Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008787.1 Corchorus capsularis cultivar CVL-1 contig08808, 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: 3230
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Found at i:441 original size:2 final size:2
Alignment explanation
Indices: 420--457 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
410 TACTGTTGAA
420 AT AT GAT AT A- AT AT -T AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
458 CATGAGTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 29 0.88
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:989 original size:7 final size:8
Alignment explanation
Indices: 972--1076 Score: 57
Period size: 7 Copynumber: 13.6 Consensus size: 8
962 TAGTTTTTGT
972 TTTATCTA
1 TTTATCTA
980 TTTA-CTA
1 TTTATCTA
*
987 TTTAT-TT
1 TTTATCTA
994 TCTTATCTA
1 T-TTATCTA
*
1003 -TT-TGTA
1 TTTATCTA
*
1009 ATTAT-TA
1 TTTATCTA
1016 TTTAT-TA
1 TTTATCTA
1023 -TTATCTA
1 TTTATCTA
1030 TTTATTGCTA
1 TTTA-T-CTA
1040 -TTATCTA
1 TTTATCTA
1047 TTTAATACTA
1 TTT-AT-CTA
*
1057 -TTATTTA
1 TTTATCTA
*
1064 TCTATCTA
1 TTTATCTA
1072 TTTAT
1 TTTAT
1077 TTTAGTATAT
Statistics
Matches: 76, Mismatches: 8, Indels: 26
0.69 0.07 0.24
Matches are distributed among these distances:
6 7 0.09
7 28 0.37
8 26 0.34
9 9 0.12
10 6 0.08
ACGTcount: A:0.27, C:0.10, G:0.02, T:0.62
Consensus pattern (8 bp):
TTTATCTA
Found at i:1031 original size:17 final size:18
Alignment explanation
Indices: 1011--1077 Score: 50
Period size: 17 Copynumber: 3.7 Consensus size: 18
1001 TATTTGTAAT
1011 TATTAT-TTATTATTATC
1 TATTATATTATTATTATC
**
1028 TATT-TATTGCTATTATC
1 TATTATATTATTATTATC
*
1045 TATTTAATACTATTATTTATC
1 TA-TT-ATATTATTA-TTATC
1066 TATCTAT-TTATT
1 TAT-TATATTATT
1078 TTAGTATATC
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
16 1 0.03
17 15 0.39
18 2 0.05
19 4 0.11
20 8 0.21
21 8 0.21
ACGTcount: A:0.28, C:0.09, G:0.01, T:0.61
Consensus pattern (18 bp):
TATTATATTATTATTATC
Found at i:1193 original size:20 final size:22
Alignment explanation
Indices: 1148--1203 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
1138 ATTGTTTACT
1148 TATTTATCTATTTGTATATATATC
1 TATTTATCT-TTT-TATATATATC
1172 TATTTATCTTTTTAT-T-TATC
1 TATTTATCTTTTTATATATATC
1192 TA-TTAT-TTTTTA
1 TATTTATCTTTTTA
1204 CTTTTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.19
19 4 0.12
20 6 0.19
21 1 0.03
22 3 0.09
23 3 0.09
24 9 0.28
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (22 bp):
TATTTATCTTTTTATATATATC
Found at i:1199 original size:39 final size:39
Alignment explanation
Indices: 1125--1199 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
1115 TGTTTATATG
*
1125 TATATATATATATATTGTTTACTTATTTATCTATTTGTA
1 TATATATATATATATTGTTTACTTATCTATCTATTTGTA
* * * *
1164 TATATATCTATTTATCTTTTTATTTATCTAT-TATTT
1 TATATATATATATAT-TGTTTACTTATCTATCTATTT
1200 TTTACTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
39 18 0.60
40 12 0.40
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.63
Consensus pattern (39 bp):
TATATATATATATATTGTTTACTTATCTATCTATTTGTA
Found at i:1708 original size:15 final size:14
Alignment explanation
Indices: 1683--1718 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
1673 TGATTTTTGA
*
1683 TTTTGTTTTTGTTT
1 TTTTTTTTTTGTTT
1697 TTTGTTTTTTTGTTT
1 TTT-TTTTTTTGTTT
1712 TTTTTTT
1 TTTTTTT
1719 GAATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (14 bp):
TTTTTTTTTTGTTT
Found at i:1725 original size:21 final size:20
Alignment explanation
Indices: 1676--1743 Score: 77
Period size: 21 Copynumber: 3.5 Consensus size: 20
1666 TTTTTCTTGA
* *
1676 TTTTTGATTTTGTT-TTTGT
1 TTTTTGATTTTTTTGTTTTT
1695 TTTTTG-TTTTTTTGTTTTT
1 TTTTTGATTTTTTTGTTTTT
*
1714 TTTTTGAATTTTTATGTTTTT
1 TTTTTG-ATTTTTTTGTTTTT
*
1735 TATTTGATT
1 TTTTTGATT
1744 GTGTTTTTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 6 0.14
19 16 0.38
20 3 0.07
21 17 0.40
ACGTcount: A:0.09, C:0.00, G:0.12, T:0.79
Consensus pattern (20 bp):
TTTTTGATTTTTTTGTTTTT
Found at i:1751 original size:36 final size:35
Alignment explanation
Indices: 1688--1756 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 35
1678 TTTGATTTTG
* ** * *
1688 TTTTTGTTTTTTGTTTTTTTGTTTTTTTTTTGAAT
1 TTTTTGTTTTTTATTTGATTGTGTTTTTCTTGAAT
1723 TTTTATGTTTTTTATTTGATTGTGTTTTTCTTGA
1 TTTT-TGTTTTTTATTTGATTGTGTTTTTCTTGA
1757 TTTCTGCCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 4 0.14
36 24 0.86
ACGTcount: A:0.09, C:0.01, G:0.13, T:0.77
Consensus pattern (35 bp):
TTTTTGTTTTTTATTTGATTGTGTTTTTCTTGAAT
Done.