Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024484.1 Corchorus olitorius cultivar O-4 contig24517, 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: 3234
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Found at i:700 original size:63 final size:64
Alignment explanation
Indices: 530--733 Score: 266
Period size: 67 Copynumber: 3.2 Consensus size: 64
520 CACACAAAAC
* *
530 AAAAAAAAAAGAGCTCGCTAAGTTGAAAATCCTGTAAAGGACGACTTAGGCAAAAGTTAGAGCAA
1 AAAAAAAAAACAGCTCGCTAAGTTGAAAATCCTGTAAAGGACGGCTTAGGCAAAAGTTAGAG---
595 CA
63 CA
*
597 AAAAAAAAAACAGCTCGCTAAGTTGAAAATCCTGTAAAGGACGGCTTAGGCAAAAGTTAGAGCG
1 AAAAAAAAAACAGCTCGCTAAGTTGAAAATCCTGTAAAGGACGGCTTAGGCAAAAGTTAGAGCA
** * *** * * *
661 GGAAAAAAAA-AGCTTGCTAAGTTGAAAATCCTACGAAGGACAGCTTAGGAAAAATTTAGAGCA
1 AAAAAAAAAACAGCTCGCTAAGTTGAAAATCCTGTAAAGGACGGCTTAGGCAAAAGTTAGAGCA
724 AAAAAAAAAA
1 AAAAAAAAAA
734 ACCAAATGAA
Statistics
Matches: 122, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
63 53 0.43
64 9 0.07
67 60 0.49
ACGTcount: A:0.49, C:0.14, G:0.21, T:0.17
Consensus pattern (64 bp):
AAAAAAAAAACAGCTCGCTAAGTTGAAAATCCTGTAAAGGACGGCTTAGGCAAAAGTTAGAGCA
Found at i:734 original size:63 final size:62
Alignment explanation
Indices: 529--734 Score: 259
Period size: 63 Copynumber: 3.2 Consensus size: 62
519 GCACACAAAA
*
529 CAAAAAAAAAAGAGCTCGCTAAGTTGAAAATCCTGTAAAGGACGACTTAGGCAAAAGTTAGAG
1 CAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGTAAAGGACG-CTTAGGCAAAAGTTAGAG
592 CAACAAAAAAAAAAACAGCTCGCTAAGTTGAAAATCCTGTAAAGGACGGCTTAGGCAAAAGTTAG
1 ---CAAAAAAAAAAA-AGCTCGCTAAGTTGAAAATCCTGTAAAGGAC-GCTTAGGCAAAAGTTAG
657 AG
61 AG
*** * *** * *
659 CGGGAAAAAAAAAGCTTGCTAAGTTGAAAATCCTACGAAGGACAGCTTAGGAAAAATTTAGAG
1 CAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGTAAAGGAC-GCTTAGGCAAAAGTTAGAG
722 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
735 CCAAATGAAC
Statistics
Matches: 124, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
63 54 0.44
64 9 0.07
66 11 0.09
67 49 0.40
68 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.21, T:0.17
Consensus pattern (62 bp):
CAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGTAAAGGACGCTTAGGCAAAAGTTAGAG
Found at i:1441 original size:16 final size:16
Alignment explanation
Indices: 1420--1454 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1410 ACAATTCAGA
1420 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
1436 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
1452 AAG
1 AAG
1455 TATTTTCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:1607 original size:41 final size:41
Alignment explanation
Indices: 1550--1873 Score: 418
Period size: 41 Copynumber: 7.9 Consensus size: 41
1540 TTTTCGTTTG
**
1550 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
1591 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
**
1632 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
** * *
1673 TTCAAGATTGAGTCTTCGAGACCCTTGAACTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* * *
1714 TTCAAGAACAAGTCATCGAGACCCTTGAATCGAATTATTAACAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAAT-TAA--ATTATCAA
* *
1758 TTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* * * *
1799 TTCAAGGTCAAGTCGTCAACACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* *
1840 TTCAAGAACAAGTCATTC--GACCCTTGAATCAAAT
1 TTCAAGATCAAGTCA-TCGAGACCCTTGAATTAAAT
1874 CAAATCAAAC
Statistics
Matches: 256, Mismatches: 23, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
40 14 0.05
41 202 0.79
42 4 0.02
43 2 0.01
44 34 0.13
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (41 bp):
TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:1824 original size:126 final size:124
Alignment explanation
Indices: 1570--1873 Score: 418
Period size: 126 Copynumber: 2.5 Consensus size: 124
1560 AGTCATCGAG
** * *
1570 ACCCTTGAATTAAATTATCAATTCAAGATTAAGTCATCGAGACCCTTGAAT-TAAATTATCAATT
1 ACCCTTGAATTAAATTATCAATTCAAGAACAAGTCATCGAGACCCTTGAATCGAAATTAACAATT
** * ** * * *
1634 CAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGATTGAGTCTTCGAG
66 CAAGATCAAGTCATCAAGACCCTTGAATTAAATTATCAATTCAAGATCAAGTCGTCAAC
*
1693 ACCCTTGAACTAAATTATCAATTCAAGAACAAGTCATCGAGACCCTTGAATCGAATTATTAACAA
1 ACCCTTGAATTAAATTATCAATTCAAGAACAAGTCATCGAGACCCTTGAATCGAA--ATTAACAA
* *
1758 TTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATCAATTCAAGGTCAAGTCGTCAAC
64 TTCAAGATCAAGTCATCAAGACCCTTGAATTAAATTATCAATTCAAGATCAAGTCGTCAAC
1819 ACCCTTGAATTAAATTATCAATTCAAGAACAAGTCATTC--GACCCTTGAATC-AAAT
1 ACCCTTGAATTAAATTATCAATTCAAGAACAAGTCA-TCGAGACCCTTGAATCGAAAT
1874 CAAATCAAAC
Statistics
Matches: 161, Mismatches: 16, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
122 2 0.01
123 48 0.30
124 4 0.02
125 12 0.07
126 93 0.58
127 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (124 bp):
ACCCTTGAATTAAATTATCAATTCAAGAACAAGTCATCGAGACCCTTGAATCGAAATTAACAATT
CAAGATCAAGTCATCAAGACCCTTGAATTAAATTATCAATTCAAGATCAAGTCGTCAAC
Done.