Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 4 of 190
Found at i:1021966 original size:19 final size:18
Alignment explanation
Indices: 1021917--1021968 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
1021907 GATTATTTAA
1021917 TCTTAGAGTTCTAA-TTG
1 TCTTAGAGTTCTAATTTG
* *
1021934 T-ATACAGCTTCTAATTATG
1 TCTTAGAG-TTCTAATT-TG
1021953 TCTTAGAGTTCTAATT
1 TCTTAGAGTTCTAATT
1021969 GTATACAGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.15
17 7 0.26
18 1 0.04
19 11 0.41
20 4 0.15
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46
Consensus pattern (18 bp):
TCTTAGAGTTCTAATTTG
Found at i:1022787 original size:16 final size:16
Alignment explanation
Indices: 1022766--1022797 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1022756 TTTGGTTCGC
1022766 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
1022782 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
1022798 CGCAAGAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:1023156 original size:120 final size:119
Alignment explanation
Indices: 1023017--1023266 Score: 437
Period size: 119 Copynumber: 2.1 Consensus size: 119
1023007 TTAATCATAT
*
1023017 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA-T
* *
1023082 AAATATTCTTATATGAACTTACTAAAATCACAATATATAATACTATAAAATATAA
65 AAATATTCCTATATGAACTTACTAAAACCACAATATATAATACTATAAAATATAA
1023137 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATA
* * *
1023202 ATTATTCCTATATGAATTTACTAAAACCATAATATATAATACTATAAAATATAA
66 AATATTCCTATATGAACTTACTAAAACCACAATATATAATACTATAAAATATAA
1023256 TTTAAAATAAT
1 TTTAAAATAAT
1023267 CTACTTTATT
Statistics
Matches: 124, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
119 62 0.50
120 62 0.50
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (119 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATA
AATATTCCTATATGAACTTACTAAAACCACAATATATAATACTATAAAATATAA
Found at i:1024013 original size:40 final size:40
Alignment explanation
Indices: 1023958--1024078 Score: 242
Period size: 40 Copynumber: 3.0 Consensus size: 40
1023948 TAAATTGGCC
1023958 AGGAAGAAAACAAACATTTGCTAAATTTAAGATTGAATTA
1 AGGAAGAAAACAAACATTTGCTAAATTTAAGATTGAATTA
1023998 AGGAAGAAAACAAACATTTGCTAAATTTAAGATTGAATTA
1 AGGAAGAAAACAAACATTTGCTAAATTTAAGATTGAATTA
1024038 AGGAAGAAAACAAACATTTGCTAAATTTAAGATTGAATTA
1 AGGAAGAAAACAAACATTTGCTAAATTTAAGATTGAATTA
1024078 A
1 A
1024079 TCTTTGGTTT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.27
Consensus pattern (40 bp):
AGGAAGAAAACAAACATTTGCTAAATTTAAGATTGAATTA
Found at i:1030204 original size:2 final size:2
Alignment explanation
Indices: 1030197--1030229 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1030187 ATAGGAAATT
1030197 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1030230 TATATTAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1031723 original size:22 final size:22
Alignment explanation
Indices: 1031692--1031734 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1031682 CCACCAAATA
*
1031692 AGAAAACGATGGAAGAAGAAGC
1 AGAAAACGATGGAAAAAGAAGC
*
1031714 AGAAATCGATGGAAAAAGAAG
1 AGAAAACGATGGAAAAAGAAG
1031735 TAAAAATTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.07, G:0.30, T:0.07
Consensus pattern (22 bp):
AGAAAACGATGGAAAAAGAAGC
Found at i:1031741 original size:22 final size:22
Alignment explanation
Indices: 1031694--1031741 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1031684 ACCAAATAAG
*
1031694 AAAA-CGATGGAAGAAGAAGCA
1 AAAATCGATGGAAAAAGAAGCA
* *
1031715 GAAATCGATGGAAAAAGAAGTA
1 AAAATCGATGGAAAAAGAAGCA
1031737 AAAAT
1 AAAAT
1031742 TACCTCTGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.58, C:0.06, G:0.25, T:0.10
Consensus pattern (22 bp):
AAAATCGATGGAAAAAGAAGCA
Found at i:1035312 original size:15 final size:15
Alignment explanation
Indices: 1035271--1035314 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
1035261 TCGCAGGCAG
*
1035271 AAATATAATTATACT
1 AAATATAATTATAAT
*
1035286 AAAAATTAAATTATAAT
1 AAATA-T-AATTATAAT
1035303 AAATATAATTAT
1 AAATATAATTAT
1035315 GCGAGACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 10 0.42
16 2 0.08
17 12 0.50
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATATAATTATAAT
Found at i:1040422 original size:3 final size:3
Alignment explanation
Indices: 1040416--1040467 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
1040406 GTAGTAACCC
1040416 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1040464 ATT A
1 ATT A
1040468 CCGTCCATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1042828 original size:5 final size:5
Alignment explanation
Indices: 1042818--1042844 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1042808 CATGACTCTC
1042818 TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TT
1042845 TCCATTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:1048001 original size:357 final size:357
Alignment explanation
Indices: 1047346--1048066 Score: 1334
Period size: 357 Copynumber: 2.0 Consensus size: 357
1047336 GTAGATCAAG
1047346 AAACAACTTGTTGTTTCTTAGAACACCATGAGACAAGTGTATGACCAAAGTAGACACAATAGCCT
1 AAACAACTTGTTGTTTCTTAGAACACCATGAGACAAGTGTATGACCAAAGTAGACACAATAGCCT
*
1047411 GTCGTAGAACGGCGGTCATCAAAATCTAGACCCCAATTAGCATCAGCATAACCAACTAAAGATAG
66 GTCGTAGAACGGCGGTCATCAAAATCTAGACCCCAATTAGCATCAGCATAACCAACTAAAAATAG
*
1047476 TCTGTCGGATCGGTGAAACACCAACCTGTGATTAATAGTGCCATGTAAATACCTCAAGATATGTT
131 TCTGTCGGATCGGTGAAACACCAACCTGTGATTAATAGTACCATGTAAATACCTCAAGATATGTT
*
1047541 TTAATCCTACCAGATGTACTGTAGTAGGTGCATGCATGAATTGACAAACGTGATTTACCACATAA
196 TTAATCCTACCAGATGTACTGTAGTAGGTGCATGCATGAATTGACAAACGCGATTTACCACATAA
1047606 GCAATATTCGATCGAGTTAAGACCATATATTGAAGAACACCGGCAAGACTTCTGTATTCAGTAGG
261 GCAATATTCGATCGAGTTAAGACCATATATTGAAGAACACCGGCAAGACTTCTGTATTCAGTAGG
1047671 ACCAGCAAGTCGATCACCCACATCTTTAGACA
326 ACCAGCAAGTCGATCACCCACATCTTTAGACA
*
1047703 AAACAACTTGTTGTTTCTTAGAACACCATGAGACAAGTGTATGGCCAAAGTAGACACAATAGCCT
1 AAACAACTTGTTGTTTCTTAGAACACCATGAGACAAGTGTATGACCAAAGTAGACACAATAGCCT
*
1047768 GTCGTAGAACGGCGGTCATCAAAATCTAGACCTCAATTAGCATCAGCATAACCAACTAAAAATAG
66 GTCGTAGAACGGCGGTCATCAAAATCTAGACCCCAATTAGCATCAGCATAACCAACTAAAAATAG
1047833 TCTGTCGGATCGGTGAAACACCAACCTGTGATTAATAGTACCATGTAAATACCTCAAGATATGTT
131 TCTGTCGGATCGGTGAAACACCAACCTGTGATTAATAGTACCATGTAAATACCTCAAGATATGTT
* *
1047898 TTAATGCTACCAGATGTACTGTAGTAGGTGCATGCATGAATTGACAAATGCGATTTACCACATAA
196 TTAATCCTACCAGATGTACTGTAGTAGGTGCATGCATGAATTGACAAACGCGATTTACCACATAA
*
1047963 GCAATATTCGGTCGAGTTAAGACCATATATTGAAGAACACCGGCAAGACTTCTGTATTCAGTAGG
261 GCAATATTCGATCGAGTTAAGACCATATATTGAAGAACACCGGCAAGACTTCTGTATTCAGTAGG
* * * *
1048028 GCTAGCAAGTCGATCGCCCTCATCTTTAGACA
326 ACCAGCAAGTCGATCACCCACATCTTTAGACA
1048060 AAACAAC
1 AAACAAC
1048067 ATGTGAGTAC
Statistics
Matches: 352, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
357 352 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (357 bp):
AAACAACTTGTTGTTTCTTAGAACACCATGAGACAAGTGTATGACCAAAGTAGACACAATAGCCT
GTCGTAGAACGGCGGTCATCAAAATCTAGACCCCAATTAGCATCAGCATAACCAACTAAAAATAG
TCTGTCGGATCGGTGAAACACCAACCTGTGATTAATAGTACCATGTAAATACCTCAAGATATGTT
TTAATCCTACCAGATGTACTGTAGTAGGTGCATGCATGAATTGACAAACGCGATTTACCACATAA
GCAATATTCGATCGAGTTAAGACCATATATTGAAGAACACCGGCAAGACTTCTGTATTCAGTAGG
ACCAGCAAGTCGATCACCCACATCTTTAGACA
Found at i:1055835 original size:4 final size:4
Alignment explanation
Indices: 1055821--1055855 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
1055811 AAAAATTAGT
1055821 TAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1055856 AAGGATAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:1056256 original size:31 final size:31
Alignment explanation
Indices: 1056163--1056258 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
1056153 GGCAAATTAC
*
1056163 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1056194 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
*
1056226 AAGAGTAGTTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1056257 AA
1 AA
1056259 ATTATCTAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 33 0.53
32 29 0.47
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:1058236 original size:16 final size:16
Alignment explanation
Indices: 1058215--1058247 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1058205 ACAATGTAAT
*
1058215 ACATACATACATGCAA
1 ACATACATACATACAA
1058231 ACATACATACATACAA
1 ACATACATACATACAA
1058247 A
1 A
1058248 GCTACTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.24, G:0.03, T:0.18
Consensus pattern (16 bp):
ACATACATACATACAA
Found at i:1064905 original size:13 final size:13
Alignment explanation
Indices: 1064872--1064898 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1064862 ACAGAGCTAA
1064872 CCTGATATGATCG
1 CCTGATATGATCG
1064885 CCTGATATGATCG
1 CCTGATATGATCG
1064898 C
1 C
1064899 TTTATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (13 bp):
CCTGATATGATCG
Found at i:1069290 original size:25 final size:22
Alignment explanation
Indices: 1069263--1069309 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
1069253 AAAAAAATTA
1069263 AGAAA-AAAAATGGAAGGTTCT
1 AGAAAGAAAAATGGAAGGTTCT
1069284 AGAAAGAAAAATGGAAGGTTCT
1 AGAAAGAAAAATGGAAGGTTCT
1069306 AGAA
1 AGAA
1069310 TGATCGGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.53, C:0.04, G:0.26, T:0.17
Consensus pattern (22 bp):
AGAAAGAAAAATGGAAGGTTCT
Found at i:1075855 original size:26 final size:26
Alignment explanation
Indices: 1075760--1075855 Score: 75
Period size: 26 Copynumber: 3.5 Consensus size: 26
1075750 GTTATTAAAT
*
1075760 TTTAATAAGATTATTATTAAAAATAA
1 TTTAATAAAATTATTATTAAAAATAA
** *
1075786 TTTAATAAAAATAATAATTAATTTAACCATAT
1 TTTAAT-AAAAT--T-ATT-A-TTAAAAATAA
* * *
1075818 TTTAACATAATTATTATTAAATATAA
1 TTTAATAAAATTATTATTAAAAATAA
1075844 TTTAATAAAATT
1 TTTAATAAAATT
1075856 CTTAATATAA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
26 23 0.43
27 5 0.09
28 3 0.06
29 2 0.04
30 3 0.06
31 5 0.09
32 12 0.23
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (26 bp):
TTTAATAAAATTATTATTAAAAATAA
Found at i:1075898 original size:36 final size:38
Alignment explanation
Indices: 1075824--1075900 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
1075814 ATATTTTAAC
*
1075824 ATAATTATTATTAAATATAATTTAATAAAATTCTTAAT
1 ATAATTATTATTAAATATAATTTAATAAAATTCATAAT
* *
1075862 ATAATTATTATTATATA-AATTTACTAAAA-TCATAAT
1 ATAATTATTATTAAATATAATTTAATAAAATTCATAAT
1075898 ATA
1 ATA
1075901 TAATACTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 9 0.25
37 11 0.31
38 16 0.44
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (38 bp):
ATAATTATTATTAAATATAATTTAATAAAATTCATAAT
Found at i:1077516 original size:13 final size:13
Alignment explanation
Indices: 1077498--1077522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1077488 GACAGTGCAA
1077498 TAATGTAAGGCTG
1 TAATGTAAGGCTG
1077511 TAATGTAAGGCT
1 TAATGTAAGGCT
1077523 CCCTCGACAA
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:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (13 bp):
TAATGTAAGGCTG
Found at i:1078534 original size:16 final size:16
Alignment explanation
Indices: 1078513--1078567 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
1078503 GTTTGATTCA
1078513 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
1078529 CTGTAATAGAATAGAG
1 CTGTAATGGAATAGAG
* * *
1078545 TTGTAATGGAATAAAA
1 CTGTAATGGAATAGAG
1078561 CTGTAAT
1 CTGTAAT
1078568 CAGTAATTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.42, C:0.05, G:0.24, T:0.29
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:1078825 original size:58 final size:58
Alignment explanation
Indices: 1078746--1078869 Score: 178
Period size: 58 Copynumber: 2.1 Consensus size: 58
1078736 TTTTAATAAG
* *
1078746 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACCATATT-TTAACATA
1 ATTATTATTAAAAATAATTTAAT-AAAATAATAAATAATTTAACAAAATTATTAACATA
* * * *
1078804 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTATTAATATA
1 ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTATTAACATA
1078862 ATTATTAT
1 ATTATTAT
1078870 ATGAATTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 22 0.37
58 37 0.63
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTATTAACATA
Found at i:1081820 original size:70 final size:69
Alignment explanation
Indices: 1081738--1081870 Score: 187
Period size: 70 Copynumber: 1.9 Consensus size: 69
1081728 ATTTAAAAAA
** *
1081738 AAAAAAGGTCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATT-TCTGAGATCATTTAAAAT
1 AAAAAAGGTCATGCCCAGTAAGTTAGGACACGATCTCCTCATAATTCTC-GAGATCATTTAAAAT
1081802 TTGGG
65 TTGGG
* * *
1081807 AAAAAGGGATCATGCTCAGTAAGTTAGGACACGATCTCCTCATAATTCTCGAGATCGTTTAAAA
1 AAAAAAGG-TCATGCCCAGTAAGTTAGGACACGATCTCCTCATAATTCTCGAGATCATTTAAAA
1081871 CTTGAGTTTG
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
69 7 0.12
70 47 0.84
71 2 0.04
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (69 bp):
AAAAAAGGTCATGCCCAGTAAGTTAGGACACGATCTCCTCATAATTCTCGAGATCATTTAAAATT
TGGG
Found at i:1085369 original size:13 final size:13
Alignment explanation
Indices: 1085346--1085398 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
1085336 AGTTCTTCAT
1085346 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
1085359 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
1085372 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
1085385 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
1085398 T
1 T
1085399 TTTGTTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:1085621 original size:31 final size:29
Alignment explanation
Indices: 1085568--1085629 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
1085558 TTATAACTTG
*
1085568 TTGTTAATATTTTAATATATAAAATATAAA
1 TTGTAAATATTTTAATATAT-AAATATAAA
*
1085598 TTGTAAATATTTTTAAGTA-ATAAATATTAA
1 TTGTAAATA-TTTTAA-TATATAAATATAAA
1085628 TT
1 TT
1085630 ATTTATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 18 0.64
31 8 0.29
32 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (29 bp):
TTGTAAATATTTTAATATATAAATATAAA
Found at i:1088126 original size:123 final size:123
Alignment explanation
Indices: 1087907--1088156 Score: 491
Period size: 123 Copynumber: 2.0 Consensus size: 123
1087897 CATTATCAAA
1087907 CAAGAAATCACGGAATAAATGGTCAATGCCCACATGATTCTCTACCCCTCCTTTCCTTTCCTCAC
1 CAAGAAATCACGGAATAAATGGTCAATGCCCACATGATTCTCTACCCCTCCTTTCCTTTCCTCAC
*
1087972 TAGAGACAATAACATTTAAGTCACCCCCGAGGAGCCACAGTATCCTATCCTGGGGAGT
66 TAGAGACAATAACATTTAAGTCACCCCCGAGGAGCCACAGTATACTATCCTGGGGAGT
1088030 CAAGAAATCACGGAATAAATGGTCAATGCCCACATGATTCTCTACCCCTCCTTTCCTTTCCTCAC
1 CAAGAAATCACGGAATAAATGGTCAATGCCCACATGATTCTCTACCCCTCCTTTCCTTTCCTCAC
1088095 TAGAGACAATAACATTTAAGTCACCCCCGAGGAGCCACAGTATACTATCCTGGGGAGT
66 TAGAGACAATAACATTTAAGTCACCCCCGAGGAGCCACAGTATACTATCCTGGGGAGT
1088153 CAAG
1 CAAG
1088157 GATGCAAGGT
Statistics
Matches: 126, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 126 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (123 bp):
CAAGAAATCACGGAATAAATGGTCAATGCCCACATGATTCTCTACCCCTCCTTTCCTTTCCTCAC
TAGAGACAATAACATTTAAGTCACCCCCGAGGAGCCACAGTATACTATCCTGGGGAGT
Found at i:1097206 original size:2 final size:2
Alignment explanation
Indices: 1097199--1097224 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1097189 TAGAAATCAG
1097199 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1097225 GTTACTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1099504 original size:54 final size:54
Alignment explanation
Indices: 1099443--1099550 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
1099433 TACCAAAGAA
* *
1099443 TATATACTTTTAAAAGCCTAATAATTGCATGATGATTAGCAAAAACGAAAAGTC
1 TATATACTTTTAAAAGCCTAATAATTGCATAATGATTAGCAAAAAAGAAAAGTC
*
1099497 TATATACTTTTAAAAGCCTAATAATTGCATAATGATTAGCAAAAAAGGAAAGTC
1 TATATACTTTTAAAAGCCTAATAATTGCATAATGATTAGCAAAAAAGAAAAGTC
1099551 GTGTTGTCGG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (54 bp):
TATATACTTTTAAAAGCCTAATAATTGCATAATGATTAGCAAAAAAGAAAAGTC
Found at i:1106325 original size:12 final size:12
Alignment explanation
Indices: 1106308--1106338 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
1106298 AATGTTTAGG
1106308 CCTGCAATGAAT
1 CCTGCAATGAAT
1106320 CCTGCAATGAAT
1 CCTGCAATGAAT
1106332 CGCTGCA
1 C-CTGCA
1106339 GTGTCGAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (12 bp):
CCTGCAATGAAT
Found at i:1114972 original size:30 final size:31
Alignment explanation
Indices: 1114929--1114990 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
1114919 GAATGGCTTG
*
1114929 GATATGCCTAGATGTTAATAATGTGTTTTGT
1 GATATGCCAAGATGTTAATAATGTGTTTTGT
1114960 GATAT-CCAAGATGTTAATAATGTGTTTTGT
1 GATATGCCAAGATGTTAATAATGTGTTTTGT
1114990 G
1 G
1114991 CCATATTGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.27, C:0.06, G:0.23, T:0.44
Consensus pattern (31 bp):
GATATGCCAAGATGTTAATAATGTGTTTTGT
Found at i:1122792 original size:30 final size:30
Alignment explanation
Indices: 1122753--1122817 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
1122743 GTGTATAATT
*
1122753 ATATCAAATC-AAATTTATATATCAAATTAA
1 ATATTAAATCAAAATTTATATAT-AAATTAA
* *
1122783 ATATTAAATCAAAATTTATGTATAAATTTA
1 ATATTAAATCAAAATTTATATATAAATTAA
1122813 ATATT
1 ATATT
1122818 TATCGCCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (30 bp):
ATATTAAATCAAAATTTATATATAAATTAA
Found at i:1127039 original size:25 final size:25
Alignment explanation
Indices: 1127011--1127060 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1127001 TTTCTCACCC
1127011 CAATTTACCTCCGATAAAATTTTGA
1 CAATTTACCTCCGATAAAATTTTGA
* **
1127036 CAATTTGCCTTTGATAAAATTTTGA
1 CAATTTACCTCCGATAAAATTTTGA
1127061 GAAAATCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (25 bp):
CAATTTACCTCCGATAAAATTTTGA
Found at i:1128833 original size:2 final size:2
Alignment explanation
Indices: 1128826--1128889 Score: 92
Period size: 2 Copynumber: 32.0 Consensus size: 2
1128816 TCGTCTGAGC
*
1128826 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CG CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
* * *
1128868 CG CA CG CA CG CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA
1128890 TAAAAAAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.44, C:0.50, G:0.06, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1140497 original size:29 final size:29
Alignment explanation
Indices: 1140465--1140546 Score: 85
Period size: 31 Copynumber: 2.8 Consensus size: 29
1140455 AAAATTTCAA
1140465 AATTTAAAAGTATAAGGCTAAAATTGATC
1 AATTTAAAAGTATAAGGCTAAAATTGATC
* * **
1140494 AATTCGAAAAGTACAAACACTAAAATTGATC
1 AATT-TAAAAGTA-TAAGGCTAAAATTGATC
*
1140525 AAATTAAAA-TATAAGGACTAAA
1 AATTTAAAAGTATAAGG-CTAAA
1140547 TTCATAAGTA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
28 2 0.05
29 11 0.27
30 11 0.27
31 17 0.41
ACGTcount: A:0.54, C:0.10, G:0.11, T:0.26
Consensus pattern (29 bp):
AATTTAAAAGTATAAGGCTAAAATTGATC
Found at i:1142592 original size:113 final size:112
Alignment explanation
Indices: 1142432--1142976 Score: 444
Period size: 114 Copynumber: 4.8 Consensus size: 112
1142422 AAATCTCAAG
* * * *
1142432 ACCAACACGCAGCGTTCTGGTGTTGATGTATATTGGC-ATTAGTGGCGCTTACGAACAAACGCCG
1 ACCAAAACGCAGCGTT-TGGTCTTGATGTATATT-TCAATTAGTGGCGCTTATGAA-AAACGCCG
* *
1142496 GTAATGTATAGTATTAGCGGCGCTTAGTGGAAGCGCCGCAAAAGATGTTA
63 CTAATGTATAGTATTAGCGGCGCTTAGTGGAAGCGCCGCAAAAGATCTTA
* *
1142546 ACCAAAACGCAGAGTTTGGTCTTGATGTATATTTCAATTAGTGGCGCTTATAAAGAAAACGCCGC
1 ACCAAAACGCAGCGTTTGGTCTTGATGTATATTTCAATTAGTGGCGCTTAT-GA-AAAACGCCGC
* ** * * * *
1142611 TAATATATAGTATTAGCGGCGCAAAGCCT-TAAACGCCGCAAGACATCTTA
64 TAATGTATAGTATTAGCGGCGCTTAG--TGGAAGCGCCGCAAAAGATCTTA
* * * * *
1142661 ATCAAAACGCAGCGTGTTGGTCTTGATGTATAATAT-AATTAGTGGCGTTTAAGGAAAACGCCAG
1 ACCAAAACGCAGCGT-TTGGTCTTGATGTAT-ATTTCAATTAGTGGCGCTTATGAAAAACGCC-G
* ** * * *
1142725 -TAAATG-ATAGT-TATAGCAGCATTTGGTGGTAAGCGCCTCAAAATATCTTA
63 CT-AATGTATAGTAT-TAGCGGCGCTTAGTGG-AAGCGCCGCAAAAGATCTTA
* * * ** *
1142775 ACCAAAACGCAGAGTTTGGTCTTGAGGTGTATTAGAATTAGTGGCGTTTGATGAAAAACGCCGCT
1 ACCAAAACGCAGCGTTTGGTCTTGATGTATATTTCAATTAGTGGCGCTT-ATGAAAAACGCCGCT
* *
1142840 AAAGTATA-TCATTAGCGGCG-TTTGTGGAACGCGCCGC-AAAGTATCTTA
65 AATGTATAGT-ATTAGCGGCGCTTAGTGGAA-GCGCCGCAAAAG-ATCTTA
* * * ** * ** *
1142888 ACCAAAACACAGCGTTTAGTTCTTGATGTATACTGGAATTAGTCGCGCAAATGGGAAAACGCCGC
1 ACCAAAACGCAGCGTTT-GGTCTTGATGTATATTTCAATTAGTGGCGCTTAT-GAAAAACGCCGC
*
1142953 TGAA-GCATAGTATTAGCGGCGCTT
64 T-AATGTATAGTATTAGCGGCGCTT
1142977 TTACCGAAAC
Statistics
Matches: 345, Mismatches: 61, Indels: 49
0.76 0.13 0.11
Matches are distributed among these distances:
112 9 0.03
113 98 0.28
114 165 0.48
115 40 0.12
116 30 0.09
117 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (112 bp):
ACCAAAACGCAGCGTTTGGTCTTGATGTATATTTCAATTAGTGGCGCTTATGAAAAACGCCGCTA
ATGTATAGTATTAGCGGCGCTTAGTGGAAGCGCCGCAAAAGATCTTA
Found at i:1143100 original size:18 final size:18
Alignment explanation
Indices: 1143079--1143114 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1143069 TCATTTTATA
1143079 TGTTT-TTTATATTTAATT
1 TGTTTATTTATA-TTAATT
1143097 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
1143115 AAAATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:1144072 original size:7 final size:7
Alignment explanation
Indices: 1144062--1144137 Score: 84
Period size: 7 Copynumber: 11.0 Consensus size: 7
1144052 TTACTGTTCG
1144062 GGGTTTA
1 GGGTTTA
1144069 GGGTTTA
1 GGGTTTA
*
1144076 GGGTTTG
1 GGGTTTA
1144083 GGGTTT-
1 GGGTTTA
1144089 GGGTTTA
1 GGGTTTA
1144096 GGGTTTA
1 GGGTTTA
*
1144103 GGGTTTG
1 GGGTTTA
1144110 GGGTTT-
1 GGGTTTA
* *
1144116 GGTTTTT
1 GGGTTTA
1144123 GAGGTTTA
1 G-GGTTTA
*
1144131 AGGTTTA
1 GGGTTTA
1144138 CAAATTATAA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
6 11 0.18
7 45 0.75
8 4 0.07
ACGTcount: A:0.11, C:0.00, G:0.43, T:0.46
Consensus pattern (7 bp):
GGGTTTA
Found at i:1144093 original size:27 final size:27
Alignment explanation
Indices: 1144062--1144136 Score: 114
Period size: 27 Copynumber: 2.7 Consensus size: 27
1144052 TTACTGTTCG
1144062 GGGTTTAGGGTTTAGGGTTTGGGGTTT
1 GGGTTTAGGGTTTAGGGTTTGGGGTTT
1144089 GGGTTTAGGGTTTAGGGTTTGGGGTTT
1 GGGTTTAGGGTTTAGGGTTTGGGGTTT
* * *
1144116 GGTTTTTGAGGTTTAAGGTTT
1 GGGTTTAG-GGTTTAGGGTTT
1144137 ACAAATTATA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
27 33 0.75
28 11 0.25
ACGTcount: A:0.09, C:0.00, G:0.44, T:0.47
Consensus pattern (27 bp):
GGGTTTAGGGTTTAGGGTTTGGGGTTT
Found at i:1144094 original size:20 final size:20
Alignment explanation
Indices: 1144061--1144111 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1144051 TTTACTGTTC
1144061 GGGGTTTAGGGTTTAGGGTTT
1 GGGGTTT-GGGTTTAGGGTTT
1144082 GGGGTTTGGGTTTAGGGTTT
1 GGGGTTTGGGTTTAGGGTTT
*
1144102 AGGGTTTGGG
1 GGGGTTTGGG
1144112 GTTTGGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.08, C:0.00, G:0.51, T:0.41
Consensus pattern (20 bp):
GGGGTTTGGGTTTAGGGTTT
Found at i:1146474 original size:16 final size:16
Alignment explanation
Indices: 1146453--1146488 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1146443 GTATTTATAA
*
1146453 TTATCGATTTGCAATT
1 TTATCGATTTACAATT
1146469 TTATCGATTTACAATT
1 TTATCGATTTACAATT
1146485 TTAT
1 TTAT
1146489 TTCAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (16 bp):
TTATCGATTTACAATT
Found at i:1147011 original size:13 final size:12
Alignment explanation
Indices: 1146965--1147011 Score: 58
Period size: 13 Copynumber: 3.7 Consensus size: 12
1146955 ACTTTATTAT
*
1146965 ATTACTTGAATA
1 ATTACTTAAATA
1146977 TATTACTTAAATA
1 -ATTACTTAAATA
1146990 ATTTACTTAAATA
1 A-TTACTTAAATA
1147003 CATTACTTA
1 -ATTACTTA
1147012 CTAAAATTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 1 0.03
13 29 0.94
14 1 0.03
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.45
Consensus pattern (12 bp):
ATTACTTAAATA
Found at i:1147730 original size:9 final size:9
Alignment explanation
Indices: 1147675--1147898 Score: 146
Period size: 9 Copynumber: 25.4 Consensus size: 9
1147665 TAGTTACATA
*
1147675 ATAACTTAT
1 ATAACTTAC
1147684 ATAAACTTAC
1 AT-AACTTAC
1147694 ATGATAC--AC
1 AT-A-ACTTAC
*
1147703 ATTACTTAC
1 ATAACTTAC
* *
1147712 ATAGCATAC
1 ATAACTTAC
1147721 ATAACTTAC
1 ATAACTTAC
* *
1147730 ACAACTTAA
1 ATAACTTAC
1147739 ATAA--TAC
1 ATAACTTAC
*
1147746 AAAACTTAC
1 ATAACTTAC
*
1147755 ATAACCTAC
1 ATAACTTAC
*
1147764 ATAACCTAC
1 ATAACTTAC
*
1147773 ATAATACATA-
1 AT-A-ACTTAC
1147783 ATAACTTAC
1 ATAACTTAC
*
1147792 ATAACATAC
1 ATAACTTAC
* **
1147801 ATTACTTTG
1 ATAACTTAC
1147810 ATAACTTAC
1 ATAACTTAC
1147819 ATAACTTAC
1 ATAACTTAC
1147828 ATAA--TAC
1 ATAACTTAC
* *
1147835 ACAACTTAA
1 ATAACTTAC
*
1147844 ATAGCTTAC
1 ATAACTTAC
*
1147853 TTAA--TAC
1 ATAACTTAC
1147860 ATAACTTAC
1 ATAACTTAC
1147869 ATAACTT--
1 ATAACTTAC
*
1147876 ATACACGTAC
1 ATA-ACTTAC
1147886 ATAACTTAC
1 ATAACTTAC
1147895 ATAA
1 ATAA
1147899 TGGACTTAAT
Statistics
Matches: 164, Mismatches: 35, Indels: 32
0.71 0.15 0.14
Matches are distributed among these distances:
7 22 0.13
8 7 0.04
9 114 0.70
10 15 0.09
11 6 0.04
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (9 bp):
ATAACTTAC
Found at i:1147780 original size:25 final size:25
Alignment explanation
Indices: 1147717--1147899 Score: 90
Period size: 25 Copynumber: 7.1 Consensus size: 25
1147707 CTTACATAGC
* *
1147717 ATACATAACTTACACAACTTAAATA
1 ATACATAACTTACATAACTTACATA
* *
1147742 ATACAAAACTTACATAACCTACATA
1 ATACATAACTTACATAACTTACATA
*
1147767 ACCTACATAATACATA-ATAACTTACATAA
1 A--TACAT-A-ACTTACATAACTTACAT-A
* **
1147796 CATACATTACTTTGATAACTTACATA
1 -ATACATAACTTACATAACTTACATA
* *
1147822 ACTTACATAA--TACACAACTTAAATA
1 A--TACATAACTTACATAACTTACATA
* *
1147847 GCTTACTTAA--TACATAACTTACATA
1 --ATACATAACTTACATAACTTACATA
* *
1147872 ACT-TATACACGTACATAACTTACATA
1 A-TACATA-ACTTACATAACTTACATA
1147898 AT
1 AT
1147900 GGACTTAATA
Statistics
Matches: 121, Mismatches: 22, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
23 2 0.02
24 2 0.02
25 54 0.45
26 20 0.17
27 21 0.17
28 16 0.13
29 5 0.04
30 1 0.01
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.31
Consensus pattern (25 bp):
ATACATAACTTACATAACTTACATA
Found at i:1147803 original size:98 final size:99
Alignment explanation
Indices: 1147648--1147828 Score: 224
Period size: 98 Copynumber: 1.8 Consensus size: 99
1147638 ATTCTCAAAT
* ** * * *
1147648 AAACTTACATAATACATTAGTTACATAATAACTTATATAAACTTACATGATACACATTACTTACA
1 AAACTTACATAATACATAACCTACATAATAACATATATAAACTTACATAACACACATTACTTACA
*
1147713 TAGCATACATAACTTACACAACTTAAATAATACA
66 TAACATACATAACTTACACAACTTAAATAATACA
* *
1147747 AAACTTACATAACCTACATAACCTACATAAT-ACATA-AT-AACTTACATAACATACATTACTTT
1 AAACTTACATAA--TACATAACCTACATAATAACATATATAAACTTACATAACACACATTACTTA
* *
1147809 GATAACTTACATAACTTACA
64 CATAACATACATAACTTACA
1147829 TAATACACAA
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
98 37 0.54
99 14 0.20
100 4 0.06
101 14 0.20
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31
Consensus pattern (99 bp):
AAACTTACATAATACATAACCTACATAATAACATATATAAACTTACATAACACACATTACTTACA
TAACATACATAACTTACACAACTTAAATAATACA
Found at i:1151310 original size:22 final size:22
Alignment explanation
Indices: 1151279--1151322 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1151269 TAGTGGCGTT
* *
1151279 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAACGCCGCTAAAGACCTA
1151301 AAAAAACGCCGCTAAAGACCTA
1 AAAAAACGCCGCTAAAGACCTA
1151323 TTTTGGTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.27, G:0.18, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAGACCTA
Found at i:1153748 original size:34 final size:34
Alignment explanation
Indices: 1153705--1153772 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
1153695 CAAAAAAAGT
*
1153705 ACATCAAGGCTAATTTAGTAGCTTATTCTTTAAA
1 ACATCAAGGCTAATTTAATAGCTTATTCTTTAAA
1153739 ACATCAAGGCTAATTTAATAGCTTATTCTTTAAA
1 ACATCAAGGCTAATTTAATAGCTTATTCTTTAAA
1153773 CGTGATTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (34 bp):
ACATCAAGGCTAATTTAATAGCTTATTCTTTAAA
Found at i:1158013 original size:26 final size:25
Alignment explanation
Indices: 1157948--1158020 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 25
1157938 AATTTTCTCG
*
1157948 AAATTTTATAGGGGGTAAAATCGTCA
1 AAATTTTATA-GGGGTAAAATTGTCA
**
1157974 AAATTTTACCGGGGATAAAATTGTCA
1 AAATTTTATAGGGG-TAAAATTGTCA
*
1158000 AAATTTTATTGGGGTAAAATT
1 AAATTTTATAGGGGTAAAATT
1158021 AGGATGAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 11 0.27
26 30 0.73
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (25 bp):
AAATTTTATAGGGGTAAAATTGTCA
Found at i:1164805 original size:22 final size:22
Alignment explanation
Indices: 1164771--1164813 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1164761 TGGTTTTTCT
*
1164771 ATTTTTAATAATTT-TTTAATG
1 ATTTTTAAGAATTTATTTAATG
1164792 ATTTTTGAAGAATTTATTTAAT
1 ATTTTT-AAGAATTTATTTAAT
1164814 TAAAATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 7 0.37
23 6 0.32
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (22 bp):
ATTTTTAAGAATTTATTTAATG
Found at i:1171397 original size:97 final size:97
Alignment explanation
Indices: 1171223--1171400 Score: 245
Period size: 97 Copynumber: 1.8 Consensus size: 97
1171213 TTGAACATGT
* * * *
1171223 GGTTACAAAATTGTGTTTTCTTTATAAATTTGAGTAAATAGTTAATGAATTTTGTAGTTGTTGTA
1 GGTTACAAAATCGTGTTTTCATTATAAATTTGAGTAAATAATTAATGAATTTTGTAGTTGTTATA
*
1171288 AAATATTGTTATTTAGAACTTTCAGTGTGTTC
66 AAATATTATTATTTAGAACTTTCAGTGTGTTC
* *
1171320 GGTTACAAAATCGTGTTTTCATTA-AGAA-TTGAAGTAAATAATTTATGATTTTTGTAGTTGTTA
1 GGTTACAAAATCGTGTTTTCATTATA-AATTTG-AGTAAATAATTAATGAATTTTGTAGTTGTTA
1171383 TAACAA-ATTATTATTTAG
64 TAA-AATATTATTATTTAG
1171401 GGAGATACTT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
96 4 0.06
97 65 0.92
98 2 0.03
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.46
Consensus pattern (97 bp):
GGTTACAAAATCGTGTTTTCATTATAAATTTGAGTAAATAATTAATGAATTTTGTAGTTGTTATA
AAATATTATTATTTAGAACTTTCAGTGTGTTC
Found at i:1172940 original size:16 final size:17
Alignment explanation
Indices: 1172909--1172941 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1172899 TAATAAATAT
*
1172909 ATATTTTTAATTTTAAA
1 ATATTTTTAATATTAAA
1172926 ATATTTTTAA-ATTAAA
1 ATATTTTTAATATTAAA
1172942 TTTTTTATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTTTTAATATTAAA
Found at i:1173550 original size:2 final size:2
Alignment explanation
Indices: 1173543--1173605 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1173533 CAAACAAACA
1173543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1173585 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
1173606 ACTTAAGACA
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1175028 original size:16 final size:15
Alignment explanation
Indices: 1175007--1175036 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1174997 CACAAAGACG
1175007 GTGGAACCAGTCCCAA
1 GTGGAACCA-TCCCAA
1175023 GTGGAACCATCCCA
1 GTGGAACCATCCCA
1175037 TGGTGTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.33, G:0.23, T:0.13
Consensus pattern (15 bp):
GTGGAACCATCCCAA
Found at i:1176039 original size:18 final size:20
Alignment explanation
Indices: 1175999--1176039 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1175989 TTATTTTAAA
*
1175999 TTTTTTATATAGTATGTAGC
1 TTTTTTATATAGTATATAGC
1176019 TTTTTTAT-TAGTATATA-C
1 TTTTTTATATAGTATATAGC
1176037 TTT
1 TTT
1176040 ATATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.24, C:0.05, G:0.10, T:0.61
Consensus pattern (20 bp):
TTTTTTATATAGTATATAGC
Found at i:1178401 original size:6 final size:6
Alignment explanation
Indices: 1178390--1178414 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1178380 TCAGCTTATC
1178390 CTAACA CTAACA CTAACA CTAACA C
1 CTAACA CTAACA CTAACA CTAACA C
1178415 CAATTTCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (6 bp):
CTAACA
Found at i:1182475 original size:24 final size:26
Alignment explanation
Indices: 1182429--1182482 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
1182419 ATTGGTTCCT
1182429 TTTTTTTTCATTTTGAGCAA-TTTAA
1 TTTTTTTTCATTTTGAGCAATTTTAA
*
1182454 TTTTTTTTC-TTTT-ATGCTATTTTAA
1 TTTTTTTTCATTTTGA-GCAATTTTAA
1182479 TTTT
1 TTTT
1182483 AATTTTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 1 0.04
24 7 0.27
25 18 0.69
ACGTcount: A:0.19, C:0.07, G:0.06, T:0.69
Consensus pattern (26 bp):
TTTTTTTTCATTTTGAGCAATTTTAA
Found at i:1184795 original size:16 final size:17
Alignment explanation
Indices: 1184774--1184808 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1184764 TATACATATG
1184774 TTTTATTTTTTA-TTTT
1 TTTTATTTTTTACTTTT
1184790 TTTTATTTTTTACTTTT
1 TTTTATTTTTTACTTTT
1184807 TT
1 TT
1184809 ATATATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTATTTTTTACTTTT
Found at i:1184831 original size:20 final size:18
Alignment explanation
Indices: 1184803--1184854 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
1184793 TATTTTTTAC
1184803 TTTTT-TATATATACTTT
1 TTTTTATATATATACTTT
*
1184820 ATATTTTATATATACACTTT
1 -T-TTTTATATATATACTTT
*
1184840 TTTTTAAATATATAC
1 TTTTTATATATATAC
1184855 ACATGTACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 13 0.45
19 5 0.17
20 11 0.38
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTTATATATATACTTT
Found at i:1184844 original size:18 final size:18
Alignment explanation
Indices: 1184803--1184856 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
1184793 TATTTTTTAC
1184803 TTTTTTATATAT--ACTT
1 TTTTTTATATATACACTT
1184819 TATATTTTATATATACACTT
1 T-T-TTTTATATATACACTT
1184839 TTTTTTAAATATATACAC
1 TTTTTT--ATATATACAC
1184857 ATGTACATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 1 0.03
17 1 0.03
18 14 0.44
19 1 0.03
20 15 0.47
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTTTATATATACACTT
Found at i:1186137 original size:2 final size:2
Alignment explanation
Indices: 1186130--1186176 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1186120 AAAATGAAGG
*
1186130 TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1186172 TA TA T
1 TA TA T
1186177 GACCTTAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1186622 original size:19 final size:18
Alignment explanation
Indices: 1186594--1186632 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1186584 TGTACTGTGT
**
1186594 ATGTTTTTTTCTTTTAAA
1 ATGTTTTTTTAATTTAAA
1186612 ATGTATTTTTTAATTTAAA
1 ATGT-TTTTTTAATTTAAA
1186631 AT
1 AT
1186633 TTTAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (18 bp):
ATGTTTTTTTAATTTAAA
Found at i:1187346 original size:28 final size:28
Alignment explanation
Indices: 1187315--1187403 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 28
1187305 AAATTTTTTA
* *
1187315 AAAACACT-AAAATAATAAAAATTATAAT
1 AAAA-ACTAAAAAAAATAAAAACTATAAT
*
1187343 AAAAACTAAAAAAAATAATAACTATAAT
1 AAAAACTAAAAAAAATAAAAACTATAAT
* * *
1187371 --AAACTAAAAAGAAGTTAAAAACTAAAAA
1 AAAAACTAAAAA-AA-ATAAAAACTATAAT
1187399 AAAAA
1 AAAAA
1187404 GTTGGCACAC
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
26 10 0.20
27 5 0.10
28 31 0.63
30 3 0.06
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.19
Consensus pattern (28 bp):
AAAAACTAAAAAAAATAAAAACTATAAT
Found at i:1187363 original size:22 final size:21
Alignment explanation
Indices: 1187323--1187363 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1187313 TAAAAACACT
* *
1187323 AAAATAATAAAAATTATAATA
1 AAAATAAAAAAAATAATAATA
1187344 AAAACTAAAAAAAATAATAA
1 AAAA-TAAAAAAAATAATAA
1187364 CTATAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAATAAAAAAAATAATAATA
Found at i:1187928 original size:29 final size:29
Alignment explanation
Indices: 1187882--1187943 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
1187872 TTTCAACTTT
*
1187882 TTTTATTTTATTTCAATAAATCATTATAC
1 TTTTATTATATTTCAATAAATCATTATAC
**
1187911 TTTTATTATA-TTCAAATAAATTGTTATAC
1 TTTTATTATATTTC-AATAAATCATTATAC
1187940 TTTT
1 TTTT
1187944 GAATCCCATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 3 0.10
29 26 0.90
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (29 bp):
TTTTATTATATTTCAATAAATCATTATAC
Found at i:1191009 original size:16 final size:17
Alignment explanation
Indices: 1190983--1191016 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1190973 AAAATTGGAA
*
1190983 TGAGAAAATTATTTAAT
1 TGAGAAAATTAATTAAT
1191000 TGAG-AAATTAATTAAT
1 TGAGAAAATTAATTAAT
1191016 T
1 T
1191017 TAAATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (17 bp):
TGAGAAAATTAATTAAT
Found at i:1192838 original size:9 final size:9
Alignment explanation
Indices: 1192820--1192852 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1192810 ATGAATAAGC
1192820 AAAT-AAAT
1 AAATAAAAT
1192828 AAATAAAAT
1 AAATAAAAT
*
1192837 AATTAAAAT
1 AAATAAAAT
1192846 AAATAAA
1 AAATAAA
1192853 GGACTTAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 4 0.18
9 18 0.82
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1214404 original size:31 final size:29
Alignment explanation
Indices: 1214366--1214443 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
1214356 CTAACGGCTC
* *
1214366 AGTGACTAAAATGTTACAACATGATAACATA
1 AGTGACTAAAATGTAAC-ACATCA-AACATA
* **
1214397 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACATCAAACATA
1214426 AGTGACTAAAATGTAACA
1 AGTGACTAAAATGTAACA
1214444 TGAACCAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 23 0.56
30 3 0.07
31 15 0.37
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.24
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACATCAAACATA
Found at i:1214460 original size:31 final size:29
Alignment explanation
Indices: 1214391--1214464 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
1214381 ACAACATGAT
**
1214391 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATACCA
*
1214420 AACATAAGTGACTAAAATGTAACATGAACCA
1 AACATAAGTGACTAAAACGTAACAT--ACCA
*
1214451 AACAAAAGTGACTA
1 AACATAAGTGACTA
1214465 TTTTAGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.20
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATACCA
Found at i:1222195 original size:9 final size:9
Alignment explanation
Indices: 1222181--1222227 Score: 55
Period size: 8 Copynumber: 5.4 Consensus size: 9
1222171 AAATGACTTC
1222181 AAAATTATA
1 AAAATTATA
1222190 AAAATT-TA
1 AAAATTATA
*
1222198 GAAATTAT-
1 AAAATTATA
1222206 AAAA-TATA
1 AAAATTATA
1222214 AAAATTATA
1 AAAATTATA
1222223 TAAAA
1 -AAAA
1222228 ATAAAATGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
7 3 0.09
8 14 0.44
9 11 0.34
10 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (9 bp):
AAAATTATA
Found at i:1222234 original size:16 final size:15
Alignment explanation
Indices: 1222181--1222248 Score: 66
Period size: 17 Copynumber: 4.3 Consensus size: 15
1222171 AAATGACTTC
*
1222181 AAAATTATAAAAATTT
1 AAAATTATAAAAA-AT
*
1222197 AGAAATTATAAAATAT
1 A-AAATTATAAAAAAT
1222213 AAAAATTATATAAAAAT
1 -AAAATTATA-AAAAAT
1222230 AAAATGTA-AAAAAAT
1 AAAAT-TATAAAAAAT
1222245 AAAA
1 AAAA
1222249 AAAATATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
15 10 0.22
16 16 0.36
17 19 0.42
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AAAATTATAAAAAAT
Found at i:1222576 original size:56 final size:59
Alignment explanation
Indices: 1222466--1222649 Score: 187
Period size: 60 Copynumber: 3.2 Consensus size: 59
1222456 GAAATGTTAG
* * * * * * *
1222466 GGACTAACTTGGACAAAAAAAAAATCAAGCCCGAAGGTGCG-AACAATTGTCAAGTTTAA
1 GGACTAACTTGAACAAAAAATAATTCAAGCCCTAATGTG-GAAACAATTATCAAGTTCAA
* ** * * *
1222525 GGACTAATTTG-GGAAAAAA-AGTTCAGGCCCTAATGT-GAAATAATTATCAAGTTCAA
1 GGACTAACTTGAACAAAAAATAATTCAAGCCCTAATGTGGAAACAATTATCAAGTTCAA
* *
1222581 GGACTAACTTGAAACAAAAAATAATTCAAGCCCTAGTGTGGGAACAATTATCAAGTTCAA
1 GGACTAACTTG-AACAAAAAATAATTCAAGCCCTAATGTGGAAACAATTATCAAGTTCAA
1222641 GGACTAACT
1 GGACTAACT
1222650 CAAACAACAA
Statistics
Matches: 101, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
55 1 0.01
56 25 0.25
57 12 0.12
58 12 0.12
59 24 0.24
60 27 0.27
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (59 bp):
GGACTAACTTGAACAAAAAATAATTCAAGCCCTAATGTGGAAACAATTATCAAGTTCAA
Found at i:1224202 original size:16 final size:17
Alignment explanation
Indices: 1224171--1224203 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1224161 TAAAATTTTA
1224171 AAAATATTAATTTAATAT
1 AAAATATT-ATTTAATAT
1224189 AAAATATT-TTTAATA
1 AAAATATTATTTAATA
1224204 CTATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATATTATTTAATAT
Found at i:1224492 original size:16 final size:16
Alignment explanation
Indices: 1224471--1224501 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1224461 AATATTTATT
*
1224471 ATTTTATTAATATTAA
1 ATTTTATTAAAATTAA
1224487 ATTTTATTAAAATTA
1 ATTTTATTAAAATTA
1224502 TTATTTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTATTAAAATTAA
Found at i:1230863 original size:57 final size:57
Alignment explanation
Indices: 1230757--1230893 Score: 159
Period size: 57 Copynumber: 2.3 Consensus size: 57
1230747 CGGTAAAAAG
*
1230757 GATCTAGCTCGGACGGGTGATCCTATCCTGATATAACCCTCCCGAAGAATATGTGTGAAAA-A
1 GATCTAGCCCGGACGGGTGAT-C--T--TGATATAACCCTCCCGAAGAATATGTG-GAAAATA
* * * *
1230819 GATCTAGCCTGGACGGGTGATCTTGATATAGCCCTCTCGAAGAATATGTGGAAAATG
1 GATCTAGCCCGGACGGGTGATCTTGATATAACCCTCCCGAAGAATATGTGGAAAATA
*
1230876 GATTTAGCCCGGACGGGT
1 GATCTAGCCCGGACGGGT
1230894 AATTCGAATT
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
56 5 0.07
57 41 0.61
59 1 0.01
61 1 0.01
62 19 0.28
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (57 bp):
GATCTAGCCCGGACGGGTGATCTTGATATAACCCTCCCGAAGAATATGTGGAAAATA
Found at i:1234012 original size:47 final size:47
Alignment explanation
Indices: 1233912--1234024 Score: 115
Period size: 47 Copynumber: 2.4 Consensus size: 47
1233902 ATGGGGTTCG
* * *
1233912 CATAAAACATAAAGGGTTCGTATAATTCAATATGTAGGGTTCGCATA
1 CATAAAACATAAAGGGTTCGCATAAGTCAATATGTAGAGTTCGCATA
* *
1233959 CCTAAAACATGAAGGGTTCGCATATAGT-AGA-ATGTAGAGTTCGCATGA
1 CATAAAACATAAAGGGTTCGCATA-AGTCA-ATATGTAGAGTTCGCAT-A
* *
1234007 -ATAAAACTTACAGGGTTC
1 CATAAAACATAAAGGGTTC
1234025 ACACCTATGC
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
47 50 0.93
48 4 0.07
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.27
Consensus pattern (47 bp):
CATAAAACATAAAGGGTTCGCATAAGTCAATATGTAGAGTTCGCATA
Found at i:1235796 original size:23 final size:22
Alignment explanation
Indices: 1235770--1235812 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1235760 TAATACATAT
1235770 ATTTAATATTTAATAATTTTATA
1 ATTTAATATTTAA-AATTTTATA
* *
1235793 ATTTTATTTTTAAAATTTTA
1 ATTTAATATTTAAAATTTTA
1235813 AAAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTAATATTTAAAATTTTATA
Found at i:1240383 original size:22 final size:22
Alignment explanation
Indices: 1240358--1240429 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
1240348 GAACTAAACC
1240358 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
1240380 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
1240402 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
1240424 CTCATG
1 CTCATG
1240430 TGCCTTTGCT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:1244569 original size:96 final size:95
Alignment explanation
Indices: 1244460--1244704 Score: 368
Period size: 96 Copynumber: 2.6 Consensus size: 95
1244450 AAACCCTAAA
* *
1244460 TACTCAAGTAACCCTAAACCCTAATTTATTTGATTTCTTCCTTAAAAACCCTAAACCCT-AACCC
1 TACTCAAGTAACCCTAAACCCTAATTTATTTAATTT-TTCCTTAAAAACCCTAAACACTAAACCC
1244524 TAATCTAATTTTTTTAAAATTTATAATTAATT
65 TAATCTAA-TTTTTTAAAATTTATAATTAATT
* *
1244556 TACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTTCTTAAAAACCATAAACACTAAACCC
1 TACTCAAGTAACCCTAAACCCTAATTTATTTAA-TTTTTCCTTAAAAACCCTAAACACTAAACCC
1244621 TAATCTAATTTTTTAAAATTTATAATTAATT
65 TAATCTAATTTTTTAAAATTTATAATTAATT
* * * * *
1244652 TAATTAAGAAACCTTAAACCCTTATTTATTTAATTTTTCCTT-AAAACCCTAAA
1 TACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTCCTTAAAAACCCTAAA
1244705 ATCTAAAAAC
Statistics
Matches: 136, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
94 10 0.07
95 8 0.06
96 102 0.75
97 16 0.12
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.40
Consensus pattern (95 bp):
TACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTCCTTAAAAACCCTAAACACTAAACCCT
AATCTAATTTTTTAAAATTTATAATTAATT
Found at i:1244903 original size:40 final size:40
Alignment explanation
Indices: 1244812--1244909 Score: 133
Period size: 40 Copynumber: 2.5 Consensus size: 40
1244802 CAACGTAGAC
* * *
1244812 ACAAAGCGCTCCCTCAAGGAAACGTTTTCTGTCCATGTGG
1 ACAAAGCGCTTCCTTAAGGAAACGTTTTCTGTCCACGTGG
* * * *
1244852 ACAAAGTGCTTCCTTGAGGAAGCGTTTTTTGTCCACGTGG
1 ACAAAGCGCTTCCTTAAGGAAACGTTTTCTGTCCACGTGG
1244892 ACAAAGCGCTTCCTTAAG
1 ACAAAGCGCTTCCTTAAG
1244910 AAAGTGTTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.28
Consensus pattern (40 bp):
ACAAAGCGCTTCCTTAAGGAAACGTTTTCTGTCCACGTGG
Found at i:1244919 original size:40 final size:40
Alignment explanation
Indices: 1244812--1244920 Score: 130
Period size: 40 Copynumber: 2.7 Consensus size: 40
1244802 CAACGTAGAC
* * *
1244812 ACAAAGCGCTCCCTCAAGGAAA-CGTTTTCTGTCCATGTGG
1 ACAAAGCGCTTCCTTAA-GAAAGCGTTTTCTGTCCACGTGG
* * * *
1244852 ACAAAGTGCTTCCTTGAGGAAGCGTTTTTTGTCCACGTGG
1 ACAAAGCGCTTCCTTAAGAAAGCGTTTTCTGTCCACGTGG
*
1244892 ACAAAGCGCTTCCTTAAGAAAGTGTTTTC
1 ACAAAGCGCTTCCTTAAGAAAGCGTTTTC
1244921 CTGCTTTATC
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
39 3 0.05
40 53 0.95
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (40 bp):
ACAAAGCGCTTCCTTAAGAAAGCGTTTTCTGTCCACGTGG
Found at i:1249450 original size:24 final size:24
Alignment explanation
Indices: 1249408--1249459 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1249398 AATCAAAGTC
1249408 AAATATATTAAGCTAATAAA-AGCT
1 AAATATATTAAGCTAATAAATA-CT
*
1249432 AAATATATTATA-CTCATAAATACT
1 AAATATATTA-AGCTAATAAATACT
1249456 AAAT
1 AAAT
1249460 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATATATTAAGCTAATAAATACT
Found at i:1253162 original size:19 final size:20
Alignment explanation
Indices: 1253123--1253167 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
1253113 ATTTATTTTC
1253123 TATA-TTTTATTAAATTGTA
1 TATATTTTTATTAAATTGTA
*
1253142 TA-ATTTTTA-TAAATTCTTA
1 TATATTTTTATTAAATT-GTA
1253161 TATATTT
1 TATATTT
1253168 GAAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 7 0.32
19 11 0.50
20 4 0.18
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
TATATTTTTATTAAATTGTA
Found at i:1261095 original size:2 final size:2
Alignment explanation
Indices: 1261088--1261113 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1261078 TACCCTTAAT
1261088 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1261114 AATAATCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1262120 original size:20 final size:21
Alignment explanation
Indices: 1262066--1262121 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
1262056 AAAAAATGAC
1262066 ATTTTAGATTTTTTTAATAAAT
1 ATTTT-GATTTTTTTAATAAAT
** *
1262088 ATTTTGAAATTTTTAA-AATT
1 ATTTTGATTTTTTTAATAAAT
1262108 ATTTTGATTTTTTT
1 ATTTTGATTTTTTT
1262122 TTTGTTGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 15 0.52
21 9 0.31
22 5 0.17
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
ATTTTGATTTTTTTAATAAAT
Found at i:1262223 original size:18 final size:18
Alignment explanation
Indices: 1262196--1262230 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1262186 CAATCTATCG
*
1262196 TTTGAGTTATTCAAATTA
1 TTTGAATTATTCAAATTA
*
1262214 TTTGAATTATTCGAATT
1 TTTGAATTATTCAAATT
1262231 GTGAAATTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTATTCAAATTA
Found at i:1263809 original size:24 final size:26
Alignment explanation
Indices: 1263776--1263831 Score: 80
Period size: 24 Copynumber: 2.2 Consensus size: 26
1263766 CATTTAATCA
* *
1263776 GTAAATATATATTTTTTAA-AAATTT
1 GTAAAAATATATTATTTAATAAATTT
1263801 -TAAAAATATATTATTTAATAAATTT
1 GTAAAAATATATTATTTAATAAATTT
1263826 GTAAAA
1 GTAAAA
1263832 TAAATTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 16 0.59
25 6 0.22
26 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
GTAAAAATATATTATTTAATAAATTT
Found at i:1263831 original size:25 final size:24
Alignment explanation
Indices: 1263776--1263833 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 24
1263766 CATTTAATCA
*
1263776 GTAAATATATATTTTTTAAAAATTT
1 GTAAA-ATATATTATTTAAAAATTT
1263801 -TAAAAATATATTATTTAATAAATTT
1 GT-AAAATATATTATTTAA-AAATTT
1263826 GTAAAATA
1 GTAAAATA
1263834 AATTTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 13 0.45
25 15 0.52
26 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (24 bp):
GTAAAATATATTATTTAAAAATTT
Found at i:1263835 original size:13 final size:13
Alignment explanation
Indices: 1263817--1263847 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1263807 TATATTATTT
*
1263817 AATAAATTTGTAA
1 AATAAATTTATAA
1263830 AATAAATTTATAA
1 AATAAATTTATAA
1263843 AATAA
1 AATAA
1263848 GGTGCAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (13 bp):
AATAAATTTATAA
Found at i:1263840 original size:26 final size:25
Alignment explanation
Indices: 1263776--1263840 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
1263766 CATTTAATCA
1263776 GTAAATATATATTT-TTTAAAAATTT
1 GTAAA-ATATATTTATTTAAAAATTT
1263801 -TAAAA-ATATATTATTTAATAAATTT
1 GTAAAATATAT-TTATTTAA-AAATTT
*
1263826 GTAAAATAAATTTAT
1 GTAAAATATATTTAT
1263841 AAAATAAGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
22 4 0.12
23 3 0.09
24 9 0.26
25 6 0.18
26 9 0.26
27 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (25 bp):
GTAAAATATATTTATTTAAAAATTT
Found at i:1269014 original size:72 final size:73
Alignment explanation
Indices: 1268862--1269125 Score: 304
Period size: 72 Copynumber: 3.6 Consensus size: 73
1268852 ACTGCTCATG
* * * *
1268862 ATTTTAATGTCGAAAATTTGGTCACAAACAAATTGAATAGTTGTGACCATTCATTTTTGTCACAA
1 ATTTTAGTGTCGAAAATTTGGT-ACAAACAAAATGAATAATTGTGACCATTTATTTTTGTCACAA
1268927 TTGCTTACA
65 TTGCTTACA
* * * * * *
1268936 ATTTTAGTGTCGACAATATGGTACAAA-AAAATGAATAATTATGACCATTTATATTTATCAAAAA
1 ATTTTAGTGTCGAAAATTTGGTACAAACAAAATGAATAATTGTGACCATTTATTTTTGTC-ACAA
**
1269000 TTGCTTATG
65 TTGCTTACA
** *
1269009 A-TTTAGTGTAAAAAATTTGGCCACAAACAAAAT-AATAATTGTGACCATTTATTTTTGTCACAA
1 ATTTTAGTGTCGAAAATTTGG-TACAAACAAAATGAATAATTGTGACCATTTATTTTTGTCACAA
1269072 TTGCTTACA
65 TTGCTTACA
* *
1269081 ATTTTAGTGTCGAAAATTTAG-ACAAA-AAAATTTAATAATTGTGAC
1 ATTTTAGTGTCGAAAATTTGGTACAAACAAAA-TGAATAATTGTGAC
1269126 AACTTTGTAA
Statistics
Matches: 158, Mismatches: 26, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
70 4 0.03
71 6 0.04
72 64 0.41
73 60 0.38
74 24 0.15
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (73 bp):
ATTTTAGTGTCGAAAATTTGGTACAAACAAAATGAATAATTGTGACCATTTATTTTTGTCACAAT
TGCTTACA
Found at i:1273496 original size:18 final size:17
Alignment explanation
Indices: 1273474--1273516 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1273464 GAACTTTTAT
1273474 TAAAATAAAAAAAATTA
1 TAAAATAAAAAAAATTA
* *
1273491 TAAAAATACAGAAAA-TA
1 T-AAAATAAAAAAAATTA
1273508 TAAAATAAA
1 TAAAATAAA
1273517 TTGTAAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 7 0.32
17 4 0.18
18 11 0.50
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (17 bp):
TAAAATAAAAAAAATTA
Found at i:1273793 original size:16 final size:17
Alignment explanation
Indices: 1273763--1273795 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1273753 TAGTTAATTA
1273763 ATTTTCTTTAAATATTT
1 ATTTTCTTTAAATATTT
*
1273780 ATTTT-TTTATATATTT
1 ATTTTCTTTAAATATTT
1273796 TTTAATATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTCTTTAAATATTT
Found at i:1285335 original size:11 final size:11
Alignment explanation
Indices: 1285319--1285352 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1285309 TCTCTCACAT
1285319 TCTCAAATCTC
1 TCTCAAATCTC
*
1285330 TCTCAAATTTC
1 TCTCAAATCTC
*
1285341 TCTCAATTCTC
1 TCTCAAATCTC
1285352 T
1 T
1285353 GTTAAATTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (11 bp):
TCTCAAATCTC
Found at i:1285351 original size:22 final size:23
Alignment explanation
Indices: 1285319--1285371 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
1285309 TCTCTCACAT
*
1285319 TCTCAAATCTCTCTCAAATT-TC
1 TCTCAATTCTCTCTCAAATTCTC
* *
1285341 TCTCAATTCTCTGTTAAATTCTC
1 TCTCAATTCTCTCTCAAATTCTC
*
1285364 CCTCAATT
1 TCTCAATT
1285372 TTTATTTATC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.25, C:0.30, G:0.02, T:0.43
Consensus pattern (23 bp):
TCTCAATTCTCTCTCAAATTCTC
Found at i:1286324 original size:44 final size:44
Alignment explanation
Indices: 1286247--1286334 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
1286237 TTTTATAAAC
** * * * *
1286247 TACATTTTATAGTTATTTTATTTTAGTTATCTATGCTATTATTT
1 TACATTTTATACCTATTTTATTGTAGTCATCTATACTATGATTT
*
1286291 TACATTTTATACCTATTTTATTGTAGTCGTCTATACTATGATTT
1 TACATTTTATACCTATTTTATTGTAGTCATCTATACTATGATTT
1286335 AAGGTTAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.57
Consensus pattern (44 bp):
TACATTTTATACCTATTTTATTGTAGTCATCTATACTATGATTT
Found at i:1289087 original size:9 final size:9
Alignment explanation
Indices: 1289073--1289138 Score: 89
Period size: 9 Copynumber: 7.2 Consensus size: 9
1289063 TTTGGTTAAA
1289073 AATTACCCG
1 AATTACCCG
1289082 AATTACCCG
1 AATTACCCG
*
1289091 -ATTAACCG
1 AATTACCCG
*
1289099 AATTAACCG
1 AATTACCCG
1289108 AATTACCCG
1 AATTACCCG
1289117 AAAATTACCCG
1 --AATTACCCG
1289128 AATTACCCG
1 AATTACCCG
1289137 AA
1 AA
1289139 AATTACCCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
8 7 0.13
9 36 0.69
11 9 0.17
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (9 bp):
AATTACCCG
Found at i:1289146 original size:20 final size:18
Alignment explanation
Indices: 1289073--1289138 Score: 89
Period size: 20 Copynumber: 3.6 Consensus size: 18
1289063 TTTGGTTAAA
1289073 AATTACCCGAATTACCCG
1 AATTACCCGAATTACCCG
* *
1289091 -ATTAACCGAATTAACCG
1 AATTACCCGAATTACCCG
1289108 AATTACCCGAAAATTACCCG
1 AATTACCCG--AATTACCCG
1289128 AATTACCCGAA
1 AATTACCCGAA
1289139 AATTACCCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 15 0.37
18 9 0.22
20 17 0.41
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (18 bp):
AATTACCCGAATTACCCG
Found at i:1289151 original size:11 final size:11
Alignment explanation
Indices: 1289108--1289150 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
1289098 GAATTAACCG
1289108 AATTACCCGAA
1 AATTACCCGAA
1289119 AATTACCCG--
1 AATTACCCGAA
1289128 AATTACCCGAA
1 AATTACCCGAA
1289139 AATTACCC-AA
1 AATTACCCGAA
1289149 AA
1 AA
1289151 AGTTCGGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.30
10 4 0.13
11 17 0.57
ACGTcount: A:0.47, C:0.28, G:0.07, T:0.19
Consensus pattern (11 bp):
AATTACCCGAA
Found at i:1290195 original size:22 final size:22
Alignment explanation
Indices: 1290161--1290202 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1290151 ATTGATACAT
*
1290161 TACACTAACATATTACATAAAAA
1 TACACTAAAATATTA-ATAAAAA
1290184 TACA-TAAAATATTAATAAA
1 TACACTAAAATATTAATAAA
1290203 TTAATATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 9 0.50
23 4 0.22
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.29
Consensus pattern (22 bp):
TACACTAAAATATTAATAAAAA
Found at i:1290553 original size:18 final size:18
Alignment explanation
Indices: 1290514--1290569 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
1290504 ATAATTTTCA
* *
1290514 AAAATTTAAAATAATTTTT
1 AAAATTCAAAAT-ATTTAT
1290533 AAAATTCAAAATATTTAT
1 AAAATTCAAAATATTTAT
*
1290551 AAAAATTCCAAA-ATTTAT
1 -AAAATTCAAAATATTTAT
1290569 A
1 A
1290570 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 1 0.03
18 11 0.33
19 21 0.64
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATTCAAAATATTTAT
Found at i:1290555 original size:19 final size:19
Alignment explanation
Indices: 1290493--1290564 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
1290483 AATTACAAAA
*
1290493 AAAAAATCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
*
1290512 CAAAAATTTAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
*
1290532 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
1290551 AAAAATTCCAAAAT
1 AAAAATT-CAAAAT
1290565 TTATATTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
18 4 0.09
19 18 0.40
20 23 0.51
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:1291867 original size:26 final size:26
Alignment explanation
Indices: 1291829--1291890 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
1291819 ACTACTAGAC
*
1291829 TAAAAATAAATAAATA-ATTAAATAAT
1 TAAAAATAAATAAA-AGATTAAAAAAT
**
1291855 TAAAAATTCATAAAAGATTAAAAAA-
1 TAAAAATAAATAAAAGATTAAAAAAT
*
1291880 TAAAAAAAAAT
1 TAAAAATAAAT
1291891 TATTAAATCA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 9 0.31
26 20 0.69
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (26 bp):
TAAAAATAAATAAAAGATTAAAAAAT
Found at i:1294879 original size:21 final size:21
Alignment explanation
Indices: 1294854--1294893 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1294844 TCTTTTAACA
1294854 AAAATA-TCATTTTTACTTTAT
1 AAAATAGTCATTTTT-CTTTAT
1294875 AAAATAGTCATTTTTCTTT
1 AAAATAGTCATTTTTCTTT
1294894 TCTAAGCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
AAAATAGTCATTTTTCTTTAT
Found at i:1297695 original size:28 final size:26
Alignment explanation
Indices: 1297650--1297703 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
1297640 NNNNNNNNNC
*
1297650 AATACTTTTTTATTTTTTTTAATTTTAA
1 AATACTTTTTTA-TATTTTT-ATTTTAA
1297678 AATACTTTTTT-TAATTTTTATTTTAA
1 AATACTTTTTTAT-ATTTTTATTTTAA
1297704 TTTTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 8 0.33
27 5 0.21
28 11 0.46
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (26 bp):
AATACTTTTTTATATTTTTATTTTAA
Found at i:1297720 original size:33 final size:29
Alignment explanation
Indices: 1297655--1297721 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 29
1297645 NNNNCAATAC
*
1297655 TTTTTTATTTTTTTTAATTTTAAAATACT
1 TTTTTTATTTTTTTTAATTTTAAAATAAT
1297684 TTTTTTAATTTTTATTTTAATTTTTAAAATAAT
1 TTTTTT-A-TTTT-TTTTAA-TTTTAAAATAAT
1297717 TTTTT
1 TTTTT
1297722 GGTATTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 6 0.18
30 1 0.03
31 4 0.12
32 6 0.18
33 16 0.48
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (29 bp):
TTTTTTATTTTTTTTAATTTTAAAATAAT
Found at i:1298630 original size:5 final size:5
Alignment explanation
Indices: 1298555--1298619 Score: 130
Period size: 5 Copynumber: 13.0 Consensus size: 5
1298545 ATTATAGCAT
1298555 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1298605 ATATC ATATC ATATC
1 ATATC ATATC ATATC
1298620 TCATATAATA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 60 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATC
Found at i:1314405 original size:63 final size:63
Alignment explanation
Indices: 1314327--1314455 Score: 177
Period size: 63 Copynumber: 2.0 Consensus size: 63
1314317 TCCAACTGAG
* * * *
1314327 TATGTTCCGCTAACTATTATGTAACTGCTGTAACTCTAATTAAGTTGCGTGCACATACACAGT
1 TATGTTCCGCTAACTATTATGTAACCGCTGTAACACAAATGAAGTTGCGTGCACATACACAGT
* * ** *
1314390 TATGTTCCGTTAACTATTATGTAACCGCTGTAGCACAAATGAAGTTGTTTGCGCATACACAGT
1 TATGTTCCGCTAACTATTATGTAACCGCTGTAACACAAATGAAGTTGCGTGCACATACACAGT
1314453 TAT
1 TAT
1314456 CAAGAAGACT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (63 bp):
TATGTTCCGCTAACTATTATGTAACCGCTGTAACACAAATGAAGTTGCGTGCACATACACAGT
Found at i:1314986 original size:16 final size:16
Alignment explanation
Indices: 1314965--1314997 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1314955 AGATCGGTCT
*
1314965 TTCTAGCACCATTCTC
1 TTCTAGCAACATTCTC
1314981 TTCTAGCAACATTCTC
1 TTCTAGCAACATTCTC
1314997 T
1 T
1314998 ATCGGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.33, G:0.06, T:0.39
Consensus pattern (16 bp):
TTCTAGCAACATTCTC
Found at i:1339306 original size:51 final size:51
Alignment explanation
Indices: 1339225--1339331 Score: 144
Period size: 51 Copynumber: 2.1 Consensus size: 51
1339215 TGATATGAGG
* ** *
1339225 TTGGAGCAGGCTGTTGAATCAAGAAAAGAAGTTGGAATATC-GAGGAGAAGT
1 TTGGAACAGGCTGCCGAATCAAGAAAAGAAGTTGGAATAGCTG-GGAGAAGT
* *
1339276 TTGGAACAGGCTGCCGAATCTAGAAGAGAAGTTGGAATAGCTGGGAGAAGT
1 TTGGAACAGGCTGCCGAATCAAGAAAAGAAGTTGGAATAGCTGGGAGAAGT
1339327 TTGGA
1 TTGGA
1339332 GCCGAGCCAG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
51 48 0.98
52 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (51 bp):
TTGGAACAGGCTGCCGAATCAAGAAAAGAAGTTGGAATAGCTGGGAGAAGT
Found at i:1351765 original size:19 final size:19
Alignment explanation
Indices: 1351741--1351851 Score: 159
Period size: 19 Copynumber: 5.8 Consensus size: 19
1351731 AATTTTTGAG
*
1351741 GATATGCAATCTTATATAT
1 GATATGCAATCTTAGATAT
*
1351760 GATATGCAATCGTAGATAT
1 GATATGCAATCTTAGATAT
1351779 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
1351798 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* ** * *
1351817 GATGTATAATATTTGATAT
1 GATATGCAATCTTAGATAT
1351836 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
1351852 AGATATGATT
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 79 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:1353013 original size:3 final size:3
Alignment explanation
Indices: 1353007--1353043 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1352997 GATGATGTAT
*
1353007 TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1353044 AGCATTTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1353799 original size:23 final size:20
Alignment explanation
Indices: 1353767--1353823 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
1353757 ACCACTGTTC
*
1353767 TTTCTCTATTTTTGCATCTACT
1 TTTCTTTATTTTTG--TCTACT
* *
1353789 GTTTCTTTATTTTTGTTTTCT
1 -TTTCTTTATTTTTGTCTACT
1353810 TTTCTTTATTTTTG
1 TTTCTTTATTTTTG
1353824 ATTATTTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 14 0.45
21 4 0.13
23 13 0.42
ACGTcount: A:0.09, C:0.14, G:0.07, T:0.70
Consensus pattern (20 bp):
TTTCTTTATTTTTGTCTACT
Found at i:1359053 original size:103 final size:103
Alignment explanation
Indices: 1358869--1359074 Score: 286
Period size: 103 Copynumber: 2.0 Consensus size: 103
1358859 GCTATTGACG
* *
1358869 CATACCGAATTGACGAGGATGTAAGTGATGGTAATTTTTAAATCTCTAAAGAATTCAAGTGTTTA
1 CATACCGAATTGACGAGGAGGTAAGTGATGGTAATTTCTAAATCTCTAAAGAATTCAAGTGTTTA
* *
1358934 CTTTGTTTGTGAGTAAAGATAAGCTAATTATTAATGAA
66 CTTTGCTTGTGAGTAAAGATAAACTAATTATTAATGAA
* ** * ** *
1358972 CATATCGAATTGGTGAGGAGGTAAGTGATGGTAGTTTCTGGATCTTTAAAGAATTCAAGTGTTTA
1 CATACCGAATTGACGAGGAGGTAAGTGATGGTAATTTCTAAATCTCTAAAGAATTCAAGTGTTTA
* * *
1359037 TTTTGCTTGTGAGTAAATATAAACTACTTATTAATGAA
66 CTTTGCTTGTGAGTAAAGATAAACTAATTATTAATGAA
1359075 GAGCGCATCA
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
103 89 1.00
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (103 bp):
CATACCGAATTGACGAGGAGGTAAGTGATGGTAATTTCTAAATCTCTAAAGAATTCAAGTGTTTA
CTTTGCTTGTGAGTAAAGATAAACTAATTATTAATGAA
Found at i:1361084 original size:3 final size:3
Alignment explanation
Indices: 1361076--1361100 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1361066 CAAAATTTTC
1361076 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
1361101 TTATTGCCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1362346 original size:2 final size:2
Alignment explanation
Indices: 1362334--1362380 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1362324 TCTTTATTAT
*
1362334 AG AG AG GG 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
1362376 AG AG A
1 AG AG A
1362381 ATTTTTCTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1370785 original size:16 final size:16
Alignment explanation
Indices: 1370764--1370805 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1370754 AATAATTTGA
*
1370764 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
1370780 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
1370796 TAGTTTTAAT
1 TAATTTTAAT
1370806 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:1370789 original size:22 final size:22
Alignment explanation
Indices: 1370779--1370833 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1370769 TTACTAACAA
* * *
1370779 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
1370801 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
1370823 TTAATTTTAAT
1 TTAATTTTAAT
1370834 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:1384697 original size:20 final size:20
Alignment explanation
Indices: 1384674--1384713 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1384664 TAATTTAGCC
*
1384674 ATTTTTATTTTTATTTTAAT
1 ATTTTTATTTTTAATTTAAT
*
1384694 ATTTTTGTTTTTAATTTAAT
1 ATTTTTATTTTTAATTTAAT
1384714 TGTTTCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
ATTTTTATTTTTAATTTAAT
Found at i:1385931 original size:20 final size:20
Alignment explanation
Indices: 1385906--1385943 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1385896 CTTTTTCTGT
*
1385906 TTGAATCGATTCATTGTTGC
1 TTGAATCAATTCATTGTTGC
*
1385926 TTGAATCAATTCTTTGTT
1 TTGAATCAATTCATTGTT
1385944 ATTTAACTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.50
Consensus pattern (20 bp):
TTGAATCAATTCATTGTTGC
Found at i:1399533 original size:2 final size:2
Alignment explanation
Indices: 1399521--1399550 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1399511 ATGTAAAAAT
1399521 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1399551 TCAGAGACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1404163 original size:30 final size:30
Alignment explanation
Indices: 1404127--1404187 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1404117 ATCATGATCA
*
1404127 AAATTCACCAGTTGATATAGCACAGAACTT
1 AAATTCACCAGTTGATATAACACAGAACTT
* *
1404157 AAATTCACGAGTTGATATAACACGGAACTT
1 AAATTCACCAGTTGATATAACACAGAACTT
1404187 A
1 A
1404188 TTTGGAAGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (30 bp):
AAATTCACCAGTTGATATAACACAGAACTT
Found at i:1413918 original size:2 final size:2
Alignment explanation
Indices: 1413911--1413945 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
1413901 TATCCTTAAA
1413911 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
1413946 TAAAACACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Done.