Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020617.1 Corchorus olitorius cultivar O-4 contig20650, 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: 7367
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:5911 original size:48 final size:48
Alignment explanation
Indices: 5845--6749 Score: 1349
Period size: 48 Copynumber: 19.0 Consensus size: 48
5835 AGACAGGATG
*
5845 AAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* *
5893 ACATATCGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* * *
5941 AAACATTGAAGACAACACCTTCCAACCGGGAAGGGCAAAACAGGAATA
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
*
5989 AAATATTGGAA-ACAACACCTTCCGACCGGGAAGGACAAAACGGGAATA
1 AAATATT-GAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* *
6037 AAACATTGAAGACAATACCTTCCGACCGGGAAGGGCAAAACGGGAATA
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* *
6085 AAATATCGAAGACAACACCTTCCGACCAGGAAGGGCAAAACGGGAATA
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* * *
6133 AAACATTGAAGACAATACCTTCCGACCAGGAAGGGCAAAACGGGAATA
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* *
6181 AAATATCGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGAGAATA
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* * *
6229 AAATATCGAAGACAATACCTTCCGACAGGGAAGGGCAAAACGGGAATA
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* * *
6277 AAACATTGAAGACAATACCTTCCAACCGGGAAGGGCAAAACGGGAATA
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* *
6325 AAATATCGAAGACAACACCTTCCGACCGAGAAGGGCAAAACGGGAATA
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* * * *
6373 AAACATTGAAGACAATACCTTCCGACCGGGAAGGGAAAAACCGGAATA
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* *
6421 ATATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGG-ATA
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* * *
6468 AAACATTGAAGACAACACCTTCCGACCGGTAAGGGCAAAACAGGAATA
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
*
6516 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATA
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* *
6564 AAACATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATA
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* *
6612 AAACATTGAAGACAACACCATCCGACCGGGAAGGGCAAAACGGGAATA
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* * *
6660 AAACATTGAAGACAACACCTTCCGACCGGGAAGGGAAAAACGAGAAT-
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* *
6707 --A-A-TGATGACAACACCTTCCGACCGAGAAGGGC-AAACTGGGAAT
1 AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAAC-GGGAAT
6750 GTAAACAACA
Statistics
Matches: 785, Mismatches: 68, Indels: 13
0.91 0.08 0.02
Matches are distributed among these distances:
42 4 0.01
43 32 0.04
44 1 0.00
45 1 0.00
47 45 0.06
48 699 0.89
49 3 0.00
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (48 bp):
AAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
Found at i:6815 original size:41 final size:40
Alignment explanation
Indices: 6714--6831 Score: 139
Period size: 41 Copynumber: 2.9 Consensus size: 40
6704 AATAATGATG
* * *
6714 ACAACACCTTCCGACCGA-GAAGGGCAAACTGGGAATGTAA
1 ACAACAACTTCCGA-TGAGGAAGGGCAAACTGGGAATTTAA
* **
6754 ACAACACCTTCTTATGAGGAAGGGCAAACTGGGAATTTAAA
1 ACAACAACTTCCGATGAGGAAGGGCAAACTGGGAATTT-AA
* *
6795 ACAACAACTTCCGATTAGGAAGGGCAAACTAGGAATT
1 ACAACAACTTCCGATGAGGAAGGGCAAACTGGGAATT
6832 ATCGAAGGAA
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
39 2 0.03
40 31 0.46
41 34 0.51
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (40 bp):
ACAACAACTTCCGATGAGGAAGGGCAAACTGGGAATTTAA
Found at i:6902 original size:43 final size:43
Alignment explanation
Indices: 6847--7146 Score: 252
Period size: 42 Copynumber: 6.8 Consensus size: 43
6837 AGGAAAACTG
*
6847 GGACCTTCCGACTAGGAAGGGGCATTTTTGGAAATGAAAACAA
1 GGACCTTCCGACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
* ** **
6890 GGACCTTACGACTGGGAAGGGGCATTTTTGGAATGAGATATCGAAAACTG
1 GGACCTTCCGACCAGGAAGGGGCATTTTT-G---GA-A-AT-GAAAACAA
* * *
6940 GGATCTTCCGACC-GAGAAGGGGCATTTTTTGGAAATGAAGATAA
1 GGACCTTCCGACCAG-GAAGGGGCA-TTTTTGGAAATGAAAACAA
* *
6984 GGACCTTCCAACCAGGAAGGGGCA-TTTTGGGAATGAAAACAA
1 GGACCTTCCGACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
* * * * *
7026 AGACCTCCCAACCAGGAAGGGGGATTTTTGG-AATGAAAGAAAA
1 GGACCTTCCGACCAGGAAGGGGCATTTTTGGAAATGAAA-ACAA
* * *
7069 CTGTGACCTTCCGACCGGGAATGGGCATTTTTGG-AAT-AAAAC-G
1 --G-GACCTTCCGACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
*
7112 GAGACCTTCCAACCAGGAAGGGGCATTTTTGGAAA
1 G-GACCTTCCGACCAGGAAGGGGCATTTTTGGAAA
7147 GAGATAAGAA
Statistics
Matches: 209, Mismatches: 32, Indels: 33
0.76 0.12 0.12
Matches are distributed among these distances:
41 28 0.13
42 45 0.22
43 36 0.17
44 26 0.12
45 6 0.03
46 29 0.14
47 4 0.02
48 1 0.00
49 3 0.01
50 26 0.12
51 5 0.02
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (43 bp):
GGACCTTCCGACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
Found at i:6936 original size:93 final size:94
Alignment explanation
Indices: 6839--7019 Score: 258
Period size: 94 Copynumber: 1.9 Consensus size: 94
6829 ATTATCGAAG
*
6839 GAAAACTGGGACCTTCCGACTAG-GAAGGGGCA-TTTTTGGAAATGAAAACAAGGACCTTACGAC
1 GAAAACTGGGACCTTCCGAC-AGAGAAGGGGCATTTTTTGGAAATGAAAACAAGGACCTTACAAC
** *
6902 TGGGAAGGGGCATTTTTGGAATGAGATATC
65 CAGGAAGGGGCATTTTGGGAATGAGATATC
* * * * *
6932 GAAAACTGGGATCTTCCGACCGAGAAGGGGCATTTTTTGGAAATGAAGATAAGGACCTTCCAACC
1 GAAAACTGGGACCTTCCGACAGAGAAGGGGCATTTTTTGGAAATGAAAACAAGGACCTTACAACC
6997 AGGAAGGGGCATTTTGGGAATGA
66 AGGAAGGGGCATTTTGGGAATGA
7020 AAACAAAGAC
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
92 1 0.01
93 28 0.36
94 48 0.62
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.22
Consensus pattern (94 bp):
GAAAACTGGGACCTTCCGACAGAGAAGGGGCATTTTTTGGAAATGAAAACAAGGACCTTACAACC
AGGAAGGGGCATTTTGGGAATGAGATATC
Found at i:7130 original size:87 final size:88
Alignment explanation
Indices: 6955--7145 Score: 248
Period size: 87 Copynumber: 2.2 Consensus size: 88
6945 TTCCGACCGA
*
6955 GAAGGGGCATTTTTTGGAAATG-AAGATAA--G-GACCTTCCAACCAGGAAGGGGCATTTTGGGA
1 GAAGGGGCA-TTTTTGG-AATGAAAGAAAACTGTGACCTTCCAACCAGGAAGGGGCATTTTGGGA
7016 ATGAAAACAAAGACCTCCCAACCAG
64 ATGAAAACAAAGACCTCCCAACCAG
* * * * *
7041 GAAGGGGGATTTTTGGAATGAAAGAAAACTGTGACCTTCCGACCGGGAATGGGCATTTTTGGAAT
1 GAAGGGGCATTTTTGGAATGAAAGAAAACTGTGACCTTCCAACCAGGAAGGGGCATTTTGGGAAT
** *
7106 -AAAACGGAGACCTTCCAACCAG
66 GAAAACAAAGACCTCCCAACCAG
7128 GAAGGGGCATTTTTGGAA
1 GAAGGGGCATTTTTGGAA
7146 AGAGATAAGA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
84 4 0.04
85 13 0.14
86 8 0.09
87 37 0.41
88 29 0.32
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.21
Consensus pattern (88 bp):
GAAGGGGCATTTTTGGAATGAAAGAAAACTGTGACCTTCCAACCAGGAAGGGGCATTTTGGGAAT
GAAAACAAAGACCTCCCAACCAG
Found at i:7136 original size:41 final size:42
Alignment explanation
Indices: 6955--7145 Score: 181
Period size: 41 Copynumber: 4.4 Consensus size: 42
6945 TTCCGACCGA
*
6955 GAAGGGGCATTTTTTGGAAATGAAGATA-AG-GACCTTCCAACCAG
1 GAAGGGGCA-TTTTTGG-AAT-AA-AAACAGAGACCTTCCAACCAG
* * * *
6999 GAAGGGGCATTTTGGGAATGAAAACAAAGACCTCCCAACCAG
1 GAAGGGGCATTTTTGGAATAAAAACAGAGACCTTCCAACCAG
* * * * *
7041 GAAGGGGGATTTTTGGAATGAAAGAAAACTGTGACCTTCCGACCGG
1 GAAGGGGCATTTTTGGAAT---A-AAAACAGAGACCTTCCAACCAG
* *
7087 GAATGGGCATTTTTGGAAT-AAAACGGAGACCTTCCAACCAG
1 GAAGGGGCATTTTTGGAATAAAAACAGAGACCTTCCAACCAG
7128 GAAGGGGCATTTTTGGAA
1 GAAGGGGCATTTTTGGAA
7146 AGAGATAAGA
Statistics
Matches: 120, Mismatches: 21, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
40 2 0.02
41 37 0.31
42 33 0.28
43 6 0.05
44 9 0.08
46 33 0.28
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.21
Consensus pattern (42 bp):
GAAGGGGCATTTTTGGAATAAAAACAGAGACCTTCCAACCAG
Done.