Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020304.1 Corchorus olitorius cultivar O-4 contig20337, 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: 12607
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:851 original size:30 final size:30
Alignment explanation
Indices: 799--1403 Score: 743
Period size: 30 Copynumber: 20.2 Consensus size: 30
789 CAAATAAACC
* * *
799 AAAGTAATAATCCT-AAATCAGGATAAAAAT
1 AAAGCAATGATCCTCAAA-CAGGATTAAAAT
* *
829 ATAGCAATGATCCTCAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * * *
859 AAAGCAATGGTCTTCAACCATGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
** *
889 AAAGCAACAATCCTCAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * *
919 GATGCAAAT-ATCCTCAACCAGGATTAAAAT
1 AAAGC-AATGATCCTCAAACAGGATTAAAAT
** *
949 GGAGCGAAT-ATCCTCAATCAGGATTAAAAT
1 AAAGC-AATGATCCTCAAACAGGATTAAAAT
* * *
979 GAAGCAATGATCCTTAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* *
1009 AAAGCAATGATCTTCAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
1039 AAAGCAATGATCCT-AAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAA-CAGGATTAAAAT
* *
1069 AAAGCAATGATCCACAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* ** *
1099 GAAGTGATGATCCTC-AACTAGGATTAGAAT
1 AAAGCAATGATCCTCAAAC-AGGATTAAAAT
*
1129 AAAGCAATGATCCTCAAACAGGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * *
1159 AAAGCAATGATTCTCAAATAGGATTACAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* *
1189 AAAGCAAAGATCCTCAAACAGGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
*
1219 AAAACAATGATCCTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * *
1249 ATAGCAATGATCCTCAAACAAGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
*
1279 AAAGCAATGATCCTCAAACAGGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
1309 AAAGCAATGATCCTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
**
1339 AAAGCAATGATCCTCAAACAGGATTAACCT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
*
1369 AAAGCAATGATCCTCAAACAGGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
1399 AAAGC
1 AAAGC
1404 TGATAAAGCA
Statistics
Matches: 504, Mismatches: 64, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
29 7 0.01
30 488 0.97
31 9 0.02
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.21
Consensus pattern (30 bp):
AAAGCAATGATCCTCAAACAGGATTAAAAT
Found at i:1741 original size:25 final size:27
Alignment explanation
Indices: 1713--1770 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
1703 TACTGAAGTA
1713 AATTGAA-G-AAAGATCACCCTAGATC
1 AATTGAAGGAAAAGATCACCCTAGATC
* *
1738 AATT-AAGGAAAAGATCGCCCTCGATC
1 AATTGAAGGAAAAGATCACCCTAGATC
*
1764 AACTGAA
1 AATTGAA
1771 ATAAACTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 2 0.07
25 5 0.19
26 18 0.67
27 2 0.07
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (27 bp):
AATTGAAGGAAAAGATCACCCTAGATC
Found at i:1785 original size:36 final size:36
Alignment explanation
Indices: 1745--2165 Score: 467
Period size: 36 Copynumber: 11.8 Consensus size: 36
1735 ATCAATTAAG
*
1745 GAAAAGATCGCCCTCGATCAACTGAAATAAACTGAA
1 GAAAAGATCGCCCTGGATCAACTGAAATAAACTGAA
* * *
1781 GAAAAGATTGCCCCGGATCAATTGAAATAAACTGAA
1 GAAAAGATCGCCCTGGATCAACTGAAATAAACTGAA
* * * * *
1817 GAAAAGATCGCCTTAGATCAATTGAAATAAATTGTA
1 GAAAAGATCGCCCTGGATCAACTGAAATAAACTGAA
*
1853 GAAAAGATCGACCTGGATCAACTGAAATAAACTGAA
1 GAAAAGATCGCCCTGGATCAACTGAAATAAACTGAA
* *
1889 G-AAAGACCGCCCTGGATCAATTGAAATAAACTGAA
1 GAAAAGATCGCCCTGGATCAACTGAAATAAACTGAA
1924 GAAAAGATCGCCCTGGATCAACTGAAATAAACTGAA
1 GAAAAGATCGCCCTGGATCAACTGAAATAAACTGAA
* * *
1960 G-AAAGACCGCCCTGGGTCAACAGAAATAAACTGAA
1 GAAAAGATCGCCCTGGATCAACTGAAATAAACTGAA
* * * * *
1995 GAAAGGATCGCCATGAATCAACTGAAGTAAAAT-AA
1 GAAAAGATCGCCCTGGATCAACTGAAATAAACTGAA
* * *
2030 AAAAAAATCACCCTGGATCAAACTGAAATAAACTGAA
1 GAAAAGATCGCCCTGGATC-AACTGAAATAAACTGAA
* * * * * * *
2067 -ATAGGACCACCCTGGGTCAACTGAAATGAATTGAA
1 GAAAAGATCGCCCTGGATCAACTGAAATAAACTGAA
* * * * *
2102 -TAAGGATCGCCCTGGATCAACTGAAGTGAATTGAA
1 GAAAAGATCGCCCTGGATCAACTGAAATAAACTGAA
2137 G-AAAGATCGCCCTGGATCAAACTGAAATA
1 GAAAAGATCGCCCTGGATC-AACTGAAATA
2166 GGACCACCCT
Statistics
Matches: 323, Mismatches: 56, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
35 139 0.43
36 182 0.56
37 2 0.01
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.18
Consensus pattern (36 bp):
GAAAAGATCGCCCTGGATCAACTGAAATAAACTGAA
Found at i:1932 original size:71 final size:71
Alignment explanation
Indices: 1747--2165 Score: 473
Period size: 71 Copynumber: 5.9 Consensus size: 71
1737 CAATTAAGGA
* * * *
1747 AAAGATCGCCCTCGATCAACTGAAATAAACTGAAGAAAAGATTGCCCCGGATCAATTGAAATAAA
1 AAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAA
1812 CTGAAG
66 CTGAAG
* * * * * *
1818 AAAAGATCGCCTTAGATCAATTGAAATAAATTGTAGAAAAGATCGACCTGGATCAACTGAAATAA
1 -AAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAA
1883 ACTGAAG
65 ACTGAAG
* *
1890 AAAGACCGCCCTGGATCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAA
1 AAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAA
1955 CTGAAG
66 CTGAAG
* * * * * * *
1961 AAAGACCGCCCTGGGTCAACAGAAATAAACTGAAGAAAGGATCGCCATGAATCAACTGAAGTAAA
1 AAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAA
* * *
2026 ATAAAA
66 CTGAAG
* * * * * * * *
2032 AAAAATCACCCTGGATCAAACTGAAATAAACTGAA-ATAGGACCACCCTGGGTCAACTGAAATGA
1 AAAGATCGCCCTGGATC-AACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAA
* *
2096 ATTGAAT
65 ACTGAAG
* * * *
2103 AAGGATCGCCCTGGATCAACTGAAGTGAATTGAAG-AAAGATCGCCCTGGATCAAACTGAAATA
1 AAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATC-AACTGAAATA
2166 GGACCACCCT
Statistics
Matches: 291, Mismatches: 53, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
70 26 0.09
71 187 0.64
72 78 0.27
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.18
Consensus pattern (71 bp):
AAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAA
CTGAAG
Found at i:3751 original size:16 final size:16
Alignment explanation
Indices: 3714--3754 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
3704 CAAAGATTGA
*
3714 TAGAAAGCAATTAAAC
1 TAGAAAACAATTAAAC
3730 -AGAAAACAATTAAAC
1 TAGAAAACAATTAAAC
3745 TAGAAAACAA
1 TAGAAAACAA
3755 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.63, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
TAGAAAACAATTAAAC
Found at i:6432 original size:21 final size:21
Alignment explanation
Indices: 6408--6462 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
6398 GGCACTGAAT
* *
6408 GGTGATGGCACGGGCATAGCC
1 GGTGGTGGCACGGGCATAACC
*
6429 GGTGGTGGCACGGGCTTAACC
1 GGTGGTGGCACGGGCATAACC
6450 GGTGGTGGCACGG
1 GGTGGTGGCACGG
6463 AAATGGGCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.15, C:0.22, G:0.47, T:0.16
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATAACC
Found at i:9841 original size:11 final size:11
Alignment explanation
Indices: 9820--9848 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
9810 TTGAAATAAA
9820 TCTTC-AATGG
1 TCTTCAAATGG
9830 TCTTCAAATGG
1 TCTTCAAATGG
9841 TCTTCAAA
1 TCTTCAAA
9849 CACGAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (11 bp):
TCTTCAAATGG
Done.