Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004946.1 Corchorus capsularis cultivar CVL-1 contig04964, 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: 18522
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:8124 original size:3 final size:3
Alignment explanation
Indices: 8116--8166 Score: 68
Period size: 3 Copynumber: 16.3 Consensus size: 3
8106 ACTTATTAAG
8116 TTA TTA TTA TTA TTA TTA TTA TATA TTA TTA TTA TATA TATA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA T-TA TTA TTA
8163 TTA T
1 TTA T
8167 AATATATTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.04
3 33 0.73
4 10 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:8144 original size:19 final size:19
Alignment explanation
Indices: 8116--8175 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
8106 ACTTATTAAG
8116 TTATTATTATTATTAT-TA
1 TTATTATTATTATTATATA
8134 TTATATATTATTATTATATA
1 TTAT-TATTATTATTATATA
*
8154 TATATTA-TATTATAATATA
1 T-TATTATTATTATTATATA
8173 TTA
1 TTA
8176 GGGGTAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
18 6 0.16
19 24 0.63
20 5 0.13
21 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATTATTATTATTATATA
Found at i:8144 original size:22 final size:24
Alignment explanation
Indices: 8117--8163 Score: 80
Period size: 22 Copynumber: 2.0 Consensus size: 24
8107 CTTATTAAGT
8117 TATTATTATTAT-TAT-TATTATA
1 TATTATTATTATATATATATTATA
8139 TATTATTATTATATATATATTATA
1 TATTATTATTATATATATATTATA
8163 T
1 T
8164 TATAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 12 0.52
23 3 0.13
24 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TATTATTATTATATATATATTATA
Found at i:8195 original size:2 final size:2
Alignment explanation
Indices: 8188--8214 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8178 GGTAAATTAC
8188 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
8215 CCCTGTGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12364 original size:39 final size:39
Alignment explanation
Indices: 12321--12409 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 39
12311 AGCTGCATTT
* *
12321 CCAATCTAATGTAAATGT-GATGGGTCAGCAATTGCAACC
1 CCAATCAAATGTAAAT-TAGATGGATCAGCAATTGCAACC
* * * * *
12360 CCAATCCAATATCAATTATATGGATCAGCAATTGCAGCC
1 CCAATCAAATGTAAATTAGATGGATCAGCAATTGCAACC
12399 CCAATCAAATG
1 CCAATCAAATG
12410 CCTTTGGAGT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
38 1 0.02
39 40 0.98
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.25
Consensus pattern (39 bp):
CCAATCAAATGTAAATTAGATGGATCAGCAATTGCAACC
Found at i:15482 original size:33 final size:33
Alignment explanation
Indices: 15445--15509 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
15435 GGTCGCGCGC
*
15445 GACCCACACCATGGTCAG-TCGCGATCCGGTCGT
1 GACCCA-ACCATGGCCAGCTCGCGATCCGGTCGT
* *
15478 GACCCATCCATGGCCTGCTCGCGATCCGGTCG
1 GACCCAACCATGGCCAGCTCGCGATCCGGTCG
15510 CAACCCGAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 8 0.29
33 20 0.71
ACGTcount: A:0.15, C:0.38, G:0.28, T:0.18
Consensus pattern (33 bp):
GACCCAACCATGGCCAGCTCGCGATCCGGTCGT
Found at i:15826 original size:20 final size:20
Alignment explanation
Indices: 15801--15842 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
15791 ATAAACTATG
*
15801 AACTAAAATTG-AATTAATTA
1 AACT-AAATTGCAAGTAATTA
15821 AACTAAATTGCAAGTAATTA
1 AACTAAATTGCAAGTAATTA
15841 AA
1 AA
15843 ATAGAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (20 bp):
AACTAAATTGCAAGTAATTA
Found at i:17394 original size:36 final size:35
Alignment explanation
Indices: 17352--17470 Score: 131
Period size: 36 Copynumber: 3.4 Consensus size: 35
17342 CCCTTTTTAG
*
17352 ATTAAGTTCTTTATTGATTTCACTTAATTATCTTGA
1 ATTAAGTTCTTTATTGATTTCACTTAATTA-CCTGA
* *
17388 ATTAAGTTATTTA-T--TCT-ACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGATTTCACTTAATTA-CCTGA
*
17420 ATTAAG-TCTTTTATTGACTTCACTTAATTACGCTGA
1 ATTAAGTTC-TTTATTGATTTCACTTAATTAC-CTGA
17456 ATTAAGTTCTTTATT
1 ATTAAGTTCTTTATT
17471 TTACTTAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
31 1 0.01
32 23 0.33
33 3 0.04
35 3 0.04
36 37 0.54
37 2 0.03
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (35 bp):
ATTAAGTTCTTTATTGATTTCACTTAATTACCTGA
Found at i:17409 original size:32 final size:30
Alignment explanation
Indices: 17373--17480 Score: 108
Period size: 32 Copynumber: 3.3 Consensus size: 30
17363 TATTGATTTC
*
17373 ACTTAATTATCTTGAATTAAGTTATTTATTCT
1 ACTTAATTA-CCTGAATTAAGTT-TTTATTCT
17405 ACTTAATTACCCTGAATTAAGTCTTTTATTGACTT
1 ACTTAATTA-CCTGAATTAAGT-TTTTATT--C-T
*
17440 CACTTAATTACGCTGAATTAAGTTCTTTATTTT
1 -ACTTAATTAC-CTGAATTAAGTT-TTTATTCT
17473 ACTTAATT
1 ACTTAATT
17481 TCCTTTCTTG
Statistics
Matches: 66, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
32 34 0.52
33 2 0.03
34 1 0.02
35 3 0.05
36 26 0.39
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.49
Consensus pattern (30 bp):
ACTTAATTACCTGAATTAAGTTTTTATTCT
Found at i:17435 original size:68 final size:68
Alignment explanation
Indices: 17352--17480 Score: 190
Period size: 68 Copynumber: 1.9 Consensus size: 68
17342 CCCTTTTTAG
* *
17352 ATTAAGTTCTTTATTGATTTCACTTAATTATC-TTGAATTAAGTTATTTATTCTACTTAATTACC
1 ATTAAGTTCTTTATTGACTTCACTTAATTA-CGCTGAATTAAGTTATTTATTCTACTTAATTACC
17416 CTGA
65 CTGA
* *
17420 ATTAAG-TCTTTTATTGACTTCACTTAATTACGCTGAATTAAGTTCTTTATTTTACTTAATT
1 ATTAAGTTC-TTTATTGACTTCACTTAATTACGCTGAATTAAGTTATTTATTCTACTTAATT
17481 TCCTTTCTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
67 3 0.05
68 52 0.95
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (68 bp):
ATTAAGTTCTTTATTGACTTCACTTAATTACGCTGAATTAAGTTATTTATTCTACTTAATTACCC
TGA
Found at i:17556 original size:36 final size:36
Alignment explanation
Indices: 17487--17908 Score: 540
Period size: 36 Copynumber: 11.6 Consensus size: 36
17477 AATTTCCTTT
* * * * *
17487 CTTGAAATTAAGCCTGTGTCTT-TTTACTTAATTTC
1 CTTGAAACTAAGCCAGTCTTTTCTTTACCTAATTTC
* *
17522 CTTGAAATTAAGCAAGTCTTTTCTTTACCTAATTTC
1 CTTGAAACTAAGCCAGTCTTTTCTTTACCTAATTTC
* *
17558 CTTGAAATTAAGCCAGTCTTATTCTTTACTTAATTTC
1 CTTGAAACTAAGCCAGTCTT-TTCTTTACCTAATTTC
* * *
17595 CTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTA
1 CTTGAAACTAAGCCAGTCTTTTCTTTACCTAATTTC
* *
17631 CTTGAAACTAAGCCAGTTCTTTTTTTTTTGTTACTTAATTTC
1 CTTGAAACTAAGCCAG-TC----TTTTCT-TTACCTAATTTC
* * * *
17673 CTTGAAATTAAGCCAGTCTATTCTTTTCCTATTTTC
1 CTTGAAACTAAGCCAGTCTTTTCTTTACCTAATTTC
*
17709 CTTGAAACTAAGCCAGTCTTTTCTTTACCTAGTTTC
1 CTTGAAACTAAGCCAGTCTTTTCTTTACCTAATTTC
*
17745 CTTGAAACTAAGCCAGTCTTTTCTTTACTTAATTTC
1 CTTGAAACTAAGCCAGTCTTTTCTTTACCTAATTTC
* * * *
17781 CTTGAAATTAAGTCAGTCTATTCTTTACCTAGTTTC
1 CTTGAAACTAAGCCAGTCTTTTCTTTACCTAATTTC
*
17817 CTTGAAACTAAGCCAGTCTTTTCTTTACCTAGTTTC
1 CTTGAAACTAAGCCAGTCTTTTCTTTACCTAATTTC
*
17853 CTTGAAACTAAGCCAGTCTTTTCTTTACCTAGTTTC
1 CTTGAAACTAAGCCAGTCTTTTCTTTACCTAATTTC
17889 CTTGAAACTAAGCCAGTCTT
1 CTTGAAACTAAGCCAGTCTT
17909 CTTTCAGTCT
Statistics
Matches: 344, Mismatches: 35, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
35 18 0.05
36 254 0.74
37 41 0.12
41 7 0.02
42 24 0.07
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (36 bp):
CTTGAAACTAAGCCAGTCTTTTCTTTACCTAATTTC
Found at i:17918 original size:11 final size:11
Alignment explanation
Indices: 17902--18072 Score: 121
Period size: 11 Copynumber: 15.5 Consensus size: 11
17892 GAAACTAAGC
*
17902 CAGTCTTCTTT
1 CAGTCTTATTT
*
17913 CAGTCTTCTTT
1 CAGTCTTATTT
*
17924 CAG-CATTCTTT
1 CAGTC-TTATTT
*
17935 CAGTCTGATTT
1 CAGTCTTATTT
* *
17946 CAAT-TTAATAT
1 CAGTCTT-ATTT
*
17957 CAGTCTTATAT
1 CAGTCTTATTT
*
17968 CAGTCTAATTT
1 CAGTCTTATTT
* *
17979 CAGTCTAATAT
1 CAGTCTTATTT
*
17990 CAGTCTTTTTT
1 CAGTCTTATTT
* *
18001 CAGTCTAATAT
1 CAGTCTTATTT
* *
18012 CAGTCTTCTAT
1 CAGTCTTATTT
*
18023 CAGTCTAATTT
1 CAGTCTTATTT
* *
18034 CAGTCTTCTAT
1 CAGTCTTATTT
*
18045 CAGTCTAATTT
1 CAGTCTTATTT
* *
18056 CAGTCTTCTAT
1 CAGTCTTATTT
18067 CAGTCT
1 CAGTCT
18073 AACTTTGCCT
Statistics
Matches: 127, Mismatches: 29, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
10 2 0.02
11 122 0.96
12 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.46
Consensus pattern (11 bp):
CAGTCTTATTT
Found at i:17976 original size:22 final size:22
Alignment explanation
Indices: 17954--18074 Score: 170
Period size: 22 Copynumber: 5.5 Consensus size: 22
17944 TTCAATTTAA
* **
17954 TATCAGTCTTATATCAGTCTAA
1 TATCAGTCTAATATCAGTCTTC
* *
17976 TTTCAGTCTAATATCAGTCTTT
1 TATCAGTCTAATATCAGTCTTC
*
17998 TTTCAGTCTAATATCAGTCTTC
1 TATCAGTCTAATATCAGTCTTC
*
18020 TATCAGTCTAATTTCAGTCTTC
1 TATCAGTCTAATATCAGTCTTC
*
18042 TATCAGTCTAATTTCAGTCTTC
1 TATCAGTCTAATATCAGTCTTC
18064 TATCAGTCTAA
1 TATCAGTCTAA
18075 CTTTGCCTAA
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 92 1.00
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.45
Consensus pattern (22 bp):
TATCAGTCTAATATCAGTCTTC
Found at i:18327 original size:41 final size:42
Alignment explanation
Indices: 18216--18350 Score: 206
Period size: 42 Copynumber: 3.3 Consensus size: 42
18206 TTGAATTAGG
* * *
18216 ACTATGTTTG-CTTTTCTTAATTACCATGGATTACAACTTCA
1 ACTATGTTTGACTTTTCTTAATCACCCTGGATTACAACTTTA
18257 ACTATGTTTGACTTTTCTTAATCACCCTGGATTACAACTTTA
1 ACTATGTTTGACTTTTCTTAATCACCCTGGATTACAACTTTA
*
18299 ACTATGTTTGAC-TTTCTTAATCGCCCTGGATT--AACTTTA
1 ACTATGTTTGACTTTTCTTAATCACCCTGGATTACAACTTTA
18338 ACTATGTTTGACT
1 ACTATGTTTGACT
18351 ATCCAAATTA
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
39 19 0.22
41 29 0.33
42 40 0.45
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (42 bp):
ACTATGTTTGACTTTTCTTAATCACCCTGGATTACAACTTTA
Found at i:18369 original size:41 final size:39
Alignment explanation
Indices: 18250--18358 Score: 103
Period size: 39 Copynumber: 2.7 Consensus size: 39
18240 CATGGATTAC
* * **
18250 AACTTCAACTATGTTTGACTTTTCTTAATC-ACCCTGGATT
1 AACTTTAACTATGTTTGAC-TATCCAAATCGA-CCTGGATT
* ** *
18290 ACAACTTTAACTATGTTTGACTTTCTTAATCGCCCTGGATT
1 --AACTTTAACTATGTTTGACTATCCAAATCGACCTGGATT
18331 AACTTTAACTATGTTTGACTATCCAAAT
1 AACTTTAACTATGTTTGACTATCCAAAT
18359 TAGGACCTGG
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
39 25 0.41
41 18 0.30
42 18 0.30
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (39 bp):
AACTTTAACTATGTTTGACTATCCAAATCGACCTGGATT
Found at i:18503 original size:15 final size:14
Alignment explanation
Indices: 18483--18512 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
18473 CAACTATGGG
18483 ACCTTGACTTTGCTT
1 ACCTTGACTTT-CTT
18498 ACCTTGACTTTCTT
1 ACCTTGACTTTCTT
18512 A
1 A
18513 ATTATCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.17, C:0.27, G:0.10, T:0.47
Consensus pattern (14 bp):
ACCTTGACTTTCTT
Done.