Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1109
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: 40075
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Found at i:146 original size:47 final size:48
Alignment explanation
Indices: 74--192 Score: 172
Period size: 47 Copynumber: 2.5 Consensus size: 48
64 TAGGGGTGTC
74 AATGTGAAAAGTGTATATATTGTGATAAGGCCTAATGGCCGATGTGA-TG
1 AATGTG-AAAGTGTATATA-TGTGATAAGGCCTAATGGCCGATGTGACTG
*
123 -ATGTGAAAGTGTAATATATGTGATGAGGCCTAATGGCCGATGTGACTG
1 AATGTGAAAGTGT-ATATATGTGATAAGGCCTAATGGCCGATGTGACTG
*
171 AAT-TGAAAGTGTATTTATGTGA
1 AATGTGAAAGTGTATATATGTGA
193 CGGGCGAGTG
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
47 42 0.65
48 21 0.32
49 2 0.03
ACGTcount: A:0.32, C:0.08, G:0.29, T:0.32
Consensus pattern (48 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGACTG
Found at i:4484 original size:35 final size:37
Alignment explanation
Indices: 4417--4646 Score: 128
Period size: 43 Copynumber: 5.5 Consensus size: 37
4407 TATATATGTG
*
4417 ATAA-GCCTAATGCCAGTGATGGAATGTGAAA-GTATATA
1 ATAAGGCCTAATGCC---GATGTAATGTGAAAGGTATATA
4455 ATAAGGCCTAATGCCGATGT-ATGTGAAAGTGTATATA
1 ATAAGGCCTAATGCCGATGTAATGTGAAAG-GTATATA
* *
4492 TGTATA-GCCTAATGCCGATGTGATGAATGTGAAAGTGTATATG
1 -ATA-AGGCCTAATGCCGA--TG-T-AATGTGAAAG-GTATATA
4535 ATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
1 ATAAGGCCTAAT-GCCGA--TG-T-AATGTGAAAG-GTATATA
4578 TGTATAAGGCCT-ATGCCGATGTGATGAATGTGAAAGTGTATATA
1 ---ATAAGGCCTAATGCCGA--TG-T-AATGTGAAAG-GTATATA
4622 TGTGATAAGGCCTAATGGCCGATGT
1 ----ATAAGGCCTAAT-GCCGATGT
4647 GAAGAAAGTA
Statistics
Matches: 166, Mismatches: 8, Indels: 30
0.81 0.04 0.15
Matches are distributed among these distances:
35 8 0.05
36 4 0.02
37 7 0.04
38 18 0.11
39 11 0.07
40 2 0.01
41 2 0.01
42 9 0.05
43 45 0.27
44 31 0.19
45 13 0.08
46 11 0.07
47 5 0.03
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (37 bp):
ATAAGGCCTAATGCCGATGTAATGTGAAAGGTATATA
Found at i:4611 original size:44 final size:45
Alignment explanation
Indices: 4393--4648 Score: 334
Period size: 44 Copynumber: 6.0 Consensus size: 45
4383 CTAATACGTG
4393 TGAATGTGAAAGTGTATATATGTGATAA-GCCTAATGCC-A-GTGA
1 TGAATGTGAAAGTGTATATATGT-ATAAGGCCTAATGCCGATGTGA
4436 TGGAATGTGAAA--GTATATA---ATAAGGCCTAATGCCGA--TG-
1 T-GAATGTGAAAGTGTATATATGTATAAGGCCTAATGCCGATGTGA
4474 T--ATGTGAAAGTGTATATATGTAT-A-GCCTAATGCCGATGTGA
1 TGAATGTGAAAGTGTATATATGTATAAGGCCTAATGCCGATGTGA
4515 TGAATGTGAAAGTG--TATATG-ATAAGGCCTAATAGCCGATGTGA
1 TGAATGTGAAAGTGTATATATGTATAAGGCCTAAT-GCCGATGTGA
4558 TGAATGTGAAAGTGTATATATGTATAAGGCCT-ATGCCGATGTGA
1 TGAATGTGAAAGTGTATATATGTATAAGGCCTAATGCCGATGTGA
4602 TGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
1 TGAATGTGAAAGTGTATATATGT-ATAAGGCCTAAT-GCCGATGTGA
4649 AGAAAGTATA
Statistics
Matches: 191, Mismatches: 0, Indels: 40
0.83 0.00 0.17
Matches are distributed among these distances:
35 8 0.04
37 7 0.04
38 17 0.09
39 13 0.07
40 7 0.04
41 8 0.04
42 14 0.07
43 36 0.19
44 43 0.23
45 17 0.09
46 11 0.06
47 10 0.05
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (45 bp):
TGAATGTGAAAGTGTATATATGTATAAGGCCTAATGCCGATGTGA
Found at i:4921 original size:37 final size:36
Alignment explanation
Indices: 4853--4930 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 36
4843 CCGAGCTCTA
* *
4853 AAGACCCGTGACTACGTGTGGGAATTTTGTCCGGGT
1 AAGACCCGTAACTACGTGTGGGAATTATGTCCGGGT
*
4889 AAGACCCGATAACTTCGTGT-GGAGATTATGTCCGGGT
1 AAGACCCG-TAACTACGTGTGGGA-ATTATGTCCGGGT
4926 AAGAC
1 AAGAC
4931 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 11 0.30
37 26 0.70
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (36 bp):
AAGACCCGTAACTACGTGTGGGAATTATGTCCGGGT
Found at i:6822 original size:43 final size:43
Alignment explanation
Indices: 6774--6876 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
6764 TTGGTTTTCA
6774 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
6817 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
6860 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
6877 TTGAAATGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:6893 original size:29 final size:29
Alignment explanation
Indices: 6858--6931 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
6848 GTTGTGAGAT
* *
6858 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
6887 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
6916 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
6932 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:7329 original size:40 final size:40
Alignment explanation
Indices: 7279--7421 Score: 159
Period size: 40 Copynumber: 3.6 Consensus size: 40
7269 CTAAGTGACC
*
7279 ATATCTGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
1 ATATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
* *
7319 GTATCCGGACTAAGTTCCGAAGAGCATTAGTGCTAGTGAT
1 ATATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
** * * *
7359 ATATCC-G-CTAA-CCCCGAAGAGCATTCGTACTGGTGTT
1 ATATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
* *
7396 ATATCCGGGCT-AGGTCCTGAAGAGCA
1 ATATCCGGACTAAGTTCC-GAAGAGCA
7422 ATCATGCTGG
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
37 26 0.30
38 6 0.07
39 5 0.06
40 50 0.57
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (40 bp):
ATATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
Found at i:11016 original size:47 final size:47
Alignment explanation
Indices: 10958--11447 Score: 793
Period size: 47 Copynumber: 10.4 Consensus size: 47
10948 CAGCCAAGAC
*
10958 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
11005 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * *
11052 AGTGTATATGTGTGATAAGGCCTAATAGCCAATGTGATGAATGTAAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
11099 AGTGTATATATGTGATAAGGCCTAATGGTCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
11146 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
11193 AGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
11242 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
11289 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
11336 AGTGTATATATGTG-TAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
11382 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
11429 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
11448 TCCCGAAGGG
Statistics
Matches: 414, Mismatches: 26, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
46 46 0.11
47 322 0.78
49 46 0.11
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:11251 original size:143 final size:141
Alignment explanation
Indices: 10958--11447 Score: 802
Period size: 143 Copynumber: 3.5 Consensus size: 141
10948 CAGCCAAGAC
10958 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
* *
11023 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCAATGTG
66 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTG
*
11088 ATGAATGTAAA
131 ATGAATGTGAA
* *
11099 AGTGTATATATGTGATAAGGCCTAATGGTCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
11164 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATG
66 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATAGCCGATG
11229 TGATGAATGTGAA
129 TGATGAATGTGAA
*
11242 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
11307 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG-TAAGGCCTAATGGCCGATGTG
66 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTG
11371 ATGAATGTGAA
131 ATGAATGTGAA
* * * * * * * * * *
11382 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGATAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
11447 G
66 G
11448 TCCCGAAGGG
Statistics
Matches: 327, Mismatches: 20, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
140 86 0.26
141 106 0.32
143 135 0.41
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (141 bp):
AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTG
ATGAATGTGAA
Found at i:13111 original size:47 final size:47
Alignment explanation
Indices: 13006--13248 Score: 441
Period size: 47 Copynumber: 5.1 Consensus size: 47
12996 GGGTGTTACA
13006 CACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTT
1 CACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTT
* *
13055 CACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTT
1 CACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTT
*
13102 CACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTT
1 CACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTT
13149 CACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTT
1 CACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTT
13196 CACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTT
1 CACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTT
13243 CACATT
1 CACATT
13249 TATTCAAATA
Statistics
Matches: 188, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
47 156 0.83
49 32 0.17
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTT
Found at i:15671 original size:25 final size:24
Alignment explanation
Indices: 15642--15694 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
15632 TGATACCATA
15642 GCTCTTTATGAG-TGTCCTGATATAG
1 GCTCTTTATGAGCT-TCCTGATAT-G
* *
15667 GCTCTTTGTGAGCTTCTTGATATG
1 GCTCTTTATGAGCTTCCTGATATG
15691 GCTC
1 GCTC
15695 GCTTGAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.20
25 19 0.76
26 1 0.04
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.42
Consensus pattern (24 bp):
GCTCTTTATGAGCTTCCTGATATG
Found at i:21956 original size:46 final size:46
Alignment explanation
Indices: 21906--22166 Score: 269
Period size: 46 Copynumber: 5.7 Consensus size: 46
21896 TGAGCATCCG
* * *
21906 AACTCGTTGAGTTGAGTCTGAGTTCACTTACGGATGCGAATGTTCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
***
21952 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTTG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
* * * *
21998 AACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATG-TAACTAGGCATCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCCA
* ***
22045 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACCCCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
* * ***
22091 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAACCCCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
*
22137 AGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTA
22167 GGGGTGGGTT
Statistics
Matches: 185, Mismatches: 21, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
42 2 0.01
43 5 0.03
45 3 0.02
46 142 0.77
47 25 0.14
48 2 0.01
50 4 0.02
51 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
Found at i:22149 original size:139 final size:139
Alignment explanation
Indices: 21899--22161 Score: 366
Period size: 139 Copynumber: 1.9 Consensus size: 139
21889 GGATGGTTGA
* * * ****
21899 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTACGGATGCGAATGTTCAAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCAAACCCCCAAACTCGTTGAGT
* ***** *
21964 TGAGTCCGAGTTCACTTATGGATGCGAATGTTTGAACTCGTTGAGTTGAGTCTGAGTTCGTGAGA
66 TGAGTCCGAGTTCACTTATGGATGAGAATCCCCCAACTCGTTGAGTTGAGTCCGAGTTCGTGAGA
22029 TGTAACTAG
131 TGTAACTAG
* *
22038 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACCCCCAAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCAAACCCCCAAACTCGTTGAGT
22103 TGAGTCCGAGTTCACTTATGGATGAGAA-CCCCCAAGCTCGTTGAGTTGAGTCCGAGTTC
66 TGAGTCCGAGTTCACTTATGGATGAGAATCCCCCAA-CTCGTTGAGTTGAGTCCGAGTTC
22162 ACTTAGGGGT
Statistics
Matches: 107, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
138 2 0.02
139 105 0.98
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.30
Consensus pattern (139 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCAAACCCCCAAACTCGTTGAGT
TGAGTCCGAGTTCACTTATGGATGAGAATCCCCCAACTCGTTGAGTTGAGTCCGAGTTCGTGAGA
TGTAACTAG
Found at i:26214 original size:43 final size:43
Alignment explanation
Indices: 26166--26336 Score: 184
Period size: 43 Copynumber: 4.0 Consensus size: 43
26156 ATCTCATACA
* *
26166 ATGCCAACGTCCCAAACATGGTCTTACATGAAATCACATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAATCACATATCG
* * *
26209 ATGCC-ACTGTCCCAGACAGGGTCTTACACGAACTCATATA-CG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGAAATCACATATCG
* * * ** * * *
26251 ATGTCGATGTCCCAGACATTATTTTACACGTAAATCACAAATCA
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AAATCACATATCG
*
26295 ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCACATATC
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAATCACATATC
26337 AGAATCCTTT
Statistics
Matches: 101, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
42 26 0.26
43 51 0.50
44 24 0.24
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAAATCACATATCG
Found at i:27446 original size:13 final size:13
Alignment explanation
Indices: 27428--27452 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27418 ACAAACAATA
27428 AAATTTTCACACG
1 AAATTTTCACACG
27441 AAATTTTCACAC
1 AAATTTTCACAC
27453 ATATAATATA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:33280 original size:78 final size:81
Alignment explanation
Indices: 33145--33328 Score: 218
Period size: 78 Copynumber: 2.3 Consensus size: 81
33135 TTGAATGATG
* *
33145 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
33209 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
33224 TTCCGGGCTAAG-CCCGAAGGCATTT-TGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
33285 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
33303 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
33329 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
77 1 0.01
78 48 0.54
79 26 0.29
80 14 0.16
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:33335 original size:40 final size:39
Alignment explanation
Indices: 33146--33328 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
33136 TGAATGATGT
* * * *
33146 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AA
* * *
33186 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
33226 CCGGGCTAAG-CCCGAAGGCATTT-TGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
33263 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
33304 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
33329 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
38 21 0.17
39 25 0.20
40 66 0.54
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Done.