Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022784.1 Corchorus olitorius cultivar O-4 contig22817, 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: 62641
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--119 Score: 231
Period size: 3 Copynumber: 40.0 Consensus size: 3
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
49 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
97 TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
120 CTAAAAATAC
Statistics
Matches: 115, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 113 0.98
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4928 original size:14 final size:14
Alignment explanation
Indices: 4895--4929 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
4885 AAACAGAGTG
*
4895 AGAAAAAAAAGAAA
1 AGAAAGAAAAGAAA
*
4909 AGAAAGAAAAGAAT
1 AGAAAGAAAAGAAA
4923 AGAAAGA
1 AGAAAGA
4930 GCAGAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (14 bp):
AGAAAGAAAAGAAA
Found at i:6958 original size:3 final size:3
Alignment explanation
Indices: 6950--6988 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
6940 AATGCTTTTA
* *
6950 CAG CAG CAG CAG CAG CAA CAA CAG CAG CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
6989 TTTCTACAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.38, C:0.33, G:0.28, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:34330 original size:22 final size:22
Alignment explanation
Indices: 34304--34347 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
34294 CTGCCGAAGC
34304 AACTTTTTCCCCGTGTAATAGA
1 AACTTTTTCCCCGTGTAATAGA
34326 AACTTTTTCCCCGTGTAATAGA
1 AACTTTTTCCCCGTGTAATAGA
34348 TATCTAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (22 bp):
AACTTTTTCCCCGTGTAATAGA
Found at i:38227 original size:3 final size:3
Alignment explanation
Indices: 38214--38255 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
38204 TAATGGGATG
* *
38214 ATC AAC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AAC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
38256 TTGTATGGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.29
Consensus pattern (3 bp):
ATC
Found at i:42557 original size:18 final size:18
Alignment explanation
Indices: 42509--42557 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
42499 TATTCAATAT
* *
42509 TATTATGTATAAAT-TTA
1 TATTATTTATATATATTA
42526 -ATTATTTA-ATTATATTA
1 TATTATTTATA-TATATTA
42543 TATTATTTATATATA
1 TATTATTTATATATA
42558 ATACGGGCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
15 1 0.04
16 9 0.35
17 3 0.12
18 12 0.46
19 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TATTATTTATATATATTA
Found at i:47202 original size:19 final size:20
Alignment explanation
Indices: 47175--47212 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
47165 CTCTCTCTTT
* *
47175 TTTTTATTC-CTTTTTTGTA
1 TTTTAATTCTCTTCTTTGTA
47194 TTTTAATTCTCTTCTTTGT
1 TTTTAATTCTCTTCTTTGT
47213 TTCTTTAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.11, C:0.13, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTTAATTCTCTTCTTTGTA
Found at i:47504 original size:2 final size:2
Alignment explanation
Indices: 47497--47525 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
47487 CAATCCCCTA
47497 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47526 AGTTTATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48958 original size:11 final size:11
Alignment explanation
Indices: 48915--48952 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
48905 CTCTTATATA
*
48915 AAATAAATTAT
1 AAATTAATTAT
48926 CAAA-TAATTAT
1 -AAATTAATTAT
48937 AAATTAATTAT
1 AAATTAATTAT
48948 AAATT
1 AAATT
48953 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:49322 original size:59 final size:59
Alignment explanation
Indices: 49230--49347 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
49220 GCTTTTGTTT
49230 TGTTATCATTTCACAACAAAATTTCATTTCTTAACTGAATTTTCTTAAAATAAATTATA
1 TGTTATCATTTCACAACAAAATTTCATTTCTTAACTGAATTTTCTTAAAATAAATTATA
*
49289 TGTTATCATTTCACAACAAAATTTCATTTCTTAACTGAATTTTCTTAAAATAATTTATA
1 TGTTATCATTTCACAACAAAATTTCATTTCTTAACTGAATTTTCTTAAAATAAATTATA
49348 AAACAAAACA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.45
Consensus pattern (59 bp):
TGTTATCATTTCACAACAAAATTTCATTTCTTAACTGAATTTTCTTAAAATAAATTATA
Found at i:50205 original size:15 final size:15
Alignment explanation
Indices: 50185--50215 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
50175 GAGAAGAACA
50185 AAATATTGAGCATAC
1 AAATATTGAGCATAC
50200 AAATATTGAGCATAC
1 AAATATTGAGCATAC
50215 A
1 A
50216 TCAGTTTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (15 bp):
AAATATTGAGCATAC
Found at i:50226 original size:146 final size:146
Alignment explanation
Indices: 49962--50241 Score: 479
Period size: 146 Copynumber: 1.9 Consensus size: 146
49952 GAGTTTTACT
49962 TTGATTATAAATCAATATTCTAAATATTATTTATAAAAACCAATAAATTTTGGACAAATGTCAAC
1 TTGATTATAAATCAATATTCTAAATATTATTTATAAAAACCAATAAATTTTGGACAAATGTCAAC
* * * *
50027 AGGAGAAGAACCAAATATTGAGCGTATAAATATTGAGCATACAACAGTCTGGGGATAACTTTAAT
66 AAGAGAAGAACAAAATATTGAGCATACAAATATTGAGCATACAACAGTCTGGGGATAACTTTAAT
50092 AGTAAAATAAAATATA
131 AGTAAAATAAAATATA
* *
50108 TTGATTATAAATTAATATTCTAAATATTATTTATAAAAACCAATAAATTTTGGACAAATGTCAGC
1 TTGATTATAAATCAATATTCTAAATATTATTTATAAAAACCAATAAATTTTGGACAAATGTCAAC
* * *
50173 AAGAGAAGAACAAAATATTGAGCATACAAATATTGAGCATACATCAGTTTGGGGATAACTTTGAT
66 AAGAGAAGAACAAAATATTGAGCATACAAATATTGAGCATACAACAGTCTGGGGATAACTTTAAT
50238 AGTA
131 AGTA
50242 TGGTATAGAT
Statistics
Matches: 125, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
146 125 1.00
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (146 bp):
TTGATTATAAATCAATATTCTAAATATTATTTATAAAAACCAATAAATTTTGGACAAATGTCAAC
AAGAGAAGAACAAAATATTGAGCATACAAATATTGAGCATACAACAGTCTGGGGATAACTTTAAT
AGTAAAATAAAATATA
Found at i:51206 original size:12 final size:13
Alignment explanation
Indices: 51174--51208 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
51164 TCTAAAAAAA
51174 AACAAAAATAAGT
1 AACAAAAATAAGT
51187 AACAAAAATAAGT
1 AACAAAAATAAGT
51200 AACAAAAAT
1 AACAAAAAT
51209 TGTGACATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.71, C:0.09, G:0.06, T:0.14
Consensus pattern (13 bp):
AACAAAAATAAGT
Found at i:54500 original size:2 final size:2
Alignment explanation
Indices: 54493--54526 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
54483 TTTTAATTTG
*
54493 AT AT AT AT TT 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
54527 TTTTGACTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:59675 original size:15 final size:15
Alignment explanation
Indices: 59655--59683 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
59645 TTTGCCAGTG
59655 TCTCCTTGTTCAAGA
1 TCTCCTTGTTCAAGA
59670 TCTCCTTGTTCAAG
1 TCTCCTTGTTCAAG
59684 CCCATTAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.28, G:0.14, T:0.41
Consensus pattern (15 bp):
TCTCCTTGTTCAAGA
Done.