Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1113
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: 2767
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Found at i:865 original size:25 final size:25
Alignment explanation
Indices: 816--887 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
806 GAGGGTAAAG
*
816 AAATGAAAT-GATGACATAAATAAAT
1 AAAT-AAATAGATGACATAAAAAAAT
841 AAATAAATAGATGA-ATAAAGAAAAT
1 AAATAAATAGATGACATAAA-AAAAT
* * *
866 AAATAAAAAGATAAAATAAAAA
1 AAATAAATAGATGACATAAAAA
888 TGTCATACTC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 9 0.22
25 27 0.66
26 5 0.12
ACGTcount: A:0.69, C:0.01, G:0.10, T:0.19
Consensus pattern (25 bp):
AAATAAATAGATGACATAAAAAAAT
Found at i:1193 original size:127 final size:127
Alignment explanation
Indices: 1051--1505 Score: 874
Period size: 127 Copynumber: 3.6 Consensus size: 127
1041 TATGAATGCT
1051 AATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAATAATAATAAATA
1 AATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAATAATAATAAATA
1116 AATAGATAATATAAATAATATCAAATTTAAATTTTAAAAAGTAAAAGAATAACAAATACATA
66 AATAGATAATATAAATAATATCAAATTTAAATTTTAAAAAGTAAAAGAATAACAAATACATA
1178 AATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAATAATAATAAATA
1 AATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAATAATAATAAATA
1243 AATAGATAATATAAATAATATCAAATTTAAATTTTAAAAAGTAAAAGAATAACAAATACATA
66 AATAGATAATATAAATAATATCAAATTTAAATTTTAAAAAGTAAAAGAATAACAAATACATA
1305 AATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAATAATAATAAATA
1 AATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAATAATAATAAATA
1370 AATAGATAATATAAATAATATCAAATTTAAATTTTAAAAAGTAAAAGAATAACAAATACATA
66 AATAGATAATATAAATAATATCAAATTTAAATTTTAAAAAGTAAAAGAATAACAAATACATA
* ** *
1432 AATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAGAGGAATAACAAATA
1 AATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAATAATAATAAATA
1497 AATAGATAA
66 AATAGATAA
1506 AACAACCCAT
Statistics
Matches: 324, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 324 1.00
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (127 bp):
AATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAATAATAATAAATA
AATAGATAATATAAATAATATCAAATTTAAATTTTAAAAAGTAAAAGAATAACAAATACATA
Found at i:1495 original size:69 final size:64
Alignment explanation
Indices: 1127--1510 Score: 477
Period size: 68 Copynumber: 6.0 Consensus size: 64
1117 ATAGATAATA
1127 TAAATAATATCAAATTTAAATTTTAAAAAGTAAAAGAATAACAAATACATAAATAGATAAAACAA
1 TAAATAATATCAAATTTAAATTTTAAAAAGTAAAAGAATAAC--A-A-ATAAATAGATAAAACAA
1192 ATT
62 ATT
* * *
1195 TAAATAATATCAAATTTAAATATTTAAAAAGTAAAATAATAATAAATAAATAGAT------AATA
1 TAAATAATATCAAATTTAAAT-TTTAAAAAGTAAAAGAATAACAAATAAATAGATAAAACAAATT
1254 TAAATAATATCAAATTTAAATTTTAAAAAGTAAAAGAATAACAAATACATAAATAGATAAAACAA
1 TAAATAATATCAAATTTAAATTTTAAAAAGTAAAAGAATAAC--A-A-ATAAATAGATAAAACAA
1319 ATT
62 ATT
* * *
1322 TAAATAATATCAAATTTAAATATTTAAAAAGTAAAATAATAATAAATAAATAGAT------AATA
1 TAAATAATATCAAATTTAAAT-TTTAAAAAGTAAAAGAATAACAAATAAATAGATAAAACAAATT
1381 TAAATAATATCAAATTTAAATTTTAAAAAGTAAAAGAATAACAAATACATAAATAGATAAAACAA
1 TAAATAATATCAAATTTAAATTTTAAAAAGTAAAAGAATAAC--A-A-ATAAATAGATAAAACAA
1446 ATT
62 ATT
* *
1449 TAAATAATATCAAATTTAAATATTTAAAAAGTAGAGGAATAACAAATAAATAGATAAAACAA
1 TAAATAATATCAAATTTAAAT-TTTAAAAAGTAAAAGAATAACAAATAAATAGATAAAACAA
1511 CCCATAAAAG
Statistics
Matches: 279, Mismatches: 14, Indels: 49
0.82 0.04 0.14
Matches are distributed among these distances:
58 38 0.14
59 48 0.17
60 2 0.01
61 2 0.01
62 20 0.07
65 37 0.13
66 3 0.01
67 3 0.01
68 69 0.25
69 57 0.20
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (64 bp):
TAAATAATATCAAATTTAAATTTTAAAAAGTAAAAGAATAACAAATAAATAGATAAAACAAATT
Found at i:1993 original size:26 final size:26
Alignment explanation
Indices: 1944--1994 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1934 TTAAAATTCT
* *
1944 TTTAAAAAAAATTCATTTCCCTTTTA
1 TTTAAAAAAAAATCACTTCCCTTTTA
* *
1970 TTTAAAAAAAAATCCCTTCTCTTTT
1 TTTAAAAAAAAATCACTTCCCTTTT
1995 TTTTTTTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (26 bp):
TTTAAAAAAAAATCACTTCCCTTTTA
Found at i:2351 original size:15 final size:16
Alignment explanation
Indices: 2326--2356 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2316 TTATTTTTAT
2326 AAAATATAACAAATAA
1 AAAATATAACAAATAA
2342 AAAATA-AACAAATAA
1 AAAATATAACAAATAA
2357 TGGAATCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAATATAACAAATAA
Found at i:2410 original size:18 final size:18
Alignment explanation
Indices: 2374--2411 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2364 ACCTTCTGAA
*
2374 GTTTTTTTTTTGTATTCT
1 GTTTTTTTTTTGTACTCT
2392 GTTTTTTTTATTGT-CTCT
1 GTTTTTTTT-TTGTACTCT
2410 GT
1 GT
2412 ATTCGATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.05, C:0.08, G:0.13, T:0.74
Consensus pattern (18 bp):
GTTTTTTTTTTGTACTCT
Done.