Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004884.1 Hibiscus syriacus cultivar Beakdansim tig00011002_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: 71526
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:8906 original size:13 final size:14
Alignment explanation
Indices: 8880--8910 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
8870 GGCTTGTAAT
8880 TTATTTTATTATTA
1 TTATTTTATTATTA
8894 TTATTTT-TTATTA
1 TTATTTTATTATTA
8907 TTAT
1 TTAT
8911 CTATATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTTATTATTA
Found at i:8933 original size:12 final size:11
Alignment explanation
Indices: 8915--9007 Score: 62
Period size: 9 Copynumber: 9.1 Consensus size: 11
8905 TATTATCTAT
8915 ATTTAAT-AT-
1 ATTTAATAATA
8924 ATTTAATAATA
1 ATTTAATAATA
8935 A--TAATAATA
1 ATTTAATAATA
*
8944 ATAATAATAATA
1 AT-TTAATAATA
*
8956 ATATTTATAATA
1 AT-TTAATAATA
8968 A-TT-ATAATA
1 ATTTAATAATA
*
8977 A--TAATAATT
1 ATTTAATAATA
8986 ATTATAATAATA
1 ATT-TAATAATA
8998 A--TAATAATA
1 ATTTAATAATA
9007 A
1 A
9008 ATAAATCAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 18
0.76 0.04 0.19
Matches are distributed among these distances:
8 1 0.01
9 38 0.54
10 4 0.06
11 1 0.01
12 27 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:8935 original size:3 final size:3
Alignment explanation
Indices: 8927--9007 Score: 117
Period size: 3 Copynumber: 27.0 Consensus size: 3
8917 TTAATATATT
* * *
8927 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
8975 TAA TAA TAA TTA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9008 ATAAATCAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:13547 original size:6 final size:6
Alignment explanation
Indices: 13540--13575 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
13530 CGTATTACCA
*
13540 CGACCA CGACCC CGACCC CGACCC CGACCC CGACCC
1 CGACCC CGACCC CGACCC CGACCC CGACCC CGACCC
13576 GAGACGGACG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.19, C:0.64, G:0.17, T:0.00
Consensus pattern (6 bp):
CGACCC
Found at i:14078 original size:6 final size:6
Alignment explanation
Indices: 14067--14099 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
14057 TCTCGTCTCA
14067 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
14100 AATACGTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:20105 original size:3 final size:3
Alignment explanation
Indices: 20097--20135 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
20087 CGGTTTGTAG
20097 TTA TTA TTA TTA -TA TTA TTA TTA TTTA TTTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TT
20136 TTTTTAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 25 0.74
4 7 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20114 original size:11 final size:11
Alignment explanation
Indices: 20098--20131 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
20088 GGTTTGTAGT
20098 TATTATTATTA
1 TATTATTATTA
20109 TATTATTATTA
1 TATTATTATTA
20120 T-TTATTTATTA
1 TATTA-TTATTA
20131 T
1 T
20132 TATTTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 3 0.14
11 19 0.86
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTATTATTA
Found at i:20116 original size:14 final size:14
Alignment explanation
Indices: 20097--20141 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
20087 CGGTTTGTAG
20097 TTATTATTA-TTAT
1 TTATTATTATTTAT
20110 ATTATTATTATTTAT
1 -TTATTATTATTTAT
*
20125 TTATTATTATTTTT
1 TTATTATTATTTAT
20139 TTA
1 TTA
20142 ATAATAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 25 0.86
15 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTATTATTTAT
Found at i:20146 original size:3 final size:3
Alignment explanation
Indices: 20140--20205 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
20130 ATTATTTTTT
*
20140 TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TATA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA
*
20185 TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
20206 ACAAATAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 4 0.07
3 45 0.82
4 6 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:21086 original size:336 final size:334
Alignment explanation
Indices: 20478--21428 Score: 1353
Period size: 336 Copynumber: 2.8 Consensus size: 334
20468 TCTTGATGAG
*
20478 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT-TTCATTATGAACTTTTTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT-ATTATGAACTTTATCT
* * * *
20542 GGAAAGGCTGATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAA---TTCTCATTATGAA
65 GGAAA-GCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
*
20604 CTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAAC-TCTCTGGCAAAGCTAATCCATCA
129 TTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTTCTCTGGCAAAGCTAATCCATCA
20668 AGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTTATGAACTTCTTCTTCCTTCTTCAGAT
194 AGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTTATGAACTTCTTCTTCCTTCTTCAGAT
* *
20733 GAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTCAG-GCAAA
259 GAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATAGATT-AGAACAAA
20797 AGGTTGAACAAA
323 AGGTTGAACAAA
* * *
20809 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAGGAGTTCTTCTTATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTATCTG
20874 GCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
66 G-AAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
* *
20939 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGCAAAGCTAATCCATCA
130 TTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAAC-TTCTCTGGCAAAGCTAATCCATCA
21004 AGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTTATGAACTTCTTCTTCCTTCTTCAGAT
194 AGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTTATGAACTTCTTCTTCCTTCTTCAGAT
* *
21069 GAGTTCTTCTTATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATAGATTTGAACAAAA
259 GAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATAGATTAGAACAAAA
*
21134 GGTTGGACAAA
324 GGTTGAACAAA
* * * * ** *
21145 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTTTTCTCATTATGAAGTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTATCTG
* * * * *
21210 GAAAAGATAATCCATCAAGTGATAGATT-TGAACAAAAGGTTGGACAAATTCTTCTCATTATGAA
66 G-AAAGCTAATCCATCAAGTGATGGATTCAG-GCAAAAGGTTGAACAAATTCTTCTCATTATGAA
* * * * * *
21274 TTTTTTCTTCTTTCTTCAGATGAGTTTTTCTCATTATGAAC-TCGAACTGGAAAAGATAATCCAT
129 TTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTTC--TCTGGCAAAGCTAATCCAT
* * * * * * *
21338 CAAGTGATAGATT-TGAACAAAAGGTTGGACAAATTCTTCTCATTATGAATTTTTTCTTCATTCT
192 CAAGTGATGGATTCAG-GCAAAAGGTTGAACAAATTC-T-TC-TTATGAACTTCTTCTTCCTTCT
21402 TCAGATGAGTTCTTCTCATTATGAACT
253 TCAGATGAGTTCTTCTCATTATGAACT
21429 CGAACTGGTA
Statistics
Matches: 559, Mismatches: 46, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
331 99 0.18
332 5 0.01
334 53 0.09
335 3 0.01
336 351 0.63
337 1 0.00
338 2 0.00
339 45 0.08
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (334 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTATCTG
GAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAATT
TCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTTCTCTGGCAAAGCTAATCCATCAAG
TGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTTATGAACTTCTTCTTCCTTCTTCAGATGA
GTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATAGATTAGAACAAAAGG
TTGAACAAA
Found at i:21436 original size:226 final size:226
Alignment explanation
Indices: 20478--21428 Score: 1318
Period size: 223 Copynumber: 4.3 Consensus size: 226
20468 TCTTGATGAG
* *
20478 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTTCATTATGAACTTTTTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTG
* * * * *
20543 GAAAGGCTGATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAA---TTCTCATTATGAAC
66 GAAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
*
20605 TTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAA--CTCTCTGGCAAAGCTAATCCATCA
131 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGCAAAGCTAATCCATCA
* *
20668 AGTGATGGATTCAGGCAAAAGGTTGAACAAA
196 AGTGATAGATTCAGACAAAAGGTTGAACAAA
*
20699 TTC-T-TC-TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTG
* *
20761 GCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
66 GAAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * *
20826 TTCTTCTTCCTTCTTCAGAGGAGTTCTTCTTATTATGAACTTTCTCTGGCAAAGCTAATCCATCA
131 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGCAAAGCTAATCCATCA
* *
20891 AGTGATGGATTCAGGCAAAAGGTTGAACAAA
196 AGTGATAGATTCAGACAAAAGGTTGAACAAA
* * *
20922 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTG
*
20987 GCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTC-T-TC-TTATGAAC
66 GAAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
21049 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGCAAAGCTAATCCATCA
131 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGCAAAGCTAATCCATCA
* *
21114 AGTGATAGATT-TGAACAAAAGGTTGGACAAA
196 AGTGATAGATTCAG-ACAAAAGGTTGAACAAA
* * * ** *
21145 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTTTTCTCATTATGAAGTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTG
* * * * *
21210 GAAAAGATAATCCATCAAGTGATAGATT-TGAACAAAAGGTTGGACAAATTCTTCTCATTATGAA
66 GAAAAGCTAATCCATCAAGTGATGGATTCAG-GCAAAAGGTTGAACAAATTCTTCTCATTATGAA
* * * * *** * *
21274 TTTTTTCTTCTTTCTTCAGATGAGTTTTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATC
130 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGCAAAGCTAATCCATC
* *
21339 AAGTGATAGATT-TGAACAAAAGGTTGGACAAA
195 AAGTGATAGATTCAG-ACAAAAGGTTGAACAAA
* * *
21371 TTCTTCTCATTATGAATTTTTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
21429 CGAACTGGTA
Statistics
Matches: 664, Mismatches: 53, Indels: 21
0.90 0.07 0.03
Matches are distributed among these distances:
218 96 0.14
219 2 0.00
220 1 0.00
221 52 0.08
222 2 0.00
223 252 0.38
224 4 0.01
225 5 0.01
226 250 0.38
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (226 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTG
GAAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGCAAAGCTAATCCATCA
AGTGATAGATTCAGACAAAAGGTTGAACAAA
Found at i:21464 original size:113 final size:113
Alignment explanation
Indices: 20478--21428 Score: 1338
Period size: 113 Copynumber: 8.5 Consensus size: 113
20468 TCTTGATGAG
* *
20478 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTTCATTATGAACTTTTTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
20543 G-AAAGGCTGATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAA
66 GCAAA-GCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
*
20591 ---TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAAC--TCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
20651 GCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
66 GCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
20699 TTC-T-TC-TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
20761 GCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
66 GCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
* * *
20809 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAGGAGTTCTTCTTATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
20874 GCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
66 GCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
* *
20922 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
20987 GCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
66 GCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
*
21035 TTC-T-TC-TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
21097 GCAAAGCTAATCCATCAAGTGATAGATT-TGAACAAAAGGTTGGACAAA
66 GCAAAGCTAATCCATCAAGTGATGGATTCAG-GCAAAAGGTTGAACAAA
* * * ****
21145 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTTTTCTCATTATGAAGTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * *
21210 GAAAAGATAATCCATCAAGTGATAGATT-TGAACAAAAGGTTGGACAAA
66 GCAAAGCTAATCCATCAAGTGATGGATTCAG-GCAAAAGGTTGAACAAA
* * * * ****
21258 TTCTTCTCATTATGAATTTTTTCTTCTTTCTTCAGATGAGTTTTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * *
21323 GAAAAGATAATCCATCAAGTGATAGATT-TGAACAAAAGGTTGGACAAA
66 GCAAAGCTAATCCATCAAGTGATGGATTCAG-GCAAAAGGTTGAACAAA
* * *
21371 TTCTTCTCATTATGAATTTTTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
21429 CGAACTGGTA
Statistics
Matches: 791, Mismatches: 34, Indels: 26
0.93 0.04 0.03
Matches are distributed among these distances:
108 92 0.12
109 6 0.01
110 210 0.27
111 4 0.01
112 5 0.01
113 474 0.60
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
Found at i:21945 original size:22 final size:22
Alignment explanation
Indices: 21867--21940 Score: 112
Period size: 22 Copynumber: 3.4 Consensus size: 22
21857 GATAAAGCTT
* *
21867 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTAAAAAGAGAATCTA
*
21889 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
*
21911 TCATCTTTAAAGAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
21933 TCATCTTT
1 TCATCTTT
21941 GAAGAATGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:24880 original size:83 final size:83
Alignment explanation
Indices: 24606--25147 Score: 959
Period size: 83 Copynumber: 6.6 Consensus size: 83
24596 CATACCGAAT
* * **
24606 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACATTCCTC-T-CAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
24669 TGATTGGTTTTACCAAAC
66 TGATTGGTTTTACCAAAC
* * **
24687 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACATTCCTC-T-CAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
24750 TGATTGGTTTTACCAAAC
66 TGATTGGTTTTACCAAAC
24768 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
24833 TGATTGGTTTTACCAAAC
66 TGATTGGTTTTACCAAAC
24851 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
24916 TGATTGGTTTTACCAAAC
66 TGATTGGTTTTACCAAAC
24934 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
24999 TGATTGG-TTTACCAAAC
66 TGATTGGTTTTACCAAAC
*
25016 CAGATCAGCTAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
25081 TGATTGGTTTTACCAAAC
66 TGATTGGTTTTACCAAAC
*
25099 CAGATCAGCTAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
25148 GCATTTATTC
Statistics
Matches: 453, Mismatches: 5, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
81 130 0.29
82 82 0.18
83 241 0.53
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
TGATTGGTTTTACCAAAC
Found at i:25069 original size:248 final size:245
Alignment explanation
Indices: 24606--25147 Score: 951
Period size: 248 Copynumber: 2.2 Consensus size: 245
24596 CATACCGAAT
* * *
24606 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACATTCCTCTCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTCAAATTCAATG
*
24671 ATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACATT
66 ATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATT
*
24736 CCTCTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
131 ACTCTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
24801 ATGCTATGAGCACATTATTCTTCCAAATTCAATGATTGGTTTTACCAAAC
196 ATGCTATGAGCACATTATTCTTCCAAATTCAATGATTGGTTTTACCAAAC
*
24851 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTC-T-CAAATTCAA
*
24916 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
64 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACA
* *
24981 TTATTCTTCCAAATTCAATGATTGG-TTTACCAAACCAGATCAGCTAACTCAAAGAACACTTCCA
129 TTACTC-T-CAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCA
25045 GAAGATGCTATGAGCACATTATTCTTCCAAATTCAATGATTGGTTTTACCAAAC
192 GAAGATGCTATGAGCACATTATTCTTCCAAATTCAATGATTGGTTTTACCAAAC
*
25099 CAGATCAGCTAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
25148 GCATTTATTC
Statistics
Matches: 283, Mismatches: 10, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
245 49 0.17
246 1 0.00
247 76 0.27
248 141 0.50
249 16 0.06
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (245 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTCAAATTCAATG
ATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATT
ACTCTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
ATGCTATGAGCACATTATTCTTCCAAATTCAATGATTGGTTTTACCAAAC
Found at i:25114 original size:165 final size:166
Alignment explanation
Indices: 24606--25147 Score: 959
Period size: 165 Copynumber: 3.3 Consensus size: 166
24596 CATACCGAAT
* * **
24606 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACATTCCTC-T-CAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
* *
24669 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACA
66 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
**
24734 TTCCTC-T-CAAATTCAATGATTGGTTTTACCAAAC
131 TTATTCTTCCAAATTCAATGATTGGTTTTACCAAAC
24768 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
24833 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
66 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
24898 TTATTCTTCCAAATTCAATGATTGGTTTTACCAAAC
131 TTATTCTTCCAAATTCAATGATTGGTTTTACCAAAC
24934 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
*
24999 TGATTGG-TTTACCAAACCAGATCAGCTAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
66 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
25063 TTATTCTTCCAAATTCAATGATTGGTTTTACCAAAC
131 TTATTCTTCCAAATTCAATGATTGGTTTTACCAAAC
*
25099 CAGATCAGCTAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
25148 GCATTTATTC
Statistics
Matches: 366, Mismatches: 10, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
162 49 0.13
163 1 0.00
164 76 0.21
165 141 0.39
166 99 0.27
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (166 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
TTATTCTTCCAAATTCAATGATTGGTTTTACCAAAC
Found at i:34175 original size:3 final size:3
Alignment explanation
Indices: 34169--34234 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
34159 ATTATTTTTC
*
34169 TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TATA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA
*
34214 TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
34235 ACAAATAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 4 0.07
3 45 0.82
4 6 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:44118 original size:24 final size:24
Alignment explanation
Indices: 44080--44131 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
44070 AAGATCGTTC
* *
44080 ACATGAGAACAGCTTCACATTGGA
1 ACATGAAAACAGCTTCACATGGGA
*
44104 ACATGAAAACCGCTTCACATGGGA
1 ACATGAAAACAGCTTCACATGGGA
44128 ACAT
1 ACAT
44132 AGTTGAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (24 bp):
ACATGAAAACAGCTTCACATGGGA
Found at i:49480 original size:29 final size:29
Alignment explanation
Indices: 49442--49676 Score: 105
Period size: 29 Copynumber: 7.9 Consensus size: 29
49432 TTTTCATTCC
* *
49442 TGACTCCCTCATGAAGAGGAAACAATCCT
1 TGACTTCCTCATGAAGAGGAATCAATCCT
*
49471 TGACTTCCTCGTGAAGA-GAAGTCAAT-CT
1 TGACTTCCTCATGAAGAGGAA-TCAATCCT
** ** * *
49499 T-TTTTATTCCTGAAGAGGAGTCAATCCT
1 TGACTTCCTCATGAAGAGGAATCAATCCT
49527 TGACTTCCTCATGAAGA-GAAGTCAATCTTTATCATT
1 TGACTTCCTCATGAAGAGGAA-TCAATC-----C--T
* * *
49563 CATGACTCCCTCGTAAAGAGGAA-CAAATCCT
1 --TGACTTCCTCATGAAGAGGAATC-AATCCT
* *
49594 TAACTTCCTCATGAAGA-GAATTCAATCTT
1 TGACTTCCTCATGAAGAGGAA-TCAATCCT
*
49623 TGATATTCCT-A--AAGA-GAAGTCAATCCT
1 TGA-CTTCCTCATGAAGAGGAA-TCAATCCT
*
49650 TGACTTCCTCGTGAAGA-GAAGTCAATC
1 TGACTTCCTCATGAAGAGGAA-TCAATC
49677 TTTGTTATTC
Statistics
Matches: 155, Mismatches: 29, Indels: 44
0.68 0.13 0.19
Matches are distributed among these distances:
26 5 0.03
27 32 0.21
28 16 0.10
29 70 0.45
30 6 0.04
31 1 0.01
33 1 0.01
34 1 0.01
36 1 0.01
37 1 0.01
38 18 0.12
39 3 0.02
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (29 bp):
TGACTTCCTCATGAAGAGGAATCAATCCT
Found at i:49506 original size:123 final size:123
Alignment explanation
Indices: 49282--50357 Score: 1341
Period size: 123 Copynumber: 8.8 Consensus size: 123
49272 TCTTCAACTA
* * ** **
49282 GACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTTTTCTCTCCCTCGTGAAGAGGAACCAATCC
1 GACTTCCTCGTGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCC
* * * * *
49347 TTGACTTTCTTGTGAAGAGAAGTTAATCTTTGTTATTCCTGAAATAG-AGTCAATCCAT
66 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCT-AAAGAGAAGTCAATCCTT
* ** * * * *
49405 GTCTTCCTCGCAAAGAGAAGTTAATCTTT-TTCATTCCTGACTCCCTCATGAAGAGGAAACAATC
1 GACTTCCTCGTGAAGAGAAGTCAATCTTTATT-ATTCATGACTCCCTCGTGAAGAGGAACCAATC
* * *
49469 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCCTGAAGAGGAGTCAATCCTT
65 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTT
* * * *
49528 GACTTCCTCATGAAGAGAAGTCAATCTTTATCATTCATGACTCCCTCGTAAAGAGGAACAAATCC
1 GACTTCCTCGTGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCC
* * * *
49593 TTAACTTCCTCATGAAGAGAATTCAATCTTTGATATTCCTAAAGAGAAGTCAATCCTT
66 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTT
* *
49651 GACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCATGACTCCCTCATGAAGA-G-A--AA-CC
1 GACTTCCTCGTGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCC
* * * * **
49711 ---A-ATCCT--TGAAGAGAAGTCAATCTTTGATATTCCTAAAGAGAAGTTAGTTGTT
66 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTT
** * *
49763 GACTTCCTCACGAAGAGAAGTCAATCTTTATTATTCATAACTCCCTCATGAAGAGGAACCAATCC
1 GACTTCCTCGTGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCC
*
49828 TTGACTTCCTCGTAAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTT
66 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTT
* *
49886 GACTTCCTTGTGAAGAGAAGTCAATCTTTGTTATTCATGACTCCCTCGTGAAGAGGAACCAATCC
1 GACTTCCTCGTGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCC
* * * * *
49951 TTGACTTCCTCGTGAAGAAAAATTAATCTTTGCTATTCCTAAAGAGGAGTCAATCCTT
66 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTT
*** * * * *
50009 GACTTCCTTAAGAAGAGAAGTCAATCTTTGTTATTCATGACTTCCTCGTGAAGAGGAGCCAATGC
1 GACTTCCTCGTGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCC
* * * * * ** * *
50074 TTGACTTCCTCATAAAAAGACGTTAATCTTTACTGTTCCTAAAAAGAAGTCAATCCTT
66 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTT
* * *
50132 GAATTCCTCTTGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTTGTGAAGAGGAACCAATCC
1 GACTTCCTCGTGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCC
* * *
50197 TTGACTTCCTCGTGAATAGAAGTCGATATTTGTTATTCCTAAAGAGAAGTCAATCCTT
66 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTT
* * *
50255 GACTTCCTCGTGAAGAGAAATCAATCTTTATTATTCTTGACTCCCTCGTGAAGAGGAACCAATCA
1 GACTTCCTCGTGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCC
* * * *
50320 TTGACTTCCTCATGAAGAGAAGTTAATTTTTATTATTC
66 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTC
50358 ATGACTCCCT
Statistics
Matches: 822, Mismatches: 117, Indels: 28
0.85 0.12 0.03
Matches are distributed among these distances:
112 91 0.11
113 1 0.00
114 5 0.01
115 1 0.00
116 2 0.00
117 2 0.00
118 2 0.00
119 2 0.00
120 1 0.00
121 5 0.01
122 7 0.01
123 702 0.85
124 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (123 bp):
GACTTCCTCGTGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCC
TTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTT
Found at i:49508 original size:67 final size:67
Alignment explanation
Indices: 49396--50568 Score: 699
Period size: 67 Copynumber: 19.0 Consensus size: 67
49386 TGAAATAGAG
* * ** * * *
49396 TCAATCCATGTCTTCCTCGCAAAGAGAAGTTAATCTTTTTCATTCCTGACTCCCTCATGAAGAGG
1 TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAGG
49461 AA
66 AA
*
49463 ACAATCCTTGACTTCCTCGTGAAGAGAAGTCAATC--TTTT-TT-AT---T--C-C-TGAAGAGG
1 TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAGG
*
49517 AG
66 AA
* * * * *
49519 TCAATCCTTGACTTCCTCATGAAGAGAAGTCAATCTTTATCATTCATGACTCCCTCGTAAAGAGG
1 TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAGG
49584 AA
66 AA
* * * *
49586 -CAAATCCTTAACTTCCTCATGAAGAGAATTCAATC--TTTGA-T-AT---T-CCT-A--AAGA-
1 TC-AATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAG
49638 GAA
65 GAA
*
49641 GTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCATGACTCCCTCATGAAGA-
1 -TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAG
49705 G-A
65 GAA
* *
49707 --AA-CC---A-ATCCT--TGAAGAGAAGTCAATC-T-TTGA-T-AT---T-CCT-A--AAGA-G
1 TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAGG
49751 AA
66 AA
* * ** ** * *
49753 GTTAGTTGTTGACTTCCTCACGAAGAGAAGTCAATCTTTATTATTCATAACTCCCTCATGAAGAG
1 -TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAG
49818 GAA
65 GAA
* * *
49821 CCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATC---TTTGTT-AT---T-CCT-A--AAGA-G
1 TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAGG
49874 AA
66 AA
* * *
49876 GTCAATCCTTGACTTCCTTGTGAAGAGAAGTCAATCTTTGTTATTCATGACTCCCTCGTGAAGAG
1 -TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAG
49941 GAA
65 GAA
* * * * * *
49944 CCAATCCTTGACTTCCTCGTGAAGAAAAATTAATC----TT-TGC-T-A-TTCCT-A--AAGAGG
1 TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAGG
*
49998 AG
66 AA
*** * * *
50000 TCAATCCTTGACTTCCTTAAGAAGAGAAGTCAATCTTTGTTATTCATGACTTCCTCGTGAAGAGG
1 TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAGG
*
50065 AG
66 AA
* * * * * * * * *
50067 CCAATGCTTGACTTCCTCATAAAAAGACGTTAATC---TTTA--C-TG--TTCCT-A--AA-AAG
1 TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAGG
50120 AA
66 AA
* * * **
50122 GTCAATCCTTGAATTCCTCTTGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTTGTGAAGAG
1 -TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAG
50187 GAA
65 GAA
* * * * *
50190 CCAATCCTTGACTTCCTCGTGAATAGAAGTCGA---TATTTGTT-AT---T-CCT-A--AAGA-G
1 TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAGG
50243 AA
66 AA
* * * *
50245 GTCAATCCTTGACTTCCTCGTGAAGAGAAATCAATCTTTATTATTCTTGACTCCCTCGTGAAGAG
1 -TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAG
50310 GAA
65 GAA
* * * * *
50313 CCAATCATTGACTTCCTCATGAAGAGAAGTTAAT-TTTTATTATTCATGACTCCCTCGTGAAGAG
1 TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTT-TTATTCATGACTCCCTCATGAAGAG
50377 GAA
65 GAA
* *
50380 CCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATC---TTTGTT-A--A-T-CCT-A--AAGA-G
1 TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAGG
50433 AA
66 AA
** * * * * * *
50435 GTCAATTATTGACTTACTCGTAAAGAGAAGTCTATCTTTGTTATTCCTGACTCCCT-AGTGAAGT
1 -TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCA-TGAAGA
50499 GGAA
64 GGAA
** *
50503 TCAATCCTTGACTTCCTTATGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCGTGAAGAGG
1 TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAGG
50568 A
66 A
50569 GAAGTCAATA
Statistics
Matches: 848, Mismatches: 144, Indels: 228
0.70 0.12 0.19
Matches are distributed among these distances:
45 5 0.01
46 1 0.00
47 1 0.00
48 3 0.00
49 2 0.00
52 2 0.00
53 2 0.00
54 6 0.01
55 16 0.02
56 273 0.32
57 3 0.00
58 13 0.02
59 42 0.05
60 17 0.02
61 7 0.01
62 9 0.01
63 19 0.02
64 44 0.05
65 10 0.01
66 6 0.01
67 351 0.41
68 16 0.02
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (67 bp):
TCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCATGAAGAGG
AA
Found at i:49542 original size:56 final size:56
Alignment explanation
Indices: 49453--50547 Score: 444
Period size: 56 Copynumber: 18.0 Consensus size: 56
49443 GACTCCCTCA
**
49453 TGAAGAGGAAACAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCC
1 TGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCC
*
49509 TGAAGAGGAGTCAATCCTTGACTTCCTCATGAAGAGAAGTCAATCTTTATCATTCATGACTCCC
1 TGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTT-T--TT-AT---T-CC
* * * * **
49573 TCGTAAAGAGGA-ACAAATCCTTAACTTCCTCATGAAGAGAATTCAATCTTTGATATTCC
1 T-G--AAGAGGAGTC-AATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCC
* *
49632 TAAAGAGAAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCATGACTCCC
1 TGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT-TT-TT-AT---T-CC
* * * * * **
49696 TCATGAAGAG--AAACC---A-ATCCT--TGAAGAGAAGTCAATCTTTGATATTCC
1 TGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCC
* * * * ** **
49744 TAAAGAGAAGTTAGTTGTTGACTTCCTCACGAAGAGAAGTCAATCTTTATTATTCATAACTCCCT
1 TGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT-TT-TT-AT---T--C-
49809 C
56 C
** * *
49810 ATGAAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTGTTATTCC
1 -TGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCC
* * *
49867 TAAAGAGAAGTCAATCCTTGACTTCCTTGTGAAGAGAAGTCAATCTTTGTTATTCATGACTCCCT
1 TGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT-TT-TT-AT---T--C-
49932 C
56 C
** * * * **
49933 GTGAAGAGGAACCAATCCTTGACTTCCTCGTGAAGAAAAATTAATCTTTGCTATTCC
1 -TGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCC
* ***
49990 TAAAGAGGAGTCAATCCTTGACTTCCTTAAGAAGAGAAGTCAATCTTTGTTATTCATGACTTCCT
1 TGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATC--T-TT-TT--T-A-TT-C-
50055 C
56 C
* * * * * * * ** *
50056 GTGAAGAGGAGCCAATGCTTGACTTCCTCATAAAAAGACGTTAATCTTTACTGTTCC
1 -TGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCC
* * * * *
50113 TAAAAAGAAGTCAATCCTTGAATTCCTCTTGAAGAGAAGTCAATCTTTATTATTCATGACTCCC
1 TGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT-TT-TT-AT---T-CC
** * * * *
50177 TTGTGAAGAGGAACCAATCCTTGACTTCCTCGTGAATAGAAGTCGATATTTGTTATTCC
1 ---TGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCC
* * *
50236 TAAAGAGAAGTCAATCCTTGACTTCCTCGTGAAGAGAAATCAATCTTTATTATTCTTGACTCCCT
1 TGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATC----TT-TT-TT-A-T---T
*
50301 CG
55 CC
** * * * *
50303 TGAAGAGGAACCAATCATTGACTTCCTCATGAAGAGAAGTTAATTTTTATTATTCATGACTCCCT
1 TGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAA-TCTT-TT-TT-AT---T--C-
50368 C
56 C
** * *
50369 GTGAAGAGGAACCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTAATCC
1 -TGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCC
* * ** * * * *
50426 TAAAGAGAAGTCAATTATTGACTTACTCGTAAAGAGAAGTCTATCTTTGTTATTCC
1 TGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCC
* **
50482 TGACTCCCTAGTGAAGTGGAATCAATCCTTGACTTCCTTATGAAGAGAAGTCAATCTTTTTTATT
1 TGA------A--G-A--GGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATT
50547 C
55 C
50548 ATGACTCCCT
Statistics
Matches: 775, Mismatches: 164, Indels: 189
0.69 0.15 0.17
Matches are distributed among these distances:
48 8 0.01
49 1 0.00
50 1 0.00
52 2 0.00
53 2 0.00
54 5 0.01
55 2 0.00
56 306 0.39
57 14 0.02
58 13 0.02
59 17 0.02
60 16 0.02
61 2 0.00
62 8 0.01
63 19 0.02
64 35 0.05
65 11 0.01
66 13 0.02
67 299 0.39
68 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (56 bp):
TGAAGAGGAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCC
Found at i:49716 original size:246 final size:245
Alignment explanation
Indices: 49282--50568 Score: 1359
Period size: 246 Copynumber: 5.2 Consensus size: 245
49272 TCTTCAACTA
* ** **
49282 GACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTTTTCTCTCCCTCGTGAAGAGGAACCAATCC
1 GACTTCCTCATGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCC
* ** * * * *
49347 TTGACTTTCTTGTGAAGAGAAGTTAATCTTTGTTATTCCTGAAATAG-AGTCAATCCATGTCTTC
66 TTGACTTCCTCATGAAGAGAA-TTAATCTTTGATATTCCT-AAAGAGAAGTCAATCCTTGACTTC
** * *
49411 CTCGCAAAGAGAAGTTAATCTTT-TTCATTCCTGACTCCCTCATGAAGAGGAAA-CAATCCTTGA
129 CTCGTGAAGAGAAGTCAATCTTTGTT-ATTCATGACTCCCTCATGAAGA-GAAACCAATCCTTGA
* * *
49474 CTTCCTCGTGAAGAGAAGTCAATCTTTTTTATTCCTGAAGAGGAGTCAATCCTT
192 CTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTT
* * *
49528 GACTTCCTCATGAAGAGAAGTCAATCTTTATCATTCATGACTCCCTCGTAAAGAGGAACAAATCC
1 GACTTCCTCATGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCC
*
49593 TTAACTTCCTCATGAAGAGAATTCAATCTTTGATATTCCTAAAGAGAAGTCAATCCTTGACTTCC
66 TTGACTTCCTCATGAAGAGAATT-AATCTTTGATATTCCTAAAGAGAAGTCAATCCTTGACTTCC
49658 TCGTGAAGAGAAGTCAATCTTTGTTATTCATGACTCCCTCATGAAGAGAAACC-A------A--T
130 TCGTGAAGAGAAGTCAATCTTTGTTATTCATGACTCCCTCATGAAGAGAAACCAATCCTTGACTT
* * * **
49714 CCT--TGAAGAGAAGTCAATCTTTGATATTCCTAAAGAGAAGTTAGTTGTT
195 CCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTT
* * *
49763 GACTTCCTCACGAAGAGAAGTCAATCTTTATTATTCATAACTCCCTCATGAAGAGGAACCAATCC
1 GACTTCCTCATGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCC
* * * *
49828 TTGACTTCCTCGTAAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTTGACTTCC
66 TTGACTTCCTCATGAAGAGAA-TTAATCTTTGATATTCCTAAAGAGAAGTCAATCCTTGACTTCC
* * *
49893 TTGTGAAGAGAAGTCAATCTTTGTTATTCATGACTCCCTCGTGAAGAGGAACCAATCCTTGACTT
130 TCGTGAAGAGAAGTCAATCTTTGTTATTCATGACTCCCTCATGAAGAGAAACCAATCCTTGACTT
* * * * *
49958 CCTCGTGAAGAAAAATTAATCTTTGCTATTCCTAAAGAGGAGTCAATCCTT
195 CCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTT
* * * * * *
50009 GACTTCCTTAAGAAGAGAAGTCAATCTTTGTTATTCATGACTTCCTCGTGAAGAGGAGCCAATGC
1 GACTTCCTCATGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCC
* * * * * *
50074 TTGACTTCCTCATAAAAAGACGTTAATCTTT-ACTGTTCCTAAAAAGAAGTCAATCCTTGAATTC
66 TTGACTTCCTCATGAAGAGA-ATTAATCTTTGA-TATTCCTAAAGAGAAGTCAATCCTTGACTTC
* * ** *
50138 CTCTTGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTTGTGAAGAGGAACCAATCCTTGACT
129 CTCGTGAAGAGAAGTCAATCTTTGTTATTCATGACTCCCTCATGAAGAGAAACCAATCCTTGACT
* * *
50203 TCCTCGTGAATAGAAGTCGATATTTGTTATTCCTAAAGAGAAGTCAATCCTT
194 TCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTT
* * * *
50255 GACTTCCTCGTGAAGAGAAATCAATCTTTATTATTCTTGACTCCCTCGTGAAGAGGAACCAATCA
1 GACTTCCTCATGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCC
* * * *
50320 TTGACTTCCTCATGAAGAGAAGTTAATTTTTATTATTCATGACTCCCTCGTGAAGAGGAA-CCAA
66 TTGACTTCCTCATGAAGAGAA-TTAA-TCTT-TGA-T-AT---T--C-C-TAAAGA-GAAGTCAA
**
50384 TCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTG---TT-A--A-T-CCT-A--AAGAGAAGTC
118 TCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCATGACTCCCTCATGAAGAGAAACC
** * * * * *
50438 AATTATTGACTTACTCGTAAAGAGAAGTCTATCTTTGTTATTCCTGACTCCCTAGTGAAGTGGAA
183 AATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCT-A-----AAGAGAA---G--
50503 TCAATCCTT
237 TCAATCCTT
* *
50512 GACTTCCTTATGAAGAGAAGTCAATCTTTTTTATTCATGACTCCCTCGTGAAGAGGA
1 GACTTCCTCATGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTCGTGAAGAGGA
50569 GAAGTCAATA
Statistics
Matches: 880, Mismatches: 119, Indels: 73
0.82 0.11 0.07
Matches are distributed among these distances:
235 205 0.23
236 2 0.00
237 4 0.00
239 1 0.00
242 1 0.00
244 4 0.00
245 12 0.01
246 521 0.59
247 6 0.01
248 1 0.00
249 5 0.01
250 2 0.00
251 1 0.00
252 5 0.01
253 2 0.00
254 2 0.00
255 2 0.00
256 1 0.00
257 100 0.11
258 3 0.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (245 bp):
GACTTCCTCATGAAGAGAAGTCAATCTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCC
TTGACTTCCTCATGAAGAGAATTAATCTTTGATATTCCTAAAGAGAAGTCAATCCTTGACTTCCT
CGTGAAGAGAAGTCAATCTTTGTTATTCATGACTCCCTCATGAAGAGAAACCAATCCTTGACTTC
CTCGTGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTT
Found at i:49854 original size:29 final size:29
Alignment explanation
Indices: 49822--49911 Score: 112
Period size: 29 Copynumber: 3.2 Consensus size: 29
49812 GAAGAGGAAC
49822 CAATCCTTGACTTCCTCGTAAAGAGAAGT
1 CAATCCTTGACTTCCTCGTAAAGAGAAGT
* ** *
49851 CAATCTTTG--TTATTCCTAAAGAGAAGT
1 CAATCCTTGACTTCCTCGTAAAGAGAAGT
* *
49878 CAATCCTTGACTTCCTTGTGAAGAGAAGT
1 CAATCCTTGACTTCCTCGTAAAGAGAAGT
49907 CAATC
1 CAATC
49912 TTTGTTATTC
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
27 23 0.47
29 26 0.53
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (29 bp):
CAATCCTTGACTTCCTCGTAAAGAGAAGT
Found at i:49875 original size:27 final size:28
Alignment explanation
Indices: 49840--49921 Score: 98
Period size: 27 Copynumber: 2.9 Consensus size: 28
49830 GACTTCCTCG
49840 TAAAGAGAAGTCAATCTTTGTTATTCC-
1 TAAAGAGAAGTCAATCTTTGTTATTCCT
*
49867 TAAAGAGAAGTCAATCCTTG--ACTTCCTT
1 TAAAGAGAAGTCAATCTTTGTTA-TTCC-T
*
49895 GTGAAGAGAAGTCAATCTTTGTTATTC
1 -TAAAGAGAAGTCAATCTTTGTTATTC
49922 ATGACTCCCT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
25 1 0.02
26 4 0.09
27 19 0.41
29 18 0.39
30 3 0.07
31 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (28 bp):
TAAAGAGAAGTCAATCTTTGTTATTCCT
Found at i:50354 original size:190 final size:190
Alignment explanation
Indices: 49417--50568 Score: 877
Period size: 190 Copynumber: 6.2 Consensus size: 190
49407 CTTCCTCGCA
* * * * *
49417 AAGAGAAGTTAATCTTTT-TCATTCCTGACTCCCTCATGAAGAGGAAACAATCCTTGACTTCCTC
1 AAGAGAAGTCAAT-TTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCCTTGACTTCCTC
* * * *
49481 GTGAAGAGAAGTCAATCTTTTTTATTCCTGAAGAGGAGTCAATCCTTGACTTCCTCATGAAGAGA
65 GTGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTTGACTTCCTCGTGAAGAGA
* * * * * *
49546 AGTCAATCTTTATCATTCATGACTCCCTCGTAAAGAGGAACAAATCCTTAACTTCCTCATG
130 AATCAATCTTTATTATTCTTGACTCCCTCGTGAAGAGGAACCAATCCTTGACTTCCTCATG
* * * * *
49607 AAGAGAATTCAA-TCTT-TGA-T-AT---T--C-C-TAAAGA-GAAGTCAATCCTTGACTTCCTC
1 AAGAGAAGTCAATTTTTATTATTCATGACTCCCTCGTGAAGAGGAA-CCAATCCTTGACTTCCTC
**** ** * *
49660 GTGAAGAGAAGTCAATCTTTGTTATTCATGACTCCCTCATGAAGAGAAACC---A-ATCCT--TG
65 GTGAAGAGAAGTCAATCTTTGTTATTC----CT-AAAGA-GAAGTCAATCCTTGACTTCCTCGTG
* * ** * **
49719 AAGAGAAGTCAATCTTTGA-TA----T---T--C-C-TAAAGA-GAAGTTAGTTGTTGACTTCCT
124 AAGAGAAATCAATCTTT-ATTATTCTTGACTCCCTCGTGAAGAGGAA-CCAATCCTTGACTTCCT
*
49771 CACG
187 CATG
* * *
49775 AAGAGAAGTCAATCTTTATTATTCATAACTCCCTCATGAAGAGGAACCAATCCTTGACTTCCTCG
1 AAGAGAAGTCAATTTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCCTTGACTTCCTCG
* *
49840 TAAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTTGACTTCCTTGTGAAGAGAA
66 TGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTTGACTTCCTCGTGAAGAGAA
* * * *
49905 GTCAATCTTTGTTATTCATGACTCCCTCGTGAAGAGGAACCAATCCTTGACTTCCTCGTG
131 ATCAATCTTTATTATTCTTGACTCCCTCGTGAAGAGGAACCAATCCTTGACTTCCTCATG
* * ** * * ** **
49965 AAGA-AA---AA---TTAATCTT--TG-CT-ATTCCTAAAGAGGAGTCAATCCTTGACTTCCTTA
1 AAGAGAAGTCAATTTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCCTTGACTTCCTCG
* * * * *
50019 AGAAGAGAAGTCAATCTTTGTTATTCATGACTTCCTCGTGAAGAGGAGCCAATGCTTGACTTCCT
66 TGAAGAGAAGTCAATCTTTG----T--T-A-TT-C-C-TAAAGAGAAGTCAATCCTTGACTTCCT
* * * * ** * * * * *
50084 CAT--A-A-AAA--GA-CGTTA--A-TCTTTACT-GTTCCT-AAAAAGAAGTCAATCCTTGAATT
120 CGTGAAGAGAAATCAATCTTTATTATTCTTGACTCCCTCGTGAAGAGGAA-CCAATCCTTGACTT
*
50137 CCTCTTG
184 CCTCATG
* *
50144 AAGAGAAGTCAATCTTTATTATTCATGACTCCCTTGTGAAGAGGAACCAATCCTTGACTTCCTCG
1 AAGAGAAGTCAATTTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCCTTGACTTCCTCG
* * *
50209 TGAATAGAAGTCGATATTTGTTATTCCTAAAGAGAAGTCAATCCTTGACTTCCTCGTGAAGAGAA
66 TGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTTGACTTCCTCGTGAAGAGAA
*
50274 ATCAATCTTTATTATTCTTGACTCCCTCGTGAAGAGGAACCAATCATTGACTTCCTCATG
131 ATCAATCTTTATTATTCTTGACTCCCTCGTGAAGAGGAACCAATCCTTGACTTCCTCATG
*
50334 AAGAGAAGTTAATTTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCCTTGACTTCCTCG
1 AAGAGAAGTCAATTTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCCTTGACTTCCTCG
* ** * *
50399 TGAAGAGAAGTCAATCTTTGTTAATCCTAAAGAGAAGTCAATTATTGACTTACTCGTAAAGAGAA
66 TGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTTGACTTCCTCGTGAAGAGAA
* * * * * * * *
50464 GTCTATCTTTGTTATTCCTGACTCCCTAGTGAAGTGGAATCAATCCTTGACTTCCTTATG
131 ATCAATCTTTATTATTCTTGACTCCCTCGTGAAGAGGAACCAATCCTTGACTTCCTCATG
50524 AAGAGAAGTCAATCTTTT-TTATTCATGACTCCCTCGTGAAGAGGA
1 AAGAGAAGTCAAT-TTTTATTATTCATGACTCCCTCGTGAAGAGGA
50569 GAAGTCAATA
Statistics
Matches: 751, Mismatches: 135, Indels: 152
0.72 0.13 0.15
Matches are distributed among these distances:
167 3 0.00
168 31 0.04
169 3 0.00
170 3 0.00
171 1 0.00
172 3 0.00
173 8 0.01
174 1 0.00
175 4 0.01
176 1 0.00
177 5 0.01
178 10 0.01
179 231 0.31
180 16 0.02
181 9 0.01
182 4 0.01
183 20 0.03
184 3 0.00
185 9 0.01
186 18 0.02
187 4 0.01
188 11 0.01
189 13 0.02
190 327 0.44
191 13 0.02
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (190 bp):
AAGAGAAGTCAATTTTTATTATTCATGACTCCCTCGTGAAGAGGAACCAATCCTTGACTTCCTCG
TGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGAAGTCAATCCTTGACTTCCTCGTGAAGAGAA
ATCAATCTTTATTATTCTTGACTCCCTCGTGAAGAGGAACCAATCCTTGACTTCCTCATG
Found at i:50432 original size:123 final size:123
Alignment explanation
Indices: 50305--50540 Score: 323
Period size: 123 Copynumber: 1.9 Consensus size: 123
50295 CTCCCTCGTG
* * *
50305 AAGAGGAA-CCAATCATTGACTTCCTCATGAAGAGAAGT-TAATTTTTATTATTCATGACTCCCT
1 AAGA-GAAGCCAATCATTGACTTACTCATAAAGAGAAGTCT-ATCTTTATTATTCATGACTCCCT
* *
50368 CGTGAAGAGGAACCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTAATCCTA
64 AGTGAAGAGGAACCAATCCTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTAATCCTA
* * * * *
50428 AAGAGAAGTCAATTATTGACTTACTCGTAAAGAGAAGTCTATCTTTGTTATTCCTGACTCCCTAG
1 AAGAGAAGCCAATCATTGACTTACTCATAAAGAGAAGTCTATCTTTATTATTCATGACTCCCTAG
* * *
50493 TGAAGTGGAATCAATCCTTGACTTCCTTATGAAGAGAAGTCAATCTTT
66 TGAAGAGGAACCAATCCTTGACTTCCTCATGAAGAGAAGTCAATCTTT
50541 TTTATTCATG
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
122 3 0.03
123 94 0.96
124 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (123 bp):
AAGAGAAGCCAATCATTGACTTACTCATAAAGAGAAGTCTATCTTTATTATTCATGACTCCCTAG
TGAAGAGGAACCAATCCTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTAATCCTA
Found at i:50434 original size:27 final size:27
Alignment explanation
Indices: 50401--50482 Score: 94
Period size: 27 Copynumber: 3.0 Consensus size: 27
50391 CTTCCTCGTG
50401 AAGAGAAGTCAATCTTTGTTAATCCTA
1 AAGAGAAGTCAATCTTTGTTAATCCTA
* *
50428 AAGAGAAGTCAAT-TATTGACTTACTCGTA
1 AAGAGAAGTCAATCT-TTG--TTAATCCTA
* *
50457 AAGAGAAGTCTATCTTTGTTATTCCT
1 AAGAGAAGTCAATCTTTGTTAATCCT
50483 GACTCCCTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.02
27 22 0.48
29 22 0.48
30 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (27 bp):
AAGAGAAGTCAATCTTTGTTAATCCTA
Found at i:50594 original size:164 final size:161
Alignment explanation
Indices: 50388--50704 Score: 384
Period size: 164 Copynumber: 2.0 Consensus size: 161
50378 AACCAATCCT
* * * *
50388 TGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTAATCCTAAAGAGAAGTCAATTATTGACTTACT
1 TGACTCCCTCGTGAAGAGAAGTCAATATTTGTTAATCCTAAAGAGAAGTCAATTATTCACATACT
* * * * *
50453 CGTAAAGAGAAGTCTATCTTTGTTATTCCTGACTCCCTAGTGAAGTGGAATCAATCCTTGACTTC
66 CATAAAGAGAAGTCAATCTTTGTTATTCCTGACTCCCTAGCGAAGAGGAATAAATCCTTGACTTC
* *
50518 CTTATGAAGAGAAGTCAATCTTTTTTATTCA
131 CTCATGAAGAGAAATCAATCTTTTTTATTCA
* * **
50549 TGACTCCCTCGTGAAGAGGAGAAGTCAATATTT-TCTATTCCTAAAGTGGTGTCAATTATTCACA
1 TGACTCCCTCGTG-A-A-GAGAAGTCAATATTTGT-TAATCCTAAAGAGAAGTCAATTATTCACA
* * * * * *
50613 TCCTCATGAAGAGGAGTCAATCTTTGTTATTCTTGACTCCCTCGCGAAGAGGAATAAATTCTTGA
62 TACTCATAAAGAGAAGTCAATCTTTGTTATTCCTGACTCCCTAGCGAAGAGGAATAAATCCTTGA
* *
50678 CTTTCTCGTGAAGAGAAATCAATCTTT
127 CTTCCTCATGAAGAGAAATCAATCTTT
50705 CAAATTTGGT
Statistics
Matches: 129, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
161 12 0.09
162 1 0.01
163 2 0.02
164 114 0.88
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (161 bp):
TGACTCCCTCGTGAAGAGAAGTCAATATTTGTTAATCCTAAAGAGAAGTCAATTATTCACATACT
CATAAAGAGAAGTCAATCTTTGTTATTCCTGACTCCCTAGCGAAGAGGAATAAATCCTTGACTTC
CTCATGAAGAGAAATCAATCTTTTTTATTCA
Found at i:51254 original size:3 final size:3
Alignment explanation
Indices: 51246--51277 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
51236 TTCCGTCCCA
51246 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
51278 AATTTACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:58161 original size:12 final size:12
Alignment explanation
Indices: 58139--58172 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
58129 AAATAAGTTT
58139 TTATCTTTTAAAA
1 TTAT-TTTTAAAA
58152 TTATTTTTAAAA
1 TTATTTTTAAAA
*
58164 GTATTTTTA
1 TTATTTTTA
58173 GGTATTTGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (12 bp):
TTATTTTTAAAA
Found at i:61402 original size:3 final size:3
Alignment explanation
Indices: 61394--61445 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
61384 TTCTAAAAAA
*
61394 TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
61441 TAT TA
1 TAT TA
61446 ATTAAAACCA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:62962 original size:30 final size:32
Alignment explanation
Indices: 62918--62999 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
62908 GAACAACAGT
* *
62918 GCATCTTTAAAGATTCAACAACAAATATT-GG
1 GCATATTTAGAGATTCAACAACAAATATTGGG
***
62949 GCATATTT-GAGATTCAACATTGAATATTGGG
1 GCATATTTAGAGATTCAACAACAAATATTGGG
*
62980 GCATATTTAGGGATTCAACA
1 GCATATTTAGAGATTCAACA
63000 TCCTGATGTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
30 16 0.37
31 17 0.40
32 10 0.23
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (32 bp):
GCATATTTAGAGATTCAACAACAAATATTGGG
Found at i:63000 original size:32 final size:30
Alignment explanation
Indices: 62941--63000 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 30
62931 TTCAACAACA
62941 AATATTGGGCATATTTGAGATTCAACATTG
1 AATATTGGGCATATTTGAGATTCAACATTG
*
62971 AATATTGGGGCATATTTAGGGATTCAACAT
1 AATATT-GGGCATATTT-GAGATTCAACAT
63001 CCTGATGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 6 0.22
31 10 0.37
32 11 0.41
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (30 bp):
AATATTGGGCATATTTGAGATTCAACATTG
Found at i:63128 original size:34 final size:34
Alignment explanation
Indices: 63092--63391 Score: 453
Period size: 34 Copynumber: 8.9 Consensus size: 34
63082 TTTCTCTTCA
* *
63092 AAAAAAAATTT-GTCTTACTTGAGACAATTTCTC
1 AAAACAAATTTCGTCTCACTTGAGACAATTTCTC
*
63125 AAAACAAATTTTGTCTCACTTGAGACAATTTCTC
1 AAAACAAATTTCGTCTCACTTGAGACAATTTCTC
*
63159 AAAACAAATTTCGTCTCACTTGAGAGAATTTCTC
1 AAAACAAATTTCGTCTCACTTGAGACAATTTCTC
* *
63193 AAAACAAATTTTGTCTCACTTGAGAAAATTTCTC
1 AAAACAAATTTCGTCTCACTTGAGACAATTTCTC
* *
63227 AAAACAAATTTTGTCTCACTTGAGACACTTTCTC
1 AAAACAAATTTCGTCTCACTTGAGACAATTTCTC
*
63261 AAAACAAATTTCGTCTTACTT--GACAATTTCTC
1 AAAACAAATTTCGTCTCACTTGAGACAATTTCTC
* *
63293 AAAACAAATTTCGTCTCACTTGAGATAATTTCTT
1 AAAACAAATTTCGTCTCACTTGAGACAATTTCTC
* *
63327 AACACAAATTTCGTCTCACTTAAGACAATTTCTC
1 AAAACAAATTTCGTCTCACTTGAGACAATTTCTC
*
63361 AAAACAAATTTCGTCTCGCTTGAGACAATTT
1 AAAACAAATTTCGTCTCACTTGAGACAATTT
63392 TTCTCTGAGA
Statistics
Matches: 243, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
32 30 0.12
33 10 0.04
34 203 0.84
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (34 bp):
AAAACAAATTTCGTCTCACTTGAGACAATTTCTC
Found at i:63334 original size:134 final size:135
Alignment explanation
Indices: 63089--63391 Score: 464
Period size: 134 Copynumber: 2.2 Consensus size: 135
63079 TTGTTTCTCT
* * * *
63089 TCAAAAAAAAATTTGTCTTACTTGAGACAATTTCTCAAAACAAATTTTGTCTCACTTGAGACAAT
1 TCAAAACAAATTTTGTCTCACTTGAGACAATTTCTCAAAACAAATTTCGTCTCACTT-AGACAAT
* *
63154 TTCTCAAAACAAATTTCGTCTCACTTGAGAGAATTTCTCAAAACAAATTTTGTCTCACTTGAGAA
65 TTCTCAAAACAAATTTCGTCTCACTTGAGAGAATTTCTCAAAACAAATTTCGTCTCACTTAAGAA
63219 AATTTC
130 AATTTC
* *
63225 TCAAAACAAATTTTGTCTCACTTGAGACACTTTCTCAAAACAAATTTCGTCTTACTT-GACAATT
1 TCAAAACAAATTTTGTCTCACTTGAGACAATTTCTCAAAACAAATTTCGTCTCACTTAGACAATT
* * * *
63289 TCTCAAAACAAATTTCGTCTCACTTGAGATAATTTCTTAACACAAATTTCGTCTCACTTAAGACA
66 TCTCAAAACAAATTTCGTCTCACTTGAGAGAATTTCTCAAAACAAATTTCGTCTCACTTAAGAAA
63354 ATTTC
131 ATTTC
* *
63359 TCAAAACAAATTTCGTCTCGCTTGAGACAATTT
1 TCAAAACAAATTTTGTCTCACTTGAGACAATTT
63392 TTCTCTGAGA
Statistics
Matches: 152, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
134 101 0.66
136 51 0.34
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (135 bp):
TCAAAACAAATTTTGTCTCACTTGAGACAATTTCTCAAAACAAATTTCGTCTCACTTAGACAATT
TCTCAAAACAAATTTCGTCTCACTTGAGAGAATTTCTCAAAACAAATTTCGTCTCACTTAAGAAA
ATTTC
Found at i:63746 original size:33 final size:33
Alignment explanation
Indices: 63705--63786 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
63695 AAATTCTGAA
* *
63705 ATTGTTTCACTTGAAATAAAAATAATCTTTGAG
1 ATTGTTTCACTTGAAACAAAAACAATCTTTGAG
* * * *
63738 TTTGTTTCACTGGAAACAACAACCATCTTTGAG
1 ATTGTTTCACTTGAAACAAAAACAATCTTTGAG
*
63771 ATTGTTTCTCTTGAAA
1 ATTGTTTCACTTGAAA
63787 AAATCTTGTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (33 bp):
ATTGTTTCACTTGAAACAAAAACAATCTTTGAG
Found at i:64210 original size:32 final size:31
Alignment explanation
Indices: 64166--64229 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 31
64156 CCTCATCGCG
64166 TAGGAACGTGTCATCACCCGACCTGATTTCC
1 TAGGAACGTGTCATCACCCGACCTGATTTCC
64197 TAGGAACCGTGTCATCACCCGACCTGATTTCC
1 TAGGAA-CGTGTCATCACCCGACCTGATTTCC
64229 T
1 T
64230 CATCACATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 6 0.19
32 26 0.81
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.27
Consensus pattern (31 bp):
TAGGAACGTGTCATCACCCGACCTGATTTCC
Found at i:64279 original size:43 final size:43
Alignment explanation
Indices: 64226--64459 Score: 192
Period size: 43 Copynumber: 5.4 Consensus size: 43
64216 CGACCTGATT
* * *
64226 TCCTCATCACATTGGAACCATGTCAGCCCCAGATAACCAGCCG
1 TCCTCATCACATAGGAACCGTGTCAACCCCAGATAACCAGCCG
* * * **
64269 TCCTCATCACATAGGAATCGTGTTATCACCCTTAGATGGCCTA-CCG
1 TCCTCATCACATAGGAACCGTGTCA--ACCC-CAGATAACC-AGCCG
* *
64315 TCCTCATCACGTAGGAACCGTGTCAACCCCAGATAACCAGCCA
1 TCCTCATCACATAGGAACCGTGTCAACCCCAGATAACCAGCCG
* * * * *
64358 TCCTCATCACGTAGGAATCGTGTCATCACCC-G---ACCTGATC-
1 TCCTCATCACATAGGAACCGTGTCAAC-CCCAGATAACCAG-CCG
* * *
64398 TCCTCATCGCGTAGGAACCGTGTCAACCCTAGATAACCAGCCG
1 TCCTCATCACATAGGAACCGTGTCAACCCCAGATAACCAGCCG
* *
64441 TCCTCATCACGTAGAAACC
1 TCCTCATCACATAGGAACC
64460 ATGTTATCAC
Statistics
Matches: 152, Mismatches: 27, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
39 2 0.01
40 29 0.19
41 1 0.01
42 2 0.01
43 76 0.50
44 7 0.05
45 3 0.02
46 31 0.20
47 1 0.01
ACGTcount: A:0.26, C:0.35, G:0.17, T:0.21
Consensus pattern (43 bp):
TCCTCATCACATAGGAACCGTGTCAACCCCAGATAACCAGCCG
Found at i:64337 original size:46 final size:45
Alignment explanation
Indices: 64226--64644 Score: 240
Period size: 46 Copynumber: 9.7 Consensus size: 45
64216 CGACCTGATT
* * * * *
64226 TCCTCATCACATTGGAACCATGTCAGC-CCC-AGATAACC-AGCCG
1 TCCTCATCACGTAGGAACCGTGTCATCACCCTAGATAGCCTA-CCG
* * * *
64269 TCCTCATCACATAGGAATCGTGTTATCACCCTTAGATGGCCTACCG
1 TCCTCATCACGTAGGAACCGTGTCATCACCC-TAGATAGCCTACCG
* * *
64315 TCCTCATCACGTAGGAACCGTGTCA--ACCCCAGATAACC-AGCCA
1 TCCTCATCACGTAGGAACCGTGTCATCACCCTAGATAGCCTA-CCG
* *
64358 TCCTCATCACGTAGGAATCGTGTCATCACCC--G--A-CCTGATC-
1 TCCTCATCACGTAGGAACCGTGTCATCACCCTAGATAGCCT-ACCG
* *
64398 TCCTCATCGCGTAGGAACCGTGTCA--ACCCTAGATAACC-AGCCG
1 TCCTCATCACGTAGGAACCGTGTCATCACCCTAGATAGCCTA-CCG
* * * * * * ** *
64441 TCCTCATCACGTAGAAACCATGTTATCACTCTTAGATGGCATGTCT
1 TCCTCATCACGTAGGAACCGTGTCATCAC-CCTAGATAGCCTACCG
* *
64487 TCCTCATCACGTAGGAACTGTGTCATCACCC--G--A-CCTGATC-
1 TCCTCATCACGTAGGAACCGTGTCATCACCCTAGATAGCCT-ACCG
** * * **
64527 TCCTCAT--CGTAGGAGTCGTGTCA--ACCCCAGATAGCCAACAA
1 TCCTCATCACGTAGGAACCGTGTCATCACCCTAGATAGCCTACCG
* * * *
64568 TCCTCATCACGCAGGAACCGTGTTATCACCCTTAGATGGCCTGCCG
1 TCCTCATCACGTAGGAACCGTGTCATCACCC-TAGATAGCCTACCG
* *
64614 TCCTCATCATGTAGGAACCGTGACATCACCC
1 TCCTCATCACGTAGGAACCGTGTCATCACCC
64645 ACCTGATATC
Statistics
Matches: 286, Mismatches: 58, Indels: 61
0.71 0.14 0.15
Matches are distributed among these distances:
36 4 0.01
38 18 0.06
40 37 0.13
41 14 0.05
42 4 0.01
43 91 0.32
44 7 0.02
45 11 0.04
46 99 0.35
47 1 0.00
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (45 bp):
TCCTCATCACGTAGGAACCGTGTCATCACCCTAGATAGCCTACCG
Found at i:64345 original size:89 final size:88
Alignment explanation
Indices: 64226--64511 Score: 350
Period size: 89 Copynumber: 3.3 Consensus size: 88
64216 CGACCTGATT
* * * * *
64226 TCCTCATCACATTGGAACCATGTCAGCCCCAGATAACCAGCCGTCCTCATCACATAGGAATCGTG
1 TCCTCATCACGTAGGAACCGTGTCAACCCCAGATAACCAGCCGTCCTCATCACGTAGGAATCGTG
*
64291 TTATCACCCTTAGATGGCCTACC
66 TTATCACCCTTAGATGGCCTATC
*
64314 GTCCTCATCACGTAGGAACCGTGTCAACCCCAGATAACCAGCCATCCTCATCACGTAGGAATCGT
1 -TCCTCATCACGTAGGAACCGTGTCAACCCCAGATAACCAGCCGTCCTCATCACGTAGGAATCGT
*
64379 GTCATCACCC---GA---CCTGATC
65 GTTATCACCCTTAGATGGCCT-ATC
* * * * *
64398 TCCTCATCGCGTAGGAACCGTGTCAACCCTAGATAACCAGCCGTCCTCATCACGTAGAAACCATG
1 TCCTCATCACGTAGGAACCGTGTCAACCCCAGATAACCAGCCGTCCTCATCACGTAGGAATCGTG
* * *
64463 TTATCACTCTTAGATGGCATGTC
66 TTATCACCCTTAGATGGCCTATC
*
64486 TTCCTCATCACGTAGGAACTGTGTCA
1 -TCCTCATCACGTAGGAACCGTGTCA
64512 TCACCCGACC
Statistics
Matches: 169, Mismatches: 20, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
83 69 0.41
84 2 0.01
86 4 0.02
88 2 0.01
89 92 0.54
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (88 bp):
TCCTCATCACGTAGGAACCGTGTCAACCCCAGATAACCAGCCGTCCTCATCACGTAGGAATCGTG
TTATCACCCTTAGATGGCCTATC
Found at i:64445 original size:83 final size:83
Alignment explanation
Indices: 64197--64713 Score: 349
Period size: 83 Copynumber: 6.1 Consensus size: 83
64187 CCTGATTTCC
* * * * * *
64197 TAGGAACCGTGTCATCACCCGACCTGATTTCCTCATCACATTGGAACCATGTCAGCCCCAGATAA
1 TAGGAATCGTGTCATCACCCGACCTGATCTCCTCATCACGTAGGAACCGTGTCAACCCCAGATAA
*
64262 CCAGCCGTCCTCATCACA
66 CCAGCCGTCCTCATCACG
* *
64280 TAGGAATCGTGTTATCACCCTTAGATGGCCT-ACCGTCCTCATCACGTAGGAACCGTGTCAACCC
1 TAGGAATCGTGTCATCACCC---GA---CCTGATC-TCCTCATCACGTAGGAACCGTGTCAACCC
*
64344 CAGATAACCAGCCATCCTCATCACG
59 CAGATAACCAGCCGTCCTCATCACG
* *
64369 TAGGAATCGTGTCATCACCCGACCTGATCTCCTCATCGCGTAGGAACCGTGTCAACCCTAGATAA
1 TAGGAATCGTGTCATCACCCGACCTGATCTCCTCATCACGTAGGAACCGTGTCAACCCCAGATAA
64434 CCAGCCGTCCTCATCACG
66 CCAGCCGTCCTCATCACG
* * * * * * * *
64452 TAGAAACCATGTTATCACTCTTAGATGGCATG-TCTTCCTCATCACGTAGGAACTGTGTCATCAC
1 TAGGAATCGTGTCATCAC-C--CGA---CCTGATC-TCCTCATCACGTAGGAACCGTGTCAAC-C
* *
64516 CC-G---ACCTGATC-TCCTCAT--CG
58 CCAGATAACCAG-CCGTCCTCATCACG
* * * * *
64536 TAGGAGTCGTGTCAAC-CCCAGA--TAGCCAACAATCCTCATCACGCAGGAACCGTGTTATCACC
1 TAGGAATCGTGTCATCACCC-GACCT-G--ATC--TCCTCATCACGTAGGAACCGTGTCA--ACC
* ** * *
64598 CTTAGATGGCCTGCCGTCCTCATCATG
58 C-CAGATAACCAGCCGTCCTCATCACG
* * * ***
64625 TAGGAACCGTGACATCACCC-ACCTGATATCCTCATCACGTAGGAGTTGTGTCAACCCCAGAATA
1 TAGGAATCGTGTCATCACCCGACCTGATCTCCTCATCACGTAGGAACCGTGTCAACCCCAG-ATA
* *
64689 ACCAGTCATCCTCATCACG
65 ACCAGCCGTCCTCATCACG
64708 TAGGAA
1 TAGGAA
64714 CCGTTTTATC
Statistics
Matches: 335, Mismatches: 62, Indels: 74
0.71 0.13 0.16
Matches are distributed among these distances:
76 1 0.00
77 1 0.00
80 1 0.00
81 24 0.07
82 5 0.01
83 114 0.34
84 16 0.05
85 20 0.06
86 18 0.05
87 13 0.04
88 4 0.01
89 112 0.33
90 6 0.02
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (83 bp):
TAGGAATCGTGTCATCACCCGACCTGATCTCCTCATCACGTAGGAACCGTGTCAACCCCAGATAA
CCAGCCGTCCTCATCACG
Found at i:64491 original size:129 final size:127
Alignment explanation
Indices: 64315--64774 Score: 538
Period size: 127 Copynumber: 3.6 Consensus size: 127
64305 TGGCCTACCG
* ** ** * * * *
64315 TCCTCATCACGTAGGAACCGTGTCA--ACCCCAGATAACCAGCCATCCTCATCACGTAGGAATCG
1 TCCTCATCACGTAGGAACCGTGTTATCACCTTAGATGGCCTGTCTTCCTCATCACGTAGGAACCG
** * *
64378 TGTCATCACCCGACCTGATCTCCTCATCGCGTAGGAACCGTGTCAACCCTAGATAACCAGCCG
66 TGTCATCACCCGACCTGATCTCCTCATC-CGTAGGAGTCGTGTCAACCCCAGATAACCAGCCA
* * * *
64441 TCCTCATCACGTAGAAACCATGTTATCACTCTTAGATGGCATGTCTTCCTCATCACGTAGGAACT
1 TCCTCATCACGTAGGAACCGTGTTATCAC-CTTAGATGGCCTGTCTTCCTCATCACGTAGGAACC
* * *
64506 GTGTCATCACCCGACCTGATCTCCTCAT-CGTAGGAGTCGTGTCAACCCCAGATAGCCAACAA
65 GTGTCATCACCCGACCTGATCTCCTCATCCGTAGGAGTCGTGTCAACCCCAGATAACCAGCCA
* * * *
64568 TCCTCATCACGCAGGAACCGTGTTATCACCCTTAGATGGCCTGCCGTCCTCATCATGTAGGAACC
1 TCCTCATCACGTAGGAACCGTGTTATCA-CCTTAGATGGCCTGTCTTCCTCATCACGTAGGAACC
* * * *
64633 GTGACATCACCC-ACCTGATATCCTCATCACGTAGGAGTTGTGTCAACCCCAGAATAACCAGTCA
65 GTGTCATCACCCGACCTGATCTCCTCATC-CGTAGGAGTCGTGTCAACCCCAG-ATAACCAGCCA
* * *
64697 TCCTCATCACGTAGGAACCGTTTTAT--CCTTAGATGACCTGTCGTT-CTCATCGCGTAGGAACC
1 TCCTCATCACGTAGGAACCGTGTTATCACCTTAGATGGCCTGTC-TTCCTCATCACGTAGGAACC
64759 GTGTCATCACCCGACC
65 GTGTCATCACCCGACC
64775 AAAACTCTTC
Statistics
Matches: 282, Mismatches: 43, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
126 76 0.27
127 97 0.34
128 25 0.09
129 84 0.30
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (127 bp):
TCCTCATCACGTAGGAACCGTGTTATCACCTTAGATGGCCTGTCTTCCTCATCACGTAGGAACCG
TGTCATCACCCGACCTGATCTCCTCATCCGTAGGAGTCGTGTCAACCCCAGATAACCAGCCA
Found at i:64493 original size:172 final size:172
Alignment explanation
Indices: 64197--64511 Score: 468
Period size: 172 Copynumber: 1.8 Consensus size: 172
64187 CCTGATTTCC
* * *
64197 TAGGAACCGTGTCATCACCCGACCTGATTTCCTCATCACATTGGAACCATGTCAGCCCCAGATAA
1 TAGGAACCGTGTCATCACCCGACCTGATCTCCTCATCACATAGGAACCATGTCAACCCCAGATAA
* * * *
64262 CCAGCCGTCCTCATCACATAGGAATCGTGTTATCACCCTTAGATGGCCTACCGTCCTCATCACGT
66 CCAGCCGTCCTCATCACATAGAAACCATGTTATCACCCTTAGATGGCATACCGTCCTCATCACGT
64327 AGGAACCGTGTCAACCCCAGATAACCAGCCATCCTCATCACG
131 AGGAACCGTGTCAACCCCAGATAACCAGCCATCCTCATCACG
* * * * *
64369 TAGGAATCGTGTCATCACCCGACCTGATCTCCTCATCGCGTAGGAACCGTGTCAACCCTAGATAA
1 TAGGAACCGTGTCATCACCCGACCTGATCTCCTCATCACATAGGAACCATGTCAACCCCAGATAA
* * ** *
64434 CCAGCCGTCCTCATCACGTAGAAACCATGTTATCACTCTTAGATGGCATGTCTTCCTCATCACGT
66 CCAGCCGTCCTCATCACATAGAAACCATGTTATCACCCTTAGATGGCATACCGTCCTCATCACGT
*
64499 AGGAACTGTGTCA
131 AGGAACCGTGTCA
64512 TCACCCGACC
Statistics
Matches: 125, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
172 125 1.00
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.24
Consensus pattern (172 bp):
TAGGAACCGTGTCATCACCCGACCTGATCTCCTCATCACATAGGAACCATGTCAACCCCAGATAA
CCAGCCGTCCTCATCACATAGAAACCATGTTATCACCCTTAGATGGCATACCGTCCTCATCACGT
AGGAACCGTGTCAACCCCAGATAACCAGCCATCCTCATCACG
Found at i:64843 original size:40 final size:40
Alignment explanation
Indices: 64742--64844 Score: 93
Period size: 40 Copynumber: 2.6 Consensus size: 40
64732 ACCTGTCGTT
* * *
64742 CTCATCGCGTAGGAACCGTGTCATCACCCGACCAAAACTC
1 CTCATCACGTAGGAGCTGTGTCATCACCCGACCAAAACTC
* * * * * *
64782 TTCATAATGTATGAG-TCGTGTCATC-CCCTGACCAGATCTC
1 CTCATCACGTAGGAGCT-GTGTCATCACCC-GACCAAAACTC
64822 CTCATCACGTAGGAGCTGTGTCA
1 CTCATCACGTAGGAGCTGTGTCA
64845 CCCTTAGACG
Statistics
Matches: 47, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
39 3 0.06
40 43 0.91
41 1 0.02
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.25
Consensus pattern (40 bp):
CTCATCACGTAGGAGCTGTGTCATCACCCGACCAAAACTC
Found at i:64886 original size:43 final size:40
Alignment explanation
Indices: 64759--64892 Score: 112
Period size: 40 Copynumber: 3.3 Consensus size: 40
64749 CGTAGGAACC
* * * *
64759 GTGTCATCACC-CGACCAAAACTCTTCATAATGTATGAGT
1 GTGTCATCCCCTCGACCAGAACTCTTCATCACGTATGAGT
* * *
64798 CGTGTCATCCCCT-GACCAGATCTCCTCATCACGTAGGAGCT
1 -GTGTCATCCCCTCGACCAGAACTCTTCATCACGTATGAG-T
*
64839 GTGTCA-CCCTTAGACGACCAGAACTCTTCATCACGTATGAGT
1 GTGTCATCCCCT---CGACCAGAACTCTTCATCACGTATGAGT
*
64881 AGTGTCGTCCCC
1 -GTGTCATCCCC
64893 CAAATCAAAA
Statistics
Matches: 73, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
39 4 0.05
40 36 0.49
41 1 0.01
42 1 0.01
43 28 0.38
44 3 0.04
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (40 bp):
GTGTCATCCCCTCGACCAGAACTCTTCATCACGTATGAGT
Found at i:65044 original size:3 final size:3
Alignment explanation
Indices: 65038--65074 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
65028 TCTAAAAAAA
65038 TAT TAT TAT TA- TAT TAT TAT TAT TA- TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
65075 AAACCACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.13
3 24 0.77
4 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:65053 original size:11 final size:11
Alignment explanation
Indices: 65037--65074 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
65027 TTCTAAAAAA
65037 ATATTATTATT
1 ATATTATTATT
65048 ATATTATTATT
1 ATATTATTATT
65059 AT-TATATTA-T
1 ATAT-TATTATT
65069 ATATTA
1 ATATTA
65075 AAACCACTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATATTATTATT
Found at i:65057 original size:14 final size:14
Alignment explanation
Indices: 65038--65074 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
65028 TCTAAAAAAA
65038 TATTATTATTATAT
1 TATTATTATTATAT
65052 TATTATTATTATAT
1 TATTATTATTATAT
65066 TATATATTA
1 TAT-TATTA
65075 AAACCACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTATTATTATAT
Done.