Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009493.1 Corchorus capsularis cultivar CVL-1 contig09514, 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: 71581
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6957 original size:26 final size:26
Alignment explanation
Indices: 6921--6973 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
6911 ACTTTTTTTT
*
6921 TTTTTTTTTTGAAG-TAAGGAAAAAGA
1 TTTTCTTTTTG-AGTTAAGGAAAAAGA
*
6947 TTTTCTTTTTGAGTTCAGGAAAAAGA
1 TTTTCTTTTTGAGTTAAGGAAAAAGA
6973 T
1 T
6974 ATATTCTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.34, C:0.04, G:0.19, T:0.43
Consensus pattern (26 bp):
TTTTCTTTTTGAGTTAAGGAAAAAGA
Found at i:12538 original size:18 final size:18
Alignment explanation
Indices: 12511--12552 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
12501 GGCCGCATTT
*
12511 TCCAACTCCTCCTATTCC
1 TCCAAATCCTCCTATTCC
*
12529 TCCAAATCCTCCTATTCG
1 TCCAAATCCTCCTATTCC
12547 TCCAAA
1 TCCAAA
12553 ATCCATAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.43, G:0.02, T:0.31
Consensus pattern (18 bp):
TCCAAATCCTCCTATTCC
Found at i:13280 original size:18 final size:18
Alignment explanation
Indices: 13257--13305 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
13247 CTTTTTGTAC
*
13257 TTTTTATGTGGTTTTTTT
1 TTTTTATGTGGTTTTTTA
**
13275 TTTTTAAT-TTATTTTTTA
1 TTTTT-ATGTGGTTTTTTA
13293 TTTTTATGTGGTT
1 TTTTTATGTGGTT
13306 CAAACTGATT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (18 bp):
TTTTTATGTGGTTTTTTA
Found at i:14967 original size:22 final size:22
Alignment explanation
Indices: 14939--14985 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
14929 ATTGCAAGGA
14939 GATGAACATGTAGTACATATTT
1 GATGAACATGTAGTACATATTT
14961 GATGAACATGTAGTACATATTT
1 GATGAACATGTAGTACATATTT
14983 GAT
1 GAT
14986 AATGATGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (22 bp):
GATGAACATGTAGTACATATTT
Found at i:17025 original size:7 final size:7
Alignment explanation
Indices: 17013--17047 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
17003 TGGCTTTGTA
17013 AATGGTG
1 AATGGTG
17020 AATGGTG
1 AATGGTG
17027 AATGGTG
1 AATGGTG
17034 AATGGTG
1 AATGGTG
17041 AATGGTG
1 AATGGTG
17048 GGTGGAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.43, T:0.29
Consensus pattern (7 bp):
AATGGTG
Found at i:17525 original size:11 final size:11
Alignment explanation
Indices: 17509--17533 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17499 TCATAGTGGC
17509 AGACAAGCACA
1 AGACAAGCACA
17520 AGACAAGCACA
1 AGACAAGCACA
17531 AGA
1 AGA
17534 ACATCGTCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.24, G:0.20, T:0.00
Consensus pattern (11 bp):
AGACAAGCACA
Found at i:24159 original size:13 final size:13
Alignment explanation
Indices: 24141--24165 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24131 GGAAGTAATT
24141 TATACTAATTATC
1 TATACTAATTATC
24154 TATACTAATTAT
1 TATACTAATTAT
24166 AATGTGAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
TATACTAATTATC
Found at i:31429 original size:7 final size:7
Alignment explanation
Indices: 31417--31450 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
31407 AAATGTATGT
31417 ATGTATC
1 ATGTATC
31424 ATGTATC
1 ATGTATC
31431 ATGTATC
1 ATGTATC
31438 ATGTATC
1 ATGTATC
31445 ATGTAT
1 ATGTAT
31451 GTATGTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (7 bp):
ATGTATC
Found at i:31685 original size:7 final size:7
Alignment explanation
Indices: 31673--31698 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31663 AACCTAATAC
31673 TAGCAAT
1 TAGCAAT
31680 TAGCAAT
1 TAGCAAT
31687 TAGCAAT
1 TAGCAAT
31694 TAGCA
1 TAGCA
31699 TGCATGGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (7 bp):
TAGCAAT
Found at i:38034 original size:6 final size:6
Alignment explanation
Indices: 38019--38052 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
38009 TTCTCTTATT
*
38019 GATTGG GATTGA GATTGA GATTGA GATTGA GATT
1 GATTGA GATTGA GATTGA GATTGA GATTGA GATT
38053 AAACAAATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (6 bp):
GATTGA
Found at i:47312 original size:2 final size:2
Alignment explanation
Indices: 47305--47329 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47295 ATAACACTAC
47305 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
47330 GCTAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51292 original size:48 final size:48
Alignment explanation
Indices: 51226--51353 Score: 177
Period size: 48 Copynumber: 2.7 Consensus size: 48
51216 AATCCTGATC
* * **
51226 ATCACTAATATATATAGGATCCTTCAGAGTCGCTGAAGTAGAATCCTG
1 ATCACTAATATATGTAGGATCCTTCAGAGTAGCTGAAGTAGAATCCCA
*
51274 ATCACTAATATATGTAGGATCCTT-AGAAGTAGCTGGAGTAGAATCCCA
1 ATCACTAATATATGTAGGATCCTTCAG-AGTAGCTGAAGTAGAATCCCA
* *
51322 ATCACTAATGTATGTAGGATCCATCAGAGTAG
1 ATCACTAATATATGTAGGATCCTTCAGAGTAG
51354 ATGGAGTTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
47 2 0.03
48 67 0.94
49 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (48 bp):
ATCACTAATATATGTAGGATCCTTCAGAGTAGCTGAAGTAGAATCCCA
Found at i:52914 original size:28 final size:28
Alignment explanation
Indices: 52873--52929 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
52863 GGTGAGTCTC
*
52873 CCAACAGGGGCAGCTACGTACGCAAGGT
1 CCAACAGGGACAGCTACGTACGCAAGGT
*
52901 CCAACAGGGACAGCTACGTACGTAAGGT
1 CCAACAGGGACAGCTACGTACGCAAGGT
52929 C
1 C
52930 TCGAACCCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.30, C:0.28, G:0.30, T:0.12
Consensus pattern (28 bp):
CCAACAGGGACAGCTACGTACGCAAGGT
Found at i:55881 original size:2 final size:2
Alignment explanation
Indices: 55874--55899 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55864 AAATTGCCAG
55874 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
55900 CTTATTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62260 original size:2 final size:2
Alignment explanation
Indices: 62249--62282 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
62239 ATAGTATTAT
62249 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62283 TGTAGGAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.