Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6509.1
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: 11301
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1402 original size:68 final size:68
Alignment explanation
Indices: 1293--1429 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
1283 AAAGCTATAT
1293 ATGTAGTCTATTTTATGTAAAGAAACTCTTTATCTAGTAAAGTTTTTTAATGAAGTTGAATTAGA
1 ATGTAGTCTATTTTATGTAAAGAAACTCTTTATCTAGTAAAGTTTTTTAATGAAGTTGAATTAGA
1358 ATC
66 ATC
1361 ATGTAGTCTATTTTATGTAAAGAAACTCTTTATCTAGTAAAGTTTTTTAATGAAGTTGAATTAGA
1 ATGTAGTCTATTTTATGTAAAGAAACTCTTTATCTAGTAAAGTTTTTTAATGAAGTTGAATTAGA
1426 ATC
66 ATC
1429 A
1 A
1430 GTGCCTCTTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (68 bp):
ATGTAGTCTATTTTATGTAAAGAAACTCTTTATCTAGTAAAGTTTTTTAATGAAGTTGAATTAGA
ATC
Found at i:9988 original size:44 final size:42
Alignment explanation
Indices: 9873--10752 Score: 374
Period size: 44 Copynumber: 20.6 Consensus size: 42
9863 GGTTTATTAT
* * ***
9873 ACAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAG
1 ACAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
* *
9915 AATTTCAGATCTTATCTCCCTAAGGTTACAGTGGAGCAGATTGAAG
1 -A---CAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
* * *
9961 CCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGA-TCAAGG
1 ACAG--ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA-G
* * * *
10005 ATAGTAATCCTATCTCCTTGAGATTACAATGGAGCAGATT-AA-
1 ACAG--ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
* * * * * *
10047 A-GGATCTTATCTCTCTGA-AGTTACAGTAGAGAAGA-TCACAT
1 ACAGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGA-AG
* * * * ** *
10088 ACAGGTCTCATCTGCCTGAGATTACAGTGGAACAGGCCAAAGAATT
1 ACAGATCTTATCTCCCTGAGATTACAGTGGAGCA-G--ATTGAA-G
* * * *
10134 TCAGATCTTATCTCCCTAAGATTACAGCGGAGCAGA-TCAAGG
1 ACAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA-G
* * * *
10176 ATAGTAATCCTATCTCCTTGAGATTACAATGGAGCAGATT-AA-
1 ACAG--ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
* * * * *
10218 A-GGATCTTATCTCTCTGA-AGTTACAGTAGAGAAGA-TCACA-
1 ACAGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGA-AG
* * *
10258 TCAGGTCTTATCTCCCTGAGATTACAGTGGA--ACA--G-A-
1 ACAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
* * * ** *
10294 CCA-ANTCTTATCTCCCTGAGGTTACAGTGGAGCACCAAAGAATT
1 ACAGA-TCTTATCTCCCTGAGATTACAGTGGAGCA-GATTGAA-G
* * *
10338 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG
1 ACAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
* * * * *
10380 ACACTATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAATA
1 ACA-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATT-GAA-G
* * **
10425 AGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG
1 ACAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
* * * * **
10467 ATAGTAATCCTATCTCCTTGAGATTACAATGGAGTGGATT-AA-
1 ACAG--ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
* * * * *
10509 A-GGATCTTATCTCTCTGA-AGTTACAGTGGAGAAGATCGCA-
1 ACAGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAG
* * * * * ** *
10549 TCAGGTCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAG
1 ACAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
*
10591 AATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAG
1 -A---CAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
* * * *
10637 CCAGTGATATTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG
1 ACA--GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
* * * * *
10681 ACACTATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAAT
1 ACA-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATT-GAAG
* * *
10725 AAAGGATCTTATCTCTCTGAGGTTACAG
1 ACA-GATCTTATCTCCCTGAGATTACAG
10753 CAGAGTAGAT
Statistics
Matches: 633, Mismatches: 147, Indels: 113
0.71 0.16 0.13
Matches are distributed among these distances:
36 28 0.04
38 6 0.01
39 79 0.12
40 3 0.00
41 58 0.09
42 43 0.07
43 71 0.11
44 238 0.38
45 9 0.01
46 98 0.15
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (42 bp):
ACAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG
Found at i:10165 original size:171 final size:170
Alignment explanation
Indices: 9967--10297 Score: 617
Period size: 171 Copynumber: 1.9 Consensus size: 170
9957 GAAGCCAGAA
*
9967 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAGGATAGTAATCCTATCTCCTTGAGATTAC
1 ATCTTATCTCCCTAAGATTACAGCGGAGCAGATCAAGGATAGTAATCCTATCTCCTTGAGATTAC
10032 AATGGAGCAGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATACAGGTCTC
66 AATGGAGCAGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACAT-CAGGTCTC
* *
10097 ATCTGCCTGAGATTACAGTGGAACAGGCCAAAGAATTTCAG
130 ATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAG
10138 ATCTTATCTCCCTAAGATTACAGCGGAGCAGATCAAGGATAGTAATCCTATCTCCTTGAGATTAC
1 ATCTTATCTCCCTAAGATTACAGCGGAGCAGATCAAGGATAGTAATCCTATCTCCTTGAGATTAC
*
10203 AATGGAGCAGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTA
66 AATGGAGCAGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTCA
10268 TCTCCCTGAGATTACAGTGGAACAGACCAA
131 TCTCCCTGAGATTACAGTGGAACAGACCAA
10298 NTCTTATCTC
Statistics
Matches: 156, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
170 36 0.23
171 120 0.77
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (170 bp):
ATCTTATCTCCCTAAGATTACAGCGGAGCAGATCAAGGATAGTAATCCTATCTCCTTGAGATTAC
AATGGAGCAGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTCA
TCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAG
Found at i:10448 original size:87 final size:88
Alignment explanation
Indices: 10340--10509 Score: 263
Period size: 87 Copynumber: 1.9 Consensus size: 88
10330 AAAGAATTTC
*
10340 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGA-AGT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGA-T
*
10403 TACAGTGGAGCGGATTAAAATAAG
65 TACAATGGAGCGGATTAAAATAAG
* * *
10427 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATT
*
10492 ACAATGGAGTGGATTAAA
66 ACAATGGAGCGGATTAAA
10510 GGATCTTATC
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
87 42 0.56
88 32 0.43
89 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (88 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATT
ACAATGGAGCGGATTAAAATAAG
Found at i:10737 original size:87 final size:87
Alignment explanation
Indices: 10603--10764 Score: 209
Period size: 87 Copynumber: 1.9 Consensus size: 87
10593 TTTCAGATCT
* * ** *
10603 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGTGATATTATCTCCCTGAGATTACAGCG
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGAAAGTGATATTATCTCCCTGAGATTACAGCA
10668 GAGCAGATCGAAGACACTATCC
66 GAGCAGATCGAAGACACTATCC
* * * * *
10690 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAG-GATCTTATCTCTCTGAGGTTACAGC
1 TATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAGAAAGTGATATTATCTCCCTGAGATTACAGC
*
10754 AGAGTAGATCG
65 AGAGCAGATCG
10765 CATCAAGTCT
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
87 59 0.94
88 4 0.06
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (87 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGAAAGTGATATTATCTCCCTGAGATTACAGCA
GAGCAGATCGAAGACACTATCC
Done.