Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014544.1 Corchorus olitorius cultivar O-4 contig14577, 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: 24493
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:135 original size:47 final size:49
Alignment explanation
Indices: 46--145 Score: 134
Period size: 47 Copynumber: 2.1 Consensus size: 49
36 CAAATGAAGA
* * *
46 TTATATTTTTTATATGTTATATTATAAATTAATATGCGATTTATTATAT
1 TTATATTTTATATATGTTATATTAGAAATTAATATGCAATTTATTATAT
*
95 TTATATTTTATA-AT-TTATGATTAGAAATTAATATG-AATTTATTTTAT
1 TTATATTTTATATATGTTAT-ATTAGAAATTAATATGCAATTTATTATAT
142 TTAT
1 TTAT
146 TTATTTATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
47 18 0.39
48 17 0.37
49 11 0.24
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (49 bp):
TTATATTTTATATATGTTATATTAGAAATTAATATGCAATTTATTATAT
Found at i:12974 original size:2 final size:2
Alignment explanation
Indices: 12967--13019 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
12957 CTCACAAATA
12967 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
13009 GT GT GT GT GT G
1 GT GT GT GT GT G
13020 ATTACCAACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:13515 original size:19 final size:19
Alignment explanation
Indices: 13481--13521 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
13471 AATTTTCTCC
13481 AATTAGGGCTAATTGCAACA
1 AATTAGGGCTAATTGC-ACA
*
13501 AATTAGGTC-AATTGCACA
1 AATTAGGGCTAATTGCACA
13519 AAT
1 AAT
13522 CAAGAACCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 6 0.30
20 8 0.40
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (19 bp):
AATTAGGGCTAATTGCACA
Found at i:15510 original size:22 final size:22
Alignment explanation
Indices: 15483--15551 Score: 138
Period size: 22 Copynumber: 3.1 Consensus size: 22
15473 CCAATTTGAT
15483 GGCGGGAGGCTCGCCGATTGGC
1 GGCGGGAGGCTCGCCGATTGGC
15505 GGCGGGAGGCTCGCCGATTGGC
1 GGCGGGAGGCTCGCCGATTGGC
15527 GGCGGGAGGCTCGCCGATTGGC
1 GGCGGGAGGCTCGCCGATTGGC
15549 GGC
1 GGC
15552 CGGTGGCCAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.09, C:0.28, G:0.51, T:0.13
Consensus pattern (22 bp):
GGCGGGAGGCTCGCCGATTGGC
Found at i:16518 original size:12 final size:12
Alignment explanation
Indices: 16501--16529 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
16491 AACTTATTAT
16501 ACCGAACCGAAA
1 ACCGAACCGAAA
16513 ACCGAACCGAAA
1 ACCGAACCGAAA
16525 ACCGA
1 ACCGA
16530 CAAACCGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.34, G:0.17, T:0.00
Consensus pattern (12 bp):
ACCGAACCGAAA
Found at i:17369 original size:28 final size:29
Alignment explanation
Indices: 17304--17370 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
17294 TAATACCCTT
*
17304 TTTGCCCCCTGAACTTCTACGATTTTGACG
1 TTTGCCCCCTAAACTTCTAC-ATTTTGACG
*
17334 TTTTCCCCCTAAACTT-TA-ATTTTGGACG
1 TTTGCCCCCTAAACTTCTACATTTT-GACG
17362 TTTGCCCCC
1 TTTGCCCCC
17371 AGAACTCGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 5 0.15
28 12 0.36
29 2 0.06
30 14 0.42
ACGTcount: A:0.16, C:0.31, G:0.13, T:0.39
Consensus pattern (29 bp):
TTTGCCCCCTAAACTTCTACATTTTGACG
Found at i:17376 original size:28 final size:29
Alignment explanation
Indices: 17304--17376 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 29
17294 TAATACCCTT
*
17304 TTTGCCCCCTGAACTTCTACGATTTTGACG
1 TTTGCCCCCAGAACTTCTAC-ATTTTGACG
*
17334 TTTTCCCCCTA-AACTT-TA-ATTTTGGACG
1 TTTGCCCCC-AGAACTTCTACATTTT-GACG
17362 TTTGCCCCCAGAACT
1 TTTGCCCCCAGAACT
17377 CGCAATTTGG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
27 6 0.16
28 16 0.43
29 2 0.05
30 13 0.35
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.37
Consensus pattern (29 bp):
TTTGCCCCCAGAACTTCTACATTTTGACG
Found at i:19049 original size:21 final size:21
Alignment explanation
Indices: 19025--19064 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19015 TAATCTTATA
*
19025 AGATCTTTTAATAAGTTTAGT
1 AGATCTTTTAATAACTTTAGT
* *
19046 AGATTTTTTAGTAACTTTA
1 AGATCTTTTAATAACTTTA
19065 TAAGTTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (21 bp):
AGATCTTTTAATAACTTTAGT
Found at i:19089 original size:35 final size:37
Alignment explanation
Indices: 19043--19112 Score: 90
Period size: 35 Copynumber: 1.9 Consensus size: 37
19033 TAATAAGTTT
* *
19043 AGTAGATTTTTTAGTAAC-T-TTATAAGTTTTTTTGA
1 AGTAGAATTTTTAGTAACTTCTTAAAAGTTTTTTTGA
**
19078 AGTAGAATTTTTTTTAACTTCTTAAAAGTTTTTTT
1 AGTAGAATTTTTAGTAACTTCTTAAAAGTTTTTTT
19113 AATTAATTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 15 0.52
36 1 0.03
37 13 0.45
ACGTcount: A:0.29, C:0.04, G:0.11, T:0.56
Consensus pattern (37 bp):
AGTAGAATTTTTAGTAACTTCTTAAAAGTTTTTTTGA
Found at i:19573 original size:30 final size:31
Alignment explanation
Indices: 19506--19575 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
19496 AAAAAGTGAG
*
19506 TCAGGGACCTAATTGCTCAATTAACTCCACT
1 TCAGGGACCTAATTGCTCAACTAACTCCACT
* * *
19537 TTAGGGA-CTCAATTGCTC-ACTAAGTTCACT
1 TCAGGGACCT-AATTGCTCAACTAACTCCACT
19567 TCAGGGACC
1 TCAGGGACC
19576 CATTTGCACA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (31 bp):
TCAGGGACCTAATTGCTCAACTAACTCCACT
Found at i:19665 original size:9 final size:9
Alignment explanation
Indices: 19623--19665 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
19613 CAATAAAAAG
19623 TTTTTCATTT
1 TTTTTC-TTT
19633 TTTCTTCTTT
1 TTT-TTCTTT
19643 TTTTTCTTT
1 TTTTTCTTT
* *
19652 ATTTTGTTT
1 TTTTTCTTT
19661 TTTTT
1 TTTTT
19666 AAATCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
9 17 0.59
10 9 0.31
11 3 0.10
ACGTcount: A:0.05, C:0.09, G:0.02, T:0.84
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:20466 original size:21 final size:19
Alignment explanation
Indices: 20435--20485 Score: 84
Period size: 19 Copynumber: 2.6 Consensus size: 19
20425 CCCTAACCCA
20435 ATTTTTTAAAAATTATATAT
1 ATTTTTTAAAAA-TATATAT
20455 ATTTTTTAAAAATATATAT
1 ATTTTTTAAAAATATATAT
*
20474 ATATTTTAAAAA
1 ATTTTTTAAAAA
20486 AATAGTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTTTTAAAAATATATAT
Found at i:20486 original size:21 final size:21
Alignment explanation
Indices: 20442--20489 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
20432 CCAATTTTTT
**
20442 AAAAAT-TATATATATTTTTT
1 AAAAATATATATATATTTTAA
20462 AAAAATATATATATATTTTAA
1 AAAAATATATATATATTTTAA
20483 AAAAATA
1 AAAAATA
20490 GTTTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAAATATATATATATTTTAA
Found at i:23710 original size:19 final size:19
Alignment explanation
Indices: 23686--23724 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
23676 TTCATTTTCT
23686 AACTCTCAAAACTTCTTCA
1 AACTCTCAAAACTTCTTCA
*
23705 AACTCTCTAAACTTCTTCA
1 AACTCTCAAAACTTCTTCA
23724 A
1 A
23725 GAACATCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (19 bp):
AACTCTCAAAACTTCTTCA
Found at i:23876 original size:33 final size:33
Alignment explanation
Indices: 23832--23991 Score: 214
Period size: 33 Copynumber: 4.8 Consensus size: 33
23822 TAGAAAAAAT
**
23832 TGGCGGTGTCGCCCAACTT-GGGCGGCACCACCA
1 TGGCGGTGTCGCCC-TGTTGGGGCGGCACCACCA
* * * *
23865 TAGCGGTGTCGCCCTGTTGGGCCGGCACCTCCT
1 TGGCGGTGTCGCCCTGTTGGGGCGGCACCACCA
*
23898 TGGCGGTGTCGCCCTGTTGGGGCGGCACCACCT
1 TGGCGGTGTCGCCCTGTTGGGGCGGCACCACCA
*
23931 TGGCGGTGTCACCCTGTTGGGGCGGCACCACCA
1 TGGCGGTGTCGCCCTGTTGGGGCGGCACCACCA
* *
23964 TGACGGCGTCGCCCTGTTGGGGCGGCAC
1 TGGCGGTGTCGCCCTGTTGGGGCGGCAC
23992 TGCCGGAAAG
Statistics
Matches: 112, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
32 2 0.02
33 110 0.98
ACGTcount: A:0.09, C:0.34, G:0.37, T:0.19
Consensus pattern (33 bp):
TGGCGGTGTCGCCCTGTTGGGGCGGCACCACCA
Found at i:24443 original size:39 final size:39
Alignment explanation
Indices: 24389--24472 Score: 159
Period size: 39 Copynumber: 2.2 Consensus size: 39
24379 GCAGTTGCAA
24389 AGGGAGAGAGAGGCTGAGGCTGCTCGGATGTATAGGGAG
1 AGGGAGAGAGAGGCTGAGGCTGCTCGGATGTATAGGGAG
*
24428 AGGGAGAGGGAGGCTGAGGCTGCTCGGATGTATAGGGAG
1 AGGGAGAGAGAGGCTGAGGCTGCTCGGATGTATAGGGAG
24467 AGGGAG
1 AGGGAG
24473 GGTGCTGCTG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.25, C:0.10, G:0.51, T:0.14
Consensus pattern (39 bp):
AGGGAGAGAGAGGCTGAGGCTGCTCGGATGTATAGGGAG
Found at i:24483 original size:33 final size:33
Alignment explanation
Indices: 24389--24484 Score: 93
Period size: 39 Copynumber: 2.7 Consensus size: 33
24379 GCAGTTGCAA
* * **
24389 AGGGAGAGAGAGGCTGAGGCTGCTCGGATGTAT
1 AGGGAGAGGGAGGGTGCTGCTGCTCGGATGTAT
*
24422 AGGGAGAGGGAGAGGGAGGCTGAGGCTGCTCGGATGTAT
1 AGGGAGA-GG-GAGGG-TGCT---GCTGCTCGGATGTAT
24461 AGGGAGAGGGAGGGTGCTGCTGCT
1 AGGGAGAGGGAGGGTGCTGCTGCT
24485 GCTCAGATT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
33 13 0.25
34 1 0.02
35 4 0.08
36 4 0.08
37 5 0.10
38 2 0.04
39 22 0.43
ACGTcount: A:0.22, C:0.11, G:0.50, T:0.17
Consensus pattern (33 bp):
AGGGAGAGGGAGGGTGCTGCTGCTCGGATGTAT
Done.