Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold709
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: 9152
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Found at i:3980 original size:15 final size:15
Alignment explanation
Indices: 3954--3998 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
3944 AAAATTAGAG
*
3954 GAAAAGAAAGAAGAAT
1 GAAAA-AAAGAAAAAT
3970 GAAAAAAAGAAAAAT
1 GAAAAAAAGAAAAAT
3985 GACAAAAAAGAAAA
1 GA-AAAAAAGAAAA
3999 GGAGAGGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (15 bp):
GAAAAAAAGAAAAAT
Found at i:4885 original size:14 final size:15
Alignment explanation
Indices: 4861--4889 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4851 AAAAAATGGG
4861 TGAATAATGAAAAAA
1 TGAATAATGAAAAAA
4876 TGAA-AATGAAAAAA
1 TGAATAATGAAAAAA
4890 GTAAAAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (15 bp):
TGAATAATGAAAAAA
Found at i:6460 original size:129 final size:129
Alignment explanation
Indices: 6241--6478 Score: 309
Period size: 129 Copynumber: 1.8 Consensus size: 129
6231 GAAGACGGTA
* * *
6241 AATCTTATCTTCAAGTGTAAGGAAGCAAATTTAAGCCACAAGTCCTTTCTCCCTGAGGTTGAAGT
1 AATCTTATCTTCAAGTGTAAGGAAGCAAATTGAAGCCACAAGTCCTATCTCCCTGAAGTTGAAGT
* *
6306 GGAGCAGACTAAGTAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGGGACAGATGAAAGACGACG
66 GGAGCAGACTAAGTAAGCAGATCTTATCCCCCTGAAGTGGCAGTGGGACAGATGAAAGACGACG
* * * *
6370 AATCTTATCTTCAAGTGTAAGGAAGTAGATTGAAGCCGATAA-TCCTATCTCCCTGAAGTTGTAG
1 AATCTTATCTTCAAGTGTAAGGAAGCAAATTGAAGCC-ACAAGTCCTATCTCCCTGAAGTTGAAG
** * * * *
6434 TGGAGTGGATTAAAGTAA-TAGATCTTATCTCTCTGAAGTGGCAGT
65 TGGAGCAGACT-AAGTAAGCAGATCTTATCCCCCTGAAGTGGCAGT
6479 AGAGTGGATC
Statistics
Matches: 92, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
129 83 0.90
130 9 0.10
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (129 bp):
AATCTTATCTTCAAGTGTAAGGAAGCAAATTGAAGCCACAAGTCCTATCTCCCTGAAGTTGAAGT
GGAGCAGACTAAGTAAGCAGATCTTATCCCCCTGAAGTGGCAGTGGGACAGATGAAAGACGACG
Found at i:6654 original size:217 final size:217
Alignment explanation
Indices: 6396--6934 Score: 918
Period size: 217 Copynumber: 2.5 Consensus size: 217
6386 GTAAGGAAGT
**
6396 AGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAGTAATAGATCTTA
1 AGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTAATAGATCTTA
*
6461 TCTCTCTGAAGTGGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTCAGGTTGCAGCGGAGCA
66 TCTCTCTGAAGTGGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTAAGGTTGCAGCGGAGCA
6526 GACTGAGAAAATGAGTCTTATCCCCCTAAAGTCACAGTGGGGCAGACTGAAGAAGCAAATCTTAT
131 GACTGAGAAAATGAGTCTTATCCCCCTAAAGTCACAGTGGGGCAGACTGAAGAAGCAAATCTTAT
6591 CTCCCTAAGGTTGCAGAGGAGC
196 CTCCCTAAGGTTGCAGAGGAGC
*
6613 AGATTGAAGCCGATAATCCTATCTCCCTGAAGTTATAGTGGAGCAGATTAAAGTAATAGATCTTA
1 AGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTAATAGATCTTA
*
6678 TCTCTCTGAAGTGGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTAAGGTTGCAGTGGAGCA
66 TCTCTCTGAAGTGGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTAAGGTTGCAGCGGAGCA
* *
6743 GACTGAGAAAATGAGTCTTATCCCCCTGAAGTCATAGTGGGGCAGACTGAAGAAGCAAATCTTAT
131 GACTGAGAAAATGAGTCTTATCCCCCTAAAGTCACAGTGGGGCAGACTGAAGAAGCAAATCTTAT
*
6808 CTCCCTAAGGTTGCAGTGGAGC
196 CTCCCTAAGGTTGCAGAGGAGC
** * *
6830 AGATTGAATTCGATAATCCTATCTCCCTGAATTTGTAGCT-GAACAGATTAAAGTAATAGATCTT
1 AGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAG-TGGAGCAGATTAAAGTAATAGATCTT
* ** *
6894 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTT
65 ATCTCTCTGAAGTGGCAGTAGAGTGGATCGCATCAGGTCTT
6935 GCTGACTAAA
Statistics
Matches: 304, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
217 303 1.00
218 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (217 bp):
AGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTAATAGATCTTA
TCTCTCTGAAGTGGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTAAGGTTGCAGCGGAGCA
GACTGAGAAAATGAGTCTTATCCCCCTAAAGTCACAGTGGGGCAGACTGAAGAAGCAAATCTTAT
CTCCCTAAGGTTGCAGAGGAGC
Found at i:6921 original size:44 final size:43
Alignment explanation
Indices: 6415--6921 Score: 202
Period size: 44 Copynumber: 11.7 Consensus size: 43
6405 CCGATAATCC
* **
6415 TATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-AATAGATCT
* * * ** * * *
6459 TATCTCTCTGAAGTGGCAGTAGAGTGGA-T--CGCATCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGAAT-AGATCT
* * * *
6500 TATCTCCCTCAGGTTGCAGCGGAGCAGACTGAGAA-AAT-GAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA-AAGAATAGA-TCT
* * ** * * * * *
6544 TATCCCCCTAAAGTCACAGTGGGGCAGACTGAAGAAGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGAA-TAGATCT
* * * *
6588 TATCTCCCT-AAGGTTGCAGAGGAGCAGATTGAAGCCGATA-ATCC
1 TATCTCCCTGAA-GTTGCAGTGGAGCAGATTAAAG--AATAGATCT
**
6632 TATCTCCCTGAAGTTATAGTGGAGCAGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-AATAGATCT
* * * ** * * *
6676 TATCTCTCTGAAGTGGCAGTAGAGTGGA-T--CGCATCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGAAT-AGATCT
*
6717 TATCTCCCT-AAGGTTGCAGTGGAGCAGACTGAGAA-AAT-GAGTCT
1 TATCTCCCTGAA-GTTGCAGTGGAGCAGA-TTA-AAGAATAGA-TCT
* *** * * * * *
6761 TATCCCCCTGAAGTCATAGTGGGGCAGACTGAAGAAGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGAA-TAGATCT
* *
6805 TATCTCCCT-AAGGTTGCAGTGGAGCAGATTGAATTCG-ATA-ATCC
1 TATCTCCCTGAA-GTTGCAGTGGAGCAGATT-AA--AGAATAGATCT
* * *
6849 TATCTCCCTGAATTTGTAGCT-GAACAGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAG-TGGAGCAGATTAAAG-AATAGATCT
* *
6893 TATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAT
6922 CGCATCAAGT
Statistics
Matches: 331, Mismatches: 95, Indels: 74
0.66 0.19 0.15
Matches are distributed among these distances:
40 6 0.02
41 53 0.16
42 4 0.01
43 21 0.06
44 228 0.69
45 16 0.05
46 2 0.01
47 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGAATAGATCT
Done.