Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009126.1 Corchorus capsularis cultivar CVL-1 contig09147, 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: 15621
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:102 original size:14 final size:15
Alignment explanation
Indices: 73--114 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
63 GGCTCAGTGT
*
73 AAAAGTGTAAAAAGGGT
1 AAAAGTGT--AAAGGGC
90 AAAAG-GTAAAGGGC
1 AAAAGTGTAAAGGGC
104 AAAAGTGTAAA
1 AAAAGTGTAAA
115 AAGTGGGGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 11 0.48
15 5 0.22
16 2 0.09
17 5 0.22
ACGTcount: A:0.55, C:0.02, G:0.29, T:0.14
Consensus pattern (15 bp):
AAAAGTGTAAAGGGC
Found at i:1653 original size:21 final size:19
Alignment explanation
Indices: 1629--1672 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
1619 ATTTGTAAAA
*
1629 TAAATCAAATAATAGGTATAT
1 TAAAT-AAA-AATAAGTATAT
*
1650 TAAATAAAATTAAGTATAT
1 TAAATAAAAATAAGTATAT
1669 TAAA
1 TAAA
1673 CATTAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
20 3 0.14
21 5 0.24
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (19 bp):
TAAATAAAAATAAGTATAT
Found at i:2298 original size:29 final size:29
Alignment explanation
Indices: 2257--2314 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
2247 TGACTATCCA
*
2257 TTTTGGGACAAATTGGCCCCTTATCTTTT
1 TTTTGGGACAAATTGGCCCCTTAACTTTT
2286 TTTTGGGACAAATTGGCCCCTTAACTTTT
1 TTTTGGGACAAATTGGCCCCTTAACTTTT
2315 AAAAATGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (29 bp):
TTTTGGGACAAATTGGCCCCTTAACTTTT
Found at i:3033 original size:28 final size:28
Alignment explanation
Indices: 2998--3077 Score: 115
Period size: 28 Copynumber: 2.8 Consensus size: 28
2988 TCTCGTTTTT
2998 AAAAGTTAAGGGGCCAATTTGTCCCAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAA
3026 AAAAGTTAAGGGGCCAATTTGTCCCAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAA
* *
3054 ATGGATAGTTAAGGGGCTAATTTG
1 A---AAAGTTAAGGGGCCAATTTG
3078 GGTATTGCCT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
28 29 0.62
31 18 0.38
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (28 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAA
Found at i:6922 original size:2 final size:2
Alignment explanation
Indices: 6915--6997 Score: 70
Period size: 2 Copynumber: 44.0 Consensus size: 2
6905 GAAAATTTTA
* *
6915 AT AT AT AT AT AT AT AT AT AA AT A- AT -T AT AT CAG AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
* * *
6955 AT A- AT AT AT AT AT AT AT AT A- AT AT AA AA AT AT A- AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6994 AT AT
1 AT AT
6998 TATTATTATT
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
1 6 0.09
2 59 0.89
3 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:10704 original size:32 final size:32
Alignment explanation
Indices: 10663--10729 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
10653 TGGTAAATGC
10663 TTGTGATTGGTTTAGTGATATAGGATTAGCTT
1 TTGTGATTGGTTTAGTGATATAGGATTAGCTT
10695 TTGTGATTGGTTTAGTGATATAGGATTAGCTT
1 TTGTGATTGGTTTAGTGATATAGGATTAGCTT
10727 TTG
1 TTG
10730 ATATTAATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.21, C:0.03, G:0.28, T:0.48
Consensus pattern (32 bp):
TTGTGATTGGTTTAGTGATATAGGATTAGCTT
Found at i:10733 original size:18 final size:18
Alignment explanation
Indices: 10678--10733 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
10668 ATTGGTTTAG
10678 TGATATAGGATTAGCTTT
1 TGATATAGGATTAGCTTT
* *
10696 TG-TGATTGGTTTAG----
1 TGAT-ATAGGATTAGCTTT
10710 TGATATAGGATTAGCTTT
1 TGATATAGGATTAGCTTT
10728 TGATAT
1 TGATAT
10734 TAATTGTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
14 10 0.36
15 1 0.04
17 1 0.04
18 16 0.57
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.46
Consensus pattern (18 bp):
TGATATAGGATTAGCTTT
Done.