Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021117.1 Corchorus olitorius cultivar O-4 contig21150, 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: 23832
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:46 original size:31 final size:31
Alignment explanation
Indices: 10--73 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
1 ACAGCCAAT
10 AAAGCCCAATACTAA-CTAAAATAAGAAAATA
1 AAAGCCCAATACTAATCT-AAATAAGAAAATA
*
41 AAAGCCTAATACTAATCTAAATAAGAAAATA
1 AAAGCCCAATACTAATCTAAATAAGAAAATA
72 AA
1 AA
74 GACAAACTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.61, C:0.14, G:0.06, T:0.19
Consensus pattern (31 bp):
AAAGCCCAATACTAATCTAAATAAGAAAATA
Found at i:248 original size:21 final size:20
Alignment explanation
Indices: 202--248 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
192 TCCTCTTGCC
*
202 TTTCCATCGAGTCCTTGTCT
1 TTTCCATCGAGTCCTTGTAT
222 TCTTCCATCGAGTCCTTGTAT
1 T-TTCCATCGAGTCCTTGTAT
243 ATTTCC
1 -TTTCC
249 TGTAAATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.13, C:0.30, G:0.13, T:0.45
Consensus pattern (20 bp):
TTTCCATCGAGTCCTTGTAT
Found at i:710 original size:68 final size:68
Alignment explanation
Indices: 627--763 Score: 258
Period size: 68 Copynumber: 2.0 Consensus size: 68
617 TCATCATACT
627 TATCATAAACAGGTTCTAACTCTTCTTCTATGCACAAATCCATCTCCAATCCACCTCCTATCGCT
1 TATCATAAACAGGTTCTAACTCTTCTTCTATGCACAAATCCATCTCCAATCCACCTCCTATCGCT
692 TGA
66 TGA
695 TATCATAAAGC-GGTTCTAACTCTTCTTCTATGCACAAATCCATCTCCAATCCACCTCCTATCGC
1 TATCATAAA-CAGGTTCTAACTCTTCTTCTATGCACAAATCCATCTCCAATCCACCTCCTATCGC
759 TTGA
65 TTGA
763 T
1 T
764 CTGCGATTCC
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
68 67 0.99
69 1 0.01
ACGTcount: A:0.27, C:0.32, G:0.08, T:0.33
Consensus pattern (68 bp):
TATCATAAACAGGTTCTAACTCTTCTTCTATGCACAAATCCATCTCCAATCCACCTCCTATCGCT
TGA
Found at i:1362 original size:31 final size:31
Alignment explanation
Indices: 1320--1383 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
1310 AACAGCCAAT
1320 AAAGCCCAATACTAA-CTAAAATAAGAAAATA
1 AAAGCCCAATACTAATCT-AAATAAGAAAATA
*
1351 AAAGCCTAATACTAATCTAAATAAGAAAATA
1 AAAGCCCAATACTAATCTAAATAAGAAAATA
1382 AA
1 AA
1384 GACAAACTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.61, C:0.14, G:0.06, T:0.19
Consensus pattern (31 bp):
AAAGCCCAATACTAATCTAAATAAGAAAATA
Found at i:14474 original size:100 final size:99
Alignment explanation
Indices: 14296--14566 Score: 461
Period size: 100 Copynumber: 2.7 Consensus size: 99
14286 TCTTGATGGC
*
14296 TGTCCTCATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTTGAGCTCCTTAACAAGTTTGGAG
1 TGTCATCATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTTGAGCTCCTTAACAAGTTTGGAG
14361 GACAATTGATGTGGCAAAGAAATTTCCTTCATTAT
66 GACAATTGATGTGGCAAAG-AATTTCCTTCATTAT
*
14396 TGTCATCATTTTTGTGGAAGTAAGCTGTGGTATTCTTGTCCTTGAGCTCCTTAACAAGTTTGGAG
1 TGTCATCATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTTGAGCTCCTTAACAAGTTTGGAG
*
14461 GACAATTGATGTGGCAAAGATTTTCCTTCATTAT
66 GACAATTGATGTGGCAAAGAATTTCCTTCATTAT
* * * * *
14495 TGTCACCATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTCGGGCTCCTTAACAAGTTCGAAG
1 TGTCATCATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTTGAGCTCCTTAACAAGTTTGGAG
14560 GACAATT
66 GACAATT
14567 TGAGCTCGAT
Statistics
Matches: 162, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
99 80 0.49
100 82 0.51
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.37
Consensus pattern (99 bp):
TGTCATCATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTTGAGCTCCTTAACAAGTTTGGAG
GACAATTGATGTGGCAAAGAATTTCCTTCATTAT
Found at i:14534 original size:99 final size:100
Alignment explanation
Indices: 14302--14566 Score: 460
Period size: 99 Copynumber: 2.7 Consensus size: 100
14292 TGGCTGTCCT
14302 CATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTTGAGCTCCTTAACAAGTTTGGAGGACAAT
1 CATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTTGAGCTCCTTAACAAGTTTGGAGGACAAT
*
14367 TGATGTGGCAAAGAAATTTCCTTCATTATTGTCAT
66 TGATGTGGCAAAGAAATTTCCTTCATTATTGTCAC
*
14402 CATTTTTGTGGAAGTAAGCTGTGGTATTCTTGTCCTTGAGCTCCTTAACAAGTTTGGAGGACAAT
1 CATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTTGAGCTCCTTAACAAGTTTGGAGGACAAT
*
14467 TGATGTGGCAAAG-ATTTTCCTTCATTATTGTCAC
66 TGATGTGGCAAAGAAATTTCCTTCATTATTGTCAC
* * * *
14501 CATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTCGGGCTCCTTAACAAGTTCGAAGGACAAT
1 CATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTTGAGCTCCTTAACAAGTTTGGAGGACAAT
14566 T
66 T
14567 TGAGCTCGAT
Statistics
Matches: 157, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
99 80 0.51
100 77 0.49
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.37
Consensus pattern (100 bp):
CATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTTGAGCTCCTTAACAAGTTTGGAGGACAAT
TGATGTGGCAAAGAAATTTCCTTCATTATTGTCAC
Found at i:14772 original size:140 final size:141
Alignment explanation
Indices: 14500--14772 Score: 372
Period size: 140 Copynumber: 1.9 Consensus size: 141
14490 ATTATTGTCA
* * * ** *
14500 CCATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTCGGGCTCCTTAACAAGTTCGAAGGACAA
1 CCATTCTTGTGAAAGTAAGCAGTGGTATACTTGTCCTCAAGCTCCTTAAAAAGTTCGAAGGACAA
14565 TTTGAGCTCGATGTCCCCATTTTTGTGGAAGTAAGCCATGGTATACTTATCCTCGAGCTCCTTAA
66 TTTGAGCTCGATGTCCCCATTTTTGTGGAAGTAAGCCATGGTATACTTATCCTCGAGCTCCTTAA
14630 CAACTTCATCT
131 CAACTTCATCT
* *
14641 CCATTCTTGTGAAAGTAAGCAGTGGTATACTTGTCCTCAATCTCCTTAAAAAAGTTC-AGTGGAC
1 CCATTCTTGTGAAAGTAAGCAGTGGTATACTTGTCCTCAAGCTCCTT-AAAAAGTTCGA-AGGAC
* * * ** * *
14705 AA-TTGAGGT-GCTGTCCTCATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTTGAGCTCCTT
64 AATTTGAGCTCGATGTCCCCATTTTTGTGGAAGTAAGCCATGGTATACTTATCCTCGAGCTCCTT
14768 AACAA
129 AACAA
14773 GTTTGGAGGA
Statistics
Matches: 115, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
140 53 0.46
141 48 0.42
142 14 0.12
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (141 bp):
CCATTCTTGTGAAAGTAAGCAGTGGTATACTTGTCCTCAAGCTCCTTAAAAAGTTCGAAGGACAA
TTTGAGCTCGATGTCCCCATTTTTGTGGAAGTAAGCCATGGTATACTTATCCTCGAGCTCCTTAA
CAACTTCATCT
Found at i:14955 original size:180 final size:176
Alignment explanation
Indices: 14641--15054 Score: 476
Period size: 180 Copynumber: 2.3 Consensus size: 176
14631 AACTTCATCT
* * * * * *
14641 CCATTCTTGTGAAAGTAAGCAGTGGTATACTTGTCCTCAATCTCCTTAAAAAAGTTCAGTGGACA
1 CCATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTCGAGCTCCTT-AAAAAGTTCAGAGGACA
* * * * *
14706 ATTGAGGTGCTGTCCTCATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTTGAGCTCCTTAAC
65 ATTGAGCTGATGTCCCCATTTTTGTGGAAATAAGCTGTGGTATACTTGTCCTCGAGCTCCTTAAC
*
14771 AAGTTTGGAGGACAATTGATGAG-GCATAGAATTTCCTTCAT-T-AT-TGTC
130 AAGTTTGGAGGACAATTGA-G-GCG-A-AGAATTACCTTCATATCATAT-TC
*
14819 ACCATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTCGAGCTCCTTAATAAGTTCAGAGGACA
1 -CCATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTCGAGCTCCTTAAAAAGTTCAGAGGACA
* * * *
14884 ATTTGAGCTCGATGTCCCCATTTTTGTTGAAATAAGCTGTGGTATACTTGTTCTCGAGCTCTTTT
65 A-TTGAGCT-GATGTCCCCATTTTTGTGGAAATAAGCTGTGGTATACTTGTCCTCGAGCTCCTTA
** *
14949 ACAAGTTTGGAGGGTAATTGAGGCGAAGAATTACTTTCATGATCATAATTC
128 ACAAGTTTGGAGGACAATTGAGGCGAAGAATTACCTTCAT-ATCAT-ATTC
* * * * *
15000 CCATTTTTATGGAAGTAAGCTGTGGTATACATGTCCCCGAGCTTCTTAAAGAGTT
1 CCATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTCGAGCTCCTTAAAAAGTT
15055 GAGAAGGATT
Statistics
Matches: 201, Mismatches: 26, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
177 12 0.06
178 18 0.09
179 51 0.25
180 117 0.58
181 2 0.01
182 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (176 bp):
CCATTTTTGTGGAAGTAAGCTGTGGTATACTTGTCCTCGAGCTCCTTAAAAAGTTCAGAGGACAA
TTGAGCTGATGTCCCCATTTTTGTGGAAATAAGCTGTGGTATACTTGTCCTCGAGCTCCTTAACA
AGTTTGGAGGACAATTGAGGCGAAGAATTACCTTCATATCATATTC
Found at i:23067 original size:31 final size:30
Alignment explanation
Indices: 23012--23116 Score: 83
Period size: 31 Copynumber: 3.5 Consensus size: 30
23002 AAAATGGCTG
* *
23012 AAATCTCAAAT-AGGTCCCCGAACTTTGCCAT
1 AAATCTCAAATAAGG-GCCCAAACTTTG-CAT
23043 AAATCTCAAATAAGGGCCCAAACTTT--AT
1 AAATCTCAAATAAGGGCCCAAACTTTGCAT
** * *
23071 AAAAGGTCAAATAAGGGCCCCAAC-TTGTCAG
1 -AAATCTCAAATAAGGGCCCAAACTTTG-CAT
23102 AAAGTCTCAAATAAG
1 AAA-TCTCAAATAAG
23117 TCCATTTCGT
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
28 4 0.07
29 20 0.33
30 3 0.05
31 30 0.50
32 3 0.05
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (30 bp):
AAATCTCAAATAAGGGCCCAAACTTTGCAT
Found at i:23469 original size:27 final size:26
Alignment explanation
Indices: 23397--23459 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
23387 GTTTGAAGGT
23397 TGCGAAATCTGCCACATTTTTGAGCG
1 TGCGAAATCTGCCACATTTTTGAGCG
23423 TGCGAAATCTGCCACATTTTTGAGCG
1 TGCGAAATCTGCCACATTTTTGAGCG
23449 TGCGAAATCTG
1 TGCGAAATCTG
23460 TTGATGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (26 bp):
TGCGAAATCTGCCACATTTTTGAGCG
Done.