Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014983.1 Corchorus capsularis cultivar CVL-1 contig15004, 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: 20648
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:1066 original size:2 final size:2
Alignment explanation
Indices: 1061--1140 Score: 97
Period size: 2 Copynumber: 39.5 Consensus size: 2
1051 AGAAAAAAAG
* * * * *
1061 AT AT AT AT AT AT AT AT CT AT AT CT AT AT AT CT AT CT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1103 CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
1141 AGTCTAAACT
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
2 63 0.97
3 2 0.03
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1781 original size:47 final size:47
Alignment explanation
Indices: 1724--1817 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
1714 AGAAATATAT
*
1724 TAAAAAAATAAGGATATAATTGTCGATTTAAAAGTTTTACAAAACTC
1 TAAAAAAATAAGGATATAATTGTCGATTCAAAAGTTTTACAAAACTC
*
1771 TAAAAAAATAAGGATATAATTGTCGATTCAAAATTTTTACAAAACTC
1 TAAAAAAATAAGGATATAATTGTCGATTCAAAAGTTTTACAAAACTC
1818 GTACTTTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.32
Consensus pattern (47 bp):
TAAAAAAATAAGGATATAATTGTCGATTCAAAAGTTTTACAAAACTC
Found at i:4095 original size:109 final size:109
Alignment explanation
Indices: 3963--4237 Score: 455
Period size: 109 Copynumber: 2.5 Consensus size: 109
3953 AAAAAAATTA
3963 TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
4026 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
65 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
4071 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
*
4136 AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
66 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
* *
4180 TATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAA
1 TATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAGAATAAAA
4238 CTATAATAGT
Statistics
Matches: 157, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
108 6 0.04
109 119 0.76
110 3 0.02
111 1 0.01
114 28 0.18
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
Found at i:4336 original size:2 final size:2
Alignment explanation
Indices: 4329--4365 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
4319 CTCGTATTTT
*
4329 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4366 CACCCTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:5616 original size:21 final size:21
Alignment explanation
Indices: 5588--5628 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
5578 CCAATCTTGA
5588 CTATATATATG-ACACTTTCC
1 CTATATATATGAACACTTTCC
5608 CTATGATATATGTAACACTTT
1 CTAT-ATATATG-AACACTTT
5629 TGATCCTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
23 7 0.39
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (21 bp):
CTATATATATGAACACTTTCC
Found at i:6113 original size:2 final size:2
Alignment explanation
Indices: 6106--6133 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6096 TAAAATGAAT
6106 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6134 ATAAGAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8171 original size:2 final size:2
Alignment explanation
Indices: 8164--8198 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
8154 ATAAATCATG
*
8164 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8199 TGTTTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:14959 original size:78 final size:78
Alignment explanation
Indices: 14812--14963 Score: 207
Period size: 78 Copynumber: 1.9 Consensus size: 78
14802 AGGCAAGTCT
* * * *
14812 ACAATAGAAAGCCAAGGGTGGAGATGGCTCATGGTGACCCTATTGAAAAACCTGTATCTGTTTAC
1 ACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAACTGTTCAC
14877 AGAAATCCTGTCG
66 AGAAATCCTGTCG
* * * *
14890 ACAATAGAAAGCCAGGGGTGGAAATAGCTCATGGTGGCCCTATTGAAAGACCTG-AACATGTTCG
1 ACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAAC-TGTTCA
*
14954 TAGAAATCCT
65 CAGAAATCCT
14964 ATCTATGATA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
77 2 0.03
78 62 0.97
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (78 bp):
ACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAACTGTTCAC
AGAAATCCTGTCG
Found at i:16328 original size:15 final size:15
Alignment explanation
Indices: 16308--16338 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
16298 TAGCAAAGAC
16308 AAAATACAACAAGGT
1 AAAATACAACAAGGT
16323 AAAATACAACAAGGT
1 AAAATACAACAAGGT
16338 A
1 A
16339 GTTTATACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13
Consensus pattern (15 bp):
AAAATACAACAAGGT
Found at i:18682 original size:7 final size:7
Alignment explanation
Indices: 18670--18705 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
18660 AGTTACTTGC
18670 TTTTTTA
1 TTTTTTA
18677 TTTTTTA
1 TTTTTTA
18684 TTTTTTA
1 TTTTTTA
18691 TTTTTTA
1 TTTTTTA
18698 TTTTTTA
1 TTTTTTA
18705 T
1 T
18706 ATTTAGGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTA
Found at i:20553 original size:19 final size:19
Alignment explanation
Indices: 20519--20555 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20509 AAAAAATATT
**
20519 TTAAAAAAAATTTAAAAAA
1 TTAAAAAAAAAATAAAAAA
20538 TTAAAAAAAAAATAAAAA
1 TTAAAAAAAAAATAAAAA
20556 TGGCCTAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (19 bp):
TTAAAAAAAAAATAAAAAA
Done.