Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008774.1 Corchorus capsularis cultivar CVL-1 contig08795, 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: 18542
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Found at i:6231 original size:15 final size:15
Alignment explanation
Indices: 6207--6237 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6197 CAATTTAGGC
*
6207 TAAAAGTTCAAGCTT
1 TAAAAATTCAAGCTT
6222 TAAAAATTCAAGCTT
1 TAAAAATTCAAGCTT
6237 T
1 T
6238 TCCTTCTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (15 bp):
TAAAAATTCAAGCTT
Found at i:14202 original size:24 final size:26
Alignment explanation
Indices: 14170--14233 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
14160 AGGATTTTGG
* *
14170 TTATCCACACCATCGTT-G-ATGGCA
1 TTATTCACACCATCATTGGAATGGCA
**
14194 TTATTCACACCATTCATTGGAATTTCA
1 TTATTCACACCA-TCATTGGAATGGCA
14221 TTATTCACACCAT
1 TTATTCACACCAT
14234 GATGGAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 11 0.33
25 4 0.12
26 2 0.06
27 16 0.48
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.36
Consensus pattern (26 bp):
TTATTCACACCATCATTGGAATGGCA
Found at i:16723 original size:2 final size:2
Alignment explanation
Indices: 16718--16743 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16708 TTTTATGACC
16718 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
16744 CTAGTTTTAA
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):
TA
Found at i:16788 original size:142 final size:142
Alignment explanation
Indices: 16576--16859 Score: 523
Period size: 142 Copynumber: 2.0 Consensus size: 142
16566 TAAAAGGATA
* * * *
16576 TATATATATATATATGTATGTATATACTGGTTTTAGCTTTCACGTACGTTGCACGTGACGCAACG
1 TATATATATATATATATATATATATACTAGTTTTAACTTTCACGTACGTTGCACGTGACGCAACG
16641 TGTTTAAATAAAATATTCATATGAAATTATAATAATCTCTCTATTAAATTATGATAATTACATTA
66 TGTTTAAATAAAATATTCATATGAAATTATAATAATCTCTCTATTAAATTATGATAATTACATTA
16706 TTTTTTATGACC
131 TTTTTTATGACC
*
16718 TATATATATATATATATATATATATACTAGTTTTAACTTTCACGTACGTTGCACGTGGCGCAACG
1 TATATATATATATATATATATATATACTAGTTTTAACTTTCACGTACGTTGCACGTGACGCAACG
16783 TGTTTAAATAAAATATTCATATGAAATTATAATAATCTCTCTATTAAATTATGATAATTACATTA
66 TGTTTAAATAAAATATTCATATGAAATTATAATAATCTCTCTATTAAATTATGATAATTACATTA
16848 TTTTTTATGACC
131 TTTTTTATGACC
16860 CCATTATGAA
Statistics
Matches: 137, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
142 137 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (142 bp):
TATATATATATATATATATATATATACTAGTTTTAACTTTCACGTACGTTGCACGTGACGCAACG
TGTTTAAATAAAATATTCATATGAAATTATAATAATCTCTCTATTAAATTATGATAATTACATTA
TTTTTTATGACC
Found at i:17049 original size:22 final size:22
Alignment explanation
Indices: 16863--17227 Score: 137
Period size: 22 Copynumber: 16.7 Consensus size: 22
16853 TATGACCCCA
*
16863 TTATGAAATTTTGATAACATTCC
1 TTATGAAATTTTGATAACCTT-C
* * * *
16886 CTATGAAATTTTAATAACGATAC
1 TTATGAAATTTTGATAAC-CTTC
* * * *
16909 -TATGTAATTTCGAGAACCTTT
1 TTATGAAATTTTGATAACCTTC
**
16930 TTAT-AAATTTTTTTTAACCTTC
1 TTATGAAA-TTTTGATAACCTTC
* ** *
16952 TTATAAAATTCGGTTAACCTTC
1 TTATGAAATTTTGATAACCTTC
* * * **
16974 CTAAGGAATTTT-A-AAGATCTC
1 TTATGAAATTTTGATAACCT-TC
* *
16995 AATATGAAATTTTGATAAACCTCC
1 -TTATGAAATTTTGAT-AACCTTC
* *
17019 TTATAAAATTTTGATAACTTTC
1 TTATGAAATTTTGATAACCTTC
*
17041 TTATGAAATATTGATAA----C
1 TTATGAAATTTTGATAACCTTC
* *
17059 -TA-CAAATTTTGATAACCTCC
1 TTATGAAATTTTGATAACCTTC
* **
17079 CTATGATTTTTTTGATAACC-TC
1 TTATGA-AATTTTGATAACCTTC
* * * *
17101 ATTACGAAATTTTGTTAATCTCC
1 -TTATGAAATTTTGATAACCTTC
* * ***
17124 CTATGAAGTTTTGATATACAAAC
1 TTATGAAATTTTGATA-ACCTTC
*
17147 -TATGAAATTTTGATAACCCTC
1 TTATGAAATTTTGATAACCTTC
* * *
17168 TTGTGAAATTTTGA-AAACTAAAC
1 TTATGAAATTTTGATAACCT--TC
17191 -TATGAAATTTTGATAACCTTC
1 TTATGAAATTTTGATAACCTTC
*
17212 ATATGAAATTTTGATA
1 TTATGAAATTTTGATA
17228 TCATCCCTAA
Statistics
Matches: 246, Mismatches: 72, Indels: 49
0.67 0.20 0.13
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
18 1 0.00
20 4 0.02
21 14 0.06
22 151 0.61
23 57 0.23
24 3 0.01
25 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCTTC
Found at i:17470 original size:22 final size:22
Alignment explanation
Indices: 17423--17497 Score: 64
Period size: 25 Copynumber: 3.4 Consensus size: 22
17413 TCTATGAAAT
*
17423 AAATTTTGATAATCCGATCTCTATG
1 AAATTTTGATAAT-C-A-ATCTATG
17448 AAATTTTGATAATCAATCTATG
1 AAATTTTGATAATCAATCTATG
* ** *
17470 ATA-TTTGATAA-CCTTCTATC
1 AAATTTTGATAATCAATCTATG
17490 AAATTTTG
1 AAATTTTG
17498 GTACTCCTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 8 0.19
21 12 0.28
22 8 0.19
23 1 0.02
24 1 0.02
25 13 0.30
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (22 bp):
AAATTTTGATAATCAATCTATG
Found at i:17655 original size:22 final size:22
Alignment explanation
Indices: 17325--17655 Score: 102
Period size: 22 Copynumber: 14.9 Consensus size: 22
17315 CCAGAAATAC
17325 CACTATGAAATTTTTG-TAA--T
1 CACTATGAAA-TTTTGATAACCT
* *
17345 CACATTTGAAAATTTGATAACCT
1 CAC-TATGAAATTTTGATAACCT
** *
17368 CTTTATCAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCT
** * * * *
17390 CTTTATAAAATTTTGTTGACCC
1 CACTATGAAATTTTGATAACCT
*
17412 CTCTATGAAATAAATTTTGATAATCCGAT
1 CACTATG----AAATTTTGATAA-CC--T
*
17441 CTCTATGAAATTTTGATAA--T
1 CACTATGAAATTTTGATAACCT
*
17461 CAATCTATGATA-TTTGATAACCT
1 C-A-CTATGAAATTTTGATAACCT
* * *
17484 -TCTATCAAATTTTGGT-A-CT
1 CACTATGAAATTTTGATAACCT
*
17503 C-CTTATGAAATTGAGACTTTTATAACCTT
1 CAC-TATGAAA-T-----TTTGATAACC-T
*
17532 CA-TATGAAATTTTGATAACCA
1 CACTATGAAATTTTGATAACCT
*
17553 CACTATAAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCT
* * **
17575 CCCCATGAAACATT-AGTAACCT
1 CACTATGAAATTTTGA-TAACCT
* *
17597 C-C--T-AAATTTTGTTAACCA
1 CACTATGAAATTTTGATAACCT
17615 CACTATGAAATTCTT-ATAACCT
1 CACTATGAAATT-TTGATAACCT
* *
17637 CGCTATGACATTTTGATAA
1 CACTATGAAATTTTGATAA
17656 TCTCTTTGAT
Statistics
Matches: 232, Mismatches: 42, Indels: 72
0.67 0.12 0.21
Matches are distributed among these distances:
18 11 0.05
19 5 0.02
20 22 0.09
21 30 0.13
22 112 0.48
23 5 0.02
25 12 0.05
26 14 0.06
27 4 0.02
28 8 0.03
29 9 0.04
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.39
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCT
Found at i:17843 original size:44 final size:45
Alignment explanation
Indices: 17745--17855 Score: 115
Period size: 44 Copynumber: 2.5 Consensus size: 45
17735 TAAACTTATC
* * * **
17745 CTATGAAATTTTGGTAA-CTACATTATGAAATTTTGGTAACCATA
1 CTATGAAATTTTGATAACCTACATCATGAAATTATAATAACCATA
17789 CTATTG-AATTTTGATAACCTAC-TCATGAAATTATAATAACCAT-
1 CTA-TGAAATTTTGATAACCTACATCATGAAATTATAATAACCATA
*
17832 CTTATGAAATTTTGACAACC-ACAT
1 C-TATGAAATTTTGATAACCTACAT
17856 AGAGACAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
43 5 0.09
44 45 0.80
45 6 0.11
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (45 bp):
CTATGAAATTTTGATAACCTACATCATGAAATTATAATAACCATA
Found at i:17851 original size:22 final size:23
Alignment explanation
Indices: 17746--17852 Score: 100
Period size: 22 Copynumber: 4.8 Consensus size: 23
17736 AAACTTATCC
*
17746 TATGAAATTTTGGTAA-C-TACAT
1 TATGAAATTTTGATAACCATAC-T
*
17768 TATGAAATTTTGGTAACCATAC-
1 TATGAAATTTTGATAACCATACT
17790 TATTG-AATTTTGATAACC-TACT
1 TA-TGAAATTTTGATAACCATACT
* * *
17812 CATGAAATTATAATAACCAT-CT
1 TATGAAATTTTGATAACCATACT
*
17834 TATGAAATTTTGACAACCA
1 TATGAAATTTTGATAACCA
17853 CATAGAGACA
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
21 5 0.07
22 59 0.83
23 4 0.06
24 3 0.04
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.37
Consensus pattern (23 bp):
TATGAAATTTTGATAACCATACT
Found at i:18049 original size:19 final size:20
Alignment explanation
Indices: 18018--18055 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
18008 TATTGACATT
18018 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
18037 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
18056 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
Done.