Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024250.1 Corchorus olitorius cultivar O-4 contig24283, 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: 55559
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3999 original size:31 final size:32
Alignment explanation
Indices: 3972--4042 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 32
3962 AATAGGACTG
*
3972 AATTGAGCAAC-CGTTCAAAGGTTTAGGACCA
1 AATTGAGCAACTCGCTCAAAGGTTTAGGACCA
*
4003 AATTGAGC-GCTCGCTCAAAGGTTTAGGACCA
1 AATTGAGCAACTCGCTCAAAGGTTTAGGACCA
4034 AATTGAGCA
1 AATTGAGCA
4043 TTTAGCCCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (32 bp):
AATTGAGCAACTCGCTCAAAGGTTTAGGACCA
Found at i:5366 original size:18 final size:19
Alignment explanation
Indices: 5343--5380 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5333 CAATCCTAAC
5343 TATCTAA-TCTTAAAACTA
1 TATCTAATTCTTAAAACTA
5361 TATCTAATTCTTAAAACTA
1 TATCTAATTCTTAAAACTA
5380 T
1 T
5381 CGTAACTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (19 bp):
TATCTAATTCTTAAAACTA
Found at i:10115 original size:20 final size:20
Alignment explanation
Indices: 10090--10131 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
10080 GGCATCATCG
10090 GTCTTAAAACATGCAATAAA
1 GTCTTAAAACATGCAATAAA
10110 GTCTTAAAACATGCAATAAA
1 GTCTTAAAACATGCAATAAA
10130 GT
1 GT
10132 GTGCCATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (20 bp):
GTCTTAAAACATGCAATAAA
Found at i:20348 original size:42 final size:42
Alignment explanation
Indices: 20324--20462 Score: 251
Period size: 42 Copynumber: 3.3 Consensus size: 42
20314 AGGATGAGAC
*
20324 CTTTCCCTAAATTAAAAACTTTTGAAAACTACTTGAGGGGAT
1 CTTTCCCTAAATTAAAAACTTTTGAAAACTACATGAGGGGAT
*
20366 CTTTTCCTAAATTAAAAACTTTTGAAAACTACATGAGGGGAT
1 CTTTCCCTAAATTAAAAACTTTTGAAAACTACATGAGGGGAT
*
20408 CTTTCCCTAAATTAAAAACTTTTGAAAACTACTTGAGGGGAT
1 CTTTCCCTAAATTAAAAACTTTTGAAAACTACATGAGGGGAT
20450 CTTTCCCTAAATT
1 CTTTCCCTAAATT
20463 GGAATCTTTG
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 93 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (42 bp):
CTTTCCCTAAATTAAAAACTTTTGAAAACTACATGAGGGGAT
Found at i:20491 original size:42 final size:41
Alignment explanation
Indices: 20260--20568 Score: 225
Period size: 42 Copynumber: 7.4 Consensus size: 41
20250 AAAGACTCAA
* * ***
20260 TTTGAAAAAAACTTTGATGGGATCTTTCCCCT-AATGGGAAAC
1 TTTGAAAAATAC-TTGGTGGGATCTTT-CCCTAAATTAAAAAC
* * * *
20302 TTTGAAAAAGAC-AGGATGAGACCTTTCCCTAAATTAAAAAC
1 TTTGAAAAATACTTGG-TGGGATCTTTCCCTAAATTAAAAAC
* *
20343 TTTTGAAAACTACTTGAG-GGGATCTTTTCCTAAATTAAAAAC
1 -TTTGAAAAATACTTG-GTGGGATCTTTCCCTAAATTAAAAAC
* *
20385 TTTTGAAAACTACATGAG-GGGATCTTTCCCTAAATTAAAAAC
1 -TTTGAAAAATACTTG-GTGGGATCTTTCCCTAAATTAAAAAC
* ** *
20427 TTTTGAAAACTACTTGAG-GGGATCTTTCCCTAAATTGGAATC
1 -TTTGAAAAATACTTG-GTGGGATCTTTCCCTAAATTAAAAAC
* * * *
20469 TTTGAAAAATACTTTGGTGGGATCTTTCCATAATTTGAAATC
1 TTTGAAAAATAC-TTGGTGGGATCTTTCCCTAAATTAAAAAC
* * * * *
20511 TTTAAAAAAAATAATTTGGTGGGATCTTCCCCTAAATTGATAAC
1 TTT--GAAAAAT-ACTTGGTGGGATCTTTCCCTAAATTAAAAAC
20555 TTTGAAAAA-ACTTG
1 TTTGAAAAATACTTG
20569 ATTTTTGATT
Statistics
Matches: 224, Mismatches: 33, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
40 9 0.04
41 27 0.12
42 152 0.68
43 1 0.00
44 34 0.15
45 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (41 bp):
TTTGAAAAATACTTGGTGGGATCTTTCCCTAAATTAAAAAC
Found at i:20491 original size:84 final size:82
Alignment explanation
Indices: 20273--20563 Score: 275
Period size: 84 Copynumber: 3.5 Consensus size: 82
20263 GAAAAAAACT
* * * * * *
20273 TTGATGGGATCTTTCCCCT-AATGGGAAACTTTGAAAAAGACAGGATGAGACCTTTCCCTAAATT
1 TTGAGGGGATCTTT-CCCTAAATTGGAAACTTTGAAAAATACTGG-TGGGATCTTTCCCTAAATT
20337 AAAAACTTTTGAAAACTAC
64 AAAAACTTTTGAAAACTAC
* ** *
20356 TTGAGGGGATCTTTTCCTAAATTAAAAACTTTTGAAAACTACATGAG-GGGATCTTTCCCTAAAT
1 TTGAGGGGATCTTTCCCTAAATTGGAAAC-TTTGAAAAATAC-TG-GTGGGATCTTTCCCTAAAT
20420 TAAAAACTTTTGAAAACTAC
63 TAAAAACTTTTGAAAACTAC
* * *
20440 TTGAGGGGATCTTTCCCTAAATTGGAATCTTTGAAAAATACTTTGGTGGGATCTTTCCATAATTT
1 TTGAGGGGATCTTTCCCTAAATTGGAAACTTTGAAAAATAC--TGGTGGGATCTTTCCCTAAATT
* * ** * *
20505 GAAATCTTTAAAAAAAATAAT
64 AAAAACTTT-TGAAAACT-AC
*
20526 TTG-GTGGGATCTTCCCCTAAATT-GATAACTTTGAAAAA
1 TTGAG-GGGATCTTTCCCTAAATTGGA-AACTTTGAAAAA
20564 ACTTGATTTT
Statistics
Matches: 172, Mismatches: 26, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
82 3 0.02
83 32 0.19
84 95 0.55
85 9 0.05
86 33 0.19
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Consensus pattern (82 bp):
TTGAGGGGATCTTTCCCTAAATTGGAAACTTTGAAAAATACTGGTGGGATCTTTCCCTAAATTAA
AAACTTTTGAAAACTAC
Found at i:21159 original size:22 final size:23
Alignment explanation
Indices: 21109--21169 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
21099 ATAGAAAGGT
*
21109 CAAGCCCAAATAACTAAAACAAAC
1 CAAGCCCAAATTA-TAAAACAAAC
* *
21133 AAAGCCCAAATTATAACA-AAAC
1 CAAGCCCAAATTATAAAACAAAC
* *
21155 CAAGCCTAAAGTATA
1 CAAGCCCAAATTATA
21170 TATGTTAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 16 0.52
23 4 0.13
24 11 0.35
ACGTcount: A:0.56, C:0.25, G:0.07, T:0.13
Consensus pattern (23 bp):
CAAGCCCAAATTATAAAACAAAC
Found at i:26910 original size:49 final size:49
Alignment explanation
Indices: 26833--26930 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
26823 TGCATGCCTT
*
26833 TATTCGGGCTTTCCAAGTCTCAAAGCCCAAAAGCAACTCCCAAATGAGC
1 TATTCGGGCTTTCCAAGTCTCAAAGCCCAAAAGCAAATCCCAAATGAGC
*
26882 TATTTGGGCTTTCCAAGTCTCAAAGCCCAAAAGCAAATCCCAAATGAGC
1 TATTCGGGCTTTCCAAGTCTCAAAGCCCAAAAGCAAATCCCAAATGAGC
26931 AAACGGACTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (49 bp):
TATTCGGGCTTTCCAAGTCTCAAAGCCCAAAAGCAAATCCCAAATGAGC
Found at i:30852 original size:22 final size:22
Alignment explanation
Indices: 30805--30853 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
30795 TAGCCTTATC
* *
30805 TTTTTATTTTTCGTTATTTTTC
1 TTTTTAATTTTCGTTATTTTTA
*
30827 TTTTTAATTTT-GTTTTTGTTTA
1 TTTTTAATTTTCGTTATT-TTTA
30849 TTTTT
1 TTTTT
30854 CTTAGTTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.10, C:0.04, G:0.06, T:0.80
Consensus pattern (22 bp):
TTTTTAATTTTCGTTATTTTTA
Found at i:33523 original size:26 final size:27
Alignment explanation
Indices: 33476--33538 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 27
33466 TTCTAAGGGC
** **
33476 TTGGTCATTTTTACATTAA-GGGCATT
1 TTGGTCATTTGCACATTAAGGGGCACG
* *
33502 TTGGTCATTTGCATATTCAGGGGCACG
1 TTGGTCATTTGCACATTAAGGGGCACG
33529 TTGGTCATTT
1 TTGGTCATTT
33539 TAAGTCCACT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 15 0.50
27 15 0.50
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (27 bp):
TTGGTCATTTGCACATTAAGGGGCACG
Found at i:35950 original size:22 final size:24
Alignment explanation
Indices: 35920--35978 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
35910 TAAATCTGAC
35920 TTGGGCCTTT-TCCTTTTA-GCAT
1 TTGGGCCTTTATCCTTTTATGCAT
* * *
35942 TTGGTCCTTTATTCTTTTATGCTT
1 TTGGGCCTTTATCCTTTTATGCAT
35966 TTGGGCCTCTTAT
1 TTGGGCCT-TTAT
35979 TTATGCCTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 9 0.30
23 7 0.23
24 10 0.33
25 4 0.13
ACGTcount: A:0.08, C:0.20, G:0.17, T:0.54
Consensus pattern (24 bp):
TTGGGCCTTTATCCTTTTATGCAT
Found at i:37722 original size:21 final size:22
Alignment explanation
Indices: 37697--37737 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
37687 CTTCTATTAC
*
37697 CTTTATTCAT-AAATTCACTCA
1 CTTTAATCATCAAATTCACTCA
*
37718 CTTTAATCATCAATTTCACT
1 CTTTAATCATCAAATTCACT
37738 ACTCCATCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (22 bp):
CTTTAATCATCAAATTCACTCA
Found at i:44036 original size:23 final size:23
Alignment explanation
Indices: 43998--44066 Score: 95
Period size: 25 Copynumber: 3.0 Consensus size: 23
43988 TTCTTTTTTT
*
43998 TTCTTGTTTTTC-GTTTTCGGTA
1 TTCTTTTTTTTCTGTTTTCGGTA
*
44020 TTCTTTTTTTTCTGTTTTCGATA
1 TTCTTTTTTTTCTGTTTTCGGTA
44043 TTCTTTTTTTTTTCTGTTTTCGGT
1 TTC--TTTTTTTTCTGTTTTCGGT
44067 TTTTTTAGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
22 11 0.27
23 12 0.29
25 18 0.44
ACGTcount: A:0.04, C:0.13, G:0.13, T:0.70
Consensus pattern (23 bp):
TTCTTTTTTTTCTGTTTTCGGTA
Found at i:55524 original size:2 final size:2
Alignment explanation
Indices: 55517--55559 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
55507 GTTGAAAGGG
55517 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
55559 G
1 G
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.