Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022214.1 Corchorus olitorius cultivar O-4 contig22247, 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: 15447
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:3606 original size:13 final size:13
Alignment explanation
Indices: 3588--3612 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3578 TTTTTACCAC
3588 CTTAAAATTATTG
1 CTTAAAATTATTG
3601 CTTAAAATTATT
1 CTTAAAATTATT
3613 TTTTGGCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
CTTAAAATTATTG
Found at i:5584 original size:18 final size:18
Alignment explanation
Indices: 5561--5606 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
5551 TGAAATTAAT
5561 TAATTATTAATTAAATAA
1 TAATTATTAATTAAATAA
** *
5579 TAATTATTTTTTGAATAA
1 TAATTATTAATTAAATAA
*
5597 TTATTATTAA
1 TAATTATTAA
5607 ATTTCTAGTG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATTATTAATTAAATAA
Found at i:9073 original size:6 final size:6
Alignment explanation
Indices: 9062--9092 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
9052 CAAATCAAAT
*
9062 AGAAAA AGAAAA AGAAAC AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A
9093 TAATACACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:11513 original size:31 final size:30
Alignment explanation
Indices: 11449--11514 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 30
11439 TATGGGATTT
*
11449 ATTTGTCCCAAAAAAAAAGTTAAGGGGCCA
1 ATTTGTCCCAAAAAAAAAGTTAAGGGGACA
** * *
11479 ATTTGTCCCAAAATGGATAGTTAAGGGGATA
1 ATTTGTCCCAAAA-AAAAAGTTAAGGGGACA
11510 ATTTG
1 ATTTG
11515 GGTATTAAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (30 bp):
ATTTGTCCCAAAAAAAAAGTTAAGGGGACA
Found at i:12374 original size:14 final size:14
Alignment explanation
Indices: 12355--12384 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12345 GAAGACTTAA
*
12355 AAATCATTAAGAAC
1 AAATCATTAACAAC
12369 AAATCATTAACAAC
1 AAATCATTAACAAC
12383 AA
1 AA
12385 TTATTCACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.17, G:0.03, T:0.20
Consensus pattern (14 bp):
AAATCATTAACAAC
Found at i:14969 original size:22 final size:22
Alignment explanation
Indices: 14942--15426 Score: 185
Period size: 22 Copynumber: 22.3 Consensus size: 22
14932 ATTACACTAT
*
14942 TTTTGATGACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
14964 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* ** * *
14986 TTTTAATAACGATACTATGGAA
1 TTTTGATAACCTTCCTATGAAA
** ** **
15008 TTTCAATAATATTTTTAT--AA
1 TTTTGATAACCTTCCTATGAAA
** *
15028 TTTTTTTAACCTTCTTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* *
15050 TTTT-ATTAACCTCCCTGA-GGAA
1 TTTTGA-TAACCTTCCT-ATGAAA
15072 TTTTGA-AGACC-TCACTATGAAA
1 TTTTGATA-ACCTTC-CTATGAAA
*
15094 TTTTGATAA-CTTCCAATGAAA
1 TTTTGATAACCTTCCTATGAAA
* ** *
15115 TTTTGATGACCAACACTATGAGA
1 TTTTGATAACCTTC-CTATGAAA
* *
15138 TGTTGATAACC-TCCATATGATA
1 TTTTGATAACCTTCC-TATGAAA
* * *
15160 TATTGATAACC-ACGTTATGAAAA
1 TTTTGATAACCTTC-CTATG-AAA
*
15183 TTTT-AAAACC-TCCATATG-AA
1 TTTTGATAACCTTCC-TATGAAA
* *
15203 TCGTT-AGTAA--TTACACTCTGAAA
1 T-TTTGA-TAACCTT-C-CTATGAAA
* * *
15226 TTTTGATAATCATACTATGAAA
1 TTTTGATAACCTTCCTATGAAA
*
15248 TTGTGATAACC-TCGCTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
*
15270 TTTTGATAAACCTTCCTATAAAA
1 TTTTGAT-AACCTTCCTATGAAA
*
15293 TTTTGATAAACC-TCCTTATAAAA
1 TTTTGAT-AACCTTCC-TATGAAA
*
15316 TTTTGATAA-CATCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
* *
15338 TCTTGATAA-----CTA-CAAA
1 TTTTGATAACCTTCCTATGAAA
*
15354 TTTTGATAACCTCCCTATG-AA
1 TTTTGATAACCTTCCTATGAAA
***
15375 TGTTTGATAACCTAATTATGAAA
1 T-TTTGATAACCTTCCTATGAAA
* * *
15398 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
*
15420 ATTTGAT
1 TTTTGAT
15427 CTACATATAT
Statistics
Matches: 355, Mismatches: 69, Indels: 78
0.71 0.14 0.16
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 17 0.05
21 32 0.09
22 218 0.61
23 71 0.20
24 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:15345 original size:45 final size:44
Alignment explanation
Indices: 15223--15346 Score: 128
Period size: 45 Copynumber: 2.8 Consensus size: 44
15213 TTACACTCTG
* * *
15223 AAATTTTGATAATCATACTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAACCATCCTATGAAATT-TGATAAACCTCGCTATA
* *
15267 AAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTC-CTTATA
1 AAATTTTGAT-AACCATCCTATGAAA-TTTGATAAACCTCGC-TATA
15313 AAATTTTGATAA-CATCCTTATGAAATCTTGATAA
1 AAATTTTGATAACCATCC-TATGAAAT-TTGATAA
15347 CTACAAATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
44 15 0.22
45 31 0.46
46 21 0.31
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.38
Consensus pattern (44 bp):
AAATTTTGATAACCATCCTATGAAATTTGATAAACCTCGCTATA
Found at i:15426 original size:82 final size:84
Alignment explanation
Indices: 15267--15419 Score: 197
Period size: 82 Copynumber: 1.8 Consensus size: 84
15257 CCTCGCTATG
* ** *
15267 AAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCCTTATAAAATTTTGATAACATCCTT
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAAACCTAATTATAAAATTTTGATAACATCCCT
15332 ATGAAATCTTGATAACTAC
66 ATGAAATCTTGATAACTAC
* * *
15351 AAATTTTGAT-AACCTCCCTAT-GAATGTTTGAT-AACCTAATTATGAAATTTTGTTAATC-TCC
1 AAATTTTGATAAACCTCCCTATAAAAT-TTTGATAAACCTAATTATAAAATTTTGATAA-CATCC
15412 CTATGAAA
64 CTATGAAA
15420 ATTTGATCTA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
82 33 0.55
83 17 0.28
84 10 0.17
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (84 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAAACCTAATTATAAAATTTTGATAACATCCCT
ATGAAATCTTGATAACTAC
Done.