Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023558.1 Corchorus olitorius cultivar O-4 contig23591, 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: 22010
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Found at i:7910 original size:21 final size:21
Alignment explanation
Indices: 7886--7942 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 21
7876 AATTGCTAAA
*
7886 TACCGCCCCTTTTTTACTACT
1 TACCGCCCCTTTTTTACTACC
*
7907 TACCGCCCCCCTTTTTACTACC
1 TACCG-CCCCTTTTTTACTACC
7929 TACCGCCCTCTTTT
1 TACCGCCC-CTTTT
7943 GACAATTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.26
22 23 0.74
ACGTcount: A:0.12, C:0.44, G:0.05, T:0.39
Consensus pattern (21 bp):
TACCGCCCCTTTTTTACTACC
Found at i:8307 original size:33 final size:33
Alignment explanation
Indices: 8260--8330 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
8250 ATCCAGGCGC
* * *
8260 GGAGGCGTCTCCAGGGGGCGCCCCACTACGGTG
1 GGAGGCGTCCCCAGGGGGCGCCCCACCACAGTG
*
8293 GGAGGCGTCCCCAGGGGGTGCCCCACCACAGTG
1 GGAGGCGTCCCCAGGGGGCGCCCCACCACAGTG
8326 GGAGG
1 GGAGG
8331 TGCCCCACCG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.14, C:0.32, G:0.44, T:0.10
Consensus pattern (33 bp):
GGAGGCGTCCCCAGGGGGCGCCCCACCACAGTG
Found at i:9102 original size:70 final size:67
Alignment explanation
Indices: 9029--9159 Score: 176
Period size: 69 Copynumber: 1.9 Consensus size: 67
9019 CTAATTAGGA
* *
9029 AAAAAATTG-TGGAAGCACCATTAATTACATCTC-AATGCTAAAATTACATATAAAGATAATACA
1 AAAAAA-TGATGGAA-CACCATTAATTACATC-CAAATGCTAAAATCACATATAAA-ACAATACA
9092 CTAAGG
62 CTAAGG
*
9098 AAAAAATGATTGGAACACCATTAATTACATCCAAATGCTAAAATCACGTATAAAACAATACA
1 AAAAAATGA-TGGAACACCATTAATTACATCCAAATGCTAAAATCACATATAAAACAATACA
9160 TTAATTTCAA
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
68 10 0.18
69 41 0.73
70 5 0.09
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.24
Consensus pattern (67 bp):
AAAAAATGATGGAACACCATTAATTACATCCAAATGCTAAAATCACATATAAAACAATACACTAA
GG
Found at i:13461 original size:15 final size:14
Alignment explanation
Indices: 13433--13487 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 14
13423 TTTTCTCAAA
*
13433 CCCCTCCCAAACCCTC
1 CCCCTCCC-CACCC-C
13449 CCCCTCCCCACCCC
1 CCCCTCCCCACCCC
*
13463 ACCCCTTCCCACCCC
1 -CCCCTCCCCACCCC
*
13478 ACCCTCCCCA
1 CCCCTCCCCA
13488 ATTGAACCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
14 9 0.26
15 17 0.50
16 8 0.24
ACGTcount: A:0.15, C:0.75, G:0.00, T:0.11
Consensus pattern (14 bp):
CCCCTCCCCACCCC
Found at i:17335 original size:21 final size:21
Alignment explanation
Indices: 17305--17344 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17295 CTAAAAACAG
* *
17305 GACAAGTCCTGCCCAGGACTT
1 GACAACTCCTACCCAGGACTT
17326 GACAACTCCTACCCAGGAC
1 GACAACTCCTACCCAGGAC
17345 CTGGTCTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.38, G:0.20, T:0.15
Consensus pattern (21 bp):
GACAACTCCTACCCAGGACTT
Found at i:17402 original size:50 final size:50
Alignment explanation
Indices: 17327--17448 Score: 174
Period size: 50 Copynumber: 2.4 Consensus size: 50
17317 CCAGGACTTG
* * *
17327 ACAACTCCTACCCAGGACCTGGTCTGTTGAAAGATGGAAGAAAAA-TCAGA
1 ACAACTCCTACCCAGGACTTGGTCTGTTGAAAGA-CGAAAAAAAATTCAGA
*
17377 ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAGACGAAAAAAAATTCAGA
1 ACAACTCCTACCCAGGACTTGGTCTGTTGAAAGACGAAAAAAAATTCAGA
* *
17427 ACAAGTCCTATCCAGGACTTGG
1 ACAACTCCTACCCAGGACTTGG
17449 ACAACTCCTG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
49 8 0.12
50 56 0.88
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (50 bp):
ACAACTCCTACCCAGGACTTGGTCTGTTGAAAGACGAAAAAAAATTCAGA
Found at i:17457 original size:22 final size:22
Alignment explanation
Indices: 17427--17469 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17417 AAAATTCAGA
* *
17427 ACAAGTCCTATCCAGGACTTGG
1 ACAACTCCTACCCAGGACTTGG
*
17449 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTACCCAGGACTTG
17470 TTGCGGGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.21
Consensus pattern (22 bp):
ACAACTCCTACCCAGGACTTGG
Found at i:18918 original size:22 final size:21
Alignment explanation
Indices: 18860--19179 Score: 110
Period size: 22 Copynumber: 14.5 Consensus size: 21
18850 TATAACAACA
*
18860 CTATGAAATTTTGACAATCTC
1 CTATGAAATTTTGATAATCTC
18881 CTTATGAAATTTTGATAGGAT-TC
1 C-TATGAAATTTTGATA--ATCTC
*
18904 CTATGAAATTTTGATAA-CGAC
1 CTATGAAATTTTGATAATC-TC
* * * *
18925 ACTATGGAGTTTCGAGAA-CGTC
1 -CTATGAAATTTTGATAATC-TC
* * * * *
18947 GCTATAAAATTTCGAGAACCTGT
1 -CTATGAAATTTTGATAATCT-C
* *
18970 CTATGAAATTTTGTTAACCTTC
1 CTATGAAATTTTGATAATC-TC
* * * *
18992 CCATGAAATTTTGTTATTTTTC
1 CTATGAAATTTTGATA-ATCTC
* * * *
19014 CTATGGAATTTGGAAAAACTC
1 CTATGAAATTTTGATAATCTC
*
19035 GCTATGAAATTTTGATAAGGCTTC
1 -CTATGAAATTTTGATAA-TC-TC
* * *
19059 CTATAAAATTTTGATAAACCTTA
1 CTATGAAATTTTGAT-AATC-TC
* *
19082 CTATAAAATTTTGATAACCTC
1 CTATGAAATTTTGATAATCTC
* * *
19103 CTTATGGAATTTAGATAACCTCC
1 C-TATGAAATTTTGATAATCT-C
**
19126 CTATGATTTTTTGATAA-CTTC
1 CTATGAAATTTTGATAATC-TC
* *
19147 ACTATGAGAA-TTTGTTAACCTCC
1 -CTATGA-AATTTTGATAATCT-C
19170 CTATGAAATT
1 CTATGAAATT
19180 AGTTATCTAC
Statistics
Matches: 230, Mismatches: 47, Indels: 43
0.72 0.15 0.13
Matches are distributed among these distances:
20 1 0.00
21 10 0.04
22 171 0.74
23 42 0.18
24 6 0.03
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.38
Consensus pattern (21 bp):
CTATGAAATTTTGATAATCTC
Found at i:19062 original size:23 final size:23
Alignment explanation
Indices: 19036--19098 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
19026 GAAAAACTCG
* ** *
19036 CTATGAAATTTTGATAAGGCTTC
1 CTATAAAATTTTGATAAACCTTA
19059 CTATAAAATTTTGATAAACCTTA
1 CTATAAAATTTTGATAAACCTTA
19082 CTATAAAATTTTGATAA
1 CTATAAAATTTTGATAA
19099 CCTCCTTATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.40
Consensus pattern (23 bp):
CTATAAAATTTTGATAAACCTTA
Found at i:19069 original size:45 final size:46
Alignment explanation
Indices: 19011--19098 Score: 106
Period size: 46 Copynumber: 1.9 Consensus size: 46
19001 TTTGTTATTT
** * *
19011 TTCCTATGGAATTTGGA-AAAACTCGCTATGAAATTTTGATAAGGC
1 TTCCTATAAAATTTGGATAAAACTCACTATAAAATTTTGATAAGGC
* * *
19056 TTCCTATAAAATTTTGATAAACCTTACTATAAAATTTTGATAA
1 TTCCTATAAAATTTGGATAAAACTCACTATAAAATTTTGATAA
19099 CCTCCTTATG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
45 14 0.40
46 21 0.60
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (46 bp):
TTCCTATAAAATTTGGATAAAACTCACTATAAAATTTTGATAAGGC
Found at i:19140 original size:44 final size:44
Alignment explanation
Indices: 19090--19175 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
19080 TACTATAAAA
19090 TTTTGATAACCTC-CTTATG-GAATTTAGATAACCTCCCTATGATT
1 TTTTGATAACCTCAC-TATGAGAATTT-GATAACCTCCCTATGATT
* *
19134 TTTTGATAACTTCACTATGAGAATTTGTTAACCTCCCTATGA
1 TTTTGATAACCTCACTATGAGAATTTGATAACCTCCCTATGA
19176 AATTAGTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
44 31 0.82
45 7 0.18
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.41
Consensus pattern (44 bp):
TTTTGATAACCTCACTATGAGAATTTGATAACCTCCCTATGATT
Found at i:19653 original size:27 final size:26
Alignment explanation
Indices: 19609--19677 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
19599 AAAAATACAC
* *
19609 AAAATTATATTTTAATAATGGCATTATT
1 AAAA-TATACTTTAATAATGGCAAT-TT
*
19637 AAAATATACTTTGATAATGGCAATTT
1 AAAATATACTTTAATAATGGCAATTT
*
19663 AGAAATATATTTTAA
1 A-AAATATACTTTAA
19678 AAAAAGAGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 3 0.09
27 28 0.80
28 4 0.11
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (26 bp):
AAAATATACTTTAATAATGGCAATTT
Done.