Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold668
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: 46421
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.28
Found at i:3258 original size:58 final size:59
Alignment explanation
Indices: 3159--3276 Score: 184
Period size: 58 Copynumber: 2.0 Consensus size: 59
3149 TTCCCCGGTT
* *
3159 ACAGGATCTGTTTATGCCCCCGCCAATACAGAAACAAGTAATTTCCAATTCTAAGACATA
1 ACAGGATCTGTTTATG-CCCCGCAAATACAGAAACAAGTAATTTCCAATTCCAAGACATA
* *
3219 ACAGGATCTGTTTATG-CCTGCAAATACAGAAACAAGTAATTTCTAATTCCAAGACATA
1 ACAGGATCTGTTTATGCCCCGCAAATACAGAAACAAGTAATTTCCAATTCCAAGACATA
3277 GCATGGCATT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 38 0.70
60 16 0.30
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (59 bp):
ACAGGATCTGTTTATGCCCCGCAAATACAGAAACAAGTAATTTCCAATTCCAAGACATA
Found at i:8480 original size:16 final size:17
Alignment explanation
Indices: 8461--8502 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
8451 GATATAGCTT
*
8461 TAAAAAAATTA-AAAAA
1 TAAATAAATTATAAAAA
*
8477 TAAATATA-TATAAAAA
1 TAAATAAATTATAAAAA
8493 TAAATAAATT
1 TAAATAAATT
8503 TTTTTAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 2 0.10
16 18 0.86
17 1 0.05
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAATAAATTATAAAAA
Found at i:15240 original size:15 final size:14
Alignment explanation
Indices: 15207--15257 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
15197 CCAGTGAAAA
*
15207 AATATTTTAATTTT
1 AATATTTTAAATTT
*
15221 TATATTATTAAATTT
1 AATATT-TTAAATTT
15236 AATATTTTAATATTT
1 AATATTTTAA-ATTT
15251 -ATATTTT
1 AATATTTT
15258 TAAAATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 16 0.50
15 16 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATATTTTAAATTT
Found at i:15246 original size:8 final size:8
Alignment explanation
Indices: 15207--15250 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
15197 CCAGTGAAAA
15207 AATATTTT
1 AATATTTT
15215 AAT-TTTT
1 AATATTTT
15222 -ATATTATT
1 AATATT-TT
15230 AA-A-TTT
1 AATATTTT
15236 AATATTTT
1 AATATTTT
15244 AATATTT
1 AATATTT
15251 ATATTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
6 6 0.19
7 8 0.26
8 16 0.52
9 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
AATATTTT
Found at i:15258 original size:15 final size:15
Alignment explanation
Indices: 15211--15260 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
15201 TGAAAAAATA
*
15211 TTTTAATTTTTATAT
1 TTTTAATATTTATAT
*
15226 TATTAA-ATTTA-AT
1 TTTTAATATTTATAT
15239 ATTTTAATATTTATAT
1 -TTTTAATATTTATAT
15255 TTTTAA
1 TTTTAA
15261 AATATAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 2 0.07
14 9 0.31
15 16 0.55
16 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTAATATTTATAT
Found at i:16761 original size:14 final size:14
Alignment explanation
Indices: 16742--16792 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
16732 ACAATTTTAA
16742 AAAATATAAAAATT
1 AAAATATAAAAATT
* *
16756 AAAATATTAAATTT
1 AAAATATAAAAATT
16770 AATAATATAAAAATT
1 AA-AATATAAAAATT
16785 AAAATATA
1 AAAATATA
16793 TTTTACTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:27902 original size:2 final size:2
Alignment explanation
Indices: 27895--27928 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
27885 GGGAGGAGGG
27895 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
27929 AGCTAAACCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35419 original size:2 final size:2
Alignment explanation
Indices: 35414--35459 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
35404 TCTCTCTCTC
* *
35414 TA TA TA TA TA TA TA TA TA CA TA TA TA AA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35456 TA TA
1 TA TA
35460 CACACACATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:38690 original size:84 final size:84
Alignment explanation
Indices: 38549--38716 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
38539 AAGTATTATT
38549 TCACAATAATAAATATTAAAAAGAAAAAGGAGAATGTAATGAGAGTGGGTGACGTGAAATTAGCA
1 TCACAATAATAAATATTAAAAAGAAAAAGGAGAATGTAATGAGAGTGGGTGACGTGAAATTAGCA
38614 TGTTTACCGAGCACCTGAG
66 TGTTTACCGAGCACCTGAG
38633 TCACAATAATAAATATTAAAAAGAAAAAGGAGAATGTAATGAGAGTGGGTGACGTGAAATTAGCA
1 TCACAATAATAAATATTAAAAAGAAAAAGGAGAATGTAATGAGAGTGGGTGACGTGAAATTAGCA
38698 TGTTTACCGAGCACCTGAG
66 TGTTTACCGAGCACCTGAG
38717 ACTATGTATT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.23
Consensus pattern (84 bp):
TCACAATAATAAATATTAAAAAGAAAAAGGAGAATGTAATGAGAGTGGGTGACGTGAAATTAGCA
TGTTTACCGAGCACCTGAG
Found at i:43498 original size:17 final size:17
Alignment explanation
Indices: 43464--43501 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
43454 TAAATTCGAT
43464 TATAACATATAAAAAAA
1 TATAACATATAAAAAAA
*
43481 TATAA-ATATAATATAAA
1 TATAACATATAA-AAAAA
43498 TATA
1 TATA
43502 CTAATCACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
TATAACATATAAAAAAA
Found at i:43760 original size:7 final size:7
Alignment explanation
Indices: 43716--43773 Score: 53
Period size: 8 Copynumber: 7.7 Consensus size: 7
43706 AATATCTTAA
43716 AAAATCAT
1 AAAAT-AT
*
43724 AAAAAAT
1 AAAATAT
43731 AGAAATAT
1 A-AAATAT
*
43739 CAAAATTT
1 -AAAATAT
43747 CAAAATAT
1 -AAAATAT
43755 AAAATAT
1 AAAATAT
*
43762 AAGATAT
1 AAAATAT
43769 AAAAT
1 AAAAT
43774 TATTTTTCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
7 20 0.48
8 21 0.50
9 1 0.02
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (7 bp):
AAAATAT
Found at i:44133 original size:33 final size:30
Alignment explanation
Indices: 44090--44175 Score: 100
Period size: 33 Copynumber: 2.7 Consensus size: 30
44080 TAAATATATT
* *
44090 TTTATGTAATATAAATTTTTTATTACACAAATA
1 TTTATTTAATATAAAATTTTTA-T--ACAAATA
**
44123 TTTATTTAATATAAAATTTTTATATTAATA
1 TTTATTTAATATAAAATTTTTATACAAATA
44153 TTTATTTAATATTAAAATTTTTA
1 TTTATTTAATA-TAAAATTTTTA
44176 ATTAAATCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
30 16 0.33
31 11 0.23
32 1 0.02
33 20 0.42
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (30 bp):
TTTATTTAATATAAAATTTTTATACAAATA
Found at i:44139 original size:18 final size:19
Alignment explanation
Indices: 44118--44153 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
44108 TTTATTACAC
44118 AAATATTTAT-TTAATATA
1 AAATATTTATATTAATATA
*
44136 AAATTTTTATATTAATAT
1 AAATATTTATATTAATAT
44154 TTATTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATATTTATATTAATATA
Found at i:44155 original size:30 final size:30
Alignment explanation
Indices: 44119--44180 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
44109 TTATTACACA
44119 AATATTTATTTAATA-TAAAATTTTTATATT
1 AATATTTATTTAATATTAAAATTTTTA-ATT
44149 AATATTTATTTAATATTAAAATTTTTAATT
1 AATATTTATTTAATATTAAAATTTTTAATT
44179 AA
1 AA
44181 ATCATTCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
AATATTTATTTAATATTAAAATTTTTAATT
Found at i:44166 original size:17 final size:17
Alignment explanation
Indices: 44119--44172 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
44109 TTATTACACA
44119 AATATTTATTTAATA-T
1 AATATTTATTTAATATT
*
44135 AA-AATT-TTT-ATATT
1 AATATTTATTTAATATT
44149 AATATTTATTTAATATT
1 AATATTTATTTAATATT
*
44166 AAAATTT
1 AATATTT
44173 TTAATTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 3 0.10
14 6 0.19
15 6 0.19
16 5 0.16
17 11 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATATTTATTTAATATT
Found at i:44179 original size:13 final size:14
Alignment explanation
Indices: 44134--44181 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 14
44124 TTATTTAATA
44134 TAAAATTTTTATAT
1 TAAAATTTTTATAT
*
44148 TAATATTTATTTAATAT
1 TAA-AATT-TTT-ATAT
44165 TAAAATTTTTA-AT
1 TAAAATTTTTATAT
44178 TAAA
1 TAAA
44182 TCATTCAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 6 0.21
14 4 0.14
15 6 0.21
16 6 0.21
17 7 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TAAAATTTTTATAT
Found at i:45880 original size:1 final size:1
Alignment explanation
Indices: 45874--45908 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
45864 ATGAGTGAAA
45874 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
45909 AAAAAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:46238 original size:28 final size:28
Alignment explanation
Indices: 46167--46244 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
46157 GGGCACATTG
* *
46167 ATTAAATTACTATTAATTTTTAAATAAATT
1 ATTAAAATATTATTAA--TTTAAATAAATT
*
46197 -TTAAAATATGATTAATTTAAATAAATT
1 ATTAAAATATTATTAATTTAAATAAATT
*
46224 ATTAAAATATTATTATTTTAA
1 ATTAAAATATTATTAATTTAA
46245 TTAACGAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 12 0.29
28 18 0.43
29 12 0.29
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (28 bp):
ATTAAAATATTATTAATTTAAATAAATT
Found at i:46310 original size:32 final size:31
Alignment explanation
Indices: 46243--46311 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
46233 TTATTATTTT
* * * *
46243 AATTAACGAAAAATCACTAAATTGATTAATG
1 AATTCACGAAAAATCACTAAAATAATTAATA
*
46274 AATTCACGTAAAAATCACTAAAATAATTAGTA
1 AATTCACG-AAAAATCACTAAAATAATTAATA
46306 AATTCA
1 AATTCA
46312 TATAAAACTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 7 0.22
32 25 0.78
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (31 bp):
AATTCACGAAAAATCACTAAAATAATTAATA
Found at i:46318 original size:32 final size:32
Alignment explanation
Indices: 46251--46318 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
46241 TTAATTAACG
* * * *
46251 AAAAATCACTAAATTGATTAATGAATTCACGT
1 AAAAATCACTAAAATAATTAATAAATTCACAT
* *
46283 AAAAATCACTAAAATAATTAGTAAATTCATAT
1 AAAAATCACTAAAATAATTAATAAATTCACAT
46315 AAAA
1 AAAA
46319 CTTCTCTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.29
Consensus pattern (32 bp):
AAAAATCACTAAAATAATTAATAAATTCACAT
Done.