Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015464.1 Corchorus olitorius cultivar O-4 contig15497, 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: 91944
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:1715 original size:14 final size:13
Alignment explanation
Indices: 1696--1745 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 13
1686 AGCGAAGTTA
*
1696 AAATCAAAGAAACG
1 AAATC-AAGAAAAG
1710 AAATCAAGAAAAG
1 AAATCAAGAAAAG
*
1723 AAA--ATGAAAAG
1 AAATCAAGAAAAG
1734 AAATACAAGAAA
1 AAAT-CAAGAAA
1746 TCAGATCTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 10 0.33
13 10 0.33
14 10 0.33
ACGTcount: A:0.70, C:0.08, G:0.14, T:0.08
Consensus pattern (13 bp):
AAATCAAGAAAAG
Found at i:14955 original size:26 final size:26
Alignment explanation
Indices: 14925--14977 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
14915 AGGCCGGCCT
14925 TGAACAAGCTATATTAGTATAAATCA
1 TGAACAAGCTATATTAGTATAAATCA
14951 TGAACAAGCTATATTAGTATAAATCA
1 TGAACAAGCTATATTAGTATAAATCA
14977 T
1 T
14978 AGCTTTGGCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (26 bp):
TGAACAAGCTATATTAGTATAAATCA
Found at i:15870 original size:35 final size:35
Alignment explanation
Indices: 15824--15893 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
15814 TAGTCAAGAC
15824 ATTAATGATGAAATTCAATCTATTGTAATTTATGT
1 ATTAATGATGAAATTCAATCTATTGTAATTTATGT
15859 ATTAATGATGAAATTCAATCTATTGTAATTTATGT
1 ATTAATGATGAAATTCAATCTATTGTAATTTATGT
15894 TATGAACGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (35 bp):
ATTAATGATGAAATTCAATCTATTGTAATTTATGT
Found at i:16798 original size:20 final size:20
Alignment explanation
Indices: 16770--16810 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
16760 GGGTGTTTGG
16770 TTTGGGGTGATCTTTGATCA
1 TTTGGGGTGATCTTTGATCA
* * *
16790 TTTGTGGTGATTTTTTATCA
1 TTTGGGGTGATCTTTGATCA
16810 T
1 T
16811 CCCGTTTGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.07, G:0.24, T:0.54
Consensus pattern (20 bp):
TTTGGGGTGATCTTTGATCA
Found at i:16952 original size:17 final size:16
Alignment explanation
Indices: 16912--16961 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
16902 CATGTAATCT
* *
16912 TTGATCACCGATGATC
1 TTGATCACTGGTGATC
16928 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
16945 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
16962 CGGGGGTGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:18547 original size:2 final size:2
Alignment explanation
Indices: 18540--18566 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18530 GATTTGTGAC
18540 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
18567 CTACATATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28345 original size:21 final size:20
Alignment explanation
Indices: 28319--28382 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
28309 GCTATTCTAA
28319 TAATCTCATCTGTACAGTATC
1 TAATCTCATCTGTACAGT-TC
* ** *
28340 TAATCTAATCCATACAG-TG
1 TAATCTCATCTGTACAGTTC
*
28359 TAATCCCATCTGTACAGTTGC
1 TAATCTCATCTGTACAGTT-C
28380 TAA
1 TAA
28383 ACAGTGTCAA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
19 14 0.44
20 1 0.03
21 17 0.53
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTTC
Found at i:42397 original size:50 final size:50
Alignment explanation
Indices: 42317--42418 Score: 161
Period size: 50 Copynumber: 2.0 Consensus size: 50
42307 TCCTCAAAGG
* * *
42317 GACACCCCGGTGGTTAAAACTTTGGGCTTCTTGTTAGAGATTCTGGGTTC
1 GACACCCCGATGGTTAAAACTTTGGGCTTCTTGTGAGAGATCCTGGGTTC
42367 GACACCCCGATGGTTAAAA-TTTGGGCCTTCTTGTGAGAGATCCTGGGTTC
1 GACACCCCGATGGTTAAAACTTTGGG-CTTCTTGTGAGAGATCCTGGGTTC
42417 GA
1 GA
42419 ATCCTAGGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
49 6 0.12
50 42 0.88
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (50 bp):
GACACCCCGATGGTTAAAACTTTGGGCTTCTTGTGAGAGATCCTGGGTTC
Found at i:42665 original size:51 final size:51
Alignment explanation
Indices: 42610--42706 Score: 158
Period size: 51 Copynumber: 1.9 Consensus size: 51
42600 TGTTCATGAG
* *
42610 GAAAAATAAACATAGCACTAGATCTTTGTAATCAGGTATTTGACATAAAAA
1 GAAAAAAAAACATAGCACCAGATCTTTGTAATCAGGTATTTGACATAAAAA
* *
42661 GAAAAAAAAACATAGCACCCGATCTTTGTAATCGGGTATTTGACAT
1 GAAAAAAAAACATAGCACCAGATCTTTGTAATCAGGTATTTGACAT
42707 GATGGTAGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.27
Consensus pattern (51 bp):
GAAAAAAAAACATAGCACCAGATCTTTGTAATCAGGTATTTGACATAAAAA
Found at i:42667 original size:107 final size:108
Alignment explanation
Indices: 42481--42701 Score: 374
Period size: 107 Copynumber: 2.0 Consensus size: 108
42471 TGTGTAGCTC
*
42481 ATTTCAATATCATGTTCATGAGGGAAAAAAAACATAGTACTAGATCTTTGTAATCAGGTATTTGA
1 ATTTCAATATCATGTTCATGAGGGAAAAAAAACATAGCACTAGATCTTTGTAATCAGGTATTTGA
**
42546 CAT-AAAAAAAAAAAACATAGCACTGGATCTTTGTAATCGGGT
66 CATAAAAAAAAAAAAACATAGCACCCGATCTTTGTAATCGGGT
42588 ATTTCAATATCATGTTCATGA-GGAAAAATAAACATAGCACTAGATCTTTGTAATCAGGTATTTG
1 ATTTCAATATCATGTTCATGAGGGAAAAA-AAACATAGCACTAGATCTTTGTAATCAGGTATTTG
42652 ACATAAAAAGAAAAAAAAACATAGCACCCGATCTTTGTAATCGGGT
65 ACAT-AAAA-AAAAAAAAACATAGCACCCGATCTTTGTAATCGGGT
42698 ATTT
1 ATTT
42702 GACATGATGG
Statistics
Matches: 107, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
106 7 0.07
107 59 0.55
109 3 0.03
110 38 0.36
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (108 bp):
ATTTCAATATCATGTTCATGAGGGAAAAAAAACATAGCACTAGATCTTTGTAATCAGGTATTTGA
CATAAAAAAAAAAAAACATAGCACCCGATCTTTGTAATCGGGT
Found at i:42887 original size:109 final size:107
Alignment explanation
Indices: 42663--42889 Score: 253
Period size: 109 Copynumber: 2.1 Consensus size: 107
42653 CATAAAAAGA
*
42663 AAAAAAAACATAGCACCCGATCTTTGTAATCGGGTATTTGACATGATGGTAGAGTGTTGCACTCT
1 AAAAAAAACATAGCACCCGATCTTTGTAATCGGGTATTTGACATAATGGTAGAGTGTTGCACTCT
* *** ** ***
42728 TAATTTCAGTGGTTAAGGGATCTTTGTAATCAGGTATTTGGCAT
66 TAATTTCAGTGGCTAAGGGATCTCCCTAATCA-G-ACCTCAAAT
*
42772 AAAAAAAACATAGCACCCGATCTTTGTAATCGGGTATTTGACATAATGGTAGAGTGTTGGACTCT
1 AAAAAAAACATAGCACCCGATCTTTGTAATCGGGTATTTGACATAATGGTAGAGTGTTGCACTCT
*
42837 TAATTGT-AGTGGCTAA-GGTTCAGTCCCTAATACA-ACCTCAAAT
66 TAATT-TCAGTGGCTAAGGGATC--TCCCTAAT-CAGACCTCAAAT
42880 ACCAAAAAAA
1 A--AAAAAAA
42890 AAAATTAGGC
Statistics
Matches: 100, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
108 9 0.09
109 76 0.76
110 13 0.13
111 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (107 bp):
AAAAAAAACATAGCACCCGATCTTTGTAATCGGGTATTTGACATAATGGTAGAGTGTTGCACTCT
TAATTTCAGTGGCTAAGGGATCTCCCTAATCAGACCTCAAAT
Found at i:47950 original size:20 final size:21
Alignment explanation
Indices: 47925--47963 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
47915 ATAGTTACGG
47925 CTAATTTAAAGT-TAATTGAA
1 CTAATTTAAAGTCTAATTGAA
47945 CTAATTTAAAGTCTAATTG
1 CTAATTTAAAGTCTAATTG
47964 TGTTTAGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (21 bp):
CTAATTTAAAGTCTAATTGAA
Found at i:48133 original size:25 final size:26
Alignment explanation
Indices: 48104--48171 Score: 129
Period size: 25 Copynumber: 2.7 Consensus size: 26
48094 ATGAACTTTC
48104 AAAAATTACTTAATCCATAATTG-AA
1 AAAAATTACTTAATCCATAATTGAAA
48129 AAAAATTACTTAATCCATAATTGAAA
1 AAAAATTACTTAATCCATAATTGAAA
48155 AAAAATTACTTAATCCA
1 AAAAATTACTTAATCCA
48172 AAAACTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 23 0.55
26 19 0.45
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.31
Consensus pattern (26 bp):
AAAAATTACTTAATCCATAATTGAAA
Found at i:55315 original size:20 final size:20
Alignment explanation
Indices: 55290--55329 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
55280 ACCAGGGTCA
55290 ACTAACTAGGTAATTCTTTT
1 ACTAACTAGGTAATTCTTTT
55310 ACTAACTAGGTAATTCTTTT
1 ACTAACTAGGTAATTCTTTT
55330 CAACCATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (20 bp):
ACTAACTAGGTAATTCTTTT
Found at i:62586 original size:240 final size:240
Alignment explanation
Indices: 62158--62880 Score: 1293
Period size: 240 Copynumber: 3.0 Consensus size: 240
62148 TCCACAGCTC
* * *
62158 CTATAAGACTAACTCGCTCATCAGCTCAGAAAGGGGCTATAATCTCAAATGATGGCATCCAGGTG
1 CTATAAGACTAACTCGCTCAGCAGCTCGGAAAGGGGCTATAATCCCAAATGATGGCATCCAGGTG
* * * * *
62223 GAGATTCGCGATGATGATATGAAGAGAAGGGTTCCAGGCAAGAAAAACAGGTTGAGTCAGCCAGC
66 GAGATCCACGATGATGATATGAAGAGAAGGATTCCAGGGAAGAAAAACAGGTCGAGTCAGCCAGC
* *
62288 AGTTTGCCAAGGAAATGAAAATTTGGCCAATGCAGAGGAGAATGACTTGACTCATGTGACAGATT
131 AGTTTGTCAAGGAAATGAAAATTTGGCCAATGAAGAGGAGAATGACTTGACTCATGTGACAGATT
*
62353 CAGATTCATCTAATGGGAAGATTGCAGCTGCTGAGAGCGATGTGG
196 CAGATTCATCTAATGGGAAGATTGCAGCTGCTGAGAGCAATGTGG
62398 CTATAAGACTAACTCGCTCAGCAGCTCGGAAAGGGGCTATAATCCCAAATGATGGCATCCAGGTG
1 CTATAAGACTAACTCGCTCAGCAGCTCGGAAAGGGGCTATAATCCCAAATGATGGCATCCAGGTG
*
62463 GAGATCCACGATGATGATATGAAGAGAAGGATTCCAGGGAAGAAAAACAGGTCGAGTCAGCCAGT
66 GAGATCCACGATGATGATATGAAGAGAAGGATTCCAGGGAAGAAAAACAGGTCGAGTCAGCCAGC
* *
62528 AGTTTGTCAAGGAAATGAAAATTTGGCCAATGAAGAGGAGAATGACTTGACACATGTGATAGATT
131 AGTTTGTCAAGGAAATGAAAATTTGGCCAATGAAGAGGAGAATGACTTGACTCATGTGACAGATT
62593 CAGATTCATCTAATGGGAAGATTGCAGCTGCTGAGAGCAATGTGG
196 CAGATTCATCTAATGGGAAGATTGCAGCTGCTGAGAGCAATGTGG
62638 CTATAAGACTAACTCGCTCAGCAGCTCGGAAAGGGGCTATAATCCCAAATGATGGCATCCAGGTG
1 CTATAAGACTAACTCGCTCAGCAGCTCGGAAAGGGGCTATAATCCCAAATGATGGCATCCAGGTG
*
62703 GAGATCCACGATGATGATACGAAGAGAAGGATTCCAGGGAAGAAAAACAGGTCGAGTCAGCCAGC
66 GAGATCCACGATGATGATATGAAGAGAAGGATTCCAGGGAAGAAAAACAGGTCGAGTCAGCCAGC
*
62768 AGTTTGTCAAGGAAATGAAAATTTGGGCAATGAAGAGGAGAATGACTTGACTCATGTGACAGATT
131 AGTTTGTCAAGGAAATGAAAATTTGGCCAATGAAGAGGAGAATGACTTGACTCATGTGACAGATT
*
62833 TAGATTCATCTAATGGGAAGATTGCAGCTGCTGAGAGCAATGTGG
196 CAGATTCATCTAATGGGAAGATTGCAGCTGCTGAGAGCAATGTGG
62878 CTA
1 CTA
62881 CAATGAAATC
Statistics
Matches: 463, Mismatches: 20, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
240 463 1.00
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (240 bp):
CTATAAGACTAACTCGCTCAGCAGCTCGGAAAGGGGCTATAATCCCAAATGATGGCATCCAGGTG
GAGATCCACGATGATGATATGAAGAGAAGGATTCCAGGGAAGAAAAACAGGTCGAGTCAGCCAGC
AGTTTGTCAAGGAAATGAAAATTTGGCCAATGAAGAGGAGAATGACTTGACTCATGTGACAGATT
CAGATTCATCTAATGGGAAGATTGCAGCTGCTGAGAGCAATGTGG
Found at i:81443 original size:354 final size:354
Alignment explanation
Indices: 80814--81472 Score: 957
Period size: 354 Copynumber: 1.9 Consensus size: 354
80804 AATTAGGTAG
* * * **
80814 TGCAGCTGACATGGATTGTTCTCACGATGTGGCTGAGCAGACTAATGCTGCTGTTGATGATGGCA
1 TGCAGCTGACATGGATTCTTCTCACAATGTAGCTGAGCAGACTAATGCTGCTGCCGATGATGGCA
* * * *
80879 GCACAGAGAAGGATGCAGCTAACTTGCCGGGATCTATTCAGAGAGTAAATCATTCTCCACCGAAC
66 GCACACACAAGGATGCAGCTAACTTGCCAGGATCTATTCAGAGAGTAAATCATTCTCCACCAAAC
* * * *
80944 ATGGAAACTAATAAAGTAAAAGGCAGAAGAAACAAGAACGAAGCAAATGTCAGCCAATACATTGT
131 ACGGAAACCAATAAAGTAAAAGGCAGAAGAAACAAAAACGAAGCAAATGTCAGCCAATACATTCT
* * * * * *
81009 TGGAACTAGAACAACCAGAAGTAATGTTCGGATGACAAAATGCAGTCAGAAAGAGAACTTTAAGG
196 TAGAACTAGAACAACCAGAAATAATGTTCAGATGACAAAATGCAGTCAGAAAAAGAACATAAAGG
81074 ATGGATTTTCTACAACGCACAAGGATAGAGCTTCAAGAATGGAGCAAAAGCTGAATAGGAAGAAG
261 ATGGATTTTCTACAACGCACAAGGATAGAGCTTCAAGAATGGAGCAAAAGCTGAATAGGAAGAAG
81139 CCACACAATGAAAGATTGAAAGTAGACAA
326 CCACACAATGAAAGATTGAAAGTAGACAA
* * **
81168 TGCAGTTGACATGGATTCTTCTCACAATGTAGCTGAGCAGGCTAATGCTGCTGCCGATGATGGTG
1 TGCAGCTGACATGGATTCTTCTCACAATGTAGCTGAGCAGACTAATGCTGCTGCCGATGATGGCA
*
81233 GCACACACAA-GAGTGCAGCTAAC-TGCCCAGGATCTTTTCAGAGAGTAAATCATTCTCCACCAA
66 GCACACACAAGGA-TGCAGCTAACTTG-CCAGGATCTATTCAGAGAGTAAATCATTCTCCACCAA
* * * *
81296 ATACGGAAACCAATAAAG-AAAATGGTAGAAGAAACAAAAACGAAGTAAATGTCAGCCCATACGA
129 ACACGGAAACCAATAAAGTAAAA-GGCAGAAGAAACAAAAACGAAGCAAATGTCAGCCAATAC-A
* * *
81360 -TCTTAGAACTAGAACAACCAGAAATCATGTTCAGATTACAGAATGCAGTCAGAAAAAGAACATA
192 TTCTTAGAACTAGAACAACCAGAAATAATGTTCAGATGACAAAATGCAGTCAGAAAAAGAACATA
* *
81424 AAGGCTGGATTTTCTACAACGCACAAGGATAGAGTTTCAAGAATGGAGC
257 AAGGATGGATTTTCTACAACGCACAAGGATAGAGCTTCAAGAATGGAGC
81473 TTCAAGATGA
Statistics
Matches: 268, Mismatches: 33, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
353 8 0.03
354 259 0.97
355 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (354 bp):
TGCAGCTGACATGGATTCTTCTCACAATGTAGCTGAGCAGACTAATGCTGCTGCCGATGATGGCA
GCACACACAAGGATGCAGCTAACTTGCCAGGATCTATTCAGAGAGTAAATCATTCTCCACCAAAC
ACGGAAACCAATAAAGTAAAAGGCAGAAGAAACAAAAACGAAGCAAATGTCAGCCAATACATTCT
TAGAACTAGAACAACCAGAAATAATGTTCAGATGACAAAATGCAGTCAGAAAAAGAACATAAAGG
ATGGATTTTCTACAACGCACAAGGATAGAGCTTCAAGAATGGAGCAAAAGCTGAATAGGAAGAAG
CCACACAATGAAAGATTGAAAGTAGACAA
Done.