Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008212.1 Corchorus capsularis cultivar CVL-1 contig08233, 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: 29917
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:534 original size:23 final size:23
Alignment explanation
Indices: 457--536 Score: 106
Period size: 23 Copynumber: 3.5 Consensus size: 23
447 AAATCTTGAT
*
457 GGAGTCCGGTTTGGGGCCAAGTG
1 GGAGCCCGGTTTGGGGCCAAGTG
* *
480 GGGGCCCGATTTGGGGCCAAGTG
1 GGAGCCCGGTTTGGGGCCAAGTG
* * *
503 GTAGCCCGGTTGGGGGTCAAGTG
1 GGAGCCCGGTTTGGGGCCAAGTG
526 GGAGCCCGGTT
1 GGAGCCCGGTT
537 AGAACAGCCA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.12, C:0.20, G:0.47, T:0.20
Consensus pattern (23 bp):
GGAGCCCGGTTTGGGGCCAAGTG
Found at i:595 original size:63 final size:63
Alignment explanation
Indices: 496--618 Score: 219
Period size: 63 Copynumber: 2.0 Consensus size: 63
486 CGATTTGGGG
*
496 CCAAGTGGTAGCCCGGTTGGGGGTCAAGTGGGAGCCCGGTTAGAACAGCCATGATGAACAGCC
1 CCAAGTGGGAGCCCGGTTGGGGGTCAAGTGGGAGCCCGGTTAGAACAGCCATGATGAACAGCC
* *
559 CCAAGTGGGGGCCCGGTTTGGGGTCAAGTGGGAGCCCGGTTAGAACAGCCATGATGAACA
1 CCAAGTGGGAGCCCGGTTGGGGGTCAAGTGGGAGCCCGGTTAGAACAGCCATGATGAACA
619 AAACGACTGT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.24, C:0.23, G:0.37, T:0.16
Consensus pattern (63 bp):
CCAAGTGGGAGCCCGGTTGGGGGTCAAGTGGGAGCCCGGTTAGAACAGCCATGATGAACAGCC
Found at i:2992 original size:27 final size:27
Alignment explanation
Indices: 2954--3016 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
2944 GCTCAGCAGC
* * *
2954 AGCAACAGCAAGTTCTCTCTCCCTCTG
1 AGCAGCAGCAAGCTCTATCTCCCTCTG
2981 AGCAGCAGCAAGCTCTATCTCCCTCTG
1 AGCAGCAGCAAGCTCTATCTCCCTCTG
3008 AGCAGCAGC
1 AGCAGCAGC
3017 TACTGCCCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.21
Consensus pattern (27 bp):
AGCAGCAGCAAGCTCTATCTCCCTCTG
Found at i:3011 original size:21 final size:22
Alignment explanation
Indices: 3001--3049 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
2991 AGCTCTATCT
3001 CCCTCTGAGC-AGCAGCTACTG
1 CCCTCTGAGCAAGCAGCTACTG
* *
3022 CCCTCTGAGC-AGCAACTGCTG
1 CCCTCTGAGCAAGCAGCTACTG
3043 CCTCTCT
1 CC-CTCT
3050 CTCCTTCTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.16, C:0.41, G:0.20, T:0.22
Consensus pattern (22 bp):
CCCTCTGAGCAAGCAGCTACTG
Found at i:3335 original size:26 final size:26
Alignment explanation
Indices: 3302--3379 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 26
3292 AAAATTAATG
3302 AACTAATTAATTATAAACTAATTAAA
1 AACTAATTAATTATAAACTAATTAAA
* ** *
3328 TACTAATTAAACATAAACTAATAAAAA
1 AACTAATTAATTATAAACTAAT-TAAA
3355 AACTAATT--TTA-ATAACTAATTAAA
1 AACTAATTAATTATA-AACTAATTAAA
3379 A
1 A
3380 TTAATCATCA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
24 5 0.12
25 8 0.19
26 19 0.45
27 10 0.24
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (26 bp):
AACTAATTAATTATAAACTAATTAAA
Found at i:3349 original size:15 final size:14
Alignment explanation
Indices: 3302--3380 Score: 71
Period size: 13 Copynumber: 5.9 Consensus size: 14
3292 AAAATTAATG
*
3302 AACTAATTAATTATA
1 AACTAATTAA-AATA
3317 AACTAATT-AAAT-
1 AACTAATTAAAATA
3329 -ACTAATTAAACATA
1 AACTAATTAAA-ATA
3343 AACTAA-TAAAA-A
1 AACTAATTAAAATA
**
3355 AACTAATTTTAAT-
1 AACTAATTAAAATA
3368 AACTAATTAAAAT
1 AACTAATTAAAAT
3381 TAATCATCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
11 7 0.13
12 9 0.17
13 19 0.36
14 5 0.09
15 13 0.25
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (14 bp):
AACTAATTAAAATA
Found at i:3534 original size:32 final size:32
Alignment explanation
Indices: 3493--3645 Score: 234
Period size: 32 Copynumber: 4.8 Consensus size: 32
3483 AAAACCATGG
*
3493 CCAAGCCGCCCAAAATGGGCGGCCTGCCATAA
1 CCAAGCCGCCCAAAATGGGCGGCCTGCTATAA
* *
3525 CCAAGCCGCCCAAGATGGGCGGCCTGCTTTAA
1 CCAAGCCGCCCAAAATGGGCGGCCTGCTATAA
* * *
3557 CGAAGCCGCCCAAAATGGGCGGTCTGCTTTAA
1 CCAAGCCGCCCAAAATGGGCGGCCTGCTATAA
3589 CCAAGCCGCCCAAAATGGGCGGCCTGCTATAA
1 CCAAGCCGCCCAAAATGGGCGGCCTGCTATAA
**
3621 CCAAGCCGCCCAACCTGGGCGGCCT
1 CCAAGCCGCCCAAAATGGGCGGCCT
3646 TTCTATGGCC
Statistics
Matches: 110, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 110 1.00
ACGTcount: A:0.24, C:0.36, G:0.27, T:0.13
Consensus pattern (32 bp):
CCAAGCCGCCCAAAATGGGCGGCCTGCTATAA
Found at i:3888 original size:25 final size:25
Alignment explanation
Indices: 3839--3922 Score: 127
Period size: 25 Copynumber: 3.4 Consensus size: 25
3829 AAATGATGGA
*
3839 AAATG-AGTTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
*
3862 AAATGAAGTTTGGAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
3887 AAATGAAGTTTGAAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
*
3912 GAATGAAGTTT
1 AAATGAAGTTT
3923 AGGGTTTGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
23 5 0.09
24 8 0.15
25 42 0.76
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.35
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAG
Found at i:4857 original size:31 final size:28
Alignment explanation
Indices: 4779--4858 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 28
4769 CTCATTTTTA
4779 AAGTTAAGGGGCCAATTTGTCCCAAAAT
1 AAGTTAAGGGGCCAATTTGTCCCAAAAT
*
4807 AAGTTAAAAGGGACCAATTTGTCCCAAAAT
1 AAGTT--AAGGGGCCAATTTGTCCCAAAAT
*
4837 GGATAGTTAAGGGGCTAATTTG
1 --A-AGTTAAGGGGCCAATTTG
4859 GGTATTAAGC
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 5 0.11
30 22 0.50
31 12 0.27
32 1 0.02
33 4 0.09
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (28 bp):
AAGTTAAGGGGCCAATTTGTCCCAAAAT
Found at i:5007 original size:2 final size:2
Alignment explanation
Indices: 5000--5035 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4990 ATTAGAATCA
*
5000 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5036 GGTATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7097 original size:25 final size:24
Alignment explanation
Indices: 7056--7111 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
7046 AAATATCATA
*
7056 TATATATATTAATATATATTTGATAT
1 TATATATATTAAAATATATTT-A-AT
7082 TATATATA-TAAAATATATTTAAT
1 TATATATATTAAAATATATTTAAT
7105 TATATAT
1 TATATAT
7112 GTATTAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 9 0.31
24 1 0.03
25 11 0.38
26 8 0.28
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TATATATATTAAAATATATTTAAT
Found at i:20116 original size:7 final size:6
Alignment explanation
Indices: 20074--20115 Score: 66
Period size: 6 Copynumber: 6.7 Consensus size: 6
20064 ATGATTTTAG
20074 AAAAGAA AAAAGAA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
1 AAAAG-A AAAAG-A AAAAGA AAAAGA AAAAGA AAAAGA AAAA
20116 ATGATATTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.66
7 12 0.34
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:20291 original size:30 final size:31
Alignment explanation
Indices: 20228--20294 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
20218 CCATATCCTT
*
20228 AATTGACACAAAACGATAACGGTATATCCTG
1 AATTGACACAAAACGATAACGGTATATCATG
** * *
20259 AATTGACAC-AAGTGATAATGGTGTATCATG
1 AATTGACACAAAACGATAACGGTATATCATG
20289 AATTGA
1 AATTGA
20295 ATTTTGGGGC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (31 bp):
AATTGACACAAAACGATAACGGTATATCATG
Found at i:23188 original size:13 final size:13
Alignment explanation
Indices: 23170--23194 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23160 AGTTATAAGA
23170 ATAAAAATAAAAT
1 ATAAAAATAAAAT
23183 ATAAAAATAAAA
1 ATAAAAATAAAA
23195 ACTATAAGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
ATAAAAATAAAAT
Found at i:27429 original size:179 final size:179
Alignment explanation
Indices: 27129--27486 Score: 716
Period size: 179 Copynumber: 2.0 Consensus size: 179
27119 ACTTTAGTTA
27129 TTTCTAAAGGATCTGAACTAGATAATAAGGTAGTCGCCTGGATTGTACCCTCATTCGGGTCGTGT
1 TTTCTAAAGGATCTGAACTAGATAATAAGGTAGTCGCCTGGATTGTACCCTCATTCGGGTCGTGT
27194 CCACATTTCATACCAAATACCTGAATTGAAATTGTAAAACTATTTAAATGACAATATATAGTTAT
66 CCACATTTCATACCAAATACCTGAATTGAAATTGTAAAACTATTTAAATGACAATATATAGTTAT
27259 AAGAAAATAAATAAAATATATAAAAATTATAAGATTTAAATATATATAG
131 AAGAAAATAAATAAAATATATAAAAATTATAAGATTTAAATATATATAG
27308 TTTCTAAAGGATCTGAACTAGATAATAAGGTAGTCGCCTGGATTGTACCCTCATTCGGGTCGTGT
1 TTTCTAAAGGATCTGAACTAGATAATAAGGTAGTCGCCTGGATTGTACCCTCATTCGGGTCGTGT
27373 CCACATTTCATACCAAATACCTGAATTGAAATTGTAAAACTATTTAAATGACAATATATAGTTAT
66 CCACATTTCATACCAAATACCTGAATTGAAATTGTAAAACTATTTAAATGACAATATATAGTTAT
27438 AAGAAAATAAATAAAATATATAAAAATTATAAGATTTAAATATATATAG
131 AAGAAAATAAATAAAATATATAAAAATTATAAGATTTAAATATATATAG
27487 CTTTATTAGG
Statistics
Matches: 179, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
179 179 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.32
Consensus pattern (179 bp):
TTTCTAAAGGATCTGAACTAGATAATAAGGTAGTCGCCTGGATTGTACCCTCATTCGGGTCGTGT
CCACATTTCATACCAAATACCTGAATTGAAATTGTAAAACTATTTAAATGACAATATATAGTTAT
AAGAAAATAAATAAAATATATAAAAATTATAAGATTTAAATATATATAG
Done.