Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold379
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: 56864
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Found at i:4352 original size:18 final size:20
Alignment explanation
Indices: 4325--4366 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
4315 TTCATTGCTC
*
4325 TTTTTTCATG-ATTTTTA-A
1 TTTTTCCATGCATTTTTATA
*
4343 TTTTTCCATGCCTTTTTATA
1 TTTTTCCATGCATTTTTATA
4363 TTTT
1 TTTT
4367 AATTTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 6 0.30
20 5 0.25
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTTTCCATGCATTTTTATA
Found at i:4821 original size:12 final size:12
Alignment explanation
Indices: 4804--4835 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
4794 TTTTCTTTAA
*
4804 GGGGGGGGTGGG
1 GGGGGGGGAGGG
4816 GGGGGGGGAGGG
1 GGGGGGGGAGGG
4828 GGGGGGGG
1 GGGGGGGG
4836 GAACCCCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.03, C:0.00, G:0.94, T:0.03
Consensus pattern (12 bp):
GGGGGGGGAGGG
Found at i:4822 original size:13 final size:13
Alignment explanation
Indices: 4804--4837 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
4794 TTTTCTTTAA
*
4804 GGGGGGGG-TGGG
1 GGGGGGGGAGGGG
4816 GGGGGGGGAGGGG
1 GGGGGGGGAGGGG
4829 GGGGGGGGA
1 GGGGGGGGA
4838 ACCCCCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.06, C:0.00, G:0.91, T:0.03
Consensus pattern (13 bp):
GGGGGGGGAGGGG
Found at i:16162 original size:16 final size:16
Alignment explanation
Indices: 16137--16220 Score: 75
Period size: 16 Copynumber: 5.2 Consensus size: 16
16127 TGGTTCACTA
*
16137 TAATGGAATAGGGTTG
1 TAATTGAATAGGGTTG
*
16153 TAATTAAATAGAGG-TG
1 TAATTGAATAG-GGTTG
* *
16169 TAATGGAATAGAGTTG
1 TAATTGAATAGGGTTG
16185 TAATTGAATAGAGG-TG
1 TAATTGAATAG-GGTTG
*
16201 TAA-TGTAATAGAGTTG
1 TAATTG-AATAGGGTTG
16217 TAAT
1 TAAT
16221 CAGTAATTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
15 4 0.07
16 47 0.87
17 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.33
Consensus pattern (16 bp):
TAATTGAATAGGGTTG
Found at i:16178 original size:32 final size:32
Alignment explanation
Indices: 16137--16220 Score: 141
Period size: 32 Copynumber: 2.6 Consensus size: 32
16127 TGGTTCACTA
*
16137 TAATGGAATAGGGTTGTAATTAAATAGAGGTG
1 TAATGGAATAGAGTTGTAATTAAATAGAGGTG
*
16169 TAATGGAATAGAGTTGTAATTGAATAGAGGTG
1 TAATGGAATAGAGTTGTAATTAAATAGAGGTG
*
16201 TAATGTAATAGAGTTGTAAT
1 TAATGGAATAGAGTTGTAAT
16221 CAGTAATTCT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.33
Consensus pattern (32 bp):
TAATGGAATAGAGTTGTAATTAAATAGAGGTG
Found at i:16291 original size:44 final size:46
Alignment explanation
Indices: 16202--16294 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 46
16192 ATAGAGGTGT
* * * *
16202 AATGTAATAGAGTTGTAATCAGTAATTCTATTGTTTGGTTTAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTCTATTGTTTCGTTGAATGG
16248 AATGGAATAGAGCTGTAAT-AGT-ATTCT-TGTGTTTCGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTCTAT-TGTTTCGTTGAATGG
16292 AAT
1 AAT
16295 AGATGTTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.50
45 3 0.07
46 17 0.40
ACGTcount: A:0.30, C:0.05, G:0.24, T:0.41
Consensus pattern (46 bp):
AATGGAATAGAGCTGTAATCAGTAATTCTATTGTTTCGTTGAATGG
Found at i:16475 original size:61 final size:56
Alignment explanation
Indices: 16384--16525 Score: 158
Period size: 61 Copynumber: 2.4 Consensus size: 56
16374 TTATTGTTAT
* * * * *
16384 TTTATTAAATTTTAATAAAATTATTGTTAAATATATTTTAATAAAAATAAAAATAAATAA
1 TTTAATAAATTTTAATATAATTATTATTAAATACAATTTAAT-AAAAT---AATAAATAA
* *
16444 TTTAATCAAATTTTAATATAATTCTTATTAAATACAATTTAATAAAATAATATATAA
1 TTTAAT-AAATTTTAATATAATTATTATTAAATACAATTTAATAAAATAATAAATAA
16501 TTTAATAACATTCTTAATATAATTA
1 TTTAATAA-ATT-TTAATATAATTA
16526 CTATATGAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
56 2 0.03
57 17 0.24
58 11 0.15
60 10 0.14
61 31 0.44
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (56 bp):
TTTAATAAATTTTAATATAATTATTATTAAATACAATTTAATAAAATAATAAATAA
Found at i:19317 original size:43 final size:42
Alignment explanation
Indices: 19172--19328 Score: 167
Period size: 43 Copynumber: 3.7 Consensus size: 42
19162 TGTGTTCTCG
* * * *
19172 TGTAAGACCATGTCTAGGACTTTGGCATCG-ACTTATGATTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGTA-TT-TGA-TTACA
* * *
19216 TGCAAGACCACGTCTGGGACGTTGGCATCGTATTTGATTTCG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGTATTTGATTACA
19258 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCG-TATTTGATTACA
*
19301 TGTAAGACCACATCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
19329 TGTACATGTT
Statistics
Matches: 98, Mismatches: 9, Indels: 13
0.82 0.08 0.11
Matches are distributed among these distances:
41 1 0.01
42 30 0.31
43 37 0.38
44 29 0.30
45 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGTATTTGATTACA
Found at i:24784 original size:48 final size:49
Alignment explanation
Indices: 24730--24851 Score: 142
Period size: 49 Copynumber: 2.5 Consensus size: 49
24720 TCAGTGCAAT
**
24730 ACCATGTCTACGACATGGCATCGGCAC-GTAT-AGAGGTAT-TAGTGTAAG
1 ACCATGTCTGGGACATGGCATCGGCACGGTATGAGA-G-ATCTAGTGTAAG
* * * *
24778 ACCATGTTTGGGACATAGCATTGGCACGGTATGTGAGATCTAGTGTAAG
1 ACCATGTCTGGGACATGGCATCGGCACGGTATGAGAGATCTAGTGTAAG
*
24827 ACCATGTCTGGGACATGTCATCGGC
1 ACCATGTCTGGGACATGGCATCGGC
24852 TTAATGGATG
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
48 24 0.39
49 35 0.57
50 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (49 bp):
ACCATGTCTGGGACATGGCATCGGCACGGTATGAGAGATCTAGTGTAAG
Found at i:25891 original size:28 final size:28
Alignment explanation
Indices: 25851--25914 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
25841 ACACGGGCTA
25851 GGACACAGACGTGTCATGGCCGTATGAG
1 GGACACAGACGTGTCATGGCCGTATGAG
* * *
25879 GGACACGGGCGTGTCATGGCCGTGTGAG
1 GGACACAGACGTGTCATGGCCGTATGAG
*
25907 GTACACAG
1 GGACACAG
25915 GCATGTGTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.22, C:0.22, G:0.39, T:0.17
Consensus pattern (28 bp):
GGACACAGACGTGTCATGGCCGTATGAG
Found at i:32295 original size:48 final size:48
Alignment explanation
Indices: 32191--32361 Score: 185
Period size: 48 Copynumber: 3.6 Consensus size: 48
32181 ATTGTGCGCT
*
32191 AGTGTAAGA-CATGTCTGGGACAT-GCATCGG--C-TATGAGATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTAT-AGAGGTGTC
* *
32235 AGTGTAATACCATGTTTGGGACATGGCATCGGCACGTATAGAGGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGTC
* * * *
32283 AGTGTAAGACCATGTTTGGGACATGGCATCGGCATAG-ATATGTGAGAG-C
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CGTATA-GAG-GTGTC
32332 TAGTGTAAGACCATGTCTGGGACATGGCAT
1 -AGTGTAAGACCATGTCTGGGACATGGCAT
32362 TGACTTAATG
Statistics
Matches: 110, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
44 8 0.07
45 13 0.12
46 7 0.06
48 45 0.41
49 7 0.06
50 30 0.27
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGTC
Found at i:33280 original size:30 final size:30
Alignment explanation
Indices: 33240--33338 Score: 153
Period size: 30 Copynumber: 3.3 Consensus size: 30
33230 CACGGGCAGA
*
33240 GACACGGCCGTGTGTCTCAGCCATGTGGAG
1 GACACAGCCGTGTGTCTCAGCCATGTGGAG
*
33270 GACACAGCCGTGTGTCTCAGCCATGTAGAG
1 GACACAGCCGTGTGTCTCAGCCATGTGGAG
* * *
33300 GACACGGCCGTGTGTCTTAGCCGTGTGGAG
1 GACACAGCCGTGTGTCTCAGCCATGTGGAG
33330 GACACAGCC
1 GACACAGCC
33339 TCTGGCCACA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.19, C:0.27, G:0.34, T:0.19
Consensus pattern (30 bp):
GACACAGCCGTGTGTCTCAGCCATGTGGAG
Found at i:33355 original size:60 final size:60
Alignment explanation
Indices: 33240--33355 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
33230 CACGGGCAGA
* * *
33240 GACACGGCCGTGTGTCTCAGCCATGTGGAGGACACAGCCGTGTGTCTCAGCCATGTAGAG
1 GACACGGCCGTGTGTCTCAGCCATGTGGAGGACACAGCCCTGTGCCACAGCCATGTAGAG
* * *
33300 GACACGGCCGTGTGTCTTAGCCGTGTGGAGGACACAGCCTCTG-GCCACAGGCATGT
1 GACACGGCCGTGTGTCTCAGCCATGTGGAGGACACAGCC-CTGTGCCACAGCCATGT
33356 TCCTTGGCCG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 47 0.96
61 2 0.04
ACGTcount: A:0.19, C:0.28, G:0.34, T:0.20
Consensus pattern (60 bp):
GACACGGCCGTGTGTCTCAGCCATGTGGAGGACACAGCCCTGTGCCACAGCCATGTAGAG
Found at i:37360 original size:43 final size:43
Alignment explanation
Indices: 37236--37387 Score: 157
Period size: 43 Copynumber: 3.5 Consensus size: 43
37226 ATATGTGTTC
* * *
37236 TCGTGTAAGACCATGTTTGGGAC-GTGGGCATCGACT-TATGATT
1 TCGTGTAAGACCACGTCTGGGACAGT-GGCATCGA-TATTTGATT
* *
37279 TACGTGTAAGACCACGTCTGGGACATTAGCATCG-TATTTGATT
1 T-CGTGTAAGACCACGTCTGGGACAGTGGCATCGATATTTGATT
* * * *
37322 TTGTGTAAAACCATGTCTGGGACAGTGGCATTGATATTTGATT
1 TCGTGTAAGACCACGTCTGGGACAGTGGCATCGATATTTGATT
* *
37365 ACATGTAAGACCACGTCTGGGAC
1 TCGTGTAAGACCACGTCTGGGAC
37388 GTTTGCATTG
Statistics
Matches: 89, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
42 27 0.30
43 35 0.39
44 26 0.29
45 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
TCGTGTAAGACCACGTCTGGGACAGTGGCATCGATATTTGATT
Found at i:39968 original size:47 final size:47
Alignment explanation
Indices: 39905--40106 Score: 280
Period size: 47 Copynumber: 4.3 Consensus size: 47
39895 TGAATGTATA
39905 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
* *
39952 TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
* *
39999 TATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
* * * * * * * *
40046 TATATATGCGACAGGGCCGAGTGGCCAACGTGA-GGATGTGAAATTG
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
*
40092 TATAAATGTGATAAG
1 TATATATGTGATAAG
40107 TCCCGAAGGG
Statistics
Matches: 137, Mismatches: 18, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
46 22 0.16
47 115 0.84
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
Done.