Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021200.1 Corchorus olitorius cultivar O-4 contig21233, 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: 9592
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:622 original size:43 final size:42
Alignment explanation
Indices: 460--655 Score: 135
Period size: 43 Copynumber: 4.6 Consensus size: 42
450 TTTTTTATTG
* ** *
460 GAAGATCAACTTAGATCTTTGAAAATTAATTAAAAGACAATTC
1 GAAGATCAACATAGATCTCCGAAAATTAA-CAAAAGACAATTC
* * * ** * *
503 GAAGATCAGCCTAGATCTCCGAATATTATTAAAATGGCAACTC
1 GAAGATCAACATAGATCTCCGAAAATTAACAAAA-GACAATTC
* ** * * * **
546 GAAGATCATCGCAGACCTCTGAAAGTTTTCAAGAAGACAATTC
1 GAAGATCAACATAGATCTCCGAAAATTAACAA-AAGACAATTC
* *
589 GCAGATCAACATAGATCTCCGAAAATTAACAAGAAGACGATTC
1 GAAGATCAACATAGATCTCCGAAAATTAACAA-AAGACAATTC
632 -AAGAATCAACATAGAT-TCCTGAAA
1 GAAG-ATCAACATAGATCTCC-GAAA
656 TTGAATGAAA
Statistics
Matches: 119, Mismatches: 30, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
42 10 0.08
43 107 0.90
44 2 0.02
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.24
Consensus pattern (42 bp):
GAAGATCAACATAGATCTCCGAAAATTAACAAAAGACAATTC
Found at i:1126 original size:71 final size:71
Alignment explanation
Indices: 1044--1257 Score: 360
Period size: 71 Copynumber: 3.0 Consensus size: 71
1034 AAACCTCATT
* *
1044 GAAC-TTGGCTTATGGAAAAGCCCCCTAATGCTTGGGTGGAACCAAGGGC-TAAATTGACTCGTA
1 GAACTTTGGCTTATGGAAAAGCCCCCTGATGCTTGGGTGGAACCAA-GGCTTAAACTGACTCGTA
1107 TGGAAAC
65 TGGAAAC
* *
1114 GAACTTTGGCTTATGGAAAAGCCCCCTGATGCTTGGGTGGAACCAAGGCTTAACCTGACTCATAT
1 GAACTTTGGCTTATGGAAAAGCCCCCTGATGCTTGGGTGGAACCAAGGCTTAAACTGACTCGTAT
1179 GGAAAC
66 GGAAAC
*
1185 GAACTTTGGCTTATGGAAAAGCCCCCTGATGCTTGGATGGAACCAAGGCTTAAACTGACTCGTAT
1 GAACTTTGGCTTATGGAAAAGCCCCCTGATGCTTGGGTGGAACCAAGGCTTAAACTGACTCGTAT
1250 GGAAAC
66 GGAAAC
1256 GA
1 GA
1258 GCTTAGTCTT
Statistics
Matches: 135, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
70 7 0.05
71 128 0.95
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.23
Consensus pattern (71 bp):
GAACTTTGGCTTATGGAAAAGCCCCCTGATGCTTGGGTGGAACCAAGGCTTAAACTGACTCGTAT
GGAAAC
Found at i:1367 original size:102 final size:102
Alignment explanation
Indices: 1190--1667 Score: 841
Period size: 102 Copynumber: 4.7 Consensus size: 102
1180 GAAACGAACT
* *
1190 TTGGCTTATGGAAAAGCCCCCTGATGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAA
1 TTGGCTTATGGAAAAG-CCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAA
1255 CGAGCT-TAGTCTTGGAAGACTGAATTCATGTGGAAAAC
65 CGAG-TATAGTCTTGGAAGACTGAATTCATGTGGAAAAC
1293 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1358 GAGTATAGTCTTGGAAGACTGAATTCATGTGGAAAAC
66 GAGTATAGTCTTGGAAGACTGAATTCATGTGGAAAAC
* **
1395 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAATCAAGGCTTAAACTGACTCGTATATAAAC
1 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
*
1460 GAGTATAGTCTTGGAAGACAGAATTCATGTGGAAAAC
66 GAGTATAGTCTTGGAAGACTGAATTCATGTGGAAAAC
*
1497 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAATCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1562 GAGTATAGTCTTGGAAGACTGAATTCATGTGGAAAAC
66 GAGTATAGTCTTGGAAGACTGAATTCATGTGGAAAAC
* * *
1599 TTGGCTTATGGAAAAGCCCATGTTGCTTGGACGGAACCAAGGCTTAAACTGAGTCGTATGGAAAT
1 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1664 GAGT
66 GAGT
1668 TTGACTTATG
Statistics
Matches: 361, Mismatches: 13, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
101 1 0.00
102 344 0.95
103 16 0.04
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (102 bp):
TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
GAGTATAGTCTTGGAAGACTGAATTCATGTGGAAAAC
Found at i:1575 original size:49 final size:49
Alignment explanation
Indices: 1318--1576 Score: 129
Period size: 49 Copynumber: 5.1 Consensus size: 49
1308 GCCCATGTTG
*
1318 CTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTATAGT
1 CTTGGATGGAATCAAGGCTTAAACTGACTCGTATGGAAACGAGTATAGT
* * ** * * ***
1367 CTTGGAAGACTGAATTCATGTG-GAAAACTTGGCT--TATGGAAAAGCCCAT-GTT
1 CTTGGATG---GAA-TCAAG-GCTTAAAC-TGACTCGTATGGAAACGAGTATAG-T
**
1419 GCTTGGATGGAATCAAGGCTTAAACTGACTCGTATATAAACGAGTATAGT
1 -CTTGGATGGAATCAAGGCTTAAACTGACTCGTATGGAAACGAGTATAGT
* * ** * * ***
1469 CTTGGAAGACAGAATTCATGTG-GAAAACTTGGCT--TATGGAAAAGCCCAT-GTT
1 CTTGGATG---GAA-TCAAG-GCTTAAAC-TGACTCGTATGGAAACGAGTATAG-T
1521 GCTTGGATGGAATCAAGGCTTAAACTGACTCGTATGGAAACGAGTATAGT
1 -CTTGGATGGAATCAAGGCTTAAACTGACTCGTATGGAAACGAGTATAGT
1571 CTTGGA
1 CTTGGA
1577 AGACTGAATT
Statistics
Matches: 145, Mismatches: 41, Indels: 48
0.62 0.18 0.21
Matches are distributed among these distances:
48 10 0.07
49 36 0.25
50 28 0.19
51 4 0.03
52 28 0.19
53 29 0.20
54 10 0.07
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (49 bp):
CTTGGATGGAATCAAGGCTTAAACTGACTCGTATGGAAACGAGTATAGT
Found at i:3745 original size:14 final size:14
Alignment explanation
Indices: 3707--3746 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3697 CTAGTTTCTG
*
3707 GAAAATCCTTTTTT
1 GAAAAACCTTTTTT
3721 G-AAAACACTTTTTT
1 GAAAAAC-CTTTTTT
3735 GAAAAACCTTTT
1 GAAAAACCTTTT
3747 GTTTTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 4 0.17
14 14 0.61
15 5 0.22
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.42
Consensus pattern (14 bp):
GAAAAACCTTTTTT
Done.