Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2987
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: 12177
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Found at i:584 original size:40 final size:40
Alignment explanation
Indices: 504--677 Score: 259
Period size: 40 Copynumber: 4.5 Consensus size: 40
494 CGTTCAAATC
* * * *
504 TCGGGACATAGCCCGG-TTTAGTAACTCACAC-AAT-CCT
1 TCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCT
* *
541 TCGGGACTTAACCCGGATTTAACAACTAGCACGAATGCCT
1 TCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCT
581 TCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCT
1 TCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCT
621 TCGGGACTTAACCC-GATTTAATAACTCGCACGAATGCCT
1 TCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCT
660 TC-GGACTTAACCCGGATT
1 TCGGGACTTAACCCGGATT
678 AGTATCTCGC
Statistics
Matches: 125, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
37 14 0.11
38 22 0.18
39 34 0.27
40 55 0.44
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
TCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCT
Found at i:658 original size:79 final size:78
Alignment explanation
Indices: 504--677 Score: 255
Period size: 78 Copynumber: 2.2 Consensus size: 78
494 CGTTCAAATC
* * *
504 TCGGGACATAGCCCGG-TTTAGTAACTCACACAATCCTTCGGGACTTAACCCGGATTTAACAACT
1 TCGGGACTTAACCCGGATTTAATAACTCACACAATCCTTCGGGACTTAACCCGGATTTAACAACT
568 AGCACGAATGCCT
66 AGCACGAATGCCT
* *
581 TCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCC-GATTTAATAA
1 TCGGGACTTAACCCGGATTTAATAACTCACAC-AAT-CCTTCGGGACTTAACCCGGATTTAACAA
*
645 CTCGCACGAATGCCT
64 CTAGCACGAATGCCT
660 TC-GGACTTAACCCGGATT
1 TCGGGACTTAACCCGGATT
678 AGTATCTCGC
Statistics
Matches: 88, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
77 14 0.16
78 29 0.33
79 28 0.32
80 17 0.19
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (78 bp):
TCGGGACTTAACCCGGATTTAATAACTCACACAATCCTTCGGGACTTAACCCGGATTTAACAACT
AGCACGAATGCCT
Found at i:8325 original size:39 final size:40
Alignment explanation
Indices: 8282--8447 Score: 182
Period size: 39 Copynumber: 4.3 Consensus size: 40
8272 TCCTCGTTCA
* * *
8282 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCACG
* **
8321 AATGCCTTCGGGACATAACCCGGATTCAACAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCACG
*
8361 AATGCCTTCGGGACTTAACCC-GA-TTA-TAAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAGT-AACTCGCACG
* * *
8399 AATGCCTTCGGGACTTAACCCAGATTTAGT-ATTCGCAC-
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCACG
*
8437 AAGGCCTTCGG
1 AATGCCTTCGG
8448 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
38 43 0.39
39 44 0.40
40 23 0.21
41 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.23
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCACG
Found at i:8508 original size:40 final size:40
Alignment explanation
Indices: 8433--8508 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
8423 TTTAGTATTC
* * * *
8433 GCACAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGCCTTCGGATCTTAGCCCGGACACATTCACTTA
8473 GCACAAAGCCTTCGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGCCTTCGGATCTTAGCCCGGACA-CATTCA
8509 ATTAATCATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 11 0.35
40 20 0.65
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAAGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:10351 original size:44 final size:43
Alignment explanation
Indices: 10262--10351 Score: 155
Period size: 45 Copynumber: 2.1 Consensus size: 43
10252 ACATGTATTG
10262 CATCCAAATGAACTCGACCAAACTCAACGAGCTCAGATGCTCA
1 CATCCAAATGAACTCGACCAAACTCAACGAGCTCAGATGCTCA
10305 CATCCATAATGAACTCAGACCAAACTCAACGAGCTCAGATGC-CA
1 CATCCA-AATGAACTC-GACCAAACTCAACGAGCTCAGATGCTCA
10349 CAT
1 CAT
10352 ATATCATGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
43 6 0.13
44 14 0.31
45 25 0.56
ACGTcount: A:0.38, C:0.32, G:0.13, T:0.17
Consensus pattern (43 bp):
CATCCAAATGAACTCGACCAAACTCAACGAGCTCAGATGCTCA
Found at i:10361 original size:44 final size:44
Alignment explanation
Indices: 10268--10361 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 44
10258 ATTGCATCCA
*
10268 AATGAACTCGACCAAACTCAACGAGCTCAGATGCTCACATCCAT
1 AATGAACTCGACCAAACTCAACGAGCTCAGATGCTCACATACAT
*
10312 AATGAACTCAGACCAAACTCAACGAGCTCAGATGC-CACATATAT
1 AATGAACTC-GACCAAACTCAACGAGCTCAGATGCTCACATACAT
*
10356 CATGAA
1 AATGAA
10362 TCCGGACTAC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 21 0.46
45 25 0.54
ACGTcount: A:0.39, C:0.29, G:0.14, T:0.18
Consensus pattern (44 bp):
AATGAACTCGACCAAACTCAACGAGCTCAGATGCTCACATACAT
Done.