Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014896.1 Corchorus capsularis cultivar CVL-1 contig14917, 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: 24064
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1712 original size:12 final size:12
Alignment explanation
Indices: 1689--1728 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1679 TAAAAAAAAA
*
1689 TATTATTGTTGT
1 TATTATTATTGT
*
1701 TGTTATTATTGT
1 TATTATTATTGT
*
1713 TATTATTATTTT
1 TATTATTATTGT
1725 TATT
1 TATT
1729 TTTTTGAGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (12 bp):
TATTATTATTGT
Found at i:1721 original size:15 final size:15
Alignment explanation
Indices: 1689--1722 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1679 TAAAAAAAAA
* *
1689 TATTATTGTTGTTGT
1 TATTATTGTTATTAT
1704 TATTATTGTTATTAT
1 TATTATTGTTATTAT
1719 TATT
1 TATT
1723 TTTATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.68
Consensus pattern (15 bp):
TATTATTGTTATTAT
Found at i:1808 original size:17 final size:17
Alignment explanation
Indices: 1776--1808 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1766 TTTTTTGAGA
1776 AAAATTATTAAAATATT
1 AAAATTATTAAAATATT
1793 AAAA-TATTAAATATAT
1 AAAATTATTAAA-ATAT
1809 GGATTAACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATTATTAAAATATT
Found at i:4902 original size:20 final size:20
Alignment explanation
Indices: 4879--4917 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4869 ACTGGCGGGC
4879 TTTACTTGCTGAAGAAGGCA
1 TTTACTTGCTGAAGAAGGCA
*
4899 TTTACTTGCTGAGGAAGGC
1 TTTACTTGCTGAAGAAGGC
4918 GAACTCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (20 bp):
TTTACTTGCTGAAGAAGGCA
Found at i:5631 original size:155 final size:154
Alignment explanation
Indices: 5436--5804 Score: 417
Period size: 156 Copynumber: 2.4 Consensus size: 154
5426 TAAACCGAGC
* * *
5436 TTCTCACCTCAAATTGTCCTTAATTGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-AGA-ATG
1 TTCTCTCCTCAAA-TGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTA-ACAAG
*
5499 AGCTGAAATTTTGCCA-AG-GGACTTAGAATATCCACATAAGACTAT-GAAAAAATTCTAAGTAA
64 -GCT--AATTTT-CCACAGTAGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAA
* * * *
5561 AACCGAGCTTCCCTTG-GTAGTGAACTAGGT
125 AACCGAAC-TCCCTAGCATAGAGAACTAGGT
*
5591 TTCTCTCCCCAAATGGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTAACAAGG
1 TTCTCTCCTCAAAT-GTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTAACAAGG
* * *
5656 CTAATTTTCCACCAGTAGACTTAGATTATCCCCATAAGGCTATGGAAAAAATTCTAAGTAAAACC
65 CTAATTTTCCA-CAGTAGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACC
* * *
5721 GAACTCTCTAGCATAGAGAAGTTGGT
129 GAACTCCCTAGCATAGAGAACTAGGT
** * * * *
5747 TTGACTCCTCAAACTGTACTTAACTGAAAAACTAGCATAAGTTTTTCATACCAAGTCT
1 TTCTCTCCTCAAA-TGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCT
5805 GTTTGAGATG
Statistics
Matches: 183, Mismatches: 22, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
152 3 0.02
153 6 0.03
154 3 0.02
155 84 0.46
156 86 0.47
157 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (154 bp):
TTCTCTCCTCAAATGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTAACAAGGC
TAATTTTCCACAGTAGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGA
ACTCCCTAGCATAGAGAACTAGGT
Found at i:6618 original size:2 final size:2
Alignment explanation
Indices: 6611--6642 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6601 TTCCAATGTA
*
6611 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6643 GGAAATCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13159 original size:2 final size:2
Alignment explanation
Indices: 13148--13183 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
13138 CCCGAATTGC
13148 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13184 TAGTTTTACC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13315 original size:22 final size:21
Alignment explanation
Indices: 13290--13779 Score: 164
Period size: 22 Copynumber: 22.6 Consensus size: 21
13280 ATGATCCCAT
13290 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACC-TCC
* * * *
13312 TATGAAATTTTAACAACGATAC
1 TATGAAATTTTGATAAC-CTCC
**
13334 TATCG-AATTTTGATAACCTTTT
1 TAT-GAAATTTTGATAACC-TCC
** *
13356 TAT-AAATTTTTTTAACCTTCT
1 TATGAAATTTTGATAACC-TCC
13377 TATGAAATTTT-ATTAACCTCCC
1 TATGAAATTTTGA-TAACCT-CC
* * * *
13399 TAAGGAATTTTGA-AGATCTCAA
1 TATGAAATTTTGATA-ACCTC-C
* *
13421 TATAAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCT-CC
* *
13443 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TC-C
* * *
13466 TATGAGATGTTGATAACCCCC
1 TATGAAATTTTGATAACCTCC
* * *
13487 ATATG--ATATTGATAACCACAT
1 -TATGAAATTTTGATAACCTC-C
* * *
13508 TATGAAAATTTAAAAACCTCC
1 TATGAAATTTTGATAACCTCC
*
13529 ATATG-AATTGTT-AGTAACCACAC
1 -TATGAAATT-TTGA-TAACCTC-C
* * *
13552 -ATTGAAATTTTGATAATCACAT
1 TA-TGAAATTTTGATAACCTC-C
* *
13574 TGTGAAATTGTGATAACCTCAC
1 TATGAAATTTTGATAACCTC-C
* *
13596 TACGAAATTTTGATGAATCTTCC
1 TATGAAATTTTGAT-AA-CCTCC
*
13619 TATAAAATTTTGATAAACCTCTC
1 TATGAAATTTTGAT-AACCTC-C
* * *
13642 TATAAAATTTTGATAACTTGCT
1 TATGAAATTTTGATAACCT-CC
* *
13664 TATAAAATCTTGATAA----C
1 TATGAAATTTTGATAACCTCC
* *
13681 TA-CAAATTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTC-C
* *
13702 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCT-CC
* * * *
13724 TATGAACTTTTGATCTACAT-A
1 TATGAAATTTTGAT-AACCTCC
*
13745 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAA-CCTCC
13767 TATGAAATTTTGA
1 TATGAAATTTTGA
13780 AAACTAAATT
Statistics
Matches: 348, Mismatches: 80, Indels: 80
0.69 0.16 0.16
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
20 17 0.05
21 43 0.12
22 210 0.60
23 62 0.18
24 3 0.01
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:13365 original size:21 final size:21
Alignment explanation
Indices: 13339--13395 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 21
13329 GATACTATCG
*
13339 AATTTTGATAACCTTTTTAT-A
1 AATTTT-ATAACCTTCTTATGA
*
13360 AATTTTTTTAACCTTCTTATGA
1 AA-TTTTATAACCTTCTTATGA
13382 AATTTTATTAACCT
1 AATTTTA-TAACCT
13396 CCCTAAGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.32, C:0.12, G:0.04, T:0.53
Consensus pattern (21 bp):
AATTTTATAACCTTCTTATGA
Found at i:13511 original size:20 final size:19
Alignment explanation
Indices: 13452--13512 Score: 50
Period size: 20 Copynumber: 2.9 Consensus size: 19
13442 CAATGAAATT
*
13452 TTGATAACCAACACTATGAGATG
1 TTGATAACC-ACA-TAT--GATA
*
13475 TTGATAACCCCCATATGATA
1 TTGATAA-CCACATATGATA
13495 TTGATAACCACATTATGA
1 TTGATAACCACA-TATGA
13513 AAATTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 4 0.12
20 15 0.45
22 3 0.09
23 9 0.27
24 2 0.06
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.30
Consensus pattern (19 bp):
TTGATAACCACATATGATA
Found at i:13626 original size:23 final size:21
Alignment explanation
Indices: 13600--13681 Score: 92
Period size: 23 Copynumber: 3.7 Consensus size: 21
13590 CCTCACTACG
13600 AAATTTTGATGAATCTTCCTATA
1 AAATTTTGAT-AA-CTTCCTATA
*
13623 AAATTTTGATAAACCTCTCTATA
1 AAATTTTGAT-AACTTC-CTATA
*
13646 AAATTTTGATAACTTGCTTATA
1 AAATTTTGATAACTT-CCTATA
*
13668 AAATCTTGATAACT
1 AAATTTTGATAACT
13682 ACAAATTTTG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
22 24 0.46
23 28 0.54
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.41
Consensus pattern (21 bp):
AAATTTTGATAACTTCCTATA
Found at i:13668 original size:45 final size:46
Alignment explanation
Indices: 13578--13679 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 46
13568 TCACATTGTG
* *
13578 AAATTGTGAT-AACCTCACTACGAAATTTTGATGAATCTTCCTATA
1 AAATTTTGATAAACCTCACTACAAAATTTTGATGAATCTTCCTATA
* * *
13623 AAATTTTGATAAACCTCTCTATAAAATTTTGAT-AA-CTTGCTTATA
1 AAATTTTGATAAACCTCACTACAAAATTTTGATGAATCTT-CCTATA
*
13668 AAATCTTGATAA
1 AAATTTTGATAA
13680 CTACAAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
44 3 0.06
45 27 0.55
46 19 0.39
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (46 bp):
AAATTTTGATAAACCTCACTACAAAATTTTGATGAATCTTCCTATA
Found at i:13933 original size:22 final size:22
Alignment explanation
Indices: 13908--14032 Score: 85
Period size: 22 Copynumber: 5.7 Consensus size: 22
13898 AATCAGATTT
13908 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* *
13930 TGAAATTTTGATAGCCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* * *
13952 T-AAAATTTTGTTGACCCCTTTA
1 TGAAAA-TTTGATAACCTCTTTA
* * * *
13974 T-AAAATTCTTATAATCACATTA
1 TGAAAATT-TGATAACCTCTTTA
* * *
13996 TGTAATTTTGATAACCTCGCTT-
1 TGAAAATTTGATAACCTC-TTTA
*
14018 TGAAATTTTGATAAC
1 TGAAAATTTGATAAC
14033 AACGCTATGA
Statistics
Matches: 79, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
21 5 0.06
22 68 0.86
23 6 0.08
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:14062 original size:22 final size:22
Alignment explanation
Indices: 13994--14072 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
13984 ATAATCACAT
* *
13994 TATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACATCGC
* *
14016 TTTGAAATTTTGATAACAACGC
1 TATGAAATTTTGATAACATCGC
*
14038 TATGAAATTTTGATAATCTTC-C
1 TATGAAATTTTGATAA-CATCGC
14060 TAT-AAATTTTGAT
1 TATGAAATTTTGAT
14073 GGTACTCCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
21 10 0.20
22 37 0.76
23 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAACATCGC
Found at i:14164 original size:22 final size:22
Alignment explanation
Indices: 14110--14425 Score: 119
Period size: 22 Copynumber: 14.6 Consensus size: 22
14100 ATAACTATAG
*
14110 AATTTTGATAACCTC-CCATGA
1 AATTTTGATAACCTCACTATGA
*
14131 AATATT-AGTAACCTC-CTAATGA
1 AATTTTGA-TAACCTCACT-ATGA
* *
14153 AATTTTGTTAACCACACTATGA
1 AATTTTGATAACCTCACTATGA
*
14175 AATTCTT-ATAACCTCGCTATGA
1 AATT-TTGATAACCTCACTATGA
* * ** *
14197 CATTTTGATAACATCTTTGATAA
1 AATTTTGATAACCTCACT-ATGA
* * *
14220 AATTTCT-ATAA---AATTGTGA
1 AATTT-TGATAACCTCACTATGA
* *
14239 TAA--TTAATCA-C-C-CTATGA
1 -AATTTTGATAACCTCACTATGA
** * *
14257 AATTTCAATAACC-AACCTAAGA
1 AATTTTGATAACCTCA-CTATGA
* *
14279 AATTTTAATAACCTGATCCTATGA
1 AATTTTGATAACCTCA--CTATGA
* *
14303 AATTTTGGTAACCACACTATGA
1 AATTTTGATAACCTCACTATGA
* *
14325 AAATTTGATAACTTC-CATATGA
1 AATTTTGATAACCTCAC-TATGA
* * *
14347 AATTTTGGTAACCACACTATGG
1 AATTTTGATAACCTCACTATGA
14369 AATTTTGATAACCTC-CTCATGA
1 AATTTTGATAACCTCACT-ATGA
* *
14391 AATTATAATAA-CT-ATCTTATGA
1 AATTTTGATAACCTCA-C-TATGA
14413 AATTTTGATAACC
1 AATTTTGATAACC
14426 ACATAGAGAC
Statistics
Matches: 221, Mismatches: 49, Indels: 48
0.69 0.15 0.15
Matches are distributed among these distances:
17 3 0.01
18 8 0.04
19 7 0.03
20 6 0.03
21 20 0.09
22 139 0.63
23 19 0.09
24 19 0.09
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.35
Consensus pattern (22 bp):
AATTTTGATAACCTCACTATGA
Found at i:14353 original size:44 final size:43
Alignment explanation
Indices: 14295--14394 Score: 155
Period size: 44 Copynumber: 2.3 Consensus size: 43
14285 AATAACCTGA
*
14295 TCCTATGAAATTTTGGTAACCACACTATGAAAATTTGATAACT
1 TCCTATGAAATTTTGGTAACCACACTATGAAAATTTGATAACC
* *
14338 TCCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC
1 TCC-TATGAAATTTTGGTAACCACACTATGAAAATTTGATAACC
14382 TCCTCATGAAATT
1 TCCT-ATGAAATT
14395 ATAATAACTA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
43 4 0.08
44 48 0.92
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (43 bp):
TCCTATGAAATTTTGGTAACCACACTATGAAAATTTGATAACC
Found at i:14402 original size:66 final size:66
Alignment explanation
Indices: 14297--14428 Score: 162
Period size: 66 Copynumber: 2.0 Consensus size: 66
14287 TAACCTGATC
* * *
14297 CTATGAAATTTTGGTAACCACACTATGAAAATTTGATAACT-TCCATATGAAATTTTGGTAACCA
1 CTATGAAATTTTGATAACCACACTATGAAAATTTAATAACTAT-CATATGAAATTTTGATAACCA
14361 CA
65 CA
* * *
14363 CTATGGAATTTTGATAACCTC-CTCATG-AAATTATAATAACTATCTTATGAAATTTTGATAACC
1 CTATGAAATTTTGATAACCACACT-ATGAAAATT-TAATAACTATCATATGAAATTTTGATAACC
14426 ACA
64 ACA
14429 TAGAGACAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
65 7 0.12
66 49 0.86
67 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (66 bp):
CTATGAAATTTTGATAACCACACTATGAAAATTTAATAACTATCATATGAAATTTTGATAACCAC
A
Found at i:14496 original size:13 final size:13
Alignment explanation
Indices: 14478--14502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14468 ATTATGATTA
14478 AAAAAATAATTTT
1 AAAAAATAATTTT
14491 AAAAAATAATTT
1 AAAAAATAATTT
14503 AATAAGGAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAAAATAATTTT
Found at i:14503 original size:12 final size:12
Alignment explanation
Indices: 14478--14527 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 12
14468 ATTATGATTA
14478 AAAAAATAATTTT
1 AAAAAATAA-TTT
14491 AAAAAATAATTT
1 AAAAAATAATTT
*
14503 AATAAGGAATAATTA
1 AA-AA--AATAATTT
14518 AAAAAATAAT
1 AAAAAATAAT
14528 GGAATAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
12 11 0.33
13 11 0.33
14 2 0.06
15 9 0.27
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (12 bp):
AAAAAATAATTT
Found at i:14533 original size:20 final size:19
Alignment explanation
Indices: 14503--14540 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
14493 AAAATAATTT
14503 AATAAGGAATAATTAAAAA
1 AATAAGGAATAATTAAAAA
14522 AATAATGGAATAATTAAAA
1 AATAA-GGAATAATTAAAA
14541 TATTATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.24
Consensus pattern (19 bp):
AATAAGGAATAATTAAAAA
Found at i:14533 original size:27 final size:28
Alignment explanation
Indices: 14482--14534 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
14472 TGATTAAAAA
* **
14482 AATAATTTTAAAAAATAATTTAATAAGG
1 AATAATTTAAAAAAATAATGGAATAAGG
14510 AATAA-TTAAAAAAATAATGGAATAA
1 AATAATTTAAAAAAATAATGGAATAA
14535 TTAAAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (28 bp):
AATAATTTAAAAAAATAATGGAATAAGG
Found at i:15622 original size:11 final size:11
Alignment explanation
Indices: 15608--15645 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
15598 ATTCATAACA
15608 AATTTATAATT
1 AATTTATAATT
15619 AATTTATAATT
1 AATTTATAATT
15630 -ATTTGATAATT
1 AATTT-ATAATT
*
15641 TATTT
1 AATTT
15646 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:16346 original size:10 final size:10
Alignment explanation
Indices: 16331--16361 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
16321 TTAATTATAA
16331 AAACATAGAT
1 AAACATAGAT
16341 AAACATAGAT
1 AAACATAGAT
16351 AAACATAGAT
1 AAACATAGAT
16361 A
1 A
16362 TTGGTACTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.19
Consensus pattern (10 bp):
AAACATAGAT
Found at i:16456 original size:20 final size:21
Alignment explanation
Indices: 16431--16473 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
16421 GTTTTATGGA
16431 TTGCTAAA-CACCG-CCCCCTT
1 TTGCTAAATC-CCGCCCCCCTT
16451 TTGCTAAATCCCGCCCCCCTT
1 TTGCTAAATCCCGCCCCCCTT
16472 TT
1 TT
16474 TACCCTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.16, C:0.44, G:0.09, T:0.30
Consensus pattern (21 bp):
TTGCTAAATCCCGCCCCCCTT
Found at i:16604 original size:24 final size:25
Alignment explanation
Indices: 16548--16602 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
16538 AACCCTAAAT
*
16548 TTCATTTCTAACAACTTCTTCAAAC
1 TTCATTTCTAACAACATCTTCAAAC
16573 TTCATTTCTAACAA-ATCTTCAAA-
1 TTCATTTCTAACAACATCTTCAAAC
16596 TTCATTT
1 TTCATTT
16603 TCCTTCATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 7 0.24
24 8 0.28
25 14 0.48
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.44
Consensus pattern (25 bp):
TTCATTTCTAACAACATCTTCAAAC
Found at i:16635 original size:11 final size:11
Alignment explanation
Indices: 16621--16667 Score: 58
Period size: 11 Copynumber: 3.9 Consensus size: 11
16611 TTAATCAGAA
16621 ACTAATTAAAT
1 ACTAATTAAAT
16632 ACTAATTAATCAT
1 ACTAATTAA--AT
16645 AAACTAATTAAAT
1 --ACTAATTAAAT
16658 ACTAATTAAA
1 ACTAATTAAA
16668 CATAAACTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 19 0.59
13 4 0.12
15 9 0.28
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (11 bp):
ACTAATTAAAT
Found at i:16640 original size:26 final size:26
Alignment explanation
Indices: 16611--16678 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
16601 TTTCCTTCAT
*
16611 TTAATCAGAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
16637 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
16663 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
16679 AAACTAAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.32
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:16678 original size:15 final size:15
Alignment explanation
Indices: 16632--16682 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
16622 CTAATTAAAT
*
16632 ACTAATTAATCATAA
1 ACTAATTAAACATAA
16647 ACTAATT-AA-AT--
1 ACTAATTAAACATAA
16658 ACTAATTAAACATAA
1 ACTAATTAAACATAA
16673 ACTAA-TAAAC
1 ACTAATTAAAC
16683 TAAGTACTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
11 7 0.23
12 2 0.06
13 4 0.13
14 6 0.19
15 12 0.39
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (15 bp):
ACTAATTAAACATAA
Found at i:16768 original size:16 final size:18
Alignment explanation
Indices: 16732--16772 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
16722 CTAATTAATA
*
16732 TTAAAAAAAAAATAATTT
1 TTAAAAAAAAAATAATCT
16750 TTAAAAAAAAAA-AA-CT
1 TTAAAAAAAAAATAATCT
16766 TTAAAAA
1 TTAAAAA
16773 TGGCCTAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 2 0.09
18 12 0.55
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
TTAAAAAAAAAATAATCT
Found at i:17027 original size:20 final size:21
Alignment explanation
Indices: 16996--17039 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
16986 AAAAATTATG
16996 AAAAGAGGGGCGGTATTTAGC
1 AAAAGAGGGGCGGTATTTAGC
*
17017 AAAAG-GGGGCGGTGTTTAGC
1 AAAAGAGGGGCGGTATTTAGC
17037 AAA
1 AAA
17040 CCCCGTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.34, C:0.09, G:0.39, T:0.18
Consensus pattern (21 bp):
AAAAGAGGGGCGGTATTTAGC
Found at i:20740 original size:40 final size:41
Alignment explanation
Indices: 20684--20767 Score: 125
Period size: 40 Copynumber: 2.1 Consensus size: 41
20674 TCCAACTTGA
* * *
20684 CCCTCCTAATAATTAAGGAAATAAATTAAATTCAGGTTTAG
1 CCCTCCTAATAATTAAGGAAAGAAATTAAATCCAGCTTTAG
*
20725 CCCT-CTAATAATTAAGGTAAGAAATTAAATCCAGCTTTAG
1 CCCTCCTAATAATTAAGGAAAGAAATTAAATCCAGCTTTAG
20765 CCC
1 CCC
20768 CTAGTTATAG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 35 0.90
41 4 0.10
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (41 bp):
CCCTCCTAATAATTAAGGAAAGAAATTAAATCCAGCTTTAG
Done.