Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016235.1 Corchorus olitorius cultivar O-4 contig16268, 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: 28080
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:249 original size:14 final size:13
Alignment explanation
Indices: 230--268 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
220 AAATTGTAAA
230 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
243 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
257 ATTTAAAAAATT
1 ATTTAAAAAATT
269 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:497 original size:123 final size:127
Alignment explanation
Indices: 254--508 Score: 419
Period size: 131 Copynumber: 2.0 Consensus size: 127
244 ATTTAAGAAA
254 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---A
* *
319 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 TA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAAAA
384 G
127 G
385 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAG
*
448 TA-AA-GATATTTGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAAAAG
66 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAAAAG
508 T
1 T
509 TTAAATAATG
Statistics
Matches: 121, Mismatches: 3, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
123 54 0.45
124 2 0.02
125 2 0.02
127 2 0.02
131 61 0.50
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAAAAG
Found at i:534 original size:123 final size:127
Alignment explanation
Indices: 260--516 Score: 360
Period size: 123 Copynumber: 2.0 Consensus size: 127
250 GAAATATATT
* *
260 TAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTA
1 TAAAAAATTCTAAGAAATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---ATA-GTA
* * *
325 TAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAGTATAT
62 TAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAAAAGTATAA
*
390 T
127 A
* *
391 TAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-TA-AA-
1 TAAAAAATTCTAAGAAATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTATAAG
* *
452 GATATTTGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAAAAGTTTAAA
66 GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAAAAGTATAAA
514 TAA
1 TAA
517 TGGCATTTAA
Statistics
Matches: 120, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
123 59 0.49
124 2 0.02
125 2 0.02
127 2 0.02
131 55 0.46
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.37
Consensus pattern (127 bp):
TAAAAAATTCTAAGAAATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTATAAG
GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAAAAGTATAAA
Found at i:940 original size:48 final size:48
Alignment explanation
Indices: 869--964 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
859 GTGTCCCGGT
**
869 CCTACACAAAAATAAATGTAATTATTATATAAAGTTAAAAGTAAAAGA
1 CCTACACAAAAATAAATGTAATTATTATATAAAACTAAAAGTAAAAGA
* *
917 CCTACACAAAAATAGATGTAATTATTATATAAAACTAAAATTAAAAGA
1 CCTACACAAAAATAAATGTAATTATTATATAAAACTAAAAGTAAAAGA
965 AAAGTACATA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.27
Consensus pattern (48 bp):
CCTACACAAAAATAAATGTAATTATTATATAAAACTAAAAGTAAAAGA
Found at i:1353 original size:36 final size:36
Alignment explanation
Indices: 1313--1386 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
1303 CACATGGTAG
1313 ATCATAATTGAAGTCTCAAGGTGCTAGCTATCTTCA
1 ATCATAATTGAAGTCTCAAGGTGCTAGCTATCTTCA
*
1349 ATCATAATTGAAGTCTCGAGGTGCTAGCTATCTTCA
1 ATCATAATTGAAGTCTCAAGGTGCTAGCTATCTTCA
1385 AT
1 AT
1387 TAAAGTTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (36 bp):
ATCATAATTGAAGTCTCAAGGTGCTAGCTATCTTCA
Found at i:4011 original size:46 final size:47
Alignment explanation
Indices: 3953--4046 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 47
3943 ATTTAACAAA
*
3953 TAAGAGTATAATGGGTGATTCAAAAGTTTTACAGGTGAACGTA-TTT
1 TAAGAGTATAATGGGTAATTCAAAAGTTTTACAGGTGAACGTACTTT
*
3999 TAAGGGTATAATGGGTAATTCAAAAGTTTTACAGGTGAACGTACTTT
1 TAAGAGTATAATGGGTAATTCAAAAGTTTTACAGGTGAACGTACTTT
4046 T
1 T
4047 TAATATAGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 41 0.91
47 4 0.09
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.35
Consensus pattern (47 bp):
TAAGAGTATAATGGGTAATTCAAAAGTTTTACAGGTGAACGTACTTT
Found at i:6011 original size:10 final size:10
Alignment explanation
Indices: 5995--6028 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
5985 ATACCTCGAT
5995 ATATCCGTAA
1 ATATCCGTAA
*
6005 GTATCCGTAA
1 ATATCCGTAA
6015 ATATCCGTAA
1 ATATCCGTAA
6025 ATAT
1 ATAT
6029 TCATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:7037 original size:12 final size:13
Alignment explanation
Indices: 7020--7055 Score: 65
Period size: 12 Copynumber: 2.8 Consensus size: 13
7010 CATCGATACC
7020 TCGATATATCCG-
1 TCGATATATCCGT
7032 TCGATATATCCGT
1 TCGATATATCCGT
7045 TCGATATATCC
1 TCGATATATCC
7056 ATGGATACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (13 bp):
TCGATATATCCGT
Found at i:7062 original size:12 final size:12
Alignment explanation
Indices: 7020--7062 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
7010 CATCGATACC
*
7020 TCGATATATCCG
1 TCGATATATCCA
*
7032 TCGATATATCCGT
1 TCGATATATCC-A
7045 TCGATATATCCA
1 TCGATATATCCA
*
7057 TGGATA
1 TCGATA
7063 CCTGATGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (12 bp):
TCGATATATCCA
Found at i:8925 original size:30 final size:29
Alignment explanation
Indices: 8827--8926 Score: 76
Period size: 30 Copynumber: 3.3 Consensus size: 29
8817 GCTAAATGCT
* * * *
8827 TAATTAAGGGCAAAATGTTTCTGACTCGGCC
1 TAATT-AGGGCAAAACGTTTC-AATTCGGTC
* * *
8858 TAATTTGGGGCACAACGTTTCAATTTGGTC
1 TAA-TTAGGGCAAAACGTTTCAATTCGGTC
*
8888 TATTTAGGGCAAAACGTTTTCAATTCGCGTC
1 TAATTAGGGCAAAACG-TTTCAATTCG-GTC
8919 -AATTAGGG
1 TAATTAGGG
8927 GTAGACCGTC
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
29 11 0.20
30 23 0.43
31 18 0.33
32 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (29 bp):
TAATTAGGGCAAAACGTTTCAATTCGGTC
Found at i:10728 original size:19 final size:20
Alignment explanation
Indices: 10700--10740 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
10690 TTGAAGAGTG
*
10700 TTTGTGATTTT-TATTTAAT
1 TTTGTAATTTTATATTTAAT
*
10719 TTTGTAATTTTATTTTTAAT
1 TTTGTAATTTTATATTTAAT
10739 TT
1 TT
10741 CAAAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (20 bp):
TTTGTAATTTTATATTTAAT
Found at i:13238 original size:6 final size:6
Alignment explanation
Indices: 13229--13271 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
13219 ATTTTCGTTT
*
13229 TTTTTG TTTTTTG TTTTTG -TTTTA TTTTTG -TTTTG TTTTTG TT
1 TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TT
13272 GCGCTGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 9 0.28
6 17 0.53
7 6 0.19
ACGTcount: A:0.02, C:0.00, G:0.14, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:13251 original size:11 final size:11
Alignment explanation
Indices: 13237--13271 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
13227 TTTTTTTGTT
13237 TTTTGTTTTTG
1 TTTTGTTTTTG
*
13248 TTTTATTTTTG
1 TTTTGTTTTTG
13259 TTTTGTTTTTG
1 TTTTGTTTTTG
13270 TT
1 TT
13272 GCGCTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.03, C:0.00, G:0.14, T:0.83
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:13268 original size:22 final size:22
Alignment explanation
Indices: 13220--13271 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
13210 TTTGGCATAA
* *
13220 TTTTCGTTTTTTTTGTTTTTTG
1 TTTTTGTTTTTTTTGTGTTTTG
13242 TTTTTGTTTTATTTT-TGTTTTG
1 TTTTTGTTTT-TTTTGTGTTTTG
13264 TTTTTGTT
1 TTTTTGTT
13272 GCGCTGTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.83
Consensus pattern (22 bp):
TTTTTGTTTTTTTTGTGTTTTG
Found at i:14492 original size:21 final size:21
Alignment explanation
Indices: 14468--14534 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
14458 AATTATCTGT
14468 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
14489 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
14510 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
14531 AAAT
1 AAAT
14535 CCTGATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:14514 original size:42 final size:42
Alignment explanation
Indices: 14455--14535 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
14445 GCTAACTCTT
14455 GAAAATTATCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTATCTGTAAATTAAGAAATACTCAACTCAAATCATA
* *
14497 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTATCTGTAAATTAAGAAATACTCAACTCAAATC
14536 CTGATCCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTATCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:14695 original size:56 final size:57
Alignment explanation
Indices: 14601--14715 Score: 178
Period size: 56 Copynumber: 2.0 Consensus size: 57
14591 TTTATTTTAT
*
14601 AGAATAATTAAGTATAGATAGGAGGGATAACATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGAGGGATAACATTTATTATAACATTTATTGTGTGAA
* ** *
14658 AGAATAATTAAGTAGAGAT-GGGGGGATAGGATTTATTATAATATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGAGGGATAACATTTATTATAACATTTATTGTGTGAA
14714 AG
1 AG
14716 GAAACGAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
56 35 0.66
57 18 0.34
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (57 bp):
AGAATAATTAAGTAGAGATAGGAGGGATAACATTTATTATAACATTTATTGTGTGAA
Found at i:16866 original size:7 final size:7
Alignment explanation
Indices: 16854--16886 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
16844 GGTTTAGCGG
16854 TTTTTT-
1 TTTTTTC
16860 TTTTTT-
1 TTTTTTC
16866 TTTTTTC
1 TTTTTTC
16873 TTTTTTC
1 TTTTTTC
16880 TTTTTTC
1 TTTTTTC
16887 AAGAGACGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (7 bp):
TTTTTTC
Done.