Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009508.1 Corchorus capsularis cultivar CVL-1 contig09529, 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: 97009
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:3022 original size:15 final size:15
Alignment explanation
Indices: 3004--3038 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2994 TAACTCTCCA
3004 TGGGAGAGTGATTCT
1 TGGGAGAGTGATTCT
3019 TGGGAGAGTGATTCT
1 TGGGAGAGTGATTCT
*
3034 AGGGA
1 TGGGA
3039 AAGTAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.23, C:0.06, G:0.43, T:0.29
Consensus pattern (15 bp):
TGGGAGAGTGATTCT
Found at i:4688 original size:18 final size:18
Alignment explanation
Indices: 4657--4703 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
4647 TTTGATCAGT
* *
4657 ATTACCTTTTCGATCAAA
1 ATTACCTCTGCGATCAAA
* *
4675 GTTGCCTCTGCGATCAAA
1 ATTACCTCTGCGATCAAA
4693 ATTACCTCTGC
1 ATTACCTCTGC
4704 CAAAACCTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.34
Consensus pattern (18 bp):
ATTACCTCTGCGATCAAA
Found at i:5374 original size:17 final size:17
Alignment explanation
Indices: 5352--5386 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5342 ATAGTGAATA
*
5352 TAAAATTTCATCTATAT
1 TAAAATTTCATCCATAT
5369 TAAAATTTCATCCATAT
1 TAAAATTTCATCCATAT
5386 T
1 T
5387 CTATAGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAATTTCATCCATAT
Found at i:6273 original size:17 final size:15
Alignment explanation
Indices: 6239--6281 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
6229 ATATTTTTTA
6239 TTAAAAAAATAATTT
1 TTAAAAAAATAATTT
6254 TTAAAAAAATATATATT
1 TTAAAAAAATA-AT-TT
6271 TTAAACAAAAT
1 TTAAA-AAAAT
6282 TGGGTGAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.44
16 2 0.08
17 7 0.28
18 5 0.20
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAAAAAAATAATTT
Found at i:7788 original size:2 final size:2
Alignment explanation
Indices: 7776--7832 Score: 52
Period size: 2 Copynumber: 30.5 Consensus size: 2
7766 GATAAAGTAT
*
7776 TA TA T- TA TA TA TA TA TA T- TA TA T- TA TA T- TA TA CA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
7813 TA TA GTG TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA T
7833 GCTCAACTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
1 5 0.11
2 39 0.87
3 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (2 bp):
TA
Found at i:8158 original size:44 final size:44
Alignment explanation
Indices: 8110--8303 Score: 154
Period size: 44 Copynumber: 4.3 Consensus size: 44
8100 AACATCCAAA
* *
8110 GAAATTTTGATAACCACATTATGAAATTTTGATAACCTTATTGT
1 GAAATTTTGATAACCACATTATGAAATTTTGATAACCTTACTAT
* * * * * * * *
8154 GAAATATTGGTAAGCATACTATGAAAATTTGATAAACTCACTAT
1 GAAATTTTGATAACCACATTATGAAATTTTGATAACCTTACTAT
* * * * * * *
8198 AAAATGTTGGTAATCACATTGTGAAATTTTGATAATCATATATATTAT
1 GAAATTTTGATAACCACATTATGAAATTTTGATAA-C--CT-TACTAT
** * *
8246 GAAATTTTGATAACTTCATTATGATATTTTGATTAACCTTCCTAT
1 GAAATTTTGATAACCACATTATGAAATTTTGA-TAACCTTACTAT
8291 GAAATTTTGATAA
1 GAAATTTTGATAA
8304 ATTTTCCTAT
Statistics
Matches: 113, Mismatches: 32, Indels: 9
0.73 0.21 0.06
Matches are distributed among these distances:
44 62 0.55
45 17 0.15
46 1 0.01
47 1 0.01
48 29 0.26
49 3 0.03
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (44 bp):
GAAATTTTGATAACCACATTATGAAATTTTGATAACCTTACTAT
Found at i:8291 original size:23 final size:23
Alignment explanation
Indices: 8243--8346 Score: 99
Period size: 23 Copynumber: 4.6 Consensus size: 23
8233 TCATATATAT
*
8243 TATGAAATTTTGA-TAA-CTTCAT
1 TATGAAATTTTGATTAACCTTC-C
*
8265 TATGATATTTTGATTAACCTTCC
1 TATGAAATTTTGATTAACCTTCC
* **
8288 TATGAAATTTTGATAAATTTTCC
1 TATGAAATTTTGATTAACCTTCC
* *
8311 TATAAAATTGTGA-TAACC-TCC
1 TATGAAATTTTGATTAACCTTCC
8332 TTATGAAATTTTGAT
1 -TATGAAATTTTGAT
8347 AACTTCAAAT
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
21 3 0.05
22 25 0.38
23 33 0.51
24 4 0.06
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.45
Consensus pattern (23 bp):
TATGAAATTTTGATTAACCTTCC
Found at i:8295 original size:45 final size:44
Alignment explanation
Indices: 8242--8353 Score: 129
Period size: 45 Copynumber: 2.5 Consensus size: 44
8232 ATCATATATA
* * * *
8242 TTATGAAATTTTGATAACTTCATTATGATATTTTGATTAACCTTCC
1 TTATGAAATTTTGATAACTTCACTATAAAATTGTGA-TAACC-TCC
*
8288 -TATGAAATTTTGATAAATTTTC-CTATAAAATTGTGATAACCTCC
1 TTATGAAATTTTGAT-AA-CTTCACTATAAAATTGTGATAACCTCC
8332 TTATGAAATTTTGATAACTTCA
1 TTATGAAATTTTGATAACTTCA
8354 AATTTTCATA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
43 3 0.05
44 5 0.09
45 33 0.59
46 12 0.21
47 3 0.05
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (44 bp):
TTATGAAATTTTGATAACTTCACTATAAAATTGTGATAACCTCC
Found at i:8346 original size:22 final size:22
Alignment explanation
Indices: 8110--8349 Score: 135
Period size: 22 Copynumber: 10.6 Consensus size: 22
8100 AACATCCAAA
*
8110 GAAATTTTGATAACCACATTAT
1 GAAATTTTGATAACCTCATTAT
* *
8132 GAAATTTTGATAACCTTATTGT
1 GAAATTTTGATAACCTCATTAT
* * * *
8154 GAAATATTGGTAAGCAT-ACTAT
1 GAAATTTTGATAA-CCTCATTAT
* * *
8176 GAAAATTTGATAAACTCACTAT
1 GAAATTTTGATAACCTCATTAT
* * * * * *
8198 AAAATGTTGGTAATCACATTGT
1 GAAATTTTGATAACCTCATTAT
* *
8220 GAAATTTTGATAATCATATATATTAT
1 GAAATTTTGATAA-C--CT-CATTAT
*
8246 GAAATTTTGATAACTTCATTAT
1 GAAATTTTGATAACCTCATTAT
* *
8268 GATATTTTGATTAACCTTC-CTAT
1 GAAATTTTGA-TAACC-TCATTAT
** *
8291 GAAATTTTGATAAATTTTC-CTAT
1 GAAATTTTGAT-AA-CCTCATTAT
* * *
8314 AAAATTGTGATAACCTCCTTAT
1 GAAATTTTGATAACCTCATTAT
8336 GAAATTTTGATAAC
1 GAAATTTTGATAAC
8350 TTCAAATTTT
Statistics
Matches: 163, Mismatches: 44, Indels: 22
0.71 0.19 0.10
Matches are distributed among these distances:
21 3 0.02
22 104 0.64
23 36 0.22
24 2 0.01
25 1 0.01
26 17 0.10
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (22 bp):
GAAATTTTGATAACCTCATTAT
Found at i:8472 original size:20 final size:22
Alignment explanation
Indices: 8398--8475 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
8388 GTTAATCTCT
* * *
8398 CTATTAAATTTTGATATATATATA
1 CTATGAAATTTTGATA-AT-CACA
8422 CTATGAAATTTTGATAATCACA
1 CTATGAAATTTTGATAATCACA
* *
8444 CTATAAAATTTTGATAA-C-CC
1 CTATGAAATTTTGATAATCACA
8464 CTATGAAATTTT
1 CTATGAAATTTT
8476 AAAAACTAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 12 0.25
21 1 0.02
22 18 0.38
23 2 0.04
24 15 0.31
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACA
Found at i:8548 original size:22 final size:22
Alignment explanation
Indices: 8511--8611 Score: 71
Period size: 22 Copynumber: 4.6 Consensus size: 22
8501 AACCACCCTC
*
8511 TAAAA-TTTCATAACCTTTATA
1 TAAAATTTTCATAACCTTCATA
*
8532 TAAAATTTTGATAACCTTCATA
1 TAAAATTTTCATAACCTTCATA
* ** * *
8554 TGAAATTTTTGTTA-CTTCACA
1 TAAAATTTTCATAACCTTCATA
* * *
8575 GTAAAATTTTAATAACATTCCTA
1 -TAAAATTTTCATAACCTTCATA
* *
8598 TGAAATTTTTATAA
1 TAAAATTTTCATAA
8612 TCTACCTTTG
Statistics
Matches: 61, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
21 11 0.18
22 46 0.75
23 4 0.07
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.44
Consensus pattern (22 bp):
TAAAATTTTCATAACCTTCATA
Found at i:8655 original size:22 final size:22
Alignment explanation
Indices: 8629--8670 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
8619 TTGAAATACT
*
8629 ACACTCTAAAATTTTGATAATC
1 ACACTATAAAATTTTGATAATC
8651 ACACTATAAAATTTTGATAA
1 ACACTATAAAATTTTGATAA
8671 CCTCCTTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (22 bp):
ACACTATAAAATTTTGATAATC
Found at i:8685 original size:44 final size:43
Alignment explanation
Indices: 8637--8732 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 43
8627 CTACACTCTA
8637 AAATTTTGAT-AATCACACTATAAAATTTTGATAA-CCTCCTTATG
1 AAATTTTGATCAAT-ACACTATAAAATTTTGATAATCC-CC-TATG
* * * * *
8681 AAATTTTTATCTATATACTATGAAATTTTGATAATCCCCTGTG
1 AAATTTTGATCAATACACTATAAAATTTTGATAATCCCCTATG
8724 AAATTTTGA
1 AAATTTTGA
8733 AAAGTAAACC
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
43 11 0.25
44 29 0.66
45 4 0.09
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (43 bp):
AAATTTTGATCAATACACTATAAAATTTTGATAATCCCCTATG
Found at i:9455 original size:16 final size:16
Alignment explanation
Indices: 9436--9539 Score: 115
Period size: 16 Copynumber: 6.5 Consensus size: 16
9426 AACCCGCCCA
9436 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
9452 ACCCGCA-ACCC-AGATG
1 ACCCG-AGACCCGA-ATG
*
9468 ATCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
*
9484 ACCCGTA-ACCCGAGTG
1 ACCCG-AGACCCGAATG
*
9500 ACCCGAGACCCGTATG
1 ACCCGAGACCCGAATG
* *
9516 ACCCGAAACCCGAATA
1 ACCCGAGACCCGAATG
9532 ACCCGAGA
1 ACCCGAGA
9540 AGTTAACCCG
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
15 3 0.04
16 67 0.92
17 3 0.04
ACGTcount: A:0.32, C:0.38, G:0.22, T:0.09
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:9474 original size:32 final size:32
Alignment explanation
Indices: 9436--9539 Score: 138
Period size: 32 Copynumber: 3.2 Consensus size: 32
9426 AACCCGCCCA
*
9436 ACCCGAGACCCGAATGACCCGCAACCC-AGATG
1 ACCCGAGACCCGAATGACCCGAAACCCGAG-TG
* *
9468 ATCCGAGACCCGAATGACCCGTAACCCGAGTG
1 ACCCGAGACCCGAATGACCCGAAACCCGAGTG
* * *
9500 ACCCGAGACCCGTATGACCCGAAACCCGAATA
1 ACCCGAGACCCGAATGACCCGAAACCCGAGTG
9532 ACCCGAGA
1 ACCCGAGA
9540 AGTTAACCCG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
32 62 0.97
33 2 0.03
ACGTcount: A:0.32, C:0.38, G:0.22, T:0.09
Consensus pattern (32 bp):
ACCCGAGACCCGAATGACCCGAAACCCGAGTG
Found at i:10619 original size:9 final size:9
Alignment explanation
Indices: 10607--10655 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
10597 GTAGACCCCA
10607 GACCCGAAT
1 GACCCGAAT
10616 GACCCGGAA-
1 GACCC-GAAT
10625 -A-CCGAAT
1 GACCCGAAT
10632 GACCCG-A-
1 GACCCGAAT
10639 GACCCGAAT
1 GACCCGAAT
10648 GACCCGAA
1 GACCCGAA
10656 ACCTGTATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
6 3 0.09
7 8 0.24
8 4 0.12
9 16 0.47
10 3 0.09
ACGTcount: A:0.35, C:0.35, G:0.24, T:0.06
Consensus pattern (9 bp):
GACCCGAAT
Found at i:10619 original size:16 final size:16
Alignment explanation
Indices: 10600--10678 Score: 70
Period size: 16 Copynumber: 4.9 Consensus size: 16
10590 AGACCCGGTA
10600 GACCCCAGACCCGAAT
1 GACCCCAGACCCGAAT
* *
10616 GA-CCCGGAAACCGAAT
1 GACCCCAG-ACCCGAAT
*
10632 GACCCGAGACCCGAAT
1 GACCCCAGACCCGAAT
* * * *
10648 GACCCGAAACCTGTAT
1 GACCCCAGACCCGAAT
*
10664 GACCCAAGACCCGAA
1 GACCCCAGACCCGAA
10679 ACTTGAATAA
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
15 4 0.08
16 42 0.86
17 3 0.06
ACGTcount: A:0.34, C:0.37, G:0.22, T:0.08
Consensus pattern (16 bp):
GACCCCAGACCCGAAT
Found at i:10621 original size:32 final size:32
Alignment explanation
Indices: 10585--10678 Score: 104
Period size: 32 Copynumber: 2.9 Consensus size: 32
10575 AACCCGCCCA
* *
10585 ACCCGAGACCCGGTA-GACCCCAGACCCGAATG
1 ACCCGAGAACC-GTATGACCCAAGACCCGAATG
* *
10617 ACCCG-GAAACCGAATGACCCGAGACCCGAATG
1 ACCCGAG-AACCGTATGACCCAAGACCCGAATG
10649 ACCCGA-AACCTGTATGACCCAAGACCCGAA
1 ACCCGAGAACC-GTATGACCCAAGACCCGAA
10679 ACTTGAATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
31 7 0.13
32 46 0.87
ACGTcount: A:0.33, C:0.37, G:0.22, T:0.07
Consensus pattern (32 bp):
ACCCGAGAACCGTATGACCCAAGACCCGAATG
Found at i:10691 original size:23 final size:23
Alignment explanation
Indices: 10648--10691 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
10638 AGACCCGAAT
* *
10648 GACCCGAAACCTGTATGACCCAA
1 GACCCGAAACCTGAATAACCCAA
*
10671 GACCCGAAACTTGAATAACCC
1 GACCCGAAACCTGAATAACCC
10692 GAACCCAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.34, G:0.16, T:0.14
Consensus pattern (23 bp):
GACCCGAAACCTGAATAACCCAA
Found at i:10712 original size:16 final size:16
Alignment explanation
Indices: 10671--10724 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
10661 TATGACCCAA
**
10671 GACCCGAAACTTGAAT
1 GACCCGAAACCCGAAT
*
10687 AACCCG-AACCC-AGAT
1 GACCCGAAACCCGA-AT
10702 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
10718 GACCCGA
1 GACCCGA
10725 GAAAACAGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 10 0.32
16 19 0.61
17 1 0.03
ACGTcount: A:0.37, C:0.35, G:0.19, T:0.09
Consensus pattern (16 bp):
GACCCGAAACCCGAAT
Found at i:24604 original size:13 final size:13
Alignment explanation
Indices: 24586--24620 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
24576 AGAAACTTCA
24586 GGAGGGTCAACTT
1 GGAGGGTCAACTT
* *
24599 GGAGGGACAAGTT
1 GGAGGGTCAACTT
24612 GGAGGGTCA
1 GGAGGGTCA
24621 TGTAGCAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.46, T:0.17
Consensus pattern (13 bp):
GGAGGGTCAACTT
Found at i:28031 original size:20 final size:20
Alignment explanation
Indices: 28006--28046 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
27996 TGAAGATGTC
28006 TTAAAAACCCACTTAACATA
1 TTAAAAACCCACTTAACATA
*
28026 TTAAAAATCCACTTAACATA
1 TTAAAAACCCACTTAACATA
28046 T
1 T
28047 CAATAATTAA
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:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (20 bp):
TTAAAAACCCACTTAACATA
Found at i:29847 original size:31 final size:31
Alignment explanation
Indices: 29809--29873 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
29799 AACTGAACTA
29809 ACTCAAACATCCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
*
29840 ACTCAAACATTCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
29871 ACT
1 ACT
29874 GATAACCCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.22
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAGATCTGGAG
Found at i:65641 original size:23 final size:23
Alignment explanation
Indices: 65594--65638 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
65584 TAAACAGAAT
65594 CAGAGACTGGACTTGCAGCAAAA
1 CAGAGACTGGACTTGCAGCAAAA
65617 CAGAGACTGGACTT-CAGCAAAA
1 CAGAGACTGGACTTGCAGCAAAA
65639 ACAAAACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.13
Consensus pattern (23 bp):
CAGAGACTGGACTTGCAGCAAAA
Found at i:66766 original size:30 final size:31
Alignment explanation
Indices: 66707--66766 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
66697 AAAAGTCACA
*
66707 TGTGATTTTTTAATAACACCTGGCCAAATAG
1 TGTGATTTTTTAATAACACATGGCCAAATAG
** *
66738 TGTGA-TTTTTAATGGCACATGGCTAAATA
1 TGTGATTTTTTAATAACACATGGCCAAATA
66767 AATTACACCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (31 bp):
TGTGATTTTTTAATAACACATGGCCAAATAG
Found at i:69362 original size:16 final size:16
Alignment explanation
Indices: 69341--69373 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
69331 AAAAAAAAAC
69341 ACATATACAACTATAT
1 ACATATACAACTATAT
69357 ACATATACAACTATAT
1 ACATATACAACTATAT
69373 A
1 A
69374 TTTCATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (16 bp):
ACATATACAACTATAT
Found at i:70207 original size:11 final size:11
Alignment explanation
Indices: 70191--70221 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
70181 TTCTGTTTTT
70191 GTTTTTGTTTC
1 GTTTTTGTTTC
*
70202 GTTTTTGTTTT
1 GTTTTTGTTTC
70213 GTTTTTGTT
1 GTTTTTGTT
70222 GCGCTGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.03, G:0.19, T:0.77
Consensus pattern (11 bp):
GTTTTTGTTTC
Found at i:70207 original size:17 final size:17
Alignment explanation
Indices: 70180--70221 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
70170 CGTTTTCGTT
70180 TTTCTGTTTTTGTTTTTG
1 TTTCTGTTTTTG-TTTTG
70198 TTTC-GTTTTTGTTTTG
1 TTTCTGTTTTTGTTTTG
*
70214 TTTTTGTT
1 TTTCTGTT
70222 GCGCTGTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 8 0.36
17 10 0.45
18 4 0.18
ACGTcount: A:0.00, C:0.05, G:0.17, T:0.79
Consensus pattern (17 bp):
TTTCTGTTTTTGTTTTG
Found at i:70218 original size:6 final size:6
Alignment explanation
Indices: 70179--70221 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
70169 TCGTTTTCGT
*
70179 TTTTCTG TTTTTG TTTTTG -TTTCG TTTTTG -TTTTG TTTTTG TT
1 TTTT-TG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TT
70222 GCGCTGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 9 0.28
6 19 0.59
7 4 0.12
ACGTcount: A:0.00, C:0.05, G:0.16, T:0.79
Consensus pattern (6 bp):
TTTTTG
Found at i:83114 original size:5 final size:5
Alignment explanation
Indices: 83099--83136 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
83089 ACTTATATTA
*
83099 GTTGCT GTTGT GTTGT GTTGT GTTGT GTCGT GTTGT GT
1 GTTG-T GTTGT GTTGT GTTGT GTTGT GTTGT GTTGT GT
83137 GCTTCCATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.00, C:0.05, G:0.39, T:0.55
Consensus pattern (5 bp):
GTTGT
Found at i:83533 original size:31 final size:31
Alignment explanation
Indices: 83498--83559 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
83488 GTCCCACCTA
83498 ATAATTTCTCATCTTTTGGGAGTCCCATAGC
1 ATAATTTCTCATCTTTTGGGAGTCCCATAGC
83529 ATAATTTCTCATCTTTTGGGAGTCCCATAGC
1 ATAATTTCTCATCTTTTGGGAGTCCCATAGC
83560 GTATTGGCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.39
Consensus pattern (31 bp):
ATAATTTCTCATCTTTTGGGAGTCCCATAGC
Found at i:86291 original size:6 final size:6
Alignment explanation
Indices: 86282--86324 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
86272 GCGTCCACGA
* * * *
86282 CCACCT CCACCA CCACCA CCACCA CCACCT CCACGT CCACCT C
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT C
86325 TGCCTCTAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.23, C:0.65, G:0.02, T:0.09
Consensus pattern (6 bp):
CCACCT
Found at i:86296 original size:3 final size:3
Alignment explanation
Indices: 86276--86315 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
86266 TCCTGAGCGT
* * *
86276 CCA CGA CCA CCT CCA CCA CCA CCA CCA CCA CCA CCT CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA C
86316 GTCCACCTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.28, C:0.65, G:0.03, T:0.05
Consensus pattern (3 bp):
CCA
Found at i:86324 original size:12 final size:12
Alignment explanation
Indices: 86275--86315 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
86265 CTCCTGAGCG
*
86275 TCCACGACCACC
1 TCCACCACCACC
86287 TCCACCACCACC
1 TCCACCACCACC
*
86299 ACCACCACCACC
1 TCCACCACCACC
86311 TCCAC
1 TCCAC
86316 GTCCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.27, C:0.63, G:0.02, T:0.07
Consensus pattern (12 bp):
TCCACCACCACC
Found at i:94214 original size:29 final size:31
Alignment explanation
Indices: 94182--94247 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
94172 TGGTATTGAT
94182 TTGAGCAAGTT-G-AAAGGTTTGGTACCAAA
1 TTGAGCAAGTTAGAAAAGGTTTGGTACCAAA
**
94211 TTGAGCATTTTAGAAAAGGTTTGGTACCAAA
1 TTGAGCAAGTTAGAAAAGGTTTGGTACCAAA
94242 TTGAGC
1 TTGAGC
94248 TTTTAGCCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 9 0.27
30 1 0.03
31 23 0.70
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (31 bp):
TTGAGCAAGTTAGAAAAGGTTTGGTACCAAA
Found at i:94232 original size:31 final size:30
Alignment explanation
Indices: 94194--94253 Score: 111
Period size: 31 Copynumber: 2.0 Consensus size: 30
94184 GAGCAAGTTG
94194 AAAGGTTTGGTACCAAATTGAGCATTTTAGA
1 AAAGGTTTGGTACCAAATTGAGC-TTTTAGA
94225 AAAGGTTTGGTACCAAATTGAGCTTTTAG
1 AAAGGTTTGGTACCAAATTGAGCTTTTAG
94254 CCTTGTATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 6 0.21
31 23 0.79
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (30 bp):
AAAGGTTTGGTACCAAATTGAGCTTTTAGA
Found at i:94729 original size:29 final size:29
Alignment explanation
Indices: 94694--94771 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
94684 ACTTATAGTG
* *
94694 TTTGGACGTTTTGTCCCCTGAACTTTAAT
1 TTTGGACATTTTGACCCCTGAACTTTAAT
94723 TTTGGACATTTT-ACCCCATGAACTTTAAT
1 TTTGGACATTTTGACCCC-TGAACTTTAAT
*
94752 TTTGGAACATTTTGCCCCCT
1 TTTGG-ACATTTTGACCCCT
94772 CAGCCAAACG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 4 0.09
29 27 0.63
30 8 0.19
31 4 0.09
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (29 bp):
TTTGGACATTTTGACCCCTGAACTTTAAT
Found at i:96293 original size:109 final size:109
Alignment explanation
Indices: 96026--96320 Score: 441
Period size: 109 Copynumber: 2.7 Consensus size: 109
96016 ACTATTATAG
* * *
96026 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA-T---TCTAATATCTTTATAATTACTT
96091 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTCTAATATACAA
62 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTCTAATATACAA
*
96139 TTTTATTCTACTAAAAACTCTATTTTCATTTATTTAAA-TCTAATATCTTTATAATTACTTTATT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATT
*
96203 TTTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTTACCAAAAAATTTGGATATACTAAAA-TTTTTCTAATATACAA
* **
96248 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTC-AATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTT-TATAA-TTACTTTA
96312 TTTTTACCA
64 TTTTTACCA
96321 TTTTAATTTA
Statistics
Matches: 169, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
108 53 0.31
109 60 0.36
110 7 0.04
111 15 0.09
113 34 0.20
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATT
TTTACCAAAAAATTTGGATATACTAAAATTTTTCTAATATACAA
Done.