Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005111.1 Corchorus capsularis cultivar CVL-1 contig05129, 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: 9080
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Found at i:1063 original size:42 final size:43
Alignment explanation
Indices: 1016--1098 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
1006 CGTGTTTGGC
*
1016 TTATCGTGTCTCGTGTC-TGAATCGTGTC-GGACACGATTAAGA
1 TTATCGTGTCTCGTGTCGT-AATCGTGTCAAGACACGATTAAGA
* *
1058 TTATCGTGTTTTGTGTCGTAATCGTGTCAAGACACGATTAA
1 TTATCGTGTCTCGTGTCGTAATCGTGTCAAGACACGATTAA
1099 CACGTTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 24 0.67
43 12 0.33
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (43 bp):
TTATCGTGTCTCGTGTCGTAATCGTGTCAAGACACGATTAAGA
Found at i:1287 original size:14 final size:14
Alignment explanation
Indices: 1268--1295 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1258 AAATTATCTT
1268 TAATTATATATATA
1 TAATTATATATATA
1282 TAATTATATATATA
1 TAATTATATATATA
1296 GTTTAGCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTATATATATA
Found at i:1644 original size:26 final size:27
Alignment explanation
Indices: 1610--1662 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
1600 ATCTCCTAAA
*
1610 AAAAGTATT-TTTCAACAAATTAAATTT
1 AAAAGTATTATAT-AACAAATTAAATTT
*
1637 AAAA-TATTATATATCAAATTAAATTT
1 AAAAGTATTATATAACAAATTAAATTT
1663 TATGGATAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (27 bp):
AAAAGTATTATATAACAAATTAAATTT
Found at i:1699 original size:80 final size:81
Alignment explanation
Indices: 1590--1749 Score: 313
Period size: 80 Copynumber: 2.0 Consensus size: 81
1580 ATCTAACGTT
1590 GTTGTATTGTATCTCCTAAAAAAAGTATTTTTCAACAAATTAAATTTAAAATATTATATATCAAA
1 GTTGTATTGTATCTCCTAAAAAAAGTATTTTTCAACAAATTAAATTTAAAATATTATATATCAAA
1655 TTAAATTTTATGGATA
66 TTAAATTTTATGGATA
1671 GTTGTATTGTATCTCCT-AAAAAAGTATTTTTCAACAAATTAAATTTAAAATATTATATATCAAA
1 GTTGTATTGTATCTCCTAAAAAAAGTATTTTTCAACAAATTAAATTTAAAATATTATATATCAAA
1735 TTAAATTTTATGGAT
66 TTAAATTTTATGGAT
1750 GGTTAGTCTT
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 62 0.78
81 17 0.22
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.42
Consensus pattern (81 bp):
GTTGTATTGTATCTCCTAAAAAAAGTATTTTTCAACAAATTAAATTTAAAATATTATATATCAAA
TTAAATTTTATGGATA
Found at i:4242 original size:3 final size:3
Alignment explanation
Indices: 4234--4272 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
4224 ATATTAATTA
4234 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
4273 GAAAAGATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4954 original size:27 final size:25
Alignment explanation
Indices: 4898--4954 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
4888 AAGGATATCG
* *
4898 AATATTTTTTAAAAAAATAATAATA
1 AATATATTTTAAAAAAATAATAAAA
*
4923 TATATATTTTAAAAAAATTAATCAAAA
1 AATATATTTTAAAAAAA-TAAT-AAAA
4950 AATAT
1 AATAT
4955 GACATGGCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 15 0.58
26 4 0.15
27 7 0.27
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
AATATATTTTAAAAAAATAATAAAA
Found at i:7109 original size:2 final size:2
Alignment explanation
Indices: 7102--7128 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7092 AATTAATTTA
7102 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
7129 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:7133 original size:2 final size:2
Alignment explanation
Indices: 7128--7153 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7118 ACACACACAC
7128 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
7154 TCCAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.