Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002440.1 Hibiscus syriacus cultivar Beakdansim tig00004996_pilon, whole genome shotgun sequence
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: 77051
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:472 original size:14 final size:15
Alignment explanation
Indices: 447--476 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
437 AGCATTAGCA
447 AAACACAAAGTTATC
1 AAACACAAAGTTATC
462 AAACA-AAAGTTATC
1 AAACACAAAGTTATC
476 A
1 A
477 CCAGTTACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.57, C:0.17, G:0.07, T:0.20
Consensus pattern (15 bp):
AAACACAAAGTTATC
Found at i:1274 original size:192 final size:193
Alignment explanation
Indices: 935--1308 Score: 606
Period size: 192 Copynumber: 1.9 Consensus size: 193
925 CTTTTGTTAG
* * * *
935 AGCACCTTAACCCAACGTTTCAATTTTTTGGTCAAAACAGTTCCTGCCGTATGAAAATAGTTAGT
1 AGCACCTTAACCCAACGTTTCAATTTTTTAGTCAAAACAATTCCTGACGGATGAAAATAGTTAGT
* * *
1000 TAACCGATAATCAATATGTGTTATTGATATGACATTTTTACATGTATTTAATTGATGGCATGACA
66 TAACCGATAATCAATACGTATTATTGATATGACATTTTCACATGTATTTAATTGATGGCATGACA
* *
1065 CGTGTTAAAATACTCAAAGTTATAATGTCGCATACGTTATATCACCTAAAGTAATGTTTTTAA
131 CGTGTCAAAACACTCAAAGTTATAATGTCGCATACGTTATATCACCTAAAGTAATGTTTTTAA
* * *
1128 AGCACTTTAACCCAACGTTTCAA-TTTTTAGTCAAAATAATTCCTGATGGATGAAAATAGTTAGT
1 AGCACCTTAACCCAACGTTTCAATTTTTTAGTCAAAACAATTCCTGACGGATGAAAATAGTTAGT
* * *
1192 TGACTGATAATTAATACGTATTATTGATATGACATTTTCACATGTATTTAATTGATGGCATGACA
66 TAACCGATAATCAATACGTATTATTGATATGACATTTTCACATGTATTTAATTGATGGCATGACA
1257 CGTGTCAAAACACTCAAAGTTATAATGTCGCATACGTTATATCACCTAAAGT
131 CGTGTCAAAACACTCAAAGTTATAATGTCGCATACGTTATATCACCTAAAGT
1309 GAGGTTGTGA
Statistics
Matches: 166, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
192 144 0.87
193 22 0.13
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (193 bp):
AGCACCTTAACCCAACGTTTCAATTTTTTAGTCAAAACAATTCCTGACGGATGAAAATAGTTAGT
TAACCGATAATCAATACGTATTATTGATATGACATTTTCACATGTATTTAATTGATGGCATGACA
CGTGTCAAAACACTCAAAGTTATAATGTCGCATACGTTATATCACCTAAAGTAATGTTTTTAA
Found at i:3766 original size:4 final size:4
Alignment explanation
Indices: 3757--3783 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3747 CAATTCATAT
3757 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
3784 CATAGTAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:3812 original size:13 final size:13
Alignment explanation
Indices: 3794--3820 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3784 CATAGTAGAA
3794 CAGTCTTCATATG
1 CAGTCTTCATATG
3807 CAGTCTTCATATG
1 CAGTCTTCATATG
3820 C
1 C
3821 GCGTCTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:5422 original size:17 final size:18
Alignment explanation
Indices: 5400--5433 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5390 TGAAACTCGA
5400 CTCGAACTCAA-AAAATG
1 CTCGAACTCAACAAAATG
5417 CTCGAACTCAACAAAAT
1 CTCGAACTCAACAAAAT
5434 TTCAGGAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.47, C:0.26, G:0.09, T:0.18
Consensus pattern (18 bp):
CTCGAACTCAACAAAATG
Found at i:5502 original size:11 final size:11
Alignment explanation
Indices: 5466--5515 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
5456 GAGACTCGAG
5466 CTCGATTCAAA
1 CTCGATTCAAA
*
5477 CACGATTCAAA
1 CTCGATTCAAA
*
5488 CTCGATTCAAG
1 CTCGATTCAAA
*
5499 CTCGAACTCAAA
1 CTCG-ATTCAAA
5511 CTCGA
1 CTCGA
5516 ATTTGAACCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
11 24 0.73
12 9 0.27
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22
Consensus pattern (11 bp):
CTCGATTCAAA
Found at i:5567 original size:14 final size:15
Alignment explanation
Indices: 5548--5613 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 15
5538 TATTACATTT
5548 AAAAATAT-ATTTTA
1 AAAAATATAATTTTA
* *
5562 AAAAATTTATAATTATC
1 AAAAA--TATAATTTTA
* *
5579 AATAATAT-ATTTTT
1 AAAAATATAATTTTA
*
5593 AATAATATAATTTTA
1 AAAAATATAATTTTA
5608 AAAAAT
1 AAAAAT
5614 CTAAAATTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
14 17 0.41
15 13 0.32
16 3 0.07
17 8 0.20
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AAAAATATAATTTTA
Found at i:5636 original size:45 final size:45
Alignment explanation
Indices: 5545--5637 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 45
5535 TTATATTACA
* * *
5545 TTTAAAAATATATTTTAAAAAATTTATAATTATCAATAATATATT
1 TTTAAAAATATATTTTAAAAAATCTAAAATTATCAATAATACATT
*
5590 TTTAATAATATAATTTTAAAAAATCTAAAATTAT-AAT-ATAACATT
1 TTTAAAAATAT-ATTTTAAAAAATCTAAAATTATCAATAAT-ACATT
5635 TTT
1 TTT
5638 TCTAGTAGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 2 0.05
45 20 0.48
46 20 0.48
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (45 bp):
TTTAAAAATATATTTTAAAAAATCTAAAATTATCAATAATACATT
Found at i:5638 original size:46 final size:45
Alignment explanation
Indices: 5545--5638 Score: 118
Period size: 46 Copynumber: 2.1 Consensus size: 45
5535 TTATATTACA
* * * *
5545 TTTAAAAATATATTTTAAAAAATTTATAATTATCAATAATATATT
1 TTTAAAAATATATTTTAAAAAATCTAAAATTATAAATAACATATT
*
5590 TTTAATAATATAATTTTAAAAAATCTAAAATTATAATATAACAT-TT
1 TTTAAAAATAT-ATTTTAAAAAATCTAAAATTATAA-ATAACATATT
5636 TTT
1 TTT
5639 CTAGTAGCTC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
45 10 0.24
46 26 0.62
47 6 0.14
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (45 bp):
TTTAAAAATATATTTTAAAAAATCTAAAATTATAAATAACATATT
Found at i:8421 original size:2 final size:2
Alignment explanation
Indices: 8414--8439 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8404 AAACTGAAGC
8414 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
8440 CAAACAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13121 original size:83 final size:82
Alignment explanation
Indices: 12983--13137 Score: 256
Period size: 83 Copynumber: 1.9 Consensus size: 82
12973 GCCTATCCTA
* *
12983 GGGGTGCCTCATTTTCTCTTTAGTTCATAGTATATATAAATAATGAAGAGCAAGTATACGCTTAT
1 GGGGTGCCTCATTTTCTCTTTAGTTCATAGTATATATAAATAACGAAGACCAAGTATACGCTTAT
13048 ACTAATTTAGTAGTTGT
66 ACTAATTTAGTAGTTGT
* * *
13065 GGGGTGCCTCATTTTTTTCTTTAGTTCATAGTATATATAAGTAACGAAGACCAAGTATATGCTTA
1 GGGGTGCCTCA-TTTTCTCTTTAGTTCATAGTATATATAAATAACGAAGACCAAGTATACGCTTA
13130 TACTAATT
65 TACTAATT
13138 ATGTTAAGGG
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
82 11 0.16
83 56 0.84
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (82 bp):
GGGGTGCCTCATTTTCTCTTTAGTTCATAGTATATATAAATAACGAAGACCAAGTATACGCTTAT
ACTAATTTAGTAGTTGT
Found at i:16915 original size:2 final size:2
Alignment explanation
Indices: 16908--16957 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
16898 ATTGCACTAC
16908 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16950 AT AT AT AT
1 AT AT AT AT
16958 TTTGTTTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16976 original size:18 final size:18
Alignment explanation
Indices: 16955--17014 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
16945 TATATATATA
*
16955 TATTTTGTTTTTTATTTT
1 TATTTTCTTTTTTATTTT
*
16973 TATTTTCTTTGTTA-TTT
1 TATTTTCTTTTTTATTTT
*
16990 TCTTTTCTTTTGTTATTTT
1 TATTTTCTTTT-TTATTTT
17009 TCATTT
1 T-ATTT
17015 GTTATTTACA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 12 0.35
18 15 0.44
19 4 0.12
20 3 0.09
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (18 bp):
TATTTTCTTTTTTATTTT
Found at i:17015 original size:14 final size:14
Alignment explanation
Indices: 16992--17021 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16982 TGTTATTTTC
*
16992 TTTTCTTTTGTTAT
1 TTTTCATTTGTTAT
17006 TTTTCATTTGTTAT
1 TTTTCATTTGTTAT
17020 TT
1 TT
17022 ACAAAATCAA
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:0.10, C:0.07, G:0.07, T:0.77
Consensus pattern (14 bp):
TTTTCATTTGTTAT
Found at i:18320 original size:2 final size:2
Alignment explanation
Indices: 18313--18338 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18303 TTTTCAAATA
18313 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
18339 TATGAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25308 original size:231 final size:231
Alignment explanation
Indices: 24857--25567 Score: 857
Period size: 231 Copynumber: 3.0 Consensus size: 231
24847 CCCAGCCCTT
* *
24857 TGAATTTGATTCTCAGTTTCCCGATTCTCCTTTTCCTGGTACGTTTATCTCAATCTTTGATTCTT
1 TGAATTTGATTCTCAGTTTCCCGATTCTCCTTTTCGTGGTATGTTTATCTCAATCTTTGATT-TT
** * *
24922 TTCCCGCTTAATATTTTAGTATTATTAGTTA-TGTACGCTTCAAATCATTTGAATTTTATGTGAA
65 TTTTCGCTTAATATTTTAGTATTATTAGTTATTG-ACGCTTTAAATCATTTGAAATTTATGTGAA
* * * *
24986 TTACGAGTTTTAAAAAGAATGCATATAGGTGACGGTTGTGATAATGAATTAAGCTTTCTACAAGA
129 TTACGAGTTTGAAAAA-AATACATATAGGTGACGATTGTGATAACGAATTAAGCTTTCTACAAGA
*
25051 TACGGTTCCTGTGGATGATAACAATGTTCCAATTGAAGA
193 TACGGTTCCTGTAGATGATAACAATGTTCCAATTGAAGA
* * * * * * *
25090 TGAATTTGACTATCAGTTACCCGATTCTCCATGTCGTGGTATGTTTATCGCGATCTTTGATTTTT
1 TGAATTTGATTCTCAGTTTCCCGATTCTCCTTTTCGTGGTATGTTTATCTCAATCTTTGATTTTT
* * *
25155 TTTGGCTTAATATTGTAGTATTATTAGTTATTGACGCTTTAAATTATTTGAAATTTATGTGAATT
66 TTTCGCTTAATATTTTAGTATTATTAGTTATTGACGCTTTAAATCATTTGAAATTTATGTGAATT
* *
25220 ACGAGTTTGAAAAAAATACATATAGGTGACGATTGTGATAACGAATTGAA-TTTTCTTCAAGATA
131 ACGAGTTTGAAAAAAATACATATAGGTGACGATTGTGATAACGAATT-AAGCTTTCTACAAGATA
25284 CGGTTCCTGTAGATGATAACAATGTTCCAATTGAAGA
195 CGGTTCCTGTAGATGATAACAATGTTCCAATTGAAGA
25321 TGAATTTGATTCTCAGTTTCCCGATTCTCCTTTTCGTGGTATGTTTATCTCAATCTTTG---TTT
1 TGAATTTGATTCTCAGTTTCCCGATTCTCCTTTTCGTGGTATGTTTATCTCAATCTTTGATTTTT
* * * * *
25383 TTTCACTTAATATTTTAGTATTGGTT-GTT-TATG-C-TTTTAAATCATTTGCAATTTATATGAA
66 TTTCGCTTAATATTTTAGTATT-ATTAGTTAT-TGACGCTTTAAATCATTTGAAATTTATGTGAA
* * * * * *
25444 TTATGGGTTTGAAAAAAATACATATAGGTGACAGAGATGATAATGAGGATGGTGTTGAATTAAAC
129 TTACGAGTTTGAAAAAAATACATATAGGTGAC-GA-TTG-TGAT-A--A------CGAATTAAGC
* *
25509 TTTCTACAAGATACGGTTCCTGTAGATGATAA-AATTGTTTCAATTGAGGA
182 TTTCTACAAGATACGGTTCCTGTAGATGATAACAA-TGTTCCAATTGAAGA
25559 TGAATTTGA
1 TGAATTTGA
25568 GATTCGATGT
Statistics
Matches: 413, Mismatches: 47, Indels: 31
0.84 0.10 0.06
Matches are distributed among these distances:
226 53 0.13
227 4 0.01
228 29 0.07
229 5 0.01
230 1 0.00
231 130 0.31
232 74 0.18
233 55 0.13
237 4 0.01
238 58 0.14
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (231 bp):
TGAATTTGATTCTCAGTTTCCCGATTCTCCTTTTCGTGGTATGTTTATCTCAATCTTTGATTTTT
TTTCGCTTAATATTTTAGTATTATTAGTTATTGACGCTTTAAATCATTTGAAATTTATGTGAATT
ACGAGTTTGAAAAAAATACATATAGGTGACGATTGTGATAACGAATTAAGCTTTCTACAAGATAC
GGTTCCTGTAGATGATAACAATGTTCCAATTGAAGA
Found at i:26308 original size:145 final size:145
Alignment explanation
Indices: 26075--26337 Score: 436
Period size: 145 Copynumber: 1.8 Consensus size: 145
26065 TTTCTATCAC
* * *
26075 TTGTTCATGGTCGGGAATGATTGATTTTCTTGATACGTTGTGGCTCTATTTGAATCAACTACTAT
1 TTGTTCATGGTAGGGAATGATCGACTTTCTTGATACGTTGTGGCTCTATTTGAATCAACTACTAT
* * * *
26140 TTAATGTCTTAGGGGATTAATTGATTTTGGTTTGCGGTTTGATAAACTTTGAACCTGGTAATTTT
66 TTAATGTCTTAGGGGATCAATTGAATTTGATTAGCGGTTTGATAAACTTTGAACCTGGTAATTTT
26205 CTATGGCATGTTCAA
131 CTATGGCATGTTCAA
* *
26220 TTGTTCATGGTAGGGAATGCTCGACTTTCTTGATACGTTGTGGCTCTATTTGATTCAACTACTAT
1 TTGTTCATGGTAGGGAATGATCGACTTTCTTGATACGTTGTGGCTCTATTTGAATCAACTACTAT
*
26285 TTAATGTCTTAGGGGATCAATTGAATTTGATTAGTGGTTTGATAAACTTTGAA
66 TTAATGTCTTAGGGGATCAATTGAATTTGATTAGCGGTTTGATAAACTTTGAA
26338 GCGATTTCAA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
145 108 1.00
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.43
Consensus pattern (145 bp):
TTGTTCATGGTAGGGAATGATCGACTTTCTTGATACGTTGTGGCTCTATTTGAATCAACTACTAT
TTAATGTCTTAGGGGATCAATTGAATTTGATTAGCGGTTTGATAAACTTTGAACCTGGTAATTTT
CTATGGCATGTTCAA
Found at i:34486 original size:21 final size:21
Alignment explanation
Indices: 34461--34508 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
34451 GACTCGGTTT
34461 TTTCATACATAATTCAATTTG
1 TTTCATACATAATTCAATTTG
**
34482 TTTCATTTATAATTCAATTTG
1 TTTCATACATAATTCAATTTG
34503 TTTCAT
1 TTTCAT
34509 TTGTTCATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTCATACATAATTCAATTTG
Found at i:34509 original size:21 final size:21
Alignment explanation
Indices: 34469--34510 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
34459 TTTTTCATAC
34469 ATAATTCAATTTGTTTCATTT
1 ATAATTCAATTTGTTTCATTT
34490 ATAATTCAATTTGTTTCATTT
1 ATAATTCAATTTGTTTCATTT
34511 GTTCATGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.57
Consensus pattern (21 bp):
ATAATTCAATTTGTTTCATTT
Found at i:36681 original size:97 final size:96
Alignment explanation
Indices: 36568--36763 Score: 365
Period size: 97 Copynumber: 2.0 Consensus size: 96
36558 ATTATAGATA
36568 TTAATTAAATAAATCTCTTTTATTTATTTTATTAATTCGTTTACTTTTATTATACTTATCCATGG
1 TTAATTAAATAAATCTCTTTTATTTATTTTATTAATTCGTTTACTTTTATTATACTTATCCATGG
*
36633 TATTTTATTATTAATATAACGTTAAGTGTGT
66 TATTTTATTATTAATATAACGTTAAGTGTAT
36664 TTAATTAATATAAATCTCTTTTATTTATTTTATTAATTCGTTTACTTTTATTATACTTATCCATG
1 TTAATTAA-ATAAATCTCTTTTATTTATTTTATTAATTCGTTTACTTTTATTATACTTATCCATG
*
36729 GTATTTTATTATTAATATAATGTTAAGTGTAT
65 GTATTTTATTATTAATATAACGTTAAGTGTAT
36761 TTA
1 TTA
36764 TATTGTAGTT
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
96 8 0.08
97 89 0.92
ACGTcount: A:0.31, C:0.08, G:0.07, T:0.55
Consensus pattern (96 bp):
TTAATTAAATAAATCTCTTTTATTTATTTTATTAATTCGTTTACTTTTATTATACTTATCCATGG
TATTTTATTATTAATATAACGTTAAGTGTAT
Found at i:36838 original size:23 final size:23
Alignment explanation
Indices: 36793--36882 Score: 112
Period size: 23 Copynumber: 3.9 Consensus size: 23
36783 TTTAGTTATT
* *
36793 TTATTTCATTATTTATTTGTAATA
1 TTATTTTATTA-TTATTTTTAATA
36817 TTATTTTATTATTATTTTTAATA
1 TTATTTTATTATTATTTTTAATA
*
36840 -TATTTTAATTATTA-ATTTAATTA
1 TTATTTT-ATTATTATTTTTAA-TA
36863 TTATTTTATTATTATTTTTA
1 TTATTTTATTATTATTTTTA
36883 TCTTAGTCTT
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
22 11 0.19
23 27 0.47
24 20 0.34
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (23 bp):
TTATTTTATTATTATTTTTAATA
Found at i:36843 original size:14 final size:12
Alignment explanation
Indices: 36805--36911 Score: 61
Period size: 12 Copynumber: 9.2 Consensus size: 12
36795 ATTTCATTAT
36805 TTATTTGTA-ATA
1 TTATTT-TATATA
36817 TTATTTTAT-TA
1 TTATTTTATATA
36828 TTATTTT-TA-A
1 TTATTTTATATA
36838 TATATTTTA-ATTA
1 T-TATTTTATA-TA
*
36851 TTAATTTA-ATTA
1 TTATTTTATA-TA
36863 TTATTTTAT-TA
1 TTATTTTATATA
*
36874 TTATTTT-TATC
1 TTATTTTATATA
*
36885 TTAGTCTTATATA
1 TTA-TTTTATATA
*
36898 -TATGTATATATA
1 TTAT-TTTATATA
36910 TT
1 TT
36912 TGTTTAAATA
Statistics
Matches: 76, Mismatches: 7, Indels: 23
0.72 0.07 0.22
Matches are distributed among these distances:
10 4 0.05
11 32 0.42
12 34 0.45
13 6 0.08
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (12 bp):
TTATTTTATATA
Found at i:36881 original size:12 final size:12
Alignment explanation
Indices: 36788--36883 Score: 85
Period size: 12 Copynumber: 8.3 Consensus size: 12
36778 TTTTATTTAG
36788 TTATT-TTA-TT
1 TTATTATTATTT
*
36798 TCATTATTTATTT
1 TTATTA-TTATTT
* *
36811 GTAATATTA-TT
1 TTATTATTATTT
36822 TTATTATTATTT
1 TTATTATTATTT
*
36834 TTAATA-TATTT
1 TTATTATTATTT
* *
36845 TAATTATTAATT
1 TTATTATTATTT
*
36857 TAATTATTA-TT
1 TTATTATTATTT
36868 TTATTATTATTT
1 TTATTATTATTT
36880 TTAT
1 TTAT
36884 CTTAGTCTTA
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
10 4 0.06
11 28 0.41
12 32 0.46
13 5 0.07
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (12 bp):
TTATTATTATTT
Found at i:37180 original size:21 final size:19
Alignment explanation
Indices: 37156--37203 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
37146 ATATTCTTAA
37156 ATAAATAAATATCTTACTTTT
1 ATAAATAAATATC-TA-TTTT
*
37177 ATAAAT-TATATCTATTTT
1 ATAAATAAATATCTATTTT
37195 -TAAATAAAT
1 ATAAATAAAT
37204 GTTTTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 5 0.21
18 6 0.25
19 2 0.08
20 5 0.21
21 6 0.25
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAAATAAATATCTATTTT
Found at i:42426 original size:2 final size:2
Alignment explanation
Indices: 42419--42454 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
42409 ATTTCCTTTA
42419 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42455 CCTTTGTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42774 original size:16 final size:17
Alignment explanation
Indices: 42748--42779 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
42738 CTCATCCAAC
42748 AAAGAAAGAAGAAAAAA
1 AAAGAAAGAAGAAAAAA
42765 AAAG-AAGAAGAAAAA
1 AAAGAAAGAAGAAAAA
42780 GGAAAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAGAAAAAA
Found at i:45247 original size:114 final size:114
Alignment explanation
Indices: 45047--45386 Score: 556
Period size: 114 Copynumber: 3.0 Consensus size: 114
45037 AAGTGCCATG
*
45047 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
45112 TGATTTGGTATGAACCCCAAAACCAATCATTGGTTTTGAAAGATGAATT
66 TGATTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATT
*
45161 TGCTCATAGTAGAAATAAGAAGACCCAATATCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
45226 TGATTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGAAGAATT
66 TGATTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATT
* *
45275 TGCTCATAGTAGAAATAAGGAGACCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
** * * * *
45340 T-AGTTCAGTAGGAACCCCAGAACCAATCATTGGAATTAAAAGATGAA
66 TGA-TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAA
45387 CTGCATGATC
Statistics
Matches: 211, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
113 1 0.00
114 210 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGATTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATT
Found at i:47535 original size:54 final size:54
Alignment explanation
Indices: 47449--47614 Score: 269
Period size: 54 Copynumber: 3.1 Consensus size: 54
47439 CAATGATTGA
*
47449 GAACATCTGAGCAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
*
47503 GAACATCTGAGCAGAAACTACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
* ** **
47557 GAACATCTGAGCAGAAGCCACAGGAAAGGATGAATACGCCGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
47611 GAAC
1 GAAC
47615 CTGTTATTCT
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 104 1.00
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.23
Consensus pattern (54 bp):
GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
Found at i:48000 original size:22 final size:22
Alignment explanation
Indices: 47974--48050 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
47964 ATCTACATTC
47974 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
47996 TTCAAAGATGATAGATTC-CCT
1 TTCAAAGATGATAGATTCTCTT
*
48017 TTCTAAAGATGACAGATTCTCTT
1 TTC-AAAGATGATAGATTCTCTT
*
48040 TTCAAATATGA
1 TTCAAAGATGA
48051 AAGCTTTATC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.10
22 39 0.80
23 5 0.10
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:48569 original size:34 final size:40
Alignment explanation
Indices: 48489--48580 Score: 133
Period size: 40 Copynumber: 2.5 Consensus size: 40
48479 TGCCAGGTCG
48489 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
48529 AGTTCATAATGAGAATAACTCATCTG-A-AA-GAAG-A-A
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
48564 A-TTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
48581 TTTATTCAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
34 15 0.30
35 2 0.04
36 1 0.02
37 4 0.08
38 2 0.04
39 1 0.02
40 25 0.50
ACGTcount: A:0.49, C:0.10, G:0.21, T:0.21
Consensus pattern (40 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
Found at i:48687 original size:113 final size:112
Alignment explanation
Indices: 48527--49041 Score: 642
Period size: 113 Copynumber: 4.7 Consensus size: 112
48517 GAAGGAAGAA
* *
48527 GAAGTTCATAATGAGAATAACTCATCT---G-A-AAGAAGAAATTCATAATGAGAAGAATTTATT
1 GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTT
* * *
48587 CAACTTTTTGTTCAAAACCATCACTTGATGGATCAAAC-TTTCCAGAG
66 CAACCTTTTGCTCAAATCCATCACTTGATGGATC-AACTTTTCCAGAG
* *
48634 GAAGTTCGTAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
1 GAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAATTCATAATGAGAAGAATTTGT
*
48699 TCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACTTTTCCAGAG
65 TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAG
* *
48747 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 GAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAATTCATAATGAGAAGAATTTGT
* * * * * * *
48812 TCAACCTTTTGTTTAAATTCATCATTTGATAGATTAACATTGT-CAG-G
65 TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAAC-TTTTCCAGAG
* * ** *
48859 TAGAGTTCATAATGAGAAGAACTCTTCAT-CTGAAGAAGAATAAATTCATAATGAGAAGAATTTG
1 GA-AGTTCATAATGAGAAGAACTCATC-TGAAGAAGAAGAAGAAATTCATAATGAGAAGAATTTG
* *
48923 TTCAACCTTTTGCTCAAATCTATCACTTGATGGATCAGCTTTTCCAGA-
64 TTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAG
* **
48971 GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAG---TTCACAATGAGAAGAGCTTGTT
1 GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTT
49033 CAACCTTTT
66 CAACCTTTT
49042 ACATAATTTT
Statistics
Matches: 354, Mismatches: 41, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
107 24 0.07
108 28 0.08
110 2 0.01
111 36 0.10
112 68 0.19
113 192 0.54
114 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (112 bp):
GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTT
CAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAG
Found at i:48690 original size:24 final size:23
Alignment explanation
Indices: 48647--48691 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
48637 GTTCGTAATG
*
48647 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
48670 AGAAGAAATTCATAATG-AGAAG
1 AGAAG-AATTCAT-ATGAAGAAG
48692 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:48926 original size:20 final size:20
Alignment explanation
Indices: 48863--48926 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
48853 GTCAGGTAGA
*
48863 GTTCATAATGAGAAGAA-CT
1 GTTCATAATGAGAAGAATAT
* * *
48882 CTTCAT-CTGAAGAAGAATAA
1 GTTCATAATG-AGAAGAATAT
* *
48902 ATTCATAATGAGAAGAATTT
1 GTTCATAATGAGAAGAATAT
48922 GTTCA
1 GTTCA
48927 ACCTTTTGCT
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
18 2 0.06
19 12 0.36
20 17 0.52
21 2 0.06
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (20 bp):
GTTCATAATGAGAAGAATAT
Found at i:48955 original size:225 final size:221
Alignment explanation
Indices: 48526--49041 Score: 694
Period size: 225 Copynumber: 2.3 Consensus size: 221
48516 AGAAGGAAGA
* *
48526 AGAAGTTCATAATGAGAATAACTCATCTGA-AAGAAG-A-AA-TTCATAATGAGAAGAATTTATT
1 AGAAGTTCATAATGAGAAGAACTCATCTGAGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * *
48587 CAACTTTTTGTTCAAAACCATCACTTGATGGATCAAACTTTCCAGAGGAAGTTCGTAATGAGAAG
66 CAACCTTTTGTTCAAAACCATCACTTGATAGATCAAACTTTCCAGAGGAAGTTCATAATGAGAAG
48652 AATTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAAT
131 AATTCATCT--AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAAT
*
48717 CCATCATTTGATGGATCAACTTTTCCAG
194 CCATCACTTGATGGATCAACTTTTCCAG
48745 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
1 AG-AAGTTCATAATGAGAAGAACTCATCTG-AGAA-GAAGAAGAAGTTCATAATGAGAAGAATTT
* ** * * *
48810 GTTCAACCTTTTGTTTAAATTCATCATTTGATAGAT-TAACATTGT-CAG-GTAGAGTTCATAAT
63 GTTCAACCTTTTGTTCAAAACCATCACTTGATAGATCAAAC-TT-TCCAGAGGA-AGTTCATAAT
*
48872 GAGAAGAACTCTTCATCT-GAA-GAAGAATAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
125 GAGAAGAA---TTCATCTAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
* *
48935 CTCAAATCTATCACTTGATGGATCAGCTTTTCCAG
187 CTCAAATCCATCACTTGATGGATCAACTTTTCCAG
* **
48970 AGAAGTTCATAATGAGAAGAACTCATCT--GAAGAAGAAGAAGTTCACAATGAGAAGAGCTTGTT
1 AGAAGTTCATAATGAGAAGAACTCATCTGAGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
49033 CAACCTTTT
66 CAACCTTTT
49042 ACATAATTTT
Statistics
Matches: 266, Mismatches: 18, Indels: 25
0.86 0.06 0.08
Matches are distributed among these distances:
219 2 0.01
220 64 0.24
221 4 0.02
222 2 0.01
223 4 0.02
224 27 0.10
225 82 0.31
226 73 0.27
227 1 0.00
229 7 0.03
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (221 bp):
AGAAGTTCATAATGAGAAGAACTCATCTGAGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
CAACCTTTTGTTCAAAACCATCACTTGATAGATCAAACTTTCCAGAGGAAGTTCATAATGAGAAG
AATTCATCTAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCC
ATCACTTGATGGATCAACTTTTCCAG
Found at i:49168 original size:83 final size:82
Alignment explanation
Indices: 49003--49189 Score: 216
Period size: 83 Copynumber: 2.3 Consensus size: 82
48993 CATCTGAAGA
* * *
49003 AGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTACATAATTTTATCACAGAAGCAAATA
1 AGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTA-ATAATTCTATCACAGAAGCAAATA
*
49068 GATTAGCATCAACTTTCC
65 GATCAGCATCAACTTTCC
* * * *
49086 AGAGAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTGT-TTGATTCTATCACAGAATG-AGAT
1 AGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT-TAATAATTCTATCACAGAA-GCAAAT
* *
49149 AGATCAGTATCAGCATTTCC
64 AGATCAGCATCAAC-TTTCC
* *
49169 ATAAAAAGTTCATAATAAGAA
1 AGAAAAAGTTCATAATGAGAA
49190 TAACTCATCT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
82 28 0.32
83 59 0.67
84 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (82 bp):
AGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTAATAATTCTATCACAGAAGCAAATAG
ATCAGCATCAACTTTCC
Found at i:49231 original size:17 final size:17
Alignment explanation
Indices: 49209--49271 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
49199 TGAAGAAGGA
49209 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
* *
49226 AGAAGAACTCATCTGAAGAATG
1 AGAAGAAGT--TC---ATAATG
49248 AAGAAGAAGTTCATAATG
1 -AGAAGAAGTTCATAATG
49266 AGAAGA
1 AGAAGA
49272 GCTTGTTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
17 14 0.39
18 5 0.14
19 2 0.06
21 2 0.06
22 5 0.14
23 8 0.22
ACGTcount: A:0.49, C:0.08, G:0.24, T:0.19
Consensus pattern (17 bp):
AGAAGAAGTTCATAATG
Found at i:49235 original size:40 final size:40
Alignment explanation
Indices: 49174--49271 Score: 169
Period size: 40 Copynumber: 2.5 Consensus size: 40
49164 TTTCCATAAA
* *
49174 AAGTTCATAATAAGAATAACTCATCTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
*
49214 AAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
49254 AAGTTCATAATGAGAAGA
1 AAGTTCATAATGAGAAGA
49272 GCTTGTTCAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.20
Consensus pattern (40 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
Found at i:49573 original size:103 final size:101
Alignment explanation
Indices: 49273--49578 Score: 325
Period size: 102 Copynumber: 3.0 Consensus size: 101
49263 ATGAGAAGAG
* * *
49273 CTTGTTCAACC-TTTGTTTGATTCTATCACAGAATGAGATAGATCAGTATCAACATTTCCATAAA
1 CTTGTTCAACCTTTTGCTTGATTCTATCACAGAA-G-G-TAGATCA-AATCAAC-TTTCCAGAAA
49337 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAGAA
61 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAGAA
* * * * * * *** **
49378 TTTGTTCAACTTTTTGCTAGATTAC-ATTACAGAA-GAAAAT-AAATTGTCATCCCCAGCGAAAA
1 CTTGTTCAACCTTTTGCTTGATT-CTATCACAGAAGGTAGATCAAATCAAC-TTTCCA--GAAAA
*
49440 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGGAGAA
62 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAGAA
*
49480 CTTGTTCAACCTTTTGCTTGATTCTATCACATAAGGTAGATCAACATCAACTTTGCCAGAAAAAG
1 CTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGGTAGATCAA-ATCAACTTT-CCAGAAAAAG
*
49545 TTCATAATGAGAAGAACTCATCTGAAGAA-GAAGA
64 TTCATAATAAGAAGAACTCATCTGAAGAAGGAAGA
49579 AGTTCGTAAT
Statistics
Matches: 163, Mismatches: 29, Indels: 21
0.77 0.14 0.10
Matches are distributed among these distances:
100 8 0.05
101 2 0.01
102 77 0.47
103 40 0.25
104 3 0.02
105 15 0.09
106 17 0.10
107 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.28
Consensus pattern (101 bp):
CTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGGTAGATCAAATCAACTTTCCAGAAAAAGTT
CATAATAAGAAGAACTCATCTGAAGAAGGAAGAGAA
Found at i:51253 original size:97 final size:98
Alignment explanation
Indices: 51133--51331 Score: 382
Period size: 97 Copynumber: 2.0 Consensus size: 98
51123 TTATATAGAT
51133 TTTAATTAAATATAAATCTCTTTTATTTATTTTATTAATTCGTTTACTTTTATTATACTTATCCA
1 TTTAATTAAATATAAATCTCTTTTATTTATTTTATTAATTCGTTTACTTTTATTATACTTATCCA
*
51198 TGGTATTTTATTATTAATATAACGTTAAGTGTG
66 TGGTATTTTATTATTAATATAACGTTAAGTGTA
51231 TTTAATT-AATATAAATCTCTTTTATTTATTTTATTAATTCGTTTACTTTTATTATACTTATCCA
1 TTTAATTAAATATAAATCTCTTTTATTTATTTTATTAATTCGTTTACTTTTATTATACTTATCCA
51295 TGGTATTTTATTATTAATATAACGTTAAGTGTA
66 TGGTATTTTATTATTAATATAACGTTAAGTGTA
51328 TTTA
1 TTTA
51332 TATTGTAGTT
Statistics
Matches: 100, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
97 93 0.93
98 7 0.07
ACGTcount: A:0.31, C:0.08, G:0.07, T:0.55
Consensus pattern (98 bp):
TTTAATTAAATATAAATCTCTTTTATTTATTTTATTAATTCGTTTACTTTTATTATACTTATCCA
TGGTATTTTATTATTAATATAACGTTAAGTGTA
Found at i:51388 original size:12 final size:11
Alignment explanation
Indices: 51373--51447 Score: 66
Period size: 11 Copynumber: 6.7 Consensus size: 11
51363 ATTTCATTAT
51373 TTATTTGTAATA
1 TTATTT-TAATA
*
51385 TTATTTTATTA
1 TTATTTTAATA
51396 TTATTTTTAATA
1 TTA-TTTTAATA
51408 -TA-TTTAATTA
1 TTATTTTAA-TA
*
51418 TTACTTTAAT-
1 TTATTTTAATA
*
51428 TATATTTTATTA
1 T-TATTTTAATA
51440 TTATTTTA
1 TTATTTTA
51448 TCTTAGTCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
9 5 0.09
10 3 0.06
11 26 0.49
12 19 0.36
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:51415 original size:9 final size:10
Alignment explanation
Indices: 51395--51445 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
51385 TTATTTTATT
*
51395 ATTATTTTTA
1 ATTATATTTA
51405 A-TATATTTA
1 ATTATATTTA
51414 ATTATTACTTTA
1 ATTA-TA-TTTA
*
51426 ATTATATTTT
1 ATTATATTTA
51436 ATTATTATTT
1 ATTA-TATTT
51446 TATCTTAGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
9 8 0.23
10 10 0.29
11 9 0.26
12 8 0.23
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTATATTTA
Found at i:51447 original size:22 final size:21
Alignment explanation
Indices: 51362--51447 Score: 100
Period size: 22 Copynumber: 3.9 Consensus size: 21
51352 TTAGTTATTT
*
51362 TATTTCATTATTTATTTGTAATA
1 TATTTTATTA-TTATTT-TAATA
51385 TTATTTTATTATTATTTTTAATA
1 -TATTTTATTATTA-TTTTAATA
* *
51408 TATTTAATTATTACTTTAATTA
1 TATTTTATTATTATTTTAA-TA
51430 TATTTTATTATTATTTTA
1 TATTTTATTATTATTTTA
51448 TCTTAGTCTT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
21 5 0.09
22 30 0.55
23 8 0.15
24 12 0.22
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (21 bp):
TATTTTATTATTATTTTAATA
Found at i:51745 original size:21 final size:19
Alignment explanation
Indices: 51721--51768 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
51711 ATATTCTTAA
51721 ATAAATAAATATCTTACTTTT
1 ATAAATAAATATC-TA-TTTT
*
51742 ATAAAT-TATATCTATTTT
1 ATAAATAAATATCTATTTT
51760 -TAAATAAAT
1 ATAAATAAAT
51769 GTTTTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 5 0.21
18 6 0.25
19 2 0.08
20 5 0.21
21 6 0.25
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAAATAAATATCTATTTT
Found at i:51789 original size:129 final size:129
Alignment explanation
Indices: 51648--51881 Score: 343
Period size: 130 Copynumber: 1.8 Consensus size: 129
51638 CATATTTATA
* * *
51648 TATTTATATATTTTTTAATAT-TAAGAAATG-GACTGTCTTAAAG-CACCTAGAAGTCCTTTTCT
1 TATTTATATATTTTTTAATATCGAAGAAAAGAG-CTGTCTT-AAGTCACCTAAAAGTCCTTTTCT
51710 GATA-TTCTTAAATAAATAAATATCTTACTTTTATAAAT-TATATCTATTTTTAAATAAATGTTT
64 GATATTTC-TAAATAAATAAATATCTTA--TTTATAAATATATATCTATTTTTAAATAAATGTTT
51773 TAAT
126 TAAT
*
51777 TATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGTCACCTAAAAGTCCTTTTCTGA
1 TATTTATATATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGTCACCTAAAAGTCCTTTTCTGA
*
51842 TATTTCTAAATAAATAAATATTTTATTTATAAATATATAT
66 TATTTCTAAATAAATAAATATCTTATTTATAAATATATAT
51882 AAATTAATAT
Statistics
Matches: 95, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
128 9 0.09
129 28 0.29
130 54 0.57
131 4 0.04
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (129 bp):
TATTTATATATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGTCACCTAAAAGTCCTTTTCTGA
TATTTCTAAATAAATAAATATCTTATTTATAAATATATATCTATTTTTAAATAAATGTTTTAAT
Found at i:53476 original size:37 final size:37
Alignment explanation
Indices: 53403--53477 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
53393 GTTGAAAAAT
* *
53403 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
53440 ATTTATATAATTTTTTTTATAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
53477 A
1 A
53478 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:56403 original size:28 final size:28
Alignment explanation
Indices: 56370--56427 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
56360 TTTAATACAC
*
56370 ATATTAATACGTAAATTTAGAATAATGA
1 ATATTAATACGTAAATTTAAAATAATGA
56398 ATATTAATACGTAAATTTAAAATAATGA
1 ATATTAATACGTAAATTTAAAATAATGA
56426 AT
1 AT
56428 TCTATGTAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (28 bp):
ATATTAATACGTAAATTTAAAATAATGA
Found at i:57584 original size:17 final size:17
Alignment explanation
Indices: 57562--57600 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
57552 GACCCATCCA
57562 GCCCAAAATCCAAACCG
1 GCCCAAAATCCAAACCG
*
57579 GCCC-AAATCTAAACCG
1 GCCCAAAATCCAAACCG
*
57595 ACCCAA
1 GCCCAA
57601 CCAAGCCAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.41, C:0.41, G:0.10, T:0.08
Consensus pattern (17 bp):
GCCCAAAATCCAAACCG
Found at i:57666 original size:21 final size:21
Alignment explanation
Indices: 57638--57697 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
57628 ACTGAAATGA
57638 ACCATTGACAGTTGACTGTTG
1 ACCATTGACAGTTGACTGTTG
* *
57659 ACCTTTGACAGTTGATTGTTG
1 ACCATTGACAGTTGACTGTTG
*
57680 ATCATTGACCA-TTGACTG
1 ACCATTGA-CAGTTGACTG
57698 CCGACATTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (21 bp):
ACCATTGACAGTTGACTGTTG
Found at i:57909 original size:2 final size:2
Alignment explanation
Indices: 57896--57947 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
57886 TATATTTTTA
*
57896 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57938 AT AT AT AT AT
1 AT AT AT AT AT
57948 TAGGATATCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66392 original size:24 final size:24
Alignment explanation
Indices: 66358--66414 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
66348 ATGGTGAATA
*
66358 CGATGGAGATGGTGAATACGACGG
1 CGATGGTGATGGTGAATACGACGG
*
66382 CGATGGTGATGGTGAATACGATGG
1 CGATGGTGATGGTGAATACGACGG
66406 CGATGGTGA
1 CGATGGTGA
66415 AGAAGATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.26, C:0.11, G:0.42, T:0.21
Consensus pattern (24 bp):
CGATGGTGATGGTGAATACGACGG
Found at i:66403 original size:18 final size:18
Alignment explanation
Indices: 66337--66415 Score: 68
Period size: 18 Copynumber: 4.1 Consensus size: 18
66327 TCTGGAATTG
* *
66337 ATACGATAGTAATGGTGA
1 ATACGATGGTGATGGTGA
*
66355 ATACGATGGAGATGGTGA
1 ATACGATGGTGATGGTGA
66373 ATACGACGGCGATGGTGATGGTGA
1 AT---A---CGATGGTGATGGTGA
*
66397 ATACGATGGCGATGGTGA
1 ATACGATGGTGATGGTGA
66415 A
1 A
66416 GAAGATTTGG
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
18 32 0.64
21 2 0.04
24 16 0.32
ACGTcount: A:0.32, C:0.09, G:0.37, T:0.23
Consensus pattern (18 bp):
ATACGATGGTGATGGTGA
Found at i:71013 original size:3 final size:3
Alignment explanation
Indices: 71005--71038 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
70995 TTTAAGGATA
71005 AGG AGG AGG AGG AGG AGG AGG AGG ATGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG A-GG AGG AGG
71039 GTGTTGAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.65, T:0.03
Consensus pattern (3 bp):
AGG
Found at i:75924 original size:3 final size:3
Alignment explanation
Indices: 75916--75992 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
75906 TCCTGAAGCT
75916 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
75964 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
75993 TTAATTATAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:76005 original size:11 final size:12
Alignment explanation
Indices: 75924--76005 Score: 77
Period size: 12 Copynumber: 6.9 Consensus size: 12
75914 CTTTATTATT
75924 ATTATTATTATT-
1 ATTATTATT-TTA
75936 ATTATTATTATT-
1 ATTATTATT-TTA
75948 ATTATTATTATT-
1 ATTATTATT-TTA
75960 ATTATTATTATT-
1 ATTATTATT-TTA
75972 ATTATTATTATT-
1 ATTATTATT-TTA
75984 ATTATTATTTTA
1 ATTATTATTTTA
75996 ATTA-TATTTT
1 ATTATTATTTT
76006 GTGCATTGAA
Statistics
Matches: 69, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
11 8 0.12
12 61 0.88
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTATTATTTTA
Done.