Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1191
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: 17551
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Found at i:15128 original size:44 final size:44
Alignment explanation
Indices: 14757--15130 Score: 194
Period size: 44 Copynumber: 8.7 Consensus size: 44
14747 TAGGTTTATT
* * **
14757 ATACAGG-TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGA
1 ATACAGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGA-TTAA-A
* * * *
14802 ATTTCA-GATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAA
1 A-TACAGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAA
* * * * * *
14846 GAT--AGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATT---
1 -ATACAG-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAA
* * * * * *
14887 A-A-AGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGA-TCAC
1 ATACAGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAA
*
14928 AT-CAGG-TCTTAT-TCCCTGAGATTACAGTGGAGACCAGAATT---
1 ATACAGGATCTTATCTCCCTGAGGTTACAGTGGAG--CAG-ATTAAA
*
14969 -T-CA-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT-GA
1 ATACAGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAA
** * * *
15009 AGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATATCGAAG
1 ATACAG-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGAT-T--AAA
* * * * *
15057 TTACAGTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA
1 ATACAGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAA
* *
15101 ATAAAGGATCTTATCTCTCTGAGGTTACAG
1 ATACAGGATCTTATCTCCCTGAGGTTACAG
15131 CAGAGTAGAT
Statistics
Matches: 253, Mismatches: 49, Indels: 55
0.71 0.14 0.15
Matches are distributed among these distances:
38 4 0.02
39 27 0.11
40 28 0.11
41 26 0.10
42 8 0.03
43 1 0.00
44 89 0.35
45 6 0.02
46 33 0.13
47 28 0.11
48 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
ATACAGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAA
Found at i:15198 original size:216 final size:207
Alignment explanation
Indices: 14807--15216 Score: 499
Period size: 216 Copynumber: 1.9 Consensus size: 207
14797 AAAGAATTTC
* *
14807 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACAGTAATCCTATCTCCCTGAGATT
* *
14872 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
66 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTCT
*** *
14937 TATTCCCTGAGATTACAGTGGAGACCAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGC
131 TATTCCCTGAGATTACAGTGGAGACCAGAAAAACAGATCTTATCTCCCT-AAGTTACAGTGGAGC
15002 AGATTGAAGCCAG
195 AGATTGAAGCCAG
*
15015 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATATCGAAGTTACAGT-ATCCTATCTCCCTGA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAG--ATCAAAG--ACAGTAATCCTATCTCCCTGA
* * * *
15079 -AGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCG
62 GA-TTACAATGGAGCGGA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCA
* *
15143 CATCAAGTCTTATTTCCCTGAAGA-TGCAGTGGATAGA-CTGAAAAACA-AT-TTATCTCCCTAA
121 CATCAAGTCTTA-TTCCCTG-AGATTACAGTGG--AGACCAGAAAAACAGATCTTATCTCCCTAA
*
15204 GTTGCAGTGGAGC
182 GTTACAGTGGAGC
15217 GGACAATAGA
Statistics
Matches: 172, Mismatches: 16, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
208 33 0.19
210 7 0.04
211 28 0.16
212 5 0.03
215 13 0.08
216 58 0.34
217 16 0.09
218 9 0.05
219 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (207 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACAGTAATCCTATCTCCCTGAGATT
ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTCT
TATTCCCTGAGATTACAGTGGAGACCAGAAAAACAGATCTTATCTCCCTAAGTTACAGTGGAGCA
GATTGAAGCCAG
Found at i:15509 original size:14 final size:14
Alignment explanation
Indices: 15490--15535 Score: 76
Period size: 15 Copynumber: 3.3 Consensus size: 14
15480 TTCTGCCCGG
15490 CCCAATACCACAAA
1 CCCAATACCACAAA
15504 CCCAATACCCACAAA
1 CCCAATA-CCACAAA
15519 CCCAATACC-CAAA
1 CCCAATACCACAAA
15532 CCCA
1 CCCA
15536 TACAAACCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.26
14 9 0.29
15 14 0.45
ACGTcount: A:0.46, C:0.48, G:0.00, T:0.07
Consensus pattern (14 bp):
CCCAATACCACAAA
Found at i:15528 original size:7 final size:7
Alignment explanation
Indices: 15490--15535 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
15480 TTCTGCCCGG
15490 CCCAATA
1 CCCAATA
15497 CCACAA-A
1 CC-CAATA
15504 CCCAATA
1 CCCAATA
*
15511 CCCACAAA
1 CCCA-ATA
15519 CCCAATA
1 CCCAATA
15526 CCCAA-A
1 CCCAATA
15532 CCCA
1 CCCA
15536 TACAAACCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
6 8 0.24
7 17 0.50
8 9 0.26
ACGTcount: A:0.46, C:0.48, G:0.00, T:0.07
Consensus pattern (7 bp):
CCCAATA
Done.