Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016578.1 Corchorus olitorius cultivar O-4 contig16611, 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: 26592
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:232 original size:121 final size:120
Alignment explanation
Indices: 87--311 Score: 407
Period size: 121 Copynumber: 1.9 Consensus size: 120
77 TTTATTAGTA
87 ATTCTCAAAAAAGAAAACAGTTAACAACCAAAAAGTAAAATGACAACTAAAAAT-AATTTTTAAT
1 ATTCTCAAAAAAGAAAACAGTTAACAACCAAAAAGTAAAATGACAACTAAAAATAAATTTTTAAT
*
151 TACAAAATAGAGAAATGACAATTTTTTAAAAAGGAAAAAATAAAATTATAATTTAT
66 TACAAAATAGAGAAATGA-AAATTTTTAAAAAGGAAAAAATAAAATTATAATTTAT
*
207 ATTCTCAAAAAAGAAAAACAGTTAACAACCAAAAAGTAAAATGACAATTAAAAATAAATTTTTAA
1 ATTCTCAAAAAAG-AAAACAGTTAACAACCAAAAAGTAAAATGACAACTAAAAATAAATTTTTAA
272 TTACAAAATAGAGAAATGAAAATTTTTAAAAAGGAAAAAA
65 TTACAAAATAGAGAAATGAAAATTTTTAAAAAGGAAAAAA
312 ATTAGAGAAA
Statistics
Matches: 101, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
120 13 0.13
121 60 0.59
122 28 0.28
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.25
Consensus pattern (120 bp):
ATTCTCAAAAAAGAAAACAGTTAACAACCAAAAAGTAAAATGACAACTAAAAATAAATTTTTAAT
TACAAAATAGAGAAATGAAAATTTTTAAAAAGGAAAAAATAAAATTATAATTTAT
Found at i:323 original size:34 final size:34
Alignment explanation
Indices: 276--379 Score: 192
Period size: 34 Copynumber: 3.1 Consensus size: 34
266 TTTTAATTAC
*
276 AAAA-TAGAGAAATGAAAATTTTTAAAAAGGAAA
1 AAAATTAGAGAAATGACAATTTTTAAAAAGGAAA
309 AAAATTAGAGAAATGACAATTTTTAAAAAGGAAA
1 AAAATTAGAGAAATGACAATTTTTAAAAAGGAAA
343 AAAATTAGAGAAATGACAATTTTTAAAAAGGAAA
1 AAAATTAGAGAAATGACAATTTTTAAAAAGGAAA
377 AAA
1 AAA
380 TTATAATCTA
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
33 4 0.06
34 65 0.94
ACGTcount: A:0.62, C:0.02, G:0.14, T:0.22
Consensus pattern (34 bp):
AAAATTAGAGAAATGACAATTTTTAAAAAGGAAA
Found at i:728 original size:121 final size:121
Alignment explanation
Indices: 589--814 Score: 443
Period size: 121 Copynumber: 1.9 Consensus size: 121
579 TTTATTAGTA
*
589 ATTCTCAAAAAAGAAAAACAGTTAACAACCAAAAAGTAAAATGACAATTAATAATAAATTTTTAA
1 ATTCTCAAAAAAGAAAAACAGTTAACAACCAAAAAGTAAAATGACAATTAAAAATAAATTTTTAA
654 TTACAAAATAGAGAAATGACAATTTTTAAAAAGGAAAAAATAAAATTATAATTTAT
66 TTACAAAATAGAGAAATGACAATTTTTAAAAAGGAAAAAATAAAATTATAATTTAT
710 ATTCTCAAAAAAGAAAAACAGTTAACAACCAAAAAGTAAAATGACAATTAAAAATAAATTTTTAA
1 ATTCTCAAAAAAGAAAAACAGTTAACAACCAAAAAGTAAAATGACAATTAAAAATAAATTTTTAA
775 TTACAAAATAGAGAAATGACAATTTTTAAAAAGGAAAAAA
66 TTACAAAATAGAGAAATGACAATTTTTAAAAAGGAAAAAA
815 ATTAGAGAAA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 104 1.00
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.25
Consensus pattern (121 bp):
ATTCTCAAAAAAGAAAAACAGTTAACAACCAAAAAGTAAAATGACAATTAAAAATAAATTTTTAA
TTACAAAATAGAGAAATGACAATTTTTAAAAAGGAAAAAATAAAATTATAATTTAT
Found at i:821 original size:34 final size:34
Alignment explanation
Indices: 779--852 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
769 TTTTAATTAC
779 AAAA-TAGAGAAATGACAATTTTTAAAAAGGAAA
1 AAAATTAGAGAAATGACAATTTTTAAAAAGGAAA
812 AAAATTAGAGAAATGACAATTTTTAAAAAGGAAA
1 AAAATTAGAGAAATGACAATTTTTAAAAAGGAAA
846 AAAATTA
1 AAAATTA
853 TAATCTAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 4 0.10
34 36 0.90
ACGTcount: A:0.61, C:0.03, G:0.14, T:0.23
Consensus pattern (34 bp):
AAAATTAGAGAAATGACAATTTTTAAAAAGGAAA
Found at i:6313 original size:21 final size:21
Alignment explanation
Indices: 6288--6329 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6278 AGGAATCGCT
*
6288 CTCATCAGAGTCACTCTCATC
1 CTCATCAGAATCACTCTCATC
*
6309 CTCATCAGAATCGCTCTCATC
1 CTCATCAGAATCACTCTCATC
6330 AGAGTCTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.38, G:0.10, T:0.29
Consensus pattern (21 bp):
CTCATCAGAATCACTCTCATC
Found at i:6654 original size:28 final size:29
Alignment explanation
Indices: 6622--6680 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
6612 ATTCATTAAG
*
6622 AACAGA-AATTCAGTCATCACAATAAATA
1 AACAGATAATTCAGTCATCAAAATAAATA
6650 AACAGATAATTCAGTCATCAAAATAAATA
1 AACAGATAATTCAGTCATCAAAATAAATA
6679 AA
1 AA
6681 TTTAACTTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (29 bp):
AACAGATAATTCAGTCATCAAAATAAATA
Found at i:7298 original size:110 final size:111
Alignment explanation
Indices: 7095--7312 Score: 411
Period size: 110 Copynumber: 2.0 Consensus size: 111
7085 ATATTAACAC
*
7095 GAATTAATATAAATCAGAAAAACAGTTCTAAGCATAAAACCACAAAAAAAAAACCATTCCACAGA
1 GAATTAATATAAATCAGAAAAACAGTTCTAAGCATAAAACAACAAAAAAAAAACCATTCCACAGA
7160 AATCCTTTTCGTTCAATCACCAATAATAAACCCAAAATTCCTAAAT
66 AATCCTTTTCGTTCAATCACCAATAATAAACCCAAAATTCCTAAAT
*
7206 GAATTAATATAAATCAGAAAAACAGTTCTAAGCATAGAACAACAAAAAAAAAA-CATTCCACAGA
1 GAATTAATATAAATCAGAAAAACAGTTCTAAGCATAAAACAACAAAAAAAAAACCATTCCACAGA
7270 AATCCTTTTCGTTCAATCACCAATAATAAACCCAAAATTCCTA
66 AATCCTTTTCGTTCAATCACCAATAATAAACCCAAAATTCCTA
7313 TTATGGCAAA
Statistics
Matches: 105, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
110 54 0.51
111 51 0.49
ACGTcount: A:0.50, C:0.21, G:0.06, T:0.22
Consensus pattern (111 bp):
GAATTAATATAAATCAGAAAAACAGTTCTAAGCATAAAACAACAAAAAAAAAACCATTCCACAGA
AATCCTTTTCGTTCAATCACCAATAATAAACCCAAAATTCCTAAAT
Found at i:14882 original size:159 final size:162
Alignment explanation
Indices: 14631--14957 Score: 473
Period size: 159 Copynumber: 2.0 Consensus size: 162
14621 TTGTTTAGAC
* * *
14631 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTCCCTAAAAAAACTAAAAGTAAAAACTCTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTTTTACC---AAAAAC-AAAACTAAAAACTCTA
* *
14696 TTTTTATTTTATTAAATATAATATCCTTATAACTATTTAATTTTTACCATTTTACT-ATTTAATT
62 TTTTTATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACCAATTTACTAATTTAATT
* * *
14760 AAAAAA-TTATATATATTATAATTTTTTAAATATAT
127 AAAAAACTTAGATATATTAGAATTTTTAAAATATAT
14795 TTTTATAATTTTACTCAACTAAAAACTCTATTTTTTGACC-AAAA-AAAACTAAAAACTCTATTT
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTTTT-ACCAAAAACAAAACTAAAAACTCTATTT
* * * *
14858 TTATTTAATTAAATCTAATATCCTTATACCTATTTTATTTTTATCAATTTACTAATTTAATTAAA
65 TTATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACCAATTTACTAATTTAATTAAA
14923 AAACTTAGATATATTAGAATTTTTAAAATATAT
130 AAACTTAGATATATTAGAATTTTTAAAATATAT
14956 TT
1 TT
14958 CTTAAATGAC
Statistics
Matches: 148, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
159 65 0.44
160 14 0.09
161 32 0.22
164 35 0.24
165 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.47
Consensus pattern (162 bp):
TTTTATAATTTTACTCAACTAAAAACTCTATTTTTTACCAAAAACAAAACTAAAAACTCTATTTT
TATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACCAATTTACTAATTTAATTAAAA
AACTTAGATATATTAGAATTTTTAAAATATAT
Found at i:16016 original size:21 final size:22
Alignment explanation
Indices: 15992--16032 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
15982 GTTTATAATA
*
15992 TTCTTGGGTCA-TCGGGTTATT
1 TTCTCGGGTCATTCGGGTTATT
*
16013 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
16033 CAAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.15, G:0.29, T:0.46
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATT
Done.