Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019981.1 Corchorus olitorius cultivar O-4 contig20014, 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: 35977
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:548 original size:13 final size:13
Alignment explanation
Indices: 530--554 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
520 GGGGGACGGC
530 ACTAGAAGAAAAA
1 ACTAGAAGAAAAA
543 ACTAGAAGAAAA
1 ACTAGAAGAAAA
555 GAAAATTGGT
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:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (13 bp):
ACTAGAAGAAAAA
Found at i:3013 original size:21 final size:22
Alignment explanation
Indices: 2989--3035 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
2979 TTGGAATGGC
*
2989 GATGGCACGG-GCATGGCCGGT
1 GATGGCACGGTGAATGGCCGGT
*
3010 GATGGCACGGTGAATGGGCGGT
1 GATGGCACGGTGAATGGCCGGT
3032 GATG
1 GATG
3036 ACTTGGTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.17, C:0.17, G:0.49, T:0.17
Consensus pattern (22 bp):
GATGGCACGGTGAATGGCCGGT
Found at i:5526 original size:29 final size:29
Alignment explanation
Indices: 5494--5551 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
5484 TTTATCTAAA
*
5494 AACGCAAGAAC-AAGAAATTTTTTTTTTTC
1 AACGCAA-AACAAACAAATTTTTTTTTTTC
5523 AACGCAAAACAAAACAAATTTTTTTTTTT
1 AACGCAAAAC-AAACAAATTTTTTTTTTT
5552 TTTTGAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 3 0.12
29 7 0.27
30 16 0.62
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (29 bp):
AACGCAAAACAAACAAATTTTTTTTTTTC
Found at i:6042 original size:16 final size:15
Alignment explanation
Indices: 6002--6044 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 15
5992 ACGGAGGTTG
6002 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
6017 ACAGAAAAACAATTAA
1 ACAG-AAAACAATTAA
6033 ACTAGAAAACAA
1 AC-AGAAAACAA
6045 AACAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.15
16 20 0.77
17 2 0.08
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:13240 original size:21 final size:21
Alignment explanation
Indices: 13214--13254 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13204 TTAGAAACCC
13214 TAGTACCACTTAAATCCAATT
1 TAGTACCACTTAAATCCAATT
**
13235 TAGTACCACTTGTATCCAAT
1 TAGTACCACTTAAATCCAAT
13255 AGGGCTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.34
Consensus pattern (21 bp):
TAGTACCACTTAAATCCAATT
Found at i:18621 original size:22 final size:21
Alignment explanation
Indices: 18569--18622 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
18559 GCTTCTTGGA
18569 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
18590 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
18609 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
18623 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:19065 original size:15 final size:15
Alignment explanation
Indices: 19045--19074 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19035 CATCATTCTT
19045 AAGTAGCTATAATCA
1 AAGTAGCTATAATCA
*
19060 AAGTAGCTTTAATCA
1 AAGTAGCTATAATCA
19075 CTTACCATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (15 bp):
AAGTAGCTATAATCA
Found at i:19994 original size:29 final size:31
Alignment explanation
Indices: 19962--20028 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
19952 ATGCAATTTG
19962 GGATATAACGTT-ACAAAA-CAAGCAATTAA
1 GGATATAACGTTAACAAAAGCAAGCAATTAA
* *
19991 GGATATAACGTTAAGAAAAGCGAGCAATTAA
1 GGATATAACGTTAACAAAAGCAAGCAATTAA
20022 GGATATA
1 GGATATA
20029 GTCCGTTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 12 0.35
30 5 0.15
31 17 0.50
ACGTcount: A:0.49, C:0.10, G:0.19, T:0.21
Consensus pattern (31 bp):
GGATATAACGTTAACAAAAGCAAGCAATTAA
Found at i:20195 original size:31 final size:31
Alignment explanation
Indices: 20158--20269 Score: 136
Period size: 31 Copynumber: 3.6 Consensus size: 31
20148 CCCTAACTGA
20158 TTATATCCTTAATTGCTTGACATCGAAAACG
1 TTATATCCTTAATTGCTTGACATCGAAAACG
* * **
20189 TCATATCCTTAATTGCTTGAAATAAAAAACG
1 TTATATCCTTAATTGCTTGACATCGAAAACG
**
20220 TTATATCCTTAATTGCTTG-CGGCAGAAAACG
1 TTATATCCTTAATTGCTTGACATC-GAAAACG
* *
20251 TTATATCCTAAATTTCTTG
1 TTATATCCTTAATTGCTTG
20270 CTTATCATCT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGACATCGAAAACG
Found at i:21092 original size:70 final size:70
Alignment explanation
Indices: 21018--21155 Score: 267
Period size: 70 Copynumber: 2.0 Consensus size: 70
21008 AAAATGGTAA
*
21018 AAAAAAAAGAGATTAGATTTAATTAAATATGTTTAAAATGATTGTTTGTGTGAGTGAATTTCAGT
1 AAAAAAAAGAGATTAGATTTAATTAAATATGTTTAAAATGACTGTTTGTGTGAGTGAATTTCAGT
21083 AATAG
66 AATAG
21088 AAAAAAAAGAGATTAGATTTAATTAAATATGTTTAAAATGACTGTTTGTGTGAGTGAATTTCAGT
1 AAAAAAAAGAGATTAGATTTAATTAAATATGTTTAAAATGACTGTTTGTGTGAGTGAATTTCAGT
21153 AAT
66 AAT
21156 GCAGATGTTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.43, C:0.02, G:0.18, T:0.37
Consensus pattern (70 bp):
AAAAAAAAGAGATTAGATTTAATTAAATATGTTTAAAATGACTGTTTGTGTGAGTGAATTTCAGT
AATAG
Found at i:22078 original size:31 final size:31
Alignment explanation
Indices: 22011--22120 Score: 143
Period size: 31 Copynumber: 3.6 Consensus size: 31
22001 TTTGCTGCCA
* **
22011 CAAGCAATTAAGGATATAACG-TTACAA-AA
1 CAAGCAATTAAGGATATAACGTTTTCAATTT
*
22040 CAAGCAATTAAGGATATAACGTTTTTAATTT
1 CAAGCAATTAAGGATATAACGTTTTCAATTT
* * *
22071 CAAGCAATTAAGGATATGAGGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCAATTT
22102 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
22121 TCAGTTAGGG
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
29 21 0.30
30 4 0.06
31 45 0.64
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCAATTT
Found at i:22311 original size:29 final size:31
Alignment explanation
Indices: 22237--22303 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
22227 TTTAACGGGC
*
22237 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACAT
*
22268 TATATCCTTAATTGCTTG-TTTT-GTAACAT
1 TATATCCTTAATTGCTCGCTTTTCGTAACAT
22297 TATATCC
1 TATATCC
22304 CAAATTGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 13 0.38
30 4 0.12
31 17 0.50
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.48
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGCTTTTCGTAACAT
Found at i:25427 original size:22 final size:20
Alignment explanation
Indices: 25378--25454 Score: 75
Period size: 22 Copynumber: 3.6 Consensus size: 20
25368 AATTGTTTCA
* * *
25378 CCTTAAGTCGAAAATTGCTT
1 CCTTTAGTCGACAATTTCTT
25398 CCTTTAGTCGACTAATTTCTT
1 CCTTTAGTCGAC-AATTTCTT
25419 CTCTTTAGTCGACAATTTTGCTT
1 C-CTTTAGTCGACAA-TTT-CTT
25442 CCTCTTA-TCGACA
1 CCT-TTAGTCGACA
25455 CTTTTGCTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
20 10 0.20
21 10 0.20
22 22 0.45
23 7 0.14
ACGTcount: A:0.22, C:0.25, G:0.12, T:0.42
Consensus pattern (20 bp):
CCTTTAGTCGACAATTTCTT
Found at i:25474 original size:22 final size:22
Alignment explanation
Indices: 25426--25481 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
25416 CTTCTCTTTA
* **
25426 GTCGACAATTTTGCTTCCTCTT
1 GTCGACACTTTTGCTTCCTCAC
*
25448 ATCGACACTTTTGCTTCCTCAC
1 GTCGACACTTTTGCTTCCTCAC
25470 GTCGACAACTTT
1 GTCGAC-ACTTT
25482 GCCTCTTCCT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 23 0.82
23 5 0.18
ACGTcount: A:0.18, C:0.30, G:0.12, T:0.39
Consensus pattern (22 bp):
GTCGACACTTTTGCTTCCTCAC
Found at i:30858 original size:21 final size:21
Alignment explanation
Indices: 30832--30872 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
30822 TTGAAGACCT
30832 ATTGGATAC-AAGTGGTACTAA
1 ATTGGAT-CTAAGTGGTACTAA
30853 ATTGGATCTAAGTGGTACTA
1 ATTGGATCTAAGTGGTACTA
30873 GGGTTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (21 bp):
ATTGGATCTAAGTGGTACTAA
Done.