Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021446.1 Corchorus olitorius cultivar O-4 contig21479, 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: 16530
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:9 original size:2 final size:2
Alignment explanation
Indices: 3--36 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 CG
3 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
37 ACACACACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:87 original size:2 final size:2
Alignment explanation
Indices: 36--74 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
26 CTCTCTCTCT
**
36 CA CA CA CA CA CA CA CA CA CA CA CA CA CA TG CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
75 GCGCGCACAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.49, G:0.03, T:0.03
Consensus pattern (2 bp):
CA
Found at i:970 original size:18 final size:18
Alignment explanation
Indices: 947--986 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
937 CTAATTTTCT
947 TCTCTCTCTAGACTCGAG
1 TCTCTCTCTAGACTCGAG
965 TCTCTCTCTAGACTCGAG
1 TCTCTCTCTAGACTCGAG
983 TCTC
1 TCTC
987 GCTACTAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.15, C:0.35, G:0.15, T:0.35
Consensus pattern (18 bp):
TCTCTCTCTAGACTCGAG
Found at i:1914 original size:6 final size:6
Alignment explanation
Indices: 1903--1929 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1893 GTAGGTTACT
1903 TCCTAA TCCTAA TCCTAA TCCTAA TCC
1 TCCTAA TCCTAA TCCTAA TCCTAA TCC
1930 CAAGACTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (6 bp):
TCCTAA
Found at i:2238 original size:2 final size:2
Alignment explanation
Indices: 2231--2268 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2221 ATCTGTATTG
2231 AT AT AT AT AT 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 AT AT AT AT AT
2269 CCCTGCAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3590 original size:21 final size:21
Alignment explanation
Indices: 3564--3605 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3554 ACCATAATAG
3564 GTAGAAGTGAAATTATTACAC
1 GTAGAAGTGAAATTATTACAC
3585 GTAGAAGTGAAATTATTACAC
1 GTAGAAGTGAAATTATTACAC
3606 AAAATAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
GTAGAAGTGAAATTATTACAC
Found at i:3641 original size:20 final size:20
Alignment explanation
Indices: 3616--3655 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3606 AAAATAATAG
3616 GTAGAAGTGAAATTAAAAAA
1 GTAGAAGTGAAATTAAAAAA
3636 GTAGAAGTGAAATTAAAAAA
1 GTAGAAGTGAAATTAAAAAA
3656 AATGGTCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (20 bp):
GTAGAAGTGAAATTAAAAAA
Found at i:4204 original size:178 final size:177
Alignment explanation
Indices: 3864--4318 Score: 522
Period size: 178 Copynumber: 2.6 Consensus size: 177
3854 TATCCTATCA
* *
3864 AGGTGATTCAAGTGTCTATTAAAAGGTTGTTTCATGATCTACAACTTTCATGAAAGACTCGAAAA
1 AGGTGATTCAAGTGTCTA-TAAAAGGTTGTTTCATGATCTACAACTTTCATGAAGGACTCGAAAG
* * *
3929 CTAAATTTAATGTTTCAAGTATCAAAAAA-GCTTCCGAAAAATTAGTTGTTTCGGTTAGCGGGAA
65 CTAAATTTAATGTTTCAAGTAT-AAAAAATGCTTCCAAAAAATTAATTGTTTCGATTAGCGGGAA
* * * ***
3993 TGGACGATCCACTTAGTATAACATTACTTTTGCTCCAGATGTCTTCTTG
129 TGAACGATCCACTTAATATAACATAACTTTTGCTCCAGATGTCCGATTG
* * * * *
4042 AGTTGATCCAAGTGTCTCATAAAAGGTTATTTTATGATCTACAACTTTCATGCAGGACTCGAAAG
1 AGGTGATTCAAGTGTCT-ATAAAAGGTTGTTTCATGATCTACAACTTTCATGAAGGACTCGAAAG
*
4107 CTAAATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAAAATTAATTTTTTCGATTAG-GGAGAA
65 CTAAATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAAAATTAATTGTTTCGATTAGCGG-GAA
* * *
4171 TGAAC-AGTCCATTTAATA-ATACATAATTTTTGCTTCAGATGTCCGATTG
129 TGAACGA-TCCACTTAATATA-ACATAACTTTTGCTCCAGATGTCCGATTG
* * * * * * * *
4220 AGGTGATTTAAGTGTCTGTTAAAAGGCTGTTTCATGATTTTCAGCTTTCATGTAGGACTTGAAAG
1 AGGTGATTCAAGTGTCT-ATAAAAGGTTGTTTCATGATCTACAACTTTCATGAAGGACTCGAAAG
* * * **
4285 CTAAATTTTATTTTTCAAATACCAAAAATGCTTC
65 CTAAATTTAATGTTTCAAGTATAAAAAATGCTTC
4319 TGAAAATTTT
Statistics
Matches: 234, Mismatches: 38, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
177 10 0.04
178 223 0.95
179 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (177 bp):
AGGTGATTCAAGTGTCTATAAAAGGTTGTTTCATGATCTACAACTTTCATGAAGGACTCGAAAGC
TAAATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAAAATTAATTGTTTCGATTAGCGGGAATG
AACGATCCACTTAATATAACATAACTTTTGCTCCAGATGTCCGATTG
Found at i:4869 original size:6 final size:6
Alignment explanation
Indices: 4858--4904 Score: 76
Period size: 6 Copynumber: 7.5 Consensus size: 6
4848 ATATACTAAT
4858 ATACTA ATACTA ATACTA ATTACTA ATACTA ATTACTA ATACTA ATA
1 ATACTA ATACTA ATACTA A-TACTA ATACTA A-TACTA ATACTA ATA
4905 AATATATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 27 0.69
7 12 0.31
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (6 bp):
ATACTA
Found at i:4875 original size:20 final size:20
Alignment explanation
Indices: 4850--4898 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
4840 CCCATTATAT
4850 ATACTAATATACTAATACTA
1 ATACTAATATACTAATACTA
4870 ATACTAAT-TACTAATACTA
1 ATACTAATATACTAATACTA
4889 ATTACTAATA
1 A-TACTAATA
4899 CTAATAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (20 bp):
ATACTAATATACTAATACTA
Found at i:4883 original size:13 final size:13
Alignment explanation
Indices: 4858--4903 Score: 85
Period size: 13 Copynumber: 3.6 Consensus size: 13
4848 ATATACTAAT
4858 ATACTAA-TACTA
1 ATACTAATTACTA
4870 ATACTAATTACTA
1 ATACTAATTACTA
4883 ATACTAATTACTA
1 ATACTAATTACTA
4896 ATACTAAT
1 ATACTAAT
4904 AAATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 7 0.21
13 26 0.79
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
ATACTAATTACTA
Found at i:4883 original size:19 final size:19
Alignment explanation
Indices: 4850--4904 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 19
4840 CCCATTATAT
4850 ATACTAATATACTAATACTA
1 ATACTAAT-TACTAATACTA
4870 ATACTAATTACTAATACTA
1 ATACTAATTACTAATACTA
4889 ATTACTAA-TACTAATA
1 A-TACTAATTACTAATA
4905 AATATATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 20 0.59
20 14 0.41
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (19 bp):
ATACTAATTACTAATACTA
Found at i:10322 original size:20 final size:20
Alignment explanation
Indices: 10294--10333 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
10284 TAACTGATGT
*
10294 TTCTTATCTCTGTTGTTTTC
1 TTCTCATCTCTGTTGTTTTC
*
10314 TTCTCATCTGTGTTGTTTTC
1 TTCTCATCTCTGTTGTTTTC
10334 AACTAATCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.20, G:0.12, T:0.62
Consensus pattern (20 bp):
TTCTCATCTCTGTTGTTTTC
Found at i:11511 original size:3 final size:3
Alignment explanation
Indices: 11505--11570 Score: 109
Period size: 3 Copynumber: 22.7 Consensus size: 3
11495 AAAACCATTC
11505 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
11553 ATT A-T ATT GTT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT AT
11571 GTAAAATTTG
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 4 0.07
3 55 0.93
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:13349 original size:9 final size:9
Alignment explanation
Indices: 13335--13361 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
13325 GATGAATAAA
13335 ACATGGTAG
1 ACATGGTAG
13344 ACATGGTAG
1 ACATGGTAG
13353 ACATGGTAG
1 ACATGGTAG
13362 GCGTAGTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.22
Consensus pattern (9 bp):
ACATGGTAG
Found at i:13910 original size:16 final size:16
Alignment explanation
Indices: 13889--13921 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
13879 ATGGGACCCG
13889 CCTCATATTTTTGCAA
1 CCTCATATTTTTGCAA
*
13905 CCTCATGTTTTTGCAA
1 CCTCATATTTTTGCAA
13921 C
1 C
13922 AAATGGAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.27, G:0.09, T:0.42
Consensus pattern (16 bp):
CCTCATATTTTTGCAA
Done.