Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024313.1 Corchorus olitorius cultivar O-4 contig24346, 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: 35236
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Found at i:472 original size:22 final size:23
Alignment explanation
Indices: 433--475 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
423 AATCCTAATC
433 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
456 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
476 ACTCCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:3551 original size:32 final size:32
Alignment explanation
Indices: 3510--3592 Score: 166
Period size: 32 Copynumber: 2.6 Consensus size: 32
3500 TCATCTCTCT
3510 CATAAAAAAGCAATGTTTTTTTCTTTTTTGGC
1 CATAAAAAAGCAATGTTTTTTTCTTTTTTGGC
3542 CATAAAAAAGCAATGTTTTTTTCTTTTTTGGC
1 CATAAAAAAGCAATGTTTTTTTCTTTTTTGGC
3574 CATAAAAAAGCAATGTTTT
1 CATAAAAAAGCAATGTTTT
3593 GGCAGGATTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (32 bp):
CATAAAAAAGCAATGTTTTTTTCTTTTTTGGC
Found at i:7185 original size:3 final size:3
Alignment explanation
Indices: 7177--7221 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
7167 ACACACCAAA
7177 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
7222 CAGACTTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16005 original size:22 final size:22
Alignment explanation
Indices: 15980--16564 Score: 232
Period size: 22 Copynumber: 26.8 Consensus size: 22
15970 TGAAAATCTA
* * *
15980 ATAACCTCATTGTGAAATTTCG
1 ATAACCTCACTATGAAATTTTG
* * *
16002 ATAACCTCCCAATGAAAGTTTG
1 ATAACCTCACTATGAAATTTTG
* *
16024 ATAACCACACTGTGAAATTTTG
1 ATAACCTCACTATGAAATTTTG
16046 ATAACCAT-ACTATGAAATTTTG
1 ATAACC-TCACTATGAAATTTTG
16068 ATAACCAT-ACTATGAAATTTTG
1 ATAACC-TCACTATGAAATTTTG
* * * *
16090 ATAACTTCAGTGTAAAATTTTG
1 ATAACCTCACTATGAAATTTTG
* *
16112 ATAATCTCCCTATGAAATTTTG
1 ATAACCTCACTATGAAATTTTG
* * *
16134 ATAATCACACTAT-AAA-ATTG
1 ATAACCTCACTATGAAATTTTG
* * *
16154 GTAACCGCACTATGAAAAGTTTG
1 ATAACCTCACTATG-AAATTTTG
*
16177 ATAA---CA--AT-AACATATTG
1 ATAACCTCACTATGAA-ATTTTG
** * *
16194 ATAACCAAACCATGAAATTTCG
1 ATAACCTCACTATGAAATTTTG
*
16216 ATAACCTTCTTA-TGAGAATGAAATTGTG
1 ATAACC-TC--ACT----ATGAAATTTTG
* * *
16244 ATATCCTCTCTATGTAATTTTG
1 ATAACCTCACTATGAAATTTTG
* * * *
16266 ATAACCTCTCCATAAAATTTTC
1 ATAACCTCACTATGAAATTTTG
*
16288 ATAACCTCCCTATGAAATTTTG
1 ATAACCTCACTATGAAATTTTG
* * ** *
16310 -TTA-GTCTTTAGGAAATTTTG
1 ATAACCTCACTATGAAATTTTG
*
16330 ATAA--GCAC---G-AATTTTG
1 ATAACCTCACTATGAAATTTTG
* *
16346 ATAATTACCCTCCCTATGATATTTTG
1 AT-A--A-CCTCACTATGAAATTTTG
* * *
16372 TTAACCTTC-TTATGAAAGTTTG
1 ATAACC-TCACTATGAAATTTTG
* * *
16394 ATAACCACACTATAAAATTTCG
1 ATAACCTCACTATGAAATTTTG
*
16416 ATAACCTTC-GTATGAAATTTTG
1 ATAACC-TCACTATGAAATTTTG
* *
16438 TTAACCTTC-CTAAGAAATTTTG
1 ATAACC-TCACTATGAAATTTTG
* ***
16460 ATAACATTTTTATGAAATTTT-
1 ATAACCTCACTATGAAATTTTG
*
16481 AGTAGCCTCTA-TATGAAATTTTG
1 A-TAACCTC-ACTATGAAATTTTG
* *
16504 ATAACAAT-ACTATGAAGTTTTG
1 ATAAC-CTCACTATGAAATTTTG
*
16526 ATAACCTC-CATTTGAAATTTTG
1 ATAACCTCAC-TATGAAATTTTG
* * *
16548 GTAATCACACTATGAAA
1 ATAACCTCACTATGAAA
16565 CCTCAATATA
Statistics
Matches: 418, Mismatches: 102, Indels: 86
0.69 0.17 0.14
Matches are distributed among these distances:
16 11 0.03
17 10 0.02
18 2 0.00
19 1 0.00
20 30 0.07
21 14 0.03
22 308 0.74
23 15 0.04
25 3 0.01
26 8 0.02
27 2 0.00
28 14 0.03
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (22 bp):
ATAACCTCACTATGAAATTTTG
Found at i:16062 original size:66 final size:66
Alignment explanation
Indices: 15955--16137 Score: 176
Period size: 66 Copynumber: 2.8 Consensus size: 66
15945 TGTAGAAATA
* * * * * *
15955 TTGATAACCACA-TCGTGAAAA-TCTAATAACCTCATTGTGAAATTTCGATAACC-TCCCAATGA
1 TTGATAACCACACT-GT-AAAATTTTGATAACCTCACTATGAAATTTTGATAACCAT-ACAATGA
16017 AAGT
63 AAGT
* *
16021 TTGATAACCACACTGTGAAATTTTGATAACCAT-ACTATGAAATTTTGATAACCATACTATGAAA
1 TTGATAACCACACTGTAAAATTTTGATAACC-TCACTATGAAATTTTGATAACCATACAATGAAA
*
16085 TT
65 GT
** * * *
16087 TTGATAACTTCAGTGTAAAATTTTGATAATCTCCCTATGAAATTTTGATAA
1 TTGATAACCACACTGTAAAATTTTGATAACCTCACTATGAAATTTTGATAA
16138 TCACACTATA
Statistics
Matches: 97, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
65 4 0.04
66 90 0.93
67 3 0.03
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (66 bp):
TTGATAACCACACTGTAAAATTTTGATAACCTCACTATGAAATTTTGATAACCATACAATGAAAG
T
Found at i:17158 original size:31 final size:31
Alignment explanation
Indices: 17069--17169 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 31
17059 AAAATTATCA
* * ** *
17069 ATTAACTCCAATAAAATTGAAGTTTTACAGT
1 ATTAACCCCATTAAAATAAAAGTTTTATAGT
**
17100 ATTAA-CCTTTCTAAAATAAAAGTTTTATAGT
1 ATTAACCCCAT-TAAAATAAAAGTTTTATAGT
* *
17131 ATTAACCCCATTAAAATCAAAGTTTTATAGC
1 ATTAACCCCATTAAAATAAAAGTTTTATAGT
*
17162 ATTCACCC
1 ATTAACCC
17170 TACTGAAACT
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
30 1 0.02
31 52 0.93
32 3 0.05
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (31 bp):
ATTAACCCCATTAAAATAAAAGTTTTATAGT
Found at i:20523 original size:13 final size:13
Alignment explanation
Indices: 20505--20543 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
20495 GGCCGGCCTG
20505 GCGCGGCCCAGGC
1 GCGCGGCCCAGGC
* *
20518 GTGCGGCCTAGGC
1 GCGCGGCCCAGGC
20531 GCGCGGCCCAGGC
1 GCGCGGCCCAGGC
20544 CAGGCTTGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.08, C:0.41, G:0.46, T:0.05
Consensus pattern (13 bp):
GCGCGGCCCAGGC
Found at i:20654 original size:20 final size:20
Alignment explanation
Indices: 20612--20655 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
20602 AAAGAGAAAA
*
20612 AAAAGAGAAAAAGGGAATGG
1 AAAAGAGAAAAAGGGAATAG
20632 AAAAG-GAAAAAGGGAAATAG
1 AAAAGAGAAAAAGGG-AATAG
20652 AAAA
1 AAAA
20656 ATAAAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.05
Consensus pattern (20 bp):
AAAAGAGAAAAAGGGAATAG
Found at i:25283 original size:43 final size:44
Alignment explanation
Indices: 25236--25346 Score: 154
Period size: 43 Copynumber: 2.5 Consensus size: 44
25226 TTAATATATA
* *
25236 GATTTAAAATATATTTTCATAATTC-AAAAATAAAATTAAGAT-G
1 GATTTAAAATATCTTTTCATAATTCAAAAAAT-AAATAAAGATCG
* * *
25279 GATTTAAAATATCTTTCCATAATTTAAAAAATAAATAAATATCG
1 GATTTAAAATATCTTTTCATAATTCAAAAAATAAATAAAGATCG
25323 GATTTAAAATATCTTTTCATAATT
1 GATTTAAAATATCTTTTCATAATT
25347 AATAAAAAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
43 30 0.50
44 30 0.50
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (44 bp):
GATTTAAAATATCTTTTCATAATTCAAAAAATAAATAAAGATCG
Found at i:25326 original size:44 final size:44
Alignment explanation
Indices: 25236--25355 Score: 154
Period size: 44 Copynumber: 2.7 Consensus size: 44
25226 TTAATATATA
* * *
25236 GATTTAAAATATATTTTCATAA-TTCAAAAATAAAATTAAGATG
1 GATTTAAAATATCTTTTCATAATTTAAAAAATAAAATAAAGATG
* *
25279 GATTTAAAATATCTTTCCATAATTTAAAAAAT-AAATAAATATCG
1 GATTTAAAATATCTTTTCATAATTTAAAAAATAAAATAAAGAT-G
25323 GATTTAAAATATCTTTTCATAATTAATAAAAAA
1 GATTTAAAATATCTTTTCATAATT--TAAAAAA
25356 GTTGAATGAC
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
43 28 0.42
44 32 0.48
46 7 0.10
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.38
Consensus pattern (44 bp):
GATTTAAAATATCTTTTCATAATTTAAAAAATAAAATAAAGATG
Found at i:25497 original size:2 final size:2
Alignment explanation
Indices: 25492--25531 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
25482 TTTATATGTG
*
25492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25532 CTAGTTTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:29856 original size:23 final size:23
Alignment explanation
Indices: 29813--29856 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
29803 AAGTTTTTTT
*
29813 AATAAAATTAGTAAAATGATAAA
1 AATAAAATTAGTAAAAGGATAAA
*
29836 AATAAAA-TAGGTATAAGGATA
1 AATAAAATTA-GTAAAAGGATA
29857 TTATATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (23 bp):
AATAAAATTAGTAAAAGGATAAA
Found at i:29971 original size:104 final size:103
Alignment explanation
Indices: 29815--30012 Score: 283
Period size: 104 Copynumber: 1.9 Consensus size: 103
29805 GTTTTTTTAA
* * * *
29815 TAAAATTAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTATATTTAATTAAATAAAAGTA
1 TAAAATTAGTAAAATGATAAAAATAAAATACGTATAAGGATATTAGATTTAATCAAATAAAAATA
29880 GA-GTTTTTAGTTGAGTAAAACTATAAAAGTATTTTCAT
66 -ATGTTTTTAGTTGAGTAAAACTATAAAAGTATTTTCAT
* *
29918 TAAAA-TAGTAAAATGGTAAAAATAAATAGTACTTATAAGGATATTAGATTTAATCAAATAAAAA
1 TAAAATTAGTAAAATGATAAAAATAAA-A-TACGTATAAGGATATTAGATTTAATCAAATAAAAA
*
29982 TAATTTTTTTTAGTTGAGTAAAACTATAAAA
64 TAA-TGTTTTTAGTTGAGTAAAACTATAAAA
30013 ATTTAAGCAA
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
102 20 0.24
103 7 0.08
104 32 0.38
105 25 0.30
ACGTcount: A:0.51, C:0.03, G:0.12, T:0.35
Consensus pattern (103 bp):
TAAAATTAGTAAAATGATAAAAATAAAATACGTATAAGGATATTAGATTTAATCAAATAAAAATA
ATGTTTTTAGTTGAGTAAAACTATAAAAGTATTTTCAT
Found at i:31828 original size:13 final size:13
Alignment explanation
Indices: 31787--31829 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
31777 GCAACACAAG
31787 AAAATCGTTAAAACC
1 AAAATCG-T-AAACC
*
31802 AATATCGT-AACC
1 AAAATCGTAAACC
31814 AAAATCGTAAACC
1 AAAATCGTAAACC
31827 AAA
1 AAA
31830 GTAATAAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 11 0.44
13 7 0.28
14 1 0.04
15 6 0.24
ACGTcount: A:0.53, C:0.21, G:0.07, T:0.19
Consensus pattern (13 bp):
AAAATCGTAAACC
Found at i:32739 original size:11 final size:11
Alignment explanation
Indices: 32713--32754 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
32703 ATTCTCTTAT
32713 TTTCC-TTTTC
1 TTTCCTTTTTC
32723 -TTCCTTTTTC
1 TTTCCTTTTTC
32733 TTTCCTTTTTC
1 TTTCCTTTTTC
*
32744 TTTTCTTTTTC
1 TTTCCTTTTTC
32755 CTTCTTCCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 4 0.14
10 5 0.17
11 20 0.69
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTCCTTTTTC
Found at i:34749 original size:12 final size:12
Alignment explanation
Indices: 34732--34759 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
34722 GTACGTTTAT
34732 ACGACACGAAAC
1 ACGACACGAAAC
34744 ACGACACGAAAC
1 ACGACACGAAAC
34756 ACGA
1 ACGA
34760 ATTGCCAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.32, G:0.18, T:0.00
Consensus pattern (12 bp):
ACGACACGAAAC
Done.