Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2589
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: 29449
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:1318 original size:46 final size:46
Alignment explanation
Indices: 1268--1440 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
1258 TGGTTGAGCA
1268 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
1314 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
1359 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
1407 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
1441 GGGGGGTTAC
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:1424 original size:93 final size:93
Alignment explanation
Indices: 1265--1435 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
1255 GGATGGTTGA
* *
1265 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1330 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
1358 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1423 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
1436 ACTTAGGGGG
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
Found at i:8859 original size:47 final size:45
Alignment explanation
Indices: 8798--8917 Score: 138
Period size: 46 Copynumber: 2.6 Consensus size: 45
8788 TGAGCATCAA
*
8798 CTCGTTTGAGTTGAGTCCGAGTTC-GTGA-GATGT-AACTAGGCATCCGAG
1 CTCG-TTGAGTTGAGTCCGAGTTCACTGAGGATGTGAAC---GC--CCGAG
*
8846 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGTGAACGCCCGAG
8892 CTCGTTGAGTTGAGTCCGAGTTCACT
1 CTCGTTGAGTTGAGTCCGAGTTCACT
8918 TAGGGACGGG
Statistics
Matches: 66, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
46 31 0.47
47 19 0.29
48 8 0.12
50 5 0.08
51 3 0.05
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (45 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGTGAACGCCCGAG
Found at i:10836 original size:15 final size:15
Alignment explanation
Indices: 10759--10836 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
10749 AGAAAATCGA
10759 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
** **
10774 ATAGCGAAA-CCCGG
1 ATAAAGAAATCCAAG
10788 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
10803 AATAAAGAGATCCATG
1 -ATAAAGAAATCCAAG
*
10819 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
10834 ATA
1 ATA
10837 CGATACTATG
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
14 3 0.06
15 42 0.88
16 3 0.06
ACGTcount: A:0.54, C:0.17, G:0.17, T:0.13
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:13812 original size:46 final size:45
Alignment explanation
Indices: 13745--13918 Score: 201
Period size: 46 Copynumber: 3.8 Consensus size: 45
13735 TGTAACCCGC
*
13745 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGCATTCGCAT
* *
13791 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGC-A--T
* *** *
13837 ACATCTCTCGAACTC-GACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGG-CATTCGCAT
13883 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
13919 ATGCTCAACC
Statistics
Matches: 106, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 8 0.08
46 84 0.79
47 6 0.06
48 3 0.03
49 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCAT
Found at i:13867 original size:92 final size:93
Alignment explanation
Indices: 13753--13922 Score: 290
Period size: 92 Copynumber: 1.8 Consensus size: 93
13743 GCCCATAAGT
*
13753 GAACTCGGACTCAACTCAACGAGTTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
13817 ACGAGCTCGGATGCCTAGTTACATCTCTC
65 ACGAGCTCGGATGCCTAGTTACATCTCTC
*
13846 GAACTC-GACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
13910 CGAGTTCGGATGC
66 CGAGCTCGGATGC
13923 TCAACCATCG
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
91 2 0.03
92 65 0.89
93 6 0.08
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:24219 original size:40 final size:40
Alignment explanation
Indices: 24135--24318 Score: 198
Period size: 40 Copynumber: 4.6 Consensus size: 40
24125 TTGAATGCTG
* *
24135 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
** *
24174 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGATACTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
*
24215 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* ** *
24255 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACT-AAT
24295 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
24319 GAATGAGTTA
Statistics
Matches: 126, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
39 3 0.02
40 110 0.87
41 12 0.10
42 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:24339 original size:39 final size:38
Alignment explanation
Indices: 24216--24365 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
24206 GATACTAATT
* ** * *
24216 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
24256 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
24295 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
24335 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
24366 GAGCTAATCC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Done.