Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002199.1 Hibiscus syriacus cultivar Beakdansim tig00004480_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: 76228
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:1426 original size:40 final size:40
Alignment explanation
Indices: 1371--1451 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
1361 GATTTGGACT
*
1371 TAGTCTTCTTTTGCTTTGCAGGCCGGCAGTTGATCCATTC
1 TAGTCTTCTTTTGCTTTGCAGGACGGCAGTTGATCCATTC
* *
1411 TAGTCTTCTTTTGCTTTGCAGGACTGCAGTTGATTCATTC
1 TAGTCTTCTTTTGCTTTGCAGGACGGCAGTTGATCCATTC
1451 T
1 T
1452 TTTCAGCTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.43
Consensus pattern (40 bp):
TAGTCTTCTTTTGCTTTGCAGGACGGCAGTTGATCCATTC
Found at i:1873 original size:29 final size:29
Alignment explanation
Indices: 1831--1893 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
1821 GTTATTCATC
1831 TAAAATTTTAAAAATTTATTTCCTTAACA
1 TAAAATTTTAAAAATTTATTTCCTTAACA
1860 TAAAATTTTAAAAATTTATTTCCTTAACA
1 TAAAATTTTAAAAATTTATTTCCTTAACA
1889 TAAAA
1 TAAAA
1894 AAATTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.43
Consensus pattern (29 bp):
TAAAATTTTAAAAATTTATTTCCTTAACA
Found at i:4527 original size:59 final size:59
Alignment explanation
Indices: 4453--4564 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 59
4443 ACATATTAAT
*
4453 AGTCGGGTGACCATTTTG-AGACTTTTAATAGTTGGAGGACTAGAAAAA-TAATACGCTAC
1 AGTCGGGTGACCATTTTGTA-ACTTTTAACAGTTGGAGGACTA-AAAAAGTAATACGCTAC
*
4512 AGTCGGGTGATCATTTTGTAACTTTTAACAGTTGGAGGACTAAAAAAGTAATA
1 AGTCGGGTGACCATTTTGTAACTTTTAACAGTTGGAGGACTAAAAAAGTAATA
4565 TTTTAGTCTA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
58 5 0.10
59 43 0.88
60 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (59 bp):
AGTCGGGTGACCATTTTGTAACTTTTAACAGTTGGAGGACTAAAAAAGTAATACGCTAC
Found at i:4658 original size:25 final size:25
Alignment explanation
Indices: 4630--4696 Score: 134
Period size: 25 Copynumber: 2.7 Consensus size: 25
4620 GGCTTATGTA
4630 TTGGGAAATACACAAAATAGATTGC
1 TTGGGAAATACACAAAATAGATTGC
4655 TTGGGAAATACACAAAATAGATTGC
1 TTGGGAAATACACAAAATAGATTGC
4680 TTGGGAAATACACAAAA
1 TTGGGAAATACACAAAA
4697 AAGAGTTTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.22
Consensus pattern (25 bp):
TTGGGAAATACACAAAATAGATTGC
Found at i:6395 original size:135 final size:131
Alignment explanation
Indices: 5782--6409 Score: 411
Period size: 129 Copynumber: 4.7 Consensus size: 131
5772 AAGCATAATG
* * * * * *
5782 CATCCGGAGAGAGTGATGGCGATGATGAAAGTGGTCGTGGCATGCTTGATGAAAGTAGGTTGAAT
1 CATCCGGAGATAGTGA--GTGATGGTGAAAGTGATCGT-GTATGCTTGATGAAAGTA-GATGAAT
* * ** * * * * * * * * *
5847 GAAGGGCAGCAGAATGGAACTGGATTGTTGCGGACGGAATCTTTTGATAGATACAAGAAGGATCG
62 GAAAGGCAGCAAAATGGAACTCAACTCTTGCAGACGGAATCATTAGATCGCTACGAGAAGGATCA
*
5912 AAATG
127 AAATA
** ** * * *
5917 CATCC-G-GATA-T-AGTGATGGTGAAAGCAATCACGATATGCTTGATGGAACTCA-ATCGATTG
1 CATCCGGAGATAGTGAGTGATGGTGAAAGTGATCGTG-TATGCTTGATGAAAGT-AGAT-GAATG
* * * ** *
5977 -AAGAGAAGCTAAATCGAACTGGACTCTTGCAGACGGAACCATTAGATCGCTACGAGAAGGATCA
63 AAAG-GCAGCAAAATGGAACTCAACTCTTGCAGACGGAATCATTAGATCGCTACGAGAAGGATCA
6041 AAATA
127 AAATA
* * *
6046 TATCCCGG-G--A--GAGTGATGGTGAAAGTGCA-CGGGGTATGCTTGATAAAAGTAGATTGAAT
1 CAT-CCGGAGATAGTGAGTGATGGTGAAAGTG-ATC-GTGTATGCTTGATGAAAGTAGA-TGAAT
* * * * * * * *
6105 GAAGGGCAGCAGAATGGAAC-CGGATTTTTGCGGATGGAATCTTTAGATCGCTACGAGAAGGATC
62 GAAAGGCAGCAAAATGGAACTC-AACTCTTGCAGACGGAATCATTAGATCGCTACGAGAAGGATC
*
6169 TAAATA
126 AAAATA
* * * *
6175 CATCCGGATATAGTGAGGGCGATGATGAAAGTGATCGTGATATGCTTGATGAAAGTAGAT-CATA
1 CATCCGGAGATAGTGA--GTGATGGTGAAAGTGATCGTG-TATGCTTGATGAAAGTAGATGAAT-
* * * * * *
6239 CAAAGGGAAGCTAAATGGAACTCAACTCTTTCAGACGGAGTCATTAGATCGCTACAAGAAGGATC
62 GAAA-GGCAGCAAAATGGAACTCAACTCTTGCAGACGGAATCATTAGATCGCTACGAGAAGGATC
6304 AAAATA
126 AAAATA
* * * *
6310 CATTCGGAGATAGTGATGTTGATGGTGAAAGCGATCGTTGTATGCTTAACGAAAGTAGACTGAAT
1 CATCCGGAGATAGTGA-G-TGATGGTGAAAGTGATCG-TGTATGCTTGATGAAAGTAGA-TGAAT
* *
6375 GAAAGGCAGCAAAATGGAACTGAACTATTGCAGAC
62 GAAAGGCAGCAAAATGGAACTCAACTCTTGCAGAC
6410 AGATTCTTTC
Statistics
Matches: 376, Mismatches: 88, Indels: 58
0.72 0.17 0.11
Matches are distributed among these distances:
128 9 0.02
129 170 0.45
130 8 0.02
131 4 0.01
132 1 0.00
133 7 0.02
134 8 0.02
135 160 0.43
136 7 0.02
137 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (131 bp):
CATCCGGAGATAGTGAGTGATGGTGAAAGTGATCGTGTATGCTTGATGAAAGTAGATGAATGAAA
GGCAGCAAAATGGAACTCAACTCTTGCAGACGGAATCATTAGATCGCTACGAGAAGGATCAAAAT
A
Found at i:9438 original size:32 final size:32
Alignment explanation
Indices: 9397--9459 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
9387 AAACTCACAT
9397 TTCCCCTTCAATTCTTGGTTATAGGTTGTTTG
1 TTCCCCTTCAATTCTTGGTTATAGGTTGTTTG
9429 TTCCCCTTCAATTCTTGGTTATAGGTTGTTT
1 TTCCCCTTCAATTCTTGGTTATAGGTTGTTT
9460 CGTACATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.13, C:0.19, G:0.17, T:0.51
Consensus pattern (32 bp):
TTCCCCTTCAATTCTTGGTTATAGGTTGTTTG
Found at i:11016 original size:6 final size:6
Alignment explanation
Indices: 11007--11032 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
10997 ATGCACATGT
11007 CTATGG CTATGG CTATGG CTATGG CT
1 CTATGG CTATGG CTATGG CTATGG CT
11033 CCCAAGCCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.19, G:0.31, T:0.35
Consensus pattern (6 bp):
CTATGG
Found at i:16516 original size:2 final size:2
Alignment explanation
Indices: 16509--16542 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16499 TGCCTCTTCT
16509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16543 ATTGTATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23443 original size:30 final size:32
Alignment explanation
Indices: 23388--23449 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
23378 AGTATGCTAG
*
23388 TAATAATAAATATTGTAAAACAAATTGGACCTT
1 TAATAAAAAATATTG-AAAACAAATTGGACCTT
23421 TAATAAAAAATATTG-AAA-AAATTGGACCT
1 TAATAAAAAATATTGAAAACAAATTGGACCT
23450 ATAAAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 11 0.39
31 3 0.11
33 14 0.50
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.31
Consensus pattern (32 bp):
TAATAAAAAATATTGAAAACAAATTGGACCTT
Found at i:25558 original size:12 final size:12
Alignment explanation
Indices: 25521--25559 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
25511 TTTATTATTT
25521 TTTAATAAAATTA
1 TTTAA-AAAATTA
* *
25534 ATAAAAAAATTA
1 TTTAAAAAATTA
25546 TTTAAAAAATTA
1 TTTAAAAAATTA
25558 TT
1 TT
25560 ATTTTTATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 19 0.86
13 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TTTAAAAAATTA
Found at i:31000 original size:20 final size:21
Alignment explanation
Indices: 30975--31026 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
30965 TTTTCCCAAT
*
30975 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
30995 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
31016 TCGCAATGCGA
1 TCGCAATGCGA
31027 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:31040 original size:20 final size:20
Alignment explanation
Indices: 31015--31149 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
31005 AATTGGGAAA
31015 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
31035 ATCGCAATACGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
31055 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
31076 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
31096 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
31116 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
31136 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
31150 TTTCAAAGCG
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 64 0.68
21 24 0.26
22 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:31061 original size:61 final size:61
Alignment explanation
Indices: 31012--31143 Score: 174
Period size: 61 Copynumber: 2.2 Consensus size: 61
31002 GCGAATTGGG
* * * * *
31012 AAAATCGCAATGCGATACTGACTATCGCAATACGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATACTGACTATCGCAACGCGATAATAC
* * * *
31073 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATACTGACTATCGCAACGCGATAATAC
*
31134 ATAATCGCAA
1 AAAATCGCAA
31144 TGCGATTTTC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATACTGACTATCGCAACGCGATAATAC
Found at i:31667 original size:20 final size:20
Alignment explanation
Indices: 31623--31682 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
31613 GCGATTCTCT
** *
31623 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCA
31643 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCATTTTCA
* **
31663 TGTTGCGATTTTCATTTTCA
1 CGTTGCGATAGTCATTTTCA
31683 GAAACTATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCA
Found at i:31872 original size:25 final size:24
Alignment explanation
Indices: 31818--31872 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
31808 TGTTTATTAT
* *
31818 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
31842 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
31868 TGTTT
1 TGTTT
31873 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:33009 original size:17 final size:18
Alignment explanation
Indices: 32972--33015 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
32962 TCCACTTCGG
32972 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
32990 GAGCTATCACCTCA-CCA
1 GAGCCATCACCTCACCCA
33007 GAGCCATCA
1 GAGCCATCA
33016 TCTGATCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.30, C:0.43, G:0.14, T:0.14
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:33522 original size:20 final size:20
Alignment explanation
Indices: 33497--33542 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
33487 TAGTTTACTT
33497 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
33517 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
33537 TCGCAA
1 TCGCAA
33543 TGCGAAGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:33560 original size:19 final size:19
Alignment explanation
Indices: 33536--33618 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
33526 GGAAATGGCT
*
33536 ATCGCAATGCGAAGTGAAA
1 ATCGCAATGCGAAATGAAA
*
33555 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
33569 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
33588 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
33607 ATCGCAATGCGA
1 ATCGCAATGCGA
33619 TTTGTGTTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
14 10 0.19
16 2 0.04
17 2 0.04
18 1 0.02
19 39 0.72
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:33649 original size:14 final size:14
Alignment explanation
Indices: 33630--33719 Score: 72
Period size: 14 Copynumber: 5.8 Consensus size: 14
33620 TTGTGTTTCG
33630 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
33644 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
33660 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
33676 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
*
33693 CACATTGCGATTTTGT
1 --CGTTGCGATTTTGT
33709 CGTTGCGATTT
1 CGTTGCGATTT
33720 GCATTTCGCA
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 27 0.44
15 3 0.05
16 10 0.16
17 2 0.03
18 12 0.20
19 7 0.11
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:33699 original size:33 final size:33
Alignment explanation
Indices: 33625--33736 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
33615 GCGATTTGTG
*
33625 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
33657 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
* *
33690 TTTCACATTGCGATTTTGTCGTTGCGATTTGCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
33723 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
33737 AGCCATTTCC
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 26 0.35
33 49 0.65
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:33735 original size:19 final size:18
Alignment explanation
Indices: 33646--33736 Score: 81
Period size: 14 Copynumber: 5.4 Consensus size: 18
33636 GATTTTGTCG
33646 TTGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCGCA
*
33664 TTGCGATTT--TGTCG--
1 TTGCGATTTCATTTCGCA
*
33678 TTGCGATTTTCATTTCACA
1 TTGCGA-TTTCATTTCGCA
*
33697 TTGCGATTT--TGTCG--
1 TTGCGATTTCATTTCGCA
33711 TTGCGATTTGCATTTCGCA
1 TTGCGATTT-CATTTCGCA
33730 TTGCGAT
1 TTGCGAT
33737 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
14 15 0.26
15 3 0.05
16 7 0.12
17 7 0.12
18 12 0.21
19 13 0.23
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.46
Consensus pattern (18 bp):
TTGCGATTTCATTTCGCA
Found at i:33755 original size:20 final size:20
Alignment explanation
Indices: 33730--33776 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33720 GCATTTCGCA
33730 TTGCGATAGCCATTTCCACG
1 TTGCGATAGCCATTTCCACG
* * *
33750 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTCCACG
33770 TTGCGAT
1 TTGCGAT
33777 TTTAAGTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCACG
Found at i:34238 original size:41 final size:41
Alignment explanation
Indices: 34142--34259 Score: 128
Period size: 42 Copynumber: 2.8 Consensus size: 41
34132 GACTCACCTG
* * *
34142 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGT-CCCTCCCACCGTTCAAGAGGCCACTA
* *
34184 TCCTCCCTCAAGAGTCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCTCCCACCGTTCAAGAGGCCACTA
** * * *
34225 TCATCGTTGAAGAGGTCCCTCCCACCATTCCAGAG
1 TCATCCCTCAAGA-GTCCCTCCCACCGTTCAAGAG
34260 CCATGGAGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 31 0.48
42 33 0.52
ACGTcount: A:0.22, C:0.40, G:0.17, T:0.21
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:35753 original size:19 final size:19
Alignment explanation
Indices: 35729--35775 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
35719 GCAACGAGAG
35729 AATCGCAATACGAAATGAA
1 AATCGCAATACGAAATGAA
**
35748 AATCGCAACGCGAAATGAA
1 AATCGCAATACGAAATGAA
35767 AATCGCAAT
1 AATCGCAAT
35776 GAGGGAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.49, C:0.19, G:0.17, T:0.15
Consensus pattern (19 bp):
AATCGCAATACGAAATGAA
Found at i:35773 original size:52 final size:53
Alignment explanation
Indices: 35696--35813 Score: 159
Period size: 52 Copynumber: 2.3 Consensus size: 53
35686 CTTAATGTCT
* ** *
35696 ATCGCAACGCGGAAATTACTATCGCAACGAGAGAATCGCAATACGAAATGAAA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCACAATACGAAATGAAA
* * *
35749 ATCGCAACGC-GAAATGAAAATCGCAATGAGGGAATCACAATGCGAAATGAAA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCACAATACGAAATGAAA
35801 ATCGCAACG-GGAA
1 ATCGCAACGCGGAA
35814 TTTAATTTCG
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
52 47 0.82
53 10 0.18
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (53 bp):
ATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCACAATACGAAATGAAA
Found at i:35987 original size:14 final size:14
Alignment explanation
Indices: 35968--36004 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
35958 CATCAATTAA
35968 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
35982 ACAAATCACCTTTT
1 ACAAATCAACTTTT
35996 ACAAATCAA
1 ACAAATCAA
36005 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:37804 original size:93 final size:91
Alignment explanation
Indices: 37695--37881 Score: 288
Period size: 93 Copynumber: 2.0 Consensus size: 91
37685 ATTTCAAACT
*
37695 TTCAACCAAAAGACAAAAC-AA-AGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 TTCAACCAAAAGACAAAACAAAGAGACAAATACTAACTTCACAGTGTT----AATAAACAGTTTA
37758 GCAGAATTGGCAGCAACCGAATAAATTTAC
62 GCAGAATTGGCAGCAACCGAATAAATTTAC
37788 TTCAACCAAAAGACAAAACAAAAAGAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGC
1 TTCAACCAAAAGACAAAAC--AAAGAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGC
*
37853 AGTATTGGCAGCAACCGAATAAATTTAC
64 AGAATTGGCAGCAACCGAATAAATTTAC
37881 T
1 T
37882 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
93 61 0.69
96 2 0.02
97 25 0.28
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (91 bp):
TTCAACCAAAAGACAAAACAAAGAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAG
AATTGGCAGCAACCGAATAAATTTAC
Found at i:39599 original size:20 final size:20
Alignment explanation
Indices: 39569--39628 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
39559 CTTTTGGTTG
39569 AAATGAAAATCGCAACGAGA
1 AAATGAAAATCGCAACGAGA
* * *
39589 TAATGAGAATCGCAACGCGA
1 AAATGAAAATCGCAACGAGA
** *
39609 AAATGACTATCGTAACGAGA
1 AAATGAAAATCGCAACGAGA
39629 GAATCGCAAC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (20 bp):
AAATGAAAATCGCAACGAGA
Found at i:39639 original size:14 final size:14
Alignment explanation
Indices: 39617--39705 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
39607 GAAAATGACT
*
39617 ATCGTAACGAGAGA
1 ATCGCAACGAGAGA
*
39631 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
39648 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
*
39664 ATCGCAACGTGAAATGAAA
1 ATCGCAAC--G--A-GAGA
39683 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
39697 ATCGCAACG
1 ATCGCAACG
39706 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
14 26 0.43
15 1 0.02
16 7 0.12
17 7 0.12
18 1 0.02
19 18 0.30
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:39651 original size:33 final size:33
Alignment explanation
Indices: 39593--39722 Score: 197
Period size: 33 Copynumber: 3.9 Consensus size: 33
39583 ACGAGATAAT
*
39593 GAGAATCGCAACGCGAAAATGACTATCGTAACGA
1 GAGAATCGCAACGCG-AAATGACTATCGCAACGA
39627 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* **
39660 GAGAATCGCAACGTGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
39693 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
39723 TGTGATTTTG
Statistics
Matches: 91, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
33 76 0.84
34 15 0.16
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:39748 original size:19 final size:19
Alignment explanation
Indices: 39726--39789 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
39716 ATCGCAATGT
*
39726 GATTTTGGTTTCGCGTTGA
1 GATTTTGATTTCGCGTTGA
* *
39745 GATTTTTATTTCGCGTTGC
1 GATTTTGATTTCGCGTTGA
* *
39764 GATAGTT-ATTTCCGCGTTGT
1 GAT-TTTGATTT-CGCGTTGA
39784 GATTTT
1 GATTTT
39790 CATTCTCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 25 0.68
20 12 0.32
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (19 bp):
GATTTTGATTTCGCGTTGA
Found at i:40361 original size:20 final size:20
Alignment explanation
Indices: 40309--40415 Score: 110
Period size: 20 Copynumber: 5.3 Consensus size: 20
40299 GCTATGTAAA
* *
40309 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
*
40329 TCGCATTACGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
40349 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
40370 TCGCATTGCGATTTAC-TAAT
1 TCGCATTGCGATTTACGT-AT
* *
40390 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACGTAT
40410 TCGCAT
1 TCGCAT
40416 ATCGAATTAT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.04
20 54 0.72
21 18 0.24
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:40382 original size:41 final size:41
Alignment explanation
Indices: 40327--40604 Score: 153
Period size: 41 Copynumber: 6.8 Consensus size: 41
40317 CGATAGTAAG
*
40327 ATTCGCATTACGATTTACGTATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTA
* * *
40368 ATTCGCATTGCGATTTAC-TAATTCGCGTTGCGATTTACAT-
1 ATTCGCATTGCGATTTACGT-ATTCGCATTGCGATTTTCCTA
* * * * ** * * *
40408 ATTCGCATAT-CGAATTATGAAAATCGCAACGCGA-ATACGTA
1 ATTCGCAT-TGCGATTTACG-TATTCGCATTGCGATTTTCCTA
* * * * * * **
40449 AATCGCAATGCGAATTAGGAAAATCGCATTGCGATAGT-C-A
1 ATTCGCATTGCGATTTACG-TATTCGCATTGCGATTTTCCTA
* * *
40489 GTATCGCATTGCGATAGT-CAGTA-TCGCATTGCGATTTTCCAA
1 AT-TCGCATTGCGAT-TTAC-GTATTCGCATTGCGATTTTCCTA
* *
40531 ATTCGCATTGCGATAGT-CAGTA-TCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGAT-TTAC-GTATTCGCATTGCGATTTTCCTA
* *
40572 ATTCGCATTGCGATTTACTTATTTGCATTGCGA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGA
40605 ATTGGGAAAA
Statistics
Matches: 189, Mismatches: 34, Indels: 28
0.75 0.14 0.11
Matches are distributed among these distances:
40 37 0.20
41 147 0.78
42 5 0.03
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (41 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTA
Found at i:40442 original size:21 final size:21
Alignment explanation
Indices: 40418--40476 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 21
40408 ATTCGCATAT
*
40418 CGAATTATGAAAATCGCAACG
1 CGAATTACGAAAATCGCAACG
* *
40439 CGAA-TACGTAAATCGCAATG
1 CGAATTACGAAAATCGCAACG
*
40459 CGAATTAGGAAAATCGCA
1 CGAATTACGAAAATCGCA
40477 TTGCGATAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.19
Consensus pattern (21 bp):
CGAATTACGAAAATCGCAACG
Found at i:40481 original size:21 final size:21
Alignment explanation
Indices: 40410--40482 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
40400 ATTTACATAT
*
40410 TCGCATAT-CGAATTATGAAAA
1 TCGCA-ATGCGAATTACGAAAA
* *
40431 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
40451 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
*
40472 TCGCATTGCGA
1 TCGCAATGCGA
40483 TAGTCAGTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 18 0.42
21 25 0.58
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:40495 original size:61 final size:61
Alignment explanation
Indices: 40430--40557 Score: 143
Period size: 61 Copynumber: 2.1 Consensus size: 61
40420 AATTATGAAA
**
40430 ATCGCAACGCGAATACGT-A-AATCGCAATGCGAATTAGGAAAATCGCATTGCGATAGTCAGT
1 ATCGCAACGCG-ATA-GTCAGAATCGCAATGCGAATTACCAAAATCGCATTGCGATAGTCAGT
** * * * * *
40491 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCATTGCGATAGTCAGT
1 ATCGCAACGCGATAGTCAGAATCGCAATGCGAATTACCAAAATCGCATTGCGATAGTCAGT
40552 ATCGCA
1 ATCGCA
40558 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 2 0.04
60 4 0.07
61 50 0.89
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (61 bp):
ATCGCAACGCGATAGTCAGAATCGCAATGCGAATTACCAAAATCGCATTGCGATAGTCAGT
Found at i:40496 original size:20 final size:20
Alignment explanation
Indices: 40471--40564 Score: 136
Period size: 20 Copynumber: 4.7 Consensus size: 20
40461 AATTAGGAAA
40471 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
40491 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
** *
40511 ATCGCATTGCGATTTTCCA-A
1 ATCGCATTGCGATAGT-CAGT
40531 ATTCGCATTGCGATAGTCAGT
1 A-TCGCATTGCGATAGTCAGT
40552 ATCGCATTGCGAT
1 ATCGCATTGCGAT
40565 TTTCCAAATT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
20 49 0.75
21 16 0.25
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:40538 original size:21 final size:21
Alignment explanation
Indices: 40512--40587 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
40502 ATAGTCAGTA
40512 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
** *
40533 TCGCATTGCGATAGT-C-AGT
1 TCGCATTGCGATTTTCCAAAT
40552 ATCGCATTGCGATTTTCCAAAT
1 -TCGCATTGCGATTTTCCAAAT
40574 TCGCATTGCGATTT
1 TCGCATTGCGATTT
40588 ACTTATTTGC
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.04
20 14 0.30
21 28 0.61
22 2 0.04
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:40600 original size:61 final size:61
Alignment explanation
Indices: 40472--40604 Score: 171
Period size: 61 Copynumber: 2.2 Consensus size: 61
40462 ATTAGGAAAA
* *
40472 TCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAATATCGCATTGCGATTTTACAAAT
** **
40533 TCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCAA-ATTCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATAGTCAGTATCGCATTGCGATAGT-CAATA-TCGCATTGCGATTTTACAAAT
*
40594 TTGCATTGCGA
1 TCGCATTGCGA
40605 ATTGGGAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
61 50 0.79
62 13 0.21
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.35
Consensus pattern (61 bp):
TCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAATATCGCATTGCGATTTTACAAAT
Found at i:40646 original size:21 final size:22
Alignment explanation
Indices: 40596--40646 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
40586 TTACTTATTT
40596 GCATTGCG-AATTGGGAAAATC
1 GCATTGCGAAATTGGGAAAATC
**
40617 GCAACGCGAAATT-GGAAAATC
1 GCATTGCGAAATTGGGAAAATC
40638 GCATTGCGA
1 GCATTGCGA
40647 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (22 bp):
GCATTGCGAAATTGGGAAAATC
Found at i:42650 original size:3 final size:3
Alignment explanation
Indices: 42642--42737 Score: 102
Period size: 3 Copynumber: 32.0 Consensus size: 3
42632 ATTAATTTAT
* * * *
42642 TTA TTA TTA TTA TAA TTA TAA TTA TTA TTA TTA TTA TAA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
42690 TAA TAA TAA TAA TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42738 AATAAATATA
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:42652 original size:18 final size:18
Alignment explanation
Indices: 42631--42731 Score: 80
Period size: 18 Copynumber: 5.3 Consensus size: 18
42621 TTTTTACCCA
*
42631 TATTAATTTATTTATTAT
1 TATTAATTTAATTATTAT
42649 TATTATAATTATAATTATTAT
1 TA-T-TAATT-TAATTATTAT
42670 TATT-ATTATAATTATTAT
1 TATTAATT-TAATTATTAT
* *
42688 AATAATAATAATAATTATTAT
1 --TATTAAT-TTAATTATTAT
*
42709 TATAAATATT-ATTATTAT
1 TATTAAT-TTAATTATTAT
42727 TATTA
1 TATTA
42732 TTATTAAATA
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
18 28 0.41
19 9 0.13
20 9 0.13
21 23 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTAATTTAATTATTAT
Found at i:42879 original size:15 final size:16
Alignment explanation
Indices: 42859--42900 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
42849 CCTAATCCCT
42859 AGCCGCCTCT-AATCC
1 AGCCGCCTCTGAATCC
**
42874 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGAATCC
42890 AGCCGCCTCTG
1 AGCCGCCTCTG
42901 CCTCCACCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.12, C:0.50, G:0.19, T:0.19
Consensus pattern (16 bp):
AGCCGCCTCTGAATCC
Found at i:42892 original size:16 final size:16
Alignment explanation
Indices: 42871--42910 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
42861 CCGCCTCTAA
42871 TCCAGCCGCCTCTGCC
1 TCCAGCCGCCTCTGCC
42887 TCCAGCCGCCTCTGCC
1 TCCAGCCGCCTCTGCC
42903 TCCA-CCGC
1 TCCAGCCGC
42911 TGCCACGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.07, C:0.57, G:0.17, T:0.17
Consensus pattern (16 bp):
TCCAGCCGCCTCTGCC
Found at i:44879 original size:13 final size:15
Alignment explanation
Indices: 44848--44884 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
44838 TTATATGTTT
44848 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
44863 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
44876 TA-TTTATTT
1 TATTTTATTT
44885 TTCTGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:55428 original size:1 final size:1
Alignment explanation
Indices: 55422--55481 Score: 75
Period size: 1 Copynumber: 60.0 Consensus size: 1
55412 ATTATGCTTG
* * * * *
55422 AAAAAAAAGAAAAAAAAAAAAAAAAAAGAAAAAAAGAAAAAAAAAGAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
55482 GGGGTCAAGG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:55446 original size:19 final size:19
Alignment explanation
Indices: 55422--55481 Score: 95
Period size: 18 Copynumber: 3.2 Consensus size: 19
55412 ATTATGCTTG
55422 AAAAAAAAGAAAAAAAAAA
1 AAAAAAAAGAAAAAAAAAA
*
55441 AAAAAAAAG-AAAAAAAGA
1 AAAAAAAAGAAAAAAAAAA
55459 AAAAAAAAGAAAAAGAAAAA
1 AAAAAAAAGAAAAA-AAAAA
55479 AAA
1 AAA
55482 GGGGTCAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 17 0.46
19 13 0.35
20 7 0.19
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAAAAA
Found at i:55460 original size:27 final size:26
Alignment explanation
Indices: 55422--55481 Score: 93
Period size: 27 Copynumber: 2.3 Consensus size: 26
55412 ATTATGCTTG
55422 AAAAAAAAGAAAAAAAAAAAAAAAAA
1 AAAAAAAAGAAAAAAAAAAAAAAAAA
* *
55448 AGAAAAAAAGAAAAAAAAAGAAAAAGA
1 A-AAAAAAAGAAAAAAAAAAAAAAAAA
55475 AAAAAAA
1 AAAAAAA
55482 GGGGTCAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 7 0.23
27 24 0.77
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (26 bp):
AAAAAAAAGAAAAAAAAAAAAAAAAA
Found at i:56705 original size:81 final size:83
Alignment explanation
Indices: 56559--56722 Score: 305
Period size: 81 Copynumber: 2.0 Consensus size: 83
56549 TTAACTGGAA
56559 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACC
56624 AATCATTGAATTTAGAAG
66 AATCATTGAATTTAGAAG
*
56642 ATGAATGTG-TCATAGCATCTTCT-GAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACC
56705 AATCATTGAATTTAGAAG
66 AATCATTGAATTTAGAAG
56723 CTGGCTTTAC
Statistics
Matches: 80, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
81 57 0.71
82 14 0.17
83 9 0.11
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (83 bp):
ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACC
AATCATTGAATTTAGAAG
Found at i:56919 original size:83 final size:83
Alignment explanation
Indices: 56780--57044 Score: 476
Period size: 83 Copynumber: 3.2 Consensus size: 83
56770 ACTGGGACAA
56780 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACC
56845 AATCATTGAATTTAGAAG
66 AATCATTGAATTTAGAAG
*
56863 ATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACC
56928 AATCATTGAATTTAGAAG
66 AATCATTGAATTTAGAAG
* * *
56946 ATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAATC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACC
*
57011 AATCATTGAATTTGGAAG
66 AATCATTGAATTTAGAAG
*
57029 ATGAATTTGCTCATAG
1 ATGAATGTGCTCATAG
57045 TAGAAATAAG
Statistics
Matches: 176, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 176 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.37
Consensus pattern (83 bp):
ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACC
AATCATTGAATTTAGAAG
Found at i:58142 original size:110 final size:113
Alignment explanation
Indices: 57833--58151 Score: 551
Period size: 113 Copynumber: 2.8 Consensus size: 113
57823 TAGCAAAGAT
*
57833 TCAAATCTATCACTTGATGGATTATTTTTGCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCTATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
57898 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
57946 TCAAATCTATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCTATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
58011 AGAAGGAAGAAGAAGTTCATAATGAGAAGAA-TTGTTCAACC-TTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
58057 TC-AATCTATCACTTGATGGATTATTTTTTCCAGAG-AAGTTCATAATGAGAA-AACTCATCATC
1 TCAAATCTATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATC
58119 TGAAGAAGGAAGAA-AAGTTCATAATGAGAAGAA
63 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
58152 CTCATCATCT
Statistics
Matches: 201, Mismatches: 2, Indels: 9
0.95 0.01 0.04
Matches are distributed among these distances:
108 2 0.01
109 16 0.08
110 52 0.26
111 26 0.13
112 10 0.05
113 95 0.47
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (113 bp):
TCAAATCTATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:58193 original size:43 final size:43
Alignment explanation
Indices: 58088--58409 Score: 580
Period size: 43 Copynumber: 7.6 Consensus size: 43
58078 TATTTTTTCC
58088 AGAG-AAGTTCATAATGAGAA-AACTCATCATCTGAAGAAGGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
58129 AGA-AAAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
58171 AGAGAAAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
58214 AGAGAAAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
*
58257 AGAGAAAGTTCATAATGAGAAGAACTCATCATCTGAAGAAAGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
*
58300 ATAGAAAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
*
58343 AGAGAAAGTTCATAATGAGAAGAACACATCATCTGAAGAAGGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
58386 AGA-AGAAGTTCATAATGAGAAGAA
1 AGAGA-AAGTTCATAATGAGAAGAA
58410 TTTGTTCAAC
Statistics
Matches: 272, Mismatches: 5, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
41 19 0.07
42 25 0.09
43 228 0.84
ACGTcount: A:0.48, C:0.11, G:0.22, T:0.19
Consensus pattern (43 bp):
AGAGAAAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
Found at i:58778 original size:3 final size:3
Alignment explanation
Indices: 58770--58849 Score: 94
Period size: 3 Copynumber: 27.3 Consensus size: 3
58760 ATTTATTTAT
* * *
58770 TTA TTA TTA TTA -TA TTA -TA ATA TTA TTA TTA TAA TTA TTA -AA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
58815 TTA TTA TTA TTA TTAA ATA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA T
58850 ATATAATATA
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
2 5 0.08
3 59 0.89
4 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:58821 original size:42 final size:42
Alignment explanation
Indices: 58770--58849 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
58760 ATTTATTTAT
58770 TTATTATTATTA-TATTATAATATTATTATTATAATTATTAAA
1 TTATTATTATTATTATTA-AATATTATTATTATAATTATTAAA
*
58812 TTATTATTATTATTATTAAATATTATTATTATTATTAT
1 TTATTATTATTATTATTAAATATTATTATTATAATTAT
58850 ATATAATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
42 31 0.86
43 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (42 bp):
TTATTATTATTATTATTAAATATTATTATTATAATTATTAAA
Found at i:58989 original size:15 final size:16
Alignment explanation
Indices: 58969--59010 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
58959 CCTAATCCCT
58969 AGCCGCCTCT-AATCC
1 AGCCGCCTCTGAATCC
**
58984 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGAATCC
59000 AGCCGCCTCTG
1 AGCCGCCTCTG
59011 CCTCCACCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.12, C:0.50, G:0.19, T:0.19
Consensus pattern (16 bp):
AGCCGCCTCTGAATCC
Found at i:59002 original size:16 final size:16
Alignment explanation
Indices: 58981--59020 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
58971 CCGCCTCTAA
58981 TCCAGCCGCCTCTGCC
1 TCCAGCCGCCTCTGCC
58997 TCCAGCCGCCTCTGCC
1 TCCAGCCGCCTCTGCC
59013 TCCA-CCGC
1 TCCAGCCGC
59021 TGCCACGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.07, C:0.57, G:0.17, T:0.17
Consensus pattern (16 bp):
TCCAGCCGCCTCTGCC
Found at i:64193 original size:40 final size:41
Alignment explanation
Indices: 64114--64194 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
64104 TTTTACTCGA
*
64114 CTCAACTCGATCAAATGCTAACCCCTACATGGAAGCACTGT
1 CTCAACTCGATCAAATGCTAACCACTACATGGAAGCACTGT
64155 CTCAACTCGATCAAATGCTAA-CACTACATGGAAGCACTGT
1 CTCAACTCGATCAAATGCTAACCACTACATGGAAGCACTGT
64195 GTTTGAAAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 18 0.46
41 21 0.54
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.22
Consensus pattern (41 bp):
CTCAACTCGATCAAATGCTAACCACTACATGGAAGCACTGT
Found at i:68393 original size:6 final size:6
Alignment explanation
Indices: 68382--68442 Score: 122
Period size: 6 Copynumber: 10.2 Consensus size: 6
68372 CAGTCCTATC
68382 CCAATT CCAATT CCAATT CCAATT CCAATT CCAATT CCAATT CCAATT
1 CCAATT CCAATT CCAATT CCAATT CCAATT CCAATT CCAATT CCAATT
68430 CCAATT CCAATT C
1 CCAATT CCAATT C
68443 TTTATTGCAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.33, C:0.34, G:0.00, T:0.33
Consensus pattern (6 bp):
CCAATT
Found at i:69335 original size:10 final size:9
Alignment explanation
Indices: 69311--69338 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
69301 TTGAAATTTA
69311 AATTTTTTC
1 AATTTTTTC
69320 AATTTTTTC
1 AATTTTTTC
69329 AATTTTTTC
1 AATTTTTTC
69338 A
1 A
69339 CTTGACTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (9 bp):
AATTTTTTC
Found at i:75855 original size:59 final size:59
Alignment explanation
Indices: 75750--75869 Score: 179
Period size: 59 Copynumber: 2.0 Consensus size: 59
75740 CCAAAACAGC
*
75750 ACCAAAACGACATCTACATCAATAATCGTTTGCGTCTCATGCGATTACCGATTTAATGT
1 ACCAAAACGACATCCACATCAATAATCGTTTGCGTCTCATGCGATTACCGATTTAATGT
* * * *
75809 ACCAAAACGACATCCGCATCAATAATTGTTTGC-TCATCGTGTGATTACCGATTTAATGT
1 ACCAAAACGACATCCACATCAATAATCGTTTGCGTC-TCATGCGATTACCGATTTAATGT
75868 AC
1 AC
75870 GATATGTGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 2 0.04
59 53 0.96
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (59 bp):
ACCAAAACGACATCCACATCAATAATCGTTTGCGTCTCATGCGATTACCGATTTAATGT
Done.