Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011959.1 Corchorus olitorius cultivar O-4 contig11992, 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: 29036
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:6640 original size:15 final size:16
Alignment explanation
Indices: 6616--6655 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
6606 AGAGGTTGAA
*
6616 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
6631 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
6647 AGAAAACAA
1 AGAAAACAA
6656 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:7454 original size:10 final size:10
Alignment explanation
Indices: 7439--7465 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
7429 TAAAGAGAAT
7439 TATGTGAAGG
1 TATGTGAAGG
7449 TATGTGAAGG
1 TATGTGAAGG
7459 TATGTGA
1 TATGTGA
7466 GGTCTGTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (10 bp):
TATGTGAAGG
Found at i:12422 original size:17 final size:18
Alignment explanation
Indices: 12402--12441 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
12392 TAAAAAGGTT
*
12402 TTCAAAAATCCAAA-CAA
1 TTCAAAAATCAAAATCAA
*
12419 TTCAAAATTCAAAATCAA
1 TTCAAAAATCAAAATCAA
12437 TTCAA
1 TTCAA
12442 GTTTTTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (18 bp):
TTCAAAAATCAAAATCAA
Found at i:12540 original size:49 final size:49
Alignment explanation
Indices: 12434--12567 Score: 141
Period size: 49 Copynumber: 2.8 Consensus size: 49
12424 AATTCAAAAT
* * *
12434 CAATTCAAGTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCAAGTATT
1 CAATTCAAGTTTTTCAAAGTTTTCAATTTTGGGAAAGATCCAAAGTATC
* **
12483 CAATTCAAGTTTTTCAAAGTGTTCAATTTTGGGAAAGATTGGGAAAGT-TC
1 CAATTCAAGTTTTTCAAAGTTTTCAATTTTGGGAAAGA-T-CCAAAGTATC
* *
12533 CCA-TCAAG-TTTTCAAAGTTTTTCAA-ATTGGGAAAG
1 CAATTCAAGTTTTTCAAAG-TTTTCAATTTTGGGAAAG
12568 TTTCAATCAA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
48 18 0.25
49 47 0.64
50 4 0.05
51 4 0.05
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36
Consensus pattern (49 bp):
CAATTCAAGTTTTTCAAAGTTTTCAATTTTGGGAAAGATCCAAAGTATC
Found at i:12606 original size:37 final size:37
Alignment explanation
Indices: 12520--12758 Score: 325
Period size: 37 Copynumber: 6.4 Consensus size: 37
12510 TTTGGGAAAG
12520 ATTGGGAAAGTTCCCATCAAGTTTTCAAAGTTTTTCAA
1 ATTGGGAAAGTTCCCATCAAGTTTTCAAAG-TTTTCAA
* * * *
12558 ATTGGGAAAGTTTCAATCAATTTTTCAAAGTTTTAAA
1 ATTGGGAAAGTTCCCATCAAGTTTTCAAAGTTTTCAA
12595 ATTGGGAAAGTTCCCATCAAGTTTTCAAAGTTTTCAA
1 ATTGGGAAAGTTCCCATCAAGTTTTCAAAGTTTTCAA
* * * *
12632 ATTAGAAAAGTTCCAATCAAGTTTTCAAAGTTTGCAA
1 ATTGGGAAAGTTCCCATCAAGTTTTCAAAGTTTTCAA
* *
12669 ATTGGGAAAGTTCCCATCAAGTTTTCACAGTTTCCAA
1 ATTGGGAAAGTTCCCATCAAGTTTTCAAAGTTTTCAA
* * *
12706 TTTAGGGAAAGTTCCCATCAAGTTTTTTCAAAGATTCCAA
1 ATT-GGGAAAGTTCCCATCAAG--TTTTCAAAGTTTTCAA
12746 ATTGGGAAAGTTC
1 ATTGGGAAAGTTC
12759 TTATGGGAAT
Statistics
Matches: 177, Mismatches: 21, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
37 106 0.60
38 45 0.25
39 10 0.06
40 16 0.09
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (37 bp):
ATTGGGAAAGTTCCCATCAAGTTTTCAAAGTTTTCAA
Found at i:14563 original size:69 final size:69
Alignment explanation
Indices: 14450--14616 Score: 217
Period size: 69 Copynumber: 2.4 Consensus size: 69
14440 ACCGAATTCA
* * *** *
14450 TATGGAATCGAATTTGGTTTATGGAAAAGCCCCTGTTGCTTGGATGGAACCAAGGCTTAAACTAA
1 TATGGAAACGAGTTTGGTTTATGGAAAAGCCCCTACCGCCTGGATGGAACCAAGGCTTAAACTAA
14515 CTCG
66 CTCG
* * * * *
14519 TATGGAAATGAGTTTGGTTTGTGGAAAAGCCCTTACCGCCTGGATGGAACCAAGGCTTGAACTGA
1 TATGGAAACGAGTTTGGTTTATGGAAAAGCCCCTACCGCCTGGATGGAACCAAGGCTTAAACTAA
14584 CTCG
66 CTCG
**
14588 TATGGAAACGAGTTTGACTTATGGAAAAG
1 TATGGAAACGAGTTTGGTTTATGGAAAAG
14617 TCAAAGCATT
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 83 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (69 bp):
TATGGAAACGAGTTTGGTTTATGGAAAAGCCCCTACCGCCTGGATGGAACCAAGGCTTAAACTAA
CTCG
Found at i:16865 original size:75 final size:75
Alignment explanation
Indices: 16742--16888 Score: 249
Period size: 75 Copynumber: 2.0 Consensus size: 75
16732 GGATTCAGTC
*
16742 ACCTCGAAATCATTGCTTTGACTAAAACTGATTTTGGAACATCATTTGATTAAAACTCATCATTC
1 ACCTCGAAATCATTGCTTTGACTAAAACTGATTTTGAAACATCATTTGATTAAAACTCATCATTC
16807 CTTTGCTCAT
66 CTTTGCTCAT
* * * *
16817 ACCTCGAAATCATTGTTTTGACTAAAATTGATTTTGAAATATCTTTTGATTAAAACTCATCATTC
1 ACCTCGAAATCATTGCTTTGACTAAAACTGATTTTGAAACATCATTTGATTAAAACTCATCATTC
16882 CTTTGCT
66 CTTTGCT
16889 TCACAGTCCA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (75 bp):
ACCTCGAAATCATTGCTTTGACTAAAACTGATTTTGAAACATCATTTGATTAAAACTCATCATTC
CTTTGCTCAT
Found at i:21750 original size:40 final size:40
Alignment explanation
Indices: 21704--21866 Score: 218
Period size: 40 Copynumber: 4.0 Consensus size: 40
21694 ACTTTGAAAA
* * *
21704 AAAAAAACTTGATGTGATATTTCCCTAAACTGAAAACTTT
1 AAAAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTT
*
21744 CAAAAAAAACTTGATGGGATCTTTCCCTGAATTGAAAACTTT
1 --AAAAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTT
* ** *
21786 GAAAAAACTTGATGGTTTCTTTCCCTGAATTGAAAACTTT
1 AAAAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTT
*
21826 GAAAAAAATTTGATGGGATCTTTCCCTAAATTGAAAACTTT
1 -AAAAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTT
21867 GAAAGAGCTT
Statistics
Matches: 108, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
40 37 0.34
41 35 0.32
42 36 0.33
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (40 bp):
AAAAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTT
Found at i:21791 original size:41 final size:41
Alignment explanation
Indices: 21704--21870 Score: 237
Period size: 41 Copynumber: 4.1 Consensus size: 41
21694 ACTTTGAAAA
* * * *
21704 AAAAAAACTTGATGTGATATTTCCCTAAACTGAAAACTTTCA
1 AAAAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTT-G
*
21746 AAAAAAACTTGATGGGATCTTTCCCTGAATTGAAAACTTTG
1 AAAAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTG
** *
21787 -AAAAAACTTGATGGTTTCTTTCCCTGAATTGAAAACTTTG
1 AAAAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTG
*
21827 AAAAAAATTTGATGGGATCTTTCCCTAAATTGAAAACTTTG
1 AAAAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTG
21868 AAA
1 AAA
21871 GAGCTTCTTT
Statistics
Matches: 113, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
40 38 0.34
41 39 0.35
42 36 0.32
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (41 bp):
AAAAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTG
Found at i:21851 original size:81 final size:82
Alignment explanation
Indices: 21705--21870 Score: 246
Period size: 81 Copynumber: 2.0 Consensus size: 82
21695 CTTTGAAAAA
21705 AAAAAACTTGATGTGATATTTCCCTAAACTGAAAACTTTCAAAAAAAACTTGATGGGATCTTTCC
1 AAAAAACTTGATGTGATATTTCCCTAAACTGAAAACTTTCAAAAAAAACTTGATGGGATCTTTCC
*
21770 CTGAATTGAAAACTTTG
66 CTAAATTGAAAACTTTG
* * * * * *
21787 AAAAAACTTGATG-GTTTCTTTCCCTGAATTGAAAACTTT-GAAAAAAATTTGATGGGATCTTTC
1 AAAAAACTTGATGTG-ATATTTCCCTAAACTGAAAACTTTCAAAAAAAACTTGATGGGATCTTTC
21850 CCTAAATTGAAAACTTTG
65 CCTAAATTGAAAACTTTG
21868 AAA
1 AAA
21871 GAGCTTCTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
81 43 0.57
82 33 0.43
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (82 bp):
AAAAAACTTGATGTGATATTTCCCTAAACTGAAAACTTTCAAAAAAAACTTGATGGGATCTTTCC
CTAAATTGAAAACTTTG
Found at i:27564 original size:19 final size:20
Alignment explanation
Indices: 27518--27566 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
27508 ATGATCTATG
*
27518 GCCCAATTAGATGTTCTCAT
1 GCCCAATTAGATGTTCTCAA
*
27538 GTCCAATTGAGA-GTT-TCAA
1 GCCCAATT-AGATGTTCTCAA
27557 GCCCAATTAG
1 GCCCAATTAG
27567 TAATTATGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 10 0.40
20 10 0.40
21 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (20 bp):
GCCCAATTAGATGTTCTCAA
Found at i:28874 original size:14 final size:14
Alignment explanation
Indices: 28855--28896 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
28845 GATTTAATAT
28855 ATCTTTAGTAGTGA
1 ATCTTTAGTAGTGA
* *
28869 ATCTTTACTAACT-A
1 ATCTTTAGT-AGTGA
28883 ATCTTTAGTAGTGA
1 ATCTTTAGTAGTGA
28897 TTTACTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
13 2 0.09
14 18 0.82
15 2 0.09
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (14 bp):
ATCTTTAGTAGTGA
Done.