Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015774.1 Corchorus olitorius cultivar O-4 contig15807, 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: 20768
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:569 original size:6 final size:6
Alignment explanation
Indices: 527--632 Score: 119
Period size: 6 Copynumber: 17.5 Consensus size: 6
517 CCAAGCCAGG
527 AAAAG- AAAA-A AAAAGA GAAAAGA GAAAAGA GAAAAGA AAAAGA AAAAGGA
1 AAAAGA AAAAGA AAAAGA -AAAAGA -AAAAGA -AAAAGA AAAAGA AAAA-GA
* * * *
577 AAAGGA AAAGGA AAAGGA AAAGGA AAAAGA AAAAGA AAAAGA AAAA-A
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
624 AAAAGA AAA
1 AAAAGA AAA
633 TAAAATAAAA
Statistics
Matches: 94, Mismatches: 2, Indels: 9
0.90 0.02 0.09
Matches are distributed among these distances:
5 13 0.14
6 56 0.60
7 25 0.27
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:637 original size:12 final size:11
Alignment explanation
Indices: 527--669 Score: 90
Period size: 12 Copynumber: 11.7 Consensus size: 11
517 CCAAGCCAGG
527 AAAAGAAAAAA
1 AAAAGAAAAAA
538 AAAGAGAAAAGAGA
1 AAA-AGAAAA-A-A
*
552 AAAGAGAAAAGA
1 AAA-AGAAAAAA
564 AAAAGAAAAAGGA
1 AAAAGAAAAA--A
* *
577 AAAGGAAAAGGA
1 AAAAGAAAA-AA
* *
589 AAAGGAAAAGGA
1 AAAAGAAAA-AA
601 AAAAGAAAAAGA
1 AAAAGAAAAA-A
613 AAAAGAAAAAA
1 AAAAGAAAAAA
624 AAAAGAAAATAA
1 AAAAGAAAA-AA
636 AATAA-AATAAATA
1 AA-AAGAA-AAA-A
*
649 AGGAAATAAAAAA
1 A--AAAGAAAAAA
662 AAAAGAAA
1 AAAAGAAA
670 TTTTTAAAAA
Statistics
Matches: 111, Mismatches: 7, Indels: 28
0.76 0.05 0.19
Matches are distributed among these distances:
11 25 0.23
12 49 0.44
13 18 0.16
14 16 0.14
15 3 0.03
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.03
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:655 original size:22 final size:21
Alignment explanation
Indices: 600--665 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
590 AAGGAAAAGG
*
600 AAAAAGAAAAAGAAAAAGAAAAA
1 AAAAAG-AAAATAAAAA-AAAAA
*
623 AAAAAGAAAATAAAATAAAATA
1 AAAAAGAAAATAAAA-AAAAAA
* *
645 AATAAGGAAATAAAAAAAAAA
1 AAAAAGAAAATAAAAAAAAAA
666 GAAATTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 5 0.14
22 25 0.68
23 7 0.19
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.08
Consensus pattern (21 bp):
AAAAAGAAAATAAAAAAAAAA
Found at i:2033 original size:12 final size:11
Alignment explanation
Indices: 1988--2044 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 11
1978 CCCGTTGAGG
1988 AAATGTTTTAT
1 AAATGTTTTAT
* *
1999 TACTGTTTTATAT
1 AAATG-TTT-TAT
*
2012 AAATGATTTAT
1 AAATGTTTTAT
2023 AAAATGTTTTAGT
1 -AAATGTTTTA-T
2036 AAATGTTTT
1 AAATGTTTT
2045 GGGTGCATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
11 6 0.17
12 23 0.64
13 7 0.19
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.53
Consensus pattern (11 bp):
AAATGTTTTAT
Found at i:3668 original size:16 final size:16
Alignment explanation
Indices: 3628--3661 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3618 TTATTAAAAG
3628 GAGTTAATTGAGACTT
1 GAGTTAATTGAGACTT
*
3644 GAGTTAATTGAGGCTT
1 GAGTTAATTGAGACTT
3660 GA
1 GA
3662 TTGAATTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.35
Consensus pattern (16 bp):
GAGTTAATTGAGACTT
Found at i:5386 original size:163 final size:164
Alignment explanation
Indices: 5110--5573 Score: 693
Period size: 163 Copynumber: 2.8 Consensus size: 164
5100 TGATTGATTT
* * * * * *
5110 ATTTATGGTAAAATTAAATAATCATCAATCAGTTATAATTTTGATTGGCAAAGTTAACTAATGAC
1 ATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTCGCAAAATTAACTAACGAC
* * * * *
5175 TAACTTGATTCATTTGTCTATTTAGCATGTCCAATAATTAATTTTTTTGGTAACATAATCACTAA
66 TAACTTGATTCATTTATTTATTTAGCATGTTCAATAATTTA-TTTTTTGGTAACATAATTACTAA
5240 TTGATTTATTTA-TTATGGTAATTTTTTTGGTAGCA
130 TTGATTTATTTATTTATGGTAA-TTTTTTGGTAGCA
*
5275 ATTTATGGTAAAATTAAAT-AT-ATCAATCAATTAAAACTTTGATTCACAAAATTAACTAACGAC
1 ATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTCGCAAAATTAACTAACGAC
*
5338 TAACTTGGATTCATTTATTTATTTACCATGTTCAATAATTTATTTTTTGGTAACATAATTACTAA
66 TAACTT-GATTCATTTATTTATTTAGCATGTTCAATAATTTATTTTTTGGTAACATAATTACTAA
*
5403 TTGATTTATTTATTTATGGTAATTTTTTGGTAGCG
130 TTGATTTATTTATTTATGGTAATTTTTTGGTAGCA
* *
5438 ATTTATGGTAAAATT-AATAATCATCAATCAATTACAACTTTGATTTGCAAAATTAACTAACGAC
1 ATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTCGCAAAATTAACTAACGAC
* *
5502 TAACTTGATTCATTTATTTATTTAGCTTGTTCAATCAATTTTATTTTTTGCTAACATAATTACTA
66 TAACTTGATTCATTTATTTATTTAGCATGTTCAAT-AA-TTTATTTTTTGGTAACATAATTACTA
5567 ATTGATT
129 ATTGATT
5574 CGTTTATTCA
Statistics
Matches: 273, Mismatches: 20, Indels: 12
0.90 0.07 0.04
Matches are distributed among these distances:
162 3 0.01
163 131 0.48
164 88 0.32
165 51 0.19
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (164 bp):
ATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTCGCAAAATTAACTAACGAC
TAACTTGATTCATTTATTTATTTAGCATGTTCAATAATTTATTTTTTGGTAACATAATTACTAAT
TGATTTATTTATTTATGGTAATTTTTTGGTAGCA
Found at i:5872 original size:142 final size:142
Alignment explanation
Indices: 5601--5960 Score: 476
Period size: 142 Copynumber: 2.6 Consensus size: 142
5591 ATTATAGGAG
* * * * *
5601 TAACTTTTATTGGCAAAGTTGACTT-AGGACTAACTTGGTTCATTTGTTTATTTAGCATGTTGAA
1 TAACTTTAATTGGCAAAGTT-AATTAAGGACTAACTTGATTCATTTATTTATTTAGCATGTTCAA
* * * **
5665 GCAGTTTA--TTTTTGCTAACATAATTACTAATTGATTCATTTATTTATGGCAAAATTTAATAAT
65 TCAATTTATTTTTTTGCTAACATAATTACTAATTGATTCATTTATTTATAGCAAAATCAAATAAT
* *
5728 CATCAATTAGTTA
130 CATCAATCAATTA
* * * * *
5741 TAACTTTGATTGGCAAAGTTAATTAACGACTAATTTGATTTATTTATTTATTTAGTATGTTCAAT
1 TAACTTTAATTGGCAAAGTTAATTAAGGACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT
* * * *
5806 CAATTTATTTTTTTGCTAACATAGTTACTAATTGATTCTTTTTTTTATAGCAAAATCAAATCATC
66 CAATTTATTTTTTTGCTAACATAATTACTAATTGATTCATTTATTTATAGCAAAATCAAATAATC
5871 ATCAATCAATTA
131 ATCAATCAATTA
* *
5883 TAACTTTAATTGACAAAGTTGATTAAGGACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT
1 TAACTTTAATTGGCAAAGTTAATTAAGGACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT
5948 CAATTT-TTTTTTT
66 CAATTTATTTTTTT
5961 AGTGGCAAAA
Statistics
Matches: 190, Mismatches: 27, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
139 3 0.02
140 57 0.30
141 7 0.04
142 123 0.65
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (142 bp):
TAACTTTAATTGGCAAAGTTAATTAAGGACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT
CAATTTATTTTTTTGCTAACATAATTACTAATTGATTCATTTATTTATAGCAAAATCAAATAATC
ATCAATCAATTA
Found at i:6087 original size:170 final size:171
Alignment explanation
Indices: 5803--6121 Score: 464
Period size: 170 Copynumber: 1.9 Consensus size: 171
5793 TAGTATGTTC
* * *
5803 AATCAATTTATTTTTTTGCTAACATAGTTACTAATTGATTCTTTTTTTTATAGCAAAATCAAATC
1 AATCAATTTATTTTTTTGCTAACATAATTACTAATTGATTCTTTTATTTATAGCAAAATCAAATA
* * **
5868 ATCATCAATCAATTATAACTTTAATTGACAAAGTTGATTAAGGACTAACTTGATTCATTTATTTA
66 ATCATCAATCAATTATAACTTTAATTGACAAAGTTAACTAACAACTAACTTGATTCATTTATTTA
5933 TTTAGCATGTTCAATCAATTTTTTTTTTAGTGGCAAAAAAA
131 TTTAGCATGTTCAATCAATTTTTTTTTTAGTGGCAAAAAAA
* * *
5974 AATCAATTTA-TTTTTTGAC-AACATAATTACTAATTTATT-TATTTATTTATGGCAAAATTAAA
1 AATCAATTTATTTTTTTG-CTAACATAATTACTAATTGATTCT-TTTATTTATAGCAAAATCAAA
* * * *
6036 TAATCATCCATCAATTATAACTTTGATTGGCAAATTTAACTAACAACTAACTTGATTCATTTATT
64 TAATCATCAATCAATTATAACTTTAATTGACAAAGTTAACTAACAACTAACTTGATTCATTTATT
*
6101 TATTTTGCATGTTCAATCAAT
129 TATTTAGCATGTTCAATCAAT
6122 CATATATATT
Statistics
Matches: 131, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
169 1 0.01
170 119 0.91
171 11 0.08
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (171 bp):
AATCAATTTATTTTTTTGCTAACATAATTACTAATTGATTCTTTTATTTATAGCAAAATCAAATA
ATCATCAATCAATTATAACTTTAATTGACAAAGTTAACTAACAACTAACTTGATTCATTTATTTA
TTTAGCATGTTCAATCAATTTTTTTTTTAGTGGCAAAAAAA
Found at i:6663 original size:18 final size:20
Alignment explanation
Indices: 6630--6666 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
6620 GTTAGGTTTT
6630 TTTAAATGGCATTTTATTAA
1 TTTAAATGGCATTTTATTAA
6650 TTTAAAT-G-ATTTTATTA
1 TTTAAATGGCATTTTATTA
6667 GTGGAAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 1 0.06
20 7 0.41
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (20 bp):
TTTAAATGGCATTTTATTAA
Found at i:7798 original size:2 final size:2
Alignment explanation
Indices: 7791--7854 Score: 76
Period size: 2 Copynumber: 30.0 Consensus size: 2
7781 TACAGTTTCA
7791 AT AT AT AT AT AT AT AT AT AT AT GAT AT AT AT GAT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT -AT AT AT -AT AT
7834 GAT AT AT GAT -T AT AT AT AT AT
1 -AT AT AT -AT AT AT AT AT AT AT
7855 GATTAAAATC
Statistics
Matches: 56, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
1 1 0.02
2 45 0.80
3 10 0.18
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10953 original size:21 final size:23
Alignment explanation
Indices: 10929--10977 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
10919 AAATCACTCA
*
10929 ATTTTTG-GGGGGCCATTGATT-
1 ATTTTTGAAGGGGCCATTGATTG
10950 ATTTTTGAAGGGGCCATTGATTG
1 ATTTTTGAAGGGGCCATTGATTG
10973 ATTTT
1 ATTTT
10978 GGTATTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 7 0.28
22 13 0.52
23 5 0.20
ACGTcount: A:0.18, C:0.08, G:0.29, T:0.45
Consensus pattern (23 bp):
ATTTTTGAAGGGGCCATTGATTG
Found at i:12330 original size:23 final size:25
Alignment explanation
Indices: 12300--12347 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
12290 ATCCGTGCTA
*
12300 TTTTC-TT-TCAGGCCCTGCGCCAC
1 TTTTCTTTCTCAGGCCCTGCACCAC
12323 TTTTCTTTCTCAGGCCCTGCACCAC
1 TTTTCTTTCTCAGGCCCTGCACCAC
12348 CCCCTGCAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.23
24 2 0.09
25 15 0.68
ACGTcount: A:0.10, C:0.40, G:0.15, T:0.35
Consensus pattern (25 bp):
TTTTCTTTCTCAGGCCCTGCACCAC
Found at i:18564 original size:17 final size:17
Alignment explanation
Indices: 18542--18582 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
18532 AATTAGTAGG
18542 TATTATTGGATAATAAT
1 TATTATTGGATAATAAT
** *
18559 TATTATTTTATAATTAT
1 TATTATTGGATAATAAT
18576 TATTATT
1 TATTATT
18583 TCAGTAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
TATTATTGGATAATAAT
Found at i:18583 original size:17 final size:17
Alignment explanation
Indices: 18551--18583 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18541 GTATTATTGG
18551 ATAATAATTATTATTTT
1 ATAATAATTATTATTTT
*
18568 ATAATTATTATTATTT
1 ATAATAATTATTATTT
18584 CAGTAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAATAATTATTATTTT
Done.