Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009578.1 Corchorus olitorius cultivar O-4 contig09610, 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: 7343
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1046 original size:31 final size:30
Alignment explanation
Indices: 1008--1070 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
998 GTGTCCTTTA
*
1008 TAAACTTTCAAAATTTTGTCATTATGCCCCT
1 TAAACTTTCAAAATTCTGTCATT-TGCCCCT
* *
1039 TAAACTTTTAAAATTCTGTCATTTTCCCCT
1 TAAACTTTCAAAATTCTGTCATTTGCCCCT
1069 TA
1 TA
1071 CTCTATTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (30 bp):
TAAACTTTCAAAATTCTGTCATTTGCCCCT
Found at i:2436 original size:42 final size:43
Alignment explanation
Indices: 2385--2478 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 43
2375 CGTGCGTTAC
* *
2385 CTAA-ATTCTA-CTACATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTACATCTCTAGATAATTCATCAAAATAAAA
*
2426 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTA--CCTACATCTCTAGATAATTCATCAAAATAAAA
*
2471 TTAATATT
1 CTAATATT
2479 AATTGTTGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 35 0.78
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTACATCTCTAGATAATTCATCAAAATAAAA
Found at i:5264 original size:14 final size:14
Alignment explanation
Indices: 5242--5276 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5232 ACATATTGAA
* *
5242 ATAAAAATAAATAT
1 ATAATAATAAATAG
5256 ATAATAATAAATAG
1 ATAATAATAAATAG
5270 ATAATAA
1 ATAATAA
5277 ATAGATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
ATAATAATAAATAG
Found at i:5273 original size:11 final size:11
Alignment explanation
Indices: 5259--5284 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5249 TAAATATATA
5259 ATAATAAATAG
1 ATAATAAATAG
5270 ATAATAAATAG
1 ATAATAAATAG
5281 ATAA
1 ATAA
5285 AAAAATATAG
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:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (11 bp):
ATAATAAATAG
Found at i:5294 original size:25 final size:25
Alignment explanation
Indices: 5247--5294 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5237 TTGAAATAAA
* *
5247 AATAAATATATAATAATAAATAGAT
1 AATAAATAGATAATAAAAAATAGAT
5272 AATAAATAGATAA-AAAAATATAG
1 AATAAATAGATAATAAAAA-ATAG
5295 CAACTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (25 bp):
AATAAATAGATAATAAAAAATAGAT
Found at i:5999 original size:20 final size:20
Alignment explanation
Indices: 5962--6000 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5952 TACTATTATT
5962 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
5982 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
6001 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:6223 original size:22 final size:21
Alignment explanation
Indices: 6168--6363 Score: 158
Period size: 22 Copynumber: 8.9 Consensus size: 21
6158 TCTCGGTGTC
*
6168 GTTATCAAAATTTCATAAGATG
1 GTTATCAAAATTTCATAGGA-G
* * *
6190 GTCATTATAATTTCATGAGGAG
1 GTTATCAAAATTTCAT-AGGAG
*
6212 GTTATCAAAATTTCATAGTGTG
1 GTTATCAAAATTTCATAG-GAG
* * *
6234 ATTACCAAAATTTCATATGGAA
1 GTTATCAAAATTTCATA-GGAG
* *
6256 GTTATCAAAGTTTCATGGGAAG
1 GTTATCAAAATTTCATAGG-AG
*
6278 GTTATCAAAATTTCATAGTGTG
1 GTTATCAAAATTTCATAG-GAG
*
6300 GTTACCAAAATTTCATAGGATCAG
1 GTTATCAAAATTTCATAGG---AG
* *
6324 GTTATTAAAATTTCTTAGGAAG
1 GTTATCAAAATTTCATAGG-AG
**
6346 GTTATTGAAATTTCATAG
1 GTTATCAAAATTTCATAG
6364 TACTATCACA
Statistics
Matches: 138, Mismatches: 28, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
21 5 0.04
22 111 0.80
23 5 0.04
24 17 0.12
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.37
Consensus pattern (21 bp):
GTTATCAAAATTTCATAGGAG
Found at i:6280 original size:66 final size:67
Alignment explanation
Indices: 6198--6364 Score: 223
Period size: 66 Copynumber: 2.5 Consensus size: 67
6188 TGGTCATTAT
6198 AATTTCATGAGG-AGGTTATCAAAATTTCATAGTGTGATTACCAAAATTTCATATGGA-A-GTTA
1 AATTTCATG-GGAAGGTTATCAAAATTTCATAGTGTGATTACCAAAATTTCATA-GGACAGGTTA
6260 TCAA
64 TCAA
* *
6264 AGTTTCATGGGAAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATCAGGTTAT
1 AATTTCATGGGAAGGTTATCAAAATTTCATAGTGTGATTACCAAAATTTCATAGGA-CAGGTTAT
*
6329 TAA
65 CAA
* * **
6332 AATTTCTTAGGAAGGTTATTGAAATTTCATAGT
1 AATTTCATGGGAAGGTTATCAAAATTTCATAGT
6365 ACTATCACAA
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
65 5 0.06
66 48 0.54
67 1 0.01
68 35 0.39
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.37
Consensus pattern (67 bp):
AATTTCATGGGAAGGTTATCAAAATTTCATAGTGTGATTACCAAAATTTCATAGGACAGGTTATC
AA
Found at i:6730 original size:16 final size:16
Alignment explanation
Indices: 6709--6745 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
6699 AACCTAGACT
*
6709 AGACACAGACAGACAG
1 AGACACAGACAAACAG
*
6725 AGACACAGACAAAGAG
1 AGACACAGACAAACAG
6741 AGACA
1 AGACA
6746 GGCAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.22, G:0.24, T:0.00
Consensus pattern (16 bp):
AGACACAGACAAACAG
Done.