Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021478.1 Corchorus olitorius cultivar O-4 contig21511, 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: 17893
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:81 original size:44 final size:44
Alignment explanation
Indices: 28--215 Score: 155
Period size: 50 Copynumber: 4.4 Consensus size: 44
18 GAGGTGAGAC
28 TTCGTGAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGT
1 TTCGTGAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGT
* *
72 TTCGTGAACACCATATGCCTTTGACATTGAAAGA--G-G-CA--
1 TTCGTGAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGT
* * * *
110 --C--AAACACCATATG-TTTTAACGTTGAAAGAAGGTGATAGT
1 TTCGTGAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGT
** *
149 TTCGCCAACACCATATGCCTTTGACATTGACATTGAAAGAGGGTGATAAT
1 TTCGTGAACACCATATG-C-TT----TTGACATTGAAAGAGGGTGATAGT
*
199 TTCATGAACACCATATG
1 TTCGTGAACACCATATG
216 TCGTTGATGT
Statistics
Matches: 112, Mismatches: 15, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
33 13 0.12
34 11 0.10
35 1 0.01
36 2 0.02
37 1 0.01
40 1 0.01
41 2 0.02
42 1 0.01
43 11 0.10
44 33 0.29
46 2 0.02
50 34 0.30
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
TTCGTGAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGT
Found at i:144 original size:77 final size:78
Alignment explanation
Indices: 34--178 Score: 238
Period size: 77 Copynumber: 1.9 Consensus size: 78
24 AGACTTCGTG
* * **
34 AACACCATATGCTTTTGACATTGAAAGAGGGTGATAGTTTCGTGAACACCATATGCCTTTGACAT
1 AACACCATATGCTTTTAACATTGAAAGAAGGTGATAGTTTCGCCAACACCATATGCCTTTGACAT
99 TGAAAGAGGCACA
66 TGAAAGAGGCACA
*
112 AACACCATATG-TTTTAACGTTGAAAGAAGGTGATAGTTTCGCCAACACCATATGCCTTTGACAT
1 AACACCATATGCTTTTAACATTGAAAGAAGGTGATAGTTTCGCCAACACCATATGCCTTTGACAT
176 TGA
66 TGA
179 CATTGAAAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
77 51 0.82
78 11 0.18
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (78 bp):
AACACCATATGCTTTTAACATTGAAAGAAGGTGATAGTTTCGCCAACACCATATGCCTTTGACAT
TGAAAGAGGCACA
Found at i:407 original size:19 final size:19
Alignment explanation
Indices: 383--503 Score: 98
Period size: 19 Copynumber: 5.9 Consensus size: 19
373 GCCTTTATTG
*
383 TCGCGAATACCATACCATA
1 TCGCGAATACCATACCACA
* *
402 TCGCGAGTACCATGCCTTTAGCA
1 TCGCGAATACCATACC---A-CA
425 TCGCGAATACCATACCACA
1 TCGCGAATACCATACCACA
* * *
444 TCGCGAGTACCATGCCTTTAGCG
1 TCGCGAATACCATACC---A-CA
467 TCGCGAATACCATACCACA
1 TCGCGAATACCATACCACA
* *
486 TCGCGAGTACCATGCCAC
1 TCGCGAATACCATACCAC
504 TTGCCACTGT
Statistics
Matches: 81, Mismatches: 13, Indels: 16
0.74 0.12 0.15
Matches are distributed among these distances:
19 47 0.58
20 2 0.02
22 2 0.02
23 30 0.37
ACGTcount: A:0.28, C:0.34, G:0.17, T:0.21
Consensus pattern (19 bp):
TCGCGAATACCATACCACA
Found at i:417 original size:42 final size:42
Alignment explanation
Indices: 371--501 Score: 226
Period size: 42 Copynumber: 3.1 Consensus size: 42
361 TTGACGCCAA
** *
371 ATGCCTTTATTGTCGCGAATACCATACCATATCGCGAGTACC
1 ATGCCTTTAGCGTCGCGAATACCATACCACATCGCGAGTACC
*
413 ATGCCTTTAGCATCGCGAATACCATACCACATCGCGAGTACC
1 ATGCCTTTAGCGTCGCGAATACCATACCACATCGCGAGTACC
455 ATGCCTTTAGCGTCGCGAATACCATACCACATCGCGAGTACC
1 ATGCCTTTAGCGTCGCGAATACCATACCACATCGCGAGTACC
497 ATGCC
1 ATGCC
502 ACTTGCCACT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 84 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (42 bp):
ATGCCTTTAGCGTCGCGAATACCATACCACATCGCGAGTACC
Found at i:435 original size:23 final size:23
Alignment explanation
Indices: 401--479 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 23
391 ACCATACCAT
*
401 ATCGCGAGTACCATGCCTTTAGC
1 ATCGCGAATACCATGCCTTTAGC
*
424 ATCGCGAATACCATACC---A-C
1 ATCGCGAATACCATGCCTTTAGC
*
443 ATCGCGAGTACCATGCCTTTAGC
1 ATCGCGAATACCATGCCTTTAGC
*
466 GTCGCGAATACCAT
1 ATCGCGAATACCAT
480 ACCACATCGC
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 16 0.35
20 1 0.02
22 1 0.02
23 28 0.61
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.23
Consensus pattern (23 bp):
ATCGCGAATACCATGCCTTTAGC
Found at i:567 original size:14 final size:14
Alignment explanation
Indices: 550--618 Score: 102
Period size: 14 Copynumber: 4.9 Consensus size: 14
540 ATACTATATC
*
550 GCGAATGCCACATT
1 GCGAATACCACATT
*
564 GCGAATACCACATC
1 GCGAATACCACATT
*
578 GCGAATGCCACATT
1 GCGAATACCACATT
592 GCGAATACCACATT
1 GCGAATACCACATT
*
606 GCAAATACCACAT
1 GCGAATACCACAT
619 GCCTTTGATG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 49 1.00
ACGTcount: A:0.35, C:0.30, G:0.16, T:0.19
Consensus pattern (14 bp):
GCGAATACCACATT
Found at i:570 original size:28 final size:28
Alignment explanation
Indices: 538--618 Score: 117
Period size: 28 Copynumber: 2.9 Consensus size: 28
528 TTGGAAGAAG
* *
538 GAATACTATATCGCGAATGCCACATTGC
1 GAATACCACATCGCGAATGCCACATTGC
566 GAATACCACATCGCGAATGCCACATTGC
1 GAATACCACATCGCGAATGCCACATTGC
* * *
594 GAATACCACATTGCAAATACCACAT
1 GAATACCACATCGCGAATGCCACAT
619 GCCTTTGATG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (28 bp):
GAATACCACATCGCGAATGCCACATTGC
Found at i:680 original size:14 final size:14
Alignment explanation
Indices: 658--700 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
648 GCTTTTGATG
658 TCGCGAATACCACA
1 TCGCGAATACCACA
* *
672 TCGCAAATACCATA
1 TCGCGAATACCACA
*
686 TCGCGAATGCCACA
1 TCGCGAATACCACA
700 T
1 T
701 GTCTTTGACG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.35, C:0.33, G:0.14, T:0.19
Consensus pattern (14 bp):
TCGCGAATACCACA
Found at i:698 original size:53 final size:53
Alignment explanation
Indices: 635--736 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
625 GATGTTTGAA
*
635 GCGAACGCCACATG-CTTTTGATGTCGCGAATACCACATCGCAAATACCATATC
1 GCGAACGCCACATGTC-TTTGACGTCGCGAATACCACATCGCAAATACCATATC
* * *
688 GCGAATGCCACATGTCTTTGACGTCGCGAATACCATATTGCAAATACCA
1 GCGAACGCCACATGTCTTTGACGTCGCGAATACCACATCGCAAATACCA
737 CCACATGCCT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 43 0.98
54 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (53 bp):
GCGAACGCCACATGTCTTTGACGTCGCGAATACCACATCGCAAATACCATATC
Found at i:5272 original size:29 final size:30
Alignment explanation
Indices: 5195--5275 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 30
5185 CATTTAAAAA
* *
5195 AATGGCTAATTTATTCTTTTTTAACAAGTTC
1 AATGGCTAATTTGTTC-ATTTTAACAAGTTC
* *
5226 AAGTGTG-TAA-TTGGTCATTTTGA-AAGTTC
1 AA-TG-GCTAATTTGTTCATTTTAACAAGTTC
5255 AATGGCTAATTTGTTCATTTT
1 AATGGCTAATTTGTTCATTTT
5276 TTCACATTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
27 1 0.02
28 5 0.12
29 18 0.44
30 5 0.12
31 6 0.15
32 5 0.12
33 1 0.02
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.47
Consensus pattern (30 bp):
AATGGCTAATTTGTTCATTTTAACAAGTTC
Found at i:5897 original size:20 final size:20
Alignment explanation
Indices: 5872--5909 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5862 GCCACTTTGC
5872 ATTTTGTGCCACGTGGCATT
1 ATTTTGTGCCACGTGGCATT
*
5892 ATTTTGTGCCATGTGGCA
1 ATTTTGTGCCACGTGGCA
5910 ATGCCATGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.39
Consensus pattern (20 bp):
ATTTTGTGCCACGTGGCATT
Found at i:6022 original size:29 final size:29
Alignment explanation
Indices: 5974--6035 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
5964 AAAAGGACCC
* *
5974 AAATTAAGAATTCAGTGGGCAAAATGTTCA
1 AAATTAAGAATTCAGGGGGCAAAACG-TCA
*
6004 AAATTAA-AATTTAGGGGGCAAAACGTCA
1 AAATTAAGAATTCAGGGGGCAAAACGTCA
6032 AAAT
1 AAAT
6036 CGTACAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 7 0.24
29 15 0.52
30 7 0.24
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.24
Consensus pattern (29 bp):
AAATTAAGAATTCAGGGGGCAAAACGTCA
Found at i:7640 original size:21 final size:21
Alignment explanation
Indices: 7599--7642 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
7589 TAGATGAAAT
*
7599 AGATGAAAATTGAAGATACAA
1 AGATGAAAATTGAAGACACAA
*
7620 AGATGAGAAATTGCA-ACACAA
1 AGATGA-AAATTGAAGACACAA
7641 AG
1 AG
7643 TAAAAGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.55, C:0.09, G:0.20, T:0.16
Consensus pattern (21 bp):
AGATGAAAATTGAAGACACAA
Found at i:8104 original size:20 final size:20
Alignment explanation
Indices: 8063--8105 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
8053 CTCTCACAAG
*
8063 TTTCTAGCCGTTTGAGCTCT
1 TTTCTAGCCGTTTGAGCACT
8083 TTTCTAGCCGTTAT-AGCACT
1 TTTCTAGCCGTT-TGAGCACT
8103 TTT
1 TTT
8106 TCCACTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.47
Consensus pattern (20 bp):
TTTCTAGCCGTTTGAGCACT
Found at i:9536 original size:21 final size:21
Alignment explanation
Indices: 9512--9571 Score: 90
Period size: 19 Copynumber: 3.0 Consensus size: 21
9502 ATCATCTCTA
9512 ATGAAGAATCCTCTCACCATG
1 ATGAAGAATCCTCTCACCATG
*
9533 ATGAA-AATCCTCTCA-C-TA
1 ATGAAGAATCCTCTCACCATG
9551 ATGAAGAATCCTCTCACCATG
1 ATGAAGAATCCTCTCACCATG
9572 TCCAAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 6 0.18
19 11 0.32
20 11 0.32
21 6 0.18
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.25
Consensus pattern (21 bp):
ATGAAGAATCCTCTCACCATG
Found at i:10237 original size:7 final size:7
Alignment explanation
Indices: 10221--10251 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
10211 CTAAACTAAT
*
10221 CAATTAA
1 CAATTCA
10228 CAATTCA
1 CAATTCA
10235 CAATTCA
1 CAATTCA
10242 CAATTCA
1 CAATTCA
10249 CAA
1 CAA
10252 AAATGCATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (7 bp):
CAATTCA
Found at i:13696 original size:20 final size:20
Alignment explanation
Indices: 13655--13697 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
13645 CTCTCACAAG
*
13655 TTTCTAGCCGTTTGAGCTCT
1 TTTCTAGCCGTTTGAGCACT
13675 TTTCTAGCCGTTAT-AGCACT
1 TTTCTAGCCGTT-TGAGCACT
13695 TTT
1 TTT
13698 TCCACTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.47
Consensus pattern (20 bp):
TTTCTAGCCGTTTGAGCACT
Found at i:15571 original size:56 final size:56
Alignment explanation
Indices: 15479--15588 Score: 157
Period size: 56 Copynumber: 2.0 Consensus size: 56
15469 ATAATAATCC
* * * *
15479 AAAGTACTCGGATATTCCACACGATAGCCATTACCTTTCAGTCTTTTAGCAATTCT
1 AAAGTAATCGGATATTCAACACGATAGCCATCACCTTTCAATCTTTTAGCAATTCT
* * *
15535 AAAGTAATCGGATATTCAACACGGTAGTCATCACCTTTTAATCTTTTAGCAATT
1 AAAGTAATCGGATATTCAACACGATAGCCATCACCTTTCAATCTTTTAGCAATT
15589 TTTCGACAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.35
Consensus pattern (56 bp):
AAAGTAATCGGATATTCAACACGATAGCCATCACCTTTCAATCTTTTAGCAATTCT
Found at i:16172 original size:19 final size:18
Alignment explanation
Indices: 16145--16189 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
16135 TGAGTAATTT
*
16145 TTAAGTAAAAATATAATA
1 TTAAATAAAAATATAATA
*
16163 TATAAATAAAAATTTAATA
1 T-TAAATAAAAATATAATA
16182 TTAAATAA
1 TTAAATAA
16190 TTAATTAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:16195 original size:19 final size:19
Alignment explanation
Indices: 16150--16189 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
16140 AATTTTTAAG
*
16150 TAAAAATATAATATATAAA
1 TAAAAATTTAATATATAAA
16169 TAAAAATTTAATAT-TAAA
1 TAAAAATTTAATATATAAA
16187 TAA
1 TAA
16190 TTAATTAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATTTAATATATAAA
Done.