Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1761
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: 14192
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:693 original size:29 final size:29
Alignment explanation
Indices: 613--695 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
603 AACTAAAATG
* *
613 AGCTAAGCTTTAGCTCGTGAGCTAAAGTTG
1 AGCTAAG-TTTAGCTCGTGAGCTGAAGTTA
* * * *
643 AGCTGAAG-CTAACTCCTAAGCTGAAGTTA
1 AGCT-AAGTTTAGCTCGTGAGCTGAAGTTA
672 AGCTAAGTTTAGCTCGTGAGCTGA
1 AGCTAAGTTTAGCTCGTGAGCTGA
696 TAATGACTAG
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
28 3 0.07
29 31 0.76
30 4 0.10
31 3 0.07
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (29 bp):
AGCTAAGTTTAGCTCGTGAGCTGAAGTTA
Found at i:4227 original size:28 final size:28
Alignment explanation
Indices: 4195--4250 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
4185 GATTCAAAGA
*
4195 TGGGTTTATGGATATGAAGTTTATGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
*
4223 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
4251 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (28 bp):
TGGGTTTATGGATATAAAGTTTATGTAG
Found at i:6305 original size:11 final size:10
Alignment explanation
Indices: 6287--6316 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
6277 GTTATACAAG
6287 TCAAAAAAAT
1 TCAAAAAAAT
6297 TCGAAAAAAAT
1 TC-AAAAAAAT
6308 TCAAAAAAA
1 TCAAAAAAA
6317 AATTTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.70, C:0.10, G:0.03, T:0.17
Consensus pattern (10 bp):
TCAAAAAAAT
Found at i:7265 original size:9 final size:10
Alignment explanation
Indices: 7258--7320 Score: 58
Period size: 11 Copynumber: 6.0 Consensus size: 10
7248 AAGAGAAAAC
7258 AAAGAAAAGA
1 AAAGAAAAGA
7268 AAAGAAAAAGA
1 AAAG-AAAAGA
*
7279 AAA-AGAAGAA
1 AAAGAAAAG-A
7289 AAAGAAAAAGA
1 AAAG-AAAAGA
7300 AAATGAAATA-A
1 AAA-GAAA-AGA
7311 AAAGAAAAGA
1 AAAGAAAAGA
7321 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
9 5 0.11
10 13 0.30
11 20 0.45
12 6 0.14
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:7268 original size:5 final size:5
Alignment explanation
Indices: 7258--7320 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
7248 AAGAGAAAAC
*
7258 AAAGA AAAGA AAAGAA AAAGA AAA-A GAAGAA AAAGAA AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAG-A AAAG-A AAAGA AAA-GA
7306 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
7321 GAGGCAAGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
4 4 0.08
5 26 0.52
6 19 0.38
7 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:7289 original size:15 final size:15
Alignment explanation
Indices: 7258--7300 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
7248 AAGAGAAAAC
*
7258 AAAGAAAAGAAAAGAA
1 AAAGAAAA-AGAAGAA
7274 AAAGAAAAAGAAGAA
1 AAAGAAAAAGAAGAA
7289 AAAGAAAAAGAA
1 AAAGAAAAAGAA
7301 AATGAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGAAGAA
Found at i:7291 original size:21 final size:21
Alignment explanation
Indices: 7258--7318 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 21
7248 AAGAGAAAAC
7258 AAAGAAAAGAAAAGAAAAAGAA
1 AAAGAAAA-AAAAGAAAAAGAA
*
7280 AAAGAAGAAAAAGAAAAAGAA
1 AAAGAAAAAAAAGAAAAAGAA
*
7301 AATGAAATAAAAAGAAAA
1 AAAGAAA-AAAAAGAAAA
7319 GAGAGGCAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.03
Consensus pattern (21 bp):
AAAGAAAAAAAAGAAAAAGAA
Found at i:7318 original size:6 final size:6
Alignment explanation
Indices: 7258--7307 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
7248 AAGAGAAAAC
7258 AAAG-A AAAG-A AAAGAA AAAGAA AAAG-- -AAGAA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
*
7301 AATGAA A
1 AAAGAA A
7308 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
3 3 0.08
5 9 0.22
6 28 0.70
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:7320 original size:21 final size:21
Alignment explanation
Indices: 7258--7318 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
7248 AAGAGAAAAC
*
7258 AAAGAAAAGAAAAGAAAAAGAA
1 AAAGAAGA-AAAAGAAAAAGAA
7280 AAAGAAGAAAAAGAAAAAGAA
1 AAAGAAGAAAAAGAAAAAGAA
* *
7301 AATGAAATAAAAAGAAAA
1 AAAG-AAGAAAAAGAAAA
7319 GAGAGGCAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 16 0.46
22 19 0.54
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.03
Consensus pattern (21 bp):
AAAGAAGAAAAAGAAAAAGAA
Found at i:7423 original size:30 final size:31
Alignment explanation
Indices: 7389--7470 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
7379 TTTGAAAAGC
*
7389 AAAAAGAAAAAGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
* * *
7419 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
* *
7449 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAAAGAAAAAGAAAT
7471 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.66, C:0.01, G:0.22, T:0.11
Consensus pattern (31 bp):
AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
Found at i:7443 original size:24 final size:24
Alignment explanation
Indices: 7394--7463 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
7384 AAAGCAAAAA
*
7394 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAATGAAATT
* *
7418 GAAAAAGAGAACGAAAA-GAAATTT
1 GAAAAAGAAAAAGAAAATGAAA-TT
* ** *
7442 GAGAGTGAAAAAGAAGATGAAA
1 GAAAAAGAAAAAGAAAATGAAA
7464 AAGAAATTGA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
23 3 0.09
24 28 0.80
25 4 0.11
ACGTcount: A:0.63, C:0.01, G:0.24, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAATGAAATT
Found at i:8049 original size:19 final size:19
Alignment explanation
Indices: 8025--8064 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
8015 AGCTCCCATG
8025 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
* *
8044 TAGCTCGAGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
8063 TA
1 TA
8065 TCAGCTCACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:9705 original size:9 final size:10
Alignment explanation
Indices: 9693--9739 Score: 62
Period size: 9 Copynumber: 4.7 Consensus size: 10
9683 TATACAAGTT
9693 AAAAAAATCA
1 AAAAAAATCA
9703 AAAAAAATTCGA
1 AAAAAAA-TC-A
9715 AAAAAAAT-A
1 AAAAAAATCA
9724 AAAAAAAT-A
1 AAAAAAATCA
9733 AAAAAAA
1 AAAAAAA
9740 AGTGATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
9 17 0.49
10 7 0.20
11 3 0.09
12 8 0.23
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.11
Consensus pattern (10 bp):
AAAAAAATCA
Found at i:9740 original size:10 final size:11
Alignment explanation
Indices: 9693--9740 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
9683 TATACAAGTT
9693 AAAAAAATCAA
1 AAAAAAATCAA
* *
9704 AAAAAATTCGA
1 AAAAAAATCAA
9715 AAAAAAAT--A
1 AAAAAAATCAA
9724 AAAAAAAT-AA
1 AAAAAAATCAA
9734 AAAAAAA
1 AAAAAAA
9741 GTGATTTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
9 9 0.27
10 8 0.24
11 16 0.48
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.10
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:10951 original size:19 final size:19
Alignment explanation
Indices: 10927--10966 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
10917 AGCTCCCATG
10927 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
10946 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
10965 TA
1 TA
10967 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Done.