Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2734
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: 32558
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Found at i:3603 original size:18 final size:17
Alignment explanation
Indices: 3580--3637 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
3570 TTGGAGTCAA
3580 ATTTTTTGAACTTCCACT
1 ATTTTTTGAACTT-CACT
* * *
3598 A-TTTTTGGA-GTCA-A
1 ATTTTTTGAACTTCACT
3612 ATTTTTTGAACTTTCACT
1 ATTTTTTGAAC-TTCACT
3630 ATTTTTTG
1 ATTTTTTG
3638 TAAAAACATA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
14 1 0.03
15 9 0.30
16 1 0.03
17 10 0.33
18 9 0.30
ACGTcount: A:0.22, C:0.14, G:0.10, T:0.53
Consensus pattern (17 bp):
ATTTTTTGAACTTCACT
Found at i:3619 original size:15 final size:15
Alignment explanation
Indices: 3568--3619 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3558 CAGCTGATAA
3568 TTTTGGAGTCAAATT
1 TTTTGGAGTCAAATT
* * * *
3583 TTTTGAACTTCCACTAT
1 TTTTGGA-GTCAAAT-T
3600 TTTTGGAGTCAAATT
1 TTTTGGAGTCAAATT
3615 TTTTG
1 TTTTG
3620 AACTTTCACT
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 12 0.44
16 8 0.30
17 7 0.26
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (15 bp):
TTTTGGAGTCAAATT
Found at i:3637 original size:33 final size:32
Alignment explanation
Indices: 3568--3635 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
3558 CAGCTGATAA
3568 TTTTGGAGTCAAATTTTTTGAACTTCCACTAT
1 TTTTGGAGTCAAATTTTTTGAACTTCCACTAT
*
3600 TTTTGGAGTCAAATTTTTTGAACTTTCACTAT
1 TTTTGGAGTCAAATTTTTTGAACTTCCACTAT
3632 TTTT
1 TTTT
3636 TGTAAAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.24, C:0.13, G:0.12, T:0.51
Consensus pattern (32 bp):
TTTTGGAGTCAAATTTTTTGAACTTCCACTAT
Found at i:5319 original size:29 final size:29
Alignment explanation
Indices: 5283--5342 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
5273 TCTTGTCTTG
5283 TTCATAACATTTTTGTATTAAGATTGTAC
1 TTCATAACATTTTTGTATTAAGATTGTAC
*
5312 TTCATAACATTTTTGTATTATGATTGTAC
1 TTCATAACATTTTTGTATTAAGATTGTAC
5341 TT
1 TT
5343 AATTATGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (29 bp):
TTCATAACATTTTTGTATTAAGATTGTAC
Found at i:7858 original size:181 final size:180
Alignment explanation
Indices: 7554--7918 Score: 660
Period size: 181 Copynumber: 2.0 Consensus size: 180
7544 ATCACAAACC
*
7554 TCTCCTAAATCAAGGAGATTGAAATAAGAAAGACACTAATTACCGATCTGCAGGCAGGCAGGAAT
1 TCTCCTAAATCAAGGAGATTGAAATAAGAAAGACACTAATTACCGATCTCCAGGCAGGCAGGAAT
*
7619 ATAATGAAATCAAAGGGTGACTCAGAGCCGACTAAGTGACGAAAACAGATTCTAAAGCACACCAA
66 ATAATGAAATCAAAGGGTGACTCAGAGCCGACTAAGTGACAAAAACAGATTCTAAAGCACACCAA
7684 GAAAGGCTATTCTTCATTTTTGTGCTGTTCTTGTCAATTAGTAAGCCACCT
131 GAAAGGCTATTCTTCATTTTTGTGCTGTTCTTGTC-ATTAGTAAGCCACCT
*
7735 TCTCCTAAATCAA-GACGATTGAAATAAGAAAGACACTAATTACTGATCTCCAGGCAGGCAGGAA
1 TCTCCTAAATCAAGGA-GATTGAAATAAGAAAGACACTAATTACCGATCTCCAGGCAGGCAGGAA
* *
7799 TATAATGAAATCAAAGGGTGACTCAGAGCTGACTAATTGACAAAAACAGATTCTAAAGCACACCA
65 TATAATGAAATCAAAGGGTGACTCAGAGCCGACTAAGTGACAAAAACAGATTCTAAAGCACACCA
7864 AGAAAGGCTATTCTTCATTTTTGTGCTGTTCTTGTCATTAGTAAGCCACCT
130 AGAAAGGCTATTCTTCATTTTTGTGCTGTTCTTGTCATTAGTAAGCCACCT
7915 TCTC
1 TCTC
7919 TAAGGCATTC
Statistics
Matches: 178, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
180 21 0.12
181 157 0.88
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (180 bp):
TCTCCTAAATCAAGGAGATTGAAATAAGAAAGACACTAATTACCGATCTCCAGGCAGGCAGGAAT
ATAATGAAATCAAAGGGTGACTCAGAGCCGACTAAGTGACAAAAACAGATTCTAAAGCACACCAA
GAAAGGCTATTCTTCATTTTTGTGCTGTTCTTGTCATTAGTAAGCCACCT
Found at i:10908 original size:18 final size:16
Alignment explanation
Indices: 10854--10908 Score: 51
Period size: 18 Copynumber: 3.3 Consensus size: 16
10844 TAAATTTTAA
*
10854 TTTTATAAAA-GAATT
1 TTTTATAAAATTAATT
10869 TTTT-TAAAATTAATTT
1 TTTTATAAAATTAA-TT
10885 TATTTATAAAATTTTAATT
1 T-TTTATAAAA--TTAATT
10904 TTTTA
1 TTTTA
10909 ATATTACTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
14 5 0.15
15 6 0.18
16 3 0.09
17 3 0.09
18 9 0.27
19 3 0.09
20 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TTTTATAAAATTAATT
Found at i:18176 original size:25 final size:25
Alignment explanation
Indices: 18142--18193 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
18132 TTTAAACAAC
18142 CAGGTTTAATAGCTACTGTTTGGAT
1 CAGGTTTAATAGCTACTGTTTGGAT
18167 CAGGTTTAATAGCTACTGTTTGGAT
1 CAGGTTTAATAGCTACTGTTTGGAT
18192 CA
1 CA
18194 ATACTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (25 bp):
CAGGTTTAATAGCTACTGTTTGGAT
Found at i:19060 original size:20 final size:21
Alignment explanation
Indices: 19032--19072 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
19022 TTGGACTAAA
19032 AAATAA-TTTAAAAAATTATT
1 AAATAATTTTAAAAAATTATT
*
19052 AAATTATTTTAAAAAATTATT
1 AAATAATTTTAAAAAATTATT
19073 TAAGTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATAATTTTAAAAAATTATT
Found at i:19064 original size:21 final size:22
Alignment explanation
Indices: 19038--19081 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
19028 TAAAAAATAA
19038 TTTAAAAAATTA-TTAAATTAT
1 TTTAAAAAATTATTTAAATTAT
*
19059 TTTAAAAAATTATTTAAGTTAT
1 TTTAAAAAATTATTTAAATTAT
19081 T
1 T
19082 AGGCATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTAAAAAATTATTTAAATTAT
Found at i:30897 original size:19 final size:19
Alignment explanation
Indices: 30861--30920 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
30851 TAAGAAAGTT
* *
30861 TAATTGAATAATATACATTA
1 TAATT-AATATTACACATTA
*
30881 TAATTAATATTACACATTG
1 TAATTAATATTACACATTA
*
30900 TAATTAATATTACACAATA
1 TAATTAATATTACACATTA
30919 TA
1 TA
30921 TTATTATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.86
20 5 0.14
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.40
Consensus pattern (19 bp):
TAATTAATATTACACATTA
Done.