Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017748.1 Corchorus olitorius cultivar O-4 contig17781, 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: 10072
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:1058 original size:16 final size:15
Alignment explanation
Indices: 1037--1079 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 15
1027 TTACTCTTCT
1037 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
1053 TTGTTTTTCTGTTTAA
1 TTG-TTTTCTGTTTAA
1069 TTGTTTTCTGT
1 TTGTTTTCTGT
1080 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.31
16 12 0.46
17 6 0.23
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:6489 original size:12 final size:12
Alignment explanation
Indices: 6474--6509 Score: 63
Period size: 12 Copynumber: 2.9 Consensus size: 12
6464 GAAAAAAAAT
6474 TGAAAAATGAAA
1 TGAAAAATGAAA
6486 TGAAAAATGAAA
1 TGAAAAATGAAA
6498 TGAAAAAATGAA
1 TG-AAAAATGAA
6510 GAAAGAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (12 bp):
TGAAAAATGAAA
Found at i:8053 original size:67 final size:67
Alignment explanation
Indices: 7943--8333 Score: 602
Period size: 67 Copynumber: 5.8 Consensus size: 67
7933 GGATTTTAGA
* * ** *
7943 TACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTCGAAGACAATCTCATTAAGA
1 TACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGA
8008 AG
66 AG
* *
8010 TACACCAGAAGACGGTGTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAAA
1 TACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATT-AAG
8075 AAG
65 AAG
* * *
8078 TACACCGGAAAACGGTTTGTTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCATTAAGA
1 TACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGA
8143 AG
66 AG
* * * *
8145 TACACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTAATTGGAAGACAATCTTATTAAGG
1 TACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGA
8210 AG
66 AG
* * * *
8212 AACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTAATTGGAAGACAATCTTATTAAGG
1 TACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGA
8277 AG
66 AG
*
8279 AACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAAT
1 TACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAAT
8334 ACATCGGAAG
Statistics
Matches: 303, Mismatches: 20, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
67 241 0.80
68 62 0.20
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (67 bp):
TACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGA
AG
Found at i:8185 original size:135 final size:133
Alignment explanation
Indices: 7943--8539 Score: 700
Period size: 135 Copynumber: 4.6 Consensus size: 133
7933 GGATTTTAGA
* *
7943 TACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTCGAAGACAATCTCATTAAGA
1 TACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCATTAAGA
* *
8008 AGTACACCAGAAGACGGTGTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
66 AGAACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATT--
8073 AAAAG
129 AAAAG
* *
8078 TACACCGGAAAACGGTTTGTTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCATTAAGA
1 TACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCATTAAGA
* * * *
8143 AGTACACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTAATTGGAAGACAATCTTATTAA
66 AGAACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
*
8208 GGAG
131 -AAG
* * * * * * *
8212 AACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTAATTGGAAGACAATCTTATTAAGG
1 TACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCATTAAGA
8277 AGAACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAG---A---C-----
66 AGAACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
8331 AA-
131 AAG
* * * *
8333 TACATCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTTATTAAGG
1 TACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCATTAAGA
* * *
8398 AGAACCCCAGAAGACGGTTTGTTAGAAAGGATTTTCAAATGTCGATTGGAAGACAATCTC-----
66 AGAACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
8458 -A-
131 AAG
** * * ** *
8459 T----CGGAAGACGGTTTGCTAGAAAGAATTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGA
1 TACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCATTAAGA
* *
8520 AGTACACCAGAAGATGGTTT
66 AGAACACCAGAAGACGGTTT
8540 CTCAAAAATT
Statistics
Matches: 415, Mismatches: 40, Indels: 27
0.86 0.08 0.06
Matches are distributed among these distances:
121 109 0.26
122 70 0.17
124 1 0.00
126 2 0.00
127 1 0.00
131 1 0.00
133 2 0.00
134 109 0.26
135 120 0.29
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.27
Consensus pattern (133 bp):
TACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCATTAAGA
AGAACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAA
AAG
Found at i:8433 original size:121 final size:122
Alignment explanation
Indices: 8219--8539 Score: 493
Period size: 121 Copynumber: 2.6 Consensus size: 122
8209 GAGAACACCA
* *
8219 GAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTAATTGGAAGACAATCTTATTAAGGAGAACAC
1 GAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTTATTAAGGAGAACAC
*
8284 CAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAAT-ACATCG
66 CAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTCGATTGGAAGACAATCACATCG
*
8340 GAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTTATTAAGGAGAACCC
1 GAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTTATTAAGGAGAACAC
* *
8405 CAGAAGACGGTTTGTTAGAAAGGATTTTCAAATGTCGATTGGAAGACAATCTCATCG
66 CAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTCGATTGGAAGACAATCACATCG
* * * * * * *
8462 GAAGACGGTTTGCTAGAAAGAATTTTCAGGA-GTTGATCGGAAGACGATCTTGTCAAGAAGTACA
1 GAAGACGGTTTGCTAGAAAGAATTTTCA-AATGTTGATTGGAAGACAATCTTATTAAGGAGAACA
*
8526 CCAGAAGATGGTTT
65 CCAGAAGACGGTTT
8540 CTCAAAAATT
Statistics
Matches: 183, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
121 110 0.60
122 72 0.39
123 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (122 bp):
GAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTTATTAAGGAGAACAC
CAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTCGATTGGAAGACAATCACATCG
Found at i:8504 original size:55 final size:55
Alignment explanation
Indices: 8407--8511 Score: 140
Period size: 55 Copynumber: 1.9 Consensus size: 55
8397 GAGAACCCCA
* * *
8407 GAAGACGGTTTGTTAGAAAGGATTTTCAAATGTCGATTGGAAGACAATCTCATCG
1 GAAGACGGTTTGCTAGAAAGAATTTTCAAATGTCGATCGGAAGACAATCTCATCG
* * *
8462 GAAGACGGTTTGCTAGAAAGAATTTTCAGGA-GTTGATCGGAAGACGATCT
1 GAAGACGGTTTGCTAGAAAGAATTTTCA-AATGTCGATCGGAAGACAATCT
8512 TGTCAAGAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
55 42 0.98
56 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (55 bp):
GAAGACGGTTTGCTAGAAAGAATTTTCAAATGTCGATCGGAAGACAATCTCATCG
Found at i:8566 original size:64 final size:64
Alignment explanation
Indices: 8482--8903 Score: 488
Period size: 64 Copynumber: 6.6 Consensus size: 64
8472 TGCTAGAAAG
*
8482 AATTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
** * * *
8546 AATTTTCCTAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGTTTTCTTAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * * ** *
8610 AATTTTCAGAAGTGGATCGGAAGATGATCTTGTCAAAAAGTACATTAGAAGATGGTTTCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * ** * **
8674 AGTTTTCAGAAGTTGATCGGAAGATGATCTTGTCAAGAAGTGTACCAGAAGATAGCGTCT-AAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * * * *
8737 GAGTTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAACTACGCCAGAAGATGGATTCTC-AA
1 -AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * * * * * *
8801 AATTTTCAAAAGTCGGTCGGAAGACGATCTTGTTAAAAAGCACACCAGAAGATAGTTTCTCGAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC-AAA
** * * *
8866 AGGTTTCAGAAGTGGGTCGGAAGACGATCTTGTTAAGA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGA
8904 GATGCACAGG
Statistics
Matches: 302, Mismatches: 52, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
63 51 0.17
64 216 0.72
65 35 0.12
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (64 bp):
AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
Found at i:8705 original size:192 final size:192
Alignment explanation
Indices: 8484--8903 Score: 540
Period size: 192 Copynumber: 2.2 Consensus size: 192
8474 CTAGAAAGAA
* * **
8484 TTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA-AA
1 TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATAGCGTCT-AAAGAA
** * ** *
8548 TTTTCCTAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGTTTTCTTAACAAT
65 TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGATTCTCAA-AAT
* * * ** * *
8613 TTTCAGAAGT-GGATCGGAAGATGATCTTGTCAAAAAGTACATTAGAAGATGGTTTCTC-AACAG
129 TTTCAAAAGTCGG-TCGGAAGACGATCTTGTCAAAAAGCACACCAGAAGATAGTTTCTCGAAAAG
* ** *
8676 TTTTCAGAAGTTGATCGGAAGATGATCTTGTCAAGAAGTGTACCAGAAGATAGCGTCTAAAGAGT
1 TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATAGCGTCTAAAGAAT
* *
8741 TTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAACTACGCCAGAAGATGGATTCTCAAAATTT
66 TTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGATTCTCAAAATTT
*
8806 TCAAAAGTCGGTCGGAAGACGATCTTGTTAAAAAGCACACCAGAAGATAGTTTCTCGAAAAG
131 TCAAAAGTCGGTCGGAAGACGATCTTGTCAAAAAGCACACCAGAAGATAGTTTCTCGAAAAG
* * * *
8868 GTTTCAGAAGTGGGTCGGAAGACGATCTTGTTAAGA
1 TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGA
8904 GATGCACAGG
Statistics
Matches: 196, Mismatches: 29, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
191 54 0.28
192 142 0.72
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (192 bp):
TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATAGCGTCTAAAGAAT
TTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAACTACACCAGAAGATGGATTCTCAAAATTT
TCAAAAGTCGGTCGGAAGACGATCTTGTCAAAAAGCACACCAGAAGATAGTTTCTCGAAAAG
Found at i:9191 original size:50 final size:50
Alignment explanation
Indices: 9133--9507 Score: 578
Period size: 50 Copynumber: 7.5 Consensus size: 50
9123 GGTTTTCTCG
*
9133 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
1 AGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
* *
9183 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTA
1 AGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
9233 AGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
1 AGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
* * *
9283 AGGTTGAATTGGTAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTCTA
1 AGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
*
9333 AGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTCTA
1 AGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
* * *
9383 AGATTGAATTGGTAGACAATTCAAAGGATAAACGGAAGACGATCCTTTTA
1 AGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
*
9433 AGATTGAATTGG-AGGACAGTTCAAAGGATAAGCGGAAGAC-G-ACTCTTTA
1 AGATTGAATTGGTA-GACAGTTCAAAGGATAAGCGGAAGACGGTCCT-TTTA
* *
9482 ATATT-AGATTGGTAGACAATTCAAAG
1 AGATTGA-ATTGGTAGACAGTTCAAAG
9508 AAGTTGATCC
Statistics
Matches: 303, Mismatches: 18, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
48 3 0.01
49 25 0.08
50 275 0.91
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (50 bp):
AGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
Done.