Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2359
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: 37210
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Found at i:1499 original size:27 final size:27
Alignment explanation
Indices: 1437--1534 Score: 117
Period size: 27 Copynumber: 3.5 Consensus size: 27
1427 ATAATAAGCC
*
1437 CGCACACTTAGTGCT-TAATAGTCGAACT
1 CGCACACTTAGTGCTAT-ATAATC-AACT
1465 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
* * *
1492 CGCACACTTAGTGCTATACAATTTGAACC
1 CGCACACTTAGTGCTATATAA--TCAACT
1521 CGCACACTTAGTGC
1 CGCACACTTAGTGC
1535 CAATCTCATG
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
27 24 0.38
28 20 0.32
29 19 0.30
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:9434 original size:28 final size:29
Alignment explanation
Indices: 9402--9500 Score: 98
Period size: 28 Copynumber: 3.5 Consensus size: 29
9392 ATAATAAGCC
*
9402 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
*
9430 CGCACACTTAGTGC-TATATAATC-AACCT
1 CGCACACTTAGTGCTTACATAATCGAA-CT
* * * *
9458 CGCACACATAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
9487 CGCACACTTAGTGC
1 CGCACACTTAGTGC
9501 CAATCTCATG
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
27 4 0.07
28 34 0.58
29 16 0.27
30 5 0.08
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:14552 original size:20 final size:19
Alignment explanation
Indices: 14523--14577 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
14513 TTGGGCCTTA
14523 CCCATATCAACACAGTTGGG
1 CCCATATCAACACAGTT-GG
* * *
14543 CCCATTTCAATATAGTTGG
1 CCCATATCAACACAGTTGG
* *
14562 CCCATAACAAAACAGT
1 CCCATATCAACACAGT
14578 CTCATATGAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.24
Consensus pattern (19 bp):
CCCATATCAACACAGTTGG
Found at i:15902 original size:10 final size:10
Alignment explanation
Indices: 15887--15914 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
15877 TGAGAGAAGG
15887 ATAGAAAAGA
1 ATAGAAAAGA
15897 ATAGAAAAGA
1 ATAGAAAAGA
15907 ATAGAAAA
1 ATAGAAAA
15915 TAGAAGAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (10 bp):
ATAGAAAAGA
Found at i:17154 original size:12 final size:12
Alignment explanation
Indices: 17132--17163 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
17122 GAGGTAACTG
17132 ACGAT-GGTTCT
1 ACGATAGGTTCT
17143 ACGATAGGTTCT
1 ACGATAGGTTCT
17155 ACGATAGGT
1 ACGATAGGT
17164 AAGACAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (12 bp):
ACGATAGGTTCT
Found at i:24993 original size:39 final size:39
Alignment explanation
Indices: 24909--25072 Score: 217
Period size: 39 Copynumber: 4.2 Consensus size: 39
24899 CAAATCCAAT
* *
24909 CACCACCAC-AAAGCATGCGGGACTTTAAGCCCGGATATAA
1 CACCAGCACGAAAGCCTGCGGGAC-TT-AGCCCGGATATAA
*
24949 TACCAGCAC-AAAGCCTGCGGGACTTTAGCCCGGATATAA
1 CACCAGCACGAAAGCCTGCGGGAC-TTAGCCCGGATATAA
* *
24988 CACCAGCACGAATGCCTTC-GGACTTAGCCCGGATATAA
1 CACCAGCACGAAAGCCTGCGGGACTTAGCCCGGATATAA
* *
25026 CACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAAAGCCTGCGGGACTTAGCCCGGATATAA
25065 CACCAGCA
1 CACCAGCA
25073 TGACATATAT
Statistics
Matches: 116, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
38 34 0.29
39 52 0.45
40 30 0.26
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.16
Consensus pattern (39 bp):
CACCAGCACGAAAGCCTGCGGGACTTAGCCCGGATATAA
Found at i:25024 original size:38 final size:39
Alignment explanation
Indices: 24926--25072 Score: 226
Period size: 39 Copynumber: 3.7 Consensus size: 39
24916 ACAAAGCATG
* * *
24926 CGGGACTTTAAGCCCGGATATAATACCAGCAC-AAAGCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
24966 CGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
25006 C-GGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
25044 CGGGACTTAGCCCGGATATAACACCAGCA
1 CGGGACTTAGCCCGGATATAACACCAGCA
25073 TGACATATAT
Statistics
Matches: 102, Mismatches: 3, Indels: 5
0.93 0.03 0.05
Matches are distributed among these distances:
38 34 0.33
39 52 0.51
40 16 0.16
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:27740 original size:46 final size:46
Alignment explanation
Indices: 27688--27860 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
27678 TGGTTGAGCA
*
27688 TCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
27734 TTCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
27779 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
27827 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
27861 GGGGGGGTTA
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 57 0.55
47 28 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:27808 original size:93 final size:93
Alignment explanation
Indices: 27685--27855 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
27675 GGATGGTTGA
* * **
27685 GCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
27750 TGAGTCTGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
27778 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
27843 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
27856 ACTTAGGGGG
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:35276 original size:46 final size:46
Alignment explanation
Indices: 35226--35398 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
35216 TGGTTGAGCA
35226 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
35272 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
35317 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
35365 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
35399 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:35382 original size:93 final size:93
Alignment explanation
Indices: 35223--35393 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
35213 GGATGGTTGA
* *
35223 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
35288 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
35316 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
35381 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
35394 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.