTAAATGGTTTGTCTACAC
* *
1177490 TGATATAGACACTTAAATGGTTTGTCAATAC
1 TGATATAGACACTTAAATGGTTTGTCTACAC
*** **
1177521 TGGGGTAGATTCTTACAA-GG--T-T-TACAC
1 TGATATAGACACTTA-AATGGTTTGTCTACAC
* * * * *
1177548 TGACATAGGCACTTCAATAGTTTGTCTACAT
1 TGATATAGACACTTAAATGGTTTGTCTACAC
* * ****
1177579 TGATATAGACACATACATAACATGTCTACAC
1 TGATATAGACACTTAAATGGTTTGTCTACAC
* * *
1177610 TGA-AGTAGACAC-TAACAAGGTTTGCCTAAAC
1 TGATA-TAGACACTTAA-ATGGTTTGTCTACAC
*
1177641 TGA-AGTAGACAATTACAA-GGTTTGTCTA
1 TGATA-TAGACACTTA-AATGGTTTGTCTA
1177669 TACTTGGGTA
Statistics
Matches: 154, Mismatches: 46, Indels: 20
0.70 0.21 0.09
Matches are distributed among these distances:
26 2 0.01
27 12 0.08
28 1 0.01
29 2 0.01
30 4 0.03
31 127 0.82
32 5 0.03
33 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (31 bp):
TGATATAGACACTTAAATGGTTTGTCTACAC
Found at i:1177977 original size:31 final size:31
Alignment explanation
Indices: 1177934--1178152 Score: 172
Period size: 31 Copynumber: 6.8 Consensus size: 31
1177924 TTACTACACT
* * * *
1177934 GTTTTTCTACACTAAAATAGACACTTACTTG
1 GTTTGTCTACACTGATATAGACACTTACATG
* *
1177965 GTTTGTCTACACTAATACATGTAAAGACACTTAATATATG
1 GTTTGTCTACACTGAT--A--T--AGACAC-T--TACATG
* * *
1178005 GGTTGCCTACACTGATATAGACACTTACAAG
1 GTTTGTCTACACTGATATAGACACTTACATG
* * *
1178036 GTTTGTCTACATTGAAATAGACA--TATATG
1 GTTTGTCTACACTGATATAGACACTTACATG
* * *
1178065 GTTTGTTTACAATGATATAGACACTTACATA
1 GTTTGTCTACACTGATATAGACACTTACATG
* * *
1178096 GCTTGTCTACACTGATATAGACACTTAAAAG
1 GTTTGTCTACACTGATATAGACACTTACATG
*
1178127 GTGTGTCTACACTGATATAGACACTT
1 GTTTGTCTACACTGATATAGACACTT
1178153 GATATATGGC
Statistics
Matches: 149, Mismatches: 28, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
29 24 0.16
31 90 0.60
33 2 0.01
34 6 0.04
35 1 0.01
36 1 0.01
37 6 0.04
38 2 0.01
40 17 0.11
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (31 bp):
GTTTGTCTACACTGATATAGACACTTACATG
Found at i:1178081 original size:60 final size:60
Alignment explanation
Indices: 1177998--1178152 Score: 186
Period size: 60 Copynumber: 2.5 Consensus size: 60
1177988 AAGACACTTA
* * * *
1177998 ATATATGGGTTGCCTACACTGATATAGACACTTACA-AGGTTTGTCTACATTGAAATAGAC
1 ATATATGGTTTGTCTACACTGATATAGACACTTACATA-GCTTGTCTACACTGAAATAGAC
* * *
1178058 ATATATGGTTTGTTTACAATGATATAGACACTTACATAGCTTGTCTACACTGATATAGAC
1 ATATATGGTTTGTCTACACTGATATAGACACTTACATAGCTTGTCTACACTGAAATAGAC
* * *
1178118 ACTTAAAAGGTGTGTCTACACTGATATAGACACTT
1 A--TATATGGTTTGTCTACACTGATATAGACACTT
1178153 GATATATGGC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
60 52 0.65
61 1 0.01
62 27 0.34
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (60 bp):
ATATATGGTTTGTCTACACTGATATAGACACTTACATAGCTTGTCTACACTGAAATAGAC
Found at i:1180727 original size:189 final size:188
Alignment explanation
Indices: 1180367--1180745 Score: 618
Period size: 189 Copynumber: 2.0 Consensus size: 188
1180357 AATCAGTAAT
* *
1180367 CAAGTTAATCTTTAGTTTCTTCTTATTATGTCATTTTTTTATTTTTACTAAGTTAACTGTGTTAG
1 CAAGTAAATCTTTAGTTTCTTC-T-TTATGTCATTTTTTTATTATTACTAAGTTAACTGTGTTAG
* *
1180432 GCCAAAATAATTATCTTTTCTTTCTCAGGCAATTTAATGAATTGATAATAAGTTAACAGATATGG
64 GCCAAAAAAATTATCTTTTCTATCTCAGGCAATTTAATGAATTGATAATAAGTTAACAGATATGG
* *
1180497 CCAAAACAATTAATCTAAACTTTCTCATGCGGAACATTTCAAAATAAAATGTTGCAGGTA
129 CCAAAACAATTAATCTAAACTTTCTCATGCGAAACATTTCAAAATAAAATGTTACAGGTA
1180557 CAAGTAAATCTTTAGTTTCTTC-TTATGTCATTTATTTTAAATTATTACTAAGTTAACTGTGTTA
1 CAAGTAAATCTTTAGTTTCTTCTTTATGTCATTT-TTTT--ATTATTACTAAGTTAACTGTGTTA
*
1180621 GGCCAAAAAAATTATCTTTTCTATCTGAGGCAA-TTAATGAATTGATAATAAGTTAACAGATATG
63 GGCCAAAAAAATTATCTTTTCTATCTCAGGCAATTTAATGAATTGATAATAAGTTAACAGATATG
* *
1180685 GCCAAAACAATTAATCTTAAGTTTCTCATGCGAAACATTTCAAAATAAAATGTTACAGGTA
128 GCCAAAACAATTAATCTAAACTTTCTCATGCGAAACATTTCAAAATAAAATGTTACAGGTA
1180746 TTTAACTTTT
Statistics
Matches: 177, Mismatches: 9, Indels: 7
0.92 0.05 0.04
Matches are distributed among these distances:
187 11 0.06
188 4 0.02
189 88 0.50
190 74 0.42
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (188 bp):
CAAGTAAATCTTTAGTTTCTTCTTTATGTCATTTTTTTATTATTACTAAGTTAACTGTGTTAGGC
CAAAAAAATTATCTTTTCTATCTCAGGCAATTTAATGAATTGATAATAAGTTAACAGATATGGCC
AAAACAATTAATCTAAACTTTCTCATGCGAAACATTTCAAAATAAAATGTTACAGGTA
Found at i:1186598 original size:2 final size:2
Alignment explanation
Indices: 1186591--1186620 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1186581 CTGTTCTTTA
1186591 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
1186621 AAAAATAAGC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1190423 original size:30 final size:29
Alignment explanation
Indices: 1190384--1190445 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 29
1190374 AATTAGGAAT
*
1190384 CTACAGTACTTATTAGAATTGCATATGCA
1 CTACAGTACTTACTAGAATTGCATATGCA
1190413 CTACATGTACTTACTAGAATTGCATATGCA
1 CTACA-GTACTTACTAGAATTGCATATGCA
1190443 CTA
1 CTA
1190446 TCAAGGAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (29 bp):
CTACAGTACTTACTAGAATTGCATATGCA
Found at i:1191291 original size:14 final size:14
Alignment explanation
Indices: 1191272--1191299 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1191262 ATCACTCATG
1191272 AAGTGAACAAATAT
1 AAGTGAACAAATAT
1191286 AAGTGAACAAATAT
1 AAGTGAACAAATAT
1191300 CTGGATTCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
AAGTGAACAAATAT
Found at i:1192252 original size:46 final size:46
Alignment explanation
Indices: 1192185--1192415 Score: 453
Period size: 46 Copynumber: 5.0 Consensus size: 46
1192175 TCTTTGCATA
1192185 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG
1 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG
1192231 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG
1 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG
1192277 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG
1 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG
1192323 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG
1 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG
*
1192369 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTACCAG
1 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG
1192415 C
1 C
1192416 ATGGTCAAAA
Statistics
Matches: 184, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 184 1.00
ACGTcount: A:0.18, C:0.32, G:0.13, T:0.37
Consensus pattern (46 bp):
CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG
Found at i:1198477 original size:2 final size:2
Alignment explanation
Indices: 1198470--1198524 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
1198460 AGACATTCCT
* * *
1198470 TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TT TC TC TT TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1198512 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
1198525 GGGAATAGAC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:1202028 original size:2 final size:2
Alignment explanation
Indices: 1202023--1202059 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1202013 AAAAAATTAA
1202023 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
1202060 AAAACATTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1207922 original size:80 final size:80
Alignment explanation
Indices: 1207833--1208019 Score: 311
Period size: 80 Copynumber: 2.3 Consensus size: 80
1207823 GGGGTAACTA
* *
1207833 ATTAAAGGTAAGTCAGTATTACCTACAGTCAAATTTGCAAGTAAGTCAATTGAATTTTACCTGTG
1 ATTATAGGTAAGTCAGTATTACCTACAGTCAAATCTGCAAGTAAGTCAATTGAATTTTACCTGTG
*
1207898 CTCACTGGGCAAGTT
66 CTCACTAGGCAAGTT
*
1207913 ATTATAGGTAAGTCAGTATTACCTACAGTCAAATCTGCAGGTAAGTCAATTGAATTTTACCTGTG
1 ATTATAGGTAAGTCAGTATTACCTACAGTCAAATCTGCAAGTAAGTCAATTGAATTTTACCTGTG
*
1207978 CTCACTAGGTAAGTT
66 CTCACTAGGCAAGTT
*
1207993 ATTATAGGTAAGTCAGTTTTGACCTAC
1 ATTATAGGTAAGTCAGTATT-ACCTAC
1208020 TTCAGGTCCA
Statistics
Matches: 100, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
80 94 0.94
81 6 0.06
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (80 bp):
ATTATAGGTAAGTCAGTATTACCTACAGTCAAATCTGCAAGTAAGTCAATTGAATTTTACCTGTG
CTCACTAGGCAAGTT
Found at i:1211395 original size:21 final size:21
Alignment explanation
Indices: 1211351--1211396 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1211341 AAATCATTTA
*
1211351 TATTGTATGATATTTATTAAG
1 TATTGTATGATATTTATGAAG
*
1211372 TATTG-ATGAATATTTATGAGG
1 TATTGTATG-ATATTTATGAAG
1211393 TATT
1 TATT
1211397 AATATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (21 bp):
TATTGTATGATATTTATGAAG
Found at i:1214182 original size:24 final size:24
Alignment explanation
Indices: 1214155--1214271 Score: 135
Period size: 24 Copynumber: 4.9 Consensus size: 24
1214145 CAATTAAACT
*
1214155 TAATATTCAAGTCAGCATGTAACC
1 TAATATTCAAGTCAGCATTTAACC
* * *
1214179 TAATATCCAAGTCAGTATTTAACT
1 TAATATTCAAGTCAGCATTTAACC
* * *
1214203 TGATATTCAAGACAACATTTAACC
1 TAATATTCAAGTCAGCATTTAACC
* **
1214227 TAATATTTAAGTCAGCATTTAATT
1 TAATATTCAAGTCAGCATTTAACC
*
1214251 TAATGTTCAAGTCAGCATTTA
1 TAATATTCAAGTCAGCATTTA
1214272 TATACTCTAA
Statistics
Matches: 75, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 75 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (24 bp):
TAATATTCAAGTCAGCATTTAACC
Found at i:1214226 original size:48 final size:48
Alignment explanation
Indices: 1214151--1214271 Score: 161
Period size: 48 Copynumber: 2.5 Consensus size: 48
1214141 ATAGCAATTA
* *
1214151 AACTTAATATTCAAGTCAGCATGTAACCTAATATCCAAGTCAGTATTT
1 AACTTAATATTCAAGTCAGCATTTAACCTAATATCCAAGTCAGCATTT
* * * **
1214199 AACTTGATATTCAAGACAACATTTAACCTAATATTTAAGTCAGCATTT
1 AACTTAATATTCAAGTCAGCATTTAACCTAATATCCAAGTCAGCATTT
* *
1214247 AATTTAATGTTCAAGTCAGCATTTA
1 AACTTAATATTCAAGTCAGCATTTA
1214272 TATACTCTAA
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 61 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.36
Consensus pattern (48 bp):
AACTTAATATTCAAGTCAGCATTTAACCTAATATCCAAGTCAGCATTT
Found at i:1216238 original size:166 final size:166
Alignment explanation
Indices: 1215917--1216443 Score: 864
Period size: 166 Copynumber: 3.2 Consensus size: 166
1215907 AGAATCATCT
*
1215917 GGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTT
1 GGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTC
*
1215982 GACCCTCCATTGT-GCCCCACCCTACACCCAGGGGTCATGATTTTCACAACTTTGAATCTACACT
66 GACCCTCCATTGTGGCCCCACCCTACACCCAGGGGTCATGAATTTCACAACTTTGAATCTACACT
* *
1216046 ATCTGAGGATGCTTCCACACAAGTTTCAGCTTCCCA
131 ACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCA
*
1216082 GGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAGCTTC
1 GGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTC
*
1216147 GACCCTCCATTGTGGCCCCACCCTACATCCAGGGGTCATGAATTTCACAACTTTGAATCTACACT
66 GACCCTCCATTGTGGCCCCACCCTACACCCAGGGGTCATGAATTTCACAACTTTGAATCTACACT
*
1216212 ACCTGAGGATCCTTCCACACAAGTTTCAGCTTTCCA
131 ACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCA
*
1216248 GGCTGATTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTC
1 GGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTC
* * * * *
1216313 GACCCCCCATTGTGGCCCCA-CCTAACCCCCGGGGGCCATGAATTTCACAACTTTGAATTTACAC
66 GACCCTCCATTGTGGCCCCACCCT-ACACCCAGGGGTCATGAATTTCACAACTTTGAATCTACAC
*
1216377 TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCT
130 TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCA
*
1216414 GGCT--TTATGGTTCTTGAGAAGAAGATTTTT
1 GGCTGATTA-GTTTC-TGAGAAGAAGATTTTT
1216444 GAAAAATTCT
Statistics
Matches: 339, Mismatches: 19, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
164 3 0.01
165 82 0.24
166 254 0.75
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (166 bp):
GGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTC
GACCCTCCATTGTGGCCCCACCCTACACCCAGGGGTCATGAATTTCACAACTTTGAATCTACACT
ACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCA
Found at i:1218619 original size:18 final size:18
Alignment explanation
Indices: 1218574--1218621 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
1218564 GTGCATACAT
* *
1218574 TTAATTTGAGGTTTATAC
1 TTAACTTGAGGTTGATAC
1218592 TTAGACTTGAGGTTGAGTA-
1 TTA-ACTTGAGGTTGA-TAC
1218611 TTAACTTGAGG
1 TTAACTTGAGG
1218622 AGAGTTGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 11 0.42
19 13 0.50
20 2 0.08
ACGTcount: A:0.27, C:0.06, G:0.25, T:0.42
Consensus pattern (18 bp):
TTAACTTGAGGTTGATAC
Found at i:1220715 original size:2 final size:2
Alignment explanation
Indices: 1220708--1220755 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1220698 AATGATTGTG
1220708 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
1220750 CT CT CT
1 CT CT CT
1220756 TACAGTAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1221317 original size:18 final size:20
Alignment explanation
Indices: 1221278--1221317 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
1221268 CACAACCAGT
1221278 AAGTAATTCTTTGCAATAAA
1 AAGTAATTCTTTGCAATAAA
1221298 AAGTAA-TC-TTGCAGATAAA
1 AAGTAATTCTTTGCA-ATAAA
1221317 A
1 A
1221318 TTGTAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 8 0.42
20 6 0.32
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (20 bp):
AAGTAATTCTTTGCAATAAA
Found at i:1229226 original size:24 final size:24
Alignment explanation
Indices: 1229199--1229248 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1229189 TGGTGTATTT
1229199 ACCTGTATTTAAAAACAGTTTAAC
1 ACCTGTATTTAAAAACAGTTTAAC
1229223 ACCTGTATTTAAAAACAGTTTAAC
1 ACCTGTATTTAAAAACAGTTTAAC
1229247 AC
1 AC
1229249 ATTTGGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (24 bp):
ACCTGTATTTAAAAACAGTTTAAC
Found at i:1237360 original size:22 final size:20
Alignment explanation
Indices: 1237335--1237393 Score: 77
Period size: 19 Copynumber: 3.0 Consensus size: 20
1237325 AATTTGAGAT
*
1237335 AACGAATTCTTAAATTTGTTAA
1 AACGAATT-TTAAA-TCGTTAA
1237357 AACGAA-TTTAAATCGTTAA
1 AACGAATTTTAAATCGTTAA
1237376 AACGAA-TTTAAATCGTTA
1 AACGAATTTTAAATCGTTA
1237394 TAACAAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 24 0.67
20 5 0.14
21 1 0.03
22 6 0.17
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (20 bp):
AACGAATTTTAAATCGTTAA
Found at i:1237376 original size:19 final size:19
Alignment explanation
Indices: 1237352--1237393 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1237342 TCTTAAATTT
1237352 GTTAAAACGAATTTAAATC
1 GTTAAAACGAATTTAAATC
1237371 GTTAAAACGAATTTAAATC
1 GTTAAAACGAATTTAAATC
1237390 GTTA
1 GTTA
1237394 TAACAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (19 bp):
GTTAAAACGAATTTAAATC
Found at i:1240261 original size:21 final size:21
Alignment explanation
Indices: 1240227--1240306 Score: 117
Period size: 21 Copynumber: 3.8 Consensus size: 21
1240217 AATTTAATGC
* *
1240227 TATGCTATGGTATGCGATTT-
1 TATGCTATGCTATGAGATTTG
*
1240247 TAATGATATGCTATGAGATTTG
1 T-ATGCTATGCTATGAGATTTG
1240269 TATGCTATGCTATGAGATTTG
1 TATGCTATGCTATGAGATTTG
1240290 TATGCTATGCTATGAGA
1 TATGCTATGCTATGAGA
1240307 AATTGAAATG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
20 1 0.02
21 52 0.96
22 1 0.02
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (21 bp):
TATGCTATGCTATGAGATTTG
Found at i:1240348 original size:10 final size:10
Alignment explanation
Indices: 1240330--1240362 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
1240320 GGCTTAATGA
1240330 TATGGTATGC
1 TATGGTATGC
*
1240340 TATGCTATGC
1 TATGGTATGC
1240350 TATGGTATGC
1 TATGGTATGC
1240360 TAT
1 TAT
1240363 AAGATTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.42
Consensus pattern (10 bp):
TATGGTATGC
Found at i:1240529 original size:10 final size:10
Alignment explanation
Indices: 1240511--1240544 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1240501 AATAATGTTG
*
1240511 TATGCTATGC
1 TATGGTATGC
1240521 TATGGTATGC
1 TATGGTATGC
*
1240531 TATGGTATGA
1 TATGGTATGC
1240541 TATG
1 TATG
1240545 ACGAATGCGA
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:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (10 bp):
TATGGTATGC
Found at i:1240530 original size:15 final size:15
Alignment explanation
Indices: 1240510--1240544 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1240500 AAATAATGTT
1240510 GTATGCTATGCTATG
1 GTATGCTATGCTATG
*
1240525 GTATGCTATGGTATG
1 GTATGCTATGCTATG
*
1240540 ATATG
1 GTATG
1240545 ACGAATGCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.09, G:0.29, T:0.40
Consensus pattern (15 bp):
GTATGCTATGCTATG
Found at i:1240594 original size:21 final size:21
Alignment explanation
Indices: 1240569--1240643 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
1240559 ATGAGATTGT
* *
1240569 ATGCTATGGTATGAAATTCCA
1 ATGCTATGCTATGAGATTCCA
*
1240590 ATGCTATGCTATGAGATCCCA
1 ATGCTATGCTATGAGATTCCA
*
1240611 ATGCTATGCTATGAGATTTCA
1 ATGCTATGCTATGAGATTCCA
1240632 ATGCTATGCTAT
1 ATGCTATGCTAT
1240644 CCTATGGTGT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (21 bp):
ATGCTATGCTATGAGATTCCA
Found at i:1240921 original size:49 final size:49
Alignment explanation
Indices: 1240835--1240941 Score: 160
Period size: 49 Copynumber: 2.2 Consensus size: 49
1240825 GCAAACATAA
* * *
1240835 GGCTTAACATTTACTTCCCGAAGAATGACAAAATTGTATAACTTCCTTT
1 GGCTTAACATATACTTCCCGAAAAAGGACAAAATTGTATAACTTCCTTT
* * *
1240884 GGCTAAACATATACTTCCCGAAAAAGGACATATTTGTATAACTTCCTTT
1 GGCTTAACATATACTTCCCGAAAAAGGACAAAATTGTATAACTTCCTTT
1240933 GGCTTAACA
1 GGCTTAACA
1240942 AGCTCTTCCC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.33
Consensus pattern (49 bp):
GGCTTAACATATACTTCCCGAAAAAGGACAAAATTGTATAACTTCCTTT
Found at i:1243678 original size:22 final size:21
Alignment explanation
Indices: 1243653--1243726 Score: 64
Period size: 23 Copynumber: 3.5 Consensus size: 21
1243643 AAACTTTGAA
1243653 ATAACGAATTCAAGAATTTGTT
1 ATAACGAATTCAA-AATTTGTT
*
1243675 ATAAC-AGATT--AAATTCGTT
1 ATAACGA-ATTCAAAATTTGTT
*
1243694 AAAACGAATTCCTAAAATTTGTT
1 ATAACGAATT-C-AAAATTTGTT
*
1243717 ATAACAAATT
1 ATAACGAATT
1243727 TAATTCAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
19 14 0.34
20 2 0.05
21 1 0.02
22 8 0.20
23 16 0.39
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (21 bp):
ATAACGAATTCAAAATTTGTT
Found at i:1243701 original size:41 final size:41
Alignment explanation
Indices: 1243655--1243801 Score: 127
Period size: 41 Copynumber: 3.6 Consensus size: 41
1243645 ACTTTGAAAT
*
1243655 AACGAATTCAAGAATTTGTTATAACAGATTAAATTCGTTAA
1 AACGAATTCAAGAATTCGTTATAACAGATTAAATTCGTTAA
* * * ** *
1243696 AACGAATTCCTAA-AATTTGTTATAACAAATTTAATTCAATAT
1 AACGAATT-C-AAGAATTCGTTATAACAGATTAAATTCGTTAA
* * * * * *
1243738 AACGGATTAAAAAATTCATTATAAC-GATTTAGATTCGTTTA
1 AACGAATTCAAGAATTCGTTATAACAGA-TTAAATTCGTTAA
*
1243779 AACAAATTCAAGAATTCGTTATA
1 AACGAATTCAAGAATTCGTTATA
1243802 TCAAATTCAA
Statistics
Matches: 81, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
40 3 0.04
41 44 0.54
42 32 0.40
43 2 0.02
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (41 bp):
AACGAATTCAAGAATTCGTTATAACAGATTAAATTCGTTAA
Found at i:1243798 original size:22 final size:22
Alignment explanation
Indices: 1243770--1243811 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1243760 AACGATTTAG
1243770 ATTCGTT-TAAACAAATTCAAGA
1 ATTCGTTAT-AACAAATTCAAGA
*
1243792 ATTCGTTATATCAAATTCAA
1 ATTCGTTATAACAAATTCAA
1243812 ATATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (22 bp):
ATTCGTTATAACAAATTCAAGA
Found at i:1257955 original size:30 final size:30
Alignment explanation
Indices: 1257915--1258013 Score: 153
Period size: 30 Copynumber: 3.3 Consensus size: 30
1257905 AAAAAGAGGA
* * *
1257915 CATAGAATTCTTATATCTGTCTTAGGGCGG
1 CATAGGATTCTTATATCTGACTTAGGACGG
*
1257945 CATAGGATTCTAATATCTGACTTAGGACGG
1 CATAGGATTCTTATATCTGACTTAGGACGG
*
1257975 CATAGGATTCTTATATCTGACTCAGGACGG
1 CATAGGATTCTTATATCTGACTTAGGACGG
1258005 CATAGGATT
1 CATAGGATT
1258014 ATTCTTTCTG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (30 bp):
CATAGGATTCTTATATCTGACTTAGGACGG
Found at i:1258024 original size:30 final size:30
Alignment explanation
Indices: 1257915--1258026 Score: 125
Period size: 30 Copynumber: 3.7 Consensus size: 30
1257905 AAAAAGAGGA
* * * * *
1257915 CATAGAATTCTTATATCTGTCTTAGGGCGG
1 CATAGGATTATTATATCTGACTCAGGACGG
* * *
1257945 CATAGGATTCTAATATCTGACTTAGGACGG
1 CATAGGATTATTATATCTGACTCAGGACGG
*
1257975 CATAGGATTCTTATATCTGACTCAGGACGG
1 CATAGGATTATTATATCTGACTCAGGACGG
* *
1258005 CATAGGATTATTCTTTCTGACT
1 CATAGGATTATTATATCTGACT
1258027 AAGGGCGATA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 73 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (30 bp):
CATAGGATTATTATATCTGACTCAGGACGG
Found at i:1258170 original size:19 final size:20
Alignment explanation
Indices: 1258146--1258187 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1258136 GACTTGGAAC
1258146 GACATA-AATTCTTTTATCT
1 GACATATAATTCTTTTATCT
1258165 GACATATAATTCTTTTATCT
1 GACATATAATTCTTTTATCT
1258185 GAC
1 GAC
1258188 TTAGGACGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (20 bp):
GACATATAATTCTTTTATCT
Found at i:1258216 original size:25 final size:25
Alignment explanation
Indices: 1258182--1258246 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
1258172 AATTCTTTTA
*
1258182 TCTGACTTAGGACGGCTTAGAGAAT
1 TCTGACTTAGGACGACTTAGAGAAT
* * *
1258207 TCTGACTTAGGTCGACTTAGATAGT
1 TCTGACTTAGGACGACTTAGAGAAT
1258232 TCTGACTTAGGACGA
1 TCTGACTTAGGACGA
1258247 GATAAAGTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (25 bp):
TCTGACTTAGGACGACTTAGAGAAT
Found at i:1262217 original size:7 final size:7
Alignment explanation
Indices: 1262202--1262268 Score: 71
Period size: 7 Copynumber: 9.6 Consensus size: 7
1262192 TTTAGATATT
1262202 GAATCTC
1 GAATCTC
*
1262209 GAATTTC
1 GAATCTC
*
1262216 GAATCTT
1 GAATCTC
1262223 GAATCTC
1 GAATCTC
* *
1262230 GTATTTC
1 GAATCTC
1262237 GAATCTC
1 GAATCTC
* * *
1262244 GTATTTT
1 GAATCTC
1262251 GAATCTC
1 GAATCTC
1262258 GAATCTC
1 GAATCTC
1262265 GAAT
1 GAAT
1262269 GATCCTTCTC
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (7 bp):
GAATCTC
Found at i:1263007 original size:22 final size:22
Alignment explanation
Indices: 1262982--1263044 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 22
1262972 ATCAAATAAA
1262982 TTTAAAAGAACATAATAAAGGT
1 TTTAAAAGAACATAATAAAGGT
1263004 TTTAAAAGAAGTCCATAATAAAGGT
1 TTTAAAAGAA---CATAATAAAGGT
* *
1263029 TATAAAAGAAAATAAT
1 TTTAAAAGAACATAAT
1263045 GGAGATAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
22 15 0.42
25 21 0.58
ACGTcount: A:0.56, C:0.05, G:0.13, T:0.27
Consensus pattern (22 bp):
TTTAAAAGAACATAATAAAGGT
Found at i:1267014 original size:2 final size:2
Alignment explanation
Indices: 1267007--1267060 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1266997 TATTTTAGAG
1267007 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
1267049 CT CT CT CT CT CT
1 CT CT CT CT CT CT
1267061 TTATAATTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1271282 original size:4 final size:4
Alignment explanation
Indices: 1271273--1271303 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1271263 GAGACATTTC
1271273 TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
1271304 ACATTCATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:1273346 original size:12 final size:12
Alignment explanation
Indices: 1273329--1273358 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1273319 NNNNNNNCCC
1273329 CCCCCCCCCCCG
1 CCCCCCCCCCCG
*
1273341 CCCCCCCCCCCT
1 CCCCCCCCCCCG
1273353 CCCCCC
1 CCCCCC
1273359 GATGCTACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.93, G:0.03, T:0.03
Consensus pattern (12 bp):
CCCCCCCCCCCG
Found at i:1273801 original size:21 final size:21
Alignment explanation
Indices: 1273744--1273797 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1273734 TTTTCTCGCT
1273744 TGTCAACATACTTAT-GTTGCA
1 TGTCAACATA-TTATCGTTGCA
**
1273765 TGTTGACATGATTATCG-TGCA
1 TGTCAACAT-ATTATCGTTGCA
1273786 TGTCAACATATT
1 TGTCAACATATT
1273798 TATCTCGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 3 0.11
21 22 0.81
22 2 0.07
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (21 bp):
TGTCAACATATTATCGTTGCA
Found at i:1273807 original size:21 final size:21
Alignment explanation
Indices: 1273733--1273807 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
1273723 TTTGGTGCCG
*
1273733 ATTT-TCTCGCTTGTCAACAT
1 ATTTATCTCGCATGTCAACAT
* * * **
1273753 ACTTATGTTGCATGTTGACAT
1 ATTTATCTCGCATGTCAACAT
1273774 GA-TTATCGT-GCATGTCAACAT
1 -ATTTATC-TCGCATGTCAACAT
1273795 ATTTATCTCGCAT
1 ATTTATCTCGCAT
1273808 TTCGACATTT
Statistics
Matches: 41, Mismatches: 9, Indels: 9
0.69 0.15 0.15
Matches are distributed among these distances:
20 5 0.12
21 34 0.83
22 2 0.05
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (21 bp):
ATTTATCTCGCATGTCAACAT
Found at i:1282000 original size:13 final size:13
Alignment explanation
Indices: 1281978--1282054 Score: 57
Period size: 13 Copynumber: 5.7 Consensus size: 13
1281968 TACACCAATT
*
1281978 CATCATTACATTA
1 CATCAATACATTA
1281991 CATCAATACATTA
1 CATCAATACATTA
* *
1282004 TATTAATACGTTATTA
1 CATCAATAC---ATTA
* *
1282020 TATCATTACATTA
1 CATCAATACATTA
*
1282033 TCA-CATTACATTA
1 -CATCAATACATTA
1282046 CATCAATAC
1 CATCAATAC
1282055 CAACTATCAA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
12 2 0.04
13 38 0.73
14 1 0.02
16 11 0.21
ACGTcount: A:0.40, C:0.19, G:0.01, T:0.39
Consensus pattern (13 bp):
CATCAATACATTA
Found at i:1297639 original size:12 final size:12
Alignment explanation
Indices: 1297622--1297664 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
1297612 ATGAAGTGTT
*
1297622 GTTTTTCGAAAA
1 GTTTTTCAAAAA
1297634 GTTTTTCCAAAAA
1 GTTTTT-CAAAAA
*
1297647 ATTTTT-AAAAA
1 GTTTTTCAAAAA
1297658 GTTTTTC
1 GTTTTTC
1297665 GTCAATTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 10 0.38
12 6 0.23
13 10 0.38
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (12 bp):
GTTTTTCAAAAA
Found at i:1300039 original size:38 final size:38
Alignment explanation
Indices: 1299988--1300060 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
1299978 GAATTAACTT
* *
1299988 TGTTGTGAAAGTATTTATTAAAACAAAAGTTGCCTGTA
1 TGTTGTGAAAGTATTTAATAAAACAAAAATTGCCTGTA
1300026 TGTTGTGAAAGTATTTAATAAAACAAAAATTGCCT
1 TGTTGTGAAAGTATTTAATAAAACAAAAATTGCCT
1300061 CTCTTGGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (38 bp):
TGTTGTGAAAGTATTTAATAAAACAAAAATTGCCTGTA
Found at i:1307151 original size:16 final size:16
Alignment explanation
Indices: 1307132--1307168 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1307122 AGTTCGGTTA
1307132 AAAATTTTCCAGAAAC
1 AAAATTTTCCAGAAAC
1307148 AAAATTTTCCAGAAAC
1 AAAATTTTCCAGAAAC
1307164 AAAAT
1 AAAAT
1307169 AACTTACCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.54, C:0.16, G:0.05, T:0.24
Consensus pattern (16 bp):
AAAATTTTCCAGAAAC
Found at i:1312857 original size:42 final size:42
Alignment explanation
Indices: 1312793--1313259 Score: 580
Period size: 42 Copynumber: 11.1 Consensus size: 42
1312783 ACTATATGAA
* * * *
1312793 CATGTATATAGAGGTGATTTCACGCCATTGTGGTTTTATAAG
1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG
*
1312835 CATGTAGATAGAGGTGACTTCACGCCATTGTCG-TTATATAAG
1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTA-ATAAG
* * ** * * * *
1312877 CATGTAGACAGAGGCAACCTCAGGCCATTGTGGTTTTATAAG
1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG
* * * * * *
1312919 CATGTAGATAGAGATGGCTTCACCCCATTGTCGTTTTATATG
1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG
** * *
1312961 TTTGT-AGTCAGAGGTGACTTCACGCCATTGCCGTTTAATAAG
1 CATGTAAAT-AGAGGTGACTTCACGCCATTGTCGTTTAATAAG
1313003 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG
1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG
** *
1313045 CATGTAAATAGAGGTGACTTCACGCCATTG-CAGTTTTTTCAG
1 CATGTAAATAGAGGTGACTTCACGCCATTGTC-GTTTAATAAG
* * *
1313087 CATGTGAATAGAGGTGACTTCACGCCATTGCCGTGTAATAAG
1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG
*
1313129 CATGTAAATAGAGGTGACTTCACGCCATTGTCATTTAATAAG
1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG
* * *
1313171 CATGTAAATAGAGTTGACTTCACGCCATTGTCATTCAATAAG
1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG
*
1313213 CATGTAAATAGAGGTGACTTCACGCCATTGTCATTTAATAAG
1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG
1313255 CATGT
1 CATGT
1313260 TAATTGACTT
Statistics
Matches: 368, Mismatches: 51, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
41 4 0.01
42 359 0.98
43 5 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32
Consensus pattern (42 bp):
CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG
Found at i:1313735 original size:42 final size:42
Alignment explanation
Indices: 1313666--1313891 Score: 283
Period size: 42 Copynumber: 5.4 Consensus size: 42
1313656 AATCAGTGCC
* ** *
1313666 GGTGACTCCACGCCATTATCGTTATATAAGCATGTAGATAGA
1 GGTGACTTCACGCCATTGCCGTTTTATAAGCATGTAGATAGA
* **
1313708 AGTGACTTCACGCCATTGCCGTGATATAAGCATGTAGATAGA
1 GGTGACTTCACGCCATTGCCGTTTTATAAGCATGTAGATAGA
* * * *
1313750 GTTGACTTCACGCCATTGTCGTTTAATAAGCATGTAAATAGA
1 GGTGACTTCACGCCATTGCCGTTTTATAAGCATGTAGATAGA
* * *
1313792 GGTGACTTCACGCCATTGCAC-TTTTTTAAGCATTTTAGATATA
1 GGTGACTTCACGCCATTGC-CGTTTTATAAGCA-TGTAGATAGA
* *
1313835 GGTGACTTCGCGCCATTGCCGTTTTATAAGCATGTAAATAGA
1 GGTGACTTCACGCCATTGCCGTTTTATAAGCATGTAGATAGA
1313877 GGTGACTTCACGCCA
1 GGTGACTTCACGCCA
1313892 GGTGACTTCA
Statistics
Matches: 156, Mismatches: 25, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
42 120 0.77
43 36 0.23
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.31
Consensus pattern (42 bp):
GGTGACTTCACGCCATTGCCGTTTTATAAGCATGTAGATAGA
Found at i:1313896 original size:15 final size:15
Alignment explanation
Indices: 1313876--1313906 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1313866 ATGTAAATAG
1313876 AGGTGACTTCACGCC
1 AGGTGACTTCACGCC
*
1313891 AGGTGACTTCATGCC
1 AGGTGACTTCACGCC
1313906 A
1 A
1313907 TTGTCGTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.23
Consensus pattern (15 bp):
AGGTGACTTCACGCC
Found at i:1313933 original size:57 final size:57
Alignment explanation
Indices: 1313834--1313948 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 57
1313824 TTTTAGATAT
* *
1313834 AGGTGACTTCGCGCCATTGCCGTTTTATAAGCATGTAAATAGAGGTGACTTCACGCC
1 AGGTGACTTCACGCCATTGCCGTTTAATAAGCATGTAAATAGAGGTGACTTCACGCC
* * * * *
1313891 AGGTGACTTCATGCCATTGTCGTTTAATACGCATTTAGATAGAGGTGACTTCACGCC
1 AGGTGACTTCACGCCATTGCCGTTTAATAAGCATGTAAATAGAGGTGACTTCACGCC
1313948 A
1 A
1313949 TTGCCGTTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (57 bp):
AGGTGACTTCACGCCATTGCCGTTTAATAAGCATGTAAATAGAGGTGACTTCACGCC
Found at i:1313950 original size:42 final size:42
Alignment explanation
Indices: 1313891--1314454 Score: 620
Period size: 42 Copynumber: 13.4 Consensus size: 42
1313881 ACTTCACGCC
* * *
1313891 AGGTGACTTCATGCCATTGTCGTTTAATACGCATTTAGATAG
1 AGGTGACTTCACGCCATTGTCGTTTAATAAGCATGTAGATAG
* ** *
1313933 AGGTGACTTCACGCCATTGCCGTTTCTTAAGGATGTAGATAG
1 AGGTGACTTCACGCCATTGTCGTTTAATAAGCATGTAGATAG
* **
1313975 AGGTGACTTCACGCCATTGCCGTTTTTTAAGCATG-AGAATAG
1 AGGTGACTTCACGCCATTGTCGTTTAATAAGCATGTAG-ATAG
* * *
1314017 AGGTGACTTCACGTCATTGTGGATTT-ATAAGCATGTAGAAAG
1 AGGTGACTTCACGCCATTGTCG-TTTAATAAGCATGTAGATAG
* ** * * * *
1314059 AGTTGACTTCACGTTATTGTCGTTTTATTAGCACGAAGATAG
1 AGGTGACTTCACGCCATTGTCGTTTAATAAGCATGTAGATAG
* *
1314101 AGGTGACTTCACGCCATTGTCATTTAATAAGCATGTAAATAG
1 AGGTGACTTCACGCCATTGTCGTTTAATAAGCATGTAGATAG
* * * **
1314143 AGTTGACTTCCCGCCATTGCCGTTTTTTAAGCATGTAGATAG
1 AGGTGACTTCACGCCATTGTCGTTTAATAAGCATGTAGATAG
*
1314185 AGGTGACTTCACGCCATTGCCG-TTATATAAGCATGTAGATAG
1 AGGTGACTTCACGCCATTGTCGTTTA-ATAAGCATGTAGATAG
* *
1314227 AGGTGACTTCACGCCATTGTCG-TTATATAAGCATGAAGATAT
1 AGGTGACTTCACGCCATTGTCGTTTA-ATAAGCATGTAGATAG
* * * *
1314269 AGGTGACCTCACGCTATTGTC-ATTATATAAGCATGTAGAAAG
1 AGGTGACTTCACGCCATTGTCGTTTA-ATAAGCATGTAGATAG
* * *
1314311 AGGTGACTTCACGCCATTTTCGTTTTATAAGCATGTAGATAT
1 AGGTGACTTCACGCCATTGTCGTTTAATAAGCATGTAGATAG
* *
1314353 AGGTGATTTCACGCCATTGTCG-TTATATAAGTATGTAGATAG
1 AGGTGACTTCACGCCATTGTCGTTTA-ATAAGCATGTAGATAG
* * * * *
1314395 AGGTGGCTTCATGCTATTGCCG-TAATATAAGCATGTAGATAG
1 AGGTGACTTCACGCCATTGTCGTTTA-ATAAGCATGTAGATAG
1314437 AGGTGACTTCACGCCATT
1 AGGTGACTTCACGCCATT
1314455 TTGGTGTACT
Statistics
Matches: 443, Mismatches: 71, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
41 9 0.02
42 427 0.96
43 7 0.02
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (42 bp):
AGGTGACTTCACGCCATTGTCGTTTAATAAGCATGTAGATAG
Found at i:1315608 original size:22 final size:22
Alignment explanation
Indices: 1315583--1315626 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1315573 GAAAAAACCC
*
1315583 CGGTTTAACAAAGACGGAAAAT
1 CGGTTTAACAAAGACAGAAAAT
1315605 CGGTTTAACAAAGACAGAAAAT
1 CGGTTTAACAAAGACAGAAAAT
1315627 AGCATTTACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.18
Consensus pattern (22 bp):
CGGTTTAACAAAGACAGAAAAT
Found at i:1318146 original size:2 final size:2
Alignment explanation
Indices: 1318139--1318178 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1318129 AGTATTTACA
1318139 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1318179 GTGCGTGCGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1320844 original size:2 final size:2
Alignment explanation
Indices: 1320837--1320863 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1320827 ATGCAAAATA
1320837 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
1320864 GAATTACTGA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1321349 original size:2 final size:2
Alignment explanation
Indices: 1321342--1321419 Score: 133
Period size: 2 Copynumber: 40.0 Consensus size: 2
1321332 AGAGGTATGT
*
1321342 TC TC TC TC TC TC -C TC TC TC TC TC TC TC AC TC -C 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
1321382 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
1321420 GTTATTTAAT
Statistics
Matches: 72, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
1 2 0.03
2 70 0.97
ACGTcount: A:0.01, C:0.51, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:1325728 original size:42 final size:42
Alignment explanation
Indices: 1325638--1326807 Score: 1486
Period size: 42 Copynumber: 27.8 Consensus size: 42
1325628 TCCACATGCT
* * * * *
1325638 TGAAGTCACCTCTATGTACA-GGTTGATAAAA-GACAATGACG
1 TGAAGTCACCTCTATTTACATGCTT-AAAAAACGTCAATGGCG
* * **
1325679 TGAAGTCACCTCTATCTACATGATTATTAAACGTCAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGTCAATGGCG
1325721 TGAAGTCACCTCTATTTACATGCTTAAAAAACCG-CAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAA-CGTCAATGGCG
* * *
1325763 TGAAGTCACCTCTATTTACATGCTTCAAAAACGGCGATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGTCAATGGCG
*
1325805 TGAAGTCACCTCTATTTACATGCTTAAAAAACCG-CAATGGCA
1 TGAAGTCACCTCTATTTACATGCTTAAAAAA-CGTCAATGGCG
1325847 TGAAGTCACCTCTATTTACATGCTTAAAAAACCG-CAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAA-CGTCAATGGCG
1325889 TGAAGTCACCTCTATTTACATGCTTAAAAAA-GTGCAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGT-CAATGGCG
* * **
1325931 TGAAGTCACCTCTATCTACATGCTTTAGGAA-GTGCAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGT-CAATGGCG
* ** *
1325973 TGAAGTCACCTCTATCTACATGCTTATTAAACGACAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGTCAATGGCG
* * * *
1326015 TGAAGTCACCTCTATCTACATGATTATAAAACGGCAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGTCAATGGCG
*
1326057 TGAAGTCACCTCTATTTACATGCTTTAAAAA-GTGCAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGT-CAATGGCG
* *
1326099 TGAAGTCACCTCTATCTACATGCTTATAAAA-GTGCAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGT-CAATGGCG
** * *
1326141 TGAAGTCACCTCTATTTACATGCTTATTAAACGGCAATGGCA
1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGTCAATGGCG
1326183 TGAAGTCACCTCTATTTACATGCCTTAAAAAAC-TGCAATGGCG
1 TGAAGTCACCTCTATTTACATG-CTTAAAAAACGT-CAATGGCG
1326226 TGAAGTCACCTCTATTTACATGCTTAAAAAAC-TGCAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGT-CAATGGCG
* * * **
1326268 TGAAGTCACCTCTCTCTACATGATTATTAAACAG-CAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAAC-GTCAATGGCG
1326310 TGAAGTCACCTCTATTTACATGCTTAAAAAAC-TGCAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGT-CAATGGCG
* * *
1326352 TGAAGTCACCTCTATTTACATGCTTTAGAAACCG-CAATGGCA
1 TGAAGTCACCTCTATTTACATGC-TTAAAAAACGTCAATGGCG
*
1326394 TGAAGTCACCTCTATCTACATGCTTAAAAAACCG-CAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAA-CGTCAATGGCG
1326436 TGAAGTCACCTCTATTTACATGCTTAAAAAACCG-CAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAA-CGTCAATGGCG
*
1326478 TGAAGTCACCTCTATCTACATGCTTAAAAAACCG-CAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAA-CGTCAATGGCG
1326520 TGAAGTCACCTCTATTTACATGCTTAAAAAACCG-CAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAA-CGTCAATGGCG
* * *
1326562 TGAAGTCACTTCTATCTACATGCTT-AAAAACGACAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGTCAATGGCG
* *
1326603 TGAAGTCACCTCTATCTACATGCTTATAAAA-GTGCAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGT-CAATGGCG
*
1326645 TGAAGTCACCTCTATTTACATGCTTATAAAA-GTGCAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGT-CAATGGCG
*
1326687 TAAAGTCACCTCTATTTACATGCTTAAAAAACCG-CAATGGCG
1 TGAAGTCACCTCTATTTACATGCTTAAAAAA-CGTCAATGGCG
*
1326729 TGCAGTCACCTCTATTTACATGCCTTAAAAAAC-TGCAATGGCG
1 TGAAGTCACCTCTATTTACATG-CTTAAAAAACGT-CAATGGCG
1326772 TGAAGTCACCTCTATTAATTTACATGCTTAAAAAAC
1 TGAAGTCACCTC---T-ATTTACATGCTTAAAAAAC
1326808 TTCACGACAA
Statistics
Matches: 1024, Mismatches: 74, Indels: 57
0.89 0.06 0.05
Matches are distributed among these distances:
40 3 0.00
41 71 0.07
42 851 0.83
43 78 0.08
44 1 0.00
46 11 0.01
47 9 0.01
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (42 bp):
TGAAGTCACCTCTATTTACATGCTTAAAAAACGTCAATGGCG
Found at i:1325876 original size:126 final size:126
Alignment explanation
Indices: 1325638--1326787 Score: 1643
Period size: 126 Copynumber: 9.1 Consensus size: 126
1325628 TCCACATGCT
* * * * *
1325638 TGAAGTCACCTCTATGTACA-GGTTGATAAAA-GACAATGACGTGAAGTCACCTCTATCTACATG
1 TGAAGTCACCTCTATTTACATGCTT-ATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATG
* **
1325701 ATTATTAAA-CGTCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG
65 CTTAAAAAACCG-CAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG
*
1325763 TGAAGTCACCTCTATTTACATGCTTCA-AAAACGGCGATGGCGTGAAGTCACCTCTATTTACATG
1 TGAAGTCACCTCTATTTACATGCTT-ATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATG
*
1325827 CTTAAAAAACCGCAATGGCATGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG
65 CTTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG
* *
1325889 TGAAGTCACCTCTATTTACATGCTTA-AAAAAGTGCAATGGCGTGAAGTCACCTCTATCTACATG
1 TGAAGTCACCTCTATTTACATGCTTATAAAACG-GCAATGGCGTGAAGTCACCTCTATTTACATG
* ** ** * **
1325953 CTTTAGGAAGTGCAATGGCGTGAAGTCACCTCTATCTACATGCTTATTAAA-CGACAATGGCG
65 CTTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCG-CAATGGCG
* *
1326015 TGAAGTCACCTCTATCTACATGATTATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATGC
1 TGAAGTCACCTCTATTTACATGCTTATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATGC
* ** * * **
1326080 TTTAAAAAGTGCAATGGCGTGAAGTCACCTCTATCTACATGCTTATAAAAGTGCAATGGCG
66 TTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG
* *
1326141 TGAAGTCACCTCTATTTACATGCTTATTAAACGGCAATGGCATGAAGTCACCTCTATTTACATGC
1 TGAAGTCACCTCTATTTACATGCTTATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATG-
* *
1326206 CTTAAAAAACTGCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACTGCAATGGCG
65 CTTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG
* * * * *
1326268 TGAAGTCACCTCTCTCTACATGATTATTAAACAGCAATGGCGTGAAGTCACCTCTATTTACATGC
1 TGAAGTCACCTCTATTTACATGCTTATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATGC
* * * *
1326333 TTAAAAAACTGCAATGGCGTGAAGTCACCTCTATTTACATGCTTTAGAAACCGCAATGGCA
66 TTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG
* * *
1326394 TGAAGTCACCTCTATCTACATGCTTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATGC
1 TGAAGTCACCTCTATTTACATGCTTATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATGC
*
1326459 TTAAAAAACCGCAATGGCGTGAAGTCACCTCTATCTACATGCTTAAAAAACCGCAATGGCG
66 TTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG
* * * *
1326520 TGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCGTGAAGTCACTTCTATCTACATGC
1 TGAAGTCACCTCTATTTACATGCTTATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATGC
* * **
1326585 TT-AAAAA-CGACAATGGCGTGAAGTCACCTCTATCTACATGCTTATAAAAGTGCAATGGCG
66 TTAAAAAACCG-CAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG
*
1326645 TGAAGTCACCTCTATTTACATGCTTATAAAA-GTGCAATGGCGTAAAGTCACCTCTATTTACATG
1 TGAAGTCACCTCTATTTACATGCTTATAAAACG-GCAATGGCGTGAAGTCACCTCTATTTACATG
* *
1326709 CTTAAAAAACCGCAATGGCGTGCAGTCACCTCTATTTACATGCCTTAAAAAACTGCAATGGCG
65 CTTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATG-CTTAAAAAACCGCAATGGCG
1326772 TGAAGTCACCTCTATT
1 TGAAGTCACCTCTATT
1326788 AATTTACATG
Statistics
Matches: 938, Mismatches: 74, Indels: 24
0.91 0.07 0.02
Matches are distributed among these distances:
124 2 0.00
125 144 0.15
126 632 0.67
127 160 0.17
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (126 bp):
TGAAGTCACCTCTATTTACATGCTTATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATGC
TTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG
Found at i:1328350 original size:43 final size:43
Alignment explanation
Indices: 1328289--1328583 Score: 222
Period size: 43 Copynumber: 6.9 Consensus size: 43
1328279 AAATCTTTTT
*
1328289 TCGTAATAACGAGATCTTTTCTCGTTATTACGAGATAATTAAC
1 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAAC
*
1328332 TCGTAATAACGAGATCTTTTCTCGTAATAACGAGATAATTAAC
1 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAAC
* * * **
1328375 TCGTAATAACGAGATCTTTTCTTGTAATTAGGAGAT-CTTTTC
1 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAAC
* * ** * * ***
1328417 TCGTAATGACGAGATAATTAACTCGTAATAACGAGAT-CTTTTT
1 TCGTAATAACGAGAT-CTTTTCTCGTAATTACGAGATAATTAAC
* * * ** * * **
1328460 TCGTAATTAGGAGATAATTAACTCGTAATAACGAGAT-CTTTTC
1 TCGTAATAACGAGAT-CTTTTCTCGTAATTACGAGATAATTAAC
* * * ** * **
1328503 TCGTTATTACGAGATAATTAACTCATAATTACGAG-TTCTCT-AC
1 TCGTAATAACGAGAT-CTTTTCTCGTAATTACGAGATAAT-TAAC
1328546 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAA
1 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAA
1328584 AAATATTTTC
Statistics
Matches: 216, Mismatches: 32, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
42 33 0.15
43 182 0.84
44 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (43 bp):
TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAAC
Found at i:1328474 original size:107 final size:107
Alignment explanation
Indices: 1328281--1328583 Score: 423
Period size: 107 Copynumber: 2.8 Consensus size: 107
1328271 TTTTATATAA
* *
1328281 ATCTTTT-TTCGTAATAACGAGATCTTTTCTCGTTATTACGAGATAATTAACTCGTAATAACGAG
1 ATCTTTTCTT-GTAATTACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAG
*
1328345 ATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAG
65 ATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAG
* *
1328388 ATCTTTTCTTGTAATTAGGAGATCTTTTCTCGTAATGACGAGATAATTAACTCGTAATAACGAGA
1 ATCTTTTCTTGTAATTACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAGA
* *
1328453 TCTTTTTTCGTAATTAGGAGATAATTAACTCGTAATAACGAG
66 TCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAG
* * * ** * **
1328495 ATCTTTTCTCGTTATTACGAGATAATTAACTCATAATTACGAG-TTCTCT-ACTCGTAATAACGA
1 ATCTTTTCTTGTAATTACGAGAT-CTTTTCTCGTAATTACGAGATAAT-TAACTCGTAATAACGA
1328558 GATCTTTTCTCGTAATTACGAGATAA
64 GATCTTTTCTCGTAATTACGAGATAA
1328584 AAATATTTTC
Statistics
Matches: 174, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
107 157 0.90
108 17 0.10
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (107 bp):
ATCTTTTCTTGTAATTACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAGA
TCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAG
Found at i:1328506 original size:64 final size:64
Alignment explanation
Indices: 1328289--1328583 Score: 288
Period size: 64 Copynumber: 4.6 Consensus size: 64
1328279 AAATCTTTTT
* * *
1328289 TCGTAATAACGAGATCTTTTCTCGTTATTACGAGATAATTAACTCGTAATAACGAGATCTTTTC
1 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATTACGAGATCTTTAC
* ** * * ** * * *
1328353 TCGTAATAACGAGATAATTAACTCGTAATAACGAGAT-CTTTTCTTGTAATTAGGAGATCTTTTC
1 TCGTAATAACGAGAT-CTTTTCTCGTAATTACGAGATAATTAACTCGTAATTACGAGATCTTTAC
* * ** * * *** * * *
1328417 TCGTAATGACGAGATAATTAACTCGTAATAACGAGAT-CTTTTTTCGTAATTAGGAGATAATTAA
1 TCGTAATAACGAGAT-CTTTTCTCGTAATTACGAGATAATTAACTCGTAATTACGAGAT-CTTTA
1328481 C
64 C
* * * *
1328482 TCGTAATAACGAGATCTTTTCTCGTTATTACGAGATAATTAACTCATAATTACGAGTTCTCTAC
1 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATTACGAGATCTTTAC
1328546 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAA
1 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAA
1328584 AAATATTTTC
Statistics
Matches: 194, Mismatches: 34, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
64 147 0.76
65 47 0.24
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (64 bp):
TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATTACGAGATCTTTAC
Found at i:1342235 original size:438 final size:437
Alignment explanation
Indices: 1341291--1343153 Score: 2494
Period size: 437 Copynumber: 4.3 Consensus size: 437
1341281 ATAAACGTAT
* ** * ***
1341291 TATTATGCTT-TTGTAACATTTCACAAAATATATCTCAGTAAATCGCTACA-AATACAATTTTTT
1 TATT-TGCTTCTT-TAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTA-AAGACTTT
* * *
1341354 AGAGCCTTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAAGCCAT
63 AGAGCCCTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCAT
* * * ** * *
1341419 TTAATTCTA-ATCACATTTTTTTGAATC-AGTGTTT-GGGATTTGTTACCGTTTTTGAGATATTT
128 TTAATTCTACA-CAAATTTTGTTCAA-CAAGTGTTTAGAAATTTGTTACCGTTCTTGAGATATAT
* *
1341481 GAGAAAGAATGTTTTAGGGGCCGATCCCTAATCTCCTTTTAGGGGCCGTTTAACGAAATTTTGAA
191 GAGAAAGAAGGTTTTAGGGGCCGATCCCTTATCTCCTTTTAGGGGCCGTTTAACGAAATTTTGAA
* * * * * * ** **
1341546 GGTTGCATATTACTT-AGGACATCACTTTGAGCATCTTTCCTTCTATACTGCATTTTAAAATCCT
256 GGTTGCAT-TTTCTTAAGAACATCATTTTGAACATCTTTTCTTCTGTACTGCATTACAAAATATT
* * *
1341610 TTTCGTTTCTGAGATATGGGTGATCAAAATTTTGGACTTTTGGCCCCTAAAAACCCCTAATTACG
320 TTTCCTTTCTGAGATATGGGAGATCAAAATTTTGGACTTTTGGCCCCTAAAAACCCTTAATTACG
* * * * * *
1341675 TAACATATAATAAAATCATTACATTGTTTGGATACATTAC-TGTTAGAAAAACA
385 TAACACATAATAAAATCATTACATTGCTTGAATACATAACAT-TGAGATAAACA
* * * *
1341728 TATTTGCTTCTTTAACATTTCACAAAATATCTCTTAGTAAAGGGCTACAGATGAAAAACTTTCGA
1 TATTTGCTTCTTTAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGA
** * *
1341793 GCCCTTTAATCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATAACAGATAAAAGGTCATTTA
66 GCCCTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCATTTA
* * * * * *
1341858 ATTCTACACACATTTTGTTCAATAAGTATTTAAAAATGTGTTACCGTTCTTGAGATATTTGAGAA
131 ATTCTACACAAATTTTGTTCAACAAGTGTTTAGAAATTTGTTACCGTTCTTGAGATATATGAGAA
** * * *
1341923 AGAATATTTTAGGGGCCGATCCCTTATTTCCTTTTAGGGGCCGTTTAACGATATTTTGAAAGTTG
196 AGAAGGTTTTAGGGGCCGATCCCTTATCTCCTTTTAGGGGCCGTTTAACGAAATTTTGAAGGTTG
* * * * *
1341988 CATATTTCTT-AGGACATCATTTTGAGCATCTTTTCTTCTGTGCTGCATTTCAAAATCCTTTTTC
261 CAT-TTTCTTAAGAACATCATTTTGAACATCTTTTCTTCTGTACTGCATTACAAAAT-ATTTTTC
* * * ** *
1342052 TTTTCTGAGATATGGGTGATCGAAATTTTGGACTTTTGGCCCCTAAAAACCCTTGGTTAGGTAAC
324 CTTTCTGAGATATGGGAGATCAAAATTTTGGACTTTTGGCCCCTAAAAACCCTTAATTACGTAAC
* * *
1342117 ACATGATTAAATCATTACATTGCTT-AGATACATAAC-TGTAAGATAAACA
389 ACATAATAAAATCATTACATTGCTTGA-ATACATAACAT-TGAGATAAACA
1342166 TATTTGCTTCTTTAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGA
1 TATTTGCTTCTTTAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGA
* *
1342231 GCCCTTTGGTCCCCTAATTTTAGGGGCCAGCTCCTTTTTCTTGATATCAAATAAAAGGTCATTTA
66 GCCCTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCATTTA
*
1342296 ATTCTACACAAATTTTGTTCAACAAGTGTTTAGAAATTTGTTACCGTTCTAGAGATATATGAGAA
131 ATTCTACACAAATTTTGTTCAACAAGTGTTTAGAAATTTGTTACCGTTCTTGAGATATATGAGAA
* * * * *
1342361 AGAAGGTTTTAGGGGCTGGTCCCTTATCTCCTTTTAGGGGGCTTTTAACGAAATTTTGACGGTTG
196 AGAAGGTTTTAGGGGCCGATCCCTTATCTCCTTTTAGGGGCCGTTTAACGAAATTTTGAAGGTTG
* * *
1342426 CATTTTGTTAAGAACATCATTTTGAACAACTTTTCTTTTGTACTGCATTACAAAATATTTTTCCT
261 CATTTTCTTAAGAACATCATTTTGAACATCTTTTCTTCTGTACTGCATTACAAAATATTTTTCCT
* *
1342491 TTCTGAAATATGGGAGATCGAAATTTTGGACTTTTGGCCCCTAAAAACCCTTAATTACGTAACAC
326 TTCTGAGATATGGGAGATCAAAATTTTGGACTTTTGGCCCCTAAAAACCCTTAATTACGTAACAC
*
1342556 ATCATAAAATCATTACATTGCTTGAATACATAACATTGAGATAAACA
391 ATAATAAAATCATTACATTGCTTGAATACATAACATTGAGATAAACA
* * *
1342603 CATTTGCTTCTATAACATTTCACAAAATATCTCTCAGTAAAAGGCTACAGATTAAAGACTTTAGA
1 TATTTGCTTCTTTAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGA
1342668 GCCCTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCATTTA
66 GCCCTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCATTTA
* * * *
1342733 ATTCTACACAAAATTTGTTAAACAAGTGTTTAGAAATTCGTTACCGTTCTGGAGATATATGAGAA
131 ATTCTACACAAATTTTGTTCAACAAGTGTTTAGAAATTTGTTACCGTTCTTGAGATATATGAGAA
* * * * *
1342798 ATAAGGTTTTAGGGGCCGTTCCCTTATCTCCTTTTAGGGGCCGTTAAACGAAATTTTGACGATTG
196 AGAAGGTTTTAGGGGCCGATCCCTTATCTCCTTTTAGGGGCCGTTTAACGAAATTTTGAAGGTTG
* *
1342863 CATTTTGTTAAGAACATCATTTTGAACAAT-TTTTCTTCTGTACTGCATTACAAAATATTTGTCC
261 CATTTTCTTAAGAACATCATTTTGAAC-ATCTTTTCTTCTGTACTGCATTACAAAATATTTTTCC
* * *
1342927 TTTCTGAGATATGGGAGATCAAAATTTGGGAGTTTTGCCCCCTAAAAACCCTTAATTACGTAACA
325 TTTCTGAGATATGGGAGATCAAAATTTTGGACTTTTGGCCCCTAAAAACCCTTAATTACGTAACA
1342992 CATAATAAAATCATTACATTGCTTGAATACATAACATTGAGATAAACA
390 CATAATAAAATCATTACATTGCTTGAATACATAACATTGAGATAAACA
* * * * * * * * *
1343040 TATTTGCTTCTATAATC-TATT-ACAAAATATCCCTCGGTAAAGAGTTACGGGTAAAAGATTTTA
1 TATTTGCTTCTTTAA-CAT-TTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTA
1343103 GAGCCCTTTAGGT-CCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCA
64 GAGCCCTTT-GGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCA
1343154 GCTGAAAGAT
Statistics
Matches: 1281, Mismatches: 131, Indels: 28
0.89 0.09 0.02
Matches are distributed among these distances:
436 127 0.10
437 764 0.60
438 390 0.30
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (437 bp):
TATTTGCTTCTTTAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGA
GCCCTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCATTTA
ATTCTACACAAATTTTGTTCAACAAGTGTTTAGAAATTTGTTACCGTTCTTGAGATATATGAGAA
AGAAGGTTTTAGGGGCCGATCCCTTATCTCCTTTTAGGGGCCGTTTAACGAAATTTTGAAGGTTG
CATTTTCTTAAGAACATCATTTTGAACATCTTTTCTTCTGTACTGCATTACAAAATATTTTTCCT
TTCTGAGATATGGGAGATCAAAATTTTGGACTTTTGGCCCCTAAAAACCCTTAATTACGTAACAC
ATAATAAAATCATTACATTGCTTGAATACATAACATTGAGATAAACA
Found at i:1343806 original size:115 final size:115
Alignment explanation
Indices: 1343604--1343835 Score: 410
Period size: 115 Copynumber: 2.0 Consensus size: 115
1343594 AATAATAGGG
* * *
1343604 AAAAAGAAACCGAAGAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAAAAAGAAA
1 AAAAAGAAACCGAAGAATAACAAGAAGGTCTTCCGTTGAAAACGGAAGACCCTAATAAAAAGAAA
* *
1343669 CCGAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAAT
66 CCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAAAAT
*
1343719 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAATAAAAAGAAA
1 AAAAAGAAACCGAAGAATAACAAGAAGGTCTTCCGTTGAAAACGGAAGACCCTAATAAAAAGAAA
1343784 CCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAAAAT
66 CCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAAAAT
1343834 AA
1 AA
1343836 TAATGAAGAA
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
115 111 1.00
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (115 bp):
AAAAAGAAACCGAAGAATAACAAGAAGGTCTTCCGTTGAAAACGGAAGACCCTAATAAAAAGAAA
CCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAAAAT
Found at i:1343826 original size:56 final size:56
Alignment explanation
Indices: 1343604--1343829 Score: 380
Period size: 56 Copynumber: 4.0 Consensus size: 56
1343594 AATAATAGGG
* * * *
1343604 AAAAAGAAACCGAAGAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT
1 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAT
*
1343660 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAAT
1 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCC---TAAT
1343719 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAT
1 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAT
1343775 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAA
1 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAA
1343830 AAATAATAAT
Statistics
Matches: 163, Mismatches: 4, Indels: 6
0.94 0.02 0.03
Matches are distributed among these distances:
56 108 0.66
59 55 0.34
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (56 bp):
AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAT
Found at i:1347730 original size:129 final size:130
Alignment explanation
Indices: 1347405--1347918 Score: 895
Period size: 130 Copynumber: 4.0 Consensus size: 130
1347395 GTCATTACCC
1347405 TTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCACTGT
1 TTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCACTGT
1347470 ACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAACTCA
66 ACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAACTCA
* *
1347535 TTGTTTCACTTTCTTATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCACTGT
1 TTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCACTGT
* * ** *
1347600 ACCCTCACCATCAGCTCCTTTATTTGATTTTTTAACTTTGACAAAAATGGAGACTTCTTAAC-CC
66 ACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAACTCA
*
1347664 TTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCATTGT
1 TTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCACTGT
1347729 ACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAACTCA
66 ACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAACTCA
* * *
1347794 TTGTTTCACTTTCTTATAGTTTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCACTGT
1 TTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCACTGT
* * *
1347859 ACCCTCACCATCAGCTCCTTTATTTGATTTTTTAACTTTGACAAAAATAAAGACTTCTTA
66 ACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTA
1347919 CATCTGTTAC
Statistics
Matches: 361, Mismatches: 22, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
129 121 0.34
130 240 0.66
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.39
Consensus pattern (130 bp):
TTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCACTGT
ACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAACTCA
Found at i:1347860 original size:259 final size:259
Alignment explanation
Indices: 1347401--1347918 Score: 1000
Period size: 259 Copynumber: 2.0 Consensus size: 259
1347391 TGAAGTCATT
1347401 ACCCTTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA
1 ACCCTTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA
1347466 CTGTACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAA
66 CTGTACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAA
1347531 CTCATTGTTTCACTTTCTTATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA
131 CTCATTGTTTCACTTTCTTATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA
**
1347596 CTGTACCCTCACCATCAGCTCCTTTATTTGATTTTTTAACTTTGACAAAAATGGAGACTTCTTA
196 CTGTACCCTCACCATCAGCTCCTTTATTTGATTTTTTAACTTTGACAAAAATAAAGACTTCTTA
1347660 ACCCTTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA
1 ACCCTTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA
*
1347725 TTGTACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAA
66 CTGTACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAA
*
1347790 CTCATTGTTTCACTTTCTTATAGTTTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA
131 CTCATTGTTTCACTTTCTTATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA
1347855 CTGTACCCTCACCATCAGCTCCTTTATTTGATTTTTTAACTTTGACAAAAATAAAGACTTCTTA
196 CTGTACCCTCACCATCAGCTCCTTTATTTGATTTTTTAACTTTGACAAAAATAAAGACTTCTTA
1347919 CATCTGTTAC
Statistics
Matches: 255, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
259 255 1.00
ACGTcount: A:0.25, C:0.26, G:0.10, T:0.39
Consensus pattern (259 bp):
ACCCTTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA
CTGTACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAA
CTCATTGTTTCACTTTCTTATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA
CTGTACCCTCACCATCAGCTCCTTTATTTGATTTTTTAACTTTGACAAAAATAAAGACTTCTTA
Found at i:1349367 original size:24 final size:25
Alignment explanation
Indices: 1349340--1349391 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
1349330 TTTATCTCAC
1349340 TTTAA-TTTTTTTTAGATTCTTCTG
1 TTTAAGTTTTTTTTAGATTCTTCTG
1349364 TTTAAGTTTTTTTTAGATTCTTCTG
1 TTTAAGTTTTTTTTAGATTCTTCTG
1349389 TTT
1 TTT
1349392 TGTAGGGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.15, C:0.08, G:0.10, T:0.67
Consensus pattern (25 bp):
TTTAAGTTTTTTTTAGATTCTTCTG
Found at i:1363552 original size:54 final size:55
Alignment explanation
Indices: 1363450--1363565 Score: 173
Period size: 54 Copynumber: 2.1 Consensus size: 55
1363440 AGACGAAGAA
* **
1363450 GTGCTGTAAATCGTTAATTATTATATCCACTACGAGTGATCAACTAGACAAAAAT
1 GTGCTGTAAATCGTTAATCATTATATCCACTACGAGCCATCAACTAGACAAAAAT
*
1363505 GTGCTGTAAATCGTT-ATCATTATATCCACTATGAGCCATC-ACTTAGACAAAAAT
1 GTGCTGTAAATCGTTAATCATTATATCCACTACGAGCCATCAAC-TAGACAAAAAT
1363559 GTGCTGT
1 GTGCTGT
1363566 TATATATAGT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
53 2 0.04
54 39 0.70
55 15 0.27
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (55 bp):
GTGCTGTAAATCGTTAATCATTATATCCACTACGAGCCATCAACTAGACAAAAAT
Found at i:1364574 original size:215 final size:214
Alignment explanation
Indices: 1364203--1364631 Score: 849
Period size: 215 Copynumber: 2.0 Consensus size: 214
1364193 AACAGCGGTA
1364203 AATTCTAAAATGTATTTTAAAAGGTAATGTTAGCCCTTGTATGAAAAATTTCGGATGGTAGTCAT
1 AATTCTAAAATGTATTTTAAAAGGTAATGTTAGCCCTTGTATGAAAAATTTCGGATGGTAGTCAT
1364268 TTTTTCCGGGATCCAGACCGAGAGCTACATATATGCAGCTAAGGTAACTAATAATGCTTCCAATA
66 TTTTTCCGGGATCCAGACCGAGAGCTACATATATGCAGCTAAGGTAACTAATAATGCTTCCAATA
1364333 AAATACTTTGTTTATTAATGCAAGCTTTTAAGAAAGCAATACAGCCTACTCCGGATATATTGAAA
131 AAATACTTTGTTTATTAATGCAAGCTTTTAAGAAAGCAATACAGCCTACTCCGGATATATTGAAA
1364398 TTCTGGGGGCCATGCAAAT
196 TTCTGGGGGCCATGCAAAT
1364417 NAATTCTAAAATGTATTTTAAAAGGTAATGTTAGCCCTTGTATGAAAAATTTCGGATGGTAGTCA
1 -AATTCTAAAATGTATTTTAAAAGGTAATGTTAGCCCTTGTATGAAAAATTTCGGATGGTAGTCA
1364482 TTTTTTCCGGGATCCAGACCGAGAGCTACATATATGCAGCTAAGGTAACTAATAATGCTTCCAAT
65 TTTTTTCCGGGATCCAGACCGAGAGCTACATATATGCAGCTAAGGTAACTAATAATGCTTCCAAT
1364547 AAAATACTTTGTTTATTAATGCAAGCTTTTAAGAAAGCAATACAGCCTACTCCGGATATATTGAA
130 AAAATACTTTGTTTATTAATGCAAGCTTTTAAGAAAGCAATACAGCCTACTCCGGATATATTGAA
1364612 ATTCTGGGGGCCATGCAAAT
195 ATTCTGGGGGCCATGCAAAT
1364632 TATTTCAATA
Statistics
Matches: 214, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
215 214 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (214 bp):
AATTCTAAAATGTATTTTAAAAGGTAATGTTAGCCCTTGTATGAAAAATTTCGGATGGTAGTCAT
TTTTTCCGGGATCCAGACCGAGAGCTACATATATGCAGCTAAGGTAACTAATAATGCTTCCAATA
AAATACTTTGTTTATTAATGCAAGCTTTTAAGAAAGCAATACAGCCTACTCCGGATATATTGAAA
TTCTGGGGGCCATGCAAAT
Found at i:1365457 original size:15 final size:17
Alignment explanation
Indices: 1365420--1365464 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
1365410 ATTTATTTCT
1365420 ATTTCAAAATAAGCGGA
1 ATTTCAAAATAAGCGGA
1365437 ATTTCAAAATAAGC-G-
1 ATTTCAAAATAAGCGGA
*
1365452 ATTTCAATATAAG
1 ATTTCAAAATAAG
1365465 TGGAGTAAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 12 0.44
16 1 0.04
17 14 0.52
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (17 bp):
ATTTCAAAATAAGCGGA
Found at i:1368748 original size:2 final size:2
Alignment explanation
Indices: 1368741--1368765 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1368731 AAATTGCAAT
1368741 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 G
1368766 GGGGGCGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1371613 original size:11 final size:11
Alignment explanation
Indices: 1371597--1371628 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1371587 CTTAGAAGTC
*
1371597 AAGAAATATAG
1 AAGAAATAAAG
1371608 AAGAAATAAAG
1 AAGAAATAAAG
1371619 AAGAAATAAA
1 AAGAAATAAA
1371629 AGAATCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (11 bp):
AAGAAATAAAG
Found at i:1373234 original size:10 final size:10
Alignment explanation
Indices: 1373200--1373249 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
1373190 AATACATCAC
1373200 AATATTGTA-
1 AATATTGTAT
1373209 ACATA-TGATAT
1 A-ATATTG-TAT
*
1373220 TATATTGTAT
1 AATATTGTAT
*
1373230 AATATAGTAT
1 AATATTGTAT
1373240 AATATTGTAT
1 AATATTGTAT
1373250 TGTATGATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
9 3 0.09
10 28 0.85
11 2 0.06
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (10 bp):
AATATTGTAT
Found at i:1373234 original size:20 final size:20
Alignment explanation
Indices: 1373200--1373259 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
1373190 AATACATCAC
1373200 AATATTGTA-ACATATGATAT
1 AATATTGTATA-ATATGATAT
*
1373220 TATATTGTATAATAT-AGTAT
1 AATATTGTATAATATGA-TAT
**
1373240 AATATTGTATTGTATGATAT
1 AATATTGTATAATATGATAT
1373260 CGTATCATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 1 0.03
20 30 0.91
21 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (20 bp):
AATATTGTATAATATGATAT
Found at i:1373250 original size:25 final size:25
Alignment explanation
Indices: 1373216--1373270 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1373206 GTAACATATG
1373216 ATATTATATTGTATAATATAGTATA
1 ATATTATATTGTATAATATAGTATA
* * * *
1373241 ATATTGTATTGTATGATATCGTATC
1 ATATTATATTGTATAATATAGTATA
1373266 ATATT
1 ATATT
1373271 TGATACACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (25 bp):
ATATTATATTGTATAATATAGTATA
Found at i:1373299 original size:22 final size:23
Alignment explanation
Indices: 1373256--1373299 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1373246 GTATTGTATG
1373256 ATATCGTATCATATTTGATACACA
1 ATATCGTATCATA-TTGATACACA
*
1373280 ATATTGTATCATA-TGATACA
1 ATATCGTATCATATTGATACA
1373300 ATATAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
24 12 0.63
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (23 bp):
ATATCGTATCATATTGATACACA
Found at i:1373351 original size:15 final size:15
Alignment explanation
Indices: 1373333--1373661 Score: 128
Period size: 15 Copynumber: 21.6 Consensus size: 15
1373323 TCATATCATG
* *
1373333 ATACAATATCATCTG
1 ATACAATATCATATT
* *
1373348 ATACAGTATGATATT
1 ATACAATATCATATT
*
1373363 ATATAATA-CAATATT
1 ATACAATATC-ATATT
*
1373378 ATACAATATCATTTT
1 ATACAATATCATATT
1373393 ATACAATATCATATCATAT
1 ATACAATATC--AT-AT-T
1373412 GATACAATATCATATT
1 -ATACAATATCATATT
*
1373428 ATACAGTATCATATT
1 ATACAATATCATATT
*
1373443 ATATAATATC---TT
1 ATACAATATCATATT
*
1373455 AT--AATATCATATA
1 ATACAATATCATATT
*
1373468 ATACAATTTCATGTATTAT
1 ATACAATATCA--TA-T-T
1373487 ATAACAATAT-ATTATAT
1 AT-ACAATATCA-TAT-T
*
1373504 AAACCAATATCATATT
1 ATA-CAATATCATATT
* ** *
1373520 ATACATTATTGTATC
1 ATACAATATCATATT
* *
1373535 ATACAATATGATATA
1 ATACAATATCATATT
*
1373550 ATTATAATATACA-A-T
1 A-TACAATAT-CATATT
** *
1373565 AT--TGTATCATATG
1 ATACAATATCATATT
*
1373578 ATACAAAATCATA-T
1 ATACAATATCATATT
* * *
1373592 ATTGCAATATAATATG
1 A-TACAATATCATATT
* *
1373608 AAACAATATCAT-TCG
1 ATACAATATCATAT-T
*
1373623 ATAAAATAAT-ATATT
1 ATACAAT-ATCATATT
1373638 ATACAATATCATATT
1 ATACAATATCATATT
*
1373653 CTACAATAT
1 ATACAATAT
1373662 TGTATAATAA
Statistics
Matches: 233, Mismatches: 50, Indels: 62
0.68 0.14 0.18
Matches are distributed among these distances:
10 6 0.03
11 2 0.01
12 8 0.03
13 5 0.02
14 5 0.02
15 142 0.61
16 18 0.08
17 20 0.09
18 7 0.03
19 4 0.02
20 16 0.07
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (15 bp):
ATACAATATCATATT
Found at i:1373408 original size:5 final size:5
Alignment explanation
Indices: 1373398--1373466 Score: 52
Period size: 5 Copynumber: 13.8 Consensus size: 5
1373388 ATTTTATACA
* * * *
1373398 ATATC ATATC ATATG ATA-C AATATC ATATT ATA-C AGTATC ATATT ATATA
1 ATATC ATATC ATATC ATATC -ATATC ATATC ATATC A-TATC ATATC ATATC
* *
1373448 ATATC TTATA ATATC ATAT
1 ATATC ATATC ATATC ATAT
1373467 AATACAATTT
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
4 1 0.02
5 45 0.92
6 3 0.06
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.42
Consensus pattern (5 bp):
ATATC
Found at i:1373408 original size:20 final size:20
Alignment explanation
Indices: 1373383--1373426 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1373373 ATATTATACA
* *
1373383 ATATCATTTTATACAATATC
1 ATATCATATGATACAATATC
1373403 ATATCATATGATACAATATC
1 ATATCATATGATACAATATC
1373423 ATAT
1 ATAT
1373427 TATACAGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (20 bp):
ATATCATATGATACAATATC
Found at i:1373424 original size:35 final size:35
Alignment explanation
Indices: 1373338--1373446 Score: 120
Period size: 35 Copynumber: 3.3 Consensus size: 35
1373328 TCATGATACA
* * * *
1373338 ATATCATCTGATACAGTATGATATTATATAATA-C
1 ATATCATATGATACAATATCATATTATACAATATC
*
1373372 A-AT-AT-T-ATACAATATCATTTTATACAATATC
1 ATATCATATGATACAATATCATATTATACAATATC
*
1373403 ATATCATATGATACAATATCATATTATACAGTATC
1 ATATCATATGATACAATATCATATTATACAATATC
*
1373438 ATATTATAT
1 ATATCATAT
1373447 AATATCTTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
30 19 0.30
31 3 0.05
32 4 0.06
33 4 0.06
34 2 0.03
35 31 0.49
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (35 bp):
ATATCATATGATACAATATCATATTATACAATATC
Found at i:1373441 original size:20 final size:19
Alignment explanation
Indices: 1373383--1373472 Score: 62
Period size: 20 Copynumber: 4.8 Consensus size: 19
1373373 ATATTATACA
*
1373383 ATATCATTTTATACAATATC
1 ATATCATATTATAC-ATATC
*
1373403 ATATCATATGATAC--A--
1 ATATCATATTATACATATC
1373418 ATATCATATTATACAGTATC
1 ATATCATATTATACA-TATC
* * * *
1373438 ATATTATATAATATCTTATA
1 ATATCATATTATA-CATATC
*
1373458 ATATCATATAATACA
1 ATATCATATTATACA
1373473 ATTTCATGTA
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
15 13 0.24
17 1 0.02
18 1 0.02
19 1 0.02
20 38 0.69
21 1 0.02
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.41
Consensus pattern (19 bp):
ATATCATATTATACATATC
Found at i:1373457 original size:10 final size:10
Alignment explanation
Indices: 1373397--1373470 Score: 69
Period size: 10 Copynumber: 7.4 Consensus size: 10
1373387 CATTTTATAC
1373397 AATATCATAT
1 AATATCATAT
* * *
1373407 CATATGATAC
1 AATATCATAT
1373417 AATATCATAT
1 AATATCATAT
*
1373427 TATA-CAGTAT
1 AATATCA-TAT
* *
1373437 CATATTATAT
1 AATATCATAT
*
1373447 AATATCTTAT
1 AATATCATAT
1373457 AATATCATAT
1 AATATCATAT
1373467 AATA
1 AATA
1373471 CAATTTCATG
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
9 2 0.04
10 46 0.94
11 1 0.02
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.41
Consensus pattern (10 bp):
AATATCATAT
Found at i:1373718 original size:15 final size:15
Alignment explanation
Indices: 1373333--1373718 Score: 97
Period size: 15 Copynumber: 25.2 Consensus size: 15
1373323 TCATATCATG
* *
1373333 ATACAATATCATCTG
1 ATACAATATCATATA
* * *
1373348 ATACAGTATGATATT
1 ATACAATATCATATA
* *
1373363 ATATAATA-CAATATT
1 ATACAATATC-ATATA
* *
1373378 ATACAATATCATTTT
1 ATACAATATCATATA
1373393 ATACAATATCATATCATA
1 ATACAATATC--AT-ATA
*
1373411 TGATACAATATCATATT
1 --ATACAATATCATATA
* *
1373428 ATACAGTATCATATT
1 ATACAATATCATATA
*
1373443 ATATAATATC-T-T-
1 ATACAATATCATATA
1373455 AT--AATATCATATA
1 ATACAATATCATATA
*
1373468 ATACAATTTCATGTATTA
1 ATACAATATCA--TA-TA
1373486 TATAACAATAT-ATTATA
1 -AT-ACAATATCA-TATA
* *
1373503 TAAACCAATATCATATT
1 -ATA-CAATATCATATA
* ** *
1373520 ATACATTATTGTATC
1 ATACAATATCATATA
*
1373535 ATACAATATGATATA
1 ATACAATATCATATA
*
1373550 ATTATAATATACA-AT-
1 A-TACAATAT-CATATA
** *
1373565 AT--TGTATCATATG
1 ATACAATATCATATA
*
1373578 ATACAAAATCATATA
1 ATACAATATCATATA
* * *
1373593 TTGCAATATAATATGA
1 ATACAATATCATAT-A
*
1373609 A-ACAATATCAT-TCG
1 ATACAATATCATAT-A
* *
1373623 ATAAAATAAT-ATATT
1 ATACAAT-ATCATATA
*
1373638 ATACAATATCATATT
1 ATACAATATCATATA
* *
1373653 CTACAATATTGTATAATAA
1 ATACAATA-T-CAT-AT-A
1373672 TATACAATA-C-TATA
1 -ATACAATATCATATA
1373686 CATAACAATATC--ATA
1 -AT-ACAATATCATATA
1373701 ATACAATATCATATA
1 ATACAATATCATATA
1373716 ATA
1 ATA
1373719 ATGTACAAAA
Statistics
Matches: 277, Mismatches: 55, Indels: 78
0.68 0.13 0.19
Matches are distributed among these distances:
10 6 0.02
11 3 0.01
12 8 0.03
13 13 0.05
14 11 0.04
15 158 0.57
16 20 0.07
17 22 0.08
18 10 0.04
19 3 0.01
20 23 0.08
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (15 bp):
ATACAATATCATATA
Found at i:1379683 original size:327 final size:326
Alignment explanation
Indices: 1379052--1380138 Score: 1497
Period size: 327 Copynumber: 3.3 Consensus size: 326
1379042 TGAAATAGGG
* * *
1379052 GTGAAATGCTAAAATATTACAAAGTTCGGGT-AGCTAACTGAGCCCCTGTAGGGGTCATAGGTGC
1 GTGAAATGCTAAAATATGACAAAGTTCGGGTGAGCTAACTGAGCCCTTGCAGGGGTCATAGGTGC
* * * ** * *
1379116 CCTC-TAACACTTATTATGAATATATACCTCCTGAGGTTCTCTACCTTATCCAAGTGTTTGCAAG
66 CCTCGT-ACGCTTATGATG---A-ATA-CTTCTGAGGCCCTCTACCTAATCCAAGTGTTTCCAAG
* *
1379180 TTCTTGTGGTCAATCTCAAGTGAGATATAAACCCCTGAAATGAGCCAGAACCCCTGGGATCCT-C
125 TTCTTGTGGTCAATCTCAAGTCAGATATAAACCCCTGAAATGAGCCAGAACCCCTGGGA-GCTAC
1379244 TTGGTGGTACCCCTACAGCCCAAATTTGAGACCGGGAAATAATAGCCCTCATAGGTCCTCTACAC
189 TTGGTGGTACCCCTACAGCCCAAATTTGAGACCGGGAAATAATAGCCCTCATAGGTCCTCTACAC
* *
1379309 TGCCCTGGTATCCGTTTGATGCACACTTCAAAGATAAAAGTGATAATGGCCCGCCTTTCACCCCT
254 TGCCCTGGTATCCGTTTGATGCACACTTCAAAGATAAAAGAGATAATGGACCGCCTTTCACCCCT
1379374 ATATCATT
319 ATATCATT
* * * * *
1379382 GTGAAATGCTAAAATATGAGAGAGTTCGGGTGAGCTAACTGAACCCTTGTAGGGGCCATAGGTGC
1 GTGAAATGCTAAAATATGACAAAGTTCGGGTGAGCTAACTGAGCCCTTGCAGGGGTCATAGGTGC
* * * *
1379447 CCTCGTACGCTTATTATGAATACTTCTTGAGGTCCTCAACCTAATCCAAGTGTTTTCAAGTTCTT
66 CCTCGTACGCTTATGATGAATACTTC-TGAGGCCCTCTACCTAATCCAAGTGTTTCCAAGTTCTT
* *
1379512 GTGGTCAATCTTAAGTCAGATATAAACCCCTGAAATGAGCCAGAACCCTTGGGAGCTACTTGGTG
130 GTGGTCAATCTCAAGTCAGATATAAACCCCTGAAATGAGCCAGAACCCCTGGGAGCTACTTGGTG
*
1379577 GTACCCCTACAGCCCAAATTTGAGACCGGGAAATAACAGCCCTCATAGGTCCTCTACACTGCCCT
195 GTACCCCTACAGCCCAAATTTGAGACCGGGAAATAATAGCCCTCATAGGTCCTCTACACTGCCCT
*
1379642 GGTATCCGTTTGATGCACACTTCAAAGATAAAAGAGATAATGGTCCGCCTTTCACCCCTATATCA
260 GGTATCCGTTTGATGCACACTTCAAAGATAAAAGAGATAATGGACCGCCTTTCACCCCTATATCA
1379707 TT
325 TT
* *
1379709 GTGAAATGCTAAAATATGACAAAGTTCGGGTGAGCTTACTGGGCCCTTGCAGGGGTCATAGGTGC
1 GTGAAATGCTAAAATATGACAAAGTTCGGGTGAGCTAACTGAGCCCTTGCAGGGGTCATAGGTGC
* * *
1379774 CCTCGTACGCTTATGATGAATACCTCTGAGGCCCTCTACCTAATCCTAA-TGTTTCCCAGTTTTT
66 CCTCGTACGCTTATGATGAATACTTCTGAGGCCCTCTACCTAATCC-AAGTGTTTCCAAGTTCTT
* * * *
1379838 GTGATCAAACTCAAGTCAGATATAAACCCCTGAAATGAGCCAGAACCCCGGGGAGCGACTTGGTG
130 GTGGTCAATCTCAAGTCAGATATAAACCCCTGAAATGAGCCAGAACCCCTGGGAGCTACTTGGTG
* * * * *
1379903 GTACCCCTACAGCCCGAATTTGAGACCGGGAAATAGTATCAC-CATAGGTCCTCTACACTGCCTT
195 GTACCCCTACAGCCCAAATTTGAGACCGGGAAATAATAGCCCTCATAGGTCCTCTACACTGCCCT
* * * ** * * * *
1379967 GGCATTCGTTTGCTTTACACTTCAAAGATAAAA-ATGATATTGGACCGCTTTTCATCCATATATC
260 GGTATCCGTTTGATGCACACTTCAAAGATAAAAGA-GATAATGGACCGCCTTTCACCCCTATATC
**
1380031 GCT
324 ATT
** * *
1380034 GAAAAATGCT-AAATAAT-ACAAAGTTCGGGTGAGCTAACTGGGCCCTTGCAGGGGTTATAGGTG
1 GTGAAATGCTAAAAT-ATGACAAAGTTCGGGTGAGCTAACTGAGCCCTTGCAGGGGTCATAGGTG
*
1380097 CCCTCTTACGCTTATGATGAATACCTTCTGAGGCCCTCTACC
65 CCCTCGTACGCTTATGATGAATA-CTTCTGAGGCCCTCTACC
1380139 CTGGGAGCCA
Statistics
Matches: 686, Mismatches: 63, Indels: 21
0.89 0.08 0.03
Matches are distributed among these distances:
324 71 0.10
325 101 0.15
326 131 0.19
327 308 0.45
328 1 0.00
330 28 0.04
331 45 0.07
332 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (326 bp):
GTGAAATGCTAAAATATGACAAAGTTCGGGTGAGCTAACTGAGCCCTTGCAGGGGTCATAGGTGC
CCTCGTACGCTTATGATGAATACTTCTGAGGCCCTCTACCTAATCCAAGTGTTTCCAAGTTCTTG
TGGTCAATCTCAAGTCAGATATAAACCCCTGAAATGAGCCAGAACCCCTGGGAGCTACTTGGTGG
TACCCCTACAGCCCAAATTTGAGACCGGGAAATAATAGCCCTCATAGGTCCTCTACACTGCCCTG
GTATCCGTTTGATGCACACTTCAAAGATAAAAGAGATAATGGACCGCCTTTCACCCCTATATCAT
T
Found at i:1380818 original size:13 final size:13
Alignment explanation
Indices: 1380800--1380824 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1380790 TTTTATGGGC
1380800 TTAGTGGCTGCTG
1 TTAGTGGCTGCTG
1380813 TTAGTGGCTGCT
1 TTAGTGGCTGCT
1380825 TGCTTCAGCC
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:0.08, C:0.16, G:0.36, T:0.40
Consensus pattern (13 bp):
TTAGTGGCTGCTG
Found at i:1382117 original size:2 final size:2
Alignment explanation
Indices: 1382110--1382163 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1382100 TCATCATATA
1382110 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
1382152 AG AG AG AG AG AG
1 AG AG AG AG AG AG
1382164 TACCAGTGTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1382499 original size:2 final size:2
Alignment explanation
Indices: 1382492--1382546 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1382482 TTGTAAAATA
1382492 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
1382534 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
1382547 GTGTACTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1384017 original size:19 final size:20
Alignment explanation
Indices: 1383993--1384037 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
1383983 GTAACGATAT
*
1383993 CCACGGAGTAACACA-GTGG
1 CCACGGAGTAACACAGGCGG
*
1384012 CCACGGAGTTACACAGGCGG
1 CCACGGAGTAACACAGGCGG
1384032 CCACGG
1 CCACGG
1384038 TGCGACACGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.27, C:0.31, G:0.33, T:0.09
Consensus pattern (20 bp):
CCACGGAGTAACACAGGCGG
Found at i:1387033 original size:16 final size:16
Alignment explanation
Indices: 1387010--1387059 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
1387000 CGTCACATTG
1387010 CCATTTGACACAAATA
1 CCATTTGACACAAATA
* * *
1387026 CTATTTGATACAATTA
1 CCATTTGACACAAATA
*
1387042 CCATTTGACACAATTA
1 CCATTTGACACAAATA
1387058 CC
1 CC
1387060 CGATGTCCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (16 bp):
CCATTTGACACAAATA
Found at i:1388231 original size:46 final size:46
Alignment explanation
Indices: 1388181--1388268 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
1388171 AAAATGTTTT
* *
1388181 TATCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGAAAATAAA
1 TATCTCGTAATTACGAAAAAAAATCTCGTTATTACGAGAAAATAAA
* * *
1388227 TATCTCGTTATTACGAAAAAAAATCTTGTTATTATGAGAAAA
1 TATCTCGTAATTACGAAAAAAAATCTCGTTATTACGAGAAAA
1388269 GAGACCTCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (46 bp):
TATCTCGTAATTACGAAAAAAAATCTCGTTATTACGAGAAAATAAA
Found at i:1388268 original size:21 final size:21
Alignment explanation
Indices: 1388182--1388268 Score: 93
Period size: 21 Copynumber: 4.0 Consensus size: 21
1388172 AAATGTTTTT
* *
1388182 ATCTCGTAATTACGAGAAAAG
1 ATCTCGTTATTACGAGAAAAA
1388203 ATCTCGTTATTACGAGAAAATAAA
1 ATCTCGTTATTACGAG--AA-AAA
*
1388227 TATCTCGTTATTACGAAAAAAA
1 -ATCTCGTTATTACGAGAAAAA
* *
1388249 ATCTTGTTATTATGAGAAAA
1 ATCTCGTTATTACGAGAAAA
1388269 GAGACCTCAT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
21 32 0.57
22 3 0.05
23 4 0.07
24 2 0.04
25 15 0.27
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (21 bp):
ATCTCGTTATTACGAGAAAAA
Found at i:1388428 original size:43 final size:43
Alignment explanation
Indices: 1388349--1388444 Score: 138
Period size: 43 Copynumber: 2.2 Consensus size: 43
1388339 TATTCTTATT
* * * * *
1388349 ATTACGAGAAAAGATCTTGTTTTTACGCGTTAATTATCTCGTA
1 ATTACGAGAAAAGATATAGTTATTAAGAGTTAATTATCTCGTA
*
1388392 ATTACGAGAAAAGATATAGTTATTAAGAGTTCATTATCTCGTA
1 ATTACGAGAAAAGATATAGTTATTAAGAGTTAATTATCTCGTA
1388435 ATTACGAGAA
1 ATTACGAGAA
1388445 TTGGTCTAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.35
Consensus pattern (43 bp):
ATTACGAGAAAAGATATAGTTATTAAGAGTTAATTATCTCGTA
Found at i:1389183 original size:21 final size:21
Alignment explanation
Indices: 1389151--1389312 Score: 153
Period size: 21 Copynumber: 7.6 Consensus size: 21
1389141 TAACTCGTTA
1389151 TAATAAACGAGATCTTTTCTCG
1 TAAT-AACGAGATCTTTTCTCG
* * *
1389173 TTATTACGAGATCTTTTTTCG
1 TAATAACGAGATCTTTTCTCG
* * *
1389194 TAATAACGACATAATTATCTCG
1 TAATAACGAGAT-CTTTTCTCG
*
1389216 TAATAACGAAATCTTTTCTCG
1 TAATAACGAGATCTTTTCTCG
* ** *
1389237 TAATAACGAGATAATTAGCCCG
1 TAATAACGAGAT-CTTTTCTCG
* *
1389259 TTATAACGAGATCTTTTCTCA
1 TAATAACGAGATCTTTTCTCG
*
1389280 TAATAACGAGATATTTTCTCG
1 TAATAACGAGATCTTTTCTCG
* *
1389301 TTATCACGAGAT
1 TAATAACGAGAT
1389313 ATCTTTTATG
Statistics
Matches: 110, Mismatches: 28, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
21 74 0.67
22 36 0.33
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (21 bp):
TAATAACGAGATCTTTTCTCG
Found at i:1389199 original size:43 final size:43
Alignment explanation
Indices: 1389168--1389312 Score: 193
Period size: 43 Copynumber: 3.4 Consensus size: 43
1389158 CGAGATCTTT
* * *
1389168 TCTCGTTATTACGAGATCTTTTTTCGTAATAACGACATAATTA
1 TCTCGTTATAACGAGATCTTTTCTCGTAATAACGAGATAATTA
* *
1389211 TCTCGTAATAACGAAATCTTTTCTCGTAATAACGAGATAATTA
1 TCTCGTTATAACGAGATCTTTTCTCGTAATAACGAGATAATTA
* * * *
1389254 GCCCGTTATAACGAGATCTTTTCTCATAATAACGAGAT-ATTT
1 TCTCGTTATAACGAGATCTTTTCTCGTAATAACGAGATAATTA
*
1389296 TCTCGTTATCACGAGAT
1 TCTCGTTATAACGAGAT
1389313 ATCTTTTATG
Statistics
Matches: 88, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 17 0.19
43 71 0.81
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (43 bp):
TCTCGTTATAACGAGATCTTTTCTCGTAATAACGAGATAATTA
Found at i:1391635 original size:19 final size:18
Alignment explanation
Indices: 1391611--1391668 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 18
1391601 CTTAACATTG
1391611 TTTTTTGTTTGTTTGGTTT
1 TTTTTTGTTTGTTT-GTTT
1391630 TTTTTTGGTTT-TTTGTTT
1 TTTTTT-GTTTGTTTGTTT
*
1391648 TTTTGTG-TTGTTT-TTT
1 TTTTTTGTTTGTTTGTTT
1391664 TTTTT
1 TTTTT
1391669 GGTGTTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 9 0.26
17 4 0.11
18 9 0.26
19 9 0.26
20 4 0.11
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (18 bp):
TTTTTTGTTTGTTTGTTT
Found at i:1391652 original size:27 final size:29
Alignment explanation
Indices: 1391610--1391664 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 29
1391600 ACTTAACATT
1391610 GTTTTTTGTTTGTTTG-GTT-TTTTTTTG
1 GTTTTTTGTTTGTTTGTGTTGTTTTTTTG
*
1391637 GTTTTTTGTTTTTTTGTGTTGTTTTTTT
1 GTTTTTTGTTTGTTTGTGTTGTTTTTTT
1391665 TTTTGGTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 15 0.60
28 3 0.12
29 7 0.28
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (29 bp):
GTTTTTTGTTTGTTTGTGTTGTTTTTTTG
Found at i:1391673 original size:18 final size:17
Alignment explanation
Indices: 1391627--1391675 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
1391617 GTTTGTTTGG
1391627 TTTTTTTTTGGT-TTTT
1 TTTTTTTTTGGTGTTTT
*
1391643 TGTTTTTTT-GTGTTGTT
1 TTTTTTTTTGGTGTT-TT
1391660 TTTTTTTTTGGTGTTT
1 TTTTTTTTTGGTGTTT
1391676 ATTGTTCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 2 0.07
16 10 0.36
17 11 0.39
18 5 0.18
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTGGTGTTTT
Found at i:1398716 original size:12 final size:12
Alignment explanation
Indices: 1398695--1398736 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1398685 CAAAATTTAT
*
1398695 ATCATCATCATC
1 ATCATTATCATC
1398707 ATCATTATCATC
1 ATCATTATCATC
*
1398719 ATCA-TACTCAGC
1 ATCATTA-TCATC
1398731 ATCATT
1 ATCATT
1398737 TTACCAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 2 0.08
12 23 0.88
13 1 0.04
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.36
Consensus pattern (12 bp):
ATCATTATCATC
Found at i:1405010 original size:9 final size:9
Alignment explanation
Indices: 1404996--1405025 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1404986 TTTTCTTGTG
1404996 TTTGTGTTT
1 TTTGTGTTT
1405005 TTTGTGTTT
1 TTTGTGTTT
*
1405014 TTTATGTTT
1 TTTGTGTTT
1405023 TTT
1 TTT
1405026 CACTGAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.03, C:0.00, G:0.17, T:0.80
Consensus pattern (9 bp):
TTTGTGTTT
Found at i:1408632 original size:107 final size:105
Alignment explanation
Indices: 1408448--1408659 Score: 300
Period size: 107 Copynumber: 2.0 Consensus size: 105
1408438 GAAAGATAAT
* * *
1408448 GACCGGACACGAATTTTGCACTTTTTCTGCAAGTGACCTTGACCTTGCCCAAATGACCTTGGGTC
1 GACCGGACACGAATTTTGCACTTTTTCTCCAAGCGACCTTGACCTTGCCCAAATGACCTTGGATC
* *
1408513 AAAGTCATGACACACCCTTTGGTCCTAAGCAATATTTGTG
66 AAAGTCATGACACACCCTTAGGTCATAAGCAATATTTGTG
* *
1408553 GACCGGACACTAATTTTGCACTTTTTTTTTTCCAA-CGACCTTGACCTTGCCCAAATGACCTTGG
1 GACCGGACACGAATTTTGCAC---TTTTTCTCCAAGCGACCTTGACCTTGCCCAAATGACCTTGG
* * *
1408617 ATCAAGGTCATGACACACCCTTAGTTCATAAGCAATCTTTGTG
63 ATCAAAGTCATGACACACCCTTAGGTCATAAGCAATATTTGTG
1408660 TGAATTAACA
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
105 20 0.21
107 65 0.69
108 9 0.10
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (105 bp):
GACCGGACACGAATTTTGCACTTTTTCTCCAAGCGACCTTGACCTTGCCCAAATGACCTTGGATC
AAAGTCATGACACACCCTTAGGTCATAAGCAATATTTGTG
Found at i:1408819 original size:146 final size:146
Alignment explanation
Indices: 1408551--1409002 Score: 683
Period size: 146 Copynumber: 3.1 Consensus size: 146
1408541 GCAATATTTG
* * * **
1408551 TGGACCGGACACTAATTTTGCACTTTTTTTTTTCCAACGACCTTGACCTTGCCCAAATGACCTTG
1 TGGACCGGACACAAATTTTGCAC--TTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTG
* *
1408616 GATCAAGGTCATGACACACCCTTAGTTCATAAGCAATCTTTGTGTGAA-TTAACAACTTCCAATA
64 GGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTT-ACAACTTCCAATA
1408680 ATTCTCCATAAGAAAGATA
128 ATTCTCCATAAGAAAGATA
1408699 TGGACCGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGG
1 TGGACCGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGG
* *
1408764 TCAAGGTCATGACACACCCTTAGGTCATAGGCAATCTTTGTGTGAAGTTAGAACTTCCAATAATT
66 TCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTTACAACTTCCAATAATT
1408829 CTCCATAAGAAAGATA
131 CTCCATAAGAAAGATA
* * * ** *
1408845 TGGACCGGACACGAATTTTGTATTTTTTCTGCCAGTGACCTTGACCTTGCCGGAATGACCTTGTG
1 TGGACCGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGG
* **
1408910 TCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAG-TATTAACTTCCAATGTT
66 TCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTTA-CAACTTCCAATAAT
1408974 TCTCCATAAGAAAGATA
130 TCTCCATAAGAAAGATA
*
1408991 TGGACCGAACAC
1 TGGACCGGACAC
1409003 GATTGCACAG
Statistics
Matches: 282, Mismatches: 20, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
145 2 0.01
146 256 0.91
147 2 0.01
148 22 0.08
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (146 bp):
TGGACCGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGG
TCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTTACAACTTCCAATAATT
CTCCATAAGAAAGATA
Found at i:1409026 original size:12 final size:12
Alignment explanation
Indices: 1409009--1409042 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
1408999 ACACGATTGC
1409009 ACAGACGGACGG
1 ACAGACGGACGG
1409021 ACAGACGGACGG
1 ACAGACGGACGG
1409033 ACAGACGGAC
1 ACAGACGGAC
1409043 AAGGTGATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.35, C:0.26, G:0.38, T:0.00
Consensus pattern (12 bp):
ACAGACGGACGG
Found at i:1427266 original size:2 final size:2
Alignment explanation
Indices: 1427259--1427322 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
1427249 TTCATGTGCG
*
1427259 CT CT CT CT CA 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
*
1427301 CT CT CT CT CT CT TT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
1427323 NNNNNNNNNN
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.02, C:0.48, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Done.