Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007162.1 Corchorus capsularis cultivar CVL-1 contig07183, 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: 29186
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4640 original size:22 final size:22
Alignment explanation
Indices: 4612--4676 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
4602 TTAGTAATCA
4612 CACACTCTGAAATTTTGATAAT
1 CACACTCTGAAATTTTGATAAT
4634 CACACTCTGAAATTTTGATAAT
1 CACACTCTGAAATTTTGATAAT
* *
4656 CACACTATGAAATTGTGATAA
1 CACACTCTGAAATTTTGATAA
4677 CCTCGTTATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (22 bp):
CACACTCTGAAATTTTGATAAT
Found at i:4715 original size:23 final size:23
Alignment explanation
Indices: 4643--4744 Score: 91
Period size: 23 Copynumber: 4.5 Consensus size: 23
4633 TCACACTCTG
* * * *
4643 AAATTTTGAT-AATCACACTATG
1 AAATTTTGATAAACCTCCCTATA
* ** *
4665 AAATTGTGAT-AACCTCGTTATG
1 AAATTTTGATAAACCTCCCTATA
* * *
4687 AAATTTTGATAAATCTTCCTTTA
1 AAATTTTGATAAACCTCCCTATA
4710 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
4733 AAATTTTGATAA
1 AAATTTTGATAA
4745 CTTTCTTATG
Statistics
Matches: 64, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
22 26 0.41
23 38 0.59
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:4880 original size:22 final size:21
Alignment explanation
Indices: 4619--4952 Score: 124
Period size: 22 Copynumber: 15.6 Consensus size: 21
4609 TCACACACTC
* *
4619 TGAAATTTTGATAATCACACTC
1 TGAAATTTTGATAA-CACTCTA
*
4641 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAA-CACTCTA
*
4663 TGAAATTGTGATAAC-CTCGTTA
1 TGAAATTTTGATAACACTC--TA
*
4685 TGAAATTTTGATAA-ATCTTCCTT
1 TGAAATTTTGATAACA-C-T-CTA
*
4708 TAAAATTTTGATAA-ACCTCCCTA
1 TGAAATTTTGATAACA-CT--CTA
* **
4731 TAAAATTTTGATAACTTTCTTA
1 TGAAATTTTGATAACACTC-TA
*
4753 TGAAATCTTGAT-A-A--CTA
1 TGAAATTTTGATAACACTCTA
*
4770 -CAAATTTTGATAAC-CTTCCTA
1 TGAAATTTTGATAACAC-T-CTA
** * *
4791 TGATTTTTTGATAAC-CGTATTT
1 TGAAATTTTGATAACAC-T-CTA
* *
4813 TGAAATTTTGTTAA-TCTCCGTA
1 TGAAATTTTGATAACACT-C-TA
4835 TGAAATTTTGATCTAA-A-TACTA
1 TGAAATTTTGA--TAACACT-CTA
4857 TGAAATTTTGATAACACTCTTA
1 TGAAATTTTGATAACACTC-TA
* **
4879 TGAAATTTTGAAAACTAAACTA
1 TGAAATTTTGATAAC-ACTCTA
* * **
4901 TGAAATTGTGATATC-CTCCC
1 TGAAATTTTGATAACACTCTA
*
4921 TGAAATTTTGATATC-CTCCT-
1 TGAAATTTTGATAACACT-CTA
4941 TGAAATTTTGAT
1 TGAAATTTTGAT
4953 TACTCCATAA
Statistics
Matches: 244, Mismatches: 43, Indels: 52
0.72 0.13 0.15
Matches are distributed among these distances:
16 9 0.04
17 3 0.01
18 1 0.00
20 34 0.14
21 10 0.04
22 143 0.59
23 39 0.16
24 4 0.02
25 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (21 bp):
TGAAATTTTGATAACACTCTA
Found at i:4926 original size:20 final size:20
Alignment explanation
Indices: 4901--4952 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
4891 AACTAAACTA
*
4901 TGAAATTGTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
4921 TGAAATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
4941 TGAAATTTTGAT
1 TGAAATTTTGAT
4953 TACTCCATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.42
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:5099 original size:43 final size:43
Alignment explanation
Indices: 5024--5343 Score: 163
Period size: 44 Copynumber: 7.2 Consensus size: 43
5014 AGAAATACCA
*
5024 CTATGAAATTTTTG-TAATCACATTT-TGAAAATTTGGTAACCTCT
1 CTATGAAA-TTTTGATAATCAC-TTTAT-AAAATTTGATAACCTCT
* * * *
5068 TTATGAAATTTTGATAATCTCTTTATAAAATTTTGTTGACC-CT
1 CTATGAAATTTTGATAATCACTTTATAAAA-TTTGATAACCTCT
* * * * *
5111 CTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACTTTAT-AAAATTTGATAACCTCT
* * *
5155 CTTTGAAATTTTGATAAT--CTTCCTATAAATTTTGATAATCTGATCT
1 CTATGAAATTTTGATAATCACTT--TATAAAATTTGATAA-C--CTCT
* * * * *
5201 CTATGAAATTTCGATAATCACTCTATGAGATTTGGTAACCT-T
1 CTATGAAATTTTGATAATCACTTTATAAAATTTGATAACCTCT
* * * *
5243 CTATAAAATTTTGGT-A-CTCTTTATGAAATTGAGACTTTTATAACCT-T
1 CTATGAAATTTTGATAATCACTTTAT--AA---A-A-TTTGATAACCTCT
* ** *
5290 CATATGAAATTTTGATAACCACACTATAAAATTTTGATAACCTCC
1 C-TATGAAATTTTGATAATCACTTTATAAAA-TTTGATAACCTCT
*
5335 CCATGAAAT
1 CTATGAAAT
5344 ATTAGTAACC
Statistics
Matches: 208, Mismatches: 45, Indels: 46
0.70 0.15 0.15
Matches are distributed among these distances:
40 6 0.03
41 1 0.00
42 16 0.08
43 56 0.27
44 63 0.30
45 3 0.01
46 30 0.14
47 11 0.05
48 16 0.08
49 1 0.00
50 5 0.02
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (43 bp):
CTATGAAATTTTGATAATCACTTTATAAAATTTGATAACCTCT
Found at i:5182 original size:87 final size:86
Alignment explanation
Indices: 5024--5188 Score: 210
Period size: 87 Copynumber: 1.9 Consensus size: 86
5014 AGAAATACCA
* * * *
5024 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGGTAACCTCTTTATGAAATTTTGATAATCTC
1 CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAATCTC
*
5089 TTTATAAAATTTTGTTGACCCT
66 TCTAT-AAATTTTGTTGACCCT
* *
5111 CTATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAATC
1 CTATGAAATTTCTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAATC
5174 T-TCCTATAAATTTTG
64 TCT-CTATAAATTTTG
5189 ATAATCTGAT
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
86 13 0.19
87 53 0.78
88 2 0.03
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (86 bp):
CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAATCTC
TCTATAAATTTTGTTGACCCT
Found at i:5227 original size:22 final size:22
Alignment explanation
Indices: 5024--5233 Score: 126
Period size: 22 Copynumber: 9.5 Consensus size: 22
5014 AGAAATACCA
5024 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* * * * *
5047 -TTTGAAAATTTGGTAACCTCT
1 CTATGAAATTTTGATAATCACT
* *
5068 TTATGAAATTTTGATAATCTCT
1 CTATGAAATTTTGATAATCACT
* * * * *
5090 TTATAAAATTTTGTTGA-CCCT
1 CTATGAAATTTTGATAATCACT
*
5111 CTATGAAATTCTGATAATCACAT
1 CTATGAAATTTTGATAATCAC-T
* * * *
5134 -TATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACT
* *
5155 CTTTGAAATTTTGATAATC-TT
1 CTATGAAATTTTGATAATCACT
5176 CCTAT-AAATTTTGATAATCTGATCT
1 -CTATGAAATTTTGATAATC--A-CT
*
5201 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACT
*
5223 CTATGAGATTT
1 CTATGAAATTT
5234 GGTAACCTTC
Statistics
Matches: 144, Mismatches: 32, Indels: 23
0.72 0.16 0.12
Matches are distributed among these distances:
21 34 0.24
22 90 0.62
23 2 0.01
24 4 0.03
25 14 0.10
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:5307 original size:22 final size:21
Alignment explanation
Indices: 5278--5417 Score: 88
Period size: 22 Copynumber: 6.4 Consensus size: 21
5268 AAATTGAGAC
5278 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* *
5299 TTTTGATAACCACACTATAAAA
1 TTTTGATAACCTCA-TATGAAA
**
5321 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CATATGAAA
* *
5343 TATT-AGTAACCTCCTAATGAAA
1 TTTTGA-TAACCTCAT-ATGAAA
* * *
5365 TTTCGTTAACCACACTATGAAA
1 TTTTGATAACCTCA-TATGAAA
* *
5387 TTCTT-ATAACCTCGTTATGACA
1 TT-TTGATAACCTC-ATATGAAA
5409 TTTTGATAA
1 TTTTGATAA
5418 TCTCTTTGAT
Statistics
Matches: 91, Mismatches: 18, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
21 11 0.12
22 77 0.85
23 3 0.03
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.36
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:5366 original size:44 final size:44
Alignment explanation
Indices: 5293--5417 Score: 103
Period size: 44 Copynumber: 2.8 Consensus size: 44
5283 TAACCTTCAT
* * * *
5293 ATGAAATT-TTGATAACCACACT-ATAAAATTTTGATAACCTCCCC
1 ATGAAATTATT-ATAACCTC-CTAATGAAATTTTGATAACCACACC
* * *
5337 ATGAAA-TATTAGTAACCTCCTAATGAAATTTCGTTAACCACACT
1 ATGAAATTATTA-TAACCTCCTAATGAAATTTTGATAACCACACC
* * * *
5381 ATGAAATTCTTATAACCTCGTTATGACATTTTGATAA
1 ATGAAATTATTATAACCTCCTAATGAAATTTTGATAA
5418 TCTCTTTGAT
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
43 4 0.06
44 56 0.88
45 4 0.06
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (44 bp):
ATGAAATTATTATAACCTCCTAATGAAATTTTGATAACCACACC
Found at i:5513 original size:46 final size:46
Alignment explanation
Indices: 5460--5548 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
5450 AATTAACAAC
5460 CCTATGAAATTTCAATAACCA-ACCTAAGAAATTTCAATAACTTGAT
1 CCTATGAAATTTCAATAACCACA-CTAAGAAATTTCAATAACTTGAT
*** * *
5506 CCTATGAAATTTTGGTAACCACACTATGAAATTTTAATAACTT
1 CCTATGAAATTTCAATAACCACACTAAGAAATTTCAATAACTT
5549 CCATATGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
46 36 0.97
47 1 0.03
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (46 bp):
CCTATGAAATTTCAATAACCACACTAAGAAATTTCAATAACTTGAT
Found at i:5571 original size:44 final size:43
Alignment explanation
Indices: 5460--5604 Score: 157
Period size: 44 Copynumber: 3.3 Consensus size: 43
5450 AATTAACAAC
*** * *
5460 CCTATGAAATTTCAATAACCA-ACCTAAGAAATTTCAATAACTTGAT
1 CCTATGAAATTTTGGTAACCACA-CTATGAAATTTTAATAAC-T--T
5506 CCTATGAAATTTTGGTAACCACACTATGAAATTTTAATAACTT
1 CCTATGAAATTTTGGTAACCACACTATGAAATTTTAATAACTT
* * *
5549 CCATATGAAATTTTGTTAACCACACTATGGAATTTTGATAACTT
1 CC-TATGAAATTTTGGTAACCACACTATGAAATTTTAATAACTT
5593 CCTCATGAAATT
1 CCT-ATGAAATT
5605 ATAATAACCA
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
43 4 0.05
44 48 0.55
45 1 0.01
46 34 0.39
47 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (43 bp):
CCTATGAAATTTTGGTAACCACACTATGAAATTTTAATAACTT
Found at i:5613 original size:44 final size:44
Alignment explanation
Indices: 5521--5634 Score: 142
Period size: 44 Copynumber: 2.6 Consensus size: 44
5511 GAAATTTTGG
* * **
5521 TAACCACACTATGAAATTTTAATAACTTCCATATGAAATTTTGT
1 TAACCACACTATGAAATTTTGATAACTTCCATATGAAATTATAA
*
5565 TAACCACACTATGGAATTTTGATAACTTCC-TCATGAAATTATAA
1 TAACCACACTATGAAATTTTGATAACTTCCAT-ATGAAATTATAA
*
5609 TAACCATC-TTATGAAATTTTGATAAC
1 TAACCA-CACTATGAAATTTTGATAAC
5635 CACATAGAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 59 0.97
45 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.37
Consensus pattern (44 bp):
TAACCACACTATGAAATTTTGATAACTTCCATATGAAATTATAA
Found at i:5635 original size:22 final size:22
Alignment explanation
Indices: 5460--5636 Score: 128
Period size: 22 Copynumber: 8.0 Consensus size: 22
5450 AATTAACAAC
** *
5460 CCTATGAAATTTCAATAACCAA
1 CCTATGAAATTTTGATAACCAT
* ** *
5482 CCTAAGAAATTTCAATAACTTGAT
1 CCTATGAAATTTTGATAAC--CAT
*
5506 CCTATGAAATTTTGGTAACCA-
1 CCTATGAAATTTTGATAACCAT
* *
5527 CACTATGAAATTTTAATAA-CTT
1 C-CTATGAAATTTTGATAACCAT
*
5549 CCATATGAAATTTTGTTAACCA-
1 CC-TATGAAATTTTGATAACCAT
* *
5571 CACTATGGAATTTTGATAA-CTT
1 C-CTATGAAATTTTGATAACCAT
* *
5593 CCTCATGAAATTATAATAACCAT
1 CCT-ATGAAATTTTGATAACCAT
*
5616 CTTATGAAATTTTGATAACCA
1 CCTATGAAATTTTGATAACCA
5637 CATAGAGACA
Statistics
Matches: 121, Mismatches: 24, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
21 6 0.05
22 93 0.77
23 6 0.05
24 16 0.13
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (22 bp):
CCTATGAAATTTTGATAACCAT
Found at i:6023 original size:38 final size:38
Alignment explanation
Indices: 5981--6067 Score: 122
Period size: 38 Copynumber: 2.3 Consensus size: 38
5971 CAAATATGAC
* *
5981 ATTGGAGACAACGACAAAAAGCAAAACTAAATACAACG
1 ATTGGAAACAAAGACAAAAAGCAAAACTAAATACAACG
* * *
6019 ATTGGAAACAAAGACAAAATGCAAAATTAAATAGAACG
1 ATTGGAAACAAAGACAAAAAGCAAAACTAAATACAACG
6057 -TTGGAAACAAA
1 ATTGGAAACAAA
6068 AAGTCAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 11 0.25
38 33 0.75
ACGTcount: A:0.56, C:0.14, G:0.16, T:0.14
Consensus pattern (38 bp):
ATTGGAAACAAAGACAAAAAGCAAAACTAAATACAACG
Found at i:7435 original size:24 final size:24
Alignment explanation
Indices: 7408--7457 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
7398 ATACCTTATG
*
7408 AATGAATCAAAACAACCAGATACC
1 AATGAATCAAAACAACCAAATACC
7432 AATGAATCAAAACAACCAAATACC
1 AATGAATCAAAACAACCAAATACC
7456 AA
1 AA
7458 CTTGGGGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.58, C:0.24, G:0.06, T:0.12
Consensus pattern (24 bp):
AATGAATCAAAACAACCAAATACC
Found at i:9300 original size:16 final size:15
Alignment explanation
Indices: 9281--9352 Score: 53
Period size: 14 Copynumber: 4.9 Consensus size: 15
9271 CGAATAAATA
9281 ATATATATTAATTTT
1 ATATATATTAATTTT
*
9296 AATATATCAGTTTA-TTT
1 -ATATAT-A-TTAATTTT
*
9313 ATATATA-TAATTAT
1 ATATATATTAATTTT
*
9327 ATATATA-TAA-ATT
1 ATATATATTAATTTT
*
9340 ATAAATATTAATT
1 ATATATATTAATT
9353 CTAAATATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
13 9 0.20
14 15 0.34
15 1 0.02
16 12 0.27
17 4 0.09
18 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (15 bp):
ATATATATTAATTTT
Found at i:9302 original size:14 final size:14
Alignment explanation
Indices: 9283--9361 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 14
9273 AATAAATAAT
*
9283 ATATATTAATTTTA
1 ATATATTAATTATA
* * *
9297 ATATATCAGTTTATTT
1 ATATATTA-ATTA-TA
9313 ATATATATAATTATA
1 ATATAT-TAATTATA
*
9328 TATATATAAATTATA
1 -ATATATTAATTATA
*
9343 A-ATATTAATTCTA
1 ATATATTAATTATA
9356 A-ATATT
1 ATATATT
9362 CTCTAATCTC
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
13 16 0.31
14 8 0.16
15 10 0.20
16 16 0.31
17 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.51
Consensus pattern (14 bp):
ATATATTAATTATA
Found at i:13608 original size:2 final size:2
Alignment explanation
Indices: 13601--13626 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13591 AAAGCCTAAA
13601 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
13627 CAGTGTATTT
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:17563 original size:21 final size:21
Alignment explanation
Indices: 17532--17580 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
17522 TTTCTAGTCA
* *
17532 GGGAAA-T-CCTATTTTGATT
1 GGGAAATTGCCTATTGTAATT
*
17551 GGGATATTGCCTATTGTAATT
1 GGGAAATTGCCTATTGTAATT
17572 GGGAAATTG
1 GGGAAATTG
17581 TTTGGTTAGC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 5 0.21
20 1 0.04
21 18 0.75
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.39
Consensus pattern (21 bp):
GGGAAATTGCCTATTGTAATT
Found at i:18242 original size:31 final size:31
Alignment explanation
Indices: 18204--18307 Score: 111
Period size: 31 Copynumber: 3.4 Consensus size: 31
18194 CCAAAAAGTG
18204 TGGCACGCCACATGTA-CAAAAAAGTGACACA
1 TGGCACGCCACATGTATC-AAAAAGTGACACA
* ** *
18235 TGTCACGCCATGTGTATCAAAAAGTGACACT
1 TGGCACGCCACATGTATCAAAAAGTGACACA
* * * *
18266 TGGCATGCCACATGTTTCAAAAAGTGGCACG
1 TGGCACGCCACATGTATCAAAAAGTGACACA
*
18297 TGGCATGCCAC
1 TGGCACGCCAC
18308 GTGCACAAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 60 0.98
32 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (31 bp):
TGGCACGCCACATGTATCAAAAAGTGACACA
Found at i:21125 original size:21 final size:22
Alignment explanation
Indices: 21101--21163 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
21091 GAATTTCGAG
* *
21101 AACCTTTTTAT-AAATTTTTTT
1 AACCTTCTTATGAAATTTTGTT
*
21122 AACCTTCTTGTGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
* * *
21144 AACCTCCCTAAGAAATTTTG
1 AACCTTCTTATGAAATTTTG
21164 AAGACCTCAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 9 0.26
22 25 0.74
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.48
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:21231 original size:22 final size:23
Alignment explanation
Indices: 21183--21237 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
21173 ACATGAAATT
*
21183 TTGATAACCAACACTATGAGATG
1 TTGATAACCAACACTATGAGATA
** *
21206 TTGATAACCTCCA-TATGATATA
1 TTGATAACCAACACTATGAGATA
21228 TTGATAACCA
1 TTGATAACCA
21238 CGTTACGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (23 bp):
TTGATAACCAACACTATGAGATA
Found at i:21312 original size:22 final size:22
Alignment explanation
Indices: 21263--21322 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
21253 AAAACCTCCA
*
21263 TATGAATTGTTTG-TAATCATAC
1 TATGAATT-TTTGATAATCACAC
* *
21285 TCTGAATTTTTGATAATTACAC
1 TATGAATTTTTGATAATCACAC
* *
21307 TATGAAATTGTGATAA
1 TATGAATTTTTGATAA
21323 CCTCGTTATG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.43
Consensus pattern (22 bp):
TATGAATTTTTGATAATCACAC
Found at i:21361 original size:23 final size:23
Alignment explanation
Indices: 21306--21390 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
21296 GATAATTACA
* * *
21306 CTATGAAATTGTGAT-AACCTCG
1 CTATAAAATTTTGATAAACCTCC
* * * *
21328 TTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAACCTCC
**
21351 CTATAAAATTTTCTTAAACCTCC
1 CTATAAAATTTTGATAAACCTCC
21374 CTATAAAATTTTGATAA
1 CTATAAAATTTTGATAA
21391 CTTTCTTATG
Statistics
Matches: 49, Mismatches: 13, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
22 13 0.27
23 36 0.73
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.40
Consensus pattern (23 bp):
CTATAAAATTTTGATAAACCTCC
Found at i:21460 original size:22 final size:22
Alignment explanation
Indices: 21417--21578 Score: 120
Period size: 22 Copynumber: 7.5 Consensus size: 22
21407 TAATAATTAC
*
21417 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTCACTATG
** * *
21439 ATTTTTTGATAACCTTATTATG
1 AAATTTTGATAACCTCACTATG
*
21461 AAATTTTGTTAACCTGC-CTATG
1 AAATTTTGATAACCT-CACTATG
* *
21483 AAATTTTGATCTACAT-ACTATG
1 AAATTTTGAT-AACCTCACTATG
*
21505 AAATTTTGATAATCCTC-TTATG
1 AAATTTTGATAA-CCTCACTATG
* *
21527 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT-CACTATG
* * *
21549 AAATTGTGATATCCTC-C-CTG
1 AAATTTTGATAACCTCACTATG
21569 AAATTTTGAT
1 AAATTTTGAT
21579 TACTCCATAA
Statistics
Matches: 107, Mismatches: 25, Indels: 18
0.71 0.17 0.12
Matches are distributed among these distances:
20 13 0.12
21 4 0.04
22 84 0.79
23 6 0.06
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTCACTATG
Found at i:21505 original size:44 final size:43
Alignment explanation
Indices: 21132--22274 Score: 204
Period size: 44 Copynumber: 26.4 Consensus size: 43
21122 AACCTTCTTG
* * *
21132 TGAAATTTTGTTAACC-TCCCTAAGAAATTTTGA-AGACCTCAAC-A
1 TGAAATTTTGATAACCAT-ACTATGAAATTTTGATA-ACCTC--CTA
* * *
21176 TGAAATTTTGATAACCAACACTATGAGATGTTGATAACCTCCATA
1 TGAAATTTTGATAACC-ATACTATGAAATTTTGATAACCTCC-TA
* * *** * * * *
21221 TGATATATTGATAACCACGTTACGAAAATTTAAAAACCTCCATA
1 TGAAATTTTGATAACCATACTATGAAATTTTGATAACCTCC-TA
* * * * *
21265 TGAATTGTTTG-TAATCATACTCTGAATTTTTGATAA-TTACACTA
1 TGAAAT-TTTGATAACCATACTATGAAATTTTGATAACCT-C-CTA
* *
21309 TGAAATTGTGATAACC-T-CGTTATGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGATAACCATAC--TATGAAATTTTGAT-AA-CCTCCTA
* ** * * * *
21354 TAAAATTTTCTTAAACC-TCCCTATAAAATTTTGATAACTTTCTTA
1 TGAAATTTTGAT-AACCAT-ACTATGAAATTTTGATAAC-CTCCTA
* * * *
21399 TGAGATCTTAAT-A--AT--TA-CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCATACTATGAAATTTTGATAACCT-CCTA
** * * *
21437 TGATTTTTTGATAACCTTATTATGAAATTTTGTTAACCTGCCTA
1 TGAAATTTTGATAACCATACTATGAAATTTTGATAACCT-CCTA
* *
21481 TGAAATTTTGATCTA-CATACTATGAAATTTTGATAATCCTCTTA
1 TGAAATTTTGAT-AACCATACTATGAAATTTTGATAA-CCTCCTA
* * * * * *
21525 TGAAATTTTGAAAACTAAACTATGAAATTGTGATATCCTCC-C
1 TGAAATTTTGATAACCATACTATGAAATTTTGATAACCTCCTA
* ** * *
21567 TGAAATTTTGATTACTCCATA--AAAAAAATTTAATAACCTTCC--
1 TGAAATTTTGA-TA-ACCATACTATGAAATTTTGATAACC-TCCTA
* * *
21609 T--AA-TTTGGTAATCATACTATGAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCATACTATGAAATTTTGATAACCT-CCTA
* * * *
21650 -G-AA-----AT-ACC--ACTATGAAATTTTTG-TAATCACATTT
1 TGAAATTTTGATAACCATACTATGAAA-TTTTGATAACCTC-CTA
* * * ** *
21684 TGAAAATTTGGTAACCTTTTTATGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCATACTATGAAATTTTGATAACCTC-CTA
* * ** * * * * *
21728 TAAAATTTTGTTGTCCCCT-CTATGAAATTCTGATAATCACATTA
1 TGAAATTTTGAT-AACCATACTATGAAATTTTGATAACCTC-CTA
* * * ** *
21772 TGTAATTTTGATAACC-TCGCTTTGAAATTTTGATAACAACATTA
1 TGAAATTTTGATAACCAT-ACTATGAAATTTTGATAACCTC-CTA
* * * *
21816 TGAAATTTTGATAATCTTCCTAT-AAATTTTGATAATCTGATCTCTA
1 TGAAATTTTGATAACCATACTATGAAATTTTGATAA-C--CTC-CTA
* * * *
21862 TGAAATTTCGATAA-TATCACTCTATGAGA-TTTGATAACCTTCTA
1 TGAAATTTTGATAACCAT-A--CTATGAAATTTTGATAACCTCCTA
* * * * *
21906 TGAAATTTTGGTACTCCTTATGA-AATTGAGACTTTT-ATAACCTTCATA
1 TGAAATTTTGATA-ACC--AT-ACTA-TGA-AATTTTGATAACC-TCCTA
* * * * *
21954 TAAAATTTTGATAACCACACTATAAAATTTTGATAACGTCCCCA
1 TGAAATTTTGATAACCATACTATGAAATTTTGATAACCT-CCTA
* * * * *
21998 TGAAATATTAATAACC-TCCTAATGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCATACT-ATGAAATTTTGATAACCTC-CTA
* * *
22042 TGAAATTCTT-ATAACC-TCGCTATGACATTTTGATAATCT-CT-
1 TGAAATT-TTGATAACCAT-ACTATGAAATTTTGATAACCTCCTA
* *
22083 TCGATAATCTT--T---C-TA-TA--AAATTGTGATGATTAACCACCCTA
1 T-GA-AATTTTGATAACCATACTATGAAATT-T--TGA-TAACC-TCCTA
* * * * *
22124 TGAAATTTTAATAATCTAATCCTATGAAATTTTGGTAACCACACTA
1 TGAAATTTTGATAA-C-CATACTATGAAATTTTGATAACCTC-CTA
* * * * *
22170 TAAAATTTTGATAA-CTTCCATATGAAATTTTGGTAACCACACTA
1 TGAAATTTTGATAACCATAC-TATGAAATTTTGATAACCTC-CTA
* * * * *
22214 TGGAATTTTGATAACC-TCCTCATGAAATTATAATAACCATCTTA
1 TGAAATTTTGATAACCATACT-ATGAAATTTTGATAACC-TCCTA
22258 TGAAATTTTGATAACCA
1 TGAAATTTTGATAACCA
22275 CATAGAGAAA
Statistics
Matches: 801, Mismatches: 195, Indels: 205
0.67 0.16 0.17
Matches are distributed among these distances:
33 1 0.00
34 17 0.02
35 7 0.01
36 6 0.01
37 9 0.01
38 33 0.04
39 27 0.03
40 6 0.01
41 8 0.01
42 35 0.04
43 53 0.07
44 400 0.50
45 82 0.10
46 60 0.07
47 14 0.02
48 35 0.04
49 3 0.00
50 5 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (43 bp):
TGAAATTTTGATAACCATACTATGAAATTTTGATAACCTCCTA
Found at i:21709 original size:22 final size:22
Alignment explanation
Indices: 21684--21829 Score: 73
Period size: 22 Copynumber: 6.6 Consensus size: 22
21674 AATCACATTT
* *
21684 TGAAAATTTGGTAACCTTTTTA
1 TGAAAATTTGATAACCTCTTTA
*
21706 TGAAATTTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* ** * *
21728 T-AAAATTTTGTTGTCCCCTCTA
1 TGAAAA-TTTGATAACCTCTTTA
* * *
21750 TG-AAATTCTGATAATCACATTA
1 TGAAAATT-TGATAACCTCTTTA
* * *
21772 TGTAATTTTGATAACCTCGCTT-
1 TGAAAATTTGATAACCTC-TTTA
* ** *
21794 TGAAATTTTGATAACAACATTA
1 TGAAAATTTGATAACCTCTTTA
*
21816 TGAAATTTTGATAA
1 TGAAAATTTGATAA
21830 TCTTCCTATA
Statistics
Matches: 94, Mismatches: 24, Indels: 12
0.72 0.18 0.09
Matches are distributed among these distances:
21 7 0.07
22 81 0.86
23 6 0.06
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:21884 original size:24 final size:23
Alignment explanation
Indices: 21704--21915 Score: 133
Period size: 22 Copynumber: 9.5 Consensus size: 23
21694 GTAACCTTTT
* *
21704 TATGAAATTTTGATAACCT-CTT
1 TATGAAATTTTGATAATCTACTC
* ** **
21726 TATAAAATTTTG-TTGTCCCCTC
1 TATGAAATTTTGATAATCTACTC
*
21748 TATGAAATTCTGATAATC-ACAT-
1 TATGAAATTTTGATAATCTAC-TC
* * *
21770 TATGTAATTTTGATAACCT-CGC
1 TATGAAATTTTGATAATCTACTC
* *
21792 TTTGAAATTTTGATAA-CAACAT-
1 TATGAAATTTTGATAATCTAC-TC
*
21814 TATGAAATTTTGATAATCTTC-C
1 TATGAAATTTTGATAATCTACTC
21836 TAT-AAATTTTGATAATCTGATCTC
1 TATGAAATTTTGATAATCT-A-CTC
* *
21860 TATGAAATTTCGATAATATCACTC
1 TATGAAATTTTGATAATCT-ACTC
* *
21884 TATGAGA-TTTGATAACCT--TC
1 TATGAAATTTTGATAATCTACTC
21904 TATGAAATTTTG
1 TATGAAATTTTG
21916 GTACTCCTTA
Statistics
Matches: 145, Mismatches: 31, Indels: 29
0.71 0.15 0.14
Matches are distributed among these distances:
20 8 0.06
21 22 0.15
22 73 0.50
23 15 0.10
24 13 0.09
25 14 0.10
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.42
Consensus pattern (23 bp):
TATGAAATTTTGATAATCTACTC
Found at i:21967 original size:22 final size:22
Alignment explanation
Indices: 21952--22077 Score: 85
Period size: 22 Copynumber: 5.7 Consensus size: 22
21942 ATAACCTTCA
21952 TATAAAATTTTGATAACCACAC
1 TATAAAATTTTGATAACCACAC
** *
21974 TATAAAATTTTGATAACGTCCC
1 TATAAAATTTTGATAACCACAC
* * * * *
21996 CATGAAATATTAATAACCTC-C
1 TATAAAATTTTGATAACCACAC
* *
22017 TAATGAAATTTTGTTAACCACAC
1 T-ATAAAATTTTGATAACCACAC
* * *
22040 TATGAAATTCTT-ATAACCTCGC
1 TATAAAATT-TTGATAACCACAC
* *
22062 TATGACATTTTGATAA
1 TATAAAATTTTGATAA
22078 TCTCTTCGAT
Statistics
Matches: 83, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
21 3 0.04
22 76 0.92
23 4 0.05
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (22 bp):
TATAAAATTTTGATAACCACAC
Found at i:22175 original size:22 final size:22
Alignment explanation
Indices: 22113--22276 Score: 131
Period size: 22 Copynumber: 7.4 Consensus size: 22
22103 TTGTGATGAT
* *
22113 TAACCACCCTATGAAATTTTAA
1 TAACCACACTATGAAATTTTGA
* *
22135 TAATCTA-ATCCTATGAAATTTTGG
1 TAA-CCACA--CTATGAAATTTTGA
*
22159 TAACCACACTATAAAATTTTGA
1 TAACCACACTATGAAATTTTGA
*
22181 TAACTTC-CA-TATGAAATTTTGG
1 TAAC--CACACTATGAAATTTTGA
*
22203 TAACCACACTATGGAATTTTGA
1 TAACCACACTATGAAATTTTGA
* * *
22225 TAACCTC-CTCATGAAATTATAA
1 TAACCACACT-ATGAAATTTTGA
*
22247 TAACCATC-TTATGAAATTTTGA
1 TAACCA-CACTATGAAATTTTGA
22269 TAACCACA
1 TAACCACA
22277 TAGAGAAAAG
Statistics
Matches: 112, Mismatches: 19, Indels: 22
0.73 0.12 0.14
Matches are distributed among these distances:
20 1 0.01
21 5 0.04
22 81 0.72
23 8 0.07
24 17 0.15
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
TAACCACACTATGAAATTTTGA
Found at i:22242 original size:66 final size:66
Alignment explanation
Indices: 22145--22276 Score: 151
Period size: 66 Copynumber: 2.0 Consensus size: 66
22135 TAATCTAATC
* * * * *
22145 CTATGAAATTTTGGTAACCACACTATAAAATTTTGATAA-CTTCCATATGAAATTTTGGTAACCA
1 CTATGAAATTTTGATAACCACACTATAAAATTATAATAACCAT-CATATGAAATTTTGATAACCA
22209 CA
65 CA
* * * *
22211 CTATGGAATTTTGATAACCTC-CTCATGAAATTATAATAACCATCTTATGAAATTTTGATAACCA
1 CTATGAAATTTTGATAACCACACT-ATAAAATTATAATAACCATCATATGAAATTTTGATAACCA
22275 CA
65 CA
22277 TAGAGAAAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
65 2 0.04
66 51 0.93
67 2 0.04
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (66 bp):
CTATGAAATTTTGATAACCACACTATAAAATTATAATAACCATCATATGAAATTTTGATAACCAC
A
Found at i:22476 original size:19 final size:20
Alignment explanation
Indices: 22445--22482 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
22435 TATTGACAAT
22445 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
22464 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
22483 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:22665 original size:37 final size:37
Alignment explanation
Indices: 22624--22715 Score: 112
Period size: 38 Copynumber: 2.5 Consensus size: 37
22614 AGCTAAGCCC
* * *
22624 AAATAGGATGTTGGAGACAAAGACAAAAAGCAAAATT
1 AAATAGGACGTTGGAAACAAAGACAAAAAGAAAAATT
** * *
22661 AAATACAACGATTGGAAACAAAGATAAAAGGAAAAATT
1 AAATAGGACG-TTGGAAACAAAGACAAAAAGAAAAATT
22699 AAATAGGACGTTGGAAA
1 AAATAGGACGTTGGAAA
22716 TAAAAAGACA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
37 14 0.31
38 31 0.69
ACGTcount: A:0.55, C:0.08, G:0.21, T:0.16
Consensus pattern (37 bp):
AAATAGGACGTTGGAAACAAAGACAAAAAGAAAAATT
Found at i:22875 original size:29 final size:31
Alignment explanation
Indices: 22842--22905 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
22832 TGGCAATTTA
* * *
22842 GAAATATGTTTTTAAAA-AA-GGTACAATTG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
22871 GAAATATATTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
22902 GAAA
1 GAAA
22906 ACATAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 15 0.50
30 2 0.07
31 13 0.43
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.30
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATCG
Done.