Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3822
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: 36413
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:183 original size:39 final size:39
Alignment explanation
Indices: 88--272 Score: 178
Period size: 39 Copynumber: 4.6 Consensus size: 39
78 TCGAATGATG
* * * *
88 TCCGGGCTAAGTCCCGAA-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
127 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
* *
167 TTCGGGCTAAGCCCGAAGGCATTTGGGCGAGTTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
206 TCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTTACTATAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAG-TTACTA-AA
*
247 -CCGGGCTATGTCCCCGAAGGCATTTG
1 TCCGGGCTAAG--CCCGAAGGCATTTG
273 AACGGAGTAG
Statistics
Matches: 120, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
39 67 0.56
40 31 0.26
41 9 0.08
42 13 0.11
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:2767 original size:56 final size:55
Alignment explanation
Indices: 2700--2818 Score: 220
Period size: 56 Copynumber: 2.1 Consensus size: 55
2690 TATTAGTTTA
2700 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATG-T
*
2756 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGT
2811 TTGCCCAT
1 TTGCCCAT
2819 CATCCCTTGT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
55 9 0.15
56 53 0.85
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.45
Consensus pattern (55 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGT
Found at i:9428 original size:78 final size:80
Alignment explanation
Indices: 9287--9466 Score: 224
Period size: 78 Copynumber: 2.3 Consensus size: 80
9277 TACTCGTTCA
* **
9287 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
9352 TTAGTAAC-TCGCACC
66 ATAGTAACTTAGCA-C
**
9367 AATGCCTTCGGG-CTTAGCCCGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
* *
9429 TATGGTCACTTAGCAC
65 TATAGTAACTTAGCAC
*
9445 AAAGCCTTCGGGACTTAGCCCG
1 AATGCCTTCGGGACTTAGCCCG
9467 GACATCATTC
Statistics
Matches: 87, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
77 3 0.03
78 50 0.57
79 22 0.25
80 12 0.14
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:9468 original size:40 final size:40
Alignment explanation
Indices: 9266--9468 Score: 236
Period size: 40 Copynumber: 5.1 Consensus size: 40
9256 CGGAATTTAA
** *
9266 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
9306 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
9346 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
9385 CCGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
9424 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
9464 CCGGA
1 CCGGA
9469 CATCATTCGA
Statistics
Matches: 140, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
37 2 0.01
38 22 0.16
39 21 0.15
40 84 0.60
41 11 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:10669 original size:56 final size:56
Alignment explanation
Indices: 10603--10722 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
10593 TATTAGTTTA
*
10603 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCCTGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
10659 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
10715 TTGCCCAT
1 TTGCCCAT
10723 CATCCCTTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.22, C:0.24, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:13966 original size:17 final size:18
Alignment explanation
Indices: 13939--13973 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
13929 TGCAAAAGTT
13939 GTGTCCTAATAGCTATAG
1 GTGTCCTAATAGCTATAG
13957 GTGT-CTAATAGCTATAG
1 GTGTCCTAATAGCTATAG
13974 AATTTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (18 bp):
GTGTCCTAATAGCTATAG
Found at i:15025 original size:26 final size:25
Alignment explanation
Indices: 14995--15057 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 25
14985 CTAATCGTCT
* * *
14995 TTCAGCTTGGTGGAGCTTACCGTTTA
1 TTCAGCTTGGAGAAGCTTACC-ATTA
* *
15021 TTCAGCTCGAAGAAGCTTACCATTA
1 TTCAGCTTGGAGAAGCTTACCATTA
15046 TTCAGCTTGGAG
1 TTCAGCTTGGAG
15058 GATTTTTCTG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 13 0.43
26 17 0.57
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (25 bp):
TTCAGCTTGGAGAAGCTTACCATTA
Found at i:18918 original size:43 final size:43
Alignment explanation
Indices: 18811--18953 Score: 132
Period size: 43 Copynumber: 3.3 Consensus size: 43
18801 CCAACATTCC
* * *
18811 AGACATGGTCTTACAT-GT-ACTCAAATATCGATGCCAATTTCCC
1 AGACATGGTCTTAC-TCGTAAATCAAATAT-GATGCCAATGTCCT
* * **
18854 AGACAGGGTCTTACACG-AAATCAAATATGATGCCGCTGTCCT
1 AGACATGGTCTTACTCGTAAATCAAATATGATGCCAATGTCCT
*
18896 AGACATGGTCTTACTCGTAAATCTCAAAT-CGATGCCAATGTCCT
1 AGACATGGTCTTACTCGTAAA--TCAAATATGATGCCAATGTCCT
**
18940 AGATGTGGTCTTAC
1 AGACATGGTCTTAC
18954 ACGAAATAAC
Statistics
Matches: 81, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
42 25 0.31
43 26 0.32
44 24 0.30
45 6 0.07
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (43 bp):
AGACATGGTCTTACTCGTAAATCAAATATGATGCCAATGTCCT
Found at i:18940 original size:44 final size:41
Alignment explanation
Indices: 18811--18960 Score: 138
Period size: 42 Copynumber: 3.5 Consensus size: 41
18801 CCAACATTCC
* * * * *
18811 AGACATGGTCTTACATGTACTCAAATATCGATGCCAATTTCCC
1 AGACATGGTCTTACACGAAATC-AA-ATCGATGCCAATGTCCT
* * **
18854 AGACAGGGTCTTACACGAAATCAAATATGATGCCGCTGTCCT
1 AGACATGGTCTTACACGAAATCAAAT-CGATGCCAATGTCCT
*
18896 AGACATGGTCTTACTCGTAAATCTCAAATCGATGCCAATGTCCT
1 AGACATGGTCTTACACG-AAA--TCAAATCGATGCCAATGTCCT
**
18940 AGATGTGGTCTTACACGAAAT
1 AGACATGGTCTTACACGAAAT
18961 AACATATCAG
Statistics
Matches: 86, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
41 3 0.03
42 27 0.31
43 24 0.28
44 26 0.30
45 6 0.07
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (41 bp):
AGACATGGTCTTACACGAAATCAAATCGATGCCAATGTCCT
Found at i:20274 original size:17 final size:17
Alignment explanation
Indices: 20252--20286 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20242 CATCTTCGGG
*
20252 CTCCCACGTAGCCTTTT
1 CTCCCACCTAGCCTTTT
20269 CTCCCACCTAGCCTTTT
1 CTCCCACCTAGCCTTTT
20286 C
1 C
20287 AACACCTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.46, G:0.09, T:0.34
Consensus pattern (17 bp):
CTCCCACCTAGCCTTTT
Found at i:21284 original size:47 final size:49
Alignment explanation
Indices: 21159--21289 Score: 160
Period size: 47 Copynumber: 2.7 Consensus size: 49
21149 AGGTATGTGA
* * *
21159 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATTTTGAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGACTTGA-TTGGAT
* * * *
21209 -AGTCACTGTAAGGCCATATCTGGGACATGGCATC-GACTTGA-TGGAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGACTTGATTGGAT
*
21255 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATC
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATC
21290 AGCATTATAC
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
46 4 0.06
47 29 0.43
48 6 0.09
49 29 0.43
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (49 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGACTTGATTGGAT
Found at i:22959 original size:12 final size:12
Alignment explanation
Indices: 22942--22968 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
22932 TCTTCAAAAT
22942 GGCGTCGTATGG
1 GGCGTCGTATGG
22954 GGCGTCGTATGG
1 GGCGTCGTATGG
22966 GGC
1 GGC
22969 CATTATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.19, G:0.52, T:0.22
Consensus pattern (12 bp):
GGCGTCGTATGG
Found at i:24050 original size:41 final size:41
Alignment explanation
Indices: 23977--24121 Score: 218
Period size: 41 Copynumber: 3.5 Consensus size: 41
23967 ATCTGCTCCA
* * * ** *
23977 CTACTCCACTGTAACTTCAGGGAAATAAGGTTTGTTTTGAT
1 CTACTCTACTGCAACTTCAGAGTGATAGGGTTTGTTTTGAT
*
24018 CTGCTCTACTGCAACTTCAGAGTGATAGGGTTTGTTTTGAT
1 CTACTCTACTGCAACTTCAGAGTGATAGGGTTTGTTTTGAT
24059 CTACTCTACTGCAACTTCAGAGTGATAGGGTTTGTTTTGAT
1 CTACTCTACTGCAACTTCAGAGTGATAGGGTTTGTTTTGAT
*
24100 CTATTCTACTGCAACTTCAGAG
1 CTACTCTACTGCAACTTCAGAG
24122 AGGTAAGATC
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 95 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (41 bp):
CTACTCTACTGCAACTTCAGAGTGATAGGGTTTGTTTTGAT
Found at i:24760 original size:77 final size:75
Alignment explanation
Indices: 24595--24871 Score: 290
Period size: 77 Copynumber: 3.6 Consensus size: 75
24585 AGAGACTAAA
* * * *
24595 AGGCTCAACTCACTTCTCGCAATATGAGTCAGATTTTTTTTTGAAAAAAACATAAATTAAAAATA
1 AGGCTCAACTCACCTCTCGCAATATGAGT-TGA--TTTTTTTG---AAAA-GTAAACTAAAAATA
** *
24660 CCTCAGCATGT-ATCCCG
59 CCTCAGTGTGTGA-CCTG
**
24677 AGGCTCAACTCACCTCTCATAATATGAGTTGATTTTTTTGAGAAA-TAGAAACTAAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA-AAAGT--AAACTAAAAATACCTC
24741 AGTGTGTGACCTG
63 AGTGTGTGACCTG
* * * *
24754 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAACGTAAATTGAAAATACCTCAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGTAAACTAAAAATACCTCAGT
* **
24819 GCGTGATTTG
66 GTGTGACCTG
24829 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAA
24872 ACAGGAATAA
Statistics
Matches: 172, Mismatches: 18, Indels: 18
0.83 0.09 0.09
Matches are distributed among these distances:
74 10 0.06
75 56 0.33
76 3 0.02
77 66 0.38
78 1 0.01
79 8 0.05
81 2 0.01
82 26 0.15
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (75 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGTAAACTAAAAATACCTCAGT
GTGTGACCTG
Found at i:24836 original size:75 final size:75
Alignment explanation
Indices: 24595--24870 Score: 299
Period size: 75 Copynumber: 3.6 Consensus size: 75
24585 AGAGACTAAA
* *
24595 AGGCTCAACTCACTTCTCGCAATATGAGTCAGATTTTTTTTTGAAAAAAACATAAATTAAAAATA
1 AGGCTCAACTCACCTCTCGCAATATGAGT-TGA--TTTTTTTG----AAACATAAATTAAAAATA
* *
24660 CCTC-A-GCATGTATCCCG
59 CCTCAATGCGTG-AT-CTG
** *
24677 AGGCTCAACTCACCTCTCATAATATGAGTTGATTTTTTTGAGAA-ATAGAAACTAAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA-AACAT--AAATTAAAAATACCTC
* * *
24741 AGTGTGTGACCTG
63 AATGCGTGATCTG
* *
24754 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAACGTAAATTGAAAATACCTCAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAACATAAATTAAAAATACCTCAAT
*
24819 GCGTGATTTG
66 GCGTGATCTG
24829 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA
24871 AACAGGAATA
Statistics
Matches: 169, Mismatches: 19, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
74 10 0.06
75 58 0.34
76 4 0.02
77 57 0.34
78 1 0.01
79 11 0.07
81 2 0.01
82 26 0.15
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (75 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAACATAAATTAAAAATACCTCAAT
GCGTGATCTG
Found at i:27285 original size:27 final size:27
Alignment explanation
Indices: 27254--27431 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
27244 TAAATTGTAC
27254 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
27281 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
27307 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
27335 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
27363 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
27390 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
27417 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
27432 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:27368 original size:82 final size:81
Alignment explanation
Indices: 27255--27410 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
27245 AAATTGTACA
* *
27255 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
27319 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
27336 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
27401 TGCGAGTTGA
65 TGCGAATTGA
27411 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:27422 original size:82 final size:81
Alignment explanation
Indices: 27251--27431 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
27241 GATTAAATTG
* *
27251 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
27316 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
27332 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
27396 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
27414 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
27432 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:35378 original size:27 final size:27
Alignment explanation
Indices: 35347--35523 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
35337 TAAATTGTAC
*
35347 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
35374 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
35400 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
35428 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* *
35456 AGCACTAAGTGTGCG-ATTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
35482 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
35509 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35524 GACTCAAATA
Statistics
Matches: 126, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
26 23 0.18
27 81 0.64
28 22 0.17
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:35493 original size:81 final size:81
Alignment explanation
Indices: 35348--35502 Score: 233
Period size: 81 Copynumber: 1.9 Consensus size: 81
35338 AAATTGTACA
* *
35348 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
35413 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* *
35429 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCG-ATTGATTACG-TAGCACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAGT
*
35492 GTGCGAGTTGA
64 GTGCGAATTGA
35503 TTATATAGCA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
80 1 0.01
81 41 0.61
82 25 0.37
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:35514 original size:81 final size:81
Alignment explanation
Indices: 35344--35523 Score: 229
Period size: 81 Copynumber: 2.2 Consensus size: 81
35334 GATTAAATTG
* *
35344 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
35409 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * *
35425 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCG-ATTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
35488 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
35506 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
35524 GACTCAAATA
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
80 1 0.01
81 58 0.69
82 25 0.30
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.