Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1599
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1324113
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.30
Warning! 103357 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:430 original size:24 final size:24
Alignment explanation
Indices: 398--444 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
388 TCAGAATTGG
*
398 TGATCTGTTGATTGTACCTCTTCA
1 TGATCTGTTAATTGTACCTCTTCA
*
422 TGATCTGTTAATTGTAGCTCTTC
1 TGATCTGTTAATTGTACCTCTTC
445 CCAGATACGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (24 bp):
TGATCTGTTAATTGTACCTCTTCA
Found at i:4474 original size:13 final size:14
Alignment explanation
Indices: 4456--4485 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4446 TTTTTCTCTT
4456 GTTGTAAAC-AGGA
1 GTTGTAAACGAGGA
4469 GTTGTAAACGAGGA
1 GTTGTAAACGAGGA
4483 GTT
1 GTT
4486 CTTAAATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.27
Consensus pattern (14 bp):
GTTGTAAACGAGGA
Found at i:6554 original size:1 final size:1
Alignment explanation
Indices: 6521--6545 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
6511 CAGTACCTCA
6521 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
6546 ACNCCCCCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:7037 original size:41 final size:41
Alignment explanation
Indices: 6992--7427 Score: 276
Period size: 41 Copynumber: 10.1 Consensus size: 41
6982 TATGTGGTGC
* * *
6992 GATACTCTACATATTGTAAGATAGCTTACAGTCTATGATAT
1 GATACTCTATATATTGTAAGATAGCTTACAGTCTGTGCTAT
* **
7033 GATACTCTTTATATTGTAAGATAGCTTA-AGTCTGTGCCGT
1 GATACTCTATATATTGTAAGATAGCTTACAGTCTGTGCTAT
* *
7073 GATACTCAATGTATTGTAAGAATA-CTTACAGTCTGTGCTAT
1 GATACTCTATATATTGTAAG-ATAGCTTACAGTCTGTGCTAT
* * * * * *
7114 GATACTCAATATATTGAAATATAGCTTA-AGTATATGCAAT
1 GATACTCTATATATTGTAAGATAGCTTACAGTCTGTGCTAT
* * * *
7154 GATACTCTATACGGTATATCATATA-ATAACTTACAGCCTGTGCCAT
1 GATACTCTATA---TAT-T-GTA-AGATAGCTTACAGTCTGTGCTAT
* * *
7200 GATACTCTATATATCGTAAGATAACTTATAGTCTGTGCTAT
1 GATACTCTATATATTGTAAGATAGCTTACAGTCTGTGCTAT
* * *
7241 GATACTCTAAATATTGTTAGATAGCTTATAGTCTAGTGCTACAT
1 GATACTCTATATATTGTAAGATAGCTTACAGTCT-GTGCT--AT
* * *
7285 GGATTCTACAATGTATATATATTGTAAGGCT-GCTTA-AGTCTATGCTAT
1 -GA---TAC----TCTATATATTGTAA-GATAGCTTACAGTCTGTGCTAT
* *
7333 GATACTCATTATACTCTTTATGCTATAAAATAGCTTA-AGTCTGTGCTAT
1 GATACTC--TATA-----TAT--TGTAAGATAGCTTACAGTCTGTGCTAT
* * *
7382 GATACTCTATTTATTGTAAGATAACTTA-AGTCTATGCTAT
1 GATACTCTATATATTGTAAGATAGCTTACAGTCTGTGCTAT
7422 GATACT
1 GATACT
7428 TCGTTTACAC
Statistics
Matches: 313, Mismatches: 49, Indels: 67
0.73 0.11 0.16
Matches are distributed among these distances:
40 81 0.26
41 110 0.35
42 12 0.04
43 6 0.02
44 6 0.02
45 10 0.03
46 20 0.06
47 8 0.03
48 6 0.02
49 27 0.09
50 4 0.01
51 5 0.02
52 16 0.05
53 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (41 bp):
GATACTCTATATATTGTAAGATAGCTTACAGTCTGTGCTAT
Found at i:7157 original size:81 final size:81
Alignment explanation
Indices: 7003--7160 Score: 210
Period size: 81 Copynumber: 2.0 Consensus size: 81
6993 ATACTCTACA
** * * *
7003 TATTGTAAGATAGCTTACAGTCTATGATATGATACTCTTTATATTGTAAGATAGCTTAAGTCTGT
1 TATTGTAAGATAGCTTACAGTCTATGATATGATACTCAATATATTGAAAGATAGCTTAAGTATAT
**
7068 GCCGTGATACTCAATG
66 GCAATGATACTCAATG
* * *
7084 TATTGTAAGAATA-CTTACAGTCTGTGCTATGATACTCAATATATTGAAATATAGCTTAAGTATA
1 TATTGTAAG-ATAGCTTACAGTCTATGATATGATACTCAATATATTGAAAGATAGCTTAAGTATA
7148 TGCAATGATACTC
65 TGCAATGATACTC
7161 TATACGGTAT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
81 63 0.95
82 3 0.05
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (81 bp):
TATTGTAAGATAGCTTACAGTCTATGATATGATACTCAATATATTGAAAGATAGCTTAAGTATAT
GCAATGATACTCAATG
Found at i:11441 original size:16 final size:16
Alignment explanation
Indices: 11417--11497 Score: 135
Period size: 16 Copynumber: 5.1 Consensus size: 16
11407 GACAACCCAT
11417 ACACTAAATCATGTCC
1 ACACTAAATCATGTCC
* *
11433 ACCCTAAATCATGGCC
1 ACACTAAATCATGTCC
11449 ACACTAAATCATGTCC
1 ACACTAAATCATGTCC
*
11465 ACCCTAAATCATGTCC
1 ACACTAAATCATGTCC
11481 ACACTAAATCATGTCC
1 ACACTAAATCATGTCC
11497 A
1 A
11498 TACTGAACCA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 59 1.00
ACGTcount: A:0.36, C:0.33, G:0.07, T:0.23
Consensus pattern (16 bp):
ACACTAAATCATGTCC
Found at i:11458 original size:32 final size:32
Alignment explanation
Indices: 11417--11497 Score: 153
Period size: 32 Copynumber: 2.5 Consensus size: 32
11407 GACAACCCAT
11417 ACACTAAATCATGTCCACCCTAAATCATGGCC
1 ACACTAAATCATGTCCACCCTAAATCATGGCC
*
11449 ACACTAAATCATGTCCACCCTAAATCATGTCC
1 ACACTAAATCATGTCCACCCTAAATCATGGCC
11481 ACACTAAATCATGTCCA
1 ACACTAAATCATGTCCA
11498 TACTGAACCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.36, C:0.33, G:0.07, T:0.23
Consensus pattern (32 bp):
ACACTAAATCATGTCCACCCTAAATCATGGCC
Found at i:13208 original size:4 final size:4
Alignment explanation
Indices: 13201--13247 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
13191 TCTTTAATTA
13201 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
13248 TATATATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:13252 original size:2 final size:2
Alignment explanation
Indices: 13245--13270 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13235 AGATAGATAG
13245 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
13271 NNNNNNNNNN
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:13372 original size:18 final size:18
Alignment explanation
Indices: 13349--13384 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
13339 NNNNNNNNNN
13349 TATATATATATATTTCTA
1 TATATATATATATTTCTA
13367 TATATATATATATTTCTA
1 TATATATATATATTTCTA
13385 AATAAAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATATATATTTCTA
Found at i:17018 original size:35 final size:35
Alignment explanation
Indices: 16935--17090 Score: 269
Period size: 35 Copynumber: 4.5 Consensus size: 35
16925 TAATACCGGA
*
16935 AAATTCGTCCGAAAGTCGACTGCTTGTTTCAAT-T
1 AAATTCGTCCGAAAGTCGACTGCTTGTTTCGATGT
16969 AAATTCGTCCGAAAGTCGACTGCTTGTTTCGATGT
1 AAATTCGTCCGAAAGTCGACTGCTTGTTTCGATGT
* *
17004 AAATTCTTCAGAAAGTCGACTGCTTGTTTCGATGT
1 AAATTCGTCCGAAAGTCGACTGCTTGTTTCGATGT
17039 AAATTCGTCCGAAAGTCGACTGCTTGTTTCGATGT
1 AAATTCGTCCGAAAGTCGACTGCTTGTTTCGATGT
*
17074 AAATTCGACCGAAAGTC
1 AAATTCGTCCGAAAGTC
17091 AATCGGATGA
Statistics
Matches: 115, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
34 32 0.28
35 83 0.72
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (35 bp):
AAATTCGTCCGAAAGTCGACTGCTTGTTTCGATGT
Found at i:17496 original size:12 final size:12
Alignment explanation
Indices: 17479--17519 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
17469 CAATGGCCCC
17479 ACACACATACAT
1 ACACACATACAT
17491 ACACACATACAT
1 ACACACATACAT
* * *
17503 ACATACACACAC
1 ACACACATACAT
17515 ACACA
1 ACACA
17520 GCAGCGATCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.12
Consensus pattern (12 bp):
ACACACATACAT
Found at i:17502 original size:16 final size:16
Alignment explanation
Indices: 17478--17517 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
17468 ACAATGGCCC
17478 CACACACATACATACA
1 CACACACATACATACA
*
17494 CACATACATACATACA
1 CACACACATACATACA
17510 CACACACA
1 CACACACA
17518 CAGCAGCGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (16 bp):
CACACACATACATACA
Found at i:29413 original size:39 final size:37
Alignment explanation
Indices: 29370--29498 Score: 102
Period size: 39 Copynumber: 3.4 Consensus size: 37
29360 TAAAATGGAT
* *
29370 TCATTGAAGAGTTTCTAAATTGACTGACTTATATAGGTC
1 TCATTGAAGAGTTTCT-AATT-ACTAACTTACATAGGTC
* * * *
29409 TCATT-AATGAGCTTCTCAACTAACTCACTTACACAGGTC
1 TCATTGAA-GAGTTTCT-AA-TTACTAACTTACATAGGTC
* * *
29448 TTATTGATGAGTTTCT--TTACTAACTTACATAAGTC
1 TCATTGAAGAGTTTCTAATTACTAACTTACATAGGTC
*
29483 TCATTGATGAGTTTCT
1 TCATTGAAGAGTTTCT
29499 CCAGCGTGGT
Statistics
Matches: 73, Mismatches: 14, Indels: 10
0.75 0.14 0.10
Matches are distributed among these distances:
35 30 0.41
38 2 0.03
39 39 0.53
40 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (37 bp):
TCATTGAAGAGTTTCTAATTACTAACTTACATAGGTC
Found at i:33976 original size:49 final size:49
Alignment explanation
Indices: 33922--34019 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
33912 ATGAGAAAAC
33922 TCTACGGTAAAATCTTTTTTAAAACCTTGCTTTTAATTCGAACTATGCA
1 TCTACGGTAAAATCTTTTTTAAAACCTTGCTTTTAATTCGAACTATGCA
* * *
33971 TCTACGGTGAAATCTTTTTTAAAACCTTGCTTTTAATTCGCATTATGCA
1 TCTACGGTAAAATCTTTTTTAAAACCTTGCTTTTAATTCGAACTATGCA
34020 CTATGAATAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (49 bp):
TCTACGGTAAAATCTTTTTTAAAACCTTGCTTTTAATTCGAACTATGCA
Found at i:42526 original size:21 final size:21
Alignment explanation
Indices: 42489--42537 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
42479 GATCACTAAT
* *
42489 TATAGTTTACGAATCGTTATC
1 TATAGTTTACGAATCGTAAAC
**
42510 TATAGTTTACGGTTCGTAAAC
1 TATAGTTTACGAATCGTAAAC
42531 TATAGTT
1 TATAGTT
42538 AACAATAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (21 bp):
TATAGTTTACGAATCGTAAAC
Found at i:46813 original size:2 final size:2
Alignment explanation
Indices: 46806--46866 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
46796 TAGACACATT
46806 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
46848 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
46867 GAATTTACAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:58214 original size:14 final size:14
Alignment explanation
Indices: 58192--58221 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
58182 TGTCATTAGT
*
58192 TTCTTTGTAATATG
1 TTCTATGTAATATG
58206 TTCTATGTAATATG
1 TTCTATGTAATATG
58220 TT
1 TT
58222 GGTACAGAAT
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:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (14 bp):
TTCTATGTAATATG
Found at i:72659 original size:19 final size:20
Alignment explanation
Indices: 72635--72703 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
72625 CAGTACACCG
72635 GTAGTCAGTTAACTATACC-
1 GTAGTCAGTTAACTATACCA
*
72654 GTAGTCAGTTAACTATACCT
1 GTAGTCAGTTAACTATACCA
72674 GTAGTCAGTTAACTATACCA
1 GTAGTCAGTTAACTATACCA
72694 GTAGTCAGTT
1 GTAGTCAGTT
72704 TACTGATAAC
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 19 0.40
20 29 0.60
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (20 bp):
GTAGTCAGTTAACTATACCA
Found at i:75535 original size:34 final size:34
Alignment explanation
Indices: 75497--75579 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
75487 CCATCTCAGA
* **
75497 CAAAATTTATCTTGGGAAAAATCTAT-TTCGCAGT
1 CAAAATATATCTCAGGAAAAATCTATCTT-GCAGT
**
75531 CAAAATATATCTCAGTCAAAATCTATCTTGCAGT
1 CAAAATATATCTCAGGAAAAATCTATCTTGCAGT
*
75565 CAAAATCTATCTCAG
1 CAAAATATATCTCAG
75580 CCAAAATTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
34 40 0.95
35 2 0.05
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (34 bp):
CAAAATATATCTCAGGAAAAATCTATCTTGCAGT
Found at i:75543 original size:50 final size:50
Alignment explanation
Indices: 75463--75560 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 50
75453 GAGCAGACGT
* *
75463 AAAAATATATCTCGCAATCAAAATCCATCTCAGACAAAATTTATCTTGGG
1 AAAAATATATCTCGCAATCAAAATACATCTCAGACAAAATCTATCTTGGG
* * * * *
75513 AAAAATCTATTTCGCAGTCAAAATATATCTCAGTCAAAATCTATCTTG
1 AAAAATATATCTCGCAATCAAAATACATCTCAGACAAAATCTATCTTG
75561 CAGTCAAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (50 bp):
AAAAATATATCTCGCAATCAAAATACATCTCAGACAAAATCTATCTTGGG
Found at i:75585 original size:34 final size:34
Alignment explanation
Indices: 75514--75802 Score: 213
Period size: 34 Copynumber: 8.6 Consensus size: 34
75504 TATCTTGGGA
*
75514 AAAATCTAT-TTCGCAGTCAAAATATATCTCAGTC
1 AAAATCTATCTT-GCAGTCAAAATCTATCTCAGTC
*
75548 AAAATCTATCTTGCAGTCAAAATCTATCTCAGCC
1 AAAATCTATCTTGCAGTCAAAATCTATCTCAGTC
* * *
75582 AAAATTTATCCTGTA--CAAAATCTATCATGCAGTC
1 AAAATCTATCTTGCAGTCAAAATCTATC-T-CAGTC
* * *
75616 AAAATCTATC-T-CAGACAAAATTTATCT-TGTAC
1 AAAATCTATCTTGCAGTCAAAATCTATCTCAGT-C
* ** *
75648 AAAATTTATCTCACAGTCAAAATCTATCTCAGCC
1 AAAATCTATCTTGCAGTCAAAATCTATCTCAGTC
* * * *
75682 AAAATTTATCTTGTA--CAAAATCTTTCACGCAGTC
1 AAAATCTATCTTGCAGTCAAAATCTAT--CTCAGTC
* **
75716 AAAATCTATC-T-CAGACAAAAT-TATCTTGGTC
1 AAAATCTATCTTGCAGTCAAAATCTATCTCAGTC
* ** * *
75747 AAAATTTATCTCACAGTCAAAATTTATCTCAGAC
1 AAAATCTATCTTGCAGTCAAAATCTATCTCAGTC
**
75781 AAAATCTATCTCACAGTCAAAA
1 AAAATCTATCTTGCAGTCAAAA
75803 AATGTAAACT
Statistics
Matches: 204, Mismatches: 35, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
31 15 0.07
32 32 0.16
33 15 0.07
34 139 0.68
35 3 0.01
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (34 bp):
AAAATCTATCTTGCAGTCAAAATCTATCTCAGTC
Found at i:75585 original size:50 final size:51
Alignment explanation
Indices: 75531--75792 Score: 333
Period size: 50 Copynumber: 5.3 Consensus size: 51
75521 ATTTCGCAGT
* * * *
75531 CAAAATATATCTCAGT-CAAAATCTATCTTGCAGTCAAAATCTATCTCAGC
1 CAAAATTTATCTCTGTACAAAATCTATCTCGCAGTCAAAATCTATCTCAGA
75581 CAAAATTTATC-CTGTACAAAATCTATCAT-GCAGTCAAAATCTATCTCAGA
1 CAAAATTTATCTCTGTACAAAATCTATC-TCGCAGTCAAAATCTATCTCAGA
* * *
75631 CAAAATTTATCT-TGTACAAAATTTATCTCACAGTCAAAATCTATCTCAGC
1 CAAAATTTATCTCTGTACAAAATCTATCTCGCAGTCAAAATCTATCTCAGA
* *
75681 CAAAATTTATCT-TGTACAAAATCTTTCACGCAGTCAAAATCTATCTCAGA
1 CAAAATTTATCTCTGTACAAAATCTATCTCGCAGTCAAAATCTATCTCAGA
* * *
75731 CAAAA-TTATCT-TGGT-CAAAATTTATCTCACAGTCAAAATTTATCTCAGA
1 CAAAATTTATCTCT-GTACAAAATCTATCTCGCAGTCAAAATCTATCTCAGA
*
75780 CAAAATCTATCTC
1 CAAAATTTATCTC
75793 ACAGTCAAAA
Statistics
Matches: 188, Mismatches: 17, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
49 45 0.24
50 142 0.76
51 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (51 bp):
CAAAATTTATCTCTGTACAAAATCTATCTCGCAGTCAAAATCTATCTCAGA
Found at i:75642 original size:100 final size:99
Alignment explanation
Indices: 75531--75790 Score: 378
Period size: 100 Copynumber: 2.6 Consensus size: 99
75521 ATTTCGCAGT
* * **
75531 CAAAATATATCTCAGTCAAAATCTATCTTGCAGTCAAAATCTATCTCAGCCAAAATTTATCCTGT
1 CAAAATTTATCT-AGTCAAAATTTATCTCACAGTCAAAATCTATCTCAGCCAAAATTTATCCTGT
*
75596 ACAAAATCTATCATGCAGTCAAAATCTATCTCAGA
65 ACAAAATCTATCACGCAGTCAAAATCTATCTCAGA
* *
75631 CAAAATTTATCTTGTACAAAATTTATCTCACAGTCAAAATCTATCTCAGCCAAAATTTATCTTGT
1 CAAAATTTATCTAGT-CAAAATTTATCTCACAGTCAAAATCTATCTCAGCCAAAATTTATCCTGT
*
75696 ACAAAATCTTTCACGCAGTCAAAATCTATCTCAGA
65 ACAAAATCTATCACGCAGTCAAAATCTATCTCAGA
* * * *
75731 CAAAA-TTATCTTGGTCAAAATTTATCTCACAGTCAAAATTTATCTCAGACAAAATCTATC
1 CAAAATTTATC-TAGTCAAAATTTATCTCACAGTCAAAATCTATCTCAGCCAAAATTTATC
75791 TCACAGTCAA
Statistics
Matches: 146, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
99 49 0.34
100 97 0.66
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (99 bp):
CAAAATTTATCTAGTCAAAATTTATCTCACAGTCAAAATCTATCTCAGCCAAAATTTATCCTGTA
CAAAATCTATCACGCAGTCAAAATCTATCTCAGA
Found at i:76245 original size:24 final size:24
Alignment explanation
Indices: 76218--76285 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
76208 CATGTGATCA
* *
76218 GTCATGTGATAAGTGTAA-ATGTAT
1 GTCATGTGACAA-TCTAATATGTAT
* *
76242 GTCATTTGACCATCTAATATGTAT
1 GTCATGTGACAATCTAATATGTAT
*
76266 GTCATGTGACTAGTCTAATA
1 GTCATGTGAC-AATCTAATA
76286 AAGCATGCCA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
23 4 0.11
24 24 0.69
25 7 0.20
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (24 bp):
GTCATGTGACAATCTAATATGTAT
Found at i:84187 original size:1 final size:1
Alignment explanation
Indices: 84181--84220 Score: 62
Period size: 1 Copynumber: 40.0 Consensus size: 1
84171 GGGTCAGGCG
**
84181 CCCCCCCCCCCCCCCCCCCCCNGCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
84221 GGTTCTTCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.95, G:0.03, T:0.00
Consensus pattern (1 bp):
C
Found at i:86968 original size:2 final size:2
Alignment explanation
Indices: 86961--87003 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
86951 CCCCTTAGAG
*
86961 CT CT CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
87003 C
1 C
87004 GTCGTAATTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:89427 original size:12 final size:12
Alignment explanation
Indices: 89412--89440 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
89402 ATAAATCTTT
89412 CAATATGGAAAC
1 CAATATGGAAAC
89424 CAATATGGAAAC
1 CAATATGGAAAC
89436 CAATA
1 CAATA
89441 ATTTGAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.17
Consensus pattern (12 bp):
CAATATGGAAAC
Found at i:97286 original size:168 final size:168
Alignment explanation
Indices: 97085--97829 Score: 1163
Period size: 168 Copynumber: 4.4 Consensus size: 168
97075 CCTCATGTCC
* * * * *
97085 TGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAAAGGAGATT-GTGGATATCATAA
1 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGG-GCTTCATGGACATCATAA
* * ** ** * * * * * *
97149 CCATGTATTCAGTTTTTTGCCCACATGTGTGGGAGTAGAGAAGAAGATTTTTTAATATTTAACTA
65 CCATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAA-TA
97214 -ATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCA
129 CATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCA
*
97253 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAAT
1 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAAC
*
97318 CATGCATTTAGTTTTTAACAAATATATATGATAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
66 CATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
*
97383 TTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCC
131 TTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCA
*
97421 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTAAGGTAGAGGGCTTCATGGACATCATAAC
1 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAAC
* *
97486 CATGCATTTAATTTTTAACAAATATATATGATAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
66 CATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
* *
97551 TTTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCC
131 TTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCA
* *
97589 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGACATCATAAT
1 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAAC
97654 CATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
66 CATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
97719 TTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCA
131 TTTTTACTATATGGCCATATTGGCCCCACCCTAGAG-CA
* * * *
97758 -GAACCCCTGACCCAGGGGCCATAAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATAAC
1 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAAC
97822 CATGCATT
66 CATGCATT
97830 CATTTTTTTC
Statistics
Matches: 537, Mismatches: 37, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
167 5 0.01
168 531 0.99
169 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (168 bp):
TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAAC
CATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
TTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCA
Found at i:98052 original size:7 final size:7
Alignment explanation
Indices: 98042--98079 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
98032 AAAATTGTTA
98042 ACGCACG
1 ACGCACG
*
98049 ACGCACA
1 ACGCACG
98056 ACGCACG
1 ACGCACG
*
98063 ACGCACA
1 ACGCACG
98070 ACGCACG
1 ACGCACG
98077 ACG
1 ACG
98080 ACGGACGAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.34, C:0.42, G:0.24, T:0.00
Consensus pattern (7 bp):
ACGCACG
Found at i:98060 original size:14 final size:14
Alignment explanation
Indices: 98041--98079 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
98031 TAAAATTGTT
98041 AACGCACGACGCAC
1 AACGCACGACGCAC
98055 AACGCACGACGCAC
1 AACGCACGACGCAC
98069 AACGCACGACG
1 AACGCACGACG
98080 ACGGACGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.36, C:0.41, G:0.23, T:0.00
Consensus pattern (14 bp):
AACGCACGACGCAC
Found at i:102032 original size:2 final size:2
Alignment explanation
Indices: 102025--102075 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
102015 TTTAACTGTT
102025 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
102067 GA GA GA GA G
1 GA GA GA GA G
102076 NACAAGTAGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:103421 original size:2 final size:2
Alignment explanation
Indices: 103416--103491 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
103406 AGTTTTAAAC
103416 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
103458 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
103492 TCTCTTATAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:106186 original size:4 final size:4
Alignment explanation
Indices: 106177--106204 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
106167 TCCTCTTTAA
106177 CTGT CTGT CTGT CTGT CTGT CTGT CTGT
1 CTGT CTGT CTGT CTGT CTGT CTGT CTGT
106205 AATCATCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.25, T:0.50
Consensus pattern (4 bp):
CTGT
Found at i:109028 original size:20 final size:20
Alignment explanation
Indices: 109000--109037 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
108990 AAATGACTCA
109000 AATGAACCCAAATGGAAACT
1 AATGAACCCAAATGGAAACT
*
109020 AATGGACCCAAATGGAAA
1 AATGAACCCAAATGGAAA
109038 TTGAATGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.13
Consensus pattern (20 bp):
AATGAACCCAAATGGAAACT
Found at i:110368 original size:12 final size:12
Alignment explanation
Indices: 110347--110376 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
110337 GAAATGATTA
*
110347 TATATCAACAGT
1 TATATTAACAGT
110359 TATATTAACAGT
1 TATATTAACAGT
110371 TATATT
1 TATATT
110377 TAAATTCATA
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:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (12 bp):
TATATTAACAGT
Found at i:112093 original size:26 final size:26
Alignment explanation
Indices: 112064--112115 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
112054 GAGAACATGT
112064 ACTCCACTACATGGGTACCAGTTTTC
1 ACTCCACTACATGGGTACCAGTTTTC
112090 ACTCCACTACATGGGTACCAGTTTTC
1 ACTCCACTACATGGGTACCAGTTTTC
112116 CACGAGAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (26 bp):
ACTCCACTACATGGGTACCAGTTTTC
Found at i:117133 original size:2 final size:2
Alignment explanation
Indices: 117126--117166 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
117116 CCAGTCAGGT
117126 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
117167 TGGAGTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:122069 original size:26 final size:26
Alignment explanation
Indices: 122038--122113 Score: 116
Period size: 26 Copynumber: 2.9 Consensus size: 26
122028 CTATTTATAT
*
122038 CAAACATACCGGTATATTTACCTACA
1 CAAACATACAGGTATATTTACCTACA
*
122064 CAAACATACAGGTATAGTTACCTACA
1 CAAACATACAGGTATATTTACCTACA
**
122090 CAAGTATACAGGTATATTTACCTA
1 CAAACATACAGGTATATTTACCTA
122114 AAGAGGCAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (26 bp):
CAAACATACAGGTATATTTACCTACA
Found at i:122469 original size:24 final size:24
Alignment explanation
Indices: 122442--122503 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
122432 TTTGTTGTAC
**
122442 TTTCCTTTGTTGTCTCTCTAGTTG
1 TTTCCTTTGTTGTCTCTCTAACTG
*
122466 TTT-CTGTTGTTGTCTCTTTAACTG
1 TTTCCT-TTGTTGTCTCTCTAACTG
122490 TTTCCTTTGTTGTC
1 TTTCCTTTGTTGTC
122504 ACTGCAGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 2 0.06
24 29 0.88
25 2 0.06
ACGTcount: A:0.05, C:0.19, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTCCTTTGTTGTCTCTCTAACTG
Found at i:122515 original size:24 final size:23
Alignment explanation
Indices: 122442--122515 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 23
122432 TTTGTTGTAC
122442 TTTCCTTTGTTGTCTCTCTAGTTG
1 TTTCCTTTGTTGTCTCTC-AGTTG
* **
122466 TTT-CTGTTGTTGTCTCTTTAACTG
1 TTTCCT-TTGTTGTCTC-TCAGTTG
*
122490 TTTCCTTTGTTGTCACTGCAGTTG
1 TTTCCTTTGTTGTCTCT-CAGTTG
122514 TT
1 TT
122516 GAAATGAACT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
23 3 0.08
24 33 0.85
25 3 0.08
ACGTcount: A:0.07, C:0.19, G:0.18, T:0.57
Consensus pattern (23 bp):
TTTCCTTTGTTGTCTCTCAGTTG
Found at i:123347 original size:132 final size:132
Alignment explanation
Indices: 123195--124139 Score: 1487
Period size: 132 Copynumber: 7.1 Consensus size: 132
123185 CTTCTTCTGG
* * * *
123195 TTGTTGTTGATGTTTCTGAAGTACTTGGTGTTGAAATTGTTGTTGTGCTTGGTGTTGTTACTGAT
1 TTGTTGTTGATGTTTTTGAAGTGCTTGGAGTTGAAATTGTTGTTGTGCTTGGTGTTGTTACTGAG
*
123260 CTTTGGCTTCCAGTGGTTGTTGTCATTGCTGCTGTACTTGGTGTTGTTGTCAAAGTTGTAATTAT
66 CTTTGGCTTCCAGTGGTTGTTGTCACTGCTGCTGTACTTGGTGTTGTTGTCAAAGTTGTAATTAT
123325 CC
131 CC
* * *
123327 TTTTTGTTGATGTTTTTGAAGTGCTCGGAGTTGAAATTGTTGTCGTGCTTGGTGTTGTTACTGAG
1 TTGTTGTTGATGTTTTTGAAGTGCTTGGAGTTGAAATTGTTGTTGTGCTTGGTGTTGTTACTGAG
*
123392 CTTTGGCTTCCAGTGGTTGTTGTCAATGCTGCTGTACTTGGTGTTGTTGTCAAAGTTGTAATTAT
66 CTTTGGCTTCCAGTGGTTGTTGTCACTGCTGCTGTACTTGGTGTTGTTGTCAAAGTTGTAATTAT
123457 CC
131 CC
* *
123459 TTGTTGTTGATGTTTTTGAAGTGCTCGGAGTTGAAATTGTTGTCGTGCTTGGTGTTGTTACTGAG
1 TTGTTGTTGATGTTTTTGAAGTGCTTGGAGTTGAAATTGTTGTTGTGCTTGGTGTTGTTACTGAG
*
123524 CTTTGGCTTCCAGTGGTTGTTGTCACTGCTGCTGTACTTGGTGTTGTTGTCAAAGTTGTTATTAT
66 CTTTGGCTTCCAGTGGTTGTTGTCACTGCTGCTGTACTTGGTGTTGTTGTCAAAGTTGTAATTAT
123589 CC
131 CC
* *
123591 TTGTTATTGATGTTTTTGAAGTGCTTGGAGTTGAAATTGTTGTTGTGCTTGGTGTTGTTACTGAT
1 TTGTTGTTGATGTTTTTGAAGTGCTTGGAGTTGAAATTGTTGTTGTGCTTGGTGTTGTTACTGAG
123656 CTTTGGCTTCCAGTGGTTGTTGTCACTGCTGCTGTACTTGGTGTTGTTGTCAAAGTTGTAATTAT
66 CTTTGGCTTCCAGTGGTTGTTGTCACTGCTGCTGTACTTGGTGTTGTTGTCAAAGTTGTAATTAT
123721 CC
131 CC
* * *
123723 TAGTTGTTGATGTTTTTGAATTGCTTGGAGTTGAAATTGTTGTTGTGCTTGGTGTTGTTTCTGAG
1 TTGTTGTTGATGTTTTTGAAGTGCTTGGAGTTGAAATTGTTGTTGTGCTTGGTGTTGTTACTGAG
* * * * *
123788 CCTTGGCTTCCAGTAGTTGTTGTCACTGCTGCTGTAGTTGGTGTTGTTGTTAAAGTTGTGATTAT
66 CTTTGGCTTCCAGTGGTTGTTGTCACTGCTGCTGTACTTGGTGTTGTTGTCAAAGTTGTAATTAT
123853 CC
131 CC
* *
123855 TAGTTGTTGATGTTTTTGAAGTGCTTGGAGTTGAAATTGTTGTTGTGCTTGGTGTTGTTTCTGAG
1 TTGTTGTTGATGTTTTTGAAGTGCTTGGAGTTGAAATTGTTGTTGTGCTTGGTGTTGTTACTGAG
* * * **
123920 CCTTGGCTTCCAGTGGTTGTTGTCACTGCTGCTGTACTTGGTTTTGTTGT-TAAGCTTGGTCTTC
66 CTTTGGCTTCCAGTGGTTGTTGTCACTGCTGCTGTACTTGGTGTTGTTGTCAAAG-TT-GTAAT-
**
123984 TACTGG
128 TA-TCC
* *
123990 TTGTTGTTGATGTTTTTGAAGTACTTGGTGTTGAAATTGTTGTTGTGCTTGGTGTTGTTACTGAG
1 TTGTTGTTGATGTTTTTGAAGTGCTTGGAGTTGAAATTGTTGTTGTGCTTGGTGTTGTTACTGAG
* * * *
124055 CTTTGGATTCCAGTGGTTGTTGTCACTGCTGCTGTACTTGGTTTTGTTGTCATAGTTGTGATTAT
66 CTTTGGCTTCCAGTGGTTGTTGTCACTGCTGCTGTACTTGGTGTTGTTGTCAAAGTTGTAATTAT
124120 CC
131 CC
124122 TAGTTGTTGTTGATGTTT
1 ---TTGTTGTTGATGTTT
124140 CTGACTTGCT
Statistics
Matches: 758, Mismatches: 47, Indels: 13
0.93 0.06 0.02
Matches are distributed among these distances:
131 3 0.00
132 616 0.81
133 5 0.01
134 5 0.01
135 127 0.17
136 2 0.00
ACGTcount: A:0.13, C:0.11, G:0.28, T:0.47
Consensus pattern (132 bp):
TTGTTGTTGATGTTTTTGAAGTGCTTGGAGTTGAAATTGTTGTTGTGCTTGGTGTTGTTACTGAG
CTTTGGCTTCCAGTGGTTGTTGTCACTGCTGCTGTACTTGGTGTTGTTGTCAAAGTTGTAATTAT
CC
Found at i:126848 original size:30 final size:29
Alignment explanation
Indices: 126812--126890 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 29
126802 ACAAAAAAAG
126812 CTTCGAAAATATTTGACTTAAGAAAGAGAA
1 CTTCGAAAA-ATTTGACTTAAGAAAGAGAA
* * *
126842 CTTCGAAGAAATTTAACTTACGATAGAGAA
1 CTTCGAA-AAATTTGACTTAAGAAAGAGAA
* * *
126872 TTTAGAAGAGATTTGACTT
1 CTTCGAA-AAATTTGACTT
126891 GCGATTGAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 39 0.95
31 2 0.05
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (29 bp):
CTTCGAAAAATTTGACTTAAGAAAGAGAA
Found at i:126859 original size:16 final size:19
Alignment explanation
Indices: 126840--126875 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
126830 TAAGAAAGAG
126840 AACTT-CGA-AGA-AATTT
1 AACTTACGATAGAGAATTT
126856 AACTTACGATAGAGAATTT
1 AACTTACGATAGAGAATTT
126875 A
1 A
126876 GAAGAGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.29
17 3 0.18
18 3 0.18
19 6 0.35
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (19 bp):
AACTTACGATAGAGAATTT
Found at i:126960 original size:30 final size:29
Alignment explanation
Indices: 126822--126959 Score: 116
Period size: 30 Copynumber: 4.7 Consensus size: 29
126812 CTTCGAAAAT
* * * *
126822 ATTTGACTTAAGAAAGAGAACTTCGAAGAA
1 ATTTGACTTACGATAGAG-ACTTTGAAGGA
* *
126852 ATTTAACTTACGATAGAGAATTTAGAA-GA
1 ATTTGACTTACGATAGAGACTTT-GAAGGA
* *
126881 GATTTGACTTGCGATTGAGACTTTGAAGGA
1 -ATTTGACTTACGATAGAGACTTTGAAGGA
* * ** *
126911 ATTTAACTGATAAAAGAGAGCTTTGAAGGA
1 ATTTGACTTACGATAGAGA-CTTTGAAGGA
126941 ATTTGACTTACGATAGAGA
1 ATTTGACTTACGATAGAGA
126960 GTTGATATGG
Statistics
Matches: 82, Mismatches: 22, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
29 19 0.23
30 63 0.77
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (29 bp):
ATTTGACTTACGATAGAGACTTTGAAGGA
Found at i:130599 original size:28 final size:28
Alignment explanation
Indices: 130568--130651 Score: 125
Period size: 28 Copynumber: 3.0 Consensus size: 28
130558 TCCCGTGGAT
*
130568 TACACCTAAACACAGTCTCCCCATCTCA
1 TACACCCAAACACAGTCTCCCCATCTCA
*
130596 TACACCCAAACATAGTCTCCCCATCTCA
1 TACACCCAAACACAGTCTCCCCATCTCA
*
130624 TACACCCAAACACAGAC-CCCCAATCTCA
1 TACACCCAAACACAGTCTCCCC-ATCTCA
130652 AGTGAAAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 4 0.08
28 47 0.92
ACGTcount: A:0.35, C:0.44, G:0.04, T:0.18
Consensus pattern (28 bp):
TACACCCAAACACAGTCTCCCCATCTCA
Found at i:133267 original size:2 final size:2
Alignment explanation
Indices: 133260--133303 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
133250 TGTATTTCTA
133260 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
133302 CT
1 CT
133304 ATATATATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:133308 original size:2 final size:2
Alignment explanation
Indices: 133303--133336 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
133293 TCTCTCTCTC
*
133303 TA TA TA TA TA TA TA TA TA TA TA TG TCA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA T
133337 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.97
3 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:133447 original size:2 final size:2
Alignment explanation
Indices: 133440--133521 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
133430 NNNNNNNNNN
133440 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
133482 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
133522 ATGACATTCT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:138223 original size:14 final size:16
Alignment explanation
Indices: 138189--138224 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
138179 GCAACTATAC
*
138189 CACACCGGTCAGCAAA
1 CACACCAGTCAGCAAA
138205 CACACCAGTCAGCAAA
1 CACACCAGTCAGCAAA
138221 CACA
1 CACA
138225 AAGAGACTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.39, G:0.14, T:0.06
Consensus pattern (16 bp):
CACACCAGTCAGCAAA
Found at i:138811 original size:49 final size:49
Alignment explanation
Indices: 138754--138851 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
138744 TATCCAAGAA
138754 TTGTTGATTCAAAAACAGTTGAAAACATGT-CCTTTATTATCTAATTACG
1 TTGTTGATTCAAAAACAGTTGAAAACATGTCCCTTT-TTATCTAATTACG
* *
138803 TTGTTGATTCAAAGACAGTTGAAAACTTGTCCCTTTTTATCTAATTACG
1 TTGTTGATTCAAAAACAGTTGAAAACATGTCCCTTTTTATCTAATTACG
138852 AATACTGGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 41 0.89
50 5 0.11
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (49 bp):
TTGTTGATTCAAAAACAGTTGAAAACATGTCCCTTTTTATCTAATTACG
Found at i:143856 original size:16 final size:16
Alignment explanation
Indices: 143813--143857 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
143803 AAAGAAAGGA
*
143813 CTGTATATAAAACAGG
1 CTGTATATAAAACAAG
* *
143829 CTGTCTACAAAACAAG
1 CTGTATATAAAACAAG
*
143845 CTGTGTATAAAAC
1 CTGTATATAAAAC
143858 CACTGTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (16 bp):
CTGTATATAAAACAAG
Found at i:144261 original size:49 final size:49
Alignment explanation
Indices: 144207--145980 Score: 1791
Period size: 49 Copynumber: 35.7 Consensus size: 49
144197 CATCTTTATA
* ***
144207 GGTAAGTCTAG-TAATGTGTCATCAATACTAGCGGCGGATTATCTATACT
1 GGTAAGTCTGGCT-ATGTGTCATCAATACTAGCAATGGATTATCTATACT
144256 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
144305 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
* * *** *
144354 GGTAAGTCTGGCTATATGTCATCAATAATAGCGGCGGATTATCTTTACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
* *
144403 GGTAAGTCTGACTATGTGTCATCAATACTAGCAATGGATTATCTTTACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
*
144452 GGTCAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
* ** **** *
144501 GGTAAGTCTGGCTACGCCTCATCAATACTAGTGGCGGATTATCTTTACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
* *
144550 GGTAAGTCTGGCTTATGTGTCATCAATACTAGCAATTGATTATCTATACC
1 GGTAAGTCTGGC-TATGTGTCATCAATACTAGCAATGGATTATCTATACT
144600 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
144649 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
144698 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
* *** *
144747 GGTTAGTCTGGCTATGTGTCATCAATACTAGCGGCGGATTATCTTTACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
* ***
144796 GGTAAGTCTGGCTATGTGTCATCAATTCTAGCGGCGGATTATCTATACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
144845 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
* * * * * * * *
144894 TGTTAGTCTTGCTATGTGTTATCAGTACAAGCAATGGGTTATCTTTACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
* *
144943 GGTAAGTCTGGCTATGTTTCATCAATACTAGCAATGGATTATCTTTACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
144992 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
*** * *
145041 GGTAAGTCTGGCTATGTGTCATCAATACTAGCGGCGGAATATCTTTACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
* *
145090 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAACGGATTATCGATACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
*
145139 GGTAAGTCTGGCTATGTGTCATCAACACTAGCAATGGATTATCTATACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
**
145188 GGTAAGTCTGGCTATGTGTCATCAATACTAGCGGTGG-TATATCTTTATAGGTACAT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGAT-TATC----TA--TAC-T
* **
145244 -GTATGTCTGGCTATGTGTCATCAATACTAGCGGTGG-TATATCTTTATAGGTACAT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGAT-TATC----TA--TAC-T
* ** *
145299 -GTATGTCTGGCTATGTGTCATCAATACTAGCGGTGG-TATATCTTTA-T
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGAT-TATCTATACT
* **
145346 AAGTAAGTCTGGCTATGTGTCATCAATACTAGCGGTGG-TATATCTATACT
1 -GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGAT-TATCTATACT
145396 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
** *
145445 GGTAAGTCTGGCTATGTGTCATCAATACTAGCGGTGG-TATATCTTTA-T
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGAT-TATCTATACT
** ** *
145493 AGGTAAGTCAAGCCGTGTGTCATCAATACTAGCAGTGGCA-TATCTTTATAGGTACAT
1 -GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGG-ATTATC----TA--TAC-T
* * * ** *
145550 -GTATGTCTGGCCATGTGTCATTAATACTAGCGGTGG-TATATCTTTA-T
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGAT-TATCTATACT
* * * ** **
145597 AGATAAGTTTGGCCATGTGTCATCAATACTAGCGGTGG-TATATCTGA-AAA
1 -GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGAT-TATCT-ATACT
* *** * * *
145647 GGTAAATCTGGCTATGTGTCATCAATACTAGCGGCGTACTAACT-T-CAT
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATAC-T
* *** * * * *
145695 AAGTAAGTCTTAATATATGTCATCCATAGTAGCAGTGG-TATATCTATA-T
1 -GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGAT-TATCTATACT
* **
145744 AGCTAAGTCTGGCTATGTGTCATCAATACTAGCGGTGG-TATATCTATA-T
1 -GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGAT-TATCTATACT
* * ** * *
145793 AGCTAAGTCTGGCAATGTGTCATCAATACTAGCGGTGGTATAACTTTATAGGTACAT
1 -GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGG-AT---TATCTA--TAC-T
* * * ** *
145850 -GTATGTCTGGCCATGTGTCATTAATACTAGCGGTGG-TATATCTTTA-T
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGAT-TATCTATACT
* * * ** *
145897 AGCTAAGTCTGGCTATGCGTTATCAATACTAGCGGTGGTATATATCT-TAAGT
1 -GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGG-AT-TATCTAT-ACT
* * *
145949 GGTAAGTCTAGCCATGTGTCATCAATTCTAGC
1 GGTAAGTCTGGCTATGTGTCATCAATACTAGC
145981 GGTGGTTTAT
Statistics
Matches: 1501, Mismatches: 171, Indels: 104
0.85 0.10 0.06
Matches are distributed among these distances:
47 3 0.00
48 3 0.00
49 1230 0.82
50 44 0.03
51 40 0.03
52 1 0.00
53 8 0.01
55 169 0.11
56 1 0.00
57 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (49 bp):
GGTAAGTCTGGCTATGTGTCATCAATACTAGCAATGGATTATCTATACT
Found at i:146619 original size:2 final size:2
Alignment explanation
Indices: 146612--146654 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
146602 GTTTAGGTTC
*
146612 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT 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
146654 A
1 A
146655 GATCACTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:147981 original size:2 final size:2
Alignment explanation
Indices: 147974--148031 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
147964 TCAAAAGATA
147974 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
148016 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
148032 ATGCTTATAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:151922 original size:21 final size:20
Alignment explanation
Indices: 151898--152048 Score: 158
Period size: 21 Copynumber: 7.2 Consensus size: 20
151888 ATTTGCCACC
151898 ACTTGTCAGATAATTATGTCG
1 ACTTGTCAGAT-ATTATGTCG
*
151919 ACTTGTCAGATCTTGATGTCG
1 ACTTGTCAGATATT-ATGTCG
*
151940 ACTTGTCAGATCTTGATGTCG
1 ACTTGTCAGATATT-ATGTCG
*
151961 ACTTGTCAGATCTTGATGTCG
1 ACTTGTCAGATATT-ATGTCG
**
151982 ACTTGTCAGATAATTATGTTA
1 ACTTGTCAGAT-ATTATGTCG
* * *
152003 ACTTCTCATATGATAATGTCG
1 ACTTGTCAGAT-ATTATGTCG
*
152024 ACGTGTCAGATATTTATGTCG
1 ACTTGTCAGATA-TTATGTCG
152045 ACTT
1 ACTT
152049 ATATGGTATT
Statistics
Matches: 112, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
20 3 0.03
21 107 0.96
22 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.39
Consensus pattern (20 bp):
ACTTGTCAGATATTATGTCG
Found at i:151959 original size:42 final size:42
Alignment explanation
Indices: 151898--152048 Score: 196
Period size: 42 Copynumber: 3.6 Consensus size: 42
151888 ATTTGCCACC
151898 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTGATGTCG
1 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTGATGTCG
*
151940 ACTTGTCAGAT-CTTGATGTCGACTTGTCAGATCTTGATGTCG
1 ACTTGTCAGATAATT-ATGTCGACTTGTCAGATCTTGATGTCG
** * * ** *
151982 ACTTGTCAGATAATTATGTTAACTTCTCATATGATAATGTCG
1 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTGATGTCG
* *
152024 ACGTGTCAGATATTTATGTCGACTT
1 ACTTGTCAGATAATTATGTCGACTT
152049 ATATGGTATT
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
41 2 0.02
42 90 0.96
43 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.39
Consensus pattern (42 bp):
ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTGATGTCG
Found at i:152167 original size:21 final size:21
Alignment explanation
Indices: 152142--152235 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 21
152132 ATGGTTATTT
*
152142 TCTGACAAGTCAACATAAAGA
1 TCTGACAAGTCAACATAAATA
**
152163 TCTGACAAGTTGACATAAATA
1 TCTGACAAGTCAACATAAATA
* * *
152184 TCTGACACGTCGACAT-TATCA
1 TCTGACAAGTCAACATAAAT-A
* * * *
152205 TATGAGAAGTTAACATAATTA
1 TCTGACAAGTCAACATAAATA
152226 TCTGACAAGT
1 TCTGACAAGT
152236 GGTGGCAGAT
Statistics
Matches: 56, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
20 2 0.04
21 53 0.95
22 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (21 bp):
TCTGACAAGTCAACATAAATA
Found at i:152189 original size:42 final size:42
Alignment explanation
Indices: 152142--152235 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
152132 ATGGTTATTT
* * *
152142 TCTGACAAGTCAACATAAAGATCTGACAAGTTGACATAAATA
1 TCTGACAAGTCAACATAAACATATGACAAGTTAACATAAATA
* * * * * *
152184 TCTGACACGTCGACATTATCATATGAGAAGTTAACATAATTA
1 TCTGACAAGTCAACATAAACATATGACAAGTTAACATAAATA
152226 TCTGACAAGT
1 TCTGACAAGT
152236 GGTGGCAGAT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (42 bp):
TCTGACAAGTCAACATAAACATATGACAAGTTAACATAAATA
Found at i:157319 original size:17 final size:15
Alignment explanation
Indices: 157297--157341 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
157287 ATTTATTTCT
157297 ATTTCAAAATAAGCAGA
1 ATTTCAAAATAAGC--A
*
157314 ATTTCAAAACAAGCA
1 ATTTCAAAATAAGCA
*
157329 ATTTCAATATAAG
1 ATTTCAAAATAAG
157342 TGGAGTAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.48
17 13 0.52
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.27
Consensus pattern (15 bp):
ATTTCAAAATAAGCA
Found at i:160926 original size:33 final size:33
Alignment explanation
Indices: 160882--160947 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
160872 TTCCTGCTTA
* *
160882 CAATGGTCTTATTATTATTTACGGTCTCCATGG
1 CAATGGCCTTATTATTATTTACAGTCTCCATGG
160915 CAATGGCCTTATTATTATTTACAGTCTCCATGG
1 CAATGGCCTTATTATTATTTACAGTCTCCATGG
160948 GGATGTGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.41
Consensus pattern (33 bp):
CAATGGCCTTATTATTATTTACAGTCTCCATGG
Found at i:161818 original size:21 final size:20
Alignment explanation
Indices: 161794--161840 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
161784 TAGCACTAGG
*
161794 CTGATCTTTGCTTTGCTGG-GA
1 CTGATCTTTG--TTGCTGGCAA
*
161815 CTGACCTTTGTTGCTGGCAA
1 CTGATCTTTGTTGCTGGCAA
161835 CTGATC
1 CTGATC
161841 CGGCAGTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 7 0.32
20 6 0.27
21 9 0.41
ACGTcount: A:0.13, C:0.23, G:0.26, T:0.38
Consensus pattern (20 bp):
CTGATCTTTGTTGCTGGCAA
Found at i:171131 original size:2 final size:2
Alignment explanation
Indices: 171124--171163 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
171114 GACTTAATTT
171124 AG AG AG AG AG AG AG 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 AG AG AG AG AG AG AG
171164 TCTGAAGCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:175418 original size:14 final size:14
Alignment explanation
Indices: 175399--175431 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
175389 TTTCATTTAA
175399 TTGATAGCAAGCAT
1 TTGATAGCAAGCAT
175413 TTGATAGCAAGCAT
1 TTGATAGCAAGCAT
175427 TTGAT
1 TTGAT
175432 TATTGTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (14 bp):
TTGATAGCAAGCAT
Found at i:179432 original size:57 final size:57
Alignment explanation
Indices: 179369--179487 Score: 150
Period size: 57 Copynumber: 2.1 Consensus size: 57
179359 TAATTAACAT
* *
179369 AGCTTATTCAGACACTTGTATGTTAAGTTATCAATGTATAA-AAAGAGTTGTTAGCAC
1 AGCTTATTCAGACACTTATATATTAAGTTATCAATGTATAAGAAA-AGTTGTTAGCAC
* * * * * *
179426 AGCTTATTCATACATTTATATATTAAGTTATCAGTGTGTAAGGAAAGTTGTTAGCCC
1 AGCTTATTCAGACACTTATATATTAAGTTATCAATGTATAAGAAAAGTTGTTAGCAC
179483 AGCTT
1 AGCTT
179488 GGTTAGAAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 51 0.96
58 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.37
Consensus pattern (57 bp):
AGCTTATTCAGACACTTATATATTAAGTTATCAATGTATAAGAAAAGTTGTTAGCAC
Found at i:182390 original size:17 final size:17
Alignment explanation
Indices: 182355--182391 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
182345 AATATAGAAG
182355 AAAAATTAAGATTTAAA
1 AAAAATTAAGATTTAAA
182372 AAAACATTAAGATTTAAA
1 AAAA-ATTAAGATTTAAA
182390 AA
1 AA
182392 GCATACATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (17 bp):
AAAAATTAAGATTTAAA
Found at i:184321 original size:26 final size:26
Alignment explanation
Indices: 184287--184369 Score: 130
Period size: 26 Copynumber: 3.2 Consensus size: 26
184277 ACTAACTGCT
* *
184287 CTATTTTTACCGTGTGCATATAAATG
1 CTATCTTTACCGTATGCATATAAATG
184313 CTATCTTTACCGTATGCATATAAATG
1 CTATCTTTACCGTATGCATATAAATG
* *
184339 CTATCTTTACCGAATGCATGTAAATG
1 CTATCTTTACCGTATGCATATAAATG
184365 CTATC
1 CTATC
184370 AATGCTATCT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (26 bp):
CTATCTTTACCGTATGCATATAAATG
Found at i:184381 original size:35 final size:35
Alignment explanation
Indices: 184335--184404 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
184325 TATGCATATA
*
184335 AATGCTATCTTTACCGAATGCATGTAAATGCTATC
1 AATGCTATCTTTACCGAATGCATATAAATGCTATC
* *
184370 AATGCTATCTTTACTGTATGCATATAAATGCTATC
1 AATGCTATCTTTACCGAATGCATATAAATGCTATC
184405 TTTACTGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (35 bp):
AATGCTATCTTTACCGAATGCATATAAATGCTATC
Found at i:184427 original size:26 final size:26
Alignment explanation
Indices: 184370--184421 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
184360 AAATGCTATC
184370 AATGCTATCTTTACTGTATGCATATA
1 AATGCTATCTTTACTGTATGCATATA
184396 AATGCTATCTTTACTGTATGCATATA
1 AATGCTATCTTTACTGTATGCATATA
184422 TGTGCTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (26 bp):
AATGCTATCTTTACTGTATGCATATA
Found at i:184829 original size:47 final size:48
Alignment explanation
Indices: 184753--184848 Score: 124
Period size: 47 Copynumber: 2.0 Consensus size: 48
184743 CTTGTTTACA
* * *
184753 ACATATAAATAATGTTGTCGAATATTTGTTTACAGTTGGGAGTTATTT
1 ACATATAAATAATGTTGTCGAATAATTGTTCACAGTTGCGAGTTATTT
* *
184801 ACATAT-AATAATGTTGTTG-ATAAATTGTTCATAGTTGCGAGTTATTT
1 ACATATAAATAATGTTGTCGAAT-AATTGTTCACAGTTGCGAGTTATTT
184848 A
1 A
184849 AACATATGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
46 2 0.05
47 34 0.81
48 6 0.14
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (48 bp):
ACATATAAATAATGTTGTCGAATAATTGTTCACAGTTGCGAGTTATTT
Found at i:189370 original size:2 final size:2
Alignment explanation
Indices: 189363--189387 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
189353 NNNNNNNNNN
189363 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
189388 CTTCTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:192284 original size:23 final size:23
Alignment explanation
Indices: 192258--192305 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
192248 TAACCAAAGG
192258 TATTTGGCATGGTTATATACAAA
1 TATTTGGCATGGTTATATACAAA
192281 TATTTGGCATGGTTATATACAAA
1 TATTTGGCATGGTTATATACAAA
192304 TA
1 TA
192306 ACTATACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (23 bp):
TATTTGGCATGGTTATATACAAA
Found at i:194999 original size:11 final size:11
Alignment explanation
Indices: 194983--195009 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
194973 ATCTGTGCGT
194983 GATGTTAACGA
1 GATGTTAACGA
194994 GATGTTAACGA
1 GATGTTAACGA
195005 GATGT
1 GATGT
195010 GGAAATTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (11 bp):
GATGTTAACGA
Found at i:203961 original size:17 final size:18
Alignment explanation
Indices: 203927--203964 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
203917 ATGAGCATTT
* *
203927 TTGTACGTGCTTTTTACA
1 TTGTACGTGCTATATACA
203945 TTGTA-GTGCTATATACA
1 TTGTACGTGCTATATACA
203962 TTG
1 TTG
203965 ACCATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.47
Consensus pattern (18 bp):
TTGTACGTGCTATATACA
Found at i:213613 original size:2 final size:2
Alignment explanation
Indices: 213608--213652 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
213598 GTGTGTGTTT
213608 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
213650 GA G
1 GA G
213653 TACTTCTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:228816 original size:20 final size:20
Alignment explanation
Indices: 228791--228831 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
228781 AAATGGGTAC
*
228791 GTGAGAGAGAGATAGAGAGA
1 GTGAGAGAGAGAAAGAGAGA
228811 GTGAGAGAGAGAAAGAGAGA
1 GTGAGAGAGAGAAAGAGAGA
228831 G
1 G
228832 AGGGGGGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.46, T:0.07
Consensus pattern (20 bp):
GTGAGAGAGAGAAAGAGAGA
Found at i:228843 original size:2 final size:2
Alignment explanation
Indices: 228793--228833 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
228783 ATGGGTACGT
* * *
228793 GA GA GA GA GA TA GA GA GA GT GA GA GA GA GA AA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
228834 GGGGGAGAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.46, T:0.05
Consensus pattern (2 bp):
GA
Found at i:230778 original size:2 final size:2
Alignment explanation
Indices: 230771--230810 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
230761 GTGCGTGTTG
*
230771 GA GA GA GA GA GC GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
230811 TTACTTCTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:234302 original size:21 final size:21
Alignment explanation
Indices: 234250--234308 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
234240 TACCTATTAC
** *
234250 TTAATACTTGCTTGTTAATTG
1 TTAATACTTATTTTTTAATTG
**
234271 TTAATTTTTATTTTTTAATTG
1 TTAATACTTATTTTTTAATTG
*
234292 TTAATACTTATTATTTA
1 TTAATACTTATTTTTTA
234309 CTGGTTATTT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (21 bp):
TTAATACTTATTTTTTAATTG
Found at i:235915 original size:39 final size:41
Alignment explanation
Indices: 235835--235915 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
235825 CAAAACTAAG
235835 TCATAACAATTAAGAAGGAAGTCAATATGTCCTCCCAGGGC
1 TCATAACAATTAAGAAGGAAGTCAATATGTCCTCCCAGGGC
* *
235876 TCATAACAATTAAGGAGTAAGTC-A-ATGTCCTCCCAGGGC
1 TCATAACAATTAAGAAGGAAGTCAATATGTCCTCCCAGGGC
235915 T
1 T
235916 TCCGTACATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 16 0.42
40 1 0.03
41 21 0.55
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (41 bp):
TCATAACAATTAAGAAGGAAGTCAATATGTCCTCCCAGGGC
Found at i:241799 original size:2 final size:2
Alignment explanation
Indices: 241792--241843 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
241782 CACATTAAAT
241792 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
241834 TC TC TC TC TC
1 TC TC TC TC TC
241844 ATGTCAATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:243657 original size:12 final size:12
Alignment explanation
Indices: 243640--243665 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
243630 TCCGCTTGAA
243640 TCGCCATTTGGG
1 TCGCCATTTGGG
243652 TCGCCATTTGGG
1 TCGCCATTTGGG
243664 TC
1 TC
243666 TGAATTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.27, G:0.31, T:0.35
Consensus pattern (12 bp):
TCGCCATTTGGG
Found at i:243782 original size:10 final size:10
Alignment explanation
Indices: 243767--243806 Score: 71
Period size: 10 Copynumber: 4.0 Consensus size: 10
243757 ACTTTAATCG
243767 CCATTTGGGT
1 CCATTTGGGT
243777 CCATTTGGGT
1 CCATTTGGGT
*
243787 TCATTTGGGT
1 CCATTTGGGT
243797 CCATTTGGGT
1 CCATTTGGGT
243807 AAATCGACGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.10, C:0.17, G:0.30, T:0.42
Consensus pattern (10 bp):
CCATTTGGGT
Found at i:248809 original size:21 final size:20
Alignment explanation
Indices: 248783--248851 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 20
248773 TAAAAATTGT
248783 AAATTTCCAGATATATGTGTA
1 AAATTTCCAGAT-TATGTGTA
248804 AAATTTCCAGATTTATGTGTA
1 AAATTTCCAGA-TTATGTGTA
* *
248825 AGATTTACAGATTATTGTGTA
1 AAATTTCCAGATTA-TGTGTA
*
248846 GAATTT
1 AAATTT
248852 ACATAATAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.07
21 38 0.90
22 1 0.02
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (20 bp):
AAATTTCCAGATTATGTGTA
Found at i:250618 original size:11 final size:11
Alignment explanation
Indices: 250601--250634 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
250591 CTACTACACC
250601 ACACGCTCGCT
1 ACACGCTCGCT
*
250612 GCACGCTCGCT
1 ACACGCTCGCT
250623 ACACGCTCGCT
1 ACACGCTCGCT
250634 A
1 A
250635 AACGGTTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.18, C:0.44, G:0.21, T:0.18
Consensus pattern (11 bp):
ACACGCTCGCT
Found at i:250659 original size:21 final size:21
Alignment explanation
Indices: 250630--250736 Score: 142
Period size: 21 Copynumber: 5.1 Consensus size: 21
250620 GCTACACGCT
* *
250630 CGCTAAACGGTTCACACGAAA
1 CGCTGAACGGTTTACACGAAA
250651 CGCTGAACGGTTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
* * * *
250672 CGCTGCACGCTTTGCCCGAAA
1 CGCTGAACGGTTTACACGAAA
* *
250693 CGCTAAACGATTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
250714 CGCTGAACGGTTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
250735 CG
1 CG
250737 ATTCTCGCAC
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (21 bp):
CGCTGAACGGTTTACACGAAA
Found at i:251341 original size:123 final size:123
Alignment explanation
Indices: 251137--251382 Score: 456
Period size: 123 Copynumber: 2.0 Consensus size: 123
251127 AACTGAAATC
*
251137 GGTTTTTCAGTATTTGGCGGGATTTGTTTTTTCTTCTCACATTAATATTTTTATTGGTTTCAGAG
1 GGTTTTTCAGTATTCGGCGGGATTTGTTTTTTCTTCTCACATTAATATTTTTATTGGTTTCAGAG
251202 AATACGATGTAAAAATACTAACTATAAATAAACCTGTAATTATTTACATTGATAATTT
66 AATACGATGTAAAAATACTAACTATAAATAAACCTGTAATTATTTACATTGATAATTT
*
251260 GGTTTTTCAGTATTCGGCGGGATTTGTTTTTTGTTCTCACATTAATATTTTTATTGGTTTCAGAG
1 GGTTTTTCAGTATTCGGCGGGATTTGTTTTTTCTTCTCACATTAATATTTTTATTGGTTTCAGAG
* *
251325 AATACGATGTGAAAATACTAACTGTAAATAAACCTGTAATTATTTACATTGATAATTT
66 AATACGATGTAAAAATACTAACTATAAATAAACCTGTAATTATTTACATTGATAATTT
251383 TGAAAGTTAT
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 119 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (123 bp):
GGTTTTTCAGTATTCGGCGGGATTTGTTTTTTCTTCTCACATTAATATTTTTATTGGTTTCAGAG
AATACGATGTAAAAATACTAACTATAAATAAACCTGTAATTATTTACATTGATAATTT
Found at i:252365 original size:23 final size:21
Alignment explanation
Indices: 252335--252480 Score: 94
Period size: 21 Copynumber: 6.9 Consensus size: 21
252325 ACGGTTCTCG
*
252335 CACGCTTTGCCCGAAACGATTTA
1 CACGCTTTGCCCGAAACG--CTA
*
252358 CACGCTTTGCCCGAAACGCTG
1 CACGCTTTGCCCGAAACGCTA
*
252379 CACGCTTTGCCCGAAACGCGA
1 CACGCTTTGCCCGAAACGCTA
* * * * *
252400 AACGGTTTACACGAAACGCTT
1 CACGCTTTGCCCGAAACGCTA
* ** *
252421 CACGATTCACACGAAACGCTA
1 CACGCTTTGCCCGAAACGCTA
* * * *
252442 AACGGTTTACACGAAACGCTA
1 CACGCTTTGCCCGAAACGCTA
* * * *
252463 AACGGTTTACACGAAACG
1 CACGCTTTGCCCGAAACG
252481 TTTGTCGCAC
Statistics
Matches: 106, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
21 88 0.83
23 18 0.17
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (21 bp):
CACGCTTTGCCCGAAACGCTA
Found at i:252414 original size:21 final size:21
Alignment explanation
Indices: 252390--252480 Score: 137
Period size: 21 Copynumber: 4.3 Consensus size: 21
252380 ACGCTTTGCC
*
252390 CGAAACGCGAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
** * *
252411 CGAAACGCTTCACGATTCACA
1 CGAAACGCTAAACGGTTTACA
252432 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
252453 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
252474 CGAAACG
1 CGAAACG
252481 TTTGTCGCAC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.16
Consensus pattern (21 bp):
CGAAACGCTAAACGGTTTACA
Found at i:252674 original size:2 final size:2
Alignment explanation
Indices: 252667--252713 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
252657 TCGGTAAAAG
252667 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
252709 TC TC T
1 TC TC T
252714 TTCGTTTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:253153 original size:2 final size:2
Alignment explanation
Indices: 253146--253187 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
253136 AATACTCATA
253146 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
253188 GTTAATTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:256045 original size:21 final size:19
Alignment explanation
Indices: 256009--256051 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
255999 TATTCATGTT
256009 TATATATACATGTATATGA
1 TATATATACATGTATATGA
*
256028 TATATATCATATGATATATGA
1 TATATAT-ACATG-TATATGA
256049 TAT
1 TAT
256052 TGGTTGCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 4 0.19
21 10 0.48
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (19 bp):
TATATATACATGTATATGA
Found at i:258541 original size:2 final size:2
Alignment explanation
Indices: 258536--258575 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
258526 TTTCAAACCT
258536 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
258576 AATGATTACG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:259353 original size:10 final size:10
Alignment explanation
Indices: 259340--259364 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
259330 ATGGGTCCTT
259340 TATACAAGAA
1 TATACAAGAA
259350 TATACAAGAA
1 TATACAAGAA
259360 TATAC
1 TATAC
259365 CGGTATATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (10 bp):
TATACAAGAA
Found at i:259608 original size:134 final size:133
Alignment explanation
Indices: 259389--259795 Score: 519
Period size: 134 Copynumber: 3.0 Consensus size: 133
259379 GGGGTATAGA
* **
259389 TCTTAACCATTTTCAAGATATTTGGGCACTTCCTGTTTGAGGGGGGTCAGGACCACCCTCAAAGC
1 TCTTAACCATTTTCAAGATATTTGGGCACTTCCTGTTTGAGAGGGGTCAGGACCACCCT-AGGGC
* * *
259454 CGATGACCTACATACCATTTGATGCCCTTGACACCAGGAACAAGAATATATATAGCTTAGGGGTA
65 CCATGACCTACATACCATTTGATGCCCTTGACACCAGAAACAAGAATATATATAGTTTAGGGGTA
259519 GGAT
130 GGAT
** * *
259523 TCTTAACTGTTTTCAAGATATTCGGGCACTTTCTGTTTGAGAGGGGTCAGGACCACCCCTAGGGC
1 TCTTAACCATTTTCAAGATATTTGGGCACTTCCTGTTTGAGAGGGGTCAGGACCA-CCCTAGGGC
* * * *
259588 CCATGACCTACATACCATTTGATGCTCCTTGACACAAGTAACAAGAATATATATGGTTTAGGAGT
65 CCATGACCTACATACCATTTGATGC-CCTTGACACCAGAAACAAGAATATATATAGTTTAGGGGT
* *
259653 GGGAA
129 AGGAT
* * * * * * *
259658 TCTTAACCATTTTCAAGTTATTTGTGCACTACCGGTTTGAGAGGGGTCAGAACCAACCTGGGGCC
1 TCTTAACCATTTTCAAGATATTTGGGCACTTCCTGTTTGAGAGGGGTCAGGACCACCCTAGGGCC
* **
259723 CATGACCTACATACCATTTGATGCCCCTTAACA-CATGAAACAAGAATATATACCGTTTAGGGGT
66 CATGACCTACATACCATTTGATG-CCCTTGACACCA-GAAACAAGAATATATATAGTTTAGGGGT
259787 CAGGAT
129 -AGGAT
259793 TCT
1 TCT
259796 AAGAGTTTCT
Statistics
Matches: 234, Mismatches: 34, Indels: 9
0.84 0.12 0.03
Matches are distributed among these distances:
133 1 0.00
134 139 0.59
135 94 0.40
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (133 bp):
TCTTAACCATTTTCAAGATATTTGGGCACTTCCTGTTTGAGAGGGGTCAGGACCACCCTAGGGCC
CATGACCTACATACCATTTGATGCCCTTGACACCAGAAACAAGAATATATATAGTTTAGGGGTAG
GAT
Found at i:265705 original size:2 final size:2
Alignment explanation
Indices: 265700--265753 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
265690 TTTCAAACCT
265700 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
265742 GA GA GA GA GA GA
1 GA GA GA GA GA GA
265754 TGATTACTTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:269232 original size:2 final size:2
Alignment explanation
Indices: 269225--269265 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
269215 CCACTATCCC
269225 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GNA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G-A GA GA
269266 CCGGTACCTG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:287879 original size:18 final size:18
Alignment explanation
Indices: 287856--287891 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
287846 ATTTTCACTT
287856 AAACTTCATGAGAATTTC
1 AAACTTCATGAGAATTTC
*
287874 AAACTTCATGAGTATTTC
1 AAACTTCATGAGAATTTC
287892 CTGTGAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (18 bp):
AAACTTCATGAGAATTTC
Found at i:290101 original size:65 final size:66
Alignment explanation
Indices: 289980--290108 Score: 215
Period size: 65 Copynumber: 2.0 Consensus size: 66
289970 CCATTTTCCC
* *
289980 CCTGGCTGATTAATTTCTGAGCAGAAGATTTTTTAAAGATTTACTCTATATATTCCTATGTAAAT
1 CCTGGCTGATTAATTTCTGAGAAGAAGATTCTTTAAAGATTTACTCTATATATTCCTATGTAAAT
290045 T
66 T
**
290046 CCTGGCTGATTTGTTTCTGAGAAGAAGA-TCTTTAAAGATTTACTCTATATATTCCTATGTAAA
1 CCTGGCTGATTAATTTCTGAGAAGAAGATTCTTTAAAGATTTACTCTATATATTCCTATGTAAA
290109 ACTTCGACCC
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
65 34 0.58
66 25 0.42
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (66 bp):
CCTGGCTGATTAATTTCTGAGAAGAAGATTCTTTAAAGATTTACTCTATATATTCCTATGTAAAT
T
Found at i:290369 original size:166 final size:167
Alignment explanation
Indices: 290044--290439 Score: 677
Period size: 166 Copynumber: 2.4 Consensus size: 167
290034 CCTATGTAAA
*
290044 TTCCTGGCTGATTTGTTTCTGAGAAGAAGATCTTTAAAGATTTACTCTATATATTCCTATGTAAA
1 TTCCTGGCTGATTAGTTTCTGAGAAGAAGATCTTTAAAGATTTACTCTATATATTCCTATGTAAA
* *
290109 ACTTCGACCCCCCCCATTGTGGCCCCACTCTACCCTCGGAGGTCATGATTTTCACAACTTTGAAT
66 ACTTCGA-CCCCCCCATTGTGGCCCCACCCTACCCCCGGAGGTCATGATTTTCACAACTTTGAAT
*
290174 CTACACTACCTGAGGATGCTTCCACACAAGTTTCAGTT
130 CTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCT
* *
290212 TTCCTGGCTGATTAATTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAA
1 TTCCTGGCTGATTAGTTTCTGAGAAGAAGATCTTTAAAGATTTACTCTATATATTCCTATGTAAA
* *
290277 ACTTTGA-CCCCCCATTGTGGCCCCACCCTACCCCCGTAGGTCATGATTTTCACAACTTTGAATC
66 ACTTCGACCCCCCCATTGTGGCCCCACCCTACCCCCGGAGGTCATGATTTTCACAACTTTGAATC
*
290341 TACACTACCTGAGGATGCTTTCACACAAGTTTCAGCT
131 TACACTACCTGAGGATGCTTCCACACAAGTTTCAGCT
* *
290378 TTCCTGGCTGGTTAGTTTTTGAGAAGAAGATCTTTAAAGATTTACTCTATATATTCCTATGT
1 TTCCTGGCTGATTAGTTTCTGAGAAGAAGATCTTTAAAGATTTACTCTATATATTCCTATGT
290440 GAATTCCTGG
Statistics
Matches: 215, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
166 147 0.68
168 68 0.32
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (167 bp):
TTCCTGGCTGATTAGTTTCTGAGAAGAAGATCTTTAAAGATTTACTCTATATATTCCTATGTAAA
ACTTCGACCCCCCCATTGTGGCCCCACCCTACCCCCGGAGGTCATGATTTTCACAACTTTGAATC
TACACTACCTGAGGATGCTTCCACACAAGTTTCAGCT
Found at i:290633 original size:227 final size:230
Alignment explanation
Indices: 290212--290666 Score: 754
Period size: 227 Copynumber: 2.0 Consensus size: 230
290202 AGTTTCAGTT
290212 TTCCTGGCTGATTAATTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAA
1 TTCCTGGCTGATTAATTTCT-AGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAA
* *
290277 ACTTTGACCCCCCATTGTGGCCCCACCCTACCCCCGTAGGTCATGATTTTCACAACTTTGAATCT
65 ACTTCGACCCCCCATTGTGGCCCCACCCTACCCCCGGAGGTCATGATTTTCACAACTTTGAATCT
* * *** *
290342 ACACTACCTGAGGATGCTTTCACACAAGTTTCAGCTTTCCTGGCTGGTTAGTTTTTGAGAAGAAG
130 ACACTACCTGAGAATGCTTCCACACAAGTTTCAGCTTTCCTGGCCAATTAGTTTCTGAGAAGAAG
290407 ATCTTTAAAGATTTACTCTATATATTCCTATGTGAA
195 ATCTTTAAAGATTTACTCTATATATTCCTATGTGAA
** *
290443 TTCCTGGCTGATTCGTTTCT-G-AGAAGATTTTTAAAGATTTACTCTATATATTTCTATGTAAAA
1 TTCCTGGCTGATTAATTTCTAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAA
*
290506 CTTCGACCCCCCATTGTGGCCCCACCCTA-CCCCGGGGGTCATGATTTTCACAACTTTGAATCTA
66 CTTCGACCCCCCATTGTGGCCCCACCCTACCCCCGGAGGTCATGATTTTCACAACTTTGAATCTA
*
290570 CACTACCTGAGAATGCTTCCACACAAGTTTCAGCTTTCCTGGCCAATTAGTTTCTGGGAAGAAGA
131 CACTACCTGAGAATGCTTCCACACAAGTTTCAGCTTTCCTGGCCAATTAGTTTCTGAGAAGAAGA
*
290635 TTTTTAAAGATTTACTCTATATATTCCTATGT
196 TCTTTAAAGATTTACTCTATATATTCCTATGT
290667 AAAACTTCGA
Statistics
Matches: 210, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
227 122 0.58
228 69 0.33
229 1 0.00
231 18 0.09
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (230 bp):
TTCCTGGCTGATTAATTTCTAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAA
CTTCGACCCCCCATTGTGGCCCCACCCTACCCCCGGAGGTCATGATTTTCACAACTTTGAATCTA
CACTACCTGAGAATGCTTCCACACAAGTTTCAGCTTTCCTGGCCAATTAGTTTCTGAGAAGAAGA
TCTTTAAAGATTTACTCTATATATTCCTATGTGAA
Found at i:293274 original size:18 final size:18
Alignment explanation
Indices: 293251--293286 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
293241 ATTTTCACTT
293251 AAACTTCATGAGAATTTC
1 AAACTTCATGAGAATTTC
*
293269 AAACTTCATGAGTATTTC
1 AAACTTCATGAGAATTTC
293287 CTGTGAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (18 bp):
AAACTTCATGAGAATTTC
Found at i:294305 original size:20 final size:21
Alignment explanation
Indices: 294282--294328 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
294272 GACTCATAAA
* *
294282 ACAAGTTCA-AGACTTGTATG
1 ACAAGTTCAGAGACTTGAAGG
294302 ACAAG-TCAGAGACTTGAAGG
1 ACAAGTTCAGAGACTTGAAGG
294322 ACAAGTT
1 ACAAGTT
294329 TTTTGTGCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 3 0.13
20 19 0.83
21 1 0.04
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (21 bp):
ACAAGTTCAGAGACTTGAAGG
Found at i:297591 original size:25 final size:25
Alignment explanation
Indices: 297563--297614 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
297553 TGCAAAACAT
297563 TAATTGATGCATCATCAAATTATAA
1 TAATTGATGCATCATCAAATTATAA
297588 TAATTGATGCATCATCAAATTATAA
1 TAATTGATGCATCATCAAATTATAA
297613 TA
1 TA
297615 TTCCATGACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.37
Consensus pattern (25 bp):
TAATTGATGCATCATCAAATTATAA
Found at i:301928 original size:66 final size:66
Alignment explanation
Indices: 301852--302048 Score: 268
Period size: 74 Copynumber: 2.9 Consensus size: 66
301842 AATACATGTT
*
301852 TGTTTTGATACACATGGACTTACACTGAATGCTGATGCGCAGTCCATCACTTGTTGATGTATTGT
1 TGTTTTGATACACATGGACTTACATTGAATGCTGATGCGCAGTCCATCACTTGTTGATGTATTGT
301917 A
66 A
*
301918 TGTTTTGATACACATGGACTTACATTGAATGCTGATGCACAGTCCATCACTTGCTGACTTGTTGA
1 TGTTTTGATACACATGGACTTACATTGAATGCTGATGCGCAGT-C--CA--T-C--ACTTGTTGA
301983 TGTATTGTA
58 TGTATTGTA
* * * *
301992 TGTTTTGATACACATGAACTTACATTGAATGCTAATACGCAGTCCGTCACTTGTTGA
1 TGTTTTGATACACATGGACTTACATTGAATGCTGATGCGCAGTCCATCACTTGTTGA
302049 CTTGTTGATG
Statistics
Matches: 116, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
66 50 0.43
67 1 0.01
68 1 0.01
69 3 0.03
71 2 0.02
72 1 0.01
73 1 0.01
74 57 0.49
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (66 bp):
TGTTTTGATACACATGGACTTACATTGAATGCTGATGCGCAGTCCATCACTTGTTGATGTATTGT
A
Found at i:301988 original size:74 final size:74
Alignment explanation
Indices: 301900--302062 Score: 272
Period size: 74 Copynumber: 2.2 Consensus size: 74
301890 GCAGTCCATC
* * *
301900 ACTTGTTGATGTATTGTATGTTTTGATACACATGGACTTACATTGAATGCTGATGCACAGTCCAT
1 ACTTGTTGATGTATTGTATGTTTTGATACACATGAACTTACATTGAATGCTAATACACAGTCCAT
301965 CACTTGCTG
66 CACTTGCTG
* *
301974 ACTTGTTGATGTATTGTATGTTTTGATACACATGAACTTACATTGAATGCTAATACGCAGTCCGT
1 ACTTGTTGATGTATTGTATGTTTTGATACACATGAACTTACATTGAATGCTAATACACAGTCCAT
*
302039 CACTTGTTG
66 CACTTGCTG
302048 ACTTGTTGATGTATT
1 ACTTGTTGATGTATT
302063 CATTCTTCGC
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 83 1.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.40
Consensus pattern (74 bp):
ACTTGTTGATGTATTGTATGTTTTGATACACATGAACTTACATTGAATGCTAATACACAGTCCAT
CACTTGCTG
Found at i:304600 original size:27 final size:27
Alignment explanation
Indices: 304562--304656 Score: 136
Period size: 27 Copynumber: 3.5 Consensus size: 27
304552 GAGGGTCTGT
* * * *
304562 AAAATAGTAACATAGTCTTAATACAAC
1 AAAATAATAACATAGTCTCAATGCAAG
* *
304589 AAAATAGTAACATACTCTCAATGCAAG
1 AAAATAATAACATAGTCTCAATGCAAG
304616 AAAATAATAACATAGTCTCAATGCAAG
1 AAAATAATAACATAGTCTCAATGCAAG
304643 AAAATAATAACATA
1 AAAATAATAACATA
304657 CAGTAAATCA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (27 bp):
AAAATAATAACATAGTCTCAATGCAAG
Found at i:305212 original size:34 final size:34
Alignment explanation
Indices: 305048--305217 Score: 250
Period size: 34 Copynumber: 5.0 Consensus size: 34
305038 TTTAACTGTG
* * * *
305048 TTTTCTCAGATCTCAGTAAAACAAAACACTGACA
1 TTTTATCAGATCTCAGTAAAACAAAATAGTAACA
* *
305082 TTTTATCAGATCTCAGTAAAACAAAACAGTTACA
1 TTTTATCAGATCTCAGTAAAACAAAATAGTAACA
*
305116 TTTTATCAGATCTCAGTAAAACAAAATAGTTACA
1 TTTTATCAGATCTCAGTAAAACAAAATAGTAACA
* *
305150 TTTCATCAGATCTCAGTAAAACAGAATAGTAACA
1 TTTTATCAGATCTCAGTAAAACAAAATAGTAACA
*
305184 TTTTGTCAGATCTCAGTAAAACAAAATAGTAACA
1 TTTTATCAGATCTCAGTAAAACAAAATAGTAACA
305218 AAGTCTCAGA
Statistics
Matches: 126, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 126 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.29
Consensus pattern (34 bp):
TTTTATCAGATCTCAGTAAAACAAAATAGTAACA
Found at i:307643 original size:27 final size:27
Alignment explanation
Indices: 307605--307699 Score: 136
Period size: 27 Copynumber: 3.5 Consensus size: 27
307595 GAGGGTCTGT
* * * *
307605 AAAATAGTAACATAGTCTTAATACAAC
1 AAAATAATAACATAGTCTCAATGCAAG
* *
307632 AAAATAGTAACATACTCTCAATGCAAG
1 AAAATAATAACATAGTCTCAATGCAAG
307659 AAAATAATAACATAGTCTCAATGCAAG
1 AAAATAATAACATAGTCTCAATGCAAG
307686 AAAATAATAACATA
1 AAAATAATAACATA
307700 CAGTAAATCA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (27 bp):
AAAATAATAACATAGTCTCAATGCAAG
Found at i:308341 original size:34 final size:34
Alignment explanation
Indices: 308091--308328 Score: 368
Period size: 34 Copynumber: 7.0 Consensus size: 34
308081 TTTAACTGTG
* * * *
308091 TTTTCTCAGATCTCAGTAAAACAAAACACTGACA
1 TTTTATCAGATCTCAGTAAAACAAAATAGTAACA
* *
308125 TTTTATCAGATCTCAGTAAAACAAAACAGTTACA
1 TTTTATCAGATCTCAGTAAAACAAAATAGTAACA
*
308159 TTTTATCAGATCTCAGTAAAACAAAATAGTTACA
1 TTTTATCAGATCTCAGTAAAACAAAATAGTAACA
* *
308193 TTTCATCAGATCTCAGTAAAACAGAATAGTAACA
1 TTTTATCAGATCTCAGTAAAACAAAATAGTAACA
*
308227 TTTTGTCAGATCTCAGTAAAACAAAATAGTAACA
1 TTTTATCAGATCTCAGTAAAACAAAATAGTAACA
*
308261 TTTTATCAGATCTCAGTAAAACAGAATAGTAACA
1 TTTTATCAGATCTCAGTAAAACAAAATAGTAACA
*
308295 TTTTGTCAGATCTCAGTAAAACAAAATAGTAACA
1 TTTTATCAGATCTCAGTAAAACAAAATAGTAACA
308329 AAGTCTCAGA
Statistics
Matches: 190, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 190 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.29
Consensus pattern (34 bp):
TTTTATCAGATCTCAGTAAAACAAAATAGTAACA
Found at i:315239 original size:12 final size:12
Alignment explanation
Indices: 315222--315248 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
315212 CCTAGCCTGT
315222 AAATAGATCATC
1 AAATAGATCATC
315234 AAATAGATCATC
1 AAATAGATCATC
315246 AAA
1 AAA
315249 CTGTCAGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (12 bp):
AAATAGATCATC
Found at i:326843 original size:34 final size:34
Alignment explanation
Indices: 326800--326969 Score: 322
Period size: 34 Copynumber: 5.0 Consensus size: 34
326790 GCACTTCCTT
*
326800 AATCCTTGCTTATATTGAGGTCTTATTCCATCTC
1 AATCCTTGCTTATATTGAGGTCTTATTCTATCTC
326834 AATCCTTGCTTATATTGAGGTCTTATTCTATCTC
1 AATCCTTGCTTATATTGAGGTCTTATTCTATCTC
326868 AATCCTTGCTTATATTGAGGTCTTATTCTATCTC
1 AATCCTTGCTTATATTGAGGTCTTATTCTATCTC
326902 AATCCTTGCTTATATTGAGGTCTTATTCTATCTC
1 AATCCTTGCTTATATTGAGGTCTTATTCTATCTC
*
326936 AATCCTTGTTTATATTGAGGTCTTATTCTATCTC
1 AATCCTTGCTTATATTGAGGTCTTATTCTATCTC
326970 CAATAGAAGT
Statistics
Matches: 134, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 134 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.47
Consensus pattern (34 bp):
AATCCTTGCTTATATTGAGGTCTTATTCTATCTC
Found at i:365987 original size:15 final size:15
Alignment explanation
Indices: 365967--365996 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
365957 GATTTTGCAG
365967 TCTAATGGATTCTGT
1 TCTAATGGATTCTGT
365982 TCTAATGGATTCTGT
1 TCTAATGGATTCTGT
365997 CTGACAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (15 bp):
TCTAATGGATTCTGT
Found at i:366707 original size:2 final size:2
Alignment explanation
Indices: 366700--366741 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
366690 ACCCCTACCC
366700 AG AG AG AG AG AG AG AG 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 AG AG AG AG AG AG AG AG
366742 CCCAATACCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:366836 original size:1 final size:1
Alignment explanation
Indices: 366830--366857 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
366820 TACCTGTTTC
366830 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
366858 NCTACTCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:368579 original size:12 final size:11
Alignment explanation
Indices: 368555--368592 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
368545 GCTAATGTGT
368555 AAAAA-AAAAA
1 AAAAAGAAAAA
368565 AAAAAGAAAAGA
1 AAAAAGAAAA-A
368577 AAAAAGAAGAAA
1 AAAAAGAA-AAA
368589 AAAA
1 AAAA
368593 CCCTCTGTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.20
11 4 0.16
12 14 0.56
13 2 0.08
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:368579 original size:15 final size:15
Alignment explanation
Indices: 368556--368592 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
368546 CTAATGTGTA
368556 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
* *
368571 AAAAGAAAAAAGAAG
1 AAAAAAAAAAAAAAG
368586 AAAAAAA
1 AAAAAAA
368593 CCCTCTGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:384844 original size:32 final size:32
Alignment explanation
Indices: 384807--385094 Score: 285
Period size: 32 Copynumber: 8.3 Consensus size: 32
384797 GTGTAGGCAA
384807 GTGTAGACAAAGTCATTTATAGGTGTGGTGGT
1 GTGTAGACAAAGTCATTTATAGGTGTGGTGGT
*
384839 GTGTAGACAAAGTCATTTATAGG-GTTGGTGGG
1 GTGTAGACAAAGTCATTTATAGGTG-TGGTGGT
*
384871 GTGTAGACAAGTGTAGCATTCATTTATATGTGTGGTGGT
1 GTGTAGACAA----AG---TCATTTATAGGTGTGGTGGT
*
384910 GTGTAGACAAAGTCATTTATAGG-GTTGGTGGG
1 GTGTAGACAAAGTCATTTATAGGTG-TGGTGGT
*
384942 GTGTAGACAAGTGTAGCATTCATTTATATGTGTGGTGGT
1 GTGTAGACAA----AG---TCATTTATAGGTGTGGTGGT
*
384981 GTGTAGACAAAGTCATTTATAGG-GTTGGTGGG
1 GTGTAGACAAAGTCATTTATAGGTG-TGGTGGT
*
385013 GTGTAGACAAGTGTAGCATTCATTTATATGTGTGGTGGT
1 GTGTAGACAA----AG---TCATTTATAGGTGTGGTGGT
385052 GTGTAGACAAAGTCATTTATAGGTGTGGTGGT
1 GTGTAGACAAAGTCATTTATAGGTGTGGTGGT
385084 GTGTAGACAAA
1 GTGTAGACAAA
385095 TTGAAGACAA
Statistics
Matches: 217, Mismatches: 12, Indels: 54
0.77 0.04 0.19
Matches are distributed among these distances:
31 3 0.01
32 121 0.56
35 6 0.03
36 6 0.03
39 78 0.36
40 3 0.01
ACGTcount: A:0.25, C:0.07, G:0.34, T:0.34
Consensus pattern (32 bp):
GTGTAGACAAAGTCATTTATAGGTGTGGTGGT
Found at i:384909 original size:71 final size:71
Alignment explanation
Indices: 384790--385136 Score: 534
Period size: 71 Copynumber: 4.8 Consensus size: 71
384780 ATTATAAGTG
* * * *
384790 TGGTGGTGTGTAGGCAAGTGTAGACAAAGTCATTTATAGGTGTGGTGGTGTGTAGACAAAGTCAT
1 TGGTGGGGTGTAGACAAGTGTAG-C--ATTCATTTATATGTGTGGTGGTGTGTAGACAAAGTCAT
384855 TTATAGGGT
63 TTATAGGGT
384864 TGGTGGGGTGTAGACAAGTGTAGCATTCATTTATATGTGTGGTGGTGTGTAGACAAAGTCATTTA
1 TGGTGGGGTGTAGACAAGTGTAGCATTCATTTATATGTGTGGTGGTGTGTAGACAAAGTCATTTA
384929 TAGGGT
66 TAGGGT
384935 TGGTGGGGTGTAGACAAGTGTAGCATTCATTTATATGTGTGGTGGTGTGTAGACAAAGTCATTTA
1 TGGTGGGGTGTAGACAAGTGTAGCATTCATTTATATGTGTGGTGGTGTGTAGACAAAGTCATTTA
385000 TAGGGT
66 TAGGGT
385006 TGGTGGGGTGTAGACAAGTGTAGCATTCATTTATATGTGTGGTGGTGTGTAGACAAAGTCATTTA
1 TGGTGGGGTGTAGACAAGTGTAGCATTCATTTATATGTGTGGTGGTGTGTAGACAAAGTCATTTA
385071 TA-GGT
66 TAGGGT
* * * * *
385076 GTGGTGGTGTGTAGACAAATTGAAGACAAAGTCATTTATAAGTGTGGTGGTGTGTAGACAA
1 -TGGTGGGGTGTAGAC-AAGTGTAG-C--ATTCATTTATATGTGTGGTGGTGTGTAGACAA
385137 TATTACTTAT
Statistics
Matches: 259, Mismatches: 9, Indels: 9
0.94 0.03 0.03
Matches are distributed among these distances:
70 3 0.01
71 197 0.76
72 6 0.02
73 2 0.01
74 21 0.08
75 30 0.12
ACGTcount: A:0.26, C:0.07, G:0.34, T:0.34
Consensus pattern (71 bp):
TGGTGGGGTGTAGACAAGTGTAGCATTCATTTATATGTGTGGTGGTGTGTAGACAAAGTCATTTA
TAGGGT
Found at i:385033 original size:142 final size:144
Alignment explanation
Indices: 384774--385136 Score: 588
Period size: 142 Copynumber: 2.5 Consensus size: 144
384764 AGTCATAGGT
* * * *
384774 AAGTCAATTATAAGTGTGGTGGTGTGTAGGCAAGTGTAGACAAAGTCATTTATAGGTGTGGTGGT
1 AAGTCATTTATAGGTGTGGTGGTGTGTAGACAAGTGTAGAC-AAGTCATTTATAAGTGTGGTGGT
384839 GTGTAGACAAAGTCATTTATAGGGTTGGTGGGGTGTAGACAAGTGTAGCATTCATTTATATGTGT
65 GTGTAGACAAAGTCATTTATAGGGTTGGTGGGGTGTAGACAAGTGTAGCATTCATTTATATGTGT
384904 GGTGGTGTGTAGACA
130 GGTGGTGTGTAGACA
* * *
384919 AAGTCATTTATAGG-GTTGGTGGGGTGTAGACAAGTGTAG-C-ATTCATTTATATGTGTGGTGGT
1 AAGTCATTTATAGGTG-TGGTGGTGTGTAGACAAGTGTAGACAAGTCATTTATAAGTGTGGTGGT
384981 GTGTAGACAAAGTCATTTATAGGGTTGGTGGGGTGTAGACAAGTGTAGCATTCATTTATATGTGT
65 GTGTAGACAAAGTCATTTATAGGGTTGGTGGGGTGTAGACAAGTGTAGCATTCATTTATATGTGT
385046 GGTGGTGTGTAGACA
130 GGTGGTGTGTAGACA
* *
385061 AAGTCATTTATAGGTGTGGTGGTGTGTAGACAAATTGAAGACAAAGTCATTTATAAGTGTGGTGG
1 AAGTCATTTATAGGTGTGGTGGTGTGTAGAC-AAGTGTAGAC-AAGTCATTTATAAGTGTGGTGG
385126 TGTGTAGACAA
64 TGTGTAGACAA
385137 TATTACTTAT
Statistics
Matches: 201, Mismatches: 11, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
142 128 0.64
143 7 0.03
144 3 0.01
145 33 0.16
146 30 0.15
ACGTcount: A:0.26, C:0.07, G:0.33, T:0.34
Consensus pattern (144 bp):
AAGTCATTTATAGGTGTGGTGGTGTGTAGACAAGTGTAGACAAGTCATTTATAAGTGTGGTGGTG
TGTAGACAAAGTCATTTATAGGGTTGGTGGGGTGTAGACAAGTGTAGCATTCATTTATATGTGTG
GTGGTGTGTAGACA
Done.