Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023987.1 Corchorus olitorius cultivar O-4 contig24020, 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: 23972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:748 original size:2 final size:2
Alignment explanation
Indices: 741--798 Score: 59
Period size: 2 Copynumber: 29.5 Consensus size: 2
731 TTATTTTTAG
*
741 AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT GAT -T AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
*
781 AT AT CT AT ACT AT AT AT A
1 AT AT AT AT A-T AT AT AT A
799 AAAATACGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
1 3 0.06
2 40 0.85
3 4 0.09
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:777 original size:13 final size:13
Alignment explanation
Indices: 741--798 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
731 TTATTTTTAG
741 ATATATATA-TAT
1 ATATATATATTAT
753 ATATATATATTAT
1 ATATATATATTAT
766 AT-TATATGATTAT
1 ATATATAT-ATTAT
* *
779 CTATATCTA-TACT
1 ATATATATATTA-T
792 ATATATA
1 ATATATA
799 AAAATACGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 16 0.42
13 18 0.47
14 4 0.11
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (13 bp):
ATATATATATTAT
Found at i:2246 original size:2 final size:2
Alignment explanation
Indices: 2241--2275 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2231 GTGGAGTAAT
2241 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2276 ACATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3146 original size:22 final size:22
Alignment explanation
Indices: 3096--3148 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
3086 CATACTATAG
*
3096 TATCAAAAAATTATAGGGAAAT
1 TATCAAAAAATTACAGGGAAAT
* * **
3118 TAACAAAATATTACAGGGAGGT
1 TATCAAAAAATTACAGGGAAAT
3140 TATCAAAAA
1 TATCAAAAA
3149 TCATAGGAAG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.53, C:0.08, G:0.15, T:0.25
Consensus pattern (22 bp):
TATCAAAAAATTACAGGGAAAT
Found at i:3195 original size:22 final size:21
Alignment explanation
Indices: 3169--3286 Score: 94
Period size: 22 Copynumber: 5.4 Consensus size: 21
3159 GTTTATTAAT
3169 ATTTCATAGTTAGGTTATCAAA
1 ATTTCATAGTTA-GTTATCAAA
* * *
3191 GTTTCATA-TGGAGTTTATCACA
1 ATTTCATAGT-TAG-TTATCAAA
** *
3213 ATTTCATAGGAAAATTATCAAA
1 ATTTCATA-GTTAGTTATCAAA
*
3235 ATTTCATACTGTAGTTATCAAA
1 ATTTCATAGT-TAGTTATCAAA
* *
3257 ATTTAATAGGATAGTTATCAAA
1 ATTTCATA-GTTAGTTATCAAA
3279 ATTTCATA
1 ATTTCATA
3287 AAAATATTCA
Statistics
Matches: 74, Mismatches: 16, Indels: 12
0.73 0.16 0.12
Matches are distributed among these distances:
21 2 0.03
22 71 0.96
23 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
ATTTCATAGTTAGTTATCAAA
Found at i:3231 original size:44 final size:44
Alignment explanation
Indices: 3183--3286 Score: 138
Period size: 44 Copynumber: 2.4 Consensus size: 44
3173 CATAGTTAGG
* * *
3183 TTATCAAAGTTTCATA-TGGAGTTTATCACAATTTCATAGGAAAA
1 TTATCAAAATTTCATACTGGAG-TTATCAAAATTTAATAGGAAAA
* * *
3227 TTATCAAAATTTCATACTGTAGTTATCAAAATTTAATAGGATAG
1 TTATCAAAATTTCATACTGGAGTTATCAAAATTTAATAGGAAAA
3271 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
3287 AAAATATTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 49 0.92
45 4 0.08
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (44 bp):
TTATCAAAATTTCATACTGGAGTTATCAAAATTTAATAGGAAAA
Found at i:5776 original size:500 final size:500
Alignment explanation
Indices: 4817--5821 Score: 1493
Period size: 500 Copynumber: 2.0 Consensus size: 500
4807 ATTTAGATTC
* *
4817 ATTTGGAGAAACTACTGATTTTATCTCATTTCGGCTCAGCAGGACCATTAGGCCCGTTTGAGTCC
1 ATTTGGAGAAACTACTGATTTTATCTAATTTCGCCTCAGCAGGACCATTAGGCCCGTTTGAGTCC
* * *
4882 ATGAAACCCGAATTGCCAAGCTAGATGTCCTTAAACCTAAATCTGATATTCTTAGAGCCAATTCG
66 ATGAAACCCAAATTGCCAAGCTAGATGTCCTGAAACCTAAATCTGATATTCTTAGAGCCAACTCG
** *
4947 TTAATATGGAAGCCCAAAAAAGGAGTCCAAATCCAATCAGTAATTATGATGCAGTTTTGATTCAG
131 TTAATATGGAAGCCCAAAAAAGGAGTCCAAATCCAATCAGTAATTATGATGCAGTAATGATTCAA
* * *
5012 CCCTGATGCAGCATTGTTAAATCCTATTCAAAGGAGGGCTTCACAAGAGTAATTTTGGAAGAAAA
196 CCCTGATGCAGCATTGTTAAATCATATTCAAAGGA--GCTTCACAACAGCAATTTTGGAAGAAAA
*
5077 TTCATAACTTTTGATCTAGAGCTTAGAAAAATGCAAATAAGGTACCATTGGAAAGAGGATTCCAA
259 TTCATAACTTTTGATCTAGAGCTCAGAAAAATGCAAATAAGGTACCATTGGAAAGAGGATTCCAA
* * *
5142 GGTCTACAACTTTTATGTTTACCTCAAGACCTAATTCCGCCGTTCTAGTGAACGATTTTGCCCTT
324 GATCTACAACTTTTATGTTTACCTCAAGACCTAATTCCACCGTTCTAGTGAACAATTTTGCCCTT
* * * * *
5207 GAAAGTTATGGACTGAATTGATCTTCTCCTTAACCGACTTTGAGAATGTTTTGAACGAAATTCAG
389 CAAAGTTATGGACAGAATTGATCTTCTCCTAAACCAACTTAGAGAATGTTTTGAACGAAATTCAG
*
5272 ATACTACAGATGATGTGTAGCATTCATATTGGCCACGTTGAATCCTCA
454 ATACTACAGATGATGTGGAGCATTCATATTGGCCACGTTGAATCCT-A
* * *
5320 ATTTGGAGAAACTACTGATTTTGTCTAATTTCGACCT-AGTAGGCCCATTAGGCCCGTTTGAGTC
1 ATTTGGAGAAACTACTGATTTTATCTAATTTCG-CCTCAGCAGGACCATTAGGCCCGTTTGAGTC
* * *
5384 TATGAAGCCCAAATTGCCAAGCTAGATGTCCTGAAAGCTAAATCTGATATTCTTAGA-CTCAACT
65 CATGAAACCCAAATTGCCAAGCTAGATGTCCTGAAACCTAAATCTGATATTCTTAGAGC-CAACT
*
5448 CGTTAATATGGAAGCCCAAAGAAGGAGT-CAAAGTCCAATCAGTAATTATGATGCAGTAATGATT
129 CGTTAATATGGAAGCCCAAAAAAGGAGTCCAAA-TCCAATCAGTAATTATGATGCAGTAATGATT
* *
5512 CAACCCTGATGCAGCATTGTTAAATCATATTTAAAGGA-CTTCACAACAGCAGTTTTGGAAGAAA
193 CAACCCTGATGCAGCATTGTTAAATCATATTCAAAGGAGCTTCACAACAGCAATTTTGGAAGAAA
* * *
5576 A-TCAATAACTTTTGAT-TCAGAGCTCAGAAAAATGTAAATGAGGTACCGTTGGAAAGAGGATTC
258 ATTC-ATAACTTTTGATCT-AGAGCTCAGAAAAATGCAAATAAGGTACCATTGGAAAGAGGATTC
* * *
5639 CAAGATCTACAACTTTTATGTTTACCTCAAGACCTAATTCTACCGTTCTGGTGGACAATTTTGCC
321 CAAGATCTACAACTTTTATGTTTACCTCAAGACCTAATTCCACCGTTCTAGTGAACAATTTTGCC
* **
5704 CTTCAAATTTATGGACA-AGATTGATCTTCTCCTAAACCAACTTAGAGAATGTTTTGGGCGAAAT
386 CTTCAAAGTTATGGACAGA-ATTGATCTTCTCCTAAACCAACTTAGAGAATGTTTTGAACGAAAT
* * * *
5768 TTAGATACTACAGATGATGTGGAGTATTCTTATTGGCCACGTTGGATCCTA
450 TCAGATACTACAGATGATGTGGAGCATTCATATTGGCCACGTTGAATCCTA
5819 ATT
1 ATT
5822 AATGAGGATG
Statistics
Matches: 453, Mismatches: 43, Indels: 16
0.88 0.08 0.03
Matches are distributed among these distances:
499 8 0.02
500 235 0.52
502 5 0.01
503 203 0.45
504 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (500 bp):
ATTTGGAGAAACTACTGATTTTATCTAATTTCGCCTCAGCAGGACCATTAGGCCCGTTTGAGTCC
ATGAAACCCAAATTGCCAAGCTAGATGTCCTGAAACCTAAATCTGATATTCTTAGAGCCAACTCG
TTAATATGGAAGCCCAAAAAAGGAGTCCAAATCCAATCAGTAATTATGATGCAGTAATGATTCAA
CCCTGATGCAGCATTGTTAAATCATATTCAAAGGAGCTTCACAACAGCAATTTTGGAAGAAAATT
CATAACTTTTGATCTAGAGCTCAGAAAAATGCAAATAAGGTACCATTGGAAAGAGGATTCCAAGA
TCTACAACTTTTATGTTTACCTCAAGACCTAATTCCACCGTTCTAGTGAACAATTTTGCCCTTCA
AAGTTATGGACAGAATTGATCTTCTCCTAAACCAACTTAGAGAATGTTTTGAACGAAATTCAGAT
ACTACAGATGATGTGGAGCATTCATATTGGCCACGTTGAATCCTA
Found at i:6068 original size:25 final size:28
Alignment explanation
Indices: 6027--6085 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
6017 CTTTTTTGTC
6027 AAATATATTTCTAAATTA-CCATTATTA
1 AAATATATTTCTAAATTATCCATTATTA
6054 AAATATATTT-T-AATTATTCCATTATTA
1 AAATATATTTCTAAATTA-TCCATTATTA
6081 AAATA
1 AAATA
6086 ATAGAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 5 0.17
26 1 0.03
27 24 0.80
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (28 bp):
AAATATATTTCTAAATTATCCATTATTA
Found at i:7682 original size:44 final size:44
Alignment explanation
Indices: 7625--7708 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
7615 TCATAGAAAG
* * * *
7625 GTTTATTAAAATTTCATAATTAAGTTATCAAAGTTTCATATGGA
1 GTTTATCAAAATTTCATAAGTAAATTATCAAAATTTCATATGGA
* *
7669 GTTTATCACAATTTCATAGGTAAATTATCAAAATTTCATA
1 GTTTATCAAAATTTCATAAGTAAATTATCAAAATTTCATA
7709 GCGTGGTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.42
Consensus pattern (44 bp):
GTTTATCAAAATTTCATAAGTAAATTATCAAAATTTCATATGGA
Found at i:7709 original size:22 final size:22
Alignment explanation
Indices: 7627--7752 Score: 78
Period size: 22 Copynumber: 5.7 Consensus size: 22
7617 ATAGAAAGGT
* ** *
7627 TTATTAAAATTTCATAATTAAG
1 TTATCAAAATTTCATAGGTAAA
* **
7649 TTATCAAAGTTTCATATGG-AGT
1 TTATCAAAATTTCATA-GGTAAA
*
7671 TTATCACAATTTCATAGGTAAA
1 TTATCAAAATTTCATAGGTAAA
**
7693 TTATCAAAATTTCATAGCGT-GG
1 TTATCAAAATTTCATAG-GTAAA
* * *
7715 TTATCAAATTTTAATTGG-ATAA
1 TTATCAAAATTTCATAGGTA-AA
*
7737 TTATTAAAATTTCATA
1 TTATCAAAATTTCATA
7753 AAAATATTCA
Statistics
Matches: 77, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
21 3 0.04
22 72 0.94
23 2 0.03
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGTAAA
Found at i:7719 original size:44 final size:43
Alignment explanation
Indices: 7633--7752 Score: 109
Period size: 44 Copynumber: 2.7 Consensus size: 43
7623 AGGTTTATTA
** * * *
7633 AAATTTCATAATTAAGTTATCAAAGTTTCATATGGAGTTTATC
1 AAATTTCATAGGTAAATTATCAAAATTTCATATGGAGGTTATC
*
7676 ACAATTTCATAGGTAAATTATCAAAATTTCATA-GCGTGGTTATC
1 A-AATTTCATAGGTAAATTATCAAAATTTCATATG-GAGGTTATC
* * *
7720 AAATTTTAATTGG-ATAATTATTAAAATTTCATA
1 AAA-TTTCATAGGTA-AATTATCAAAATTTCATA
7753 AAAATATTCA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
43 5 0.08
44 59 0.92
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (43 bp):
AAATTTCATAGGTAAATTATCAAAATTTCATATGGAGGTTATC
Found at i:13147 original size:3 final size:3
Alignment explanation
Indices: 13139--13178 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
13129 TTCCTCCACT
13139 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC
13179 CAAGAGAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:18026 original size:28 final size:28
Alignment explanation
Indices: 17986--18041 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
17976 TGAAGGTGTC
17986 AGAATCAATTGAGAAACTGTCTATTCTT
1 AGAATCAATTGAGAAACTGTCTATTCTT
18014 AGAATCAATTGAGAAACTGTCTATTCTT
1 AGAATCAATTGAGAAACTGTCTATTCTT
18042 GTGAAGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (28 bp):
AGAATCAATTGAGAAACTGTCTATTCTT
Done.