Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold220
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: 3999181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 12171 characters in sequence are not A, C, G, or T
File 8 of 19
Found at i:1691950 original size:18 final size:18
Alignment explanation
Indices: 1691927--1691968 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1691917 ATGTATGGTT
1691927 GTATATT-CTGAATTCTGA
1 GTATATTACTG-ATTCTGA
*
1691945 GTATATTACTGCTTCTGA
1 GTATATTACTGATTCTGA
1691963 -TATATT
1 GTATATT
1691969 TTATGTGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 6 0.27
18 13 0.59
19 3 0.14
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (18 bp):
GTATATTACTGATTCTGA
Found at i:1696169 original size:7 final size:7
Alignment explanation
Indices: 1696157--1696189 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
1696147 TAAAATAGCC
1696157 TTTTGTT
1 TTTTGTT
1696164 TTTTGTT
1 TTTTGTT
1696171 TTTTGTT
1 TTTTGTT
*
1696178 TTTTTTT
1 TTTTGTT
1696185 TTTTG
1 TTTTG
1696190 AGGGTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTGTT
Found at i:1696876 original size:2 final size:2
Alignment explanation
Indices: 1696869--1696906 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1696859 TTATATTCAT
1696869 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
1696907 ACTGCTGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1700356 original size:21 final size:21
Alignment explanation
Indices: 1700315--1700356 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1700305 TGACACTTCA
*
1700315 TTATTCTTAATATTTGCATTT
1 TTATTCTTAATATTTGAATTT
*
1700336 TTATT-TTACATATTTTAATTT
1 TTATTCTTA-ATATTTGAATTT
1700357 GCTCCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.64
Consensus pattern (21 bp):
TTATTCTTAATATTTGAATTT
Found at i:1701753 original size:2 final size:2
Alignment explanation
Indices: 1701746--1701771 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1701736 ACTTTTCATT
1701746 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
1701772 GGTATAGCCT
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:1702031 original size:2 final size:2
Alignment explanation
Indices: 1702020--1702051 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1702010 TATGCATGTG
1702020 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1702052 TTCGTTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1703644 original size:2 final size:2
Alignment explanation
Indices: 1703637--1703665 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1703627 TTGTTTCAAT
1703637 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1703666 TAAAAACAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1703691 original size:2 final size:2
Alignment explanation
Indices: 1703684--1703708 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1703674 GCTTCTACAA
1703684 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1703709 ATCTGATGGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1704335 original size:29 final size:30
Alignment explanation
Indices: 1704293--1704362 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
1704283 AATTTTCTAG
*
1704293 AATTATTATATTTTTA-TTACA-TCTAAATAA
1 AATT-TTATTTTTTTATTTACATTC-AAATAA
*
1704323 AATTTTATTTTTTTATTTATATTCAAATAA
1 AATTTTATTTTTTTATTTACATTCAAATAA
*
1704353 AATCTTATTT
1 AATTTTATTT
1704363 GAAATGAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.29
30 23 0.66
31 2 0.06
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (30 bp):
AATTTTATTTTTTTATTTACATTCAAATAA
Found at i:1707178 original size:38 final size:37
Alignment explanation
Indices: 1707107--1707179 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 37
1707097 TTAAAGTAAT
* * **
1707107 ATTTAATAAATAAATATAATTAATATATTATTTTTTA
1 ATTTAATAAAAAAATATAATAAATATAAAATTTTTTA
1707144 ATTTAATAAAAATAATATAATAAATATAAAATTTTT
1 ATTTAATAAAAA-AATATAATAAATATAAAATTTTT
1707180 CTCAAATAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 11 0.35
38 20 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTAATAAAAAAATATAATAAATATAAAATTTTTTA
Found at i:1707179 original size:37 final size:37
Alignment explanation
Indices: 1707107--1707179 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
1707097 TTAAAGTAAT
* * * *
1707107 ATTTAATAAATAAATATAATTAATATATTATTTTTTA
1 ATTTAATAAAAAAATATAATAAATATATAAATTTTTA
1707144 ATTTAATAAAAATAATATAATAAATATA-AAATTTTT
1 ATTTAATAAAAA-AATATAATAAATATATAAATTTTT
1707180 CTCAAATAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 17 0.55
38 14 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTAATAAAAAAATATAATAAATATATAAATTTTTA
Found at i:1707269 original size:19 final size:18
Alignment explanation
Indices: 1707242--1707287 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
1707232 ACTAATTTAA
*
1707242 AAAAAAATTAATAACTTTT
1 AAAAAAATTAATAA-ATTT
* *
1707261 AAAACAATTTATAAATTT
1 AAAAAAATTAATAAATTT
1707279 AAAAAAATT
1 AAAAAAATT
1707288 TACAATTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAAAATTAATAAATTT
Found at i:1708180 original size:2 final size:2
Alignment explanation
Indices: 1708169--1708207 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1708159 ACATAGATCT
1708169 TA TA -A TA 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
1708208 CACGCACACA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1708927 original size:2 final size:2
Alignment explanation
Indices: 1708920--1708950 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1708910 AAAATAGGGG
1708920 GA GA GA GA GA GA GA GA GA GA GA -A GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1708951 AAAAGAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1714623 original size:12 final size:12
Alignment explanation
Indices: 1714606--1714648 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
1714596 TGCCTTTAAA
1714606 ATTTATTTTTTT
1 ATTTATTTTTTT
1714618 ATTTATTATTTTAT
1 ATTTATT-TTTT-T
*
1714632 TTTTCATTTTTTT
1 ATTT-ATTTTTTT
1714645 ATTT
1 ATTT
1714649 TCCAATCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 7 0.27
13 8 0.31
14 8 0.31
15 3 0.12
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTTATTTTTTT
Found at i:1714626 original size:15 final size:14
Alignment explanation
Indices: 1714607--1714649 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
1714597 GCCTTTAAAA
1714607 TTTATTTTTTTA--
1 TTTATTTTTTTATT
*
1714619 TTTATTATTTTATT
1 TTTATTTTTTTATT
1714633 TTTCATTTTTTTATT
1 TTT-ATTTTTTTATT
1714648 TT
1 TT
1714650 CCAATCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 11 0.42
14 3 0.12
15 12 0.46
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTTTTATT
Found at i:1715008 original size:14 final size:15
Alignment explanation
Indices: 1714976--1715017 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1714966 ATTGAATAAA
1714976 TTAATTTTGATTT-AT
1 TTAATTTT-ATTTAAT
1714991 TTAATTTT-TTTAAT
1 TTAATTTTATTTAAT
1715005 TTAATTTTATTTA
1 TTAATTTTATTTA
1715018 GTTAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.12
14 10 0.40
15 12 0.48
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
TTAATTTTATTTAAT
Found at i:1715022 original size:14 final size:14
Alignment explanation
Indices: 1714976--1715022 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
1714966 ATTGAATAAA
1714976 TTAATTTTGATTTAT
1 TTAATTTT-ATTTAT
1714991 TTAATTTT-TTTAAT
1 TTAATTTTATTT-AT
*
1715005 TTAATTTTATTTAG
1 TTAATTTTATTTAT
1715019 TTAA
1 TTAA
1715023 ATAATATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 3 0.10
14 15 0.52
15 11 0.38
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (14 bp):
TTAATTTTATTTAT
Found at i:1715032 original size:28 final size:28
Alignment explanation
Indices: 1715004--1715058 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1714994 ATTTTTTTAA
*
1715004 TTTAATTTTATTTAGTTAAATAATATAAT
1 TTTAA-TTAATTTAGTTAAATAATATAAT
* *
1715033 TTTAATTAATTTATTTAATTAATATA
1 TTTAATTAATTTAGTTAAATAATATA
1715059 TAATTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTAATTAATTTAGTTAAATAATATAAT
Found at i:1715293 original size:39 final size:39
Alignment explanation
Indices: 1715245--1715346 Score: 93
Period size: 39 Copynumber: 2.6 Consensus size: 39
1715235 TGATTAATTT
* * **
1715245 AATTTATTAATTTATTTAATTTTTAAAATTTTAAAAATA
1 AATTGATTAATTTATTTAATTTTTAAAAATAAAAAAATA
* * *
1715284 AATTGATTAA-ATA-TTAATTTTAAAAAAATAAAAAAATT
1 AATTGATTAATTTATTTAATTTT-TAAAAATAAAAAAATA
*
1715322 AATCTGATTAATTTATAT-ATTTTTA
1 AAT-TGATTAATTTATTTAATTTTTA
1715347 TTTAAATATT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
37 8 0.16
38 16 0.33
39 17 0.35
40 7 0.14
41 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (39 bp):
AATTGATTAATTTATTTAATTTTTAAAAATAAAAAAATA
Found at i:1717014 original size:2 final size:2
Alignment explanation
Indices: 1717007--1717031 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1716997 ATTAATGGAT
1717007 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 T
1717032 TATTAATATT
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1717778 original size:2 final size:2
Alignment explanation
Indices: 1717771--1717797 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1717761 AAACATATTG
1717771 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1717798 CCCATTAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1717885 original size:21 final size:22
Alignment explanation
Indices: 1717844--1717904 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
1717834 TCAAACTAAA
* *
1717844 TTTAAATATTAAAAATATTTATT
1 TTTAAA-ATTTAAAATATTTAAT
1717867 TTTAAAATTTAAAAT-TTTAAT
1 TTTAAAATTTAAAATATTTAAT
**
1717888 TTTATTATTT-AAATATT
1 TTTAAAATTTAAAATATT
1717905 ATAAAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 4 0.12
21 15 0.45
22 8 0.24
23 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTAAAATTTAAAATATTTAAT
Found at i:1717889 original size:22 final size:23
Alignment explanation
Indices: 1717844--1717891 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
1717834 TCAAACTAAA
1717844 TTTAAATATTAAAAATATTTATT
1 TTTAAATATTAAAAATATTTATT
* *
1717867 TTTAAA-ATTTAAAAT-TTTAAT
1 TTTAAATATTAAAAATATTTATT
1717888 TTTA
1 TTTA
1717892 TTATTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 8 0.35
23 6 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTAAATATTAAAAATATTTATT
Found at i:1719616 original size:23 final size:23
Alignment explanation
Indices: 1719590--1719691 Score: 63
Period size: 23 Copynumber: 4.4 Consensus size: 23
1719580 AAACCTCATA
1719590 ATTTATATATATATATATATATT
1 ATTTATATATATATATATATATT
* * *
1719613 ATTTACATATATTTTTATA-ATTT
1 ATTTATATATATATATATATA-TT
* *
1719636 ATTTAAAATATTATATATGTAAATATT
1 ATTT---ATA-TATATATATATATATT
1719663 -TTTATATA-ATA-ATA-AT-TT
1 ATTTATATATATATATATATATT
1719681 ATATTATATAT
1 AT-TTATATAT
1719692 TAATTTTATA
Statistics
Matches: 62, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
18 2 0.03
19 3 0.05
20 9 0.15
21 3 0.05
22 3 0.05
23 25 0.40
26 5 0.08
27 11 0.18
28 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (23 bp):
ATTTATATATATATATATATATT
Found at i:1719687 original size:20 final size:18
Alignment explanation
Indices: 1719657--1719703 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
1719647 TATATATGTA
*
1719657 AATATTTTTATA-TA-AT
1 AATAATTTTATATTATAT
1719673 AATAA-TTTATATTATAT
1 AATAATTTTATATTATAT
*
1719690 ATTAATTTTATATT
1 AATAATTTTATATT
1719704 TTAATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 6 0.23
16 6 0.23
17 6 0.23
18 8 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATAATTTTATATTATAT
Found at i:1719688 original size:18 final size:19
Alignment explanation
Indices: 1719667--1719708 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1719657 AATATTTTTA
1719667 TATAATAATAA-TTTATAT
1 TATAATAATAATTTTATAT
*
1719685 TAT-ATATTAATTTTATAT
1 TATAATAATAATTTTATAT
*
1719703 TTTAAT
1 TATAAT
1719709 TATTTTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 6 0.30
18 12 0.60
19 2 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATAATAATAATTTTATAT
Found at i:1722594 original size:64 final size:64
Alignment explanation
Indices: 1722489--1722617 Score: 213
Period size: 64 Copynumber: 2.0 Consensus size: 64
1722479 TAGTAATTAG
* *
1722489 ATTAACTCTATGCATCCAGTCAATCTTACGAAAGTCGTAAGTTTAAACACCATGATACCTGGAA
1 ATTAACTCTATGCATCCAATCAATCTTACGAAAGTCGTAAGTTCAAACACCATGATACCTGGAA
** *
1722553 ATTAACTCTATGCATCCAATCAATCTTGTGAAAGTCTTAAGTTCAAACACCATGATACCTGGAA
1 ATTAACTCTATGCATCCAATCAATCTTACGAAAGTCGTAAGTTCAAACACCATGATACCTGGAA
1722617 A
1 A
1722618 GAAGCGATGA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (64 bp):
ATTAACTCTATGCATCCAATCAATCTTACGAAAGTCGTAAGTTCAAACACCATGATACCTGGAA
Found at i:1725879 original size:19 final size:20
Alignment explanation
Indices: 1725838--1725879 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
1725828 GTCATCGATT
* *
1725838 AAATTATACTAATTCAATTA
1 AAATTATACAAATTCAATAA
*
1725858 AAATTATA-AAATTTAATAA
1 AAATTATACAAATTCAATAA
1725877 AAA
1 AAA
1725880 ATTAATTATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATTATACAAATTCAATAA
Found at i:1726243 original size:13 final size:13
Alignment explanation
Indices: 1726208--1726233 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1726198 TTATAATCAC
1726208 ATATTAAATTATT
1 ATATTAAATTATT
1726221 ATATTAAATTATT
1 ATATTAAATTATT
1726234 TTTATTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATTAAATTATT
Found at i:1727102 original size:30 final size:29
Alignment explanation
Indices: 1727034--1727102 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
1727024 TAAAAGTAAA
* *
1727034 ATATATATAATTTTAAATATGATATAATT
1 ATATATAAAATTTTAAATATAATATAATT
*
1727063 ATATAATAAAATTTTAAATTATTAATATTATT
1 ATAT-ATAAAATTTTAAA-TA-TAATATAATT
1727095 -TATATAAA
1 ATATATAAA
1727103 TATATAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 4 0.12
30 17 0.50
31 5 0.15
32 8 0.24
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (29 bp):
ATATATAAAATTTTAAATATAATATAATT
Found at i:1727581 original size:20 final size:20
Alignment explanation
Indices: 1727539--1727578 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1727529 TTTTATTTAT
* *
1727539 TTTAAATTTTTTAATATAAA
1 TTTAAATTTATTAAAATAAA
1727559 TTTAAATTATATTAAAATAA
1 TTTAAATT-TATTAAAATAA
1727579 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAAATTTATTAAAATAAA
Found at i:1728568 original size:25 final size:26
Alignment explanation
Indices: 1728513--1728593 Score: 73
Period size: 25 Copynumber: 3.2 Consensus size: 26
1728503 ATGACTGTAT
* *
1728513 AATATAAATAATATTAAAAATAAT-T-
1 AATATAAAAAATA-TAAATATAATATG
*
1728538 AA-ATAATGAAATA-AAATATAATATG
1 AATATAA-AAAATATAAATATAATATG
*
1728563 -ATATAAAAAATATAAATATTATATG
1 AATATAAAAAATATAAATATAATATG
1728588 AATATA
1 AATATA
1728594 TAAATGTATC
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
23 8 0.18
24 11 0.24
25 21 0.47
26 5 0.11
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (26 bp):
AATATAAAAAATATAAATATAATATG
Found at i:1728607 original size:28 final size:27
Alignment explanation
Indices: 1728546--1728662 Score: 77
Period size: 25 Copynumber: 4.5 Consensus size: 27
1728536 TTAAATAATG
*
1728546 AAATA-AAATATAATATG-ATATA-AA
1 AAATATAAATATTATATGAATATATAA
1728570 AAATATAAATATTATATGAATATATAA
1 AAATATAAATATTATATGAATATATAA
** * *
1728597 ATGTATCAAAT-TTATATAAAATATATTAT
1 AAATAT-AAATATTATAT-GAATATA-TAA
* * * *
1728626 TAATATATATA-TAAAT-AAAATATAA
1 AAATATAAATATTATATGAATATATAA
1728651 AAATAT-AATATT
1 AAATATAAATATT
1728663 TTAAATATAA
Statistics
Matches: 71, Mismatches: 14, Indels: 15
0.71 0.14 0.15
Matches are distributed among these distances:
24 8 0.11
25 19 0.27
26 10 0.14
27 12 0.17
28 17 0.24
29 5 0.07
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.38
Consensus pattern (27 bp):
AAATATAAATATTATATGAATATATAA
Found at i:1728702 original size:11 final size:11
Alignment explanation
Indices: 1728510--1728711 Score: 65
Period size: 11 Copynumber: 18.5 Consensus size: 11
1728500 AATATGACTG
1728510 TATAATAT-AA
1 TATAATATAAA
1728520 -ATAATATTAAA
1 TATAATA-TAAA
*
1728531 AATAAT-T-AA
1 TATAATATAAA
*
1728540 -ATAAT-GAAA
1 TATAATATAAA
*
1728549 TAAAATAT-AA
1 TATAATATAAA
*
1728559 TATGATATAAA
1 TATAATATAAA
1728570 -A-AATATAAA
1 TATAATATAAA
*
1728579 TATTATATGAATA
1 TATAATAT-AA-A
1728592 TATAAATGTATCAAA
1 TAT-AA--TAT-AAA
*
1728607 T-TTATATAAAA
1 TATAATAT-AAA
* *
1728618 TATATTATTAA
1 TATAATATAAA
1728629 TATATATATAAA
1 TATA-ATATAAA
*
1728641 TAAAATATAAAAA
1 TATAATAT--AAA
**
1728654 TATAATAT-TT
1 TATAATATAAA
*
1728664 TA-AATATAAT
1 TATAATATAAA
1728674 TATTACATAATAAA
1 TA-TA-AT-ATAAA
1728688 -ATAATATAAA
1 TATAATATAAA
1728698 TATAAT-TAAA
1 TATAATATAAA
1728708 -ATAA
1 TATAA
1728712 ATTAATGATG
Statistics
Matches: 146, Mismatches: 22, Indels: 49
0.67 0.10 0.23
Matches are distributed among these distances:
8 5 0.03
9 26 0.18
10 30 0.21
11 32 0.22
12 22 0.15
13 18 0.12
14 6 0.04
15 2 0.01
16 5 0.03
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (11 bp):
TATAATATAAA
Found at i:1729237 original size:33 final size:33
Alignment explanation
Indices: 1729162--1729229 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
1729152 AGATGATATT
* ** *
1729162 TAAAAT-ATATAATTAATATATTTTTAATCTGA
1 TAAAATAATATAATAAATATATTTTTAAAATAA
1729194 TAAAATAATATAATAAATATATTTTTAAAATAA
1 TAAAATAATATAATAAATATATTTTTAAAATAA
1729227 TAA
1 TAA
1729230 TTTAATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 6 0.19
33 25 0.81
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (33 bp):
TAAAATAATATAATAAATATATTTTTAAAATAA
Found at i:1729660 original size:17 final size:18
Alignment explanation
Indices: 1729621--1729682 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 18
1729611 AATTTAACTA
**
1729621 ATTTATACTTTTATATCAT
1 ATTTATA-TTTTATAAAAT
1729640 ATTTATATTTTA-AAAAT
1 ATTTATATTTTATAAAAT
**
1729657 ATTTA-ATTTTATATTAT
1 ATTTATATTTTATAAAAT
1729674 ATTTATATT
1 ATTTATATT
1729683 ATATTTTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 6 0.16
17 16 0.43
18 8 0.22
19 7 0.19
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTATATTTTATAAAAT
Found at i:1729681 original size:23 final size:23
Alignment explanation
Indices: 1729655--1729719 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
1729645 TATTTTAAAA
1729655 ATATTTA-ATTTTATATTATATTT
1 ATATTTATATTTTATATTAT-TTT
1729678 ATA-TTATATTTTAATATT-TTTT
1 ATATTTATATTTT-ATATTATTTT
*
1729700 A-ATATTATATTTAATATTAT
1 ATAT-TTATATTTTATATTAT
1729720 CATACCTACT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
21 1 0.03
22 12 0.33
23 18 0.50
24 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
ATATTTATATTTTATATTATTTT
Found at i:1729701 original size:10 final size:11
Alignment explanation
Indices: 1729662--1729719 Score: 59
Period size: 12 Copynumber: 5.2 Consensus size: 11
1729652 AAAATATTTA
1729662 ATTTT-ATATT
1 ATTTTAATATT
1729672 ATATTT-ATATTAT
1 AT-TTTAATA-T-T
1729685 ATTTTAATATT
1 ATTTTAATATT
1729696 -TTTTAATATT
1 ATTTTAATATT
1729706 ATATTTAATATT
1 AT-TTTAATATT
1729718 AT
1 AT
1729720 CATACCTACT
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
10 12 0.29
11 8 0.19
12 16 0.38
13 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTTTAATATT
Found at i:1731048 original size:16 final size:16
Alignment explanation
Indices: 1731023--1731074 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1731013 TTGTGGCTAT
*
1731023 TATATTTAAAAATTTA
1 TATATATAAAAATTTA
*
1731039 TATATAT-AAATTTTA
1 TATATATAAAAATTTA
*
1731054 -ATATATTAATAATTTA
1 TATATA-TAAAAATTTA
1731070 TATAT
1 TATAT
1731075 TTATTATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 5 0.17
15 8 0.28
16 12 0.41
17 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATATAAAAATTTA
Found at i:1735833 original size:17 final size:17
Alignment explanation
Indices: 1735813--1735849 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1735803 TAATATTTAC
*
1735813 TTATTAAATAAACTTAA
1 TTATAAAATAAACTTAA
*
1735830 TTATAAAATAATCTTAA
1 TTATAAAATAAACTTAA
1735847 TTA
1 TTA
1735850 AATAATTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
TTATAAAATAAACTTAA
Found at i:1735855 original size:14 final size:14
Alignment explanation
Indices: 1735815--1735866 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
1735805 ATATTTACTT
*
1735815 ATTAAATAAACTTA
1 ATTAAATAATCTTA
1735829 ATTATAAAATAATCTTA
1 A-T-T-AAATAATCTTA
*
1735846 ATTAAATAATTCTCA
1 ATTAAATAA-TCTTA
1735861 ATTAAA
1 ATTAAA
1735867 ATTTAGATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 7 0.22
15 12 0.38
16 2 0.06
17 11 0.34
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTAAATAATCTTA
Found at i:1736957 original size:2 final size:2
Alignment explanation
Indices: 1736946--1736978 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1736936 AATTTGTGTG
*
1736946 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1736979 GCAGGTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1738791 original size:25 final size:25
Alignment explanation
Indices: 1738757--1738805 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
1738747 ATGATAGTTT
1738757 TCACTAGCTTTGATTCATTGTTAAA
1 TCACTAGCTTTGATTCATTGTTAAA
1738782 TCACTAGCTTTGATTCATTGTTAA
1 TCACTAGCTTTGATTCATTGTTAA
1738806 TTTCAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (25 bp):
TCACTAGCTTTGATTCATTGTTAAA
Found at i:1740073 original size:2 final size:2
Alignment explanation
Indices: 1740066--1740090 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1740056 TTCAGTTCAT
1740066 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 T
1740091 GTATTTTCAG
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1749854 original size:2 final size:2
Alignment explanation
Indices: 1749847--1749871 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1749837 TTCTAACTCT
1749847 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 T
1749872 TTAATCTCAT
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1752106 original size:29 final size:28
Alignment explanation
Indices: 1752057--1752127 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
1752047 AAAGGTTTTA
* * * *
1752057 ATTTTAAATTAATTATTATATTT-ATAT
1 ATTTTATATTTATAATTATATTTAAAAT
1752084 ATTTTACTATATTATAATTATATTTAAAAT
1 ATTTTA-TAT-TTATAATTATATTTAAAAT
1752114 ATTTTATATTTATA
1 ATTTTATATTTATA
1752128 TAAGTTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 6 0.16
28 7 0.19
29 15 0.41
30 9 0.24
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTTTATATTTATAATTATATTTAAAAT
Found at i:1752141 original size:45 final size:49
Alignment explanation
Indices: 1752072--1752165 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 49
1752062 AAATTAATTA
1752072 TTATATTTATATATTTTACTATATT-AT-AA-TTATATT-TA-AAATATT
1 TTATATTTATATATTTTAC-ATATTAATAAATTTATATTATATAAATATT
1752117 TTATATTTATATAAGTTTTA-ATATTAATAAATTTATATTATATAAATAT
1 TTATATTTATAT-A-TTTTACATATTAATAAATTTATATTATATAAATAT
1752166 AAAAAATTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
45 17 0.40
46 3 0.07
47 7 0.17
48 7 0.17
49 2 0.05
50 6 0.14
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (49 bp):
TTATATTTATATATTTTACATATTAATAAATTTATATTATATAAATATT
Found at i:1753579 original size:2 final size:2
Alignment explanation
Indices: 1753574--1753606 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1753564 ACACACACAC
*
1753574 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1753607 CAGATTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1767112 original size:13 final size:13
Alignment explanation
Indices: 1767094--1767119 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1767084 TAAATCATTT
1767094 AAATTAATTTTTA
1 AAATTAATTTTTA
1767107 AAATTAATTTTTA
1 AAATTAATTTTTA
1767120 TTAAAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAATTAATTTTTA
Found at i:1767825 original size:20 final size:20
Alignment explanation
Indices: 1767794--1767845 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1767784 TATTTAACAT
*
1767794 AAAATT-TTTAAAAAATTAA
1 AAAATTATTTAAAAAATAAA
**
1767813 ATTATTATTTAAAAAATAAA
1 AAAATTATTTAAAAAATAAA
1767833 AAAATTATTTAAA
1 AAAATTATTTAAA
1767846 TTTAATTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATTATTTAAAAAATAAA
Found at i:1768033 original size:2 final size:2
Alignment explanation
Indices: 1768026--1768060 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1768016 TTAGCAACTC
1768026 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1768061 GCTAACATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1768740 original size:18 final size:18
Alignment explanation
Indices: 1768719--1768753 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1768709 ATTAATCAAA
* *
1768719 TAATTATTTAAATTAAAT
1 TAATTAATTAAAGTAAAT
1768737 TAATTAATTAAAGTAAA
1 TAATTAATTAAAGTAAA
1768754 ATTCTCTAAT
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:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
TAATTAATTAAAGTAAAT
Found at i:1769392 original size:14 final size:15
Alignment explanation
Indices: 1769361--1769393 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1769351 TTTTGTTTTC
*
1769361 AATAAAAAAAGTTGA
1 AATAAAAAAAATTGA
1769376 AATAAAAAAAATT-A
1 AATAAAAAAAATTGA
1769390 AATA
1 AATA
1769394 TTATAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (15 bp):
AATAAAAAAAATTGA
Found at i:1769801 original size:142 final size:142
Alignment explanation
Indices: 1769545--1769827 Score: 566
Period size: 142 Copynumber: 2.0 Consensus size: 142
1769535 TGCAGGATAT
1769545 TCGTTTTATTTCCGTAAAATTCTGGATGGTGAGATGGTGAAGTATTATTATTATTAAGGTACTTA
1 TCGTTTTATTTCCGTAAAATTCTGGATGGTGAGATGGTGAAGTATTATTATTATTAAGGTACTTA
1769610 ATTGTTTGTCGCATTCGACAGTTACGACCCCATTAATGGAGATTCTAGGCTTCGCTCAACCTGTT
66 ATTGTTTGTCGCATTCGACAGTTACGACCCCATTAATGGAGATTCTAGGCTTCGCTCAACCTGTT
1769675 GTTCAAATTGCC
131 GTTCAAATTGCC
1769687 TCGTTTTATTTCCGTAAAATTCTGGATGGTGAGATGGTGAAGTATTATTATTATTAAGGTACTTA
1 TCGTTTTATTTCCGTAAAATTCTGGATGGTGAGATGGTGAAGTATTATTATTATTAAGGTACTTA
1769752 ATTGTTTGTCGCATTCGACAGTTACGACCCCATTAATGGAGATTCTAGGCTTCGCTCAACCTGTT
66 ATTGTTTGTCGCATTCGACAGTTACGACCCCATTAATGGAGATTCTAGGCTTCGCTCAACCTGTT
1769817 GTTCAAATTGC
131 GTTCAAATTGC
1769828 AATCCGCCAA
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 141 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (142 bp):
TCGTTTTATTTCCGTAAAATTCTGGATGGTGAGATGGTGAAGTATTATTATTATTAAGGTACTTA
ATTGTTTGTCGCATTCGACAGTTACGACCCCATTAATGGAGATTCTAGGCTTCGCTCAACCTGTT
GTTCAAATTGCC
Found at i:1770153 original size:2 final size:2
Alignment explanation
Indices: 1770146--1770177 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1770136 CTCAGTCTCA
1770146 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
1770178 CAACAATACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1773084 original size:23 final size:23
Alignment explanation
Indices: 1773058--1773107 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1773048 TATTATTGAT
*
1773058 ATTTATTATGATTTTTATTTTAA
1 ATTTATTATGAATTTTATTTTAA
* * *
1773081 ATTTTTTATTAATTTTATTTTTA
1 ATTTATTATGAATTTTATTTTAA
1773104 ATTT
1 ATTT
1773108 GATTTGTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (23 bp):
ATTTATTATGAATTTTATTTTAA
Found at i:1773096 original size:11 final size:12
Alignment explanation
Indices: 1773048--1773107 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
1773038 AATTATTTAG
*
1773048 TATTATTGATATT
1 TATTATTAAT-TT
* *
1773061 TATTATGATTTT
1 TATTATTAATTT
1773073 TATT-TTAAATTT
1 TATTATT-AATTT
1773085 T-TTATTAATTT
1 TATTATTAATTT
*
1773096 TATTTTTAATTT
1 TATTATTAATTT
1773108 GATTTGTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
11 9 0.24
12 22 0.58
13 7 0.18
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (12 bp):
TATTATTAATTT
Found at i:1773185 original size:20 final size:22
Alignment explanation
Indices: 1773144--1773186 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1773134 AAATTAAAAA
*
1773144 ATATATTTTTATACTAATATTT
1 ATATATTTTTATAATAATATTT
1773166 ATATA-TTTTATAATAA-ATTT
1 ATATATTTTTATAATAATATTT
1773186 A
1 A
1773187 ATTAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATATTTTTATAATAATATTT
Found at i:1775670 original size:16 final size:17
Alignment explanation
Indices: 1775645--1775681 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1775635 ACATCATTAG
1775645 TAAAAAA-TTTTAAAAT
1 TAAAAAATTTTTAAAAT
*
1775661 TAAAAGATTTTTAAAAT
1 TAAAAAATTTTTAAAAT
1775678 TAAA
1 TAAA
1775682 TATTTCATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TAAAAAATTTTTAAAAT
Found at i:1776801 original size:2 final size:2
Alignment explanation
Indices: 1776794--1776834 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1776784 GTATTTCTTT
1776794 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1776835 CTCTTTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1783687 original size:2 final size:2
Alignment explanation
Indices: 1783680--1783713 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1783670 ATTTATGTTT
1783680 TA 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
1783714 ATAAAGTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1784708 original size:18 final size:19
Alignment explanation
Indices: 1784667--1784708 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1784657 ATTCCTTTGC
1784667 AAAGAGGAAATGAGAACAA
1 AAAGAGGAAATGAGAACAA
*
1784686 TAAGAGGAAA-G-GTAACAA
1 AAAGAGGAAATGAG-AACAA
1784704 AAAGA
1 AAAGA
1784709 CCTACAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 10 0.50
19 9 0.45
ACGTcount: A:0.62, C:0.05, G:0.26, T:0.07
Consensus pattern (19 bp):
AAAGAGGAAATGAGAACAA
Found at i:1786825 original size:23 final size:23
Alignment explanation
Indices: 1786802--1786846 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
1786792 AACCCAGAAG
1786802 ATTAAACGACCAAACAA-AACAAGA
1 ATTAAA-GACC-AACAAGAACAAGA
*
1786826 ATTTAAGACCAACAAGAACAA
1 ATTAAAGACCAACAAGAACAA
1786847 AACTTACACT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 9 0.47
24 5 0.26
ACGTcount: A:0.60, C:0.20, G:0.09, T:0.11
Consensus pattern (23 bp):
ATTAAAGACCAACAAGAACAAGA
Found at i:1788104 original size:21 final size:20
Alignment explanation
Indices: 1788061--1788112 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1788051 ATAATTACAT
* **
1788061 TTAAATAAAAAATATTTTTA
1 TTAAATAAATAATATTTAAA
1788081 TTAAATAAATAATAATTTAAA
1 TTAAATAAATAAT-ATTTAAA
1788102 TTAAATCAAAT
1 TTAAAT-AAAT
1788113 TAAATTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 12 0.44
21 11 0.41
22 4 0.15
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAAATAAATAATATTTAAA
Found at i:1788379 original size:15 final size:16
Alignment explanation
Indices: 1788353--1788382 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1788343 ATCAATATTT
1788353 ATAATAATTAATTATG
1 ATAATAATTAATTATG
1788369 ATAAT-ATTAATTAT
1 ATAATAATTAATTAT
1788383 ATTTATAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAATAATTAATTATG
Found at i:1799795 original size:47 final size:47
Alignment explanation
Indices: 1799726--1799822 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
1799716 GGTTTGTTTA
1799726 TTTTTAAATATTTTGGGGAGGAATTATGGGATACAGTATACAGATTC
1 TTTTTAAATATTTTGGGGAGGAATTATGGGATACAGTATACAGATTC
1799773 TTTTTAAATATTTTGGGGAGGAATTATGGGATACAGTATACAGATTC
1 TTTTTAAATATTTTGGGGAGGAATTATGGGATACAGTATACAGATTC
1799820 TTT
1 TTT
1799823 CTGAGCCGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (47 bp):
TTTTTAAATATTTTGGGGAGGAATTATGGGATACAGTATACAGATTC
Found at i:1801060 original size:27 final size:26
Alignment explanation
Indices: 1801030--1801094 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 26
1801020 TTAAAATATA
1801030 TTATTTAAACTAT-TAATATATTTAAAT
1 TTATTTAAA-TATATAATAT-TTTAAAT
*
1801057 TTATATAAATATATAATATTTTAAAT
1 TTATTTAAATATATAATATTTTAAAT
*
1801083 ATATTTATAATA
1 TTATTTA-AATA
1801095 AAAAATATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 15 0.45
27 18 0.55
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
TTATTTAAATATATAATATTTTAAAT
Found at i:1801079 original size:20 final size:20
Alignment explanation
Indices: 1801056--1801094 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1801046 TATATTTAAA
*
1801056 TTTATATAAATATATAATAT
1 TTTAAATAAATATATAATAT
* *
1801076 TTTAAATATATTTATAATA
1 TTTAAATAAATATATAATA
1801095 AAAAATATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAAATAAATATATAATAT
Found at i:1802048 original size:21 final size:21
Alignment explanation
Indices: 1802024--1802081 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
1802014 ATCATTAATT
1802024 TTAATTTTATTATTATAAAAA
1 TTAATTTTATTATTATAAAAA
* *
1802045 TTAATCTTATTATTATAATAA
1 TTAATTTTATTATTATAAAAA
*
1802066 TTAATTTTATCATTAT
1 TTAATTTTATTATTAT
1802082 CATTATTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAATTTTATTATTATAAAAA
Found at i:1802295 original size:3 final size:3
Alignment explanation
Indices: 1802287--1802311 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1802277 CAATTTACCC
1802287 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
1802312 AAAAAGATCG
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1802642 original size:22 final size:22
Alignment explanation
Indices: 1802614--1802657 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1802604 AAAAAATATT
*
1802614 TTTTAT-ATTAAAATTTATATAA
1 TTTTATAATT-AAATTTAAATAA
1802636 TTTTATAATTAAATTTAAATAA
1 TTTTATAATTAAATTTAAATAA
1802658 AATAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTATAATTAAATTTAAATAA
Found at i:1809232 original size:8 final size:8
Alignment explanation
Indices: 1809207--1809247 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
1809197 ATCCAATAAT
1809207 GTATTTGA
1 GTATTTGA
*
1809215 GTGTTTTGA
1 GT-ATTTGA
1809224 GTATTTGA
1 GTATTTGA
1809232 GTATTTGA
1 GTATTTGA
*
1809240 GTGTTTGA
1 GTATTTGA
1809248 TCTTTTTGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 22 0.76
9 7 0.24
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (8 bp):
GTATTTGA
Found at i:1810545 original size:45 final size:45
Alignment explanation
Indices: 1810481--1810570 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
1810471 AGTTGATAAG
1810481 GACCAAAGATAGAAGTTAGAACTCAGAAGTATTTTAGAAAATTTT
1 GACCAAAGATAGAAGTTAGAACTCAGAAGTATTTTAGAAAATTTT
1810526 GACCAAAGATAGAAGTTAGAACTCAGAAGTATTTTAGAAAATTTT
1 GACCAAAGATAGAAGTTAGAACTCAGAAGTATTTTAGAAAATTTT
1810571 TAGACATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (45 bp):
GACCAAAGATAGAAGTTAGAACTCAGAAGTATTTTAGAAAATTTT
Found at i:1816962 original size:2 final size:2
Alignment explanation
Indices: 1816957--1816990 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1816947 GTTCTTGATC
* *
1816957 AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1816991 GTTAAAGCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1817435 original size:133 final size:133
Alignment explanation
Indices: 1817197--1817441 Score: 445
Period size: 133 Copynumber: 1.8 Consensus size: 133
1817187 TTCTTCGCTC
* *
1817197 GGACCCAGTAGTCAAGGTATAAATTGGGAGCCCCACATTGTAGCTTTGGATTGTTGCAAAGTCTT
1 GGACCCAGTAGTCAAGGTACAAATTGGGAGCCCCAAATTGTAGCTTTGGATTGTTGCAAAGTCTT
* *
1817262 TTTCTTGTTGGGTTAGCCTTTTCTTAGACGGTCCACAATCCTTAATACTATAGTTTGATAATTCA
66 TTTCTCGTTGGGTTAGCCTTTTCTTAGACGCTCCACAATCCTTAATACTATAGTTTGATAATTCA
1817327 TTT
131 TTT
*
1817330 GGACCCAGTAGTCAAGGTACAAATTGGGAGCCCCAAATTGTAGCTTTGGATTGTTGCAGAGTCTT
1 GGACCCAGTAGTCAAGGTACAAATTGGGAGCCCCAAATTGTAGCTTTGGATTGTTGCAAAGTCTT
1817395 TTTCTCGTTGGGTTAGCCTTTTCTTAGACGCTCCACAATCCTTAATA
66 TTTCTCGTTGGGTTAGCCTTTTCTTAGACGCTCCACAATCCTTAATA
1817442 ATACATTTTG
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
133 107 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.36
Consensus pattern (133 bp):
GGACCCAGTAGTCAAGGTACAAATTGGGAGCCCCAAATTGTAGCTTTGGATTGTTGCAAAGTCTT
TTTCTCGTTGGGTTAGCCTTTTCTTAGACGCTCCACAATCCTTAATACTATAGTTTGATAATTCA
TTT
Found at i:1823256 original size:2 final size:2
Alignment explanation
Indices: 1823251--1823278 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1823241 TGTATGTATG
1823251 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
1823279 GAAACATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1826340 original size:29 final size:28
Alignment explanation
Indices: 1826281--1826344 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
1826271 AATATATAAA
* *
1826281 TATTAATACAAAATAATATTTTATTATT
1 TATTAATACAAAATAAAATTTTAATATT
1826309 TATTAATA-ATAAATAAAAATTTTAATATT
1 TATTAATACA-AAAT-AAAATTTTAATATT
1826338 TATTAAT
1 TATTAAT
1826345 TAATGGTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 1 0.03
28 12 0.38
29 19 0.59
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
TATTAATACAAAATAAAATTTTAATATT
Found at i:1830918 original size:22 final size:21
Alignment explanation
Indices: 1830893--1830968 Score: 90
Period size: 21 Copynumber: 3.8 Consensus size: 21
1830883 TAGAACTCAT
1830893 TATTAAATATTATTTTTTTATA
1 TATTAAATATT-TTTTTTTATA
*
1830915 TATTAAATATTTTATTTTA-A
1 TATTAAATATTTTTTTTTATA
*
1830935 T-TT--ATA-TTATTTTTATA
1 TATTAAATATTTTTTTTTATA
1830952 TATTAAATATTTTTTTT
1 TATTAAATATTTTTTTT
1830969 ATTTTTATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
16 7 0.16
17 5 0.11
18 2 0.04
19 2 0.04
20 5 0.11
21 13 0.29
22 11 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTAAATATTTTTTTTTATA
Found at i:1830964 original size:17 final size:17
Alignment explanation
Indices: 1830907--1830965 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
1830897 AAATATTATT
1830907 TTTTTATATATTAAATA
1 TTTTTATATATTAAATA
* *
1830924 -TTTTATTTTAATTTATATTA
1 TTTTTA-TAT-A-TTA-AATA
1830944 TTTTTATATATTAAATA
1 TTTTTATATATTAAATA
1830961 TTTTT
1 TTTTT
1830966 TTTATTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
16 5 0.15
17 10 0.30
18 4 0.12
19 4 0.12
20 5 0.15
21 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTATATATTAAATA
Found at i:1830988 original size:37 final size:37
Alignment explanation
Indices: 1830910--1830989 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
1830900 TATTATTTTT
* ***
1830910 TTATATATTAAATATTTTATTTTAATTTATATTATTT
1 TTATATATTAAATATTTTATTTTAATTTATACTAAAA
*
1830947 TTATATATTAAATATTTT-TTTTATTTTTATACTAAAA
1 TTATATATTAAATATTTTATTTTA-ATTTATACTAAAA
1830984 TTATAT
1 TTATAT
1830990 TAAAAATATT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 5 0.14
37 32 0.86
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (37 bp):
TTATATATTAAATATTTTATTTTAATTTATACTAAAA
Found at i:1831024 original size:32 final size:31
Alignment explanation
Indices: 1830980--1831049 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 31
1830970 TTTTTATACT
*
1830980 AAAATTATATTAAAAAT-ATTAAAATTAATTG
1 AAAATTACATTAAAAATCATTAAAA-TAATTG
* *
1831011 ATAAATTACATTAAATATCATTAAAATAATTT
1 A-AAATTACATTAAAAATCATTAAAATAATTG
1831043 AAAATTA
1 AAAATTA
1831050 TTATAATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 7 0.21
32 20 0.59
33 7 0.21
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (31 bp):
AAAATTACATTAAAAATCATTAAAATAATTG
Found at i:1831477 original size:30 final size:30
Alignment explanation
Indices: 1831416--1831477 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1831406 TTATTTTTTA
*
1831416 TTTTAAATATATTTAAAATATAAAATTATT
1 TTTTAAATATATTTAAAATATAAAATAATT
*
1831446 TTTTAATTATATTTATAAA-ATTAAAA-AATT
1 TTTTAAATATATTTA-AAATA-TAAAATAATT
1831476 TT
1 TT
1831478 ACTATACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTTAAATATATTTAAAATATAAAATAATT
Found at i:1834037 original size:15 final size:15
Alignment explanation
Indices: 1833999--1834042 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1833989 GGCTTCATAT
* *
1833999 TATATTTTTTTATAA
1 TATATTTTTTAAAAA
* *
1834014 TTTAGTTTTTAAAAA
1 TATATTTTTTAAAAA
1834029 TATATTTTTTAAAA
1 TATATTTTTTAAAA
1834043 TTTAATCTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
TATATTTTTTAAAAA
Found at i:1834179 original size:12 final size:13
Alignment explanation
Indices: 1834149--1834181 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
1834139 ATTTTTTATT
1834149 ATATAAAATATATA
1 ATAT-AAATATATA
1834163 ATATAAATATA-A
1 ATATAAATATATA
1834175 ATATAAA
1 ATATAAA
1834182 ATTAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 7 0.37
14 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
ATATAAATATATA
Found at i:1834308 original size:13 final size:14
Alignment explanation
Indices: 1834280--1834312 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1834270 AACTGAGCGT
*
1834280 AATTTTTTTATTTA
1 AATTTATTTATTTA
1834294 AATTTATTT-TTTA
1 AATTTATTTATTTA
1834307 AATTTA
1 AATTTA
1834313 ATATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATTTATTTATTTA
Found at i:1834311 original size:19 final size:19
Alignment explanation
Indices: 1834289--1834330 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1834279 TAATTTTTTT
*
1834289 ATTTAA-ATTTATTTTTTAA
1 ATTTAATATTT-TTATTTAA
1834308 ATTTAATATTTTTATTTAA
1 ATTTAATATTTTTATTTAA
1834327 ATTT
1 ATTT
1834331 TTTGAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTAATATTTTTATTTAA
Found at i:1842214 original size:17 final size:17
Alignment explanation
Indices: 1842192--1842225 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1842182 CATGTCCACC
1842192 TCACGCACGCCCCTCAG
1 TCACGCACGCCCCTCAG
*
1842209 TCACGCACGCCTCTCAG
1 TCACGCACGCCCCTCAG
1842226 ACCAAGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.50, G:0.18, T:0.15
Consensus pattern (17 bp):
TCACGCACGCCCCTCAG
Found at i:1842374 original size:12 final size:13
Alignment explanation
Indices: 1842357--1842385 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1842347 TTCCTTCCGA
1842357 CAAAACC-AAAAC
1 CAAAACCAAAAAC
1842369 CAAAACCAAAAAC
1 CAAAACCAAAAAC
1842382 CAAA
1 CAAA
1842386 CAAGAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAACCAAAAAC
Found at i:1849118 original size:26 final size:26
Alignment explanation
Indices: 1849071--1849123 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1849061 TTTTATGTAA
*
1849071 ATTTTATATATTTTATATAATATAAT
1 ATTTTATATATTTTATATAATAGAAT
* *
1849097 ATTTT-TATTTTTTATTTGAATAGAAT
1 ATTTTATATATTTTATAT-AATAGAAT
1849123 A
1 A
1849124 AATTTTAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (26 bp):
ATTTTATATATTTTATATAATAGAAT
Found at i:1853993 original size:16 final size:16
Alignment explanation
Indices: 1853972--1854005 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1853962 GCTGTAAGCA
1853972 TTGTCGTGCTCTGTGG
1 TTGTCGTGCTCTGTGG
1853988 TTGTCGTGCTCTGTGG
1 TTGTCGTGCTCTGTGG
1854004 TT
1 TT
1854006 ATCAGATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.18, G:0.35, T:0.47
Consensus pattern (16 bp):
TTGTCGTGCTCTGTGG
Found at i:1854523 original size:23 final size:23
Alignment explanation
Indices: 1854492--1854552 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
1854482 AGTTAATATT
*
1854492 TATTATTATTCATTTAA-TAAAAA
1 TATTATTA-TAATTTAATTAAAAA
* *
1854515 TATTTTTATAATTTAATTATAAA
1 TATTATTATAATTTAATTAAAAA
1854538 TATATATATATAATT
1 TAT-TAT-TATAATT
1854553 ATTAATATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 7 0.23
23 15 0.48
24 2 0.06
25 7 0.23
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTATTATAATTTAATTAAAAA
Found at i:1854961 original size:14 final size:14
Alignment explanation
Indices: 1854940--1854984 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
1854930 TATTATCTAA
1854940 TAAA-TTTAATATT
1 TAAATTTTAATATT
1854953 TAAATTTTAATATT
1 TAAATTTTAATATT
*
1854967 TATAATTTT-TTATT
1 TA-AATTTTAATATT
1854981 TAAA
1 TAAA
1854985 ATTGTGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 6 0.21
14 17 0.59
15 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TAAATTTTAATATT
Found at i:1855939 original size:2 final size:2
Alignment explanation
Indices: 1855932--1855967 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1855922 GCAAGTGTAC
1855932 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
1855968 TCATTGATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1859185 original size:19 final size:19
Alignment explanation
Indices: 1859161--1859200 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1859151 CCATATCTGA
*
1859161 CTATATGACAGACATAAGT
1 CTATATGACAAACATAAGT
*
1859180 CTATATGACAAACATATGT
1 CTATATGACAAACATAAGT
1859199 CT
1 CT
1859201 CAAACAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.30
Consensus pattern (19 bp):
CTATATGACAAACATAAGT
Found at i:1860674 original size:16 final size:16
Alignment explanation
Indices: 1860655--1860689 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1860645 AGCTCTGGTT
1860655 CAAAACAACACATTCA
1 CAAAACAACACATTCA
* *
1860671 CAAAACAACTCATTTA
1 CAAAACAACACATTCA
1860687 CAA
1 CAA
1860690 TAGCACATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.29, G:0.00, T:0.17
Consensus pattern (16 bp):
CAAAACAACACATTCA
Found at i:1866821 original size:5 final size:5
Alignment explanation
Indices: 1866800--1866832 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1866790 ATAAGTTAGA
*
1866800 AAAAT -AAAT AAAGT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1866833 AGAAATAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1867738 original size:9 final size:9
Alignment explanation
Indices: 1867725--1867767 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
1867715 TGTGCAAGTA
*
1867725 TAAATATAA
1 TAAATATAT
*
1867734 TAAATTTAT
1 TAAATATAT
1867743 TAAATATAT
1 TAAATATAT
*
1867752 TAAATTTAT
1 TAAATATAT
1867761 TAAATAT
1 TAAATAT
1867768 TTTTAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TAAATATAT
Found at i:1867782 original size:19 final size:18
Alignment explanation
Indices: 1867725--1867767 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1867715 TGTGCAAGTA
*
1867725 TAAATATAATAAATTTAT
1 TAAATATATTAAATTTAT
1867743 TAAATATATTAAATTTAT
1 TAAATATATTAAATTTAT
1867761 TAAATAT
1 TAAATAT
1867768 TTTTAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATATATTAAATTTAT
Found at i:1870948 original size:12 final size:12
Alignment explanation
Indices: 1870933--1870965 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1870923 GAGTATTAAA
1870933 ATTGTTATTATT
1 ATTGTTATTATT
1870945 ATTGTTATTATT
1 ATTGTTATTATT
*
1870957 ATTATTATT
1 ATTGTTATT
1870966 TAAACAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (12 bp):
ATTGTTATTATT
Found at i:1874472 original size:2 final size:2
Alignment explanation
Indices: 1874465--1874504 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1874455 ACGACAAAGC
* *
1874465 AG AG AG AG AG AG AG AG AG AG AG AG AG AG TG AG TG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1874505 TTTCTGCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.50, T:0.05
Consensus pattern (2 bp):
AG
Found at i:1877095 original size:33 final size:32
Alignment explanation
Indices: 1877053--1877130 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
1877043 TTATATTTAA
*
1877053 AATATTTTATATTTATATAAATTTTAACATATT
1 AATAATTTATATTTATATAAATTTTAACAT-TT
*
1877086 AATAATTTATA-TTATATAAATTTTAATATTT
1 AATAATTTATATTTATATAAATTTTAACATTT
1877117 ATATATATTTATAT
1 A-ATA-ATTTATAT
1877131 CATATTGATA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
31 3 0.08
32 20 0.50
33 17 0.43
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (32 bp):
AATAATTTATATTTATATAAATTTTAACATTT
Found at i:1877118 original size:18 final size:17
Alignment explanation
Indices: 1877043--1877130 Score: 73
Period size: 16 Copynumber: 5.4 Consensus size: 17
1877033 TTTATTATTA
1877043 TTATATTTA-A-AATATT
1 TTATATTTATATAA-ATT
1877059 TTATATTTATATAAATT
1 TTATATTTATATAAATT
*
1877076 TTAACATATTA-AT-AA-T
1 TT-ATAT-TTATATAAATT
1877092 TTATA-TTATATAAATT
1 TTATATTTATATAAATT
*
1877108 TTAATATTTATATATA-T
1 TT-ATATTTATATAAATT
1877125 TTATAT
1 TTATAT
1877131 CATATTGATA
Statistics
Matches: 60, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
13 3 0.05
14 2 0.03
15 4 0.07
16 19 0.32
17 14 0.23
18 15 0.25
19 3 0.05
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:1877141 original size:27 final size:26
Alignment explanation
Indices: 1877040--1877142 Score: 74
Period size: 27 Copynumber: 4.0 Consensus size: 26
1877030 ATTTTTATTA
* *
1877040 TTAT-TATATTTA-AAATATTTTATAT
1 TTATATATATTTATACATA-TTAATAT
*
1877065 TTATATAAATTT-TAACATATTAATAAT
1 TTATATATATTTAT-ACATATTAAT-AT
* *
1877092 TTATAT-TA--TATAAATTTTAATAT
1 TTATATATATTTATACATATTAATAT
*
1877115 TTATATATATTTATATCATATTGATAT
1 TTATATATATTTATA-CATATTAATAT
1877142 T
1 T
1877143 ATTATTTAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
23 8 0.13
24 11 0.18
25 5 0.08
26 15 0.25
27 21 0.35
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (26 bp):
TTATATATATTTATACATATTAATAT
Found at i:1877168 original size:16 final size:19
Alignment explanation
Indices: 1877107--1877171 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 19
1877097 TTATATAAAT
*
1877107 TTTAATATTTATATATATTTA
1 TTTAATATTGATAT-TA-TTA
* *
1877128 TATCATATTGATATTATTA
1 TTTAATATTGATATTATTA
1877147 TTTAATATT-ATATT-TT-
1 TTTAATATTGATATTATTA
1877163 TTTAATATT
1 TTTAATATT
1877172 TTAATTAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
16 9 0.23
17 2 0.05
18 5 0.13
19 10 0.26
20 2 0.05
21 11 0.28
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTAATATTGATATTATTA
Found at i:1878714 original size:19 final size:19
Alignment explanation
Indices: 1878649--1878715 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
1878639 ATTGATTAAA
* * *
1878649 ATATAATATAATATAA-TA
1 ATATAATATATTAAAATTT
* *
1878667 ATATAAATACATTATAAATAT
1 ATAT-AATATATTA-AAATTT
1878688 A-ATAATATATTAAAATTT
1 ATATAATATATTAAAATTT
1878706 ATATAATATA
1 ATATAATATA
1878716 AATTATTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
18 10 0.26
19 23 0.61
20 4 0.11
21 1 0.03
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATAATATATTAAAATTT
Found at i:1891514 original size:23 final size:22
Alignment explanation
Indices: 1891465--1891514 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
1891455 TAATATGATG
*
1891465 AAAAA-ATTATAATATTTATCA
1 AAAAATATTATAAAATTTATCA
1891486 AAAAATATTATTAAAATTTAT-A
1 AAAAATATTA-TAAAATTTATCA
1891508 AATAAAT
1 AA-AAAT
1891515 TTAACAGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 5 0.20
22 7 0.28
23 13 0.52
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAAATATTATAAAATTTATCA
Found at i:1892079 original size:2 final size:2
Alignment explanation
Indices: 1892072--1892101 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1892062 TTCTGACTCT
1892072 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1892102 TCCAAGCTAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1893604 original size:27 final size:25
Alignment explanation
Indices: 1893558--1893616 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 25
1893548 ATCTAAATTT
1893558 TTTAATAAATAAAAAATTTTAAATA
1 TTTAATAAATAAAAAATTTTAAATA
* * *
1893583 TTTAATTAATATAAATACTTTTTAATA
1 TTTAA-TAA-ATAAAAAATTTTAAATA
*
1893610 TTAAATA
1 TTTAATA
1893617 TATTTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 5 0.18
26 5 0.18
27 18 0.64
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TTTAATAAATAAAAAATTTTAAATA
Found at i:1893737 original size:16 final size:18
Alignment explanation
Indices: 1893699--1893740 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
1893689 TAAATATAAT
1893699 TATATT-ATTTAATTTAA
1 TATATTAATTTAATTTAA
1893716 TA-ATTAATTT-A-TTAA
1 TATATTAATTTAATTTAA
1893731 TATATTAATT
1 TATATTAATT
1893741 ATATATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 6 0.26
16 11 0.48
17 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATTAATTTAATTTAA
Found at i:1894034 original size:28 final size:28
Alignment explanation
Indices: 1893979--1894054 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
1893969 TAGAATATTT
** *
1893979 AATTAATTGTAATA-ATTATTTTATTATG
1 AATTAATT-TAATATATTATAATAATATG
1894007 AATTAATTTAATATATTATAATAATATG
1 AATTAATTTAATATATTATAATAATATG
*
1894035 --TTAATTTAATTTATTA-AATA
1 AATTAATTTAATATATTATAATA
1894055 TTTATTTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
25 4 0.09
26 15 0.35
27 5 0.12
28 19 0.44
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (28 bp):
AATTAATTTAATATATTATAATAATATG
Found at i:1894180 original size:16 final size:16
Alignment explanation
Indices: 1894161--1894210 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1894151 TAAAAGATTT
1894161 AAATTTATTTTATTAA
1 AAATTTATTTTATTAA
1894177 AAATTTAAATTTTA-TAA
1 AAATTT--ATTTTATTAA
* *
1894194 AATTTTATTTCATTAA
1 AAATTTATTTTATTAA
1894210 A
1 A
1894211 TCAAATTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 5 0.17
16 10 0.34
17 8 0.28
18 6 0.21
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
AAATTTATTTTATTAA
Found at i:1894200 original size:17 final size:18
Alignment explanation
Indices: 1894167--1894200 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1894157 ATTTAAATTT
1894167 ATTTTATTAAAAATTTAA
1 ATTTTATTAAAAATTTAA
*
1894185 ATTTTA-TAAAATTTTA
1 ATTTTATTAAAAATTTA
1894201 TTTCATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTATTAAAAATTTAA
Found at i:1894289 original size:16 final size:16
Alignment explanation
Indices: 1894270--1894300 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1894260 TAAAAAATAA
1894270 TTATTTTATTATAATT
1 TTATTTTATTATAATT
*
1894286 TTATTTTATTTTAAT
1 TTATTTTATTATAAT
1894301 AAATTAAATA
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTTATTATAATT
Found at i:1894297 original size:38 final size:39
Alignment explanation
Indices: 1894257--1894343 Score: 97
Period size: 38 Copynumber: 2.2 Consensus size: 39
1894247 CTCTAAATAT
* *
1894257 TTTTAA-AAAATAATTATTTTATT-ATAATTTTATTTTA
1 TTTTAATAAAATAAATATATTATTAATAATTTTATTTTA
* *
1894294 TTTTAATAAATTAAATATATTATTAATTATTTTATTATTGA
1 TTTTAATAAAATAAATATATTATTAATAATTTTATT-TT-A
*
1894335 TTTCAATAA
1 TTTTAATAA
1894344 TATTATAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
37 6 0.15
38 14 0.34
39 10 0.24
40 2 0.05
41 9 0.22
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (39 bp):
TTTTAATAAAATAAATATATTATTAATAATTTTATTTTA
Found at i:1900126 original size:2 final size:2
Alignment explanation
Indices: 1900119--1900157 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1900109 ATGGGATTGC
1900119 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1900158 GCGCAAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1902873 original size:34 final size:34
Alignment explanation
Indices: 1902827--1902895 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
1902817 ATGCACATTA
* *
1902827 TCAGTTACATGGTAAAGATACATGGAATTTTAGC
1 TCAGTTACATGGTAAAGATACATAGAATTTGAGC
*
1902861 TCAGTTATATGGTAAAGATACATAGAATTTGAGC
1 TCAGTTACATGGTAAAGATACATAGAATTTGAGC
1902895 T
1 T
1902896 GGTTTATTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.33
Consensus pattern (34 bp):
TCAGTTACATGGTAAAGATACATAGAATTTGAGC
Found at i:1904969 original size:42 final size:42
Alignment explanation
Indices: 1904910--1904994 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
1904900 GTCTCAAAAT
1904910 GCATGAATTCCTTCACTTGGTACAATATTTCTTTGCTTGTAC
1 GCATGAATTCCTTCACTTGGTACAATATTTCTTTGCTTGTAC
1904952 GCATGAATTCCTTCACTTGGTACAATATTTCTTTGCTTGTAC
1 GCATGAATTCCTTCACTTGGTACAATATTTCTTTGCTTGTAC
1904994 G
1 G
1904995 TATATGTGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.42
Consensus pattern (42 bp):
GCATGAATTCCTTCACTTGGTACAATATTTCTTTGCTTGTAC
Found at i:1904970 original size:22 final size:22
Alignment explanation
Indices: 1904910--1904970 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 22
1904900 GTCTCAAAAT
1904910 GCATGAATTCCTTCACTTGGTAC
1 GCATGAATTCCTTCACTT-GTAC
* * **
1904933 -AAT--ATTTCTTTGCTTGTAC
1 GCATGAATTCCTTCACTTGTAC
1904952 GCATGAATTCCTTCACTTG
1 GCATGAATTCCTTCACTTG
1904971 GTACAATATT
Statistics
Matches: 27, Mismatches: 8, Indels: 7
0.64 0.19 0.17
Matches are distributed among these distances:
19 4 0.15
20 11 0.41
22 12 0.44
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (22 bp):
GCATGAATTCCTTCACTTGTAC
Found at i:1904999 original size:20 final size:20
Alignment explanation
Indices: 1904929--1904999 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
1904919 CCTTCACTTG
1904929 GTAC-AATATTTCTTTGCTT
1 GTACGAATATTTCTTTGCTT
* * **
1904948 GTACGCATGAATTCCTTCACTT
1 GTACGAAT--ATTTCTTTGCTT
1904970 GGTAC-AATATTTCTTTGCTT
1 -GTACGAATATTTCTTTGCTT
*
1904990 GTACGTATAT
1 GTACGAATAT
1905000 GTGTGTGTGT
Statistics
Matches: 38, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
19 8 0.21
20 15 0.39
22 11 0.29
23 4 0.11
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (20 bp):
GTACGAATATTTCTTTGCTT
Done.