Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014089.1 Corchorus capsularis cultivar CVL-1 contig14110, 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: 29695
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:6901 original size:46 final size:46
Alignment explanation
Indices: 6834--6943 Score: 193
Period size: 46 Copynumber: 2.4 Consensus size: 46
6824 TATTAGATAA
**
6834 AATTACCTTGGTCCAATTTAAATTATCCCTTTTATTTAAAACAATT
1 AATTACCTTGGTCCAGCTTAAATTATCCCTTTTATTTAAAACAATT
6880 AATTACCTTGGTCCAGCTTAAATTATCCCTTTTATTTAAAACAATT
1 AATTACCTTGGTCCAGCTTAAATTATCCCTTTTATTTAAAACAATT
*
6926 AATTACCTTGATCCAGCT
1 AATTACCTTGGTCCAGCT
6944 AAAAAATTGT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 61 1.00
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (46 bp):
AATTACCTTGGTCCAGCTTAAATTATCCCTTTTATTTAAAACAATT
Found at i:16648 original size:17 final size:17
Alignment explanation
Indices: 16626--16661 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
16616 GTTTTTTTGT
16626 TTTTTGTTTT-TGTTTCG
1 TTTTTGTTTTGT-TTTCG
16643 TTTTTGTTTTGTTTTCG
1 TTTTTGTTTTGTTTTCG
16660 TT
1 TT
16662 GCGCTGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.94
18 1 0.06
ACGTcount: A:0.00, C:0.06, G:0.17, T:0.78
Consensus pattern (17 bp):
TTTTTGTTTTGTTTTCG
Found at i:19096 original size:24 final size:25
Alignment explanation
Indices: 19036--19094 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
19026 TTCAAACTCT
* *
19036 AAACTTCGTTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACATCTTC
19061 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
19085 AAA-TTCATTT
1 AAACTTCATTT
19095 TCCTTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 7 0.22
24 8 0.25
25 17 0.53
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.41
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:19133 original size:26 final size:26
Alignment explanation
Indices: 19104--19175 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
19094 TTCCTTCATT
19104 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* * * *
19130 TTAATAATAAATTAATCAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
19156 TTAAACATAAACTAA-TAAAT
1 TTAATCATAAACTAATTAAAT
19176 TAAGTAATTT
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
25 3 0.08
26 34 0.92
ACGTcount: A:0.56, C:0.10, G:0.01, T:0.33
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:19239 original size:9 final size:9
Alignment explanation
Indices: 19223--19329 Score: 98
Period size: 9 Copynumber: 12.2 Consensus size: 9
19213 ACTAATTAAT
19223 ATTAAAAAA
1 ATTAAAAAA
*
19232 AAT-AAAAA
1 ATTAAAAAA
*
19240 TTTAAAAAA
1 ATTAAAAAA
*
19249 ATTTAAAAA
1 ATTAAAAAA
*
19258 ATTTAAAAA
1 ATTAAAAAA
19267 ATTAAAAAA
1 ATTAAAAAA
*
19276 TTTAAAAAA
1 ATTAAAAAA
19285 A-T-AAAAA
1 ATTAAAAAA
19292 A-TAAATAAA
1 ATTAAA-AAA
*
19301 AATAAAAAA
1 ATTAAAAAA
19310 A-TAAATAAA
1 ATTAAA-AAA
*
19319 ATAAAAAAA
1 ATTAAAAAA
19328 AT
1 AT
19330 GGCCGAGCCG
Statistics
Matches: 83, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
7 7 0.08
8 13 0.16
9 56 0.67
10 7 0.08
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:19307 original size:23 final size:23
Alignment explanation
Indices: 19281--19325 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
19271 AAAAATTTAA
19281 AAAAATAAAAAAT-AAATAAAAAT
1 AAAAA-AAAAAATAAAATAAAAAT
*
19304 AAAAAAATAAATAAAATAAAAA
1 AAAAAAAAAAATAAAATAAAAA
19326 AAATGGCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (23 bp):
AAAAAAAAAAATAAAATAAAAAT
Found at i:19309 original size:18 final size:17
Alignment explanation
Indices: 19225--19327 Score: 100
Period size: 17 Copynumber: 6.0 Consensus size: 17
19215 TAATTAATAT
**
19225 TAAAAAAAATAAAAATT
1 TAAAAAAAATAAAAAAA
* *
19242 TAAAAAAATTTAAAAAAT
1 TAAAAAAA-ATAAAAAAA
* * *
19260 TTAAAAAATTAAAAAAT
1 TAAAAAAAATAAAAAAA
*
19277 TTAAAAAAAT-AAAAAA
1 TAAAAAAAATAAAAAAA
19293 TAAATAAAAATAAAAAAA
1 TAAA-AAAAATAAAAAAA
*
19311 TAAATAAAATAAAAAAA
1 TAAAAAAAATAAAAAAA
19328 ATGGCCGAGC
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
16 8 0.11
17 44 0.58
18 24 0.32
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
TAAAAAAAATAAAAAAA
Found at i:22747 original size:88 final size:87
Alignment explanation
Indices: 22598--22785 Score: 229
Period size: 88 Copynumber: 2.1 Consensus size: 87
22588 TGGAGAATAA
* * * * *
22598 TTTGAATTC-AATTGATTGTGATCTTTCTAATGGAGTTATGGGTGGTTATGGTGCAAAATCTTTG
1 TTTGAATTCAAATT-ATTGTGATCTTCCTAATAGAGTTATGGGTAGTAATGATGCAAAATCTTTG
22662 GAAAAT-ATTATGGTAGAGGATAG
65 GAAAATGATT-TGGTAGAGGATAG
*
22685 TTTGAATTCAAATT-TTAGTGATCTTCCCTAATAGAGTTATGGTTAGTAATGATGCAAAATCTTT
1 TTTGAATTCAAATTATT-GTGATCTT-CCTAATAGAGTTATGGGTAGTAATGATGCAAAATCTTT
* * * *
22749 GGAAACTGATTTGGTGGTGGATAT
64 GGAAAATGATTTGGTAGAGGATAG
22773 TTTGAATTCAAAT
1 TTTGAATTCAAAT
22786 CGGAGTGGTT
Statistics
Matches: 87, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
86 2 0.02
87 17 0.20
88 65 0.75
89 3 0.03
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (87 bp):
TTTGAATTCAAATTATTGTGATCTTCCTAATAGAGTTATGGGTAGTAATGATGCAAAATCTTTGG
AAAATGATTTGGTAGAGGATAG
Found at i:23786 original size:32 final size:33
Alignment explanation
Indices: 23745--23810 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 33
23735 AAATTTCTTT
*
23745 ACCTTTGTTTATTC-TTGAAGGATTG-CCCCAAG
1 ACCTTTGTTTA-ACATTGAAGGATTGCCCCCAAG
*
23777 ACCTTTGTTTAACATTGAAGGCTTGCCCCCAAG
1 ACCTTTGTTTAACATTGAAGGATTGCCCCCAAG
23810 A
1 A
23811 TTCCATTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 1 0.03
32 21 0.70
33 8 0.27
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (33 bp):
ACCTTTGTTTAACATTGAAGGATTGCCCCCAAG
Found at i:24265 original size:20 final size:20
Alignment explanation
Indices: 24228--24266 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
24218 CAAAGTTAAC
24228 CCTATTTTTATGGTTATTTA
1 CCTATTTTTATGGTTATTTA
*
24248 CCTATGTTTTTTGG-TATTT
1 CCTAT-TTTTATGGTTATTT
24267 TTATGTGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.15, C:0.10, G:0.13, T:0.62
Consensus pattern (20 bp):
CCTATTTTTATGGTTATTTA
Found at i:25575 original size:14 final size:15
Alignment explanation
Indices: 25556--25586 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
25546 ATGTGAATTA
25556 TTGTTCTTAATG-TT
1 TTGTTCTTAATGATT
25570 TTGTTCTTAATGATT
1 TTGTTCTTAATGATT
25585 TT
1 TT
25587 TAAGCCCGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.16, C:0.06, G:0.13, T:0.65
Consensus pattern (15 bp):
TTGTTCTTAATGATT
Done.