Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010786.1 Corchorus olitorius cultivar O-4 contig10818, 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: 26721
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:7764 original size:14 final size:14
Alignment explanation
Indices: 7747--7832 Score: 64
Period size: 14 Copynumber: 6.1 Consensus size: 14
7737 GAAATTCAGG
*
7747 TTTTGAAATTTGAT
1 TTTTGAAATTTGAA
* **
7761 TTTTGAGACATGAA
1 TTTTGAAATTTGAA
7775 TTTTGAAATTTGAA
1 TTTTGAAATTTGAA
** *
7789 TTTTGAGTTTTGAG
1 TTTTGAAATTTGAA
* ** *
7803 TTTCGAGTTTTGAG
1 TTTTGAAATTTGAA
*
7817 TTTTGAATTTTGAA
1 TTTTGAAATTTGAA
7831 TT
1 TT
7833 GCCTATTTGG
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 58 1.00
ACGTcount: A:0.26, C:0.02, G:0.20, T:0.52
Consensus pattern (14 bp):
TTTTGAAATTTGAA
Found at i:7781 original size:7 final size:7
Alignment explanation
Indices: 7771--7832 Score: 70
Period size: 7 Copynumber: 8.9 Consensus size: 7
7761 TTTTGAGACA
7771 TGAATTT
1 TGAATTT
*
7778 TGAAATT
1 TGAATTT
7785 TGAATTT
1 TGAATTT
*
7792 TGAGTTT
1 TGAATTT
*
7799 TGAGTTT
1 TGAATTT
* *
7806 CGAGTTT
1 TGAATTT
*
7813 TGAGTTT
1 TGAATTT
7820 TGAATTT
1 TGAATTT
7827 TGAATT
1 TGAATT
7833 GCCTATTTGG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.24, C:0.02, G:0.21, T:0.53
Consensus pattern (7 bp):
TGAATTT
Found at i:8027 original size:33 final size:33
Alignment explanation
Indices: 7985--8062 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
7975 AGAAACTGTG
* * *
7985 AATTTTGAACTTTGAGTTTTGATATGATATGCA
1 AATTTTGAACTTTGAATTTTGAAATGAAATGCA
8018 AATTTTGAACTTTGAATTTTGAAATGAAATGCA
1 AATTTTGAACTTTGAATTTTGAAATGAAATGCA
8051 AATTTTGAACTT
1 AATTTTGAACTT
8063 CTTAATTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (33 bp):
AATTTTGAACTTTGAATTTTGAAATGAAATGCA
Found at i:8254 original size:54 final size:54
Alignment explanation
Indices: 8190--8737 Score: 863
Period size: 54 Copynumber: 10.2 Consensus size: 54
8180 GACCACACTG
* * * ** *
8190 GATCAACTTAGATTTTTGAAAACTTCTATGGAAGACCACACAAGGTCATCTGAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
*
8244 GATCAACTTAGACCTCT-AAAAGCTTCTATGAAAGACCACACTGGGTCATCTTAA
1 GATCAACTTAGATCTCTGAAAA-CTTCTATGAAAGACCACACTGGGTCATCTTAA
8298 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACT-GGTCATCTTAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
*
8351 GATCAACTTAGATCTCTGAAAAACTTCTATGAAAGACCACACT-GGTCAACTTAA
1 GATCAACTTAGATCTCTG-AAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
*
8405 GATCAACTTAGATCTCTGAAAAGTTCTATGAAAGACCACACTGGGTCATCTTAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
*
8459 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTAGGTCATCTTAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
* *
8513 GATAAACTTAGATCTCTAAAAACTTCTATGAAAGACCACACT-GGTCATCTTAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
8566 GATCAACTTAGATCTCTGAAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
1 GATCAACTTAGATCTCTG-AAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
* * * *
8621 GATCGAA-TTAAATCTCTGAAAACTTCTATGAAAGACCACAGTGGATCAACTTAA
1 GATC-AACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
**
8675 GATCAACTTAGAAATCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
8729 GATCAACTT
1 GATCAACTT
8738 TCTAGAGAGA
Statistics
Matches: 459, Mismatches: 27, Indels: 16
0.91 0.05 0.03
Matches are distributed among these distances:
53 85 0.19
54 343 0.75
55 29 0.06
56 2 0.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (54 bp):
GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
Found at i:8561 original size:215 final size:216
Alignment explanation
Indices: 8190--8737 Score: 895
Period size: 215 Copynumber: 2.5 Consensus size: 216
8180 GACCACACTG
* * * ** *
8190 GATCAACTTAGATTTTTGAAAACTTCTATGGAAGACCACACAAGGTCATCTGAAGATCAACTTAG
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAG
* *
8255 ACCTCT-AAAAGCTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGAAA
66 AACTCTGAAAA-CTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTAAAA
8319 ACTTCTATGAAAGACCACACTGGTCATCTTAAGATCAACTTAGATCTCTGAAAAACTTCTATGAA
130 ACTTCTATGAAAGACCACACTGGTCATCTTAAGATCAACTTAGATCTCTGAAAAACTTCTATGAA
8384 AGACCACACT-GGTCAACTTAA
195 AGACCACACTGGGTCAACTTAA
*
8405 GATCAACTTAGATCTCTGAAAAGTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAG
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAG
* * *
8470 ATCTCTGAAAACTTCTATGAAAGACCACACTAGGTCATCTTAAGATAAACTTAGATCTCTAAAAA
66 AACTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTAAAAA
8535 CTTCTATGAAAGACCACACTGGTCATCTTAAGATCAACTTAGATCTCTGAAAAACTTCTATGAAA
131 CTTCTATGAAAGACCACACTGGTCATCTTAAGATCAACTTAGATCTCTGAAAAACTTCTATGAAA
*
8600 GACCACACTGGGTCATCTTAA
196 GACCACACTGGGTCAACTTAA
* * * *
8621 GATCGAA-TTAAATCTCTGAAAACTTCTATGAAAGACCACAGTGGATCAACTTAAGATCAACTTA
1 GATC-AACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTA
*
8685 GAAATCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTT
65 GAACTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTT
8738 TCTAGAGAGA
Statistics
Matches: 309, Mismatches: 21, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
215 188 0.61
216 119 0.39
217 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (216 bp):
GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAG
AACTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTAAAAA
CTTCTATGAAAGACCACACTGGTCATCTTAAGATCAACTTAGATCTCTGAAAAACTTCTATGAAA
GACCACACTGGGTCAACTTAA
Found at i:9398 original size:37 final size:37
Alignment explanation
Indices: 8844--9375 Score: 511
Period size: 37 Copynumber: 14.4 Consensus size: 37
8834 GATTTTAAAG
* * *
8844 AGACACCTAAACAGGTACCTTAAATAAGGATTTAATA
1 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
* * ** * *
8881 AGAAACCTAAACAGGAATTTTGAACAA-GATTTTGATG
1 AGACACCTAAACAGGGACCTTAAACAAGGA-TTTGATA
* *
8918 AGACACCTAAACATGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
* * * **
8955 AGAAAACTAAACAGGGATCTTAAACAAAAATTTTGACT-
1 AGACACCTAAACAGGGACCTTAAACAAGGA-TTTGA-TA
* * * *
8993 AGAAACCTAAACAGGCACCTTAAATAAGGATTCGATA
1 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
* * * *
9030 AGAAACCTAAACAAGGATCTTAAACAA-GATTTTGATG
1 AGACACCTAAACAGGGACCTTAAACAAGGA-TTTGATA
* * * *
9067 AGACACCTAAATAGGGACCTTAAATAAAGATTTAATA
1 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
* * * * *
9104 AGAAACCTAAACAGGAAACTTGAACAA-GATTTTGATG
1 AGACACCTAAACAGGGACCTTAAACAAGGA-TTTGATA
* * * * * *
9141 GGACACCTAAATAGGGATCTTGAACCA-GATTTTGATG
1 AGACACCTAAACAGGGACCTTAAACAAGGA-TTTGATA
* *
9178 AGGCACCTAAACAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
* *
9215 AGACACCTAAACAGGGACCTTAAATAAGGATTTAATA
1 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
9252 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
* * * *
9289 AGACACCTAAACACGAATCTTGAACAA-GATTTTGATGA
1 AGACACCTAAACAGGGACCTTAAACAAGGA-TTTGAT-A
*
9327 A-ACACCTAAACAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
9363 AGACACCTAAACA
1 AGACACCTAAACA
9376 AAAATCTTGA
Statistics
Matches: 404, Mismatches: 78, Indels: 26
0.80 0.15 0.05
Matches are distributed among these distances:
36 11 0.03
37 353 0.87
38 39 0.10
39 1 0.00
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (37 bp):
AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
Found at i:10010 original size:20 final size:21
Alignment explanation
Indices: 9977--10015 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
9967 AGTGAAATAC
*
9977 ATATATATTCAAGGAAAGAGT
1 ATATATAATCAAGGAAAGAGT
9998 ATATATAAT-AAGGAAAGA
1 ATATATAATCAAGGAAAGA
10016 TCAAGTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.54, C:0.03, G:0.18, T:0.26
Consensus pattern (21 bp):
ATATATAATCAAGGAAAGAGT
Found at i:10434 original size:28 final size:28
Alignment explanation
Indices: 10403--10472 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 28
10393 TTCCTTTTGA
*
10403 TTTTTTTTTCTTTCTTTCTTT--TTTTTC
1 TTTTTTTTTCTTT-TTTCTTTGCTTTCTC
10430 TTTTTTTTTCACTTTTTTCTTTGCTTTCTC
1 TTTTTTTTT--CTTTTTTCTTTGCTTTCTC
10460 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
10473 AGATTGCTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
27 9 0.24
28 11 0.29
29 4 0.11
30 14 0.37
ACGTcount: A:0.01, C:0.16, G:0.01, T:0.81
Consensus pattern (28 bp):
TTTTTTTTTCTTTTTTCTTTGCTTTCTC
Found at i:11134 original size:14 final size:14
Alignment explanation
Indices: 11117--11164 Score: 73
Period size: 14 Copynumber: 3.5 Consensus size: 14
11107 AAACTTAATT
11117 TTGAAAATCATTTC
1 TTGAAAATCATTTC
11131 TTGAAAA-CAGTTTC
1 TTGAAAATCA-TTTC
11145 TTGAAAATCATTT-
1 TTGAAAATCATTTC
11158 TTGAAAA
1 TTGAAAA
11165 ACGTCATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.28
14 21 0.66
15 2 0.06
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (14 bp):
TTGAAAATCATTTC
Found at i:11135 original size:28 final size:26
Alignment explanation
Indices: 11100--11164 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 26
11090 ACTCAAAACC
*
11100 TTTTTGAAAAC-TTAATTTTGAAAATCA
1 TTTTTGAAAACATT--TCTTGAAAATCA
11127 TTTCTTGAAAACAGTTTCTTGAAAATCA
1 TTT-TTGAAAACA-TTTCTTGAAAATCA
11155 TTTTTGAAAA
1 TTTTTGAAAA
11165 ACGTCATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
27 10 0.29
28 22 0.65
30 2 0.06
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.43
Consensus pattern (26 bp):
TTTTTGAAAACATTTCTTGAAAATCA
Found at i:11165 original size:14 final size:13
Alignment explanation
Indices: 11100--11164 Score: 69
Period size: 14 Copynumber: 4.8 Consensus size: 13
11090 ACTCAAAACC
*
11100 TTTTTGAAAACTTA
1 TTTTTGAAAA-TCA
*
11114 ATTTTGAAAATCA
1 TTTTTGAAAATCA
11127 TTTCTTGAAAA-CA
1 TTT-TTGAAAATCA
11140 GTTTCTTGAAAATCA
1 -TTT-TTGAAAATCA
11155 TTTTTGAAAA
1 TTTTTGAAAA
11165 ACGTCATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
13 13 0.29
14 30 0.67
15 2 0.04
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.43
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:19439 original size:34 final size:34
Alignment explanation
Indices: 19387--19545 Score: 261
Period size: 34 Copynumber: 4.8 Consensus size: 34
19377 CGTCTCCCAG
*
19387 TTATTACAACCCACTGGGCAGGGTCTTCCAGTTA
1 TTATCACAACCCACTGGGCAGGGTCTTCCAGTTA
* *
19421 TTATCTCAACCCATTGGGCAGGGTCTTCCAGTTA
1 TTATCACAACCCACTGGGCAGGGTCTTCCAGTTA
*
19455 TTATCACAACCCACTGGGCATGGTCTTCCAGTTA
1 TTATCACAACCCACTGGGCAGGGTCTTCCAGTTA
19489 TTATCACAACCCACTGGGCAGGGTCTTCCAGTTA
1 TTATCACAACCCACTGGGCAGGGTCTTCCAGTTA
19523 TTAT---AACCCACTGGGCAGGGTCT
1 TTATCACAACCCACTGGGCAGGGTCT
19546 ATAAAACATG
Statistics
Matches: 118, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
31 19 0.16
34 99 0.84
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.29
Consensus pattern (34 bp):
TTATCACAACCCACTGGGCAGGGTCTTCCAGTTA
Found at i:24661 original size:60 final size:59
Alignment explanation
Indices: 24549--24664 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 59
24539 ATTAATCAAA
*
24549 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAACGACGTTTTCGGACCGAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAACGACGTTTTAGGACCGAGACT
* * *
24608 TATCGAGTGACATGTTTTTTTAATTAGATGCCT-AAAAAACGACGTTTTAGGACCGAG
1 TATCAAGTGACATG-TTCTTT-ATTAGATGCATAAAAAAACGACGTTTTAGGACCGAG
24665 GCATGATGCT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 13 0.25
60 28 0.55
61 10 0.20
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (59 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAACGACGTTTTAGGACCGAGACT
Found at i:25986 original size:36 final size:36
Alignment explanation
Indices: 25939--26008 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
25929 TTCAATAACC
* *
25939 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
25975 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
26009 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Done.