Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009678.1 Corchorus capsularis cultivar CVL-1 contig09699, 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: 21875
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:3223 original size:23 final size:23
Alignment explanation
Indices: 3175--3254 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
3165 TCACACTTTG
* * *
3175 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAACCTCCCTATA
* *
3197 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
*
3220 AAATTTTAATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
3243 AAATTTTGATAA
1 AAATTTTGATAA
3255 CTTTTTTATG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
22 9 0.19
23 39 0.81
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:3331 original size:22 final size:22
Alignment explanation
Indices: 2992--3469 Score: 204
Period size: 22 Copynumber: 21.9 Consensus size: 22
2982 TTTTTTAACT
* *
2992 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* * *
3014 TAAGGAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACCTCAC
*
3036 TATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCAC
* *
3059 TATGAGATGTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * *
3080 ATATGATATATATTGATAACCACTC
1 -TATGA-A-ATTTTGATAACCTCAC
* * * * *
3105 TATAAAAATTTAAAAACC-CCC
1 TATGAAATTTTGATAACCTCAC
*
3126 ATATG-AATTGTT-AGTAA-TTACAC
1 -TATGAAATT-TTGA-TAACCT-CAC
* * * *
3149 TTTAAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTCAC
* * *
3171 TTTGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCAC
*
3193 TATGAAATTTTGATAAATCTTC-C
1 TATGAAATTTTGAT-AA-CCTCAC
* * *
3216 TATAAAATTTTAATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCAC
* * ***
3239 TATAAAATTTTGATAACTTTTT
1 TATGAAATTTTGATAACCTCAC
*
3261 TATGAAATCTTGATAA-CT-AC
1 TATGAAATTTTGATAACCTCAC
* *
3281 ----AAATTTTGATAAGCTCCC
1 TATGAAATTTTGATAACCTCAC
** * *
3299 TATGATTTTTTGATTACCTCAT
1 TATGAAATTTTGATAACCTCAC
* * * *
3321 TATTAAATTTTGCTAATCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
3343 TATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGAT-AACCTCAC
*
3365 TATGAAATTTTGATAACCCTC-T
1 TATGAAATTTTGATAA-CCTCAC
* *
3387 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CAC
*
3409 TATGAAAATTTGATAACCTTCA-
1 TATGAAATTTTGATAACC-TCAC
*
3431 TATGAAATTTTGATATCCTCAC
1 TATGAAATTTTGATAACCTCAC
*
3453 --TG-AATTTTGATATCCTC
1 TATGAAATTTTGATAACCTC
3470 CCTGAATTTT
Statistics
Matches: 340, Mismatches: 84, Indels: 67
0.69 0.17 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
19 15 0.04
20 4 0.01
21 15 0.04
22 206 0.61
23 65 0.19
24 20 0.06
25 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:3508 original size:19 final size:19
Alignment explanation
Indices: 3436--3502 Score: 107
Period size: 19 Copynumber: 3.5 Consensus size: 19
3426 CTTCATATGA
*
3436 AATTTTGATATCCTCACTG
1 AATTTTGATATCCTCCCTG
3455 AATTTTGATATCCTCCCTG
1 AATTTTGATATCCTCCCTG
*
3474 AATTTTGGTATCCTCCCTG
1 AATTTTGATATCCTCCCTG
3493 AAATTTTGAT
1 -AATTTTGAT
3503 TACTCCATCA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 36 0.82
20 8 0.18
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (19 bp):
AATTTTGATATCCTCCCTG
Found at i:3640 original size:22 final size:22
Alignment explanation
Indices: 3608--3799 Score: 131
Period size: 22 Copynumber: 8.6 Consensus size: 22
3598 AATCACATTT
* *
3608 TGAAAATTTGATAAGCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* *
3630 TGGAATTTTGATAACATCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
3652 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
3674 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
3696 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
3718 TGAAATTTTGATAACAACAATA
1 TGAAATTTTGATAACCTCTTTA
3740 TGAAATTTTGATAA--TCTTCATA
1 TGAAATTTTGATAACCTCTT--TA
3762 T-AAATTTTGATAACCCTATCTTTA
1 TGAAATTTTGATAA-CC--TCTTTA
*
3786 TGAAATTTCGATAA
1 TGAAATTTTGATAA
3800 TCACTCTATG
Statistics
Matches: 129, Mismatches: 31, Indels: 17
0.73 0.18 0.10
Matches are distributed among these distances:
20 1 0.01
21 13 0.10
22 95 0.74
23 2 0.02
24 3 0.02
25 11 0.09
26 4 0.03
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:3683 original size:44 final size:43
Alignment explanation
Indices: 3583--3753 Score: 130
Period size: 44 Copynumber: 3.9 Consensus size: 43
3573 AGAAATACCA
* * * *
3583 CTATGAAATTTTTG-TAATCACATTTTGAAAA-TTTGATAAGCTCT
1 CTATGAAA-TTTTGATAA-CACATTAT-AAAATTTTGATAACCCCG
* * * * * *
3627 TTATGGAATTTTGATAACATCTTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAACA-CATTATAAAATTTTGATAACCCCG
** *
3671 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAA-CACATTATAAAATTTTGATAACCCCG
* * *
3715 CTTTGAAATTTTGATAACAACAATATGAAATTTTGATAA
1 CTATGAAATTTTGATAAC-ACATTATAAAATTTTGATAA
3754 TCTTCATATA
Statistics
Matches: 102, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
43 12 0.12
44 88 0.86
45 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (43 bp):
CTATGAAATTTTGATAACACATTATAAAATTTTGATAACCCCG
Found at i:3724 original size:66 final size:66
Alignment explanation
Indices: 3608--3776 Score: 164
Period size: 66 Copynumber: 2.6 Consensus size: 66
3598 AATCACATTT
* * * * * * * * ** **
3608 TGAAAATTTGATAAGCTCTTTATGGAATTTTGATAACATCTTTATAAAATTTTGTTGACCCCTCT
1 TGAAATTTTGATAATCTCATTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACAAT
3673 A
66 A
* * *
3674 TGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACAA
1 TGAAATTTTGATAATCTCATTATGAAATTTTGATAACCTC-CTTATAAAATTTTGATAACAACAA
3738 TA
65 TA
3740 TGAAATTTTGATAATCTTCA-TAT-AAATTTTGATAACC
1 TGAAATTTTGATAATC-TCATTATGAAATTTTGATAACC
3777 CTATCTTTAT
Statistics
Matches: 85, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
65 13 0.15
66 68 0.80
67 4 0.05
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (66 bp):
TGAAATTTTGATAATCTCATTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACAAT
A
Found at i:3746 original size:88 final size:88
Alignment explanation
Indices: 3583--3749 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 88
3573 AGAAATACCA
* * * * *
3583 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAAGCTCTTTATGGAATTTTGATAACATC
1 CTATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
3648 TTTATAAAATTTTGTTGACCCCT
66 AATATAAAATTTTGTTGACCCCT
* *
3671 CTATGAAA-TTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACA
1 CTATGAAATTTTTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACA
*
3734 ACAATATGAAATTTTG
64 ACAATATAAAATTTTG
3750 ATAATCTTCA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 5 0.07
88 60 0.90
89 2 0.03
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (88 bp):
CTATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
AATATAAAATTTTGTTGACCCCT
Found at i:3934 original size:22 final size:20
Alignment explanation
Indices: 3860--3935 Score: 53
Period size: 22 Copynumber: 3.5 Consensus size: 20
3850 AAATTGAGAT
*
3860 TTTTATAACCTTCATATGAAA
1 TTTTGTAACCTTCA-ATGAAA
* * *
3881 TTTTGATAACCTCCCGATGAAG
1 TTTTG-TAACCT-TCAATGAAA
*
3903 TATTAGTAACCTTCTAATGAAA
1 T-TTTGTAACCTTC-AATGAAA
3925 TTTTGTTAACC
1 TTTTG-TAACC
3936 ACACTATGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 9
0.69 0.15 0.15
Matches are distributed among these distances:
21 8 0.20
22 29 0.71
23 4 0.10
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (20 bp):
TTTTGTAACCTTCAATGAAA
Found at i:4044 original size:22 final size:22
Alignment explanation
Indices: 4012--4195 Score: 124
Period size: 22 Copynumber: 8.3 Consensus size: 22
4002 TTGTGATAAT
* *
4012 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
4034 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* *
4056 TAACCTGATCCTATGAAATTTTGA
1 TAACC--AACCTATGAAATTTTAA
* **
4080 TAGCC-ACTCTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* **
4102 TAA-CTACACTATGAAATTTTTG
1 TAACCAAC-CTATGAAATTTTAA
* *
4124 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* * *
4146 TAACC-TCCTCATGGAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* *
4168 TAACCATCTTATGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
4190 TAACCA
1 TAACCA
4196 CATAGAGACA
Statistics
Matches: 134, Mismatches: 21, Indels: 14
0.79 0.12 0.08
Matches are distributed among these distances:
21 4 0.03
22 108 0.81
23 4 0.03
24 18 0.13
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:4501 original size:30 final size:31
Alignment explanation
Indices: 4460--4521 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
4450 AGTAATGACA
4460 ATTTAGAAATATG-TTTAAAAAAAAGGGTAC
1 ATTTAGAAATATGTTTTAAAAAAAAGGGTAC
* *
4490 ATTTGGAAATATGTTTTAAAAATAAGGGTAC
1 ATTTAGAAATATGTTTTAAAAAAAAGGGTAC
4521 A
1 A
4522 ATCGGAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (31 bp):
ATTTAGAAATATGTTTTAAAAAAAAGGGTAC
Found at i:4529 original size:31 final size:30
Alignment explanation
Indices: 4465--4529 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
4455 TGACAATTTA
* *
4465 GAAATATGTTTAAAAAAAAGGGTACATTTG
1 GAAATATGTTTAAAAAAAAGGGTACAATCG
*
4495 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATG-TTTAAAAAAAAGGGTACAATCG
4526 GAAA
1 GAAA
4530 ACATAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.28
Consensus pattern (30 bp):
GAAATATGTTTAAAAAAAAGGGTACAATCG
Found at i:6373 original size:28 final size:24
Alignment explanation
Indices: 6356--6402 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
6346 CTCTTAACCC
*
6356 ATTTTAATCTCAACCAAACTCCTA
1 ATTTTAATCTCAACCAAACTCTTA
*
6380 ATTTTAATCTCAACCAACCTCTT
1 ATTTTAATCTCAACCAAACTCTT
6403 CAAGATTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.30, G:0.00, T:0.36
Consensus pattern (24 bp):
ATTTTAATCTCAACCAAACTCTTA
Found at i:8606 original size:15 final size:16
Alignment explanation
Indices: 8586--8617 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
8576 ACAACAATAA
8586 TACTTTT-TTTTAATT
1 TACTTTTCTTTTAATT
8601 TACTTTTCTTTTAATT
1 TACTTTTCTTTTAATT
8617 T
1 T
8618 TAAATTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (16 bp):
TACTTTTCTTTTAATT
Found at i:9324 original size:29 final size:30
Alignment explanation
Indices: 9250--9319 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 30
9240 ATTTCTTATA
9250 TTGACCCCATTGAAATT-GTGAAATATACAT
1 TTGACCCCATTG-AATTAGTGAAATATACAT
*
9280 TTGA-CCCATTGAATTAGTGAAATATGCAT
1 TTGACCCCATTGAATTAGTGAAATATACAT
9309 TTGACCCCATT
1 TTGACCCCATT
9320 TATTAACGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
28 4 0.11
29 23 0.62
30 10 0.27
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (30 bp):
TTGACCCCATTGAATTAGTGAAATATACAT
Found at i:20502 original size:30 final size:29
Alignment explanation
Indices: 20424--20483 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
20414 TACCATCCTA
*
20424 ATAGAATTCCTTCTATACTTTTTCCATAC
1 ATAGAATTCTTTCTATACTTTTTCCATAC
20453 ATAGAATTCTTTCTATACTTTTTCCATAC
1 ATAGAATTCTTTCTATACTTTTTCCATAC
20482 AT
1 AT
20484 CAATATTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.28, C:0.22, G:0.03, T:0.47
Consensus pattern (29 bp):
ATAGAATTCTTTCTATACTTTTTCCATAC
Done.