Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold603
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: 43842
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.16
Warning! 21251 characters in sequence are not A, C, G, or T
Found at i:24266 original size:13 final size:13
Alignment explanation
Indices: 24245--24279 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
24235 ATAAGTTGCT
* *
24245 GTTAGTTAAATTA
1 GTTAATTAAATAA
24258 GTTAATTAAATAA
1 GTTAATTAAATAA
24271 GTTAATTAA
1 GTTAATTAA
24280 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:26206 original size:12 final size:12
Alignment explanation
Indices: 26160--26213 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
26150 AAAGAAGAGG
26160 AAATTCAAAAAA
1 AAATTCAAAAAA
*
26172 AAA-TC-GAAAA
1 AAATTCAAAAAA
*
26182 AAATTGATTAAAAA
1 AAATTCA--AAAAA
26196 AAATTCAAAAAA
1 AAATTCAAAAAA
26208 AAATTC
1 AAATTC
26214 GAAGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 7 0.21
11 3 0.09
12 14 0.41
14 10 0.29
ACGTcount: A:0.69, C:0.07, G:0.04, T:0.20
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:27201 original size:18 final size:18
Alignment explanation
Indices: 27145--27204 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
27135 AGTGCGAGCG
27145 AGAAAAAGAAATCGAAAGAAA
1 AGAAAAAGAAATC--AA-AAA
* **
27166 AGAAAAAGAGATTGAAAA
1 AGAAAAAGAAATCAAAAA
27184 AGAAAAAGAAATCAAAAA
1 AGAAAAAGAAATCAAAAA
27202 AGA
1 AGA
27205 GAGTGAGGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 21 0.64
19 1 0.03
21 11 0.33
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCAAAAA
Found at i:29039 original size:13 final size:13
Alignment explanation
Indices: 29018--29052 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
29008 ATAAGTTGCT
* *
29018 GTTAGTTAAATTA
1 GTTAATTAAATAA
29031 GTTAATTAAATAA
1 GTTAATTAAATAA
29044 GTTAATTAA
1 GTTAATTAA
29053 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:38473 original size:21 final size:21
Alignment explanation
Indices: 38449--38506 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
38439 TTTATTTCGG
38449 CTCATTCTCTTGTTCAACGGC
1 CTCATTCTCTTGTTCAACGGC
*
38470 CTCATCCTCTTGTTCAACGGC
1 CTCATTCTCTTGTTCAACGGC
38491 CTCATTCTCTTGTTCA
1 CTCATTCTCTTGTTCA
38507 CTTTCAGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.14, C:0.34, G:0.12, T:0.40
Consensus pattern (21 bp):
CTCATTCTCTTGTTCAACGGC
Found at i:38675 original size:255 final size:255
Alignment explanation
Indices: 38224--38706 Score: 912
Period size: 255 Copynumber: 1.9 Consensus size: 255
38214 CATCTTCGGG
*
38224 TTGTTCAACGGCCTCATTCTCTTGTTCACTTTCAGATTCAATCTCTCTATCATCTCAGACAAACA
1 TTGTTCAACGGCCTCATTCTCTTGTTCACTTTCAGATTCAATCTCTCCATCATCTCAGACAAACA
*
38289 TCACATTCCGGTTTGGAGATTGGCTTGTGATGTGGCCCCTTCTAAGACATTTGAAACACTTTATG
66 TCACATTCCGGTTTGGACATTGGCTTGTGATGTGGCCCCTTCTAAGACATTTGAAACACTTTATG
38354 CCTCGGGATCTATTTGGTTGGGCATCCATCTTCCTTTACTCGTTTCAACAATCGGTTTGTTGAAC
131 CCTCGGGATCTATTTGGTTGGGCATCCATCTTCCTTTACTCGTTTCAACAATCGGTTTGTTGAAC
38419 TTGGTTGCACCACTCACTTCTTTATTTCGGCTCATTCTCTTGTTCAACGGCCTCATCCTC
196 TTGGTTGCACCACTCACTTCTTTATTTCGGCTCATTCTCTTGTTCAACGGCCTCATCCTC
*
38479 TTGTTCAACGGCCTCATTCTCTTGTTCACTTTCAGATTCAATCTCTCCATCATCTCGGACAAACA
1 TTGTTCAACGGCCTCATTCTCTTGTTCACTTTCAGATTCAATCTCTCCATCATCTCAGACAAACA
38544 TCACATTCCGGTTTGGACATTGGCTTGTGATGTGGCCCCTTCTAAGACATTTGAAACACTTTATG
66 TCACATTCCGGTTTGGACATTGGCTTGTGATGTGGCCCCTTCTAAGACATTTGAAACACTTTATG
* *
38609 TCTTGGGATCTATTTGGTTGGGCATCCATCTTCCTTTACTCGTTTCAACAATCGGTTTGTTGAAC
131 CCTCGGGATCTATTTGGTTGGGCATCCATCTTCCTTTACTCGTTTCAACAATCGGTTTGTTGAAC
*
38674 TTGGTTGCACCACTCACTTCTTTATTTTGGCTC
196 TTGGTTGCACCACTCACTTCTTTATTTCGGCTC
38707 GGCATGTCAC
Statistics
Matches: 222, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
255 222 1.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (255 bp):
TTGTTCAACGGCCTCATTCTCTTGTTCACTTTCAGATTCAATCTCTCCATCATCTCAGACAAACA
TCACATTCCGGTTTGGACATTGGCTTGTGATGTGGCCCCTTCTAAGACATTTGAAACACTTTATG
CCTCGGGATCTATTTGGTTGGGCATCCATCTTCCTTTACTCGTTTCAACAATCGGTTTGTTGAAC
TTGGTTGCACCACTCACTTCTTTATTTCGGCTCATTCTCTTGTTCAACGGCCTCATCCTC
Done.