Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018682.1 Corchorus olitorius cultivar O-4 contig18715, 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: 37292
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1258 original size:15 final size:15
Alignment explanation
Indices: 1238--1279 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
1228 ACAGAGGTTG
1238 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
1253 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
*
1268 ACTACAAAACAA
1 AC-AGAAAACAA
1280 AACAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 17 0.68
16 8 0.32
ACGTcount: A:0.67, C:0.17, G:0.05, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:6783 original size:330 final size:330
Alignment explanation
Indices: 6182--6847 Score: 1287
Period size: 330 Copynumber: 2.0 Consensus size: 330
6172 AGTGGATGCT
6182 CACAATCCACCCCCTACCGAGGATAGCAAAGAAATGATTGAAGTTCTTCAAACAATACACTCGGG
1 CACAATCCACCCCCTACCGAGGATAGCAAAGAAATGATTGAAGTTCTTCAAACAATACACTCGGG
6247 GGGAACGATTATGAAGATGCTAAGGCTATAGTTTTTACTAAGCCTGATGAAACATCTACATACCA
66 GGGAACGATTATGAAGATGCTAAGGCTATAGTTTTTACTAAGCCTGATGAAACATCTACATACCA
6312 CATTAAGCCTTTACACATTAAGGCTTACGTTGATGGTATTCTTATAAACATAGTTCTAGTCGACA
131 CATTAAGCCTTTACACATTAAGGCTTACGTTGATGGTATTCTTATAAACATAGTTCTAGTCGACA
*
6377 ACGGGGCAACTGTTAACCTGCTTCCTTTTTCCTCATTGAAAAAGATTGGCAAGTGCAGTGACGAC
196 ACAGGGCAACTGTTAACCTGCTTCCTTTTTCCTCATTGAAAAAGATTGGCAAGTGCAGTGACGAC
*
6442 CTGATGCCTTCATATGTTACTGTCAGTGACTTCTCTGACGCTGTCAGGAAGACTAGAGGGATACT
261 CTGATGCCTTCAGATGTTACTGTCAGTGACTTCTCTGACGCTGTCAGGAAGACTAGAGGGATACT
6507 CCCTA
326 CCCTA
6512 CACAATCCACCCCCTACCGAGGATAGCAAAGAAATGATTGAAGTTCTTCAAACAATACACTCGGG
1 CACAATCCACCCCCTACCGAGGATAGCAAAGAAATGATTGAAGTTCTTCAAACAATACACTCGGG
6577 GGGAACGATTATGAAGATGCTAAGGCTATAGTTTTTACTAAGCCTGATGAAACATCTACATACCA
66 GGGAACGATTATGAAGATGCTAAGGCTATAGTTTTTACTAAGCCTGATGAAACATCTACATACCA
6642 CATTAAGCCTTTACACATTAAGGCTTACGTTGATGGTATTCTTATAAACATAGTTCTAGTCGACA
131 CATTAAGCCTTTACACATTAAGGCTTACGTTGATGGTATTCTTATAAACATAGTTCTAGTCGACA
* *
6707 ACAGGGCAACTGTTAACCTGCTTCTTTTTTCCTCATTGAAAAAGATTGGCAAGTGCAGTGATGAC
196 ACAGGGCAACTGTTAACCTGCTTCCTTTTTCCTCATTGAAAAAGATTGGCAAGTGCAGTGACGAC
*
6772 CTGATGCCTTCAGATGTTACTGTCAGTGACTTCTCTGGCGCTGTCAGGAAGACTAGAGGGATACT
261 CTGATGCCTTCAGATGTTACTGTCAGTGACTTCTCTGACGCTGTCAGGAAGACTAGAGGGATACT
6837 CCCTA
326 CCCTA
6842 CACAAT
1 CACAAT
6848 TAACTGTTGG
Statistics
Matches: 331, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
330 331 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (330 bp):
CACAATCCACCCCCTACCGAGGATAGCAAAGAAATGATTGAAGTTCTTCAAACAATACACTCGGG
GGGAACGATTATGAAGATGCTAAGGCTATAGTTTTTACTAAGCCTGATGAAACATCTACATACCA
CATTAAGCCTTTACACATTAAGGCTTACGTTGATGGTATTCTTATAAACATAGTTCTAGTCGACA
ACAGGGCAACTGTTAACCTGCTTCCTTTTTCCTCATTGAAAAAGATTGGCAAGTGCAGTGACGAC
CTGATGCCTTCAGATGTTACTGTCAGTGACTTCTCTGACGCTGTCAGGAAGACTAGAGGGATACT
CCCTA
Found at i:16481 original size:24 final size:24
Alignment explanation
Indices: 16449--16520 Score: 144
Period size: 24 Copynumber: 3.0 Consensus size: 24
16439 GCAATCGAGA
16449 CCACAAAATTTCAGAAGCATTTTT
1 CCACAAAATTTCAGAAGCATTTTT
16473 CCACAAAATTTCAGAAGCATTTTT
1 CCACAAAATTTCAGAAGCATTTTT
16497 CCACAAAATTTCAGAAGCATTTTT
1 CCACAAAATTTCAGAAGCATTTTT
16521 TAAAACCAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (24 bp):
CCACAAAATTTCAGAAGCATTTTT
Found at i:16989 original size:12 final size:12
Alignment explanation
Indices: 16972--16997 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16962 TATATAATAT
16972 ATGTTATTATAG
1 ATGTTATTATAG
16984 ATGTTATTATAG
1 ATGTTATTATAG
16996 AT
1 AT
16998 ATATATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (12 bp):
ATGTTATTATAG
Found at i:18651 original size:21 final size:21
Alignment explanation
Indices: 18625--18678 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
18615 GCCATTTTCA
18625 ACTTGTTCATCACGAGTTCTT
1 ACTTGTTCATCACGAGTTCTT
18646 ACTTGTTCATCACGAGTTCTT
1 ACTTGTTCATCACGAGTTCTT
*
18667 ACTCGTTCATCA
1 ACTTGTTCATCA
18679 ACTTTTCCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.41
Consensus pattern (21 bp):
ACTTGTTCATCACGAGTTCTT
Found at i:19525 original size:102 final size:100
Alignment explanation
Indices: 19338--19526 Score: 288
Period size: 101 Copynumber: 1.9 Consensus size: 100
19328 TTGCATATTG
* * * * * *
19338 TAAACAACCATAATAGAAGATGTGAAAATACTAATTAACCAATCCGACCCTTTCTTCCCATGAAT
1 TAAACAACCACAATAGAAGATATGAAAATACTAATTAACCAATCCAAACCTCTCTTCCCATGAAA
*
19403 TGAAGAACAAATGAGGAGGGGTTGTAAATAATAAA
66 TGAAGAAAAAATGAGGAGGGGTTGTAAATAATAAA
*
19438 TAAAGAACCACAATAGAAAGATATGAAAATACTAATTAACCAATCCAAACCTCTCTTACCCATGA
1 TAAACAACCACAATAG-AAGATATGAAAATACTAATTAACCAATCCAAACCTCTCTT-CCCATGA
19503 AATGAAGAAAAAATGAGGAGGGGT
64 AATGAAGAAAAAATGAGGAGGGGT
19527 ATATAGGTAA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
100 14 0.18
101 36 0.46
102 29 0.37
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (100 bp):
TAAACAACCACAATAGAAGATATGAAAATACTAATTAACCAATCCAAACCTCTCTTCCCATGAAA
TGAAGAAAAAATGAGGAGGGGTTGTAAATAATAAA
Found at i:21688 original size:15 final size:15
Alignment explanation
Indices: 21622--21657 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
21612 CATGGAAAGT
21622 ACTCTCATTGGAATC
1 ACTCTCATTGGAATC
* *
21637 ACTCTCTTTGGAATG
1 ACTCTCATTGGAATC
21652 ACTCTC
1 ACTCTC
21658 CATAAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.36
Consensus pattern (15 bp):
ACTCTCATTGGAATC
Found at i:25887 original size:12 final size:11
Alignment explanation
Indices: 25866--25893 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
25856 TCTGCTATGT
25866 AAAAAGAAAAA
1 AAAAAGAAAAA
25877 AAAAAGAAAAA
1 AAAAAGAAAAA
25888 AAAAAG
1 AAAAAG
25894 GAAGAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:26717 original size:13 final size:13
Alignment explanation
Indices: 26699--26728 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
26689 TTCCTACGTA
26699 TTAAAATTTTATT
1 TTAAAATTTTATT
26712 TTAAAATTTTATT
1 TTAAAATTTTATT
26725 TTAA
1 TTAA
26729 TTGATTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTAAAATTTTATT
Found at i:29206 original size:14 final size:14
Alignment explanation
Indices: 29187--29217 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
29177 GATAATTCTC
29187 ATATTATATAAAAA
1 ATATTATATAAAAA
29201 ATATTATATAAAAA
1 ATATTATATAAAAA
29215 ATA
1 ATA
29218 ATAATTATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATATTATATAAAAA
Found at i:29685 original size:178 final size:178
Alignment explanation
Indices: 29416--29753 Score: 457
Period size: 178 Copynumber: 1.9 Consensus size: 178
29406 CCGATTAAGG
* *
29416 TGATTTAAATGTCTATTAAAAGATTGTTTAATGATCTACAACTTTCATGCAGGACTCGAAAACTA
1 TGATTCAAATGTCTATTAAAAGATTGTTTAATGATCTACAACTTTCATGAAGGACTCGAAAACTA
* * * * ** *
29481 AATTTAATGTTTTAAGTATCAAAAATGCTTCCGAAAG-ATTTGTTGTTTCGGTTAACGGGAATAT
66 AATTTAATGTTTCAAGTATAAAAAATGATTCC-AAAGAATTAGTTGTTTCGGTTAACGAAAATAG
*
29545 ACGATCCACTTAATATTATATAACTTT-TGCTCCAGATGTCTGATTGAGA
130 ACGATCCACTTAATATTACATAA-TTTGTGCTCCAGATGTCTGATTGAGA
* * * * * * *
29594 TGATTCAATTGTCTCTTGAAAGGTTGTTTCATGATCTACAGCTTTCATGAAGGACTTGAAAACTA
1 TGATTCAAATGTCTATTAAAAGATTGTTTAATGATCTACAACTTTCATGAAGGACTCGAAAACTA
29659 AATTTAATG-TTCAAGGTATAAAAAATGATTCCAAAGAATTAGTTGTTTCGGTTAACGAAAATAG
66 AATTTAATGTTTCAA-GTATAAAAAATGATTCCAAAGAATTAGTTGTTTCGGTTAACGAAAATAG
* *
29723 ACGGTCTACTTAATATTACATAATTTGTGCT
130 ACGATCCACTTAATATTACATAATTTGTGCT
29754 TATGGTAGAA
Statistics
Matches: 138, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
177 11 0.08
178 127 0.92
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (178 bp):
TGATTCAAATGTCTATTAAAAGATTGTTTAATGATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGATTCCAAAGAATTAGTTGTTTCGGTTAACGAAAATAGA
CGATCCACTTAATATTACATAATTTGTGCTCCAGATGTCTGATTGAGA
Found at i:32380 original size:21 final size:21
Alignment explanation
Indices: 32333--32394 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
32323 GTTTCTATGT
*
32333 AATTAAAAAAAAAAACTATCC
1 AATTAAAAAAAAAAACTACCC
* *
32354 AATTAAAAAAGAAAACTGCCC
1 AATTAAAAAAAAAAACTACCC
* **
32375 ATTTAAAAATTAAAACTACC
1 AATTAAAAAAAAAAACTACC
32395 ATGCCTTTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.60, C:0.16, G:0.03, T:0.21
Consensus pattern (21 bp):
AATTAAAAAAAAAAACTACCC
Found at i:34220 original size:21 final size:21
Alignment explanation
Indices: 34196--34260 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
34186 AATTCTCTGT
34196 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
34217 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
34238 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
34259 AA
1 AA
34261 GTACTGATTC
Statistics
Matches: 30, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
20 6 0.20
21 18 0.60
22 6 0.20
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:34401 original size:56 final size:56
Alignment explanation
Indices: 34329--34442 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
34319 TTTATTTTAT
*
34329 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTATGAA
34385 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTATGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTATGAA
34441 AG
1 AG
34443 GAAATGGATA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.33
Consensus pattern (56 bp):
AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTATGAA
Done.