Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1568
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: 27442
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Found at i:5365 original size:21 final size:21
Alignment explanation
Indices: 5351--5432 Score: 110
Period size: 21 Copynumber: 3.8 Consensus size: 21
5341 GACACATAAA
5351 GTGCCTAAAACGACACACGAG
1 GTGCCTAAAACGACACACGAG
* *
5372 GTGCCTGATACGACACACGAG
1 GTGCCTAAAACGACACACGAG
* *
5393 GTGCCTGATACGACACACGAG
1 GTGCCTAAAACGACACACGAG
5414 GTGCCTAAAATACGACACA
1 GTGCCT-AAA-ACGACACA
5433 TAAAGTGCCT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
21 46 0.84
22 1 0.02
23 8 0.15
ACGTcount: A:0.34, C:0.28, G:0.24, T:0.13
Consensus pattern (21 bp):
GTGCCTAAAACGACACACGAG
Found at i:5442 original size:44 final size:42
Alignment explanation
Indices: 5337--5445 Score: 146
Period size: 42 Copynumber: 2.5 Consensus size: 42
5327 CCTGATCAGT
* * *
5337 ATACGACACATAAAGTGCCTAAAACGACACACGAGGTGCCTG
1 ATACGACACATAAAGTGCCTGATACGACACACGAGGTGCCTA
** *
5379 ATACGACACACGAGGTGCCTGATACGACACACGAGGTGCCTAAA
1 ATACGACACATAAAGTGCCTGATACGACACACGAGGTGCCT--A
5423 ATACGACACATAAAGTGCCTGAT
1 ATACGACACATAAAGTGCCTGAT
5446 CGATAAAGCC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 36 0.64
44 20 0.36
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.16
Consensus pattern (42 bp):
ATACGACACATAAAGTGCCTGATACGACACACGAGGTGCCTA
Found at i:5835 original size:14 final size:14
Alignment explanation
Indices: 5816--5869 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
5806 CATATATATT
5816 ATATAATTCAATCA
1 ATATAATTCAATCA
*
5830 ATATAAATCAATCA
1 ATATAATTCAATCA
* *
5844 AAAT-TTTCAATCA
1 ATATAATTCAATCA
5857 ATATAAATTCAAT
1 ATAT-AATTCAAT
5870 AAATTCATCG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
13 10 0.31
14 16 0.50
15 6 0.19
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (14 bp):
ATATAATTCAATCA
Found at i:11206 original size:21 final size:21
Alignment explanation
Indices: 11192--11271 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
11182 GACACATAAA
11192 GTGCCTAAAACGACACACGAG
1 GTGCCTAAAACGACACACGAG
* *
11213 GTGCCTGATACG--ACACGAG
1 GTGCCTAAAACGACACACGAG
* *
11232 GTGCCTGATACGACACACGAG
1 GTGCCTAAAACGACACACGAG
11253 GTGCCTGAAATACGACACA
1 GTGCCT-AAA-ACGACACA
11272 TAAAGTGCCT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
19 19 0.37
21 23 0.45
22 1 0.02
23 8 0.16
ACGTcount: A:0.33, C:0.28, G:0.26, T:0.14
Consensus pattern (21 bp):
GTGCCTAAAACGACACACGAG
Found at i:11230 original size:19 final size:19
Alignment explanation
Indices: 11206--11270 Score: 94
Period size: 19 Copynumber: 3.2 Consensus size: 19
11196 CTAAAACGAC
11206 ACACGAGGTGCCTGATACG
1 ACACGAGGTGCCTGATACG
11225 ACACGAGGTGCCTGATACG
1 ACACGAGGTGCCTGATACG
11244 ACACACGAGGTGCCTGAAATACG
1 --ACACGAGGTGCCTG--ATACG
11267 ACAC
1 ACAC
11271 ATAAAGTGCC
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
19 19 0.45
21 18 0.43
23 5 0.12
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.14
Consensus pattern (19 bp):
ACACGAGGTGCCTGATACG
Found at i:11245 original size:40 final size:41
Alignment explanation
Indices: 11192--11270 Score: 124
Period size: 40 Copynumber: 1.9 Consensus size: 41
11182 GACACATAAA
11192 GTGCCTAAAACGACACACGAGGTGCCTG-ATACGACACGAG
1 GTGCCTAAAACGACACACGAGGTGCCTGAATACGACACGAG
* *
11232 GTGCCTGATACGACACACGAGGTGCCTGAAATACGACAC
1 GTGCCTAAAACGACACACGAGGTGCCTG-AATACGACAC
11271 ATAAAGTGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 26 0.74
42 9 0.26
ACGTcount: A:0.32, C:0.28, G:0.27, T:0.14
Consensus pattern (41 bp):
GTGCCTAAAACGACACACGAGGTGCCTGAATACGACACGAG
Found at i:11677 original size:15 final size:15
Alignment explanation
Indices: 11652--11709 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
11642 AATCATATAT
11652 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
11668 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
11683 AATAATTTCAATCAA
1 TATAAATTCAATCAA
11698 TATAAATTCAAT
1 TATAAATTCAAT
11710 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:17577 original size:21 final size:21
Alignment explanation
Indices: 17563--17643 Score: 101
Period size: 21 Copynumber: 3.8 Consensus size: 21
17553 GACACATAAA
17563 GTGCCTAAAACGACACACGAG
1 GTGCCTAAAACGACACACGAG
* *
17584 GTGCCTGATACGACACA-GAG
1 GTGCCTAAAACGACACACGAG
* *
17604 GTGCCTGATACGACACACGAG
1 GTGCCTAAAACGACACACGAG
17625 GTGCCTGAAATACGACACA
1 GTGCCT-AAA-ACGACACA
17644 TAAAGTGCCT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
20 20 0.38
21 24 0.45
22 1 0.02
23 8 0.15
ACGTcount: A:0.33, C:0.27, G:0.26, T:0.14
Consensus pattern (21 bp):
GTGCCTAAAACGACACACGAG
Found at i:17617 original size:41 final size:43
Alignment explanation
Indices: 17549--17653 Score: 151
Period size: 41 Copynumber: 2.5 Consensus size: 43
17539 CCTGATCAGT
17549 ATACGACACATAAAGTGCCTAAAACGACACACGAGGTGCCTG-
1 ATACGACACATAAAGTGCCTAAAACGACACACGAGGTGCCTGA
* * * *
17591 ATACGACACA-GAGGTGCCTGATACGACACACGAGGTGCCTGAA
1 ATACGACACATAAAGTGCCTAAAACGACACACGAGGTGCCTG-A
17634 ATACGACACATAAAGTGCCT
1 ATACGACACATAAAGTGCCT
17654 GATCGATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
41 27 0.50
42 10 0.19
43 10 0.19
44 7 0.13
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (43 bp):
ATACGACACATAAAGTGCCTAAAACGACACACGAGGTGCCTGA
Found at i:18051 original size:15 final size:15
Alignment explanation
Indices: 18026--18082 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
18016 TCATATATAT
18026 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
18042 TATAAATTCAATCAA
1 TATAAATTCAATCAA
*
18057 -ATAATTTCAATCAA
1 TATAAATTCAATCAA
18071 TATAAATTCAAT
1 TATAAATTCAAT
18083 AAATTCATCG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 13 0.34
15 21 0.55
16 4 0.11
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:18067 original size:29 final size:27
Alignment explanation
Indices: 18029--18086 Score: 98
Period size: 29 Copynumber: 2.1 Consensus size: 27
18019 TATATATTAT
18029 ATAATTCAATCAATATAAATTCAATCAA
1 ATAATTCAATCAATATAAATTCAAT-AA
18057 ATAATTTCAATCAATATAAATTCAATAA
1 ATAA-TTCAATCAATATAAATTCAATAA
18085 AT
1 AT
18087 TCATCGCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (27 bp):
ATAATTCAATCAATATAAATTCAATAA
Found at i:23994 original size:23 final size:23
Alignment explanation
Indices: 23940--24000 Score: 94
Period size: 21 Copynumber: 2.8 Consensus size: 23
23930 GGCACATAAA
23940 GTGCCT-AAA-ACGACACACGAG
1 GTGCCTGAAATACGACACACGAG
23961 GTGCCTG--ATACGACACACGAG
1 GTGCCTGAAATACGACACACGAG
23982 GTGCCTGAAATACGACACA
1 GTGCCTGAAATACGACACA
24001 TAAAGTGCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.03
21 25 0.69
23 10 0.28
ACGTcount: A:0.34, C:0.28, G:0.25, T:0.13
Consensus pattern (23 bp):
GTGCCTGAAATACGACACACGAG
Found at i:24008 original size:23 final size:23
Alignment explanation
Indices: 23926--24012 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
23916 CCTGATCAAT
* *
23926 ATACGGCACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
23948 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
23968 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
23991 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
24013 TCGATAAAGC
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.02
21 33 0.61
22 1 0.02
23 19 0.35
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:24190 original size:17 final size:18
Alignment explanation
Indices: 24160--24205 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
24150 AATCACATAT
* *
24160 ATTCATCCATTTTCA-CA
1 ATTCATACAATTTCATCA
24177 ATTCATACAATTTCATTCA
1 ATTCATACAATTTCA-TCA
24196 ATTCA-ACAAT
1 ATTCATACAAT
24206 ATATTTCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 13 0.52
18 5 0.20
19 7 0.28
ACGTcount: A:0.37, C:0.24, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTCATACAATTTCATCA
Found at i:24408 original size:15 final size:15
Alignment explanation
Indices: 24383--24439 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
24373 TCATATATAT
24383 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
24399 TATAAATTCAATCAA
1 TATAAATTCAATCAA
*
24414 -ATAATTTCAATCAA
1 TATAAATTCAATCAA
24428 TATAAATTCAAT
1 TATAAATTCAAT
24440 AAATTCATCG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 13 0.34
15 21 0.55
16 4 0.11
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:24424 original size:29 final size:27
Alignment explanation
Indices: 24386--24443 Score: 98
Period size: 29 Copynumber: 2.1 Consensus size: 27
24376 TATATATTAT
24386 ATAATTCAATCAATATAAATTCAATCAA
1 ATAATTCAATCAATATAAATTCAAT-AA
24414 ATAATTTCAATCAATATAAATTCAATAA
1 ATAA-TTCAATCAATATAAATTCAATAA
24442 AT
1 AT
24444 TCATCGCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (27 bp):
ATAATTCAATCAATATAAATTCAATAA
Found at i:27072 original size:9 final size:9
Alignment explanation
Indices: 27058--27148 Score: 67
Period size: 9 Copynumber: 9.8 Consensus size: 9
27048 TTTTATGTGG
27058 TTTGTTTTT
1 TTTGTTTTT
*
27067 TTTGTTTTGA
1 TTTGTTTT-T
27077 TTTGTTTTT
1 TTTGTTTTT
* *
27086 ATTGTTTTG
1 TTTGTTTTT
*
27095 TTTGTTGTT
1 TTTGTTTTT
* *
27104 TTTATTTGT
1 TTTGTTTTT
*
27113 TTTGTATTGAT
1 TTTGT-TT-TT
27124 TTT-TTTTT
1 TTTGTTTTT
27132 TTTGATTTTT
1 TTTG-TTTTT
*
27142 TTAGTTT
1 TTTGTTT
27149 GGTTTTTGTG
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
8 4 0.06
9 36 0.57
10 19 0.30
11 4 0.06
ACGTcount: A:0.08, C:0.00, G:0.14, T:0.78
Consensus pattern (9 bp):
TTTGTTTTT
Found at i:27075 original size:14 final size:14
Alignment explanation
Indices: 27058--27177 Score: 68
Period size: 14 Copynumber: 8.4 Consensus size: 14
27048 TTTTATGTGG
27058 TTTGTTTT-TTTTGT
1 TTTGTTTTGTTTT-T
*
27072 TTTGATTTGTTTTT
1 TTTGTTTTGTTTTT
* *
27086 ATTGTTTTGTTTGT
1 TTTGTTTTGTTTTT
* * *
27100 TGT-TTTTATTTGT
1 TTTGTTTTGTTTTT
*
27113 TTTGTATTGATTTTT
1 TTTGTTTTG-TTTTT
27128 TTT-TTTTGATTTTT
1 TTTGTTTTG-TTTTT
* *
27142 TTAGTTTGGTTTTT
1 TTTGTTTTGTTTTT
27156 GTGTATGTTTT-TTTTT
1 -T-T-TGTTTTGTTTTT
*
27172 GTTGTT
1 TTTGTT
27178 ATCACATAGG
Statistics
Matches: 82, Mismatches: 17, Indels: 15
0.72 0.15 0.13
Matches are distributed among these distances:
13 15 0.18
14 41 0.50
15 16 0.20
16 6 0.07
17 4 0.05
ACGTcount: A:0.07, C:0.00, G:0.17, T:0.77
Consensus pattern (14 bp):
TTTGTTTTGTTTTT
Done.