Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold429
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: 134018
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
File 2 of 2
Found at i:127569 original size:11 final size:11
Alignment explanation
Indices: 127528--127571 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
127518 AAATAATTAA
127528 AATAT-AATAT
1 AATATAAATAT
*
127538 AATATAAAAAT
1 AATATAAATAT
127549 AATATAAATAT
1 AATATAAATAT
*
127560 AATATGAATAT
1 AATATAAATAT
127571 A
1 A
127572 TAAATATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 5 0.17
11 25 0.83
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (11 bp):
AATATAAATAT
Found at i:128437 original size:2 final size:2
Alignment explanation
Indices: 128430--128468 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
128420 ATTGGTCCAT
128430 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
128469 CATCTTGGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:129300 original size:33 final size:34
Alignment explanation
Indices: 129219--129303 Score: 129
Period size: 34 Copynumber: 2.5 Consensus size: 34
129209 TGGTAAAAAC
*
129219 CACCATTTAATCAACAATGGTAAGCTACCAAATTT
1 CACCATTTAATCAACAATGGTAAACTACCAAA-TT
*
129254 C-CCATTTAGTCAACAATGGTAAACTACCAAA-T
1 CACCATTTAATCAACAATGGTAAACTACCAAATT
129286 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
129304 TCTCCCACTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
32 2 0.04
33 15 0.33
34 28 0.61
35 1 0.02
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (34 bp):
CACCATTTAATCAACAATGGTAAACTACCAAATT
Found at i:133271 original size:14 final size:14
Alignment explanation
Indices: 133252--133278 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
133242 CATCTATCTC
133252 TATATAGATATAGA
1 TATATAGATATAGA
133266 TATATAGATATAG
1 TATATAGATATAG
133279 TGGATTGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (14 bp):
TATATAGATATAGA
Found at i:133435 original size:34 final size:34
Alignment explanation
Indices: 133336--133516 Score: 242
Period size: 34 Copynumber: 5.4 Consensus size: 34
133326 GACATATATG
* *
133336 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
133369 TGTTGACTAAATGGGAAATTTGG--GCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
133401 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
133435 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
133469 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
133503 TGTTGATTAAATGG
1 TGTTGATTAAATGG
133517 TGGTTTTTAC
Statistics
Matches: 128, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
32 29 0.23
33 11 0.09
34 88 0.69
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:133837 original size:18 final size:18
Alignment explanation
Indices: 133816--133869 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
133806 TTGGTTGTCG
133816 AGGTACTATTCACGTATT
1 AGGTACTATTCACGTATT
*
133834 AGGTACTATTCACATA-T
1 AGGTACTATTCACGTATT
*
133851 ACGGTTACTATTCAAGTAT
1 A-GG-TACTATTCACGTAT
133870 ACGGTTACTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 2 0.07
18 17 0.57
19 11 0.37
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (18 bp):
AGGTACTATTCACGTATT
Found at i:133861 original size:19 final size:19
Alignment explanation
Indices: 133819--133878 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
133809 GTTGTCGAGG
*
133819 TACTATTCACGTATTA-GG-
1 TACTATTCACATA-TACGGT
133837 TACTATTCACATATACGGT
1 TACTATTCACATATACGGT
133856 TACTATTCA-AGTATACGGT
1 TACTATTCACA-TATACGGT
133875 TACT
1 TACT
133879 GTACAGTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
17 2 0.05
18 15 0.39
19 21 0.55
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (19 bp):
TACTATTCACATATACGGT
Done.