Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 64 of 276
Found at i:19824711 original size:15 final size:15
Alignment explanation
Indices: 19824691--19824724 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
19824681 ACCCCAAATT
*
19824691 AGATACAGAAATAGC
1 AGATACAGAAATAAC
19824706 AGATACAGAAATAAC
1 AGATACAGAAATAAC
19824721 AGAT
1 AGAT
19824725 TAAACACGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.18, T:0.15
Consensus pattern (15 bp):
AGATACAGAAATAAC
Found at i:19829919 original size:21 final size:21
Alignment explanation
Indices: 19829895--19829936 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
19829885 TAAGAGTGAG
19829895 TTTTTTAAATAAAAAAATTAA
1 TTTTTTAAATAAAAAAATTAA
* *
19829916 TTTTTTAAATATAAGAATTAA
1 TTTTTTAAATAAAAAAATTAA
19829937 ATCTCAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTTTTAAATAAAAAAATTAA
Found at i:19833744 original size:25 final size:27
Alignment explanation
Indices: 19833686--19833737 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
19833676 TTTGATATAC
* *
19833686 ATACATATTTTTAATTATAAAAATGAA
1 ATACAAATTTATAATTATAAAAATGAA
19833713 ATACAAATTTATAATTATAAAAATG
1 ATACAAATTTATAATTATAAAAATG
19833738 TAACAAACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (27 bp):
ATACAAATTTATAATTATAAAAATGAA
Found at i:19838505 original size:46 final size:47
Alignment explanation
Indices: 19838398--19838526 Score: 154
Period size: 46 Copynumber: 2.7 Consensus size: 47
19838388 TCATAATAGA
**
19838398 GGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTTTCACATATCC
1 GGCCGATGCCATGTCCCAGACATGGTCTTACACTA--TGACACATATCC
* * *
19838447 GTGTCGATGCCATGTCCCAGACATGGTCTTACA-T-TGACACATCTCAT
1 G-GCCGATGCCATGTCCCAGACATGGTCTTACACTATGACACATATC-C
*
19838494 GGCCGATGCCATGTCCCAGACATGGTTTTACAC
1 GGCCGATGCCATGTCCCAGACATGGTCTTACAC
19838527 AGGCTCTCAC
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
46 37 0.53
47 1 0.01
49 2 0.03
50 30 0.43
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.27
Consensus pattern (47 bp):
GGCCGATGCCATGTCCCAGACATGGTCTTACACTATGACACATATCC
Found at i:19841371 original size:11 final size:11
Alignment explanation
Indices: 19841357--19841398 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
19841347 ATTTTAAAGA
19841357 TTTTTTTTACT
1 TTTTTTTTACT
**
19841368 TTTTTCATA-T
1 TTTTTTTTACT
19841378 TTTTTTTTACT
1 TTTTTTTTACT
19841389 TTTTTATTTA
1 TTTTT-TTTA
19841399 AAAAGAAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 8 0.32
11 13 0.52
12 4 0.16
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTTTACT
Found at i:19845869 original size:35 final size:36
Alignment explanation
Indices: 19845816--19845888 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 36
19845806 GAGTTATTCG
* * *
19845816 TTTTTATTTTAGTAAGATTTTAGGATTTTTAGTTTA
1 TTTTAATTTTAGTAAGATTTTAGAAATTTTAGTTTA
* *
19845852 TTTTAATTTTA-TTAGATTTTAGAAATTTTATTTTA
1 TTTTAATTTTAGTAAGATTTTAGAAATTTTAGTTTA
19845887 TT
1 TT
19845889 AATGTTTTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
35 22 0.69
36 10 0.31
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (36 bp):
TTTTAATTTTAGTAAGATTTTAGAAATTTTAGTTTA
Found at i:19855353 original size:22 final size:20
Alignment explanation
Indices: 19855302--19855363 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
19855292 TTTTATCATA
* * * *
19855302 TATTATTTTTCACAAATTAT
1 TATTATTATTAACATATTTT
19855322 TATTATTATTAACATTATTTT
1 TATTATTATTAACA-TATTTT
*
19855343 TATATATTATTAATATATTTT
1 TAT-TATTATTAACATATTTT
19855364 ACTTGTATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 12 0.34
21 13 0.37
22 10 0.29
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTATTATTAACATATTTT
Found at i:19855515 original size:23 final size:22
Alignment explanation
Indices: 19855467--19855521 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
19855457 ATATATTCAA
19855467 ATTATGTTTTATTCTATAACGTTT
1 ATTAT-TTTTATTCTATAACG-TT
19855491 ATTATTTTTATTCTATATTAC-TT
1 ATTATTTTTATTCTATA--ACGTT
19855514 ATTATTTT
1 ATTATTTT
19855522 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 22 0.76
24 5 0.17
25 2 0.07
ACGTcount: A:0.25, C:0.07, G:0.04, T:0.64
Consensus pattern (22 bp):
ATTATTTTTATTCTATAACGTT
Found at i:19855530 original size:23 final size:22
Alignment explanation
Indices: 19855489--19855566 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 22
19855479 TCTATAACGT
*
19855489 TTATTATTTT-TATTCTATATTA
1 TTATTATTTTATA-TATATATTA
19855511 CTTATTATTTTATATATATATTTA
1 -TTATTATTTTATATATATA-TTA
* *
19855535 TATATATATGTTATGTATATATTA
1 T-TAT-TATTTTATATATATATTA
19855559 TTTATTAT
1 -TTATTAT
19855567 ATTTTTTGCT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
23 19 0.40
24 14 0.30
25 14 0.30
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (22 bp):
TTATTATTTTATATATATATTA
Found at i:19859012 original size:14 final size:14
Alignment explanation
Indices: 19858993--19859022 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19858983 AAGATATTCT
19858993 TTTTCTAAATAAAA
1 TTTTCTAAATAAAA
*
19859007 TTTTCTAAATGAAA
1 TTTTCTAAATAAAA
19859021 TT
1 TT
19859023 GAACCAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (14 bp):
TTTTCTAAATAAAA
Found at i:19862172 original size:44 final size:44
Alignment explanation
Indices: 19862109--19862197 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
19862099 CGGGAAAAGG
19862109 GCTAGGAAGACAGTTGCAAGGAGGGGTTCAAATCTCAAAACTGA
1 GCTAGGAAGACAGTTGCAAGGAGGGGTTCAAATCTCAAAACTGA
19862153 GCTAGGAAGACAGTTGCAAGGAGGGGTTCAAATCTCAAAACTGA
1 GCTAGGAAGACAGTTGCAAGGAGGGGTTCAAATCTCAAAACTGA
19862197 G
1 G
19862198 TGAGAAGAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.18
Consensus pattern (44 bp):
GCTAGGAAGACAGTTGCAAGGAGGGGTTCAAATCTCAAAACTGA
Found at i:19874748 original size:18 final size:18
Alignment explanation
Indices: 19874725--19874762 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
19874715 AGGAGCTATT
19874725 GAGATTTGGAAATAACCA
1 GAGATTTGGAAATAACCA
19874743 GAGATTTGGAAATAACCA
1 GAGATTTGGAAATAACCA
19874761 GA
1 GA
19874763 TAATCTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (18 bp):
GAGATTTGGAAATAACCA
Found at i:19881429 original size:47 final size:47
Alignment explanation
Indices: 19881322--19881530 Score: 188
Period size: 47 Copynumber: 4.3 Consensus size: 47
19881312 AATGTGATTT
* * * *
19881322 CCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGCTT
1 CCGTATAAGACCATATCTGGGATATGGCATC-G-G---TGTGATATGTGCTA
* *
19881374 CCATATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTA
1 CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
* * *
19881421 CTGTATAAGACCATATCTGGGATATGGCATCAGTGTGATATGTGAT-
1 CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
* ** * *
19881467 CCGTGTAAGACCATGGCTGGGCTATGGCCTCGGTATGTGATATGTGACTA
1 CCGTATAAGACCATATCTGGGATATGGCATCGG--TGTGATATGTG-CTA
* *
19881517 -TGTGTAAGACCATA
1 CCGTATAAGACCATA
19881531 GTTTTACTAT
Statistics
Matches: 132, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
46 26 0.20
47 54 0.41
48 11 0.08
49 13 0.10
50 1 0.01
51 1 0.01
52 26 0.20
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (47 bp):
CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
Found at i:19884386 original size:43 final size:43
Alignment explanation
Indices: 19884291--19884429 Score: 124
Period size: 43 Copynumber: 3.2 Consensus size: 43
19884281 CGGTTTACCT
** * *
19884291 AATGATGTGCTATGTGTGCTAGTATAATTGCTTC-GACTTGTCT
1 AATGATGCACTATGTGTGCCAGTATAATTGCTTCAG-CTTGTCC
*
19884334 AA-AATTGCACTATGTGTGCCAGTATAATTGCTTCAGCTTGTCC
1 AATGA-TGCACTATGTGTGCCAGTATAATTGCTTCAGCTTGTCC
* * * * *
19884377 AATGATGCAC-AAGATGT-CTCAATATAATTGCTTTAGTTTATCC
1 AATGATGCACTATG-TGTGC-CAGTATAATTGCTTCAGCTTGTCC
19884420 AATGATGCAC
1 AATGATGCAC
19884430 CGCAGTGCTA
Statistics
Matches: 80, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
42 4 0.05
43 74 0.93
44 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (43 bp):
AATGATGCACTATGTGTGCCAGTATAATTGCTTCAGCTTGTCC
Found at i:19885148 original size:22 final size:23
Alignment explanation
Indices: 19885106--19885148 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
19885096 ACTTGGTTAG
19885106 TTAAATATAGCTTGTAAATGGAT
1 TTAAATATAGCTTGTAAATGGAT
* *
19885129 TTAAATGTAGTTTG-AAATGG
1 TTAAATATAGCTTGTAAATGG
19885149 TATGAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (23 bp):
TTAAATATAGCTTGTAAATGGAT
Found at i:19894813 original size:10 final size:10
Alignment explanation
Indices: 19894798--19894857 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
19894788 TAAATTTAGG
*
19894798 ATTTATTTTT
1 ATTTATCTTT
19894808 ATTTATCTTT
1 ATTTATCTTT
* *
19894818 AATTATCATT
1 ATTTATCTTT
* *
19894828 AATTATCATT
1 ATTTATCTTT
*
19894838 AATTAT-TTGT
1 ATTTATCTT-T
19894848 ATTTATCTTT
1 ATTTATCTTT
19894858 TAGAATTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
9 1 0.02
10 40 0.93
11 2 0.05
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:19894853 original size:20 final size:19
Alignment explanation
Indices: 19894804--19894854 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
19894794 TAGGATTTAT
*
19894804 TTTTATTTATCTTTAATTA
1 TTTTATTTATCATTAATTA
* *
19894823 TCATTAATTATCATTAATTA
1 T-TTTATTTATCATTAATTA
19894843 TTTGTATTTATC
1 TTT-TATTTATC
19894855 TTTTAGAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTATTTATCATTAATTA
Found at i:19896101 original size:45 final size:44
Alignment explanation
Indices: 19896041--19896130 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 44
19896031 AATCGACGAT
19896041 GAAGTAGAGTCTAGGGTTAACAAAAACCCTACTCAAACATTTGAA
1 GAAGTAGAGTCTAGGGTTAACAAAAA-CCTACTCAAACATTTGAA
*
19896086 GAAGTAGAGTCTAGGGTTAACGAAAACCTACTCAAACATTTGAA
1 GAAGTAGAGTCTAGGGTTAACAAAAACCTACTCAAACATTTGAA
19896130 G
1 G
19896131 GCGAAAAAGT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 19 0.43
45 25 0.57
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (44 bp):
GAAGTAGAGTCTAGGGTTAACAAAAACCTACTCAAACATTTGAA
Found at i:19898535 original size:29 final size:27
Alignment explanation
Indices: 19898487--19898599 Score: 90
Period size: 29 Copynumber: 4.0 Consensus size: 27
19898477 GCAACCCAAC
*
19898487 CTTTATTTATTTAT-TTATTTATTTTTA
1 CTTT-TTTATTTTTATTATTTATTTTTA
19898514 CTTTTCTTAATTTTTATTATTTATTATTT-
1 CTTTT-TT-ATTTTTATTATTTATT-TTTA
* *
19898543 -TATTTTATTATTATTATTT-TATTTTA
1 CTTTTTTATTTTTATTATTTAT-TTTTA
19898569 CTTTATTTTATTATTTATTATTTTATTTTTA
1 C-TT-TTTTATT-TTTATTA-TTTATTTTTA
19898600 GATATTAATA
Statistics
Matches: 69, Mismatches: 5, Indels: 20
0.73 0.05 0.21
Matches are distributed among these distances:
25 4 0.06
26 14 0.20
27 8 0.12
28 9 0.13
29 16 0.23
30 9 0.13
31 8 0.12
32 1 0.01
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (27 bp):
CTTTTTTATTTTTATTATTTATTTTTA
Found at i:19898540 original size:3 final size:3
Alignment explanation
Indices: 19898527--19898595 Score: 62
Period size: 3 Copynumber: 24.7 Consensus size: 3
19898517 TTCTTAATTT
19898527 TTA TTA TTTA TTA TT- TTA TT- TTA TTA TTA TTA TT- TTA TT- TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
19898569 CT- TTA TT- TTA TTA TTTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TT
19898596 TTTAGATATT
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
2 13 0.24
3 36 0.65
4 6 0.11
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:19898543 original size:15 final size:15
Alignment explanation
Indices: 19898525--19898599 Score: 82
Period size: 15 Copynumber: 4.8 Consensus size: 15
19898515 TTTTCTTAAT
19898525 TTTTATTATTTATTA
1 TTTTATTATTTATTA
*
19898540 TTTTATTTTATTATTA
1 TTTTATTAT-TTATTA
19898556 TTATT-TTATTTTACTTTA
1 TT-TTATTA-TTTA--TTA
19898574 TTTTATTATTTATTA
1 TTTTATTATTTATTA
19898589 TTTTATT-TTTA
1 TTTTATTATTTA
19898600 GATATTAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
14 4 0.08
15 18 0.35
16 13 0.25
17 9 0.17
18 8 0.15
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTATTATTTATTA
Found at i:19898547 original size:5 final size:5
Alignment explanation
Indices: 19898537--19898597 Score: 65
Period size: 5 Copynumber: 12.4 Consensus size: 5
19898527 TTATTATTTA
* *
19898537 TTATT TTATT TTA-- TTATT ATTATT TTATT TTACT TTATT TTATT ATT-TA
1 TTATT TTATT TTATT TTATT -TTATT TTATT TTATT TTATT TTATT -TTATT
19898586 TTATT TTATT TT
1 TTATT TTATT TT
19898598 TAGATATTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
3 3 0.06
4 2 0.04
5 35 0.74
6 7 0.15
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (5 bp):
TTATT
Found at i:19898550 original size:20 final size:20
Alignment explanation
Indices: 19898525--19898599 Score: 91
Period size: 19 Copynumber: 3.6 Consensus size: 20
19898515 TTTTCTTAAT
19898525 TTTTATTATTTATTATTTTA
1 TTTTATTATTTATTATTTTA
19898545 TTTTATTA-TTATTATTTTA
1 TTTTATTATTTATTATTTTA
19898564 TTTTACTTTATTTTATTATTTATTA
1 TTTTA--TTA-TTTATTA-TT-TTA
19898589 TTTTATT-TTTA
1 TTTTATTATTTA
19898600 GATATTAATA
Statistics
Matches: 49, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
19 16 0.33
20 8 0.16
21 7 0.14
23 8 0.16
24 2 0.04
25 8 0.16
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTATTATTTATTATTTTA
Found at i:19898605 original size:15 final size:15
Alignment explanation
Indices: 19898520--19898605 Score: 52
Period size: 15 Copynumber: 5.5 Consensus size: 15
19898510 TTTACTTTTC
19898520 TTAAT-TTTTATTAT
1 TTAATATTTTATTAT
* *
19898534 TTATTATTTTATTTT
1 TTAATATTTTATTAT
*
19898549 ATTATTATTATT-TTATT
1 -TTAATATT-TTATTA-T
*
19898566 TTACTTTATTTTATTAT
1 TTA--ATATTTTATTAT
*
19898583 TTATTATTTTATT-T
1 TTAATATTTTATTAT
19898597 TTAGATATT
1 TTA-ATATT
19898606 AATAAATTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
14 8 0.13
15 22 0.37
16 13 0.22
17 9 0.15
18 8 0.13
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.72
Consensus pattern (15 bp):
TTAATATTTTATTAT
Found at i:19900296 original size:10 final size:10
Alignment explanation
Indices: 19900281--19900332 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
19900271 TAAATTTAGG
19900281 ATTTATTTTT
1 ATTTATTTTT
*
19900291 ATTTATCTTT
1 ATTTATTTTT
* *
19900301 AATTATGTTT
1 ATTTATTTTT
*
19900311 ATTTATTTGT
1 ATTTATTTTT
19900321 ATTTATCTTTT
1 ATTTAT-TTTT
19900332 A
1 A
19900333 GAATTTAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
10 30 0.88
11 4 0.12
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:19908196 original size:9 final size:9
Alignment explanation
Indices: 19908184--19908292 Score: 50
Period size: 9 Copynumber: 11.7 Consensus size: 9
19908174 TTTGATTACA
19908184 TAAAAATAT
1 TAAAAATAT
19908193 TAAAAATAT
1 TAAAAATAT
*
19908202 ATTAAAA-A-
1 -TAAAAATAT
*
19908210 TACAAATAT
1 TAAAAATAT
19908219 TAAAAAT-T
1 TAAAAATAT
19908227 ATAAAAA-AT
1 -TAAAAATAT
19908236 GTAAAAAGCTCA-
1 -TAAAAA--T-AT
19908248 TAAAAATAT
1 TAAAAATAT
*
19908257 TAAATA-AT
1 TAAAAATAT
*
19908265 TACAAAATTTT
1 TA-AAAA-TAT
19908276 GTAAAAATAT
1 -TAAAAATAT
19908286 TATAAAA
1 TA-AAAA
19908293 ACATGGAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 29
0.67 0.08 0.25
Matches are distributed among these distances:
7 4 0.05
8 7 0.09
9 40 0.53
10 11 0.14
11 11 0.14
12 2 0.03
13 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (9 bp):
TAAAAATAT
Found at i:19908233 original size:25 final size:26
Alignment explanation
Indices: 19908187--19908235 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
19908177 GATTACATAA
*
19908187 AAATATTAAAAATATATTAAAAATAC
1 AAATATTAAAAATATATAAAAAATAC
19908213 AAATATTAAAAAT-TATAAAAAAT
1 AAATATTAAAAATATATAAAAAAT
19908236 GTAAAAAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
AAATATTAAAAATATATAAAAAATAC
Found at i:19908890 original size:32 final size:32
Alignment explanation
Indices: 19908849--19908914 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
19908839 CACCATCGTC
19908849 CCATGCAAATCCTCTACCTAGTCCATTGCTCA
1 CCATGCAAATCCTCTACCTAGTCCATTGCTCA
19908881 CCATGCAAATCCTCTACCTAGTCCATTGCTCA
1 CCATGCAAATCCTCTACCTAGTCCATTGCTCA
19908913 CC
1 CC
19908915 TTTACCTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.24, C:0.39, G:0.09, T:0.27
Consensus pattern (32 bp):
CCATGCAAATCCTCTACCTAGTCCATTGCTCA
Found at i:19910017 original size:16 final size:18
Alignment explanation
Indices: 19909996--19910033 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19909986 GAATGTACAT
19909996 TATAAT-ATCATA-ATTA
1 TATAATAATCATATATTA
*
19910012 TATAATAATTATATATTA
1 TATAATAATCATATATTA
19910030 TATA
1 TATA
19910034 TTCGTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 5 0.26
18 8 0.42
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TATAATAATCATATATTA
Found at i:19912982 original size:20 final size:19
Alignment explanation
Indices: 19912918--19912985 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
19912908 TAATAATATC
19912918 ATATAATATATATTAAAA-A
1 ATATAATA-ATATTAAAAGA
* *
19912937 A-ATGAA-AATA-AAAAAGT
1 ATAT-AATAATATTAAAAGA
19912954 ATATAATAATATTAAAAGA
1 ATATAATAATATTAAAAGA
19912973 ATATACATAATAT
1 ATATA-ATAATAT
19912986 ATATAATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
16 4 0.10
17 6 0.15
18 9 0.23
19 13 0.33
20 7 0.18
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (19 bp):
ATATAATAATATTAAAAGA
Found at i:19913026 original size:21 final size:22
Alignment explanation
Indices: 19912972--19913052 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 22
19912962 ATATTAAAAG
*
19912972 AATATACATAATATATATA-AT
1 AATATACATAAAATATATACAT
* * * *
19912993 -ATACAAAACAAAATATATGCAT
1 AATA-TACATAAAATATATACAT
*
19913015 AATATA-TTAAAATATATACAT
1 AATATACATAAAATATATACAT
*
19913036 AATGTACATAAAATATA
1 AATATACATAAAATATA
19913053 CGTATATACG
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
20 3 0.07
21 27 0.60
22 12 0.27
23 3 0.07
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.32
Consensus pattern (22 bp):
AATATACATAAAATATATACAT
Found at i:19917754 original size:11 final size:11
Alignment explanation
Indices: 19917733--19917770 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
19917723 AATTTAGTGA
*
19917733 AAGAAAGAGAG
1 AAGAAAAAGAG
*
19917744 AAGAAGAAGAG
1 AAGAAAAAGAG
19917755 AAGAAAAAGA-
1 AAGAAAAAGAG
19917765 AAGAAA
1 AAGAAA
19917771 GAAAGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (11 bp):
AAGAAAAAGAG
Found at i:19917772 original size:14 final size:14
Alignment explanation
Indices: 19917732--19917774 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
19917722 GAATTTAGTG
*
19917732 AAAGAAAGAGAGAA
1 AAAGAAAGAAAGAA
*
19917746 GAAG-AAGAGAAGAA
1 AAAGAAAGA-AAGAA
19917760 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
19917774 A
1 A
19917775 GAAAAAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 4 0.17
14 16 0.67
15 4 0.17
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Found at i:19920604 original size:51 final size:50
Alignment explanation
Indices: 19920524--19920621 Score: 178
Period size: 51 Copynumber: 1.9 Consensus size: 50
19920514 CTTAGCATAT
*
19920524 TTGGTTTCTACTTCATAGGTACGATACATACTTTTACAAGGTATTCAAAG
1 TTGGTTTCTACTTCATAGGTACGAAACATACTTTTACAAGGTATTCAAAG
19920574 TTGGTTTTCTACTTCATAGGTACGAAACATACTTTTACAAGGTATTCA
1 TTGG-TTTCTACTTCATAGGTACGAAACATACTTTTACAAGGTATTCA
19920622 TACGCTCAGT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 4 0.09
51 42 0.91
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (50 bp):
TTGGTTTCTACTTCATAGGTACGAAACATACTTTTACAAGGTATTCAAAG
Found at i:19922045 original size:97 final size:98
Alignment explanation
Indices: 19921874--19922066 Score: 271
Period size: 97 Copynumber: 2.0 Consensus size: 98
19921864 ATATAGCTTT
19921874 AAATGTTGAATTCATTTTGCCACATCCGTAATTAATGAATTAAAAATAGCTTGTAATCTATCTCT
1 AAATGTTGAATTCATTTTGCCACATCCGTAATTAATGAATTAAAAATAGCTTGTAATCTATCTCT
19921939 TTCTACTGTTTACTCTCAATCAGGTCAAATTAA
66 TTCTACTGTTTACTCTCAATCAGGTCAAATTAA
* * * ** * * *
19921972 AAATGTTGAATTCATTTTTCTACTTTTGTCA-TAATGAATTAAAAATAGTTTGTAATCTATCTTT
1 AAATGTTGAATTCATTTTGCCACATCCGTAATTAATGAATTAAAAATAGCTTGTAATCTATCTCT
* * **
19922036 TTCTCCTGTTTATTCTTGATCAGGTCAAATT
66 TTCTACTGTTTACTCTCAATCAGGTCAAATT
19922067 TTCAGAGCTC
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
97 58 0.70
98 25 0.30
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (98 bp):
AAATGTTGAATTCATTTTGCCACATCCGTAATTAATGAATTAAAAATAGCTTGTAATCTATCTCT
TTCTACTGTTTACTCTCAATCAGGTCAAATTAA
Found at i:19926587 original size:2 final size:2
Alignment explanation
Indices: 19926580--19926634 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
19926570 CATAGTTTTG
* * *
19926580 TC TC TC TC TC CC CC TC TC -C CC T- TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
19926620 TC TC TC TC TT TC TC T
1 TC TC TC TC TC TC TC T
19926635 GTGCAAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:19931110 original size:29 final size:29
Alignment explanation
Indices: 19931077--19931134 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
19931067 AAAATTTAAA
19931077 AGCCTATTATTTTCAATCAATAACATTAT
1 AGCCTATTATTTTCAATCAATAACATTAT
19931106 AGCCTATTATTTTCAATCAATAACATTAT
1 AGCCTATTATTTTCAATCAATAACATTAT
19931135 GGACTAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.41
Consensus pattern (29 bp):
AGCCTATTATTTTCAATCAATAACATTAT
Found at i:19932248 original size:30 final size:30
Alignment explanation
Indices: 19932212--19932278 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
19932202 CTAAAATGAC
*
19932212 TATTATATAAAAAGGTCTTTTAAGGTCTTA
1 TATTATATAAAAAGCTCTTTTAAGGTCTTA
19932242 TATTATATAAAAAGCTCTTTTAAGGTCTTA
1 TATTATATAAAAAGCTCTTTTAAGGTCTTA
19932272 TATTATA
1 TATTATA
19932279 CATATAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.45
Consensus pattern (30 bp):
TATTATATAAAAAGCTCTTTTAAGGTCTTA
Found at i:19947550 original size:14 final size:15
Alignment explanation
Indices: 19947531--19947560 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
19947521 ATATTTGACT
19947531 TGTTCTTAATT-TTG
1 TGTTCTTAATTCTTG
19947545 TGTTCTTAATTCTTG
1 TGTTCTTAATTCTTG
19947560 T
1 T
19947561 TTTGATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.13, C:0.10, G:0.13, T:0.63
Consensus pattern (15 bp):
TGTTCTTAATTCTTG
Found at i:19948982 original size:174 final size:174
Alignment explanation
Indices: 19948704--19949042 Score: 507
Period size: 174 Copynumber: 1.9 Consensus size: 174
19948694 TCAAGCTGTG
* * *
19948704 GAAATGAATCGGATGAAAAGAGTGGAGACCATCAAAGGCATAACACATGCTTTGTCGTACTTGCA
1 GAAATGAATCAGACGAAAAGAGTGGAGACCATCAAAGGCATAACACATGCTTTGTCATACTTGCA
* * * * *
19948769 CTTTGATTGTAGTCGTCCAGCAGTTCATAGAGATATATCAAGTAACATTGTTCTTTTAAACTCAA
66 CTATGATTGTAGTCGTCCAACAGTTCATAGAGATATATCAAATAACAATGTTATTTTAAACTCAA
* *
19948834 GCTTTAAGGCCTTTATAGCTGACTTTGGAGCTGCTCAAGTAGTT
131 GCTTTAAGGCCTTTATAGCTGACTTTAGAACTGCTCAAGTAGTT
* *
19948878 GAAATGAATCAGACGAAAAGAGTGGAGATCATCAAAGGCATAGCACATGCTTTGTCATACTTGCA
1 GAAATGAATCAGACGAAAAGAGTGGAGACCATCAAAGGCATAACACATGCTTTGTCATACTTGCA
* * ** *
19948943 CTATGATTGTAGTCGTCCAATAGTTTATCTAGATATATCAAATAACAATGTTATTTTAAACTCGA
66 CTATGATTGTAGTCGTCCAACAGTTCATAGAGATATATCAAATAACAATGTTATTTTAAACTCAA
* *
19949008 GCTTTAAGGCCTTTGTAGCTTACTTTAGAACTGCT
131 GCTTTAAGGCCTTTATAGCTGACTTTAGAACTGCT
19949043 AAAATGCTAA
Statistics
Matches: 146, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
174 146 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (174 bp):
GAAATGAATCAGACGAAAAGAGTGGAGACCATCAAAGGCATAACACATGCTTTGTCATACTTGCA
CTATGATTGTAGTCGTCCAACAGTTCATAGAGATATATCAAATAACAATGTTATTTTAAACTCAA
GCTTTAAGGCCTTTATAGCTGACTTTAGAACTGCTCAAGTAGTT
Found at i:19952428 original size:16 final size:16
Alignment explanation
Indices: 19952407--19952439 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
19952397 AGACGGTAAG
19952407 CAAAGTGCGAGCCTGT
1 CAAAGTGCGAGCCTGT
*
19952423 CAAAGTGTGAGCCTGT
1 CAAAGTGCGAGCCTGT
19952439 C
1 C
19952440 GAATTGTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.21
Consensus pattern (16 bp):
CAAAGTGCGAGCCTGT
Found at i:19955460 original size:54 final size:52
Alignment explanation
Indices: 19955384--19955556 Score: 190
Period size: 54 Copynumber: 3.2 Consensus size: 52
19955374 TAATTCTCAA
* *
19955384 CTGCATTATTGATGTTAAAAAAAGAAAGCTGAAAGATGGATTACTAATTTTGAT
1 CTGCATTATTGTTGTT-AAAAAAGAAAGTTGAAAG-TGGATTACTAATTTTGAT
* * * *
19955438 TTGCATTATTGTTGTTAGAAAAAAAAAGTTGAAAGT--ATTACTCATTTTTCAT
1 CTGCATTATTGTTGTTA-AAAAAGAAAGTTGAAAGTGGATTACT-AATTTTGAT
* *
19955490 CCT-CATTATTGTTATTAATAAAAGAAAGTTGAAAGGTGGATTACTCATTTTGAT
1 -CTGCATTATTGTTGTTAA-AAAAGAAAGTTGAAA-GTGGATTACTAATTTTGAT
19955544 CTGCATTATTGTT
1 CTGCATTATTGTT
19955557 AATAAAACAC
Statistics
Matches: 99, Mismatches: 12, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
51 7 0.07
52 34 0.34
53 7 0.07
54 45 0.45
55 6 0.06
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (52 bp):
CTGCATTATTGTTGTTAAAAAAGAAAGTTGAAAGTGGATTACTAATTTTGAT
Found at i:19955571 original size:52 final size:52
Alignment explanation
Indices: 19955384--19955576 Score: 182
Period size: 52 Copynumber: 3.6 Consensus size: 52
19955374 TAATTCTCAA
* * * *
19955384 CTGCATTATTGATGTTAAAAAAAGAAAGCTGAAAGATGGATTACTAATTTTGAT
1 CTGCATTATTG-T-TTAATAAAAGAAAGTTGAAAGGTGGATTACTCATTTTGAT
* * *
19955438 TTGCATTATTGTTGTTAGA-AAAAAAAAGTTGAAA-GT--ATTACTCATTTTTCAT
1 CTGCATTATTG-T-TTA-ATAAAAGAAAGTTGAAAGGTGGATTACTCA-TTTTGAT
19955490 CCT-CATTATTGTTATTAATAAAAGAAAGTTGAAAGGTGGATTACTCATTTTGAT
1 -CTGCATTATTG-T-TTAATAAAAGAAAGTTGAAAGGTGGATTACTCATTTTGAT
*
19955544 CTGCATTATTG-TTAATAAAACACAAGTTGAAAG
1 CTGCATTATTGTTTAATAAAAGA-AAGTTGAAAG
19955577 CTACTTCTTT
Statistics
Matches: 118, Mismatches: 12, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
51 18 0.15
52 43 0.36
53 6 0.05
54 42 0.36
55 9 0.08
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (52 bp):
CTGCATTATTGTTTAATAAAAGAAAGTTGAAAGGTGGATTACTCATTTTGAT
Found at i:19960387 original size:14 final size:15
Alignment explanation
Indices: 19960360--19960388 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19960350 GGGAAGAAGA
19960360 AAAGAAAGGAGAAAG
1 AAAGAAAGGAGAAAG
19960375 AAAGAAA-GAGAAAG
1 AAAGAAAGGAGAAAG
19960389 GGGAAAGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (15 bp):
AAAGAAAGGAGAAAG
Found at i:19960388 original size:21 final size:20
Alignment explanation
Indices: 19960356--19960395 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
19960346 AGAGGGGAAG
19960356 AAGAAAAGAAAGGAGAAAGA
1 AAGAAAAGAAAGGAGAAAGA
*
19960376 AAGAAAGAGAAAGGGGAAAG
1 AAGAAA-AGAAAGGAGAAAG
19960396 GGAAGGTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (20 bp):
AAGAAAAGAAAGGAGAAAGA
Found at i:19963825 original size:28 final size:30
Alignment explanation
Indices: 19963767--19963827 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
19963757 TGCCAGAAGC
* *
19963767 AAACAAAAGAAAAATTAGTAATTAAAATAA
1 AAACAAAAGAAAAATTAGCAATAAAAATAA
*
19963797 AAACAAAA-TAAAATT-GCAATAAAAATAA
1 AAACAAAAGAAAAATTAGCAATAAAAATAA
19963825 AAA
1 AAA
19963828 ATGGCTAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 14 0.50
29 6 0.21
30 8 0.29
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (30 bp):
AAACAAAAGAAAAATTAGCAATAAAAATAA
Found at i:19967583 original size:14 final size:14
Alignment explanation
Indices: 19967561--19967612 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
19967551 ACAATAAAAG
*
19967561 AAATGATAAAATAGA
1 AAATAATAAAATA-A
19967576 AAA-AATAAAATAA
1 AAATAATAAAATAA
* *
19967589 AAATAATACAACAA
1 AAATAATAAAATAA
*
19967603 TAATAATAAA
1 AAATAATAAA
19967613 CGAGCTGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 4 0.13
14 24 0.77
15 3 0.10
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (14 bp):
AAATAATAAAATAA
Found at i:19969795 original size:13 final size:13
Alignment explanation
Indices: 19969777--19969854 Score: 68
Period size: 13 Copynumber: 5.9 Consensus size: 13
19969767 TGGAATTTAA
19969777 GGTTTAAGGTTTG
1 GGTTTAAGGTTTG
*
19969790 GGTTTAAGTTTTG
1 GGTTTAAGGTTTG
* *
19969803 GGTTTGAGGTTTAA
1 GGTTTAAGGTTT-G
* *
19969817 TGTTT-AGGTTTAT
1 GGTTTAAGGTTT-G
* *
19969830 GGTTTAATGTTTT
1 GGTTTAAGGTTTG
19969843 GGTTTAAGGTTT
1 GGTTTAAGGTTT
19969855 AAGGGTTCAT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
13 45 0.83
14 9 0.17
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.53
Consensus pattern (13 bp):
GGTTTAAGGTTTG
Found at i:19969797 original size:20 final size:20
Alignment explanation
Indices: 19969772--19969858 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
19969762 GGGTCTGGAA
*
19969772 TTTAAGGTTTAAGGTTT-GGG
1 TTTAAGGTTT-AGGTTTAAGG
* * *
19969792 TTTAAGTTTTGGGTTTGAGG
1 TTTAAGGTTTAGGTTTAAGG
* *
19969812 TTTAATGTTTAGGTTTATGG
1 TTTAAGGTTTAGGTTTAAGG
* *
19969832 TTTAATGTTTTGGTTTAAGG
1 TTTAAGGTTTAGGTTTAAGG
19969852 TTTAAGG
1 TTTAAGG
19969859 GTTCATGGTT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
19 5 0.09
20 50 0.91
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.51
Consensus pattern (20 bp):
TTTAAGGTTTAGGTTTAAGG
Found at i:19969800 original size:6 final size:7
Alignment explanation
Indices: 19969772--19969858 Score: 74
Period size: 7 Copynumber: 13.0 Consensus size: 7
19969762 GGGTCTGGAA
19969772 TTTAAGG
1 TTTAAGG
19969779 TTTAAGG
1 TTTAAGG
*
19969786 TTT-GGG
1 TTTAAGG
19969792 TTTAA-G
1 TTTAAGG
**
19969798 TTTTGGG
1 TTTAAGG
*
19969805 TTTGAGG
1 TTTAAGG
*
19969812 TTTAATG
1 TTTAAGG
19969819 TTT-AGG
1 TTTAAGG
*
19969825 TTTATGG
1 TTTAAGG
*
19969832 TTTAATG
1 TTTAAGG
*
19969839 TTT-TGG
1 TTTAAGG
19969845 TTTAAGG
1 TTTAAGG
19969852 TTTAAGG
1 TTTAAGG
19969859 GTTCATGGTT
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
6 18 0.30
7 43 0.70
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.51
Consensus pattern (7 bp):
TTTAAGG
Found at i:19969902 original size:20 final size:20
Alignment explanation
Indices: 19969772--19969891 Score: 61
Period size: 20 Copynumber: 5.8 Consensus size: 20
19969762 GGGTCTGGAA
* *
19969772 TTTAAGGTTTAAGGTTT-GGG
1 TTTAAGG-TTATGGTTTATGG
*
19969792 TTTAA-GTTTTGGGTTTGA-GG
1 TTTAAGGTTAT-GGTTT-ATGG
*
19969812 TTTAATGTT-TAGGTTTATGG
1 TTTAAGGTTAT-GGTTTATGG
* * *
19969832 TTTAATGTTTTGGTTTAAGG
1 TTTAAGGTTATGGTTTATGG
19969852 TTTAAGGGTTCATGG-TTATGAG
1 TTTAA-GGTT-ATGGTTTATG-G
*
19969874 TTTGAGGTTTATGGTTTA
1 TTTAAGG-TTATGGTTTA
19969892 AGTTCATGGT
Statistics
Matches: 81, Mismatches: 8, Indels: 20
0.74 0.07 0.18
Matches are distributed among these distances:
18 2 0.02
19 7 0.09
20 42 0.52
21 17 0.21
22 13 0.16
ACGTcount: A:0.19, C:0.01, G:0.30, T:0.50
Consensus pattern (20 bp):
TTTAAGGTTATGGTTTATGG
Found at i:19970043 original size:27 final size:28
Alignment explanation
Indices: 19969993--19970096 Score: 95
Period size: 27 Copynumber: 3.8 Consensus size: 28
19969983 GGGTTATGGG
* * *
19969993 TTTGGGTTTAAGGTTTGAGCTTTTATGT
1 TTTGGGTTTAGGGTTTAAGATTTTATGT
*
19970021 TTTGGGTTTAGGG-TTAAGATTTTAGGT
1 TTTGGGTTTAGGGTTTAAGATTTTATGT
** * * * *
19970048 TTAAGATTTAGGGTTTAGGATTAT-TGG
1 TTTGGGTTTAGGGTTTAAGATTTTATGT
*
19970075 TTTGAGTTTAGGGTTTAAGATT
1 TTTGGGTTTAGGGTTTAAGATT
19970097 CAAGATTTTA
Statistics
Matches: 59, Mismatches: 16, Indels: 3
0.76 0.21 0.04
Matches are distributed among these distances:
27 39 0.66
28 20 0.34
ACGTcount: A:0.20, C:0.01, G:0.30, T:0.49
Consensus pattern (28 bp):
TTTGGGTTTAGGGTTTAAGATTTTATGT
Found at i:19970063 original size:14 final size:14
Alignment explanation
Indices: 19970027--19970096 Score: 67
Period size: 14 Copynumber: 5.1 Consensus size: 14
19970017 ATGTTTTGGG
19970027 TTTAGGG-TTAAGA
1 TTTAGGGTTTAAGA
19970040 TTTTA-GGTTTAAGA
1 -TTTAGGGTTTAAGA
*
19970054 TTTAGGGTTTAGGA
1 TTTAGGGTTTAAGA
* *
19970068 -TTATTGGTTTGAG-
1 TTTA-GGGTTTAAGA
19970081 TTTAGGGTTTAAGA
1 TTTAGGGTTTAAGA
19970095 TT
1 TT
19970097 CAAGATTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
13 16 0.36
14 29 0.64
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (14 bp):
TTTAGGGTTTAAGA
Found at i:19970143 original size:21 final size:22
Alignment explanation
Indices: 19970119--19970175 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
19970109 TTTAATGTCT
19970119 TGGCTTAGT-GTTTA-GGTTTTA
1 TGGCTTA-TAGTTTATGGTTTTA
19970140 TGGCTTATAGTTTATGG-TTTA
1 TGGCTTATAGTTTATGGTTTTA
* *
19970161 AGGTTTATAGTTTAT
1 TGGCTTATAGTTTAT
19970176 ATGTTCGAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 1 0.03
21 29 0.91
22 2 0.06
ACGTcount: A:0.19, C:0.04, G:0.25, T:0.53
Consensus pattern (22 bp):
TGGCTTATAGTTTATGGTTTTA
Found at i:19970313 original size:35 final size:34
Alignment explanation
Indices: 19970269--19970355 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 34
19970259 GCTTTTATGT
*
19970269 TTTAT-GTTTAGCGTTTAAGATTTTAGATTTAGGG
1 TTTATGGTTTAG-GTTTAAGATTTTAGATTTAGAG
* * *
19970303 TTTATGGTTTATGGTTCAAGATTTTAGGTTTATAG
1 TTTATGGTTTA-GGTTTAAGATTTTAGATTTAGAG
*
19970338 TTCATGGTTTAGTGTTTA
1 TTTATGGTTTAG-GTTTA
19970356 GAGTTCAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
34 6 0.14
35 37 0.84
36 1 0.02
ACGTcount: A:0.22, C:0.03, G:0.23, T:0.52
Consensus pattern (34 bp):
TTTATGGTTTAGGTTTAAGATTTTAGATTTAGAG
Found at i:19970332 original size:21 final size:21
Alignment explanation
Indices: 19970303--19970367 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
19970293 AGATTTAGGG
19970303 TTTATGGTTTATGGTTCAAGAT
1 TTTA-GGTTTATGGTTCAAGAT
* * *
19970325 TTTAGGTTTATAGTTCATG-G
1 TTTAGGTTTATGGTTCAAGAT
19970345 TTTAGTGTTTA-GAGTTCAAGAT
1 TTTAG-GTTTATG-GTTCAAGAT
19970367 T
1 T
19970368 CAATGTTATG
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
20 5 0.15
21 24 0.71
22 5 0.15
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (21 bp):
TTTAGGTTTATGGTTCAAGAT
Found at i:19970415 original size:14 final size:13
Alignment explanation
Indices: 19970385--19970463 Score: 63
Period size: 14 Copynumber: 5.8 Consensus size: 13
19970375 ATGGGTTCAA
19970385 GTTTAA-GTTTAT
1 GTTTAAGGTTTAT
19970397 GTTTAAGGTTTAGT
1 GTTTAAGGTTTA-T
*
19970411 GTTTAGGGTTTAAT
1 GTTTAAGGTTT-AT
19970425 GTTT-AGAGTTTAT
1 GTTTAAG-GTTTAT
* *
19970438 GATTTTAGGTTTTTT
1 G-TTTAAGG-TTTAT
*
19970453 GTTTATGGTTT
1 GTTTAAGGTTT
19970464 GAGATTCCAG
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
12 6 0.11
13 12 0.22
14 29 0.53
15 8 0.15
ACGTcount: A:0.19, C:0.00, G:0.24, T:0.57
Consensus pattern (13 bp):
GTTTAAGGTTTAT
Found at i:19970422 original size:21 final size:21
Alignment explanation
Indices: 19970401--19970463 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
19970391 GTTTATGTTT
*
19970401 AAGGTTTAGTGTTTAGGGTTT
1 AAGGTTTAGTGTTTATGGTTT
* * *
19970422 AATGTTTAGAGTTTATGATTT
1 AAGGTTTAGTGTTTATGGTTT
* **
19970443 TAGGTTTTTTGTTTATGGTTT
1 AAGGTTTAGTGTTTATGGTTT
19970464 GAGATTCCAG
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.00, G:0.25, T:0.56
Consensus pattern (21 bp):
AAGGTTTAGTGTTTATGGTTT
Found at i:19970899 original size:20 final size:21
Alignment explanation
Indices: 19970849--19970909 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 21
19970839 AGGGTTCATG
19970849 GTTTAAGGTTTGTGATTTACTA
1 GTTTAAGGTTTGTGATTTA-TA
*
19970871 -TTTAGGGTTATGTG-TTT-TA
1 GTTTAAGGTT-TGTGATTTATA
19970890 GTTTAAGGTTTAGTG-TTTAT
1 GTTTAAGGTTT-GTGATTTAT
19970910 GATTATGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
19 3 0.09
20 14 0.42
21 12 0.36
22 4 0.12
ACGTcount: A:0.20, C:0.02, G:0.25, T:0.54
Consensus pattern (21 bp):
GTTTAAGGTTTGTGATTTATA
Found at i:19971529 original size:20 final size:21
Alignment explanation
Indices: 19971497--19971535 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19971487 CCTCAAACCC
19971497 TTGAACCATAAA-CCTAAATT
1 TTGAACCATAAACCCTAAATT
19971517 TTGAATCCA-AAACCCTAAA
1 TTGAA-CCATAAACCCTAAA
19971536 CCTCAAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.46, C:0.23, G:0.05, T:0.26
Consensus pattern (21 bp):
TTGAACCATAAACCCTAAATT
Found at i:19972534 original size:44 final size:43
Alignment explanation
Indices: 19972470--19972557 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 43
19972460 AATCTTGCTG
*
19972470 GCCACTGATGCCTCCAACTTTGAGTAAAAGTCTTGTGGAAAGA
1 GCCACTGATGCCTCCAACTTTGAGTAAAAGGCTTGTGGAAAGA
19972513 GNCCACTGATGCCTCCAACTTTGAGTAAAAGGCTTGTGGAAAGA
1 G-CCACTGATGCCTCCAACTTTGAGTAAAAGGCTTGTGGAAAGA
19972557 G
1 G
19972558 TGTCAATGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 1 0.02
44 42 0.98
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.24
Consensus pattern (43 bp):
GCCACTGATGCCTCCAACTTTGAGTAAAAGGCTTGTGGAAAGA
Found at i:19976199 original size:26 final size:24
Alignment explanation
Indices: 19976164--19976212 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
19976154 CAATTTAAAT
19976164 TCAGTTAAATT-TACTAAAAACTCAA
1 TCAGTTAAATTAT-C-AAAAACTCAA
19976189 TCAGTTTAAATTATCAAAAACTCA
1 TCAG-TTAAATTATCAAAAACTCA
19976213 CCATAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 13 0.59
26 8 0.36
27 1 0.05
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (24 bp):
TCAGTTAAATTATCAAAAACTCAA
Found at i:19979468 original size:10 final size:10
Alignment explanation
Indices: 19979449--19979529 Score: 85
Period size: 10 Copynumber: 7.9 Consensus size: 10
19979439 TTAAATTCTA
19979449 AAAGATAAAT
1 AAAGATAAAT
19979459 ACAA-ATAAAT
1 A-AAGATAAAT
*
19979469 AAAGATAATT
1 AAAGATAAAT
19979479 AAAGATAAAT
1 AAAGATAAAT
19979489 -AAGAATAAAT
1 AAAG-ATAAAT
19979499 AAAGATAAAAGT
1 AAAGAT-AAA-T
* *
19979511 TAGGATAAAT
1 AAAGATAAAT
19979521 AAAGATAAA
1 AAAGATAAA
19979530 AGCTAAAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
9 5 0.08
10 38 0.64
11 11 0.19
12 5 0.08
ACGTcount: A:0.67, C:0.01, G:0.11, T:0.21
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:19979483 original size:30 final size:30
Alignment explanation
Indices: 19979449--19979506 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
19979439 TTAAATTCTA
19979449 AAAGATAAATACA-AATAAATAAAGATAATT
1 AAAGATAAATA-AGAATAAATAAAGATAATT
19979479 AAAGATAAATAAGAATAAATAAAGATAA
1 AAAGATAAATAAGAATAAATAAAGATAA
19979507 AAGTTAGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.69, C:0.02, G:0.09, T:0.21
Consensus pattern (30 bp):
AAAGATAAATAAGAATAAATAAAGATAATT
Found at i:19987472 original size:8 final size:8
Alignment explanation
Indices: 19987440--19987469 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
19987430 TTTTAGATTT
19987440 TATATAAA
1 TATATAAA
19987448 TATATAAA
1 TATATAAA
*
19987456 TATATATA
1 TATATAAA
19987464 TATATA
1 TATATA
19987470 TATTCTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
TATATAAA
Found at i:19988867 original size:3 final size:3
Alignment explanation
Indices: 19988848--19988992 Score: 69
Period size: 3 Copynumber: 47.3 Consensus size: 3
19988838 TTAGTTAATT
* * * * *
19988848 TTA TTA TTT TTA CTA TTA TTA TTA TTA TAA ATA -TA TTA TTA TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
19988895 TTA TTA TTA TTTA CATG TTA TTA TTTC TTT TTC TT- TTA TTA TGGTC
1 TTA TTA TTA -TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA T--TA
** * * * * *
19988941 TTA TTA TTA TTA CCA TTA TTA ATA TTT TTA TTT TTA TTT TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19988989 TTA T
1 TTA T
19988993 CATCTTATTT
Statistics
Matches: 103, Mismatches: 33, Indels: 12
0.70 0.22 0.08
Matches are distributed among these distances:
2 4 0.04
3 91 0.88
4 6 0.06
5 2 0.02
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:19989082 original size:23 final size:23
Alignment explanation
Indices: 19989016--19989082 Score: 75
Period size: 23 Copynumber: 2.9 Consensus size: 23
19989006 TACTATTGTC
19989016 ATTTTTGTACTATTATTATTATTTT
1 ATTTTT-TACTATTATTATT-TTTT
*
19989041 -TTTTTTA-TATTTTATATTTTTT
1 ATTTTTTACTATTAT-TATTTTTT
*
19989063 ATTTTTTACTACTATTATTT
1 ATTTTTTACTATTATTATTT
19989083 ATTGTCGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
22 9 0.25
23 18 0.50
24 9 0.25
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.72
Consensus pattern (23 bp):
ATTTTTTACTATTATTATTTTTT
Found at i:19989190 original size:16 final size:15
Alignment explanation
Indices: 19989171--19989212 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
19989161 TTATATTTAC
*
19989171 TATTGTTATTATTATT
1 TATTGTTATTACTA-T
19989187 TATTGTTATTACTAT
1 TATTGTTATTACTAT
*
19989202 TATTCTTATTA
1 TATTGTTATTA
19989213 ATGTAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (15 bp):
TATTGTTATTACTAT
Found at i:19989224 original size:3 final size:3
Alignment explanation
Indices: 19989136--19989212 Score: 50
Period size: 3 Copynumber: 25.3 Consensus size: 3
19989126 TTTTGCTATC
* * * *
19989136 ATT ATT ATT ACT -TT ATTT ATT ATC ATT A-T ATTT ACT ATT GTT ATT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
* * *
19989181 ATT ATTT ATT GTT ATT ACT ATT ATT CTT ATT A
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT A
19989213 ATGTAATTAT
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
2 3 0.05
3 44 0.80
4 8 0.15
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:19989461 original size:15 final size:15
Alignment explanation
Indices: 19989443--19989480 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
19989433 CCTCTTTAAC
19989443 TATTATTACTATTAT
1 TATTATTACTATTAT
*
19989458 TATTTTTACTATTAT
1 TATTATTACTATTAT
*
19989473 AATTATTA
1 TATTATTA
19989481 TTAATTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTATTACTATTAT
Found at i:19990717 original size:25 final size:24
Alignment explanation
Indices: 19990680--19990746 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
19990670 ATTCTAAATT
*
19990680 CTATATTA-CGTATATATATT-ATA
1 CTATATTATTGTATATAT-TTAATA
* *
19990703 CTATTTTATGTGTATATCTTTAATA
1 CTATATTAT-TGTATATATTTAATA
19990728 CTATATTATT-TATATATTT
1 CTATATTATTGTATATATTT
19990747 TTTTTTCTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
23 15 0.42
24 3 0.08
25 18 0.50
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.55
Consensus pattern (24 bp):
CTATATTATTGTATATATTTAATA
Found at i:19990785 original size:22 final size:22
Alignment explanation
Indices: 19990760--19990801 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19990750 TTTCTACATG
*
19990760 TTATCTTATGTATATATTTTAA
1 TTATATTATGTATATATTTTAA
*
19990782 TTATATTATGTATGTATTTT
1 TTATATTATGTATATATTTT
19990802 TTACACTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (22 bp):
TTATATTATGTATATATTTTAA
Found at i:20001162 original size:75 final size:74
Alignment explanation
Indices: 20001057--20002698 Score: 2034
Period size: 75 Copynumber: 22.0 Consensus size: 74
20001047 ATGTTTCAAA
* * *
20001057 AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGTTAAGGTATTTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
20001122 TCTGTATTTC
66 TCTGT-TTTC
20001132 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
20001197 TCTGTATTTC
66 TCTGT-TTTC
20001207 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
20001272 TCTGTATTTC
66 TCTGT-TTTC
20001282 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
20001347 TCTGTATTTC
66 TCTGT-TTTC
20001357 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
20001422 TCTGTATTTC
66 TCTGT-TTTC
20001432 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
20001497 TCTGTATTTC
66 TCTGT-TTTC
* * * *
20001507 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGTGTTTTCCATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
20001570 TCTGTTCTTC
66 TCTGTT-TTC
* * * * ** * * *
20001580 AATTTCTGTTTTTCAAAAA-CA--TCA-ACT-C-ATATTGCGAGAGGTGAG--TTGAGCCTCAGG
1 AA------------AAAAATCAGCTCATATTGCGAGA--G-GTGAGTTGAGCCTCAAGACAC-GT
** * ** ** *
20001637 ACACGCTGAGGTAATTTCAATTTTTGTTTGTC
50 TGA-GGT-A--TTTTCA--ATTTCTGTTT-TC
* * * *
20001669 --AAAACTCAACTCATATTGGGAGAGGTGAGTTGAGCCTCAAGACATGTTGAGGTATTTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
20001732 TCTGTTTTTC
66 TCTG-TTTTC
* * * * *
20001742 AAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
*
20001807 TTTGTTTGTC
66 TCTGTTT-TC
*
20001817 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
20001881 TCTGTATTTC
66 TCTGT-TTTC
* * *
20001891 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGTAATTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
*
20001954 TTTGTTTGTC
66 TCTGTTT-TC
*
20001964 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
20002028 TCTGTATTTC
66 TCTGT-TTTC
* * *
20002038 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTT--GCCTCAGGACACGCTGAGGTAATTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
*
20002101 TTTGTTTGTC
66 TCTGTTT-TC
* *
20002111 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGGGGTATTTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
20002175 TCTGTCTTTC
66 TCTGT-TTTC
* * *
20002185 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGTAATTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
*
20002248 TTTGTTTGTC
66 TCTGTTT-TC
* *
20002258 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGGGGTATTTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
20002322 TCTGTCTTTC
66 TCTGT-TTTC
* * *
20002332 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGTAATTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
*
20002395 TTTGTTTGTC
66 TCTGTTT-TC
* *
20002405 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGGGGTATTTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
20002469 TCTGTCTTTC
66 TCTGT-TTTC
* * *
20002479 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGTAATTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
*
20002542 TTTGTTTGTC
66 TCTGTTT-TC
* * * *
20002552 --AAAAA-CAACTCATATTGTGAGAGGTAAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
20002614 TCTGTCTTTC
66 TCTGT-TTTC
* * * *
20002624 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACAC--TAAGGTGTTTTCTATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
20002687 TCTGTTCTTC
66 TCTGTT-TTC
20002697 AA
1 AA
20002699 TTTCTGTGTT
Statistics
Matches: 1375, Mismatches: 124, Indels: 138
0.84 0.08 0.08
Matches are distributed among these distances:
70 31 0.02
71 5 0.00
72 186 0.14
73 186 0.14
74 179 0.13
75 717 0.52
76 2 0.00
77 1 0.00
78 13 0.01
79 7 0.01
80 8 0.01
81 5 0.00
82 11 0.01
83 2 0.00
84 4 0.00
85 5 0.00
87 2 0.00
88 1 0.00
89 10 0.01
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (74 bp):
AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
TCTGTTTTC
Found at i:20002010 original size:147 final size:147
Alignment explanation
Indices: 20001058--20002668 Score: 2477
Period size: 147 Copynumber: 10.8 Consensus size: 147
20001048 TGTTTCAAAA
* *
20001058 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGTTAAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
* *
20001123 CTGTATTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
66 CTGTATTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGTA
* *
20001188 TTTTCAATTTCTGTATT-TC
129 ATTTCAATTTTTGT-TTGTC
*
20001207 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
* *
20001272 TCTGTATTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGT
65 TCTGTATTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGT
* *
20001337 ATTTTCAATTTCTGTATT-TC
128 AATTTCAATTTTTGT-TTGTC
*
20001357 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
* *
20001422 TCTGTATTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGT
65 TCTGTATTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGT
* *
20001487 ATTTTCAATTTCTGTATT-TC
128 AATTTCAATTTTTGT-TTGTC
* * *
20001507 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGTGTTTTCCATT
1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGA-G-G---T--A--
* * * *
20001570 TCTGTTCTTCAATTTCTGTTTTTCAAAAACATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
56 ----TT-TTCAATTTCTGTATTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCA
*
20001635 GGACACGCTGAGGTAATTTCAATTTTTGTTTGTC
116 --AGACGCTGAGGTAATTTCAATTTTTGTTTGTC
* * *
20001669 -AAAACTCAACTCATATTGGGAGAGGTGAGTTGAGCCTCAAGACATGTTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
* * * * *
20001733 CTGTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
66 CTGTATTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCA--AGACGCTGAGGTA
20001798 ATTTCAATTTTTGTTTGTC
129 ATTTCAATTTTTGTTTGTC
20001817 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
20001882 CTGTATTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAAT
66 CTGTATTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAAT
20001947 TTCAATTTTTGTTTGTC
131 TTCAATTTTTGTTTGTC
20001964 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
*
20002029 CTGTATTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTG--CCTCAGGACACGCTGAGGTA
66 CTGTATTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCA--AGACGCTGAGGTA
20002092 ATTTCAATTTTTGTTTGTC
129 ATTTCAATTTTTGTTTGTC
*
20002111 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGGGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
*
20002176 CTGTCTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAAT
66 CTGTATTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAAT
20002241 TTCAATTTTTGTTTGTC
131 TTCAATTTTTGTTTGTC
*
20002258 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGGGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
*
20002323 CTGTCTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAAT
66 CTGTATTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAAT
20002388 TTCAATTTTTGTTTGTC
131 TTCAATTTTTGTTTGTC
*
20002405 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGGGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
*
20002470 CTGTCTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAAT
66 CTGTATTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAAT
20002535 TTCAATTTTTGTTTGTC
131 TTCAATTTTTGTTTGTC
* * *
20002552 -AAAAA-CAACTCATATTGTGAGAGGTAAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
*
20002615 CTGTCTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGAC
66 CTGTATTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGAC
20002669 ACTAAGGTGT
Statistics
Matches: 1401, Mismatches: 36, Indels: 53
0.94 0.02 0.04
Matches are distributed among these distances:
145 113 0.08
146 5 0.00
147 601 0.43
148 96 0.07
149 115 0.08
150 339 0.24
153 1 0.00
155 2 0.00
157 1 0.00
160 38 0.03
161 5 0.00
162 84 0.06
164 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (147 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
CTGTATTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAAT
TTCAATTTTTGTTTGTC
Found at i:20002821 original size:92 final size:90
Alignment explanation
Indices: 20002605--20003187 Score: 353
Period size: 87 Copynumber: 6.5 Consensus size: 90
20002595 CATTGAGGTA
* * *
20002605 TTTTCAATTTCTGTCTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACC-TCA---A
1 TTTTCAATTTATGT-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTCACTCA
* * * * * * *
20002666 GACACTAAGGTGTTTTCTATTTCTGT
65 CACGCTGAGGTATTTTCAAATTATGT
* * * * *
20002692 TCTTCAATTTCTGTGTTTCAAAAAAATCAGCTCATATTGCGAGTGGTGAGTTGAGCCTTGACTCA
1 TTTTCAATTTATGT-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTCACTCA
*
20002757 CACGTTGAGGTATTTTCAAATTATGT
65 CACGCTGAGGTATTTTCAAATTATGT
* * * *
20002783 TTTTCAAATTT-TGTCTTTCCAAAAAAATCAACTCATATTGCGAGATGTGAGTTCAACC-TCA-G
1 TTTTC-AATTTATGT-TTT-CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTCACT
* * * * *
20002845 GACACGCTAAGGTATTTTCAATTTCTTTTTT
63 CACACGCTGAGGTATTTTCAA---ATTATGT
* * * *
20002876 TTTTCAATTTATGTTTGTCAAAAAAATCAACTTATATTGCAAGAGGTAAGTTGAGCC-TCAGGTC
1 TTTTCAATTTATGTTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTCA-CTC
* * * *
20002940 ACACGCCGATGTATTTTCAATTGATATTTTT
64 ACACGCTGAGGTATTTTCAA---AT-TATGT
* * ** **
20002971 TTTTTAATTTATGCTTTGC--AAAAATCAACTCATATTAAGAGAGGTGAGTTGAGCC-TCGGGTC
1 TTTTCAATTTATG-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTC-ACTC
** *
20003033 ACATACCGAGGTATTTTCAAAATT-TGT
64 ACACGCTGAGGTATTTTC-AAATTATGT
* * * *
20003060 TTTACAAATTT-TG--TTC-TAAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTT-AGCTC
1 TTTTC-AATTTATGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTCA-CTC
* * * *
20003120 ACGCGCTGAGCTATTTTCAATTTTTGT
64 ACACGCTGAGGTATTTTCAAATTATGT
* * *
20003147 TTTT-AATATCTA-GTTTT--AAAGAGTCAATTCATATTGCGAGA
1 TTTTCAAT-T-TATGTTTTCAAAAAAATCAACTCATATTGCGAGA
20003188 AATGAGTTAA
Statistics
Matches: 396, Mismatches: 73, Indels: 53
0.76 0.14 0.10
Matches are distributed among these distances:
85 3 0.01
86 7 0.02
87 109 0.28
88 22 0.06
89 9 0.02
90 24 0.06
91 33 0.08
92 82 0.21
93 64 0.16
94 22 0.06
95 18 0.05
96 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (90 bp):
TTTTCAATTTATGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTCACTCAC
ACGCTGAGGTATTTTCAAATTATGT
Found at i:20002944 original size:184 final size:178
Alignment explanation
Indices: 20002605--20003020 Score: 439
Period size: 184 Copynumber: 2.3 Consensus size: 178
20002595 CATTGAGGTA
* *
20002605 TTTTCAATTTCTGTCTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
1 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAACCTCAAGACA
* * * * *
20002670 CTAAGGTGTTTTCTATTTCTGTTCTTCAATTTCTGTGTTTCAAAAAAATCAGCTCATATTGCGAG
66 CTAAGGTATTTTCAATTTCTGTTCTTCAATTTATGTGTTTCAAAAAAATCAACTCATATTGCAAG
* * * **
20002735 TGGTGAGTTGAGCCTTGACTCACACGTTGAGGTATTTTCAAATTATGT
131 AGGTAAGTTGAGCCTAGACTCACACGCCGAGGTATTTTCAAATTATGT
* *
20002783 TTTTCAAATTT-TGTCTTTCCAAAAAAATCAACTCATATTGCGAGATGTGAGTTCAACCTCAGGA
1 TTTTC-AATTTCTGTCTTT-CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAACCTCAAGA
* * *
20002847 CACGCTAAGGTATTTTCAATTTCTTTTTTTTTTCAATTTATGT-TTGTCAAAAAAATCAACTTAT
64 CA--CTAAGGTATTTTCAATTTC---TGTTCTTCAATTTATGTGTT-TCAAAAAAATCAACTCAT
* * * *
20002911 ATTGCAAGAGGTAAGTTGAGCCTCAG-GTCACACGCCGATGTATTTTCAATTGATATTTTT
123 ATTGCAAGAGGTAAGTTGAGCCT-AGACTCACACGCCGAGGTATTTTCAA---AT-TATGT
* * **
20002971 TTTTTAATTTATG-CTTTGC--AAAAATCAACTCATATTAAGAGAGGTGAGTT
1 TTTTCAATTTCTGTCTTT-CAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
20003021 GAGCCTCGGG
Statistics
Matches: 198, Mismatches: 26, Indels: 21
0.81 0.11 0.09
Matches are distributed among these distances:
178 12 0.06
179 48 0.24
181 17 0.09
183 2 0.01
184 69 0.35
185 29 0.15
187 12 0.06
188 9 0.05
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (178 bp):
TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAACCTCAAGACA
CTAAGGTATTTTCAATTTCTGTTCTTCAATTTATGTGTTTCAAAAAAATCAACTCATATTGCAAG
AGGTAAGTTGAGCCTAGACTCACACGCCGAGGTATTTTCAAATTATGT
Found at i:20003021 original size:93 final size:93
Alignment explanation
Indices: 20002694--20003150 Score: 299
Period size: 92 Copynumber: 5.0 Consensus size: 93
20002684 ATTTCTGTTC
* * ** * * *
20002694 TTCAATTTCTGTGTT-TCAAAAAAATCAGCTCATATTGCGAGTGGTGAGTTGAGCCT-TGACTCA
1 TTCAATTTATGT-TTGTC-AAAAAATCAACTCATATTAAGAGAGGTGAGTTGAGCCTCAG-GTCA
** * *
20002757 CACGTTGAGGTATTTTCAA---ATTATGTTT
63 CACGCCGAGGTATTTTCAATTTATTTTTTTT
** * * *
20002785 TTCAAATTT-TGTCTT-TCCAAAAAAATCAACTCATATTGCGAGATGTGAGTTCAACCTCAGG--
1 TTC-AATTTATGT-TTGT-C-AAAAAATCAACTCATATTAAGAGAGGTGAGTTGAGCCTCAGGTC
** *
20002846 ACACGCTAAGGTATTTTCAATTTCTTTTTTTT
62 ACACGCCGAGGTATTTTCAATTTATTTTTTTT
* * *
20002878 TTCAATTTATGTTTGTCAAAAAAATCAACTTATATTGCA-AGAGGTAAGTTGAGCCTCAGGTCAC
1 TTCAATTTATGTTTGTC-AAAAAATCAACTCATATT-AAGAGAGGTGAGTTGAGCCTCAGGTCAC
*
20002942 ACGCCGATGTATTTTCAATTGATATTTTTTTT
64 ACGCCGAGGTATTTTCAATT--TATTTTTTTT
*
20002974 TT-AATTTATGCTTTG-C-AAAAATCAACTCATATTAAGAGAGGTGAGTTGAGCCTCGGGTCACA
1 TTCAATTTATG-TTTGTCAAAAAATCAACTCATATTAAGAGAGGTGAGTTGAGCCTCAGGTCACA
** * *
20003036 TACCGAGGTATTTTCAA---AATTTGTTT
65 CGCCGAGGTATTTTCAATTTATTTTTTTT
* * ** * * * *
20003062 TACAA---AT-TTTGTTCTAAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTAGCTCACG
1 TTCAATTTATGTTTG-TCAAAAAATCAACTCATATTAAGAGAGGTGAGTTGAGCCTCAGGTCACA
* * *
20003123 CGCTGAGCTATTTTCAATTT-TTGTTTTT
65 CGCCGAGGTATTTTCAATTTATTTTTTTT
20003151 AATATCTAGT
Statistics
Matches: 296, Mismatches: 48, Indels: 46
0.76 0.12 0.12
Matches are distributed among these distances:
84 4 0.01
86 3 0.01
87 52 0.18
88 8 0.03
89 7 0.02
90 18 0.06
91 9 0.03
92 84 0.28
93 68 0.23
94 19 0.06
95 9 0.03
96 15 0.05
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.39
Consensus pattern (93 bp):
TTCAATTTATGTTTGTCAAAAAATCAACTCATATTAAGAGAGGTGAGTTGAGCCTCAGGTCACAC
GCCGAGGTATTTTCAATTTATTTTTTTT
Found at i:20003841 original size:12 final size:12
Alignment explanation
Indices: 20003824--20003859 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
20003814 CCATTGTCTG
* *
20003824 CCACTTACTCCT
1 CCACTTGCTCCA
20003836 CCACTTGCTCCA
1 CCACTTGCTCCA
20003848 CCACTTGCTCCA
1 CCACTTGCTCCA
20003860 TCTTGCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.17, C:0.50, G:0.06, T:0.28
Consensus pattern (12 bp):
CCACTTGCTCCA
Found at i:20003977 original size:17 final size:16
Alignment explanation
Indices: 20003946--20003999 Score: 81
Period size: 17 Copynumber: 3.2 Consensus size: 16
20003936 GTAGTAGGGG
*
20003946 TTTTTTGAGGAGTTTT
1 TTTTTTGAGAAGTTTT
20003962 TTTTTTGAGAAGGTTTT
1 TTTTTTGAGAA-GTTTT
20003979 TTTTTTGAAGAAGTTTT
1 TTTTTTG-AGAAGTTTT
20003996 TTTT
1 TTTT
20004000 GGGGGGGGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
16 10 0.29
17 21 0.60
18 4 0.11
ACGTcount: A:0.17, C:0.00, G:0.20, T:0.63
Consensus pattern (16 bp):
TTTTTTGAGAAGTTTT
Found at i:20012199 original size:21 final size:22
Alignment explanation
Indices: 20012162--20012202 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
20012152 AATAAGAAGA
20012162 AAGCAATAAGAAAATAGCATAC
1 AAGCAATAAGAAAATAGCATAC
*
20012184 AAGCAATAA-TAAATAGCAT
1 AAGCAATAAGAAAATAGCAT
20012203 TTTTTTGTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.17
Consensus pattern (22 bp):
AAGCAATAAGAAAATAGCATAC
Found at i:20016979 original size:12 final size:12
Alignment explanation
Indices: 20016964--20016993 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20016954 ACAATAATAC
20016964 TATATATAAATG
1 TATATATAAATG
*
20016976 TATATATATATG
1 TATATATAAATG
20016988 TATATA
1 TATATA
20016994 ATAGAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
TATATATAAATG
Found at i:20017096 original size:19 final size:17
Alignment explanation
Indices: 20017072--20017118 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
20017062 AATTAAAGTA
*
20017072 ATAAAAAATAATACTATAT
1 ATAAAAAAT-ATA-TATAC
*
20017091 ATAAAATATATATATAC
1 ATAAAAAATATATATAC
20017108 AT-AAAAATATA
1 ATAAAAAATATA
20017119 CACTAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 3 0.12
19 8 0.32
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAATATATATAC
Found at i:20017114 original size:18 final size:19
Alignment explanation
Indices: 20017075--20017123 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
20017065 TAAAGTAATA
*
20017075 AAAAATA-ATACTATATAT
1 AAAAATATATACTATACAT
20017093 -AAAATATATA-TATACAT
1 AAAAATATATACTATACAT
*
20017110 AAAAATATACACTA
1 AAAAATATATACTA
20017124 ATATATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 12 0.46
18 12 0.46
19 2 0.08
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATATATACTATACAT
Found at i:20017611 original size:40 final size:40
Alignment explanation
Indices: 20017567--20017718 Score: 196
Period size: 40 Copynumber: 3.8 Consensus size: 40
20017557 GTGTTTTTAG
*
20017567 TCTGCTCCACTACTACTTAGGGAGATAAGACTTGATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
* * * * ***
20017607 TCTGCTTCACTATTGCTTAGGGAAATAAGATCTGTGGTTTTA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGATGCGA
*
20017649 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTAATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
*
20017689 TCTACTCCACTACTGCTTAGGGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
20017719 TTGTAATCTT
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
40 58 0.62
41 4 0.04
42 31 0.33
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (40 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
Found at i:20017658 original size:82 final size:83
Alignment explanation
Indices: 20017551--20017719 Score: 259
Period size: 82 Copynumber: 2.0 Consensus size: 83
20017541 CATGGGGATG
* * * * *
20017551 AGATTTGTGTTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTGATGCGATCTGCTTCA
1 AGATCTGTGGTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCA
*
20017616 CTATTGCTTAGGGAAATA
66 CTACTGCTTAGGGAAATA
*
20017634 AGATCTGTGGTTTTA-TCTGCTCCACTACTGCTTAGGGAGATAAGACTTAATGCGATCTACTCCA
1 AGATCTGTGGTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCA
*
20017698 CTACTGCTTAGGGAGATA
66 CTACTGCTTAGGGAAATA
20017716 AGAT
1 AGAT
20017720 TGTAATCTTC
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
82 65 0.83
83 13 0.17
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (83 bp):
AGATCTGTGGTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCA
CTACTGCTTAGGGAAATA
Found at i:20018061 original size:46 final size:46
Alignment explanation
Indices: 20017881--20018338 Score: 175
Period size: 46 Copynumber: 10.2 Consensus size: 46
20017871 ACTTCCTACC
* * *
20017881 AATATAGGAAGGCAGGATCTGCAATCTTCAATCTATTCCACTGCC-
1 AATACAGGAAGGTAAGATCTGCAATCTTCAATCTATTCCACTGCCT
* * * ** * *
20017926 AGATACAGGAAGATAGAGTTAT-C-GGCTTCAATGTACTCCACTG--T
1 A-ATACAGGAAGGTA-AGATCTGCAATCTTCAATCTATTCCACTGCCT
* * * * * * *
20017970 AGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTT-CGCTGCCT
1 AAT-ACAGGAAGGTAAGATCTGCAATCTTCAATCT-ATTCCACTGCCT
*
20018017 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCC-
1 AATACAGGAAGGTAAGATCTGCAATCTTCAATCTATTCCACTGCCT
* * * ** * *
20018062 AGATACAGTG-AGATAGAGTTAT-C-GGCTTCAATGTACTCCACTG--T
1 A-ATACAG-GAAGGTA-AGATCTGCAATCTTCAATCTATTCCACTGCCT
* * * * * * * *
20018106 AGT-CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTT-CGCTGCCG
1 AATACAGGAAGGTAAGATCTGCAATCTTCAATCT-ATTCCACTGCCT
* *
20018151 AATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCC-
1 AATACAGGAAGGTAAGATCTGCAATCTTCAATCTATTCCACTGCCT
* * * * ** * *
20018196 AGATACAGGGAGATAGAGTTAT-C-GGCTTCAATGTACTCCACTG--T
1 A-ATACAGGAAGGTA-AGATCTGCAATCTTCAATCTATTCCACTGCCT
** * * * ** * * *
20018240 GGT-CAGGGAGGTAAAATCTGCCATCTTTGATCTGCTT-CGCTGCCA
1 AATACAGGAAGGTAAGATCTGCAATCTTCAATCT-ATTCCACTGCCT
* *
20018285 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
1 AATACAGGAAGGTAAGATCTGCAATCTTCAATCTATTCCACTGCCT
20018331 AATACAGG
1 AATACAGG
20018339 GAGATAGAAT
Statistics
Matches: 285, Mismatches: 96, Indels: 63
0.64 0.22 0.14
Matches are distributed among these distances:
41 7 0.02
42 18 0.06
43 27 0.09
44 14 0.05
45 70 0.25
46 134 0.47
47 15 0.05
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.26
Consensus pattern (46 bp):
AATACAGGAAGGTAAGATCTGCAATCTTCAATCTATTCCACTGCCT
Found at i:20018187 original size:134 final size:134
Alignment explanation
Indices: 20017881--20018453 Score: 984
Period size: 134 Copynumber: 4.3 Consensus size: 134
20017871 ACTTCCTACC
* * *
20017881 AATATAGGAAGGCAGGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGAAGATAGAGTT
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
20017946 ATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCG
66 ATCGGCTTCAATGTACTCCACTGTAGT--CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCG
*
20018011 CTGCCT
129 CTGCCA
*
20018017 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGTGAGATAGAGTT
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
20018082 ATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCT
66 ATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCT
*
20018147 GCCG
131 GCCA
*
20018151 AATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
* *
20018216 ATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCT
66 ATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCT
20018281 GCCA
131 GCCA
* *
20018285 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATT
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
* * * * *
20018350 ATCGGCTTCAGTGTACTCCACTGTGGTCAGGAAAGTAAAATCTGCCATCTTTGATCTGCTTCGCT
66 ATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCT
20018415 GCCA
131 GCCA
20018419 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
20018454 CTTCACCACC
Statistics
Matches: 421, Mismatches: 16, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
134 333 0.79
136 88 0.21
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (134 bp):
AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
ATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCT
GCCA
Found at i:20018656 original size:132 final size:132
Alignment explanation
Indices: 20018391--20019499 Score: 2020
Period size: 132 Copynumber: 8.4 Consensus size: 132
20018381 AAAGTAAAAT
* * * * * ** * *
20018391 CTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTACT
1 CTGCTATCTTCGATCTGCTTCAC-GCC-AATACATGAAGACAAGATCTGCTTTCTGCGATCTACT
* *
20018456 TCACCACCAGTATGGGAAGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAGGAAGATA
64 TCGCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAGGAAGATA
20018521 GGAC
129 GGAC
*
20018525 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
1 CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
20018590 GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAGGAAGATAGG
66 GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAGGAAGATAGG
20018655 AC
131 AC
*
20018657 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
1 CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
20018722 GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAGGAAGATAGG
66 GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAGGAAGATAGG
20018787 AC
131 AC
20018789 CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
1 CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
20018854 GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAGGAAGATAGG
66 GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAGGAAGATAGG
20018919 AC
131 AC
20018921 CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
1 CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
20018986 GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAGGAAGATAGG
66 GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAGGAAGATAGG
20019051 AC
131 AC
20019053 CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
1 CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
20019118 GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAGGAAGATAGG
66 GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAGGAAGATAGG
20019183 AC
131 AC
* *
20019185 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTACGATCTACTTC
1 CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
* *
20019250 GCCACCAATATGGGAAGACAAGATCTGCATATTGGATCCACTTCCTATCAATATAGGAAGATAGG
66 GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAGGAAGATAGG
20019315 AC
131 AC
20019317 CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
1 CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
* *
20019382 GCCACCAATATGGGAAGACAAGATCTGCATCCTGGATCCACTTCCTATCAATATAGGAAGATAGG
66 GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAGGAAGATAGG
20019447 AC
131 AC
*
20019449 CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTACTTT
1 CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTT
20019500 AATGACTTCA
Statistics
Matches: 953, Mismatches: 22, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
132 931 0.98
133 3 0.00
134 19 0.02
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (132 bp):
CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAGGAAGATAGG
AC
Found at i:20031784 original size:19 final size:17
Alignment explanation
Indices: 20031760--20031806 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
20031750 AATTAAAGTA
*
20031760 ATAAAAAATAATACTATAT
1 ATAAAAAAT-ATA-TATAC
*
20031779 ATAAAATATATATATAC
1 ATAAAAAATATATATAC
20031796 AT-AAAAATATA
1 ATAAAAAATATA
20031807 CACTAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 3 0.12
19 8 0.32
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAATATATATAC
Found at i:20031802 original size:18 final size:19
Alignment explanation
Indices: 20031763--20031811 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
20031753 TAAAGTAATA
*
20031763 AAAAATA-ATACTATATAT
1 AAAAATATATACTATACAT
20031781 -AAAATATATA-TATACAT
1 AAAAATATATACTATACAT
*
20031798 AAAAATATACACTA
1 AAAAATATATACTA
20031812 ATATATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 12 0.46
18 12 0.46
19 2 0.08
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATATATACTATACAT
Found at i:20032038 original size:3 final size:3
Alignment explanation
Indices: 20032025--20032110 Score: 60
Period size: 3 Copynumber: 29.3 Consensus size: 3
20032015 GAGGGCATAT
20032025 ATA AT- ATA ATA ATA AT- ATA A-A A-A ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A -ATA ATA
* *
20032069 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
20032111 AACAAAGCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 13 0.19
3 46 0.68
4 7 0.10
5 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:20032051 original size:18 final size:18
Alignment explanation
Indices: 20032030--20032110 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
20032020 CATATATAAT
20032030 ATAATAATAATATAAAAA
1 ATAATAATAATATAAAAA
* *
20032048 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-ATAAAAA
*
20032069 ATAATAATAATATAAATA
1 ATAATAATAATATAAAAA
*
20032087 ATAGTAA-AA-ATAATAAA
1 ATAATAATAATATAA-AAA
20032104 ATAATAA
1 ATAATAA
20032111 AACAAAGCTC
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
16 4 0.08
17 10 0.19
18 18 0.34
19 5 0.09
20 5 0.09
21 11 0.21
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (18 bp):
ATAATAATAATATAAAAA
Found at i:20032484 original size:23 final size:23
Alignment explanation
Indices: 20032439--20032507 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
20032429 AACCTTTTTT
* **
20032439 ACAAAAAAAACACCTCC-AAAAA
1 ACAAAAAAAAAACCTCCTCCAAA
20032461 ACAAAAAAAAAACCTCCTCCAAA
1 ACAAAAAAAAAACCTCCTCCAAA
* * * *
20032484 ACAAAGAACAATCCTTCTCCAAA
1 ACAAAAAAAAAACCTCCTCCAAA
20032507 A
1 A
20032508 AACCAAAAAC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 16 0.41
23 23 0.59
ACGTcount: A:0.59, C:0.29, G:0.01, T:0.10
Consensus pattern (23 bp):
ACAAAAAAAAAACCTCCTCCAAA
Found at i:20034611 original size:15 final size:16
Alignment explanation
Indices: 20034580--20034613 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
20034570 AAAGTTGTAG
20034580 AGAGAAAATTCTTTAA
1 AGAGAAAATTCTTTAA
20034596 AGAGAAAATT-TTTAA
1 AGAGAAAATTCTTTAA
20034611 AGA
1 AGA
20034614 TATTTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.29
Consensus pattern (16 bp):
AGAGAAAATTCTTTAA
Found at i:20041635 original size:220 final size:219
Alignment explanation
Indices: 20041253--20041691 Score: 833
Period size: 220 Copynumber: 2.0 Consensus size: 219
20041243 TTAAATTAAA
*
20041253 AGACGACCTTGTGCTCGGGAATTCATGGTATTGTGTCCTAACTTACGGGATGTGATACTCCGATA
1 AGACGACCTTGTGCTCGGGAATTCATGGTACTGTGTCCTAACTTACGGGATGTGATACTCCGATA
20041318 TCTCGAGATAAGGAAATCTTTAAACAAATCGATTTAAGCTAATTCAAGAATTTTAAAATCAGTAT
66 TCTCGAGATAAGGAAATCTTTAAACAAATCGATTTAAGCTAATTCAAGAATTTTAAAATCAGTAT
*
20041383 TAATAGAAAAGATCGTATTTCAAGTCCCTTCCCGATTTTTAATTTTCGATATTAAGACACTAACT
131 TAATAGAAAAGATCGTATTTCAAGTCCCTTCCCGATTTTTAATTTTCGACA-TAAGACACTAACT
**
20041448 AATCAATTTGGTACCAATTTTTTGG
195 AATCAATTCAGTACCAATTTTTTGG
20041473 AGACGACCTTGTGCTCGGGAATTCATGGTACTGTGTCCTAACTTACGGGATGTGATACTCCGATA
1 AGACGACCTTGTGCTCGGGAATTCATGGTACTGTGTCCTAACTTACGGGATGTGATACTCCGATA
20041538 TCTCGAGATAAGGAAATCTTTAAACAAATCGATTTAAGCTAATTCAAGAATTTTAAAATCAGTAT
66 TCTCGAGATAAGGAAATCTTTAAACAAATCGATTTAAGCTAATTCAAGAATTTTAAAATCAGTAT
20041603 TAATAGAAAAGATCGTATTTCAAGTCCCTTCCCGATTTTTAATTTTCGACATAAGACACTAACTA
131 TAATAGAAAAGATCGTATTTCAAGTCCCTTCCCGATTTTTAATTTTCGACATAAGACACTAACTA
20041668 ATCAATTCAGTACCAATTTTTTGG
196 ATCAATTCAGTACCAATTTTTTGG
20041692 GCGTGTTGAG
Statistics
Matches: 215, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
219 36 0.17
220 179 0.83
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (219 bp):
AGACGACCTTGTGCTCGGGAATTCATGGTACTGTGTCCTAACTTACGGGATGTGATACTCCGATA
TCTCGAGATAAGGAAATCTTTAAACAAATCGATTTAAGCTAATTCAAGAATTTTAAAATCAGTAT
TAATAGAAAAGATCGTATTTCAAGTCCCTTCCCGATTTTTAATTTTCGACATAAGACACTAACTA
ATCAATTCAGTACCAATTTTTTGG
Found at i:20052344 original size:17 final size:16
Alignment explanation
Indices: 20052319--20052352 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
20052309 AAGGGCATCT
*
20052319 TAAAAAAAAGAGAAAA
1 TAAAAAAAAAAGAAAA
20052335 TAAAAGAAAAAAGAAAA
1 TAAAA-AAAAAAGAAAA
20052352 T
1 T
20052353 GAGAGAGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (16 bp):
TAAAAAAAAAAGAAAA
Found at i:20053390 original size:14 final size:13
Alignment explanation
Indices: 20053368--20053412 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
20053358 CGCCGAGGTA
20053368 TTTTTAATTTCTG
1 TTTTTAATTTCTG
20053381 TTTTTCAATTTCTG
1 TTTTT-AATTTCTG
* *
20053395 CTTTTAATTTCTA
1 TTTTTAATTTCTG
20053408 TTTTT
1 TTTTT
20053413 CAAAAATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.16, C:0.11, G:0.04, T:0.69
Consensus pattern (13 bp):
TTTTTAATTTCTG
Found at i:20053403 original size:13 final size:13
Alignment explanation
Indices: 20053369--20053406 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
20053359 GCCGAGGTAT
*
20053369 TTTTAATTTCTGT
1 TTTTAATTTCTGC
20053382 TTTTCAATTTCTGC
1 TTTT-AATTTCTGC
20053396 TTTTAATTTCT
1 TTTTAATTTCT
20053407 ATTTTTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.16, C:0.13, G:0.05, T:0.66
Consensus pattern (13 bp):
TTTTAATTTCTGC
Found at i:20053473 original size:100 final size:99
Alignment explanation
Indices: 20053295--20053656 Score: 424
Period size: 100 Copynumber: 3.7 Consensus size: 99
20053285 AATTTCCGTT
* * * * *
20053295 TTTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGGCACG
1 TTTT-AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
*
20053360 CCGAGGTATTTTTAATTTCTGTTTTTCAATTTCTGC
65 CTGAGGTATTTTTAATTTCTGTTTTTCAATTT-TGC
* *
20053396 TTTTAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
20053461 TGAGGTATTTTTAATTTCTGTTTTTCAATTTTTGCC
66 TGAGGTATTTTTAATTTCTGTTTTTCAA-TTTTG-C
** * * *
20053497 TTACAAATTCTGCTTTTC--AAATCAACTCATATTGCGAGAGGTGAGTTGATCCTCAGGACACGC
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
* *
20053560 TGAGGTATTTTCAA-------TTTTC-GTTTT--
66 TGAGGTATTTTTAATTTCTGTTTTTCAATTTTGC
* ** *
20053584 TTTTAATTTATGTTTCTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACG
1 TTTTAATTTCTGTTT-TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
20053649 CTGAGGTA
65 CTGAGGTA
20053657 ATTTCAGTTT
Statistics
Matches: 232, Mismatches: 24, Indels: 21
0.84 0.09 0.08
Matches are distributed among these distances:
87 10 0.04
88 1 0.00
90 54 0.23
92 5 0.02
99 56 0.24
100 85 0.37
101 21 0.09
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (99 bp):
TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTATTTTTAATTTCTGTTTTTCAATTTTGC
Found at i:20053704 original size:73 final size:73
Alignment explanation
Indices: 20053603--20054163 Score: 689
Period size: 73 Copynumber: 7.6 Consensus size: 73
20053593 ATGTTTCTAA
* * * * *
20053603 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAGTTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTT
20053668 TGTTTGTC
66 TGTTTGTC
* * * * *
20053676 AAAACTCAACTTATATTGCAAGATGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTT
* *
20053741 TCTTTTTC
66 TGTTTGTC
* * * *
20053749 AAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
20053814 TTTGTTTGTC
64 TTTGTTTGTC
* * *
20053824 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAAGATATGTTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTT
*
20053889 TGTCTT-TAAA
66 TGT-TTGT--C
* * * *
20053899 AAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTTGAGATATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTT
*
20053964 TGTTTTTC
66 TGTTTGTC
* * * * *
20053972 AAAAAAATCAACTCATATTGCAATAGGTGAGTTGAACCTCAAG--ACGCTGAGGTAATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
20054035 TTTGTTTGTC
64 TTTGTTTGTC
*
20054045 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTT
20054110 TGTCTT-TC
66 TGT-TTGTC
* * *
20054118 AAAAAAAATCAGCTCATATTGCGAGAAGTGAGTTGAACCTCAAGAC
1 ---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
20054164 GCTAAGGTAT
Statistics
Matches: 419, Mismatches: 55, Indels: 25
0.84 0.11 0.05
Matches are distributed among these distances:
71 38 0.09
73 173 0.41
74 6 0.01
75 162 0.39
76 40 0.10
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (73 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTT
TGTTTGTC
Found at i:20053782 original size:148 final size:147
Alignment explanation
Indices: 20053583--20054193 Score: 730
Period size: 148 Copynumber: 4.1 Consensus size: 147
20053573 ATTTTCGTTT
* * * * *
20053583 TTTTTAATTTATGTTTCT-AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* * * * * *
20053647 CGCTGAGGTAATTTCAGTTTTTGTTTGTC-AAAACTCAACTTATATTGCAAGATGTGAGTTGAGC
66 CGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAAC
*
20053711 CTCAAGACACGTTGAGGTA
131 CTCAAG--ACGCTGAGGTA
* * *
20053730 TTTTCAATTTCTCTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* * * *
20053795 CGCTGAGGTAATTTCAATTTTTGTTTGTC-AAAAATCAACTCATATTACGAGAGGTGAGTTGAGC
66 CGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAAC
* *
20053859 CTCAAGATATGTTGAGGTA
131 CTCAAG--ACGCTGAGGTA
* * * * *
20053878 TTTTCAATTTTTGTCTTTAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* * * * *
20053943 CGTTGAGATATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCAATAGGTGAGTTGAA
66 CGCTGAGGTAATTTCAATTTCTGTTTGTC-AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAA
20054008 CCTCAAGACGCTGAGGTA
130 CCTCAAGACGCTGAGGTA
* * *
20054026 ATTTCAATTTTTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* * * * *
20054089 CGTTGAGGTATTTTCAATTTCTGTCTT-TCAAAAAAAATCAGCTCATATTGCGAGAAGTGAGTTG
66 CGCTGAGGTAATTTCAATTTCTGT-TTGTC--AAAAAATCAACTCATATTGCAAGAGGTGAGTTG
*
20054153 AACCTCAAGACGCTAAGGTA
128 AACCTCAAGACGCTGAGGTA
* *
20054173 TTTTCCATTTCTGTTCTTCAA
1 TTTTCAATTTCTGTTTTTCAA
20054194 TTTCTGTGTT
Statistics
Matches: 407, Mismatches: 50, Indels: 12
0.87 0.11 0.03
Matches are distributed among these distances:
146 67 0.16
147 79 0.19
148 224 0.55
150 37 0.09
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (147 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
CGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAAC
CTCAAGACGCTGAGGTA
Found at i:20054034 original size:221 final size:222
Alignment explanation
Indices: 20053603--20054193 Score: 879
Period size: 221 Copynumber: 2.7 Consensus size: 222
20053593 ATGTTTCTAA
* * * * *
20053603 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAGTTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTT
* * * * * * *
20053668 TGT-TTGT--CAAAACTCAACTTATATTGCAAGATGTGAGTTGAGCCTCAAGACACGTTGAGGTA
66 TGTCTT-TAAAAAAAATCAGCTCATATTGCGAGAAGTGAGTTGAACCTCAAGACACGTTGAGGTA
* * *
20053730 TTTTCAATTTCTCTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACA
130 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCAATAGGTGAGTTGAACCTCA-GACA
20053795 CGCTGAGGTAATTTCAATTTTTGTTTGTC
194 CGCTGAGGTAATTTCAATTTTTGTTTGTC
* * *
20053824 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAAGATATGTTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTT
* *
20053889 TGTCTTTAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTTGAGATAT
66 TGTCTTTAAAAAAAATCAGCTCATATTGCGAGAAGTGAGTTGAACCTCAAGACACGTTGAGGTAT
*
20053954 TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCAATAGGTGAGTTGAACCTCA-AGACG
131 TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCAATAGGTGAGTTGAACCTCAGACACG
20054018 CTGAGGTAATTTCAATTTTTGTTTGTC
196 CTGAGGTAATTTCAATTTTTGTTTGTC
*
20054045 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTT
* *
20054110 TGTCTTTCAAAAAAAATCAGCTCATATTGCGAGAAGTGAGTTGAACCTCAAG--ACGCTAAGGTA
66 TGTCTTT-AAAAAAAATCAGCTCATATTGCGAGAAGTGAGTTGAACCTCAAGACACGTTGAGGTA
* *
20054173 TTTTCCATTTCTGTTCTTCAA
130 TTTTCAATTTCTGTTTTTCAA
20054194 TTTCTGTGTT
Statistics
Matches: 336, Mismatches: 30, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
220 27 0.08
221 160 0.48
222 45 0.13
223 104 0.31
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (222 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTT
TGTCTTTAAAAAAAATCAGCTCATATTGCGAGAAGTGAGTTGAACCTCAAGACACGTTGAGGTAT
TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCAATAGGTGAGTTGAACCTCAGACACG
CTGAGGTAATTTCAATTTTTGTTTGTC
Found at i:20054300 original size:15 final size:14
Alignment explanation
Indices: 20054264--20054296 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
20054254 CGCTGAGGTA
20054264 TTTTCAAATTCTGT
1 TTTTCAAATTCTGT
*
20054278 TTTTCAAATTTTGT
1 TTTTCAAATTCTGT
20054292 TTTTC
1 TTTTC
20054297 CAAAAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (14 bp):
TTTTCAAATTCTGT
Found at i:20054303 original size:91 final size:91
Alignment explanation
Indices: 20054099--20054656 Score: 413
Period size: 87 Copynumber: 6.0 Consensus size: 91
20054089 CGTTGAGGTA
* * * * *
20054099 TTTTCAATTTCTGTCTTTCAAAAAAAATCAGCTCATATTGCGAGAAGTGAGTTGAACCTC--A--
1 TTTTCAATTTATGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATC
* * *
20054160 AGACGCTAAGGTATTTTCCATTTCTGT
65 ACACGCTGAGGTATTTTCAATTTCTGT
* * * * * *
20054187 TCTTCAATTTCTGTGTTTCAAAAAAATCAGCTCATATTGCGAGTGGTGAGTTGAGCCT-TGACTC
1 TTTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA-TC
*
20054251 ACACGCTGAGGTATTTTCAAATTCTGT
65 ACACGCTGAGGTATTTTCAATTTCTGT
* *
20054278 TTTTCAAATTT-TGTTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGA--
1 TTTTC-AATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATC
* *
20054340 ACACGCTGAGATATTTTCAATTTCTTTTTTT
65 ACACGCTGAGGTATTTTCAATTTC----TGT
* *
20054371 TTTTCAATTTATGTTTGTCAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGATC
1 TTTTCAATTTATGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATC
* * *
20054436 ACACGCTGATGTATTTTCAATTGATTTTT
65 ACACGCTGAGGTATTTTCAATT--TCTGT
* * * * ** *
20054465 ATTTTTATTTTTTTTTCAATTTATGCTTTGCAAAAATCAACTCATATTACGAGAGGTGAGTTGAG
1 -TTTTCA-ATTTATGT---TTT-T-C---AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
* * ** * **
20054530 CCTCGGGTCACATACCGAGGTATTTTCAAAATCTGT
56 CCTCAGATCACACGCTGAGGTATTTTCAATTTCTGT
* * ** *
20054566 TTTACAAATTT-TG-TTTT---AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTC
1 TTTTC-AATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATC
*** *
20054626 ACGTTCTGAGCTATTTTCAATTTCTGT
65 ACACGCTGAGGTATTTTCAATTTCTGT
20054653 TTTT
1 TTTT
20054657 AATGTTTAGT
Statistics
Matches: 382, Mismatches: 61, Indels: 55
0.77 0.12 0.11
Matches are distributed among these distances:
87 99 0.26
88 18 0.05
89 22 0.06
91 69 0.18
92 12 0.03
93 14 0.04
94 44 0.12
95 8 0.02
96 25 0.07
98 1 0.00
99 3 0.01
100 7 0.02
101 5 0.01
103 55 0.14
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (91 bp):
TTTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCA
CACGCTGAGGTATTTTCAATTTCTGT
Found at i:20054426 original size:185 final size:178
Alignment explanation
Indices: 20054120--20054455 Score: 433
Period size: 185 Copynumber: 1.8 Consensus size: 178
20054110 TGTCTTTCAA
* * * * *
20054120 AAAAAATCAGCTCATATTGCGAGAAGTGAGTTGAACCTCAAGACGCTAAGGTATTTTCCATTTCT
1 AAAAAATCAACTCATATTGCGAGAAGTGAGTTCAACCTCAACACGCTAAGATATTTTCAATTTCT
* * * *
20054185 GTTCTTCAATTTCTGTGTTTCAAAAAAATCAGCTCATATTGCGAGTGGTGAGTTGAGCCT-TGAC
66 GTTCTTCAATTTATGTGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA-
20054249 TCACACGCTGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCC
130 TCACACGCTGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCC
* * *
20054298 AAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGAACACGCTGAGATATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAAGTGAGTTCAACCTC--AACACGCTAAGATATTTTCAATTT
* * *
20054363 CTTTTTTTTTTTCAATTTATGT-TTGTCAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAG
64 C----TGTTCTTCAATTTATGTGTT-TC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
*
20054427 CCTCAGATCACACGCTGATGTATTTTCAA
123 CCTCAGATCACACGCTGAGGTATTTTCAA
20054456 TTGATTTTTA
Statistics
Matches: 133, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
178 35 0.26
180 21 0.16
183 2 0.02
184 16 0.12
185 57 0.43
186 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (178 bp):
AAAAAATCAACTCATATTGCGAGAAGTGAGTTCAACCTCAACACGCTAAGATATTTTCAATTTCT
GTTCTTCAATTTATGTGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAT
CACACGCTGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCC
Found at i:20054553 original size:103 final size:104
Alignment explanation
Indices: 20054366--20054558 Score: 273
Period size: 103 Copynumber: 1.8 Consensus size: 104
20054356 TCAATTTCTT
**
20054366 TTTTTTTTTCAATTTATGTTTGTCAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTC
1 TTTTTTTTTCAATTTATGTTTGTC--AAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTC
* * *
20054431 AGATCACACGCTGATGTATTTTCAATTGATTTTTATTTTTA
64 AGATCACACACCGAGGTATTTTCAATTGATTTTTATTTTTA
*
20054472 TTTTTTTTTCAATTTATGCTTTG-C-AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCG
1 TTTTTTTTTCAATTTATG-TTTGTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCA
* *
20054535 GGTCACATACCGAGGTATTTTCAA
65 GATCACACACCGAGGTATTTTCAA
20054559 AATCTGTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
103 55 0.71
106 19 0.24
107 4 0.05
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.41
Consensus pattern (104 bp):
TTTTTTTTTCAATTTATGTTTGTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAG
ATCACACACCGAGGTATTTTCAATTGATTTTTATTTTTA
Found at i:20054642 original size:87 final size:87
Alignment explanation
Indices: 20054496--20054723 Score: 246
Period size: 87 Copynumber: 2.6 Consensus size: 87
20054486 TATGCTTTGC
* * * *
20054496 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATACCGAGGTATTTTCAAAA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAA
20054561 TCTGTTTTACAAAT-TTT-GTTTT
66 TCTGTTTT--AAATGTTTAGTTTT
* * * * **
20054583 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTTCTGAGCTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAA
*
20054648 TCTGTTTTTAATGTTTAGTTTT
66 TCTGTTTTAAATGTTTAGTTTT
* * * * * *
20054670 AAAGAGTCAATTCATATTGCGAGAAATGAGTTAAG-CTCAGGATCACATGCCGAG
1 AAA-AATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGCTCACATACCGAG
20054724 TAAAGAATAA
Statistics
Matches: 117, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
85 3 0.03
86 3 0.03
87 73 0.62
88 38 0.32
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (87 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAA
TCTGTTTTAAATGTTTAGTTTT
Found at i:20055381 original size:30 final size:30
Alignment explanation
Indices: 20055339--20055466 Score: 213
Period size: 30 Copynumber: 4.3 Consensus size: 30
20055329 CTAGCCTTTG
20055339 CCACCA-CAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
20055368 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
20055398 CCACCACCTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
20055428 CCACCACCTACTCCATTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
20055458 CTACCACCA
1 CCACCACCA
20055467 CTTGTACCTA
Statistics
Matches: 94, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 6 0.06
30 88 0.94
ACGTcount: A:0.26, C:0.49, G:0.06, T:0.19
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:20055764 original size:17 final size:17
Alignment explanation
Indices: 20055742--20055779 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
20055732 TTGCTTATTG
20055742 TTTTCCTTTCAGTTTTA
1 TTTTCCTTTCAGTTTTA
20055759 TTTTCCTTTCAGTTTTA
1 TTTTCCTTTCAGTTTTA
20055776 TTTT
1 TTTT
20055780 GTTTCTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.16, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTTCCTTTCAGTTTTA
Found at i:20055977 original size:15 final size:15
Alignment explanation
Indices: 20055957--20055988 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20055947 CCTCTCTTTT
*
20055957 TTTTTTATTATTATA
1 TTTTTTAATATTATA
20055972 TTTTTTAATATTATA
1 TTTTTTAATATTATA
20055987 TT
1 TT
20055989 ATATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTTAATATTATA
Found at i:20056067 original size:25 final size:25
Alignment explanation
Indices: 20055962--20056097 Score: 90
Period size: 23 Copynumber: 5.7 Consensus size: 25
20055952 CTTTTTTTTT
* *
20055962 TATTAT-TATAT-TTTTTAATATTA
1 TATTATGTATATATATTTAATACTA
** *
20055985 TATTA--TATATATATTCTTTTAATA
1 TATTATGTATATATATT-TAATACTA
* * * *
20056009 TATTAGGTATAT-T-CTAAATTCTA
1 TATTATGTATATATATTTAATACTA
*
20056032 TATTACGTATATATA-TT-ATACTA
1 TATTATGTATATATATTTAATACTA
* *
20056055 TTTTATGTATATATCTTTAATACTA
1 TATTATGTATATATATTTAATACTA
*
20056080 TATTATTTATATATATTT
1 TATTATGTATATATATTT
20056098 TTTTTTACAT
Statistics
Matches: 86, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
22 5 0.06
23 39 0.45
24 15 0.17
25 22 0.26
26 5 0.06
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (25 bp):
TATTATGTATATATATTTAATACTA
Found at i:20056087 original size:30 final size:28
Alignment explanation
Indices: 20056056--20056164 Score: 95
Period size: 28 Copynumber: 4.0 Consensus size: 28
20056046 ATTATACTAT
20056056 TTTATGTATATATCTTTAATACTATATTA
1 TTTATGTATATAT-TTTAATACTATATTA
* * ** *
20056085 TTTATATATATTTTTTTTTAC-ATGTTA
1 TTTATGTATATATTTTAATACTATATTA
20056112 TCTTATGTATATATTTTAAT--TATATTA
1 T-TTATGTATATATTTTAATACTATATTA
* *
20056139 TGTATGTAT-T-TTTT-ACACTATATTA
1 TTTATGTATATATTTTAATACTATATTA
20056164 T
1 T
20056165 GTACATATTT
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
23 1 0.02
24 4 0.06
25 9 0.14
26 7 0.11
27 12 0.19
28 20 0.31
29 11 0.17
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.60
Consensus pattern (28 bp):
TTTATGTATATATTTTAATACTATATTA
Found at i:20056139 original size:22 final size:23
Alignment explanation
Indices: 20056100--20056175 Score: 73
Period size: 25 Copynumber: 3.2 Consensus size: 23
20056090 ATATATTTTT
*
20056100 TTTTACATGTTATCTTATGTATATA
1 TTTTACA--TTATATTATGTATATA
*
20056125 TTTTA-ATTATATTATGTATGTATT
1 TTTTACATTATATTATGTA--TATA
* *
20056149 TTTTACACTATATTATGTACATA
1 TTTTACATTATATTATGTATATA
20056172 TTTT
1 TTTT
20056176 TTTTTTATCT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 11 0.26
23 6 0.14
24 9 0.21
25 17 0.40
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.58
Consensus pattern (23 bp):
TTTTACATTATATTATGTATATA
Found at i:20056215 original size:79 final size:78
Alignment explanation
Indices: 20056041--20056215 Score: 194
Period size: 79 Copynumber: 2.2 Consensus size: 78
20056031 ATATTACGTA
* * * *
20056041 TATATATTATACTATTTTATGTATATATCTTTAATACTATATTATTTATATATATTTTTTTTTAC
1 TATATATTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATATTTTTTTTTAC
*
20056106 ATGTTATCTTATG
66 ATGTTATCATATG
* * * * *
20056119 TATATATTTTAATTATATTATGTATGTATTTTTTACACTATATTATGTACATAT-TTTTTTTTTA
1 TATATATTAT-ACTATATTATGTATATATCTTTAACACTATATTATGTACATATATTTTTTTTTA
20056183 TCTAT-TTCATACATATG
65 -C-ATGTT-AT-CATATG
20056200 TATATATTATA-TATAT
1 TATATATTATACTATAT
20056216 CTTAACATTA
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
78 19 0.23
79 43 0.53
80 5 0.06
81 14 0.17
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.58
Consensus pattern (78 bp):
TATATATTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATATTTTTTTTTAC
ATGTTATCATATG
Found at i:20056267 original size:25 final size:24
Alignment explanation
Indices: 20056239--20056294 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
20056229 GTTATATTTT
*
20056239 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
20056264 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
20056287 CACTATTA
1 CACTATTA
20056295 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:20059064 original size:17 final size:17
Alignment explanation
Indices: 20059042--20059075 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
20059032 ATTTTGGGCC
20059042 CTAAACCAAACAACCCA
1 CTAAACCAAACAACCCA
20059059 CTAAACCAAACAACCCA
1 CTAAACCAAACAACCCA
20059076 ATAACCCGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.41, G:0.00, T:0.06
Consensus pattern (17 bp):
CTAAACCAAACAACCCA
Found at i:20060270 original size:3 final size:3
Alignment explanation
Indices: 20060262--20060323 Score: 97
Period size: 3 Copynumber: 20.0 Consensus size: 3
20060252 TGTATTTTCA
20060262 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
*
20060308 TAT ATAT TTT TAT TAT
1 TAT -TAT TAT TAT TAT
20060324 ATGCATATAC
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:20063065 original size:6 final size:6
Alignment explanation
Indices: 20063054--20063089 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
20063044 GTTAAAAAAC
*
20063054 ATATTA ATATTA ATATTA ATAATA ATATTA ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
20063090 CATAAAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
ATATTA
Found at i:20063079 original size:18 final size:19
Alignment explanation
Indices: 20063052--20063094 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
20063042 ATGTTAAAAA
*
20063052 ACATATTAATATTAATATT
1 ACATAATAATATTAATATT
20063071 A-ATAATAATATTAATATT
1 ACATAATAATATTAATATT
20063089 ACATAA
1 ACATAA
20063095 AGATATACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
ACATAATAATATTAATATT
Found at i:20063133 original size:25 final size:26
Alignment explanation
Indices: 20063092--20063141 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
20063082 TAATATTACA
*
20063092 TAAAGATATACTTATATAT-ATATAT
1 TAAAGATATACTCATATATGATATAT
20063117 TAAAGATATA-TGCATATATGATATA
1 TAAAGATATACT-CATATATGATATA
20063142 ATACATGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 16 0.73
26 5 0.23
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (26 bp):
TAAAGATATACTCATATATGATATAT
Done.