Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2777
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: 15174
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Found at i:405 original size:43 final size:43
Alignment explanation
Indices: 369--683 Score: 178
Period size: 43 Copynumber: 7.4 Consensus size: 43
359 AAAATGCTAT
*
369 TATAAAACATGACCTTTAGCGGTGCTTTTCCCAAAAACGCCAC
1 TATAAAACATGACCTTTAGCGGCGCTTTTCCCAAAAACGCCAC
* * * ** * *
412 TATAGAATATGACTTTTAGCGGCGCTTTTCCCCTAAACACCGC
1 TATAAAACATGACCTTTAGCGGCGCTTTTCCCAAAAACGCCAC
* * * * * ** * * *
455 CATAGAACCTAACTTTTAGCGGCGCTTTT-TTACAAACACCGC
1 TATAAAACATGACCTTTAGCGGCGCTTTTCCCAAAAACGCCAC
* * * * * *
497 TATAGAACATGACCTTTAGTGGTGTTTTTTCCACAAAA-GCCGC
1 TATAAAACATGACCTTTAGCGGCGCTTTTCCCA-AAAACGCCAC
* * * *
540 TATAGAATCA-GACCTTTAGCGGCGC-TCTCCCACAAATG-CAGC
1 TATA-AAACATGACCTTTAGCGGCGCTTTTCCCAAAAACGCCA-C
* ** *
582 TATAAAACATGACTTTTAGCGTTGCTTTTCCCAAAAATGCCAC
1 TATAAAACATGACCTTTAGCGGCGCTTTTCCCAAAAACGCCAC
* * * * * * * *
625 TATTAAACA-AACCTTTAACGACGC-TTTCTCACAAACGTCGC
1 TATAAAACATGACCTTTAGCGGCGCTTTTCCCAAAAACGCCAC
666 TA-AAGAACATGACCTTTA
1 TATAA-AACATGACCTTTA
684 AAAAAATATT
Statistics
Matches: 207, Mismatches: 55, Indels: 21
0.73 0.19 0.07
Matches are distributed among these distances:
40 1 0.00
41 26 0.13
42 71 0.34
43 101 0.49
44 8 0.04
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (43 bp):
TATAAAACATGACCTTTAGCGGCGCTTTTCCCAAAAACGCCAC
Found at i:4936 original size:15 final size:15
Alignment explanation
Indices: 4910--4945 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
4900 AATTATAAAT
4910 CATAAA-CCATAATC
1 CATAAACCCATAATC
*
4924 CCTAAACCCATAATC
1 CATAAACCCATAATC
4939 CATAAAC
1 CATAAAC
4946 TTTAAAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.19
Consensus pattern (15 bp):
CATAAACCCATAATC
Found at i:5145 original size:40 final size:41
Alignment explanation
Indices: 5090--5196 Score: 155
Period size: 40 Copynumber: 2.7 Consensus size: 41
5080 AATTTTTTGC
* * *
5090 GGCGTTTTTCAAAAAGCGCCGCTAGTGGTCGACCTATAG-A
1 GGCGTTTTTTAAAAAGCGCCGCTAATGATCGACCTATAGCA
*
5130 GGCGTTTTTTAAAAAGCGCCGCTAATGATCGATCTATAGCA
1 GGCGTTTTTTAAAAAGCGCCGCTAATGATCGACCTATAGCA
*
5171 -ACGTTTTTTAAAAAGCGCCGCTAATG
1 GGCGTTTTTTAAAAAGCGCCGCTAATG
5197 CCACTAAACT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 60 0.98
41 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (41 bp):
GGCGTTTTTTAAAAAGCGCCGCTAATGATCGACCTATAGCA
Found at i:5322 original size:39 final size:39
Alignment explanation
Indices: 5250--5402 Score: 175
Period size: 39 Copynumber: 3.9 Consensus size: 39
5240 TTTCAGCGTT
* * *
5250 TTTTTCAAAAAGCGCCGCTAATGGTCGACCTATAACAGTG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTAT-AGAGTG
*
5290 TTTTTTAAAAAGCGCC-CTAATGCTCGATCTATAGAG-G
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGAGTG
* * * ** *
5327 CATTTTTCAAAAAGCGCCACTGATGTTTAATCTATAGTGTG
1 --TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGAGTG
5368 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAG
5403 CGACGTTTTT
Statistics
Matches: 94, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
37 1 0.01
38 3 0.03
39 59 0.63
40 30 0.32
41 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (39 bp):
TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGAGTG
Found at i:5333 original size:154 final size:155
Alignment explanation
Indices: 5022--5347 Score: 430
Period size: 154 Copynumber: 2.1 Consensus size: 155
5012 ATGATAATTA
* * * * *
5022 TTTCAAAAAGCGTCACTAATTCCACTAAAGCCCAACATAAAATGACGGCGTTGTGCTTAATTTTT
1 TTTCAAAAAGCGCCACTAATGCCACTAAAGCCCAACATAAAACGACGACGTTCTGCTTAATTTTT
* * *
5087 TGCGGCGTTTTTCAAAAAGCGCCGCTAGTGGTCGACCTATAGAGGCGTTTTTTAAAAAGCGCCGC
66 TGCAGCGTTTTTCAAAAAGCGCCGCTAATGGTCGACCTATAGAAGCGTTTTTTAAAAAGCGCCGC
5152 TAATGATCGATCTATAGCAACG-TT
131 TAATGATCGATCTATAGCAACGATT
* * *
5176 TTTTAAAAAGCGCCGCTAATGCCACTAAA-CTTCAACATAAAACGACGACGTTCTGCTTAATTTT
1 TTTCAAAAAGCGCCACTAATGCCACTAAAGC-CCAACATAAAACGACGACGTTCTGCTTAATTTT
* *
5240 TTTCAGCGTTTTTTTCAAAAAGCGCCGCTAATGGTCGACCTATA-ACAGTGTTTTTTAAAAAGCG
65 TTGCAGCG--TTTTTCAAAAAGCGCCGCTAATGGTCGACCTATAGA-AGCGTTTTTTAAAAAGCG
* *
5304 CC-CTAATGCTCGATCTATAG--AGGCATT
127 CCGCTAATGATCGATCTATAGCAACG-ATT
5331 TTTCAAAAAGCGCCACT
1 TTTCAAAAAGCGCCACT
5348 GATGTTTAAT
Statistics
Matches: 149, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
153 3 0.02
154 60 0.40
155 35 0.23
156 51 0.34
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (155 bp):
TTTCAAAAAGCGCCACTAATGCCACTAAAGCCCAACATAAAACGACGACGTTCTGCTTAATTTTT
TGCAGCGTTTTTCAAAAAGCGCCGCTAATGGTCGACCTATAGAAGCGTTTTTTAAAAAGCGCCGC
TAATGATCGATCTATAGCAACGATT
Found at i:8688 original size:27 final size:27
Alignment explanation
Indices: 8640--8794 Score: 169
Period size: 27 Copynumber: 5.7 Consensus size: 27
8630 GCGAGGCTGC
* *
8640 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
8667 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
8693 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
8720 CAGATAATTGTGGCATAACCACCAGGA-A
1 CAGAT-ATTGTGGCAGAGCCACCA-GATA
8748 -AGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
8774 CAGATAATTGTGGCATAGCCA
1 CAGAT-ATTGTGGCAGAGCCA
8795 TCAGGACGCT
Statistics
Matches: 111, Mismatches: 7, Indels: 20
0.80 0.05 0.14
Matches are distributed among these distances:
26 12 0.11
27 92 0.83
28 7 0.06
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:8730 original size:54 final size:54
Alignment explanation
Indices: 8658--8800 Score: 227
Period size: 54 Copynumber: 2.6 Consensus size: 54
8648 GTGACGAAGT
*
8658 CACCAGATACAGAT-ATTGTGGCAGAGCCACCA-GAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGAA-AGATATATGTGGCAGAGC
*
8712 CACCAGATCAGATAATTGTGGCATAACCACCAGGAAAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAAAGATATATGTGGCAGAGC
*
8766 CACCAGATCAGATAATTGTGGCATAGCCATCAGGA
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGA
8801 CGCTTCCTCC
Statistics
Matches: 83, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
53 5 0.06
54 75 0.90
55 3 0.04
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGAAAGATATATGTGGCAGAGC
Found at i:10421 original size:26 final size:26
Alignment explanation
Indices: 10390--10497 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
10380 TGAAATGCCC
*
10390 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
10416 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
10442 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
10468 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
10494 ATCA
1 ATCA
10498 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Done.