Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2711
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: 29356
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Found at i:4035 original size:15 final size:15
Alignment explanation
Indices: 3989--4040 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
3979 AAATTAATTG
3989 TTTAAATTTAAATAA
1 TTTAAATTTAAATAA
* *
4004 TTCAAAACTTAAATAA
1 TT-TAAATTTAAATAA
*
4020 TTTAAATTTGAATAA
1 TTTAAATTTAAATAA
4035 TTTAAA
1 TTTAAA
4041 ATATATTTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 18 0.58
16 13 0.42
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (15 bp):
TTTAAATTTAAATAA
Found at i:4500 original size:18 final size:17
Alignment explanation
Indices: 4476--4514 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 17
4466 TGTTTTACAA
4476 TTATATAATATATATTAATT
1 TTATAT-AT-TATA-TAATT
4496 TTATATATTATATAATT
1 TTATATATTATATAATT
4513 TT
1 TT
4515 TATCACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 2 0.11
20 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATATTATATAATT
Found at i:8174 original size:29 final size:29
Alignment explanation
Indices: 8119--8177 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
8109 ATAATAAAAA
* *
8119 ATTATTTTAATTTTTATATTATTAAATTT
1 ATTATTTTAAGTTTCATATTATTAAATTT
* *
8148 ATTATTTT-AGTTTCATATTTTTAAAATT
1 ATTATTTTAAGTTTCATATTATTAAATTT
8176 AT
1 AT
8178 AATAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (29 bp):
ATTATTTTAAGTTTCATATTATTAAATTT
Found at i:8339 original size:20 final size:20
Alignment explanation
Indices: 8314--8352 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
8304 TTACATCATA
8314 TAATATATT-AATATTTTTAT
1 TAATAT-TTAAATATTTTTAT
8334 TAATATTTAAATATTTTTA
1 TAATATTTAAATATTTTTA
8353 ACACTGTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TAATATTTAAATATTTTTAT
Found at i:8402 original size:15 final size:15
Alignment explanation
Indices: 8382--8433 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
8372 TTATTATAAT
8382 TTAAAAATATAAATA
1 TTAAAAATATAAATA
8397 TT-AAAATATTAAAT-
1 TTAAAAATA-TAAATA
* * *
8411 TTAATAACATAAAAA
1 TTAAAAATATAAATA
8426 TTAAAAAT
1 TTAAAAAT
8434 TCCTTTCATT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
TTAAAAATATAAATA
Found at i:8412 original size:29 final size:30
Alignment explanation
Indices: 8373--8431 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
8363 TTTTTTTATT
* *
8373 TATTATAATTTAAAAATATAAATATTAAAA
1 TATTATAATTTAAAAACATAAAAATTAAAA
*
8403 TATTA-AATTTAATAACATAAAAATTAAAA
1 TATTATAATTTAAAAACATAAAAATTAAAA
8432 ATTCCTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (30 bp):
TATTATAATTTAAAAACATAAAAATTAAAA
Found at i:9352 original size:3 final size:3
Alignment explanation
Indices: 9344--9379 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
9334 TATGAAATTT
9344 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9380 CTTGGACAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10642 original size:2 final size:2
Alignment explanation
Indices: 10635--10668 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10625 TTTATAACAA
10635 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10669 GTAGTTATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11145 original size:5 final size:5
Alignment explanation
Indices: 11130--11178 Score: 64
Period size: 5 Copynumber: 9.6 Consensus size: 5
11120 TACTTTATCT
*
11130 TATTA TAATTA TATTA TATTA TACTA GT-TTA TATTA TATTA TATTA TAT
1 TATTA T-ATTA TATTA TATTA TATTA -TATTA TATTA TATTA TATTA TAT
11179 CCTAGGAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 1 0.03
5 32 0.82
6 6 0.15
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:11350 original size:23 final size:23
Alignment explanation
Indices: 11314--11358 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
11304 CATCAATCAT
11314 ATTTTAATAGTATATAAATATAA
1 ATTTTAATAGTATATAAATATAA
*
11337 ATTTTAGATA-TATATATATATA
1 ATTTTA-ATAGTATATAAATATA
11359 TAAAGTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
ATTTTAATAGTATATAAATATAA
Found at i:12277 original size:2 final size:2
Alignment explanation
Indices: 12270--12303 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12260 CATTTATTAG
12270 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12304 TGGCTGTCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17664 original size:28 final size:28
Alignment explanation
Indices: 17620--17674 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
17610 CATCACTTAT
17620 AGGTTTGATTTCCTAAACCACCAACAAC
1 AGGTTTGATTTCCTAAACCACCAACAAC
*
17648 AGGTTTGATTTCTTAAACCACCAACAA
1 AGGTTTGATTTCCTAAACCACCAACAA
17675 TAGTAGTAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.27
Consensus pattern (28 bp):
AGGTTTGATTTCCTAAACCACCAACAAC
Found at i:18234 original size:13 final size:12
Alignment explanation
Indices: 18218--18283 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 12
18208 AACAAGAGAG
18218 AAGAAGGAAAAAA
1 AAGAA-GAAAAAA
*
18231 AAGATAAAAAAAA
1 AAGA-AGAAAAAA
18244 AAGAAAGAAAGAAAA
1 AAG-AAG-AA-AAAA
*
18259 AAGAA-AAAGAA
1 AAGAAGAAAAAA
18270 AAGATAGAAAAAA
1 AAGA-AGAAAAAA
18283 A
1 A
18284 GTGAAAAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
11 7 0.16
12 3 0.07
13 20 0.47
14 6 0.14
15 7 0.16
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (12 bp):
AAGAAGAAAAAA
Found at i:18247 original size:26 final size:24
Alignment explanation
Indices: 18218--18283 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 24
18208 AACAAGAGAG
*
18218 AAGAAGGAAAAAAAAGATAAAAAAAA
1 AAGAA-GAAAAAAAA-AGAAAAAAAA
*
18244 AAGAAAGAAAGAAAAAAGAAAAAGAA
1 AAG-AAGAAA-AAAAAAGAAAAAAAA
18270 AAGATAGAAAAAAA
1 AAGA-AGAAAAAAA
18284 GTGAAAAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
25 5 0.14
26 23 0.66
27 7 0.20
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (24 bp):
AAGAAGAAAAAAAAAGAAAAAAAA
Found at i:18261 original size:11 final size:11
Alignment explanation
Indices: 18225--18282 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
18215 GAGAAGAAGG
18225 AAAAA-AAAGA
1 AAAAAGAAAGA
18235 TAAAAA-AAA-A
1 -AAAAAGAAAGA
*
18245 AGAAAGAAAGA
1 AAAAAGAAAGA
18256 AAAAAGAAA-A
1 AAAAAGAAAGA
*
18266 AGAAAAGATAGA
1 A-AAAAGAAAGA
18278 AAAAA
1 AAAAA
18283 AGTGAAAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 4 0.10
10 6 0.15
11 28 0.70
12 2 0.05
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:18272 original size:22 final size:21
Alignment explanation
Indices: 18224--18283 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
18214 AGAGAAGAAG
*
18224 GAAAAAAAAGATAAAAAAAAAA
1 GAAAAGAAAGA-AAAAAAAAAA
18246 G-AAAGAAAGAAAAAAGAAAAA
1 GAAAAGAAAGAAAAAA-AAAAA
*
18267 GAAAAGATAGAAAAAAA
1 GAAAAGAAAGAAAAAAA
18284 GTGAAAAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 5 0.15
21 15 0.44
22 14 0.41
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (21 bp):
GAAAAGAAAGAAAAAAAAAAA
Found at i:18291 original size:26 final size:25
Alignment explanation
Indices: 18226--18291 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
18216 AGAAGAAGGA
18226 AAAAAAAGAT-AAAAAAAAAAGAAAG
1 AAAAAAAG-TGAAAAAAAAAAGAAAG
** * *
18251 AAAGAAAAAAGAAAAAGAAAAGATAG
1 AAA-AAAAGTGAAAAAAAAAAGAAAG
18277 AAAAAAAGTGAAAAA
1 AAAAAAAGTGAAAAA
18292 GGATAAGTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
25 13 0.39
26 20 0.61
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (25 bp):
AAAAAAAGTGAAAAAAAAAAGAAAG
Found at i:28061 original size:52 final size:52
Alignment explanation
Indices: 27913--28041 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
27903 CGAAATATGA
27913 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* * *
27965 AAATTTACCTGCATGTATCAATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
28017 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
28042 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:28141 original size:19 final size:18
Alignment explanation
Indices: 28117--28214 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
28107 TAGCTTACAT
28117 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
28136 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
28149 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
28168 TGTATCGATAC--A-TT-
1 TGTATCGATACAAACTTA
28182 T-TATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
28201 TGTATCGATACAAA
1 TGTATCGATACAAA
28215 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 20 0.30
14 2 0.03
15 2 0.03
16 4 0.06
18 3 0.05
19 24 0.36
20 11 0.17
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:28153 original size:32 final size:32
Alignment explanation
Indices: 28112--28212 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
28102 GGCAGTAGCT
*
28112 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
28144 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
*
28176 TACATTTTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
28209 TACA
1 TACA
28213 AATCGTTGAA
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 51 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:28154 original size:13 final size:13
Alignment explanation
Indices: 28136--28192 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
28126 ACAAAACTTA
28136 TGTATCGATACAT
1 TGTATCGATACAT
28149 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
28167 ATGTATCGATACAT
1 -TGTATCGATACAT
*
28181 TTTATCGATACA
1 TGTATCGATACA
28193 ACACTTTATG
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 20 0.54
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Done.