Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010761.1 Corchorus capsularis cultivar CVL-1 contig10782, 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: 36301
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3033 original size:17 final size:18
Alignment explanation
Indices: 3013--3046 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3003 ATTATTATAC
3013 TAAAAAA-TAAATAATTA
1 TAAAAAATTAAATAATTA
3030 TAAAAAATTAAATAATT
1 TAAAAAATTAAATAATT
3047 TTAACACCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAAATTAAATAATTA
Found at i:16234 original size:18 final size:18
Alignment explanation
Indices: 16211--16249 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
16201 ATGGATAATC
*
16211 CTTAAGTTTTTTTTTAGA
1 CTTAAGTTTTCTTTTAGA
16229 CTTAAGTTTTCTTTTAGA
1 CTTAAGTTTTCTTTTAGA
16247 CTT
1 CTT
16250 GTGGCATGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59
Consensus pattern (18 bp):
CTTAAGTTTTCTTTTAGA
Found at i:23712 original size:22 final size:22
Alignment explanation
Indices: 23687--24230 Score: 122
Period size: 22 Copynumber: 24.7 Consensus size: 22
23677 ATGATCCCAT
23687 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* * ** *
23709 TATGAAACTTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
** * * **
23731 TAT-AGAATTTCAAGAATCTTTT
1 TATGA-AATTTTGATAACCTTCC
* ** * *
23753 TAT-AATTTTTTTTAACTTTCT
1 TATGAAATTTTGATAACCTTCC
* *
23774 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
23796 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
23818 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
23840 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
23863 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
23884 ATATGATATATTGATAACCACTT--
1 -TATGAAATTTTGATAA-C-CTTCC
* * * *
23907 TATAAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
23928 ATATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * * *
23951 TTTAAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
* * *
23973 TATAAAATTGTGATAACC-TCGT
1 TATGAAATTTTGATAACCTTC-C
* *
23995 TATGAAATTTTGATAAATCTTCT
1 TATGAAATTTTGAT-AACCTTCC
* * *
24018 TATAAAATTTTAATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
24041 TATAAAATTTTGATAATAACTTTCT
1 TATGAAATTTTG---ATAACCTTCC
** *
24066 TATGAAATCGTGATAA-C-T-A
1 TATGAAATTTTGATAACCTTCC
* * *
24085 TA-CAAATTTTGATAAGCTCCC
1 TATGAAATTTTGATAACCTTCC
** * *
24106 TATGATTTTTTGATTACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
24128 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
24150 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
24172 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* *
24194 TATGAAAATTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
24216 TATGAAATTTTGATA
1 TATGAAATTTTGATA
24231 TCCTCACTGA
Statistics
Matches: 376, Mismatches: 110, Indels: 72
0.67 0.20 0.13
Matches are distributed among these distances:
18 10 0.03
19 4 0.01
20 2 0.01
21 29 0.08
22 245 0.65
23 66 0.18
24 3 0.01
25 15 0.04
26 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:23876 original size:45 final size:45
Alignment explanation
Indices: 23818--23903 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
23808 AAGACCTCAA
* * *
23818 TATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACCT-CCATATGAAATATTGATAACCAACAC
* *
23863 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCA
23904 CTTTATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAACAC
Found at i:24004 original size:44 final size:43
Alignment explanation
Indices: 23955--24230 Score: 143
Period size: 44 Copynumber: 6.3 Consensus size: 43
23945 TCACACTTTA
*
23955 AAATTTTGATAATCACACTATAAAATTGTGATAACCTCGTTATG
1 AAATTTTGATAATCACACTATAAAATTTTGATAACCTC-TTATG
* * * * *
23999 AAATTTTGATAAATCTTC-TTATAAAATTTTAATAAACCTCCCTATA
1 AAATTTTGAT-AATC-ACACTATAAAATTTTGAT-AACCT-CTTATG
* * * ** * *
24045 AAATTTTGATAATAACTTTCTTATGAAATCGTGATAA-CT-ATA-C
1 AAATTTTGATAATCAC--AC-TATAAAATTTTGATAACCTCTTATG
* * * * ** *
24088 AAATTTTGATAAGCTCCCTATGATTTTTTGATTACCTCATTATG
1 AAATTTTGATAATCACACTATAAAATTTTGATAACCTC-TTATG
* * *
24132 AAATTTTGAT-CTACATACTATGAAATTTTGATAACCCTCTTATG
1 AAATTTTGATAAT-CACACTATAAAATTTTGATAA-CCTCTTATG
* * *
24176 AAATTTTGA-AAACTAAACTATGAAAA-TTTGATAACCTTCATATG
1 AAATTTTGATAATC-ACACTAT-AAAATTTTGATAACC-TCTTATG
24220 AAATTTTGATA
1 AAATTTTGATA
24231 TCCTCACTGA
Statistics
Matches: 174, Mismatches: 39, Indels: 37
0.70 0.16 0.15
Matches are distributed among these distances:
40 11 0.06
41 3 0.02
43 18 0.10
44 81 0.47
45 27 0.16
46 21 0.12
47 3 0.02
48 10 0.06
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (43 bp):
AAATTTTGATAATCACACTATAAAATTTTGATAACCTCTTATG
Found at i:24025 original size:23 final size:22
Alignment explanation
Indices: 23973--24056 Score: 80
Period size: 23 Copynumber: 3.7 Consensus size: 22
23963 ATAATCACAC
* *
23973 TATAAAATTGTGAT-AACCTCGT
1 TATAAAATTTTGATAAACTTC-T
*
23995 TATGAAATTTTGATAAATCTTCT
1 TATAAAATTTTGATAAA-CTTCT
* * *
24018 TATAAAATTTTAATAAACCTCCC
1 TATAAAATTTTGATAAA-CTTCT
24041 TATAAAATTTTGATAA
1 TATAAAATTTTGATAA
24057 TAACTTTCTT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
22 12 0.24
23 36 0.71
24 3 0.06
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (22 bp):
TATAAAATTTTGATAAACTTCT
Found at i:24274 original size:19 final size:20
Alignment explanation
Indices: 24218--24268 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
24208 AACCTTCATA
*
24218 TGAAATTTTGATATCCTCAC
1 TGAAATTTTGATATCCTCCC
*
24238 TG-AATTTCGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
24257 TGAAATTTTGAT
1 TGAAATTTTGAT
24269 TACTCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:24426 original size:22 final size:22
Alignment explanation
Indices: 24376--24427 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
24366 TCACATTTTG
*
24376 AAAA-TTTAATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
* *
24397 GAAATTTTGATAACTTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
24419 AAAATTTTG
1 AAAATTTTG
24428 TTGATAATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Found at i:24471 original size:22 final size:22
Alignment explanation
Indices: 24445--24541 Score: 78
Period size: 22 Copynumber: 4.5 Consensus size: 22
24435 TCACATGAAA
24445 TTTGATAATC-ACATTATATAAT
1 TTTGATAATCAACATTATA-AAT
* *
24467 TTTGATAACCTC-GCCTTA-AAAT
1 TTTGATAA--TCAACATTATAAAT
*
24489 TTTGATAA-CAACACTATGAAAT
1 TTTGATAATCAACATTAT-AAAT
**
24511 TTTGATAATCTTCA-TATAAAT
1 TTTGATAATCAACATTATAAAT
24532 TTTGATAATC
1 TTTGATAATC
24542 CTATCTTTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
19 1 0.02
20 3 0.05
21 14 0.23
22 34 0.55
23 4 0.06
24 6 0.10
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.41
Consensus pattern (22 bp):
TTTGATAATCAACATTATAAAT
Found at i:24654 original size:22 final size:22
Alignment explanation
Indices: 24485--24679 Score: 93
Period size: 22 Copynumber: 8.7 Consensus size: 22
24475 CCTCGCCTTA
**
24485 AAATTTTGATAA-CAACACTATG
1 AAATTTTGATAACCTTCA-TATG
*
24507 AAATTTTGATAATCTTCATAT-
1 AAATTTTGATAACCTTCATATG
*
24528 AAATTTTGATAATCCTATCTTTATG
1 AAATTTTGATAA-CCT-TC-ATATG
* *
24553 ATATTTCGATAATCAC-TC-TATG
1 AAATTTTGATAA-C-CTTCATATG
* *
24575 AGA-TTTGATAACCTTC-TATC
1 AAATTTTGATAACCTTCATATG
* *
24595 AAATTTTGGTACTCCTT-ATGAAATTG
1 AAATTTTGATA-ACCTTCAT---A-TG
*
24621 AGACTTTT-ATAACCTTCATATG
1 A-AATTTTGATAACCTTCATATG
* *
24643 AAATTTTGATAACC-ACACTATA
1 AAATTTTGATAACCTTCA-TATG
24665 AAATTTTGATAACCT
1 AAATTTTGATAACCT
24680 CCCGATGAAG
Statistics
Matches: 135, Mismatches: 19, Indels: 37
0.71 0.10 0.19
Matches are distributed among these distances:
19 1 0.01
20 8 0.06
21 32 0.24
22 54 0.40
23 6 0.04
24 5 0.04
25 17 0.13
26 7 0.05
27 5 0.04
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTTCATATG
Found at i:24863 original size:24 final size:22
Alignment explanation
Indices: 24799--24938 Score: 86
Period size: 22 Copynumber: 6.3 Consensus size: 22
24789 TTGTGATAAT
* *
24799 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
* *
24821 TAACCAACGTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
24843 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
**
24867 TAACC-ACTCTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* *
24889 TAACCACACC-ATGGAATTATAA
1 TAACCA-ACCTATGAAATTTTAA
** * * *
24911 TAACCTTCTTATAAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
24933 TAACCA
1 TAACCA
24939 CATAGAGACA
Statistics
Matches: 90, Mismatches: 22, Indels: 12
0.73 0.18 0.10
Matches are distributed among these distances:
21 2 0.02
22 68 0.76
23 1 0.01
24 19 0.21
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.32
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:26051 original size:29 final size:29
Alignment explanation
Indices: 26003--26062 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
25993 GGTTTGCCTG
*
26003 AAAACGCAATTCAGGATATAACGTTA-CA
1 AAAACGCAATTAAGGATATAACGTTATCA
26031 AAAACGCCAATTAAGGATATAACGTTATCA
1 AAAACG-CAATTAAGGATATAACGTTATCA
26061 AA
1 AA
26063 TCCAGTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 6 0.21
29 19 0.66
30 4 0.14
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (29 bp):
AAAACGCAATTAAGGATATAACGTTATCA
Found at i:26080 original size:31 final size:29
Alignment explanation
Indices: 26015--26080 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
26005 AACGCAATTC
*
26015 AGGATATAACGTTACAAAAACGCCAATTA
1 AGGATATAACGTTACAAAAACGCCAAATA
** *
26044 AGGATATAACGTTATCAAATCCAGTCAAATA
1 AGGATATAACGTTA-CAAAAAC-GCCAAATA
26075 AGGATA
1 AGGATA
26081 ATTTTGTACG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 14 0.45
30 5 0.16
31 12 0.39
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (29 bp):
AGGATATAACGTTACAAAAACGCCAAATA
Found at i:27802 original size:31 final size:29
Alignment explanation
Indices: 27767--27838 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
27757 CGTCCAAAAT
*
27767 TATCCTTATTTGACTGGATTTGATAACGTTA
1 TATCCTTAATTGAC-GGATTTG-TAACGTTA
* **
27798 TATCCTTAATTGGCGTTTTTGTAACGTTA
1 TATCCTTAATTGACGGATTTGTAACGTTA
*
27827 TATCCTGAATTG
1 TATCCTTAATTG
27839 CGTTTTCAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 19 0.53
30 5 0.14
31 12 0.33
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.46
Consensus pattern (29 bp):
TATCCTTAATTGACGGATTTGTAACGTTA
Found at i:27822 original size:29 final size:29
Alignment explanation
Indices: 27785--27844 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
27775 TTTGACTGGA
*
27785 TTTGATAACGTTATATCCTTAATTGGCGTT
1 TTTGATAACGTTATATCCTGAATT-GCGTT
27815 TTTG-TAACGTTATATCCTGAATTGCGTT
1 TTTGATAACGTTATATCCTGAATTGCGTT
27843 TT
1 TT
27845 CAGACAAACC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 7 0.24
29 18 0.62
30 4 0.14
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (29 bp):
TTTGATAACGTTATATCCTGAATTGCGTT
Found at i:36189 original size:30 final size:30
Alignment explanation
Indices: 36155--36215 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
36145 GAAGACCATG
* *
36155 AAGACGATGAACGTGAAAGAGAAGATGACA
1 AAGACAATGAACATGAAAGAGAAGATGACA
* *
36185 AAGACAATGAATATGAAGGAGAAGATGACA
1 AAGACAATGAACATGAAAGAGAAGATGACA
36215 A
1 A
36216 TGATAATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.52, C:0.08, G:0.28, T:0.11
Consensus pattern (30 bp):
AAGACAATGAACATGAAAGAGAAGATGACA
Done.