Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018936.1 Corchorus olitorius cultivar O-4 contig18969, 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: 42344
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:9347 original size:21 final size:23
Alignment explanation
Indices: 9323--9365 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
9313 CATTTTTCAT
9323 TTTCTCAATCT-GA-TTTAGCAG
1 TTTCTCAATCTCGACTTTAGCAG
*
9344 TTTCTCATTCTCGACTTTAGCA
1 TTTCTCAATCTCGACTTTAGCA
9366 TGCTCAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 2 0.11
23 7 0.37
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (23 bp):
TTTCTCAATCTCGACTTTAGCAG
Found at i:12834 original size:41 final size:41
Alignment explanation
Indices: 12697--13019 Score: 427
Period size: 41 Copynumber: 7.9 Consensus size: 41
12687 GTTGGATTTG
* * * *
12697 ATTTGATTCAAGGG--TCGAATGACTTGGTCTTAAATTGACA
1 ATTTAATTCAAGGGTCTCG-ATGACTTGATCTTGAATTGATA
* * * * *
12737 ATCTAATTCATGGGTCT-TACGACTTGGTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
* *
12777 ATAATTCGATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
1 AT--TT-AATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
**
12821 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
**
12862 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
**
12903 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
*
12944 ATTTAATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
12985 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA
13020 CAAACAAAAA
Statistics
Matches: 256, Mismatches: 21, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
40 32 0.12
41 187 0.73
42 4 0.02
43 11 0.04
44 22 0.09
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (41 bp):
ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
Found at i:17376 original size:14 final size:15
Alignment explanation
Indices: 17356--17394 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 15
17346 CTTCACTACT
17356 GTATATTTTCATATA
1 GTATATTTTCATATA
17371 -TATA--TT-ATATA
1 GTATATTTTCATATA
17382 GTATATTTTCATA
1 GTATATTTTCATA
17395 ATCGGGTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 8
0.71 0.00 0.29
Matches are distributed among these distances:
11 5 0.25
12 6 0.30
14 6 0.30
15 3 0.15
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (15 bp):
GTATATTTTCATATA
Found at i:20597 original size:31 final size:31
Alignment explanation
Indices: 20559--20617 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
20549 TTTGTAAAAC
*
20559 TTTTGAAACGCCTATTGTACCCTTATTTAAT
1 TTTTGAAACGCCTATTATACCCTTATTTAAT
*
20590 TTTTGAAACGCCTATTATATCCTTATTT
1 TTTTGAAACGCCTATTATACCCTTATTT
20618 GTCTAGCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.47
Consensus pattern (31 bp):
TTTTGAAACGCCTATTATACCCTTATTTAAT
Found at i:25040 original size:15 final size:16
Alignment explanation
Indices: 25010--25042 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25000 GCAAAAGGCC
*
25010 AAAAAAAAGAGTAAGA
1 AAAAAAAAGAGCAAGA
25026 AAAAAAAAGA-CAAGA
1 AAAAAAAAGAGCAAGA
25041 AA
1 AA
25043 GATGGGTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAAAAAAGAGCAAGA
Found at i:27195 original size:7 final size:7
Alignment explanation
Indices: 27183--27220 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
27173 CTTTAATGAG
27183 ATATAAT
1 ATATAAT
27190 ATATAAT
1 ATATAAT
27197 ATATAAT
1 ATATAAT
27204 ATAT-AT
1 ATATAAT
27210 A-ATAAT
1 ATATAAT
27216 ATATA
1 ATATA
27221 CATACTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 2 0.07
6 6 0.21
7 21 0.72
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:27205 original size:12 final size:13
Alignment explanation
Indices: 27183--27218 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
27173 CTTTAATGAG
27183 ATATAAT-ATATA
1 ATATAATAATATA
27195 ATAT-ATAATAT-
1 ATATAATAATATA
27206 ATATAATAATATA
1 ATATAATAATATA
27219 TACATACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATAATAATATA
Found at i:30022 original size:23 final size:23
Alignment explanation
Indices: 29996--30044 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
29986 AGAAATTTAG
* * *
29996 CTTTATAGAGTTGAGTGTTTAAA
1 CTTTATAGAGATGACTATTTAAA
30019 CTTTATAGAGATGACTATTTAAA
1 CTTTATAGAGATGACTATTTAAA
30042 CTT
1 CTT
30045 AGAAATTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (23 bp):
CTTTATAGAGATGACTATTTAAA
Found at i:32610 original size:21 final size:21
Alignment explanation
Indices: 32593--32654 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
32583 TTTGAACACT
32593 TGATATCCAAAACAGAACAAG
1 TGATATCCAAAACAGAACAAG
32614 TGATATCCAAAACAGAACAAG
1 TGATATCCAAAACAGAACAAG
32635 TGATATCCAAAACAG-ACAAG
1 TGATATCCAAAACAGAACAAG
32655 ATCATAGATC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
20 5 0.12
21 36 0.88
ACGTcount: A:0.52, C:0.19, G:0.15, T:0.15
Consensus pattern (21 bp):
TGATATCCAAAACAGAACAAG
Found at i:38618 original size:15 final size:15
Alignment explanation
Indices: 38590--38638 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
38580 TGGTATGGAG
38590 GAAATGGGAAGGAAA
1 GAAATGGGAAGGAAA
* *
38605 GAAGTGGGACGGAAA
1 GAAATGGGAAGGAAA
* *
38620 GAAATGGGGAGGAAG
1 GAAATGGGAAGGAAA
38635 GAAA
1 GAAA
38639 AAGCTTCCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.47, C:0.02, G:0.45, T:0.06
Consensus pattern (15 bp):
GAAATGGGAAGGAAA
Found at i:39843 original size:15 final size:16
Alignment explanation
Indices: 39786--39844 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
39776 TATAACTTCC
* * *
39786 TTTCCCTTCCTCCCTA
1 TTTCCTTTCCTTCTTA
* *
39802 TTTCCCTTCCCTTGTTA
1 TTT-CCTTTCCTTCTTA
39819 TTTCCTTTCCTTCTTA
1 TTTCCTTTCCTTCTTA
39835 TTT-CTTTCCT
1 TTTCCTTTCCT
39845 CTCAACCAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
15 7 0.20
16 17 0.49
17 11 0.31
ACGTcount: A:0.05, C:0.37, G:0.02, T:0.56
Consensus pattern (16 bp):
TTTCCTTTCCTTCTTA
Found at i:39891 original size:16 final size:16
Alignment explanation
Indices: 39863--39922 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
39853 AACAGACTCT
39863 AAGGAAA-GAAATAAG
1 AAGGAAAGGAAATAAG
*
39878 AAGGAAAGGAAATAAC
1 AAGGAAAGGAAATAAG
* *
39894 AAGGGAAGGGAAATAGG
1 AA-GGAAAGGAAATAAG
* *
39911 GAGGAAGGGAAA
1 AAGGAAAGGAAA
39923 GGAAGTTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
15 7 0.18
16 19 0.50
17 12 0.32
ACGTcount: A:0.57, C:0.02, G:0.37, T:0.05
Consensus pattern (16 bp):
AAGGAAAGGAAATAAG
Found at i:39905 original size:17 final size:16
Alignment explanation
Indices: 39863--39908 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
39853 AACAGACTCT
*
39863 AAGGAAA-GAAATAAG
1 AAGGAAAGGAAATAAC
39878 AAGGAAAGGAAATAAC
1 AAGGAAAGGAAATAAC
*
39894 AAGGGAAGGGAAATA
1 AA-GGAAAGGAAATA
39909 GGGAGGAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 7 0.26
16 9 0.33
17 11 0.41
ACGTcount: A:0.61, C:0.02, G:0.30, T:0.07
Consensus pattern (16 bp):
AAGGAAAGGAAATAAC
Done.