Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024590.1 Corchorus olitorius cultivar O-4 contig24623, 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: 30062
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Found at i:5061 original size:171 final size:171
Alignment explanation
Indices: 4776--5118 Score: 677
Period size: 171 Copynumber: 2.0 Consensus size: 171
4766 GGTTTGGAAG
4776 TATTCGGTCAGTGTGTATTTTGTGGAATTAATTGGGGTCAATCTGCTGCAGAGTTGGAAACTTTG
1 TATTCGGTCAGTGTGTATTTTGTGGAATTAATTGGGGTCAATCTGCTGCAGAGTTGGAAACTTTG
4841 CTGAATCTGAAATTGGACTTTGTTTTAGCTTCGATTATTGGAATCTGCATAATTTCTGGGAATTG
66 CTGAATCTGAAATTGGACTTTGTTTTAGCTTCGATTATTGGAATCTGCATAATTTCTGGGAATTG
4906 CTTCTGATTTATATATTTGGCTTATTAACAGGATGTTGAAA
131 CTTCTGATTTATATATTTGGCTTATTAACAGGATGTTGAAA
4947 TATTCGGTCAGTGTGTATTTTGTGGAATTAATTGGGGTCAATCTGCTGCAGAGTTGGAAACTTTG
1 TATTCGGTCAGTGTGTATTTTGTGGAATTAATTGGGGTCAATCTGCTGCAGAGTTGGAAACTTTG
*
5012 CTGAATCTGAAATTGGACTTTGTTTTAGCTTCGATTATTGTAATCTGCATAATTTCTGGGAATTG
66 CTGAATCTGAAATTGGACTTTGTTTTAGCTTCGATTATTGGAATCTGCATAATTTCTGGGAATTG
5077 CTTCTGATTTATATATTTGGCTTATTAACAGGATGTTGAAA
131 CTTCTGATTTATATATTTGGCTTATTAACAGGATGTTGAAA
5118 T
1 T
5119 TCAAGAAATC
Statistics
Matches: 171, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 171 1.00
ACGTcount: A:0.24, C:0.11, G:0.23, T:0.41
Consensus pattern (171 bp):
TATTCGGTCAGTGTGTATTTTGTGGAATTAATTGGGGTCAATCTGCTGCAGAGTTGGAAACTTTG
CTGAATCTGAAATTGGACTTTGTTTTAGCTTCGATTATTGGAATCTGCATAATTTCTGGGAATTG
CTTCTGATTTATATATTTGGCTTATTAACAGGATGTTGAAA
Found at i:14010 original size:27 final size:27
Alignment explanation
Indices: 13941--14013 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
13931 TCCGACATTT
13941 AAGGGCAAAACTA-TAATTTAGTCAACC
1 AAGGGCAAAA-TAGTAATTTAGTCAACC
* *
13968 AAGGGTAAAATGGTAATTTAGTCAACC
1 AAGGGCAAAATAGTAATTTAGTCAACC
13995 AAGGGC-AAATAAGTAATTT
1 AAGGGCAAAAT-AGTAATTT
14014 TAACATCTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
26 5 0.12
27 35 0.88
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (27 bp):
AAGGGCAAAATAGTAATTTAGTCAACC
Found at i:16141 original size:20 final size:21
Alignment explanation
Indices: 16113--16167 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
16103 CTTGGTTTTG
*
16113 AGTCATTTG-CTCTTTAAGTA
1 AGTCATTTGACTCCTTAAGTA
*
16133 AGTCGTTTGACTCCTTAAGT-
1 AGTCATTTGACTCCTTAAGTA
*
16153 TGATCATTTGACTCC
1 AG-TCATTTGACTCC
16168 CTTATTCGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 9 0.31
21 20 0.69
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (21 bp):
AGTCATTTGACTCCTTAAGTA
Found at i:21691 original size:47 final size:47
Alignment explanation
Indices: 21637--21750 Score: 201
Period size: 47 Copynumber: 2.4 Consensus size: 47
21627 CTACCAAATC
21637 TTTAAGACTTGATGGCTAATTGATTAGTTAGGAGGAGAAAGGGGTAA
1 TTTAAGACTTGATGGCTAATTGATTAGTTAGGAGGAGAAAGGGGTAA
*
21684 TTTAAGACTTGATGGCTAATTGATTAGTTAGGAGGATAAAGGGGTAA
1 TTTAAGACTTGATGGCTAATTGATTAGTTAGGAGGAGAAAGGGGTAA
* *
21731 TTTAAGGCTTGACGGCTAAT
1 TTTAAGACTTGATGGCTAAT
21751 CTTATCTAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 64 1.00
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (47 bp):
TTTAAGACTTGATGGCTAATTGATTAGTTAGGAGGAGAAAGGGGTAA
Found at i:22410 original size:26 final size:26
Alignment explanation
Indices: 22381--22448 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 26
22371 TTTGTTTTGT
**
22381 GTCAAAGAAAAAAAAAGAGTTTCTGC
1 GTCAAAGAAAAAAAAAGAGTCCCTGC
* **
22407 GTCATA-AAAAAAAAATTGTCCCTGC
1 GTCAAAGAAAAAAAAAGAGTCCCTGC
*
22432 ATCGAAAGAAAAAAAAA
1 GTC-AAAGAAAAAAAAA
22449 TATTTTTTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
25 17 0.52
26 7 0.21
27 9 0.27
ACGTcount: A:0.54, C:0.13, G:0.15, T:0.18
Consensus pattern (26 bp):
GTCAAAGAAAAAAAAAGAGTCCCTGC
Found at i:24304 original size:16 final size:16
Alignment explanation
Indices: 24271--24390 Score: 134
Period size: 16 Copynumber: 7.6 Consensus size: 16
24261 TGGGCGGGTA
*
24271 CGGGTTCGGG-TATTT
1 CGGGTTCGGGTTTTTT
24286 CGGGTTCGGGTTTTTT
1 CGGGTTCGGGTTTTTT
*
24302 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTTTTTT
* ***
24318 CGGGCTCGGGTTAAGT
1 CGGGTTCGGGTTTTTT
*
24334 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTTTTTT
* * *
24350 CGGGCTCGGGTTATGT
1 CGGGTTCGGGTTTTTT
*
24366 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTTTTTT
24382 CGGGTTCGG
1 CGGGTTCGG
24391 TCTCGGGTAG
Statistics
Matches: 84, Mismatches: 20, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
15 10 0.12
16 74 0.88
ACGTcount: A:0.06, C:0.15, G:0.41, T:0.38
Consensus pattern (16 bp):
CGGGTTCGGGTTTTTT
Found at i:24327 original size:32 final size:32
Alignment explanation
Indices: 24271--24390 Score: 188
Period size: 32 Copynumber: 3.8 Consensus size: 32
24261 TGGGCGGGTA
* * *
24271 CGGGTTCGGGTA-TTTCGGGTTCGGGTTTTTT
1 CGGGTTCGGGTATTTTCGGGCTCGGGTTATGT
*
24302 CGGGTTCGGGTATTTTCGGGCTCGGGTTAAGT
1 CGGGTTCGGGTATTTTCGGGCTCGGGTTATGT
24334 CGGGTTCGGGTATTTTCGGGCTCGGGTTATGT
1 CGGGTTCGGGTATTTTCGGGCTCGGGTTATGT
*
24366 CGGGTTCGGGTATTTTCGGGTTCGG
1 CGGGTTCGGGTATTTTCGGGCTCGG
24391 TCTCGGGTAG
Statistics
Matches: 82, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
31 12 0.15
32 70 0.85
ACGTcount: A:0.06, C:0.15, G:0.41, T:0.38
Consensus pattern (32 bp):
CGGGTTCGGGTATTTTCGGGCTCGGGTTATGT
Found at i:24870 original size:31 final size:31
Alignment explanation
Indices: 24835--24906 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
24825 TAAATTATTG
*
24835 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
24866 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
24897 CAAATTAAAA
1 CAAATTAAAA
24907 GCTGATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:25138 original size:2 final size:2
Alignment explanation
Indices: 25133--25171 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
25123 TTATATAAGT
*
25133 TA TA TA TA TA TA TA CA 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 TA TA T
25172 TTAGTAGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:25379 original size:23 final size:23
Alignment explanation
Indices: 25347--25409 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
25337 TCAAATTATT
25347 TCGGGTTCGGGTTCGGGCTCGGG
1 TCGGGTTCGGGTTCGGGCTCGGG
* *
25370 TCGGGATCGGGTTCGGTCTCGGG
1 TCGGGTTCGGGTTCGGGCTCGGG
*
25393 TCGGGTTCGGGCTCGGG
1 TCGGGTTCGGGTTCGGG
25410 TAATTTCGGG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.02, C:0.22, G:0.51, T:0.25
Consensus pattern (23 bp):
TCGGGTTCGGGTTCGGGCTCGGG
Found at i:25410 original size:17 final size:18
Alignment explanation
Indices: 25346--25409 Score: 78
Period size: 17 Copynumber: 3.7 Consensus size: 18
25336 TTCAAATTAT
* *
25346 TTCGGGTTCGGGTTCGGG
1 TTCGGGCTCGGGATCGGG
*
25364 CTCGGG-TCGGGATCGGG
1 TTCGGGCTCGGGATCGGG
*
25381 TTCGGTCTCGGG-TCGGG
1 TTCGGGCTCGGGATCGGG
25398 TTCGGGCTCGGG
1 TTCGGGCTCGGG
25410 TAATTTCGGG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
17 30 0.75
18 10 0.25
ACGTcount: A:0.02, C:0.22, G:0.50, T:0.27
Consensus pattern (18 bp):
TTCGGGCTCGGGATCGGG
Found at i:25425 original size:6 final size:6
Alignment explanation
Indices: 25346--25410 Score: 73
Period size: 6 Copynumber: 11.2 Consensus size: 6
25336 TTCAAATTAT
* *
25346 TTCGGG TTCGGG TTCGGG CTCGGG -TCGGG ATCGGG TTC-GG TCTCGGG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG T-TCGGG
*
25393 -TCGGG TTCGGG CTCGGG T
1 TTCGGG TTCGGG TTCGGG T
25411 AATTTCGGGT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
5 13 0.25
6 36 0.71
7 2 0.04
ACGTcount: A:0.02, C:0.22, G:0.49, T:0.28
Consensus pattern (6 bp):
TTCGGG
Found at i:26924 original size:21 final size:21
Alignment explanation
Indices: 26898--26947 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
26888 CGGCCATTCA
*
26898 CCGTGCCACCACCGGTAAAGC
1 CCGTGCCACCACCGGCAAAGC
* *
26919 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCAAAGC
26940 CCGTGCCA
1 CCGTGCCA
26948 TTACCATTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.18, C:0.48, G:0.24, T:0.10
Consensus pattern (21 bp):
CCGTGCCACCACCGGCAAAGC
Found at i:27371 original size:15 final size:14
Alignment explanation
Indices: 27351--27380 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
27341 ATCTTTTTAA
27351 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
27366 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
27380 T
1 T
27381 GCTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Done.