Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3743
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: 18966
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Found at i:4720 original size:20 final size:20
Alignment explanation
Indices: 4687--4761 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
4677 ATACGTGGGA
4687 TATGATAT--ACATGAT-TG
1 TATGATATGCACATGATATG
4704 ATATGATATGCACATGATATG
1 -TATGATATGCACATGATATG
*
4725 TATGATATACACATGATATG
1 TATGATATGCACATGATATG
*
4745 TATGAAATGCACATGAT
1 TATGATATGCACATGAT
4762 GTAATCATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
18 8 0.16
20 41 0.80
21 2 0.04
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:4871 original size:26 final size:26
Alignment explanation
Indices: 4811--4920 Score: 165
Period size: 26 Copynumber: 4.4 Consensus size: 26
4801 GAGGAAGTGC
4811 AAAAGGGC-TATGCCCCAGTTTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
4835 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* *
4861 AAAAGGGCTTATGCACAAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
4887 AAAAGGGCTT-TGCCCCAGTTTA-TC
1 AAAAGGGCTTATGCCCCAGTTTATTG
4911 AAAAGGGCTT
1 AAAAGGGCTT
4921 TGCTATGCTG
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
24 19 0.24
25 26 0.33
26 34 0.43
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:4901 original size:51 final size:50
Alignment explanation
Indices: 4810--4920 Score: 163
Period size: 51 Copynumber: 2.2 Consensus size: 50
4800 GGAGGAAGTG
* *
4810 CAAAAGGGC-TATGCCCCAGTTTATTAAAAGGGCTTATGCCCCAGTTTATT
1 CAAAAGGGCTTATGCACAAGTTTATTAAAAGGGCTTATGCCCCAGTTTA-T
*
4860 GAAAAGGGCTTATGCACAAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTAT
1 CAAAAGGGCTTATGCACAAGTTTATT-AAAAGGGCTTATGCCCCAGTTTAT
4910 CAAAAGGGCTT
1 CAAAAGGGCTT
4921 TGCTATGCTG
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
50 19 0.35
51 26 0.47
52 10 0.18
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (50 bp):
CAAAAGGGCTTATGCACAAGTTTATTAAAAGGGCTTATGCCCCAGTTTAT
Found at i:5518 original size:18 final size:18
Alignment explanation
Indices: 5495--5530 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5485 GACTTAGGAT
*
5495 TTGTTTTCAAAACGACAC
1 TTGTTTTCAAAACAACAC
*
5513 TTGTTTTCGAAACAACAC
1 TTGTTTTCAAAACAACAC
5531 AACCTTACGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (18 bp):
TTGTTTTCAAAACAACAC
Found at i:7344 original size:12 final size:12
Alignment explanation
Indices: 7327--7351 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7317 AATATGTTAT
7327 TATAATAAAACA
1 TATAATAAAACA
7339 TATAATAAAACA
1 TATAATAAAACA
7351 T
1 T
7352 CATGCATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (12 bp):
TATAATAAAACA
Found at i:9202 original size:28 final size:27
Alignment explanation
Indices: 9133--9203 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
9123 TACATATATT
*
9133 TTTGTGGCAGTGCCACCAGAACAGATA
1 TTTGTGGCAGGGCCACCAGAACAGATA
*
9160 TATGTGGCAGGGCCACCAGAACAGATAA
1 TTTGTGGCAGGGCCACCAGAACAGAT-A
9188 TTTGTGGCAGGGCCAC
1 TTTGTGGCAGGGCCAC
9204 TAGGACGCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.60
28 16 0.40
ACGTcount: A:0.28, C:0.23, G:0.30, T:0.20
Consensus pattern (27 bp):
TTTGTGGCAGGGCCACCAGAACAGATA
Found at i:9357 original size:27 final size:27
Alignment explanation
Indices: 9312--9399 Score: 142
Period size: 27 Copynumber: 3.2 Consensus size: 27
9302 AAATTAACCC
*
9312 TAGGGTATAGA-GGTCATTTTGCATACA
1 TAGGGTATA-ATGGTAATTTTGCATACA
9339 TAGGGTATAATGGTAATTTTGCATACA
1 TAGGGTATAATGGTAATTTTGCATACA
9366 TAGGGGTATAATGGTAATTTTGCATACA
1 TA-GGGTATAATGGTAATTTTGCATACA
9394 TAGGGT
1 TAGGGT
9400 TATTCTAGTA
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
26 1 0.02
27 30 0.52
28 27 0.47
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (27 bp):
TAGGGTATAATGGTAATTTTGCATACA
Found at i:9381 original size:28 final size:28
Alignment explanation
Indices: 9314--9398 Score: 138
Period size: 28 Copynumber: 3.1 Consensus size: 28
9304 ATTAACCCTA
*
9314 GGGTATAGA-GGTCATTTTGCATACATA-
1 GGGTATA-ATGGTAATTTTGCATACATAG
9341 GGGTATAATGGTAATTTTGCATACATAG
1 GGGTATAATGGTAATTTTGCATACATAG
9369 GGGTATAATGGTAATTTTGCATACATAG
1 GGGTATAATGGTAATTTTGCATACATAG
9397 GG
1 GG
9399 TTATTCTAGT
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
26 1 0.02
27 24 0.44
28 30 0.55
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.34
Consensus pattern (28 bp):
GGGTATAATGGTAATTTTGCATACATAG
Found at i:9673 original size:16 final size:15
Alignment explanation
Indices: 9652--9681 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
9642 AAAATACCGG
9652 CTTTTCGGCATTTTGA
1 CTTTTCGGC-TTTTGA
9668 CTTTTCGGCTTTTG
1 CTTTTCGGCTTTTG
9682 CCGATCTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.07, C:0.20, G:0.20, T:0.53
Consensus pattern (15 bp):
CTTTTCGGCTTTTGA
Found at i:17054 original size:26 final size:27
Alignment explanation
Indices: 17003--17091 Score: 119
Period size: 26 Copynumber: 3.2 Consensus size: 27
16993 GTGACAGAGT
17003 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
*
17032 CACCAGAACAGATA-TTGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
17058 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
17086 CACCAG
1 CACCAG
17092 GACGCTTCCT
Statistics
Matches: 55, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
26 24 0.44
27 1 0.02
28 23 0.42
29 7 0.13
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:17246 original size:28 final size:27
Alignment explanation
Indices: 17199--17258 Score: 102
Period size: 28 Copynumber: 2.2 Consensus size: 27
17189 ATTAACCCTA
*
17199 GGGTATAAGGTCATTTTGCATACATAG
1 GGGTATAAGGTAATTTTGCATACATAG
17226 GGGTATAATGGTAATTTTGCATACATAG
1 GGGTATAA-GGTAATTTTGCATACATAG
17254 GGGTA
1 GGGTA
17259 ATTGCATACA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 8 0.26
28 23 0.74
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.33
Consensus pattern (27 bp):
GGGTATAAGGTAATTTTGCATACATAG
Done.