Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023752.1 Corchorus olitorius cultivar O-4 contig23785, 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: 10327
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Found at i:1718 original size:19 final size:19
Alignment explanation
Indices: 1684--1741 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1674 CTGTTTGGCA
*
1684 ACTGTACAGCTGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
1703 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
*
1724 ACTGTATAGATGAGATTA
1 ACTGTACAGATGAGATTA
1742 TTAGAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:3906 original size:39 final size:39
Alignment explanation
Indices: 3851--4431 Score: 410
Period size: 39 Copynumber: 13.9 Consensus size: 39
3841 TCTAGTCCAC
* * * *
3851 ATTCCTAGTTTTCCCTTCCCCACCAGAAGGTATTGTTTA
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA
* ** * * *
3890 ATTCCTAGTTTGCCCTTCCCCACCGGTTGGTATTATCTAA
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT-TTA
* *
3930 ATTTCCAATTTGCCCTTCCCCATCC-GAACGTGTTGTTTAAAGTTTGA
1 ATTCCCAGTTTGCCCTTCCCCA-CCGGAA-G-G-TG-TT---GTTT-A
* * * * *
3977 TTTACCCAGTTTGCCCTTCCACACCAGATGGTGTTGTTTG
1 ATT-CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA
* * *
4017 ATTCCCAGTTTGCCCTTCTCCACCAGAAGGTGTT-TTTG
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA
* * * *
4055 ATTCTCAGTTCGCCATTCCCCACCGGAAGGTGTTGTCTAA
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT-TTA
* *
4095 ATTCCCAATTTGCCCTTCCCCCATCGGAAGGTGTTGTTTAAAGTA
1 ATTCCCAGTTTGCCCTT-CCCCACCGGAAGGTGTTG-TT----TA
* * *
4140 TGACTTACCCAGTTTTCCCTTCCTCACCGGAAGGTGTTGTCTAA
1 --A-TT-CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT-TTA
* * *
4184 ATTCCCAATTTGTCCTTCCCCATCGGAAGGTGTTGTTTAAA
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTT--A
**
4225 GTCTGATTTACCCAGTTTGCCCTTCATCACCGGAAGGTGTTGTTTA
1 -----A-TT-CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA
4271 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA
**
4310 ATTCCTTGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA
* * * *
4349 ATTCCCCAGTTTGCACTTCCTCATCGGAAGGTGTTGTCTA
1 ATT-CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA
* *
4389 AGTCTACCTTTCCAGATTGCCCTTCCCCGCCGGAAGGTGTTGT
1 A-T-T--C---CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
4432 CTATATTTTA
Statistics
Matches: 433, Mismatches: 68, Indels: 75
0.75 0.12 0.13
Matches are distributed among these distances:
38 33 0.08
39 135 0.31
40 99 0.23
41 30 0.07
42 4 0.01
43 3 0.01
44 5 0.01
45 3 0.01
46 31 0.07
47 11 0.03
48 67 0.15
49 12 0.03
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.35
Consensus pattern (39 bp):
ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA
Found at i:4177 original size:48 final size:47
Alignment explanation
Indices: 4119--4310 Score: 164
Period size: 48 Copynumber: 4.4 Consensus size: 47
4109 CTTCCCCCAT
4119 CGGAAGGTGTTGTTTAAAGTATGACTTACCCAGTTTTCCCTTCCTCAC
1 CGGAAGGTGTTGTTTAAAGTATGA-TTACCCAGTTTTCCCTTCCTCAC
* * * *
4167 CGGAAGGTGTTGTCT--A--A--ATT-CCCAATTTGT-CCTTCCCCAT
1 CGGAAGGTGTTGTTTAAAGTATGATTACCCAGTTT-TCCCTTCCTCAC
* * *
4207 CGGAAGGTGTTGTTTAAAGTCTGATTTACCCAGTTTGCCCTTCATCAC
1 CGGAAGGTGTTGTTTAAAGTATGA-TTACCCAGTTTTCCCTTCCTCAC
* *
4255 CGGAAGGTGTTG-TT----TA--ATT-CCCAGTTTGCCCTTCCCCAC
1 CGGAAGGTGTTGTTTAAAGTATGATTACCCAGTTTTCCCTTCCTCAC
4294 CGGAAGGTGTTGTTTAA
1 CGGAAGGTGTTGTTTAA
4311 TTCCTTGTTT
Statistics
Matches: 117, Mismatches: 14, Indels: 32
0.72 0.09 0.20
Matches are distributed among these distances:
39 30 0.26
40 33 0.28
41 4 0.03
42 2 0.02
43 1 0.01
44 1 0.01
46 2 0.02
47 4 0.03
48 40 0.34
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (47 bp):
CGGAAGGTGTTGTTTAAAGTATGATTACCCAGTTTTCCCTTCCTCAC
Found at i:4248 original size:88 final size:85
Alignment explanation
Indices: 4060--4434 Score: 408
Period size: 88 Copynumber: 4.4 Consensus size: 85
4050 TTTTGATTCT
* *
4060 CAGTTCGCCATTCCCCACCGGAAGGTGTTGTCTAAATTCCCAATTTGCCCTTCCCCCATCGGAAG
1 CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAATTTGCCCTT-CCCCATCGGAAG
* *
4125 GTGTTGTTTAAAGTATGACTTACC
65 GTGTTGTTT-AAGTCT-A-TTTCC
* * *
4149 CAGTTTTCCCTTCCTCACCGGAAGGTGTTGTCTAAATTCCCAATTTGTCCTTCCCCATCGGAAGG
1 CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAATTTGCCCTTCCCCATCGGAAGG
4214 TGTTGTTTAAAGTCTGATTTACC
66 TGTTGTTT-AAGTCT-ATTT-CC
** * * *
4237 CAGTTTGCCCTTCATCACCGGAAGGTGTTGT-TTAATTCCCAGTTTGCCCTTCCCCACCGGAAGG
1 CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAATTTGCCCTTCCCCATCGGAAGG
4301 TGTTGTTT-A----A-TTCC
66 TGTTGTTTAAGTCTATTTCC
** * * * *
4315 TTGTTTGCCCTTCCCCACCGGAAGGTGTTGT-TTAATTCCCCAGTTTGCACTTCCTCATCGGAAG
1 CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATT-CCCAATTTGCCCTTCCCCATCGGAAG
*
4379 GTGTTGTCTAAGTCTACCTTT-C
65 GTGTTGTTTAAGTCTA--TTTCC
* *
4401 CAGATTGCCCTTCCCCGCCGGAAGGTGTTGTCTA
1 CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTA
4435 TATTTTAGTC
Statistics
Matches: 249, Mismatches: 26, Indels: 24
0.83 0.09 0.08
Matches are distributed among these distances:
78 35 0.14
79 33 0.13
80 2 0.01
84 1 0.00
85 1 0.00
86 28 0.11
87 42 0.17
88 60 0.24
89 47 0.19
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (85 bp):
CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAATTTGCCCTTCCCCATCGGAAGG
TGTTGTTTAAGTCTATTTCC
Found at i:4354 original size:254 final size:252
Alignment explanation
Indices: 3891--4434 Score: 720
Period size: 254 Copynumber: 2.2 Consensus size: 252
3881 TATTGTTTAA
* ** * * *
3891 TTCCTAGTTTGCCCTTCCCCACCGGTTGGTATTATCTAAATTTCCAATTTGCCCTTCCCCATCCG
1 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAATTTGCCCTTCCCCATCCG
* * *
3956 AACGTGTTGTTTAAAGTTTGATTTACCCAGTTTGCCCTTCCACACCAGATGGTGTTGTTTGATTC
66 AACGTGTTGTTTAAAGTCTGATTTACCCAGTTTGCCCTTCCACACCAGAAGGTGTTGTTTAATTC
* *
4021 CCAGTTTGCCCTTCTCCACCAGAAGGTGTTTTTGATTCTCAGTTCGCCATTCCCCACCGGAAGGT
131 CCAGTTTGCCCTTCCCCACCAGAAGGTGTTTTTAATTCTCAGTTCGCCATTCCCCACCGGAAGGT
* *
4086 GTTGTCTAAATT-CCCAATTTGCCCTTCCCCCATCGGAAGGTGTTGTTTAAAGTATGA-C
196 GTTGTCTAAATTCCCCAATTTGCACTT-CCCCATCGGAAGGTGTTGTCT-AAGTAT-ACC
* * * *
4144 TTACCCAGTTTTCCCTTCCTCACCGGAAGGTGTTGTCTAAATTCCCAATTTGTCCTTCCCCATCG
1 TT-CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAATTTGCCCTTCCCCATCC
* *
4209 GAAGGTGTTGTTTAAAGTCTGATTTACCCAGTTTGCCCTT-CATCACCGGAAGGTGTTGTTTAAT
65 GAACGTGTTGTTTAAAGTCTGATTTACCCAGTTTGCCCTTCCA-CACCAGAAGGTGTTGTTTAAT
* * * *
4273 TCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTC-CTTGTTTGCCCTTCCCCACCGGA
129 TCCCAGTTTGCCCTTCCCCACCAGAAGGTGTT-TTTAATTCTC-AGTTCGCCATTCCCCACCGGA
* * * *
4337 AGGTGTTGT-TTAATTCCCCAGTTTGCACTTCCTCATCGGAAGGTGTTGTCTAAGTCTACC
192 AGGTGTTGTCTAAATTCCCCAATTTGCACTTCCCCATCGGAAGGTGTTGTCTAAGTATACC
* * *
4397 TTTCCAGATTGCCCTTCCCCGCCGGAAGGTGTTGTCTA
1 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTA
4435 TATTTTAGTC
Statistics
Matches: 253, Mismatches: 32, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
252 32 0.13
253 12 0.05
254 163 0.64
255 46 0.18
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.35
Consensus pattern (252 bp):
TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAATTTGCCCTTCCCCATCCG
AACGTGTTGTTTAAAGTCTGATTTACCCAGTTTGCCCTTCCACACCAGAAGGTGTTGTTTAATTC
CCAGTTTGCCCTTCCCCACCAGAAGGTGTTTTTAATTCTCAGTTCGCCATTCCCCACCGGAAGGT
GTTGTCTAAATTCCCCAATTTGCACTTCCCCATCGGAAGGTGTTGTCTAAGTATACC
Found at i:8451 original size:15 final size:15
Alignment explanation
Indices: 8421--8462 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
8411 TTACTTTGCT
8421 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
8437 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
8452 TTGCTTTCTGT
1 TTGTTTTCTGT
8463 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:8870 original size:26 final size:24
Alignment explanation
Indices: 8799--8871 Score: 67
Period size: 26 Copynumber: 2.9 Consensus size: 24
8789 CTTTTTGAAA
8799 AAAAAAAAATTTTGTGTTTTGCGTCG
1 AAAAAAAAA-TTTGTG-TTTGCGTCG
* * *
8825 AAAAAAAAA-TAGTTTTTGCGTCATT
1 AAAAAAAAATTTGTGTTTGCGTC--G
*
8850 AAAAAAAAATTTGTGTCTGCGT
1 AAAAAAAAATTTGTGTTTGCGT
8872 TTTTATTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
23 8 0.21
24 3 0.08
25 9 0.24
26 18 0.47
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (24 bp):
AAAAAAAAATTTGTGTTTGCGTCG
Done.