Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6257.1
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: 12834
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.26
Warning! 1993 characters in sequence are not A, C, G, or T
Found at i:542 original size:56 final size:56
Alignment explanation
Indices: 456--564 Score: 209
Period size: 56 Copynumber: 1.9 Consensus size: 56
446 GGGTGTTACA
456 CTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTTTTGCCCTTG
1 CTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTTTTGCCCTTG
*
512 CTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTTTTGCCC
1 CTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTTTTGCCC
565 ATCATCCCTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.22, C:0.23, G:0.08, T:0.47
Consensus pattern (56 bp):
CTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTTTTGCCCTTG
Found at i:1879 original size:40 final size:40
Alignment explanation
Indices: 1834--2834 Score: 1842
Period size: 40 Copynumber: 25.1 Consensus size: 40
1824 CGAATACACG
* * * * *
1834 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
* * * *** * *
1874 ACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
*
1914 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
*
1954 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
*
1994 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2034 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2074 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2114 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2154 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2194 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2234 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2274 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2314 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2354 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2394 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2434 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2474 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2514 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2554 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2594 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2634 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2674 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2714 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2754 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
*
2794 TCACTAGCATGAATGCTCTTCGGTACTTAGCCCGGAT-CA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
2833 TC
1 TC
2835 GTCGAGACCT
Statistics
Matches: 941, Mismatches: 20, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
39 4 0.00
40 937 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
Found at i:3998 original size:32 final size:32
Alignment explanation
Indices: 3962--4026 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
3952 AAGTTTCAAG
3962 TAATGAAATCGGCTTTGACTAAAGTATTACAT
1 TAATGAAATCGGCTTTGACTAAAGTATTACAT
3994 TAATGAAATCGGCTTTGACTAAAGTATTACAT
1 TAATGAAATCGGCTTTGACTAAAGTATTACAT
4026 T
1 T
4027 CACATAGCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.35
Consensus pattern (32 bp):
TAATGAAATCGGCTTTGACTAAAGTATTACAT
Found at i:4375 original size:40 final size:40
Alignment explanation
Indices: 4315--4537 Score: 365
Period size: 40 Copynumber: 5.6 Consensus size: 40
4305 CAAGCTCAAT
* * * * *
4315 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
*
4355 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
*
4395 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGAACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
* *
4435 TGCCTTCGGGTCTTAGCCCGTATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
4475 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
4515 TGCCTTCGGGTCTTAGCCCGGAT
1 TGCCTTCGGGTCTTAGCCCGGAT
4538 GTATTCAAAT
Statistics
Matches: 170, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 170 1.00
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
Found at i:6564 original size:38 final size:38
Alignment explanation
Indices: 6522--6596 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
6512 GAATTTTAAT
*
6522 CCGGACATAATCTCTGT-ACATAGCCATCGGGTCTTTAC
1 CCGGACATAATCTCT-TCACATAGCCAGCGGGTCTTTAC
* *
6560 CCGGACATAATCTCTTCATATAGTCAGCGGGTCTTTA
1 CCGGACATAATCTCTTCACATAGCCAGCGGGTCTTTA
6597 AACTCGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (38 bp):
CCGGACATAATCTCTTCACATAGCCAGCGGGTCTTTAC
Found at i:10856 original size:60 final size:60
Alignment explanation
Indices: 10772--10911 Score: 169
Period size: 60 Copynumber: 2.3 Consensus size: 60
10762 CAGTGTTAAC
*
10772 TGGGCCTCAGCCCATATCAATATTAATCTGGGCCATAGCCC-CTTAC-AGT-ATCAGAGTATAT
1 TGGGCCT-AGCCCATATCAATATTAATCTGGGCCATAGCCCTATTACGAGTCA--AGA-TATAT
* * * *
10833 TGGGCCTAGCCCATATCATTATTAATCTGGGTCGTCGCCCTATTACGAGTCAAGATATAT
1 TGGGCCTAGCCCATATCAATATTAATCTGGGCCATAGCCCTATTACGAGTCAAGATATAT
*
10893 TGGGCCTTGCCCATATCAA
1 TGGGCCTAGCCCATATCAA
10912 CACAGTTGGG
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
60 51 0.74
61 14 0.20
62 3 0.04
63 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (60 bp):
TGGGCCTAGCCCATATCAATATTAATCTGGGCCATAGCCCTATTACGAGTCAAGATATAT
Found at i:10926 original size:20 final size:19
Alignment explanation
Indices: 10901--10946 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
10891 ATTGGGCCTT
10901 GCCCATATCAACACAGTTGG
1 GCCCATATCAACACAGTT-G
* * *
10921 GCCCATTTTAATACAGTTG
1 GCCCATATCAACACAGTTG
10940 GCCCATA
1 GCCCATA
10947 ACAAAATAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (19 bp):
GCCCATATCAACACAGTTG
Done.