Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024856.1 Corchorus olitorius cultivar O-4 contig24889, 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: 15119
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:1878 original size:31 final size:31
Alignment explanation
Indices: 1833--1905 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
1823 TTTTTTTTAC
1833 AAAACGC-AAACAATATATTTTTTT-AAATTA
1 AAAACGCAAAACAATAT-TTTTTTTAAAATTA
1863 AAAACGCAAAACAATATTTTTTTTAAAATTA
1 AAAACGCAAAACAATATTTTTTTTAAAATTA
*
1894 AAAACACAAAAC
1 AAAACGCAAAAC
1906 CCTTTTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 14 0.35
31 26 0.65
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (31 bp):
AAAACGCAAAACAATATTTTTTTTAAAATTA
Found at i:1914 original size:31 final size:30
Alignment explanation
Indices: 1840--1948 Score: 105
Period size: 30 Copynumber: 3.6 Consensus size: 30
1830 TACAAAACGC
*
1840 AAACAATATATTTTTTTAAATTAAAAACGCA
1 AAACAATAT-TTTTTTTAAATTAAAAACACA
1871 AAACAATATTTTTTTTAAAATTAAAAACACA
1 AAACAATATTTTTTTT-AAATTAAAAACACA
** * *** *
1902 AAACCCT-TTTTTTTATGACGCAAAAACACG
1 AAACAATATTTTTTT-TAAATTAAAAACACA
1932 AAACAAT-TTTTTTTTAA
1 AAACAATATTTTTTTTAA
1949 GAAAAAACGC
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
29 2 0.03
30 35 0.54
31 28 0.43
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.37
Consensus pattern (30 bp):
AAACAATATTTTTTTTAAATTAAAAACACA
Found at i:2299 original size:15 final size:16
Alignment explanation
Indices: 2275--2314 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
2265 AGAGGTTGAA
*
2275 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
2290 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
2306 AGAAAACAA
1 AGAAAACAA
2315 AACAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:7611 original size:27 final size:27
Alignment explanation
Indices: 7585--7679 Score: 163
Period size: 27 Copynumber: 3.5 Consensus size: 27
7575 ATCTAAAAAT
*
7585 GACCAAAACGCCCCTGGACATGCAAAT
1 GACCAAAACGCCCCTGGACATGCAAAC
7612 GACCAAAACGCCCCTGGACATGCAAAC
1 GACCAAAACGCCCCTGGACATGCAAAC
*
7639 GACCAAAACGCCCTTGGACATGCAAAC
1 GACCAAAACGCCCCTGGACATGCAAAC
*
7666 GACCAAAATGCCCC
1 GACCAAAACGCCCC
7680 CAGGTGACCC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.37, C:0.36, G:0.18, T:0.09
Consensus pattern (27 bp):
GACCAAAACGCCCCTGGACATGCAAAC
Found at i:8024 original size:51 final size:51
Alignment explanation
Indices: 7921--8205 Score: 484
Period size: 51 Copynumber: 5.6 Consensus size: 51
7911 CGATCAACTT
*
7921 CTTTGAATTGTCTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
* *
7971 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGATCATCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
* *
8022 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCATCTTCCACTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
* * *
8073 CTTTCAACTGCCTTCCAATTCAATCTTAAAAAGGACTGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
8124 CTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
8174 CTTTGAACTGTCTTCCAATTCAATCTTAAAAA
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAA
8206 TCATATTTTG
Statistics
Matches: 220, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
50 75 0.34
51 145 0.66
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (51 bp):
CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
Found at i:8133 original size:23 final size:23
Alignment explanation
Indices: 8107--8189 Score: 69
Period size: 23 Copynumber: 3.4 Consensus size: 23
8097 CTTAAAAAGG
8107 ACTGTCTTCCGCTTATCCTTTGA
1 ACTGTCTTCCGCTTATCCTTTGA
** * *
8130 ACTGTCTTCCAATTCAAT-CTTAAAAGG
1 ACTGTCTTCCGCTT--ATCCTT---TGA
*
8157 ACCGTCTTCCGCTTATCCTTTGA
1 ACTGTCTTCCGCTTATCCTTTGA
8180 ACTGTCTTCC
1 ACTGTCTTCC
8190 AATTCAATCT
Statistics
Matches: 44, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
23 22 0.50
24 3 0.07
25 4 0.09
26 3 0.07
27 12 0.27
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.39
Consensus pattern (23 bp):
ACTGTCTTCCGCTTATCCTTTGA
Found at i:8268 original size:152 final size:151
Alignment explanation
Indices: 7932--8205 Score: 462
Period size: 152 Copynumber: 1.8 Consensus size: 151
7922 TTTGAATTGT
7932 CTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATC
1 CTTCCAATTCAATCTTAAAAAGGA-CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATC
* *
7996 TTAAAAAGGATCATCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCAT
65 TTAAAAAGGACCATCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGCACCAT
* *
8061 CTTCCACTTATCCTTTCAACTGC
130 CTTCCAC-TATCCTTTAAACTCC
8084 CTTCCAATTCAATCTTAAAAAGGACTGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATC
1 CTTCCAATTCAATCTTAAAAAGGAC-GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATC
*
8149 TT-AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAA
65 TTAAAAAGGACCATCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAA
8206 TCATATTTTG
Statistics
Matches: 118, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
152 70 0.59
153 48 0.41
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.36
Consensus pattern (151 bp):
CTTCCAATTCAATCTTAAAAAGGACGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCT
TAAAAAGGACCATCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGCACCATC
TTCCACTATCCTTTAAACTCC
Found at i:8560 original size:64 final size:64
Alignment explanation
Indices: 8426--9005 Score: 783
Period size: 64 Copynumber: 9.1 Consensus size: 64
8416 CCGGTGCATC
* * *
8426 TCTTAACAAGATCGTCTTCCGATCAACTTCTGAAACCTTTTCGAGAAACTATCTTCTGGTGTACT
1 TCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTT-GAGAAACCATCTTCTGGTGTACT
* * * *
8491 TTTTAATAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
1 TCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
* * * *
8555 TTTTAACAAGATCGTCTTCCAAACAACTTTTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
1 TCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
* * * *
8619 TCTTGATAAGATCATCTTCCGATCAAC-TCTTGAAAACTCTTGAGAAACCATCTTCTGGTGCACT
1 TCTTAACAAGATCGTCTTCCGATCAACTTC-TGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
* * *
8683 TCTTGATAAGATCAG-CTTCCGATGAAC-TCGTGAAAACTCTTGAGAAACCATCTTCTGGTGTAC
1 TCTTAACAAGATC-GTCTTCCGATCAACTTC-TGAAAACTCTTGAGAAACCATCTTCTGGTGTAC
8746 T
64 T
* *
8747 TCTTGACAAGATCGTCTTCCGATCAAC-TCTTGAAAACTCTTGAGCAACCATCTTCTGGTGTACT
1 TCTTAACAAGATCGTCTTCCGATCAACTTC-TGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
* *
8811 TTTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTAAT
1 TCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
* * * * *
8875 TCTTGACAAGATCGTCTTCCGATCATCTTTTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
1 TCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
* ** * * *
8939 TCTTGACAAGATCGTCTTCCGATCATTTTCTGAAAAATTTTTAGAAACCATCTTCTGGTGTA-T
1 TCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
9002 TCTT
1 TCTT
9006 TAATGAGATC
Statistics
Matches: 468, Mismatches: 43, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
63 7 0.01
64 422 0.90
65 39 0.08
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (64 bp):
TCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
Found at i:10921 original size:91 final size:91
Alignment explanation
Indices: 10766--10934 Score: 284
Period size: 91 Copynumber: 1.9 Consensus size: 91
10756 AAGAAAGGAT
* *
10766 TAAAGGCTCAAAATATGTTTGAGGGTGCTCGATCTAAGTATCACTTTCTCTGTTGTGAAGGATGC
1 TAAAGGCTCAAAATATGTTTGAGGGTGCTCGATCCAAGGATCACTTTCTCTGTTGTGAAGGATGC
10831 TACTGAACCTGATTTGTAATGTAATG
66 TACTGAACCTGATTTGTAATGTAATG
* *
10857 TAAAGGCTCAAAATGTGTTTGAGGGTGCTCGATCCAAGGATCACTTTCTCTGTTGTGAGGGATGC
1 TAAAGGCTCAAAATATGTTTGAGGGTGCTCGATCCAAGGATCACTTTCTCTGTTGTGAAGGATGC
* *
10922 TATTGAACTTGAT
66 TACTGAACCTGAT
10935 CTTCCATTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 72 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (91 bp):
TAAAGGCTCAAAATATGTTTGAGGGTGCTCGATCCAAGGATCACTTTCTCTGTTGTGAAGGATGC
TACTGAACCTGATTTGTAATGTAATG
Done.