Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 110 of 297
Found at i:39455360 original size:48 final size:48
Alignment explanation
Indices: 39455308--39455486 Score: 148
Period size: 48 Copynumber: 3.7 Consensus size: 48
39455298 TAAAGTACCA
* * *
39455308 ATGCCATGTCCCCGACATGGTCTTACA-T-GAATCCACATATCAACACTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCA--CACATATCAACACCG
** * * *
39455356 ATGCCATGTCTTAGATATGGTCTTACACTGGCACAGATATCATCACCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACACCG
* * * * * *
39455404 ATTCCATGTCCCAGACATGGTCTTACACAT-GCTCATATATCATCGCTG
1 ATGCCATGTCCCAGACATGGTCTTACAC-TGGCACACATATCAACACCG
* * * *
39455452 ATGCCATGTCCTAGATATGGTTTTACACAGGCACA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACA
39455487 TTTAGCACAG
Statistics
Matches: 105, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
48 101 0.96
49 2 0.02
50 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACACCG
Found at i:39455478 original size:96 final size:96
Alignment explanation
Indices: 39455311--39455486 Score: 248
Period size: 96 Copynumber: 1.8 Consensus size: 96
39455301 AGTACCAATG
* *
39455311 CCATGTCCCCGACATGGTCTTACATGAATCCACATATCAACACTGATGCCATGTCTTAGATATGG
1 CCATGTCCCAGACATGGTCTTACATGAATCCACATATCAACACTGATGCCATGTCCTAGATATGG
*
39455376 TCTTACACTGGCACAGATATCATCACCGATT
66 TCTTACACAGGCACAGATATCATCACCGATT
* * * *
39455407 CCATGTCCCAGACATGGTCTTACA--CATGCTCATATATCATCGCTGATGCCATGTCCTAGATAT
1 CCATGTCCCAGACATGGTCTTACATGAAT-C-CACATATCAACACTGATGCCATGTCCTAGATAT
*
39455470 GGTTTTACACAGGCACA
64 GGTCTTACACAGGCACA
39455487 TTTAGCACAG
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
94 2 0.03
95 1 0.01
96 67 0.96
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.28
Consensus pattern (96 bp):
CCATGTCCCAGACATGGTCTTACATGAATCCACATATCAACACTGATGCCATGTCCTAGATATGG
TCTTACACAGGCACAGATATCATCACCGATT
Found at i:39460235 original size:48 final size:48
Alignment explanation
Indices: 39460056--39460234 Score: 220
Period size: 48 Copynumber: 3.7 Consensus size: 48
39460046 TAAAGTACCA
** **
39460056 ATGCCATGTCCCCGACATGGTCTTACATGAATC-CACATATCATTGCTG
1 ATGCCATGTCCCAAACATGGTCTTACAT-AGGCACACATATCATTGCTG
* * *
39460104 ATTG-CATGTCCCAGACATGGTCTTACACT-GGCACGCATATCATCGCTG
1 A-TGCCATGTCCCAAACATGGTCTTACA-TAGGCACACATATCATTGCTG
* * *
39460152 ATGCCATGTCCCAAACATGGTCTTACACAGGCACATATATCATTGCCG
1 ATGCCATGTCCCAAACATGGTCTTACATAGGCACACATATCATTGCTG
39460200 ATGCCATGTCCCAAACATGGTCTTACATAGGCACA
1 ATGCCATGTCCCAAACATGGTCTTACATAGGCACA
39460235 TTTAGCACAG
Statistics
Matches: 114, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
47 3 0.03
48 108 0.95
49 3 0.03
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAAACATGGTCTTACATAGGCACACATATCATTGCTG
Found at i:39473423 original size:37 final size:37
Alignment explanation
Indices: 39473365--39473440 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
39473355 TTACGAAGTA
* *
39473365 TTACCCGGACATAATCTCCACACGAAGTTATCGGGTC
1 TTACCCGGACAAAATCTCCACACGAAGTCATCGGGTC
*
39473402 TTACCCGGACAAAAT-TCCCACACGTAGTCATCGGGTC
1 TTACCCGGACAAAATCT-CCACACGAAGTCATCGGGTC
39473439 TT
1 TT
39473441 TAGAGCTCGG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
36 1 0.03
37 34 0.97
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.25
Consensus pattern (37 bp):
TTACCCGGACAAAATCTCCACACGAAGTCATCGGGTC
Found at i:39473661 original size:47 final size:47
Alignment explanation
Indices: 39473559--39474032 Score: 752
Period size: 47 Copynumber: 10.1 Consensus size: 47
39473549 CCCTTCGGGA
* * * * * * * *
39473559 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* * *
39473606 CCTGTCACATATATACACTTTCACATTCA-CACGTCGGCCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGG-CTATTAGGC
39473653 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
39473700 CTTATCACAGATCTACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
39473747 CTTATCACAGATCTACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
39473794 CTTATCACAGATCTACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
39473841 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
39473888 CTTATCACAGATCTACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
39473935 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
39473982 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
39474029 CTTA
1 CTTA
39474033 CTATCATTTC
Statistics
Matches: 404, Mismatches: 21, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
46 7 0.02
47 390 0.97
48 7 0.02
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
Found at i:39483944 original size:27 final size:28
Alignment explanation
Indices: 39483914--39483970 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
39483904 ATTTTTGATG
39483914 AAATGAGCTATTTG-GG-CTAATTTGTGA
1 AAATGAGCT-TTTGAGGACTAATTTGTGA
*
39483941 AAATGAGGTTTTGAAGGACTAATTTGTGA
1 AAATGAGCTTTTG-AGGACTAATTTGTGA
39483970 A
1 A
39483971 TTTAACATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 4 0.15
27 8 0.31
28 2 0.08
29 12 0.46
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (28 bp):
AAATGAGCTTTTGAGGACTAATTTGTGA
Found at i:39485874 original size:27 final size:27
Alignment explanation
Indices: 39485845--39485963 Score: 157
Period size: 27 Copynumber: 4.4 Consensus size: 27
39485835 AGGGCAAAAT
* *
39485845 GGTAATTTTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
39485872 GGTATTTCTACCTTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
39485899 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** *
39485926 AATAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
39485953 GGTAATTCTAC
1 GGTAATTCTAC
39485964 AACTTATCCA
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:39485903 original size:54 final size:54
Alignment explanation
Indices: 39485845--39485963 Score: 175
Period size: 54 Copynumber: 2.2 Consensus size: 54
39485835 AGGGCAAAAT
* *** *
39485845 GGTAATTTTACCCTACAGGGGTATTTTGGTATTTCTACCTTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCTTACAAGGGTATTTC
* *
39485899 GGTAATTCTACCCTATAGGGGTATTTCAATAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCTTACAAGGGTATTTC
39485953 GGTAATTCTAC
1 GGTAATTCTAC
39485964 AACTTATCCA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (54 bp):
GGTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCTTACAAGGGTATTTC
Found at i:39493582 original size:27 final size:28
Alignment explanation
Indices: 39493552--39493608 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
39493542 ATTTTTGATG
39493552 AAATGAGCTATTT-AGG-CTAATTTGTGA
1 AAATGAGCT-TTTAAGGACTAATTTGTGA
*
39493579 AAATGAGGTTTTGAAGGACTAATTTGTGA
1 AAATGAGCTTTT-AAGGACTAATTTGTGA
39493608 A
1 A
39493609 TTTAACATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 3 0.12
27 8 0.31
28 3 0.12
29 12 0.46
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (28 bp):
AAATGAGCTTTTAAGGACTAATTTGTGA
Found at i:39506530 original size:10 final size:10
Alignment explanation
Indices: 39506517--39506542 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
39506507 AAAATTGTAG
39506517 AAATGGAATT
1 AAATGGAATT
39506527 AAATGGAATT
1 AAATGGAATT
39506537 AAATGG
1 AAATGG
39506543 TGAATGAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (10 bp):
AAATGGAATT
Found at i:39507573 original size:52 final size:50
Alignment explanation
Indices: 39507493--39507677 Score: 165
Period size: 50 Copynumber: 3.6 Consensus size: 50
39507483 TGAGAACATT
** * ** *
39507493 TGTGTAGTACTATCTGCAGGCTATTATGTGTTTAAAATGGTTTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAAATGG--TTAGGTCACA
* * **
39507545 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGGTTAGGTTGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAAATGGTTAGGTCACA
* * * * * *
39507595 TGTGTAGTACTAAGTGCAGGCTACTATGAGTACCCGATAT-CTTTGATCACA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTA--CAAAATGGTTAGGTCACA
* *
39507646 TGTGTGGTACTAAGTGCAGGCCACTATGTGTA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTA
39507678 AAAGATAGCT
Statistics
Matches: 110, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
50 38 0.35
51 35 0.32
52 37 0.34
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.34
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAAATGGTTAGGTCACA
Found at i:39507610 original size:50 final size:51
Alignment explanation
Indices: 39507535--39507688 Score: 175
Period size: 50 Copynumber: 3.0 Consensus size: 51
39507525 TAAAATGGTT
* * *
39507535 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAT-GG
1 TTAGATCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGC
* ** * * *
39507585 TTAGGTTGCATGTGTAGTACTAAGTGCAGGCTACTATGAGTACCCGATATC
1 TTAGATCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGC
* * * **
39507636 TTTGATCACATGTGTGGTACTAAGTGCAGGCCACTATGTGTAAAAGATAGC
1 TTAGATCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGC
39507687 TT
1 TT
39507689 TGGTCACGAG
Statistics
Matches: 85, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
50 43 0.51
51 42 0.49
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (51 bp):
TTAGATCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGC
Found at i:39507707 original size:51 final size:51
Alignment explanation
Indices: 39507493--39507695 Score: 192
Period size: 51 Copynumber: 4.0 Consensus size: 51
39507483 TGAGAACATT
** * *** * * * *
39507493 TGTGTAGTACTATCTGCAGGCTATTATGTGTTTAAAATGGTTTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCTTT-GGTCACA
* * **
39507545 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAT-GGTTAGGTTGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCTTTGGTCACA
* * * *
39507595 TGTGTAGTACTAAGTGCAGGCTACTATGAGTACCCGATATCTTTGATCACA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCTTTGGTCACA
* * **
39507646 TGTGTGGTACTAAGTGCAGGCCACTATGTGTAAAAGATAGCTTTGGTCAC
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCTTTGGTCAC
39507696 GAGTGTGGTA
Statistics
Matches: 122, Mismatches: 28, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
50 40 0.33
51 51 0.42
52 31 0.25
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.33
Consensus pattern (51 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCTTTGGTCACA
Found at i:39507720 original size:51 final size:51
Alignment explanation
Indices: 39507593--39507759 Score: 122
Period size: 51 Copynumber: 3.3 Consensus size: 51
39507583 GGTTAGGTTG
* * * * * *** *
39507593 CATGTGTAGTACTAAGTGCAGGCTACTATGAGTACCCGATATCTTTGATCA
1 CATGTGTGGTACTAAGTGAAGGCCACTATGTGCAAAAGATAGCTTTGATCA
* * *
39507644 CATGTGTGGTACTAAGTGCAGGCCACTATGTGTAAAAGATAGCTTTGGTCA
1 CATGTGTGGTACTAAGTGAAGGCCACTATGTGCAAAAGATAGCTTTGATCA
** * * * *
39507695 CGA-GTGTGGTACTGTGTGAATGCCACTTTGTGCAGAAGGTAGCTTTGA-CTA
1 C-ATGTGTGGTACTAAGTGAAGGCCACTATGTGCAAAAGATAGCTTTGATC-A
* *
39507746 CAAGGGTGGTACTA
1 CATGTGTGGTACTA
39507760 TGCGCAGGCT
Statistics
Matches: 94, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
50 2 0.02
51 91 0.97
52 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (51 bp):
CATGTGTGGTACTAAGTGAAGGCCACTATGTGCAAAAGATAGCTTTGATCA
Found at i:39511607 original size:39 final size:40
Alignment explanation
Indices: 39511403--39511625 Score: 245
Period size: 40 Copynumber: 5.6 Consensus size: 40
39511393 TTGAATGCTG
* * * * * *
39511403 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
* * * *
39511443 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
39511483 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
39511523 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
39511563 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
39511602 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
39511626 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 35 0.22
40 118 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:39511645 original size:79 final size:80
Alignment explanation
Indices: 39511478--39511660 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
39511468 GTGCGAGATA
* * *
39511478 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
39511543 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
39511558 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
39511622 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
39511637 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
39511661 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:39526451 original size:31 final size:31
Alignment explanation
Indices: 39526402--39526487 Score: 138
Period size: 31 Copynumber: 2.8 Consensus size: 31
39526392 TCAATCTCAG
39526402 CATAT-ACTGGGCCGAAGCCTTTACATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
* * *
39526432 CATATCACTAGGCCAAAGCCTTTTCATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
39526463 CATATCACTGGGCCGAAGCCTTTAC
1 CATATCACTGGGCCGAAGCCTTTAC
39526488 TGTAACAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
30 5 0.10
31 44 0.90
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTACATTATT
Found at i:39526920 original size:25 final size:25
Alignment explanation
Indices: 39526883--39526930 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39526873 ACAATTAAAC
* **
39526883 CCTAGGGGTAAAATGGTCATTTTTA
1 CCTAGGGGCAAAACAGTCATTTTTA
39526908 CCTAGGGGCAAAACAGTCATTTT
1 CCTAGGGGCAAAACAGTCATTTT
39526931 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (25 bp):
CCTAGGGGCAAAACAGTCATTTTTA
Found at i:39529190 original size:40 final size:39
Alignment explanation
Indices: 39529128--39529383 Score: 318
Period size: 40 Copynumber: 6.4 Consensus size: 39
39529118 CAACCAAGTA
* * *
39529128 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGA-ATAG-TAACTCGCACAAATG
**
39529167 CCTTCGGGACTTAGCCCGGATATAGTAGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGA-ATAGTAACTCGCACAAATG
39529207 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGA-ATAGTAACTCGCACAAATG
*
39529247 CCTTCGGGACTTAGCCCGGAATTCGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACAAATG
** * *
39529287 CCTTCTTGACTTAGCCCGGAATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACAAATG
** *
39529327 CCTTCGGGACTTAGCCCGGAATTAGTCGCTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACAAATG
39529367 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
39529384 CGTTATCATC
Statistics
Matches: 198, Mismatches: 16, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
39 14 0.07
40 184 0.93
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGAATAGTAACTCGCACAAATG
Found at i:39530603 original size:21 final size:21
Alignment explanation
Indices: 39530577--39530618 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
39530567 ACCATAGCCG
*
39530577 ATTTTCTCCAAGCTCTTTCCC
1 ATTTTCTCCAAGCTCATTCCC
39530598 ATTTTCTCCAAGCTCATTCCC
1 ATTTTCTCCAAGCTCATTCCC
39530619 TTCTTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.38, G:0.05, T:0.40
Consensus pattern (21 bp):
ATTTTCTCCAAGCTCATTCCC
Found at i:39534038 original size:27 final size:26
Alignment explanation
Indices: 39534007--39534299 Score: 271
Period size: 27 Copynumber: 10.9 Consensus size: 26
39533997 TTAGTTTACC
* *
39534007 AAATTACCAAAATACCCTCGATTAGGA
1 AAATTACCAAAATACCC-CGATTTGTA
* *
39534034 AAATTACCAAAATACCCTCGATTAGCA
1 AAATTACCAAAATACCC-CGATTTGTA
*
39534061 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCC-GATTTGTA
*
39534088 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCC-GATTTGTA
* *
39534115 AACTTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCC-GATTTGTA
*
39534142 AAATTACCAAAATACCCCTAATTTGTA
1 AAATTACCAAAATACCCC-GATTTGTA
* * * *
39534169 AAATTATCGAAATACGCCTGATTTGCA
1 AAATTACCAAAATAC-CCCGATTTGTA
* * * * *
39534196 CAATTACCGAAATATCTCTGATTTGAA
1 AAATTACCAAAATA-CCCCGATTTGTA
**
39534223 AAATTACTGAAATACCCCGATTTGTA
1 AAATTACCAAAATACCCCGATTTGTA
* * * *
39534249 AAATTACTAAAATACCTTCAACTTGTA
1 AAATTACCAAAATACC-CCGATTTGTA
*
39534276 AAATTACCAAAGTACCCCCGATTT
1 AAATTACCAAAATA-CCCCGATTT
39534300 ACAGAATTAC
Statistics
Matches: 230, Mismatches: 31, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
26 25 0.11
27 200 0.87
28 5 0.02
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.29
Consensus pattern (26 bp):
AAATTACCAAAATACCCCGATTTGTA
Found at i:39534325 original size:107 final size:108
Alignment explanation
Indices: 39534001--39534348 Score: 264
Period size: 108 Copynumber: 3.2 Consensus size: 108
39533991 AATACTTTAG
* * * * * *
39534001 TTTACCAAATTACCAAAATA-CCCTCGATTAGGAAAATTACCAAAATA-CCCTCGA-TTAGCAAA
1 TTTACAAAATTACCGAAATACCCCT-GATTTGTAAAATTACCAAAATACCCCT-AACTT-GTAAA
* * ** * * * *
39534063 ATTA-CCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGG
63 ATTATCC-AAATACCCCCGATTTACACAATTACCGAAATACCTCTGA
** * * * *
39534109 TTTGTAAACTTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTAATTTGTAAAATT
1 TTTACAAAATTACCGAAATACCCCTGATTTGTAAAATTACCAAAATACCCCTAACTTGTAAAATT
* * * * *
39534174 ATCGAAATACGCCTGATTTGCACAATTACCGAAATATCTCTGA
66 ATCCAAATACCCCCGATTTACACAATTACCGAAATACCTCTGA
* * *
39534217 TTTGA-AAAATTACTGAAATACCCC-GATTTGTAAAATTACTAAAATA-CCTTCAACTTGTAAAA
1 TTT-ACAAAATTACCGAAATACCCCTGATTTGTAAAATTACCAAAATACCCCT-AACTTGTAAAA
* ** *
39534279 TTA-CCAAAGTACCCCCGATTTACAGAATTACC-ATTTTACCTTTGA
64 TTATCCAAA-TACCCCCGATTTACACAATTACCGA-AATACCTCTGA
*
39534324 TTTACAAAATTACCGAAACACCCCT
1 TTTACAAAATTACCGAAATACCCCT
39534349 ATAGGGTAGA
Statistics
Matches: 193, Mismatches: 37, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
106 9 0.05
107 79 0.41
108 94 0.49
109 11 0.06
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.29
Consensus pattern (108 bp):
TTTACAAAATTACCGAAATACCCCTGATTTGTAAAATTACCAAAATACCCCTAACTTGTAAAATT
ATCCAAATACCCCCGATTTACACAATTACCGAAATACCTCTGA
Found at i:39534361 original size:27 final size:27
Alignment explanation
Indices: 39534331--39534927 Score: 749
Period size: 27 Copynumber: 22.2 Consensus size: 27
39534321 TGATTTACAA
* * *
39534331 AATTACCGAAACACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
39534358 AATTA-TCGAAATACCCTTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
* *
39534385 AACTACTGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
**
39534412 AATTACCAAAATA-CCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
39534438 AATTACTGAAATACCCCT-AAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
39534464 AATTA-TCGAAATACCCCTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
*
39534491 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
**
39534518 AATTA-TCGAAATACCATTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
* *
39534545 AAATACTGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* **
39534572 AATTATTGAAATACCTTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
39534599 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
39534626 AATTACTAAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * *
39534653 AATTACTAAAATAACCTTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
39534680 AAATACCGAAATA-CCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
39534706 AATTACCGAAATACCCTTGTAGGATAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
39534733 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
**
39534760 AATTACTGAAATACCATTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
39534787 AAATACTGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
39534814 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
39534841 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
39534868 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * *
39534895 AATTAGC-GAGATACCCTTGTGGGGTAA
1 AATTA-CTGAAATACCCCTGTAGGGTAG
39534922 AATTAC
1 AATTAC
39534928 CATTTTTCCT
Statistics
Matches: 502, Mismatches: 58, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
25 1 0.00
26 71 0.14
27 426 0.85
28 4 0.01
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:39535368 original size:22 final size:22
Alignment explanation
Indices: 39535317--39535380 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
39535307 CCAATTATTT
*
39535317 TGATTATGGCTTTGTGCAAACC
1 TGATTATGGCTTTGTGCCAACC
*
39535339 T-ACATATGGCTTTGTGCCAACC
1 TGA-TTATGGCTTTGTGCCAACC
*
39535361 TGATTATGGCTGTGTGCCAA
1 TGATTATGGCTTTGTGCCAA
39535381 ACGTATTTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.34
Consensus pattern (22 bp):
TGATTATGGCTTTGTGCCAACC
Found at i:39535569 original size:27 final size:27
Alignment explanation
Indices: 39535539--39535646 Score: 112
Period size: 27 Copynumber: 4.0 Consensus size: 27
39535529 ATTCTGTTAA
* *
39535539 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
* * *
39535566 GTGGTTATGCCACAAATATCT-ATTCTG
1 GTGGCTCTGCCAC-AATATCTGTTTCTG
* *
39535593 GTGGCTCTGCCACAATATATGTATCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
* *
39535620 GTGACTCTGTCACAATATCTG-TTCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
39535646 G
1 G
39535647 CAGCCATGCT
Statistics
Matches: 66, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
26 11 0.17
27 49 0.74
28 6 0.09
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTTTCTG
Found at i:39535634 original size:54 final size:53
Alignment explanation
Indices: 39535539--39535646 Score: 126
Period size: 54 Copynumber: 2.0 Consensus size: 53
39535529 ATTCTGTTAA
* * * * **
39535539 GTGGCTTTGCCACATTATCTGTTTCTGGTGGTTATGCCACAAATATCTATTCTG
1 GTGGCTCTGCCACAATATATGTATCTGGTGACTATGCCAC-AATATCTATTCTG
* * *
39535593 GTGGCTCTGCCACAATATATGTATCTGGTGACTCTGTCACAATATCTGTTCTG
1 GTGGCTCTGCCACAATATATGTATCTGGTGACTATGCCACAATATCTATTCTG
39535646 G
1 G
39535647 CAGCCATGCT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
53 13 0.29
54 32 0.71
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (53 bp):
GTGGCTCTGCCACAATATATGTATCTGGTGACTATGCCACAATATCTATTCTG
Found at i:39535801 original size:6 final size:6
Alignment explanation
Indices: 39535786--39535888 Score: 68
Period size: 6 Copynumber: 16.8 Consensus size: 6
39535776 ATTCTCTTAC
* * * *
39535786 CTGATA CTGATT CTGATT CTG-TCAC CTAATT CTGATT CTGATT TTGATT
1 CTGATT CTGATT CTGATT CTGAT--T CTGATT CTGATT CTGATT CTGATT
* * * *
39535835 CTGATT CTG-TCAC CTGATT TTGATT CTGATT CTCATT TTGATT CT-AGTT
1 CTGATT CTGAT--T CTGATT CTGATT CTGATT CTGATT CTGATT CTGA-TT
39535884 CTGAT
1 CTGAT
39535889 AATGTTTCTT
Statistics
Matches: 74, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
5 3 0.04
6 63 0.85
7 6 0.08
8 2 0.03
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (6 bp):
CTGATT
Found at i:39535812 original size:25 final size:25
Alignment explanation
Indices: 39535774--39535828 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
39535764 ATTCTAATTT
* *
39535774 TGATTCTCTTACCTGATACTGATTC
1 TGATTCTCTCACCTAATACTGATTC
* *
39535799 TGATTCTGTCACCTAATTCTGATTC
1 TGATTCTCTCACCTAATACTGATTC
39535824 TGATT
1 TGATT
39535829 TTGATTCTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (25 bp):
TGATTCTCTCACCTAATACTGATTC
Found at i:39535827 original size:37 final size:37
Alignment explanation
Indices: 39535786--39535879 Score: 134
Period size: 37 Copynumber: 2.5 Consensus size: 37
39535776 ATTCTCTTAC
*
39535786 CTGATACTGATTCTGATTCTGTCACCTAATTCTGATT
1 CTGATTCTGATTCTGATTCTGTCACCTAATTCTGATT
* * *
39535823 CTGATTTTGATTCTGATTCTGTCACCTGATTTTGATT
1 CTGATTCTGATTCTGATTCTGTCACCTAATTCTGATT
* *
39535860 CTGATTCTCATTTTGATTCT
1 CTGATTCTGATTCTGATTCT
39535880 AGTTCTGATA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.18, C:0.19, G:0.14, T:0.49
Consensus pattern (37 bp):
CTGATTCTGATTCTGATTCTGTCACCTAATTCTGATT
Found at i:39543856 original size:42 final size:42
Alignment explanation
Indices: 39543809--39543892 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
39543799 TGAGACAACG
39543809 GAGATGGTTAGAATTAATTAAGGATTATGATCTGATTATTGA
1 GAGATGGTTAGAATTAATTAAGGATTATGATCTGATTATTGA
39543851 GAGATGGTTAGAATTAATTAAGGATTATGATCTGATTATTGA
1 GAGATGGTTAGAATTAATTAAGGATTATGATCTGATTATTGA
39543893 CTATCACCCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (42 bp):
GAGATGGTTAGAATTAATTAAGGATTATGATCTGATTATTGA
Found at i:39547096 original size:27 final size:27
Alignment explanation
Indices: 39547063--39547118 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
39547053 CTAGAAACTC
39547063 AACGGGATTAATATGATGTATGTCAAT
1 AACGGGATTAATATGATGTATGTCAAT
39547090 AACGGGATTAATATGATGTATGTCAAT
1 AACGGGATTAATATGATGTATGTCAAT
39547117 AA
1 AA
39547119 TATGATGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.32
Consensus pattern (27 bp):
AACGGGATTAATATGATGTATGTCAAT
Found at i:39555489 original size:20 final size:20
Alignment explanation
Indices: 39555461--39555510 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
39555451 AAGACTATGA
*
39555461 ACCACTCCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
39555481 ACCATTCCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
**
39555501 TTCATTCCAT
1 ACCATTCCAT
39555511 GTTCTTAGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (20 bp):
ACCATTCCATTTACTTACTT
Found at i:39558978 original size:29 final size:29
Alignment explanation
Indices: 39558936--39559025 Score: 162
Period size: 29 Copynumber: 3.1 Consensus size: 29
39558926 TTCCTGGATG
*
39558936 ATAGTCAATAACCAAATCATAATCTTTGA
1 ATAGTCAATAACCAAATCATAATCTTTCA
39558965 ATAGTCAATAACCAAATCATAATCTTTCA
1 ATAGTCAATAACCAAATCATAATCTTTCA
*
39558994 ATAGTCAATACCCAAATCATAATCTTTCA
1 ATAGTCAATAACCAAATCATAATCTTTCA
39559023 ATA
1 ATA
39559026 ACTCAAGCCA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.31
Consensus pattern (29 bp):
ATAGTCAATAACCAAATCATAATCTTTCA
Found at i:39566066 original size:43 final size:43
Alignment explanation
Indices: 39565999--39566110 Score: 138
Period size: 43 Copynumber: 2.7 Consensus size: 43
39565989 TACCATACCA
* * **
39565999 ATGCC-ATATCCCAGATATGGTCTTACATGGGATCTCATATCG
1 ATGCCAATAGCCCAGATATGATCTTACATGAAATCTCATATCG
*
39566041 ATGCCAATAGCCCAGCTATGATCTTACATGAAATCTCATATCG
1 ATGCCAATAGCCCAGATATGATCTTACATGAAATCTCATATCG
* * *
39566084 ATGCC-ATATCCTAGATATGGTCTTACA
1 ATGCCAATAGCCCAGATATGATCTTACA
39566111 CGTAATCTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
42 23 0.38
43 37 0.62
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.30
Consensus pattern (43 bp):
ATGCCAATAGCCCAGATATGATCTTACATGAAATCTCATATCG
Found at i:39568552 original size:25 final size:25
Alignment explanation
Indices: 39568506--39568553 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
39568496 CTGAGCTAAA
*
39568506 CAGGAAACTCATAAGAGTTTTTACC
1 CAGGAAACTCATAAGAGCTTTTACC
*
39568531 CAGGAAGCTCAT-AGAGCCTTTTA
1 CAGGAAACTCATAAGAG-CTTTTA
39568554 GATATCTACG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (25 bp):
CAGGAAACTCATAAGAGCTTTTACC
Found at i:39574779 original size:53 final size:53
Alignment explanation
Indices: 39574699--39574804 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
39574689 TAATTAATGA
*
39574699 GATTTGTGTTCCTAGTCATGGTTAGGGCCATTAATGTTGTTTTTATATATATG
1 GATTTGTGTTACTAGTCATGGTTAGGGCCATTAATGTTGTTTTTATATATATG
39574752 GATTTGTGTTACTAGTCATGGTTAGGGCCATTAATGTTGTTTTTATATATATG
1 GATTTGTGTTACTAGTCATGGTTAGGGCCATTAATGTTGTTTTTATATATATG
39574805 TTACATAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.22, C:0.08, G:0.23, T:0.47
Consensus pattern (53 bp):
GATTTGTGTTACTAGTCATGGTTAGGGCCATTAATGTTGTTTTTATATATATG
Found at i:39574817 original size:3 final size:3
Alignment explanation
Indices: 39574809--39574845 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
39574799 TATATGTTAC
39574809 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
39574846 ATAGTAGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:39574878 original size:24 final size:24
Alignment explanation
Indices: 39574834--39574879 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
39574824 ATAATAATAA
* *
39574834 TAATAATAATAAATAGTAGAAACT
1 TAATAATAAGAAATAGAAGAAACT
39574858 TAATAA-AAGAAATAGAAAGAAA
1 TAATAATAAGAAATAG-AAGAAA
39574880 GTGGAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.65, C:0.02, G:0.11, T:0.22
Consensus pattern (24 bp):
TAATAATAAGAAATAGAAGAAACT
Found at i:39578345 original size:27 final size:27
Alignment explanation
Indices: 39578028--39578344 Score: 400
Period size: 27 Copynumber: 11.7 Consensus size: 27
39578018 TACTAAAATG
** *
39578028 CCCTCGATTTGTAGAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* * *
39578055 CTCTCGATTTATAGAATTACTGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* *
39578082 CCCTCGATTTATAGCATTACCGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
*
39578109 TCCTCGATTTACAGAATTACCGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* *
39578136 TCCTCGATTTACAGAATTATCGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
*
39578163 CCCTCGATTTACAGAATTACCGCTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* *
39578190 CCCTCGATTTACAGAATAACCATTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* * *
39578217 CTCTCGATTTATAGAATTATCGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* *
39578244 CCCTCGATTTACAAAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* *
39578271 CCCTCAATTTACAGAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* * *
39578298 CCCTTGATTTGCAGAATTACTGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* *
39578325 CCCTCAATTTACAAAATTAC
1 CCCTCGATTTACAGAATTAC
39578345 TAAAATACTC
Statistics
Matches: 252, Mismatches: 38, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 252 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTACAGAATTACCGTTTTA
Found at i:39578363 original size:81 final size:81
Alignment explanation
Indices: 39578008--39578373 Score: 367
Period size: 81 Copynumber: 4.5 Consensus size: 81
39577998 AATACTTTAG
* * * ** * *
39578008 TTTACCAAATTACTAAAATGCCCTCGATTTGTAGAATTACCATTTTACTCTCGATTTATAGAATT
1 TTTACAAAATTACTAATATACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAGAATT
39578073 A-CTGTTTTACCCTCGA
66 ATC-GTTTTACCCTCGA
* ** *** * * * *
39578089 TTTATAGCATTACCGTTTTATCCTCGATTTACAGAATTACCGTTTTATCCTCGATTTACAGAATT
1 TTTACAAAATTACTAATATACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAGAATT
39578154 ATCGTTTTACCCTCGA
66 ATCGTTTTACCCTCGA
* *** * * * *
39578170 TTTACAGAATTACCGCTTTACCCTCGATTTACAGAATAACCATTTTACTCTCGATTTATAGAATT
1 TTTACAAAATTACTAATATACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAGAATT
39578235 ATCGTTTTACCCTCGA
66 ATCGTTTTACCCTCGA
* * * * * *
39578251 TTTACAAAATTACCATTTTACCCTCAATTTACAGAATTACCATTTTACCCTTGATTTGCAGAATT
1 TTTACAAAATTACTAATATACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAGAATT
*
39578316 A-CTGTTTTACCCTCAA
66 ATC-GTTTTACCCTCGA
* * * * *
39578332 TTTACAAAATTACTAAAATACTCTTGGTTTACAAAATTACCA
1 TTTACAAAATTACTAATATACCCTCGATTTACAGAATTACCA
39578374 AAATACCCTC
Statistics
Matches: 238, Mismatches: 45, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
80 1 0.00
81 236 0.99
82 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (81 bp):
TTTACAAAATTACTAATATACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAGAATT
ATCGTTTTACCCTCGA
Found at i:39578370 original size:54 final size:54
Alignment explanation
Indices: 39578141--39578409 Score: 180
Period size: 54 Copynumber: 5.0 Consensus size: 54
39578131 TTTTATCCTC
* * * * * **** *
39578141 GATTTACAGAATTATCGTTTTACCCTCGATTTACAGAATTACCGCTTTACCCTC
1 GATTTACAAAATTACCATTTTACCCTCAATTTACAAAATTACCAAAATACCCTT
* * * * * * * **** *
39578195 GATTTACAGAATAACCATTTTACTCTCGATTTATAGAATTATCGTTTTACCCTC
1 GATTTACAAAATTACCATTTTACCCTCAATTTACAAAATTACCAAAATACCCTT
* ***
39578249 GATTTACAAAATTACCATTTTACCCTCAATTTACAGAATTACCATTTTACCCTT
1 GATTTACAAAATTACCATTTTACCCTCAATTTACAAAATTACCAAAATACCCTT
* * ** * *
39578303 GATTTGCAGAATTACTGTTTTACCCTCAATTTACAAAATTACTAAAATACTCTT
1 GATTTACAAAATTACCATTTTACCCTCAATTTACAAAATTACCAAAATACCCTT
* *** * *
39578357 GGTTTACAAAATTACCAAAATACCCTCAA-TCAGTAAAATTACCAAAATACCCT
1 GATTTACAAAATTACCATTTTACCCTCAATTTA-CAAAATTACCAAAATACCCT
39578410 GGTCTGTAAA
Statistics
Matches: 177, Mismatches: 37, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
53 2 0.01
54 175 0.99
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (54 bp):
GATTTACAAAATTACCATTTTACCCTCAATTTACAAAATTACCAAAATACCCTT
Found at i:39578394 original size:27 final size:27
Alignment explanation
Indices: 39578323--39578543 Score: 171
Period size: 27 Copynumber: 8.2 Consensus size: 27
39578313 ATTACTGTTT
* ** *
39578323 TACCCTCAATTTACAAAATTACTAAAA
1 TACCCTCAGTTTGTAAAATTACCAAAA
* ** **
39578350 TACTCTTGGTTTACAAAATTACCAAAA
1 TACCCTCAGTTTGTAAAATTACCAAAA
* **
39578377 TACCCTCAATCAGTAAAATTACCAAAA
1 TACCCTCAGTTTGTAAAATTACCAAAA
* * * *
39578404 TACCCT-GGTCTGTAAAATTGCTAAAA
1 TACCCTCAGTTTGTAAAATTACCAAAA
*
39578430 TACCC-CTGGTTTGTAAAATTACCAAAA
1 TACCCTC-AGTTTGTAAAATTACCAAAA
* *
39578457 TACCACT-AGTTTGTGAAATTACCGAAA
1 TACC-CTCAGTTTGTAAAATTACCAAAA
*
39578484 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCAGTTTGTAAAATTACCAAAA
* * **
39578511 TACCCTTAATTTACAAAATTA-CAGAAA
1 TACCCTCAGTTTGTAAAATTACCA-AAA
39578538 TACCCT
1 TACCCT
39578544 TGACTTTCTA
Statistics
Matches: 158, Mismatches: 30, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
26 24 0.15
27 133 0.84
28 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29
Consensus pattern (27 bp):
TACCCTCAGTTTGTAAAATTACCAAAA
Found at i:39578476 original size:80 final size:80
Alignment explanation
Indices: 39578337--39578543 Score: 220
Period size: 80 Copynumber: 2.6 Consensus size: 80
39578327 CTCAATTTAC
* *
39578337 AAAATTACTAAAATACTCTTGGTTTACAAAATTACCAAAATACCCTCAATCAGTAAAATTACCAA
1 AAAATTACTAAAATACCCCTGGTTTACAAAATTACCAAAATACCCTCAATCAGTAAAATTACCAA
39578402 AATACCCTGGTCTGT
66 AATACCCTGGTCTGT
* ** * ** * *
39578417 AAAATTGCTAAAATACCCCTGGTTTGTAAAATTACCAAAATACCACT-AGTTTGTGAAATTACCG
1 AAAATTACTAAAATACCCCTGGTTTACAAAATTACCAAAATACC-CTCAATCAGTAAAATTACCA
** *
39578481 AAATACCCTCAATTTGT
65 AAATACCCT-GGTCTGT
* * **
39578498 AAAATTACCAAAATACCCTTAATTTACAAAATTA-CAGAAATACCCT
1 AAAATTACTAAAATACCCCTGGTTTACAAAATTACCA-AAATACCCT
39578544 TGACTTTCTA
Statistics
Matches: 104, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
80 64 0.62
81 40 0.38
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.29
Consensus pattern (80 bp):
AAAATTACTAAAATACCCCTGGTTTACAAAATTACCAAAATACCCTCAATCAGTAAAATTACCAA
AATACCCTGGTCTGT
Found at i:39578530 original size:54 final size:54
Alignment explanation
Indices: 39578323--39578627 Score: 231
Period size: 54 Copynumber: 5.6 Consensus size: 54
39578313 ATTACTGTTT
** * * * *
39578323 TACCCTCAATTTACAAAATTACTAAAATACTCTTGGTTTACAAAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCCTTAGTTTACAAAATTACCGAAA
** * * ** * **
39578377 TACCCTCAATCAGTAAAATTACCAAAATACCC-TGGTCTGTAAAATTGCTAAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCCTTAGTTTACAAAATTACCGAAA
** ***
39578430 TACCC-CTGGTTTGTAAAATTACCAAAATACCAC-TAGTTTGTGAAATTACCGAAA
1 TACCCTC-AATTTGTAAAATTACCAAAATACC-CTTAGTTTACAAAATTACCGAAA
* *
39578484 TACCCTCAATTTGTAAAATTACCAAAATACCCTTAATTTACAAAATTACAGAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCCTTAGTTTACAAAATTACCGAAA
* * * * * *
39578538 TACCCTTGACTTTCTAAAAATTA-TAGAAATACCATTAGTTTACAAAATTACTGAAA
1 TACCC-TCAATTTGT-AAAATTACCA-AAATACCCTTAGTTTACAAAATTACCGAAA
*** * * *
39578594 TACCCTTGGTTTGTAGATTTACCAAAACACCCTT
1 TACCCTCAATTTGTAAAATTACCAAAATACCCTT
39578628 GTAGGATGAA
Statistics
Matches: 199, Mismatches: 44, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
52 1 0.01
53 42 0.21
54 103 0.52
55 14 0.07
56 39 0.20
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (54 bp):
TACCCTCAATTTGTAAAATTACCAAAATACCCTTAGTTTACAAAATTACCGAAA
Found at i:39578605 original size:27 final size:27
Alignment explanation
Indices: 39578332--39578628 Score: 147
Period size: 27 Copynumber: 11.0 Consensus size: 27
39578322 TTACCCTCAA
* *
39578332 TTTACAAAATTACTAAAATACTCTTGG
1 TTTACAAAATTACCAAAATACCCTTGG
**
39578359 TTTACAAAATTACCAAAATACCC-TCA
1 TTTACAAAATTACCAAAATACCCTTGG
* * *
39578385 ATCAGTAAAATTACCAAAATACCC-TGG
1 TTTA-CAAAATTACCAAAATACCCTTGG
* ** * * *
39578412 TCTGTAAAATTGCTAAAATACCCCTGG
1 TTTACAAAATTACCAAAATACCCTTGG
** *
39578439 TTTGTAAAATTACCAAAATACCAC-TAG
1 TTTACAAAATTACCAAAATACC-CTTGG
*** * ***
39578466 TTTGTGAAATTACCGAAATACCCTCAA
1 TTTACAAAATTACCAAAATACCCTTGG
** **
39578493 TTTGTAAAATTACCAAAATACCCTTAA
1 TTTACAAAATTACCAAAATACCCTTGG
*
39578520 TTTACAAAATTA-CAGAAATACCCTTGAC
1 TTTACAAAATTACCA-AAATACCCTTG-G
* * *
39578548 TTT-CTAAAAATTA-TAGAAATACCATTAG
1 TTTAC--AAAATTACCA-AAATACCCTTGG
**
39578576 TTTACAAAATTACTGAAATACCCTTGG
1 TTTACAAAATTACCAAAATACCCTTGG
** * * *
39578603 TTTGTAGATTTACCAAAACACCCTTG
1 TTTACAAAATTACCAAAATACCCTTG
39578629 TAGGATGAAA
Statistics
Matches: 216, Mismatches: 44, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
26 23 0.11
27 166 0.77
28 8 0.04
29 19 0.09
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
TTTACAAAATTACCAAAATACCCTTGG
Found at i:39578689 original size:27 final size:27
Alignment explanation
Indices: 39578645--39578719 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
39578635 GAAATGACTA
*
39578645 TAATACCCCTAATA-GGTAAAAAGACCG
1 TAATACCCCT-GTAGGGTAAAAAGACCG
**
39578672 TAA-AGCCCCTGTAGGGTAAAGTGACCG
1 TAATA-CCCCTGTAGGGTAAAAAGACCG
* *
39578699 TAATACCCTTGTATGGTAAAA
1 TAATACCCCTGTAGGGTAAAA
39578720 TGACGAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 35 0.90
28 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (27 bp):
TAATACCCCTGTAGGGTAAAAAGACCG
Found at i:39578723 original size:27 final size:27
Alignment explanation
Indices: 39578659--39578723 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
39578649 ACCCCTAATA
*
39578659 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * *
39578686 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
39578713 GGTAAAATGAC
1 GGTAAAATGAC
39578724 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:39579355 original size:25 final size:25
Alignment explanation
Indices: 39579326--39579373 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
39579316 TTATAATGTG
39579326 AAAATGACTGTTTTGCCCCTAGGTA
1 AAAATGACTGTTTTGCCCCTAGGTA
39579351 AAAATGACTGTTTTGCCCCTAGG
1 AAAATGACTGTTTTGCCCCTAGG
39579374 GTTTAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (25 bp):
AAAATGACTGTTTTGCCCCTAGGTA
Found at i:39579434 original size:20 final size:20
Alignment explanation
Indices: 39579400--39579475 Score: 104
Period size: 20 Copynumber: 3.9 Consensus size: 20
39579390 GATACGTGGG
39579400 GTATGATAT--ACATGAT-T
1 GTATGATATGCACATGATAT
39579417 GATATGATATGCACATGATAT
1 G-TATGATATGCACATGATAT
*
39579438 GCATGATATGCACATGATAT
1 GTATGATATGCACATGATAT
*
39579458 GTATGAAATGCACATGAT
1 GTATGATATGCACATGAT
39579476 GAATTCATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
17 1 0.02
18 8 0.15
20 41 0.79
21 2 0.04
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.33
Consensus pattern (20 bp):
GTATGATATGCACATGATAT
Found at i:39579436 original size:11 final size:11
Alignment explanation
Indices: 39579420--39579475 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
39579410 CATGATTGAT
39579420 ATGATATGCAC
1 ATGATATGCAC
39579431 ATGATATG--C
1 ATGATATGCAC
39579440 ATGATATGCAC
1 ATGATATGCAC
*
39579451 ATGATATG--T
1 ATGATATGCAC
*
39579460 ATGAAATGCAC
1 ATGATATGCAC
39579471 ATGAT
1 ATGAT
39579476 GAATTCATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 16 0.43
11 21 0.57
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:39579603 original size:52 final size:51
Alignment explanation
Indices: 39579525--39579647 Score: 221
Period size: 52 Copynumber: 2.4 Consensus size: 51
39579515 GAGGAAGTGC
*
39579525 AAAAGGGCTTATGCCCTAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
39579577 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
39579628 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
39579648 ATTAAAGAGG
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
50 10 0.14
51 25 0.36
52 35 0.50
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.28
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
Found at i:39579622 original size:25 final size:26
Alignment explanation
Indices: 39579525--39579647 Score: 187
Period size: 26 Copynumber: 4.8 Consensus size: 26
39579515 GAGGAAGTGC
* **
39579525 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
39579551 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
39579577 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
39579603 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
39579628 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
39579648 ATTAAAGAGG
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
25 33 0.37
26 57 0.63
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:39579856 original size:42 final size:42
Alignment explanation
Indices: 39579792--39579883 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
39579782 TAGTCTCCCC
* * *
39579792 AAATAGGCTTTCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
*
39579834 AAATGGGCTTGCATACATTCATTGATATTTCATGTGTTATTG
1 AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
39579876 AAATGGGC
1 AAATGGGC
39579884 CTATGGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
Found at i:39579974 original size:30 final size:31
Alignment explanation
Indices: 39579907--39579984 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
39579897 CGTTTACAAT
39579907 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
39579938 AAAGGCTTTGGCCCAGTGATTTGATTTATG-
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
39579968 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
39579985 AACCGTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 16 0.36
31 28 0.64
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:39583751 original size:24 final size:24
Alignment explanation
Indices: 39583724--39583801 Score: 111
Period size: 24 Copynumber: 3.2 Consensus size: 24
39583714 AAGGCTGTCA
*
39583724 GGAGAAGATTTGGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* *
39583748 GGAGAGGATTTAGGAGCGGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* *
39583772 GGAGAGGATTTAGGAGCTGATTAG
1 GGAGAAGATTTAGGAGCTGATAAG
39583796 GGAGAA
1 GGAGAA
39583802 CGGTGTTGGC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.33, C:0.04, G:0.44, T:0.19
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:39585271 original size:27 final size:26
Alignment explanation
Indices: 39585229--39585312 Score: 114
Period size: 27 Copynumber: 3.2 Consensus size: 26
39585219 AGGAAGCATC
*
39585229 CTGGTGGCTATGCCACATTTATCTGTT
1 CTGGTGGCTCTGCCACA-TTATCTGTT
*
39585256 CTGGTGGCTCTACCACAATTATCTGTT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
* *
39585283 CTGGTGACTCTGCCACATTATTTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
39585309 CTGG
1 CTGG
39585313 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
26 13 0.25
27 37 0.73
28 1 0.02
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.39
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:39591692 original size:259 final size:250
Alignment explanation
Indices: 39591232--39591739 Score: 854
Period size: 259 Copynumber: 2.0 Consensus size: 250
39591222 TATGTTAGTG
39591232 GGCCTCTAGAAGGCCCAAGCTTAAGCTAAATCCCGGTAATTTTAAGTGATTTTAATCCATAGGGA
1 GGCCTCTAGAAGGCCCAAGCTTAAGCTAAATCCCGGTAATTTTAAGTGATTTTAATCCATAGGGA
*
39591297 AAAGAGGTTCTGGTTAGCTAGGTTTTTAAGTATTAACTGGGTAAAATAAAACACAAGGAAGCCTG
66 AAAGAGGTTCTGGTTAGCTAGGCTTTTAAGTATTAACTGGGTAAAATAAAACACAAGGAAGCCTG
* * * *
39591362 TGGTAAGTTGGCATGTGACGCCACTTGGGGGCTTTAGAGGTGGCGTGTGGATGACCAAGGTGAGA
131 TGGTAAGTTGGCATGTGACACCACTTGGGGGCTTTAGAGGTGGCATGTAGATGACCAAGGTAAGA
* *
39591427 TAAGGTTTGAGTTGCAAGGTAAGCAAATTAGTGATATTAATTTTTATGTATAGAAAAGGTAAGT
196 TAAGGTTCGAG-T-C-------GCAAATTAGTGATATTAATTTTTATGTACAGAAAAGGTAAGT
39591491 GGCCTCTAGAAGGCCCAAGCTTAAGCTAAATCCCGGTAATTTTAAGTGATTTTAATCCATAGGGA
1 GGCCTCTAGAAGGCCCAAGCTTAAGCTAAATCCCGGTAATTTTAAGTGATTTTAATCCATAGGGA
*
39591556 AAAGAGGTTCTGGTTAGCTAGGCTTTTAAGTATTGACTGGGTAAAATAAAACACAAGGAAGCCTG
66 AAAGAGGTTCTGGTTAGCTAGGCTTTTAAGTATTAACTGGGTAAAATAAAACACAAGGAAGCCTG
*
39591621 TGGTAAGTTGGCATGTGACACCACTTGGGGGCTTTAGAGGTGGCATGTAGATGACCAAGGTAAGC
131 TGGTAAGTTGGCATGTGACACCACTTGGGGGCTTTAGAGGTGGCATGTAGATGACCAAGGTAAGA
39591686 TAAGGTTCGAGTCGCAAATTAGTGATATTAATTTTTATGTACAGAAAAGGTAAG
196 TAAGGTTCGAGTCGCAAATTAGTGATATTAATTTTTATGTACAGAAAAGGTAAG
39591740 CAGTGGAACT
Statistics
Matches: 240, Mismatches: 9, Indels: 9
0.93 0.03 0.03
Matches are distributed among these distances:
250 40 0.17
257 1 0.00
258 1 0.00
259 198 0.82
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.28
Consensus pattern (250 bp):
GGCCTCTAGAAGGCCCAAGCTTAAGCTAAATCCCGGTAATTTTAAGTGATTTTAATCCATAGGGA
AAAGAGGTTCTGGTTAGCTAGGCTTTTAAGTATTAACTGGGTAAAATAAAACACAAGGAAGCCTG
TGGTAAGTTGGCATGTGACACCACTTGGGGGCTTTAGAGGTGGCATGTAGATGACCAAGGTAAGA
TAAGGTTCGAGTCGCAAATTAGTGATATTAATTTTTATGTACAGAAAAGGTAAGT
Found at i:39591794 original size:24 final size:24
Alignment explanation
Indices: 39591767--39591820 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
39591757 AAGGCTGTCA
*
39591767 GGAGAAGATTTGGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* * *
39591791 GGAGAGGATTTAGGAGTTGATTAG
1 GGAGAAGATTTAGGAGCTGATAAG
39591815 GGAGAA
1 GGAGAA
39591821 CGGTGTTGGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.43, T:0.22
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:39608336 original size:27 final size:27
Alignment explanation
Indices: 39608271--39608347 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 27
39608261 AAATTACTGA
* * *
39608271 AATACCCTTGTAGTGTAAAATGATCGT
1 AATACCCTTGTAGGGTAAAATGACCAT
*
39608298 AATGCCCTTGTAGGGTAAAATGACCAT
1 AATACCCTTGTAGGGTAAAATGACCAT
* *
39608325 AATACTCC-TGTATGGTAGAATGA
1 AATAC-CCTTGTAGGGTAAAATGA
39608348 TGATTATGCC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 40 0.95
28 2 0.05
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.30
Consensus pattern (27 bp):
AATACCCTTGTAGGGTAAAATGACCAT
Found at i:39608533 original size:22 final size:22
Alignment explanation
Indices: 39608505--39608550 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
39608495 GTAGTCATTT
*
39608505 TGTACAAGGCTTTTAGCCGTTC
1 TGTACAAGGCTTTCAGCCGTTC
*
39608527 TGTACAAGGCTTTCAGCCTTTC
1 TGTACAAGGCTTTCAGCCGTTC
39608549 TG
1 TG
39608551 CGATACTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (22 bp):
TGTACAAGGCTTTCAGCCGTTC
Found at i:39610881 original size:11 final size:11
Alignment explanation
Indices: 39610865--39610889 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39610855 ATATGATATT
39610865 TTATTATTTTA
1 TTATTATTTTA
39610876 TTATTATTTTA
1 TTATTATTTTA
39610887 TTA
1 TTA
39610890 GTATATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:39616018 original size:24 final size:24
Alignment explanation
Indices: 39615980--39616039 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
39615970 CCAACACTGT
* *
39615980 TCTCCCTAATTAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
39616004 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
39616028 TCTCCCTTATCA
1 TCTCCCTTATCA
39616040 ACTCACAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.22, C:0.40, G:0.03, T:0.35
Consensus pattern (24 bp):
TCTCCCTTATCAGCTCCTAAATCC
Found at i:39618057 original size:25 final size:25
Alignment explanation
Indices: 39618028--39618077 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
39618018 AGTCATAATC
39618028 CTTAAGCAACTCAATCCATCTCCTT
1 CTTAAGCAACTCAATCCATCTCCTT
39618053 CTTAAGCAACTCAATCCATCTCCTT
1 CTTAAGCAACTCAATCCATCTCCTT
39618078 TGCCTAAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.36, G:0.04, T:0.32
Consensus pattern (25 bp):
CTTAAGCAACTCAATCCATCTCCTT
Found at i:39622371 original size:27 final size:27
Alignment explanation
Indices: 39622315--39622425 Score: 127
Period size: 27 Copynumber: 4.1 Consensus size: 27
39622305 AGCATGGCTG
* *
39622315 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
* *
39622341 CCAGAATAGATAATTATGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
39622368 CCAGAACAGAT-ATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* * * *
39622395 GCAGATCAGATAAATGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
39622422 CCAG
1 CCAG
39622426 GACGCTTCCT
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
26 14 0.20
27 56 0.79
28 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:39622406 original size:54 final size:53
Alignment explanation
Indices: 39622315--39622425 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 53
39622305 AGCATGGCTG
* *
39622315 CCAGAACAGATAATGTGACAGAGTCACCAGAATAGATAATTATGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGAATAGATAAATATGGCAGAGCCA
* * * *
39622368 CCAGAACAGATATATGTGGCAGAGCCAGCAG-ATCAGATAAATGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGAAT-AGATAAATATGGCAGAGCCA
39622422 CCAG
1 CCAG
39622426 GACGCTTCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
53 14 0.28
54 36 0.72
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (53 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGAATAGATAAATATGGCAGAGCCA
Found at i:39622794 original size:57 final size:57
Alignment explanation
Indices: 39622704--39622812 Score: 209
Period size: 57 Copynumber: 1.9 Consensus size: 57
39622694 CCCATTAACT
*
39622704 CGTTTTCGGCCCGTTAAGCCCAAAATATTATTAATGCACGAAATTGCACGTACAACC
1 CGTTTTCGGCCCGTTAAGCCCAAAATATCATTAATGCACGAAATTGCACGTACAACC
39622761 CGTTTTCGGCCCGTTAAGCCCAAAATATCATTAATGCACGAAATTGCACGTA
1 CGTTTTCGGCCCGTTAAGCCCAAAATATCATTAATGCACGAAATTGCACGTA
39622813 TTGCAGTTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.27
Consensus pattern (57 bp):
CGTTTTCGGCCCGTTAAGCCCAAAATATCATTAATGCACGAAATTGCACGTACAACC
Found at i:39623953 original size:24 final size:24
Alignment explanation
Indices: 39623915--39623991 Score: 118
Period size: 24 Copynumber: 3.2 Consensus size: 24
39623905 CCAACACCAT
* *
39623915 TCTCCCTAATTAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
39623939 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
* *
39623963 TCTCCCTTATCAGCTCCCAAATCT
1 TCTCCCTTATCAGCTCCTAAATCC
39623987 TCTCC
1 TCTCC
39623992 AAATAGCCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.21, C:0.42, G:0.04, T:0.34
Consensus pattern (24 bp):
TCTCCCTTATCAGCTCCTAAATCC
Found at i:39625703 original size:28 final size:28
Alignment explanation
Indices: 39625633--39625735 Score: 125
Period size: 28 Copynumber: 3.7 Consensus size: 28
39625623 CATATTCGAC
* * * *
39625633 ATCTCGCACATTAAGTGCCATTCTTAGT
1 ATCTCGCACACTAAGTGCCATACTCAAT
* * * * *
39625661 GTTTCGTACATTAAGTTCCATACTCAAT
1 ATCTCGCACACTAAGTGCCATACTCAAT
39625689 ATCTCGCACACTAAGTGCCATACTCAAT
1 ATCTCGCACACTAAGTGCCATACTCAAT
39625717 ATCTCGCACACTAAGTGCC
1 ATCTCGCACACTAAGTGCC
39625736 GTACATAGCC
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (28 bp):
ATCTCGCACACTAAGTGCCATACTCAAT
Found at i:39625785 original size:40 final size:41
Alignment explanation
Indices: 39625721--39625828 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 41
39625711 CTCAATATCT
39625721 CGCACACTAAGTGCCGTACA--TAGCCGAAGC-AATGTCGAAC
1 CGCACACTAAGTGCC--ACATTTAGCCGAAGCTAATGTCGAAC
* * *
39625761 CGCACACTAAGTGCCACATTTAGCCAAAGCTATTTTCGAAC
1 CGCACACTAAGTGCCACATTTAGCCGAAGCTAATGTCGAAC
**
39625802 TACACACTAAGTGCCACATTTAGCCGA
1 CGCACACTAAGTGCCACATTTAGCCGA
39625829 TATGTCGTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
38 3 0.05
40 24 0.41
41 32 0.54
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (41 bp):
CGCACACTAAGTGCCACATTTAGCCGAAGCTAATGTCGAAC
Found at i:39631201 original size:14 final size:14
Alignment explanation
Indices: 39631182--39631211 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
39631172 TTTTGATTAA
39631182 ATAACTGAAGGTAT
1 ATAACTGAAGGTAT
39631196 ATAACTGAAGGTAT
1 ATAACTGAAGGTAT
39631210 AT
1 AT
39631212 GTGAAACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (14 bp):
ATAACTGAAGGTAT
Found at i:39631700 original size:53 final size:53
Alignment explanation
Indices: 39631642--39632428 Score: 926
Period size: 53 Copynumber: 14.8 Consensus size: 53
39631632 ATAATAAAGA
* *
39631642 GAAATTACTGAAATACCCTCGATTTTTAAAATTACCGAAATACCCTCGATTGT
1 GAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTGT
* * **
39631695 AAAATTATTAAAATACCCTCGATTTGTAAAATTACTAAAATACCCTCGATTGT
1 GAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTGT
* *
39631748 GAAATTATTAAAATACCCTCGATTTGT-AAATTACCGAAATACCCTCAATTGT
1 GAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTGT
* *
39631800 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCGATTGT
1 GAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTGT
* **
39631853 GAAATTATTAAAATACCCTCGATTTGTAAAATTACTAAAATACCCTCGATTGT
1 GAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTGT
* *
39631906 GAAATTATTAAAATACCCTCGATTTGT-AAATTACCGAAATACCCTCAATTGT
1 GAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTGT
* **
39631958 GAAATTACTGAAATACCCTCGATTTGTAAAATTACTAAAATACCCTCGATTGT
1 GAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTGT
* *
39632011 GAAATTATTAAAATACCCTCGATTTGT-AAATTACCGAAATACCCTCAATTGT
1 GAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTGT
* *
39632063 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCTATTGT
1 GAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTGT
* * * *
39632116 GAAATTACCAAAACACTCTCGATTTGTAAAATTACTGAAATACCCTCGATTTGT
1 GAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGA-TTGT
* * * ** *
39632170 AAAATTACCAAAATACCCTCGA-TTGTGAAATTACTAAAATACCCTCAATTTGT
1 GAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGA-TTGT
* * * * *
39632223 AAAATTACTGAAATACCCTCGA-TTGTGAAATTATCGAAACACCCTCGATTTGT
1 GAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGA-TTGT
* * * * *
39632276 AAAATTA-TCGAAATACCCCCGATTTGTAAAATTACCAAAATACCCTCAATTTGT
1 GAAATTACT-AAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGA-TTGT
* * * * * * * *
39632330 AAAATTTCCAAAACA-CTTCCGATTTGTAAAATTATCAAAATACCCT-TATAGTGT
1 GAAATTACTAAAATACCCT-CGATTTGTAAAATTACCGAAATACCCTCGAT--TGT
* * * * * *
39632384 TAAATTACCAAAATACCCTTG-TAGTGTAAAATAACCGACATACCC
1 GAAATTACTAAAATACCCTCGAT-TTGTAAAATTACCGAAATACCC
39632429 CTATAGGGTA
Statistics
Matches: 646, Mismatches: 76, Indels: 23
0.87 0.10 0.03
Matches are distributed among these distances:
52 143 0.22
53 383 0.59
54 118 0.18
55 2 0.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.32
Consensus pattern (53 bp):
GAAATTACTAAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTGT
Found at i:39631805 original size:105 final size:106
Alignment explanation
Indices: 39631642--39632335 Score: 916
Period size: 105 Copynumber: 6.6 Consensus size: 106
39631632 ATAATAAAGA
* * * *
39631642 GAAATTACTGAAATACCCTCGATTTTTAAAATTACCGAAATACCCTCGATTGTAAAATTATTAAA
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCAATTGTGAAATTATTAAA
*
39631707 ATACCCTCGATTTGTAAAATTACTAAAATACCCTCGATTGT
66 ATACCCTCGATTTGTAAAATTACTGAAATACCCTCGATTGT
* * * * *
39631748 GAAATTATTAAAATACCCTCGATTTGT-AAATTACCGAAATACCCTCAATTGTGAAATTACTGAA
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCAATTGTGAAATTATTAAA
**
39631812 ATACCCTCGATTTGTAAAATTACCAAAATACCCTCGATTGT
66 ATACCCTCGATTTGTAAAATTACTGAAATACCCTCGATTGT
* * * *
39631853 GAAATTATTAAAATACCCTCGATTTGTAAAATTACTAAAATACCCTCGATTGTGAAATTATTAAA
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCAATTGTGAAATTATTAAA
* *
39631918 ATACCCTCGATTTGT-AAATTACCGAAATACCCTCAATTGT
66 ATACCCTCGATTTGTAAAATTACTGAAATACCCTCGATTGT
* *
39631958 GAAATTACTGAAATACCCTCGATTTGTAAAATTACTAAAATACCCTCGATTGTGAAATTATTAAA
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCAATTGTGAAATTATTAAA
* *
39632023 ATACCCTCGATTTGT-AAATTACCGAAATACCCTCAATTGT
66 ATACCCTCGATTTGTAAAATTACTGAAATACCCTCGATTGT
* * **
39632063 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCTATTGTGAAATTACCAAA
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCAATTGTGAAATTATTAAA
* *
39632128 ACACTCTCGATTTGTAAAATTACTGAAATACCCTCGATTTGT
66 ATACCCTCGATTTGTAAAATTACTGAAATACCCTCGA-TTGT
* ** * * * * *
39632170 AAAATTACCAAAATACCCTCGA-TTGTGAAATTACTAAAATACCCTCAATTTGTAAAATTACTGA
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCAA-TTGTGAAATTATTAA
* *
39632234 AATACCCTCGA-TTGTGAAATTA-TCGAAACACCCTCGATTTGT
65 AATACCCTCGATTTGTAAAATTACT-GAAATACCCTCGA-TTGT
* * *
39632276 AAAATTA-TCGAAATACCCCCGATTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATT
1 GAAATTACT-GAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCAA-TTGTGAAATT
39632336 TCCAAAACAC
Statistics
Matches: 536, Mismatches: 45, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
105 300 0.56
106 157 0.29
107 79 0.15
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.32
Consensus pattern (106 bp):
GAAATTACTGAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCAATTGTGAAATTATTAAA
ATACCCTCGATTTGTAAAATTACTGAAATACCCTCGATTGT
Found at i:39631862 original size:158 final size:159
Alignment explanation
Indices: 39631642--39632428 Score: 1036
Period size: 158 Copynumber: 4.9 Consensus size: 159
39631632 ATAATAAAGA
* *
39631642 GAAATTACTGAAATACCCTCGATTTTTAAAATTACCGAAATACCCTCGATTGTAAAATTATTAAA
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCGATTGTAAAATTATTAAA
* *
39631707 ATACCCTCGATTTGTAAAATTACTAAAATACCCTCGATTGTGAAATTATTAAAATACCCTCGATT
66 ATACCCTCGATTTGTAAAATTACTAAAATACCCTCAATTGTGAAATTACTAAAATACCCTCGATT
39631772 TGT-AAATTACCGAAATACCCTCAATTGT
131 TGTAAAATTACCGAAATACCCTCAATTGT
*
39631800 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCGATTGTGAAATTATTAAA
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCGATTGTAAAATTATTAAA
* *
39631865 ATACCCTCGATTTGTAAAATTACTAAAATACCCTCGATTGTGAAATTATTAAAATACCCTCGATT
66 ATACCCTCGATTTGTAAAATTACTAAAATACCCTCAATTGTGAAATTACTAAAATACCCTCGATT
39631930 TGT-AAATTACCGAAATACCCTCAATTGT
131 TGTAAAATTACCGAAATACCCTCAATTGT
* *
39631958 GAAATTACTGAAATACCCTCGATTTGTAAAATTACTAAAATACCCTCGATTGTGAAATTATTAAA
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCGATTGTAAAATTATTAAA
** *
39632023 ATACCCTCGATTTGT-AAATTACCGAAATACCCTCAATTGTGAAATTACTGAAATACCCTCGATT
66 ATACCCTCGATTTGTAAAATTACTAAAATACCCTCAATTGTGAAATTACTAAAATACCCTCGATT
*
39632087 TGTAAAATTACCGAAATACCCTCTATTGT
131 TGTAAAATTACCGAAATACCCTCAATTGT
** * * ** **
39632116 GAAATTACCAAAACACTCTCGATTTGTAAAATTACTGAAATACCCTCGATTTGTAAAATTACCAA
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCGA-TTGTAAAATTATTAA
* * *
39632181 AATACCCTCGA-TTGTGAAATTACTAAAATACCCTCAATTTGTAAAATTACTGAAATACCCTCGA
65 AATACCCTCGATTTGTAAAATTACTAAAATACCCTCAA-TTGTGAAATTACTAAAATACCCTCGA
* * * *
39632245 -TTGTGAAATTATCGAAACACCCTCGATTTGT
129 TTTGTAAAATTACCGAAATACCCTC-AATTGT
* * * **
39632276 AAAATTA-TCGAAATACCCCCGATTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATT-TCC
1 GAAATTACT-GAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCGA-TTGTAAAATTATTA
* * * * *
39632339 AAA-ACACTTCCGATTTGTAAAATTA-TCAAAATACCCTTATAGTGTTAAATTACCAAAATACCC
64 AAATAC-CCT-CGATTTGTAAAATTACT-AAAATACCCTCA-ATTGTGAAATTACTAAAATACCC
* * * *
39632402 TTG-TAGTGTAAAATAACCGACATACCC
125 TCGAT-TTGTAAAATTACCGAAATACCC
39632429 CTATAGGGTA
Statistics
Matches: 565, Mismatches: 51, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
157 47 0.08
158 308 0.55
159 69 0.12
160 83 0.15
161 41 0.07
162 17 0.03
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.32
Consensus pattern (159 bp):
GAAATTACTGAAATACCCTCGATTTGTAAAATTACCAAAATACCCTCGATTGTAAAATTATTAAA
ATACCCTCGATTTGTAAAATTACTAAAATACCCTCAATTGTGAAATTACTAAAATACCCTCGATT
TGTAAAATTACCGAAATACCCTCAATTGT
Found at i:39632388 original size:27 final size:27
Alignment explanation
Indices: 39631668--39632442 Score: 168
Period size: 27 Copynumber: 29.2 Consensus size: 27
39631658 CCTCGATTTT
* *
39631668 TAAAATTACCGAAATACCCTCGAT--TG
1 TAAAATTACCAAAATACCCT-TATAGTG
** * *
39631694 TAAAATTATTAAAATACCCTCGAT-TTG
1 TAAAATTACCAAAATACCCT-TATAGTG
* *
39631721 TAAAATTACTAAAATACCCTCGAT--TG
1 TAAAATTACCAAAATACCCT-TATAGTG
* ** * *
39631747 TGAAATTATTAAAATACCCTCGAT-TTG
1 TAAAATTACCAAAATACCCT-TATAGTG
* * *
39631774 T-AAATTACCGAAATACCCTCA-ATTG
1 TAAAATTACCAAAATACCCTTATAGTG
* ** * *
39631799 TGAAATTACTGAAATACCCTCGAT-TTG
1 TAAAATTACCAAAATACCCT-TATAGTG
*
39631826 TAAAATTACCAAAATACCCTCGAT--TG
1 TAAAATTACCAAAATACCCT-TATAGTG
* ** * *
39631852 TGAAATTATTAAAATACCCTCGAT-TTG
1 TAAAATTACCAAAATACCCT-TATAGTG
* *
39631879 TAAAATTACTAAAATACCCTCGAT--TG
1 TAAAATTACCAAAATACCCT-TATAGTG
* ** * *
39631905 TGAAATTATTAAAATACCCTCGAT-TTG
1 TAAAATTACCAAAATACCCT-TATAGTG
* * *
39631932 T-AAATTACCGAAATACCCTCA-ATTG
1 TAAAATTACCAAAATACCCTTATAGTG
* ** * *
39631957 TGAAATTACTGAAATACCCTCGAT-TTG
1 TAAAATTACCAAAATACCCT-TATAGTG
* *
39631984 TAAAATTACTAAAATACCCTCGAT--TG
1 TAAAATTACCAAAATACCCT-TATAGTG
* ** * *
39632010 TGAAATTATTAAAATACCCTCGAT-TTG
1 TAAAATTACCAAAATACCCT-TATAGTG
* * *
39632037 T-AAATTACCGAAATACCCTCA-ATTG
1 TAAAATTACCAAAATACCCTTATAGTG
* ** * *
39632062 TGAAATTACTGAAATACCCTCGAT-TTG
1 TAAAATTACCAAAATACCCT-TATAGTG
*
39632089 TAAAATTACCGAAATACCCTCTAT--TG
1 TAAAATTACCAAAATACCCT-TATAGTG
* * * * *
39632115 TGAAATTACCAAAACACTCTCGAT-TTG
1 TAAAATTACCAAAATACCCT-TATAGTG
** * *
39632142 TAAAATTACTGAAATACCCTCGAT-TTG
1 TAAAATTACCAAAATACCCT-TATAGTG
*
39632169 TAAAATTACCAAAATACCCTCGAT--TG
1 TAAAATTACCAAAATACCCT-TATAGTG
* * * *
39632195 TGAAATTACTAAAATACCCTCA-ATTTG
1 TAAAATTACCAAAATACCCTTATA-GTG
** *
39632222 TAAAATTACTGAAATACCCTCGAT--TG
1 TAAAATTACCAAAATACCCT-TATAGTG
* * * * * *
39632248 TGAAATTATCGAAACACCCTCGAT-TTG
1 TAAAATTACCAAAATACCCT-TATAGTG
* * ** *
39632275 TAAAATTATCGAAATACCCCCGAT-TTG
1 TAAAATTACCAAAATA-CCCTTATAGTG
* *
39632302 TAAAATTACCAAAATACCCTCA-ATTTG
1 TAAAATTACCAAAATACCCTTATA-GTG
* * * *
39632329 TAAAATTTCCAAAACACTTCC-GAT-TTG
1 TAAAATTACCAAAATAC--CCTTATAGTG
*
39632356 TAAAATTATCAAAATACCCTTATAGTG
1 TAAAATTACCAAAATACCCTTATAGTG
* *
39632383 TTAAATTACCAAAATACCCTTGTAGTG
1 TAAAATTACCAAAATACCCTTATAGTG
* * * * *
39632410 TAAAATAACCGACATACCCCTATAGGG
1 TAAAATTACCAAAATACCCTTATAGTG
39632437 TAAAAT
1 TAAAAT
39632443 GACTATTTTG
Statistics
Matches: 629, Mismatches: 88, Indels: 63
0.81 0.11 0.08
Matches are distributed among these distances:
25 18 0.03
26 281 0.45
27 323 0.51
28 5 0.01
29 2 0.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCTTATAGTG
Found at i:39632918 original size:11 final size:11
Alignment explanation
Indices: 39632902--39632927 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39632892 ATTGCATGTA
39632902 TGATATTATTG
1 TGATATTATTG
39632913 TGATATTATTG
1 TGATATTATTG
39632924 TGAT
1 TGAT
39632928 GTAGCCTTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (11 bp):
TGATATTATTG
Found at i:39636129 original size:14 final size:14
Alignment explanation
Indices: 39636110--39636139 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
39636100 TTTTGATTAA
39636110 ATAACTGAAGGTAT
1 ATAACTGAAGGTAT
39636124 ATAACTGAAGGTAT
1 ATAACTGAAGGTAT
39636138 AT
1 AT
39636140 GTGAAACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (14 bp):
ATAACTGAAGGTAT
Found at i:39640183 original size:28 final size:27
Alignment explanation
Indices: 39640134--39640192 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
39640124 TAACGCCCCA
*
39640134 ATTTTCAGGATTTTCAGGATTTCTGTG
1 ATTTTCAGGATTTTCAGAATTTCTGTG
39640161 ATTTTCAAGGAATTTT-AGAATTTCTGTG
1 ATTTTC-AGG-ATTTTCAGAATTTCTGTG
39640189 -TTTT
1 ATTTT
39640193 GACTATCTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 10 0.34
28 14 0.48
29 5 0.17
ACGTcount: A:0.22, C:0.08, G:0.19, T:0.51
Consensus pattern (27 bp):
ATTTTCAGGATTTTCAGAATTTCTGTG
Found at i:39651820 original size:43 final size:43
Alignment explanation
Indices: 39651772--39651896 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 43
39651762 CTAATATGTT
* ** * *
39651772 ATCATATATCGATGCCTCTGTCCCAGGCAGGGTTTTACACGAA
1 ATCATATAACGATGCCAATGTCCCAGACAGGGTCTTACACGAA
* *
39651815 ATCATATAACGATGCCAATGTCCCAGACATGGTCTTACACGTA
1 ATCATATAACGATGCCAATGTCCCAGACAGGGTCTTACACGAA
* * *
39651858 ATCACA-ATACAATGCCAATGTCCCAGACATGGTCTTACA
1 ATCATATA-ACGATGCCAATGTCCCAGACAGGGTCTTACA
39651897 TGTAATCACA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 1 0.01
43 71 0.99
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (43 bp):
ATCATATAACGATGCCAATGTCCCAGACAGGGTCTTACACGAA
Found at i:39653652 original size:135 final size:135
Alignment explanation
Indices: 39653410--39653804 Score: 610
Period size: 135 Copynumber: 2.9 Consensus size: 135
39653400 CTCGACTGCC
* * * * *
39653410 ACTAACATTACTGGGGTGACGGGGTGGTCTACCTTTTTAGACAGGATTACTCGGCTTTTGAGCTG
1 ACTAACATTACTGAGGTGACGGGGTGGTCTGCCTCTCTAGACAGGATTACTCGGCTTTTAAGCTG
* * *
39653475 GTTCTATCTCTTTTTCAACTCTTTCTGGATAGTCCCTGAGAAAATGGTCAAGTGAACCACATCCG
66 GTTCTATCTCTTTTTCAACTCTTTCTGGACAATCCCTAAGAAAATGGTCAAGTGAACCACATCCG
39653540 GAACT
131 GAACT
* **
39653545 ACTAACATTACTGAGGTAACGGGGTGGTCTGCCTCTCTAGACAGGATTACTCGATTTTTAAGCTG
1 ACTAACATTACTGAGGTGACGGGGTGGTCTGCCTCTCTAGACAGGATTACTCGGCTTTTAAGCTG
* * *
39653610 GTGCTATCTCTTTTTCAGCCCTTTCTGGACAATCCCTAAGAAAATGGTCAAGTGAACCACATCCG
66 GTTCTATCTCTTTTTCAACTCTTTCTGGACAATCCCTAAGAAAATGGTCAAGTGAACCACATCCG
39653675 GAACT
131 GAACT
* * * *
39653680 ACTAACATTACCGAGGTGACGGGGTGGTCTGCCTCTCTAGACAGGATTACTTGGCTTTGAAGATG
1 ACTAACATTACTGAGGTGACGGGGTGGTCTGCCTCTCTAGACAGGATTACTCGGCTTTTAAGCTG
* *
39653745 GTTCTATCTCCTTTTCAACTCTTTTTGGACAATCCCTAAGAAAATGGTCAAGTGAACCAC
66 GTTCTATCTCTTTTTCAACTCTTTCTGGACAATCCCTAAGAAAATGGTCAAGTGAACCAC
39653805 TTTCAAAAGA
Statistics
Matches: 234, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
135 234 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (135 bp):
ACTAACATTACTGAGGTGACGGGGTGGTCTGCCTCTCTAGACAGGATTACTCGGCTTTTAAGCTG
GTTCTATCTCTTTTTCAACTCTTTCTGGACAATCCCTAAGAAAATGGTCAAGTGAACCACATCCG
GAACT
Found at i:39655262 original size:22 final size:21
Alignment explanation
Indices: 39655237--39655290 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
39655227 TGCAGGGCTT
*
39655237 ACACGCCCGTGTGGTCCAAGGG
1 ACACGCCCGTGTGGTCC-AGGC
* ** *
39655259 ACACACCTATGTGGTCCTGGC
1 ACACGCCCGTGTGGTCCAGGC
39655280 ACACGCCCGTG
1 ACACGCCCGTG
39655291 CTAGAGGCTA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.19, C:0.35, G:0.30, T:0.17
Consensus pattern (21 bp):
ACACGCCCGTGTGGTCCAGGC
Found at i:39658185 original size:27 final size:27
Alignment explanation
Indices: 39658070--39658186 Score: 135
Period size: 27 Copynumber: 4.3 Consensus size: 27
39658060 GGCAAAAAGC
* * *
39658070 TAATTTTACCCCACAAGGGTATCTCGG
1 TAATTCTACCCTACAAGGGTATTTCGG
*
39658097 TAATTCTACCCTATAAGGGTATTTCGG
1 TAATTCTACCCTACAAGGGTATTTCGG
* * **
39658124 TATTTCTACCCTACATGGGTATTTTAG
1 TAATTCTACCCTACAAGGGTATTTCGG
* * *
39658151 TAACTCTACCCTACAGGGGTATTTTGG
1 TAATTCTACCCTACAAGGGTATTTCGG
39658178 TAATTCTAC
1 TAATTCTAC
39658187 AACTTATCCA
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 76 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (27 bp):
TAATTCTACCCTACAAGGGTATTTCGG
Found at i:39665112 original size:40 final size:39
Alignment explanation
Indices: 39665068--39665249 Score: 183
Period size: 39 Copynumber: 4.6 Consensus size: 39
39665058 AGTGACCATA
*
39665068 TCCGGACTAAGATCCAAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGACTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAT
* * * *
39665108 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGACTAAGTCCGAAGGCATTTGTGCGAGTTACTAAT
*
39665147 TCCAGG-TTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCC-GGACTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAT
*
39665186 AACCGGACTAAGATCCGAAGGCA-TTGTGCGAGTTACT-AT
1 -TCCGGACTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAT
* * * *
39665225 AACCGGGCTATGACCGAAGGCATTT
1 -TCCGGACTAAGTCCGAAGGCATTT
39665250 TAACGAGTAG
Statistics
Matches: 122, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
38 9 0.07
39 62 0.51
40 50 0.41
41 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (39 bp):
TCCGGACTAAGTCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:39665136 original size:39 final size:40
Alignment explanation
Indices: 39665029--39665249 Score: 220
Period size: 40 Copynumber: 5.6 Consensus size: 40
39665019 TGAATGATGT
* * * * * *
39665029 CCGGGCTAAGTCCCGAAGGC-TTTATGCTAAGTGACCATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGC-GAGTTACTATAA
* * * *
39665069 CCGGACTAAGATCCAAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATA-A
*
39665109 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATAA
* * *
39665147 TCCAGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATAA
* *
39665188 CCGGACTAAGATCCGAAGGCA-TTGTGCGAGTTACTATAA
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATAA
*
39665227 CCGGGCTATGA-CCGAAGGCATTT
1 CCGGGCTAAGACCCGAAGGCATTT
39665250 TAACGAGTAG
Statistics
Matches: 152, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
38 9 0.06
39 62 0.41
40 73 0.48
41 8 0.05
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:39665264 original size:78 final size:80
Alignment explanation
Indices: 39665084--39665257 Score: 198
Period size: 79 Copynumber: 2.2 Consensus size: 80
39665074 CTAAGATCCA
* * * *
39665084 AAGGCATTTGTGCGAGTTACTA-ATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 AAGGCATTTGTACGAGTTACTATA-ACCGGACTAAGATCCGAAGGCATTGGTGCGAGTTACTAAA
* *
39665147 TCCAGGTTAAGTCCCG
65 TCCAGGCTAAGTACCG
*
39665163 AAGGCATTTGTGCGAGTTACTATAACCGGACTAAGATCCGAAGGCATT-GTGCGAGTTACTATAA
1 AAGGCATTTGTACGAGTTACTATAACCGGACTAAGATCCGAAGGCATTGGTGCGAGTTACTA-AA
* *
39665227 -CCGGGCTATG-ACCG
65 TCCAGGCTAAGTACCG
39665241 AAGGCATTT-TAACGAGT
1 AAGGCATTTGT-ACGAGT
39665258 AGCTATATCC
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
77 1 0.01
78 17 0.20
79 51 0.61
80 14 0.17
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (80 bp):
AAGGCATTTGTACGAGTTACTATAACCGGACTAAGATCCGAAGGCATTGGTGCGAGTTACTAAAT
CCAGGCTAAGTACCG
Found at i:39672478 original size:79 final size:79
Alignment explanation
Indices: 39672394--39673353 Score: 1802
Period size: 79 Copynumber: 12.2 Consensus size: 79
39672384 GGACTAAGAT
39672394 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
39672459 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
39672473 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
39672538 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
39672552 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
39672617 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
39672631 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
39672696 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
39672710 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
39672775 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
39672789 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
39672854 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
39672868 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
39672933 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
39672947 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
39673012 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
39673026 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
39673091 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
39673105 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
39673170 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
39673184 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
*
39673249 ATCCAGGTTAAGTC
66 ATCCGGGTTAAGTC
* * *
39673263 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGACTAAGATCCGAAGGCATT-GTGCGAGTTACT
1 CCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACT
* * *
39673326 ATAA-CCGGGCTATG-A
64 A-AATCCGGGTTAAGTC
39673341 CCGAAGGCATTTG
1 CCGAAGGCATTTG
39673354 AACGAGTAGC
Statistics
Matches: 870, Mismatches: 8, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
78 15 0.02
79 842 0.97
80 13 0.01
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:39673367 original size:39 final size:38
Alignment explanation
Indices: 39672382--39673353 Score: 389
Period size: 39 Copynumber: 24.7 Consensus size: 38
39672372 GTGACCATAT
*
39672382 CCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGACTAAGATCCGAAGGCA-TT-TGCGAGTTACTATA-A
* *
39672422 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGACTAAGATCCGAAGGCATT--TGCGAGTTACTATAA
** *
39672460 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA-ATT
1 -CCGGACTAAGAT-CCGAAGGCA-TT-TGCGAGTTACTATA-A
* *
39672501 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGACTAAGATCCGAAGGCATT--TGCGAGTTACTATAA
** *
39672539 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA-ATT
1 -CCGGACTAAGAT-CCGAAGGCA-TT-TGCGAGTTACTATA-A
* *
39672580 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGACTAAGATCCGAAGGCATT--TGCGAGTTACTATAA
** *
39672618 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA-ATT
1 -CCGGACTAAGAT-CCGAAGGCA-TT-TGCGAGTTACTATA-A
* *
39672659 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGACTAAGATCCGAAGGCATT--TGCGAGTTACTATAA
** *
39672697 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA-ATT
1 -CCGGACTAAGAT-CCGAAGGCA-TT-TGCGAGTTACTATA-A
* *
39672738 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGACTAAGATCCGAAGGCATT--TGCGAGTTACTATAA
** *
39672776 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA-ATT
1 -CCGGACTAAGAT-CCGAAGGCA-TT-TGCGAGTTACTATA-A
* *
39672817 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGACTAAGATCCGAAGGCATT--TGCGAGTTACTATAA
** *
39672855 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA-ATT
1 -CCGGACTAAGAT-CCGAAGGCA-TT-TGCGAGTTACTATA-A
* *
39672896 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGACTAAGATCCGAAGGCATT--TGCGAGTTACTATAA
** *
39672934 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA-ATT
1 -CCGGACTAAGAT-CCGAAGGCA-TT-TGCGAGTTACTATA-A
* *
39672975 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGACTAAGATCCGAAGGCATT--TGCGAGTTACTATAA
** *
39673013 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA-ATT
1 -CCGGACTAAGAT-CCGAAGGCA-TT-TGCGAGTTACTATA-A
* *
39673054 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGACTAAGATCCGAAGGCATT--TGCGAGTTACTATAA
** *
39673092 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA-ATT
1 -CCGGACTAAGAT-CCGAAGGCA-TT-TGCGAGTTACTATA-A
* *
39673133 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGACTAAGATCCGAAGGCATT--TGCGAGTTACTATAA
** *
39673171 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA-ATT
1 -CCGGACTAAGAT-CCGAAGGCA-TT-TGCGAGTTACTATA-A
* *
39673212 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGACTAAGATCCGAAGGCATT--TGCGAGTTACTATAA
*
39673250 TCCAGG-TTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CC-GGACTAAGAT-CCGAAGGCA-TT-TGCGAGTTACTATAA
39673291 CCGGACTAAGATCCGAAGGCATTGTGCGAGTTACTATAA
1 CCGGACTAAGATCCGAAGGCATT-TGCGAGTTACTATAA
* *
39673330 CCGGGCTATGA-CCGAAGGCATTTG
1 CCGGACTAAGATCCGAAGGCATTTG
39673354 AACGAGTAGC
Statistics
Matches: 806, Mismatches: 68, Indels: 119
0.81 0.07 0.12
Matches are distributed among these distances:
37 2 0.00
38 33 0.04
39 378 0.47
40 368 0.46
41 25 0.03
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (38 bp):
CCGGACTAAGATCCGAAGGCATTTGCGAGTTACTATAA
Found at i:39675050 original size:28 final size:29
Alignment explanation
Indices: 39675013--39675079 Score: 100
Period size: 28 Copynumber: 2.3 Consensus size: 29
39675003 AAGTCTACAT
*
39675013 ACATACATATGGCCCACTAGGCCC-AATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
* *
39675041 TCATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
39675070 ACATTCATAT
1 ACATTCATAT
39675080 TCATGCTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 21 0.62
29 13 0.38
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.25
Consensus pattern (29 bp):
ACATTCATATGGCCCACTAGGCCCAAATC
Found at i:39680700 original size:39 final size:39
Alignment explanation
Indices: 39680642--39680718 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
39680632 TTTAACTAAA
39680642 AAACTGTACTAATTAGCCCAACCAAAAATTATAGAAAAT
1 AAACTGTACTAATTAGCCCAACCAAAAATTATAGAAAAT
* * *
39680681 AAACTGTACTAATTGGCCCAATCAAAAATTCTAGAAAA
1 AAACTGTACTAATTAGCCCAACCAAAAATTATAGAAAA
39680719 AATTTAGTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.49, C:0.18, G:0.09, T:0.23
Consensus pattern (39 bp):
AAACTGTACTAATTAGCCCAACCAAAAATTATAGAAAAT
Found at i:39685939 original size:26 final size:25
Alignment explanation
Indices: 39685900--39685951 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
39685890 AAAGTGTTCG
*
39685900 AGTAATGATATATAGTCTACCATTC
1 AGTAATGATATATAATCTACCATTC
39685925 AGTAATGCATATATAATCTACCATTC
1 AGTAATG-ATATATAATCTACCATTC
39685951 A
1 A
39685952 CTCAGGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (25 bp):
AGTAATGATATATAATCTACCATTC
Found at i:39687006 original size:69 final size:69
Alignment explanation
Indices: 39686765--39687016 Score: 276
Period size: 68 Copynumber: 3.7 Consensus size: 69
39686755 CTTCACCTGG
* * * *
39686765 TGCCATAGTCAAGCTACGGTCTTACACATTGTAACCGCATATTTAA-AGTCCTAGA-GGACTCTT
1 TGCCATAGTCAAGCTACGGTCTTACACATTGTAACCCCATGTTTAATA-TCCTTGACAGACTCTT
39686828 TATGA
65 TATGA
* ** * * * *
39686833 TGTCATAGTTGAGTTACGGTCTTACACATTGTAACCCTATGTTTAATGTCC-TGGCAGACTCTTT
1 TGCCATAGTCAAGCTACGGTCTTACACATTGTAACCCCATGTTTAATATCCTTGACAGACTCTTT
39686897 ATGA
66 ATGA
* ** * * *
39686901 TGTCATAGTTGAGCTATGGTCTTACACATTGAAACCCCATGTTTAATATCCTTGACAAACTCTTT
1 TGCCATAGTCAAGCTACGGTCTTACACATTGTAACCCCATGTTTAATATCCTTGACAGACTCTTT
*
39686966 ACGA
66 ATGA
* * * *
39686970 AGCCATAGTCAAGCTATGGTCTCACACTTTGTAACCCCATGTTTAAT
1 TGCCATAGTCAAGCTACGGTCTTACACATTGTAACCCCATGTTTAAT
39687017 GTATTGGTAG
Statistics
Matches: 155, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
67 1 0.01
68 100 0.65
69 54 0.35
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (69 bp):
TGCCATAGTCAAGCTACGGTCTTACACATTGTAACCCCATGTTTAATATCCTTGACAGACTCTTT
ATGA
Found at i:39687754 original size:21 final size:21
Alignment explanation
Indices: 39687704--39687755 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
39687694 AAGCTACTAC
* **
39687704 AGAAAAAGAAGTTGTTGCTGA
1 AGAAAAAGAAGTTATTGAAGA
*
39687725 AGAAGAAGAAGTTATTGAAGA
1 AGAAAAAGAAGTTATTGAAGA
*
39687746 TGAAAAAGAA
1 AGAAAAAGAA
39687756 AACGAAGAGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.52, C:0.02, G:0.27, T:0.19
Consensus pattern (21 bp):
AGAAAAAGAAGTTATTGAAGA
Found at i:39689330 original size:215 final size:214
Alignment explanation
Indices: 39688939--39689331 Score: 693
Period size: 215 Copynumber: 1.8 Consensus size: 214
39688929 CAAATTACCC
39688939 AAAATTTCAGCTAGTGGCCGGCCATGCTATGAGTGGAAACATGTTGGGAACATGTTGGCTTAGTG
1 AAAATTTCAGCTAGTGGCCGGCCATGCTATGAGTGGAAACATGTTGGGAACATGTTGGCTTAGTG
39689004 AGGTATGTTAGAAAAAAATAAAATAGGGAGTATGGGTAATAAAGAAATAAAAACAAAAAAATGTG
66 AGGTATGTTAGAAAAAAATAAAATAGGGAGTATGGGTAATAAAGAAATAAAAACAAAAAAA-GTG
* *
39689069 TGGTTGTTTTCCCCCCCCCCCGCCGTGAGTTAAAGAAAAGAAAAGAAAAAATTTTGTTCATCCTT
130 TGGTTGTTTCCCCCCCCCCCCGCCGTGAGCTAAAGAAAAGAAAAGAAAAAATTTTGTTCATCCTT
39689134 TTTCATCTTCTTTTGGCCGA
195 TTTCATCTTCTTTTGGCCGA
*
39689154 AAAATTTGAGCTAGTGGCCGGCCATGCTATGAGTGGAAACATGTTGGGAACATGTTGGCTTAGTG
1 AAAATTTCAGCTAGTGGCCGGCCATGCTATGAGTGGAAACATGTTGGGAACATGTTGGCTTAGTG
39689219 AGGTATGTTAGAAAAAAATAAAATAGGGAGTATGGGTAATAAAGAAATAAAAACAAAAAAA-TGT
66 AGGTATGTTAGAAAAAAATAAAATAGGGAGTATGGGTAATAAAGAAATAAAAACAAAAAAAGTGT
39689283 -GTT-TTTCCCCCCCCCCCCATGGCCGTGAGCTAAAGAAAAGAAAAAGAAA
131 GGTTGTTTCCCCCCCCCCCC---GCCGTGAGCTAAAGAAAAG-AAAAGAAA
39689332 GGATAATAGA
Statistics
Matches: 171, Mismatches: 3, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
211 14 0.08
212 3 0.02
213 3 0.02
214 18 0.11
215 133 0.78
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (214 bp):
AAAATTTCAGCTAGTGGCCGGCCATGCTATGAGTGGAAACATGTTGGGAACATGTTGGCTTAGTG
AGGTATGTTAGAAAAAAATAAAATAGGGAGTATGGGTAATAAAGAAATAAAAACAAAAAAAGTGT
GGTTGTTTCCCCCCCCCCCCGCCGTGAGCTAAAGAAAAGAAAAGAAAAAATTTTGTTCATCCTTT
TTCATCTTCTTTTGGCCGA
Found at i:39690500 original size:29 final size:28
Alignment explanation
Indices: 39690458--39690570 Score: 122
Period size: 29 Copynumber: 4.0 Consensus size: 28
39690448 CATGAGATTG
*
39690458 GCACTAAGTGTGCGGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGGGTTT-AATTATAT-A
*
39690487 GCACTAAGTGTGCGGGTTTGATTATATA
1 GCACTAAGTGTGCGGGTTTAATTATATA
* *
39690515 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGGGTTTAATTATATA
* **
39690542 GCACTGAGTGTGCGGACTTAATATATATA
1 GCACTAAGTGTGCGGGTTTAAT-TATATA
39690571 TTTTTGAATC
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
27 24 0.32
28 24 0.32
29 26 0.35
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (28 bp):
GCACTAAGTGTGCGGGTTTAATTATATA
Found at i:39690526 original size:28 final size:28
Alignment explanation
Indices: 39690458--39690556 Score: 130
Period size: 27 Copynumber: 3.5 Consensus size: 28
39690448 CATGAGATTG
* *
39690458 GCACTAAGTGTGCGGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGGGTTT-GATTATAT-A
39690487 GCACTAAGTGTGCGGGTTTGATTATATA
1 GCACTAAGTGTGCGGGTTTGATTATATA
*
39690515 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGGGTTTGATTATATA
*
39690542 GCACTGAGTGTGCGG
1 GCACTAAGTGTGCGG
39690557 ACTTAATATA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
27 24 0.38
28 20 0.31
29 20 0.31
ACGTcount: A:0.24, C:0.13, G:0.30, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGGGTTTGATTATATA
Found at i:39690566 original size:27 final size:28
Alignment explanation
Indices: 39690486--39690570 Score: 109
Period size: 27 Copynumber: 3.0 Consensus size: 28
39690476 TAAATTGTTC
**
39690486 AGCACTAAGTGTGCGGGTTTGATTATAT
1 AGCACTAAGTGTGCGGACTTGATTATAT
*
39690514 AGCACTAAGTGTGC-GAGTTGATTATAT
1 AGCACTAAGTGTGCGGACTTGATTATAT
* *
39690541 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGCGGACTTGAT-TATAT
39690570 A
1 A
39690571 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
27 24 0.48
28 20 0.40
29 6 0.12
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGGACTTGATTATAT
Found at i:39698542 original size:28 final size:28
Alignment explanation
Indices: 39698474--39698571 Score: 119
Period size: 27 Copynumber: 3.5 Consensus size: 28
39698464 CATGAGATTG
* * *
39698474 GCACTAAGTGTGCGGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGAGTTT-GATTATAT-A
39698503 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
39698531 GCACTAAGTGTGCAAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
39698558 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
39698572 GACTTAATAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
27 23 0.37
28 20 0.32
29 19 0.31
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:39698585 original size:29 final size:27
Alignment explanation
Indices: 39698502--39698586 Score: 80
Period size: 27 Copynumber: 3.0 Consensus size: 27
39698492 TAAATTGTTC
** *
39698502 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGC-AACTTAATTATAT
* *
39698530 AGCACTAAGTGTGCAAGTTGATTATAT
1 AGCACTAAGTGTGCAACTTAATTATAT
* *
39698557 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGC-AACTTAAT-TATAT
39698586 A
1 A
39698587 TTTTTGAATC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
27 24 0.49
28 19 0.39
29 6 0.12
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCAACTTAATTATAT
Found at i:39702217 original size:27 final size:26
Alignment explanation
Indices: 39702187--39702244 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
39702177 ATTTATAGTA
*
39702187 AAATTATCAATTAG-GGATTAAATTGTG
1 AAATTATAAATT-GTGG-TTAAATTGTG
*
39702214 AAATTTGTAAATTGTGGTTAAATTGTG
1 AAA-TTATAAATTGTGGTTAAATTGTG
39702241 AAAT
1 AAAT
39702245 AAATGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
26 1 0.04
27 17 0.63
28 9 0.33
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (26 bp):
AAATTATAAATTGTGGTTAAATTGTG
Found at i:39703534 original size:14 final size:16
Alignment explanation
Indices: 39703515--39703548 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
39703505 AATGCTTGTG
39703515 GTGAA-TGGT-TGTTT
1 GTGAATTGGTATGTTT
39703529 GTGAATTGGTATGTTT
1 GTGAATTGGTATGTTT
39703545 GTGA
1 GTGA
39703549 TTTAGGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 4 0.22
16 9 0.50
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (16 bp):
GTGAATTGGTATGTTT
Found at i:39704910 original size:43 final size:43
Alignment explanation
Indices: 39704862--39704969 Score: 162
Period size: 43 Copynumber: 2.5 Consensus size: 43
39704852 GATTAACAAG
* *
39704862 ATGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATCTTT
1 ATGTGATTATGTGTAAGACCATGTCTAGGACATTGGCATCGTT
**
39704905 ATGTGATTCCGTGTAAGACCATGTCTAGGACATTGGCATCGTT
1 ATGTGATTATGTGTAAGACCATGTCTAGGACATTGGCATCGTT
* *
39704948 ATTTGATTTTGTGTAAGACCAT
1 ATGTGATTATGTGTAAGACCAT
39704970 AGTTGGGCTA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (43 bp):
ATGTGATTATGTGTAAGACCATGTCTAGGACATTGGCATCGTT
Found at i:39704986 original size:43 final size:42
Alignment explanation
Indices: 39704862--39704996 Score: 155
Period size: 43 Copynumber: 3.1 Consensus size: 42
39704852 GATTAACAAG
*
39704862 ATGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATCTTT
1 ATGTGATTATGTGTAAGACCATGTCTGGG-CATTGGCATCGTT
** *
39704905 ATGTGATTCCGTGTAAGACCATGTCTAGGACATTGGCATCGTT
1 ATGTGATTATGTGTAAGACCATGTCT-GGGCATTGGCATCGTT
* * * *
39704948 ATTTGATTTTGTGTAAGACCATAGT-TGGGCTATCGGCATCGAT
1 ATGTGATTATGTGTAAGACCAT-GTCTGGGC-ATTGGCATCGTT
39704991 ATGTGA
1 ATGTGA
39704997 AAACATGTGA
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
42 3 0.04
43 71 0.91
44 4 0.05
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.36
Consensus pattern (42 bp):
ATGTGATTATGTGTAAGACCATGTCTGGGCATTGGCATCGTT
Found at i:39706242 original size:18 final size:18
Alignment explanation
Indices: 39706221--39706260 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
39706211 ACAATATGAT
*
39706221 TATACTGAATG-ATATATG
1 TATA-TGAATGTATAAATG
39706239 TATATGAATGTATAAATG
1 TATATGAATGTATAAATG
39706257 TATA
1 TATA
39706261 AGATTTGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (18 bp):
TATATGAATGTATAAATG
Found at i:39710498 original size:40 final size:40
Alignment explanation
Indices: 39710428--39710844 Score: 725
Period size: 40 Copynumber: 10.5 Consensus size: 40
39710418 AAACCAAGTA
* *
39710428 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
39710467 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39710507 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39710547 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39710587 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39710627 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39710667 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39710707 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
39710747 CCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
39710787 CCTTCGGGACTT-GCCCGGA-ACTAGTCACTAGCGCAGATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
39710826 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
39710845 TTATCATCCA
Statistics
Matches: 366, Mismatches: 8, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
39 47 0.13
40 319 0.87
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:39728903 original size:4 final size:5
Alignment explanation
Indices: 39728844--39728932 Score: 67
Period size: 5 Copynumber: 16.8 Consensus size: 5
39728834 TATGTCTTTC
* *
39728844 AAAAT AAAAT --AAT AAAATT GAAAT GAAAAT AAAAAT CAAAAGA AAAAT
1 AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT -AAAAT -AAAA-T AAAAT
39728892 AAAA- ATAAAT AAAAT AAAAT AAAAT AAAAAT AAGAAT AAAA
1 AAAAT A-AAAT AAAAT AAAAT AAAAT -AAAAT AA-AAT AAAA
39728933 AAATAGGAGG
Statistics
Matches: 69, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
3 3 0.04
4 1 0.01
5 33 0.48
6 32 0.46
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:39728935 original size:25 final size:24
Alignment explanation
Indices: 39728844--39728937 Score: 84
Period size: 25 Copynumber: 3.8 Consensus size: 24
39728834 TATGTCTTTC
* * *
39728844 AAAATAAAATAATAAAATTGAAATG
1 AAAATAAAATAA-AAAAATAAAATA
* *
39728869 AAAATAAAAATCAAAAGA-AAAATA
1 AAAAT-AAAATAAAAAAATAAAATA
39728893 AAAAT-AAATAAAATAAAATAAAATA
1 AAAATAAAAT-AAA-AAAATAAAATA
39728918 AAAATAAGAATAAAAAAATA
1 AAAATAA-AATAAAAAAATA
39728938 GGAGGATTCA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
22 4 0.07
23 2 0.04
24 12 0.21
25 25 0.45
26 10 0.18
27 3 0.05
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (24 bp):
AAAATAAAATAAAAAAATAAAATA
Found at i:39734314 original size:13 final size:13
Alignment explanation
Indices: 39734292--39734324 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
39734282 AAGGATTTGT
39734292 TTAT-TAAACTAA
1 TTATCTAAACTAA
39734304 TTATCTAAACTAA
1 TTATCTAAACTAA
*
39734317 TTAACTAA
1 TTATCTAA
39734325 TTTAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:39735563 original size:37 final size:37
Alignment explanation
Indices: 39735499--39735607 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
39735489 AGCTCAGACG
* * * *
39735499 AAATCTCCACATGAAGTTATCGAGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
39735536 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
39735573 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
39735608 ATATATTTCC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:39736131 original size:51 final size:51
Alignment explanation
Indices: 39735819--39736817 Score: 1558
Period size: 51 Copynumber: 19.7 Consensus size: 51
39735809 ATATATTCAT
* * * **
39735819 GTTCACATTCATCACATTGGCCATTCGGCCTTATCTC----ATATATGCAT
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
* * *
39735866 GTTCACATTCATCACATTGGCCATTCGGCCTTATCACGCATATATATATACAG
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCA--CAGATATATATACGG
* * * * * ***
39735919 GTTCACATTCATCACATTGACCATTCGGACTTATCCCACATACGCAT----
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
* * *
39735966 GTTCACATTCATCACATTGGCCATTCGGCCTTATCACGCATATATATATACAG
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCA--CAGATATATATACGG
* * * * ***
39736019 GTTCACATTCATCACATTGACCATTCGGACTTATCACACATACGCAT----
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
39736066 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
* * * * *
39736117 GTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTC--
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATA--TATATACGG
39736168 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
39736219 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
39736270 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
39736321 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
39736372 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
39736423 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
39736474 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
39736525 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
39736576 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
39736627 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
39736678 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
39736729 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
*
39736780 GTTCACATTCATCACATTGGCCATTCGGCCTTATCACA
1 GTTCACATTCATCACATTGGCCATTCAGCCTTATCACA
39736818 CATACGCATG
Statistics
Matches: 891, Mismatches: 41, Indels: 36
0.92 0.04 0.04
Matches are distributed among these distances:
47 108 0.12
49 12 0.01
51 692 0.78
53 79 0.09
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (51 bp):
GTTCACATTCATCACATTGGCCATTCAGCCTTATCACAGATATATATACGG
Found at i:39740916 original size:40 final size:40
Alignment explanation
Indices: 39740872--39741330 Score: 810
Period size: 40 Copynumber: 11.5 Consensus size: 40
39740862 TCTTCGGGGT
* * *
39740872 TTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
*
39740912 TTAGCCCGGATACATCACTAGCACGAATGCTCCTCGGGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
*
39740952 GTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
39740992 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
*
39741032 TTAGCCCGAATATATCACTAGCACGAATGCTCCTCGGGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
39741072 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
*
39741112 TTAGCCCGAATATATCACTAGCACGAATGCTCCTCGGGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
39741152 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
*
39741192 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGAGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
39741232 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
* * * *
39741272 TTAGCACGGATACATCACTAGCACGAATGCTCTTCGAGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
39741312 TTAGCCCGGATATATCACT
1 TTAGCCCGGATATATCACT
39741331 CTCAGTTCTC
Statistics
Matches: 400, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 400 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
Found at i:39741526 original size:43 final size:43
Alignment explanation
Indices: 39741473--39741560 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
39741463 ATAGTCATAA
39741473 CACTCCTTCAAAATTGCATCACTTATACCCTTATAATTCAATC
1 CACTCCTTCAAAATTGCATCACTTATACCCTTATAATTCAATC
* *
39741516 CACTCTTTCAAAATTGCGTCACTTATACCCTTATAATTCAATC
1 CACTCCTTCAAAATTGCATCACTTATACCCTTATAATTCAATC
39741559 CA
1 CA
39741561 AATCGAAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.35
Consensus pattern (43 bp):
CACTCCTTCAAAATTGCATCACTTATACCCTTATAATTCAATC
Found at i:39742691 original size:37 final size:37
Alignment explanation
Indices: 39742627--39742735 Score: 155
Period size: 37 Copynumber: 2.9 Consensus size: 37
39742617 AGCTTAGACG
* * * *
39742627 AAATCTCCACATGAAGTTATCGAGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
39742664 AAATCTCCACACGTAGTCATCGGGTCTTACCCGAACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
39742701 TAATCTCTACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
39742736 ATATATTTCC
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.25
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:39743006 original size:47 final size:47
Alignment explanation
Indices: 39742944--39743140 Score: 223
Period size: 47 Copynumber: 4.1 Consensus size: 47
39742934 ACACGCTTCG
* * **
39742944 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTACCACACATACGCATGTTCACATTCATCA
* * ** *
39742991 CATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCC-T-T-AC-C--ACACATACGCATGTTCACATTCATCA
* *
39743044 CATTGGCCATTCGGACTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTACCACACATACGCATGTTCACATTCATCA
* *
39743091 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTACCACACATACGCATGTTCACATTCATCA
39743138 CAT
1 CAT
39743141 AAAATCCTAA
Statistics
Matches: 131, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
47 84 0.64
48 1 0.01
49 2 0.02
50 3 0.02
51 2 0.02
52 1 0.01
53 38 0.29
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTACCACACATACGCATGTTCACATTCATCA
Found at i:39745422 original size:44 final size:44
Alignment explanation
Indices: 39745374--39745592 Score: 128
Period size: 44 Copynumber: 5.1 Consensus size: 44
39745364 CCCCAACATG
39745374 TTTATGACATGTTTTTAGCCATAACATCTTGTCCACCCAAGCTC
1 TTTATGACATGTTTTTAGCCATAACATCTTGTCCACCCAAGCTC
* * * ** *
39745418 TTTAT----T-TTATTAATCC-TTACATAATG-CACTACCCCAA-CATG
1 TTTATGACATGTT-TTTAGCCATAACATCTTGTC-C-A-CCCAAGC-TC
39745459 TTTATGACATGTTTTTAGCCATAACATCTTGTCCACCCAAGCTC
1 TTTATGACATGTTTTTAGCCATAACATCTTGTCCACCCAAGCTC
* * * ** *
39745503 TTTAT----T-TTATTAATCC-TTACATAATG-CACTACCCCAA-CATG
1 TTTATGACATGTT-TTTAGCCATAACATCTTGTC-C-A-CCCAAGC-TC
39745544 TTTATGACATGTTTTTAGCCATAACATCTTGTCCACCCAAGCTC
1 TTTATGACATGTTTTTAGCCATAACATCTTGTCCACCCAAGCTC
39745588 TTTAT
1 TTTAT
39745593 TTTATTAATC
Statistics
Matches: 125, Mismatches: 24, Indels: 52
0.62 0.12 0.26
Matches are distributed among these distances:
38 2 0.02
39 20 0.16
40 16 0.13
41 22 0.18
44 27 0.22
45 16 0.13
46 20 0.16
47 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.09, T:0.38
Consensus pattern (44 bp):
TTTATGACATGTTTTTAGCCATAACATCTTGTCCACCCAAGCTC
Found at i:39745430 original size:85 final size:85
Alignment explanation
Indices: 39745332--39745672 Score: 664
Period size: 85 Copynumber: 4.0 Consensus size: 85
39745322 TGTCCATGCC
39745332 CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
1 CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
39745397 ACATCTTGTCCACCCAAGCT
66 ACATCTTGTCCACCCAAGCT
39745417 CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
1 CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
39745482 ACATCTTGTCCACCCAAGCT
66 ACATCTTGTCCACCCAAGCT
39745502 CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
1 CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
39745567 ACATCTTGTCCACCCAAGCT
66 ACATCTTGTCCACCCAAGCT
39745587 CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
1 CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
* *
39745652 ACATCTTGCCCACCCATGCT
66 ACATCTTGTCCACCCAAGCT
39745672 C
1 C
39745673 ATGGCCGGCC
Statistics
Matches: 254, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 254 1.00
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (85 bp):
CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATA
ACATCTTGTCCACCCAAGCT
Found at i:39773834 original size:12 final size:12
Alignment explanation
Indices: 39773813--39773880 Score: 57
Period size: 12 Copynumber: 5.4 Consensus size: 12
39773803 TAATAAGAAT
*
39773813 TAAAACTAATAA
1 TAAAAATAATAA
39773825 TAAAAATAATAA
1 TAAAAATAATAA
* *
39773837 -AGAAATGGATATAG
1 TAAAAAT--A-ATAA
39773851 TAAATAATAATAA
1 TAAA-AATAATAA
*
39773864 TAATAATAATAA
1 TAAAAATAATAA
39773876 TAAAA
1 TAAAA
39773881 GAAGTTGAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
11 5 0.11
12 23 0.52
13 7 0.16
14 4 0.09
15 2 0.05
16 3 0.07
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.26
Consensus pattern (12 bp):
TAAAAATAATAA
Found at i:39773864 original size:6 final size:6
Alignment explanation
Indices: 39773853--39773878 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
39773843 GGATATAGTA
39773853 AATAAT AATAAT AATAAT AATAAT AA
1 AATAAT AATAAT AATAAT AATAAT AA
39773879 AAGAAGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATAAT
Found at i:39775144 original size:56 final size:56
Alignment explanation
Indices: 39775058--39775167 Score: 211
Period size: 56 Copynumber: 2.0 Consensus size: 56
39775048 ATATTCGCAT
*
39775058 GTCAAAACTCCTCTTTCTTGTGGTCAATTCTATTATTAAAATATGGTTTGAGTCGA
1 GTCAAAACTCCTCTTTCTTGCGGTCAATTCTATTATTAAAATATGGTTTGAGTCGA
39775114 GTCAAAACTCCTCTTTCTTGCGGTCAATTCTATTATTAAAATATGGTTTGAGTC
1 GTCAAAACTCCTCTTTCTTGCGGTCAATTCTATTATTAAAATATGGTTTGAGTC
39775168 AAGTAATATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (56 bp):
GTCAAAACTCCTCTTTCTTGCGGTCAATTCTATTATTAAAATATGGTTTGAGTCGA
Found at i:39779429 original size:17 final size:19
Alignment explanation
Indices: 39779397--39779434 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
39779387 AAACCTTCAA
39779397 TTTTCTCTTTTCTTCTTTC
1 TTTTCTCTTTTCTTCTTTC
39779416 TTTTCTC-TTT-TTCTTTC
1 TTTTCTCTTTTCTTCTTTC
39779433 TT
1 TT
39779435 CCTTCCCCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 3 0.16
19 7 0.37
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCTCTTTTCTTCTTTC
Found at i:39786295 original size:44 final size:43
Alignment explanation
Indices: 39786227--39786311 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 43
39786217 ATTGACTTTT
* * * *
39786227 GATTTACGTGTAAGACCATTTCTGGGACGTTGGCATCGATTTGA
1 GATTCACGTGTAAGACCATGTCTGGGACATCGGCATC-ATTTGA
39786271 GATTCACGTGTAAGACCCA-GTCTGGGACATCGGCATCATTT
1 GATTCACGTGTAAGA-CCATGTCTGGGACATCGGCATCATTT
39786312 TTTATTTCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 4 0.11
44 29 0.81
45 3 0.08
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (43 bp):
GATTCACGTGTAAGACCATGTCTGGGACATCGGCATCATTTGA
Found at i:39790100 original size:27 final size:28
Alignment explanation
Indices: 39790070--39790140 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 28
39790060 TATTTTAATG
39790070 CATGTTTTTAATATGTCATAGT-TAGTA
1 CATGTTTTTAATATGTCATAGTCTAGTA
* * * * *
39790097 CATGTTATTAATTTGTCTTGGTCTATTA
1 CATGTTTTTAATATGTCATAGTCTAGTA
*
39790125 CATATTTTTAATATGT
1 CATGTTTTTAATATGT
39790141 TCTAGCTTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 18 0.51
28 17 0.49
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.52
Consensus pattern (28 bp):
CATGTTTTTAATATGTCATAGTCTAGTA
Done.