Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013948.1 Corchorus olitorius cultivar O-4 contig13981, 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: 9770
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Found at i:1127 original size:35 final size:35
Alignment explanation
Indices: 1087--1162 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
1077 CCGTTAGCCT
*
1087 TTAATTGCCCAAGTTTTTGTGCAAAAAGGTAAGTA
1 TTAATTGCACAAGTTTTTGTGCAAAAAGGTAAGTA
*
1122 TTAATTGCACATGTTTTTGTGCAAAAAGGTAAGTA
1 TTAATTGCACAAGTTTTTGTGCAAAAAGGTAAGTA
1157 TTAATT
1 TTAATT
1163 ATAATCTGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.38
Consensus pattern (35 bp):
TTAATTGCACAAGTTTTTGTGCAAAAAGGTAAGTA
Found at i:4562 original size:78 final size:78
Alignment explanation
Indices: 4468--4874 Score: 362
Period size: 78 Copynumber: 5.1 Consensus size: 78
4458 GTTTTCTAGT
* *
4468 TAAAATAGTTAAATGGTAAACTGAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAACTAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGA
4533 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
* *
4546 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAACTAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAAT--A
* * *
4611 GGAGTTTTGAGTAGAA
64 -GAGTTTTTAGTTGAG
* * ** * * * ***
4627 TAAAATTGTAAAA-GTTTATTTCTAAAAAAAAACTGTA-AAAG-T-TTAAA--CAATGCCATAAA
1 TAAAATAGTAAAATG-GTA-AACT---AAAATAGT-TATAAAGATATTAAATTTAATTAAATAAA
* *
4686 AA-A-ATTCTAATATATCAAGTTTTCTAG
60 AATAGAGT-T--T-T-T--AG--TT-GAG
* * *
4713 TTAAAATAGTTAAATGGTAAACTGAAATAGTTATAAAAATATTAAATTTAATTAAATAAAAATAG
1 -TAAAATAGTAAAATGGTAAACTAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAG
4778 AGTTTTTAGTTGAG
65 AGTTTTTAGTTGAG
* *
4792 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAACTAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGA
4857 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
4870 TAAAA
1 TAAAA
4875 GTATAAATCT
Statistics
Matches: 257, Mismatches: 44, Indels: 56
0.72 0.12 0.16
Matches are distributed among these distances:
76 2 0.01
77 1 0.00
78 137 0.53
79 3 0.01
80 5 0.02
81 36 0.14
82 5 0.02
83 14 0.05
84 3 0.01
85 17 0.07
86 6 0.02
87 23 0.09
88 3 0.01
89 2 0.01
ACGTcount: A:0.51, C:0.02, G:0.13, T:0.34
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAACTAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGA
GTTTTTAGTTGAG
Found at i:4742 original size:246 final size:244
Alignment explanation
Indices: 4311--4857 Score: 958
Period size: 246 Copynumber: 2.2 Consensus size: 244
4301 TTTTTAAAAT
* * *
4311 TAAAATGGTAAAAATAAAATATTTATAAAAATAAT-GAATTTAATTTAAATAAAAAT--A-GAGT
1 TAAAATGGT-AAAATAAAATAGTTATAAAGATATTAG-ATTTAA-TTAAATAAAAATAGAGGAGT
* *
4372 TTTGAGTATAATAAAATTGTAAAAGTTTATTTCTTAAAAAAACTGTAAAAGTTTAAACAATGCCA
63 TTTGAGTAGAATAAAATTGTAAAAGTTTATTTCTAAAAAAAACTGTAAAAGTTTAAACAATGCCA
4437 TAAAAAATTATAATATATCAAGTTTTCTAGTTAAAATAGTTAAATGGTAAACTGAAATAGTTATA
128 TAAAAAATTATAATATATCAAGTTTTCTAGTTAAAATAGTTAAATGGTAAACTGAAATAGTTATA
*
4502 AAGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATAG
193 AAAATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATAG
4554 TAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAGGAGTTTT
1 TAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAGGAGTTTT
4619 GAGTAGAATAAAATTGTAAAAGTTTATTTCTAAAAAAAAACTGTAAAAGTTTAAACAATGCCATA
66 GAGTAGAATAAAATTGTAAAAGTTTATTTCT-AAAAAAAACTGTAAAAGTTTAAACAATGCCAT-
*
4684 AAAAAATTCTAATATATCAAGTTTTCTAGTTAAAATAGTTAAATGGTAAACTGAAATAGTTATAA
129 AAAAAATTATAATATATCAAGTTTTCTAGTTAAAATAGTTAAATGGTAAACTGAAATAGTTATAA
4749 AAATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATAG
194 AAATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATAG
4800 TAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAG
1 TAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAG
4858 TTTTTAGTTG
Statistics
Matches: 291, Mismatches: 7, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
241 12 0.04
242 28 0.10
243 11 0.04
244 37 0.13
245 31 0.11
246 172 0.59
ACGTcount: A:0.51, C:0.03, G:0.12, T:0.34
Consensus pattern (244 bp):
TAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAGGAGTTTT
GAGTAGAATAAAATTGTAAAAGTTTATTTCTAAAAAAAACTGTAAAAGTTTAAACAATGCCATAA
AAAATTATAATATATCAAGTTTTCTAGTTAAAATAGTTAAATGGTAAACTGAAATAGTTATAAAA
ATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATAG
Found at i:7144 original size:72 final size:72
Alignment explanation
Indices: 7007--7149 Score: 223
Period size: 72 Copynumber: 2.0 Consensus size: 72
6997 TTGGCTAGGC
* * **
7007 AATTGAGAGAGGAGTTGTCTAGGTCACAAGTTGAGGTGCTTTATTATTTACCTAGATCTGGAATT
1 AATTGAGAGAGAAGTTGTCTAGGTCACAAGTTCAGGTGCTTTATTATTTACCTAGATCTAAAATT
7072 TCTGATG
66 TCTGATG
* *
7079 AATTGAGAGAGAAGTTGTCTGGGTCACAAGTTCAGGTGCTTTATTATTTACCTGGATCTAAAATT
1 AATTGAGAGAGAAGTTGTCTAGGTCACAAGTTCAGGTGCTTTATTATTTACCTAGATCTAAAATT
*
7144 TTTGAT
66 TCTGAT
7150 AAGTTCGGGA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.37
Consensus pattern (72 bp):
AATTGAGAGAGAAGTTGTCTAGGTCACAAGTTCAGGTGCTTTATTATTTACCTAGATCTAAAATT
TCTGATG
Found at i:8900 original size:24 final size:25
Alignment explanation
Indices: 8864--8911 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
8854 AGTAACAATA
*
8864 AAAATAAATAAACAAGA-AAATAAT
1 AAAATAAAGAAACAAGATAAATAAT
*
8888 AAAATTAAGAAACAAGATAAATAA
1 AAAATAAAGAAACAAGATAAATAA
8912 ATACTCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (25 bp):
AAAATAAAGAAACAAGATAAATAAT
Done.