Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016445.1 Corchorus capsularis cultivar CVL-1 contig16466, 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: 23985
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:267 original size:11 final size:11
Alignment explanation
Indices: 248--282 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
238 ATAATTTTTC
*
248 AATTGTCTTCA
1 AATTATCTTCA
259 AATTATCTTCA
1 AATTATCTTCA
*
270 AATAATCTTCA
1 AATTATCTTCA
281 AA
1 AA
283 CACGAACTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (11 bp):
AATTATCTTCA
Found at i:4869 original size:18 final size:18
Alignment explanation
Indices: 4846--4884 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
4836 CCTAAATTTA
4846 TTTCGACACAATTTTTTT
1 TTTCGACACAATTTTTTT
*
4864 TTTCGACGCAATTTTTTT
1 TTTCGACACAATTTTTTT
4882 TTT
1 TTT
4885 TAGAAAAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.15, G:0.08, T:0.59
Consensus pattern (18 bp):
TTTCGACACAATTTTTTT
Found at i:5213 original size:6 final size:6
Alignment explanation
Indices: 5197--5233 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
5187 CAAAACAAAA
5197 TAAAT- TAAATC TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TA
5234 TGGCAATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:6602 original size:11 final size:11
Alignment explanation
Indices: 6583--6617 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
6573 ATAATTTTTC
*
6583 AATTGTCTTCA
1 AATTATCTTCA
6594 AATTATCTTCA
1 AATTATCTTCA
*
6605 AATAATCTTCA
1 AATTATCTTCA
6616 AA
1 AA
6618 CACGAACTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (11 bp):
AATTATCTTCA
Found at i:9262 original size:52 final size:52
Alignment explanation
Indices: 9179--9282 Score: 154
Period size: 52 Copynumber: 2.0 Consensus size: 52
9169 ACAAGAATTT
* *
9179 CAGGACAACTTCGGCCTAAAACTTGTTCAACTTCGGGACAGAAGTTGTTGCA
1 CAGGACAACTTCGGCCCAAAACTTGTACAACTTCGGGACAGAAGTTGTTGCA
* * * *
9231 CAGGAGAACTTCGGCCCAGAAGTTGTACAACTTTGGGACAGAAGTTGTTGCA
1 CAGGACAACTTCGGCCCAAAACTTGTACAACTTCGGGACAGAAGTTGTTGCA
9283 GGAAAAACCT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (52 bp):
CAGGACAACTTCGGCCCAAAACTTGTACAACTTCGGGACAGAAGTTGTTGCA
Found at i:16989 original size:3 final size:3
Alignment explanation
Indices: 16976--17030 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
16966 AAAGGGATGG
* *
16976 ATA AGA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17024 ATA ATA A
1 ATA ATA A
17031 AAGGATTAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:17648 original size:59 final size:59
Alignment explanation
Indices: 17514--17761 Score: 329
Period size: 59 Copynumber: 4.2 Consensus size: 59
17504 TTTAAGAATC
* * * * *
17514 GAAGAATTGAAGAAAGACCACCCTGGATCA-T-TGAAGTAAATTGAAACATTGGAATTT
1 GAAGAATTAAAGAAAGACCACCCTCGATCATTCTGAAATAAACTGAAGCATTGGAATTT
* * * * * *
17571 GAGGAACTCATGAAAGACCACCCTCGATCATTCTGAAATAAGCTGAAGCATTGAAATTT
1 GAAGAATTAAAGAAAGACCACCCTCGATCATTCTGAAATAAACTGAAGCATTGGAATTT
* * *
17630 GAAGAATTAAAGAAAGACCACCCTCGATCCTTTTTAAATAAACTGAAGCATTGGAATTT
1 GAAGAATTAAAGAAAGACCACCCTCGATCATTCTGAAATAAACTGAAGCATTGGAATTT
*
17689 GAAGAATTAAAGAAAGACCACCCTCGATCCTTCTGAAATAAACTGAAGCATTGGAATTT
1 GAAGAATTAAAGAAAGACCACCCTCGATCATTCTGAAATAAACTGAAGCATTGGAATTT
* *
17748 GAAGACTTGAAGAA
1 GAAGAATTAAAGAA
17762 TAGAAGAATT
Statistics
Matches: 166, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
57 25 0.15
58 1 0.01
59 140 0.84
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (59 bp):
GAAGAATTAAAGAAAGACCACCCTCGATCATTCTGAAATAAACTGAAGCATTGGAATTT
Done.