Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5449.1
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: 23596
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.31
Warning! 799 characters in sequence are not A, C, G, or T
Found at i:1345 original size:40 final size:40
Alignment explanation
Indices: 872--1333 Score: 771
Period size: 40 Copynumber: 11.6 Consensus size: 40
862 GTTACTATAA
* * *
872 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
912 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
952 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
992 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
1032 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
1072 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
1112 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
1152 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
1192 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
* *
1232 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATAT
1 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
* *** * * * * *
1272 CCGTGCTAAACCCCGAAGAGCATTCATGCTGGTGTTATAT
1 CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
* * *
1312 CCGGGCTAGGTCCCGAAGAGCA
1 CCGGGCTAAGTTCCGCAGAGCA
1334 ATCATGCTGG
Statistics
Matches: 406, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 406 1.00
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTTCCGCAGAGCATTCGTGCTAGTGATGTAT
Found at i:8955 original size:19 final size:20
Alignment explanation
Indices: 8931--8968 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
8921 GGTACCACCA
8931 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
8950 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
8969 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:9264 original size:46 final size:45
Alignment explanation
Indices: 9197--9411 Score: 193
Period size: 46 Copynumber: 4.6 Consensus size: 45
9187 CGCCCCTAAG
*
9197 TGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGCATCCATAAA
* * * * **
9243 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TTACATTTCA
1 TGAACTCGGACTCAACTCAACGAGTTCGG--GCTTCGCATCCA-TAAA
* * * *
9290 CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGCATCCATAAA
* **
9336 TGAACTCGGACTCAACTCAACGAGTTCGGATGC-TCAACCATCC-TTCA
1 TGAACTCGGACTCAACTCAACGAGTTCGG--GCTTC--GCATCCATAAA
*
9383 CGAACTCGGACTCAACTCAACGAGTTCGG
1 TGAACTCGGACTCAACTCAACGAGTTCGG
9412 ATGCTCAACC
Statistics
Matches: 135, Mismatches: 25, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
45 1 0.01
46 63 0.47
47 63 0.47
48 8 0.06
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.22
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGGCTTCGCATCCATAAA
Found at i:9308 original size:93 final size:92
Alignment explanation
Indices: 9198--9412 Score: 319
Period size: 93 Copynumber: 2.3 Consensus size: 92
9188 GCCCCTAAGT
* * *
9198 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
9263 CGAGTTCGGATGC-CTAGTTA-CAT-TTCAC
66 CGAGTTCGGATGCTC-A---ACCATCTTCAC
* *
9291 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
9356 CGAGTTCGGATGCTCAACCATCCTTCAC
66 CGAGTTCGGATGCTCAACCAT-CTTCAC
9384 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
9413 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
90 1 0.01
91 3 0.03
93 107 0.96
94 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCTCAACCATCTTCAC
Found at i:9411 original size:20 final size:20
Alignment explanation
Indices: 9341--9412 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 20
9331 ATAAGTGAAC
9341 TCGGACTCAACTCAACGAGT
1 TCGGACTCAACTCAACGAGT
* **
9361 TCGGATGCTCAACCATCCTTCACGAAC
1 TCGGA--CTCAA-C-T-C--AACGAGT
9388 TCGGACTCAACTCAACGAGT
1 TCGGACTCAACTCAACGAGT
9408 TCGGA
1 TCGGA
9413 TGCTCAACCA
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
20 14 0.36
22 6 0.15
23 2 0.05
24 2 0.05
25 6 0.15
27 9 0.23
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGGACTCAACTCAACGAGT
Found at i:9416 original size:47 final size:47
Alignment explanation
Indices: 9244--9426 Score: 207
Period size: 47 Copynumber: 3.9 Consensus size: 47
9234 ATCCATAAAT
9244 GAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CAT--TTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCCTTCAC
* *** * * * *
9291 GAACTCGGACTCAACTCAACGAGTTCAGACATTC--GCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTTCA-C
9337 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTTCAC
9384 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
9427 AGTGACATGT
Statistics
Matches: 114, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 3 0.03
45 2 0.02
46 30 0.26
47 71 0.62
48 8 0.07
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTTCAC
Found at i:9868 original size:30 final size:30
Alignment explanation
Indices: 9834--9893 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
9824 ATTTAATACG
9834 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
9864 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
9894 GGCTCAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Done.