Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013860.1 Corchorus capsularis cultivar CVL-1 contig13881, 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: 38714
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:6535 original size:2 final size:2
Alignment explanation
Indices: 6528--6555 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6518 TTTAAAATAA
6528 AT 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 AT
6556 TACAAACACC
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):
AT
Found at i:7653 original size:19 final size:19
Alignment explanation
Indices: 7593--7652 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
7583 TTGGTGTTTG
7593 TTAAAAAAAAATCTT-TATT
1 TTAAAAAAAAAT-TTATATT
**
7612 TTAAATAAATATTTTTATATT
1 TTAAA-AAA-AAATTTATATT
7633 TTAAAAAAAAATTTAT-TT
1 TTAAAAAAAAATTTATATT
7651 TT
1 TT
7653 TTAATTCCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 4 0.12
19 11 0.32
20 8 0.24
21 11 0.32
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAAAAAAAAATTTATATT
Found at i:7883 original size:2 final size:2
Alignment explanation
Indices: 7876--7908 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
7866 TTGATACGTT
*
7876 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7909 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7913 original size:2 final size:2
Alignment explanation
Indices: 7908--7941 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
7898 TATATGTATA
*
7908 TG TG TG TG TG TG TG TG TG TG TG TG TG CG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
7942 GTTATATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:10186 original size:1 final size:1
Alignment explanation
Indices: 10180--10211 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
10170 AAACTAATAT
10180 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10212 CCTACCTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:14620 original size:24 final size:25
Alignment explanation
Indices: 14575--14621 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
14565 TAAATTAAAT
*
14575 ATAGATAATTTAATTGAATTTAGAC
1 ATAGATAATTTAATAGAATTTAGAC
* *
14600 ATAG-TAATTTAGTAGAGTTTAG
1 ATAGATAATTTAATAGAATTTAG
14622 CCCAAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.17, T:0.40
Consensus pattern (25 bp):
ATAGATAATTTAATAGAATTTAGAC
Found at i:15151 original size:9 final size:9
Alignment explanation
Indices: 15137--15166 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
15127 CCGTTGGGTC
15137 GGTGAACGG
1 GGTGAACGG
15146 GGTGAACGG
1 GGTGAACGG
15155 GGTGAACGG
1 GGTGAACGG
15164 GGT
1 GGT
15167 CTTAATTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.57, T:0.13
Consensus pattern (9 bp):
GGTGAACGG
Found at i:16036 original size:26 final size:26
Alignment explanation
Indices: 15980--16036 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
15970 AATTACTTTT
** *
15980 GAATTTATATGATTTTTTTGTATAAA
1 GAATTTATATGATTTTAATGTAAAAA
*
16006 TAATTTATATGATTTTAAT-TAAAAA
1 GAATTTATATGATTTTAATGTAAAAA
16031 CGAATT
1 -GAATT
16037 CATAATTTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (26 bp):
GAATTTATATGATTTTAATGTAAAAA
Found at i:23400 original size:18 final size:19
Alignment explanation
Indices: 23377--23414 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
23367 ATAGTTTTTC
23377 TTTGCATTT-TTACATTAT
1 TTTGCATTTATTACATTAT
*
23395 TTTGCATTTATTGCATTAT
1 TTTGCATTTATTACATTAT
23414 T
1 T
23415 AGGAAATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.61
Consensus pattern (19 bp):
TTTGCATTTATTACATTAT
Found at i:29862 original size:13 final size:13
Alignment explanation
Indices: 29844--29869 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29834 ATATTAGATT
29844 TAATTAAATAAAA
1 TAATTAAATAAAA
29857 TAATTAAATAAAA
1 TAATTAAATAAAA
29870 ATAGAGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATTAAATAAAA
Found at i:29908 original size:16 final size:16
Alignment explanation
Indices: 29887--29917 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29877 TTTTAGTTGA
29887 GTAAAATAGTAAAATG
1 GTAAAATAGTAAAATG
*
29903 GTAAAATGGTAAAAT
1 GTAAAATAGTAAAAT
29918 AAAATAGTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.19, T:0.26
Consensus pattern (16 bp):
GTAAAATAGTAAAATG
Found at i:31384 original size:23 final size:23
Alignment explanation
Indices: 31352--31426 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
31342 AGACAATAGA
*
31352 CAAAAGCTCTCACAAAGGAGTCC
1 CAAAAACTCTCACAAAGGAGTCC
*
31375 CAAAAACTCTCACAAAGGAGTTC
1 CAAAAACTCTCACAAAGGAGTCC
* *
31398 CAAAAACTCTCACTAATGAGTCC
1 CAAAAACTCTCACAAAGGAGTCC
31421 CAAAAA
1 CAAAAA
31427 AAATAAAGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.44, C:0.28, G:0.12, T:0.16
Consensus pattern (23 bp):
CAAAAACTCTCACAAAGGAGTCC
Found at i:36741 original size:122 final size:122
Alignment explanation
Indices: 36531--36773 Score: 337
Period size: 122 Copynumber: 2.0 Consensus size: 122
36521 ATTCAAGATA
* * * * * *
36531 CTAAATTGCATAGAAGAAAAATGTCTGAGGACGTTTCTATGAAAGGAATAAATTTGAAGGGTTAA
1 CTAAATTACATAGAAGAAAAATGTCTAAGGACGTTTCCATGAAAAGAATAAATTTGAAAGGCTAA
** *
36596 ATTATATATAGGGAAATAATATAAGGACTAAATTGAATAAAGTAAAAATAGCTAAGGG
66 ATTATATATAAAGAAATAATATAAGGACTAAACTGAATAAAGTAAAAA-AGCTAAGGG
* *
36654 CTAAATTACATAGAAGAAAATTGTCTAAGG-TGTTTCCATGAAAAGAATTAAA-TTGAAAGGCTA
1 CTAAATTACATAGAAGAAAAATGTCTAAGGACGTTTCCATGAAAAGAA-TAAATTTGAAAGGCTA
* *
36717 AGTTATATATAAAGAAATAATATAAGGACTAAACTGAATAAAGTGAAAAAGCTAAGG
65 AATTATATATAAAGAAATAATATAAGGACTAAACTGAATAAAGTAAAAAAGCTAAGG
36774 TTTTTTTCTA
Statistics
Matches: 106, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
121 8 0.08
122 67 0.63
123 31 0.29
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (122 bp):
CTAAATTACATAGAAGAAAAATGTCTAAGGACGTTTCCATGAAAAGAATAAATTTGAAAGGCTAA
ATTATATATAAAGAAATAATATAAGGACTAAACTGAATAAAGTAAAAAAGCTAAGGG
Found at i:37090 original size:12 final size:12
Alignment explanation
Indices: 37073--37097 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37063 TATGGCTATC
37073 GAATACCAAAAG
1 GAATACCAAAAG
37085 GAATACCAAAAG
1 GAATACCAAAAG
37097 G
1 G
37098 TTTCATACCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.16, G:0.20, T:0.08
Consensus pattern (12 bp):
GAATACCAAAAG
Found at i:37123 original size:24 final size:24
Alignment explanation
Indices: 37094--37143 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
37084 GGAATACCAA
37094 AAGGTTTCATACCAGAAGATAAAT
1 AAGGTTTCATACCAGAAGATAAAT
*
37118 AAGGTTTCATACCAGAAGGTAAAT
1 AAGGTTTCATACCAGAAGATAAAT
37142 AA
1 AA
37144 TTGTTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (24 bp):
AAGGTTTCATACCAGAAGATAAAT
Found at i:38682 original size:2 final size:2
Alignment explanation
Indices: 38675--38713 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
38665 TTATGTCATA
38675 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38714 T
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.