Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007584.1 Corchorus capsularis cultivar CVL-1 contig07605, 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: 7615
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Found at i:3524 original size:12 final size:12
Alignment explanation
Indices: 3499--3536 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
3489 TGGTCGAAAC
3499 TTTTTTTT-TAT
1 TTTTTTTTATAT
*
3510 TTTATTTTA-AT
1 TTTTTTTTATAT
3521 TTTTTTTTATAT
1 TTTTTTTTATAT
3533 TTTT
1 TTTT
3537 CGATATAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 17 0.74
12 6 0.26
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTTATAT
Found at i:5945 original size:26 final size:26
Alignment explanation
Indices: 5880--5950 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 26
5870 AGTGGACTCA
*
5880 AAATGACCAAAATGCCCCTGAATGCAT
1 AAATGACCAAAATGCCCCGGAATG-AT
* **
5907 TAATGACTGAAATGCCCCGGAATG-T
1 AAATGACCAAAATGCCCCGGAATGAT
5932 GAAATGACCAAAATGCCCC
1 -AAATGACCAAAATGCCCC
5951 TAGGTGACCC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
25 1 0.03
26 15 0.42
27 20 0.56
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (26 bp):
AAATGACCAAAATGCCCCGGAATGAT
Found at i:5981 original size:10 final size:10
Alignment explanation
Indices: 5968--5994 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
5958 CCCTAATGCG
5968 AAATTGATTT
1 AAATTGATTT
5978 AAATTGATTT
1 AAATTGATTT
5988 AAATTGA
1 AAATTGA
5995 AGGATACAGG
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:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (10 bp):
AAATTGATTT
Found at i:6468 original size:70 final size:70
Alignment explanation
Indices: 6338--6756 Score: 518
Period size: 70 Copynumber: 6.0 Consensus size: 70
6328 AGACCACCCA
* * * * * * *
6338 GGATCAACTTGGAAACAACTGATGAAAAACCGCCCT-GAT-GAATGAATCAATCATTTTGACATA
1 GGATAAACTTGGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATA
*
6401 AACTA
66 AACTT
* * * * *
6406 GGATAAACATGGAAACTACTGAAGAAATACCACCCTAGGTCGACTGAATCGATCATTCTGACATA
1 GGATAAACTTGGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATA
6471 AACTT
66 AACTT
* * *
6476 GGAATAAACTTGAAAACAACTGAAGAAAGACCGCCTTGGGTCGACTGAATCGATCATTTTGACAT
1 GG-ATAAACTTGGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACAT
6541 AAACTT
65 AAACTT
* ** * * *
6547 GGATAAACGTGGAAACTGCTGAAGAAAGACCACCCTGGGTCGACCGAATCGATCATTCTGACACA
1 GGATAAACTTGGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATA
6612 AACTT
66 AACTT
* * *
6617 GGATAAACTTGGAAACAACTGAAGAAAGGCCGCCCTAGGTCAACTGAATCGATCATTCTGACATA
1 GGATAAACTTGGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATA
6682 AACTT
66 AACTT
* * * * * * *
6687 CGAATAAACTTGAAAACAATTAAAGAAAGATCGCCCTGGGTCGACTGAATCAATCATTCTAACAT
1 -GGATAAACTTGGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACAT
6752 AAACT
65 AAACT
6757 GAAGAAAGAC
Statistics
Matches: 300, Mismatches: 47, Indels: 5
0.85 0.13 0.01
Matches are distributed among these distances:
68 30 0.10
69 2 0.01
70 147 0.49
71 121 0.40
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (70 bp):
GGATAAACTTGGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATA
AACTT
Found at i:6596 original size:141 final size:139
Alignment explanation
Indices: 6338--6756 Score: 543
Period size: 141 Copynumber: 3.0 Consensus size: 139
6328 AGACCACCCA
* * * * * *
6338 GGATCAACTTGGAAACAACTGATGAAAAACCGCCCTGAT-GAATGAATCAATCATTTTGACATAA
1 GGATAAACTTGGAAACAACTGAAGAAAGACCGCCCTGGTCGACTGAATCGATCATTTTGACATAA
* * *
6402 ACTAGGATAAACATGGAAACTACTGAAGAAATACCACCCTAGGTCGACTGAATCGATCATTCTGA
66 ACTTGGATAAACATGGAAACTACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGA
6467 CATAAACTT
131 CATAAACTT
* *
6476 GGAATAAACTTGAAAACAACTGAAGAAAGACCGCCTTGGGTCGACTGAATCGATCATTTTGACAT
1 GG-ATAAACTTGGAAACAACTGAAGAAAGACCGCCCT-GGTCGACTGAATCGATCATTTTGACAT
* * *
6541 AAACTTGGATAAACGTGGAAACTGCTGAAGAAAGACCACCCTGGGTCGACCGAATCGATCATTCT
64 AAACTTGGATAAACATGGAAACTACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCT
*
6606 GACACAAACTT
129 GACATAAACTT
* * *
6617 GGATAAACTTGGAAACAACTGAAGAAAGGCCGCCCTAGGTCAACTGAATCGATCATTCTGACATA
1 GGATAAACTTGGAAACAACTGAAGAAAGACCGCCCT-GGTCGACTGAATCGATCATTTTGACATA
* * * * * * * * *
6682 AACTTCGAATAAACTTGAAAACAATTAAAGAAAGATCGCCCTGGGTCGACTGAATCAATCATTCT
65 AACTT-GGATAAACATGGAAACTACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCT
*
6747 AACATAAACT
129 GACATAAACT
6757 GAAGAAAGAC
Statistics
Matches: 243, Mismatches: 34, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
138 2 0.01
139 29 0.12
140 64 0.26
141 148 0.61
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (139 bp):
GGATAAACTTGGAAACAACTGAAGAAAGACCGCCCTGGTCGACTGAATCGATCATTTTGACATAA
ACTTGGATAAACATGGAAACTACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGA
CATAAACTT
Found at i:6804 original size:35 final size:35
Alignment explanation
Indices: 6750--6851 Score: 123
Period size: 36 Copynumber: 2.9 Consensus size: 35
6740 TCATTCTAAC
* *
6750 ATAAACTGAAGAAAGACCACCCTAGGTCAACCGAA
1 ATAAACTAAAGAAAAACCACCCTAGGTCAACCGAA
* * * * *
6785 ATAATCTAAAGAAAAACCACCCTCGATCATTCCGAC
1 ATAAACTAAAGAAAAACCACCCTAGGTCA-ACCGAA
*
6821 ATAAACTTAAGAAAAACCACCCTAGGTCAAC
1 ATAAACTAAAGAAAAACCACCCTAGGTCAAC
6852 TGAATCGATC
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
35 25 0.46
36 29 0.54
ACGTcount: A:0.45, C:0.27, G:0.12, T:0.16
Consensus pattern (35 bp):
ATAAACTAAAGAAAAACCACCCTAGGTCAACCGAA
Found at i:6836 original size:36 final size:36
Alignment explanation
Indices: 6739--6845 Score: 117
Period size: 36 Copynumber: 3.0 Consensus size: 36
6729 GACTGAATCA
** * *
6739 ATCATTCTAACATAAACTGAAGAAAGACCACCCTAG
1 ATCATTCCGACATAAACTAAAGAAAAACCACCCTAG
* * * * *
6775 GTCA-ACCGAAATAATCTAAAGAAAAACCACCCTCG
1 ATCATTCCGACATAAACTAAAGAAAAACCACCCTAG
*
6810 ATCATTCCGACATAAACTTAAGAAAAACCACCCTAG
1 ATCATTCCGACATAAACTAAAGAAAAACCACCCTAG
6846 GTCAACTGAA
Statistics
Matches: 55, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
35 26 0.47
36 29 0.53
ACGTcount: A:0.45, C:0.27, G:0.10, T:0.18
Consensus pattern (36 bp):
ATCATTCCGACATAAACTAAAGAAAAACCACCCTAG
Found at i:6942 original size:70 final size:71
Alignment explanation
Indices: 6824--7017 Score: 300
Period size: 71 Copynumber: 2.7 Consensus size: 71
6814 TTCCGACATA
* * * * *
6824 AACTTAAGAAAAACCACCCTAGGTCAACTGAATCGATCATTCTGACATAAACTT-GGATAAACTT
1 AACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
*
6888 GGAAAC
66 GAAAAC
6894 AACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
1 AACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
6959 GAAAAC
66 GAAAAC
* * *
6965 AACTGAAGAAAGACCGTCCTGGGTCGACTGAATCGATCATTCTAACATAAACT
1 AACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACT
7018 GAAGAAAGAC
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
70 50 0.44
71 64 0.56
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.22
Consensus pattern (71 bp):
AACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
GAAAAC
Found at i:7041 original size:261 final size:261
Alignment explanation
Indices: 6568--7278 Score: 1199
Period size: 261 Copynumber: 2.7 Consensus size: 261
6558 GAAACTGCTG
* * * *
6568 AAGAAAGACCACCCTGGGTCGACCGAATCGATCATTCTGACACAAACTTGGATAAACTTGGAAAC
1 AAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGATAAACTTGGAAAC
* *
6633 AACTGAAGAAAGGCCGCCCTAGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
66 AACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
* * *
6698 GAAAACAATTAAAGAAAGATCGCCCTGGGTCGACTGAATCAATCATTCTAACATAAACTGAAGAA
131 GAAAACAATTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTAACATAAACTGAAGAA
* *
6763 AGACCACCCTAGGTCAACCGAAATAATCTAAAGAAAAACCACCCTCGATCATTCCGACATAAACT
196 AGACCACCCTAGGTCAACCGAAATAAACTAAAGAAAAACCACACTCGATCATTCCGACATAAACT
*
6828 T
261 A
*
6829 AAGAAAAACCACCCTAGGTCAACTGAATCGATCATTCTGACATAAACTTGGATAAACTTGGAAAC
1 AAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGATAAACTTGGAAAC
6894 AACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
66 AACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
* *
6959 GAAAACAACTGAAGAAAGACCGTCCTGGGTCGACTGAATCGATCATTCTAACATAAACTGAAGAA
131 GAAAACAATTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTAACATAAACTGAAGAA
* *
7024 AGACCACCCTGGGTCAACCGAAATAAACTAAAGAAAGACCACACTCGATCATTCCGACATAAACT
196 AGACCACCCTAGGTCAACCGAAATAAACTAAAGAAAAACCACACTCGATCATTCCGACATAAACT
7089 A
261 A
*
7090 AAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGATAATCTT-GAAAC
1 AAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGATAAACTTGGAAAC
* * * * *
7154 AACTGAAGAAAGATCGCCCTAGGTTGACTGAATCGATCATTCTGACATATAGTTCGGATAAACTT
66 AACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
7219 GAAAACAATTGAAGAAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTAACATAAACT
131 GAAAACAATTGAAG-AAAGACCGCCCTGGGTCGACTGAATCGATCATTCTAACATAAACT
7279 TCGAATAAAC
Statistics
Matches: 423, Mismatches: 26, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
260 78 0.18
261 345 0.82
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.21
Consensus pattern (261 bp):
AAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGATAAACTTGGAAAC
AACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
GAAAACAATTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTAACATAAACTGAAGAA
AGACCACCCTAGGTCAACCGAAATAAACTAAAGAAAAACCACACTCGATCATTCCGACATAAACT
A
Found at i:7058 original size:35 final size:35
Alignment explanation
Indices: 7011--7112 Score: 132
Period size: 36 Copynumber: 2.9 Consensus size: 35
7001 TCATTCTAAC
*
7011 ATAAACTGAAGAAAGACCACCCTGGGTCAACCGAA
1 ATAAACTAAAGAAAGACCACCCTGGGTCAACCGAA
* * * * *
7046 ATAAACTAAAGAAAGACCACACTCGATCATTCCGAC
1 ATAAACTAAAGAAAGACCACCCTGGGTCA-ACCGAA
*
7082 ATAAACTAAAGAAAAACCACCCTGGGTCAAC
1 ATAAACTAAAGAAAGACCACCCTGGGTCAAC
7113 TGAATCGATC
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
35 26 0.47
36 29 0.53
ACGTcount: A:0.45, C:0.26, G:0.15, T:0.14
Consensus pattern (35 bp):
ATAAACTAAAGAAAGACCACCCTGGGTCAACCGAA
Found at i:7093 original size:36 final size:36
Alignment explanation
Indices: 6997--7101 Score: 122
Period size: 36 Copynumber: 2.9 Consensus size: 36
6987 GTCGACTGAA
** * *
6997 TCGATCATTCTAACATAAACTGAAGAAAGACCACCC
1 TCGATCATTCCGACATAAACTAAAGAAAGACCACAC
* * * *
7033 TGGGTCA-ACCGAAATAAACTAAAGAAAGACCACAC
1 TCGATCATTCCGACATAAACTAAAGAAAGACCACAC
*
7068 TCGATCATTCCGACATAAACTAAAGAAAAACCAC
1 TCGATCATTCCGACATAAACTAAAGAAAGACCAC
7102 CCTGGGTCAA
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
35 27 0.49
36 28 0.51
ACGTcount: A:0.46, C:0.26, G:0.12, T:0.16
Consensus pattern (36 bp):
TCGATCATTCCGACATAAACTAAAGAAAGACCACAC
Found at i:7406 original size:71 final size:71
Alignment explanation
Indices: 7090--7421 Score: 497
Period size: 72 Copynumber: 4.7 Consensus size: 71
7080 ACATAAACTA
* * * * *
7090 AAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTT-GGATAATCTTG-AAA
1 AAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAA
*
7153 CAACTG
66 CAATTG
* * * * * *
7159 AAGAAAGATCGCCCTAGGTTGACTGAATCGATCATTCTGACATATAGTTCGGATAAACTTGAAAA
1 AAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAA
7224 CAATTG
66 CAATTG
*
7230 AAGAAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTAACATAAACTTCGAATAAACTTTGAA
1 AAG-AAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAAC-TTGAA
7295 AACAATTG
64 AACAATTG
7303 AAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAA
1 AAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAA
*
7368 CATTTG
66 CAATTG
*
7374 AAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTATGACATAAACT
1 AAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
7422 GAAGAAAGGC
Statistics
Matches: 239, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
69 41 0.17
70 10 0.04
71 70 0.29
72 102 0.43
73 16 0.07
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (71 bp):
AAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAA
CAATTG
Done.