Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010178.1 Corchorus capsularis cultivar CVL-1 contig10199, 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: 25639
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:403 original size:10 final size:10
Alignment explanation
Indices: 390--423 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
380 CAAAAAGGCC
390 AAAAAAA-AA
1 AAAAAAAGAA
399 AAAAAAAGAA
1 AAAAAAAGAA
*
409 AAGAAAAGAA
1 AAAAAAAGAA
419 AAAAA
1 AAAAA
424 GAGGAGAGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:415 original size:18 final size:17
Alignment explanation
Indices: 390--425 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
380 CAAAAAGGCC
390 AAAAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAAG
*
407 AAAAGAAAAGAAAAAAAG
1 AAAA-AAAAAAAAAAAAG
425 A
1 A
426 GGAGAGCCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAAAG
Found at i:1472 original size:20 final size:21
Alignment explanation
Indices: 1437--1478 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1427 AATCGTGTAA
*
1437 AAGACACGATTAACATA-TTT
1 AAGACACGAGTAACATACTTT
*
1457 AAGACACGAGTGACATACTTT
1 AAGACACGAGTAACATACTTT
1478 A
1 A
1479 GTTGATAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (21 bp):
AAGACACGAGTAACATACTTT
Found at i:7447 original size:2 final size:2
Alignment explanation
Indices: 7440--7465 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7430 ACTAATTAGT
7440 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
7466 CTATTGTTTA
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:9661 original size:155 final size:154
Alignment explanation
Indices: 9464--10025 Score: 591
Period size: 155 Copynumber: 3.6 Consensus size: 154
9454 ATGTAGGTTA
* *
9464 TCTTGGCCAAGTTTCATCTCAAACAGACTTA-AGATGAAAAACTTATGCTAGTTTTTCATTTAAG
1 TCTTGGCCAAATTTCAGCTCAAACAGACTTAGA-ATGAAAAACTTATGCTAGTTTTTCATTTAAG
* * * *
9528 GACAGTTTGGGGTGAGAAACC-ACTTCACCATGATAGGGAGTTCATTTTTACTTAGAATTTTTTC
65 GACAATTTGGGGTGAGAAACCAAGTTCACCATCA-AGGGAGCTCA-TTTTACTTAGAATTTTTTC
* *
9592 CATA-ACTT-TGGGGAGATAATATAAGTC
128 CATAGTCTTAT--GGAGATAATCTAAGTC
* *
9619 TCTTGGCCAAATTTCATCTCAAACATACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGG
1 TCTTGGCCAAATTTCAGCTCAAACAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGG
* ** * * * * *
9684 ACAATTTGAGGTGAGAAGTC-GGTTCACTACCAAGGAGAGCTCGGTTTTACTTATAATTTTTTCC
66 ACAATTTGGGGTGAGAAACCAAGTTCACCATCAAGG-GAGCTC-ATTTTACTTAGAATTTTTTCC
*
9748 ATAGTCTTATGGAGATAATCTAAGAC
129 ATAGTCTTATGGAGATAATCTAAGTC
** ** * * *** *
9774 TAATGGTGGAAA-ATCAGC-CTTATTGGACTTAGAATGACAAACTTATGCTAGTTTTTCATTTAA
1 TCTTGG-CCAAATTTCAGCTC-AAACAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAA
* * * * *
9837 GGACAGTTTAGGGAGAGAAACCAAGTTCACCATCAAGGGGAGGTCGATTTTACTTGGAATTTTTT
64 GGACAATTTGGGGTGAGAAACCAAGTTCACCATCAA-GGGAGCTC-ATTTTACTTAGAATTTTTT
*
9902 CCATAGTCTTATGGAGATAGTCTAAGTC
127 CCATAGTCTTATGGAGATAATCTAAGTC
* * * *
9930 TCGTGG-AAAAGTTTCAGCTCAAACAGACTTAGAATGAAAAGCTTATGCAAGTTTTTCATTTAAG
1 TCTTGGCCAAA-TTTCAGCTCAAACAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAG
* *
9994 GACAATTTGGGGTGTGAAACCTAGTTCACCAT
65 GACAATTTGGGGTGAGAAACCAAGTTCACCAT
10026 GAAGAAGGCT
Statistics
Matches: 335, Mismatches: 60, Indels: 23
0.80 0.14 0.06
Matches are distributed among these distances:
154 7 0.02
155 186 0.56
156 138 0.41
157 4 0.01
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (154 bp):
TCTTGGCCAAATTTCAGCTCAAACAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGG
ACAATTTGGGGTGAGAAACCAAGTTCACCATCAAGGGAGCTCATTTTACTTAGAATTTTTTCCAT
AGTCTTATGGAGATAATCTAAGTC
Found at i:10445 original size:45 final size:45
Alignment explanation
Indices: 10394--10480 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
10384 TAGAGTAGTG
*
10394 GAATTACTAAAAGATCCCTACCCCAAATTAATGATAAGCTGGGCA
1 GAATTACTAAAAGATCCCTACCCCAAATTAATAATAAGCTGGGCA
* ** *
10439 GAATTACTAAAAGATCTCTACCCCGGATTAATAATGAGCTGG
1 GAATTACTAAAAGATCCCTACCCCAAATTAATAATAAGCTGG
10481 AGAAGTAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (45 bp):
GAATTACTAAAAGATCCCTACCCCAAATTAATAATAAGCTGGGCA
Found at i:13638 original size:5 final size:5
Alignment explanation
Indices: 13628--13658 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
13618 TTTACGAAGT
*
13628 AAATA AAATA AAATA AAATA AGATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA AAATA A
13659 CAAAATAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:14107 original size:19 final size:21
Alignment explanation
Indices: 14080--14130 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
14070 GTAATCTATG
14080 TTTGGTGTAAT-G-ATCATTA
1 TTTGGTGTAATGGTATCATTA
*
14099 TTTGTTGTAATGGTATCATTA
1 TTTGGTGTAATGGTATCATTA
14120 -TTGAGTGTAAT
1 TTTG-GTGTAAT
14131 ATAAAATCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 10 0.37
20 4 0.15
21 13 0.48
ACGTcount: A:0.25, C:0.04, G:0.22, T:0.49
Consensus pattern (21 bp):
TTTGGTGTAATGGTATCATTA
Found at i:16286 original size:12 final size:12
Alignment explanation
Indices: 16271--16304 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
16261 TGTCACTACT
16271 TCTGTCACAAAA
1 TCTGTCACAAAA
*
16283 TCTGTCACAAAC
1 TCTGTCACAAAA
16295 TCTGTCACAA
1 TCTGTCACAA
16305 TGAATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.35, C:0.29, G:0.09, T:0.26
Consensus pattern (12 bp):
TCTGTCACAAAA
Found at i:18649 original size:218 final size:218
Alignment explanation
Indices: 18373--18809 Score: 847
Period size: 218 Copynumber: 2.0 Consensus size: 218
18363 GTAGGAGAGG
* *
18373 GGTGGAGAAGAACACGTGAAAGGGCGAGGCAGTTTTCCTTTTTTAGACTAACGGTGTTATAACAT
1 GGTGGAGAAGAACACGTGAAAGGGAGAGGCAGTTTTCCTTTTTCAGACTAACGGTGTTATAACAT
*
18438 GAAGTAACTATAATTTCCGGTTTTATTTTGTTTAAATAGAAAATTAGATTTAGGGATGATGTGAC
66 GAAGTAACTATAATTTCCGGTTTTATTTTGTTTAAATAGAAAATTAGATTTAGGAATGATGTGAC
18503 GAAAAACATCATAGATTGGGAAATAATTTTAAAAGTATAACATTTTGGGAAATAAGTTTTCAAAC
131 GAAAAACATCATAGATTGGGAAATAATTTTAAAAGTATAACATTTTGGGAAATAAGTTTTCAAAC
18568 TATAATACCTTGGTAAAAAACTC
196 TATAATACCTTGGTAAAAAACTC
18591 GGTGGAGAAGAACACGTGAAAGGGAGAGGCAGTTTTCCTTTTTCAGACTAACGGTGTTATAACAT
1 GGTGGAGAAGAACACGTGAAAGGGAGAGGCAGTTTTCCTTTTTCAGACTAACGGTGTTATAACAT
18656 GAAGTAACTATAATTTCCGGTTTTATTTTGTTTAAATAGAAAATTAGATTTAGGAATGATGTGAC
66 GAAGTAACTATAATTTCCGGTTTTATTTTGTTTAAATAGAAAATTAGATTTAGGAATGATGTGAC
18721 GAAAAACATCATAGATTGGGAAATAATTTTAAAAGTATAACATTTTGGGAAATAAGTTTTCAAAC
131 GAAAAACATCATAGATTGGGAAATAATTTTAAAAGTATAACATTTTGGGAAATAAGTTTTCAAAC
18786 TATAATACCTTGGTAAAAAACTC
196 TATAATACCTTGGTAAAAAACTC
18809 G
1 G
18810 CTTTCATGTC
Statistics
Matches: 216, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
218 216 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (218 bp):
GGTGGAGAAGAACACGTGAAAGGGAGAGGCAGTTTTCCTTTTTCAGACTAACGGTGTTATAACAT
GAAGTAACTATAATTTCCGGTTTTATTTTGTTTAAATAGAAAATTAGATTTAGGAATGATGTGAC
GAAAAACATCATAGATTGGGAAATAATTTTAAAAGTATAACATTTTGGGAAATAAGTTTTCAAAC
TATAATACCTTGGTAAAAAACTC
Found at i:20192 original size:24 final size:25
Alignment explanation
Indices: 20156--20205 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
20146 AACTCTAATA
* *
20156 TTTTGGTATATATGTATCAAATTTT
1 TTTTGGTAGATATGTATCAAAATTT
20181 TTTTGG-AGATATGTATCAAAATTT
1 TTTTGGTAGATATGTATCAAAATTT
20205 T
1 T
20206 GAATCAGCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (25 bp):
TTTTGGTAGATATGTATCAAAATTT
Found at i:25507 original size:2 final size:2
Alignment explanation
Indices: 25495--25617 Score: 72
Period size: 2 Copynumber: 66.0 Consensus size: 2
25485 CTTTTATTCT
* *
25495 TA TA T- TA TA TA TA GTA TA T- TA TA TA TA TA TA TA TT TA GA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
25536 T- TA TA TA TA TA TA T- TA T- TA GA T- TA TA TG GA T- TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
25572 TA T- TA TA TGA AA TA T- TT TA T- TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25611 TA CTA TA
1 TA -TA TA
25618 ATTAATAACA
Statistics
Matches: 93, Mismatches: 13, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
1 12 0.13
2 76 0.82
3 5 0.05
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25559 original size:21 final size:19
Alignment explanation
Indices: 25500--25609 Score: 61
Period size: 19 Copynumber: 5.7 Consensus size: 19
25490 ATTCTTATAT
25500 TATATATAGTATATTA-T-A
1 TATATATA-TATATTATTAA
* *
25518 TATATATATAT-TTAGATAT
1 TATATATATATATTA-TTAA
25537 TATATATATATATTATTAGA
1 TATATATATATATTATTA-A
*
25557 T-TATATGGAT-TATTA-TAT
1 TATATAT--ATATATTATTAA
* *
25575 TATATGAAATATTTTATTATA
1 TATAT-ATATATATTATTA-A
25596 TATATTATATATAT
1 TATA-TATATATAT
25610 ATACTATAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 23
0.69 0.09 0.23
Matches are distributed among these distances:
16 3 0.04
17 3 0.04
18 12 0.17
19 27 0.39
20 12 0.17
21 12 0.17
22 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
TATATATATATATTATTAA
Found at i:25561 original size:17 final size:17
Alignment explanation
Indices: 25489--25612 Score: 92
Period size: 17 Copynumber: 7.0 Consensus size: 17
25479 GGATTACTTT
*
25489 TATTCTTATATTATATA
1 TATTATTATATTATATA
25506 TAGTATATTATATATATATA
1 TA-T-TATTATAT-TATATA
*
25526 TATTTAGATATTATATATATA
1 TA-TTA-TTA-TAT-TATATA
* *
25547 TATTATTAGATTATATG
1 TATTATTATATTATATA
*
25564 GATTATTATATTATATGA
1 TATTATTATATTATAT-A
* *
25582 -AATATTTTATTATATA
1 TATTATTATATTATATA
25598 TATTA-TATA-TATATA
1 TATTATTATATTATATA
25613 CTATAATTAA
Statistics
Matches: 87, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
15 6 0.07
16 4 0.05
17 37 0.43
18 3 0.03
19 11 0.13
20 14 0.16
21 12 0.14
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (17 bp):
TATTATTATATTATATA
Done.