Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5226.1
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: 29196
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1644 original size:12 final size:12
Alignment explanation
Indices: 1629--1659 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1619 TTCTTTTTGC
1629 TTTTCAAAGGCT
1 TTTTCAAAGGCT
1641 TTTTCAAAGGCT
1 TTTTCAAAGGCT
1653 TTTTCAA
1 TTTTCAA
1660 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:1752 original size:37 final size:37
Alignment explanation
Indices: 1709--1779 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
1699 CTTGCCTCTC
1709 TTTTCTTTTTATTTAATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTATTTAATTTTCTTTGTT-TTCTCTTGCT
* **
1746 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTATTTAATTTTCTTTGTTTTCTCTT
1780 TACAAGAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
37 28 0.93
38 2 0.07
ACGTcount: A:0.04, C:0.17, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTATTTAATTTTCTTTGTTTTCTCTTGCT
Found at i:1765 original size:16 final size:16
Alignment explanation
Indices: 1707--1769 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
1697 CTCTTGCCTC
*
1707 TCTTTTCTTTTTATTT
1 TCTTTTCTTTTTCTTT
** *
1723 AATTTTCTTTTTCTTC
1 TCTTTTCTTTTTCTTT
*
1739 TC-TTGCTTTTTCTTTT
1 TCTTTTCTTTTTC-TTT
1755 TCTTTTC-TTTTCTTT
1 TCTTTTCTTTTTCTTT
1770 GTTTTCTCTT
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
15 12 0.33
16 21 0.58
17 3 0.08
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (16 bp):
TCTTTTCTTTTTCTTT
Found at i:2712 original size:12 final size:11
Alignment explanation
Indices: 2697--2737 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 11
2687 TTTAACTCGA
2697 TTTTTTTTTCAC
1 TTTTTTTTT-AC
2709 TTTTTTTTT-C
1 TTTTTTTTTAC
2719 TTTTTTTTTGA-
1 TTTTTTTTT-AC
2730 TTTTTTTT
1 TTTTTTTT
2738 GAATTTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 10 0.37
11 8 0.30
12 9 0.33
ACGTcount: A:0.05, C:0.07, G:0.02, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTAC
Found at i:9927 original size:71 final size:71
Alignment explanation
Indices: 9811--9957 Score: 258
Period size: 71 Copynumber: 2.1 Consensus size: 71
9801 TCAGCTAGCC
* *
9811 AAGGACAACTCAAGAGACATTTTTAAGACATTGAAGACATTCAAATCAGCTGAATTAAAATGATT
1 AAGGACAACTCAAGAGACATTTTTAAAACATTAAAGACATTCAAATCAGCTGAATTAAAATGATT
9876 TTATGA
66 TTATGA
*
9882 AAGGACAACTCAAGAGACATTTTTAAAACATTAAAGACATTCAAATCAGCTGAATTGAAATGATT
1 AAGGACAACTCAAGAGACATTTTTAAAACATTAAAGACATTCAAATCAGCTGAATTAAAATGATT
*
9947 TTATGG
66 TTATGA
9953 AAGGA
1 AAGGA
9958 GTTATTTGGT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.27
Consensus pattern (71 bp):
AAGGACAACTCAAGAGACATTTTTAAAACATTAAAGACATTCAAATCAGCTGAATTAAAATGATT
TTATGA
Found at i:10639 original size:10 final size:11
Alignment explanation
Indices: 10599--10637 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
10589 TAGTTTCTTT
*
10599 AAAAAAATACA
1 AAAAAAATTCA
10610 AAAAAAATTCA
1 AAAAAAATTCA
10621 AAAAAAATTCA
1 AAAAAAATTCA
10632 AAAAAA
1 AAAAAA
10638 TTGGTTTCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:20333 original size:15 final size:16
Alignment explanation
Indices: 20308--20339 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
20298 TATCTCACAC
20308 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
20324 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
20339 T
1 T
20340 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:21358 original size:23 final size:23
Alignment explanation
Indices: 21338--21380 Score: 65
Period size: 20 Copynumber: 2.0 Consensus size: 23
21328 TAATAATTAA
21338 TTTTTTTT--ATTTTTTT-CAAT
1 TTTTTTTTCAATTTTTTTACAAT
21358 TTTTTTTTCAATTTTTTTACAAT
1 TTTTTTTTCAATTTTTTTACAAT
21381 CTCGTAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
22 8 0.40
23 4 0.20
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTTTTCAATTTTTTTACAAT
Found at i:21361 original size:11 final size:11
Alignment explanation
Indices: 21336--21380 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
21326 AATAATAATT
21336 AATTTTTTTT-
1 AATTTTTTTTC
21346 -A-TTTTTTTC
1 AATTTTTTTTC
21355 AATTTTTTTTTC
1 AA-TTTTTTTTC
*
21367 AATTTTTTTAC
1 AATTTTTTTTC
21378 AAT
1 AAT
21381 CTCGTAATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
8 7 0.23
9 1 0.03
10 1 0.03
11 11 0.37
12 10 0.33
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (11 bp):
AATTTTTTTTC
Found at i:21362 original size:12 final size:12
Alignment explanation
Indices: 21347--21375 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
21337 ATTTTTTTTA
21347 TTTTTTTCAATT
1 TTTTTTTCAATT
21359 TTTTTTTCAATT
1 TTTTTTTCAATT
21371 TTTTT
1 TTTTT
21376 ACAATCTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTTTCAATT
Done.