Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024702.1 Corchorus olitorius cultivar O-4 contig24735, 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: 45791
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2084 original size:22 final size:22
Alignment explanation
Indices: 2056--2104 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
2046 CCTGTACAAA
2056 ATATCGGGTCATATAGGTCCTT
1 ATATCGGGTCATATAGGTCCTT
2078 ATATCGGGTCATATAGGTCCTT
1 ATATCGGGTCATATAGGTCCTT
2100 ATATC
1 ATATC
2105 CTATTAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.37
Consensus pattern (22 bp):
ATATCGGGTCATATAGGTCCTT
Found at i:2455 original size:18 final size:18
Alignment explanation
Indices: 2434--2471 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2424 TTTTTAAAAA
2434 AAAAATAAC-TGTTAATTT
1 AAAAA-AACATGTTAATTT
*
2452 AAAAAAACATTTTAATTT
1 AAAAAAACATGTTAATTT
2470 AA
1 AA
2472 TCAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (18 bp):
AAAAAAACATGTTAATTT
Found at i:2930 original size:19 final size:19
Alignment explanation
Indices: 2902--2938 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2892 TTTGGGCCCA
2902 AAACGATGGTAAAACGGTC
1 AAACGATGGTAAAACGGTC
* *
2921 AAACGGTGGTGAAACGGT
1 AAACGATGGTAAAACGGT
2939 TACAGATAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.32, T:0.16
Consensus pattern (19 bp):
AAACGATGGTAAAACGGTC
Found at i:4566 original size:15 final size:16
Alignment explanation
Indices: 4540--4573 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4530 AATTCTCCCA
4540 AGAAGAAAGAGAAAAT
1 AGAAGAAAGAGAAAAT
*
4556 AGAAG-AAGAGAAGAT
1 AGAAGAAAGAGAAAAT
4571 AGA
1 AGA
4574 TTTAAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (16 bp):
AGAAGAAAGAGAAAAT
Found at i:7234 original size:22 final size:19
Alignment explanation
Indices: 7206--7255 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 19
7196 GGTTAATAAC
7206 AAGAAAAACAAAGAAACTGGAA
1 AAGAAAAA-AAAGAAA--GGAA
*
7228 AAGAAAATAAAATAAAGGAA
1 AAGAAAA-AAAAGAAAGGAA
7248 AAGAAAAA
1 AAGAAAAA
7256 GTAATCTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.04
20 11 0.42
22 13 0.50
23 1 0.04
ACGTcount: A:0.74, C:0.04, G:0.16, T:0.06
Consensus pattern (19 bp):
AAGAAAAAAAAGAAAGGAA
Found at i:8363 original size:328 final size:328
Alignment explanation
Indices: 7766--8423 Score: 1316
Period size: 328 Copynumber: 2.0 Consensus size: 328
7756 TATCTGTCAA
7766 TCGTAGCTCATTGGTGCTGTTGGCGGGAAACACATTCTGTCGGAAAATATAGGCAAGGAGTCGGT
1 TCGTAGCTCATTGGTGCTGTTGGCGGGAAACACATTCTGTCGGAAAATATAGGCAAGGAGTCGGT
7831 GTCCAATCGCACTATGCTTAGCATAAACTGTCCATTGTTTTTTTCGGCTCCATGACCAAGCTACA
66 GTCCAATCGCACTATGCTTAGCATAAACTGTCCATTGTTTTTTTCGGCTCCATGACCAAGCTACA
7896 TCAAGCTTCTTAATAGCTTCAAACTTATCCCAAGCAGGAAGAGTAAGACAAAGTTTTTCTCCGTG
131 TCAAGCTTCTTAATAGCTTCAAACTTATCCCAAGCAGGAAGAGTAAGACAAAGTTTTTCTCCGTG
7961 ACCATCAGGTTGAAATTGAACTTTGTCTCCAACACCCTTTAGTCCAAACCAAGTGTTGAGCTTCC
196 ACCATCAGGTTGAAATTGAACTTTGTCTCCAACACCCTTTAGTCCAAACCAAGTGTTGAGCTTCC
8026 TTTCCGTAATCTCAATTGCTACCCCAGCAACAGTAGAGTGTAAAGAGACACAAATATTTTTCTCT
261 TTTCCGTAATCTCAATTGCTACCCCAGCAACAGTAGAGTGTAAAGAGACACAAATATTTTTCTCT
8091 CTT
326 CTT
8094 TCGTAGCTCATTGGTGCTGTTGGCGGGAAACACATTCTGTCGGAAAATATAGGCAAGGAGTCGGT
1 TCGTAGCTCATTGGTGCTGTTGGCGGGAAACACATTCTGTCGGAAAATATAGGCAAGGAGTCGGT
8159 GTCCAATCGCACTATGCTTAGCATAAACTGTCCATTGTTTTTTTCGGCTCCATGACCAAGCTACA
66 GTCCAATCGCACTATGCTTAGCATAAACTGTCCATTGTTTTTTTCGGCTCCATGACCAAGCTACA
8224 TCAAGCTTCTTAATAGCTTCAAACTTATCCCAAGCAGGAAGAGTAAGACAAAGTTTTTCTCCGTG
131 TCAAGCTTCTTAATAGCTTCAAACTTATCCCAAGCAGGAAGAGTAAGACAAAGTTTTTCTCCGTG
8289 ACCATCAGGTTGAAATTGAACTTTGTCTCCAACACCCTTTAGTCCAAACCAAGTGTTGAGCTTCC
196 ACCATCAGGTTGAAATTGAACTTTGTCTCCAACACCCTTTAGTCCAAACCAAGTGTTGAGCTTCC
8354 TTTCCGTAATCTCAATTGCTACCCCAGCAACAGTAGAGTGTAAAGAGACACAAATATTTTTCTCT
261 TTTCCGTAATCTCAATTGCTACCCCAGCAACAGTAGAGTGTAAAGAGACACAAATATTTTTCTCT
8419 CTT
326 CTT
8422 TC
1 TC
8424 CTCTAAGTTT
Statistics
Matches: 330, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
328 330 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (328 bp):
TCGTAGCTCATTGGTGCTGTTGGCGGGAAACACATTCTGTCGGAAAATATAGGCAAGGAGTCGGT
GTCCAATCGCACTATGCTTAGCATAAACTGTCCATTGTTTTTTTCGGCTCCATGACCAAGCTACA
TCAAGCTTCTTAATAGCTTCAAACTTATCCCAAGCAGGAAGAGTAAGACAAAGTTTTTCTCCGTG
ACCATCAGGTTGAAATTGAACTTTGTCTCCAACACCCTTTAGTCCAAACCAAGTGTTGAGCTTCC
TTTCCGTAATCTCAATTGCTACCCCAGCAACAGTAGAGTGTAAAGAGACACAAATATTTTTCTCT
CTT
Found at i:19135 original size:15 final size:16
Alignment explanation
Indices: 19109--19142 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
19099 AATTCTCCCA
19109 AGAAGAAAGAGAAAAT
1 AGAAGAAAGAGAAAAT
*
19125 AGAAG-AAGAGAAGAT
1 AGAAGAAAGAGAAAAT
19140 AGA
1 AGA
19143 TTTAAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (16 bp):
AGAAGAAAGAGAAAAT
Found at i:22302 original size:30 final size:31
Alignment explanation
Indices: 22244--22302 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
22234 GTTTTGTAAG
22244 ACTTTTGAATCGTCTATTATATCCTTATTAA
1 ACTTTTGAATCGTCTATTATATCCTTATTAA
22275 ACTTTTGAATCGTCTATTATA-CCTTATT
1 ACTTTTGAATCGTCTATTATATCCTTATT
22303 TTTTGAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 7 0.25
31 21 0.75
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49
Consensus pattern (31 bp):
ACTTTTGAATCGTCTATTATATCCTTATTAA
Found at i:22306 original size:26 final size:28
Alignment explanation
Indices: 22246--22310 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 28
22236 TTTGTAAGAC
22246 TTTTGAATCGTCTATTATATCCTTATTAAA
1 TTTTGAATCGTCTATTATATCCTTATT--A
22276 CTTTTGAATCGTCTATTATA-CCTTATT-
1 -TTTTGAATCGTCTATTATATCCTTATTA
22303 TTTTGAAT
1 TTTTGAAT
22311 ATATTTCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
26 8 0.24
30 7 0.21
31 19 0.56
ACGTcount: A:0.26, C:0.14, G:0.08, T:0.52
Consensus pattern (28 bp):
TTTTGAATCGTCTATTATATCCTTATTA
Found at i:24786 original size:59 final size:59
Alignment explanation
Indices: 24723--24837 Score: 178
Period size: 59 Copynumber: 1.9 Consensus size: 59
24713 TCATATATGA
* *
24723 CCCAAAATTTTGTACAGAGACTTGTTTGCACAATA-TTTATAGTACAGGGACCTATATCT
1 CCCAAAATTTTGTACAGAGACTTGTTTGCACAATACTTAATAGTACAAGGA-CTATATCT
* *
24782 CCCAAAATTTTGTATAGAGACTTGTTTGCAGAATACTTAATAGTACAAGGACTATA
1 CCCAAAATTTTGTACAGAGACTTGTTTGCACAATACTTAATAGTACAAGGACTATA
24838 GGGTACTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 38 0.75
60 13 0.25
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (59 bp):
CCCAAAATTTTGTACAGAGACTTGTTTGCACAATACTTAATAGTACAAGGACTATATCT
Found at i:30031 original size:19 final size:20
Alignment explanation
Indices: 29993--30043 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
29983 TTTTTTTTTT
*
29993 GGTTCGGACCGGATCAAACC
1 GGTTCGGACCGGACCAAACC
*
30013 GGTTCGGTCC-GACCAAACC
1 GGTTCGGACCGGACCAAACC
30032 GGTTCGGACCGG
1 GGTTCGGACCGG
30044 TCAAGTCGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.20, C:0.31, G:0.33, T:0.16
Consensus pattern (20 bp):
GGTTCGGACCGGACCAAACC
Found at i:37675 original size:20 final size:19
Alignment explanation
Indices: 37650--37690 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
37640 CTTTTTTTTT
37650 GGTTCGGACCGGATCAAACC
1 GGTTCGGACCGG-TCAAACC
*
37670 GGTTCGGACCGGTCAAGCC
1 GGTTCGGACCGGTCAAACC
37689 GG
1 GG
37691 CTCGAGCCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.20, C:0.29, G:0.37, T:0.15
Consensus pattern (19 bp):
GGTTCGGACCGGTCAAACC
Found at i:41554 original size:18 final size:19
Alignment explanation
Indices: 41531--41567 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
41521 AAAAAGTTTG
41531 CTTTTTTTTCT-TCAAATT
1 CTTTTTTTTCTGTCAAATT
41549 CTTTTTTTTCTGTCAAATT
1 CTTTTTTTTCTGTCAAATT
41568 TAAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.16, C:0.16, G:0.03, T:0.65
Consensus pattern (19 bp):
CTTTTTTTTCTGTCAAATT
Found at i:44758 original size:2 final size:2
Alignment explanation
Indices: 44751--44817 Score: 107
Period size: 2 Copynumber: 33.5 Consensus size: 2
44741 GGGCTTCTTT
* *
44751 TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA CA TA 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
*
44793 TA TA TA TA TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
44818 GGTCATGTCT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Done.