Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold619
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: 17214
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.29
Warning! 378 characters in sequence are not A, C, G, or T
Found at i:12289 original size:24 final size:24
Alignment explanation
Indices: 12257--12312 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
12247 ATGTCCCGAA
*
12257 ATTACAGTGGATTGAACTTTAAAG
1 ATTACAGTGGATTGAACCTTAAAG
*
12281 ATTACAGTGGATTGAACCTTGAAG
1 ATTACAGTGGATTGAACCTTAAAG
12305 ATTACAGT
1 ATTACAGT
12313 AGGGGCAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (24 bp):
ATTACAGTGGATTGAACCTTAAAG
Found at i:12774 original size:21 final size:21
Alignment explanation
Indices: 12748--12791 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
12738 CTGACATTGC
12748 AGTGGAATAGATTAAAGCTGA
1 AGTGGAATAGATTAAAGCTGA
*
12769 AGTGGAGTAGATTAAAGCTGA
1 AGTGGAATAGATTAAAGCTGA
12790 AG
1 AG
12792 GCAGTGAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.32, T:0.23
Consensus pattern (21 bp):
AGTGGAATAGATTAAAGCTGA
Found at i:12904 original size:51 final size:51
Alignment explanation
Indices: 12769--12911 Score: 153
Period size: 51 Copynumber: 2.8 Consensus size: 51
12759 TTAAAGCTGA
* * *
12769 AGTGGAGTAGATTAAAGCTGAAGGCAGT-GAATCTTATCTCTTTGGCCCGGC
1 AGTGGAGTAGATTAAAGCTAAAGGCA-TCGAATCTTATCTCCTTGACCCGGC
** * * * ****
12820 AGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTATTTCCTTGATGTTGC
1 AGTGGAGTAGATTAAAGCTAAAGGCATCGAATCTTATCTCCTTGACCCGGC
*
12871 AGTGGAGTAGATTAAAGCTAAAGGCATCAAATCTTATCTCC
1 AGTGGAGTAGATTAAAGCTAAAGGCATCGAATCTTATCTCC
12912 CTAGCGTTAA
Statistics
Matches: 73, Mismatches: 18, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
51 73 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (51 bp):
AGTGGAGTAGATTAAAGCTAAAGGCATCGAATCTTATCTCCTTGACCCGGC
Found at i:12991 original size:87 final size:87
Alignment explanation
Indices: 12845--13006 Score: 200
Period size: 87 Copynumber: 1.9 Consensus size: 87
12835 AGCTAAAGGT
* * * * * *
12845 AGCGAATCTTATTTCCTTGATGTTGCAGTGGAGTAGATTAAAGCTAAAGGCATCAAATCTTATCT
1 AGCGAATCTTATTTCCCTGACGTTGCAGTGAACTAGATTAAAGCTAAAAGCAGCAAATCTTATCT
12910 CCCTAGCGTTAAGACTGAAAGC
66 CCCTAGCGTTAAGACTGAAAGC
* * * * *
12932 AGCGAATCTTATTTCCCTGGCGTTGCAGTAGAACT-GATTAAAGCTAAAAGTAGCGAATCTTGTT
1 AGCGAATCTTATTTCCCTGACGTTGCAGT-GAACTAGATTAAAGCTAAAAGCAGCAAATCTTATC
*
12996 TCCCTGGCGTT
65 TCCCTAGCGTT
13007 TCAATGGAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
87 59 0.95
88 3 0.05
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (87 bp):
AGCGAATCTTATTTCCCTGACGTTGCAGTGAACTAGATTAAAGCTAAAAGCAGCAAATCTTATCT
CCCTAGCGTTAAGACTGAAAGC
Found at i:13023 original size:51 final size:51
Alignment explanation
Indices: 12927--13027 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 51
12917 GTTAAGACTG
* *
12927 AAAGCAGCGAATCTTATTTCCCTGGCGTTGCAGTAGAACTGATTAAAGCTA
1 AAAGCAGCGAATCTTATTTCCCTGGCGTTGCAATAGAACTAATTAAAGCTA
* * * *
12978 AAAGTAGCGAATCTTGTTTCCCTGGCGTTTCAATGGAA-TAAATTAAAGCT
1 AAAGCAGCGAATCTTATTTCCCTGGCGTTGCAATAGAACT-AATTAAAGCT
13028 GAAGTGGAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 1 0.02
51 42 0.98
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (51 bp):
AAAGCAGCGAATCTTATTTCCCTGGCGTTGCAATAGAACTAATTAAAGCTA
Found at i:13064 original size:21 final size:20
Alignment explanation
Indices: 13018--13069 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
13008 CAATGGAATA
* *
13018 AATTAAAGCTGAAGTGGAGT
1 AATTAAAGCTGAAGTAGAGG
13038 AGATTAAAGCTGAAGTAGAGCG
1 A-ATTAAAGCTGAAGTAGAG-G
13060 AATTAAAGCT
1 AATTAAAGCT
13070 AAAGGCAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.42, C:0.08, G:0.27, T:0.23
Consensus pattern (20 bp):
AATTAAAGCTGAAGTAGAGG
Found at i:13280 original size:281 final size:282
Alignment explanation
Indices: 12748--13326 Score: 892
Period size: 281 Copynumber: 2.1 Consensus size: 282
12738 CTGACATTGC
* * * * *
12748 AGTGGAATAGATTAAAGCTGAAGTGGAGTAGATTAAAGCTGAAGGCAGTGAATCTTATCTCTTTG
1 AGTGGAGTAGATTAAAGCTGAAGTAGAGGAGATTAAAGCTAAAGGCAGTGAATATTATCTCTTTG
* * * *
12813 GCCCGGCAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTATTTCCTTGATGTTGCAGTGGAG
66 GACCGACAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTATTTCCCTGACGTTGCAGTGGAG
* *
12878 TAGATTAAAGCTAAAGGCATCAAATCTTATCTCCCTAGCGTTAAGACTGAAAGCAGCGAATCTTA
131 TAGATTAAAGCTAAAGGCAACAAATCTTATCTCCCTAGCATTAAGACTGAAAGCAGCGAATCTTA
* *
12943 TTTCCCTGGCGTTGCAGTAGAACTGATTAAAGCTAAAAGTAGCGAATCTTGTTTCCCTGGCGTTT
196 TTTCCCTGGCGTGGCAGTAGAACAGATTAAAGCTAAAAGTAGCGAATCTTGTTTCCCTGGCGTTT
13008 CAATGGAATAAATTAAAGCTGA
261 CAATGGAATAAATTAAAGCTGA
13030 AGTGGAGTAGATTAAAGCTGAAGTAGAGCGA-ATTAAAGCTAAAGGCAGTGAATATTATCTCTTT
1 AGTGGAGTAGATTAAAGCTGAAGTAGAG-GAGATTAAAGCTAAAGGCAGTGAATATTATCTCTTT
*** * *
13094 GGATTTATAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGACGTTGCAGTGGA
65 GGACCGACAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTATTTCCCTGACGTTGCAGTGGA
* * * **
13159 G-AGATTAAAGCTGAAGGCAACAAATCTTATCTCCCTGGTATTAAGACTGATGGCAGCGAATCTT
130 GTAGATTAAAGCTAAAGGCAACAAATCTTATCTCCCTAGCATTAAGACTGAAAGCAGCGAATCTT
* *
13223 ATTTCCTTGGCGTGGCAGTAGAACAGATTAAAGCTAAGAGTAGCGAATCTTGTTTCCCTGGCGTT
195 ATTTCCCTGGCGTGGCAGTAGAACAGATTAAAGCTAAAAGTAGCGAATCTTGTTTCCCTGGCGTT
13288 TCAATGGAATAAATTAAAGCTGA
260 TCAATGGAATAAATTAAAGCTGA
**
13311 AGTGGAGCGGATTAAA
1 AGTGGAGTAGATTAAA
13327 TTTGAAGTCA
Statistics
Matches: 269, Mismatches: 27, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
281 154 0.57
282 114 0.42
283 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (282 bp):
AGTGGAGTAGATTAAAGCTGAAGTAGAGGAGATTAAAGCTAAAGGCAGTGAATATTATCTCTTTG
GACCGACAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTATTTCCCTGACGTTGCAGTGGAG
TAGATTAAAGCTAAAGGCAACAAATCTTATCTCCCTAGCATTAAGACTGAAAGCAGCGAATCTTA
TTTCCCTGGCGTGGCAGTAGAACAGATTAAAGCTAAAAGTAGCGAATCTTGTTTCCCTGGCGTTT
CAATGGAATAAATTAAAGCTGA
Found at i:14357 original size:3 final size:3
Alignment explanation
Indices: 14349--14389 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
14339 AGTTTAATAC
* *
14349 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
14390 GTAGTAGTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Done.