Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011309.1 Corchorus olitorius cultivar O-4 contig11342, 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: 53458
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:603 original size:25 final size:26
Alignment explanation
Indices: 546--616 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 26
536 GACATTACAT
546 AATTTTAGTAACCTCTCATCTAAAAA
1 AATTTTAGTAACCTCTCATCTAAAAA
**
572 AATTTTAGTAACC-CTGCAT-TTTAAA
1 AATTTTAGTAACCTCT-CATCTAAAAA
*
597 AATTTTAGTAACCTTTCATC
1 AATTTTAGTAACCTCTCATC
617 GACATCAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
25 22 0.56
26 17 0.44
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (26 bp):
AATTTTAGTAACCTCTCATCTAAAAA
Found at i:1500 original size:22 final size:23
Alignment explanation
Indices: 1461--1503 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
1451 TTTTTTGTAA
1461 TATTTTGAATTATCATAGTAATC
1 TATTTTGAATTATCATAGTAATC
1484 TATTTT-AATTGAT-ATAGTAA
1 TATTTTGAATT-ATCATAGTAA
1504 ATTAATTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (23 bp):
TATTTTGAATTATCATAGTAATC
Found at i:9465 original size:22 final size:21
Alignment explanation
Indices: 9440--9498 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 21
9430 CAATTTTATT
9440 AATTTCCAAAATCTTCTTTTG
1 AATTTCCAAAATCTTCTTTTG
*
9461 AAATTACCAAAA----CTTTT-
1 -AATTTCCAAAATCTTCTTTTG
*
9478 ATTTTCCAAAATCTTCTTTTG
1 AATTTCCAAAATCTTCTTTTG
9499 GAGTTGCTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 11
0.67 0.07 0.26
Matches are distributed among these distances:
16 9 0.31
18 5 0.17
20 5 0.17
22 10 0.34
ACGTcount: A:0.32, C:0.19, G:0.03, T:0.46
Consensus pattern (21 bp):
AATTTCCAAAATCTTCTTTTG
Found at i:10492 original size:21 final size:22
Alignment explanation
Indices: 10466--10516 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
10456 AACGATGCCG
10466 TTTCTTTCAAATTCTTTT-TTT
1 TTTCTTTCAAATTCTTTTCTTT
****
10487 TTTCTTTTTCCTTCTTTTCTTT
1 TTTCTTTCAAATTCTTTTCTTT
10509 TTTCTTTC
1 TTTCTTTC
10517 CTTCTTCTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTCTTTCAAATTCTTTTCTTT
Found at i:10509 original size:20 final size:20
Alignment explanation
Indices: 10477--10522 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 20
10467 TTCTTTCAAA
10477 TTCTTTT-TTTTTTCTTTTTCC
1 TTCTTTTCTTTTTTC--TTTCC
10498 TTCTTTTCTTTTTTCTTTCC
1 TTCTTTTCTTTTTTCTTTCC
10518 TTCTT
1 TTCTT
10523 CTTCCTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.42
21 7 0.29
22 7 0.29
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (20 bp):
TTCTTTTCTTTTTTCTTTCC
Found at i:12278 original size:39 final size:39
Alignment explanation
Indices: 12224--12301 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
12214 TATAACTTAT
*
12224 GTATTTGGTATTTTGTGACTAAGTGAACAAAAATGTAAA
1 GTATTTGGTATTTTGTAACTAAGTGAACAAAAATGTAAA
12263 GTATTTGGTATTTTGTAACTAAGTGAACAAAAATGTAAA
1 GTATTTGGTATTTTGTAACTAAGTGAACAAAAATGTAAA
12302 ATGAAAACTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (39 bp):
GTATTTGGTATTTTGTAACTAAGTGAACAAAAATGTAAA
Found at i:12775 original size:27 final size:27
Alignment explanation
Indices: 12745--12807 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
12735 TTAAGAAAAG
* *
12745 GACCAAAATAACCCTAAATGTACAAAT
1 GACCAAAATAACCCCAAACGTACAAAT
** * *
12772 GACCAAAATGCCCCCAGACGTGCAAAT
1 GACCAAAATAACCCCAAACGTACAAAT
12799 GACCAAAAT
1 GACCAAAAT
12808 GCCCCTGGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.46, C:0.27, G:0.13, T:0.14
Consensus pattern (27 bp):
GACCAAAATAACCCCAAACGTACAAAT
Found at i:13978 original size:15 final size:15
Alignment explanation
Indices: 13955--13996 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
13945 CATGAATGAA
13955 GAGAAAATCGAATAC
1 GAGAAAATCGAATAC
* *
13970 GAGATAATCGAATAT
1 GAGAAAATCGAATAC
*
13985 GAGACAATCGAA
1 GAGAAAATCGAA
13997 GAAGTTTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.17
Consensus pattern (15 bp):
GAGAAAATCGAATAC
Found at i:15451 original size:17 final size:16
Alignment explanation
Indices: 15404--15453 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
15394 ATAAACCTAT
*
15404 GTAATCTTTGATCACCG
1 GTAATC-TTGATCACTG
*
15421 GTGATCTTGCATCACTG
1 GTAATCTTG-ATCACTG
15438 GTAATCTTAGATCACT
1 GTAATCTT-GATCACT
15454 AGTGATCTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 3 0.11
17 24 0.86
18 1 0.04
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (16 bp):
GTAATCTTGATCACTG
Found at i:15461 original size:17 final size:16
Alignment explanation
Indices: 15411--15461 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
15401 TATGTAATCT
*
15411 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
*
15427 TTGCATCACTGGTAATC
1 TTG-ATCACTGGTGATC
*
15444 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
15461 T
1 T
15462 GGGGGTGATC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:17162 original size:2 final size:2
Alignment explanation
Indices: 17155--17183 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17145 TGCGGCTAAA
17155 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17184 ATCCTAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20027 original size:14 final size:14
Alignment explanation
Indices: 20002--20045 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
19992 AAACTAAATG
20002 ATAAACGAAAAAGAA
1 ATAAA-GAAAAAGAA
20017 ATAAAGAAAAAGAA
1 ATAAAGAAAAAGAA
20031 ATAAAGAAAAAGAA
1 ATAAAGAAAAAGAA
20045 A
1 A
20046 AACTAACTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 24 0.83
15 5 0.17
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (14 bp):
ATAAAGAAAAAGAA
Done.