Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014103.1 Corchorus olitorius cultivar O-4 contig14136, 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: 46600
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:1411 original size:30 final size:30
Alignment explanation
Indices: 1377--1470 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
1367 CCTGCATATG
1377 AACTTTCAAATTTAGACAATTAGCTCCCTA
1 AACTTTCAAATTTAGACAATTAGCTCCCTA
* * * * *
1407 AACTTCCTAA-TT-CA-AATT-GCCTGCATA
1 AACTTTCAAATTTAGACAATTAG-CTCCCTA
*
1434 TGAACTTTCAAATTTAGACAATTAGCTCCCTG
1 --AACTTTCAAATTTAGACAATTAGCTCCCTA
1466 AACTT
1 AACTT
1471 CCTAATTCAA
Statistics
Matches: 46, Mismatches: 11, Indels: 14
0.65 0.15 0.20
Matches are distributed among these distances:
26 1 0.02
27 9 0.20
28 1 0.02
29 10 0.22
30 15 0.33
31 1 0.02
32 8 0.17
33 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (30 bp):
AACTTTCAAATTTAGACAATTAGCTCCCTA
Found at i:1436 original size:59 final size:59
Alignment explanation
Indices: 1364--1481 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
1354 TCAGGACAAC
1364 TTGCCTGCATATGAACTTTCAAATTTAGACAATTAGCTCCCTAAACTTCCTAATTCAAA
1 TTGCCTGCATATGAACTTTCAAATTTAGACAATTAGCTCCCTAAACTTCCTAATTCAAA
*
1423 TTGCCTGCATATGAACTTTCAAATTTAGACAATTAGCTCCCTGAACTTCCTAATTCAAA
1 TTGCCTGCATATGAACTTTCAAATTTAGACAATTAGCTCCCTAAACTTCCTAATTCAAA
1482 AACAATTTGC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (59 bp):
TTGCCTGCATATGAACTTTCAAATTTAGACAATTAGCTCCCTAAACTTCCTAATTCAAA
Found at i:12333 original size:12 final size:12
Alignment explanation
Indices: 12316--12341 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12306 TTTGAAAGAC
12316 ATATACATATAT
1 ATATACATATAT
12328 ATATACATATAT
1 ATATACATATAT
12340 AT
1 AT
12342 TATGTACTAT
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:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATACATATAT
Found at i:12372 original size:23 final size:22
Alignment explanation
Indices: 12327--12373 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
12317 TATACATATA
*
12327 TATATACATATATATTATGTAC
1 TATATACATATATATTATCTAC
12349 TATAGTACATATATATT-TCCTAC
1 TATA-TACATATATATTAT-CTAC
12372 TA
1 TA
12374 AACTCTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (22 bp):
TATATACATATATATTATCTAC
Found at i:19747 original size:6 final size:6
Alignment explanation
Indices: 19738--19792 Score: 76
Period size: 6 Copynumber: 9.0 Consensus size: 6
19728 AAAAAAAAAC
19738 TTTTTG TTTTTG TTTTTTTG TTTTTG TTTTTG TTTTTG TTTTT- TTTTTG
1 TTTTTG TTTTTG --TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
*
19787 TATTTG
1 TTTTTG
19793 CAAAAGGGCT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
5 5 0.11
6 34 0.76
8 6 0.13
ACGTcount: A:0.02, C:0.00, G:0.15, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:19763 original size:20 final size:19
Alignment explanation
Indices: 19738--19787 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
19728 AAAAAAAAAC
19738 TTTTTGTTTTTGTTTTTTTG
1 TTTTTGTTTTTG-TTTTTTG
19758 TTTTTGTTTTTG-TTTTTG
1 TTTTTGTTTTTGTTTTTTG
19776 TTTTT-TTTTTGT
1 TTTTTGTTTTTGT
19788 ATTTGCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.21
18 11 0.38
20 12 0.41
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (19 bp):
TTTTTGTTTTTGTTTTTTG
Found at i:23760 original size:26 final size:26
Alignment explanation
Indices: 23731--23782 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
23721 TACAAGATTG
23731 ATCCAATGTTGCATATCCTTTTTTAT
1 ATCCAATGTTGCATATCCTTTTTTAT
23757 ATCCAATGTTGCATATCCTTTTTTAT
1 ATCCAATGTTGCATATCCTTTTTTAT
23783 CATGAGATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.08, T:0.50
Consensus pattern (26 bp):
ATCCAATGTTGCATATCCTTTTTTAT
Found at i:25807 original size:24 final size:24
Alignment explanation
Indices: 25745--25813 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
25735 TGTCATTGCT
25745 AGTCATCCCATGTTTTGTAGCAAA
1 AGTCATCCCATGTTTTGTAGCAAA
* *
25769 ACTC--CACCA---TCTGTAGCAAA
1 AGTCATC-CCATGTTTTGTAGCAAA
25789 AGTCATCCCATGTTTTGTAGCAAA
1 AGTCATCCCATGTTTTGTAGCAAA
25813 A
1 A
25814 CTCCACTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
20 13 0.37
21 3 0.09
22 2 0.06
23 3 0.09
24 14 0.40
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (24 bp):
AGTCATCCCATGTTTTGTAGCAAA
Found at i:25837 original size:26 final size:26
Alignment explanation
Indices: 25804--25873 Score: 131
Period size: 26 Copynumber: 2.7 Consensus size: 26
25794 TCCCATGTTT
*
25804 TGTAGCAAAACTCCACTTCTACCATC
1 TGTAGCAAAACTCCACTTCCACCATC
25830 TGTAGCAAAACTCCACTTCCACCATC
1 TGTAGCAAAACTCCACTTCCACCATC
25856 TGTAGCAAAACTCCACTT
1 TGTAGCAAAACTCCACTT
25874 AAATAATCCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.31, C:0.34, G:0.09, T:0.26
Consensus pattern (26 bp):
TGTAGCAAAACTCCACTTCCACCATC
Found at i:29043 original size:30 final size:31
Alignment explanation
Indices: 29009--29067 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
28999 AAATTAAGAA
29009 ACACATTAAGAACT-AAAAGCAATTGCAGTT
1 ACACATTAAGAACTAAAAAGCAATTGCAGTT
*
29039 ACACATTAAGAACTAAAAAGCATTTGCAG
1 ACACATTAAGAACTAAAAAGCAATTGCAG
29068 GGAGAGAGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 14 0.52
31 13 0.48
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (31 bp):
ACACATTAAGAACTAAAAAGCAATTGCAGTT
Found at i:40881 original size:23 final size:23
Alignment explanation
Indices: 40851--40895 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
40841 ACCACCATTT
40851 TTGAGGTAATAATTTAACAATTG
1 TTGAGGTAATAATTTAACAATTG
*
40874 TTGAGGTAATAATTTATCAATT
1 TTGAGGTAATAATTTAACAATT
40896 AACTTTAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (23 bp):
TTGAGGTAATAATTTAACAATTG
Found at i:43195 original size:26 final size:26
Alignment explanation
Indices: 43154--43205 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
43144 TTAGCAAAAT
43154 TCATTTATAATCGCGACAAATAGTTA
1 TCATTTATAATCGCGACAAATAGTTA
* *
43180 TCATTTATGATTGCGACAAATAGTTA
1 TCATTTATAATCGCGACAAATAGTTA
43206 AGTGTCATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (26 bp):
TCATTTATAATCGCGACAAATAGTTA
Found at i:44048 original size:11 final size:11
Alignment explanation
Indices: 44005--44042 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
43995 CCTATATATA
*
44005 AAATAAATTAT
1 AAATTAATTAT
44016 CAAA-TAATTAT
1 -AAATTAATTAT
44027 AAATTAATTAT
1 AAATTAATTAT
44038 AAATT
1 AAATT
44043 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:46448 original size:30 final size:28
Alignment explanation
Indices: 46400--46457 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
46390 TCAGTTTTTA
**
46400 ATATAGTAAAAATAAAATATTTATAAAG
1 ATATAGTAAAAATAAAATAAATATAAAG
*
46428 ATATAGATATAAAATTAAATAAATATAAAG
1 ATATAG-TA-AAAATAAAATAAATATAAAG
46458 TTTTTAGTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.24
29 2 0.08
30 17 0.68
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (28 bp):
ATATAGTAAAAATAAAATAAATATAAAG
Found at i:46573 original size:2 final size:2
Alignment explanation
Indices: 46566--46600 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
46556 TTCGTACTTT
46566 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.