Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 143 of 427
Found at i:38700445 original size:27 final size:28
Alignment explanation
Indices: 38700403--38700482 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 28
38700393 TTCAATTATT
38700403 AAATTCAAATAGTAAAAAAATAAAAATT-G
1 AAATT-AAAT-GTAAAAAAATAAAAATTAG
38700432 AAATTAAATGTAAAAAAACT-AAAATTAG
1 AAATTAAATGTAAAAAAA-TAAAAATTAG
38700460 AAA-TAAA---AATAAAAATAAAAATT
1 AAATTAAATGTAA-AAAAATAAAAATT
38700483 TAATTTTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
24 3 0.06
25 11 0.23
27 19 0.40
28 9 0.19
29 5 0.11
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.24
Consensus pattern (28 bp):
AAATTAAATGTAAAAAAATAAAAATTAG
Found at i:38700447 original size:28 final size:29
Alignment explanation
Indices: 38700403--38700482 Score: 75
Period size: 28 Copynumber: 2.9 Consensus size: 29
38700393 TTCAATTATT
38700403 AAATTCAAATAGT-AAAAAAATAAAAATT-G
1 AAATT-AAAT-GTAAAAAAAATAAAAATTAG
*
38700432 AAATTAAATGTAAAAAAACT-AAAATTAG
1 AAATTAAATGTAAAAAAAATAAAAATTAG
*
38700460 AAA-TAAA---AATAAAAATAAAAATT
1 AAATTAAATGTAAAAAAAATAAAAATT
38700483 TAATTTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
24 7 0.16
25 6 0.13
27 12 0.27
28 15 0.33
29 5 0.11
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.24
Consensus pattern (29 bp):
AAATTAAATGTAAAAAAAATAAAAATTAG
Found at i:38707691 original size:16 final size:16
Alignment explanation
Indices: 38707670--38707706 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
38707660 GTAGATCGGC
38707670 AAAAGTCAAAATGCCG
1 AAAAGTCAAAATGCCG
*
38707686 AAAAGTCGAAATGCCG
1 AAAAGTCAAAATGCCG
38707702 AAAAG
1 AAAAG
38707707 CTAAAAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (16 bp):
AAAAGTCAAAATGCCG
Found at i:38707960 original size:28 final size:28
Alignment explanation
Indices: 38707928--38708043 Score: 108
Period size: 28 Copynumber: 4.1 Consensus size: 28
38707918 GCATGACTGA
* * *
38707928 AAAAGTGATTGGGCCTAGTGGGCCATAT
1 AAAAGTGATTAGACCTAATGGGCCATAT
*
38707956 AAAAGTGATTTA-AGCCTAATGGACCATAT
1 AAAAGTGA-TTAGA-CCTAATGGGCCATAT
* * *
38707985 AAATGTGATTGGACTTAATGGGCCATAT
1 AAAAGTGATTAGACCTAATGGGCCATAT
* * * *
38708013 GAAAGAGATTAGACCTAGTAGGCCATAT
1 AAAAGTGATTAGACCTAATGGGCCATAT
38708041 AAA
1 AAA
38708044 GGTATGTGGA
Statistics
Matches: 69, Mismatches: 16, Indels: 6
0.76 0.18 0.07
Matches are distributed among these distances:
28 46 0.67
29 23 0.33
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (28 bp):
AAAAGTGATTAGACCTAATGGGCCATAT
Found at i:38715465 original size:16 final size:16
Alignment explanation
Indices: 38715438--38715480 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
38715428 ATAGATCAGC
*
38715438 AAAAGCCGAAATGCCA
1 AAAAGCCAAAATGCCA
* *
38715454 AAAAGTCAAAATGCCG
1 AAAAGCCAAAATGCCA
38715470 AAAAGCCAAAA
1 AAAAGCCAAAA
38715481 GTTTGGCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.56, C:0.21, G:0.16, T:0.07
Consensus pattern (16 bp):
AAAAGCCAAAATGCCA
Found at i:38715737 original size:29 final size:28
Alignment explanation
Indices: 38715696--38715809 Score: 149
Period size: 28 Copynumber: 4.0 Consensus size: 28
38715686 GCATGACTGA
*
38715696 AAAAGTGATTGGGCCTAGTGGGCCATAT
1 AAAAGTGATTGGGCCTAATGGGCCATAT
*
38715724 AAAAGTGATTTGGGCCTAATGGGCCACAT
1 AAAAGTGA-TTGGGCCTAATGGGCCATAT
*
38715753 AAATGTGATTGGG-CTAAATGGGCCATAT
1 AAAAGTGATTGGGCCT-AATGGGCCATAT
* * *
38715781 GAAAGAGATTGGGCCTAGTGGGCCATAT
1 AAAAGTGATTGGGCCTAATGGGCCATAT
38715809 A
1 A
38715810 TAGGTATGTG
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
27 2 0.03
28 45 0.61
29 27 0.36
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.25
Consensus pattern (28 bp):
AAAAGTGATTGGGCCTAATGGGCCATAT
Found at i:38720559 original size:17 final size:17
Alignment explanation
Indices: 38720539--38720581 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
38720529 ATCGAAAAAG
*
38720539 TAAAAAAAATAAAAATT
1 TAAAAAAAAGAAAAATT
*
38720556 TAAAAATAAAGAAAAGTT
1 TAAAAA-AAAGAAAAATT
38720574 TAAAAAAA
1 TAAAAAAA
38720582 TATTTTGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
TAAAAAAAAGAAAAATT
Found at i:38729714 original size:23 final size:23
Alignment explanation
Indices: 38729688--38729732 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
38729678 TGGGTATGTG
*
38729688 ATGACGTTAT-TTTATAAATATGC
1 ATGAAGTTATCTTTA-AAATATGC
*
38729711 ATGAATTTATCTTTAAAATATG
1 ATGAAGTTATCTTTAAAATATG
38729733 TTGAATTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (23 bp):
ATGAAGTTATCTTTAAAATATGC
Found at i:38742194 original size:29 final size:29
Alignment explanation
Indices: 38742168--38742240 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
38742158 TTTTCAGCTT
* *
38742168 GCACACATAGTGTCATATTTTTCCAGCAC
1 GCACACTTAGTGCCATATTTTTCCAGCAC
*
38742197 GCACACTTAGTGCCATATATTTCCAGCAC
1 GCACACTTAGTGCCATATTTTTCCAGCAC
38742226 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
38742241 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (29 bp):
GCACACTTAGTGCCATATTTTTCCAGCAC
Found at i:38748279 original size:29 final size:29
Alignment explanation
Indices: 38748268--38748340 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
38748258 TTTTCAGCTT
*
38748268 GCACACATAGTGTCATATTTTTCCAGCAC
1 GCACACATAGTGCCATATTTTTCCAGCAC
* *
38748297 GCACACTTAGTGCCATATATTTCCAGCAC
1 GCACACATAGTGCCATATTTTTCCAGCAC
*
38748326 GCACACTTAGTGCCA
1 GCACACATAGTGCCA
38748341 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (29 bp):
GCACACATAGTGCCATATTTTTCCAGCAC
Found at i:38754845 original size:39 final size:39
Alignment explanation
Indices: 38754651--38754843 Score: 262
Period size: 39 Copynumber: 4.9 Consensus size: 39
38754641 TCATTCAAAC
* * * * * * *
38754651 GCCTTCGGGACATAGCCCGGTTATGATAACCCGCGCAAAT
1 GCCTTCGGG-CTTAGCCCGGATATCACAACTCGCACAATT
*
38754691 GCCTTCGGGACTTA-ACCGGATATCACAACTCGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCACAACTCGCACAATT
*
38754730 GCCTTCGGGATTAGCCCGGATATCACAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATT
*
38754769 GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACATTT
1 GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATT
*
38754808 GCCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACA
38754844 TTCATACACA
Statistics
Matches: 139, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
38 3 0.02
39 123 0.88
40 13 0.09
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATT
Found at i:38762675 original size:39 final size:40
Alignment explanation
Indices: 38762574--38762729 Score: 190
Period size: 39 Copynumber: 4.0 Consensus size: 40
38762564 CTCGTTCAAA
* * * * * *
38762574 TGCCTTCAGGACATAGCCCGGTTATGATAACCCGCACAAA
1 TGCCTTCAGGACTTAGCCCGGATATCACAACTCGCACAAT
* * *
38762614 TGCCGTCGGGACTTAACCCGGATATCACAACTCGCACAAT
1 TGCCTTCAGGACTTAGCCCGGATATCACAACTCGCACAAT
*
38762654 TGCCTTCAGG-CTTAGCCCGGATATCACAACTCGCACATT
1 TGCCTTCAGGACTTAGCCCGGATATCACAACTCGCACAAT
* *
38762693 TGCCTTC-GGGCTTAGCCCGGATATCACAATTCGCACA
1 TGCCTTCAGGACTTAGCCCGGATATCACAACTCGCACA
38762730 TTCATACACA
Statistics
Matches: 101, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
38 2 0.02
39 60 0.59
40 39 0.39
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (40 bp):
TGCCTTCAGGACTTAGCCCGGATATCACAACTCGCACAAT
Found at i:38762702 original size:79 final size:79
Alignment explanation
Indices: 38762574--38762729 Score: 206
Period size: 79 Copynumber: 2.0 Consensus size: 79
38762564 CTCGTTCAAA
* * *
38762574 TGCCTTCAGGACATAGCCCGGTTATGATAACCCGCACAAATGCCGTCGGGACTTAACCCGGATAT
1 TGCCTTCAGGACATAGCCCGGATATCACAACCCGCACAAATGCCGTCGGG-CTTAACCCGGATAT
38762639 CACAACTCGCACAAT
65 CACAACTCGCACAAT
* * ** * *
38762654 TGCCTTCAGG-CTTAGCCCGGATATCACAACTCGCACATTTGCCTTCGGGCTTAGCCCGGATATC
1 TGCCTTCAGGACATAGCCCGGATATCACAACCCGCACAAATGCCGTCGGGCTTAACCCGGATATC
*
38762718 ACAATTCGCACA
66 ACAACTCGCACA
38762730 TTCATACACA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
78 25 0.38
79 31 0.47
80 10 0.15
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (79 bp):
TGCCTTCAGGACATAGCCCGGATATCACAACCCGCACAAATGCCGTCGGGCTTAACCCGGATATC
ACAACTCGCACAAT
Found at i:38764370 original size:15 final size:15
Alignment explanation
Indices: 38764350--38764378 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38764340 TTGCACATAA
38764350 AAAAATAAATAAATG
1 AAAAATAAATAAATG
38764365 AAAAATAAATAAAT
1 AAAAATAAATAAAT
38764379 AAAGGCTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAAAATAAATAAATG
Found at i:38767778 original size:44 final size:44
Alignment explanation
Indices: 38767715--38767800 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
38767705 TAACAATAGC
*
38767715 AGTACGACACACATGGTGCCTCATCGACTCAAAGTCAAAGTAAT
1 AGTACGACACACATAGTGCCTCATCGACTCAAAGTCAAAGTAAT
** * *
38767759 AGTACGACACTTATAGTGCCTCATCGACTCAAGGTCGAAGTA
1 AGTACGACACACATAGTGCCTCATCGACTCAAAGTCAAAGTA
38767801 TCCCTGAACA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (44 bp):
AGTACGACACACATAGTGCCTCATCGACTCAAAGTCAAAGTAAT
Found at i:38768593 original size:4 final size:4
Alignment explanation
Indices: 38768584--38768663 Score: 51
Period size: 4 Copynumber: 19.8 Consensus size: 4
38768574 ATTTTTCCTT
* *
38768584 TTTC TTTC TTTC CTTC TTTC TTTC TCTC -TT- TTTC TTTTC TTTC --TC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC
* *
38768629 TGTTC TAATTC TTTAC TTTA TTTC TTTA TTTC TTT
1 T-TTC T--TTC TTT-C TTTC TTTC TTTC TTTC TTT
38768664 TTATTTCTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
2 2 0.03
3 3 0.05
4 39 0.66
5 11 0.19
6 4 0.07
ACGTcount: A:0.06, C:0.23, G:0.01, T:0.70
Consensus pattern (4 bp):
TTTC
Found at i:38770319 original size:14 final size:15
Alignment explanation
Indices: 38770300--38770329 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
38770290 ATTTATTTTG
38770300 GAAATTA-AAAATTT
1 GAAATTATAAAATTT
38770314 GAAATTATAAAATTT
1 GAAATTATAAAATTT
38770329 G
1 G
38770330 CTTTATACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (15 bp):
GAAATTATAAAATTT
Found at i:38770862 original size:52 final size:52
Alignment explanation
Indices: 38770804--38770907 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
38770794 TAGAAACATG
*
38770804 TTTAAATGCATATATCAGCGTGAGCATGGTATAATCAAATAGAATAATCCTA
1 TTTAAATGCATATATCAACGTGAGCATGGTATAATCAAATAGAATAATCCTA
38770856 TTTAAATGCATATATCAACGTGAGCATGGTATAATCAAATAGAATAATCCTA
1 TTTAAATGCATATATCAACGTGAGCATGGTATAATCAAATAGAATAATCCTA
38770908 CCCCCATTCA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (52 bp):
TTTAAATGCATATATCAACGTGAGCATGGTATAATCAAATAGAATAATCCTA
Found at i:38771550 original size:22 final size:22
Alignment explanation
Indices: 38771525--38771568 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
38771515 TAGTCATATA
38771525 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
38771547 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
38771569 TATTTAATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:38773097 original size:10 final size:10
Alignment explanation
Indices: 38773082--38773106 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
38773072 CTGTATATAT
38773082 CTATTACGTA
1 CTATTACGTA
38773092 CTATTACGTA
1 CTATTACGTA
38773102 CTATT
1 CTATT
38773107 TAACGGTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.20, G:0.08, T:0.44
Consensus pattern (10 bp):
CTATTACGTA
Found at i:38777239 original size:26 final size:26
Alignment explanation
Indices: 38777203--38777258 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
38777193 CCATAGACAA
38777203 GTCTGTAAGGTGATGTCCCTATGGGG
1 GTCTGTAAGGTGATGTCCCTATGGGG
38777229 GTCTGTAAGGTGATGTCCCTATGGGG
1 GTCTGTAAGGTGATGTCCCTATGGGG
38777255 GTCT
1 GTCT
38777259 TAAAAGCAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.14, C:0.16, G:0.38, T:0.32
Consensus pattern (26 bp):
GTCTGTAAGGTGATGTCCCTATGGGG
Found at i:38785777 original size:21 final size:21
Alignment explanation
Indices: 38785753--38785834 Score: 146
Period size: 21 Copynumber: 3.9 Consensus size: 21
38785743 ACGGGTGCTA
38785753 GACACGCCCGTGTTCATTTTT
1 GACACGCCCGTGTTCATTTTT
38785774 GACACGCCCGTGTTCATTTTT
1 GACACGCCCGTGTTCATTTTT
*
38785795 GACACGCCTGTGTTCATTTTT
1 GACACGCCCGTGTTCATTTTT
*
38785816 GACATGCCCGTGTTCATTT
1 GACACGCCCGTGTTCATTT
38785835 GGCAGATTTG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.15, C:0.27, G:0.20, T:0.39
Consensus pattern (21 bp):
GACACGCCCGTGTTCATTTTT
Found at i:38789925 original size:13 final size:13
Alignment explanation
Indices: 38789903--38789941 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
38789893 GCTCGGCAGA
*
38789903 GACACACCCGTGT
1 GACACGCCCGTGT
38789916 GACACGCCCGTGT
1 GACACGCCCGTGT
38789929 GACACGCCCGTGT
1 GACACGCCCGTGT
38789942 ACGATTACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.18, C:0.38, G:0.28, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:38791993 original size:3 final size:3
Alignment explanation
Indices: 38791985--38792138 Score: 130
Period size: 3 Copynumber: 48.7 Consensus size: 3
38791975 ATAACTATTG
* * *
38791985 ATA ATA ATA GTA ATA ATA ATA ATA ATA ACA ATA TATA ATA AT- CTAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA AT-A
* * * * * * *
38792031 ATC TTT TTA TATA TATA CATA AAA AGA GTA ATAA ATA GATTA ATA GATA
1 ATA ATA ATA -ATA -ATA -ATA ATA ATA ATA AT-A ATA -A-TA ATA -ATA
38792080 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
38792128 ATA ATA ATA AT
1 ATA ATA ATA AT
38792139 GATGATGATG
Statistics
Matches: 126, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
2 1 0.01
3 102 0.81
4 21 0.17
5 2 0.02
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:38792143 original size:3 final size:3
Alignment explanation
Indices: 38792137--38792163 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
38792127 AATAATAATA
38792137 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
38792164 GCACAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:38792322 original size:16 final size:16
Alignment explanation
Indices: 38792296--38792340 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
38792286 AAATGTAAAG
38792296 AATAA-TGAATAAAT-
1 AATAAGTGAATAAATA
38792310 AATCAAGTGAATAAATA
1 AAT-AAGTGAATAAATA
*
38792327 AATAAGTAAATAAA
1 AATAAGTGAATAAA
38792341 AGGATTAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 3 0.11
15 2 0.07
16 19 0.70
17 3 0.11
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.24
Consensus pattern (16 bp):
AATAAGTGAATAAATA
Found at i:38793621 original size:13 final size:13
Alignment explanation
Indices: 38793603--38793634 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
38793593 AATAGACTTT
38793603 TTATTTGGATTTA
1 TTATTTGGATTTA
*
38793616 TTATTTGGTTTTA
1 TTATTTGGATTTA
38793629 TTATTT
1 TTATTT
38793635 TTGGTTTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (13 bp):
TTATTTGGATTTA
Found at i:38793894 original size:44 final size:44
Alignment explanation
Indices: 38793841--38794096 Score: 234
Period size: 44 Copynumber: 5.8 Consensus size: 44
38793831 TGTCGCTTCG
* *
38793841 ATCTGCTCCACTGCAACTTCATG-GAGATAAGATTTGTAGTTTTA
1 ATCTGCTCCACTGCAACTTCA-GAGAGATAAGATTCGTAGCTTTA
** * *
38793885 ATCCACTCCACTGCAACTTCAGAGAGATAAGATTCATGGCTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATTCGTAGCTTTA
** *
38793929 ATCTGCT-CGTTGCAACTTCAGGGAGATAAGA-T--TAGCCATTTACA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATTCGTAG-C-TTT--A
* * * * *
38793973 ATCTGCTCCACTGCAACTTCAGGGAGTTGAGATTCGTAACTTCA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATTCGTAGCTTTA
* * * * * *
38794017 ACCTGCTTCACTGCAACTTTAGTGAGATAAGGTTCGTGGCTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATTCGTAGCTTTA
* *
38794061 ATCTACACCACTGCAACTTCAGAGAGATAAGATTCG
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATTCG
38794097 CTATGATAAC
Statistics
Matches: 168, Mismatches: 35, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
40 2 0.01
41 1 0.01
42 4 0.02
43 22 0.13
44 113 0.67
45 20 0.12
46 3 0.02
47 1 0.01
48 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGAGAGATAAGATTCGTAGCTTTA
Found at i:38794186 original size:95 final size:95
Alignment explanation
Indices: 38794068--38794247 Score: 254
Period size: 95 Copynumber: 1.9 Consensus size: 95
38794058 TTAATCTACA
** * * *
38794068 CCACTGCAACTTCAGAGAGATAA-GATTCGCTATGATAACTTCAATCCATCCTACTGCAACTTTA
1 CCACTGCAACTTCAGAGAGATAAGGCCT-GCCATAATAACTTCAATCCATCCGACTGCAACTTTA
38794132 GGGGTATAGGATTTGTAACTTTTGACCTGCT
65 GGGGTATAGGATTTGTAACTTTTGACCTGCT
* * * * *
38794163 CCACTGCAATTTCAGGGAGATAAGGCCTGCCATAATAACTTTAATCCGTCCGATTGCAACTTTAG
1 CCACTGCAACTTCAGAGAGATAAGGCCTGCCATAATAACTTCAATCCATCCGACTGCAACTTTAG
38794228 GGGTATAGGATTTGTAACTT
66 GGGTATAGGATTTGTAACTT
38794248 GTAGCTTAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 72 0.97
96 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (95 bp):
CCACTGCAACTTCAGAGAGATAAGGCCTGCCATAATAACTTCAATCCATCCGACTGCAACTTTAG
GGGTATAGGATTTGTAACTTTTGACCTGCT
Found at i:38807758 original size:39 final size:39
Alignment explanation
Indices: 38807704--38807866 Score: 254
Period size: 39 Copynumber: 4.2 Consensus size: 39
38807694 TGTGTATGAA
*
38807704 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
38807743 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * * *
38807782 GGTGCGAGCTATGATATCTGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
38807821 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
38807861 TGTGCG
1 TGTGCG
38807867 GTTTACCATA
Statistics
Matches: 112, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 95 0.85
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.25
Consensus pattern (39 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:38807882 original size:40 final size:40
Alignment explanation
Indices: 38807704--38807902 Score: 174
Period size: 39 Copynumber: 5.0 Consensus size: 40
38807694 TGTGTATGAA
* * * *
38807704 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
1 TGTGCGAGTTGTCATAACCGGGCTAAGTCCCGAAGGCATT
* * *
38807743 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
1 TGTGCGAGTTGTCATAACCGGGCTAAGTCCCGAAGGCATT
* * * * * * *
38807782 GGTGCGAGCTATGATATCTGGGCTAAG-CCCGAAGGCAAT
1 TGTGCGAGTTGTCATAACCGGGCTAAGTCCCGAAGGCATT
* * *
38807821 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTCATAACCGGGCTAAGTCCCGAAGGCATT
* *
38807861 TGTGCG-GTT-TACCATAACCGGGCTATGTCCCGAAGGCGTT
1 TGTGCGAGTTGT--CATAACCGGGCTAAGTCCCGAAGGCATT
38807901 TG
1 TG
38807903 AACGAGTAGC
Statistics
Matches: 141, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
38 1 0.01
39 98 0.70
40 42 0.30
ACGTcount: A:0.22, C:0.21, G:0.32, T:0.25
Consensus pattern (40 bp):
TGTGCGAGTTGTCATAACCGGGCTAAGTCCCGAAGGCATT
Found at i:38813595 original size:21 final size:21
Alignment explanation
Indices: 38813548--38813589 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
38813538 TGTCATAATG
*
38813548 GCCACACGGGCGTGTTGCCCT
1 GCCATACGGGCGTGTTGCCCT
38813569 GCCATACGGGCGTGTTGCCCT
1 GCCATACGGGCGTGTTGCCCT
38813590 TTCATATAGG
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:0.10, C:0.36, G:0.33, T:0.21
Consensus pattern (21 bp):
GCCATACGGGCGTGTTGCCCT
Found at i:38813601 original size:21 final size:21
Alignment explanation
Indices: 38813556--38813610 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
38813546 TGGCCACACG
*
38813556 GGCGTGTTGCCCTGCCATACG
1 GGCGTGTTGCCCTGCCATACA
** *
38813577 GGCGTGTTGCCCTTTCATATA
1 GGCGTGTTGCCCTGCCATACA
38813598 GGCGTG-TGCCCTG
1 GGCGTGTTGCCCTG
38813611 TTTCAAGGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.09, C:0.29, G:0.33, T:0.29
Consensus pattern (21 bp):
GGCGTGTTGCCCTGCCATACA
Found at i:38815115 original size:25 final size:25
Alignment explanation
Indices: 38815087--38815153 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
38815077 TATAAAATCT
*
38815087 AATGCATATGATGCAATGTAATGCG
1 AATGCATAGGATGCAATGTAATGCG
*
38815112 AATGCATGGGATGCAATGTAATGCG
1 AATGCATAGGATGCAATGTAATGCG
*
38815137 AATGCATGGGATG-AATG
1 AATGCATAGGATGCAATG
38815154 CAAAAAGAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 4 0.10
25 36 0.90
ACGTcount: A:0.34, C:0.10, G:0.30, T:0.25
Consensus pattern (25 bp):
AATGCATAGGATGCAATGTAATGCG
Found at i:38818862 original size:3 final size:3
Alignment explanation
Indices: 38818837--38818894 Score: 89
Period size: 3 Copynumber: 19.3 Consensus size: 3
38818827 AGATAAAAAT
* * *
38818837 ATA ACA ATA ATA GTA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
38818885 ATA ATA ATA A
1 ATA ATA ATA A
38818895 AAATGTGTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:38819151 original size:3 final size:3
Alignment explanation
Indices: 38819133--38819173 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
38819123 TAAATAGATG
*
38819133 AAT AGAT AAT AA- AAT AAT AAT AAT AAT GAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
38819174 AGGCACAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:38819334 original size:16 final size:16
Alignment explanation
Indices: 38819308--38819352 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
38819298 AAATGTAAAG
38819308 AATAA-TGAATAAAT-
1 AATAAGTGAATAAATA
38819322 AATCAAGTGAATAAATA
1 AAT-AAGTGAATAAATA
*
38819339 AATAAGTAAATAAA
1 AATAAGTGAATAAA
38819353 AGGATTAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 3 0.11
15 2 0.07
16 19 0.70
17 3 0.11
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.24
Consensus pattern (16 bp):
AATAAGTGAATAAATA
Found at i:38819448 original size:85 final size:87
Alignment explanation
Indices: 38819350--38819524 Score: 291
Period size: 85 Copynumber: 2.0 Consensus size: 87
38819340 ATAAGTAAAT
*
38819350 AAAAGGATTAAAGTAAGAACAAATAAAATAAATAATAAAGGGACTAAAAT-AAAAAA-AATCGTA
1 AAAAGGATTAAAGTAAGAACAAATAAAATAAATAAAAAAGGGACTAAAATAAAAAAACAATCGTA
38819413 AAAATAAATAATTTAGGAAGAA
66 AAAATAAATAATTTAGGAAGAA
*
38819435 AAAAGGATTAAAGTAAGAACAAATGAAATAAATAAAAAAGGGACTAAAATAAAAAAAAAGCAATC
1 AAAAGGATTAAAGTAAGAACAAATAAAATAAATAAAAAAGGGACTAAAAT--AAAAAAA-CAATC
38819500 GTAAAAATAAATAATTTAGGAAGAA
63 GTAAAAATAAATAATTTAGGAAGAA
38819525 TCCAAAATAA
Statistics
Matches: 83, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
85 48 0.58
88 6 0.07
90 29 0.35
ACGTcount: A:0.65, C:0.04, G:0.14, T:0.18
Consensus pattern (87 bp):
AAAAGGATTAAAGTAAGAACAAATAAAATAAATAAAAAAGGGACTAAAATAAAAAAACAATCGTA
AAAATAAATAATTTAGGAAGAA
Found at i:38820757 original size:16 final size:17
Alignment explanation
Indices: 38820736--38820774 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
38820726 GCTGGACTGT
38820736 TTATTTAGA-TTTATTA
1 TTATTTAGATTTTATTA
38820752 TTATTT-GATTTTATTA
1 TTATTTAGATTTTATTA
38820768 TT-TTTAG
1 TTATTTAG
38820775 TTTCTGTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (17 bp):
TTATTTAGATTTTATTA
Found at i:38823954 original size:23 final size:23
Alignment explanation
Indices: 38823928--38823974 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
38823918 GAATGTAATT
38823928 ATATAATTAGAGAAAAAATAACA
1 ATATAATTAGAGAAAAAATAACA
* *
38823951 ATATAATTAGGGAAACAATAACA
1 ATATAATTAGAGAAAAAATAACA
38823974 A
1 A
38823975 ACACTCGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.21
Consensus pattern (23 bp):
ATATAATTAGAGAAAAAATAACA
Found at i:38825415 original size:10 final size:10
Alignment explanation
Indices: 38825402--38825443 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
38825392 GATCCAATTT
*
38825402 AAAAATTATT
1 AAAAATTATA
38825412 AAAAATT-TA
1 AAAAATTATA
*
38825421 AAAAATAATA
1 AAAAATTATA
38825431 AAAAATTA-A
1 AAAAATTATA
38825440 AAAA
1 AAAA
38825444 TCCGATTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 12 0.43
10 16 0.57
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAATTATA
Found at i:38825420 original size:18 final size:18
Alignment explanation
Indices: 38825397--38825444 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
38825387 CAATCGATCC
* *
38825397 AATTTAAAAATTATTAAA
1 AATTTAAAAAATAATAAA
38825415 AATTTAAAAAATAATAAA
1 AATTTAAAAAATAATAAA
*
38825433 AAATTAAAAAAT
1 AATTTAAAAAAT
38825445 CCGATTCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATTTAAAAAATAATAAA
Found at i:38827110 original size:24 final size:24
Alignment explanation
Indices: 38827083--38827128 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
38827073 ATTCAAATTT
38827083 AGATACAAATGCAGACACAGATTC
1 AGATACAAATGCAGACACAGATTC
* * * *
38827107 AGATTCAGATGTAGCCACAGAT
1 AGATACAAATGCAGACACAGAT
38827129 CCTACCCCCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (24 bp):
AGATACAAATGCAGACACAGATTC
Found at i:38831322 original size:47 final size:46
Alignment explanation
Indices: 38831265--38831393 Score: 150
Period size: 47 Copynumber: 2.7 Consensus size: 46
38831255 TGCGAATAAG
* *
38831265 ACCTTGATTTGGCTATGGGCCATGGTATAGGTATTCAGAGAGGAGTT
1 ACCTTGATTTGG-TATGGGCCATGGTATAGGTACTCAGAGAGAAGTT
* * * * *
38831312 ACCTTTATTTGGTTATGGGCTATGGTATAGGTACTCCGGGATAAGTT
1 ACCTTGATTTGG-TATGGGCCATGGTATAGGTACTCAGAGAGAAGTT
* *
38831359 ACCTTGATTTGGTTTCGGACCATGGTATAGGTACT
1 ACCTTGATTTGGTAT-GGGCCATGGTATAGGTACT
38831394 TATCGATTCA
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
46 2 0.03
47 67 0.97
ACGTcount: A:0.22, C:0.14, G:0.29, T:0.36
Consensus pattern (46 bp):
ACCTTGATTTGGTATGGGCCATGGTATAGGTACTCAGAGAGAAGTT
Found at i:38833086 original size:19 final size:19
Alignment explanation
Indices: 38833052--38833088 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
38833042 TTTAATTTCT
38833052 ACATAATAAAACTTAACAA
1 ACATAATAAAACTTAACAA
38833071 ACATGAATAAAA-TTAACA
1 ACAT-AATAAAACTTAACA
38833089 CTTCTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.62, C:0.14, G:0.03, T:0.22
Consensus pattern (19 bp):
ACATAATAAAACTTAACAA
Found at i:38836778 original size:41 final size:41
Alignment explanation
Indices: 38836663--38836812 Score: 203
Period size: 41 Copynumber: 3.7 Consensus size: 41
38836653 CGCTGACTCA
* *
38836663 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACATTGGCCC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
* * * * * * *
38836704 GAAGGCCCTTCGAAACTAGGTTCGG-TTATGACACTGGCTT
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
38836744 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
*
38836785 AAAAGCCCTTCGAGACCAAGCTAGGATT
1 AAAAGCCCTTCGAGACCAAGCTCGGATT
38836813 TAAGCCCCGA
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 31 0.34
41 60 0.66
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (41 bp):
AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
Found at i:38838851 original size:39 final size:39
Alignment explanation
Indices: 38838741--38838973 Score: 331
Period size: 39 Copynumber: 5.9 Consensus size: 39
38838731 TCGTTCAAAC
* * * * * *
38838741 GCCTTCGGGACATAGCCCGGTTATGATAACCCGCACAAAT
1 GCCTTCGGG-CTTAGCCCGGATATCACAACTCGCACAATT
*
38838781 GCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCACAACTCGCACAATT
*
38838821 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATT
*
38838860 GCCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATT
* * *
38838899 GCCTTCGGGCTTCGCCCGGATATCACAATTCGCACATTT
1 GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATT
*
38838938 GCCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACA
38838974 TTCATACACA
Statistics
Matches: 179, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 137 0.77
40 42 0.23
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATT
Found at i:38838975 original size:39 final size:39
Alignment explanation
Indices: 38838772--38838973 Score: 332
Period size: 39 Copynumber: 5.2 Consensus size: 39
38838762 TATGATAACC
* * *
38838772 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAATT
* *
38838812 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
38838851 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
*
38838890 CGCACAATTGCCTTCGGGCTTCGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
*
38838929 CGCACATTTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
38838968 CGCACA
1 CGCACA
38838974 TTCATACACA
Statistics
Matches: 154, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
39 137 0.89
40 17 0.11
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
Found at i:38846899 original size:39 final size:39
Alignment explanation
Indices: 38846789--38847020 Score: 304
Period size: 39 Copynumber: 5.9 Consensus size: 39
38846779 TCGTTCAAAC
* * * * * *
38846789 GCCTTCGGGACATAGCCCGGTTATGATAACCCGCACAAAT
1 GCCTTCGGG-CTTAGCCCGGATATCACAACTCGCACAATT
*
38846829 GCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCACAACTCGCACAATT
*
38846869 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATT
* *
38846908 GCCTTCAGGCTT-GCCCGGATATCACAATTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATT
* * * *
38846946 GCCTTCGGGCTTCGCCCCGATATCACAATTCGCACATTT
1 GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATT
*
38846985 GCCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACA
38847021 TTCATACACA
Statistics
Matches: 174, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
38 35 0.20
39 97 0.56
40 42 0.24
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATT
Found at i:38846948 original size:77 final size:78
Alignment explanation
Indices: 38846789--38847020 Score: 322
Period size: 77 Copynumber: 3.0 Consensus size: 78
38846779 TCGTTCAAAC
* * * * * *
38846789 GCCTTCGGGACATAGCCCGGTTATGATAACCCGCACAAATGCCTTCGGGACTTAACCCGGATATC
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGG-CTTAGCCCGGATATC
*
38846854 ACAACTCGCACAATT
64 ACAATTCGCACAATT
*
38846869 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCAGGCTT-GCCCGGATATCAC
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
38846933 AATTCGCACAATT
66 AATTCGCACAATT
* * * * *
38846946 GCCTTCGGGCTTCGCCCCGATATCACAATTCGCACATTTGCCTTCGGGCTTAGCCCGGATATCAC
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
38847011 AATTCGCACA
66 AATTCGCACA
38847021 TTCATACACA
Statistics
Matches: 137, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
77 69 0.50
78 26 0.19
79 33 0.24
80 9 0.07
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (78 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
AATTCGCACAATT
Found at i:38847022 original size:39 final size:39
Alignment explanation
Indices: 38846820--38847020 Score: 305
Period size: 39 Copynumber: 5.2 Consensus size: 39
38846810 TATGATAACC
* * *
38846820 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAATT
* *
38846860 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
*
38846899 CGCACAATTGCCTTCAGGCTT-GCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
* *
38846937 CGCACAATTGCCTTCGGGCTTCGCCCCGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
*
38846976 CGCACATTTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
38847015 CGCACA
1 CGCACA
38847021 TTCATACACA
Statistics
Matches: 149, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
38 35 0.23
39 97 0.65
40 17 0.11
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
Found at i:38847047 original size:116 final size:117
Alignment explanation
Indices: 38846820--38847028 Score: 289
Period size: 116 Copynumber: 1.8 Consensus size: 117
38846810 TATGATAACC
*
38846820 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
1 CGCACAAATGCCTTCGGGACTTAACCCCGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
* * * * *
38846885 CGGATATCATAACTCGCACAATTGCCTTCAGGCTTGCCCGGATATCACAATT
66 CGGATATCACAACTCGCACAATTGCATACAAGCTTGCCCGAATATCACAATT
* ** * *
38846937 CGCACAATTGCCTTCGGG-CTTCGCCCCGATATCACAATTCGCACATTTGCCTTCGGGCTTAGCC
1 CGCACAAATGCCTTCGGGACTTAACCCCGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
*
38847001 CGGATATCACAATTCGCAC-ATT-CATACA
66 CGGATATCACAACTCGCACAATTGCATACA
38847029 CATCTTTGTT
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
114 4 0.05
115 3 0.04
116 58 0.71
117 17 0.21
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (117 bp):
CGCACAAATGCCTTCGGGACTTAACCCCGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
CGGATATCACAACTCGCACAATTGCATACAAGCTTGCCCGAATATCACAATT
Found at i:38854219 original size:41 final size:38
Alignment explanation
Indices: 38854112--38854219 Score: 126
Period size: 39 Copynumber: 2.7 Consensus size: 38
38854102 ATCACGATTT
*
38854112 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAGAAACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAAGAAACTA
* **
38854151 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCTACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-AAG-AAACTA
*
38854192 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
38854220 TTATAATTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
39 29 0.48
40 4 0.07
41 27 0.45
ACGTcount: A:0.22, C:0.30, G:0.25, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATAAGAAACTA
Found at i:38862326 original size:39 final size:37
Alignment explanation
Indices: 38862191--38862330 Score: 140
Period size: 37 Copynumber: 3.7 Consensus size: 37
38862181 CCGCACCAAG
* * * *
38862191 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAACCCGGATAT-AC-ACTAGCAC-AAT
* * *
38862231 GCCTTCGGGTCTTAGCCCGGATA-AAACTCGCACGAAT
1 GCCTTCGGGTCTTAACCCGGATATACACTAGCAC-AAT
*
38862268 GCCTTCGGGTCTTAGCCCGGATATAGCACTAGCACAATT
1 GCCTTCGGGTCTTAACCCGGATATA-CACTAGCACAA-T
38862307 GCCTTCGGGTCTTAACCCGG-TATA
1 GCCTTCGGGTCTTAACCCGGATATA
38862331 ATTTCCAGCA
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
37 32 0.37
38 8 0.09
39 27 0.31
40 20 0.23
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (37 bp):
GCCTTCGGGTCTTAACCCGGATATACACTAGCACAAT
Found at i:38862346 original size:39 final size:39
Alignment explanation
Indices: 38862223--38862369 Score: 151
Period size: 39 Copynumber: 3.8 Consensus size: 39
38862213 ATCACGATTT
* * *
38862223 GCACAAATGCCTTCGGGTCTTAGCCCGGATA-A-AACTC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCACTA
38862260 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAGCACTA
* **
38862299 GCACAATTGCCTTCGGGTCTTAACCCGGTATAATTTC-C-A
1 GCACAATTGCCTTCGGGTCTTAGCCCGG-AT-ATAGCACTA
* * *
38862338 GCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
38862370 CATTCAATTT
Statistics
Matches: 95, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
37 30 0.32
38 7 0.07
39 52 0.55
40 3 0.03
41 3 0.03
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (39 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCACTA
Found at i:38867718 original size:40 final size:41
Alignment explanation
Indices: 38867591--38867778 Score: 173
Period size: 41 Copynumber: 4.6 Consensus size: 41
38867581 CGTCACAGAC
* * * *
38867591 GCCCTTCGAAACCAAGC-CCGATTCTTAGCACTGACTCAAAAA
1 GCCCTTCGAAACCAAGCTCGGATTATGA-CACTGGCTC-AAAA
** * * * * *
38867633 GCCCTTCGAGGCCAAGCTCGAATTATGACATTGGCCCGAAG
1 GCCCTTCGAAACCAAGCTCGGATTATGACACTGGCTCAAAA
* * * *
38867674 GCCCTTCGAAACTAGGTTCGG-TTATGACACTGGCTTAAAA
1 GCCCTTCGAAACCAAGCTCGGATTATGACACTGGCTCAAAA
* *
38867714 GCCCTTCGAGACCAAGCTCGGATTATGACATTGGCTCAAAA
1 GCCCTTCGAAACCAAGCTCGGATTATGACACTGGCTCAAAA
* *
38867755 GCCCTTCGAGACCAAGCTCAGATT
1 GCCCTTCGAAACCAAGCTCGGATT
38867779 TAAACCCCGA
Statistics
Matches: 115, Mismatches: 29, Indels: 5
0.77 0.19 0.03
Matches are distributed among these distances:
40 31 0.27
41 57 0.50
42 21 0.18
43 6 0.05
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (41 bp):
GCCCTTCGAAACCAAGCTCGGATTATGACACTGGCTCAAAA
Found at i:38867749 original size:41 final size:41
Alignment explanation
Indices: 38867629--38867778 Score: 185
Period size: 41 Copynumber: 3.7 Consensus size: 41
38867619 CACTGACTCA
* * *
38867629 AAAAGCCCTTCGAGGCCAAGCTCGAATTATGACATTGGCCC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACATTGGCTC
* * * * * * * *
38867670 GAAGGCCCTTCGAAACTAGGTTCGG-TTATGACACTGGCTT
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACATTGGCTC
38867710 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACATTGGCTC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACATTGGCTC
*
38867751 AAAAGCCCTTCGAGACCAAGCTCAGATT
1 AAAAGCCCTTCGAGACCAAGCTCGGATT
38867779 TAAACCCCGA
Statistics
Matches: 88, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
40 31 0.35
41 57 0.65
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.22
Consensus pattern (41 bp):
AAAAGCCCTTCGAGACCAAGCTCGGATTATGACATTGGCTC
Found at i:38872707 original size:25 final size:25
Alignment explanation
Indices: 38872677--38872724 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
38872667 TTATACCATG
* * *
38872677 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
38872702 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
38872725 GTTTATGTAT
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:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:38872827 original size:20 final size:20
Alignment explanation
Indices: 38872767--38872827 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
38872757 ATAAATATGG
*
38872767 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
38872787 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
38872807 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
38872827 T
1 T
38872828 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:38872904 original size:24 final size:24
Alignment explanation
Indices: 38872877--38873019 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
38872867 GAGGAAGTGA
*
38872877 AAAAGGGATTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
38872901 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
38872925 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
38872948 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* *
38872972 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
38872996 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
38873020 ATGATAAAGC
Statistics
Matches: 112, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
23 23 0.21
24 78 0.70
25 11 0.10
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:38872969 original size:47 final size:47
Alignment explanation
Indices: 38872877--38873019 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
38872867 GAGGAAGTGA
*
38872877 AAAAGGGATTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
38872925 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* *
38872972 AAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
38873020 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 44 0.50
48 33 0.38
49 11 0.12
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:38872993 original size:71 final size:72
Alignment explanation
Indices: 38872877--38873020 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
38872867 GAGGAAGTGA
*
38872877 AAAAGGGATTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGATTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
38872940 CCAGTTAT
65 CCAGTTAT
* * * *
38872948 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGATTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
38873013 CAGTTAT
66 CAGTTAT
38873020 A
1 A
38873021 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGATTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:38873246 original size:31 final size:31
Alignment explanation
Indices: 38873211--38873275 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
38873201 CGTTTACAGT
38873211 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
38873242 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
38873273 AAA
1 AAA
38873276 TGAAAAGGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:38874974 original size:23 final size:23
Alignment explanation
Indices: 38874948--38874992 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
38874938 TGTATATGGC
38874948 TATGAGATATG-ACTCATATTAAT
1 TATGAGA-ATGTACTCATATTAAT
* *
38874971 TATGGGAATGTAGTCATATTAA
1 TATGAGAATGTACTCATATTAA
38874993 AAAATGCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
TATGAGAATGTACTCATATTAAT
Found at i:38876670 original size:46 final size:46
Alignment explanation
Indices: 38876603--38876868 Score: 233
Period size: 46 Copynumber: 5.7 Consensus size: 46
38876593 TAACCCGCCT
38876603 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCC
1 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCC
* * * *
38876649 ATAAGTGAACTCAGACTCAACTCAACGAGCTTGGATGCCTAGTT-ACAT-C
1 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G-C-A-TTCGCATCC
* *
38876698 -TCA-CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCC
1 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCC
* * * *
38876742 ATAAGTGAACTCAGACTCAACTCAACGAGCTCAGATGCCTAGTT-ACAT-C
1 ATAAGCGAACTCGGACTCAACTCAACGAGCTC-G--GGC-A-TTCGCATCC
* * * *
38876791 -TCA-CGAACTCGGACTCAACTCAACGAGTTCTGACATTCGCATCC
1 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCC
* * *
38876835 ATAAGTGAACTTGGACTCAACTCAACGAGTTCGG
1 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGG
38876869 ATGCCCAAAT
Statistics
Matches: 175, Mismatches: 27, Indels: 36
0.74 0.11 0.15
Matches are distributed among these distances:
42 4 0.02
43 7 0.04
44 5 0.03
45 5 0.03
46 82 0.47
47 51 0.29
48 5 0.03
49 5 0.03
50 7 0.04
51 4 0.02
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCC
Found at i:38876720 original size:47 final size:47
Alignment explanation
Indices: 38876655--38876817 Score: 192
Period size: 47 Copynumber: 3.5 Consensus size: 47
38876645 ATCCATAAGT
*
38876655 GAACTCAGACTCAACTCAACGAGCTTGGATGCCTAGTTACATCTCAC
1 GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
* * * *
38876702 GAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCATCCATAAGT
1 GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT-C-TCA-C
*
38876748 GAACTCAGACTCAACTCAACGAGCTCAGATGCCTAGTTACATCTCAC
1 GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
*
38876795 GAACTCGGACTCAACTCAACGAG
1 GAACTCAGACTCAACTCAACGAG
38876818 TTCTGACATT
Statistics
Matches: 96, Mismatches: 11, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 2 0.02
45 3 0.03
46 26 0.27
47 48 0.50
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (47 bp):
GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:38876767 original size:93 final size:93
Alignment explanation
Indices: 38876608--38876873 Score: 444
Period size: 93 Copynumber: 2.9 Consensus size: 93
38876598 CGCCTATAAG
38876608 CGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCA
38876673 ACGAGCTTGGATGCCTAGTTACATCTCA
66 ACGAGCTTGGATGCCTAGTTACATCTCA
*
38876701 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCA
**
38876766 ACGAGCTCAGATGCCTAGTTACATCTCA
66 ACGAGCTTGGATGCCTAGTTACATCTCA
* * * **
38876794 CGAACTCGGACTCAACTCAACGAGTTCTGACATTCGCATCCATAAGTGAACTTGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCA
38876859 ACGAG-TTCGGATGCC
66 ACGAGCTT-GGATGCC
38876874 CAAATATCCC
Statistics
Matches: 161, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
92 1 0.01
93 160 0.99
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGCTTGGATGCCTAGTTACATCTCA
Found at i:38880242 original size:15 final size:13
Alignment explanation
Indices: 38880225--38880277 Score: 63
Period size: 13 Copynumber: 3.9 Consensus size: 13
38880215 AGTTTCCATC
38880225 TATTATTATATTAT
1 TATTA-TATATTAT
38880239 CTATTTATATATTAT
1 -TA-TTATATATTAT
*
38880254 TTTTATATATTAT
1 TATTATATATTAT
38880267 TA-TATATATTA
1 TATTATATATTA
38880278 AAGCCTTAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 9 0.26
13 12 0.34
14 1 0.03
15 10 0.29
16 3 0.09
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATATATTAT
Found at i:38880251 original size:23 final size:25
Alignment explanation
Indices: 38880225--38880277 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
38880215 AGTTTCCATC
38880225 TATTA-TTATAT-TATCTATT-TATA
1 TATTATTTATATATAT-TATTATATA
*
38880248 TATTATTTTTATATATTATTATATA
1 TATTATTTATATATATTATTATATA
38880273 TATTA
1 TATTA
38880278 AAGCCTTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 9 0.35
25 12 0.46
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TATTATTTATATATATTATTATATA
Found at i:38886977 original size:18 final size:19
Alignment explanation
Indices: 38886942--38886979 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
38886932 CTTATTACAA
*
38886942 AATTTAAAACCCAAATTAG
1 AATTTAAAACCAAAATTAG
38886961 AATTTAAAA-CAAAATTAG
1 AATTTAAAACCAAAATTAG
38886979 A
1 A
38886980 GTCCAAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (19 bp):
AATTTAAAACCAAAATTAG
Found at i:38891146 original size:47 final size:48
Alignment explanation
Indices: 38891092--38891211 Score: 133
Period size: 47 Copynumber: 2.5 Consensus size: 48
38891082 CAGTTTATCA
38891092 ATGTCCCAGACATGTCTTACACTAGCACTCGTC-TCA-AT-GCCGATGCC
1 ATGTCCCAGACATGTCTTACACTAGCACTC-TCATCATATGGCCGATG-C
* * * * *
38891139 ATGTCCCAGACATGGTCTTAAACT-G-GCTCTCATGATGTGGCTGATGC
1 ATGTCCCAGACAT-GTCTTACACTAGCACTCTCATCATATGGCCGATGC
38891186 ATGTCCCAGACATGTCTTACACTAGC
1 ATGTCCCAGACATGTCTTACACTAGC
38891212 TCACACAAGT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
45 2 0.03
46 14 0.23
47 30 0.49
48 15 0.25
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (48 bp):
ATGTCCCAGACATGTCTTACACTAGCACTCTCATCATATGGCCGATGC
Found at i:38891590 original size:30 final size:30
Alignment explanation
Indices: 38891547--38891603 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
38891537 TAAAATTCAC
* *
38891547 GTCTTAGGTAAAATGATCATTTTGCCCTTA
1 GTCTTAGGCAAAATGACCATTTTGCCCTTA
*
38891577 GTCTTTGGCAAAATGACCATTTTGCCC
1 GTCTTAGGCAAAATGACCATTTTGCCC
38891604 CTATGCTCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (30 bp):
GTCTTAGGCAAAATGACCATTTTGCCCTTA
Found at i:38893135 original size:26 final size:26
Alignment explanation
Indices: 38893084--38893134 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
38893074 AGTTGTAGTG
*
38893084 AGAAAATTATCTGAAGAGATTATTTT
1 AGAAAATTATCTAAAGAGATTATTTT
*
38893110 AGAAAATT-TCTAAAGATATTATTTT
1 AGAAAATTATCTAAAGAGATTATTTT
38893135 TGATTCACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (26 bp):
AGAAAATTATCTAAAGAGATTATTTT
Found at i:38896481 original size:39 final size:39
Alignment explanation
Indices: 38896424--38896523 Score: 121
Period size: 39 Copynumber: 2.6 Consensus size: 39
38896414 CACGTTTTTT
* *
38896424 AGTATTGCAATATATGCTTGAACATTATGTAATTATATG
1 AGTATTACAATATATGCTTAAACATTATGTAATTATATG
* * *
38896463 AGTATTACGATATGTGCTTAAACATTATGTAATTATACG
1 AGTATTACAATATATGCTTAAACATTATGTAATTATATG
* *
38896502 TA-TAATACGATATATGCTTAAA
1 -AGTATTACAATATATGCTTAAA
38896524 AGTGAATATG
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
39 52 0.98
40 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (39 bp):
AGTATTACAATATATGCTTAAACATTATGTAATTATATG
Found at i:38904523 original size:39 final size:39
Alignment explanation
Indices: 38904469--38904662 Score: 291
Period size: 39 Copynumber: 4.9 Consensus size: 39
38904459 GATGTGTATG
*
38904469 AATGTGCGAATTGTGATATCCGGGATAAGCCCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
38904508 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
*
38904547 AATGTGCGAATTATGATATCCGGGCTAAGCCCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
* * *
38904586 ATTGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
* * *
38904625 ATTGTGC-AAGTTGTGATACCCGGGTTAAGTCCCGAAGG
1 AATGTGCGAA-TTGTGATATCCGGGCTAAG-CCCGAAGG
38904663 AATTTGTGCG
Statistics
Matches: 145, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
38 1 0.01
39 136 0.94
40 8 0.06
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (39 bp):
AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
Found at i:38912508 original size:39 final size:39
Alignment explanation
Indices: 38912454--38912649 Score: 293
Period size: 39 Copynumber: 5.0 Consensus size: 39
38912444 GATGTGTATG
*
38912454 AATGTGCGAATTGTGATATCCAGGCTAAGCCCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
*
38912493 AATGTGCGAATTGTGATATCCAGGCTAAGCCCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
*
38912532 AATGTGCGAATTGTGATATCTGGGCTAAGCCCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
* * *
38912571 ATTGTGCGAGTTCTGATATCCGGGCTAAGCCCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
* * * *
38912610 ATTGTGCGAGTTGTGATACCCGGGTTAAGTCCCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCA
38912650 TTTGTGCGGG
Statistics
Matches: 147, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 137 0.93
40 10 0.07
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.22
Consensus pattern (39 bp):
AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
Found at i:38917364 original size:14 final size:14
Alignment explanation
Indices: 38917328--38917365 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
38917318 TATCTGTATT
*
38917328 CATACATCCGCATA
1 CATACATCTGCATA
38917342 CATACATCTGCATA
1 CATACATCTGCATA
38917356 CATACATCTG
1 CATACATCTG
38917366 TATATAAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.34, C:0.32, G:0.08, T:0.26
Consensus pattern (14 bp):
CATACATCTGCATA
Found at i:38920987 original size:24 final size:24
Alignment explanation
Indices: 38920960--38921012 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
38920950 TGGGGGTAGG
38920960 ATCTGTGACTGCATCTGTATCTGA
1 ATCTGTGACTGCATCTGTATCTGA
* *
38920984 ATCTGTGTCTGCATTTGTATCTGA
1 ATCTGTGACTGCATCTGTATCTGA
38921008 ATCTG
1 ATCTG
38921013 AATACGCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (24 bp):
ATCTGTGACTGCATCTGTATCTGA
Found at i:38921006 original size:12 final size:12
Alignment explanation
Indices: 38920968--38921030 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
38920958 GGATCTGTGA
38920968 CTGCATCTGTAT
1 CTGCATCTGTAT
* *
38920980 CTGAATCTGTGT
1 CTGCATCTGTAT
*
38920992 CTGCATTTGTAT
1 CTGCATCTGTAT
* *
38921004 CTGAATCTGAAT
1 CTGCATCTGTAT
*
38921016 AC-GCATATGTAT
1 -CTGCATCTGTAT
38921028 CTG
1 CTG
38921031 ATTATGAAAA
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
11 1 0.03
12 36 0.95
13 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (12 bp):
CTGCATCTGTAT
Found at i:38921021 original size:24 final size:24
Alignment explanation
Indices: 38920968--38921031 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
38920958 GGATCTGTGA
* **
38920968 CTGCATCTGTATCTGAATCTGTGT
1 CTGCATATGTATCTGAATCTGAAT
*
38920992 CTGCATTTGTATCTGAATCTGAAT
1 CTGCATATGTATCTGAATCTGAAT
38921016 AC-GCATATGTATCTGA
1 -CTGCATATGTATCTGA
38921032 TTATGAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 34 0.97
25 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (24 bp):
CTGCATATGTATCTGAATCTGAAT
Found at i:38934012 original size:11 final size:11
Alignment explanation
Indices: 38933992--38934022 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
38933982 TCAAATCATC
*
38933992 AAGAATAAATT
1 AAGAACAAATT
38934003 AAGAACAAATT
1 AAGAACAAATT
38934014 AAGAACAAA
1 AAGAACAAA
38934023 ACTAGATGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.68, C:0.06, G:0.10, T:0.16
Consensus pattern (11 bp):
AAGAACAAATT
Found at i:38935837 original size:29 final size:31
Alignment explanation
Indices: 38935801--38935863 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
38935791 AAGAAGGAGG
38935801 GATTTTTGCTCCA-TTT-TTGGTTTAGAAGA
1 GATTTTTGCTCCATTTTCTTGGTTTAGAAGA
* *
38935830 GATTTTTGCTTCATTTTCTTTGTTTAGAAGA
1 GATTTTTGCTCCATTTTCTTGGTTTAGAAGA
38935861 GAT
1 GAT
38935864 CTAGAAGGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 12 0.40
30 3 0.10
31 15 0.50
ACGTcount: A:0.21, C:0.10, G:0.19, T:0.51
Consensus pattern (31 bp):
GATTTTTGCTCCATTTTCTTGGTTTAGAAGA
Found at i:38937159 original size:78 final size:80
Alignment explanation
Indices: 38937016--38937199 Score: 196
Period size: 78 Copynumber: 2.3 Consensus size: 80
38937006 TCGAATGATG
* * * * *
38937016 TCCGGGCTAAGTCCCGAAGGCTTTTTGCTAAGTGACTATATCTGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
*
38937081 GTGCGAGTTAATAAA
66 GTGCAAGTTAATAAA
* **
38937096 TCCGGGCTAA-TCCCGAAGGCTTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATT
**
38937158 CGTGCAAGTTGCTATAA
65 CGTGCAAGTTAATA-AA
**
38937175 -CCGGGCTTCGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGC-TTTG
38937200 AACGAGTCGT
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
77 1 0.01
78 44 0.51
79 28 0.32
80 14 0.16
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
GTGCAAGTTAATAAA
Found at i:38937179 original size:40 final size:40
Alignment explanation
Indices: 38937069--38937197 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 40
38937059 GGACTAGGAT
* * * *
38937069 CCGAAGGCATTCGTGCGAGTTAATAAATCCGGGCTAA-TC
1 CCGAAGGCATTCGTGCAAGTTACTAAACCCGGGTTAAGTC
*
38937108 CCGAAGGC-TTTGTGCAAGTTACTAAACCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCAAGTTACTAAACCCGGGTTAAGTC
* *
38937147 CCGAAGGCATTCGTGCAAGTTGCTATAA-CCGGGCTT-CGTC
1 CCGAAGGCATTCGTGCAAGTTACTA-AACCCGGG-TTAAGTC
38937187 CCGAAGGCATT
1 CCGAAGGCATT
38937198 TGAACGAGTC
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
38 23 0.29
39 18 0.23
40 33 0.42
41 4 0.05
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.24
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCAAGTTACTAAACCCGGGTTAAGTC
Found at i:38943446 original size:26 final size:28
Alignment explanation
Indices: 38943405--38943467 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
38943395 TACTCCATAC
38943405 TAATTTTTATGAAC-T-TTTTATATTTT-
1 TAATTTTTATGAACTTATTTTA-ATTTTA
38943431 TAATTTTTATTG-ACTTATTTTAATTTTA
1 TAATTTTTA-TGAACTTATTTTAATTTTA
38943459 TAATTTTTA
1 TAATTTTTA
38943468 AATTATTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 11 0.33
27 8 0.24
28 14 0.42
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (28 bp):
TAATTTTTATGAACTTATTTTAATTTTA
Found at i:38943462 original size:28 final size:26
Alignment explanation
Indices: 38943405--38943467 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 26
38943395 TACTCCATAC
38943405 TAATTTTTATGAACTTTTTATATTTT
1 TAATTTTTATGAACTTTTTATATTTT
38943431 TAATTTTTATTG-ACTTATTT-TAATTTT
1 TAATTTTTA-TGAACTT-TTTAT-ATTTT
38943458 ATAATTTTTA
1 -TAATTTTTA
38943468 AATTATTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 14 0.42
27 10 0.30
28 9 0.27
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (26 bp):
TAATTTTTATGAACTTTTTATATTTT
Found at i:38945087 original size:5 final size:5
Alignment explanation
Indices: 38945077--38945104 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
38945067 GACATTATTT
38945077 ATTAA ATTAA ATTAA ATTAA ATTAA ATT
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATT
38945105 TTCAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
ATTAA
Found at i:38946397 original size:3 final size:3
Alignment explanation
Indices: 38946368--38946435 Score: 100
Period size: 3 Copynumber: 22.7 Consensus size: 3
38946358 AATGTCCTTG
* * * *
38946368 TTA TTT TTA TAA TTA GTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38946416 TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
38946436 GTTGTTACTA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:38946960 original size:2 final size:2
Alignment explanation
Indices: 38946948--38946978 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
38946938 TGAAATTATG
*
38946948 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38946979 TTTAATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:38959622 original size:54 final size:52
Alignment explanation
Indices: 38959531--38959683 Score: 183
Period size: 54 Copynumber: 3.0 Consensus size: 52
38959521 TCTACTTTCC
*
38959531 AATTCCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
1 AATTTCTG-TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC--TT
* *
38959586 AATTTCTGTTTTTCAAAAAGCAACTCATATTACGAGAGGTGAGTTGTA-CC-T
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG-AGCCTT
* *
38959637 --TTT-TGTTTTTC-AAAATCAACTCATATTGCAAGAGATGAGTTGAGCCT
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
38959684 CGGGTCACAT
Statistics
Matches: 88, Mismatches: 7, Indels: 13
0.81 0.06 0.12
Matches are distributed among these distances:
46 1 0.01
47 29 0.33
48 8 0.09
49 3 0.03
51 1 0.01
54 38 0.43
55 8 0.09
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (52 bp):
AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
Found at i:38959724 original size:14 final size:14
Alignment explanation
Indices: 38959705--38959731 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38959695 TCGAGGTATT
38959705 TTCAAATTCTGTTA
1 TTCAAATTCTGTTA
38959719 TTCAAATTCTGTT
1 TTCAAATTCTGTT
38959732 TTTAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (14 bp):
TTCAAATTCTGTTA
Found at i:38959822 original size:14 final size:14
Alignment explanation
Indices: 38959803--38959837 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
38959793 AGCTGAGGTA
* *
38959803 TTTTCAATTTCTGC
1 TTTTCAATTCCTAC
38959817 TTTTCAATTCCTAC
1 TTTTCAATTCCTAC
38959831 TTTTCAA
1 TTTTCAA
38959838 AAAAATCAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.03, T:0.54
Consensus pattern (14 bp):
TTTTCAATTCCTAC
Found at i:38959910 original size:13 final size:13
Alignment explanation
Indices: 38959892--38959925 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
38959882 CGCTGAGGTA
*
38959892 TTTTCAATTTCTG
1 TTTTCAATTTATG
38959905 TTTTCAATTTATG
1 TTTTCAATTTATG
38959918 TTGTTCAA
1 TT-TTCAA
38959926 GAATCAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTTCAATTTATG
Found at i:38959956 original size:86 final size:87
Alignment explanation
Indices: 38959750--38959956 Score: 240
Period size: 89 Copynumber: 2.4 Consensus size: 87
38959740 TTACTTTCCT
* ** **
38959750 AAAACCAACTCATATTGCGAGAGGTGAGTCAAGCCTTGGGGCAAGCTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAAGCTGAGGTATTTTCAATTTCT
38959815 GCTTTTCAATTCCTACTTTTCAAA
66 GCTTTTCAATT-CTACTTTTC-AA
* * ** *
38959839 AAAATCAGCTCATATTGCAAGAGGTGAGTTGAGCCTCAGGTTACGCTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAAGCTGAGGTATTTTCAATTTCT
*
38959904 G-TTTTCAATT-TATGTTGTTC-A
66 GCTTTTCAATTCTA-CTT-TTCAA
* *
38959925 AGAATCAACTCATATTGCGAGAGGTGGGTTGA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGA
38959957 ACCTTTTAAT
Statistics
Matches: 101, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
86 31 0.31
87 2 0.02
88 12 0.12
89 56 0.55
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (87 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAAGCTGAGGTATTTTCAATTTCT
GCTTTTCAATTCTACTTTTCAA
Found at i:38961912 original size:21 final size:21
Alignment explanation
Indices: 38961887--38961942 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
38961877 TTAAATGTCC
*
38961887 TTGTTATTTTTATAATTAGTA
1 TTGTTATTATTATAATTAGTA
* *
38961908 TTGTTATTATTATTATTATTA
1 TTGTTATTATTATAATTAGTA
* *
38961929 TTGTTGTTACTATA
1 TTGTTATTATTATA
38961943 TATATTGGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (21 bp):
TTGTTATTATTATAATTAGTA
Found at i:38962113 original size:2 final size:2
Alignment explanation
Indices: 38962106--38962130 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38962096 GTATGCTTAA
38962106 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
38962131 CTCTTACATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38965445 original size:2 final size:2
Alignment explanation
Indices: 38965438--38965486 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
38965428 CTTTTTAACT
38965438 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38965480 TA TA TA T
1 TA TA TA T
38965487 CACAATTCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38966004 original size:2 final size:2
Alignment explanation
Indices: 38965997--38966030 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
38965987 CATCAGCTAG
38965997 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38966031 GGCTGAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38970772 original size:47 final size:46
Alignment explanation
Indices: 38970707--38970797 Score: 146
Period size: 47 Copynumber: 2.0 Consensus size: 46
38970697 CCTAAACTAA
* *
38970707 AAAAGAAAAGAAAAAGAAAAGAGAGAGAAAACCTAATCTAAAAATG
1 AAAAGAAAAGAAAAAGAAAAAAGAAAGAAAACCTAATCTAAAAATG
*
38970753 AAAAGAAAAAGAAAAAGAAAAAAGAAAGAAATCCTAATCTAAAAA
1 AAAAG-AAAAGAAAAAGAAAAAAGAAAGAAAACCTAATCTAAAAA
38970798 CTATAAACCC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 5 0.12
47 36 0.88
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09
Consensus pattern (46 bp):
AAAAGAAAAGAAAAAGAAAAAAGAAAGAAAACCTAATCTAAAAATG
Found at i:38977316 original size:29 final size:29
Alignment explanation
Indices: 38977274--38977331 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
38977264 TGTCTTAGGC
38977274 CGTGTGGGCATTCAAAATAAGGCACACAG
1 CGTGTGGGCATTCAAAATAAGGCACACAG
*
38977303 CGTGTGGGCATTCAAAATAGGGCACACAG
1 CGTGTGGGCATTCAAAATAAGGCACACAG
38977332 TCAAGTCCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.21, G:0.29, T:0.17
Consensus pattern (29 bp):
CGTGTGGGCATTCAAAATAAGGCACACAG
Found at i:38978748 original size:26 final size:25
Alignment explanation
Indices: 38978719--38978767 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
38978709 TGGAGAGCCA
*
38978719 TTAATCGGGAAGCTTACAAAGATCTT
1 TTAATCGAGAAGCTT-CAAAGATCTT
*
38978745 TTAATCGAGAAGCTTCGAAGATC
1 TTAATCGAGAAGCTTCAAAGATC
38978768 CATATCTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (25 bp):
TTAATCGAGAAGCTTCAAAGATCTT
Found at i:38979411 original size:26 final size:26
Alignment explanation
Indices: 38979378--38979487 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
38979368 TGATACAAAT
38979378 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* * * *
38979404 TGACAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
38979430 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
38979456 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
38979482 TGATAA
1 TGATAA
38979488 GAATTTCATG
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:38984992 original size:30 final size:31
Alignment explanation
Indices: 38984925--38984994 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
38984915 CCACCCTTAA
* * *
38984925 AATATTTACACTATTAGTCCTTCAGATTTTT
1 AATATTTACACTATTAATCCCTCAGAATTTT
38984956 AATATTTACACT-TTAATCCCTCA-AATTTT
1 AATATTTACACTATTAATCCCTCAGAATTTT
38984985 AAGTATTTAC
1 AA-TATTTAC
38984995 TCTTGGGCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 7 0.20
30 16 0.46
31 12 0.34
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (31 bp):
AATATTTACACTATTAATCCCTCAGAATTTT
Found at i:38988283 original size:7 final size:7
Alignment explanation
Indices: 38988271--38988296 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38988261 GAATGAGGTA
38988271 TTGAATG
1 TTGAATG
38988278 TTGAATG
1 TTGAATG
38988285 TTGAATG
1 TTGAATG
38988292 TTGAA
1 TTGAA
38988297 ATGAATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (7 bp):
TTGAATG
Found at i:38990697 original size:12 final size:12
Alignment explanation
Indices: 38990670--38990702 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
38990660 TTAAATGTAA
38990670 AAAAATAAAACT
1 AAAAATAAAACT
*
38990682 -AAAATAAAATT
1 AAAAATAAAACT
38990693 AAAAATAAAA
1 AAAAATAAAA
38990703 ATTTAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAATAAAACT
Found at i:38995734 original size:13 final size:12
Alignment explanation
Indices: 38995718--38995762 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 12
38995708 CATCTGTTCC
38995718 ATTTATCTTTTTT
1 ATTT-TCTTTTTT
38995731 ATTTTCTTTTTT
1 ATTTTCTTTTTT
38995743 ATTTTTCTAATTTTT
1 A-TTTTCT--TTTTT
38995758 ATTTT
1 ATTTT
38995763 TTGTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.31
13 10 0.34
14 4 0.14
15 6 0.21
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (12 bp):
ATTTTCTTTTTT
Found at i:38995758 original size:15 final size:13
Alignment explanation
Indices: 38995718--38995763 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
38995708 CATCTGTTCC
*
38995718 ATTTATCTTTTTT
1 ATTTTTCTTTTTT
38995731 A-TTTTCTTTTTT
1 ATTTTTCTTTTTT
38995743 ATTTTTCTAATTTTT
1 ATTTTTCT--TTTTT
38995758 ATTTTT
1 ATTTTT
38995764 TGTTTTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 11 0.38
13 7 0.24
15 11 0.38
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (13 bp):
ATTTTTCTTTTTT
Found at i:38997812 original size:89 final size:87
Alignment explanation
Indices: 38997702--38997940 Score: 243
Period size: 89 Copynumber: 2.7 Consensus size: 87
38997692 AAAAAATTTG
* * * *
38997702 AATTAAACCCCTGTTTTTTTTTGCACTTAATT-GATATTTAAACTTTCAAAATGCATAAAAAAAT
1 AATTAAGCCCCTGATTTTTTTT-CACTCAATTGGATACTTAAACTTTCAAAATGCATAAAAAAAT
* *
38997766 GTCATCAAACT-TTTTCAAAAAAAGC
65 -CCATC-AACTGTTTTCAAAAAAA-A
* * *
38997791 AATTAAGTCCCT-ACTTTTTTTTCACTCAATTGGATACTTGAACTTTCAAAATGCATTAAAAAAT
1 AATTAAGCCCCTGA-TTTTTTTTCACTCAATTGGATACTTAAACTTTCAAAATGCATAAAAAAAT
* *
38997855 CCCTCAATTGTTTTCAAAAAAAA
65 CCATCAACTGTTTTCAAAAAAAA
* * * * * *
38997878 AATTAAGCCCCTGATTTTTTTTACACTCAATTAGTTACTTGAACTGT-AAAATGCCTCAAAAAA
1 AATTAAGCCCCTGATTTTTTTT-CACTCAATTGGATACTTAAACTTTCAAAATGCATAAAAAAA
38997941 GCTGTTTAAC
Statistics
Matches: 128, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
87 36 0.28
88 45 0.35
89 47 0.37
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (87 bp):
AATTAAGCCCCTGATTTTTTTTCACTCAATTGGATACTTAAACTTTCAAAATGCATAAAAAAATC
CATCAACTGTTTTCAAAAAAAA
Found at i:39003499 original size:174 final size:176
Alignment explanation
Indices: 39003087--39003571 Score: 739
Period size: 174 Copynumber: 2.8 Consensus size: 176
39003077 ATGCCAAATC
* * * * * * *
39003087 ATCTTGGATCTGC-TTCA-GT-ATAAACATCTGAAGGTCAAACCTACTATTTCTTCGATTTGCTT
1 ATCTTGGATCTGCTTTTATGTGA-AAACATCTGAAAGTCAGATCTGCTATGTCTTCGATTTGCTC
* *
39003149 CTTGTAAACACAAGGATGCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTAAAGGTTAGAT
65 CTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAAACATCTAAAGGTTAGAT
* * *
39003214 CTGCTATGTGTCTACTCTCCGTCGAATATGGAGATGCCAGATCTGTT
130 CTGCTATGTGTCTACTCTCCATCGAATATGGAGACGCCAAATCTGTT
** *
39003261 ATCTTGGATCTGCTTTTATGTGAAAACATCTGAAAGTCAGATCTGCCGTGTCTTCTATTTGCTCC
1 ATCTTGGATCTGCTTTTATGTGAAAACATCTGAAAGTCAGATCTGCTATGTCTTCGATTTGCTCC
*
39003326 TTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAAAGATCTAAAGGTTAGATC
66 TTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAAACATCTAAAGGTTAGATC
*
39003391 TGCTATGTGTCTGCTCTCCATCG-A-ATGGAGACGCCAAATCTGTT
131 TGCTATGTGTCTACTCTCCATCGAATATGGAGACGCCAAATCTGTT
39003435 ATCTTGGATCTGCTTTGT-TGTGAAAACATCTGAAAGTCAGATCTGCTATGTCTTCGATTTGCTC
1 ATCTTGGATCTGCTTT-TATGTGAAAACATCTGAAAGTCAGATCTGCTATGTCTTCGATTTGCTC
*
39003499 CTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAAACATCTGAAGGTTAGAT
65 CTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAAACATCTAAAGGTTAGAT
*
39003564 CTGTTATG
130 CTGCTATG
39003572 CTTTGGTCTG
Statistics
Matches: 284, Mismatches: 23, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
174 160 0.56
175 5 0.02
176 118 0.42
177 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (176 bp):
ATCTTGGATCTGCTTTTATGTGAAAACATCTGAAAGTCAGATCTGCTATGTCTTCGATTTGCTCC
TTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAAACATCTAAAGGTTAGATC
TGCTATGTGTCTACTCTCCATCGAATATGGAGACGCCAAATCTGTT
Found at i:39003549 original size:87 final size:87
Alignment explanation
Indices: 39003048--39003571 Score: 382
Period size: 87 Copynumber: 6.0 Consensus size: 87
39003038 CAAATCTGCT
* * *
39003048 TCTTCGATTTGTTCCTTG-ACAATAC-AGAGATGCCAAATCATCTTGGATCTGCTTCAGTATAAA
1 TCTTCGATTTGCTCCTTGTA-AACACAAGA-ATGCCAAATCATCTTGGATCTGCTTCAGTAAAAA
* * * * *
39003111 CATCTGAAGGTCAAACCTACTATT
64 CATCTGAAAGTCAGATCTGCTATG
* * *
39003135 TCTTCGATTTGCTTCTTGTAAACACAAGGATGCCAAATCATCTTGGATCTGCTTCAGTATAAACA
1 TCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAAACA
*
39003200 TCT-AAAGGTTAGATCTGCTATG
66 TCTGAAA-GTCAGATCTGCTATG
* * * * * ** * *
39003222 T-GTCTA-CT-CTCC--GTCGAATA-TGGAGATGCCAGATCTGTTATCTTGGATCTGCTTTTATG
1 TCTTCGATTTGCTCCTTGT-AAACACAAGA-ATGCCAAATC----ATCTTGGATCTGC-TTCA-G
* **
39003281 TGAAAACATCTGAAAGTCAGATCTGCCGTG
58 TAAAAACATCTGAAAGTCAGATCTGCTATG
* *
39003311 TCTTCTATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAAAGA
1 TCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAAACA
*
39003376 TCT-AAAGGTTAGATCTGCTATG
66 TCTGAAA-GTCAGATCTGCTATG
* * * *** * **
39003398 T-GTC--TGCT-CTCCATCG--AA-TGGAG-ACGCCAAATCTGTTATCTTGGATCTGCTTTGTTG
1 TCTTCGAT-TTGCTCC-TTGTAAACACAAGAATGCCAAATC----ATCTTGGATCTGC-TT-CAG
*
39003455 TGAAAACATCTGAAAGTCAGATCTGCTATG
58 TAAAAACATCTGAAAGTCAGATCTGCTATG
39003485 TCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAAACA
1 TCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAAACA
* * *
39003550 TCTGAAGGTTAGATCTGTTATG
66 TCTGAAAGTCAGATCTGCTATG
39003572 CTTTGGTCTG
Statistics
Matches: 337, Mismatches: 64, Indels: 72
0.71 0.14 0.15
Matches are distributed among these distances:
81 9 0.03
82 5 0.01
83 14 0.04
84 8 0.02
85 17 0.05
86 12 0.04
87 158 0.47
88 16 0.05
89 52 0.15
90 12 0.04
91 3 0.01
92 6 0.02
93 21 0.06
94 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (87 bp):
TCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAAACA
TCTGAAAGTCAGATCTGCTATG
Found at i:39017045 original size:4 final size:4
Alignment explanation
Indices: 39017038--39017066 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
39017028 GTTTAATAAA
39017038 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
39017067 TCTTTTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:39019953 original size:30 final size:30
Alignment explanation
Indices: 39019917--39020019 Score: 120
Period size: 28 Copynumber: 3.5 Consensus size: 30
39019907 GACAAGATTG
* * *
39019917 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
*
39019947 GCACTAAGTGTGCGAGTTT--GATTATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* * *
39019975 GCACTAAGTGTGCGAGCTGAATATATATATA
1 GCACTAAGTGTGCGAGTTTAAAAT-TATATA
39020006 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
39020020 GATTCACTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 23 0.37
30 20 0.32
31 20 0.32
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:39020007 original size:31 final size:28
Alignment explanation
Indices: 39019946--39020019 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 28
39019936 AAAATTGTAC
*
39019946 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTATGATTATAT
39019974 AGCACTAAGTGTGCGAGCTGAAT-ATATATAT
1 AGCACTAAGTGTGCGAG-T--ATGAT-TATAT
39020005 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
39020020 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
28 17 0.41
29 1 0.02
30 2 0.05
31 21 0.51
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTATGATTATAT
Found at i:39027552 original size:30 final size:30
Alignment explanation
Indices: 39027516--39027618 Score: 120
Period size: 28 Copynumber: 3.5 Consensus size: 30
39027506 GACAAGATTG
* * *
39027516 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
*
39027546 GCACTAAGTGTGCGAGTTT--GATTATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* * *
39027574 GCACTAAGTGTGCGAGCTGAATATATATATA
1 GCACTAAGTGTGCGAGTTTAAAAT-TATATA
39027605 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
39027619 GATTCACTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 23 0.37
30 20 0.32
31 20 0.32
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:39027606 original size:31 final size:28
Alignment explanation
Indices: 39027545--39027618 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 28
39027535 AAAATTGTAC
*
39027545 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTATGATTATAT
39027573 AGCACTAAGTGTGCGAGCTGAAT-ATATATAT
1 AGCACTAAGTGTGCGAG-T--ATGAT-TATAT
39027604 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
39027619 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
28 17 0.41
29 1 0.02
30 2 0.05
31 21 0.51
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTATGATTATAT
Found at i:39032233 original size:25 final size:25
Alignment explanation
Indices: 39032204--39032251 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39032194 TTATAATATG
* * *
39032204 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
39032229 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
39032252 GTTTATAATG
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:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:39032315 original size:20 final size:20
Alignment explanation
Indices: 39032286--39032332 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
39032276 ATTTTGATAA
*
39032286 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
39032306 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
39032326 ACATGAT
1 ACATGAT
39032333 GTATTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:39032445 original size:45 final size:45
Alignment explanation
Indices: 39032381--39032539 Score: 234
Period size: 46 Copynumber: 3.5 Consensus size: 45
39032371 GAGGAAGTGC
39032381 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTTGCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTTGCCCAGTTATT
*
39032426 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTGCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTTGCCCAGTTATT
*
39032472 AAAAGGGCTTATGCCCCAGTTA-T-CAGGGCTTTGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTTGCCC-AGTTATT
*
39032516 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
39032540 ATGATAAAGC
Statistics
Matches: 105, Mismatches: 4, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
43 12 0.11
44 16 0.15
45 35 0.33
46 42 0.40
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (45 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTTGCCCAGTTATT
Found at i:39032448 original size:24 final size:24
Alignment explanation
Indices: 39032381--39032539 Score: 194
Period size: 24 Copynumber: 7.0 Consensus size: 24
39032371 GAGGAAGTGC
39032381 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
39032405 -AAAGGGCTT-TG-CCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
39032426 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
39032450 AAAAGGGCTT-TG-CCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
39032472 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
* *
39032495 --CAGGGCTT-TGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
39032516 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
39032540 ATGATAAAGC
Statistics
Matches: 117, Mismatches: 7, Indels: 21
0.81 0.05 0.14
Matches are distributed among these distances:
20 10 0.09
21 18 0.15
22 30 0.26
23 18 0.15
24 34 0.29
25 7 0.06
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:39032782 original size:38 final size:39
Alignment explanation
Indices: 39032731--39032812 Score: 139
Period size: 38 Copynumber: 2.1 Consensus size: 39
39032721 CGTTTACAGT
39032731 AAAGGCTTCGGCCCAGTAATATGAAA-TATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATTATGAAATATGA
**
39032769 AAAGGCTTCGGCCCAGTGTTATGAAATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATTATGAAATATGA
39032808 AAAGG
1 AAAGG
39032813 GCTATGGCCA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 24 0.59
39 17 0.41
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.24
Consensus pattern (39 bp):
AAAGGCTTCGGCCCAGTAATATGAAATTATGAAATATGA
Done.