Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1241
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: 2295
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.26
Warning! 433 characters in sequence are not A, C, G, or T
Found at i:75 original size:14 final size:13
Alignment explanation
Indices: 56--95 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
46 TATTCATAAA
56 TTAATTCATTTTAT
1 TTAATTCATTTT-T
*
70 TTAATTCATATTT
1 TTAATTCATTTTT
*
83 TAAATTCATTTTT
1 TTAATTCATTTTT
96 CAATCAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (13 bp):
TTAATTCATTTTT
Found at i:852 original size:43 final size:43
Alignment explanation
Indices: 787--1121 Score: 463
Period size: 43 Copynumber: 7.8 Consensus size: 43
777 GCGTCACTAA
* *
787 CTTTAGCGGCGCTTTGCTCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* *
830 CTTTAGCGGCGCTTATCCCACAAATGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* * **
873 CTTTAGCGGCGTTTTTCCCACAAATGCCGCTAAAGGTCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* ***
916 CTTTAGCGGCACTTTTTTTACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* *
959 CTTTAGCGGCGCTTATCCCACAAATGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* * **
1002 CTTTAGCGGCGTTTTTCCCACAAATGCCGCTAAAGGTCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* ***
1045 CTTTAGCGGCACTTTTTTTACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
*
1088 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
1122 AACATGACTT
Statistics
Matches: 253, Mismatches: 39, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 253 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:946 original size:129 final size:129
Alignment explanation
Indices: 787--1121 Score: 607
Period size: 129 Copynumber: 2.6 Consensus size: 129
777 GCGTCACTAA
* ** *
787 CTTTAGCGGCGCTTTGCTCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTATCCCACA
1 CTTTAGCGGCACTTTTTTTACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTATCCCACA
852 AATGCCGCTAAAGACCAAGACCTTTAGCGGCGTTTTTCCCACAAATGCCGCTAAAGGTCAAGAC
66 AATGCCGCTAAAGACCAAGACCTTTAGCGGCGTTTTTCCCACAAATGCCGCTAAAGGTCAAGAC
916 CTTTAGCGGCACTTTTTTTACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTATCCCACA
1 CTTTAGCGGCACTTTTTTTACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTATCCCACA
981 AATGCCGCTAAAGACCAAGACCTTTAGCGGCGTTTTTCCCACAAATGCCGCTAAAGGTCAAGAC
66 AATGCCGCTAAAGACCAAGACCTTTAGCGGCGTTTTTCCCACAAATGCCGCTAAAGGTCAAGAC
* *
1045 CTTTAGCGGCACTTTTTTTACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTCCCACA
1 CTTTAGCGGCACTTTTTTTACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTATCCCACA
*
1110 AACGCCGCTAAA
66 AATGCCGCTAAA
1122 AACATGACTT
Statistics
Matches: 199, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 199 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (129 bp):
CTTTAGCGGCACTTTTTTTACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTATCCCACA
AATGCCGCTAAAGACCAAGACCTTTAGCGGCGTTTTTCCCACAAATGCCGCTAAAGGTCAAGAC
Done.