Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1828
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: 27590
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Found at i:120 original size:15 final size:16
Alignment explanation
Indices: 90--155 Score: 86
Period size: 15 Copynumber: 4.4 Consensus size: 16
80 ACAAGATAAC
90 AAGAAAA-CC-GAATA
1 AAGAAAATCCAGAATA
104 AAGAAAATCCA-AATA
1 AAGAAAATCCAGAATA
119 AAG-AAATCCAGAATA
1 AAGAAAATCCAGAATA
* *
134 AAGAAGATCCAGGATA
1 AAGAAAATCCAGAATA
150 AAGAAA
1 AAGAAA
156 CCCAAGATAC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
14 14 0.31
15 16 0.36
16 15 0.33
ACGTcount: A:0.62, C:0.12, G:0.15, T:0.11
Consensus pattern (16 bp):
AAGAAAATCCAGAATA
Found at i:3193 original size:46 final size:46
Alignment explanation
Indices: 3043--3217 Score: 162
Period size: 46 Copynumber: 3.8 Consensus size: 46
3033 TGTAACCCGC
* * *
3043 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCAGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAATGAGTTC-GGACATTTGCAT
* ** * *
3089 CCATGAGTGAACTCAAACTCAACTCAA-GAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA---C-ATTTGCAT
* * * *
3138 -C-TCA-CGAACTCGGACTCAAATCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGACATTTGCAT
3181 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
3218 TGCCCAAATA
Statistics
Matches: 101, Mismatches: 19, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
43 6 0.06
44 4 0.04
45 7 0.07
46 67 0.66
47 11 0.11
48 2 0.02
49 4 0.04
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGACATTTGCAT
Found at i:7741 original size:64 final size:64
Alignment explanation
Indices: 7661--7844 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
7651 AGACATTATG
* * * *
7661 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTATGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
7725 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
7790 AA
63 AA
* * *
7792 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
7845 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.26
66 21 0.21
67 32 0.33
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:10428 original size:19 final size:19
Alignment explanation
Indices: 10404--10441 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
10394 GTGAAAAGTC
10404 TGATAAATTTCAAGAGTTT
1 TGATAAATTTCAAGAGTTT
10423 TGATAAATTTCAAGAGTTT
1 TGATAAATTTCAAGAGTTT
10442 CGTGCAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (19 bp):
TGATAAATTTCAAGAGTTT
Found at i:13156 original size:13 final size:13
Alignment explanation
Indices: 13138--13162 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13128 CGGCAGGGTT
13138 ACGCCCGTGTGAC
1 ACGCCCGTGTGAC
13151 ACGCCCGTGTGA
1 ACGCCCGTGTGA
13163 GTCGTGCTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.36, G:0.32, T:0.16
Consensus pattern (13 bp):
ACGCCCGTGTGAC
Found at i:18224 original size:40 final size:40
Alignment explanation
Indices: 18141--18364 Score: 245
Period size: 40 Copynumber: 5.6 Consensus size: 40
18131 TTGAATGCTG
* * * * * *
18141 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
18181 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
18221 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
18261 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
18301 TCCGGGTTAAGTCCCGAAGGCATTGGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
18341 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
18365 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.01
40 152 0.94
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:18384 original size:80 final size:80
Alignment explanation
Indices: 18216--18399 Score: 235
Period size: 80 Copynumber: 2.3 Consensus size: 80
18206 GTGCGAGATA
* * *
18216 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
18281 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
18296 TTAAATCCGGGTTAAGTCCCGAAGGCATTGGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
18361 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
18376 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
18400 TACGTGATTT
Statistics
Matches: 89, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
79 15 0.17
80 74 0.83
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Done.