Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013042.1 Corchorus olitorius cultivar O-4 contig13075, 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: 46108
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:5572 original size:78 final size:79
Alignment explanation
Indices: 5436--5596 Score: 288
Period size: 78 Copynumber: 2.1 Consensus size: 79
5426 TTTTGATCCC
*
5436 TTTATTCTATCTTGCCTTCCCATGTTCTTTTTAAGGCTCATATATGTCCCTATATTTCTTTACTT
1 TTTATTCTATCTTGCCTTCCCATGTTCTTTTTAAGACTCATATATGTCCCTATATTTCTTTACTT
5501 TGATTTGCTTGCAA
66 TGATTTGCTTGCAA
*
5515 TTTATTCTATCTTGCCTTCCCTTGTTC-TTTTAAGACTCATATATGTCCCTATATTTCTTTACTT
1 TTTATTCTATCTTGCCTTCCCATGTTCTTTTTAAGACTCATATATGTCCCTATATTTCTTTACTT
*
5579 TGATTTGCTTGCCA
66 TGATTTGCTTGCAA
5593 TTTA
1 TTTA
5597 GATAAACCGA
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 53 0.67
79 26 0.33
ACGTcount: A:0.17, C:0.22, G:0.09, T:0.52
Consensus pattern (79 bp):
TTTATTCTATCTTGCCTTCCCATGTTCTTTTTAAGACTCATATATGTCCCTATATTTCTTTACTT
TGATTTGCTTGCAA
Found at i:8168 original size:12 final size:12
Alignment explanation
Indices: 8151--8176 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8141 GCCTTAATGT
8151 TTATGTTTGGGC
1 TTATGTTTGGGC
8163 TTATGTTTGGGC
1 TTATGTTTGGGC
8175 TT
1 TT
8177 TGGGCTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.31, T:0.54
Consensus pattern (12 bp):
TTATGTTTGGGC
Found at i:9231 original size:41 final size:37
Alignment explanation
Indices: 9176--9408 Score: 177
Period size: 41 Copynumber: 5.9 Consensus size: 37
9166 ACAAAAGTAT
*
9176 TTTTCAAAGATTTTAATTTAGGGAAAGATCCCTTCAAATAG
1 TTTTCAAAG-TTTTAATTTAGGGAAAGATCCCATC---TAG
* *
9217 TTTTCAAAAGTTTTAATTTAGGAAAAGGTCCCATCCTA-
1 TTTTC-AAAGTTTTAATTTAGGGAAAGATCCCAT-CTAG
**
9255 TCTTTCTCAGTTTTAATTTAGGGAAAGATCCCATCTAG
1 T-TTTCAAAGTTTTAATTTAGGGAAAGATCCCATCTAG
* * * *
9293 TCTTCTTCAAAATTTTTAAATTTAGGGAAGGATCCCGTCGAG
1 --TT-TTC-AAAGTTTT-AATTTAGGGAAAGATCCCATCTAG
*
9335 TTTTC-AAGTTTTCAATTTAGGGAAAGATCCCATTTAG
1 TTTTCAAAGTTTT-AATTTAGGGAAAGATCCCATCTAG
*
9372 TCTTTTTC-AAGCTTTCAA-TTAGGGGAAAGATCCCATC
1 ---TTTTCAAAG-TTTTAATTTA-GGGAAAGATCCCATC
9409 CAAGACTTTA
Statistics
Matches: 157, Mismatches: 21, Indels: 29
0.76 0.10 0.14
Matches are distributed among these distances:
37 29 0.18
38 25 0.16
39 13 0.08
40 30 0.19
41 34 0.22
42 26 0.17
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (37 bp):
TTTTCAAAGTTTTAATTTAGGGAAAGATCCCATCTAG
Found at i:9317 original size:42 final size:40
Alignment explanation
Indices: 9100--9408 Score: 196
Period size: 42 Copynumber: 7.6 Consensus size: 40
9090 AATTCAAGTT
9100 TTTTAATTTAGGGAAAGATCCCATCTAGTCATTATTTC-AAAG
1 TTTTAATTTAGGGAAAGATCCCATCTAGTC--T-TTTCAAAAG
* * * * * *
9142 ATTTCAAAATTAAGGAAGGATCCCA-CAAAAGTATTTTTC-AAAG
1 -TTT-TAATTTAGGGAAAGATCCCATC--TAGT-CTTTTCAAAAG
* * * *
9185 ATTTTAATTTAGGGAAAGATCCCTTCAAATAGTTTTCAAAAG
1 -TTTTAATTTAGGGAAAGATCCCATCTAGT-CTTTTCAAAAG
* *
9227 TTTTAATTTAGGAAAAGGTCCCATCCTA-TCTTTCTC---AG
1 TTTTAATTTAGGGAAAGATCCCAT-CTAGTCTTT-TCAAAAG
*
9265 TTTTAATTTAGGGAAAGATCCCATCTAGTCTTCTTCAAAAT
1 TTTTAATTTAGGGAAAGATCCCATCTAGTCTT-TTCAAAAG
* * *
9306 TTTTAAATTTAGGGAAGGATCCCGTCGAG--TTTTC--AAG
1 TTTT-AATTTAGGGAAAGATCCCATCTAGTCTTTTCAAAAG
*
9343 TTTTCAATTTAGGGAAAGATCCCATTTAGTCTTTTTC--AAG
1 TTTT-AATTTAGGGAAAGATCCCATCTAGTC-TTTTCAAAAG
*
9383 CTTTCAA-TTAGGGGAAAGATCCCATC
1 -TTTTAATTTA-GGGAAAGATCCCATC
9409 CAAGACTTTA
Statistics
Matches: 215, Mismatches: 32, Indels: 41
0.75 0.11 0.14
Matches are distributed among these distances:
37 29 0.13
38 30 0.14
39 7 0.03
40 29 0.13
41 41 0.19
42 42 0.20
43 17 0.08
44 17 0.08
45 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (40 bp):
TTTTAATTTAGGGAAAGATCCCATCTAGTCTTTTCAAAAG
Found at i:9352 original size:79 final size:77
Alignment explanation
Indices: 9100--9381 Score: 232
Period size: 79 Copynumber: 3.5 Consensus size: 77
9090 AATTCAAGTT
* * *
9100 TTTTAATTTAGGGAAAGATCCCATCTAGTCATTATTTCAAAGATTTCAAAATTAAGGAAGGATCC
1 TTTTAATTTAGGGAAAGATCCCATCTAGTC-TT-TTTCAAA-ATTTTAAATTTAGGGAAGGATCC
*
9165 CACAAAAGTATTTTTCAAAGA
63 CTC----G-A-TTTTCAAAGA
* * * ** *
9186 TTTTAATTTAGGGAAAGATCCCTTCAAATAGTTTTCAAAAGTTTT-AATTTAGGAAAAGG-TCCC
1 TTTTAATTTAGGGAAAGATCCCATCTAGTCTTTTTCAAAA-TTTTAAATTTAGG-GAAGGATCCC
* **
9249 ATCCTATCTTTCTCAG-
64 -T-CGAT-TTTCAAAGA
*
9265 TTTTAATTTAGGGAAAGATCCCATCTAGTCTTCTTCAAAATTTTTAAATTTAGGGAAGGATCCCG
1 TTTTAATTTAGGGAAAGATCCCATCTAGTCTTTTTCAAAA-TTTTAAATTTAGGGAAGGATCCC-
9330 TCGAGTTTTC-AAG-
64 TCGA-TTTTCAAAGA
*
9343 TTTTCAATTTAGGGAAAGATCCCATTTAGTCTTTTTCAA
1 TTTT-AATTTAGGGAAAGATCCCATCTAGTCTTTTTCAA
9382 GCTTTCAATT
Statistics
Matches: 161, Mismatches: 26, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
78 6 0.04
79 81 0.50
80 21 0.13
83 11 0.07
84 14 0.09
85 2 0.01
86 26 0.16
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (77 bp):
TTTTAATTTAGGGAAAGATCCCATCTAGTCTTTTTCAAAATTTTAAATTTAGGGAAGGATCCCTC
GATTTTCAAAGA
Found at i:13068 original size:25 final size:25
Alignment explanation
Indices: 13030--13081 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
13020 ATGCAATCCC
13030 TCATAGAAAGACACCTTTTCATATT
1 TCATAGAAAGACACCTTTTCATATT
** *
13055 TCATAGAATTACACCTTTTCATGTT
1 TCATAGAAAGACACCTTTTCATATT
13080 TC
1 TC
13082 TGCAGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (25 bp):
TCATAGAAAGACACCTTTTCATATT
Found at i:16264 original size:13 final size:13
Alignment explanation
Indices: 16246--16273 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
16236 TATAGATCTC
16246 AAGAGGTGTGTTA
1 AAGAGGTGTGTTA
16259 AAGAGGTGTGTTA
1 AAGAGGTGTGTTA
16272 AA
1 AA
16274 CACCCTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (13 bp):
AAGAGGTGTGTTA
Found at i:18631 original size:59 final size:61
Alignment explanation
Indices: 18567--18708 Score: 209
Period size: 62 Copynumber: 2.3 Consensus size: 61
18557 TTTAAATTTA
*
18567 ATTGACACCAGAAGTTATCATATTA-A-ATTATCATGACACCAGAAGTTGTCAT-AGAAATT
1 ATTGACACCAGAAGTTGTCATATTATATATTATCATGACACCAGAAGTTGTCATGA-AAATT
* * *
18626 GTTGACACCAGAAGTTGTCATATTATATTATTATCTTGACACTAGAAGTTGTCATGAAAATT
1 ATTGACACCAGAAGTTGTCATATTATA-TATTATCATGACACCAGAAGTTGTCATGAAAATT
18688 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
18709 CCCAATATTG
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
59 23 0.31
60 1 0.01
62 49 0.66
63 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (61 bp):
ATTGACACCAGAAGTTGTCATATTATATATTATCATGACACCAGAAGTTGTCATGAAAATT
Found at i:18640 original size:28 final size:29
Alignment explanation
Indices: 18567--18708 Score: 146
Period size: 28 Copynumber: 4.7 Consensus size: 29
18557 TTTAAATTTA
* *
18567 ATTGACACCAGAAGTTATCATATTAAATT
1 ATTGACACCAGAAGTTGTCATATGAAATT
18596 ATCATGACACCAGAAGTTGTCATA-GAAATT
1 AT--TGACACCAGAAGTTGTCATATGAAATT
* *
18626 GTTGACACCAGAAGTTGTCATATTATATTATT
1 ATTGACACCAGAAGTTGTCATATGA-A--ATT
*
18658 ATCTTGACACTAGAAGTTGTC--ATGAAAATT
1 A--TTGACACCAGAAGTTGTCATATG-AAATT
18688 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
18709 CCCAATATTG
Statistics
Matches: 94, Mismatches: 8, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
28 37 0.39
29 3 0.03
30 11 0.12
31 19 0.20
32 6 0.06
33 1 0.01
34 17 0.18
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (29 bp):
ATTGACACCAGAAGTTGTCATATGAAATT
Found at i:25247 original size:31 final size:30
Alignment explanation
Indices: 25212--25318 Score: 96
Period size: 31 Copynumber: 3.5 Consensus size: 30
25202 TAAAAGATCG
25212 GGCCCTTATTTGAGCATTTTGGCAAACGTTA
1 GGCCCTTATTTGAGCATTTTGG-AAACGTTA
* ** * *
25243 GGCCCCTATTTG-GCCAAATT--AAAAGATCA
1 GGCCCTTATTTGAG-CATTTTGGAAACG-TTA
25272 GGCCCTTATTT-AGGCATTTTGGAAAACGTTA
1 GGCCCTTATTTGA-GCATTTTGG-AAACGTTA
25303 GGCCCTTATTTGAGCA
1 GGCCCTTATTTGAGCA
25319 ATTAGCCTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
28 4 0.07
29 16 0.28
30 2 0.03
31 31 0.53
32 5 0.09
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (30 bp):
GGCCCTTATTTGAGCATTTTGGAAACGTTA
Found at i:25276 original size:60 final size:60
Alignment explanation
Indices: 25198--25314 Score: 191
Period size: 60 Copynumber: 1.9 Consensus size: 60
25188 TAAGTCTTGA
* *
25198 AAATTAAAAGATCGGGCCCTTATTT-GAGCATTTTGGCAAACGTTAGGCCCCTATTTGGCC
1 AAATTAAAAGATCAGGCCCTTATTTAG-GCATTTTGGAAAACGTTAGGCCCCTATTTGGCC
*
25258 AAATTAAAAGATCAGGCCCTTATTTAGGCATTTTGGAAAACGTTAGGCCCTTATTTG
1 AAATTAAAAGATCAGGCCCTTATTTAGGCATTTTGGAAAACGTTAGGCCCCTATTTG
25315 AGCAATTAGC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
60 52 0.98
61 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (60 bp):
AAATTAAAAGATCAGGCCCTTATTTAGGCATTTTGGAAAACGTTAGGCCCCTATTTGGCC
Found at i:41151 original size:2 final size:2
Alignment explanation
Indices: 41144--41184 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
41134 TATGGTTTTG
*
41144 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
41185 CTATGCTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Done.