Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017634.1 Corchorus olitorius cultivar O-4 contig17667, 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: 31868
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3846 original size:19 final size:19
Alignment explanation
Indices: 3822--3858 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3812 CTTTTTTTTT
3822 AAAAAAAAGTAGTATACTA
1 AAAAAAAAGTAGTATACTA
3841 AAAAAAAAGTAGTATACT
1 AAAAAAAAGTAGTATACT
3859 TAAGATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.05, G:0.11, T:0.22
Consensus pattern (19 bp):
AAAAAAAAGTAGTATACTA
Found at i:4340 original size:15 final size:17
Alignment explanation
Indices: 4320--4353 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
4310 AATGATGGTG
4320 ATAATAAT-ATA-ATAT
1 ATAATAATAATACATAT
4335 ATAATAATAATACATAT
1 ATAATAATAATACATAT
4352 AT
1 AT
4354 GTATTTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 3 0.18
17 6 0.35
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATAATAATACATAT
Found at i:4367 original size:82 final size:80
Alignment explanation
Indices: 4217--4371 Score: 213
Period size: 82 Copynumber: 1.9 Consensus size: 80
4207 AACTACTATT
* *
4217 TTATATATATAAAATGATGGTGATTATAATAATAATATAATAATAATACATATATATACCCGAGT
1 TTATATATATAAAATGATGGTGATAATAATAATAATATAATAATAATACATATATATACCCGAAT
4282 TGTTAGCTAAAATTA
66 TGTTAGCTAAAATTA
* * ***
4297 TTATATTATGTAAAATGATGGTGATAATAAT-ATAATATATAATAATAATACATATATGTATTTG
1 TTATA-TATATAAAATGATGGTGATAATAATAAT-A-ATATAATAATAATACATATATATACCCG
4361 AATTGTTAGCT
63 AATTGTTAGCT
4372 TAGCAGGTGA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
80 7 0.11
81 24 0.37
82 34 0.52
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.40
Consensus pattern (80 bp):
TTATATATATAAAATGATGGTGATAATAATAATAATATAATAATAATACATATATATACCCGAAT
TGTTAGCTAAAATTA
Found at i:6170 original size:15 final size:13
Alignment explanation
Indices: 6145--6183 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
6135 CTCCTCCCTC
*
6145 TTTTTAATTTCCA
1 TTTTCAATTTCCA
6158 TTATTACAATTTCCA
1 TT-TT-CAATTTCCA
6173 TTTTCAATTTC
1 TTTTCAATTTC
6184 TTTTTTACTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 9 0.39
14 4 0.17
15 10 0.43
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTCAATTTCCA
Found at i:20510 original size:19 final size:19
Alignment explanation
Indices: 20483--20521 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20473 GGGATTTGTA
20483 AAATGATTAA-AAAATTAAC
1 AAATGATTAATAAAA-TAAC
*
20502 AAATTATTAATAAAATAAC
1 AAATGATTAATAAAATAAC
20521 A
1 A
20522 TTTTGTTCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (19 bp):
AAATGATTAATAAAATAAC
Found at i:20758 original size:25 final size:25
Alignment explanation
Indices: 20730--20781 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
20720 CATGGCTTTA
*
20730 AATTATTACAGTAAAAACATTTTCT
1 AATTATTACACTAAAAACATTTTCT
* *
20755 AATTATTACACTAAGAACTTTTTCT
1 AATTATTACACTAAAAACATTTTCT
20780 AA
1 AA
20782 CTTTTTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (25 bp):
AATTATTACACTAAAAACATTTTCT
Found at i:30887 original size:20 final size:20
Alignment explanation
Indices: 30862--30901 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
30852 TTAAAACAGT
30862 GTCCAAATTAAACATGTACA
1 GTCCAAATTAAACATGTACA
30882 GTCCAAATTAAACATGTACA
1 GTCCAAATTAAACATGTACA
30902 ATTTAACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (20 bp):
GTCCAAATTAAACATGTACA
Found at i:31427 original size:30 final size:30
Alignment explanation
Indices: 31391--31491 Score: 177
Period size: 30 Copynumber: 3.4 Consensus size: 30
31381 TTGAACTAGT
31391 AACAGATTTGATAAGGCTTAGGTTCAAACC
1 AACAGATTTGATAAGGCTTAGGTTCAAACC
31421 AACAGATTTGATAAGGCTTAGGTTCAAACC
1 AACAGATTTGATAAGGCTTAGGTTCAAACC
*
31451 AACAGATTTGATAAGGCTTAGGTTCAAATC
1 AACAGATTTGATAAGGCTTAGGTTCAAACC
31481 AA-AGGATTTGA
1 AACA-GATTTGA
31492 ACAATTCAAT
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
29 1 0.01
30 68 0.99
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (30 bp):
AACAGATTTGATAAGGCTTAGGTTCAAACC
Done.