Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold969
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: 20280
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Found at i:10174 original size:13 final size:13
Alignment explanation
Indices: 10156--10180 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10146 CAAAGATCAG
10156 TGTATCGATACAA
1 TGTATCGATACAA
10169 TGTATCGATACA
1 TGTATCGATACA
10181 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:10258 original size:33 final size:33
Alignment explanation
Indices: 10221--10287 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
10211 AGTAGCTTAA
10221 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
10254 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
10287 A
1 A
10288 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:10261 original size:13 final size:13
Alignment explanation
Indices: 10243--10267 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10233 CAAAAAAATA
10243 TGTATCGATACAT
1 TGTATCGATACAT
10256 TGTATCGATACA
1 TGTATCGATACA
10268 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10457 original size:10 final size:10
Alignment explanation
Indices: 10442--10494 Score: 63
Period size: 10 Copynumber: 5.2 Consensus size: 10
10432 GGATTCGGGC
10442 TTAACAAAAT
1 TTAACAAAAT
10452 TTAACAAAAT
1 TTAACAAAAT
*
10462 TTAACAAAAAG
1 TTAAC-AAAAT
*
10473 TTATA-AAAAG
1 TTA-ACAAAAT
10483 TTAACAAAAT
1 TTAACAAAAT
10493 TT
1 TT
10495 TTCGTCCCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
9 1 0.03
10 29 0.76
11 7 0.18
12 1 0.03
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.30
Consensus pattern (10 bp):
TTAACAAAAT
Found at i:15308 original size:97 final size:97
Alignment explanation
Indices: 15207--15394 Score: 225
Period size: 97 Copynumber: 1.9 Consensus size: 97
15197 TCCTCGGAGG
* * **
15207 AATGGGGTTGGAGTGTCCATGACGATGACAATTTAAGCAAAAATAAGACT-TAAATCTTGACAAG
1 AATGGGATTGGAGTATCCACAACGATGACAATTTAAGCAAAAATAAGA-TGTAAATCTTGACAAG
15271 TTTAAAAACGGAGTTAGAGTATCCTCTCGAAAT
65 TTTAAAAACGGAGTTAGAGTATCCTCTCGAAAT
* * * * * **
15304 AATGGGATTGGAGTATCCCCAATGTTGATAATTTAGGTGAAAATAAGATGTAAATCTTGACAAGT
1 AATGGGATTGGAGTATCCACAACGATGACAATTTAAGCAAAAATAAGATGTAAATCTTGACAAGT
* * * *
15369 TTAAAAATGGGGTTAGTGTATTCTCT
66 TTAAAAACGGAGTTAGAGTATCCTCT
15395 TAGAAGATGG
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
96 1 0.01
97 74 0.99
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.30
Consensus pattern (97 bp):
AATGGGATTGGAGTATCCACAACGATGACAATTTAAGCAAAAATAAGATGTAAATCTTGACAAGT
TTAAAAACGGAGTTAGAGTATCCTCTCGAAAT
Found at i:17850 original size:32 final size:32
Alignment explanation
Indices: 17803--17882 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
17793 GATACATTGA
* *
17803 AGAATATATCAATACATTT-GGCTAAAAAACCT
1 AGAATGTATCGATACATTTAGG-TAAAAAACCT
*
17835 AGAATGTATCGATACATTTAGGTCAAAAACCT
1 AGAATGTATCGATACATTTAGGTAAAAAACCT
*
17867 ATAATGTATCGATACA
1 AGAATGTATCGATACA
17883 ATTAAAAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 41 0.95
33 2 0.05
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (32 bp):
AGAATGTATCGATACATTTAGGTAAAAAACCT
Found at i:17971 original size:20 final size:20
Alignment explanation
Indices: 17943--18012 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
17933 ACAAGGTCTA
* *
17943 GTATTGATACATTCACTTAT
1 GTATCGATACATTAACTTAT
*
17963 GTATCGATACATTTACTTAT
1 GTATCGATACATTAACTTAT
* *
17983 GTTTCGATACATTAACTTGTT
1 GTATCGATACATTAACTT-AT
18004 GTATCGATA
1 GTATCGATA
18013 AAAATTGTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
20 34 0.79
21 9 0.21
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (20 bp):
GTATCGATACATTAACTTAT
Done.