Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5721.1
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: 18819
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.33
Warning! 644 characters in sequence are not A, C, G, or T
Found at i:1871 original size:30 final size:29
Alignment explanation
Indices: 1837--1893 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
1827 ATAGTATCGT
1837 ATCTTGGATTTCTTTATTCTGGGTTTCTCA
1 ATCTTGGATTTCTTTATTC-GGGTTTCTCA
* *
1867 ATCTTGGATTTTTTTATTCGGTTTTCT
1 ATCTTGGATTTCTTTATTCGGGTTTCT
1894 TGTTATCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.12, C:0.14, G:0.16, T:0.58
Consensus pattern (29 bp):
ATCTTGGATTTCTTTATTCGGGTTTCTCA
Found at i:10446 original size:52 final size:53
Alignment explanation
Indices: 10390--10499 Score: 213
Period size: 53 Copynumber: 2.1 Consensus size: 53
10380 GTTAATTTCT
10390 TTCATAAAAAAAAA-CTTTATAGACAAGTTAATTCTTAATATTGGAATCAATC
1 TTCATAAAAAAAAACCTTTATAGACAAGTTAATTCTTAATATTGGAATCAATC
10442 TTCATAAAAAAAAACCTTTATAGACAAGTTAATTCTTAATATTGGAATCAATC
1 TTCATAAAAAAAAACCTTTATAGACAAGTTAATTCTTAATATTGGAATCAATC
10495 TTCAT
1 TTCAT
10500 CGAAAAGTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 14 0.25
53 43 0.75
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (53 bp):
TTCATAAAAAAAAACCTTTATAGACAAGTTAATTCTTAATATTGGAATCAATC
Found at i:13005 original size:99 final size:99
Alignment explanation
Indices: 12834--13057 Score: 270
Period size: 99 Copynumber: 2.3 Consensus size: 99
12824 CTTATAGTCC
* * * * *
12834 GCTGATTTACGATCACAACTGTCATTTTTCAAGCTCGCTGATTTACAAACATGGCTTAAGTTCAT
1 GCTGATTTACGATCACAACTATCATTTTTAAAGCTCGCTAATTTACAAACAAGGCTTAAGTTAAT
*
12899 TGATTTACGATCATAAATAGTACATTAAAAGTTT
66 TGATTTACAATCATAAATAGTACATTAAAAGTTT
* * * * *
12933 GCTGATTTACTATCACAACTATCATTTTTAAAGCTTGCTAATTTACGATCAAGGCTTCAGTTAAT
1 GCTGATTTACGATCACAACTATCATTTTTAAAGCTCGCTAATTTACAAACAAGGCTTAAGTTAAT
* * * * *
12998 TGATTTACAATCATAAAAACTTCATTAAGAGTTC
66 TGATTTACAATCATAAATAGTACATTAAAAGTTT
* **
13032 ACCAATTTACGATCACAACT-TCATTT
1 GCTGATTTACGATCACAACTATCATTT
13058 AAATAATTTG
Statistics
Matches: 105, Mismatches: 20, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
98 6 0.06
99 99 0.94
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (99 bp):
GCTGATTTACGATCACAACTATCATTTTTAAAGCTCGCTAATTTACAAACAAGGCTTAAGTTAAT
TGATTTACAATCATAAATAGTACATTAAAAGTTT
Found at i:13559 original size:11 final size:11
Alignment explanation
Indices: 13545--13589 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
13535 AGATAAATAT
13545 TATTTTATTAA
1 TATTTTATTAA
*
13556 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
13569 TATTTTATTAT
1 TATTTTATTAA
13580 TATTTTATTA
1 TATTTTATTA
13590 GTAGATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:15502 original size:46 final size:46
Alignment explanation
Indices: 15373--15508 Score: 175
Period size: 46 Copynumber: 3.0 Consensus size: 46
15363 GCTCTCTGAA
* * *
15373 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGACAGCGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
15419 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * * *
15465 A-GAAAATGAGTAAAACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
15509 TCAAAGATAA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 1 0.01
46 79 0.99
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Done.