Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021173.1 Corchorus olitorius cultivar O-4 contig21206, 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: 17212
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3589 original size:13 final size:13
Alignment explanation
Indices: 3572--3603 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
3562 TAAATTATTA
3572 AAAAAATGAAAAAT
1 AAAAAAT-AAAAAT
3586 AAAAAATAAAAAT
1 AAAAAATAAAAAT
3599 AAAAA
1 AAAAA
3604 TTATCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:4524 original size:22 final size:21
Alignment explanation
Indices: 4499--5063 Score: 245
Period size: 22 Copynumber: 26.0 Consensus size: 21
4489 ATTTTTTATG
4499 ACCTCCTTATGAAATTTTGATA
1 ACCTCC-TATGAAATTTTGATA
4521 ACCTCCCTATGAAATTTTGATA
1 ACCT-CCTATGAAATTTTGATA
* *
4543 ACATTCCTATGAAATTTTAATA
1 AC-CTCCTATGAAATTTTGATA
* * ** * *
4565 ACGATACTATGGCATTTCGAGA
1 AC-CTCCTATGAAATTTTGATA
** * **
4587 ACCTTTTTATTAAATTTTTTTA
1 ACC-TCCTATGAAATTTTGATA
* *
4609 ACCTTCTTATGAAATTTTGTTA
1 ACC-TCCTATGAAATTTTGATA
* *
4631 ACCTCCCTAAGGAATTTTGA-A
1 ACCT-CCTATGAAATTTTGATA
4652 GACCTCAC-AGTGAAATTTTGATA
1 -ACCTC-CTA-TGAAATTTTGATA
* *
4675 ACTTCCAAATGAAA-TTTGATA
1 ACCTCC-TATGAAATTTTGATA
* * *
4696 ACCAACACTATGAGATGTTGATA
1 ACC-TC-CTATGAAATTTTGATA
* *
4719 ACCTCCATATGATATATTGATA
1 ACCTCC-TATGAAATTTTGATA
* * * * * *
4741 ACCACGTTATAAAAATTTAAAA
1 ACCTC-CTATGAAATTTTGATA
4763 ACCTCCATATG-AATTGTT-AGTA
1 ACCTCC-TATGAAATT-TTGA-TA
* * *
4785 ATCACACTCTGAAATTTTGATA
1 ACCTC-CTATGAAATTTTGATA
* * * * *
4807 ATCACACTATAAAATTGTAATA
1 ACCTC-CTATGAAATTTTGATA
*
4829 ACCTCGTTATGAAATTTTGATAA
1 ACCTC-CTATGAAATTTTGAT-A
*
4852 ACCTCCCTATAAAATTTTGATA
1 ACCT-CCTATGAAATTTTGATA
*
4874 ACCTCCTTATGAAATCTTGATA
1 ACCTCC-TATGAAATTTTGATA
*
4896 A----CTA-CAAATTTTGATA
1 ACCTCCTATGAAATTTTGATA
* **
4912 ATCTCCCTATGATTTTTTGATA
1 ACCT-CCTATGAAATTTTGATA
* *
4934 ACCTCATTATGAAATTTTGTTA
1 ACCTC-CTATGAAATTTTGATA
* * *
4956 ATCTCCCGATGAAATTTTGATCT
1 ACCT-CCTATGAAATTTTGAT-A
* *
4979 ACATACTATGAAATTTTGATA
1 ACCTCCTATGAAATTTTGATA
*
5000 ACTCTCTTATGAAAATTTTGA-A
1 AC-CTCCTATG-AAATTTTGATA
* *
5022 AACTAAACTATGAAATTTTGATA
1 ACCT--CCTATGAAATTTTGATA
* *
5045 TCCTCC-CTGAAATTTTGAT
1 ACCTCCTATGAAATTTTGAT
5064 TACTTCATAA
Statistics
Matches: 406, Mismatches: 99, Indels: 78
0.70 0.17 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
18 1 0.00
20 12 0.03
21 30 0.07
22 291 0.72
23 58 0.14
24 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
ACCTCCTATGAAATTTTGATA
Found at i:4862 original size:45 final size:45
Alignment explanation
Indices: 4794--4896 Score: 136
Period size: 45 Copynumber: 2.3 Consensus size: 45
4784 AATCACACTC
* *
4794 TGAAATTTTGAT-AATCACACTATAAAATTGTAATAACCTCGTTA
1 TGAAATTTTGATAAACCACACTATAAAATTGTAATAACCTCCTTA
* * * *
4838 TGAAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCCTTA
1 TGAAATTTTGATAAACCACACTATAAAATTGTAATAACCTCCTTA
*
4883 TGAAATCTTGATAA
1 TGAAATTTTGATAA
4897 CTACAAATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 12 0.24
45 39 0.76
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.37
Consensus pattern (45 bp):
TGAAATTTTGATAAACCACACTATAAAATTGTAATAACCTCCTTA
Found at i:5194 original size:22 final size:22
Alignment explanation
Indices: 5169--5248 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
5159 AATCAAATTT
*
5169 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTCTA
*
5191 TGAAATTTTGATAACCTCTCTA
1 TGAAAATTTGATAACCTCTCTA
* * *
5213 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTCTA
*
5235 TGAAATTTTGATAA
1 TGAAAATTTGATAA
5249 TAACATTAAG
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 3 0.06
22 41 0.87
23 3 0.06
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTCTA
Found at i:5346 original size:25 final size:22
Alignment explanation
Indices: 5297--5355 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
5287 TGATAACAAC
*
5297 AAATTTTGATAA-TCTTCCTAT
1 AAATTTTGATAATTCATCCTAT
5318 AAATTTTGATAATTCGATCTCTAT
1 AAATTTTGATAATTC-ATC-CTAT
*
5342 GAAATTTCGATAAT
1 -AAATTTTGATAAT
5356 CACTTGATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 12 0.38
22 2 0.06
23 2 0.06
24 4 0.12
25 12 0.38
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (22 bp):
AAATTTTGATAATTCATCCTAT
Found at i:10683 original size:24 final size:24
Alignment explanation
Indices: 10627--10674 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
10617 TTTTGTAAAG
10627 AACAGTATATTGTATAATTTTCCT
1 AACAGTATATTGTATAATTTTCCT
10651 AACAGTATATTGTATAATTTTCCT
1 AACAGTATATTGTATAATTTTCCT
10675 TTATATATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.46
Consensus pattern (24 bp):
AACAGTATATTGTATAATTTTCCT
Found at i:11246 original size:21 final size:21
Alignment explanation
Indices: 11222--11278 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
11212 AATTTAGATA
*
11222 TAAATTTAGATATTATAATAT
1 TAAATTTAAATATTATAATAT
* * *
11243 TAAA-ATAATATCTTATATTAT
1 TAAATTTAA-ATATTATAATAT
*
11264 TTAATTTAAATATTA
1 TAAATTTAAATATTA
11279 AATTTCTATT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
20 2 0.07
21 22 0.81
22 3 0.11
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
TAAATTTAAATATTATAATAT
Found at i:13619 original size:15 final size:16
Alignment explanation
Indices: 13595--13634 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
13585 AGAGGTTGAA
*
13595 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
13610 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
13626 AGAAAACAA
1 AGAAAACAA
13635 AGCAAAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:15369 original size:22 final size:23
Alignment explanation
Indices: 15340--15479 Score: 86
Period size: 22 Copynumber: 6.4 Consensus size: 23
15330 AAATTGAGAC
*
15340 TTTT-ATAACCTTCA-TATGAAA
1 TTTTGATAACCTACACTATGAAA
15361 TTTTGATAACC-ACACTATGAAA
1 TTTTGATAACCTACACTATGAAA
* * *
15383 TTTTGATAACCT-CCCCATGATA
1 TTTTGATAACCTACACTATGAAA
* *
15405 TATT-AGTAACCT-C-CTTATAAAA
1 TTTTGA-TAACCTACAC-TATGAAA
* *
15427 TTTTGTTAACC-ACACTATAAAA
1 TTTTGATAACCTACACTATGAAA
*
15449 TTCTT-ATAACCT-CGCTAT-AACA
1 TT-TTGATAACCTACACTATGAA-A
15471 TTTTGATAA
1 TTTTGATAA
15480 TCCCTTTGAT
Statistics
Matches: 95, Mismatches: 12, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
21 12 0.13
22 80 0.84
23 3 0.03
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.38
Consensus pattern (23 bp):
TTTTGATAACCTACACTATGAAA
Found at i:15586 original size:68 final size:65
Alignment explanation
Indices: 15488--15650 Score: 200
Period size: 68 Copynumber: 2.4 Consensus size: 65
15478 AATCCCTTTG
* * * * *
15488 ATAACTTTTCTATAAAATTGTGATAACCACACTATGAAATTTCAATAACCTTCCTAAGAAATTTT
1 ATAAC-TTCCTATGAAATTTTGGTAACCACACTATGAAATTTCAATAACCTTCCCAAGAAATTTT
15553 A
65 A
** *
15554 ATAACCTGATCCTATGAAATTTTGGTAACCACACTATGAAATTTGGATAACCTTCCCATGAAATT
1 ATAA-CT--TCCTATGAAATTTTGGTAACCACACTATGAAATTTCAATAACCTTCCCAAGAAATT
*
15619 TTG
63 TTA
15622 ATAACTTCCATATGAAATTTTGGTAACCA
1 ATAACTTCC-TATGAAATTTTGGTAACCA
15651 TACTTCTGAC
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
65 3 0.04
66 24 0.29
67 3 0.04
68 54 0.64
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (65 bp):
ATAACTTCCTATGAAATTTTGGTAACCACACTATGAAATTTCAATAACCTTCCCAAGAAATTTTA
Found at i:15643 original size:22 final size:22
Alignment explanation
Indices: 15484--15649 Score: 140
Period size: 22 Copynumber: 7.5 Consensus size: 22
15474 TGATAATCCC
* * *
15484 TTTGATAACTTTTCTATAAAAT
1 TTTGATAACCTTCCTATGAAAT
* *
15506 TGTGATAACC-ACACTATGAAAT
1 TTTGATAACCTTC-CTATGAAAT
** *
15528 TTCAATAACCTTCCTAAGAAAT
1 TTTGATAACCTTCCTATGAAAT
*
15550 TTTAATAACCTGATCCTATGAAAT
1 TTTGATAACCT--TCCTATGAAAT
* *
15574 TTTGGTAACC-ACACTATGAAAT
1 TTTGATAACCTTC-CTATGAAAT
* *
15596 TTGGATAACCTTCCCATGAAAT
1 TTTGATAACCTTCCTATGAAAT
15618 TTTGATAA-CTTCCATATGAAAT
1 TTTGATAACCTTCC-TATGAAAT
*
15640 TTTGGTAACC
1 TTTGATAACC
15650 ATACTTCTGA
Statistics
Matches: 114, Mismatches: 22, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
21 6 0.05
22 87 0.76
23 3 0.03
24 18 0.16
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
TTTGATAACCTTCCTATGAAAT
Done.