Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016546.1 Corchorus olitorius cultivar O-4 contig16579, 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: 50733
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:483 original size:159 final size:160
Alignment explanation
Indices: 188--488 Score: 496
Period size: 159 Copynumber: 1.9 Consensus size: 160
178 CAAAATGGAT
188 CCATTTTGAACGGAAATTTGGAATTGTAATAACAGCACGTTCCAAATTTCCGTCCAAAATAGACC
1 CCATTTTGAACGGAAATTTGGAATTGTAATAACAGCACGTTCCAAATTTCCGTCCAAAATAGACC
* *
253 CAATTTGGTGCAATTTACTAATATTTAGACCCAATTTGGTCTTGTTTAAAGGTTTAAATTCAAAT
66 CAATTTGGTGCAATTTACTAATATATAGACCCAATTTGGTCTTGTTTAAAGGTTTAAACTCAAAT
*
318 TGAGCAATTTTGAAATACACTTAATTGGGC
131 TAAGCAATTTTGAAATACACTTAATTGGGC
* * * *
348 CCATTTTGGACGGAAATTTGGAATTGTAATAACGGCGCG-TCCAAATTTTCGTCCAAAATAGACC
1 CCATTTTGAACGGAAATTTGGAATTGTAATAACAGCACGTTCCAAATTTCCGTCCAAAATAGACC
* * * *
412 CAATTTGGTGTAATTTGCTAATGTATAGACCCAATTTGGTCTTGTTTAAAGGTTTAGACTCAAAT
66 CAATTTGGTGCAATTTACTAATATATAGACCCAATTTGGTCTTGTTTAAAGGTTTAAACTCAAAT
477 TAAGCAATTTTG
131 TAAGCAATTTTG
489 TAAAGGTTTA
Statistics
Matches: 130, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
159 94 0.72
160 36 0.28
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (160 bp):
CCATTTTGAACGGAAATTTGGAATTGTAATAACAGCACGTTCCAAATTTCCGTCCAAAATAGACC
CAATTTGGTGCAATTTACTAATATATAGACCCAATTTGGTCTTGTTTAAAGGTTTAAACTCAAAT
TAAGCAATTTTGAAATACACTTAATTGGGC
Found at i:5741 original size:43 final size:42
Alignment explanation
Indices: 5636--5884 Score: 306
Period size: 43 Copynumber: 5.8 Consensus size: 42
5626 CAATAACCAA
* * *
5636 AAAGTCCCCAAACACATATATAACACAGGGGTATTTCTATTCC
1 AAAGTCCCCAAACACATATATAACACA-GGGCAATTCTATTAC
*
5679 AAAAGTCCTCAAACACATATATAACACAGGGACAATTCTATTAC
1 -AAAGTCCCCAAACACATATATAACACAGGG-CAATTCTATTAC
* *
5723 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTCCAA
1 AAAGTCCCCAAACACATATATAACACA-GGGCAATTCTATT--AC
*
5768 AAAGTCCTCAAACACATATATAACACAGAGGC-A-TCTA-TACC
1 AAAGTCCCCAAACACATATATAACACAG-GGCAATTCTATTA-C
*
5809 AAAGTCCCCAAACACATATATAACACATGGGCAATTCTATTAT
1 AAAGTCCCCAAACACATATATAACACA-GGGCAATTCTATTAC
*
5852 AAAGTCCTCAAACACATATATAACACAGAGGCA
1 AAAGTCCCCAAACACATATATAACACAG-GGCA
5885 TTTTTCCTTA
Statistics
Matches: 181, Mismatches: 13, Indels: 23
0.83 0.06 0.11
Matches are distributed among these distances:
40 1 0.01
41 29 0.16
42 4 0.02
43 76 0.42
44 41 0.23
45 30 0.17
ACGTcount: A:0.43, C:0.25, G:0.10, T:0.22
Consensus pattern (42 bp):
AAAGTCCCCAAACACATATATAACACAGGGCAATTCTATTAC
Found at i:5841 original size:86 final size:86
Alignment explanation
Indices: 5636--5885 Score: 393
Period size: 86 Copynumber: 2.9 Consensus size: 86
5626 CAATAACCAA
*
5636 AAAGTCCCCAAACACATATATAACACAGGGGTATTTCTATTCC-AAAAGTCCTCAAACACATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTCCAAAAAGTCCTCAAACACATATA
5700 TAACACAG-GGACAATTCTATTAC
66 TAACACAGAGG-C-A-TCTATTAC
5723 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTCCAAAAAGTCCTCAAACACATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTCCAAAAAGTCCTCAAACACATATA
5788 TAACACAGAGGCATCTA-TACC
66 TAACACAGAGGCATCTATTA-C
* * *
5809 AAAGTCCCCAAACACATATATAACACATGGGCAATTCTATT--ATAAAGTCCTCAAACACATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTCCAAAAAGTCCTCAAACACATATA
5872 TAACACAGAGGCAT
66 TAACACAGAGGCAT
5886 TTTTCCTTAT
Statistics
Matches: 156, Mismatches: 4, Indels: 9
0.92 0.02 0.05
Matches are distributed among these distances:
84 35 0.22
85 2 0.01
86 44 0.28
87 43 0.28
88 30 0.19
89 2 0.01
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.22
Consensus pattern (86 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTCCAAAAAGTCCTCAAACACATATA
TAACACAGAGGCATCTATTAC
Found at i:5844 original size:129 final size:131
Alignment explanation
Indices: 5632--5887 Score: 401
Period size: 129 Copynumber: 2.0 Consensus size: 131
5622 CACCCAATAA
* * * *
5632 CCAAAAAGTCCCCAAACACATATATAACACAGGGGTATTTCTATTCCAAAAGTCCTCAAACACAT
1 CCAAAAAGTCCCCAAACACATATATAACACAGAGGCA-TTCTATACCAAAAGTCCCCAAACACAT
*
5697 ATATAACACAGGGACAATTCTATTACAAAGTCCCCAAACACATATATAACACAGGGGCATTTCTA
65 ATATAACACAGGGACAATTCTATTACAAAGTCCCCAAACACATATATAACACAGAGGCATTTCTA
5762 TT
130 TT
*
5764 CCAAAAAGTCCTCAAACACATATATAACACAGAGGCA-TCTATACC-AAAGTCCCCAAACACATA
1 CCAAAAAGTCCCCAAACACATATATAACACAGAGGCATTCTATACCAAAAGTCCCCAAACACATA
* *
5827 TATAACACATGGG-CAATTCTATTATAAAGTCCTCAAACACATATATAACACAGAGGCATTT
66 TATAACACA-GGGACAATTCTATTACAAAGTCCCCAAACACATATATAACACAGAGGCATTT
5888 TTCCTTATGG
Statistics
Matches: 115, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
129 71 0.62
130 10 0.09
132 34 0.30
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (131 bp):
CCAAAAAGTCCCCAAACACATATATAACACAGAGGCATTCTATACCAAAAGTCCCCAAACACATA
TATAACACAGGGACAATTCTATTACAAAGTCCCCAAACACATATATAACACAGAGGCATTTCTAT
T
Found at i:22133 original size:2 final size:2
Alignment explanation
Indices: 22126--22173 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
22116 CTCGATACAA
* *
22126 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22167 -T AT AT AT
1 AT AT AT AT
22174 CTAATTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:23430 original size:18 final size:19
Alignment explanation
Indices: 23409--23446 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
23399 TCGAAACTCG
*
23409 ATCGAGCTTGAG-TCGAGT
1 ATCGAGCTCGAGCTCGAGT
23427 ATCGAGCTCGAGCTCGAGT
1 ATCGAGCTCGAGCTCGAGT
23446 A
1 A
23447 GCTCACTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (19 bp):
ATCGAGCTCGAGCTCGAGT
Found at i:37006 original size:42 final size:42
Alignment explanation
Indices: 36944--37144 Score: 161
Period size: 42 Copynumber: 4.8 Consensus size: 42
36934 CCCCAGATTC
* * * * *
36944 TCGATACTATAGAAGACGTGACCGTTCCTACTCTCCTGATGA
1 TCGATACTATAGAAGGCGTGACAGGTCCTACTCACCAGATGA
*
36986 TCGATACTATAGAAGGCGTGATAGGTCCTACTCACCAGATGA
1 TCGATACTATAGAAGGCGTGACAGGTCCTACTCACCAGATGA
* * ** * * * * *
37028 CCGCTACTACCGTAGGCGTGAAAGGTCCTACACGCCAGATCA
1 TCGATACTATAGAAGGCGTGACAGGTCCTACTCACCAGATGA
* * ** * * * *
37070 CCGCTACTACCGTAGGCGGGACCA-TTCCTACTCACCTGATGA
1 TCGATACTATAGAAGGCGTGA-CAGGTCCTACTCACCAGATGA
* *
37112 TCGATACTATAGAAGGCGCGATAGGTCCTACTC
1 TCGATACTATAGAAGGCGTGACAGGTCCTACTC
37145 TCCATATGGC
Statistics
Matches: 127, Mismatches: 30, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
41 1 0.01
42 125 0.98
43 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (42 bp):
TCGATACTATAGAAGGCGTGACAGGTCCTACTCACCAGATGA
Found at i:47689 original size:40 final size:40
Alignment explanation
Indices: 47634--47709 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
47624 CAGAAAAACT
47634 AATGTAACAAAGAGCCATTTAATCAAGTCATTATCTTAGA
1 AATGTAACAAAGAGCCATTTAATCAAGTCATTATCTTAGA
47674 AATGTAACAAAGAGCCATTTAATCAAGTCATTATCT
1 AATGTAACAAAGAGCCATTTAATCAAGTCATTATCT
47710 GAGATGTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (40 bp):
AATGTAACAAAGAGCCATTTAATCAAGTCATTATCTTAGA
Found at i:49815 original size:22 final size:21
Alignment explanation
Indices: 49790--49830 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
49780 TCAAAGAGTA
*
49790 TTTTAATAAATTTAACTTTACT
1 TTTTAAGAAATTTAA-TTTACT
*
49812 TTTTTAGAAATTTAATTTA
1 TTTTAAGAAATTTAATTTA
49831 AACTTTAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTAAGAAATTTAATTTACT
Done.