Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1953
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: 15333
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Found at i:444 original size:50 final size:51
Alignment explanation
Indices: 343--499 Score: 271
Period size: 52 Copynumber: 3.0 Consensus size: 51
333 TGTGGGGACG
343 AATTTGCCCAGATGTATCGATACACTATAAAATGTATCGATACATGCAGGCA
1 AATTTGCCCAGATGTATCGATACACTAT-AAATGTATCGATACATGCAGGCA
395 AATTTGCCCAGATGTATCGATAC-CTATAAATGTATCGATACATGCAGGCA
1 AATTTGCCCAGATGTATCGATACACTATAAATGTATCGATACATGCAGGCA
*
445 AATTTTGCCCAGATGTATCGATACACTATTCAATGTATCGATACATGCAGGCA
1 AA-TTTGCCCAGATGTATCGATACACTA-TAAATGTATCGATACATGCAGGCA
498 AA
1 AA
500 ATTTTTTCAT
Statistics
Matches: 101, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
50 25 0.25
51 25 0.25
52 26 0.26
53 25 0.25
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (51 bp):
AATTTGCCCAGATGTATCGATACACTATAAATGTATCGATACATGCAGGCA
Found at i:499 original size:53 final size:53
Alignment explanation
Indices: 345--504 Score: 272
Period size: 50 Copynumber: 3.1 Consensus size: 53
335 TGGGGACGAA
*
345 TTTGCCCAGATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAA-
1 TTTGCCCAGATGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAAT
397 TTTGCCCAGATGTATCGATAC-CTA-TAAATGTATCGATACATGCAGGCAAAT
1 TTTGCCCAGATGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAAT
*
448 TTTGCCCAGATGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAAAT
1 TTTGCCCAGATGTATCGATACACTATTAAATGTATCGATACATGCAGGC-AAAT
502 TTT
1 TTT
505 TTCATATTTC
Statistics
Matches: 102, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
50 25 0.25
51 24 0.24
52 24 0.24
53 22 0.22
54 7 0.07
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (53 bp):
TTTGCCCAGATGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAAT
Found at i:7066 original size:12 final size:12
Alignment explanation
Indices: 7049--7073 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7039 AATAATCATC
7049 ATAATGACAAGT
1 ATAATGACAAGT
7061 ATAATGACAAGT
1 ATAATGACAAGT
7073 A
1 A
7074 AAAGAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (12 bp):
ATAATGACAAGT
Found at i:8129 original size:23 final size:24
Alignment explanation
Indices: 8081--8130 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
8071 ATATTTTTTA
* *
8081 TTTTTTAAAACAAATAAAGATCAT
1 TTTTTTAAAACAAATAAACATAAT
*
8105 TTTTTTAAAA-AAA-AAACATAAA
1 TTTTTTAAAACAAATAAACATAAT
8127 TTTT
1 TTTT
8131 GAACTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 10 0.43
23 3 0.13
24 10 0.43
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (24 bp):
TTTTTTAAAACAAATAAACATAAT
Found at i:8287 original size:12 final size:12
Alignment explanation
Indices: 8270--8298 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
8260 TTTTCAAAAT
8270 ATATATATATAC
1 ATATATATATAC
8282 ATATATATATAC
1 ATATATATATAC
8294 ATATA
1 ATATA
8299 AATAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:11114 original size:3 final size:3
Alignment explanation
Indices: 11106--11139 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
11096 TCTGAGTCAA
* *
11106 CAT CAT CAT CAT CAT CAC CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
11140 TTTGATGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.38, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:12756 original size:13 final size:13
Alignment explanation
Indices: 12738--12762 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12728 CAATTCTTCA
12738 TGTATCGATACAT
1 TGTATCGATACAT
12751 TGTATCGATACA
1 TGTATCGATACA
12763 ATGTGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:12760 original size:33 final size:33
Alignment explanation
Indices: 12718--12782 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
12708 TTTGAGTCAA
12718 TGTATCGATACAAT-T-CTTCATGTATCGATACAT
1 TGTATCGATACAATGTGC--CATGTATCGATACAT
12751 TGTATCGATACAATGTGCCATGTATCGATACA
1 TGTATCGATACAATGTGCCATGTATCGATACA
12783 AACAGTGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATCGATACAT
Found at i:14630 original size:153 final size:152
Alignment explanation
Indices: 14462--15042 Score: 570
Period size: 153 Copynumber: 3.8 Consensus size: 152
14452 AAATATGGAG
* * * * *
14462 TTTTTTACTTTATAAATTTCTCCGGTAGGATTTTTCTAAATTTATAATTTTTACAATTCTTTAAA
1 TTTTCTACTCTATAAATTTCTCCGGTAGGATTTTTCTAAGTTTATAATTTTTAAAATTCTTCAAA
* * *
14527 TATTATTGTTTAACTCATATT-AATTCAGTTTTGAAAATTTTAATTTATTTTAAGAGTTTTAGAA
66 TATTATTGTTTAACTCATATTAAATT-AGTTTTGAAAAATTCAATTTATTTTAAGAGTTTTAAAA
* * * *
14591 TTTTTCTGTTACAAAAATATAGAA
130 ATTTTCTATTAC-AAGATACAGAA
* * * *
14615 TTTTCTACTCCATAAATTTCTCAC-GTAGGATTTTTCTGAGTTTATAATTTTCAAAATTCTTCAG
1 TTTTCTACTCTATAAATTTCTC-CGGTAGGATTTTTCTAAGTTTATAATTTTTAAAATTCTTCAA
* *
14679 ATATTATGGTTTAATTCATATTAAATTA-TTTTGAAAAAATT-AATTTATTTTATA-AGTTTTAA
65 ATATTATTGTTTAACTCATATTAAATTAGTTTTG-AAAAATTCAATTTATTTTA-AGAGTTTTAA
* *
14741 AAATTTTCTTTTTATCAAGATCCA-AA
128 AAATTTTC-TATTA-CAAGATACAGAA
* * * ** *
14767 GTTTTCTATTCTGTAATTTTCTCTAGTCGGA--TTTCTAAGTTTATAATTTTTAAAATTCTTCAA
1 -TTTTCTACTCTATAAATTTCTCCGGTAGGATTTTTCTAAGTTTATAATTTTTAAAATTCTTCAA
* * * * *
14830 ATATTATTGTTTAACTCACATTTAA-TCGGTTTGAAAAATTCAATTTATTTTATGAGTTTTAAAA
65 ATATTATTGTTTAACTCATATTAAATTAGTTTTGAAAAATTCAATTTATTTTAAGAGTTTTAAAA
* *
14894 ATTTTCTAATACCAAGATACAGAG
130 ATTTTCTATTA-CAAGATACAGAA
* * * * * * * *
14918 TGTTT-TACTCTATAAATTTTTTCGATTGGATTTTTCTCAGCTTAAAATTTTTAAAATTCATCAA
1 T-TTTCTACTCTATAAATTTCTCCGGTAGGATTTTTCTAAGTTTATAATTTTTAAAATTCTTCAA
* * * * * * *
14982 ATATTTTTATTAAATTCATATTAAATTAGTTTTTAAAAATTCAATTTATTTGATGAGTTTT
65 ATATTATTGTTTAACTCATATTAAATTAGTTTTGAAAAATTCAATTTATTTTAAGAGTTTT
15043 GCATTTTTTT
Statistics
Matches: 350, Mismatches: 62, Indels: 32
0.79 0.14 0.07
Matches are distributed among these distances:
150 36 0.10
151 85 0.24
152 79 0.23
153 144 0.41
154 6 0.02
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.49
Consensus pattern (152 bp):
TTTTCTACTCTATAAATTTCTCCGGTAGGATTTTTCTAAGTTTATAATTTTTAAAATTCTTCAAA
TATTATTGTTTAACTCATATTAAATTAGTTTTGAAAAATTCAATTTATTTTAAGAGTTTTAAAAA
TTTTCTATTACAAGATACAGAA
Found at i:15231 original size:13 final size:13
Alignment explanation
Indices: 15213--15260 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
15203 TTAGTCCTTC
15213 TAATATATTTTTA
1 TAATATATTTTTA
*
15226 TAATATAATTTTA
1 TAATATATTTTTA
* * *
15239 CAATATATATATA
1 TAATATATTTTTA
15252 TATATATAT
1 TA-ATATAT
15261 AAATATCTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 22 0.79
14 6 0.21
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATATATTTTTA
Done.