Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019114.1 Corchorus olitorius cultivar O-4 contig19147, 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: 10215
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:5459 original size:18 final size:18
Alignment explanation
Indices: 5436--5476 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5426 ATTTTCTGCA
*
5436 TGTTTGA-CCTCTTGGTCT
1 TGTTTGACCCT-TTGGTCC
5454 TGTTTGACCCTTTGGTCC
1 TGTTTGACCCTTTGGTCC
5472 TGTTT
1 TGTTT
5477 TCTGCATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (18 bp):
TGTTTGACCCTTTGGTCC
Found at i:5466 original size:47 final size:46
Alignment explanation
Indices: 5409--5599 Score: 222
Period size: 47 Copynumber: 4.1 Consensus size: 46
5399 AGTTTGCTCC
* * *
5409 GTTTGACCTTTCGTTCTATTTTCTGCATGTTTGACCTCTTGGTCTT
1 GTTTGACCTTTCGTCCTGTTTTCTGCATGTTTGACCTCTTGGTCCT
* *
5455 GTTTGACCCTTTGGTCCTGTTTTCTGCATGTTCGACCTCTTGGTCCT
1 GTTTGA-CCTTTCGTCCTGTTTTCTGCATGTTTGACCTCTTGGTCCT
* * *
5502 GTTTGACCTTTCGGTCCTGTTTTATGCCTGTTTTGACCCCTTGGTCCT
1 GTTTGACCTTTC-GTCCTGTTTTCTGCATG-TTTGACCTCTTGGTCCT
* * * * *
5550 GTTTGACCTTTTGGTCTTGTTTTCCGCCTGATTGACCT-TTGGTCCT
1 GTTTGACC-TTTCGTCCTGTTTTCTGCATGTTTGACCTCTTGGTCCT
5596 GTTT
1 GTTT
5600 TTTAGCCCTT
Statistics
Matches: 125, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
46 23 0.18
47 62 0.50
48 37 0.30
49 3 0.02
ACGTcount: A:0.07, C:0.25, G:0.20, T:0.48
Consensus pattern (46 bp):
GTTTGACCTTTCGTCCTGTTTTCTGCATGTTTGACCTCTTGGTCCT
Found at i:5509 original size:18 final size:17
Alignment explanation
Indices: 5483--5523 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
5473 GTTTTCTGCA
*
5483 TGTTCGACCTCTTGGTCC
1 TGTTTGACCT-TTGGTCC
5501 TGTTTGACCTTTCGGTCC
1 TGTTTGACCTTT-GGTCC
5519 TGTTT
1 TGTTT
5524 TATGCCTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.05, C:0.27, G:0.22, T:0.46
Consensus pattern (17 bp):
TGTTTGACCTTTGGTCC
Found at i:5552 original size:19 final size:19
Alignment explanation
Indices: 5528--5572 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
5518 CTGTTTTATG
5528 CCTGTTTTGACCCCTTGGT
1 CCTGTTTTGACCCCTTGGT
**
5547 CCTG-TTTGACCTTTTGGT
1 CCTGTTTTGACCCCTTGGT
*
5565 CTTGTTTT
1 CCTGTTTT
5573 CCGCCTGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.04, C:0.24, G:0.20, T:0.51
Consensus pattern (19 bp):
CCTGTTTTGACCCCTTGGT
Found at i:5571 original size:95 final size:92
Alignment explanation
Indices: 5401--5599 Score: 249
Period size: 95 Copynumber: 2.1 Consensus size: 92
5391 GATGAAGAAG
* * * * *
5401 TTTGCTCC-GTTTGACCTTTCGTTCTATTTTCTGCATGTTTGACCTCTTGGTCTTGTTTGACCCT
1 TTTGGTCCTGTTTGACCTTTCGTCCTATTTTATGCATGTTTGACCCCTTGGTCCTGTTTGACCCT
*
5465 TTGGTCCTGTTTTCTGCATG-TTCGACC
66 TTGGTCCTGTTTTCCGCATGATT-GACC
* *
5492 TCTTGGTCCTGTTTGACCTTTCGGTCCTGTTTTATGCCTGTTTTGACCCCTTGGTCCTGTTTGAC
1 T-TTGGTCCTGTTTGACCTTTC-GTCCTATTTTATGCATG-TTTGACCCCTTGGTCCTGTTTGAC
* * *
5557 CTTTTGGTCTTGTTTTCCGCCTGATTGACC
63 CCTTTGGTCCTGTTTTCCGCATGATTGACC
5587 TTTGGTCCTGTTT
1 TTTGGTCCTGTTT
5600 TTTAGCCCTT
Statistics
Matches: 92, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
91 1 0.01
92 6 0.07
93 12 0.13
94 25 0.27
95 46 0.50
96 2 0.02
ACGTcount: A:0.07, C:0.25, G:0.20, T:0.48
Consensus pattern (92 bp):
TTTGGTCCTGTTTGACCTTTCGTCCTATTTTATGCATGTTTGACCCCTTGGTCCTGTTTGACCCT
TTGGTCCTGTTTTCCGCATGATTGACC
Found at i:8243 original size:15 final size:16
Alignment explanation
Indices: 8218--8247 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
8208 AATAATTATT
8218 TTTAGATTATAATATA
1 TTTAGATTATAATATA
8234 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
8248 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:9731 original size:336 final size:333
Alignment explanation
Indices: 8624--9967 Score: 1534
Period size: 336 Copynumber: 4.0 Consensus size: 333
8614 ATTCTCAGTA
*
8624 ACATTGGATTTAAGAATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
1 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * * * * * *
8689 TTTAGAAAAAATAAGAAATACGATATTAAAAGCATGGAAAGCCCTCCAATATTTTTGGCGTTCAA
66 TTCAGAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAA
* *
8754 -T-TATATATTTTAGAGAGTATTTTAGCCAAGAATTGAGGAGAA-ATCTTTC-GAGTCAATTTTT
131 TTATATATATTTTA-TGAGTATTTTAGCCAAAAATTGAGGA-AATATCTTTCGGA-TCAATTTTT
** ** * *
8815 GCAAAAAGTTAGCCGAAATCGTATACTAACTAACCATCACGGTTTTTGGCTAAAAACACATTTCG
193 GCAAAATTTTAGCCGAAATC--ATGTTAA-TAACCATCACGATTTTTGGCTAAAAACGCATTTCG
* * * * * *
8880 GGGACCCGCCTCAATATTGCATGATTTTTGACTCCGAGACTACTTGAAATATCTATATTCATCTA
255 GGGCCCCGACTCAGTTTTGCATGATTTTTGACGCCGAGACTCCTTGAAATATCTATATTCATCTA
* *
8945 ATCAAATCTCAGTC
320 ATAAAATCTCAGCC
* * *
8959 ACATTGGATTTAAGGATTTGTTTTTATGAGCAATCTGAATCCTGTTTCGATTTAATTAGAAATTA
1 ACATTGGATTTAAGAATTTGTTTTTACGAGC-ATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * *
9024 ATTCAGAAAAAATAGGAAAAACAATATTAGAAA-CGTCAAAAACCCTTCAATCTTTTCAATCTTT
65 ATTCAGAAAAAATATGAAAAACAATATTA-AAAGCGT-GAAAAGCC--C--TC----CAATCTTT
* * *
9088 TTGGCGTTGAATTATATATTTTTTATGAGTATTTTAACCAAAAATTGATGAAATATCTTTCGGAT
120 TTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGAT
* * *
9153 CAATTTTTGCAAAATTTTAGCCGAAATCATG-TAATAACCATCA-TAGTTTTTGCCTAAAAAAGC
185 CAATTTTTGCAAAATTTTAGCCGAAATCATGTTAATAACCATCACGA-TTTTTGGCTAAAAACGC
* * * * ** *
9216 -GTTCGAGGGCCCCGACTCAGTTTTGCATGATTTTTGATGCCAAGTCTCCTTGGGATATCCATAT
249 ATTTCG-GGGCCCCGACTCAGTTTTGCATGATTTTTGACGCCGAGACTCCTTGAAATATCTATAT
* * *
9280 ACATCTAATCAAATCACAGCC
313 TCATCTAATAAAATCTCAGCC
* * *
9301 ATATAGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
1 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * *
9366 TTCAGAAAAAATATGAAAAAACAATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGAGTTAA
66 TTCAGAAAAAATATG-AAAAACAATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGA
* * * * *
9431 ATTATATATATTTTATGAGTGTTTTATCCAAAAATTGAGGAAACATTTTTCAGG-TCATTTTTTG
130 ATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTC-GGATCAATTTTTG
* * * *
9495 CAAAATTTTAGCCAAAATCGTGTACTAACTAACCATCACGATTTTTGGCTAAAAACGCGTTTTGG
194 CAAAATTTTAGCCGAAATCATGT--TAA-TAACCATCACGATTTTTGGCTAAAAACGCATTTCGG
* * * *
9560 GGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAAAATCTATATTCATTTAA
256 GGCCCCGACTCAGTTTTGCATGATTTTTGACGCCGAGACTCCTTGAAATATCTATATTCATCTAA
*
9625 TAAAATCTTAGCC
321 TAAAATCTCAGCC
* * * * *
9638 ACATTGCATTTAAGGATTT-TTTTTACGAGCATCTAAATCTTCTTTCGATTTAATTAGAAATTAT
1 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * *
9702 TTCAGAAAAAATTATGAAAAACAATATTAAAAGCGTGAAAAGCCCTTCGATCTTTTTGGTGTTGA
66 TTCAGAAAAAA-TATGAAAAACAATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGA
* * * * * *
9767 ATTATAT-T-TTTTATTAGTATTGT-GGCAAAATTTGACGAAATATCTTTCGGTTCAATTTTCT-
130 ATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGATCAATTTT-TG
* * *
9828 TAAAATTTTAGCCGAAATCAT-TTAATAATCATCACGCTTTTTGGGCTAAAAACGCATTTCGGGG
194 CAAAATTTTAGCCGAAATCATGTTAATAACCATCACGATTTTT-GGCTAAAAACGCATTTCGGGG
* * *
9892 -CCCGATTCAGTTTTGCATGGTTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAA-A
258 CCCCGACTCAGTTTTGCATGATTTTTGACGCCGAGACTCCTTGAAATATCTATATTCATCTAATA
9955 CAAATCTCAGCC
323 -AAATCTCAGCC
9967 A
1 A
9968 TTTTTTTACA
Statistics
Matches: 859, Mismatches: 119, Indels: 68
0.82 0.11 0.07
Matches are distributed among these distances:
328 1 0.00
329 83 0.10
330 22 0.03
332 3 0.00
333 134 0.16
334 15 0.02
335 29 0.03
336 166 0.19
337 117 0.14
338 4 0.00
339 2 0.00
341 61 0.07
342 129 0.15
343 3 0.00
344 2 0.00
345 19 0.02
346 57 0.07
347 12 0.01
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (333 bp):
ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
TTCAGAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAA
TTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGATCAATTTTTGCA
AAATTTTAGCCGAAATCATGTTAATAACCATCACGATTTTTGGCTAAAAACGCATTTCGGGGCCC
CGACTCAGTTTTGCATGATTTTTGACGCCGAGACTCCTTGAAATATCTATATTCATCTAATAAAA
TCTCAGCC
Found at i:10156 original size:2 final size:2
Alignment explanation
Indices: 10144--10179 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
10134 TTTTTGGCGT
10144 TA TA T- TA 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 TA T
10180 CTACTATACT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Done.