Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016272.1 Corchorus olitorius cultivar O-4 contig16305, 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: 55300
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2180 original size:23 final size:23
Alignment explanation
Indices: 2130--2181 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
2120 GCTAAAGCTC
* *
2130 GAGCTCGACCGAGTTTTGATTATC
1 GAGCTCGACCGAG-TTTGAGTATA
2154 GAGCTCGACTCGA-TTTGAGTATA
1 GAGCTCGAC-CGAGTTTGAGTATA
2177 GAGCT
1 GAGCT
2182 ACTCGAGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 13 0.52
24 9 0.36
25 3 0.12
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (23 bp):
GAGCTCGACCGAGTTTGAGTATA
Found at i:2994 original size:44 final size:44
Alignment explanation
Indices: 2889--3024 Score: 200
Period size: 44 Copynumber: 3.0 Consensus size: 44
2879 AGGAGGATTT
* *
2889 TTGAAAGAAGATCCACGTATGTGGATGATTATCGTCATCAGAGAAGA
1 TTGAAAGAAGATCCACGTATGTGGAGGATTAT--T-ATCAAAGAAGA
2936 TTGAAAGAAGATCCACGTATGTGGAGGATTATTATCAAAGAAGA
1 TTGAAAGAAGATCCACGTATGTGGAGGATTATTATCAAAGAAGA
* * *
2980 TTGAGAGAAAATCCACGTATGTGGAGGATTATTTTCAAAGAAGA
1 TTGAAAGAAGATCCACGTATGTGGAGGATTATTATCAAAGAAGA
3024 T
1 T
3025 CCAAGGAGGA
Statistics
Matches: 84, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
44 52 0.62
45 1 0.01
47 31 0.37
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.26
Consensus pattern (44 bp):
TTGAAAGAAGATCCACGTATGTGGAGGATTATTATCAAAGAAGA
Found at i:4960 original size:6 final size:6
Alignment explanation
Indices: 4949--4977 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
4939 TTACTCTAGC
4949 AGCTCG AGCTCG AGCTCG AGCTCG -GCTCG
1 AGCTCG AGCTCG AGCTCG AGCTCG AGCTCG
4978 TGAATAATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.14, C:0.34, G:0.34, T:0.17
Consensus pattern (6 bp):
AGCTCG
Found at i:6318 original size:44 final size:46
Alignment explanation
Indices: 6220--6323 Score: 158
Period size: 47 Copynumber: 2.3 Consensus size: 46
6210 GGAGCATTAC
*
6220 TGAAAGAAGATCCACATATGTGGAGGATTATCATCATCAAATAAGAT
1 TGAAAGAAGATCCACATATGTGGAGGATTAT-ATCATCAAAGAAGAT
* *
6267 TGAAAGAAGATCCACGTATGTGGAGGATTAT-T-ATCAAAGAATAT
1 TGAAAGAAGATCCACATATGTGGAGGATTATATCATCAAAGAAGAT
6311 TGAAAGAAGATCC
1 TGAAAGAAGATCC
6324 GTGCGATGCT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
44 23 0.43
45 1 0.02
47 30 0.56
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (46 bp):
TGAAAGAAGATCCACATATGTGGAGGATTATATCATCAAAGAAGAT
Found at i:11601 original size:17 final size:17
Alignment explanation
Indices: 11561--11601 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
11551 TGAGTGGTTT
* *
11561 ATGACAGTTTTTTTTAA
1 ATGATAGTTTTTTTAAA
11578 ATAGATAGTTTTTTTAAA
1 AT-GATAGTTTTTTTAAA
11596 ATGATA
1 ATGATA
11602 TAAATAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (17 bp):
ATGATAGTTTTTTTAAA
Found at i:11806 original size:18 final size:19
Alignment explanation
Indices: 11767--11806 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
11757 GTGCTCCCGT
11767 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
11788 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
11806 T
1 T
11807 TCTGACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:12191 original size:30 final size:30
Alignment explanation
Indices: 12146--12218 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 30
12136 GAAGTAGTTG
*
12146 ATAAAAAATAAAATAA-AAAGCTAGAAAACGA
1 ATAAAAAATAAAATAAGAAAGAT-GAAAA-GA
*
12177 ATAAAAAA-AGAATAAGAAAGATGAAAAGA
1 ATAAAAAATAAAATAAGAAAGATGAAAAGA
12206 ATAAAAAATAAAA
1 ATAAAAAATAAAA
12219 AGTTAGAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 10 0.27
30 14 0.38
31 13 0.35
ACGTcount: A:0.74, C:0.03, G:0.11, T:0.12
Consensus pattern (30 bp):
ATAAAAAATAAAATAAGAAAGATGAAAAGA
Found at i:12229 original size:27 final size:27
Alignment explanation
Indices: 12155--12240 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 27
12145 GATAAAAAAT
* *
12155 AAAATAAAAAGCTAGA-AAACGAATAA
1 AAAATAAAAAGATAGAGAAAAGAATAA
*
12181 AAAA-AGAATAAGAAAGATGAAAAGAATAA
1 AAAATA-AA-AAGATAGA-GAAAAGAATAA
*
12210 AAAATAAAAAGTTAGAGAAAAG-ATAA
1 AAAATAAAAAGATAGAGAAAAGAATAA
*
12236 TAAAT
1 AAAAT
12241 CAAGTAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
25 1 0.02
26 14 0.29
27 12 0.24
28 6 0.12
29 15 0.31
30 1 0.02
ACGTcount: A:0.70, C:0.02, G:0.14, T:0.14
Consensus pattern (27 bp):
AAAATAAAAAGATAGAGAAAAGAATAA
Found at i:25291 original size:6 final size:6
Alignment explanation
Indices: 25280--25312 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
25270 TAACTAATGC
25280 TTTCAA TTTCAA TTTCAA TTTCAA TTT-AA TTTC
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTC
25313 TTCTTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTCAA
Found at i:29229 original size:21 final size:19
Alignment explanation
Indices: 29204--29261 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
29194 GCTGCTCTAA
29204 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* * *
29225 TAATCTAATCTATACAGTG
1 TAATCTCATCTGTACAGTC
*
29244 TAATATCATCTGTACAGT
1 TAATCTCATCTGTACAGT
29262 TGCTAAACAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:34428 original size:21 final size:21
Alignment explanation
Indices: 34399--34439 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
34389 CACGGACCAA
*
34399 CACTTTTCATCATGATCATCC
1 CACTGTTCATCATGATCATCC
* *
34420 CACTGTTCATGATGTTCATC
1 CACTGTTCATCATGATCATC
34440 AGTCAAACCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.29, G:0.10, T:0.39
Consensus pattern (21 bp):
CACTGTTCATCATGATCATCC
Found at i:35995 original size:29 final size:29
Alignment explanation
Indices: 35877--35997 Score: 102
Period size: 29 Copynumber: 4.1 Consensus size: 29
35867 TCTCATACAT
* *
35877 CATAATGATATCCGTGTGCATCTCACACA
1 CATAATGATATCCGTGTGCATCTCTCGCA
* *
35906 CATAGT-AGTATCCATGTGCATCTCTCGCATAA
1 CATAATGA-TATCCGTGTGCATCTCTCGC---A
* * *
35938 CATAATGATACCCCGTGTGTA-CTTTCGCA
1 CATAATGATA-TCCGTGTGCATCTCTCGCA
* *
35967 CATAATGGTATCCGTGTGCATCTCCCGCA
1 CATAATGATATCCGTGTGCATCTCTCGCA
35996 CA
1 CA
35998 CTGTTTATTT
Statistics
Matches: 71, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
28 9 0.13
29 40 0.56
32 14 0.20
33 8 0.11
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (29 bp):
CATAATGATATCCGTGTGCATCTCTCGCA
Found at i:45787 original size:2 final size:2
Alignment explanation
Indices: 45780--45821 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
45770 ATCGAAAATA
* * *
45780 AT AT AT AT AT AT AT AT AT AT AT GT AT AT A- AG AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45821 A
1 A
45822 ACATACAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (2 bp):
AT
Done.