Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018016.1 Corchorus olitorius cultivar O-4 contig18049, 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: 46935
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:13088 original size:31 final size:32
Alignment explanation
Indices: 13050--13114 Score: 96
Period size: 35 Copynumber: 2.0 Consensus size: 32
13040 AAGAACCAAC
13050 TTCATGTTAT-AAATTAAGTTTCTATTTAAGT
1 TTCATGTTATAAAATTAAGTTTCTATTTAAGT
13081 TTCATGTTATCAAAAAATTAAGTTTCTATTTAAG
1 TTCATGTTAT---AAAATTAAGTTTCTATTTAAG
13115 GAAACTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 10 0.33
35 20 0.67
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48
Consensus pattern (32 bp):
TTCATGTTATAAAATTAAGTTTCTATTTAAGT
Found at i:13410 original size:4 final size:4
Alignment explanation
Indices: 13403--13462 Score: 120
Period size: 4 Copynumber: 15.0 Consensus size: 4
13393 ATATATATAC
13403 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
13451 ACAT ACAT ACAT
1 ACAT ACAT ACAT
13463 TATATGTTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:14888 original size:17 final size:17
Alignment explanation
Indices: 14848--14909 Score: 63
Period size: 17 Copynumber: 3.4 Consensus size: 17
14838 ACATAATATT
*
14848 TATTTATT-TTTAACTCA
1 TATTTATTATTTAAAT-A
14865 TTATTTATTATTTAAATA
1 -TATTTATTATTTAAATA
14883 TATTTATTATTTATTAATA
1 TATTTATTATTTA--AATA
14902 TATATTAT
1 TAT-TTAT
14910 ATCTAAGATA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
17 13 0.33
18 9 0.23
19 13 0.33
20 4 0.10
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTATTATTTAAATA
Found at i:14889 original size:21 final size:20
Alignment explanation
Indices: 14843--14907 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
14833 TGAATACATA
*
14843 ATATTTATTTATTTTTAACT
1 ATATTTATTTATTTTTAAAT
*
14863 -CA-TTATTTATTATTTAAAT
1 ATATTTATTTATT-TTTAAAT
14882 ATATTTA-TTATTTATTAATAT
1 ATATTTATTTATTT-TTAA-AT
14903 ATATT
1 ATATT
14908 ATATCTAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 9 0.24
19 8 0.22
20 10 0.27
21 10 0.27
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
ATATTTATTTATTTTTAAAT
Found at i:16389 original size:29 final size:29
Alignment explanation
Indices: 16352--16407 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
16342 ATGAAAGATA
*
16352 AATTTTTTTAAGAAGTTAAAAAGAAAAGG
1 AATTATTTTAAGAAGTTAAAAAGAAAAGG
*
16381 AATTATTTTAAGGAGTTAAAAAGAAAA
1 AATTATTTTAAGAAGTTAAAAAGAAAA
16408 AATTCAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (29 bp):
AATTATTTTAAGAAGTTAAAAAGAAAAGG
Found at i:16579 original size:23 final size:23
Alignment explanation
Indices: 16553--16597 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16543 GATTTCTTGA
* *
16553 AAAGGATCAATTTATAAATTTTT
1 AAAGGACCAAATTATAAATTTTT
*
16576 AAAGGGCCAAATTATAAATTTT
1 AAAGGACCAAATTATAAATTTT
16598 CCAGTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (23 bp):
AAAGGACCAAATTATAAATTTTT
Found at i:25853 original size:22 final size:22
Alignment explanation
Indices: 25802--25853 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
25792 TCATATTATT
* *
25802 ATTTTTTATTTATAAGGTTCCA
1 ATTTATTATGTATAAGGTTCCA
**
25824 ATAAATTATGTATAAGGTTCCA
1 ATTTATTATGTATAAGGTTCCA
25846 ATTTATTA
1 ATTTATTA
25854 AGATAAAACT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.48
Consensus pattern (22 bp):
ATTTATTATGTATAAGGTTCCA
Found at i:26178 original size:19 final size:17
Alignment explanation
Indices: 26148--26182 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
26138 TAAAAATTGC
26148 AAAAAAAAAAAGAAAAG
1 AAAAAAAAAAAGAAAAG
26165 AAAAGAAAAGAAAGAAAA
1 AAAA-AAAA-AAAGAAAA
26183 TGGCAGTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAGAAAAG
Found at i:26180 original size:4 final size:5
Alignment explanation
Indices: 26150--26182 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
26140 AAAATTGCAA
*
26150 AAAAA AAAAG AAAAG AAAAG AAAAG -AAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
26183 TGGCAGTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:27689 original size:22 final size:23
Alignment explanation
Indices: 27533--27728 Score: 92
Period size: 22 Copynumber: 8.9 Consensus size: 23
27523 TTAATAATCA
* **
27533 CTATA-AAATTTTTATAACCTTC
1 CTATAGAAATTTTGATAACCACC
* ** *
27555 ATATA-AAATTTTGATAATTACA
1 CTATAGAAATTTTGATAACCACC
* * **
27577 CTATA-AAATTTTTATAACGATA
1 CTATAGAAATTTTGATAACCACC
* *
27599 CTATAG-AATTTCGAGAACC-CC
1 CTATAGAAATTTTGATAACCACC
**
27620 C-ATATGAAATTTT-ATCAACTTCC
1 CTATA-GAAATTTTGAT-AACCACC
* *
27643 CTATA-AAATTTTG-TTACACTCC
1 CTATAGAAATTTTGATAAC-CACC
*
27665 CTATAGAAACTTTGATAACCA-C
1 CTATAGAAATTTTGATAACCACC
*
27687 CTA-ATGAAATTTTGATAATCACC
1 CTATA-GAAATTTTGATAACCACC
*
27710 CTAT-CAAATTTTGATAACC
1 CTATAGAAATTTTGATAACC
27729 TCCCAATGAA
Statistics
Matches: 131, Mismatches: 30, Indels: 26
0.70 0.16 0.14
Matches are distributed among these distances:
20 3 0.02
21 6 0.05
22 101 0.77
23 15 0.11
24 6 0.05
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (23 bp):
CTATAGAAATTTTGATAACCACC
Found at i:27910 original size:41 final size:41
Alignment explanation
Indices: 27865--28003 Score: 124
Period size: 41 Copynumber: 3.3 Consensus size: 41
27855 TATCCCTATA
*
27865 AAATTTTGATAACCTCATGAAATTTTGAAAACCACCTCATG
1 AAATTTTGATAACCTCATGAAATTTTGATAACCACCTCATG
*
27906 AAATTTTGATAACCATCTTACGAAATTTTGATAA-CATCC-CTAT-
1 AAATTTTGATAACC-TC--ATGAAATTTTGATAACCA-CCTC-ATG
* * * * * *
27949 AATTTTTTTATAACCTCATAAAATTTTGTTAACCTCCT-ACG
1 AA-ATTTTGATAACCTCATGAAATTTTGATAACCACCTCATG
27990 AAATTTTGATAACC
1 AAATTTTGATAACC
28004 CCCGATGAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
40 11 0.14
41 30 0.38
42 3 0.04
43 7 0.09
44 27 0.35
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (41 bp):
AAATTTTGATAACCTCATGAAATTTTGATAACCACCTCATG
Found at i:27937 original size:22 final size:20
Alignment explanation
Indices: 27865--28003 Score: 111
Period size: 22 Copynumber: 6.7 Consensus size: 20
27855 TATCCCTATA
*
27865 AAATTTTGATAACCTCAT-G
1 AAATTTTGATAACCTCCTAG
* *
27884 AAATTTTGAAAACCACCTCATG
1 AAATTTTGATAACCTCCT-A-G
*
27906 AAATTTTGATAACCATCTTACG
1 AAATTTTGATAACC-TCCTA-G
* *
27928 AAATTTTGATAACATCCCTAT
1 AAATTTTGATAACCT-CCTAG
* * *
27949 AATTTTTTTATAACCTCATA-
1 AA-ATTTTGATAACCTCCTAG
*
27969 AAATTTTGTTAACCTCCTACG
1 AAATTTTGATAACCTCCTA-G
27990 AAATTTTGATAACC
1 AAATTTTGATAACC
28004 CCCGATGAAA
Statistics
Matches: 93, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
19 28 0.30
20 2 0.02
21 19 0.20
22 42 0.45
23 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (20 bp):
AAATTTTGATAACCTCCTAG
Found at i:28199 original size:22 final size:22
Alignment explanation
Indices: 28163--28314 Score: 100
Period size: 22 Copynumber: 7.0 Consensus size: 22
28153 CCTCTGAATT
* *
28163 ACCACATTATAAAATTTTGATA
1 ACCACACTATGAAATTTTGATA
28185 ACCACACTATGAAATTTTGATA
1 ACCACACTATGAAATTTTGATA
* *
28207 TTATCC-CTCTA--AAATTTCGATA
1 --A-CCACACTATGAAATTTTGATA
* * * *
28229 ACCTCCCCATGAAATTTTGTTA
1 ACCACACTATGAAATTTTGATA
* * *
28251 A-C-CTCTATGAAATTGTGATT
1 ACCACACTATGAAATTTTGATA
** *
28271 ATTACACTATGAAATTTTGGTA
1 ACCACACTATGAAATTTTGATA
*
28293 ACGACACT-TGAAATTTTGATA
1 ACCACACTATGAAATTTTGATA
28314 A
1 A
28315 GCTCACTCTA
Statistics
Matches: 101, Mismatches: 21, Indels: 17
0.73 0.15 0.12
Matches are distributed among these distances:
19 2 0.02
20 18 0.18
21 14 0.14
22 60 0.59
24 5 0.05
25 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
ACCACACTATGAAATTTTGATA
Found at i:28495 original size:22 final size:22
Alignment explanation
Indices: 28354--28657 Score: 93
Period size: 22 Copynumber: 13.8 Consensus size: 22
28344 TAAGCACATT
*
28354 ATGAAATTTTGATAATCTTCCT-
1 ATGAAATTTTGATAA-CCTCCTA
* *
28376 ATAAAATTTTGATAACTTCC-A
1 ATGAAATTTTGATAACCTCCTA
* * ***
28397 TATAAAATTTCGATAACCAGAGT-
1 -ATGAAATTTTGATAACC-TCCTA
*
28420 ATGAAATGTT-AGTAACC-CC-A
1 ATGAAATTTTGA-TAACCTCCTA
* *
28440 GTGAAA-TTTGATAACCTTCC-C
1 ATGAAATTTTGATAACC-TCCTA
*
28461 ATG-AATTTCGATAACCTCCTA
1 ATGAAATTTTGATAACCTCCTA
*
28482 ATGAAATTTTGATAAGCTCC-A
1 ATGAAATTTTGATAACCTCCTA
*
28503 TATGAAAATTTTTATAACAC-CCTA
1 -ATG-AAATTTTGATAAC-CTCCTA
* *
28527 ATGAAATTTTATTTTAATAACCTCCTT
1 ATG-AA----ATTTTGATAACCTCCTA
* *
28554 ATTAAATTTTGATAACAC-CC-C
1 ATGAAATTTTGATAAC-CTCCTA
* *
28575 ATGAAATTGTGATAA-CTACAC-C
1 ATGAAATTTTGATAACCT-C-CTA
* * *
28597 ATAAAATTTTAATATCCTACCT-
1 ATGAAATTTTGATAACCT-CCTA
* *
28619 ATGAAAATTTGGTAACCTCACT-
1 ATGAAATTTTGATAACCTC-CTA
*
28641 ATAAAATTTTGATAACC
1 ATGAAATTTTGATAACC
28658 ACACTATAAA
Statistics
Matches: 214, Mismatches: 40, Indels: 56
0.69 0.13 0.18
Matches are distributed among these distances:
19 8 0.04
20 11 0.05
21 38 0.18
22 113 0.53
23 24 0.11
24 2 0.01
26 3 0.01
27 15 0.07
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCCTA
Found at i:28530 original size:23 final size:23
Alignment explanation
Indices: 28478--28536 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
28468 TCGATAACCT
*
28478 CCTAATGAAATTTTGATAAGCTC
1 CCTAATGAAATTTTGATAAGCAC
* *
28501 CAT-ATGAAAATTTTTATAA-CAC
1 CCTAATG-AAATTTTGATAAGCAC
28523 CCTAATGAAATTTT
1 CCTAATGAAATTTT
28537 ATTTTAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
22 14 0.47
23 16 0.53
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.37
Consensus pattern (23 bp):
CCTAATGAAATTTTGATAAGCAC
Found at i:28587 original size:21 final size:22
Alignment explanation
Indices: 28557--28604 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
28547 CCTCCTTATT
* * *
28557 AAATTTTGATAAC-ACCCCATG
1 AAATTGTGATAACTACACCATA
28578 AAATTGTGATAACTACACCATA
1 AAATTGTGATAACTACACCATA
28600 AAATT
1 AAATT
28605 TTAATATCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (22 bp):
AAATTGTGATAACTACACCATA
Found at i:28662 original size:22 final size:22
Alignment explanation
Indices: 28557--28673 Score: 96
Period size: 22 Copynumber: 5.3 Consensus size: 22
28547 CCTCCTTATT
* * *
28557 AAATTTTGATAA-CACCCCATG
1 AAATTTTGATAACCACACTATA
* * *
28578 AAATTGTGATAACTACACCATA
1 AAATTTTGATAACCACACTATA
* *
28600 AAATTTTAATATCCTAC-CTATGA
1 AAATTTTGATAACC-ACACTAT-A
* *
28623 AAA-TTTGGTAACCTCACTATA
1 AAATTTTGATAACCACACTATA
28644 AAATTTTGATAACCACACTATA
1 AAATTTTGATAACCACACTATA
28666 AAACTTTT
1 AAA-TTTT
28674 AGAATTACAC
Statistics
Matches: 75, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
21 16 0.21
22 49 0.65
23 10 0.13
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATA
Found at i:33235 original size:2 final size:2
Alignment explanation
Indices: 33228--33260 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
33218 TTATTACTCC
*
33228 TA TA TA TA TA TA TA TC TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33261 TCAACTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36584 original size:27 final size:25
Alignment explanation
Indices: 36535--36590 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 25
36525 TTTTTATTAT
36535 TTTAATAATGTAATAATTAAAATAATA
1 TTTAATAATGTAAT-ATTAAAAT-ATA
36562 TTTAATAATGGTAAT-TTAGAAATATA
1 TTTAATAAT-GTAATATTA-AAATATA
36588 TTT
1 TTT
36591 GGAAAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 9 0.33
27 13 0.48
28 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (25 bp):
TTTAATAATGTAATATTAAAATATA
Found at i:37057 original size:12 final size:13
Alignment explanation
Indices: 37040--37068 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
37030 CGTTGGATCT
37040 TGATTAATGAGG-
1 TGATTAATGAGGA
37052 TGATTAATGAGGA
1 TGATTAATGAGGA
37065 TGAT
1 TGAT
37069 CTAAATTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (13 bp):
TGATTAATGAGGA
Found at i:37200 original size:2 final size:2
Alignment explanation
Indices: 37193--37240 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
37183 TTCGTACTTT
* *
37193 TA TA TA TA GTA TA GA TA TA TA -A T- TA TA TA TA TG TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37234 TA TA TA T
1 TA TA TA T
37241 TTTTACAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 2 0.05
2 35 0.90
3 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:38730 original size:2 final size:2
Alignment explanation
Indices: 38723--38757 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
38713 CTTAATTAAG
*
38723 AT AT AT AT A- AG AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38758 TAAAAGATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:43311 original size:42 final size:43
Alignment explanation
Indices: 43260--43353 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 43
43250 AGTGCATTAC
* * *
43260 CTAA-ATTCTA-CTCCATATCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATATCTAGATAATTAATCAAAATAAAA
*
43301 CTAATATTCTACTCCTCCATCTCTAGATAATTAATCAAAATAAAA
1 CTAATATTCTA--CCTCCATATCTAGATAATTAATCAAAATAAAA
43346 CTAATATT
1 CTAATATT
43354 AATTGTTGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 35 0.78
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATATCTAGATAATTAATCAAAATAAAA
Found at i:45660 original size:28 final size:27
Alignment explanation
Indices: 45618--45672 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
45608 TTTTTATTTG
*
45618 AGTTTGTTTTTGAGTCGGTTT-GAGTC
1 AGTTTGTTTTTGAGTCAGTTTCGAGTC
45644 AGTTTGTTTTTTCGAGTCAGTTTCGAGTC
1 AGTTTG-TTTTT-GAGTCAGTTTCGAGTC
45673 TAGTCTCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
28 9 0.36
29 5 0.20
ACGTcount: A:0.13, C:0.11, G:0.27, T:0.49
Consensus pattern (27 bp):
AGTTTGTTTTTGAGTCAGTTTCGAGTC
Done.