Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010698.1 Corchorus olitorius cultivar O-4 contig10730, 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: 8247
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:383 original size:31 final size:31
Alignment explanation
Indices: 345--408 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
335 CCAAATCAAA
345 AATAAAAAATAGAAACTTTAATCAACTAAAG
1 AATAAAAAATAGAAACTTTAATCAACTAAAG
376 AATAAAAAATAGAAACTTTAATCAACTAAAG
1 AATAAAAAATAGAAACTTTAATCAACTAAAG
407 AA
1 AA
409 GAGTTGTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.22
Consensus pattern (31 bp):
AATAAAAAATAGAAACTTTAATCAACTAAAG
Found at i:1157 original size:54 final size:54
Alignment explanation
Indices: 1092--2206 Score: 809
Period size: 54 Copynumber: 20.8 Consensus size: 54
1082 TGGATCAAAT
* *
1092 TGGAGATCAACTCTGATCATCGAAAACTTCTTAAAATGACCGCACCGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * * *
1146 CGGAGATCAACTCTGATCTTCGAAAACTTCTTAAAACGACTGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * *
1200 TGGAGATCAACTCTGATCATCGAAGACTTCTTAAAATGACTGCACCGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * *
1254 TGGAGATCAACTCTGATCTTTGAAAACTTCTTGAAACGATCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * *
1308 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGGAAGGACTGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * *
1362 TGGATATCAACTCTGATCTTCGAAAACTTCTTGGAAGGACCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * * *
1416 TGGATATCAACTCTGATCATTGAAAACTTTTTTG-AATGACCACACTGGATAATC
1 TGGAGATCAACTCTGATCATCGAAAAC-TTCTTGAAATGACCGCACTGGATCATC
* * *
1470 TGG-GATCAACTCTGATCA-CTGGAAACTTCTTCAAATGACAGCACTGGATCATC
1 TGGAGATCAACTCTGATCATC-GAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * *
1523 T-GAGGATCAACTCTAATCATTGAAAACTTCTTTGGAATGACCGCACTGGATCATG
1 TGGA-GATCAACTCTGATCATCGAAAACTTC-TTGAAATGACCGCACTGGATCATC
* * * *
1578 TAGG-GATCAACCCTGATC-TCTAAAAACTTCTT-AGAATGACCGCATTGGGTCATC
1 T-GGAGATCAACTCTGATCATC-GAAAACTTCTTGA-AATGACCGCACTGGATCATC
* * * *
1632 TAG-GATCGACTCTG---ATC--AAACTTATTGGAATGACCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* ** * *
1680 TGGGGATCAACTCTGATCA-CTGAAAACTTCTTGAAATGATTGCACTAGATCATT
1 TGGAGATCAACTCTGATCATC-GAAAACTTCTTGAAATGACCGCACTGGATCATC
* * *
1734 TGGGGATCAACTCTGATCAT-TAAACACTTCTTGAAATGATCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAA-ACTTCTTGAAATGACCGCACTGGATCATC
* * * * *
1788 TAGG-GATCAACTCTGATC-TCTAAAAACTTCTACGAAAGGTA--ACACCGGATCATC
1 T-GGAGATCAACTCTGATCATC-GAAAACTTCT-TGAAATG-ACCGCACTGGATCATC
* * * *
1842 TGAAGATCAACT-TAGAT-TTCTGAAAGCTT-TATGAAA-GACCGCA-TAGGGTCATC
1 TGGAGATCAACTCT-GATCATC-GAAAACTTCT-TGAAATGACCGCACT-GGATCATC
* * * * *
1895 AT-AAAATCAACT-TAAATC-TCTGAAAACTTCTATGAAA-GACCGCACAGGGTCATC
1 -TGGAGATCAACTCT-GATCATC-GAAAACTTCT-TGAAATGACCGCACTGGATCATC
* * * * * * *
1949 TGAAGATCAACT-TAAACCTAT-GAAAACTTCTATGAAA-GACCGAACAGGGTTATC
1 TGGAGATCAACTCT-GATC-ATCGAAAACTTCT-TGAAATGACCGCACTGGATCATC
* * * * * * *
2003 TGAAGATCAACT-TAAACCTCTGAAAACTTCTATGAAA-GACCGCACAGGGTCATT
1 TGGAGATCAACTCTGATCATC-GAAAACTTCT-TGAAATGACCGCACTGGATCATC
* * * * * * *
2057 TGAAGATCAACT-TAAACCTCTGAAAGCTTCTATGAAAT-ACCGCACAGGGTCATC
1 TGGAGATCAACTCTGATCATC-GAAAACTTCT-TGAAATGACCGCACTGGATCATC
* * * *
2111 TGAAGATCAACT-TAAATC-TCTGAAAACTTCTATGAAAT-ACCGCACAGGGTCATC
1 TGGAGATCAACTCT-GATCATC-GAAAACTTCT-TGAAATGACCGCACTGGATCATC
* *
2165 TGAAGATCAACT-TAAATC-TCTGAAAACTTCTATGAAA-GACCG
1 TGGAGATCAACTCT-GATCATC-GAAAACTTCT-TGAAATGACCG
2207 TGCAGGGTTA
Statistics
Matches: 914, Mismatches: 102, Indels: 90
0.83 0.09 0.08
Matches are distributed among these distances:
48 28 0.03
49 10 0.01
51 4 0.00
52 8 0.01
53 95 0.10
54 707 0.77
55 59 0.06
56 2 0.00
57 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (54 bp):
TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
Found at i:2213 original size:54 final size:54
Alignment explanation
Indices: 1837--2299 Score: 648
Period size: 54 Copynumber: 8.6 Consensus size: 54
1827 TAACACCGGA
* * * *
1837 TCATCTGAAGATCAACTTAGATTTCTGAAAGCTT-TATGAAAGACCGCATAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
*
1890 TCATCAT-AAAATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
1 TCATC-TGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* * *
1944 TCATCTGAAGATCAACTTAAACCTATGAAAACTTCTATGAAAGACCGAACAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* *
1998 TTATCTGAAGATCAACTTAAACCTCTGAAAACTTCTATGAAAGACCGCACAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* * * *
2052 TCATTTGAAGATCAACTTAAACCTCTGAAAGCTTCTATGAAATACCGCACAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
*
2106 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAATACCGCACAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
**
2160 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGTGCAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* * * * *
2214 TTATTTGAAGATCAACTTAAACCTCTTAAAACTTATATGAAAGACCGCACAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* * *
2268 CCA--TGAACG-TTAACTTAGATCTCTGAAAACTT
1 TCATCTGAA-GATCAACTTAAATCTCTGAAAACTT
2300 TAGAAGATCA
Statistics
Matches: 371, Mismatches: 35, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
52 23 0.06
53 30 0.08
54 318 0.86
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (54 bp):
TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
Found at i:7613 original size:38 final size:39
Alignment explanation
Indices: 7536--7615 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 39
7526 ATCTTTTTGA
** * *
7536 AAAACATTTTTTCTCTTTTGAAAAGATTGCACTTTGAGG
1 AAAACATTTTTTCTCTTTTGAAAAGATCACACCTAGAGG
7575 AAAACATTTTTT-TCTTTTGAAAAGATCACACCTAGAGG
1 AAAACATTTTTTCTCTTTTGAAAAGATCACACCTAGAGG
7613 AAA
1 AAA
7616 GTTTCATTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 25 0.68
39 12 0.32
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (39 bp):
AAAACATTTTTTCTCTTTTGAAAAGATCACACCTAGAGG
Found at i:7826 original size:20 final size:19
Alignment explanation
Indices: 7794--7859 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 19
7784 CTTTCCTCCG
7794 TCTTTTGCTTTTTCAACTTTT
1 TCTTTT-CTTTTTCAA-TTTT
7815 TCTTTTCTTTTTCAATTCTT
1 TCTTTTCTTTTTCAATT-TT
*
7835 T-TATTCTTTCTTC-ATTTT
1 TCTTTTCTTT-TTCAATTTT
7853 TCTTTTC
1 TCTTTTC
7860 CTCTCCTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 3 0.08
19 16 0.40
20 15 0.38
21 6 0.15
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTTTTCAATTTT
Done.