Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014764.1 Corchorus olitorius cultivar O-4 contig14797, 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: 24277
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:274 original size:30 final size:30
Alignment explanation
Indices: 211--272 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 30
201 TATTTTGTCA
211 TTATTTTTTATTTAGGTTAGTATTAGGCTT
1 TTATTTTTTATTTAGGTTAGTATTAGGCTT
*
241 TTATTTTCTTATTTTA-GTTAGTATTGGGCTT
1 TTATTTT-TTA-TTTAGGTTAGTATTAGGCTT
272 T
1 T
273 ATGGGCTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.24
31 18 0.62
32 4 0.14
ACGTcount: A:0.18, C:0.05, G:0.16, T:0.61
Consensus pattern (30 bp):
TTATTTTTTATTTAGGTTAGTATTAGGCTT
Found at i:2607 original size:221 final size:221
Alignment explanation
Indices: 2216--2664 Score: 828
Period size: 221 Copynumber: 2.0 Consensus size: 221
2206 TCTTGATCCT
*
2216 TATAAGTCCACCTTTTTTGGTACTCCAATTTGGAGTACCAACAAGAACCAACAAAGTTTTTATTT
1 TATAAGTCCACCTTTTTTGGTACTCCAAATTGGAGTACCAACAAGAACCAACAAAGTTTTTATTT
*
2281 ATTAAATGTTAGGTGATCCCTCATGTTCCTTACTTTTTATATTTTAAACAATTCAAACAAGGATT
66 ATTAAATGTTAGGTGATCCCTCATGTTCCTTACTTTTTATATTTTAAACAATCCAAACAAGGATT
*
2346 GGTCCTTCCCTTCCTTTCCTTTAAAAAACCCTCCTTTCCCATCCTATCCTGTCCTATACTGATCC
131 GGTCCTTCCCTTCCTTTCCTTTAAAAAACCCTCATTTCCCATCCTATCCTGTCCTATACTGATCC
2411 CTCAAAAAGTTTACCCAAACACACTG
196 CTCAAAAAGTTTACCCAAACACACTG
2437 TATAAGTCCACCTTTTTTGGTACTCCAAATTGGAGTACCAACAAGAACCAACAAAGTTTTTATTT
1 TATAAGTCCACCTTTTTTGGTACTCCAAATTGGAGTACCAACAAGAACCAACAAAGTTTTTATTT
2502 ATTAAATGTTAGGTGATCCCTCATGTTCCTTACTTTTTATATTTTAAACAATCCAAACAAGGATT
66 ATTAAATGTTAGGTGATCCCTCATGTTCCTTACTTTTTATATTTTAAACAATCCAAACAAGGATT
* * *
2567 GGTCCTTCCCTTCCTTTCCTTTAAAAAACCTTCATTTCCCATTCTATCCTGTCCTATATTGATCC
131 GGTCCTTCCCTTCCTTTCCTTTAAAAAACCCTCATTTCCCATCCTATCCTGTCCTATACTGATCC
*
2632 CTCAAAAAGTTTATCCAAACACACTG
196 CTCAAAAAGTTTACCCAAACACACTG
2658 TA-AAGTC
1 TATAAGTC
2665 TGCAGAAACC
Statistics
Matches: 221, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
220 5 0.02
221 216 0.98
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.36
Consensus pattern (221 bp):
TATAAGTCCACCTTTTTTGGTACTCCAAATTGGAGTACCAACAAGAACCAACAAAGTTTTTATTT
ATTAAATGTTAGGTGATCCCTCATGTTCCTTACTTTTTATATTTTAAACAATCCAAACAAGGATT
GGTCCTTCCCTTCCTTTCCTTTAAAAAACCCTCATTTCCCATCCTATCCTGTCCTATACTGATCC
CTCAAAAAGTTTACCCAAACACACTG
Found at i:4938 original size:2 final size:2
Alignment explanation
Indices: 4933--4958 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4923 TCTCTCTCTC
4933 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
4959 GTGTGGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5768 original size:22 final size:22
Alignment explanation
Indices: 5742--5790 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
5732 ACTATAGTAT
5742 CAAAAAATTATAGGGAGATTAA
1 CAAAAAATTATAGGGAGATTAA
5764 CAAAAAATTATAGGGAGATTAA
1 CAAAAAATTATAGGGAGATTAA
5786 CAAAA
1 CAAAA
5791 TCTCATAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.57, C:0.06, G:0.16, T:0.20
Consensus pattern (22 bp):
CAAAAAATTATAGGGAGATTAA
Found at i:5798 original size:22 final size:22
Alignment explanation
Indices: 5742--5819 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 22
5732 ACTATAGTAT
* *
5742 CAAAAAATTATAGGGAGATTAA
1 CAAAATATCATAGGGAGATTAA
* *
5764 CAAAAAATTATAGGGAGATTAA
1 CAAAATATCATAGGGAGATTAA
* * *
5786 CAAAATCTCATAGGTA-ATTAT
1 CAAAATATCATAGGGAGATTAA
*
5807 CAAAATTTCATAG
1 CAAAATATCATAG
5820 CATGATTATC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
21 16 0.32
22 34 0.68
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.27
Consensus pattern (22 bp):
CAAAATATCATAGGGAGATTAA
Found at i:5827 original size:43 final size:43
Alignment explanation
Indices: 5780--5861 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
5770 ATTATAGGGA
* *
5780 GATTAACAAAATCTCATAGG-TAATTATCAAAATTTCATAGCAT
1 GATTAACAAAATCTAATAGGAT-AGTATCAAAATTTCATAGCAT
* *
5823 GATTATCAAAATTTAATAGGATAGTATCAAAATTTCATA
1 GATTAACAAAATCTAATAGGATAGTATCAAAATTTCATA
5862 AAAATATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 33 0.97
44 1 0.03
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (43 bp):
GATTAACAAAATCTAATAGGATAGTATCAAAATTTCATAGCAT
Found at i:5830 original size:22 final size:21
Alignment explanation
Indices: 5780--5861 Score: 85
Period size: 21 Copynumber: 3.9 Consensus size: 21
5770 ATTATAGGGA
* * *
5780 GATTAACAAAATCTCATAGGT
1 GATTATCAAAATTTCATAGAT
*
5801 AATTATCAAAATTTCATAGCAT
1 GATTATCAAAATTTCATAG-AT
*
5823 GATTATCAAAATTTAATAGGAT
1 GATTATCAAAATTTCATA-GAT
*
5845 -AGTATCAAAATTTCATA
1 GATTATCAAAATTTCATA
5862 AAAATATTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 31 0.61
22 19 0.37
23 1 0.02
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (21 bp):
GATTATCAAAATTTCATAGAT
Found at i:5852 original size:21 final size:22
Alignment explanation
Indices: 5804--5857 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5794 CATAGGTAAT
* *
5804 TATCAAAATTTCATAGCATGAT
1 TATCAAAATTTAATAGCATGAG
*
5826 TATCAAAATTTAATAGGAT-AG
1 TATCAAAATTTAATAGCATGAG
5847 TATCAAAATTT
1 TATCAAAATTT
5858 CATAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTAATAGCATGAG
Found at i:7949 original size:33 final size:33
Alignment explanation
Indices: 7921--7983 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
7911 ACGGCACTCG
7921 CCATGGCATGCCGCCCTTGGAGGGCGGCACGAA
1 CCATGGCATGCCGCCCTTGGAGGGCGGCACGAA
* *
7954 CCATGGCATGCGGCCTTTGGAGGGCGGCAC
1 CCATGGCATGCCGCCCTTGGAGGGCGGCAC
7984 CAATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.16, C:0.32, G:0.38, T:0.14
Consensus pattern (33 bp):
CCATGGCATGCCGCCCTTGGAGGGCGGCACGAA
Found at i:8051 original size:6 final size:7
Alignment explanation
Indices: 8003--8053 Score: 54
Period size: 6 Copynumber: 7.6 Consensus size: 7
7993 TTTTTAAATT
8003 ATTATTA
1 ATTATTA
8010 ATTATTTA
1 ATTA-TTA
8018 ATTATTA
1 ATTATTA
*
8025 ATT-TAA
1 ATTATTA
*
8031 ATTGTT-
1 ATTATTA
8037 ATTATTA
1 ATTATTA
8044 ATTA-TA
1 ATTATTA
8050 ATTA
1 ATTA
8054 AAAATTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
6 16 0.42
7 15 0.39
8 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (7 bp):
ATTATTA
Found at i:8062 original size:31 final size:33
Alignment explanation
Indices: 8001--8062 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
7991 TTTTTTTAAA
* *
8001 TTATTATTAATTATTTAATTATTAATTTAAATTG
1 TTATTATTAATTA-TTAATTATAAAATTAAATTG
8035 TTATTATTAATTA-TAATTA-AAAATTAAA
1 TTATTATTAATTATTAATTATAAAATTAAA
8063 AAAATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 7 0.27
32 6 0.23
34 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (33 bp):
TTATTATTAATTATTAATTATAAAATTAAATTG
Found at i:8173 original size:21 final size:21
Alignment explanation
Indices: 8131--8173 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
8121 GTAAAATTGT
***
8131 CAAAAAGGGGGCGGTGTTTAG
1 CAAAAAGGGGGCGGTAAATAG
8152 CAAAAAGGGGGCGGTAAATAG
1 CAAAAAGGGGGCGGTAAATAG
8173 C
1 C
8174 TAGGGCTGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.40, T:0.14
Consensus pattern (21 bp):
CAAAAAGGGGGCGGTAAATAG
Found at i:13374 original size:25 final size:25
Alignment explanation
Indices: 13340--13388 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
13330 TCCTAACTTG
13340 AAATCTTTTTGTTTGCTTAAATCTT
1 AAATCTTTTTGTTTGCTTAAATCTT
*
13365 AAATCTTTTTGTTTGCTTAGATCT
1 AAATCTTTTTGTTTGCTTAAATCT
13389 GAAAAACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.55
Consensus pattern (25 bp):
AAATCTTTTTGTTTGCTTAAATCTT
Found at i:14827 original size:104 final size:105
Alignment explanation
Indices: 14707--14899 Score: 370
Period size: 105 Copynumber: 1.8 Consensus size: 105
14697 ATTTATTAAA
*
14707 AAAATTTATTTAGAAAGTCAAGTTGCAAGT-AAAAAAAAGTTAAAAATAAAATTTATTAATAAAA
1 AAAATTTATTAAGAAAGTCAAGTTGCAAGTAAAAAAAAAGTTAAAAATAAAATTTATTAATAAAA
14771 TTATTCAATTTAGTTTATGTTTTTGTTATAATGCAAAAAC
66 TTATTCAATTTAGTTTATGTTTTTGTTATAATGCAAAAAC
14811 AAAATTTATTAAGAAAGTCAAGTTGCAAGTAAAAAAAAAGTTAAAAATAAAATTTATTAATAAAA
1 AAAATTTATTAAGAAAGTCAAGTTGCAAGTAAAAAAAAAGTTAAAAATAAAATTTATTAATAAAA
14876 TTATTCAATTTAGTTTATGTTTTT
66 TTATTCAATTTAGTTTATGTTTTT
14900 TTCTTTTTAT
Statistics
Matches: 87, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
104 29 0.33
105 58 0.67
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (105 bp):
AAAATTTATTAAGAAAGTCAAGTTGCAAGTAAAAAAAAAGTTAAAAATAAAATTTATTAATAAAA
TTATTCAATTTAGTTTATGTTTTTGTTATAATGCAAAAAC
Found at i:15332 original size:162 final size:161
Alignment explanation
Indices: 15131--15549 Score: 535
Period size: 161 Copynumber: 2.6 Consensus size: 161
15121 CTGAAATTGA
* * * * * * * * *
15131 ATATAGCGGCGTCT-GACATGAAGACGCCGCCATTTAGTGGCGTTTCG-ATAGAAAGACGCTGCC
1 ATATAGCGGCGTTTCGACAT-CAGACGCCGCTAATTAGTGGCATCTAGAAAAGAAA-ACGCCGCC
*
15194 ATATTAATATATGGAGGGAGATA-TTTTTTTTT-CTTTTTTTGGAGGGAAAAATTCACTCCCCCT
64 ATATTAATATATGGAGGGAGAAATTTTTTTTTTCCTTTTTTTGGAGGGAAAAATTCACT-CCCC-
15257 TAAAACAAAGAAAGTTTCCAACTCTACCCCTATAAT
127 TAAAA-AAAGAAAGTTTCCAACTCTACCCCTATAAT
*
15293 ATATAGCGGCGTTTCGACATCAGACGCCGCTAATTAGTGGCATCTAGAAAAGGAAACGCCGCCAT
1 ATATAGCGGCGTTTCGACATCAGACGCCGCTAATTAGTGGCATCTAGAAAAGAAAACGCCGCCAT
* *
15358 TTTAATATATGGAGGGAGAAATTTTTTTTTTCCTTTTTTTGGAGGGAAAAATTCCCTCCCCTAAA
66 ATTAATATATGGAGGGAGAAATTTTTTTTTTCCTTTTTTTGGAGGGAAAAATTCACTCCCCTAAA
*
15423 AAAAGAAAGTTTCCAACTCTACGCCTATAAT
131 AAAAGAAAGTTTCCAACTCTACCCCTATAAT
* * * * * *
15454 ATATAGCAGCGTATTC-AGATCAGACGCCGCTAATTAGTGGCATCTAGGAAAGGAAGCGCCGCAA
1 ATATAGCGGCGT-TTCGACATCAGACGCCGCTAATTAGTGGCATCTAGAAAAGAAAACGCCGCCA
*
15518 T-TGTAATATATGGAGTGAGAGAATTTTTTTTT
65 TAT-TAATATATGGAGGGAGA-AATTTTTTTTT
15550 CAGGAAAAAA
Statistics
Matches: 230, Mismatches: 20, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
160 1 0.00
161 101 0.44
162 81 0.35
163 23 0.10
164 24 0.10
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (161 bp):
ATATAGCGGCGTTTCGACATCAGACGCCGCTAATTAGTGGCATCTAGAAAAGAAAACGCCGCCAT
ATTAATATATGGAGGGAGAAATTTTTTTTTTCCTTTTTTTGGAGGGAAAAATTCACTCCCCTAAA
AAAAGAAAGTTTCCAACTCTACCCCTATAAT
Found at i:15478 original size:161 final size:163
Alignment explanation
Indices: 15186--15549 Score: 558
Period size: 161 Copynumber: 2.2 Consensus size: 163
15176 CGATAGAAAG
* * *
15186 ACGCTGCCATATTAATATATGGAGGGAGATA-TTTTTTTTTCTTTTTTTGGAGGGAAAAATTCAC
1 ACGCCGCCATTTTAATATATGGAGGGAGAAATTTTTTTTTTCTTTTTTTGGAGGGAAAAATTCAC
*
15250 TCCCCCTTAAAACAAAGAAAGTTTCCAACTCTACCCCTATAATATATAGCGGCGTTTCGACATCA
66 TCCCCCTTAAAACAAAGAAAGTTTCCAACTCTACCCCTATAATATATAGCAGCGTTTCGACATCA
15315 GACGCCGCTAATTAGTGGCATCTAGAAAAGGAA
131 GACGCCGCTAATTAGTGGCATCTAGAAAAGGAA
*
15348 ACGCCGCCATTTTAATATATGGAGGGAGAAATTTTTTTTTTCCTTTTTTTGGAGGGAAAAATTCC
1 ACGCCGCCATTTTAATATATGGAGGGAGAAATTTTTTTTTT-CTTTTTTTGGAGGGAAAAATTCA
* *
15413 CT-CCCC-TAAAA-AAAGAAAGTTTCCAACTCTACGCCTATAATATATAGCAGCGTATTC-AGAT
65 CTCCCCCTTAAAACAAAGAAAGTTTCCAACTCTACCCCTATAATATATAGCAGCGT-TTCGACAT
*
15474 CAGACGCCGCTAATTAGTGGCATCTAGGAAAGGAA
129 CAGACGCCGCTAATTAGTGGCATCTAGAAAAGGAA
* * * *
15509 GCGCCGCAATTGTAATATATGGAGTGAGAGAATTTTTTTTT
1 ACGCCGCCATTTTAATATATGGAGGGAGA-AATTTTTTTTT
15550 CAGGAAAAAA
Statistics
Matches: 186, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
161 102 0.55
162 47 0.25
163 13 0.07
164 24 0.13
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (163 bp):
ACGCCGCCATTTTAATATATGGAGGGAGAAATTTTTTTTTTCTTTTTTTGGAGGGAAAAATTCAC
TCCCCCTTAAAACAAAGAAAGTTTCCAACTCTACCCCTATAATATATAGCAGCGTTTCGACATCA
GACGCCGCTAATTAGTGGCATCTAGAAAAGGAA
Found at i:20623 original size:20 final size:21
Alignment explanation
Indices: 20585--20623 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20575 TTTTCACAAT
*
20585 TATTTCTTTTATCTTTACTAA
1 TATTTCTTTTATCTATACTAA
*
20606 TATTTTTTTTAT-TATACT
1 TATTTCTTTTATCTATACT
20624 CGTTAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTCTTTTATCTATACTAA
Found at i:21286 original size:36 final size:37
Alignment explanation
Indices: 21236--21306 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
21226 CATTTATAAG
21236 GCTACTTTCTCTTCCA-TCTCGAACCAACTGGCTTGA
1 GCTACTTTCTCTTCCATTCTCGAACCAACTGGCTTGA
* *
21272 GCTACTTT-TCCTTCCATTTTCGAACCAATTGGCTT
1 GCTACTTTCT-CTTCCATTCTCGAACCAACTGGCTT
21307 AGAACTCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 1 0.03
36 14 0.45
37 16 0.52
ACGTcount: A:0.18, C:0.31, G:0.13, T:0.38
Consensus pattern (37 bp):
GCTACTTTCTCTTCCATTCTCGAACCAACTGGCTTGA
Found at i:21446 original size:72 final size:72
Alignment explanation
Indices: 21329--21478 Score: 246
Period size: 72 Copynumber: 2.1 Consensus size: 72
21319 CCTGTTGCAT
* *
21329 TTGGACTTATATTGCTTCAAGTGGGCTGATCATTTCTTGGCATTATCTGCTTGGGCTTGTATTGT
1 TTGGACTTATATTGCTTCAAATGGGCTGATCATTTCTTGGCATTATCTGCTTGGCCTTGTATTGT
21394 TAACATC
66 TAACATC
* *
21401 TTGGATTTATATTGCTTCAAATGGGCTGATCATTTCTTGGCATTATTTGCTTGGCCTTGTATTGT
1 TTGGACTTATATTGCTTCAAATGGGCTGATCATTTCTTGGCATTATCTGCTTGGCCTTGTATTGT
*
21466 TAACGTC
66 TAACATC
*
21473 CTGGAC
1 TTGGAC
21479 CTTGGGCCTT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.43
Consensus pattern (72 bp):
TTGGACTTATATTGCTTCAAATGGGCTGATCATTTCTTGGCATTATCTGCTTGGCCTTGTATTGT
TAACATC
Done.