Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2407
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: 42366
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Found at i:5025 original size:46 final size:45
Alignment explanation
Indices: 4975--5145 Score: 222
Period size: 46 Copynumber: 3.8 Consensus size: 45
4965 TGGTTGAGCA
4975 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
5021 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GA-T-GCGAAG
5066 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
5112 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
5146 GGGCGGGTTA
Statistics
Matches: 108, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 34 0.31
46 66 0.61
47 3 0.03
48 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:5127 original size:91 final size:91
Alignment explanation
Indices: 4972--5140 Score: 311
Period size: 91 Copynumber: 1.9 Consensus size: 91
4962 GGATGGTTGA
* *
4972 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5037 TGAGTCCGAGTTCGTGATGTAACTAG
66 TGAGTCCGAGTTCGTGATGTAACTAG
*
5063 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5128 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
5141 ACTTAGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (91 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGATGTAACTAG
Found at i:12560 original size:46 final size:46
Alignment explanation
Indices: 12510--12685 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
12500 TGGTTGAGCA
12510 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
12556 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
12601 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* ** *
12649 CCCGTGCTCGTTGAGTTGAGTTCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12686 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.58
47 28 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:12666 original size:93 final size:93
Alignment explanation
Indices: 12507--12677 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
12497 GGATGGTTGA
* *
12507 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
12572 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* **
12600 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGTGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
12665 TGAGTTCGAGTTC
66 TGAGTCCGAGTTC
12678 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:14109 original size:47 final size:47
Alignment explanation
Indices: 14040--14132 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
14030 GCCAACACTT
14040 AGGCTATTTTCCAAGCCTTTATGTTACTCATAATCCCTTACAACCTC
1 AGGCTATTTTCCAAGCCTTTATGTTACTCATAATCCCTTACAACCTC
14087 AGGCTATTTTCCAAGCCTTTATGTTACTCATAATCCCTTACAACCT
1 AGGCTATTTTCCAAGCCTTTATGTTACTCATAATCCCTTACAACCT
14133 TGCACACATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.37
Consensus pattern (47 bp):
AGGCTATTTTCCAAGCCTTTATGTTACTCATAATCCCTTACAACCTC
Found at i:15754 original size:59 final size:59
Alignment explanation
Indices: 15662--15857 Score: 304
Period size: 59 Copynumber: 3.3 Consensus size: 59
15652 AGTGCCACAG
* * * *
15662 ATCACAGAATTACATGCCTTTCAATGGGGCTACTCAAAAGCAC-CTGGACCCTAGCATGT
1 ATCACATAATCACATGCCTCTCAACGGGGCTACTCAAAAGCACTC-GGACCCTAGCATGT
*
15721 ATCACATATTCACATGCCTCTCAACGGGGCTACTCAAAAGCACTCGGACCCTAGCATGT
1 ATCACATAATCACATGCCTCTCAACGGGGCTACTCAAAAGCACTCGGACCCTAGCATGT
* * *
15780 ATCACATAATCACATGCCTCTTATCGGGGCTACTCAAAAGCACTCGGACCCTAGCATGC
1 ATCACATAATCACATGCCTCTCAACGGGGCTACTCAAAAGCACTCGGACCCTAGCATGT
15839 ATCACATAATCACATGCCT
1 ATCACATAATCACATGCCT
15858 TACGTATCAA
Statistics
Matches: 127, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
59 126 0.99
60 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (59 bp):
ATCACATAATCACATGCCTCTCAACGGGGCTACTCAAAAGCACTCGGACCCTAGCATGT
Found at i:24823 original size:11 final size:11
Alignment explanation
Indices: 24807--24831 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24797 TGCAGGATAA
24807 TGGTAAAATTT
1 TGGTAAAATTT
24818 TGGTAAAATTT
1 TGGTAAAATTT
24829 TGG
1 TGG
24832 GTGAGAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (11 bp):
TGGTAAAATTT
Found at i:28500 original size:51 final size:51
Alignment explanation
Indices: 28416--28514 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
28406 ATGCTTCAAG
** *
28416 ATAGCTAAAACCACACAAAAAGTGTTACCCGATACATGATCTTGAATTTGA
1 ATAGCTAAAACCACACAAAAAGAATTACCCGATACATGATCTTAAATTTGA
** *
28467 ATAGCTAAAACCACATGAAAAGAATTACTCGATACATGATCTTAAATT
1 ATAGCTAAAACCACACAAAAAGAATTACCCGATACATGATCTTAAATT
28515 GCCAGCCATA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.26
Consensus pattern (51 bp):
ATAGCTAAAACCACACAAAAAGAATTACCCGATACATGATCTTAAATTTGA
Found at i:33008 original size:40 final size:40
Alignment explanation
Indices: 32914--33058 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
32904 TACTCGAATG
*
32914 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
32955 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
32995 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
33035 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
33059 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:40995 original size:40 final size:39
Alignment explanation
Indices: 40918--41061 Score: 171
Period size: 40 Copynumber: 3.6 Consensus size: 39
40908 TACTCGAATG
* *
40918 ATATCCGGGCTAAGTCCCAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCGAAGGCATTTGTGCT-AGCGACT
* *
40958 ACATCCGGACTAAGATCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCGAAGGCATTTGTGCTAGCGACT
* * *
40998 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGT-CCGAAGGCATTTGTGCTAGCGACT
* *
41038 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAG-TCCGAAGGC
41062 CTTGTGCGAG
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
39 1 0.01
40 73 0.81
41 16 0.18
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.24
Consensus pattern (39 bp):
ATATCCGGGCTAAGTCCGAAGGCATTTGTGCTAGCGACT
Done.