Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017538.1 Corchorus olitorius cultivar O-4 contig17571, 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: 25155
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:228 original size:2 final size:2
Alignment explanation
Indices: 216--251 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
206 AATTGACCTC
216 AT AT A- AT AT AT AT -T AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
252 CCTACTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:245 original size:19 final size:18
Alignment explanation
Indices: 216--251 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
206 AATTGACCTC
216 ATATAATATATATTATAT
1 ATATAATATATATTATAT
234 ATATATATATATATTATA
1 ATATA-ATATATATTATA
252 CCTACTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATAATATATATTATAT
Found at i:267 original size:16 final size:16
Alignment explanation
Indices: 246--280 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
236 ATATATATAT
*
246 ATTATACCTACTATTA
1 ATTATACCAACTATTA
262 ATTATACCAACTATTA
1 ATTATACCAACTATTA
278 ATT
1 ATT
281 TTATGAGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTATACCAACTATTA
Found at i:1439 original size:45 final size:42
Alignment explanation
Indices: 1375--1468 Score: 127
Period size: 45 Copynumber: 2.2 Consensus size: 42
1365 AACAACAATT
* * *
1375 AATATTAACTTTATTTTGATGAATTATCTAGAGATTGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAACTACCTAGAGA-T--GGAGTAG
1420 AATATTAGCTTTATTTTGATGAACTACCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAACTACCTAGAGATGGAGTAG
1462 AAT-TTAG
1 AATATTAG
1469 GTAATACACT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 10 0.22
44 1 0.02
45 31 0.67
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.38
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAACTACCTAGAGATGGAGTAG
Found at i:1805 original size:106 final size:106
Alignment explanation
Indices: 1672--1883 Score: 388
Period size: 106 Copynumber: 2.0 Consensus size: 106
1662 AGCTTGTATA
1672 TATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAA
1 TATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAA
* *
1737 AATGCAATGAATTATTGGATTTGAAGAAAAATACAAGCACC
66 AATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
*
1778 TATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAA
1 TATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAA
*
1843 AGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 AATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
1884 AAAATGACTA
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 102 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (106 bp):
TATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAA
AATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
Found at i:3168 original size:109 final size:109
Alignment explanation
Indices: 2977--3192 Score: 369
Period size: 109 Copynumber: 2.0 Consensus size: 109
2967 GAACCACTTG
2977 TTATTATTAATTGTATGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATAAA
1 TTATTATTAATTGTATGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATAAA
* *
3042 AAATGCAATGAATTATTGGATTTAAAGAAAAATACAAGCACCTA
66 AAATGCAATGAACTATTGGATTAAAAGAAAAATACAAGCACCTA
* * *
3086 TTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACA
1 TTATTATTAATTGTATGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATAAA
* *
3151 AAGTGCAATGAACTATTGGATTAAAATAAAAATACAAGCACC
66 AAATGCAATGAACTATTGGATTAAAAGAAAAATACAAGCACC
3193 AAATTGACTA
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
109 100 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (109 bp):
TTATTATTAATTGTATGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATAAA
AAATGCAATGAACTATTGGATTAAAAGAAAAATACAAGCACCTA
Found at i:5546 original size:33 final size:33
Alignment explanation
Indices: 5485--5559 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
5475 CACGTAGCCA
* * *
5485 AGCCTCGGCACCGTCACGAACCGAACGCGACTG
1 AGCCACGGCACAGTCACGAACCGAACGCGACCG
* * * *
5518 CGCCACGGCACAGTCGCGAGCCGCACGCGACCG
1 AGCCACGGCACAGTCACGAACCGAACGCGACCG
5551 AGCCACGGC
1 AGCCACGGC
5560 TCGCGATCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.21, C:0.43, G:0.31, T:0.05
Consensus pattern (33 bp):
AGCCACGGCACAGTCACGAACCGAACGCGACCG
Found at i:6876 original size:3 final size:3
Alignment explanation
Indices: 6870--6898 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6860 GAATTATTAT
6870 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
6899 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:11395 original size:19 final size:19
Alignment explanation
Indices: 11371--11409 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
11361 CTCCGCATAT
*
11371 TTTAACTTATTTTGAGTCA
1 TTTAACTTATTTTGAATCA
11390 TTTAACTTATTTTGAATCA
1 TTTAACTTATTTTGAATCA
11409 T
1 T
11410 GGGAGTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (19 bp):
TTTAACTTATTTTGAATCA
Found at i:17919 original size:2 final size:2
Alignment explanation
Indices: 17912--17949 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
17902 TTTCAAATGC
17912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17950 TGCTTTGCAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23903 original size:26 final size:26
Alignment explanation
Indices: 23853--23903 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
23843 ATTATTAAAA
23853 TATTTTATTTAGAAAAATTCAATTTT
1 TATTTTATTTAGAAAAATTCAATTTT
23879 TATTTTATTTAGAAAAATTCAATTT
1 TATTTTATTTAGAAAAATTCAATTT
23904 CTACAGTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (26 bp):
TATTTTATTTAGAAAAATTCAATTTT
Done.