Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022125.1 Corchorus olitorius cultivar O-4 contig22158, 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: 12304
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4116 original size:104 final size:104
Alignment explanation
Indices: 3926--4117 Score: 330
Period size: 104 Copynumber: 1.8 Consensus size: 104
3916 GGTTAATTTG
*
3926 ATTACCCTGAATTAAGCCAACAAAAATTGATTACCTTTCTTAGCTTCTTAACTAACTCAGTTACC
1 ATTACCCTGAATTAAGCCAACAAAAATTGATTACCTTTCTTAGCTTCTTAACTAACTCAATTACC
*
3991 CTGAATTAAGCCACTTGATTATCCTCCTCACTTAACTTA
66 CTGAATTAAGCCACTTCATTATCCTCCTCACTTAACTTA
*
4030 ATTACCCTGAATTAAGCCAACTAAAATTGATTACCTTTCTTAGCTTCTTAACTAACTCAATTACC
1 ATTACCCTGAATTAAGCCAACAAAAATTGATTACCTTTCTTAGCTTCTTAACTAACTCAATTACC
* * *
4095 TTGAATTAAGCTAGTTCATTATC
66 CTGAATTAAGCCACTTCATTATC
4118 TTTCTTACCT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
104 82 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (104 bp):
ATTACCCTGAATTAAGCCAACAAAAATTGATTACCTTTCTTAGCTTCTTAACTAACTCAATTACC
CTGAATTAAGCCACTTCATTATCCTCCTCACTTAACTTA
Found at i:4180 original size:54 final size:53
Alignment explanation
Indices: 4023--4164 Score: 140
Period size: 53 Copynumber: 2.5 Consensus size: 53
4013 CCTCCTCACT
* * * *
4023 TAACTTAATTACCCTGAATTAAGCCAACTAAAATTGATTACCTTTCTTAGCTTCTTAAC
1 TAACTCAATTACCCTGAATTAAGCC-AC-----TTCATTAGCTTTCTTACCTTCTTAAC
* * * *
4082 TAACTCAATTACCTTGAATTAAGCTAGTTCATTATCTTTCTTACCTTCTTAAC
1 TAACTCAATTACCCTGAATTAAGCCACTTCATTAGCTTTCTTACCTTCTTAAC
*
4135 TGACTCAATTTACCCTGAATTAAGCCACTT
1 TAACTCAA-TTACCCTGAATTAAGCCACTT
4165 ATTGCTAATT
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
53 30 0.42
54 18 0.25
58 1 0.01
59 22 0.31
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (53 bp):
TAACTCAATTACCCTGAATTAAGCCACTTCATTAGCTTTCTTACCTTCTTAAC
Found at i:4760 original size:26 final size:26
Alignment explanation
Indices: 4693--4766 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
4683 TTAACAGAAG
* * *
4693 CCCAAAACATAAC--AAAATTAGAAA
1 CCCAAAGCATAACAAAAAATAAAAAA
*
4717 CCCAAAGTATAA-ATAAAAATAAAAAA
1 CCCAAAGCATAACA-AAAAATAAAAAA
4743 CCCAAAGCATAACAAAAAACTAAA
1 CCCAAAGCATAACAAAAAA-TAAA
4767 GCCCAGACAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
24 10 0.25
26 25 0.62
27 5 0.12
ACGTcount: A:0.65, C:0.19, G:0.04, T:0.12
Consensus pattern (26 bp):
CCCAAAGCATAACAAAAAATAAAAAA
Found at i:7172 original size:19 final size:18
Alignment explanation
Indices: 7148--7183 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7138 TGAAGACTTA
7148 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
7167 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
7184 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:8716 original size:21 final size:21
Alignment explanation
Indices: 8692--8786 Score: 154
Period size: 21 Copynumber: 4.5 Consensus size: 21
8682 AGATGCTAGG
8692 AGCTCATTGGAGAAGGTTCCA
1 AGCTCATTGGAGAAGGTTCCA
* *
8713 AGCTCATTTGAGAAAGTTCCA
1 AGCTCATTGGAGAAGGTTCCA
8734 AGCTCATTGGAGAAGGTTCCA
1 AGCTCATTGGAGAAGGTTCCA
**
8755 AGCTCATTGGAGAAGGTTTTA
1 AGCTCATTGGAGAAGGTTCCA
8776 AGCTCATTGGA
1 AGCTCATTGGA
8787 ATTGTCTAAG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 68 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.27
Consensus pattern (21 bp):
AGCTCATTGGAGAAGGTTCCA
Found at i:9601 original size:9 final size:9
Alignment explanation
Indices: 9587--9615 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
9577 TCTTCTCTTT
9587 TTCCAAAAA
1 TTCCAAAAA
9596 TTCCAAAAA
1 TTCCAAAAA
9605 TT-CAAAAA
1 TTCCAAAAA
9613 TTC
1 TTC
9616 ATTGTGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (9 bp):
TTCCAAAAA
Found at i:10058 original size:21 final size:21
Alignment explanation
Indices: 10032--10072 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10022 TTGAAGCCCT
10032 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
10053 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
10073 GGGTTTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Found at i:11199 original size:33 final size:33
Alignment explanation
Indices: 11162--11258 Score: 110
Period size: 33 Copynumber: 2.9 Consensus size: 33
11152 ACTAATTTGA
*
11162 GTGTTGTTTGTGATGACACTAAA-TCTGTTTTAG
1 GTGTTGTTTGTGATGAAAC-AAATTCTGTTTTAG
11195 GTGTTGTTTGTGATGAAACAAATTCTGTTTT-G
1 GTGTTGTTTGTGATGAAACAAATTCTGTTTTAG
* **
11227 GATGCTAATTGTGATGAAAACAAA-TCTGTTTT
1 G-TGTTGTTTGTGATG-AAACAAATTCTGTTTT
11259 GGTTGATCAT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
32 5 0.09
33 45 0.79
34 7 0.12
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43
Consensus pattern (33 bp):
GTGTTGTTTGTGATGAAACAAATTCTGTTTTAG
Found at i:11894 original size:15 final size:16
Alignment explanation
Indices: 11870--11909 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
11860 AGAGGTTGAA
*
11870 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
11885 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
11901 AGAAAACAA
1 AGAAAACAA
11910 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Done.