Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010750.1 Corchorus capsularis cultivar CVL-1 contig10771, 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: 14851
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:3579 original size:22 final size:23
Alignment explanation
Indices: 3554--3596 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3544 TAACATATCT
3554 TCATTCAAATAT-ATTTGTAATC
1 TCATTCAAATATCATTTGTAATC
*
3576 TCATTCAAATTTCATTTGTAA
1 TCATTCAAATATCATTTGTAA
3597 AGTTGTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.47
Consensus pattern (23 bp):
TCATTCAAATATCATTTGTAATC
Found at i:7899 original size:22 final size:23
Alignment explanation
Indices: 7874--7916 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
7864 TAACATATCT
7874 TCATTCAAATAT-ATTTGTAATC
1 TCATTCAAATATAATTTGTAATC
* *
7896 TCATTCGAATTTAATTTGTAA
1 TCATTCAAATATAATTTGTAA
7917 AGTTGTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (23 bp):
TCATTCAAATATAATTTGTAATC
Found at i:13250 original size:72 final size:72
Alignment explanation
Indices: 13053--13282 Score: 275
Period size: 78 Copynumber: 3.1 Consensus size: 72
13043 AATTAGCTGC
* * * * *
13053 AGGTATATAGCCTACC--TATTAATGGATAGCAGTTGATACGACTAGCTTATACCAACGGGTATA
1 AGGTATATAG-CTACCTATATTAATGGATAGCAGTGGACAAGACTAGCTTATACCATCGGGCATA
13116 AATGGTGT
65 AATGGTGT
13124 AGCTATGTATATAGCTACCTATATTAATATGGATAGCAGTGGACAAGACTAGCTTATACCATCGG
1 AG----GTATATAGCTACCTATATT-A-ATGGATAGCAGTGGACAAGACTAGCTTATACCATCGG
* *
13189 CCATTAATGGTGT
60 GCATAAATGGTGT
* * *
13202 AGGTATATTGCTACCTATATTAATGGATAGAAGTGGACATGACTAGCTTATACCATCGGGCATAA
1 AGGTATATAGCTACCTATATTAATGGATAGCAGTGGACAAGACTAGCTTATACCATCGGGCAT-A
13267 AATGGTGT
65 AATGGTGT
*
13275 AGATATAT
1 AGGTATAT
13283 CTAATATATA
Statistics
Matches: 137, Mismatches: 13, Indels: 16
0.83 0.08 0.10
Matches are distributed among these distances:
71 2 0.01
72 38 0.28
73 16 0.12
74 23 0.17
75 8 0.06
76 4 0.03
77 1 0.01
78 45 0.33
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (72 bp):
AGGTATATAGCTACCTATATTAATGGATAGCAGTGGACAAGACTAGCTTATACCATCGGGCATAA
ATGGTGT
Found at i:13298 original size:72 final size:72
Alignment explanation
Indices: 13072--13299 Score: 239
Period size: 72 Copynumber: 3.1 Consensus size: 72
13062 GCCTACCTAT
* * * * *
13072 TAATGGATAGCAGTTGATACGACTAGCTTATACCAACGGGTATAAATGGTGTAGCTATGTATATA
1 TAATGGATAGCAGTGGACAAGACTAGCTTATACCATCGGGCATAAATGGTGTAG--A--TATAT-
13137 GCTACCTATAT-
61 GCTACCTATATA
* * *
13148 TAATATGGATAGCAGTGGACAAGACTAGCTTATACCATCGGCCATTAATGGTGTAGGTATATTGC
1 T-A-ATGGATAGCAGTGGACAAGACTAGCTTATACCATCGGGCATAAATGGTGTAGATATA-TGC
13213 TACCTATAT-
63 TACCTATATA
* *
13222 TAATGGATAGAAGTGGACATGACTAGCTTATACCATCGGGCATAAAATGGTGTAGATATAT-CTA
1 TAATGGATAGCAGTGGACAAGACTAGCTTATACCATCGGGCAT-AAATGGTGTAGATATATGCTA
*
13286 -ATATATA
65 CCTATATA
13293 CTAATGG
1 -TAATGG
13300 TCTGCAAAAT
Statistics
Matches: 132, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
70 5 0.04
71 3 0.02
72 45 0.34
73 15 0.11
74 16 0.12
75 1 0.01
76 1 0.01
77 1 0.01
78 45 0.34
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (72 bp):
TAATGGATAGCAGTGGACAAGACTAGCTTATACCATCGGGCATAAATGGTGTAGATATATGCTAC
CTATATA
Found at i:13533 original size:30 final size:31
Alignment explanation
Indices: 13479--13543 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
13469 AACTTTATGT
* *
13479 TTTCCGATTGTACCCTTATTTTTAAAATATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
*
13510 TTTCCAATTGTATCCTT-TTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
13540 TTTC
1 TTTC
13544 TAAATTGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.51
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:13550 original size:31 final size:31
Alignment explanation
Indices: 13485--13551 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
13475 ATGTTTTCCG
* *
13485 ATTGTACCCTTATTTTTAAAATATATTTCCA
1 ATTGTACCCTTATTTTTAAAACATATTTCAA
*
13516 ATTGTATCCTT-TTTTTAAAACATATTTCTAA
1 ATTGTACCCTTATTTTTAAAACATATTTC-AA
13547 ATTGT
1 ATTGT
13552 CATTACTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.31, C:0.13, G:0.04, T:0.51
Consensus pattern (31 bp):
ATTGTACCCTTATTTTTAAAACATATTTCAA
Found at i:13879 original size:22 final size:22
Alignment explanation
Indices: 13809--13970 Score: 107
Period size: 22 Copynumber: 7.3 Consensus size: 22
13799 TGTCTCTATA
***
13809 TGGTTATCAAAATTTCATAAAA
1 TGGTTATCAAAATTTCATAGTG
* * *
13831 TGGTTATTATAATTCCATGAG-G
1 TGGTTATCAAAATTTCAT-AGTG
* *
13853 AGGTTATCAAAATTCCATAGTG
1 TGGTTATCAAAATTTCATAGTG
13875 TGGTTA-CAAAAATTTCATAGTG
1 TGGTTATC-AAAATTTCATAGTG
* *
13897 TAGTTACCAAAATTTCATAG-G
1 TGGTTATCAAAATTTCATAGTG
* *
13918 ATCAGGTTATTAAAATTTCTTAG-G
1 -T--GGTTATCAAAATTTCATAGTG
** *
13942 TTGGTTATTGAAATTTCATAGGG
1 -TGGTTATCAAAATTTCATAGTG
13965 TGGTTA
1 TGGTTA
13971 ATTATCACAA
Statistics
Matches: 114, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
21 4 0.04
22 90 0.79
23 3 0.03
24 17 0.15
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGTG
Found at i:14059 original size:22 final size:22
Alignment explanation
Indices: 14009--14130 Score: 79
Period size: 22 Copynumber: 5.5 Consensus size: 22
13999 AAAAAGATTT
* *
14009 CAAAATGTCATAGCGAGGTTATA
1 CAAAATTTCATAGTGAGGTTA-A
* *
14032 C-GAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAGTGAGGTTAA
*
14053 CAAAATTTCATTAG-AAGGTT-A
1 CAAAATTTCA-TAGTGAGGTTAA
* * * * *
14074 CTAATACTTCATCGGGAGGTTAT
1 C-AAAATTTCATAGTGAGGTTAA
* * *
14097 CAAAATTTTATAGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAA
14119 CAAAATTTCATA
1 CAAAATTTCATA
14131 TATGAAGATT
Statistics
Matches: 75, Mismatches: 19, Indels: 11
0.71 0.18 0.10
Matches are distributed among these distances:
21 6 0.08
22 64 0.85
23 5 0.07
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAA
Found at i:14334 original size:22 final size:22
Alignment explanation
Indices: 14203--14422 Score: 121
Period size: 22 Copynumber: 9.9 Consensus size: 22
14193 ATCTAATAGA
* *
14203 GTGATTATCGAAATTTCATAAA
1 GTGATTATCAAAATTTCATAAT
14225 GATAGGATTATCAAAATTT-AT-AT
1 G-T--GATTATCAAAATTTCATAAT
* *
14248 GAAGATTATCAAAATTTCATAGT
1 G-TGATTATCAAAATTTCATAAT
* *
14271 GTTG-TTACCAAAATTTCA-AAGC
1 G-TGATTATCAAAATTTCATAA-T
* * *
14293 GGGTTTATCAAAATTACATAAT
1 GTGATTATCAAAATTTCATAAT
14315 GTGATTATCAAAATTTCATAGA-
1 GTGATTATCAAAATTTCATA-AT
* * * * *
14337 GGGATCAACAAAATTTTATAAA
1 GTGATTATCAAAATTTCATAAT
* *
14359 GATG-TTATCAAATTTTCATAAA
1 G-TGATTATCAAAATTTCATAAT
* * ** *
14381 GAGGTTATCAATTTTTCAAAAT
1 GTGATTATCAAAATTTCATAAT
14403 GTGATTA-CAAAAATTTCATA
1 GTGATTATC-AAAATTTCATA
14423 GTGGTATTTT
Statistics
Matches: 151, Mismatches: 34, Indels: 26
0.72 0.16 0.12
Matches are distributed among these distances:
21 19 0.13
22 106 0.70
23 11 0.07
24 2 0.01
25 13 0.09
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (22 bp):
GTGATTATCAAAATTTCATAAT
Found at i:14349 original size:44 final size:44
Alignment explanation
Indices: 14185--14423 Score: 159
Period size: 44 Copynumber: 5.4 Consensus size: 44
14175 TTGATAGAAG
* * * * *
14185 GTTATC-AAATCTAATAGAGTGATTATCGAAATTTCATAAAGAT
1 GTTATCAAAATTTCATAGAGGGATTATCAAAATTTCATAATGAT
* * *
14228 AGGATTATCAAAATTT-ATATGA-AGATTATCAAAATTTCATAGTGTT
1 --G-TTATCAAAATTTCATA-GAGGGATTATCAAAATTTCATAATGAT
* * * * *
14274 GTTACCAAAATTTCAAAGCGGGTTTATCAAAATTACATAATG-T
1 GTTATCAAAATTTCATAGAGGGATTATCAAAATTTCATAATGAT
* * * *
14317 GATTATCAAAATTTCATAGAGGGATCAACAAAATTTTATAAAGAT
1 G-TTATCAAAATTTCATAGAGGGATTATCAAAATTTCATAATGAT
* * ** *
14362 GTTATCAAATTTTCATAAAGAGG-TTATCAATTTTTCAAAATG-T
1 GTTATCAAAATTTCATAGAG-GGATTATCAAAATTTCATAATGAT
14405 GATTA-CAAAAATTTCATAG
1 G-TTATC-AAAATTTCATAG
14424 TGGTATTTTT
Statistics
Matches: 151, Mismatches: 33, Indels: 21
0.74 0.16 0.10
Matches are distributed among these distances:
43 17 0.11
44 95 0.63
45 5 0.03
46 27 0.18
47 7 0.05
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (44 bp):
GTTATCAAAATTTCATAGAGGGATTATCAAAATTTCATAATGAT
Found at i:14534 original size:19 final size:19
Alignment explanation
Indices: 14504--14570 Score: 116
Period size: 19 Copynumber: 3.5 Consensus size: 19
14494 TGATGGAGTA
*
14504 ATCAAAATTTCAGGGAGGAT
1 ATCAAAA-TTCAGTGAGGAT
14524 ATCAAAATTCAGTGAGGAT
1 ATCAAAATTCAGTGAGGAT
14543 ATCAAAATTCAGTGAGGAT
1 ATCAAAATTCAGTGAGGAT
14562 ATCAAAATT
1 ATCAAAATT
14571 TCATACGAAG
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 39 0.85
20 7 0.15
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.27
Consensus pattern (19 bp):
ATCAAAATTCAGTGAGGAT
Found at i:14698 original size:44 final size:44
Alignment explanation
Indices: 14542--14851 Score: 209
Period size: 44 Copynumber: 7.2 Consensus size: 44
14532 TCAGTGAGGA
* * * *
14542 TATCAAAA-TTC--AGTGAGGATATCAAAATTTCATACGAAGGT
1 TATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGAT
* * *
14583 TATCAAATTTTCATAGTTTA-GTTTTCAAAATTTCATAAGAGG-G-T
1 TATCAAAATTTCATAG-TGAGGTTATCAAAATTTCAT-AG-GGAGAT
** *
14627 TATCAAAA-TTCATAGT-ATATAGATCAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATAGTGAGGT-TATCAAAATTTCATAGGGAGAT
* * ** *
14670 TAACAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGCT
1 TATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGAT
* * *
14714 TATCAAAA-TT--T-GT-A-GTTATCAAGATTTCATA-AGAAAGT
1 TATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGA-T
* * * * *
14752 TATCAAAATTTTATAGGGAGGTTTATTAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAGTGAGG-TTATCAAAATTTCATAGGGAGA-T
** * *
14798 TATCAAAATTTCATAGTGAGGTTATCTCAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGAT
14842 TATCAAAATT
1 TATCAAAATT
Statistics
Matches: 205, Mismatches: 43, Indels: 39
0.71 0.15 0.14
Matches are distributed among these distances:
37 2 0.01
38 23 0.11
39 3 0.01
40 1 0.00
41 12 0.06
42 9 0.04
43 30 0.15
44 68 0.33
45 34 0.17
46 23 0.11
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (44 bp):
TATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGAT
Found at i:14706 original size:87 final size:87
Alignment explanation
Indices: 14562--14723 Score: 186
Period size: 87 Copynumber: 1.9 Consensus size: 87
14552 CAGTGAGGAT
* * * * * * **
14562 ATCAAAATTTCATACGAAGGTTATCAAATTTTCATAGTTTAGTTTTCAAAATTTCATAAGAGG-G
1 ATCAAAATTTCATACGAAGATTAACAAAATTTCATAGATGAGTTATCAAAAAATCAT-AG-GGAG
14626 -TTATCAAAATTCATAGTATATAG
64 CTTATCAAAATTCATAGTATATAG
* *
14649 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATA-ATGAGGTTATCAAAAAATCATAGGGAGC
1 ATCAAAATTTCATACGAAGATTAACAAAATTTCATAGATGA-GTTATCAAAAAATCATAGGGAGC
14713 TTATCAAAATT
65 TTATCAAAATT
14724 TGTAGTTATC
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
85 2 0.03
86 5 0.08
87 55 0.89
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (87 bp):
ATCAAAATTTCATACGAAGATTAACAAAATTTCATAGATGAGTTATCAAAAAATCATAGGGAGCT
TATCAAAATTCATAGTATATAG
Found at i:14782 original size:23 final size:23
Alignment explanation
Indices: 14751--14820 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
14741 CATAAGAAAG
14751 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* * *
14774 TTATTAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
14797 TTATCAAAATTTCATAGTGAGGT
1 TTATCAAAATTTTATAGGGAGGT
14820 T
1 T
14821 ATCTCAATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:14851 original size:22 final size:22
Alignment explanation
Indices: 14523--14851 Score: 160
Period size: 22 Copynumber: 15.5 Consensus size: 22
14513 TCAGGGAGGA
14523 TATCAAAA-TTC--AGTGAGGA-
1 TATCAAAATTTCATAGTGA-GAT
14542 TATCAAAA-TTC--AGTGAGGA-
1 TATCAAAATTTCATAGTGA-GAT
* *
14561 TATCAAAATTTCATACG-AAGGT
1 TATCAAAATTTCATA-GTGAGAT
* *
14583 TATCAAATTTTCATAGTTTAG-T
1 TATCAAAATTTCATAG-TGAGAT
* * *
14605 TTTCAAAATTTCATA-AGAGGGT
1 TATCAAAATTTCATAGTGA-GAT
*
14627 TATCAAAA-TTCATAGT-ATAT
1 TATCAAAATTTCATAGTGAGAT
* *
14647 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAGTGAGAT
* * *
14670 TAACAAAATTTCATAATGAGGT
1 TATCAAAATTTCATAGTGAGAT
** * *
14692 TATCAAAAAATCATAGGGAGCT
1 TATCAAAATTTCATAGTGAGAT
14714 TATCAAAA-TT--T-GT-AG-T
1 TATCAAAATTTCATAGTGAGAT
* * *
14730 TATCAAGATTTCATA-AGAAAGT
1 TATCAAAATTTCATAGTGAGA-T
* * *
14752 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGTGA-GAT
* *
14775 TATTAAAATTTTATAG-GAAGATT
1 TATCAAAATTTCATAGTG-AGA-T
*
14798 TATCAAAATTTCATAGTGAGGT
1 TATCAAAATTTCATAGTGAGAT
** *
14820 TATCTCAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGAGAT
14842 TATCAAAATT
1 TATCAAAATT
Statistics
Matches: 238, Mismatches: 47, Indels: 47
0.72 0.14 0.14
Matches are distributed among these distances:
16 8 0.03
17 4 0.02
18 1 0.00
19 29 0.12
20 6 0.03
21 18 0.08
22 129 0.54
23 42 0.18
24 1 0.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGAGAT
Done.