Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024624.1 Corchorus olitorius cultivar O-4 contig24657, 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: 30271
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:6025 original size:11 final size:11
Alignment explanation
Indices: 6009--6035 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5999 ATTGATTTTC
6009 TTTTTTTATTA
1 TTTTTTTATTA
6020 TTTTTTTATTA
1 TTTTTTTATTA
6031 TTTTT
1 TTTTT
6036 ATGAAAGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTATTA
Found at i:6977 original size:18 final size:18
Alignment explanation
Indices: 6936--6977 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
6926 ATCTAGTGAT
6936 AGAAAAAGAGAAAAATCC
1 AGAAAAAGAGAAAAATCC
* *
6954 AAAAAAAGTGAAAAAAT-C
1 AGAAAAAGAG-AAAAATCC
6972 AGAAAA
1 AGAAAA
6978 TCAAAAGAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.71, C:0.07, G:0.14, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAGAAAAATCC
Found at i:10952 original size:32 final size:32
Alignment explanation
Indices: 10863--10960 Score: 115
Period size: 32 Copynumber: 3.1 Consensus size: 32
10853 TATTTAATTG
10863 AATGAAGACAAAATAATAAGCCATTAAATGCA
1 AATGAAGACAAAATAATAAGCCATTAAATGCA
* * * * * *
10895 AATAAAGCCAAATTTACAAGGCATTAAATGCA
1 AATGAAGACAAAATAATAAGCCATTAAATGCA
* * *
10927 AATGAAGATAAAATAATAAACCATTAATTGCA
1 AATGAAGACAAAATAATAAGCCATTAAATGCA
10959 AA
1 AA
10961 AAATGCCAAA
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.55, C:0.12, G:0.11, T:0.21
Consensus pattern (32 bp):
AATGAAGACAAAATAATAAGCCATTAAATGCA
Found at i:12151 original size:52 final size:52
Alignment explanation
Indices: 12073--12178 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
12063 AGGCGCTGCT
12073 AAATTAAATGGAAGAATCTTGTCAACGTCCACCTGGAAATTTTAGGAAACAG
1 AAATTAAATGGAAGAATCTTGTCAACGTCCACCTGGAAATTTTAGGAAACAG
*
12125 AAATTAAATGGAAGGATCTTGTCAACGTCCACCTGGAAATTTTAGGAAACAG
1 AAATTAAATGGAAGAATCTTGTCAACGTCCACCTGGAAATTTTAGGAAACAG
12177 AA
1 AA
12179 CTGAGTCCAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.25
Consensus pattern (52 bp):
AAATTAAATGGAAGAATCTTGTCAACGTCCACCTGGAAATTTTAGGAAACAG
Found at i:14977 original size:25 final size:25
Alignment explanation
Indices: 14943--14995 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
14933 TAACACGCGC
*
14943 CGTTAACTGATCCACGTAGGTGCCA
1 CGTTAACTGATCCACATAGGTGCCA
14968 CGTTAACTGATCCACATAGGTGCCA
1 CGTTAACTGATCCACATAGGTGCCA
14993 CGT
1 CGT
14996 AGGATGCCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (25 bp):
CGTTAACTGATCCACATAGGTGCCA
Found at i:15112 original size:31 final size:31
Alignment explanation
Indices: 15074--15149 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
15064 TTTTGTAACT
15074 TTATATCCTGAATTGCATTTTCAGGCAAACC
1 TTATATCCTGAATTGCATTTTCAGGCAAACC
*
15105 TTATATCCTGAATTGCATTTTTAGGCAAACC
1 TTATATCCTGAATTGCATTTTCAGGCAAACC
15136 TTATA-CCTTGAATT
1 TTATATCC-TGAATT
15150 ATTTTTAAGC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
30 2 0.05
31 41 0.95
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (31 bp):
TTATATCCTGAATTGCATTTTCAGGCAAACC
Found at i:16731 original size:34 final size:34
Alignment explanation
Indices: 16693--16797 Score: 101
Period size: 34 Copynumber: 3.1 Consensus size: 34
16683 CTCTTCCTCT
16693 GAAAAAGTGAGAACAATATTAGGTTCCTACAGTA
1 GAAAAAGTGAGAACAATATTAGGTTCCTACAGTA
** * *** *
16727 G-AAAA-TGAG-GTAAT-TTAAAGCAGCTATCTGTA
1 GAAAAAGTGAGAACAATATT-AGGTTCCTA-CAGTA
16759 GAAAAAGTGAGAACAATATTAGGTTCCTACAGTA
1 GAAAAAGTGAGAACAATATTAGGTTCCTACAGTA
16793 GAAAA
1 GAAAA
16798 TGAGGTAATT
Statistics
Matches: 51, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
30 2 0.04
31 8 0.16
32 9 0.18
33 8 0.16
34 14 0.27
35 8 0.16
36 2 0.04
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (34 bp):
GAAAAAGTGAGAACAATATTAGGTTCCTACAGTA
Found at i:16774 original size:66 final size:66
Alignment explanation
Indices: 16693--16818 Score: 252
Period size: 66 Copynumber: 1.9 Consensus size: 66
16683 CTCTTCCTCT
16693 GAAAAAGTGAGAACAATATTAGGTTCCTACAGTAGAAAATGAGGTAATTTAAAGCAGCTATCTGT
1 GAAAAAGTGAGAACAATATTAGGTTCCTACAGTAGAAAATGAGGTAATTTAAAGCAGCTATCTGT
16758 A
66 A
16759 GAAAAAGTGAGAACAATATTAGGTTCCTACAGTAGAAAATGAGGTAATTTAAAGCAGCTA
1 GAAAAAGTGAGAACAATATTAGGTTCCTACAGTAGAAAATGAGGTAATTTAAAGCAGCTA
16819 GATTGATATC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (66 bp):
GAAAAAGTGAGAACAATATTAGGTTCCTACAGTAGAAAATGAGGTAATTTAAAGCAGCTATCTGT
A
Found at i:25841 original size:31 final size:30
Alignment explanation
Indices: 25789--25850 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
25779 ATTAGATGAA
* *
25789 ATAAAATGTTTGATACTAAATTGGGACTTTC
1 ATAAAAAGTTTGATACTAAATTGAGA-TTTC
*
25820 ATAAAAAGTTTGGTAGC-AAATTGAGATTTC
1 ATAAAAAGTTTGATA-CTAAATTGAGATTTC
25850 A
1 A
25851 GCCATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 5 0.19
31 21 0.78
32 1 0.04
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (30 bp):
ATAAAAAGTTTGATACTAAATTGAGATTTC
Found at i:26340 original size:3 final size:3
Alignment explanation
Indices: 26332--26483 Score: 295
Period size: 3 Copynumber: 50.3 Consensus size: 3
26322 GAAAACCAAT
26332 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
26378 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
26426 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
26474 ATA ATA ATA A
1 ATA ATA ATA A
26484 GGTAATTATT
Statistics
Matches: 148, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
3 145 0.98
4 3 0.02
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:26835 original size:203 final size:212
Alignment explanation
Indices: 26460--27075 Score: 749
Period size: 203 Copynumber: 2.9 Consensus size: 212
26450 ATAATAATAA
* *
26460 TAATAATAATAATA--ATAATAATAA-GGTAATTATTTGATACATCGGTGGTGTAAATTTCGGAC
1 TAATAATAAT-ATACCATAATAATAAGGGTAATTATTTGATACACCGGTGGTGTAAATTTTGGAC
*
26522 TCCACAAGCGGGTTGTGAAATTGATACATGTC-CATTTTCTGAATTAATTAAATTTTAAATATTT
65 TCCACAAGCGGGTTGTGAAGTTGATACATGTCTCATTTTCTGAATTAATTAAATTTTAAATATTT
*
26586 CAATCTAGTCCCTAGGGGACACATGTCACCCTTCAAGA-TCCGCTTGTGCAGTCTGCTAAACTCC
130 CAATCTAGTCCCTACGGGACACATGTCACCCTTCAAGACT-CGCTTGTGCAGTCTGCTAAACTCC
26650 ACTGACGGTG-T-A-TTG-
194 ACTGACGGTGTTAATTTGC
* * *
26665 T-AT-ATAA-A-CCCATAATAATAAGGGTAATTATTTGATACACCGATGGTGTAAATTTTGGATT
1 TAATAATAATATACCATAATAATAAGGGTAATTATTTGATACACCGGTGGTGTAAATTTTGGACT
* * * * * *
26726 CCACAAGCGTGTTGTGGAGTTGACACATGTCTAATTTT-TTAATTAATTAAGTTTTAAATATTTC
66 CCACAAGCGGGTTGTGAAGTTGATACATGTCTCATTTTCTGAATTAATTAAATTTTAAATATTTC
* * * * *
26790 AATCTAATCCCTACAGGACACATGTCACCCTTTAGGACTCGCTTGTGTAGTCTGCTAAACTCCAC
131 AATCTAGTCCCTACGGGACACATGTCACCCTTCAAGACTCGCTTGTGCAGTCTGCTAAACTCCAC
26855 TGACGGTGTATTATATAATTTGTC
196 TGACGGTG-----T-TAATTTG-C
* * * *
26879 TAATAATAATATACTATGGATTATTATATGGGTAATTATTTGATACACCGGCGGTGTAAATTTTG
1 TAATAATAATATACCAT--A--ATAATAAGGGTAATTATTTGATACACCGGTGGTGTAAATTTTG
* *
26944 GACTCCACAAGCGGGTTGTGCAGTTGATACATGT-TCATTTTCTGAATTAATTAAATTCTAAATA
62 GACTCCACAAGCGGGTTGTGAAGTTGATACATGTCTCATTTTCTGAATTAATTAAATTTTAAATA
* * * * *
27008 TTTGAATCTAGTCCCTATGGGACACATGTCACCCTTCAAGACCCGTTTATGCAGTCTGCTAAACT
127 TTTCAATCTAGTCCCTACGGGACACATGTCACCCTTCAAGACTCGCTTGTGCAGTCTGCTAAACT
27073 CCA
192 CCA
27076 TGTAATATAT
Statistics
Matches: 344, Mismatches: 42, Indels: 33
0.82 0.10 0.08
Matches are distributed among these distances:
201 1 0.00
202 10 0.03
203 155 0.45
204 8 0.02
205 1 0.00
210 1 0.00
211 1 0.00
212 3 0.01
214 1 0.00
215 2 0.01
216 4 0.01
217 1 0.00
218 3 0.01
220 1 0.00
221 6 0.02
222 146 0.42
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (212 bp):
TAATAATAATATACCATAATAATAAGGGTAATTATTTGATACACCGGTGGTGTAAATTTTGGACT
CCACAAGCGGGTTGTGAAGTTGATACATGTCTCATTTTCTGAATTAATTAAATTTTAAATATTTC
AATCTAGTCCCTACGGGACACATGTCACCCTTCAAGACTCGCTTGTGCAGTCTGCTAAACTCCAC
TGACGGTGTTAATTTGC
Found at i:27214 original size:20 final size:20
Alignment explanation
Indices: 27191--27228 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27181 ATTCAAAATA
*
27191 AAATAAAAACTACTCATTTT
1 AAATAAAAACTACCCATTTT
27211 AAATAAAAACTACCCATT
1 AAATAAAAACTACCCATT
27229 AGAGATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATAAAAACTACCCATTTT
Found at i:27517 original size:22 final size:22
Alignment explanation
Indices: 27492--27543 Score: 97
Period size: 21 Copynumber: 2.4 Consensus size: 22
27482 CACTCAAAAA
27492 AAAAGTTTTTTTTTTACCTCAC
1 AAAAGTTTTTTTTTTACCTCAC
27514 AAAAG-TTTTTTTTTACCTCAC
1 AAAAGTTTTTTTTTTACCTCAC
27535 AAAAGTTTT
1 AAAAGTTTT
27544 CTATCAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (22 bp):
AAAAGTTTTTTTTTTACCTCAC
Found at i:28163 original size:33 final size:31
Alignment explanation
Indices: 28120--28197 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 31
28110 ACACAAATGT
* * *
28120 ATTTGGTTATTTAATTCTTTTTTTTTTGCTATC
1 ATTTGATTATTTAATTC--TTTTTTTTGCCATA
28153 ATTTGATTATTTAA---TTTTTTTTGCCATA
1 ATTTGATTATTTAATTCTTTTTTTTGCCATA
28181 ATTTGATTATTTAATTC
1 ATTTGATTATTTAATTC
28198 AAAGCGATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 26 0.67
33 13 0.33
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.63
Consensus pattern (31 bp):
ATTTGATTATTTAATTCTTTTTTTTGCCATA
Found at i:28175 original size:28 final size:28
Alignment explanation
Indices: 28139--28196 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
28129 TTTAATTCTT
* *
28139 TTTTTTTTGCTATCATTTGATTATTTAA
1 TTTTTTTTGCCATAATTTGATTATTTAA
28167 TTTTTTTTGCCATAATTTGATTATTTAA
1 TTTTTTTTGCCATAATTTGATTATTTAA
28195 TT
1 TT
28197 CAAAGCGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.64
Consensus pattern (28 bp):
TTTTTTTTGCCATAATTTGATTATTTAA
Found at i:28486 original size:24 final size:27
Alignment explanation
Indices: 28418--28486 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
28408 TGTAAAAGTT
28418 TAACACATTTTAATTTTTTTTTGGTGAA
1 TAACACATTTTAA-TTTTTTTTGGTGAA
* *
28446 TAACACATTTT-ATTTTTTTTTGT-TA
1 TAACACATTTTAATTTTTTTTGGTGAA
28471 -AACACATTTTAATTTT
1 TAACACATTTTAATTTT
28487 GAAACTATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
24 10 0.26
25 6 0.16
26 10 0.26
27 1 0.03
28 11 0.29
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.57
Consensus pattern (27 bp):
TAACACATTTTAATTTTTTTTGGTGAA
Found at i:29329 original size:16 final size:16
Alignment explanation
Indices: 29282--29340 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
29272 TTGGGCGGGC
*
29282 TCGGGTTCGGGTA-CT
1 TCGGGTTCGGGTATTT
*
29297 TCGGCTTCGGGCT-TTT
1 TCGGGTTCGGG-TATTT
29313 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGTATTT
* *
29329 TCAGGCTCGGGT
1 TCGGGTTCGGGT
29341 TAAGTCGGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
15 11 0.31
16 25 0.69
ACGTcount: A:0.05, C:0.20, G:0.37, T:0.37
Consensus pattern (16 bp):
TCGGGTTCGGGTATTT
Found at i:29515 original size:13 final size:13
Alignment explanation
Indices: 29492--29544 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
29482 AAGTTTATTG
29492 ATAAT-ATATAAT
1 ATAATAATATAAT
29504 ATAATAATATAAT
1 ATAATAATATAAT
* *
29517 ATAATATTATTAT
1 ATAATAATATAAT
*
29530 -TATTAATAT-AT
1 ATAATAATATAAT
29541 ATAA
1 ATAA
29545 AGATTGAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
11 2 0.06
12 14 0.41
13 18 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATAATAATATAAT
Done.