Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013460.1 Corchorus olitorius cultivar O-4 contig13493, 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: 41221
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:5824 original size:22 final size:22
Alignment explanation
Indices: 5796--6022 Score: 148
Period size: 22 Copynumber: 9.5 Consensus size: 22
5786 CAACAAGAAG
5796 TGCTCTGCAAAGTGGAAAATAA
1 TGCTCTGCAAAGTGGAAAATAA
***
5818 TGCTCTGCAAAGATGTTTCCAATAA
1 TGCTCTGCAAAG-TG--GAAAATAA
*** *
5843 TGCAAAGCTGAAGTTGAAGAAAATAA
1 TGCTCTGC-AAAG-TG--GAAAATAA
5869 TGCACTCTGCAAAGTGGAAAATAA
1 TG--CTCTGCAAAGTGGAAAATAA
5893 TGCTCTGCAAAGTGGAAAATAA
1 TGCTCTGCAAAGTGGAAAATAA
****
5915 TGCTCTGCAGAGATGTTTCCAATAA
1 TGCTCTGCA-A-A-GTGGAAAATAA
*** *
5940 TGCAAAGCTGAAGTTGAAGAAAATAA
1 TGCTCTGC-AAAG-TG--GAAAATAA
5966 TGCACTCTGCAAAGTGGAAAATAA
1 TG--CTCTGCAAAGTGGAAAATAA
*
5990 TGCTCTGCAAAGTGGTAAATAA
1 TGCTCTGCAAAGTGGAAAATAA
6012 TGCTCTGCAAA
1 TGCTCTGCAAA
6023 AATGTTTCCA
Statistics
Matches: 156, Mismatches: 34, Indels: 30
0.71 0.15 0.14
Matches are distributed among these distances:
22 71 0.46
23 4 0.03
24 23 0.15
25 23 0.15
26 23 0.15
27 6 0.04
28 6 0.04
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (22 bp):
TGCTCTGCAAAGTGGAAAATAA
Found at i:5962 original size:97 final size:97
Alignment explanation
Indices: 5796--6039 Score: 461
Period size: 97 Copynumber: 2.5 Consensus size: 97
5786 CAACAAGAAG
5796 TGCTCTGCAAAGTGGAAAATAATGCTCTGCAAAGATGTTTCCAATAATGCAAAGCTGAAGTTGAA
1 TGCTCTGCAAAGTGGAAAATAATGCTCTGCAAAGATGTTTCCAATAATGCAAAGCTGAAGTTGAA
5861 GAAAATAATGCACTCTGCAAAGTGGAAAATAA
66 GAAAATAATGCACTCTGCAAAGTGGAAAATAA
*
5893 TGCTCTGCAAAGTGGAAAATAATGCTCTGCAGAGATGTTTCCAATAATGCAAAGCTGAAGTTGAA
1 TGCTCTGCAAAGTGGAAAATAATGCTCTGCAAAGATGTTTCCAATAATGCAAAGCTGAAGTTGAA
5958 GAAAATAATGCACTCTGCAAAGTGGAAAATAA
66 GAAAATAATGCACTCTGCAAAGTGGAAAATAA
* *
5990 TGCTCTGCAAAGTGGTAAATAATGCTCTGCAAAAATGTTTCCAATAATGC
1 TGCTCTGCAAAGTGGAAAATAATGCTCTGCAAAGATGTTTCCAATAATGC
6040 TAAACAATTC
Statistics
Matches: 143, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 143 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.25
Consensus pattern (97 bp):
TGCTCTGCAAAGTGGAAAATAATGCTCTGCAAAGATGTTTCCAATAATGCAAAGCTGAAGTTGAA
GAAAATAATGCACTCTGCAAAGTGGAAAATAA
Found at i:6277 original size:2 final size:2
Alignment explanation
Indices: 6270--6299 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6260 ATTAGCCTTC
6270 AT AT AT 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
6300 TGCTCCGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8380 original size:28 final size:28
Alignment explanation
Indices: 8340--8395 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
8330 AGAAACAAAC
8340 AATGAAGCATGTATCAATTGATTTCCAA
1 AATGAAGCATGTATCAATTGATTTCCAA
8368 AATGAAGCATGTATCAATTGATTTCCAA
1 AATGAAGCATGTATCAATTGATTTCCAA
8396 TTTGTACGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (28 bp):
AATGAAGCATGTATCAATTGATTTCCAA
Found at i:18601 original size:2 final size:2
Alignment explanation
Indices: 18594--18623 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18584 ATTTTATGTT
18594 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18624 AAGCTAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24164 original size:64 final size:64
Alignment explanation
Indices: 24056--24185 Score: 215
Period size: 64 Copynumber: 2.0 Consensus size: 64
24046 ATAAATAACA
* *
24056 AAATATCCCTCATTTTAATGGAATAGTTTGTCTAAAAAAGGGTTTATTAATTACAAGTAACATT
1 AAATATCCCTCATTTTAATGGAATAGTTTGTCTAAAAAAAGGTTTATTAATTACAAGTAAAATT
* * *
24120 AAATTTCCCTCATTTTAATGGAATAGTTTGTTTAAAAAAAGGTTTGTTAATTACAAGTAAAATT
1 AAATATCCCTCATTTTAATGGAATAGTTTGTCTAAAAAAAGGTTTATTAATTACAAGTAAAATT
24184 AA
1 AA
24186 TGGTAAATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.38
Consensus pattern (64 bp):
AAATATCCCTCATTTTAATGGAATAGTTTGTCTAAAAAAAGGTTTATTAATTACAAGTAAAATT
Found at i:26595 original size:61 final size:62
Alignment explanation
Indices: 26520--26653 Score: 198
Period size: 63 Copynumber: 2.2 Consensus size: 62
26510 CAATAGTTAA
* * *
26520 TTAATTGTTTCAATCATTAATGGAGTCAAGATC-ACACATATCAGTCTCATTTACATATTAG
1 TTAATTGTTTCAATCATTAATGGAATCAAGATCAACACATATAAGTCTCATTTACATAATAG
* * *
26581 TTAATTGTTTCAATCCTTAATGGAATCAAGATCATATATATATAAGTCTCATTTACATAATAG
1 TTAATTGTTTCAATCATTAATGGAATCAAGATCA-ACACATATAAGTCTCATTTACATAATAG
26644 TTAATTGTTT
1 TTAATTGTTT
26654 ATAGTAAGCA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 31 0.48
63 34 0.52
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.41
Consensus pattern (62 bp):
TTAATTGTTTCAATCATTAATGGAATCAAGATCAACACATATAAGTCTCATTTACATAATAG
Found at i:29555 original size:87 final size:88
Alignment explanation
Indices: 29434--29624 Score: 237
Period size: 87 Copynumber: 2.2 Consensus size: 88
29424 AAGGTGGAGA
* * * *
29434 ATAGTTTCAATTC-AATTTAATGTGATCTTCCTAATGGAGTTATGGGTGA-TTATGGTGCAAAAT
1 ATAGTTTGAATTCAAATTTAATGTGACCTTCCTAATGGAGTTAT-GGTGAGTAATGATGCAAAAT
29497 CTTTGGAAAAT-ATTATGGTAGAGG
65 CTTTGGAAAATGATT-TGGTAGAGG
* * *
29521 ATAGTTTGAATTCAAATTTTA-GTGACCTTTCTAATGGAGTTATGGTTAGTAATGATGCAAAATC
1 ATAGTTTGAATTCAAATTTAATGTGACCTTCCTAATGGAGTTATGGTGAGTAATGATGCAAAATC
* * *
29585 TTTGGAAACTGATTTGGTGGTGG
66 TTTGGAAAATGATTTGGTAGAGG
*
29608 ATATTTTGAATTCAAAT
1 ATAGTTTGAATTCAAAT
29625 CGAAGTGGTT
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
86 4 0.04
87 77 0.86
88 9 0.10
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (88 bp):
ATAGTTTGAATTCAAATTTAATGTGACCTTCCTAATGGAGTTATGGTGAGTAATGATGCAAAATC
TTTGGAAAATGATTTGGTAGAGG
Found at i:37351 original size:28 final size:29
Alignment explanation
Indices: 37279--37394 Score: 101
Period size: 33 Copynumber: 3.7 Consensus size: 29
37269 TTTAAATTTA
*
37279 ATTGACACCAGAAGTTGTCAT-ATCAAATTATT
1 ATTGACACCAGAAGTTGTCATGA--GAA--ATT
* *
37311 ATCGTGAAACCAGAAGTTATCATGA-AAATT
1 AT--TGACACCAGAAGTTGTCATGAGAAATT
37341 ATTGACACCAGAAGTTGTCATACTGAGGAAATT
1 ATTGACACCAGAAGTTGTC--A-TGA-GAAATT
37374 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
37395 CCCAAGATTG
Statistics
Matches: 72, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
28 15 0.21
30 7 0.10
31 4 0.06
32 4 0.06
33 24 0.33
34 17 0.24
35 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (29 bp):
ATTGACACCAGAAGTTGTCATGAGAAATT
Found at i:39890 original size:16 final size:16
Alignment explanation
Indices: 39872--39946 Score: 89
Period size: 16 Copynumber: 4.7 Consensus size: 16
39862 AATTTTGGGT
*
39872 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAATG
* *
39888 ACCCGAATCC-AAACG
1 ACCCGAACCCGAAATG
39903 ACCCGAACCCGAAAATG
1 ACCCGAACCCG-AAATG
* *
39920 ACCCAAACCCAAAATG
1 ACCCGAACCCGAAATG
39936 ACCCGAACCCG
1 ACCCGAACCCG
39947 TTCAACCCGA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
15 12 0.25
16 23 0.48
17 13 0.27
ACGTcount: A:0.40, C:0.40, G:0.13, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAATG
Done.