Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007952.1 Hibiscus syriacus cultivar Beakdansim tig00110377_pilon, whole genome shotgun sequence
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: 3169409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 16
Found at i:3420 original size:12 final size:12
Alignment explanation
Indices: 3405--3435 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3395 TCGTTGCACC
3405 TATTTTCTGGGA
1 TATTTTCTGGGA
3417 TATTTTCTGGGA
1 TATTTTCTGGGA
3429 TATTTTC
1 TATTTTC
3436 GCTAAACAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.10, G:0.19, T:0.55
Consensus pattern (12 bp):
TATTTTCTGGGA
Found at i:13085 original size:24 final size:24
Alignment explanation
Indices: 13035--13083 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
13025 TATTATTGTC
* *
13035 TTAACTTAAATATATATTCTTATT
1 TTAACTTAAAAATATAATCTTATT
13059 TTAACTTAAAAATATAAT-TTATT
1 TTAACTTAAAAATATAATCTTATT
13082 TT
1 TT
13084 TATCTTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (24 bp):
TTAACTTAAAAATATAATCTTATT
Found at i:13137 original size:31 final size:31
Alignment explanation
Indices: 13049--13137 Score: 121
Period size: 31 Copynumber: 2.9 Consensus size: 31
13039 CTTAAATATA
* *
13049 TATTCTTAT-TTTAAC-TTAAAAATATAATT
1 TATTTTTATCTTTAACTTTAAAAATATATTT
*
13078 TATTTTTATCTTTAACTTAAAAAATATATTT
1 TATTTTTATCTTTAACTTTAAAAATATATTT
13109 TATTTTTATC-TTAACTTTTAAAAATATAT
1 TATTTTTATCTTTAAC-TTTAAAAATATAT
13138 CTTAATTTAT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.15
30 11 0.21
31 34 0.64
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (31 bp):
TATTTTTATCTTTAACTTTAAAAATATATTT
Found at i:13221 original size:30 final size:30
Alignment explanation
Indices: 13187--13251 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
13177 AACTTATCAC
* *
13187 ATATATTATATTCTTAACTTAAATTATTAA
1 ATATATTACAGTCTTAACTTAAATTATTAA
* *
13217 ATATATTCCAGTCTTACCTTAAATTATTAA
1 ATATATTACAGTCTTAACTTAAATTATTAA
13247 ATATA
1 ATATA
13252 ATTTATCCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.46
Consensus pattern (30 bp):
ATATATTACAGTCTTAACTTAAATTATTAA
Found at i:13318 original size:27 final size:25
Alignment explanation
Indices: 13285--13348 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 25
13275 ATATATATTT
13285 TATTTTTATTTTTAACTTAAAAAAGTA
1 TATTTTTATTTTTAA-TTAAAAAA-TA
**
13312 TATTTTTATTTTT-ATTTTAAAATA
1 TATTTTTATTTTTAATTAAAAAATA
13336 T-TTTTTATTTTTA
1 TATTTTTATTTTTA
13349 TTTTAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 11 0.32
24 3 0.09
25 6 0.18
26 1 0.03
27 13 0.38
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (25 bp):
TATTTTTATTTTTAATTAAAAAATA
Found at i:13352 original size:29 final size:29
Alignment explanation
Indices: 13277--13365 Score: 110
Period size: 29 Copynumber: 3.1 Consensus size: 29
13267 AACATATAAT
**
13277 ATATATTTTATTTTTATTTTTAACTTAAA
1 ATATATTTTATTTTTATTTTTATTTTAAA
* *
13306 A-A-AGTATATTTTTATTTTTATTTTAAA
1 ATATATTTTATTTTTATTTTTATTTTAAA
* *
13333 ATATTTTTTATTTTTATTTTAATTTTAAA
1 ATATATTTTATTTTTATTTTTATTTTAAA
13362 ATAT
1 ATAT
13366 TATAATAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
27 22 0.44
28 2 0.04
29 26 0.52
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (29 bp):
ATATATTTTATTTTTATTTTTATTTTAAA
Found at i:13418 original size:28 final size:28
Alignment explanation
Indices: 13387--13484 Score: 90
Period size: 30 Copynumber: 3.4 Consensus size: 28
13377 AATATAAATA
* *
13387 TTTAAGTTAAGATAAGAATAAATTATTT
1 TTTAAGTTAAAATAAGAATAAAATATTT
* *
13415 TTTAAGATAATAAAAAGTTAA-AAAATATTT
1 TTTAAGTTAA-AATAAG--AATAAAATATTT
**
13445 TTTTGGTTAAAATAAGAATAAAATATATT
1 TTTAAGTTAAAATAAGAATAAAATAT-TT
13474 TTTAATGTTAA
1 TTTAA-GTTAA
13485 GATGATAATT
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
27 2 0.04
28 16 0.30
29 14 0.26
30 20 0.37
31 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (28 bp):
TTTAAGTTAAAATAAGAATAAAATATTT
Found at i:13842 original size:27 final size:27
Alignment explanation
Indices: 13771--13845 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 27
13761 ACAAATAAAA
*
13771 ATACATATAAATAA-AAAAAATATATAT
1 ATACATATAAA-AATATAAAATATATAT
13798 ATACATGATACCATAAATATAAAATATATAT
1 ATACAT-ATA--A-AAATATAAAATATATAT
*
13829 TTACATATAAAAATATA
1 ATACATATAAAAATATA
13846 TAAAAATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
27 13 0.32
28 4 0.10
30 6 0.15
31 18 0.44
ACGTcount: A:0.60, C:0.07, G:0.01, T:0.32
Consensus pattern (27 bp):
ATACATATAAAAATATAAAATATATAT
Found at i:14577 original size:29 final size:29
Alignment explanation
Indices: 14527--14602 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 29
14517 TCCTTTAGCG
*
14527 TTAAAAATAA-AAAAA-A-TGAAAATT-A
1 TTAAAAATAATAAAAATATTTAAAATTCA
*
14552 TTTTAAAATAATAAAAATATTTAAAATTCA
1 -TTAAAAATAATAAAAATATTTAAAATTCA
*
14582 TTAAAAAT-ATAACAATATTTA
1 TTAAAAATAATAAAAATATTTA
14603 CATTAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
26 9 0.21
27 5 0.12
28 13 0.31
29 14 0.33
30 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (29 bp):
TTAAAAATAATAAAAATATTTAAAATTCA
Found at i:17061 original size:25 final size:25
Alignment explanation
Indices: 17025--17090 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
17015 CGATTATGTA
17025 GTTAT-AA-GGTTGTTAGCATATTT
1 GTTATGAACGGTTGTTAGCATATTT
17048 GTTATGAACGGTTGTTAGCATATTT
1 GTTATGAACGGTTGTTAGCATATTT
*
17073 GTTATGAACGATTGTTAG
1 GTTATGAACGGTTGTTAG
17091 ATCTGTAGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
23 5 0.12
24 2 0.05
25 33 0.82
ACGTcount: A:0.26, C:0.06, G:0.24, T:0.44
Consensus pattern (25 bp):
GTTATGAACGGTTGTTAGCATATTT
Found at i:23092 original size:13 final size:13
Alignment explanation
Indices: 23074--23100 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23064 AGCATTGTGA
23074 AAAGAAAATAAAG
1 AAAGAAAATAAAG
23087 AAAGAAAATAAAG
1 AAAGAAAATAAAG
23100 A
1 A
23101 GATGAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (13 bp):
AAAGAAAATAAAG
Found at i:25001 original size:4 final size:4
Alignment explanation
Indices: 24994--25046 Score: 65
Period size: 4 Copynumber: 13.2 Consensus size: 4
24984 ATATATATAT
*
24994 ATAA ATAA ATAA AT-A ATAA ATAA ATAAA AGTAA GTAA ATAA ATAA AT-A
1 ATAA ATAA ATAA ATAA ATAA ATAA AT-AA A-TAA ATAA ATAA ATAA ATAA
25042 ATAA A
1 ATAA A
25047 ATAAGTTACC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
3 6 0.14
4 31 0.72
5 5 0.12
6 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:25033 original size:14 final size:15
Alignment explanation
Indices: 24994--25046 Score: 79
Period size: 15 Copynumber: 3.3 Consensus size: 15
24984 ATATATATAT
24994 ATAAATAAATAAATA
1 ATAAATAAATAAATA
25009 ATAAATAAATAAAAGTA
1 ATAAATAAAT-AAA-TA
25026 AGTAAATAAATAAATA
1 A-TAAATAAATAAATA
25042 ATAAA
1 ATAAA
25047 ATAAGTTACC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 14 0.40
16 6 0.17
17 6 0.17
18 9 0.26
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (15 bp):
ATAAATAAATAAATA
Found at i:34155 original size:21 final size:22
Alignment explanation
Indices: 34113--34168 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
34103 AATAGAGAAT
* *
34113 GGATCGATCCTTTTTCTCCAAG
1 GGATCGATCATTTCTCTCCAAG
34135 GGATCGATCATTTCT-TCCAAG
1 GGATCGATCATTTCTCTCCAAG
**
34156 GGATTAATCATTT
1 GGATCGATCATTT
34169 TGAAAATGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (22 bp):
GGATCGATCATTTCTCTCCAAG
Found at i:34569 original size:19 final size:21
Alignment explanation
Indices: 34542--34582 Score: 52
Period size: 19 Copynumber: 2.0 Consensus size: 21
34532 GAAGAATTGG
34542 ATGAGAGAATG-AGAAG-AGAA
1 ATGAGAGAA-GAAGAAGAAGAA
34562 ATGA-AGAAGAAGAAGAAGAA
1 ATGAGAGAAGAAGAAGAAGAA
34582 A
1 A
34583 AATCTAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 1 0.05
19 9 0.47
20 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.07
Consensus pattern (21 bp):
ATGAGAGAAGAAGAAGAAGAA
Found at i:39977 original size:15 final size:15
Alignment explanation
Indices: 39942--40005 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
39932 TGATTTATTT
*
39942 TTTTTCAGCATTTTA
1 TTTTTCAGTATTTTA
**
39957 AATTTCAGTATTTTA
1 TTTTTCAGTATTTTA
* * *
39972 TTTTTCTGCTCTTTAA
1 TTTTTCAG-TATTTTA
*
39988 TTTTCCAGTATTTTA
1 TTTTTCAGTATTTTA
40003 TTT
1 TTT
40006 CAGTCCTTTA
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
15 25 0.69
16 11 0.31
ACGTcount: A:0.20, C:0.12, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTTCAGTATTTTA
Found at i:40006 original size:29 final size:29
Alignment explanation
Indices: 39937--40019 Score: 75
Period size: 30 Copynumber: 2.9 Consensus size: 29
39927 TAATATGATT
* *
39937 TATTTT-TTTTCAG-CATTTTAAATTTCAG
1 TATTTTATTTTCAGTC-CTTTAATTTTCAG
*
39965 TATTTTATTTTTCTG-CTCTTTAATTTTCCAG
1 TATTTTA-TTTTCAGTC-CTTTAATTTT-CAG
39996 TATTTTA-TTTCAGTCCTTTAATTT
1 TATTTTATTTTCAGTCCTTTAATTT
40020 CCGACCTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
28 6 0.13
29 14 0.30
30 16 0.35
31 10 0.22
ACGTcount: A:0.20, C:0.13, G:0.06, T:0.60
Consensus pattern (29 bp):
TATTTTATTTTCAGTCCTTTAATTTTCAG
Found at i:40259 original size:2 final size:2
Alignment explanation
Indices: 40252--40287 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40242 ATGCTTTTTA
40252 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40288 GTAAATAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43869 original size:2 final size:2
Alignment explanation
Indices: 43862--43901 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
43852 TCATTTATCC
43862 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43902 CTTGTTGTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46433 original size:24 final size:24
Alignment explanation
Indices: 46406--46459 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
46396 TGAGGCGATC
46406 GCACAAATTCCTTGATAAGGCATT
1 GCACAAATTCCTTGATAAGGCATT
46430 GCACAAATTCCTTGATAAGGCATT
1 GCACAAATTCCTTGATAAGGCATT
46454 GCACAA
1 GCACAA
46460 TCCAAGTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (24 bp):
GCACAAATTCCTTGATAAGGCATT
Found at i:47173 original size:34 final size:33
Alignment explanation
Indices: 47122--47227 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
47112 TTTGATGTTG
* *
47122 TTTCTCTTAA-AATTTTGTCTCACTAGAGACAA
1 TTTCTCATAACAATTTTGTCTCACTTGAGACAA
*
47154 TTTCTCATAACAACTTTTGTTTCACTTGAGACAA
1 TTTCTCATAACAA-TTTTGTCTCACTTGAGACAA
* * *
47188 TTTCTCAAAACAAATTTCGTCTCGCTTGAGACAA
1 TTTCTCATAAC-AATTTTGTCTCACTTGAGACAA
47222 TTTCTC
1 TTTCTC
47228 TATGAGATAC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
32 9 0.14
33 2 0.03
34 51 0.80
35 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (33 bp):
TTTCTCATAACAATTTTGTCTCACTTGAGACAA
Found at i:48573 original size:198 final size:198
Alignment explanation
Indices: 48229--48730 Score: 720
Period size: 198 Copynumber: 2.5 Consensus size: 198
48219 CTAAAGATGG
* * ** * *
48229 CCAAGAACTCTTCATCACGGATGAACAATGTCATCTTCAGCATCAAATTGACTCGATCTCCTCAA
1 CCAAGATCTCTTCAACACGGATGAGTAGTGTCATCTTCAACATCAAATTGACTCGATCTCCTCAA
* * * * *
48294 CACGAAGGAGCAGTGTCATCTTCAGACAATCAGACTTCTTCATCATGTAGGAACTGTATTGTCCC
66 CGCGAAGGAGCAGTGTCATCTTCAGATAATCAGACTTCCTCATCATGAAGGAACCGTATTGTCCC
* * *
48359 CAAATTATCTCCTGATTGATCCGATTTCTTTAACGCGAAGGAACAACGTCATAATTTATCAAAAA
131 CAAATTATCTCCTGATTGACCCGATTTCCTCAACGCGAAGGAACAACGTCATAATTTATCAAAAA
**
48424 TGA
196 CAA
* * *
48427 -TAAGATCTCTTCAACACGGATGAGTAGTGTCATCTTCAACATCAAATTGACTGGATCTTCTCAA
1 CCAAGATCTCTTCAACACGGATGAGTAGTGTCATCTTCAACATCAAATTGACTCGATCTCCTCAA
* *
48491 CGCGAATGAGCAGTTGTCATCCTCAGATAATCAGACTTCCTCATCATGAAGGAACCGTATTGTCC
66 CGCGAAGGAGCAG-TGTCATCTTCAGATAATCAGACTTCCTCATCATGAAGGAACCGTATTGTCC
* *
48556 CCAAATTATCTCCTGATTGACCCGATTTCCTCAACGCGAAGGAACATCGTCATAATTTATCGAAA
130 CCAAATTATCTCCTGATTGACCCGATTTCCTCAACGCGAAGGAACAACGTCATAATTTATCAAAA
48621 ACAA
195 ACAA
* * * **
48625 CCCA-ATCTCTTCAACACAGATGAGTAGTGTCATCTTCAACATCAAATTAAAACGATCTCCTCAA
1 CCAAGATCTCTTCAACACGGATGAGTAGTGTCATCTTCAACATCAAATTGACTCGATCTCCTCAA
*
48689 CGCGAAGGAGCAGTGTCATCTTCAGATAATCAGACTTTCTCA
66 CGCGAAGGAGCAGTGTCATCTTCAGATAATCAGACTTCCTCA
48731 ATACGAATGA
Statistics
Matches: 268, Mismatches: 34, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
197 93 0.35
198 174 0.65
199 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (198 bp):
CCAAGATCTCTTCAACACGGATGAGTAGTGTCATCTTCAACATCAAATTGACTCGATCTCCTCAA
CGCGAAGGAGCAGTGTCATCTTCAGATAATCAGACTTCCTCATCATGAAGGAACCGTATTGTCCC
CAAATTATCTCCTGATTGACCCGATTTCCTCAACGCGAAGGAACAACGTCATAATTTATCAAAAA
CAA
Found at i:49722 original size:14 final size:14
Alignment explanation
Indices: 49703--49742 Score: 71
Period size: 14 Copynumber: 2.8 Consensus size: 14
49693 TTTGGCCGAC
49703 GTTGAGGAGAATGA
1 GTTGAGGAGAATGA
49717 GTTGAGGAGAATGA
1 GTTGAGGAGAATGA
49731 GTTGAGAGAGAA
1 GTTGAG-GAGAA
49743 GGGATAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.38, C:0.00, G:0.42, T:0.20
Consensus pattern (14 bp):
GTTGAGGAGAATGA
Found at i:50359 original size:44 final size:45
Alignment explanation
Indices: 50286--50380 Score: 122
Period size: 44 Copynumber: 2.1 Consensus size: 45
50276 GATTTATGTT
* * *
50286 TTTTTCAGTATTTTAAATTTCAGTATTTTATTTTTCTG-CTCTTTAA
1 TTTTCCAGTATTTT-AATTTCAGTATTTTAATTTTCGGCCT-TTTAA
*
50332 TTTTCCAGTATTTT-ATTTCAGTCTTTTAATTTTCGGCCTTTTAA
1 TTTTCCAGTATTTTAATTTCAGTATTTTAATTTTCGGCCTTTTAA
50376 TTTTC
1 TTTTC
50381 TGTATTTACC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
44 29 0.66
45 2 0.05
46 13 0.30
ACGTcount: A:0.19, C:0.14, G:0.07, T:0.60
Consensus pattern (45 bp):
TTTTCCAGTATTTTAATTTCAGTATTTTAATTTTCGGCCTTTTAA
Found at i:50365 original size:15 final size:15
Alignment explanation
Indices: 50287--50387 Score: 82
Period size: 15 Copynumber: 6.8 Consensus size: 15
50277 ATTTATGTTT
50287 TTTTCAGTATTTTAA
1 TTTTCAGTATTTTAA
* *
50302 ATTTCAGTATTTTAT
1 TTTTCAGTATTTTAA
* *
50317 TTTTCTGCT-CTTTAA
1 TTTTCAG-TATTTTAA
50332 TTTTCCAGTATTTT-A
1 TTTT-CAGTATTTTAA
*
50347 -TTTCAGTCTTTTAA
1 TTTTCAGTATTTTAA
* **
50361 TTTTCGGCCTTTTAA
1 TTTTCAGTATTTTAA
*
50376 TTTTCTGTATTT
1 TTTTCAGTATTT
50388 ACCTTTTAGC
Statistics
Matches: 67, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
13 8 0.12
14 4 0.06
15 49 0.73
16 6 0.09
ACGTcount: A:0.19, C:0.13, G:0.08, T:0.60
Consensus pattern (15 bp):
TTTTCAGTATTTTAA
Found at i:50601 original size:2 final size:2
Alignment explanation
Indices: 50594--50631 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
50584 ATGCTTTCTA
50594 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50632 GTGTGTGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51005 original size:33 final size:35
Alignment explanation
Indices: 50956--51028 Score: 132
Period size: 33 Copynumber: 2.1 Consensus size: 35
50946 AAAGGATCAT
50956 AATTTAAATACATTGTATAATCGTTTAGGTACCAA
1 AATTTAAATACATTGTATAATCGTTTAGGTACCAA
50991 AATTT-AA-ACATTGTATAATCGTTTAGGTACCAA
1 AATTTAAATACATTGTATAATCGTTTAGGTACCAA
51024 AATTT
1 AATTT
51029 GGGCATTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 31 0.82
34 2 0.05
35 5 0.13
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (35 bp):
AATTTAAATACATTGTATAATCGTTTAGGTACCAA
Found at i:57282 original size:45 final size:45
Alignment explanation
Indices: 57218--57316 Score: 171
Period size: 45 Copynumber: 2.2 Consensus size: 45
57208 AGGGTAACAT
* *
57218 TATCAATACGGGGGGCAATTTTTGTAGTCCAACAGTCATTTTTTG
1 TATCAATACGGGGGGCAATTTTTGTAATCCAACAGTCATTTTTGG
57263 TATCAATACGGGGGGCAATTTTTGTAATCCAACAGTCATTTTTGG
1 TATCAATACGGGGGGCAATTTTTGTAATCCAACAGTCATTTTTGG
*
57308 TATCGATAC
1 TATCAATAC
57317 TCATAAGAGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (45 bp):
TATCAATACGGGGGGCAATTTTTGTAATCCAACAGTCATTTTTGG
Found at i:58426 original size:35 final size:34
Alignment explanation
Indices: 58376--58441 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 34
58366 AGCACCTCAC
* * *
58376 TGTCAGTGTTACATTTAGATAATGCATATCAGTG
1 TGTCAGTGTCACATTTAGAGAATGCACATCAGTG
58410 TGTCATGTGTCACATTTAGAGAATGCACATCA
1 TGTCA-GTGTCACATTTAGAGAATGCACATCA
58442 ATTATAGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 5 0.18
35 23 0.82
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (34 bp):
TGTCAGTGTCACATTTAGAGAATGCACATCAGTG
Found at i:63022 original size:31 final size:31
Alignment explanation
Indices: 62987--63060 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
62977 ATTTGTACAC
62987 TTTTGGTCACTTACATTATCATTTTATTAAG
1 TTTTGGTCACTTACATTATCATTTTATTAAG
* *
63018 TTTTGGTCACTTACGTTATCGTTTTATTAAG
1 TTTTGGTCACTTACATTATCATTTTATTAAG
*
63049 TTTTGGTTACTT
1 TTTTGGTCACTT
63061 GGAAATGAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.20, C:0.12, G:0.14, T:0.54
Consensus pattern (31 bp):
TTTTGGTCACTTACATTATCATTTTATTAAG
Found at i:63824 original size:6 final size:6
Alignment explanation
Indices: 63813--63839 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
63803 ATAAAATAAC
63813 AATGAT AATGAT AATGAT AATGAT AAT
1 AATGAT AATGAT AATGAT AATGAT AAT
63840 TTAATAACGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (6 bp):
AATGAT
Found at i:72028 original size:13 final size:13
Alignment explanation
Indices: 72012--72041 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
72002 AATAGTGACC
72012 TAAATAAAAATAA
1 TAAATAAAAATAA
72025 TAAATAAAAATAA
1 TAAATAAAAATAA
72038 TAAA
1 TAAA
72042 ACCCAATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAATAAAAATAA
Found at i:73628 original size:43 final size:43
Alignment explanation
Indices: 73567--73668 Score: 195
Period size: 43 Copynumber: 2.4 Consensus size: 43
73557 ATAACACGGT
*
73567 TCCTATGTGATGAGGACGGCTGGTTATCTAAGGTTGACGCGGC
1 TCCTACGTGATGAGGACGGCTGGTTATCTAAGGTTGACGCGGC
73610 TCCTACGTGATGAGGACGGCTGGTTATCTAAGGTTGACGCGGC
1 TCCTACGTGATGAGGACGGCTGGTTATCTAAGGTTGACGCGGC
73653 TCCTACGTGATGAGGA
1 TCCTACGTGATGAGGA
73669 GATCTAGTCG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (43 bp):
TCCTACGTGATGAGGACGGCTGGTTATCTAAGGTTGACGCGGC
Found at i:73736 original size:177 final size:177
Alignment explanation
Indices: 73478--73802 Score: 515
Period size: 177 Copynumber: 1.8 Consensus size: 177
73468 AACATTGCTT
* *
73478 CTACGTGATGAGGAGATCTGGTCGGTGAATGACATGGTTCCTACGTGATGAGGACGGCTGGCCAT
1 CTACGTGATGAGGAGATCTAGTCGGTGAATGACACGGTTCCTACGTGATGAGGACGGCTGGCCAT
* * * * *
73543 CTTTAGGGATGATGATAACACGGTTCCTATGTGATGAGGACGGCTGGTTATCTAAGGTTGACGCG
66 CTTTAGGGACGATGATAACACGGTCCCTATGTGATGAGGACGACTGGTTATATAAGGTTAACGCG
* *
73608 GCTCCTACGTGATGAGGACGGCTGGTTATCTAAGGTTGACGCGGCTC
131 ACTCCTACGCGATGAGGACGGCTGGTTATCTAAGGTTGACGCGGCTC
* * * * *
73655 CTACGTGATGAGGAGATCTAGTCGGTGGATGGCACGGTTCTTACGTGATGAGGATGGCTGTCCAT
1 CTACGTGATGAGGAGATCTAGTCGGTGAATGACACGGTTCCTACGTGATGAGGACGGCTGGCCAT
*
73720 CTTTAGGGACGATGATAACACGGTCCCTATGTGATGAGGATGACTGGTTATATAAGGTTAACGCG
66 CTTTAGGGACGATGATAACACGGTCCCTATGTGATGAGGACGACTGGTTATATAAGGTTAACGCG
73785 ACTCCTACGCGATGAGGA
131 ACTCCTACGCGATGAGGA
73803 GAACTGGTCG
Statistics
Matches: 133, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
177 133 1.00
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.26
Consensus pattern (177 bp):
CTACGTGATGAGGAGATCTAGTCGGTGAATGACACGGTTCCTACGTGATGAGGACGGCTGGCCAT
CTTTAGGGACGATGATAACACGGTCCCTATGTGATGAGGACGACTGGTTATATAAGGTTAACGCG
ACTCCTACGCGATGAGGACGGCTGGTTATCTAAGGTTGACGCGGCTC
Found at i:73758 original size:134 final size:134
Alignment explanation
Indices: 73611--73859 Score: 363
Period size: 134 Copynumber: 1.9 Consensus size: 134
73601 TGACGCGGCT
* * * * * *
73611 CCTACGTGATGAGGACGGCTGGTTATCTAAGGTTGACGCGGCTCCTACGTGATGAGGAGATCTAG
1 CCTACGTGATGAGGACGACTGGTTATATAAGGTTAACGCGACTCCTACGCGATGAGGAGAACTAG
* * * * * *
73676 TCGGTGGATGGCACGGTTCTTACGTGATGAGGATGGCTGTCCATCTTTAGGGACGATGATAACAC
66 TCGGTGGATGACACGGCTCCTACGTGATGAGGACGACTGACCATCTTTAGGGACGATGATAACAC
73741 GGTC
131 GGTC
* * *
73745 CCTATGTGATGAGGATGACTGGTTATATAAGGTTAACGCGACTCCTACGCGATGAGGAGAACTGG
1 CCTACGTGATGAGGACGACTGGTTATATAAGGTTAACGCGACTCCTACGCGATGAGGAGAACTAG
73810 TCGGTGGATGACACGGCTCCTACGTGATGAGGACGACTGACCATCTTTAG
66 TCGGTGGATGACACGGCTCCTACGTGATGAGGACGACTGACCATCTTTAG
73860 CGATAATAGT
Statistics
Matches: 100, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
134 100 1.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (134 bp):
CCTACGTGATGAGGACGACTGGTTATATAAGGTTAACGCGACTCCTACGCGATGAGGAGAACTAG
TCGGTGGATGACACGGCTCCTACGTGATGAGGACGACTGACCATCTTTAGGGACGATGATAACAC
GGTC
Found at i:73979 original size:65 final size:64
Alignment explanation
Indices: 73868--74352 Score: 521
Period size: 65 Copynumber: 7.4 Consensus size: 64
73858 AGCGATAATA
* ** * *
73868 GTTTCAAGAGAAACCGTCTCAAGAGAGACAAAACTTGTTTCGAGGGAAACAATATCAATGTTTGT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT-TTTTAAGGGAAACAATCTCAATGTTTTT
* * * *
73933 GTTTCAAGGGAAACTGTCTCAAAAGAGACAAAACTTATTTTAAGGGAAACATTCTCAAAGGTTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT-TTTTAAGGGAAACAATCTC-AATGTTTT
73998 T
64 T
* * * *
73999 GTTTCAAGAGAAACTATCTCAAGAGAGATAAAAATTTGTTTCAAGGGAAAC-ATGCTCAAAGATT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTT-TTT-AAGGGAAACAAT-CTCAATG-TT
74063 TTT
62 TTT
* * * *
74066 ATTTCAAGAGAAACTGTCTCAAGAAAGAC--AACTTTGTTTCAAGGGAAACAGA-CTTAAAGATT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTT-TTT-AAGGGAAACA-ATCTCAATG-TT
74128 TTAT
62 TT-T
* * * *
74132 -TTTCAAGAGAAACTATCTCAAGAGAGAAAAAACTTTGTTTCAAGGAAAACAATATCAATGTTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTT-TTT-AAGGGAAACAATCTCAATGTTTT
74196 T
64 T
* * * * *
74197 GTTTCAAGAGAAATTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAAAAATCTCAATGCTTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT-TTTTAAGGGAAACAATCTCAATGTTTTT
* *
74262 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAACAATCTCAATGTTTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT-TTTTAAGGGAAACAATCTCAATGTTTTT
* *
74327 GTTTCAAGAGAAATTGTTTCAAGAGA
1 GTTTCAAGAGAAACTGTCTCAAGAGA
74353 AATTGTCTCA
Statistics
Matches: 362, Mismatches: 45, Indels: 26
0.84 0.10 0.06
Matches are distributed among these distances:
65 210 0.58
66 84 0.23
67 68 0.19
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (64 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTTTTAAGGGAAACAATCTCAATGTTTTT
Found at i:74012 original size:30 final size:30
Alignment explanation
Indices: 73985--74087 Score: 82
Period size: 30 Copynumber: 3.2 Consensus size: 30
73975 AGGGAAACAT
73985 TCTCAAAGGTTTTTGTTTCAAGAGAAACTA
1 TCTCAAAGGTTTTTGTTTCAAGAGAAACTA
* *
74015 TCTCAAGAGAGATAAAAATTTGTTTCAAGGGAAAC-A
1 TCTCAA-AG-G-T----TTTTGTTTCAAGAGAAACTA
* * *
74051 TGCTCAAAGATTTTTATTTCAAGAGAAACTG
1 T-CTCAAAGGTTTTTGTTTCAAGAGAAACTA
74082 TCTCAA
1 TCTCAA
74088 GAAAGACAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
30 26 0.46
31 3 0.05
32 1 0.02
33 1 0.02
34 1 0.02
36 4 0.07
37 21 0.37
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (30 bp):
TCTCAAAGGTTTTTGTTTCAAGAGAAACTA
Found at i:74253 original size:36 final size:36
Alignment explanation
Indices: 74195--74319 Score: 102
Period size: 36 Copynumber: 3.7 Consensus size: 36
74185 ATCAATGTTT
***
74195 TTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAAC
1 TTGTTTCAAGAGAAACAATCTCAAGGGAGACAAAAC
* * * **
74231 TTGTTTCAAGGGAAAAAATCTCAA---TG-C---TT
1 TTGTTTCAAGAGAAACAATCTCAAGGGAGACAAAAC
**
74260 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAC
1 TTGTTTCAAGAGAAACAATCTCAAGGGAGACAAAAC
*
74296 TTGTTTCAAGGGAAACAATCTCAA
1 TTGTTTCAAGAGAAACAATCTCAA
74320 TGTTTTTGTT
Statistics
Matches: 65, Mismatches: 17, Indels: 14
0.68 0.18 0.15
Matches are distributed among these distances:
29 20 0.31
32 2 0.03
33 2 0.03
36 41 0.63
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (36 bp):
TTGTTTCAAGAGAAACAATCTCAAGGGAGACAAAAC
Found at i:74274 original size:131 final size:130
Alignment explanation
Indices: 73868--74352 Score: 591
Period size: 132 Copynumber: 3.7 Consensus size: 130
73858 AGCGATAATA
** * * *
73868 GTTTCAAGAGAAACCGTCTCAAGAGAGACAAAACTTGTTTCGAGGGAAACAATATCAATGTTTGT
1 GTTTCAAGAGAAACTATCTCAAGAGAGAAAAAACTTGTTTCAAGGGAAACAATATCAATGTTTTT
* * * * * * *
73933 GTTTCAAGGGAAACTGTCTCAAAAGAGACAAAACTTATTTTAAGGGAAACATTCTCAAAGGTTTT
66 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAAAAATCTCAAA-GATTT
73998 T
130 T
* * *
73999 GTTTCAAGAGAAACTATCTCAAGAGAGATAAAAATTTGTTTCAAGGGAAAC-ATGCTCAAAGATT
1 GTTTCAAGAGAAACTATCTCAAGAGAGA-AAAAACTTGTTTCAAGGGAAACAAT-ATCAATG-TT
* * * *
74063 TTTATTTCAAGAGAAACTGTCTCAAGAAAGAC--AACTTTGTTTCAAGGGAAACAGA-CTTAAAG
63 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC-TTGTTTCAAGGGAAA-AAATCTCAAAG
74125 ATTTT
126 ATTTT
* *
74130 ATTTTCAAGAGAAACTATCTCAAGAGAGAAAAAACTTTGTTTCAAGGAAAACAATATCAATGTTT
1 -GTTTCAAGAGAAACTATCTCAAGAGAGAAAAAAC-TTGTTTCAAGGGAAACAATATCAATGTTT
* * * *
74195 TTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAAAAATCTCAATGCTT
64 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAAAAATCTCAAAGATT
74260 TT
129 TT
* * * *
74262 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAACAATCTCAATGTTTTT
1 GTTTCAAGAGAAACTATCTCAAGAGAGAAAAAACTTGTTTCAAGGGAAACAATATCAATGTTTTT
* *
74327 GTTTCAAGAGAAATTGTTTCAAGAGA
66 GTTTCAAGAGAAACTGTCTCAAGAGA
74353 AATTGTCTCA
Statistics
Matches: 303, Mismatches: 40, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
130 53 0.17
131 103 0.34
132 113 0.37
133 34 0.11
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (130 bp):
GTTTCAAGAGAAACTATCTCAAGAGAGAAAAAACTTGTTTCAAGGGAAACAATATCAATGTTTTT
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAAAAATCTCAAAGATTTT
Found at i:74305 original size:21 final size:20
Alignment explanation
Indices: 74272--74313 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
74262 GTTTCAAGAG
*
74272 AAACTGTCTCAAGGGAGACA
1 AAACTGTCTCAAGGGAAACA
*
74292 AAACTTGTTTCAAGGGAAACA
1 AAAC-TGTCTCAAGGGAAACA
74313 A
1 A
74314 TCTCAATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (20 bp):
AAACTGTCTCAAGGGAAACA
Found at i:74345 original size:15 final size:15
Alignment explanation
Indices: 74325--74364 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
74315 CTCAATGTTT
74325 TTGTTTCAAGAGAAA
1 TTGTTTCAAGAGAAA
74340 TTGTTTCAAGAGAAA
1 TTGTTTCAAGAGAAA
*
74355 TTGTCTCAAG
1 TTGTTTCAAG
74365 GGAGACAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (15 bp):
TTGTTTCAAGAGAAA
Found at i:74360 original size:80 final size:80
Alignment explanation
Indices: 74260--74429 Score: 304
Period size: 80 Copynumber: 2.1 Consensus size: 80
74250 CTCAATGCTT
74260 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAACAATCTCAATGTTT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAACAATCTCAATGTTT
74325 TTGTTTCAAGAGAAA
66 TTGTTTCAAGAGAAA
* *
74340 TTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAAGAATCTCAATGTTT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAACAATCTCAATGTTT
74405 TTGTTTCAAGAGAAA
66 TTGTTTCAAGAGAAA
* *
74420 CTGTCTCAAG
1 TTGTTTCAAG
74430 GGAGACAAAA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 86 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.31
Consensus pattern (80 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAACAATCTCAATGTTT
TTGTTTCAAGAGAAA
Found at i:74360 original size:145 final size:146
Alignment explanation
Indices: 74195--74458 Score: 485
Period size: 145 Copynumber: 1.8 Consensus size: 146
74185 ATCAATGTTT
74195 TTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAAAAATCTCAATGCTT
1 TTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAAAAATCTCAATGCTT
*
74260 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAC-TTGTTTCAAGGGAAACAATCTCAATGTT
66 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTGTTTCAAAGGAAACAATCTCAATGTT
74324 TTTGTTTCAAGAGAAA
131 TTTGTTTCAAGAGAAA
* *
74340 TTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAAGAATCTCAATGTTT
1 TTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAAAAATCTCAATGCTT
*
74405 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTGTTTTAAAGGAAACA
66 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTGTTTCAAAGGAAACA
74459 GACTCAAAGA
Statistics
Matches: 114, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
145 99 0.87
146 15 0.13
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (146 bp):
TTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAAAAATCTCAATGCTT
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTGTTTCAAAGGAAACAATCTCAATGTT
TTTGTTTCAAGAGAAA
Found at i:74530 original size:145 final size:144
Alignment explanation
Indices: 74198--74499 Score: 417
Period size: 145 Copynumber: 2.0 Consensus size: 144
74188 AATGTTTTTG
*
74198 TTTCAAGAGAAATTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAAAAATCTCAATGCTTTTG
1 TTTCAAGAGAAATTGTAT-AAGGGAGACAAAACTTGTTTCAAGGGAAAAAATCTCAATGCTTTTG
*
74263 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAACAATCTCAATGTTTTTG
65 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTTCAAAGGAAACAATCTCAATGTTTTTG
***
74328 TTTCAAGAGAAATTG
130 TTTCAAGAGAAACAA
* * *
74343 TTTCAAGAGAAATTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAAGAATCTCAATGTTTTTG
1 TTTCAAGAGAAATTGTAT-AAGGGAGACAAAACTTGTTTCAAGGGAAAAAATCTCAATGCTTTTG
*
74408 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTGTTTTAAAGGAAACAGA-CTCAAAGATTT
65 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAAC-TTGTTTCAAAGGAAACA-ATCTC--A-A--T
* *
74472 TTTTTTGTTTCAAGTGAAACAA
123 GTTTTTGTTTCAAGAGAAACAA
74494 TTTCAA
1 TTTCAA
74500 ATTTTGTATT
Statistics
Matches: 141, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
145 96 0.68
146 18 0.13
147 1 0.01
148 1 0.01
149 1 0.01
151 24 0.17
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (144 bp):
TTTCAAGAGAAATTGTATAAGGGAGACAAAACTTGTTTCAAGGGAAAAAATCTCAATGCTTTTGT
TTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTTCAAAGGAAACAATCTCAATGTTTTTGT
TTCAAGAGAAACAA
Found at i:75279 original size:26 final size:26
Alignment explanation
Indices: 75250--75301 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
75240 TGCTAAACAA
75250 AAAAGAAA-AAATGAATAATAAATAAT
1 AAAAGAAATAAAT-AATAATAAATAAT
*
75276 AAAATAAATAAATAATAATAAATAAT
1 AAAAGAAATAAATAATAATAAATAAT
75302 GTATTATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (26 bp):
AAAAGAAATAAATAATAATAAATAAT
Found at i:75285 original size:19 final size:19
Alignment explanation
Indices: 75257--75297 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
75247 CAAAAAAGAA
*
75257 AAAATGAAT-AATAAATAAT
1 AAAATAAATAAAT-AATAAT
75276 AAAATAAATAAATAATAAT
1 AAAATAAATAAATAATAAT
75295 AAA
1 AAA
75298 TAATGTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAATAAATAAATAATAAT
Found at i:75810 original size:33 final size:33
Alignment explanation
Indices: 75773--75853 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
75763 GTCCTACTTG
* * *
75773 GACTCAAATGC-TTCGGTTTTAGTGTTTTAATAT
1 GACTCAAATACGTT-GGTTTTAGTGTTTCAATAA
75806 GACTCAAATACGTTGGTTTTAGTGTTTCAATAA
1 GACTCAAATACGTTGGTTTTAGTGTTTCAATAA
*
75839 GACTCAAATATGTTG
1 GACTCAAATACGTTG
75854 ATTTATTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 41 0.95
34 2 0.05
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (33 bp):
GACTCAAATACGTTGGTTTTAGTGTTTCAATAA
Found at i:75937 original size:23 final size:24
Alignment explanation
Indices: 75907--75955 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
75897 GGCCTACAAA
*
75907 AATAATAAAAAAATATTAT-TAAT
1 AATAATAAAAAAATATAATATAAT
*
75930 AATAATAAATAAATATAATATAAT
1 AATAATAAAAAAATATAATATAAT
75954 AA
1 AA
75956 AATGTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AATAATAAAAAAATATAATATAAT
Found at i:77108 original size:110 final size:110
Alignment explanation
Indices: 76909--77166 Score: 353
Period size: 110 Copynumber: 2.4 Consensus size: 110
76899 GTATTGCTTC
* * * * * * *
76909 GAGTCTAATATCCTCCGCCGTGAAGTTGAAATTAGCTCTG---GAACTGGGAAA-TTGTTTGTTG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAATGAAATTGAAAAGTTTTTTGTTG
* * * *
76970 ATAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
66 ACAATCAGCCACCCCTTCGTCATGAAGTTGAGCTTGTGTTATCTT
* *
77015 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTATCTCTGAATGAAATTGAAAAGTTTTTTGTTG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAATGAAATTGAAAAGTTTTTTGTTG
77080 ACAATCAGCCACCCCTTCGTCATGAAGTTGAGCTTGTGTTATCTT
66 ACAATCAGCCACCCCTTCGTCATGAAGTTGAGCTTGTGTTATCTT
* *
77125 GGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAA
77167 ATTAGGAAGC
Statistics
Matches: 131, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
106 35 0.27
109 8 0.06
110 88 0.67
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (110 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAATGAAATTGAAAAGTTTTTTGTTG
ACAATCAGCCACCCCTTCGTCATGAAGTTGAGCTTGTGTTATCTT
Found at i:81179 original size:26 final size:26
Alignment explanation
Indices: 81150--81205 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
81140 TATTGAATGC
*
81150 TAAACAA-AAAGGAAAAAAATGAATAA
1 TAAACAATAAAAGAAAAAAAT-AATAA
* * *
81176 TAAATAATAAAATAAATAAATAATAA
1 TAAACAATAAAAGAAAAAAATAATAA
81202 TAAA
1 TAAA
81206 TAATGTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (26 bp):
TAAACAATAAAAGAAAAAAATAATAA
Found at i:81193 original size:19 final size:19
Alignment explanation
Indices: 81165--81205 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
81155 AAAAAGGAAA
*
81165 AAAATGAAT-AATAAATAAT
1 AAAATAAATAAAT-AATAAT
81184 AAAATAAATAAATAATAAT
1 AAAATAAATAAATAATAAT
81203 AAA
1 AAA
81206 TAATGTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAATAAATAAATAATAAT
Found at i:81717 original size:33 final size:33
Alignment explanation
Indices: 81680--81760 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
81670 GTCTTACTTG
* *
81680 GACTCAAATGC-TTCGGTTTTAGTGTTTCAATAT
1 GACTCAAATACGTT-GGTTTTAGTGTTTCAATAA
81713 GACTCAAATACGTTGGTTTTAGTGTTTCAATAA
1 GACTCAAATACGTTGGTTTTAGTGTTTCAATAA
*
81746 GACTCAAATATGTTG
1 GACTCAAATACGTTG
81761 ATTTATTTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 42 0.95
34 2 0.05
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (33 bp):
GACTCAAATACGTTGGTTTTAGTGTTTCAATAA
Found at i:81819 original size:3 final size:3
Alignment explanation
Indices: 81811--81871 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
81801 TGGGGCCTAC
*
81811 AAT AAT AAT AAT AA- AAT ATT AAT AAT AAT AAT AAT AA- ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
81855 -AT AAT -AT AAT -AT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
81872 AATGTTTTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
2 9 0.18
3 40 0.80
4 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:81836 original size:20 final size:19
Alignment explanation
Indices: 81811--81871 Score: 74
Period size: 20 Copynumber: 3.3 Consensus size: 19
81801 TGGGGCCTAC
81811 AATAATAATAATAAAATATT
1 AATAATAATAATAAAATA-T
81831 AATAATAATAATAATAA-AT
1 AATAATAATAATAA-AATAT
*
81850 -ATAAT-ATAATATAATAT
1 AATAATAATAATAAAATAT
81867 AATAA
1 AATAA
81872 AATGTTTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
16 2 0.05
17 8 0.22
18 9 0.24
19 1 0.03
20 15 0.41
21 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AATAATAATAATAAAATAT
Found at i:81841 original size:23 final size:25
Alignment explanation
Indices: 81811--81874 Score: 91
Period size: 23 Copynumber: 2.7 Consensus size: 25
81801 TGGGGCCTAC
81811 AATAATAATAATAAAAT-AT-TAAT
1 AATAATAATAATAAAATAATATAAT
81834 AATAATAATAATAAATATAATATAAT
1 AATAATAATAATAAA-ATAATATAAT
81860 -ATAAT-ATAATAAAAT
1 AATAATAATAATAAAAT
81875 GTTTTTGTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
23 17 0.45
24 10 0.26
25 7 0.18
26 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
AATAATAATAATAAAATAATATAAT
Found at i:82348 original size:10 final size:11
Alignment explanation
Indices: 82333--82361 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
82323 ATTTTTGAAA
82333 AAAAAAATAT-
1 AAAAAAATATG
82343 AAAAAAATATG
1 AAAAAAATATG
82354 AAAAAAAT
1 AAAAAAAT
82362 TGTCTCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.17
Consensus pattern (11 bp):
AAAAAAATATG
Found at i:85128 original size:11 final size:11
Alignment explanation
Indices: 85114--85139 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
85104 AAGGAAACAA
85114 AAAAACTTTAC
1 AAAAACTTTAC
85125 AAAAACTTTAC
1 AAAAACTTTAC
85136 AAAA
1 AAAA
85140 GCTGGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAACTTTAC
Found at i:87541 original size:24 final size:24
Alignment explanation
Indices: 87514--87562 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
87504 CTTGTTTTTC
87514 TTTTTTATCTATTTCTTCCCCGGT
1 TTTTTTATCTATTTCTTCCCCGGT
87538 TTTTTTATCTATTTCTTCCCCGGT
1 TTTTTTATCTATTTCTTCCCCGGT
87562 T
1 T
87563 AGGAATTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.08, C:0.24, G:0.08, T:0.59
Consensus pattern (24 bp):
TTTTTTATCTATTTCTTCCCCGGT
Found at i:89689 original size:3 final size:3
Alignment explanation
Indices: 89681--89808 Score: 168
Period size: 3 Copynumber: 42.7 Consensus size: 3
89671 TTTGGGTTTG
*
89681 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
* * * * * *
89726 TAA TAT TAA TAA TAA TAG TAT TAA TAA TAA TAA TAT TAT TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
89774 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
89809 TGGATATAAG
Statistics
Matches: 112, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
2 2 0.02
3 108 0.96
4 2 0.02
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:91055 original size:3 final size:3
Alignment explanation
Indices: 91041--91070 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
91031 CAAAACACAT
*
91041 TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
91071 ATAAAGAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:92606 original size:2 final size:2
Alignment explanation
Indices: 92582--92630 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
92572 CTATTCTATC
*
92582 AT AT TT AT AT -T AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
92621 AT AT AT AT AT
1 AT AT AT AT AT
92631 TATTAATAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:93714 original size:31 final size:31
Alignment explanation
Indices: 93678--93741 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
93668 CAGTGATTAT
* *
93678 ATCTTAATTAAATAAAAACAAAATTGATCAA
1 ATCTTAATTAAATAAAAACAAAAGTGACCAA
*
93709 ATCTTAATTAAATAAAAACGAAAGTGACCAA
1 ATCTTAATTAAATAAAAACAAAAGTGACCAA
93740 AT
1 AT
93742 ATTATGTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.27
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAAAAGTGACCAA
Found at i:95144 original size:2 final size:2
Alignment explanation
Indices: 95139--95173 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
95129 CCCCCAATTT
95139 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
95174 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:95178 original size:2 final size:2
Alignment explanation
Indices: 95173--95207 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
95163 TCTCTCTCTC
95173 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
95208 GAAAATCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:99676 original size:44 final size:48
Alignment explanation
Indices: 99610--99706 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 48
99600 TTATTTTCGT
99610 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
* *
99657 TTTTT-GAAT-AA-GCATGCGAATTAGATATCATGCGGTTAGGATTTC
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
99702 TTTTT
1 TTTTT
99707 ATGGATAACA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
44 28 0.60
45 10 0.21
46 4 0.09
47 5 0.11
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (48 bp):
TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:109353 original size:15 final size:16
Alignment explanation
Indices: 109345--109374 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
109335 AAGAAATAAA
109345 GAGAAAAGAAGAAAAT
1 GAGAAAAGAAGAAAAT
109361 GAGAAAA-AAGAAAA
1 GAGAAAAGAAGAAAA
109375 AATAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.03
Consensus pattern (16 bp):
GAGAAAAGAAGAAAAT
Found at i:109353 original size:18 final size:17
Alignment explanation
Indices: 109332--109445 Score: 61
Period size: 16 Copynumber: 7.1 Consensus size: 17
109322 ATTTTGCTTG
109332 AAGAAGAAATAAAGAGAA
1 AAGAAGAAA-AAAGAGAA
*
109350 AAGAAG-AAAATGAGAA
1 AAGAAGAAAAAAGAGAA
*
109366 AA-AAGAAAAAATA-AA
1 AAGAAGAAAAAAGAGAA
**
109381 AA-AA-ACGAAA-A-AA
1 AAGAAGAAAAAAGAGAA
109394 AAGAGAGAAAAAATGA-AA
1 AAGA-AGAAAAAA-GAGAA
109412 AAG--GAATAAAAGAGAA
1 AAGAAGAA-AAAAGAGAA
*
109428 AA-ATGAAAAAAAGAGAA
1 AAGAAG-AAAAAAGAGAA
109445 A
1 A
109446 TAAAAGGAGG
Statistics
Matches: 78, Mismatches: 7, Indels: 23
0.72 0.06 0.21
Matches are distributed among these distances:
13 5 0.06
14 5 0.06
15 15 0.19
16 26 0.33
17 13 0.17
18 14 0.18
ACGTcount: A:0.75, C:0.01, G:0.18, T:0.05
Consensus pattern (17 bp):
AAGAAGAAAAAAGAGAA
Found at i:109442 original size:17 final size:17
Alignment explanation
Indices: 109356--109445 Score: 76
Period size: 17 Copynumber: 5.1 Consensus size: 17
109346 AGAAAAGAAG
109356 AAAATGAGAAAAAAGA-A
1 AAAATGA-AAAAAAGAGA
* *
109373 AAAATAAAAAAAACGAAA
1 AAAATGAAAAAAA-GAGA
*
109391 AAAAAGAGAGAAAAA-ATGA
1 AAAATGA-A-AAAAAGA-GA
* *
109410 AAAAGGAATAAAAGAGA
1 AAAATGAAAAAAAGAGA
109427 AAAATGAAAAAAAGAGA
1 AAAATGAAAAAAAGAGA
109444 AA
1 AA
109446 TAAAAGGAGG
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
16 6 0.10
17 31 0.53
18 9 0.15
19 8 0.14
20 5 0.08
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.06
Consensus pattern (17 bp):
AAAATGAAAAAAAGAGA
Found at i:109658 original size:16 final size:16
Alignment explanation
Indices: 109637--109686 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
109627 TGGTGATCAG
109637 AATGAGACTAAAGATT
1 AATGAGACTAAAGATT
* *
109653 AATGAGTCT--AG--G
1 AATGAGACTAAAGATT
109665 AATGAGACTAAAGATT
1 AATGAGACTAAAGATT
109681 AATGAG
1 AATGAG
109687 TCTCGATTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
12 8 0.31
14 4 0.15
16 14 0.54
ACGTcount: A:0.46, C:0.06, G:0.24, T:0.24
Consensus pattern (16 bp):
AATGAGACTAAAGATT
Found at i:109676 original size:28 final size:28
Alignment explanation
Indices: 109636--109689 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
109626 TTGGTGATCA
109636 GAATGAGACTAAAGATTAATGAGTCTAG
1 GAATGAGACTAAAGATTAATGAGTCTAG
109664 GAATGAGACTAAAGATTAATGAGTCT
1 GAATGAGACTAAAGATTAATGAGTCT
109690 CGATTGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (28 bp):
GAATGAGACTAAAGATTAATGAGTCTAG
Found at i:110455 original size:51 final size:51
Alignment explanation
Indices: 110394--110525 Score: 264
Period size: 51 Copynumber: 2.6 Consensus size: 51
110384 TGAAGCAAAT
110394 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
110445 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
110496 AAGTTCGTTGAAGATTGAGTCCTATACTCT
1 AAGTTCGTTGAAGATTGAGTCCTATACTCT
110526 GCGGACAAGT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 81 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (51 bp):
AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
Found at i:110537 original size:36 final size:36
Alignment explanation
Indices: 110490--110561 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
110480 TGAATAGGGA
110490 GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCT
1 GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCT
110526 GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCT
1 GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCT
110562 CTGAATGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (36 bp):
GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCT
Found at i:110585 original size:87 final size:87
Alignment explanation
Indices: 110439--110711 Score: 404
Period size: 87 Copynumber: 3.0 Consensus size: 87
110429 TGAATAGGGA
110439 GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGT
1 GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGT
110504 TGAAGATTGAGTCCTATACTCT
66 TGAAGATTGAGTCCTATACTCT
110526 GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGT
1 GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGT
110591 TGAAGATTGAGTCCTACT-CTCTGAAT
66 TGAAGATTGAGTCCTA-TACTC----T
* *
110617 GAATAGGGAGCGGACAATTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 G----CGGA-C--A-AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
110682 AAGTTCGTTGAAGATTGAGTCCTATACTCT
58 AAGTTCGTTGAAGATTGAGTCCTATACTCT
110712 CTGAAGGAAT
Statistics
Matches: 170, Mismatches: 2, Indels: 20
0.89 0.01 0.10
Matches are distributed among these distances:
87 84 0.49
88 1 0.01
91 2 0.01
95 4 0.02
96 1 0.01
98 2 0.01
99 76 0.45
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (87 bp):
GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGT
TGAAGATTGAGTCCTATACTCT
Found at i:110602 original size:51 final size:51
Alignment explanation
Indices: 110526--110838 Score: 461
Period size: 51 Copynumber: 6.1 Consensus size: 51
110516 CCTATACTCT
110526 GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGA
1 GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGA
110577 GCGGACAAGTTCGTTGAAGATTGAGTCC--TACTCTCTGAATGAATAGGGA
1 GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGA
110626 GCGGACAA-TTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGA
1 GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGA
* *
110676 GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGA
1 GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGA
* * *
110727 GCGGACTAGTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGA
1 GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGA
** ** * * *
110778 GCGGACCTGTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGA
1 GCGGACAAGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGA
110833 GCGGAC
1 GCGGAC
110839 CCGTTTTATT
Statistics
Matches: 241, Mismatches: 14, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
48 19 0.08
49 29 0.12
50 29 0.12
51 131 0.54
54 2 0.01
55 31 0.13
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (51 bp):
GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGA
Found at i:110838 original size:55 final size:54
Alignment explanation
Indices: 110548--110945 Score: 303
Period size: 51 Copynumber: 7.6 Consensus size: 54
110538 GTTGAAGATT
* * ** **
110548 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA--TT-
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCTGTTTATTGAAGATTTTC
* * ** **
110599 GAGTCC--TACTCTCTGAATGAATAGGGAGCGGA-CAATTCGTTGAAGA--TT-
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCTGTTTATTGAAGATTTTC
* * ** **
110647 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA--TT-
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCTGTTTATTGAAGATTTTC
**
110698 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGA-CTAGTTCGTTGAAGA--TT-
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCT-GTTTATTGAAGATTTTC
* * *
110749 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTTC
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCTGTTTATTGAAGA-TTTTC
* * *
110804 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTAAAGATTGTTC
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCTG-TTTATTGAAGATT-TTC
* * * *
110860 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACAC-GTTT-TATGAAGATTGTTC
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGAC-CTGTTTAT-TGAAGATT-TTC
* *
110915 GAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTCCTATACTCT-CTGAAGGAATAGAGAGC
110946 AGGCTCGTCA
Statistics
Matches: 305, Mismatches: 28, Indels: 24
0.85 0.08 0.07
Matches are distributed among these distances:
48 20 0.07
49 26 0.09
50 26 0.09
51 107 0.35
52 2 0.01
54 4 0.01
55 75 0.25
56 44 0.14
57 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (54 bp):
GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCTGTTTATTGAAGATTTTC
Found at i:110916 original size:111 final size:105
Alignment explanation
Indices: 110526--110945 Score: 393
Period size: 99 Copynumber: 4.0 Consensus size: 105
110516 CCTATACTCT
* * * * *
110526 GCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGT
1 GCGGACCAGTTCATTAAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACACGTT-TT
* * *
110591 -TGAAGA--TT-GAG-TC-CTACTCTCTGAATGAATAGGGA
65 ATGAAGATTTTCGAGTTCTATACTCTCTGAAGGAATAGAGA
* * * * *
110626 GCGGA-CAATTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGT
1 GCGGACCAGTTCATTAAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACACGTT-TT
*
110690 -TGAAGA--TT-GAGTCCTATACTCTCTGAAGGAATAGAGA
65 ATGAAGATTTTCGAGTTCTATACTCTCTGAAGGAATAGAGA
* * * * *
110727 GCGGACTAGTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGAC-C-TGTTT
1 GCGGACCAGTTCATTAAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACACGT-TTT
110790 ATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGA
65 A-TGAAGA-TTTTCGAGTTCTATACTCTCTGAAGGAATAGAGA
* * * * *
110833 GCGGACCCGTTTTATTAAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACG
1 GCGGACCAG-TTCATTAAAGATTG----AGTCCTATACTCTCTGAATGAATAGGGAGCGGACACG
*
110898 TTTTATGAAGATTGTTCGAG-TCTTATACT-TCCTGAAGGAATAGGGA
61 TTTTATGAAGATT-TTCGAGTTC-TATACTCT-CTGAAGGAATAGAGA
110944 GC
1 GC
110946 AGGCTCGTCA
Statistics
Matches: 276, Mismatches: 24, Indels: 29
0.84 0.07 0.09
Matches are distributed among these distances:
99 68 0.25
100 8 0.03
101 25 0.09
102 53 0.19
105 2 0.01
106 35 0.13
107 11 0.04
110 5 0.02
111 63 0.23
112 5 0.02
113 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (105 bp):
GCGGACCAGTTCATTAAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACACGTTTTA
TGAAGATTTTCGAGTTCTATACTCTCTGAAGGAATAGAGA
Found at i:110946 original size:55 final size:55
Alignment explanation
Indices: 110698--110947 Score: 239
Period size: 55 Copynumber: 4.6 Consensus size: 55
110688 GTTGAAGATT
* * * **
110698 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACTAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
* * * * * *
110749 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACC-TGTTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGT-TTTATTGAAGATTGTTC
* *
110804 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTAAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGA-CCGTTTTATTGAAGATTGTTC
* *
110860 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
*
110915 GAGTCTTATACT-TCCTGAAGGAATAGGGAGCAG
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGCAG
110948 GCTCGTCATT
Statistics
Matches: 168, Mismatches: 19, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
51 41 0.24
54 3 0.02
55 69 0.41
56 53 0.32
57 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (55 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGTTTTATTGAAGATTGTTC
Found at i:111560 original size:2 final size:2
Alignment explanation
Indices: 111555--111592 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
111545 CTCTCTCTTC
111555 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
111593 GAAAATCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:111578 original size:17 final size:17
Alignment explanation
Indices: 111556--111589 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
111546 TCTCTCTTCT
111556 ATATATATATATATATA
1 ATATATATATATATATA
111573 ATATATATATATATATA
1 ATATATATATATATATA
111590 TATGAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:126448 original size:21 final size:23
Alignment explanation
Indices: 126418--126468 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
126408 GTAAAGTTAA
*
126418 CTAACTAATCAAG-AACT-ACTG
1 CTAACAAATCAAGTAACTAACTG
126439 CTAACAAATCAAGTAACTAACTG
1 CTAACAAATCAAGTAACTAACTG
*
126462 ATAACAA
1 CTAACAA
126469 TAAACTGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 12 0.46
22 4 0.15
23 10 0.38
ACGTcount: A:0.49, C:0.22, G:0.08, T:0.22
Consensus pattern (23 bp):
CTAACAAATCAAGTAACTAACTG
Found at i:136810 original size:20 final size:20
Alignment explanation
Indices: 136780--136829 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
136770 GGAATTTCAT
136780 CCAATTGGCTCCAAATCACTC
1 CCAA-TGGCTCCAAATCACTC
136801 CCAATGGCTCCAAATCACTC
1 CCAATGGCTCCAAATCACTC
*
136821 CCAACGGCT
1 CCAATGGCT
136830 AGAAACAGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.28, C:0.40, G:0.12, T:0.20
Consensus pattern (20 bp):
CCAATGGCTCCAAATCACTC
Found at i:137879 original size:3 final size:3
Alignment explanation
Indices: 137871--137930 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
137861 CATTTTTTAT
* *
137871 TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA -TA ATA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
137916 CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
137931 AAAAAATAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.92
4 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:137896 original size:18 final size:18
Alignment explanation
Indices: 137873--137928 Score: 85
Period size: 18 Copynumber: 2.9 Consensus size: 18
137863 TTTTTTATTT
137873 ATTATTATTATTATTATA
1 ATTATTATTATTATTATA
137891 ATTATTATTATTATTATA
1 ATTATTATTATTATTATA
137909 ATATATACTATTATTATTAT
1 AT-TAT--TATTATTATTAT
137929 TAAAAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 20 0.57
19 3 0.09
21 12 0.34
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTATTATTATTATTATA
Found at i:137897 original size:21 final size:20
Alignment explanation
Indices: 137867--137930 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 20
137857 TACCCATTTT
137867 TTAT-TTATTATTATTATTA
1 TTATATTATTATTATTATTA
137886 TTATAATTATTATTATTATTA
1 TTAT-ATTATTATTATTATTA
* *
137907 TAATATATACTATTATTATTA
1 TTATAT-TATTATTATTATTA
137928 TTA
1 TTA
137931 AAAAAATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
19 4 0.10
20 2 0.05
21 33 0.85
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATATTATTATTATTATTA
Found at i:139287 original size:19 final size:17
Alignment explanation
Indices: 139246--139350 Score: 65
Period size: 18 Copynumber: 6.1 Consensus size: 17
139236 TTTTTATTGT
* *
139246 TTATTTATGTTTTAATT
1 TTATTTATATTTTAATA
139263 TTATTTATATATTTAAATA
1 TTATTTATAT-TTT-AATA
* *
139282 TTATTT-T-TATTATTA
1 TTATTTATATTTTAATA
**
139297 TTATTATATAGTCATAA-A
1 TTATT-TATA-TTTTAATA
*
139315 TTATTTTTATTTTAATA
1 TTATTTATATTTTAATA
139332 TTTATTTAT-TTTTCAATA
1 -TTATTTATATTTT-AATA
139350 T
1 T
139351 CAAAGAAAAG
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
15 8 0.12
16 7 0.10
17 20 0.29
18 21 0.31
19 12 0.18
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
TTATTTATATTTTAATA
Found at i:150755 original size:22 final size:22
Alignment explanation
Indices: 150729--150782 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
150719 ATTATGCTTG
*
150729 AAGAAAAAAAGAACA-AAAAAGA
1 AAGAAAAAAAGAA-AGAAAAAAA
*
150751 AAGAAAGAAAGAAAGGAAAAAAA
1 AAGAAAAAAAGAAA-GAAAAAAA
150774 AAGAAAAAA
1 AAGAAAAAA
150783 GGGGGTCAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 12 0.44
23 14 0.52
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (22 bp):
AAGAAAAAAAGAAAGAAAAAAA
Found at i:152216 original size:115 final size:114
Alignment explanation
Indices: 152053--152282 Score: 370
Period size: 115 Copynumber: 2.0 Consensus size: 114
152043 AGCAAGTGCC
*
152053 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTA
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTA
* * * * *
152118 ATCTGGTTTAGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGA
66 ATCTGGTTCAGTAGGAACCAC-AAAACCAATCATTGGAATTAAAAGATGA
*
152168 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTA
* *
152233 ATCTGGTTCGGTAGGAACCACAGAACCAATCATTGGAATTAAAAGATGA
66 ATCTGGTTCAGTAGGAACCACAAAACCAATCATTGGAATTAAAAGATGA
152282 A
1 A
152283 CTGCATGATT
Statistics
Matches: 106, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
114 26 0.25
115 80 0.75
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (114 bp):
ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTA
ATCTGGTTCAGTAGGAACCACAAAACCAATCATTGGAATTAAAAGATGA
Found at i:153298 original size:113 final size:114
Alignment explanation
Indices: 152969--153367 Score: 739
Period size: 114 Copynumber: 3.5 Consensus size: 114
152959 TAGCAAAGAT
152969 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
153034 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
153083 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
* *
153148 AAGAAGGAAGAAGAAATTTATAATGAGAAGAATTTGTTTAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
153197 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
153261 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
153310 TCAAATCCATCATTTGATGGATCAGCTTTTCCA-TAAAAAGTTCATAATGAGAAGAACT
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACT
153368 TGTTCAACTT
Statistics
Matches: 277, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
113 131 0.47
114 146 0.53
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (114 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:153407 original size:186 final size:186
Alignment explanation
Indices: 153167--153513 Score: 507
Period size: 186 Copynumber: 1.9 Consensus size: 186
153157 GAAGAAATTT
* * ** * *
153167 ATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGA
1 ATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACCAGA
*
153232 GAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAA-TTCATAATGAGAAGAATTT
66 GAAAGTTCATAATAAGAAGAACTCATCTAAAGAAGGAAGAA-AAAGTTCATAATGAGAAGAATTT
153296 GTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCATAAAAAGTTC
130 GTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCATAAAAAGTTC
* ** * *
153353 ATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGT
1 ATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACCAGA
*** *
153418 TCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTG
66 GAAAGTTCATAATAAGAAGAACTCATCTAAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTG
* * *
153483 TTCAACCTTTTGTTTAAATTCATCATTTGAT
131 TTCAACCTTTTGCTCAAATCCATCATTTGAT
153514 AGATTAACAT
Statistics
Matches: 141, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
185 3 0.02
186 138 0.98
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (186 bp):
ATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACCAGA
GAAAGTTCATAATAAGAAGAACTCATCTAAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTG
TTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCATAAAAAGTTC
Found at i:153440 original size:73 final size:73
Alignment explanation
Indices: 153277--153415 Score: 197
Period size: 73 Copynumber: 1.9 Consensus size: 73
153267 GAAGAAGAAA
* ** * *
153277 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCC
1 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACC
153342 ATAAAAAG
66 ATAAAAAG
* ** *
153350 TTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACC
1 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACC
153415 A
66 A
153416 GTTCGAGTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 57 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (73 bp):
TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACC
ATAAAAAG
Found at i:153467 original size:113 final size:109
Alignment explanation
Indices: 153346--153714 Score: 445
Period size: 113 Copynumber: 3.3 Consensus size: 109
153336 TTTTCCATAA
* * *
153346 AAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCAGCAT
1 AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATT-GATGGATCAGCAT
* * *
153411 TACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAG
65 TACCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAG
* * * * *
153457 AAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATAGATTAAC
1 --AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCA-TTGATGGATCAGC
* *
153522 ATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAG
63 ATTACCAGATAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGAAG
* * * *
153572 AAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTT
1 AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCA-TTGATGGATCAGCAT
* * *
153636 TTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
65 TACCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
* *
153681 -AAGTTCACAATGAGAAGAGCTTGTTCAACCTTTT
1 AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
153715 ACATAATTTT
Statistics
Matches: 224, Mismatches: 27, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
108 2 0.01
109 44 0.20
110 1 0.00
112 77 0.34
113 81 0.36
114 2 0.01
115 5 0.02
116 12 0.05
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (109 bp):
AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTGATGGATCAGCATT
ACCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
Found at i:153540 original size:186 final size:186
Alignment explanation
Indices: 153167--153553 Score: 506
Period size: 186 Copynumber: 2.1 Consensus size: 186
153157 GAAGAAATTT
* * ** * *
153167 ATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGA
1 ATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACCAGA
*
153232 GAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
66 GAAAGTTCATAATAAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
* * * * *
153297 TTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCATAAAAAGTTC
131 TTCAACCTTTTGCTCAAATCCATCATTTGATAGATCAACATTGCCAGAAAAAGTTC
* ** * *
153353 ATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGT
1 ATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACCAGA
*** *
153418 TCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAA-AAAGTTCATAATGAGAAGAATTT
66 GAAAGTTCATAATAAGAAGAACTCATCTAAAGAAGGAAGAAGAAA-TTCATAATGAGAAGAATTT
* * * * ** *
153482 GTTCAACCTTTTGTTTAAATTCATCATTTGATAGATTAACATTGCCAGGTAGAGTTC
130 GTTCAACCTTTTGCTCAAATCCATCATTTGATAGATCAACATTGCCAGAAAAAGTTC
153539 ATAATGAGAAGAACT
1 ATAATGAGAAGAACT
153554 CGTCATCTGA
Statistics
Matches: 172, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
185 3 0.02
186 169 0.98
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (186 bp):
ATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACCAGA
GAAAGTTCATAATAAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
TTCAACCTTTTGCTCAAATCCATCATTTGATAGATCAACATTGCCAGAAAAAGTTC
Found at i:153729 original size:109 final size:108
Alignment explanation
Indices: 153347--153839 Score: 407
Period size: 112 Copynumber: 4.3 Consensus size: 108
153337 TTTCCATAAA
* * * * *
153347 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCA-TTCAATGGATCAGCAT
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC-TAAATTCATCACTT-GATGGATTAGCTT
* **** *
153411 TACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAG
64 TTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAG
* * * * *
153457 AAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATAGATTAAC
1 ---AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG-CTAAATTCATCACTTGATGGATTAGC
* * *
153522 ATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAG
62 TTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGAAG
* * * *
153572 AAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTT
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT-AAATTCATCACTTGATGGATTAGCTTT
153637 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
65 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
* * * * * * *
153681 AAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTACATAATTTTATCAC-AGAAGAAGACATATT
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC-TAAATTCATCACTTGATG--G----ATT
*
153745 AGCATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAA
59 AGC-T-----TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG---AAG-AAGAAG
* *
153805 AAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
153840 AATGACTCTA
Statistics
Matches: 318, Mismatches: 37, Indels: 39
0.81 0.09 0.10
Matches are distributed among these distances:
108 3 0.01
109 55 0.17
110 3 0.01
111 1 0.00
112 78 0.25
113 76 0.24
114 7 0.02
115 6 0.02
116 12 0.04
120 37 0.12
123 3 0.01
124 37 0.12
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (108 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTAAATTCATCACTTGATGGATTAGCTTTT
CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
Found at i:153854 original size:124 final size:121
Alignment explanation
Indices: 153635--153927 Score: 357
Period size: 124 Copynumber: 2.4 Consensus size: 121
153625 TGGATCAGCT
*
153635 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG--AAGAAGAAGAAGTTCACAATGAGAAG
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAGAAGAAAAAGTTCACAATGAGAAG
* * * * * *
153698 AGCTTGTTCAACCTTTTACATAATTTTATCACAGAAGAAGACATA-TTAGCATCAACC
66 AGCTTATTCAACCTTTTACATAACTCTATCACAGAAG--GAAATAGTCAACATCAACC
*
153755 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAAAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG-AAAAG-AAGAAAAAGTTCACAATGAGA
* *
153820 AGAGCTTATTCAACCTTTTGA-ATGACTCTATCACAGAAGGAAATAGGTCAACATCATCC
64 AGAGCTTATTCAACCTTTT-ACATAACTCTATCACAGAAGGAAATA-GTCAACATCAACC
* *
153879 ---CCAGCGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAGAGAAAAA
1 TTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAAAGA-AGAAAAA
153928 TTTATTCAGC
Statistics
Matches: 152, Mismatches: 12, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
120 38 0.25
121 15 0.10
122 34 0.22
123 3 0.02
124 61 0.40
125 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (121 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAGAAGAAAAAGTTCACAATGAGAAG
AGCTTATTCAACCTTTTACATAACTCTATCACAGAAGGAAATAGTCAACATCAACC
Found at i:154079 original size:3 final size:3
Alignment explanation
Indices: 154071--154124 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
154061 CATTTTTTAT
* * *
154071 TTA TTA TTA TTA TTA TAA TAA TTA TTA TTA -TA ATA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
154116 TTA TTA TTA
1 TTA TTA TTA
154125 AAAAAAATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:154096 original size:18 final size:18
Alignment explanation
Indices: 154072--154122 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
154062 ATTTTTTATT
154072 TATTATTATTATTATA-A
1 TATTATTATTATTATATA
*
154089 TAATTATTATTATAATATA
1 T-ATTATTATTATTATATA
154108 TATTATTATTATTAT
1 TATTATTATTATTAT
154123 TAAAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 1 0.03
18 27 0.90
19 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTATTATTATTATATA
Found at i:155310 original size:19 final size:17
Alignment explanation
Indices: 155269--155370 Score: 63
Period size: 18 Copynumber: 6.1 Consensus size: 17
155259 TTTTTATTGT
* *
155269 TTATTTATGTTTTAATT
1 TTATTTATATTTTAATA
155286 TTATTTATATATTTAA-A
1 TTATTTATAT-TTTAATA
*
155303 -TA-TTAT-TTTTATTA
1 TTATTTATATTTTAATA
**
155317 TTATTATATAGTCATAA-A
1 TTATT-TATA-TTTTAATA
*
155335 TTATTTTTATTTTAATA
1 TTATTTATATTTTAATA
155352 TTTATTTAT-TTTTCAATA
1 -TTATTTATATTTT-AATA
155370 T
1 T
155371 CAAAGAAAAG
Statistics
Matches: 65, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
13 4 0.06
14 2 0.03
15 6 0.09
16 7 0.11
17 21 0.32
18 22 0.34
19 3 0.05
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
TTATTTATATTTTAATA
Found at i:155326 original size:30 final size:29
Alignment explanation
Indices: 155273--155360 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 29
155263 TATTGTTTAT
155273 TTATGTTTTAATTTTATTTATATATTTA-AATA
1 TTAT-TTTT-ATTTTA-TTATATATTTATAA-A
* *
155305 TTATTTTTATTATTATTATATAGTCATAAA
1 TTATTTTTATT-TTATTATATATTTATAAA
* *
155335 TTATTTTTATTTTAATATTTATTTAT
1 TTATTTTTATTTTATTATATATTTAT
155361 TTTTCAATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 11 0.23
30 24 0.50
31 9 0.19
32 4 0.08
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (29 bp):
TTATTTTTATTTTATTATATATTTATAAA
Found at i:159354 original size:16 final size:16
Alignment explanation
Indices: 159333--159364 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
159323 TATTGCTGTA
159333 TATAACATTTTAAGTT
1 TATAACATTTTAAGTT
159349 TATAACATTTTAAGTT
1 TATAACATTTTAAGTT
159365 CACTTGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (16 bp):
TATAACATTTTAAGTT
Found at i:164767 original size:20 final size:19
Alignment explanation
Indices: 164722--164776 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
164712 CGTTTGAGAA
*
164722 AGGTATCGATACCGAGTTGGT
1 AGGTATCGATACC-A-TGGGT
164743 A-GTATCGATACCATGGGT
1 AGGTATCGATACCATGGGT
164761 ATGGTATCGATACCAT
1 A-GGTATCGATACCAT
164777 TTTCAAGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 5 0.16
19 1 0.03
20 24 0.77
21 1 0.03
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (19 bp):
AGGTATCGATACCATGGGT
Found at i:165279 original size:15 final size:14
Alignment explanation
Indices: 165259--165300 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
165249 TGAACAAGTG
165259 TATGTGAAAAGACTC
1 TATGTGAAAAGAC-C
165274 TATGTG-AAAGTACC
1 TATGTGAAAAG-ACC
165288 TATGTGAATAAGA
1 TATGTGAA-AAGA
165301 GACACTTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 11 0.46
15 10 0.42
16 3 0.12
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (14 bp):
TATGTGAAAAGACC
Found at i:165458 original size:23 final size:23
Alignment explanation
Indices: 165428--165488 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
165418 TCGGGACAAA
165428 TATGTGGCAATTCGGTGCAAACC
1 TATGTGGCAATTCGGTGCAAACC
*
165451 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCAATTCGGTGCAAACC
165474 TATGTGGTC-ATTCGG
1 TATGTGG-CAATTCGG
165489 GACAATTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (23 bp):
TATGTGGCAATTCGGTGCAAACC
Found at i:175062 original size:3 final size:3
Alignment explanation
Indices: 175054--175084 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
175044 ACATAAACAC
175054 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
175085 CTTGAGCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:175318 original size:18 final size:18
Alignment explanation
Indices: 175295--175348 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
175285 CCCGAGGGAC
*
175295 CACTATATTCTGAAGGAG
1 CACTATATTCCGAAGGAG
* *
175313 CACTATGTTCCGAAGGAC
1 CACTATATTCCGAAGGAG
175331 CAC-ATATGTCCCGAAGGA
1 CACTATAT-T-CCGAAGGA
175349 CCACATAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 3 0.10
18 19 0.63
19 8 0.27
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (18 bp):
CACTATATTCCGAAGGAG
Found at i:175344 original size:19 final size:19
Alignment explanation
Indices: 175282--175355 Score: 82
Period size: 19 Copynumber: 4.0 Consensus size: 19
175272 GCATAGAATT
*
175282 TGTCCCGAGGGACCACTATA
1 TGTCCCGAAGGACCAC-ATA
* *
175302 T-T-CTGAAGGAGCAC-TA
1 TGTCCCGAAGGACCACATA
*
175318 TGTTCCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
175337 TGTCCCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
175356 GAACCCTCGA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
16 3 0.07
17 1 0.02
18 19 0.42
19 21 0.47
20 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (19 bp):
TGTCCCGAAGGACCACATA
Found at i:175823 original size:2 final size:2
Alignment explanation
Indices: 175816--175886 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
175806 GCACTTAACT
175816 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
175858 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
175887 TCATGTACTC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:176251 original size:22 final size:22
Alignment explanation
Indices: 176225--176283 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
176215 ATACCACCCT
* *
176225 TAGGGTACCTATACCTCTAAGC
1 TAGGGTACCGATACCTCAAAGC
176247 TAGGGTACCGATACCTCAAAGC
1 TAGGGTACCGATACCTCAAAGC
176269 TAGGGTACCGATACC
1 TAGGGTACCGATACC
176284 CTATCTAGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (22 bp):
TAGGGTACCGATACCTCAAAGC
Found at i:176354 original size:21 final size:22
Alignment explanation
Indices: 176328--176377 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
176318 TTCCCCATGA
*
176328 ATCGATACCCTCCA-CATA-GGT
1 ATCGATA-CCTCAACCATAGGGT
176349 ATCGATACCTCAACCATAGGGT
1 ATCGATACCTCAACCATAGGGT
176371 ATCGATA
1 ATCGATA
176378 TTGTTCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 5 0.19
21 11 0.42
22 10 0.38
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (22 bp):
ATCGATACCTCAACCATAGGGT
Found at i:179159 original size:18 final size:18
Alignment explanation
Indices: 179124--179165 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
179114 ATTAACATGC
* *
179124 TTATCATTACTTATTTTA
1 TTATCATTAATTACTTTA
*
179142 TTATCATTAATTCCTTTA
1 TTATCATTAATTACTTTA
179160 -TATCAT
1 TTATCAT
179166 ATGAGCATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATCATTAATTACTTTA
Found at i:193356 original size:17 final size:17
Alignment explanation
Indices: 193309--193356 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
193299 AATGCATTTT
*
193309 TGGTATCGATACTCATA
1 TGGTATCGATACTCACA
* * *
193326 GGGTTATAGATACTCCCA
1 TGG-TATCGATACTCACA
193344 TGGTATCGATACT
1 TGGTATCGATACT
193357 ATAAGTAGAG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (17 bp):
TGGTATCGATACTCACA
Found at i:194422 original size:32 final size:32
Alignment explanation
Indices: 194386--194485 Score: 121
Period size: 32 Copynumber: 3.2 Consensus size: 32
194376 AATTCGTAAT
*
194386 AGAGTTAGTGTTGCATTCAAATGATGCACAAC
1 AGAGTTAGTGTTGCATTCAAATAATGCACAAC
* * *
194418 AGAGTTAGTGTTGTATTCAGATAATACACAAC
1 AGAGTTAGTGTTGCATTCAAATAATGCACAAC
* * * *
194450 A-AATTAGTGTTGCATTTATATAAAGCACAAC
1 AGAGTTAGTGTTGCATTCAAATAATGCACAAC
194481 AGAGT
1 AGAGT
194486 CAATATCACA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
31 25 0.45
32 31 0.55
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (32 bp):
AGAGTTAGTGTTGCATTCAAATAATGCACAAC
Found at i:194479 original size:31 final size:32
Alignment explanation
Indices: 194390--194483 Score: 102
Period size: 31 Copynumber: 3.0 Consensus size: 32
194380 CGTAATAGAG
* * *
194390 TTAGTGTTGCATTCAAATGATGCACAACAGAG
1 TTAGTGTTGCATTCAAATAAAGCACAACAGAA
* *
194422 TTAGTGTTGTATTCAGATAATA-CACAACA-AA
1 TTAGTGTTGCATTCAAATAA-AGCACAACAGAA
* *
194453 TTAGTGTTGCATTTATATAAAGCACAACAGA
1 TTAGTGTTGCATTCAAATAAAGCACAACAGA
194484 GTCAATATCA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
30 1 0.02
31 25 0.49
32 25 0.49
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (32 bp):
TTAGTGTTGCATTCAAATAAAGCACAACAGAA
Found at i:196458 original size:60 final size:59
Alignment explanation
Indices: 196376--196532 Score: 145
Period size: 60 Copynumber: 2.6 Consensus size: 59
196366 TCATTTCAAG
* * * * ** *
196376 TTAGTCCAT-AAACATTTAAACATCTCAATTTCATCCTTAAACTATGACTATTATTCTAAA
1 TTAGTCC-TCAAACTTTTGAACATTTCAATTTAATCCCCAAACTATGA-TATTATCCTAAA
* ** *
196436 TTAGTCCTCAAACTTTTGAACATTTCATTTTAATCCCCACGCTATGATCTTATCCTAAA
1 TTAGTCCTCAAACTTTTGAACATTTCAATTTAATCCCCAAACTATGATATTATCCTAAA
* * * *
196495 TTGGTCCCCAAACTTTTTGAATATTTCAATTTTATCCC
1 TTAGTCCTCAAAC-TTTTGAACATTTCAATTTAATCCC
196533 AAATTATTTG
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
59 22 0.28
60 57 0.72
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (59 bp):
TTAGTCCTCAAACTTTTGAACATTTCAATTTAATCCCCAAACTATGATATTATCCTAAA
Found at i:196507 original size:59 final size:61
Alignment explanation
Indices: 196417--196532 Score: 157
Period size: 60 Copynumber: 1.9 Consensus size: 61
196407 CATCCTTAAA
* *
196417 CTATGACTATTATTCTAAATTAGTCCTCAAAC-TTTTGAACATTTC-ATTTTAATCCCCACG
1 CTATGACTATTATCCTAAATTAGTCCCCAAACTTTTTGAACATTTCAATTTT-ATCCCCACG
* * *
196477 CTATGA-TCTTATCCTAAATTGGTCCCCAAACTTTTTGAATATTTCAATTTTATCCC
1 CTATGACTATTATCCTAAATTAGTCCCCAAACTTTTTGAACATTTCAATTTTATCCC
196533 AAATTATTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 21 0.43
60 23 0.47
61 5 0.10
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.41
Consensus pattern (61 bp):
CTATGACTATTATCCTAAATTAGTCCCCAAACTTTTTGAACATTTCAATTTTATCCCCACG
Found at i:196727 original size:59 final size:58
Alignment explanation
Indices: 196660--196796 Score: 168
Period size: 59 Copynumber: 2.3 Consensus size: 58
196650 TTTGGATGTA
* *
196660 TTTGGGGATGAAATTGAAAGAACTAAAAG-TTAGGGGCCAATTTAGAATGAGATTCATAG
1 TTTGGGGATGAAATTGAAAG--CTAAAAGTTTAAGGGCCAATTTAGAATGAGAGTCATAG
* * * *
196719 TTTGGGGATGAAATTTGAATGCTCAAAGTTTAAGGGCTAATTTAGAATGAGAGTCATGG
1 TTTGGGGATGAAA-TTGAAAGCTAAAAGTTTAAGGGCCAATTTAGAATGAGAGTCATAG
**
196778 TTTAAGGATGAAATTGAAA
1 TTTGGGGATGAAATTGAAA
196797 TATTTAAAAG
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
58 11 0.16
59 50 0.75
60 6 0.09
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.30
Consensus pattern (58 bp):
TTTGGGGATGAAATTGAAAGCTAAAAGTTTAAGGGCCAATTTAGAATGAGAGTCATAG
Found at i:196923 original size:21 final size:22
Alignment explanation
Indices: 196880--196923 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
196870 TTTACTTTGC
*
196880 AACTACTAAAATAACTTTCCAA
1 AACTACTAAAATAACTTTACAA
* *
196902 AACTATTAAATTAA-TTTACAA
1 AACTACTAAAATAACTTTACAA
196923 A
1 A
196924 TTATTTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (22 bp):
AACTACTAAAATAACTTTACAA
Found at i:197375 original size:16 final size:17
Alignment explanation
Indices: 197337--197379 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
197327 TTATAATCCG
**
197337 TAAATGATAATTGAATT
1 TAAATGATAATTGAACA
*
197354 TGAATGA-AATTGAACA
1 TAAATGATAATTGAACA
197370 TAAATGATAA
1 TAAATGATAA
197380 GATTTAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (17 bp):
TAAATGATAATTGAACA
Found at i:200060 original size:200 final size:194
Alignment explanation
Indices: 199720--200114 Score: 736
Period size: 200 Copynumber: 2.0 Consensus size: 194
199710 GAAAATTAAG
199720 ACATCCATTAATGAAAGGAATTGGTCTTTGATGAGCTTGGCCTTGGCTATGAAGATGAAACGTTA
1 ACATCCATTAATGAAAGGAATTGGTCTTTGATGAGCTTGGCCTTGGCTATGAAGATGAAACGTTA
199785 ATAAGCAAGAGAGGAAATGGTGGTGGGGTAAAAGGGGGTGGACTTCAAGAAGACGGGATTTGGTG
66 ATAAGCAAGAGAGGAAATGGTGGTGGGGTAAAAGGGGGTGGACTTCAAGAAGACGGGATTTGGTG
199850 AAAGAGTGTTTAATGAAATTGAAAGCTAAACAGAGAGCCCTAGGAGTAATGGAAATCTGGCTTC
131 AAAGAGTGTTTAATGAAATTGAAAGCTAAACAGAGAGCCCTAGGAGTAATGGAAATCTGGCTTC
199914 ACATCCATTAATGAAAGGAATTGGTCTTTGATGAGCTTGGCCTTGGCTATGAAGATGAAACGTTA
1 ACATCCATTAATGAAAGGAATTGGTCTTTGATGAGCTTGGCCTTGGCTATGAAGATGAAACGTTA
199979 ATAAAGCAAGGACAGAGAGGAAATGGTGGTGGGGTAAAAGGGGGTGGACTTCAAGAAGACGGGAT
66 AT-AAGC----A-AGAGAGGAAATGGTGGTGGGGTAAAAGGGGGTGGACTTCAAGAAGACGGGAT
200044 TTGGTGAAAGAGTGTTTAATGAAATTGAAAGCTAAACAGAGAGCCCTAGGAGTAATGGAAATCTG
125 TTGGTGAAAGAGTGTTTAATGAAATTGAAAGCTAAACAGAGAGCCCTAGGAGTAATGGAAATCTG
200109 GCTTC
190 GCTTC
200114 A
1 A
200115 TTATTCATAT
Statistics
Matches: 195, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
194 67 0.34
195 4 0.02
199 1 0.01
200 123 0.63
ACGTcount: A:0.34, C:0.11, G:0.31, T:0.24
Consensus pattern (194 bp):
ACATCCATTAATGAAAGGAATTGGTCTTTGATGAGCTTGGCCTTGGCTATGAAGATGAAACGTTA
ATAAGCAAGAGAGGAAATGGTGGTGGGGTAAAAGGGGGTGGACTTCAAGAAGACGGGATTTGGTG
AAAGAGTGTTTAATGAAATTGAAAGCTAAACAGAGAGCCCTAGGAGTAATGGAAATCTGGCTTC
Found at i:201142 original size:15 final size:15
Alignment explanation
Indices: 201122--201154 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
201112 ATTAATAAAG
201122 AAAATTGAATT-AATT
1 AAAATT-AATTGAATT
201137 AAAATTAATTGAATT
1 AAAATTAATTGAATT
201152 AAA
1 AAA
201155 TAGAACATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (15 bp):
AAAATTAATTGAATT
Found at i:201628 original size:20 final size:20
Alignment explanation
Indices: 201592--201629 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
201582 CTTTTCTGAT
*
201592 CTTATTATTTATCTTTATTG
1 CTTATTATTTATATTTATTG
201612 CTTATT-TTATATATTTAT
1 CTTATTATT-TATATTTAT
201630 CATTATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (20 bp):
CTTATTATTTATATTTATTG
Done.