Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024473.1 Corchorus olitorius cultivar O-4 contig24506, 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: 32896
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1073 original size:17 final size:19
Alignment explanation
Indices: 1034--1079 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1024 CTTTTTAAGA
*
1034 CTCTTGTCTTAATAATCCT
1 CTCTTGTATTAATAATCCT
1053 CTCTTGTATTAATAATCCT
1 CTCTTGTATTAATAATCCT
1072 CTCTTGTA
1 CTCTTGTA
1080 ATTTTCTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.22, C:0.24, G:0.07, T:0.48
Consensus pattern (19 bp):
CTCTTGTATTAATAATCCT
Found at i:4207 original size:2 final size:2
Alignment explanation
Indices: 4200--4233 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4190 ACAATAGGCC
4200 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4234 CATTGGCTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4741 original size:25 final size:25
Alignment explanation
Indices: 4713--4857 Score: 220
Period size: 25 Copynumber: 5.8 Consensus size: 25
4703 GAAAATCAAA
4713 CGGCCACATAGTTGGTCGTGAGATT
1 CGGCCACATAGTTGGTCGTGAGATT
*
4738 CGGCTACATAGTTGGTCGTGAGATT
1 CGGCCACATAGTTGGTCGTGAGATT
* **
4763 CGGCCACATCGTTGGTCGTGAGAAA
1 CGGCCACATAGTTGGTCGTGAGATT
*
4788 CGGCCACATCGTTGGTCGTGAGATT
1 CGGCCACATAGTTGGTCGTGAGATT
4813 CGGCCACATAGTTGGTCGTGAGATT
1 CGGCCACATAGTTGGTCGTGAGATT
* *
4838 TGGCCACAT-GGTGGTCGTGA
1 CGGCCACATAGTTGGTCGTGA
4858 CAAAAGACCA
Statistics
Matches: 110, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
24 10 0.09
25 100 0.91
ACGTcount: A:0.19, C:0.21, G:0.33, T:0.27
Consensus pattern (25 bp):
CGGCCACATAGTTGGTCGTGAGATT
Found at i:4833 original size:75 final size:74
Alignment explanation
Indices: 4710--4857 Score: 251
Period size: 75 Copynumber: 2.0 Consensus size: 74
4700 GAGGAAAATC
* *
4710 AAACGGCCACATAGTTGGTCGTGAGATTCGGCTACATAGTTGGTCGTGAGATTCGGCCACATCGT
1 AAACGGCCACATAGTTGGTCGTGAGATTCGGCCACATAGTTGGTCGTGAGATTCGGCCACAT-GG
4775 TGGTCGTGAG
65 TGGTCGTGAG
* *
4785 AAACGGCCACATCGTTGGTCGTGAGATTCGGCCACATAGTTGGTCGTGAGATTTGGCCACATGGT
1 AAACGGCCACATAGTTGGTCGTGAGATTCGGCCACATAGTTGGTCGTGAGATTCGGCCACATGGT
4850 GGTCGTGA
66 GGTCGTGA
4858 CAAAAGACCA
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
74 10 0.14
75 59 0.86
ACGTcount: A:0.21, C:0.20, G:0.32, T:0.26
Consensus pattern (74 bp):
AAACGGCCACATAGTTGGTCGTGAGATTCGGCCACATAGTTGGTCGTGAGATTCGGCCACATGGT
GGTCGTGAG
Found at i:5419 original size:17 final size:19
Alignment explanation
Indices: 5380--5425 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
5370 CTTTTTAAGA
*
5380 CTCTTGTCTTAATAATCCT
1 CTCTTGTATTAATAATCCT
5399 CTCTTGTATTAATAATCCT
1 CTCTTGTATTAATAATCCT
5418 CTCTTGTA
1 CTCTTGTA
5426 ATTTTCTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.22, C:0.24, G:0.07, T:0.48
Consensus pattern (19 bp):
CTCTTGTATTAATAATCCT
Found at i:10770 original size:41 final size:41
Alignment explanation
Indices: 10725--10807 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
10715 TACATGTACA
10725 TGTCTTTTAGATAAAGACAACATTAAATAGATACATGTCTT
1 TGTCTTTTAGATAAAGACAACATTAAATAGATACATGTCTT
*
10766 TGTCTTTTGGATAAAGACAACATTAAATAGATACATGTCTT
1 TGTCTTTTAGATAAAGACAACATTAAATAGATACATGTCTT
10807 T
1 T
10808 TCATAAGACA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.37
Consensus pattern (41 bp):
TGTCTTTTAGATAAAGACAACATTAAATAGATACATGTCTT
Found at i:10846 original size:37 final size:37
Alignment explanation
Indices: 10796--10909 Score: 210
Period size: 37 Copynumber: 3.1 Consensus size: 37
10786 CATTAAATAG
* *
10796 ATACATGTCTTTTCATAAGACAACTCTTAATTCATGA
1 ATACATGTCTTTTCACAAGACAACTCTTGATTCATGA
10833 ATACATGTCTTTTCACAAGACAACTCTTGATTCATGA
1 ATACATGTCTTTTCACAAGACAACTCTTGATTCATGA
10870 ATACATGTCTTTTCACAAGACAACTCTTGATTCATGA
1 ATACATGTCTTTTCACAAGACAACTCTTGATTCATGA
10907 ATA
1 ATA
10910 ATCACATTAT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 75 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (37 bp):
ATACATGTCTTTTCACAAGACAACTCTTGATTCATGA
Found at i:15690 original size:41 final size:41
Alignment explanation
Indices: 15645--15727 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
15635 TACATGTACA
15645 TGTCTTTTAGATAAAAACAACATTAAATAGATACATGTCTT
1 TGTCTTTTAGATAAAAACAACATTAAATAGATACATGTCTT
* *
15686 TGTCTTTTGGATAAAGACAACATTAAATAGATACATGTCTT
1 TGTCTTTTAGATAAAAACAACATTAAATAGATACATGTCTT
15727 T
1 T
15728 TCACAAGACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (41 bp):
TGTCTTTTAGATAAAAACAACATTAAATAGATACATGTCTT
Found at i:20192 original size:11 final size:11
Alignment explanation
Indices: 20178--20203 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20168 TCATCATAAT
20178 TTTTGCAACAA
1 TTTTGCAACAA
20189 TTTTGCAACAA
1 TTTTGCAACAA
20200 TTTT
1 TTTT
20204 AGGAAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (11 bp):
TTTTGCAACAA
Found at i:20192 original size:12 final size:12
Alignment explanation
Indices: 20175--20203 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
20165 GAATCATCAT
20175 AATTTTTGCAAC
1 AATTTTTGCAAC
20187 AA-TTTTGCAAC
1 AATTTTTGCAAC
20198 AATTTT
1 AATTTT
20204 AGGAAGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (12 bp):
AATTTTTGCAAC
Found at i:22616 original size:23 final size:23
Alignment explanation
Indices: 22586--22632 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
22576 CAAAATTTTC
22586 TGCAGATTTTCTAGATGGTGGGT
1 TGCAGATTTTCTAGATGGTGGGT
22609 TGCAGATTTTCTAGATGGTGGGT
1 TGCAGATTTTCTAGATGGTGGGT
22632 T
1 T
22633 TTTTTGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.09, G:0.34, T:0.40
Consensus pattern (23 bp):
TGCAGATTTTCTAGATGGTGGGT
Found at i:30769 original size:13 final size:13
Alignment explanation
Indices: 30751--30775 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30741 GGATGAGAAA
30751 TATAATTGTTAGG
1 TATAATTGTTAGG
30764 TATAATTGTTAG
1 TATAATTGTTAG
30776 TCTATCAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
TATAATTGTTAGG
Done.