Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007782.1 Hibiscus syriacus cultivar Beakdansim tig00110065_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: 3900615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 19
Found at i:3261483 original size:37 final size:36
Alignment explanation
Indices: 3261433--3261544 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 36
3261423 ATGCTTGTGG
*
3261433 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATC-TAGTAAAACTCT
3261470 ATCCTATTTTTAGGAGTTTGAATTCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAA-TCTAGTAAAACTCT
3261507 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAAT-CTAGTAAAACTCT
3261544 A
1 A
3261545 ACGTTATGTT
Statistics
Matches: 72, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
36 1 0.01
37 69 0.96
38 2 0.03
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCTAGTAAAACTCT
Found at i:3272602 original size:11 final size:11
Alignment explanation
Indices: 3272578--3272627 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
3272568 ATTAAAATAT
*
3272578 TAAACCTAACC
1 TAAACCTAAAC
*
3272589 TAAACTTAAAC
1 TAAACCTAAAC
* *
3272600 TAAACCCAACC
1 TAAACCTAAAC
*
3272611 TAAACTTAAAC
1 TAAACCTAAAC
3272622 TAAACC
1 TAAACC
3272628 CTCAGCCGCA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (11 bp):
TAAACCTAAAC
Found at i:3272604 original size:22 final size:22
Alignment explanation
Indices: 3272578--3272628 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
3272568 ATTAAAATAT
*
3272578 TAAACCTAACCTAAACTTAAAC
1 TAAACCCAACCTAAACTTAAAC
3272600 TAAACCCAACCTAAACTTAAAC
1 TAAACCCAACCTAAACTTAAAC
3272622 TAAACCC
1 TAAACCC
3272629 TCAGCCGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (22 bp):
TAAACCCAACCTAAACTTAAAC
Found at i:3273135 original size:23 final size:23
Alignment explanation
Indices: 3273108--3273157 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
3273098 AAATTCTTTC
3273108 TTATCTCTTATTTTCTACTATTA
1 TTATCTCTTATTTTCTACTATTA
3273131 TTATCTCTTATTTTCTACTATTA
1 TTATCTCTTATTTTCTACTATTA
3273154 TTAT
1 TTAT
3273158 TTTTATTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.16, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATCTCTTATTTTCTACTATTA
Found at i:3273154 original size:13 final size:13
Alignment explanation
Indices: 3273115--3273155 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
3273105 TTCTTATCTC
3273115 TTATTTTCTACTA
1 TTATTTTCTACTA
*
3273128 TTATTATCT-C--
1 TTATTTTCTACTA
3273138 TTATTTTCTACTA
1 TTATTTTCTACTA
3273151 TTATT
1 TTATT
3273156 ATTTTTATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
10 8 0.35
11 1 0.04
12 1 0.04
13 13 0.57
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATTTTCTACTA
Found at i:3274143 original size:5 final size:5
Alignment explanation
Indices: 3274128--3274166 Score: 51
Period size: 5 Copynumber: 7.2 Consensus size: 5
3274118 ATGGCCACAC
3274128 ATATAA ATATA ATATA ATATA ATTAGTA ATATA ATATA A
1 ATAT-A ATATA ATATA ATATA A-TA-TA ATATA ATATA A
3274167 ACCCAAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 20 0.65
6 8 0.26
7 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:3274159 original size:17 final size:16
Alignment explanation
Indices: 3274128--3274167 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
3274118 ATGGCCACAC
3274128 ATATAAATATAATATA
1 ATATAAATATAATATA
*
3274144 ATATAATTAGTAATATA
1 ATATAAATA-TAATATA
3274161 ATATAAA
1 ATATAAA
3274168 CCCAAACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
ATATAAATATAATATA
Found at i:3287580 original size:19 final size:19
Alignment explanation
Indices: 3287556--3287604 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
3287546 AAAAACCTGA
3287556 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
3287575 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
3287594 GTGCATCGATG
1 GTGCATCGATG
3287605 TTTGAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:3289850 original size:13 final size:13
Alignment explanation
Indices: 3289819--3289857 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
3289809 TGGGCAAGGT
*
3289819 TTTGAAAA-ACTA
1 TTTGAAAATAATA
*
3289831 GTTGAAAATAATA
1 TTTGAAAATAATA
3289844 TTTGAAAATAATA
1 TTTGAAAATAATA
3289857 T
1 T
3289858 GTATAGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:3298801 original size:22 final size:22
Alignment explanation
Indices: 3298776--3298874 Score: 180
Period size: 22 Copynumber: 4.5 Consensus size: 22
3298766 GGGTATATTA
*
3298776 GTCCTTCAGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
3298798 GTCCTTCGGAACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
3298820 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
3298842 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
3298864 GTCCTTCGGGA
1 GTCCTTCGGGA
3298875 TAAATATTGA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 74 1.00
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.27
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:3303841 original size:16 final size:18
Alignment explanation
Indices: 3303815--3303847 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3303805 AAAAGACCCA
3303815 AAAAGAAAAGAA-AAAAT
1 AAAAGAAAAGAATAAAAT
3303832 AAAA-AAAAGAATAAAA
1 AAAAGAAAAGAATAAAA
3303848 GGGGGTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (18 bp):
AAAAGAAAAGAATAAAAT
Found at i:3305104 original size:37 final size:37
Alignment explanation
Indices: 3305049--3305173 Score: 146
Period size: 37 Copynumber: 3.4 Consensus size: 37
3305039 TTCGACCTTC
* * * *
3305049 GAAGAAAATC-ATATTAAGCCTTCACGAAAGATTATT
1 GAAGCAAATCAATCTTAAGCCTTCACGAAAGAGTAGT
3305085 GAAGCAAATCAATCTTAAGCCTTCACGAAAGAGTAGT
1 GAAGCAAATCAATCTTAAGCCTTCACGAAAGAGTAGT
* * * *
3305122 GAAACAAGTCAATCTTAAGCCTTCGA-GGAAGAGTAGC
1 GAAGCAAATCAATCTTAAGCCTTC-ACGAAAGAGTAGT
*
3305159 GAAGAAAATCAATCT
1 GAAGCAAATCAATCT
3305174 CGGTCTGATA
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
36 9 0.12
37 66 0.87
38 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.22
Consensus pattern (37 bp):
GAAGCAAATCAATCTTAAGCCTTCACGAAAGAGTAGT
Found at i:3305302 original size:54 final size:52
Alignment explanation
Indices: 3305218--3305616 Score: 319
Period size: 55 Copynumber: 7.6 Consensus size: 52
3305208 CTATTTGCTA
*
3305218 AAGATTGTTCGA-TCCTATACTCCCTGAAAGAAGAGGAGCATACATGTTTACCG
1 AAGATTGTTCGAGTCCTATACTCCCTGAAAGAA-AGGAGCAGACATGTTT-CCG
* * * **
3305271 AAGATTGTTCGAGTCCTATACTCCTTGAAAGAAGAAGGAACGGACATGTTTGCTA
1 AAGATTGTTCGAGTCCTATACTCCCTGAAAG-A-AAGGAGCAGACATGTTT-CCG
* * * *
3305326 AAGATTGTTTGAGTCATAATACTCCCTAAAAGAATAGGGAGC-GACACGTTTACCG
1 AAGATTGTTCGAGTCCT-ATACTCCCTGAAAGAA-A-GGAGCAGACATGTTT-CCG
* * *
3305381 AAGATTGTTTGAGTCCTATACTCCTTGAAAG-AAGGAGC-GACCCAT-TTTTCG
1 AAGATTGTTCGAGTCCTATACTCCCTGAAAGAAAGGAGCAGA--CATGTTTCCG
*
3305432 AAGATT-TTCGAGTCCTATACT-CCTGAAAG-AA--AG--GACATGTTGCCG
1 AAGATTGTTCGAGTCCTATACTCCCTGAAAGAAAGGAGCAGACATGTTTCCG
* * *
3305477 AAGATTGTTCGAGTGCTATACTCCTTGAAAGAATAAGGAG-AGGACCCAT-TTTCTG
1 AAGATTGTTCGAGTCCTATACTCCCTGAAAG-A-AAGGAGCA-GA--CATGTTTCCG
* *
3305532 AAGA-TGTTTCGAGTCCTATACTCCCTGAAAGAAAGGGAGAAAACATGTTTTCCG
1 AAGATTG-TTCGAGTCCTATACTCCCTGAAAGAAA-GGAGCAGACATG-TTTCCG
* *
3305586 AATATTGTTCAAGTCCTATACT-CC-GAAAGAA
1 AAGATTGTTCGAGTCCTATACTCCCTGAAAGAA
3305617 TATAGAGGGA
Statistics
Matches: 285, Mismatches: 35, Indels: 53
0.76 0.09 0.14
Matches are distributed among these distances:
44 3 0.01
45 10 0.04
46 16 0.06
47 9 0.03
49 9 0.03
50 16 0.06
51 15 0.05
52 16 0.06
53 19 0.07
54 62 0.22
55 90 0.32
56 20 0.07
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (52 bp):
AAGATTGTTCGAGTCCTATACTCCCTGAAAGAAAGGAGCAGACATGTTTCCG
Found at i:3305631 original size:206 final size:210
Alignment explanation
Indices: 3305200--3305673 Score: 508
Period size: 206 Copynumber: 2.2 Consensus size: 210
3305190 GAAAAAAAAG
* * *
3305200 GAGCTGACCTATTTGCTAAAGATTGTTCGA-TCCTATACTCCCTGAAAGAAGAGGAGCATACATG
1 GAGC-GACCCATTTTCTGAAGATT-TTCGAGTCCTATACT-CCTGAAAGAAGAGGAG-A-ACATG
3305264 TTTACCGAAGATTGTTCGAGTCCTATACTCCTTGAAAGAAGAAGGAACGGACATGTTTGCTAAAG
61 TTTACCGAAGATTGTTCGAGTCCTATACTCCTTGAAAGAAGAAGGAACGGACATGTTTGCTAAAG
** **
3305329 ATTGTTTGAGTCATAATACTCCCTAAAAGAATAGGGAGCGACACGTTTACCGAAGATTGTTTGAG
126 ATTGTTTGAGTCATAATACTCCCTAAAAGAATAGGGAGAAACACGTTTACCGAAGATTGTTCAAG
*
3305394 TCCTATACTCCTTGAAAGAAG
191 TCCTATACTCC-TGAAAGAAA
*
3305415 GAGCGACCCATTTT-TCGAAGATTTTCGAGTCCTATACTCCTGAAAGAA-A-G-G-ACATG-TTG
1 GAGCGACCCATTTTCT-GAAGATTTTCGAGTCCTATACTCCTGAAAGAAGAGGAGAACATGTTTA
* * *
3305474 CCGAAGATTGTTCGAGTGCTATACTCCTTGAAAGAATAAGGAGA-GGACCCAT-TTT-CTGAAGA
65 CCGAAGATTGTTCGAGTCCTATACTCCTTGAAAGAAGAAGGA-ACGGA--CATGTTTGCTAAAGA
* * * * *
3305536 -TGTTTCGAGTCCT-ATACTCCCTGAAAGAA-AGGGAGAAAACATGTTTTCCGAATATTGTTCAA
127 TTGTTT-GAGTCATAATACTCCCTAAAAGAATAGGGAG-AAACACGTTTACCGAAGATTGTTCAA
3305598 GTCCTATACTCC-GAAAGAATATA
190 GTCCTATACTCCTGAAAG-A-A-A
* * * * *
3305621 GAGGGACCCATTTTCTGAAGAAGTTTCGAGTCATATATTCCTAAAAGAAGAGG
1 GAGCGACCCATTTTCTGAAG-ATTTTCGAGTCCTATACTCCTGAAAGAAGAGG
3305674 GAGCGAACCC
Statistics
Matches: 223, Mismatches: 22, Indels: 34
0.80 0.08 0.12
Matches are distributed among these distances:
203 5 0.02
204 7 0.03
205 52 0.23
206 74 0.33
207 34 0.15
208 4 0.02
209 1 0.00
210 1 0.00
211 1 0.00
212 1 0.00
213 16 0.07
214 23 0.10
215 4 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (210 bp):
GAGCGACCCATTTTCTGAAGATTTTCGAGTCCTATACTCCTGAAAGAAGAGGAGAACATGTTTAC
CGAAGATTGTTCGAGTCCTATACTCCTTGAAAGAAGAAGGAACGGACATGTTTGCTAAAGATTGT
TTGAGTCATAATACTCCCTAAAAGAATAGGGAGAAACACGTTTACCGAAGATTGTTCAAGTCCTA
TACTCCTGAAAGAAA
Found at i:3305639 original size:106 final size:107
Alignment explanation
Indices: 3305466--3305676 Score: 286
Period size: 106 Copynumber: 2.0 Consensus size: 107
3305456 GAAAGAAAGG
* *
3305466 ACATGTTGCCGAAGATTGTTCGAGTGCTATACTCCTTGAAAGAATAAGGAGAGGACCCATTTTCT
1 ACATGTTGCCGAAGATTGTTCAAGTCCTATACTCC-TGAAAGAATAAGGAGAGGACCCATTTTCT
* * *
3305531 GAAGATGTTTCGAGTCCTATACTCCCTGAAAGAA-AGGGAGAAA
65 GAAGAAGTTTCGAGTCATATA-TCCCTAAAAGAAGAGGGAGAAA
* *
3305574 ACATGTTTTCCGAATATTGTTCAAGTCCTATACTCC-GAAAGAATATA-GAG-GGACCCATTTTC
1 ACATG-TTGCCGAAGATTGTTCAAGTCCTATACTCCTGAAAGAATA-AGGAGAGGACCCATTTTC
*
3305636 TGAAGAAGTTTCGAGTCATATATTCCTAAAAGAAGAGGGAG
64 TGAAGAAGTTTCGAGTCATATATCCCTAAAAGAAGAGGGAG
3305677 CGAACCCGTC
Statistics
Matches: 92, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
105 10 0.11
106 38 0.41
107 12 0.13
108 6 0.07
109 26 0.28
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.27
Consensus pattern (107 bp):
ACATGTTGCCGAAGATTGTTCAAGTCCTATACTCCTGAAAGAATAAGGAGAGGACCCATTTTCTG
AAGAAGTTTCGAGTCATATATCCCTAAAAGAAGAGGGAGAAA
Found at i:3305703 original size:106 final size:108
Alignment explanation
Indices: 3305477--3305707 Score: 281
Period size: 106 Copynumber: 2.1 Consensus size: 108
3305467 CATGTTGCCG
* * *
3305477 AAGATTGTTCGAGTGCTATACTCCTTGAAAGAATAAGGAGAGGACCCATTTTCTGAAGATGTTTC
1 AAGATTGTTCAAGTCCTATACTCC-TGAAAGAATAAGGAGAGGACCCATTTTCTGAAGAAGTTTC
* * * * *
3305542 GAGTCCTATACTCCCTGAAAGAAAGGGAGAAAACATGTTTTCCG
65 GAGTCATATACTCCCTAAAAGAAAGGGAGAAAACACGTCTTCCA
*
3305586 AATATTGTTCAAGTCCTATACTCC-GAAAGAATATA-GAG-GGACCCATTTTCTGAAGAAGTTTC
1 AAGATTGTTCAAGTCCTATACTCCTGAAAGAATA-AGGAGAGGACCCATTTTCTGAAGAAGTTTC
* ** *
3305648 GAGTCATATA-TTCCTAAAAGAAGAGGGAGCGAACCCGTCTTCCA
65 GAGTCATATACTCCCTAAAAGAA-AGGGAGAAAACACGTCTTCCA
*
3305692 AAGATTTTTCAAGTCC
1 AAGATTGTTCAAGTCC
3305708 AACCTATTCT
Statistics
Matches: 105, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
105 10 0.10
106 61 0.58
107 12 0.11
108 1 0.01
109 21 0.20
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (108 bp):
AAGATTGTTCAAGTCCTATACTCCTGAAAGAATAAGGAGAGGACCCATTTTCTGAAGAAGTTTCG
AGTCATATACTCCCTAAAAGAAAGGGAGAAAACACGTCTTCCA
Found at i:3306463 original size:293 final size:286
Alignment explanation
Indices: 3305935--3306496 Score: 947
Period size: 293 Copynumber: 1.9 Consensus size: 286
3305925 GTGCATGGAT
3305935 TATATATTATCATAGTTAAATAAATTAATAGTTGTATATGTGTGTAAATTACATATGAATTGCTT
1 TATATATTATCATAGTTAAATAAATTAATAGTTGTATATGTGTGTAAATTACATATGAATTGCTT
3306000 TTAATTATCTAGGCTAGTTATGTTGTGGTCGTATATACATATATATTTGTATTTATAGGCATATG
66 TTAATTATCTAGGCTAGTTATGTTGTGGTCGTATATACATATATATTTGTATTTATAGGCATATG
3306065 GAATTATTATTTTATATATATACACATATGATAATCAGATTCAAGTAAATATTTTATTTTTACAC
131 GAATTATTATTTTATATATATACACATATGATAATCAGATTCAAGTAAATATTTTATTTTTACAC
3306130 GACCTACAGTAATTACAATAACCCATGCCCAATCTAAGCAAGCCTGAACAAACAGCCCAGTAGCC
196 GACCTACAGTAATTACAATAACCCATGCCCAA-CTAAGCAAGCCTGAACAAACAGCCCAGTAGCC
3306195 AAACCCGAAGTTGTGCATGTGATTATA
260 AAACCCGAAGTTGTGCATGTGATTATA
3306222 TATATATTATCAATAGTT-AATAAATTAATAGTTGTATATGTGTGTTAAATTACATATGAATTGC
1 TATATATTATC-ATAGTTAAATAAATTAATAGTTGTATATGTGTG-TAAATTACATATGAATTGC
3306286 TTATTTAATTATCTAGGCTAGTTATGCTTGTGGTCGTATATATACATATATATTTGTATTTATAG
64 -T-TTTAATTATCTAGGCTAGTTATG-TTGTGGTCG--TATATACATATATATTTGTATTTATAG
*
3306351 GCATATGGAATTATTA-TTT-TATATATACACATACT-ATGAT-AGATTCTAAGTAAATATTTTA
124 GCATATGGAATTATTATTTTATATATATACACATA-TGATAATCAGATTC-AAGTAAATATTTTA
3306412 TTTTTACACGACCGAATTACAGTAATTACAATAACCCATGCCCAA-TAAGCAAGCCTGAACAAAC
187 TTTTTACACGACC----TACAGTAATTACAATAACCCATGCCCAACTAAGCAAGCCTGAACAAAC
3306476 AGCCCAGTAGCCAAACCCGAA
248 AGCCCAGTAGCCAAACCCGAA
3306497 CCAAATGAAA
Statistics
Matches: 261, Mismatches: 1, Indels: 20
0.93 0.00 0.07
Matches are distributed among these distances:
287 37 0.14
288 25 0.10
289 1 0.00
290 29 0.11
291 54 0.21
292 4 0.02
293 83 0.32
295 28 0.11
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (286 bp):
TATATATTATCATAGTTAAATAAATTAATAGTTGTATATGTGTGTAAATTACATATGAATTGCTT
TTAATTATCTAGGCTAGTTATGTTGTGGTCGTATATACATATATATTTGTATTTATAGGCATATG
GAATTATTATTTTATATATATACACATATGATAATCAGATTCAAGTAAATATTTTATTTTTACAC
GACCTACAGTAATTACAATAACCCATGCCCAACTAAGCAAGCCTGAACAAACAGCCCAGTAGCCA
AACCCGAAGTTGTGCATGTGATTATA
Found at i:3311111 original size:20 final size:20
Alignment explanation
Indices: 3311082--3311119 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3311072 TCCCTTCAAA
*
3311082 GGGGGAATCGGTTCCCTCAG
1 GGGGGAATCGATTCCCTCAG
*
3311102 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
3311120 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.39, T:0.21
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAG
Found at i:3314925 original size:22 final size:21
Alignment explanation
Indices: 3314883--3314922 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3314873 GAGTTTGTTT
*
3314883 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3314904 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3314923 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3320091 original size:17 final size:17
Alignment explanation
Indices: 3320057--3320095 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3320047 TAAAAAGACG
** *
3320057 AAAAATATATTATCAAT
1 AAAAATATAAAATAAAT
3320074 AAAAATATAAAATAAAT
1 AAAAATATAAAATAAAT
3320091 AAAAA
1 AAAAA
3320096 AATTATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAATATAAAATAAAT
Found at i:3327305 original size:21 final size:21
Alignment explanation
Indices: 3327279--3327331 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
3327269 GTTTCCAGAT
*
3327279 TCGCAACGTGAA-TATCGACTA
1 TCGCAACGCGAACT-TCGACTA
3327300 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
3327321 TCGCAATGCGA
1 TCGCAACGCGA
3327332 TTTTCCAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:3327369 original size:21 final size:21
Alignment explanation
Indices: 3327343--3327586 Score: 231
Period size: 21 Copynumber: 11.8 Consensus size: 21
3327333 TTTCCAAATT
3327343 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
3327364 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
3327385 CGTTGCGAT-GTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
3327405 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
*
3327424 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
3327445 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
3327466 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
3327487 TGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
3327508 CGTTACGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
3327529 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
3327550 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
3327571 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
3327587 AATCGCAACG
Statistics
Matches: 183, Mismatches: 23, Indels: 36
0.76 0.10 0.15
Matches are distributed among these distances:
18 7 0.04
19 44 0.24
20 9 0.05
21 89 0.49
23 34 0.19
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:3327384 original size:42 final size:42
Alignment explanation
Indices: 3327327--3327495 Score: 267
Period size: 42 Copynumber: 4.1 Consensus size: 42
3327317 ACTATCGCAA
3327327 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
3327367 TGCGATTTATTCCAAATTCGTTGCGAT-GTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
* * *
3327408 TGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
*
3327448 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
3327490 TGCGAT
1 TGCGAT
3327496 AGTCGAAGTT
Statistics
Matches: 117, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
39 18 0.15
40 23 0.20
41 21 0.18
42 55 0.47
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (42 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:3327462 original size:81 final size:82
Alignment explanation
Indices: 3327335--3327507 Score: 303
Period size: 81 Copynumber: 2.1 Consensus size: 82
3327325 AATGCGATTT
*
3327335 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGAT-GTCCA
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
3327399 AGTTCGCGTTGCGATAG
66 AGTTCGCGTTGCGATAG
*
3327416 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
*
3327481 AGTTCGTGTTGCGATAG
66 AGTTCGCGTTGCGATAG
*
3327498 TCGAAGTTCG
1 TCCAAGTTCG
3327508 CGTTACGATT
Statistics
Matches: 87, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
81 57 0.66
82 30 0.34
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.34
Consensus pattern (82 bp):
TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
AGTTCGCGTTGCGATAG
Found at i:3327503 original size:63 final size:61
Alignment explanation
Indices: 3327327--3327558 Score: 276
Period size: 63 Copynumber: 3.8 Consensus size: 61
3327317 ACTATCGCAA
* * *
3327327 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT--CGT
1 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCGAAGTTCGCGT
* *
3327388 TGCGA-TGTCCAAGTTCGCGTTGCGATAGTCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTTCCAAATT--CGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGT
*
3327448 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTGTTGCGATAGTCGAAGTTCGCGT
1 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGT
* * *
3327511 TACGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGAT
1 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGAT
3327559 TTATTCCAAA
Statistics
Matches: 150, Mismatches: 12, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
58 8 0.05
60 24 0.16
61 24 0.16
62 20 0.13
63 74 0.49
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.34
Consensus pattern (61 bp):
TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGT
Found at i:3327546 original size:105 final size:102
Alignment explanation
Indices: 3327386--3327586 Score: 348
Period size: 105 Copynumber: 1.9 Consensus size: 102
3327376 TTCCAAATTC
*
3327386 GTTGCGATGTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGC
1 GTTGCGATGTCCAAGTTCGCGTTACGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGC
3327451 GATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGT
66 GATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGT
* *
3327488 GTTGCGATAGTCGAAGTTCGCGTTACGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 GTTGCGAT-GTCCAAGTTCGCGTTACGA--TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
3327553 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
63 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
3327587 AATCGCAACG
Statistics
Matches: 93, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
102 8 0.09
103 17 0.18
105 68 0.73
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (102 bp):
GTTGCGATGTCCAAGTTCGCGTTACGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGC
GATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGT
Found at i:3327786 original size:21 final size:20
Alignment explanation
Indices: 3327720--3327915 Score: 50
Period size: 21 Copynumber: 9.4 Consensus size: 20
3327710 ATTTTGGACT
*
3327720 ATCGCAAAGAATTTGGAATAA
1 ATCGCAACGAATTT-GAATAA
* *
3327741 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAA-TTTGAATAA
3327762 ATCGCAACGAATTTGTAATAA
1 ATCGCAACGAATTTG-AATAA
* * *
3327783 ATCGTAATGCGAACTTGGACT--
1 ATCGCAA--CGAA-TTTGAATAA
* *
3327804 ATCACAACAAATTTGGAATAA
1 ATCGCAACGAATTT-GAATAA
* *
3327825 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAA-TTTGAATAA
* *
3327846 ATCACAACAAATTTGGAATAA
1 ATCGCAACGAATTT-GAATAA
* *
3327867 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAA-TTTGAATAA
*
3327888 ATCGCAACGAATTTGGA-AA
1 ATCGCAACGAATTTGAATAA
3327907 ATCGCAACG
1 ATCGCAACG
3327916 CGAACTTGGA
Statistics
Matches: 124, Mismatches: 28, Indels: 48
0.62 0.14 0.24
Matches are distributed among these distances:
18 10 0.08
19 31 0.25
21 50 0.40
23 24 0.19
24 9 0.07
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAATTTGAATAA
Found at i:3327924 original size:21 final size:21
Alignment explanation
Indices: 3327823--3327940 Score: 91
Period size: 21 Copynumber: 5.7 Consensus size: 21
3327813 AATTTGGAAT
3327823 AAATCGCAACGCGAACTTGGA
1 AAATCGCAACGCGAACTTGGA
** * * *
3327844 CTATCACAA--CAAATTTGGAA
1 AAATCGCAACGCGAACTTGG-A
3327864 TAAATCGCAACGCGAACTTGGA
1 -AAATCGCAACGCGAACTTGGA
** *
3327886 CTATCGCAA--CGAATTTGGA
1 AAATCGCAACGCGAACTTGGA
3327905 AAATCGCAACGCGAACTTGGA
1 AAATCGCAACGCGAACTTGGA
** *
3327926 CTATCGCAATGCGAA
1 AAATCGCAACGCGAA
3327941 TATGTAAATC
Statistics
Matches: 72, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
19 23 0.32
20 1 0.01
21 40 0.56
22 1 0.01
23 7 0.10
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.19
Consensus pattern (21 bp):
AAATCGCAACGCGAACTTGGA
Found at i:3327941 original size:42 final size:42
Alignment explanation
Indices: 3327713--3327934 Score: 349
Period size: 42 Copynumber: 5.3 Consensus size: 42
3327703 CGTTGCGATT
*
3327713 TTGGACTATCGCAAAGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * * *
3327755 TTCGACTATCGCAACGAATTTGTAATAAATCGTAATGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
3327797 TTGGACTATCACAACAAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
3327839 TTGGACTATCACAACAAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
3327881 TTGGACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
3327921 TTGGACTATCGCAA
1 TTGGACTATCGCAA
3327935 TGCGAATATG
Statistics
Matches: 167, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 30 0.18
41 1 0.01
42 136 0.81
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:3327953 original size:20 final size:20
Alignment explanation
Indices: 3327928--3327979 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3327918 AACTTGGACT
3327928 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
3327948 ATCGCAATGCAAATATGTAA
1 ATCGCAATGCGAATATGTAA
3327968 ATCGCAATGCGA
1 ATCGCAATGCGA
3327980 TAGTCGAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:3327999 original size:21 final size:21
Alignment explanation
Indices: 3327975--3328063 Score: 169
Period size: 21 Copynumber: 4.2 Consensus size: 21
3327965 TAAATCGCAA
3327975 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
3327996 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
*
3328017 TGCGATAGTCGAAGTTCGTGT
1 TGCGATAGTCGAAGTTCGCGT
3328038 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
3328059 TGCGA
1 TGCGA
3328064 ATCTGGAAAC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.19, C:0.18, G:0.34, T:0.29
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCGT
Found at i:3332701 original size:3 final size:3
Alignment explanation
Indices: 3332693--3332730 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
3332683 AAAATGTAAT
*
3332693 TAA TAA TAA TTAA TAA AAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3332731 TTTTAAGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3333252 original size:131 final size:130
Alignment explanation
Indices: 3332989--3333331 Score: 409
Period size: 131 Copynumber: 2.6 Consensus size: 130
3332979 GGGTGGCACA
* * * *
3332989 ACTCTTACGTAATGAGGAGATCTAGTCGGTGGATGACACGATTCCTATGCGATGAGGATGGCT-G
1 ACTCTTACGTGATGAGGAGATCTGGTCGG-GGATGACACAATTCCTACGCGATGAGGATGGCTGG
* * *
3333053 ACATCTTTAGGGATGATGATAACACGGTTCCTACGCAATGAGGACGGCTGGTTATCTAAGGTTGA
65 CCATCTTTA-GG--GATGATAACACGATTCCTACGCAATGAGGACAGCTGGTTATCTAAGGTTGA
3333118 CGCG
127 CGCG
* * * * *
3333122 GCTCTTACGTGATGAAGAGATCTGGTCTGGGGATGACATAATTCCTACGTGATAAGGATGGCTGG
1 ACTCTTACGTGATGAGGAGATCTGGTC-GGGGATGACACAATTCCTACGCGATGAGGATGGCTGG
* ** *
3333187 CCATCTTTAGGGATGATAACACGATTCTTACGTGATGAGGACAGTTGGTTATCTAAGGTTGACGC
65 CCATCTTTAGGGATGATAACACGATTCCTACGCAATGAGGACAGCTGGTTATCTAAGGTTGACGC
3333252 G
130 G
* * * * ****
3333253 ACTCCTACGTGATGAGGAGATCTGGTCAGTGGATGAAACAATTTCTACGCGATGAGGACAATTGG
1 ACTCTTACGTGATGAGGAGATCTGGTC-GGGGATGACACAATTCCTACGCGATGAGGATGGCTGG
3333318 CCATCTTTAGGGAT
65 CCATCTTTAGGGAT
3333332 TTGTTTCAAG
Statistics
Matches: 178, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
131 114 0.64
133 53 0.30
134 11 0.06
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.27
Consensus pattern (130 bp):
ACTCTTACGTGATGAGGAGATCTGGTCGGGGATGACACAATTCCTACGCGATGAGGATGGCTGGC
CATCTTTAGGGATGATAACACGATTCCTACGCAATGAGGACAGCTGGTTATCTAAGGTTGACGCG
Found at i:3333390 original size:36 final size:36
Alignment explanation
Indices: 3333350--3333521 Score: 117
Period size: 36 Copynumber: 5.2 Consensus size: 36
3333340 AGAGAACCTG
*
3333350 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGA
1 TCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGA
**
3333386 TCTCAA-AGATG-----ATT--TTTCAAAAGAAACTG-
1 TCTCAAGAGA-GACAAAATTCGTTTCAAGGGAAAC-GA
* *
3333415 TCTCAAGGGAGACAAAACTCGTTTCAAGGGAAACGA
1 TCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGA
* **
3333451 TCTCAA-AGATG-----A-T-GTTTCAAGAGAAACTT
1 TCTCAAGAGA-GACAAAATTCGTTTCAAGGGAAACGA
*
3333480 TCTCAAGAGAGACAAAATTCGTTTCAAGGGAAATGA
1 TCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGA
3333516 TCTCAA
1 TCTCAA
3333522 AGATGATGAT
Statistics
Matches: 102, Mismatches: 14, Indels: 40
0.65 0.09 0.26
Matches are distributed among these distances:
29 38 0.37
30 7 0.07
31 4 0.04
34 3 0.03
35 7 0.07
36 43 0.42
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (36 bp):
TCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGA
Found at i:3333440 original size:65 final size:65
Alignment explanation
Indices: 3333333--3333607 Score: 415
Period size: 65 Copynumber: 4.2 Consensus size: 65
3333323 TTTAGGGATT
* *
3333333 TGTTTCAAGAGAACCTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTCATTTCAAGGGAAACGATCTCAAAGATGA
* * * *
3333398 TTTTTCAAAAGAAACTGTCTCAAGGGAGACAAAACTCGTTTCAAGGGAAACGATCTCAAAGATGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTCATTTCAAGGGAAACGATCTCAAAGATGA
* * * *
3333463 TGTTTCAAGAGAAACTTTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAATGATCTCAAAGATGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTCATTTCAAGGGAAACGATCTCAAAGATGA
* * * *
3333528 TGATTCAAGAGAAATTGTCTCAAGGGAGACAAAACTTATTTCAAGGGAAACGATCTCAAAGATGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTCATTTCAAGGGAAACGATCTCAAAGATGA
*
3333593 TGTTTCAAGTGAAAC
1 TGTTTCAAGAGAAAC
3333608 AATTTCCAAA
Statistics
Matches: 187, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 187 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.24
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTCATTTCAAGGGAAACGATCTCAAAGATGA
Found at i:3333468 original size:29 final size:29
Alignment explanation
Indices: 3333435--3333607 Score: 89
Period size: 29 Copynumber: 5.5 Consensus size: 29
3333425 GACAAAACTC
3333435 GTTTCAAGGGAAACGATCTCAAAGATGAT
1 GTTTCAAGGGAAACGATCTCAAAGATGAT
* **
3333464 GTTTCAAGAGAAACTTTCTCAAGAGA-GACAAAATT
1 GTTTCAAGGGAAACGATCTCAA-AGATG-----A-T
*
3333499 CGTTTCAAGGGAAATGATCTCAAAGATGAT
1 -GTTTCAAGGGAAACGATCTCAAAGATGAT
* * * **
3333529 GATTCAAGAGAAATTG-TCTCAAGGGAGACAAAACTT
1 GTTTCAAGGGAAA-CGATCTCAA---AG--ATGA--T
*
3333565 ATTTCAAGGGAAACGATCTCAAAGATGAT
1 GTTTCAAGGGAAACGATCTCAAAGATGAT
*
3333594 GTTTCAAGTGAAAC
1 GTTTCAAGGGAAAC
3333608 AATTTCCAAA
Statistics
Matches: 107, Mismatches: 19, Indels: 36
0.66 0.12 0.22
Matches are distributed among these distances:
29 50 0.47
30 6 0.06
31 3 0.03
32 2 0.02
33 2 0.02
34 3 0.03
35 5 0.05
36 36 0.34
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (29 bp):
GTTTCAAGGGAAACGATCTCAAAGATGAT
Found at i:3333787 original size:37 final size:37
Alignment explanation
Indices: 3333734--3333838 Score: 131
Period size: 38 Copynumber: 2.8 Consensus size: 37
3333724 GTTCCGAGGG
*
3333734 AAACTGTCTCAAGTGAGACAAAATTTGTTTTGAGTA-A
1 AAACTGCCTCAAGTGAGACAAAATTTGTTTTGAG-AGA
* * *
3333771 AAATTGCCTTAAGTGAGACAAAATTTGATTTTTAGAGA
1 AAACTGCCTCAAGTGAGACAAAATTTG-TTTTGAGAGA
* *
3333809 AAACTGTCTCAAGCGAGACAAAATTTGTTT
1 AAACTGCCTCAAGTGAGACAAAATTTGTTT
3333839 CAAAGAAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
37 28 0.48
38 30 0.52
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.32
Consensus pattern (37 bp):
AAACTGCCTCAAGTGAGACAAAATTTGTTTTGAGAGA
Found at i:3333882 original size:36 final size:36
Alignment explanation
Indices: 3333734--3333883 Score: 133
Period size: 37 Copynumber: 4.1 Consensus size: 36
3333724 GTTCCGAGGG
* *
3333734 AAACTGTCTCAAGTGAGACAAAATTTGTTT-TGAGTAA
1 AAACTGTCTCAAGCGAGACAAAATTTGTTTCAGAG--A
* * * * *
3333771 AAATTGCCTTAAGTGAGACAAAATTTGATTTTTAGAGA
1 AAACTGTCTCAAGCGAGACAAAATTTG--TTTCAGAGA
*
3333809 AAACTGTCTCAAGCGAGACAAAATTTGTTTCAAAGA
1 AAACTGTCTCAAGCGAGACAAAATTTGTTTCAGAGA
* * * *
3333845 AAATTGTCTCTAGCGAGACGACACTTTGTTTC-GAGA
1 AAACTGTCTCAAGCGAGAC-AAAATTTGTTTCAGAGA
3333881 AAA
1 AAA
3333884 AACACCCTCA
Statistics
Matches: 94, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
36 30 0.32
37 34 0.36
38 24 0.26
39 3 0.03
40 3 0.03
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (36 bp):
AAACTGTCTCAAGCGAGACAAAATTTGTTTCAGAGA
Found at i:3335085 original size:22 final size:23
Alignment explanation
Indices: 3335046--3335090 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
3335036 TTTTCTTTGC
* *
3335046 TTTTTTCTTTGTTTCTTTGATTT
1 TTTTTTCTCTGTTACTTTGATTT
3335069 TTTTTTCTCT-TTACTTTGATTT
1 TTTTTTCTCTGTTACTTTGATTT
3335091 GATCTTCGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.07, C:0.11, G:0.07, T:0.76
Consensus pattern (23 bp):
TTTTTTCTCTGTTACTTTGATTT
Found at i:3346889 original size:15 final size:15
Alignment explanation
Indices: 3346868--3346906 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3346858 GTCTTTATTT
3346868 ATCTTTATTATCTCA
1 ATCTTTATTATCTCA
* *
3346883 GTCTTTATTATCTTA
1 ATCTTTATTATCTCA
3346898 ATCTTTATT
1 ATCTTTATT
3346907 CTTGATTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.23, C:0.15, G:0.03, T:0.59
Consensus pattern (15 bp):
ATCTTTATTATCTCA
Found at i:3347319 original size:3 final size:3
Alignment explanation
Indices: 3347306--3347374 Score: 72
Period size: 3 Copynumber: 23.3 Consensus size: 3
3347296 ATAGTAATGC
*
3347306 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TCA- TAT TAC TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT
* *
3347352 TAA TAT TAA TAT T-T T-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
3347375 TCAGGTTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
2 5 0.09
3 47 0.84
4 4 0.07
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:3352610 original size:8 final size:8
Alignment explanation
Indices: 3352597--3352658 Score: 56
Period size: 8 Copynumber: 7.6 Consensus size: 8
3352587 AATAAACTCA
3352597 AAAAAAAG
1 AAAAAAAG
3352605 AAAAAAAG
1 AAAAAAAG
*
3352613 --AAGAAG
1 AAAAAAAG
*
3352619 AAAAGAAG
1 AAAAAAAG
3352627 AAAAAAAAG
1 -AAAAAAAG
*
3352636 AGGAAAAAG
1 A-AAAAAAG
3352645 AAAAAAAG
1 AAAAAAAG
3352653 AGAAAA
1 A-AAAA
3352659 TAAATCAAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
6 5 0.11
8 22 0.49
9 18 0.40
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:3352616 original size:11 final size:11
Alignment explanation
Indices: 3352596--3352643 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
3352586 AAATAAACTC
3352596 AAAAAA-AAGA
1 AAAAAAGAAGA
3352606 AAAAAAGAAGA
1 AAAAAAGAAGA
*
3352617 AGAAAAGAAGAA
1 AAAAAAGAAG-A
*
3352629 AAAAAAGAGGA
1 AAAAAAGAAGA
3352640 AAAA
1 AAAA
3352644 GAAAAAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
10 6 0.18
11 18 0.55
12 9 0.27
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAGA
Found at i:3355319 original size:113 final size:112
Alignment explanation
Indices: 3355121--3355800 Score: 800
Period size: 113 Copynumber: 6.2 Consensus size: 112
3355111 GTTTAATTTG
* * *
3355121 CAGATCTGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTCTTTTTCAAGATTTGATATTCCCT
1 CAGATCTGATATTCCCTTCAGAGTAAG-CGAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCT
* ** *
3355186 TCAGAGTATGTGGAACAAGTCTGCCTTGATTCAGTGGATCAACTCCCC
65 TCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAACTCCCC
*
3355234 CAGATCTGATATTCCCTTTAGAGTAAGCAGAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCT
1 CAGATCTGATATTCCCTTCAGAGTAAGC-GAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCT
*
3355299 TCAGAGTAAGTGGAACAAGTCTGCACCGATTCAATGGATCAACTCCCC
65 TCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAACTCCCC
* * * * *
3355347 CAGATATGTTATTCCCTTCAGAGTAAGCATAACATGTCTCACTTTTCCAAGATTTGA-ATTCCCT
1 CAGATCTGATATTCCCTTCAGAGTAAGC-GAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCT
* * *
3355411 TCAAAGTAAGTGGAACAAGTCTTCCCTGATTCAA-GGATCAACTCCCC
65 TCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAACTCCCC
* *
3355458 CAGATATGATATTCCCTTCAGAGTAAGCGAAACAAGTCTCTCTTTTCCAATATTTGATATTCCCT
1 CAGATCTGATATTCCCTTCAGAGTAAGCG-AACAAGTCTCTCTTTTCCAAGATTTGATATTCCCT
** * * *
3355523 TCAGAGTAAGCAGAACAAGTCTACCCTGATTCAATGGATCAACTCCCT
65 TCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAACTCCCC
* * * *
3355571 CAGATATGATATTCCCTTCAGAGTAAGCG--CAA----C-ATGTT------TTTGATATTCCTTT
1 CAGATCTGATATTCCCTTCAGAGTAAGCGAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCTT
* *
3355623 CAGAGTAAGTGGAACAAGTCTACCCCGATTCAATAGATCAAC-CCCC
66 CAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAACTCCCC
* * * * * *
3355669 CAGATCTGATATTCCCTTAAGAGTAAGCGGAACATGTATGTATTCTCCAAGATTTGATATTCCCT
1 CAGATCTGATATTCCCTTCAGAGTAAGC-GAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCT
** * * *
3355734 TCAGAGTAAGTGCCACATGTCTGCCCCAATTGAATGGATCAA-TCCCC
65 TCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAACTCCCC
* * *
3355781 CAAAACTGATTTTCCCTTCA
1 CAGATCTGATATTCCCTTCA
3355801 ACATCTGATA
Statistics
Matches: 493, Mismatches: 55, Indels: 39
0.84 0.09 0.07
Matches are distributed among these distances:
98 29 0.06
99 52 0.11
101 2 0.00
105 3 0.01
106 4 0.01
110 3 0.01
111 64 0.13
112 141 0.29
113 195 0.40
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (112 bp):
CAGATCTGATATTCCCTTCAGAGTAAGCGAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCTT
CAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAACTCCCC
Found at i:3355522 original size:224 final size:221
Alignment explanation
Indices: 3355121--3355800 Score: 823
Period size: 224 Copynumber: 3.1 Consensus size: 221
3355111 GTTTAATTTG
* * *
3355121 CAGATCTGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTCTTTTTCAAGATTTGATATTCCCT
1 CAGATATGATATTCCCTTCAGAGTAAGCGCAACATGTCTC-C-TTTTCAAGATTTGA-ATTCCCT
* * * *
3355186 TCAGAGTATGTGGAACAAGTCTGCCTTGATTCAGTGGATCAACTCCCCCAGATCTGATATTCCCT
63 TCAGAGTAAGTGGAACAAGTCTACCCTGATTCA-AGGATCAACTCCCCCAGATCTGATATTCCCT
*
3355251 TTAGAGTAAGC-AGAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAAC
127 TAAGAGTAAGCGA-AACAAGTCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAAC
3355315 AAGTCTGCACCGATTCAATGGATCAACTCCCC
191 AAGTCTGC-CCGATTCAATGGATCAACTCCCC
* **
3355347 CAGATATGTTATTCCCTTCAGAGTAAGCATAACATGTCTCACTTTTCCAAGATTTGAATTCCCTT
1 CAGATATGATATTCCCTTCAGAGTAAGCGCAACATGTCTC-CTTTT-CAAGATTTGAATTCCCTT
* * * *
3355412 CAAAGTAAGTGGAACAAGTCTTCCCTGATTCAAGGATCAACTCCCCCAGATATGATATTCCCTTC
64 CAGAGTAAGTGGAACAAGTCTACCCTGATTCAAGGATCAACTCCCCCAGATCTGATATTCCCTTA
* **
3355477 AGAGTAAGCGAAACAAGTCTCTCTTTTCCAATATTTGATATTCCCTTCAGAGTAAGCAGAACAAG
129 AGAGTAAGCGAAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAG
* *
3355542 TCTACCCTGATTCAATGGATCAACTCCCT
194 TCTGCCC-GATTCAATGGATCAACTCCCC
*
3355571 CAGATATGATATTCCCTTCAGAGTAAGCGCAACATG--T--TTTT---GA--T--ATTCCTTTCA
1 CAGATATGATATTCCCTTCAGAGTAAGCGCAACATGTCTCCTTTTCAAGATTTGAATTCCCTTCA
* *
3355625 GAGTAAGTGGAACAAGTCTACCCCGATTCAATAGATCAAC-CCCCCAGATCTGATATTCCCTTAA
66 GAGTAAGTGGAACAAGTCTACCCTGATTCAA-GGATCAACTCCCCCAGATCTGATATTCCCTTAA
* * * * * * ** *
3355689 GAGTAAGCGGAACATGTATGTATTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGCCACATGT
130 GAGTAAGCGAAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGT
* *
3355754 CTGCCCCAATTGAATGGATCAA-TCCCC
195 CTG-CCCGATTCAATGGATCAACTCCCC
* *
3355781 CA-AAACTGATTTTCCCTTCA
1 CAGATA-TGATATTCCCTTCA
3355801 ACATCTGATA
Statistics
Matches: 402, Mismatches: 46, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
209 2 0.00
210 19 0.05
211 127 0.32
212 10 0.02
213 1 0.00
215 2 0.00
219 4 0.01
222 1 0.00
223 2 0.00
224 147 0.37
225 41 0.10
226 46 0.11
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (221 bp):
CAGATATGATATTCCCTTCAGAGTAAGCGCAACATGTCTCCTTTTCAAGATTTGAATTCCCTTCA
GAGTAAGTGGAACAAGTCTACCCTGATTCAAGGATCAACTCCCCCAGATCTGATATTCCCTTAAG
AGTAAGCGAAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTC
TGCCCGATTCAATGGATCAACTCCCC
Found at i:3356124 original size:3 final size:3
Alignment explanation
Indices: 3356111--3356183 Score: 80
Period size: 3 Copynumber: 24.7 Consensus size: 3
3356101 AATATTATCG
3356111 TTA TTA TTTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
3356157 CTA TTA ATA TTA ATA TT- TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3356184 TCAGGTTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
2 6 0.10
3 48 0.80
4 6 0.10
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3356133 original size:26 final size:25
Alignment explanation
Indices: 3356097--3356183 Score: 84
Period size: 26 Copynumber: 3.4 Consensus size: 25
3356087 TTTTTGTCCC
* *
3356097 ATTTAATATTATCGTTATTATTTATT
1 ATTTATTATTATCATTATTA-TTATT
*
3356123 ATTTATTATTATTATTATTATTATT
1 ATTTATTATTATCATTATTATTATT
* * * *
3356148 ATTATATTACTATTAATATTAATATT
1 ATT-TATTATTATCATTATTATTATT
*
3356174 TTTTATTATT
1 ATTTATTATT
3356184 TCAGGTTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
25 14 0.27
26 38 0.73
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (25 bp):
ATTTATTATTATCATTATTATTATT
Found at i:3360793 original size:38 final size:38
Alignment explanation
Indices: 3360741--3360816 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
3360731 GCTCCCAAGC
*
3360741 GATCTCACCCTAAAAAAATCTCCAAAGGGTTTGACACT
1 GATCTCACCCTAAAAAAATCTCCAAAGGGTTTAACACT
* * *
3360779 GATCTCACCTTAAAAAAATTTCCGAAGGGTTTAACACT
1 GATCTCACCCTAAAAAAATCTCCAAAGGGTTTAACACT
3360817 CCTAAGAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (38 bp):
GATCTCACCCTAAAAAAATCTCCAAAGGGTTTAACACT
Found at i:3360855 original size:46 final size:45
Alignment explanation
Indices: 3360794--3360948 Score: 161
Period size: 46 Copynumber: 3.4 Consensus size: 45
3360784 CACCTTAAAA
* * *
3360794 AAATTTCCGAAGGGTTTAACACTCCTAAGAAAGCTCACCCTTCAA-
1 AAATCTCCAAAGGGTTTAA-ACTCCTAAGCAAGCTCACCCTTCAAC
* * *
3360839 AGAGTCTCCAAAGGGTTTGAAACTCCCAAGCGAGCTCACCC-TCTAAC
1 A-AATCTCCAAAGGGTTT-AAACTCCTAAGCAAGCTCACCCTTC-AAC
* * * *
3360886 AAATCTCCAAAGGGTTCAATGCTCCTAAGCAATCTCACCCTTTAAC
1 AAATCTCCAAAGGGTTTAA-ACTCCTAAGCAAGCTCACCCTTCAAC
3360932 AAATCTCCAAAGGGTTT
1 AAATCTCCAAAGGGTTT
3360949 GACATTCTCT
Statistics
Matches: 90, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
45 5 0.06
46 81 0.90
47 4 0.04
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (45 bp):
AAATCTCCAAAGGGTTTAAACTCCTAAGCAAGCTCACCCTTCAAC
Found at i:3363340 original size:3 final size:3
Alignment explanation
Indices: 3363327--3363395 Score: 68
Period size: 3 Copynumber: 22.3 Consensus size: 3
3363317 TATATTAAAA
* * *
3363327 AAT ACT AAT AAT AAT AAG AAT AAT AAAT ATT AAT AAT -AT GAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT -AAT AAT
*
3363373 AAT AAT AAAT ATT AAT AAT AAT A
1 AAT AAT -AAT AAT AAT AAT AAT A
3363396 TAAATATGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 2 0.04
3 44 0.81
4 8 0.15
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3363401 original size:28 final size:28
Alignment explanation
Indices: 3363332--3363395 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
3363322 TAAAAAATAC
*
3363332 TAATAATAATAAGAATAATAAATATTAA
1 TAATAATAATAATAATAATAAATATTAA
3363360 TAAT-ATGAATAATAATAATAAATATTAA
1 TAATAAT-AATAATAATAATAAATATTAA
3363388 TAATAATA
1 TAATAATA
3363396 TAAATATGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (28 bp):
TAATAATAATAATAATAATAAATATTAA
Found at i:3363407 original size:28 final size:26
Alignment explanation
Indices: 3363326--3363408 Score: 89
Period size: 28 Copynumber: 3.1 Consensus size: 26
3363316 ATATATTAAA
* *
3363326 AAATACTAATAATAATAAGA-ATAAT
1 AAATATTAATAATAATAAAATATAAT
3363351 AAATATTAATAAT-ATGAATAATAATAAT
1 AAATATTAATAATAAT-AA-AAT-ATAAT
3363379 AAATATTAATAATAATATAAATATGAAT
1 AAATATTAATAATAATA-AAATAT-AAT
3363407 AA
1 AA
3363409 CCCAAACAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
24 2 0.04
25 14 0.29
26 1 0.02
27 2 0.04
28 27 0.55
29 3 0.06
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.33
Consensus pattern (26 bp):
AAATATTAATAATAATAAAATATAAT
Found at i:3363408 original size:31 final size:28
Alignment explanation
Indices: 3363339--3363408 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 28
3363329 TACTAATAAT
* *
3363339 AATAAGAATAATAAATATTAATAATATG
1 AATATGAATAATAAATATTAATAATATA
3363367 AATAAT-AATAATAAATATTAATAATAATATA
1 AAT-ATGAATAATAAATA-T--TAATAATATA
3363398 AATATGAATAA
1 AATATGAATAA
3363409 CCCAAACAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
28 14 0.40
29 2 0.06
30 2 0.06
31 17 0.49
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (28 bp):
AATATGAATAATAAATATTAATAATATA
Found at i:3363825 original size:42 final size:41
Alignment explanation
Indices: 3363748--3363854 Score: 126
Period size: 42 Copynumber: 2.6 Consensus size: 41
3363738 GTCTGAAGGT
* **
3363748 CTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTACAGATGGCCCGAAGGACTTATCATCACGCTCGAAAGA
* * *
3363789 -TTGACAGATGACCCGAATGATTTAATCATCACGCTCGAAAGA
1 CTT-ACAGATGGCCCGAAGGACTT-ATCATCACGCTCGAAAGA
*
3363831 CTTACTGATGGCCCGAAGGACTTA
1 CTTACAGATGGCCCGAAGGACTTA
3363855 CTAATTTTGG
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
40 2 0.04
41 17 0.32
42 32 0.60
43 2 0.04
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (41 bp):
CTTACAGATGGCCCGAAGGACTTATCATCACGCTCGAAAGA
Found at i:3364833 original size:260 final size:261
Alignment explanation
Indices: 3363552--3364948 Score: 1855
Period size: 261 Copynumber: 5.4 Consensus size: 261
3363542 TAACCCGTAT
* * * *
3363552 GATTTAATCATCATGCTGGAAAGACTTACTGATGGCCAGAAGGACTTACCAATTTTGGAAATAGT
1 GATTTAATCATCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTTGGAAATAGT
* * *
3363617 TTACTAGGTAAGAAACTTTGGAAATCGCTTTCTAACTTTTCAAAATTTTCA-------GAAAACA
66 TTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTTTTGAAAATA
* * * * *
3363675 TTAAATGAGAAACTTTGAAAATTGATTTTCTCATTTTTTACAAACATCATGTGAAAACATCCTGT
131 TTAAATGAGAAACTTTGGAAA-TCACTTTCTCATTTTTCACAAACATCATGTGAAAACATCCTGC
*
3363740 CTGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGATTGACAGATGACCCGA
195 CCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGATTGACAGATGACCCGA
*
3363805 AT
260 AG
3363807 GATTTAATCATCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTTGGAAATAGT
1 GATTTAATCATCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTTGGAAATAGT
* * * * **
3363872 TTACTGGGTAAGAAACTTTGGAAATAG-TTTGCTTACTTTTCAAAGATTTCATTTTCTAAAAAAT
66 TTACTAGGTAAGAAACTTTGGAAATCGCTTT-CTTACTTTTCAAAAATTTCATTTTTTTGAAAAT
* * * ** * * *
3363936 ATTAAATTA-AAA-ATT-G----C-TTTTCTCATTTTT-TGAAA-ATCACGTGAAAACATCATGG
130 ATTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCACAAACATCATGTGAAAACATCCTGC
* * * * *
3363991 CCGAAGGTTTTATAGATGGCCCGAAGGACTTATCATTTTGCTTGAAAGATTGATAGATGACCTGA
195 CCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGATTGACAGATGACCCGA
3364056 AG
260 AG
* ** * * * *
3364058 GATCTAATCATCGTGTTCAAAAGACTTACTGATGGCCTGAAGGACTTACTAATTTTGAAAATAGT
1 GATTTAATCATCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTTGGAAATAGT
** *
3364123 TTACTCTGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTTTTGAAAATA
66 TTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTTTTGAAAATA
* * *
3364188 TTAAATGAGAAAGTTTGGAAATCGCTTTCTCATTTTTCACAAACATCAAGTGAAAACATCCTGCC
131 TTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCACAAACATCATGTGAAAACATCCTGCC
* * * * *
3364253 TGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATAACTC-TA
196 CGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGATTGACAGATGACCCGAA
3364317 G
261 G
* *
3364318 GTATTTAATCACCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGAAATAG
1 G-ATTTAATCATCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTTGGAAATAG
* * * *
3364383 TTTACTAGGTAAAAAAATTTGGAAATCGCTTTCATACTTTTCAAAATTTTCATTTTTTTGAAAAT
65 TTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTTTTGAAAAT
* ** *
3364448 ATTAAATGAGAAACTTTGGAAATCACTTTCTCGTTTTTCACAAACATCATGTGAAAACATTTTTC
130 ATTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCACAAACATCATGTGAAAACATCCTGC
* *
3364513 CCGAAGGTCTTATATATGGCCCGAAGGACTTATCATCTTGCTCGAAAGATTGACAGATGACCCAA
195 CCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGATTGACAGATGACCCGA
*
3364578 AC
260 AG
** * ** *
3364580 GATTTAATTGTCACGCTCGAAAGACTTACTGATAGCTTGAAGGAATTACTAATTTTGGAAATAGT
1 GATTTAATCATCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTTGGAAATAGT
* * **
3364645 TTACTATGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTAC-TTTTTTTTTAAATA
66 TTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTTTTGAAAATA
* * *
3364709 TTAAATGAGAAAGTTTGGAAATCACTTTCTCATTTTTCATAAACATCATGTGAAAGCATCCTGCC
131 TTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCACAAACATCATGTGAAAACATCCTGCC
* * * * *
3364774 CGAAGGACTTATAGATGACCCAAAGGACTTATCATCTTGCTCGAAAGACTGAAAGATGACCCGAA
196 CGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGATTGACAGATGACCCGAA
3364839 G
261 G
*
3364840 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTTGGAAATAGT
1 GATTTAATCATCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTTGGAAATAGT
* *
3364905 TTACTGGGTAAGAAACTTTGGAAATC-ATTTCTTACTTTTCAAAA
66 TTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAA
3364949 CAACTTAATG
Statistics
Matches: 990, Mismatches: 131, Indels: 38
0.85 0.11 0.03
Matches are distributed among these distances:
251 195 0.20
252 9 0.01
253 15 0.02
254 4 0.00
255 103 0.10
258 1 0.00
259 29 0.03
260 218 0.22
261 402 0.41
262 14 0.01
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (261 bp):
GATTTAATCATCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTTGGAAATAGT
TTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTTTTGAAAATA
TTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCACAAACATCATGTGAAAACATCCTGCC
CGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGATTGACAGATGACCCGAA
G
Found at i:3364860 original size:42 final size:41
Alignment explanation
Indices: 3364786--3364887 Score: 132
Period size: 42 Copynumber: 2.5 Consensus size: 41
3364776 AAGGACTTAT
* *
3364786 AGATGACCCAAAGGACTTATCATCTTGCTCGAAAGACTGAA
1 AGATGACCCGAAGGACTTATCATCATGCTCGAAAGACTGAA
* * *
3364827 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTAC
1 AGATGACCCGAAGGACTT-ATCATCATGCTCGAAAGACTGAA
* *
3364869 TGATGGCCCGAAGGACTTA
1 AGATGACCCGAAGGACTTA
3364888 CTAATTTTGG
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 17 0.33
42 35 0.67
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (41 bp):
AGATGACCCGAAGGACTTATCATCATGCTCGAAAGACTGAA
Found at i:3364887 original size:521 final size:509
Alignment explanation
Indices: 3363552--3364948 Score: 1917
Period size: 512 Copynumber: 2.7 Consensus size: 509
3363542 TAACCCGTAT
* * *
3363552 GATTTAATCATCATGCTGGAAAGACTTACTGATGGCCAGAAGGACTTACCAATTTTGGAAATAGT
1 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACTAATTTTGGAAATAGT
* * ** *
3363617 TTACTAGGTAAGAAACTTTGGAAATCGCTTTCTAACTTTTC--AAA--A--TTTTCAGAAAACAT
66 TTACTATGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTACTTTTTTTGAAAATAT
* * * * * *
3363676 TAAATGAGAAACTTTGAAAATTGATTTTCTCATTTTTTACAAACATCATGTGAAAACATCCTGTC
131 TAAATGAGAAAGTTTGGAAA-TCACTTTCTCATTTTTCACAAACATCATGTGAAAACATCCTGCC
*
3363741 TGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGATTGACAGATGACCCGAA
195 TGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAA
*
3363806 TGATTTAATCATCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTTGGAAATAG
260 GGATTTAATCATCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTTGGAAATAG
*
3363871 TTTACTGGGTAAGAAACTTTGGAAATAGTTTGCTTACTTTTCAAAGATTTCATTTTCTAAAAAAT
325 TTTACTGGGTAAGAAACTTTGGAAATCGTTT-CTTACTTTTCAAA-ATTTCATTTTCTAAAAAAT
* * ** * *
3363936 ATTAAATTAAAAATTGCTTTTCTCATTTTTTGAAAATCACGTGAAAACATCATGGCCGAAGGTTT
388 ATTAAATGAAAAATTGCCTTTCTCATTTTTACAAAATCACGTGAAAACATCATGCCCGAAGGTCT
* * * ** *
3364001 TATAGATGGCCCGAAGGACTTATCATTTTGCTTGAAAGATTGATAGATGACCTGAAG
453 TATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGATTGACAGATGACCCAAAC
* * * * *
3364058 GATCTAATCATCGTGTTCAAAAGACTTACTGATGGCCTGAAGGACTTACTAATTTTGAAAATAGT
1 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACTAATTTTGGAAATAGT
* * *
3364123 TTACTCTGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTTTTGAAAATA
66 TTACTATGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTAC-TTTTTTTGAAAATA
* *
3364188 TTAAATGAGAAAGTTTGGAAATCGCTTTCTCATTTTTCACAAACATCAAGTGAAAACATCCTGCC
130 TTAAATGAGAAAGTTTGGAAATCACTTTCTCATTTTTCACAAACATCATGTGAAAACATCCTGCC
* * *
3364253 TGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATAACTC-TA
195 TGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAA
* *
3364317 GGTATTTAATCACCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGAAATA
260 GG-ATTTAATCATCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTTGGAAATA
* * * * * **
3364382 GTTTACTAGGTAAAAAAATTTGGAAATCGCTTTCATACTTTTCAAAATTTTCATTTTTTTGAAAA
324 GTTTACTGGGTAAGAAACTTTGGAAATCG-TTTCTTACTTTTCAAAA-TTTCATTTTCTAAAAAA
* * * ** *
3364447 TATTAAATGAGAAACTTTGGAAATCACTTTCTCGTTTTTCACAAACATCATGTGAAAACATTTTT
387 TATTAAATGA-AAA-ATT-G----C-CTTTCTCATTTTT-ACAAA-ATCACGTGAAAACATCATG
*
3364512 CCCGAAGGTCTTATATATGGCCCGAAGGACTTATCATCTTGCTCGAAAGATTGACAGATGACCCA
442 CCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGATTGACAGATGACCCA
3364577 AAC
507 AAC
** * * * *
3364580 GATTTAATTGTCACGCTCGAAAGACTTACTGATAGCTTGAAGGAATTACTAATTTTGGAAATAGT
1 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACTAATTTTGGAAATAGT
**
3364645 TTACTATGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTACTTTTTTTTTAAATAT
66 TTACTATGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTACTTTTTTTGAAAATAT
* * *
3364710 TAAATGAGAAAGTTTGGAAATCACTTTCTCATTTTTCATAAACATCATGTGAAAGCATCCTGCCC
131 TAAATGAGAAAGTTTGGAAATCACTTTCTCATTTTTCACAAACATCATGTGAAAACATCCTGCCT
* * * *
3364775 GAAGGACTTATAGATGACCCAAAGGACTTATCATCTTGCTCGAAAGACTGAAAGATGACCCGAAG
196 GAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAG
*
3364840 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTTGGAAATAGT
261 GATTTAATCATCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTTGGAAATAGT
*
3364905 TTACTGGGTAAGAAACTTTGGAAATCATTTCTTACTTTTCAAAA
326 TTACTGGGTAAGAAACTTTGGAAATCGTTTCTTACTTTTCAAAA
3364949 CAACTTAATG
Statistics
Matches: 776, Mismatches: 94, Indels: 28
0.86 0.10 0.03
Matches are distributed among these distances:
506 94 0.12
508 3 0.00
511 3 0.00
512 217 0.28
513 35 0.05
514 2 0.00
515 1 0.00
519 1 0.00
520 27 0.03
521 215 0.28
522 178 0.23
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (509 bp):
GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACTAATTTTGGAAATAGT
TTACTATGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTACTTTTTTTGAAAATAT
TAAATGAGAAAGTTTGGAAATCACTTTCTCATTTTTCACAAACATCATGTGAAAACATCCTGCCT
GAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAG
GATTTAATCATCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTTGGAAATAGT
TTACTGGGTAAGAAACTTTGGAAATCGTTTCTTACTTTTCAAAATTTCATTTTCTAAAAAATATT
AAATGAAAAATTGCCTTTCTCATTTTTACAAAATCACGTGAAAACATCATGCCCGAAGGTCTTAT
AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGATTGACAGATGACCCAAAC
Found at i:3365977 original size:40 final size:40
Alignment explanation
Indices: 3365922--3366003 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
3365912 AATGACCTCT
* * *
3365922 TTCATTCTCAAGAGATTTTCCTGTTTGAGGATGCTTTTTC
1 TTCATTATCAAGAGATTGTCCTGTTTGAGAATGCTTTTTC
* * * *
3365962 TTCATTATCGAGAGATTGTCTTGTTTGATAATGTTTTTTC
1 TTCATTATCAAGAGATTGTCCTGTTTGAGAATGCTTTTTC
3366002 TT
1 TT
3366004 TCTCTTTCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.18, C:0.13, G:0.17, T:0.51
Consensus pattern (40 bp):
TTCATTATCAAGAGATTGTCCTGTTTGAGAATGCTTTTTC
Found at i:3367711 original size:18 final size:17
Alignment explanation
Indices: 3367657--3367705 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3367647 TTGGACTCCT
* *
3367657 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
3367675 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
3367693 AGTGCATTCGATG
1 AGTGCA-TCGATG
3367706 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:3367726 original size:64 final size:62
Alignment explanation
Indices: 3367657--3367835 Score: 182
Period size: 64 Copynumber: 2.8 Consensus size: 62
3367647 TTGGACTCCT
* *
3367657 AGTGCATCGGTGCACTAAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAA-ATAGCCT
1 AGTGCATCGATGCA-T-AGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAT-GCC-
3367721 G
62 G
* * * * * * *
3367722 -GTGCATCGATGCATGGCTTGTGTATTGATGCATCAAATGCATTTGATGTTTGAAAATATTCCG
1 AGTGCATCGATGCATAG--AGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATGCCG
*
3367785 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCAT--AGAGTGCATCGATGCATGAAATGCATTCGATGTT
3367836 CAATTAAATC
Statistics
Matches: 92, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 86 0.93
65 2 0.02
66 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (62 bp):
AGTGCATCGATGCATAGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATGCCG
Found at i:3376396 original size:18 final size:17
Alignment explanation
Indices: 3376342--3376390 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3376332 TTGGACTCCT
* *
3376342 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
3376360 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
3376378 AGTGCATTCGATG
1 AGTGCA-TCGATG
3376391 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:3376411 original size:64 final size:62
Alignment explanation
Indices: 3376342--3376520 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 62
3376332 TTGGACTCCT
* *
3376342 AGTGCATCGGTGCACTAAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAA-ATAGCCT
1 AGTGCATCGATGCA-T-AGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAT-GCC-
3376406 G
62 G
* * * *
3376407 -GTGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCCG
1 AGTGCATCGATGCATAG--AGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATGCCG
* *
3376470 ATTGCATCGATGCATGGAGAGTGCATCGGTGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCAT--AGAGTGCATCGATGCATGAAATGCATTCGATGTT
3376521 CAATTAAATC
Statistics
Matches: 97, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 91 0.94
65 2 0.02
66 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (62 bp):
AGTGCATCGATGCATAGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATGCCG
Found at i:3376542 original size:64 final size:61
Alignment explanation
Indices: 3376359--3376550 Score: 179
Period size: 64 Copynumber: 3.0 Consensus size: 61
3376349 CGGTGCACTA
* * * *
3376359 AGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGAAATGCATTCGATG-TTCAAAAAT--CATGGTTCATCGATGCATGG
*** * * * *
3376423 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTC-CGATTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGAAATGCATTCGATG-TTCAAAA-A-TCATGGTT-CATCGATGCATGG
*
3376487 AGAGTGCATCGGTGCATGAAATGCATTCGATGTTCAATTAAATCATAGGTTCATCGATGCATGG
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTCAA--AAATCAT-GGTTCATCGATGCATGG
3376551 TTTGATGCAT
Statistics
Matches: 105, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
63 8 0.08
64 90 0.86
65 6 0.06
66 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (61 bp):
AGAGTGCATCGATGCATGAAATGCATTCGATGTTCAAAAATCATGGTTCATCGATGCATGG
Found at i:3376913 original size:29 final size:28
Alignment explanation
Indices: 3376857--3376954 Score: 74
Period size: 29 Copynumber: 3.4 Consensus size: 28
3376847 TTCTTCTTCT
* *
3376857 TTTTTTATCT-TTTTTCCTTTTCATTTTTA
1 TTTTTTCTCTATTTTT-CTTCT-ATTTTTA
3376886 TTGTTTTCTCTATTTTTCTTCTATTTTTTA
1 TT-TTTTCTCTATTTTTCTTCTA-TTTTTA
* * * *
3376916 TTTTATATATATTTTTCTTCT-TTTCTTCT
1 TTTTTTCTCTATTTTTCTTCTATTT-TT-A
3376945 TTTTTTCTCT
1 TTTTTTCTCT
3376955 CTCTTTTTTC
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
27 3 0.05
28 2 0.04
29 26 0.47
30 19 0.35
31 5 0.09
ACGTcount: A:0.10, C:0.14, G:0.01, T:0.74
Consensus pattern (28 bp):
TTTTTTCTCTATTTTTCTTCTATTTTTA
Found at i:3381321 original size:12 final size:12
Alignment explanation
Indices: 3381304--3381339 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3381294 GTAAAACAAG
3381304 AATACAAATGCA
1 AATACAAATGCA
*
3381316 AATACAAATTCA
1 AATACAAATGCA
*
3381328 AATATAAATGCA
1 AATACAAATGCA
3381340 CAAGATGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.58, C:0.14, G:0.06, T:0.22
Consensus pattern (12 bp):
AATACAAATGCA
Found at i:3383959 original size:17 final size:18
Alignment explanation
Indices: 3383937--3383970 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3383927 AATATTGGGA
*
3383937 GAAATCTGGA-AAATAAG
1 GAAATCGGGACAAATAAG
3383954 GAAATCGGGACAAATAA
1 GAAATCGGGACAAATAA
3383971 AAAGGCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.53, C:0.09, G:0.24, T:0.15
Consensus pattern (18 bp):
GAAATCGGGACAAATAAG
Found at i:3385088 original size:3 final size:3
Alignment explanation
Indices: 3385080--3385127 Score: 62
Period size: 3 Copynumber: 15.7 Consensus size: 3
3385070 GTATATATTA
*
3385080 AAT AAT AAT AAT AAT AAT AAAT ATT AAT AAT AAT -AT AAAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT -AAT AAT AAT
3385126 AA
1 AA
3385128 CCCGGACAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.82
4 5 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3385441 original size:46 final size:46
Alignment explanation
Indices: 3385170--3385443 Score: 197
Period size: 46 Copynumber: 5.9 Consensus size: 46
3385160 TCTTCTAACG
* * * * * *
3385170 AAATCTCTAAAGGTTTTCACACTCCAAAGCGAGCTCACACTTCAAC
1 AAATCTCCAAAGGGTTTAACACTCCCAAGCGAGCTCACCCTCCAAC
* ** * * * *
3385216 GAATCTCCAAAGGGTTTAACACTCCCAAGAAAGCCCACTCTCTAAAG
1 AAATCTCCAAAGGGTTTAACACTCCCAAGCGAGCTCACCCTC-CAAC
* * * * ** *
3385263 AAATCTCCAAAGGGTTTGACCCTCCCAAGCAAGTTTGCCCTCCACAAG
1 AAATCTCCAAAGGGTTTAACACTCCCAAGCGAGCTCACCCT-C-CAAC
* * ** * * *
3385311 AAATCTCAAAAGAGTTTAATGCTCCCAAACGAGCTCACCCTCAAAT
1 AAATCTCCAAAGGGTTTAACACTCCCAAGCGAGCTCACCCTCCAAC
* * ** *
3385357 GAATCTCCAAAGGGTTTAACACTCCTAATTGATCTCACCCTCCAAC
1 AAATCTCCAAAGGGTTTAACACTCCCAAGCGAGCTCACCCTCCAAC
* * * *
3385403 AAATCTCTAAAGGGTTTAACTCTCCCAAGTGAGGTCACCCT
1 AAATCTCCAAAGGGTTTAACACTCCCAAGCGAGCTCACCCT
3385444 TGAAAGAAAT
Statistics
Matches: 173, Mismatches: 53, Indels: 4
0.75 0.23 0.02
Matches are distributed among these distances:
46 103 0.60
47 35 0.20
48 35 0.20
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.23
Consensus pattern (46 bp):
AAATCTCCAAAGGGTTTAACACTCCCAAGCGAGCTCACCCTCCAAC
Found at i:3385527 original size:35 final size:35
Alignment explanation
Indices: 3385463--3385529 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
3385453 TCTCTAACAG
* *
3385463 GTTTGATTCTCCTAAGAGAGCTTTCCCTCCAAAGA
1 GTTTGATGCTCCTAAGAGAGCTGTCCCTCCAAAGA
*
3385498 GTTTGATGCTCCTAAGTGAGCTCGT-CCTCCAA
1 GTTTGATGCTCCTAAGAGAGCT-GTCCCTCCAA
3385530 TTAATCCTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 27 0.96
36 1 0.04
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.31
Consensus pattern (35 bp):
GTTTGATGCTCCTAAGAGAGCTGTCCCTCCAAAGA
Found at i:3385779 original size:32 final size:32
Alignment explanation
Indices: 3385738--3385809 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
3385728 AACTTTCAAG
*
3385738 TAAGTGTGAATCGGGTTATAGCTTATTACTTC
1 TAAGTGTGAATCGGGTTATAGCTAATTACTTC
*
3385770 TAAGTGTGAATCGGGTTATAGCTAATTACTTT
1 TAAGTGTGAATCGGGTTATAGCTAATTACTTC
3385802 TAAGTGTG
1 TAAGTGTG
3385810 CCCAAAGAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (32 bp):
TAAGTGTGAATCGGGTTATAGCTAATTACTTC
Found at i:3387380 original size:12 final size:12
Alignment explanation
Indices: 3387352--3387399 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
3387342 TTCTTTTCTC
*
3387352 TTTTATTTTCAAG
1 TTTTATTTT-TAG
3387365 TTTTCATTTTTA-
1 TTTT-ATTTTTAG
*
3387377 TTTTATTTTAAG
1 TTTTATTTTTAG
3387389 TTTTATTTTTA
1 TTTTATTTTTA
3387400 AACATGCTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 6 0.20
12 14 0.47
13 5 0.17
14 5 0.17
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (12 bp):
TTTTATTTTTAG
Found at i:3387398 original size:24 final size:25
Alignment explanation
Indices: 3387352--3387399 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3387342 TTCTTTTCTC
3387352 TTTTATTTTCAAGTTTTCATTTTTA
1 TTTTATTTTCAAGTTTTCATTTTTA
3387377 TTTTATTTT-AAGTTTT-ATTTTTA
1 TTTTATTTTCAAGTTTTCATTTTTA
3387400 AACATGCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 7 0.30
24 7 0.30
25 9 0.39
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (25 bp):
TTTTATTTTCAAGTTTTCATTTTTA
Found at i:3389465 original size:20 final size:20
Alignment explanation
Indices: 3389426--3389464 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3389416 ATTAAATGTC
*
3389426 AAAAATGATGAAATTAAAAG
1 AAAAATGATGAAAATAAAAG
3389446 AAAAATGATGAAAAATAAA
1 AAAAATGATG-AAAATAAA
3389465 GTCATGAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (20 bp):
AAAAATGATGAAAATAAAAG
Found at i:3403773 original size:22 final size:21
Alignment explanation
Indices: 3403747--3403787 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3403737 CCAGTATGCT
*
3403747 AGGAGGGAACCGATTCCCCCTC
1 AGGA-GGAACCAATTCCCCCTC
*
3403769 AGGAGGTACCAATTCCCCC
1 AGGAGGAACCAATTCCCCC
3403788 CTTGTATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.24, C:0.37, G:0.24, T:0.15
Consensus pattern (21 bp):
AGGAGGAACCAATTCCCCCTC
Found at i:3404142 original size:20 final size:23
Alignment explanation
Indices: 3404114--3404157 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3404104 TTTGTGCTTA
3404114 TAATCGTTT-AA-A-GATTAATT
1 TAATCGTTTGAACATGATTAATT
*
3404134 TAATTGTTTGAACATGATTAATT
1 TAATCGTTTGAACATGATTAATT
3404157 T
1 T
3404158 TCAATATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 8 0.40
21 2 0.10
22 1 0.05
23 9 0.45
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (23 bp):
TAATCGTTTGAACATGATTAATT
Found at i:3404925 original size:21 final size:21
Alignment explanation
Indices: 3404901--3404940 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3404891 ACCGTCAACC
*
3404901 AAATCCACTTCCAAATCCTCA
1 AAATCCAATTCCAAATCCTCA
*
3404922 AAATCCAATTCCTAATCCT
1 AAATCCAATTCCAAATCCT
3404941 AATCCCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATCCAATTCCAAATCCTCA
Found at i:3405855 original size:12 final size:12
Alignment explanation
Indices: 3405840--3405869 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3405830 AAGATGAGCC
3405840 GGAGCAGCCCGA
1 GGAGCAGCCCGA
*
3405852 GGAGGAGCCCGA
1 GGAGCAGCCCGA
3405864 GGAGCA
1 GGAGCA
3405870 AGCACAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.27, C:0.27, G:0.47, T:0.00
Consensus pattern (12 bp):
GGAGCAGCCCGA
Found at i:3406219 original size:24 final size:23
Alignment explanation
Indices: 3406169--3406242 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
3406159 GCTTCAACTT
* *
3406169 TTTGGATTGTTTGATTTTGTGAC
1 TTTGGATTGTTTGATGTTGTGAA
3406192 TTTGGATTTGTTTGGATGTT-TGAA
1 TTTGGA-TTGTTT-GATGTTGTGAA
*
3406216 TTTGTGGATTGATTGAT-TT-TGAA
1 -TT-TGGATTGTTTGATGTTGTGAA
3406239 TTTG
1 TTTG
3406243 TTTGGATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 12 0.27
24 12 0.27
25 12 0.27
26 4 0.09
ACGTcount: A:0.16, C:0.01, G:0.27, T:0.55
Consensus pattern (23 bp):
TTTGGATTGTTTGATGTTGTGAA
Found at i:3406817 original size:22 final size:23
Alignment explanation
Indices: 3406792--3406835 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3406782 AATTAAGTTT
3406792 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
3406814 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
3406836 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:3406905 original size:20 final size:21
Alignment explanation
Indices: 3406874--3406948 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
3406864 CTCAGAGGGA
3406874 ACCGATTCCCCCCCAAGGGGT
1 ACCGATTCCCCCCCAAGGGGT
** **
3406895 ACCGATT-CCCCCC-TTGTAT
1 ACCGATTCCCCCCCAAGGGGT
3406914 AACCGATTCCCCCCCAAGGGGT
1 -ACCGATTCCCCCCCAAGGGGT
3406936 ACCGATTCCCCCC
1 ACCGATTCCCCCC
3406949 TTGTATAACG
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 26 0.60
22 2 0.05
ACGTcount: A:0.19, C:0.45, G:0.17, T:0.19
Consensus pattern (21 bp):
ACCGATTCCCCCCCAAGGGGT
Found at i:3406930 original size:41 final size:41
Alignment explanation
Indices: 3406873--3406957 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
3406863 GCTCAGAGGG
3406873 AACCGATTCCCCCCCAAGGGGTACCGATTCCCCCCTTGTAT
1 AACCGATTCCCCCCCAAGGGGTACCGATTCCCCCCTTGTAT
3406914 AACCGATTCCCCCCCAAGGGGTACCGATTCCCCCCTTGTAT
1 AACCGATTCCCCCCCAAGGGGTACCGATTCCCCCCTTGTAT
3406955 AAC
1 AAC
3406958 GGTTGAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.21, C:0.41, G:0.16, T:0.21
Consensus pattern (41 bp):
AACCGATTCCCCCCCAAGGGGTACCGATTCCCCCCTTGTAT
Found at i:3408231 original size:42 final size:42
Alignment explanation
Indices: 3408167--3408249 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
3408157 TTCATTTTTT
3408167 CAAGAGTTGATTGACTTATGCCTTTAAAGAATCTTCTTCTTG
1 CAAGAGTTGATTGACTTATGCCTTTAAAGAATCTTCTTCTTG
*
3408209 CAAGAGTTGATTGACTTGTGCCTTTAAAGAATCTTCTTCTT
1 CAAGAGTTGATTGACTTATGCCTTTAAAGAATCTTCTTCTT
3408250 TATTTCATCC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (42 bp):
CAAGAGTTGATTGACTTATGCCTTTAAAGAATCTTCTTCTTG
Found at i:3416949 original size:84 final size:82
Alignment explanation
Indices: 3416759--3417048 Score: 287
Period size: 84 Copynumber: 3.5 Consensus size: 82
3416749 ACGCCGTAAT
* * * * *
3416759 AGAGTAGTACTTTAGTGGC-GTTTTATATAAACGCCGCAATAGGTACATATTTAGTGGCATTTTT
1 AGAGTAGTACTTTAGCGGCATTTTTATACAAACGCCGCAATAGGTACATCTATAGTGGCATTTTT
*
3416823 TCGAAAAA-GCTATAAAA
66 TCGAAAAATGCCAT-AAA
* * * *
3416840 AAAGTAGTACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGGTCCATCTATAGTGGCGTTTTT
1 AGAGTAGTACTTTAGCGGCATTTTTATACAAACGCCGCAATAGGTACATCTATAGTGGC--ATTT
*
3416905 TTTCGAAAAATGCCATAAT
64 TTTCGAAAAATGCCATAAA
* * * ** * *
3416924 AGATTAGTACTTTAGCGGCATTTTTATAAAAAACACCATAATAGGGTTCACCTATAGTGGCATTT
1 AGAGTAGTACTTTAGCGGCATTTTTAT-ACAAACGCCGCAATA-GGTACATCTATAGTGGCATTT
* **
3416989 TTTCCAACAAATGCCGCAAA
64 TTTCGAA-AAATGCCATAAA
* * * *
3417009 AGATTAGAACTGTAGCGGCATTTTTACACAAACGCCGCAA
1 AGAGTAGTACTTTAGCGGCATTTTTATACAAACGCCGCAA
3417049 AAACATGTAC
Statistics
Matches: 171, Mismatches: 31, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
81 17 0.10
82 34 0.20
84 57 0.33
85 48 0.28
86 15 0.09
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (82 bp):
AGAGTAGTACTTTAGCGGCATTTTTATACAAACGCCGCAATAGGTACATCTATAGTGGCATTTTT
TCGAAAAATGCCATAAA
Found at i:3421373 original size:43 final size:42
Alignment explanation
Indices: 3421325--3421737 Score: 481
Period size: 43 Copynumber: 9.7 Consensus size: 42
3421315 AGAAAGGTTA
*
3421325 GCGGCGTTTGTATCCAAAAACGCTGCTATAGATATGACTTTTT
1 GCGGCGTTTGT-TCCAAAAACGCTGCTATAGATATGACCTTTT
*
3421368 GCGGCGTTTGTATCCAAAAACGCTGCTATAGATATGACTTTTT
1 GCGGCGTTTGT-TCCAAAAACGCTGCTATAGATATGACCTTTT
* * * * *
3421411 GTGGCGTTTGTTCCAAAAACACAGATACAGATATGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCTGCTATAGATATGACCTTTT
* *
3421453 ACGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCTGCTATAGATATGACCTTTT
* *
3421496 GCGGCGTTTATTCCAAAAACG-TCGCTATTGATATGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCT-GCTATAGATATGACCTTTT
* * * * *
3421538 GTGGCGTTTATTCCAAAAATGCCGCTATAGATCTTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCTGCTATAGAT-ATGACCTTTT
* *
3421581 GCGACGTTTATTCCAAAAACG-TCGCTATAGATATGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCT-GCTATAGATATGACCTTTT
* *
3421623 GCGGCGTTTGTATCCAAAAATG-TAGCTATAGTTATGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCT-GCTATAGATATGACCTTTT
* * * **
3421666 GCGGTGTTTGTTCCAAAAATGCCGCTATAGATATCGACCTTCC
1 GCGGCGTTTGTTCCAAAAACGCTGCTATAGATAT-GACCTTTT
* *
3421709 GCGGCGTTTGTTCCAAAAATGCCGCTATA
1 GCGGCGTTTGTTCCAAAAACGCTGCTATA
3421738 TACTACAGCA
Statistics
Matches: 325, Mismatches: 37, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
42 128 0.39
43 197 0.61
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCTGCTATAGATATGACCTTTT
Found at i:3421446 original size:85 final size:84
Alignment explanation
Indices: 3421325--3421737 Score: 524
Period size: 85 Copynumber: 4.8 Consensus size: 84
3421315 AGAAAGGTTA
* *
3421325 GCGGCGTTTGTATCCAAAAACGCTGCTATAGATATGACTTTTTGCGGCGTTTGTATCCAAAAACG
1 GCGGCGTTTGT-TCCAAAAACGC-GCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAATG
* *
3421390 CTGCTATAGATATGACTTTTT
64 CCGCTATAGATATGACCTTTT
* * * * * *
3421411 GTGGCGTTTGTTCCAAAAACACAGATACAGATATGACCTTTTACGGCGTTTGTATCCAAAAACGC
1 GCGGCGTTTGTTCCAAAAACGC-GCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAATGC
3421476 CGCTATAGATATGACCTTTT
65 CGCTATAGATATGACCTTTT
* * * *
3421496 GCGGCGTTTATTCCAAAAACGTCGCTATTGATATGACCTTTTGTGGCGTTTAT-TCCAAAAATGC
1 GCGGCGTTTGTTCCAAAAACG-CGCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAATGC
*
3421560 CGCTATAGATCTTGACCTTTT
65 CGCTATAGAT-ATGACCTTTT
* * *
3421581 GCGACGTTTATTCCAAAAACGTCGCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAATGT
1 GCGGCGTTTGTTCCAAAAACG-CGCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAATGC
* *
3421646 AGCTATAGTTATGACCTTTT
65 CGCTATAGATATGACCTTTT
* * **
3421666 GCGGTGTTTGTTCCAAAAATGCCGCTATAGATATCGACCTTCCGCGGCGTTTGT-TCCAAAAATG
1 GCGGCGTTTGTTCCAAAAACG-CGCTATAGATAT-GACCTTTTGCGGCGTTTGTATCCAAAAATG
3421730 CCGCTATA
64 CCGCTATA
3421738 TACTACAGCA
Statistics
Matches: 286, Mismatches: 37, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
84 20 0.07
85 220 0.77
86 46 0.16
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (84 bp):
GCGGCGTTTGTTCCAAAAACGCGCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAATGCC
GCTATAGATATGACCTTTT
Found at i:3421576 original size:128 final size:127
Alignment explanation
Indices: 3421325--3421737 Score: 542
Period size: 128 Copynumber: 3.2 Consensus size: 127
3421315 AGAAAGGTTA
* *
3421325 GCGGCGTTTGTATCCAAAAACGCTGCTATAGATATGACTTTTTGCGGCGTTTGTATCCAAAAACG
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAACG
* ** * * * *
3421390 -CTGCTATAGATATGACTTTTTGTGGCGTTTGTTCCAAAAACACAGATACAGATATGACCTTTT
65 TC-GCTATAGATATGACCTTTTGTGGCGTTTGTTCCAAAAATGCCGCTATAGATTTGACCTTTT
* *
3421453 ACGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTAT-TCCAAAAACG
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAACG
* *
3421517 TCGCTATTGATATGACCTTTTGTGGCGTTTATTCCAAAAATGCCGCTATAGATCTTGACCTTTT
65 TCGCTATAGATATGACCTTTTGTGGCGTTTGTTCCAAAAATGCCGCTATAGAT-TTGACCTTTT
* * * *
3421581 GCGACGTTTATTCCAAAAACGTCGCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAATGT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAACGT
* * * * * **
3421646 AGCTATAGTTATGACCTTTTGCGGTGTTTGTTCCAAAAATGCCGCTATAGATATCGACCTTCC
66 CGCTATAGATATGACCTTTTGTGGCGTTTGTTCCAAAAATGCCGCTATAGAT-TTGACCTTTT
*
3421709 GCGGCGTTTGTTCCAAAAATGCCGCTATA
1 GCGGCGTTTGTTCCAAAAACGCCGCTATA
3421738 TACTACAGCA
Statistics
Matches: 249, Mismatches: 33, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
127 93 0.37
128 156 0.63
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (127 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAACGT
CGCTATAGATATGACCTTTTGTGGCGTTTGTTCCAAAAATGCCGCTATAGATTTGACCTTTT
Found at i:3422063 original size:42 final size:42
Alignment explanation
Indices: 3422017--3422111 Score: 136
Period size: 42 Copynumber: 2.3 Consensus size: 42
3422007 GGTTAAACAA
** * * *
3422017 TAGCGGCGTTTATAGTAAAAACGCCGCAATATAGTGTTAATT
1 TAGCGGCGTTTATACCAAAAACGCCGCAATAGAGTGGTAAAT
*
3422059 TAGCGGCGTTTATACCAAAAACGTCGCAATAGAGTGGTAAAT
1 TAGCGGCGTTTATACCAAAAACGCCGCAATAGAGTGGTAAAT
3422101 TAGCGGCGTTT
1 TAGCGGCGTTT
3422112 TTTTGTATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (42 bp):
TAGCGGCGTTTATACCAAAAACGCCGCAATAGAGTGGTAAAT
Found at i:3423245 original size:52 final size:52
Alignment explanation
Indices: 3423180--3423338 Score: 309
Period size: 52 Copynumber: 3.1 Consensus size: 52
3423170 TACTGAACAA
3423180 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
*
3423232 TATGTTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
3423284 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
3423336 TAT
1 TAT
3423339 TTTGTTGTTA
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 105 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (52 bp):
TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
Found at i:3426262 original size:26 final size:26
Alignment explanation
Indices: 3426228--3426284 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
3426218 TTTATTTATC
*
3426228 GTGTTAAGTATTTTTTTGCATAACTT
1 GTGTCAAGTATTTTTTTGCATAACTT
3426254 GTGTCAAGTATTTTTTTGCATAACTT
1 GTGTCAAGTATTTTTTTGCATAACTT
3426280 GTGTC
1 GTGTC
3426285 TTAATTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.51
Consensus pattern (26 bp):
GTGTCAAGTATTTTTTTGCATAACTT
Found at i:3426541 original size:43 final size:43
Alignment explanation
Indices: 3426404--3426541 Score: 195
Period size: 43 Copynumber: 3.2 Consensus size: 43
3426394 AAGGTAAATA
*
3426404 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTGACTTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTT
* * *
3426447 GCAGCATTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTT
* * * * *
3426490 GCGACGTTTGTTTCCAAAAATGCCGTTATAGGTTTGACCTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTT
3426533 GCGGCGTTT
1 GCGGCGTTT
3426542 TGCACTAGAA
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 82 1.00
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTT
Found at i:3426768 original size:43 final size:44
Alignment explanation
Indices: 3426711--3426814 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 44
3426701 CATTTGCGGC
* * *
3426711 GTTCT-AAAAACGCCGTTAAACATCAACGCCTATTGCGGCGTTT
1 GTTCTGAAAAACGCCGCTAAACAACAAAGCCTATTGCGGCGTTT
* *
3426754 -TTCTGAAAAACGCCGCTAAATAACAAATCCTATTGCGGCGTTT
1 GTTCTGAAAAACGCCGCTAAACAACAAAGCCTATTGCGGCGTTT
* *
3426797 GTTCAG-AAAACACCGCTA
1 GTTCTGAAAAACGCCGCTA
3426815 TATGTTGTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 4 0.08
43 44 0.85
44 4 0.08
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (44 bp):
GTTCTGAAAAACGCCGCTAAACAACAAAGCCTATTGCGGCGTTT
Found at i:3426895 original size:12 final size:14
Alignment explanation
Indices: 3426859--3426895 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
3426849 CGCCGCTAAC
3426859 TTTAGCGGCGCTAT
1 TTTAGCGGCGCTAT
3426873 TTTCAGCGGCGCT-T
1 TTT-AGCGGCGCTAT
3426887 TTT-GCGGCG
1 TTTAGCGGCG
3426896 TTTGTCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.27
14 7 0.32
15 9 0.41
ACGTcount: A:0.08, C:0.24, G:0.32, T:0.35
Consensus pattern (14 bp):
TTTAGCGGCGCTAT
Found at i:3427132 original size:43 final size:43
Alignment explanation
Indices: 3427006--3427112 Score: 160
Period size: 43 Copynumber: 2.5 Consensus size: 43
3426996 GACCTTTCGC
* *
3427006 TCCAAAAACGCCGCTATAGATATAGACTTTTTGCGGCGTTTGT
1 TCCAAAAACGCCGCTATAGATATAGACATTTTGTGGCGTTTGT
** *
3427049 TCCAAAAACGTTGCTATAGATATCGACATTTTGTGGCGTTTGT
1 TCCAAAAACGCCGCTATAGATATAGACATTTTGTGGCGTTTGT
*
3427092 TTCAAAAACGCCGCTATAGAT
1 TCCAAAAACGCCGCTATAGAT
3427113 CTTGACCTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (43 bp):
TCCAAAAACGCCGCTATAGATATAGACATTTTGTGGCGTTTGT
Found at i:3428714 original size:28 final size:28
Alignment explanation
Indices: 3428674--3428731 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
3428664 AGCTGGCACT
3428674 GGGCCGGGGCAGGAGG-GTCGCCCGCCCA
1 GGGCCGGGGCAGGAGGTG-CGCCCGCCCA
*
3428702 GGGCTGGGGCAGGAGGTGCGCCCGCCCA
1 GGGCCGGGGCAGGAGGTGCGCCCGCCCA
3428730 GG
1 GG
3428732 ACCCATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.10, C:0.33, G:0.52, T:0.05
Consensus pattern (28 bp):
GGGCCGGGGCAGGAGGTGCGCCCGCCCA
Found at i:3431189 original size:18 final size:18
Alignment explanation
Indices: 3431151--3431189 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3431141 ATAACGGATT
* *
3431151 TAAAAATATTTTTTAAGA
1 TAAAAATATTTTATAAAA
*
3431169 TAAATATATTTTATAAAA
1 TAAAAATATTTTATAAAA
3431187 TAA
1 TAA
3431190 TTAATTAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TAAAAATATTTTATAAAA
Found at i:3434243 original size:28 final size:28
Alignment explanation
Indices: 3434207--3434271 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
3434197 TTTAATATGA
* * *
3434207 ATTTCTAAAAATTTTAGGAGCTAAATTAT
1 ATTTTTAAAAATTTAAGGACCT-AATTAT
*
3434236 -TTTTTAAAACTTTAAGGACCTAATTAT
1 ATTTTTAAAAATTTAAGGACCTAATTAT
3434263 AATTTTTAA
1 -ATTTTTAA
3434272 GTTTTAGGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 6 0.20
28 17 0.57
29 7 0.23
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (28 bp):
ATTTTTAAAAATTTAAGGACCTAATTAT
Found at i:3434244 original size:27 final size:27
Alignment explanation
Indices: 3434214--3434281 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
3434204 TGAATTTCTA
3434214 AAAATTTTAGGAGCTAAATTAT-TTTTT
1 AAAATTTTAGGAGCT-AATTATATTTTT
* *
3434241 AAAACTTTAAGGACCTAATTATAATTTTT
1 AAAA-TTTTAGGAGCTAATTAT-ATTTTT
*
3434270 -AAGTTTTAGGAG
1 AAAATTTTAGGAG
3434282 GTGTCACTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
27 17 0.52
28 11 0.33
29 5 0.15
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (27 bp):
AAAATTTTAGGAGCTAATTATATTTTT
Found at i:3434763 original size:43 final size:43
Alignment explanation
Indices: 3434716--3434798 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
3434706 AACAAAAGCC
* * *
3434716 GCAAA-AAGTCAAGTTTTTTAGCGGCGTTTTGGATACAAACGTG
1 GCAAAGAA-TCAAGTTTTATAGCAGCATTTTGGATACAAACGTG
**
3434759 GCAAAGAATCGGGTTTTATAGCAGCATTTTGGATACAAAC
1 GCAAAGAATCAAGTTTTATAGCAGCATTTTGGATACAAAC
3434799 ACAACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 32 0.94
44 2 0.06
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (43 bp):
GCAAAGAATCAAGTTTTATAGCAGCATTTTGGATACAAACGTG
Found at i:3436942 original size:2 final size:2
Alignment explanation
Indices: 3436935--3436966 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3436925 CGTATTTGAA
3436935 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
3436967 GTGAATATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3438367 original size:19 final size:20
Alignment explanation
Indices: 3438328--3438365 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3438318 ACCCCTCGTG
* *
3438328 AAAAAGGATCTATCCCTTTC
1 AAAAAGAATCGATCCCTTTC
3438348 AAAAAGAATCGATCCCTT
1 AAAAAGAATCGATCCCTT
3438366 CATTGTTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (20 bp):
AAAAAGAATCGATCCCTTTC
Found at i:3438865 original size:44 final size:44
Alignment explanation
Indices: 3438802--3438939 Score: 276
Period size: 44 Copynumber: 3.1 Consensus size: 44
3438792 GAGTATCATG
3438802 CATTGCTCTGGTTGTTGCGAGATTTCAATTATTTGTTTATTAAC
1 CATTGCTCTGGTTGTTGCGAGATTTCAATTATTTGTTTATTAAC
3438846 CATTGCTCTGGTTGTTGCGAGATTTCAATTATTTGTTTATTAAC
1 CATTGCTCTGGTTGTTGCGAGATTTCAATTATTTGTTTATTAAC
3438890 CATTGCTCTGGTTGTTGCGAGATTTCAATTATTTGTTTATTAAC
1 CATTGCTCTGGTTGTTGCGAGATTTCAATTATTTGTTTATTAAC
3438934 CATTGC
1 CATTGC
3438940 CACGTGTTAT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 94 1.00
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.47
Consensus pattern (44 bp):
CATTGCTCTGGTTGTTGCGAGATTTCAATTATTTGTTTATTAAC
Found at i:3440628 original size:14 final size:14
Alignment explanation
Indices: 3440609--3440636 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3440599 TACCAAGAGA
3440609 TAAGTAGTAAAATG
1 TAAGTAGTAAAATG
3440623 TAAGTAGTAAAATG
1 TAAGTAGTAAAATG
3440637 GGGGTTGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (14 bp):
TAAGTAGTAAAATG
Found at i:3441576 original size:27 final size:26
Alignment explanation
Indices: 3441536--3441587 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
3441526 AGAAGGCGCA
*
3441536 CTGACTAGATCTTCTAGAAAACTGCCG
1 CTGACTAGACCTTCTAG-AAACTGCCG
*
3441563 CTGACTGGACCTTCTAGAAACTGCC
1 CTGACTAGACCTTCTAGAAACTGCC
3441588 ACATCAGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (26 bp):
CTGACTAGACCTTCTAGAAACTGCCG
Found at i:3447915 original size:25 final size:27
Alignment explanation
Indices: 3447897--3447950 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
3447887 AGAAGACGCG
3447897 CTGACTAGATCTTCTAGAAAACTGCCA
1 CTGACTAGATCTTCTAGAAAACTGCCA
* *
3447924 CTGACTGGACCTTCTAG-AAACTGCCA
1 CTGACTAGATCTTCTAGAAAACTGCCA
3447950 C
1 C
3447951 GTCAGACCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (27 bp):
CTGACTAGATCTTCTAGAAAACTGCCA
Found at i:3451469 original size:22 final size:22
Alignment explanation
Indices: 3451423--3451469 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
3451413 TATAATGTAA
*
3451423 AATGAAATAAAATAAAAAAGTG
1 AATGAAATAAAATAAAAAAATG
3451445 AATGAAA-AAAGA-AAAAAAATCG
1 AATGAAATAAA-ATAAAAAAAT-G
3451467 AAT
1 AAT
3451470 TAAAGGATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.13, T:0.15
Consensus pattern (22 bp):
AATGAAATAAAATAAAAAAATG
Found at i:3452669 original size:15 final size:16
Alignment explanation
Indices: 3452649--3452706 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 16
3452639 TGTTGAAATT
3452649 TAATAAATAAATAAATAA
1 TAATAAATAAAT-AA-AA
*
3452667 TAATAATATAACCTAAAA
1 TAATAA-ATAA-ATAAAA
3452685 TAAT-AATAAATAAAA
1 TAATAAATAAATAAAA
3452700 TAATAAA
1 TAATAAA
3452707 AGAATTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
15 9 0.26
16 6 0.17
17 1 0.03
18 12 0.34
19 6 0.17
20 1 0.03
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
TAATAAATAAATAAAA
Found at i:3452887 original size:28 final size:28
Alignment explanation
Indices: 3452773--3452881 Score: 163
Period size: 28 Copynumber: 4.0 Consensus size: 28
3452763 TCGAAAAACC
*
3452773 ATTTTAAAAACTATATACATTTTCAAAATT
1 ATTTTAAAAACTATAT--GTTTTCAAAATT
3452803 A----AAAAACTATATGTTTTCAAAATT
1 ATTTTAAAAACTATATGTTTTCAAAATT
3452827 ATTTTAAAAACTATATGTTTTCAAAATT
1 ATTTTAAAAACTATATGTTTTCAAAATT
3452855 ATTTTAAAAACTATATGTTTTCAAAAT
1 ATTTTAAAAACTATATGTTTTCAAAAT
3452882 AGTTTTTTAA
Statistics
Matches: 74, Mismatches: 1, Indels: 10
0.87 0.01 0.12
Matches are distributed among these distances:
24 12 0.16
26 11 0.15
28 50 0.68
30 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (28 bp):
ATTTTAAAAACTATATGTTTTCAAAATT
Found at i:3452948 original size:37 final size:36
Alignment explanation
Indices: 3452866--3452948 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 36
3452856 TTTTAAAAAC
*** * *
3452866 TATATGTTTTCAAAATAGTTTTTTAAAATCATATAT
1 TATATGTTTTCAAAATAGTTTAAAAAAAACATATAA
*
3452902 TATACGTTTTCAAAACTA-TTTAAAAAAAACTATATAA
1 TATATGTTTTCAAAA-TAGTTTAAAAAAAAC-ATATAA
3452939 TATATGTTTT
1 TATATGTTTT
3452949 TAAATTTATC
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
36 22 0.58
37 16 0.42
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (36 bp):
TATATGTTTTCAAAATAGTTTAAAAAAAACATATAA
Found at i:3453782 original size:41 final size:41
Alignment explanation
Indices: 3453736--3453868 Score: 140
Period size: 41 Copynumber: 3.5 Consensus size: 41
3453726 CGGGAGTGAC
*
3453736 TCCTTCGTCGTGAAGTTAAGTCGAAACTTTTGGGTACGATA
1 TCCTTCGTTGTGAAGTTAAGTCGAAACTTTTGGGTACGATA
** *
3453777 TCCTTCGTTGTGAAGTT---T--AAA-TCGTGGGT--GA-C
1 TCCTTCGTTGTGAAGTTAAGTCGAAACTTTTGGGTACGATA
** *
3453809 TCCTTTATTGTGAAGTTAAGTCGAAACTTTTGGGTACAATA
1 TCCTTCGTTGTGAAGTTAAGTCGAAACTTTTGGGTACGATA
3453850 TCCTTCGTTGTGAAGTTAA
1 TCCTTCGTTGTGAAGTTAA
3453869 AATCGTGGGT
Statistics
Matches: 71, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
32 15 0.21
33 2 0.03
35 7 0.10
36 3 0.04
37 3 0.04
38 7 0.10
40 1 0.01
41 33 0.46
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (41 bp):
TCCTTCGTTGTGAAGTTAAGTCGAAACTTTTGGGTACGATA
Found at i:3453808 original size:73 final size:73
Alignment explanation
Indices: 3453674--3453903 Score: 297
Period size: 73 Copynumber: 3.2 Consensus size: 73
3453664 CTCATTTACT
* * * *
3453674 GTGAAGTTAAGTCG-ATCTATTGGGCACAATATCCTTCGATT-T-AAGTTGAAATCG-GGAGTGA
1 GTGAAGTTAAGTCGAAACTTTTGGGTACAATATCCTTCG-TTGTGAAGTTAAAATCGTGG-GTGA
3453735 CTCCTTCGTC
64 CTCCTTCGTC
* *
3453745 GTGAAGTTAAGTCGAAACTTTTGGGTACGATATCCTTCGTTGTGAAGTTTAAATCGTGGGTGACT
1 GTGAAGTTAAGTCGAAACTTTTGGGTACAATATCCTTCGTTGTGAAGTTAAAATCGTGGGTGACT
** *
3453810 CCTTTATT
66 CCTTCGTC
*
3453818 GTGAAGTTAAGTCGAAACTTTTGGGTACAATATCCTTCGTTGTGAAGTTAAAATCGTGGGTGATT
1 GTGAAGTTAAGTCGAAACTTTTGGGTACAATATCCTTCGTTGTGAAGTTAAAATCGTGGGTGACT
*
3453883 CATTCGTC
66 CCTTCGTC
* *
3453891 GTTAAGTTGAGTC
1 GTGAAGTTAAGTC
3453904 CGTATTGAAT
Statistics
Matches: 138, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
71 16 0.12
72 21 0.15
73 99 0.72
74 2 0.01
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.36
Consensus pattern (73 bp):
GTGAAGTTAAGTCGAAACTTTTGGGTACAATATCCTTCGTTGTGAAGTTAAAATCGTGGGTGACT
CCTTCGTC
Found at i:3457856 original size:20 final size:20
Alignment explanation
Indices: 3457801--3457856 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
3457791 ATCTGTACCC
*
3457801 GGGGAATC-GATACCACCTGG
1 GGGGAATCTG-TACCCCCTGG
*
3457821 GGGGAATCTGTTCCCCCTGG
1 GGGGAATCTGTACCCCCTGG
3457841 GGGGAATCTGTACCCC
1 GGGGAATCTGTACCCC
3457857 TTGGACAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.18, C:0.29, G:0.34, T:0.20
Consensus pattern (20 bp):
GGGGAATCTGTACCCCCTGG
Found at i:3461337 original size:20 final size:20
Alignment explanation
Indices: 3461300--3461358 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
3461290 ATCTGTACCC
*
3461300 GGGGAATCGATA-CCCCTGG
1 GGGGAATCTATACCCCCTGG
*
3461319 GGGGAATCTATTCCCCCTGG
1 GGGGAATCTATACCCCCTGG
*
3461339 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTATACCCCCTGG
3461359 ACAATCTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 10 0.29
20 25 0.71
ACGTcount: A:0.17, C:0.29, G:0.34, T:0.20
Consensus pattern (20 bp):
GGGGAATCTATACCCCCTGG
Found at i:3461354 original size:19 final size:19
Alignment explanation
Indices: 3461284--3461354 Score: 71
Period size: 20 Copynumber: 3.9 Consensus size: 19
3461274 AAACCATGCA
3461284 GGGGGAATCTGTA-CCC--
1 GGGGGAATCTGTACCCCTG
3461300 -GGGGAATC-GATACCCCTG
1 GGGGGAATCTG-TACCCCTG
* *
3461318 GGGGGAATCTATTCCCCCTG
1 GGGGGAATCT-GTACCCCTG
3461338 GGGGGAATCTGTACCCC
1 GGGGGAATCTGTACCCC
3461355 CTGGACAATC
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
14 1 0.02
15 10 0.23
16 3 0.07
19 13 0.30
20 17 0.39
ACGTcount: A:0.18, C:0.28, G:0.34, T:0.20
Consensus pattern (19 bp):
GGGGGAATCTGTACCCCTG
Found at i:3464887 original size:19 final size:17
Alignment explanation
Indices: 3464839--3464889 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 17
3464829 AAACCATGCA
3464839 GGGGGAATCTGTA-CCC
1 GGGGGAATCTGTACCCC
3464855 -GGGGAATC-GATACCCC
1 GGGGGAATCTG-TACCCC
3464871 TGGGGGGAATCTGTACCCC
1 --GGGGGAATCTGTACCCC
3464890 CTGGACAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 1 0.03
15 10 0.34
16 3 0.10
19 14 0.48
20 1 0.03
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (17 bp):
GGGGGAATCTGTACCCC
Found at i:3469747 original size:15 final size:16
Alignment explanation
Indices: 3469729--3469766 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3469719 AAATCTAGAG
**
3469729 TTAATATATGTATG-T
1 TTAATATACATATGTT
3469744 TTAATATACATATGTT
1 TTAATATACATATGTT
3469760 TTAATAT
1 TTAATAT
3469767 TAAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.53
Consensus pattern (16 bp):
TTAATATACATATGTT
Found at i:3470649 original size:2 final size:2
Alignment explanation
Indices: 3470644--3470677 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
3470634 ATAATGTGTG
3470644 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
3470678 GTTTGTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3477471 original size:16 final size:16
Alignment explanation
Indices: 3477438--3477472 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3477428 TAACAAAGGC
* *
3477438 ATAACAACATGTATAT
1 ATAACAACATATAAAT
3477454 ATAACAACATATAAAT
1 ATAACAACATATAAAT
3477470 ATA
1 ATA
3477473 TATATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.11, G:0.03, T:0.29
Consensus pattern (16 bp):
ATAACAACATATAAAT
Found at i:3483153 original size:20 final size:20
Alignment explanation
Indices: 3483128--3483167 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3483118 AAACAGTTTT
3483128 GAGGAAAATAAATATTGCTC
1 GAGGAAAATAAATATTGCTC
3483148 GAGGAAAATAAATATTGCTC
1 GAGGAAAATAAATATTGCTC
3483168 TCAATCAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (20 bp):
GAGGAAAATAAATATTGCTC
Found at i:3494949 original size:5 final size:5
Alignment explanation
Indices: 3494939--3494963 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3494929 AATAATAATG
3494939 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
3494964 AGTGAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:3508883 original size:35 final size:35
Alignment explanation
Indices: 3508837--3508934 Score: 169
Period size: 35 Copynumber: 2.8 Consensus size: 35
3508827 AAGTCATTTG
3508837 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGC
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGC
* **
3508872 AATCAAGCCTTCACAAAAGAGTAATGAAGCAATTT
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGC
3508907 AATCAAGCCTTCACAAAAGAGTAGTGAA
1 AATCAAGCCTTCACAAAAGAGTAGTGAA
3508935 ACAAGATCAG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 59 1.00
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.19
Consensus pattern (35 bp):
AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGC
Done.