Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013851.1 Corchorus capsularis cultivar CVL-1 contig13872, 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: 9582
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Found at i:1720 original size:80 final size:77
Alignment explanation
Indices: 1583--1738 Score: 242
Period size: 80 Copynumber: 2.0 Consensus size: 77
1573 GTTCTCTTCC
1583 TTTTTCTCGTTTCCTTCATCCAAAAAGCTGTTTTTTTAGGGTTTAGTTTAGAGAAGAGGAAAGGA
1 TTTTTCTCGTTTCCTTCATCCAAAAAGCTGTTTTTTTAGGGTTTAGTTTAGAGAAGAGGAAAGGA
*
1648 GTTTGCTGCGTGA
66 G-TTGCAGCGTGA
* *
1661 TTTTTC-CTGTTTTCTTCATCCAAAAAGCTGTGTTTTTTTTGGGTTTAGTTTAGAGAAGAGGAAA
1 TTTTTCTC-GTTTCCTTCATCCAAAAAGC--TGTTTTTTTAGGGTTTAGTTTAGAGAAGAGGAAA
1725 GGAGTTGCAGCGTG
63 GGAGTTGCAGCGTG
1739 GGTGGGGTTG
Statistics
Matches: 72, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
77 1 0.01
78 25 0.35
79 9 0.12
80 37 0.51
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.40
Consensus pattern (77 bp):
TTTTTCTCGTTTCCTTCATCCAAAAAGCTGTTTTTTTAGGGTTTAGTTTAGAGAAGAGGAAAGGA
GTTGCAGCGTGA
Found at i:2159 original size:51 final size:51
Alignment explanation
Indices: 2083--2251 Score: 239
Period size: 51 Copynumber: 3.3 Consensus size: 51
2073 GACCTTGACA
*
2083 ATAAAAATTGAATCTTTATATAGTAAGGGTTGAGTTCTAGTAATTTTAGCC
1 ATAAAAATTGAATCTTTATGTAGTAAGGGTTGAGTTCTAGTAATTTTAGCC
* * *
2134 ATAAAAATTGAATCTTTATGTAGTAAAGGTTAAGCTCTAGTAATTTTAGCC
1 ATAAAAATTGAATCTTTATGTAGTAAGGGTTGAGTTCTAGTAATTTTAGCC
* * * * * * *
2185 ATAAAAATTAAATCTTTATGTAGTAAGAGTTGGGTTTTAGTAATTCTAACA
1 ATAAAAATTGAATCTTTATGTAGTAAGGGTTGAGTTCTAGTAATTTTAGCC
2236 ATAAAAATTGAATCTT
1 ATAAAAATTGAATCTT
2252 GATAGTTTTT
Statistics
Matches: 103, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 103 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (51 bp):
ATAAAAATTGAATCTTTATGTAGTAAGGGTTGAGTTCTAGTAATTTTAGCC
Found at i:3098 original size:38 final size:38
Alignment explanation
Indices: 3019--3144 Score: 137
Period size: 38 Copynumber: 3.3 Consensus size: 38
3009 ACCTCAATAA
* *
3019 AATTAAGAGTCAAAGTAACAGTAATCAGT-GAATTAAGT
1 AATTAAGAGTCAAAGTAACAGTAATCAGTAAAATTGA-T
* * *
3057 AATTGAGAATCAAAGTAATAGTAATCAGTAAAATTGAT
1 AATTAAGAGTCAAAGTAACAGTAATCAGTAAAATTGAT
* * * * *
3095 AATTAAGGGTCAAAGCAAGAATGATCAGTAAAATTGAT
1 AATTAAGAGTCAAAGTAACAGTAATCAGTAAAATTGAT
*
3133 AATCAAGAGTCA
1 AATTAAGAGTCA
3145 TGGTAAAAAT
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
38 68 0.93
39 5 0.07
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.25
Consensus pattern (38 bp):
AATTAAGAGTCAAAGTAACAGTAATCAGTAAAATTGAT
Found at i:3451 original size:25 final size:25
Alignment explanation
Indices: 3402--3474 Score: 85
Period size: 25 Copynumber: 2.9 Consensus size: 25
3392 AGTAAAAAGG
*
3402 ATATTAAGAGTAAAAAAATGATATTAA
1 ATATTAAGAGT--AAAAATGGTATTAA
3429 ATATTAAGAGTAAAAATGGTATTAA
1 ATATTAAGAGTAAAAATGGTATTAA
* **
3454 GTAAAAAGAG-AAAAATGGTAT
1 ATATTAAGAGTAAAAATGGTAT
3475 CATGGTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
24 11 0.26
25 20 0.48
27 11 0.26
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.27
Consensus pattern (25 bp):
ATATTAAGAGTAAAAATGGTATTAA
Found at i:3482 original size:25 final size:26
Alignment explanation
Indices: 3434--3677 Score: 134
Period size: 25 Copynumber: 10.1 Consensus size: 26
3424 ATTAAATATT
*
3434 AAGAGTAAAAATGGTATTA-AGTAAA
1 AAGAGTAAAAATGGTATTATGGTAAA
*
3459 AAGAG-AAAAATGGTATCATGGT-AA
1 AAGAGTAAAAATGGTATTATGGTAAA
3483 AAGAGTAAAAA-GG-A-TAT--T---
1 AAGAGTAAAAATGGTATTATGGTAAA
* **
3501 AAGAGTAAAAAATGGTATTAAGCAAAA
1 AAGAGT-AAAAATGGTATTATGGTAAA
* *
3528 AAGAGTAAAAATGGTATTA-AGCAAA
1 AAGAGTAAAAATGGTATTATGGTAAA
* *
3553 AAGAGAAAAAATGGTATCATGGTAAA
1 AAGAGTAAAAATGGTATTATGGTAAA
* *
3579 GAGAGTAAAAA-GG-A-TAT--TAAG
1 AAGAGTAAAAATGGTATTATGGTAAA
* ** **
3600 AATA--AAAAATGGTATTA-AATATT
1 AAGAGTAAAAATGGTATTATGGTAAA
* * *
3623 ACGAGTAAAGATGGTATTA-AGTAAA
1 AAGAGTAAAAATGGTATTATGGTAAA
* *
3648 AAGAGAAAAAAATGGTATCATGGTAAA
1 AAGAG-TAAAAATGGTATTATGGTAAA
3675 AAG
1 AAG
3678 GGTATTAAAG
Statistics
Matches: 167, Mismatches: 31, Indels: 40
0.70 0.13 0.17
Matches are distributed among these distances:
18 6 0.04
19 10 0.06
20 5 0.03
21 7 0.04
22 6 0.04
23 7 0.04
24 22 0.13
25 53 0.32
26 37 0.22
27 14 0.08
ACGTcount: A:0.55, C:0.02, G:0.21, T:0.22
Consensus pattern (26 bp):
AAGAGTAAAAATGGTATTATGGTAAA
Found at i:3567 original size:51 final size:50
Alignment explanation
Indices: 3407--3665 Score: 142
Period size: 51 Copynumber: 5.4 Consensus size: 50
3397 AAAGGATATT
* **
3407 AAGAGTAAAAAAATGATATTAA-ATATTAAGAGTAAAAATGGTATTAAGTAAA
1 AAGAG-AAAAAAATGGTATTAAGA-AAAAAGAGTAAAAATGGTATTAAG-AAA
* * **
3459 AAGAG--AAAAATGGTATCATGGTAAAAGAGTAAAAA-GGATATT------
1 AAGAGAAAAAAATGGTATTAAGAAAAAAGAGTAAAAATGG-TATTAAGAAA
*
3501 AAGAGTAAAAAATGGTATTAAGCAAAAAAGAGTAAAAATGGTATTAAGCAAA
1 AAGAGAAAAAAATGGTATTAAG-AAAAAAGAGTAAAAATGGTATTAAG-AAA
* * * *
3553 AAGAG-AAAAAATGGTATCATGGTAAAGAGAGTAAAAA-GGATATTAAG---
1 AAGAGAAAAAAATGGTATTA-AGAAAAAAGAGTAAAAATGG-TATTAAGAAA
* ** * *
3600 -A-A-TAAAAAATGGTATTAA-ATATTACGAGTAAAGATGGTATTAAGTAAA
1 AAGAGAAAAAAATGGTATTAAGA-AAAAAGAGTAAAAATGGTATTAAG-AAA
3648 AAGAGAAAAAAATGGTAT
1 AAGAGAAAAAAATGGTAT
3666 CATGGTAAAA
Statistics
Matches: 158, Mismatches: 24, Indels: 51
0.68 0.10 0.22
Matches are distributed among these distances:
42 5 0.03
44 29 0.18
45 33 0.21
46 3 0.02
48 2 0.01
49 27 0.17
50 3 0.02
51 45 0.28
52 11 0.07
ACGTcount: A:0.55, C:0.02, G:0.20, T:0.23
Consensus pattern (50 bp):
AAGAGAAAAAAATGGTATTAAGAAAAAAGAGTAAAAATGGTATTAAGAAA
Found at i:3621 original size:26 final size:26
Alignment explanation
Indices: 3592--3665 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 26
3582 AGTAAAAAGG
3592 ATATTAAGAATAAAAAATGGTATTAA
1 ATATTAAGAATAAAAAATGGTATTAA
* * *
3618 ATATTACGAGT-AAAGATGGTATTAA
1 ATATTAAGAATAAAAAATGGTATTAA
* **
3643 GTAAAAAGAGA-AAAAAATGGTAT
1 ATATTAAGA-ATAAAAAATGGTAT
3666 CATGGTAAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
25 18 0.49
26 19 0.51
ACGTcount: A:0.54, C:0.01, G:0.18, T:0.27
Consensus pattern (26 bp):
ATATTAAGAATAAAAAATGGTATTAA
Found at i:3658 original size:96 final size:94
Alignment explanation
Indices: 3363--3732 Score: 526
Period size: 95 Copynumber: 4.0 Consensus size: 94
3353 AAAGAAGAAG
*
3363 AAGAGAAAAAATGGTATCATGGTAAAAAGAGTAAAAAGGATATTAAGAGTAAAAAAATGATATTA
1 AAGAGAAAAAATGGTATCATGGT-AAAAGAGTAAAAAGGATATTAAGAGT-AAAAAATGGTATTA
3428 AATATTAAGAGTAAAAATGGTATTAAGTAAA
64 AATATTAAGAGTAAAAATGGTATTAAGTAAA
3459 AAGAG-AAAAATGGTATCATGGTAAAAGAGTAAAAAGGATATTAAGAGTAAAAAATGGTATTAAG
1 AAGAGAAAAAATGGTATCATGGTAAAAGAGTAAAAAGGATATTAAGAGTAAAAAATGGTATTAA-
** *
3523 CA-AAAAAGAGTAAAAATGGTATTAAGCAAA
65 -ATATTAAGAGTAAAAATGGTATTAAGTAAA
*
3553 AAGAGAAAAAATGGTATCATGGTAAAGAGAGTAAAAAGGATATTAAGAATAAAAAATGGTATTAA
1 AAGAGAAAAAATGGTATCATGGTAAA-AGAGTAAAAAGGATATTAAGAGTAAAAAATGGTATTAA
* *
3618 ATATTACGAGTAAAGATGGTATTAAGTAAA
65 ATATTAAGAGTAAAAATGGTATTAAGTAAA
3648 AAGAGAAAAAAATGGTATCATGGTAAAA-AG------GG-TATTAAAGAGTAAAAAAATGGTATT
1 AAGAG-AAAAAATGGTATCATGGTAAAAGAGTAAAAAGGATATT-AAGAGT-AAAAAATGGTATT
*
3705 AAGTATTAAGAGTAAAAATGGTATTAAG
63 AAATATTAAGAGTAAAAATGGTATTAAG
3733 AGTAAAAAAA
Statistics
Matches: 252, Mismatches: 14, Indels: 23
0.87 0.05 0.08
Matches are distributed among these distances:
87 4 0.02
88 7 0.03
89 38 0.15
93 14 0.06
94 59 0.23
95 67 0.27
96 63 0.25
ACGTcount: A:0.54, C:0.02, G:0.21, T:0.23
Consensus pattern (94 bp):
AAGAGAAAAAATGGTATCATGGTAAAAGAGTAAAAAGGATATTAAGAGTAAAAAATGGTATTAAA
TATTAAGAGTAAAAATGGTATTAAGTAAA
Found at i:3736 original size:27 final size:27
Alignment explanation
Indices: 3679--3732 Score: 85
Period size: 25 Copynumber: 2.0 Consensus size: 27
3669 GGTAAAAAGG
3679 GTATTAAAGAGTAAAAAAATGGTATTAA
1 GTATTAAAGAGT-AAAAAATGGTATTAA
3707 GTATT-AAGAGT-AAAAATGGTATTAA
1 GTATTAAAGAGTAAAAAATGGTATTAA
3732 G
1 G
3733 AGTAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 15 0.58
27 6 0.23
28 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (27 bp):
GTATTAAAGAGTAAAAAATGGTATTAA
Found at i:3757 original size:96 final size:92
Alignment explanation
Indices: 3363--3749 Score: 423
Period size: 94 Copynumber: 4.2 Consensus size: 92
3353 AAAGAAGAAG
** *
3363 AAGAGAAAAAATGGTATCATGGTAAAAAGAGTAAAAAGGATATTAAGAGTAAAAAAATGATATTA
1 AAGAG-AAAAATGGTAAAATGGT-AAAAGAGTAAAAAGGATATTAAGAGT-AAAAAATGGTATTA
3428 AATATTAAGAGTAAAAATGGTATTAAGTAAA
63 AATATTAAGAGTAAAAATGGTATTAAGT-AA
**
3459 AAGAGAAAAATGGTATCATGGTAAAAGAGTAAAAAGGATATTAAGAGTAAAAAATGGTATTAAGC
1 AAGAGAAAAATGGTAAAATGGTAAAAGAGTAAAAAGGATATTAAGAGTAAAAAATGGTATTAA--
** *
3524 A-AAAAAGAGTAAAAATGGTATTAAGCAAA
64 ATATTAAGAGTAAAAATGGTATTAAG-TAA
** *
3553 AAGAGAAAAAATGGTATCATGGTAAAGAGAGTAAAAAGGATATTAAGAATAAAAAATGGTATTAA
1 AAGAG-AAAAATGGTAAAATGGTAAA-AGAGTAAAAAGGATATTAAGAGTAAAAAATGGTATTAA
* *
3618 ATATTACGAGTAAAGATGGTATTAAGTAA
64 ATATTAAGAGTAAAAATGGTATTAAGTAA
* * * *
3647 AA-AGAGAAA----AAAATGGTATCATG-GTAAAAAGGGTATTAAAGAGTAAAAAAATGGTATTA
1 AAGAGAAAAATGGTAAAATGGTA-AAAGAGTAAAAAGGATATT-AAGAGT-AAAAAATGGTATTA
*
3706 AGTATTAAGAGTAAAAATGGTATTAAGAGTAA
63 AATATTAAGAGTAAAAATGGTATT-A-AGTAA
3738 AA-A-AAAAATGGT
1 AAGAGAAAAATGGT
3750 GGAAAATGCT
Statistics
Matches: 255, Mismatches: 21, Indels: 32
0.83 0.07 0.10
Matches are distributed among these distances:
87 13 0.05
88 13 0.05
89 36 0.14
90 5 0.02
91 8 0.03
92 4 0.02
93 16 0.06
94 60 0.24
95 58 0.23
96 42 0.16
ACGTcount: A:0.55, C:0.02, G:0.21, T:0.23
Consensus pattern (92 bp):
AAGAGAAAAATGGTAAAATGGTAAAAGAGTAAAAAGGATATTAAGAGTAAAAAATGGTATTAAAT
ATTAAGAGTAAAAATGGTATTAAGTAA
Done.