Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008685.1 Hibiscus syriacus cultivar Beakdansim tig00111708_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: 3669133
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 19
Found at i:2366447 original size:20 final size:22
Alignment explanation
Indices: 2366406--2366464 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
2366396 TCTACATCTA
2366406 CAAAGATGATAGATTCTCTCTT
1 CAAAGATGATAGATTCTCTCTT
*
2366428 CAAAGATGATAGATTCTCTTTT
1 CAAAGATGATAGATTCTCTCTT
* *
2366450 CAAAGAAGAAAGATT
1 CAAAGATGATAGATT
2366465 TATTGGATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (22 bp):
CAAAGATGATAGATTCTCTCTT
Found at i:2367018 original size:17 final size:17
Alignment explanation
Indices: 2366967--2367021 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
2366957 ACATTTCCAT
2366967 AAGAAGTTCATAATGAG
1 AAGAAGTTCATAATGAG
* *
2366984 AAGAA-CTCAT-CTGAAG
1 AAGAAGTTCATAATG-AG
2367000 AAGAAGTTCATAATGAG
1 AAGAAGTTCATAATGAG
2367017 AAGAA
1 AAGAA
2367022 CTGTTCAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 2 0.06
16 11 0.35
17 16 0.52
18 2 0.06
ACGTcount: A:0.49, C:0.09, G:0.22, T:0.20
Consensus pattern (17 bp):
AAGAAGTTCATAATGAG
Found at i:2367164 original size:122 final size:122
Alignment explanation
Indices: 2366953--2367528 Score: 914
Period size: 122 Copynumber: 4.7 Consensus size: 122
2366943 TACTCGATGA
**
2366953 ATCAACATTTCCATAAGAAGTTCATAATGAGAAGAACTCATCT------GAAGAAGAAGTTCATA
1 ATCAACATTTCCAGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
2367012 ATGAGAAGAACTGTTCAACCTTTCGCTTGATTCTATCACAGAAAGAGATAGATCAGC
66 ATGAGAAGAACTGTTCAACCTTTCGCTTGATTCTATCACAGAAAGAGATAGATCAAC
2367069 ATCAACATTTCCAGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
2367134 ATGAGAAGAACTGTTCAACCTTTCGCTTGATTCTATCACAGAAGGAGATAAATCAGC
66 ATGAGAAGAACTGTTCAACCTTTCGCTTGATTCTATCACAGAAAGAGATAGATCAAC
*
2367191 ATCAACATTGCCAGGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGGAGA-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
2367255 AATGAGAAGAACTGTTCAACCTTTCGCTTGATTCTATCACAGAAAGAGATAGATCAAC
65 AATGAGAAGAACTGTTCAACCTTTCGCTTGATTCTATCACAGAAAGAGATAGATCAAC
* *
2367313 ATCAATATTTCCAGGAGAAGTTCATAAAGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
2367378 ATGAGAAGAACTATTCAACCTTTCGCTTGATTCTATCACAGAAAGAGATAGATCAACATCAAC
66 ATGAGAAGAACTGTTCAACCTTTCGCTTGATTCTATCACAGAAAGAGATAG------ATCAAC
* *
2367441 ATCAACATTTCTAGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGGAGAAGAAGTTCATA
1 ATCAACATTTCCAGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
2367506 ATGAAAAGAACTTGTTCAACCTT
66 ATGAGAAGAAC-TGTTCAACCTT
2367529 AGATTGATTC
Statistics
Matches: 427, Mismatches: 18, Indels: 17
0.92 0.04 0.04
Matches are distributed among these distances:
116 41 0.10
121 1 0.00
122 297 0.70
123 1 0.00
128 77 0.18
129 10 0.02
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.24
Consensus pattern (122 bp):
ATCAACATTTCCAGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAACTGTTCAACCTTTCGCTTGATTCTATCACAGAAAGAGATAGATCAAC
Found at i:2367306 original size:244 final size:245
Alignment explanation
Indices: 2366841--2367528 Score: 936
Period size: 244 Copynumber: 2.9 Consensus size: 245
2366831 CACTCAATGG
* * *
2366841 ATCAACATTTCC-GAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
1 ATCAACATTTCCAGGAGAAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCAT
* *** * * *
2366905 AATGAGAAGAATTTGTTCAACC-TT---TT-A--C--T--CA-AA-TTCATTACTCGATGAATCA
65 AATGAGAAGAA-CTGTTCAACCTTTCGCTTGATTCTATCACAGAAGGAGATAAATC-A-GCATCA
*
2366957 ACATTTCCA-TAAGAAGTTCATAATGAGAAGAACTCATCT------GAAGAAGAAGTTCATAATG
127 ACATTTCCAGGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
*
2367015 AGAAGAACTGTTCAACCTTTCGCTTGATTCTATCACAGAAAGAGATAGATCAGC
192 AGAAGAACTGTTCAACCTTTCGCTTGATTCTATCACAGAAAGAGATAGATCAAC
2367069 ATCAACATTTCCAGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
2367134 ATGAGAAGAACTGTTCAACCTTTCGCTTGATTCTATCACAGAAGGAGATAAATCAGCATCAACAT
66 ATGAGAAGAACTGTTCAACCTTTCGCTTGATTCTATCACAGAAGGAGATAAATCAGCATCAACAT
*
2367199 TGCCAGGAAG-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
131 TTCCAGGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
2367263 GAACTGTTCAACCTTTCGCTTGATTCTATCACAGAAAGAGATAGATCAAC
196 GAACTGTTCAACCTTTCGCTTGATTCTATCACAGAAAGAGATAGATCAAC
* *
2367313 ATCAATATTTCCAGGAGAAGTTCATAAAGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* *
2367378 ATGAGAAGAACTATTCAACCTTTCGCTTGATTCTATCACAGAAAGAGATAGATCAACATCAACAT
66 ATGAGAAGAACTGTTCAACCTTTCGCTTGATTCTATCACAG-AAG-G--AGAT-AA-ATCAGCAT
* *
2367443 CAACATTTCTAGG-AGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGGAGAAGAAGTTCATAA
125 CAACATTTCCAGGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
*
2367507 TGAAAAGAACTTGTTCAACCTT
190 TGAGAAGAAC-TGTTCAACCTT
2367529 AGATTGATTC
Statistics
Matches: 410, Mismatches: 21, Indels: 35
0.88 0.05 0.08
Matches are distributed among these distances:
227 9 0.02
228 41 0.10
229 32 0.08
231 2 0.00
232 1 0.00
234 1 0.00
236 1 0.00
238 40 0.10
239 6 0.01
240 5 0.01
244 175 0.43
245 3 0.01
246 1 0.00
248 4 0.01
249 4 0.01
250 74 0.18
251 11 0.03
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (245 bp):
ATCAACATTTCCAGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAACTGTTCAACCTTTCGCTTGATTCTATCACAGAAGGAGATAAATCAGCATCAACAT
TTCCAGGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
GAACTGTTCAACCTTTCGCTTGATTCTATCACAGAAAGAGATAGATCAAC
Found at i:2367771 original size:137 final size:140
Alignment explanation
Indices: 2367441--2367784 Score: 360
Period size: 140 Copynumber: 2.5 Consensus size: 140
2367431 CAACATCAAC
* * *
2367441 ATCAACATTTCTAGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGGAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* *
2367506 ATGAAAAGAACTTGTTCAACCTTAGATTGATTCAGCATCTAACGAAAATGAATAAAAGAAGAACC
66 ATGAAAAGAACTTGTTCAACCTTAGATTAATTCAGCATCTAACGAAAATGAATAAAACAAGAACC
2367571 TCACTTGAGG
131 TCACTTGAGG
* * * * *
2367581 ATTAACATTTTCAGAGGAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * * * ** * *
2367646 ATGAGAAGAACTTGTTTAACC-TAGTCTTAATTCATCA-C-ATATGAAGTTGAAT-CAACAA-CA
66 ATGAAAAGAACTTGTTCAACCTTAG-ATTAATTCAGCATCTA-ACGAAAATGAATAAAACAAGAA
* *
2367706 TCTC-TTTCGAGG
129 CCTCACTT-GAGG
* * * * * *
2367718 ATCAACATTTCCAGATAG-AGTTCGTAATTAGAAGAACTCAACTAAAGAGGAAGAATAAGTTTAT
1 ATCAACATTTCCAGA-AGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
2367782 AAT
65 AAT
2367785 CTGAAGAATT
Statistics
Matches: 168, Mismatches: 32, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
136 2 0.01
137 62 0.37
138 6 0.04
139 13 0.08
140 85 0.51
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (140 bp):
ATCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATGAAAAGAACTTGTTCAACCTTAGATTAATTCAGCATCTAACGAAAATGAATAAAACAAGAACC
TCACTTGAGG
Found at i:2367891 original size:16 final size:16
Alignment explanation
Indices: 2367868--2367911 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
2367858 AAGTTCATAA
2367868 TGAA-AAGAACTCATC
1 TGAAGAAGAACTCATC
*
2367883 TGAAGAAGAATTCATC
1 TGAAGAAGAACTCATC
*
2367899 TGAAGAAAAACTC
1 TGAAGAAGAACTC
2367912 GTCCGAAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (16 bp):
TGAAGAAGAACTCATC
Found at i:2368817 original size:2 final size:2
Alignment explanation
Indices: 2368812--2368841 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2368802 ACACACACAC
2368812 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
2368842 TCATTATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2369357 original size:9 final size:9
Alignment explanation
Indices: 2369343--2369375 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2369333 TATCTTATGC
2369343 TAATTAATT
1 TAATTAATT
2369352 TAATTAATT
1 TAATTAATT
*
2369361 TTA-TAATT
1 TAATTAATT
2369369 TAATTAA
1 TAATTAA
2369376 AGAATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAATTAATT
Found at i:2369687 original size:16 final size:15
Alignment explanation
Indices: 2369662--2369691 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2369652 TTATGCAATT
2369662 GAATATAAAATAAAA
1 GAATATAAAATAAAA
2369677 GAATCATAAAATAAA
1 GAAT-ATAAAATAAA
2369692 TTTATATTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (15 bp):
GAATATAAAATAAAA
Found at i:2384132 original size:29 final size:29
Alignment explanation
Indices: 2384090--2384148 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2384080 ATTTTCACCT
2384090 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2384119 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2384148 A
1 A
2384149 TTAATTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:2388614 original size:22 final size:22
Alignment explanation
Indices: 2388589--2388635 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
2388579 ACTCTTAAGA
2388589 AAGCTTTCAAATGCTTATAATT
1 AAGCTTTCAAATGCTTATAATT
2388611 AAGCTTTCAAATGCTTATAATT
1 AAGCTTTCAAATGCTTATAATT
2388633 AAG
1 AAG
2388636 ATTTGATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (22 bp):
AAGCTTTCAAATGCTTATAATT
Found at i:2388821 original size:29 final size:29
Alignment explanation
Indices: 2388779--2388837 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
2388769 ATTTTCACCT
2388779 AACTAAATTGATGTAAACAATGACATCAA
1 AACTAAATTGATGTAAACAATGACATCAA
*
2388808 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAACAATGACATCAA
2388837 A
1 A
2388838 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAACAATGACATCAA
Found at i:2391255 original size:15 final size:16
Alignment explanation
Indices: 2391235--2391266 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2391225 TGGCAGATCG
2391235 AAATCTAG-ACGGGAA
1 AAATCTAGAACGGGAA
2391250 AAATCTAGAACGGGAA
1 AAATCTAGAACGGGAA
2391266 A
1 A
2391267 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.12, G:0.25, T:0.12
Consensus pattern (16 bp):
AAATCTAGAACGGGAA
Found at i:2399525 original size:15 final size:15
Alignment explanation
Indices: 2399505--2399534 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2399495 TTCAAATAAA
2399505 TAATGAAATTGCAGC
1 TAATGAAATTGCAGC
2399520 TAATGAAATTGCAGC
1 TAATGAAATTGCAGC
2399535 ATTGCTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (15 bp):
TAATGAAATTGCAGC
Found at i:2416219 original size:5 final size:5
Alignment explanation
Indices: 2416194--2416240 Score: 62
Period size: 5 Copynumber: 9.6 Consensus size: 5
2416184 TCGAAACAAT
*
2416194 TATAA TAT-A TATTAA TAT-A TATTA TATAA TATAA TATAA TATAA TAT
1 TATAA TATAA TA-TAA TATAA TATAA TATAA TATAA TATAA TATAA TAT
2416241 GTATGATGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
4 7 0.18
5 28 0.74
6 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (5 bp):
TATAA
Found at i:2416300 original size:12 final size:12
Alignment explanation
Indices: 2416192--2416236 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
2416182 AATCGAAACA
2416192 ATTATAATATAT
1 ATTATAATATAT
2416204 A-T-TAATATAT
1 ATTATAATATAT
2416214 ATTAT-ATAATAT
1 ATTATAAT-ATAT
*
2416226 AATATAATATA
1 ATTATAATATA
2416237 ATATGTATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
10 9 0.32
11 4 0.14
12 13 0.46
13 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTATAATATAT
Found at i:2416576 original size:16 final size:16
Alignment explanation
Indices: 2416555--2416587 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2416545 GACTAAATTG
2416555 TACTTATTTAAAAAGT
1 TACTTATTTAAAAAGT
2416571 TACTTATTTAAAAAGT
1 TACTTATTTAAAAAGT
2416587 T
1 T
2416588 GATCAACGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (16 bp):
TACTTATTTAAAAAGT
Found at i:2424696 original size:13 final size:13
Alignment explanation
Indices: 2424679--2424711 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2424669 TTTGGTTTTT
2424679 TTTATTATTAATTA
1 TTTATTATT-ATTA
2424693 -TTATTATTATTA
1 TTTATTATTATTA
2424705 TTTATTA
1 TTTATTA
2424712 CAGGCCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:2424699 original size:16 final size:16
Alignment explanation
Indices: 2424680--2424711 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2424670 TTGGTTTTTT
2424680 TTATTATTAATTATTA
1 TTATTATTAATTATTA
*
2424696 TTATTATTATTTATTA
1 TTATTATTAATTATTA
2424712 CAGGCCCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTATTAATTATTA
Found at i:2426387 original size:20 final size:19
Alignment explanation
Indices: 2426362--2426403 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2426352 CTATTTTATA
2426362 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
2426382 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
2426401 AAT
1 AAT
2426404 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:2426512 original size:26 final size:27
Alignment explanation
Indices: 2426459--2426512 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
2426449 ATATTTCTAA
2426459 ATAAATAAATATTTTATTTATAAATAT
1 ATAAATAAATATTTTATTTATAAATAT
* *
2426486 ATAAATTAATATTTT-TTTATAATTAT
1 ATAAATAAATATTTTATTTATAAATAT
2426512 A
1 A
2426513 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
ATAAATAAATATTTTATTTATAAATAT
Found at i:2433899 original size:68 final size:68
Alignment explanation
Indices: 2433790--2433925 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
2433780 ACTCATCAAT
2433790 TGCTCCAACTGATCATCATTCAGTTCTTACACATCTGTTTTCAAAAGTATGCCAAGACAGTAAAA
1 TGCTCCAACTGATCATCATTCAGTTCTTACACATCTGTTTTCAAAAGTATGCCAAGACAGTAAAA
2433855 GGC
66 GGC
2433858 TGCTCCAACTGATCATCATTCAGTTCTTACACATCTGTTTTCAAAAGTATGCCAAGACAGTAAAA
1 TGCTCCAACTGATCATCATTCAGTTCTTACACATCTGTTTTCAAAAGTATGCCAAGACAGTAAAA
2433923 GGC
66 GGC
2433926 AACTTCTGCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (68 bp):
TGCTCCAACTGATCATCATTCAGTTCTTACACATCTGTTTTCAAAAGTATGCCAAGACAGTAAAA
GGC
Found at i:2434508 original size:115 final size:115
Alignment explanation
Indices: 2434365--2434836 Score: 784
Period size: 115 Copynumber: 4.1 Consensus size: 115
2434355 CCAAACCCAT
2434365 TTTGAAAGATGAATTTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCT
1 TTTGAAAGATGAATTTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCT
2434430 TTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAACCAATCATTAGA
66 TTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAACCAATCATTAGA
2434480 TTTGAAAGATGAATTTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCT
1 TTTGAAAGATGAATTTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCT
*
2434545 TTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAACCAATCATTGGA
66 TTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAACCAATCATTAGA
* * * * *
2434595 TTTGAAAGATGAATTCGCTAATAGTAGAAATAAGGAGACCCAATAGCATTTTCTGGAAGTTTTCT
1 TTTGAAAGATGAATTTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCT
*
2434660 TTGAGTTATCTGACCTGGTTTGGTATGAACCCCAAAAACCAATCATTAGA
66 TTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAACCAATCATTAGA
* * * *
2434710 TTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTGTTCA
1 TTTGAAAGATGAATTTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCT
** * * *
2434775 TTGAGTTATCTGATCTGGTTCAGTAGGAACCCC-AGAACCAATCATTGGA
66 TTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAACCAATCATTAGA
*
2434824 ATTGAAAGATGAA
1 TTTGAAAGATGAA
2434837 CTGCATAATC
Statistics
Matches: 335, Mismatches: 22, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
114 26 0.08
115 309 0.92
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (115 bp):
TTTGAAAGATGAATTTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCT
TTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAACCAATCATTAGA
Found at i:2436988 original size:54 final size:53
Alignment explanation
Indices: 2436906--2437059 Score: 172
Period size: 54 Copynumber: 2.9 Consensus size: 53
2436896 TGAGAAATTC
*
2436906 GAGCAGAAGCCACAGAAAATGATGAATGTGTTGTCAAATGCTTTACGAACATCT
1 GAGCAGAAACCACAGAAAATGATGAATGTGTTGTCAAATG-TTTACGAACATCT
* * * *
2436960 GAGCAGAAACCACAGAAAAGGATGAATGTGTTATCAAGTGTTT---TACATCT
1 GAGCAGAAACCACAGAAAATGATGAATGTGTTGTCAAATGTTTACGAACATCT
* * * *
2437010 GAGTAGAAATCACATG-AGATGATGCATGTGTTGTCAAATGTTTTACGAAC
1 GAGCAGAAACCACA-GAAAATGATGAATGTGTTGTCAAATG-TTTACGAAC
2437060 CAGTTATTCT
Statistics
Matches: 82, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
50 37 0.45
51 4 0.05
53 3 0.04
54 38 0.46
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (53 bp):
GAGCAGAAACCACAGAAAATGATGAATGTGTTGTCAAATGTTTACGAACATCT
Found at i:2437039 original size:50 final size:50
Alignment explanation
Indices: 2436906--2437055 Score: 149
Period size: 50 Copynumber: 2.9 Consensus size: 50
2436896 TGAGAAATTC
* * * *
2436906 GAGCAGAAGCCACAGAAAATGATGAATGTGTTGTCAAATGCTTTACGAACATCT
1 GAGCAGAAACCACAGAAAAGGATGAATGTGTTATCAAATG-TTT---TACATCT
*
2436960 GAGCAGAAACCACAGAAAAGGATGAATGTGTTATCAAGTGTTTTACATCT
1 GAGCAGAAACCACAGAAAAGGATGAATGTGTTATCAAATGTTTTACATCT
* * * * * *
2437010 GAGTAGAAATCACATG-AGATGATGCATGTGTTGTCAAATGTTTTAC
1 GAGCAGAAACCACA-GAAAAGGATGAATGTGTTATCAAATGTTTTAC
2437056 GAACCAGTTA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
50 43 0.52
51 1 0.01
53 3 0.04
54 36 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (50 bp):
GAGCAGAAACCACAGAAAAGGATGAATGTGTTATCAAATGTTTTACATCT
Found at i:2437470 original size:23 final size:22
Alignment explanation
Indices: 2437415--2437492 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
2437405 ATCTACATTC
*
2437415 TTCAAAGATGATAGATTCTCTC
1 TTCAAAGATGATAGATTCTCTT
*
2437437 TTCAAAGATGATAGATTCCCTTT
1 TTCAAAGATGATAGATTCTC-TT
*
2437460 TTAAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2437482 TTCAAAGATGA
1 TTCAAAGATGA
2437493 AAGCTTTATT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
22 31 0.62
23 19 0.38
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:2438085 original size:113 final size:113
Alignment explanation
Indices: 2437921--2438567 Score: 1111
Period size: 113 Copynumber: 5.7 Consensus size: 113
2437911 TGCCAGGTCG
2437921 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
2437986 AACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAA
66 AACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAA
*
2438034 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCACAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
2438099 AACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAA
66 AACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAA
*
2438147 AGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
2438212 AACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAA
66 AACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAA
*
2438260 AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * **
2438325 AACCTTTTTGCTTAAATTCATCA-TTCAATGGATCAGCATTGCCAG-GCCG
66 AACC-TTTTGCTTAAATTCATCACTT-GATGGATCAACTTTTCCAGAG-AA
*
2438374 AGTTCATAATGAGAAGTACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
*
2438439 AACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAAAA
66 AACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAA
** *
2438487 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
*
2438552 AACTTTTTGC-TAAATT
66 AACCTTTTGCTTAAATT
2438568 ACATTACAAA
Statistics
Matches: 504, Mismatches: 25, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
112 6 0.01
113 396 0.79
114 102 0.20
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAA
Found at i:2438504 original size:340 final size:338
Alignment explanation
Indices: 2437921--2438567 Score: 1109
Period size: 340 Copynumber: 1.9 Consensus size: 338
2437911 TGCCAGGTCG
2437921 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * *
2437986 AACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGA
66 AACCTTTTGCTTAAATTCATCACTTAATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGA
2438051 ACTCATCTGAAGAAGGAAGAAGAAGTTCACAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATT
131 ACTCATCTGAAGAAGGAAGAAGAAGTTCACAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATT
* *
2438116 CATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
196 CATCACTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
2438181 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCA
261 AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGC-TAAATTCATCACTTGATGGATCA
2438246 ACTTTTCCAGAGAA
325 ACTTTTCCAGAGAA
*
2438260 AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* **
2438325 AACCTTTTTGCTTAAATTCATCA-TTCAATGGATCAGCATTGCCAG-GCCGAGTTCATAATGAGA
66 AACC-TTTTGCTTAAATTCATCACTT-AATGGATCAACATTGCCAGAG-AAAGTTCATAATGAGA
* *
2438388 AGTACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAA
128 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCACAATGAGAAGAATTTGTTCAACCTTTTGCTTAA
2438453 ATTCATCACTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
193 ATTCATCACTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
* *
2438518 GGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACTTTTTGCTAAATT
258 GGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTAAATT
2438568 ACATTACAAA
Statistics
Matches: 290, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
339 77 0.27
340 213 0.73
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (338 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTGCTTAAATTCATCACTTAATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGA
ACTCATCTGAAGAAGGAAGAAGAAGTTCACAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATT
CATCACTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTAAATTCATCACTTGATGGATCAA
CTTTTCCAGAGAA
Found at i:2438640 original size:227 final size:222
Alignment explanation
Indices: 2437921--2438630 Score: 882
Period size: 227 Copynumber: 3.1 Consensus size: 222
2437911 TGCCAGGTCG
*
2437921 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTAATC----GAA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
2437986 AACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGA
61 AACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGA
* *
2438051 ACTCATCTGAAGAAGGAAGAAGAAGTTCACAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATT
126 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTAAATT
* * * *
2438116 -CATCACTTGATGGATCAACTT-T--TCCAGAGAA
191 ACATTAC--AATGGA-CAAATTATCATCCAGGGAA
* *
2438147 AGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACT-A-AT--CGAA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
2438212 AACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGA
61 AACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGA
*
2438277 ACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGCTTAAAT
126 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTTGCTTAAAT
* * ***
2438342 TCATCATT-CAATGGATCAGCA-T-T--GCCAGGCCG
190 T-A-CATTACAATGGA-CA-AATTATCATCCAGGGAA
* *
2438374 AGTTCATAATGAGAAGTACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTAATC----GAA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
*
2438439 AACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGA
61 AACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGA
** *
2438504 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACTTTTTGC-TAAATT
126 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTAAATT
*
2438568 ACATTACAAAAGGAAACAAATTATCATCCCCAGTGGAAA
191 ACATTAC-AATGG--ACAAATTATCAT--CCAG-GG-AA
2438607 AGTTCATAATGAGAAGAACTAATC
1 AGTTCATAATGAGAAGAACTAATC
2438631 CCAAAGAAGA
Statistics
Matches: 427, Mismatches: 32, Indels: 43
0.85 0.06 0.09
Matches are distributed among these distances:
223 4 0.01
224 2 0.00
225 12 0.03
226 181 0.42
227 196 0.46
228 1 0.00
229 1 0.00
230 3 0.01
231 4 0.01
232 1 0.00
233 22 0.05
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (222 bp):
AGTTCATAATGAGAAGAACTAATCGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCT
TTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCA
TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTAAATTACATT
ACAATGGACAAATTATCATCCAGGGAA
Found at i:2438801 original size:3 final size:3
Alignment explanation
Indices: 2438783--2438835 Score: 61
Period size: 3 Copynumber: 17.0 Consensus size: 3
2438773 TTGGTTTTTT
* * *
2438783 TTA TTT TTA TTT TTA TTA TTTA TTA TTA TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
2438829 TTTA TTA
1 -TTA TTA
2438836 CAGGCCCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
3 36 0.86
4 6 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:2438817 original size:25 final size:27
Alignment explanation
Indices: 2438783--2438835 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
2438773 TTGGTTTTTT
*
2438783 TTATTTTTATT-T-TTATTATTTATTA
1 TTATTATTATTATATTATTATTTATTA
2438808 TTATTATTATTAATATTATTATTTATTA
1 TTATTATTATT-ATATTATTATTTATTA
2438836 CAGGCCCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 10 0.42
27 1 0.04
28 13 0.54
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (27 bp):
TTATTATTATTATATTATTATTTATTA
Found at i:2442204 original size:13 final size:13
Alignment explanation
Indices: 2442186--2442211 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2442176 AAAGGGACGC
2442186 CATTAAGTTATTA
1 CATTAAGTTATTA
2442199 CATTAAGTTATTA
1 CATTAAGTTATTA
2442212 TACCTACGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
CATTAAGTTATTA
Found at i:2444030 original size:65 final size:64
Alignment explanation
Indices: 2443955--2444090 Score: 175
Period size: 65 Copynumber: 2.1 Consensus size: 64
2443945 ACACTAATTA
* * * *
2443955 CATTCGATGTTTCAA-AAGAGCCAGGAGTGTATCGATGCATGGTCTGTGCATCAATACATAAAAT
1 CATTCGATGTTTCAATAA-AACCAGGAGTGCATCGATGCACGG-CTGTGCATCAATACACAAAAT
2444019 G
64 G
* ** *
2444020 CATTCGATGTTTCAATAAAATCAGGAGTGCATCGATGCACGGCTGTGCATCGGTACACAAAATT
1 CATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCACGGCTGTGCATCAATACACAAAATG
2444084 CATTCGA
1 CATTCGA
2444091 ATTAGGGAGT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
64 25 0.40
65 35 0.56
66 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (64 bp):
CATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCACGGCTGTGCATCAATACACAAAATG
Found at i:2446215 original size:14 final size:13
Alignment explanation
Indices: 2446181--2446218 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
2446171 TAATTGGCAA
2446181 AATTTTG-AAAAC
1 AATTTTGAAAAAC
*
2446193 TATTTTGAAAAAC
1 AATTTTGAAAAAC
2446206 AATGTTTGAAAAA
1 AAT-TTTGAAAAA
2446219 TCATAGTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 6 0.27
13 7 0.32
14 9 0.41
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (13 bp):
AATTTTGAAAAAC
Found at i:2451723 original size:902 final size:902
Alignment explanation
Indices: 2449980--2451789 Score: 3476
Period size: 902 Copynumber: 2.0 Consensus size: 902
2449970 TAAAACATTT
*
2449980 TTAATTTGTATGGAAGAGGTATTACCTATAGTATCTATACCTTCAACGTGACCTTTTGAATTATC
1 TTAATTTGTATGGAAGAGGTATTACCTATAGTACCTATACCTTCAACGTGACCTTTTGAATTATC
* *
2450045 ACCAAAAGTCACCTCTCCTCTATTTTTTTCATTAAGCTTTATGAACCGGCTCTTGTCTCCGGTCA
66 ACCAAAAGTCACCTCTCCTCCATTTTTTTCATTAAGCTCTATGAACCGGCTCTTGTCTCCGGTCA
2450110 TATGTCTTGAGCATCCACTATCAAGATACCATGAGTTTGAATTTGTTTCCCGTTCCTTGTAGCAA
131 TATGTCTTGAGCATCCACTATCAAGATACCATGAGTTTGAATTTGTTTCCCGTTCCTTGTAGCAA
2450175 TGCTCCTTTCCCTACAAACATAGATTAATTTTTGATTTTTGGTACCCAAATTCTTTTGGGTCCAT
196 TGCTCCTTTCCCTACAAACATAGATTAATTTTTGATTTTTGGTACCCAAATTCTTTTGGGTCCAT
2450240 ATTCATTAGTCTCCAAAATTCTAGTCCCTTTGGGTATCCATTTGTGTAGGATATCCTTATCTTTA
261 ATTCATTAGTCTCCAAAATTCTAGTCCCTTTGGGTATCCATTTGTGTAGGATATCCTTATCTTTA
2450305 GTAGTAATGTGTTCTTTAGGAACCCATATACTTCTAACGATTTTTCCATTAGAGATTCTTCGGGG
326 GTAGTAATGTGTTCTTTAGGAACCCATATACTTCTAACGATTTTTCCATTAGAGATTCTTCGGGG
2450370 ACCTATATGATTGTAGTTTTTAAAACTTTTTCTAACAAAGTTGGATTTTGAACTTTCTCCATTTT
391 ACCTATATGATTGTAGTTTTTAAAACTTTTTCTAACAAAGTTGGATTTTGAACTTTCTCCATTTT
2450435 CAAAACTTTTTGTTCCAACTTTATTAAAAGATGCTTTAAGATCATCAATTTCTTTTTGATGATCA
456 CAAAACTTTTTGTTCCAACTTTATTAAAAGATGCTTTAAGATCATCAATTTCTTTTTGATGATCA
*
2450500 TCGTTGACCTTTGAAAGTAAATTATGCAAATCAGAAAATTTCTTTTCAAACTCATCTAGTTTGAT
521 TCGTTGACCTTTAAAAGTAAATTATGCAAATCAGAAAATTTCTTTTCAAACTCATCTAGTTTGAT
*
2450565 TTGTAAATCTTTGATTTTACTTTTAAGATCATTGTTGGTCTTGGATATGAGATTATTTTCGTTTT
586 TTGTAAATCTTTGATTTTACTTTTAAGATCATTGTTGGTCTTGGATATGAGATTATTTTCGTTAT
*
2450630 TCAATTTTGAAATATCATTTTTGTATTTTAAAAATAATTTCTCATCATCCAAAGCCAACCCAATA
651 TAAATTTTGAAATATCATTTTTGTATTTTAAAAATAATTTCTCATCATCCAAAGCCAACCCAATA
2450695 TATTCCTCTAACATCTTATCAAAAGAATAATCTTCGAAATTAAATGAGCTAGAGGTTACCTGAGA
716 TATTCCTCTAACATCTTATCAAAAGAATAATCTTCGAAATTAAATGAGCTAGAGGTTACCTGAGA
2450760 ATCCTCCTCGAAAGCCATCAAGCACAAGTTTGCTACTTCTTGTTCATCTTCATCGGAAGCTTCAT
781 ATCCTCCTCGAAAGCCATCAAGCACAAGTTTGCTACTTCTTGTTCATCTTCATCGGAAGCTTCAT
*
2450825 CATCGCTCCATGTAGCCACGTGTGCCTTATGCTTCTTCTTGGATTGACCTTTTTTCC
846 CATCGCTCCATGTAGCCACGTGTGCCTTATGCTTCTTATTGGATTGACCTTTTTTCC
*
2450882 TTAATTTGTATGGAAGAGGTATTACCTATAGTACCTATACCTTCAATGTGACCTTTTGAATTATC
1 TTAATTTGTATGGAAGAGGTATTACCTATAGTACCTATACCTTCAACGTGACCTTTTGAATTATC
*
2450947 ACCAAAAGTCACCTCTCCTCCATTTTTTTTATTAAGCTCTATGAACCGGCTCTTGTCTCCGGTCA
66 ACCAAAAGTCACCTCTCCTCCATTTTTTTCATTAAGCTCTATGAACCGGCTCTTGTCTCCGGTCA
2451012 TATGTCTTGAGCATCCACTATCAAGATACCATGAGTTTGAATTTGTTTCCCGTTCCTTGTAGCAA
131 TATGTCTTGAGCATCCACTATCAAGATACCATGAGTTTGAATTTGTTTCCCGTTCCTTGTAGCAA
*
2451077 TGCTTCTTTCCCTACAAACATAGATTAATTTTTGATTTTTGGTACCCAAATTCTTTTGGGTCCAT
196 TGCTCCTTTCCCTACAAACATAGATTAATTTTTGATTTTTGGTACCCAAATTCTTTTGGGTCCAT
2451142 ATTCATTAGTCTCCAAAATTCTAGTCCCTTTGGGTATCCATTTGTGTAGGATATCCTTATCTTTA
261 ATTCATTAGTCTCCAAAATTCTAGTCCCTTTGGGTATCCATTTGTGTAGGATATCCTTATCTTTA
2451207 GTAGTAATGTGTTCTTTAGGAACCCATATACTTCTAACGATTTTTCCATTAGAGATTCTTCGGGG
326 GTAGTAATGTGTTCTTTAGGAACCCATATACTTCTAACGATTTTTCCATTAGAGATTCTTCGGGG
2451272 ACCTATATGATTGTAGTTTTTAAAACTTTTTCTAACAAAGTTGGATTTTGAACTTTCTCCATTTT
391 ACCTATATGATTGTAGTTTTTAAAACTTTTTCTAACAAAGTTGGATTTTGAACTTTCTCCATTTT
*
2451337 CAAAACTTTTTGTTCCAACTTTATTATAAGATGCTTTAAGATCATCAATTTCTTTTTGATGATCA
456 CAAAACTTTTTGTTCCAACTTTATTAAAAGATGCTTTAAGATCATCAATTTCTTTTTGATGATCA
*
2451402 TCGTTGACCTTTAAAAGTAAATTATGCAAATCAGAAATTTTCTTTTCAAACTCATCTAGTTTGAT
521 TCGTTGACCTTTAAAAGTAAATTATGCAAATCAGAAAATTTCTTTTCAAACTCATCTAGTTTGAT
* *
2451467 TTGTAAATTTTTTATTTTACTTTTAAGATCATTGTTGGTCTTGGATATGAGATTATTTTCGTTAT
586 TTGTAAATCTTTGATTTTACTTTTAAGATCATTGTTGGTCTTGGATATGAGATTATTTTCGTTAT
2451532 TAAATTTTGAAATATCATTTTTGTATTTTAAAAATAATTTCTCATCATCCAAAGCCAACCCAATA
651 TAAATTTTGAAATATCATTTTTGTATTTTAAAAATAATTTCTCATCATCCAAAGCCAACCCAATA
2451597 TATTCCTCTAACATCTTATCAAAAGAATAATCTTCGAAATTAAATGAGCTAGAGGTTACCTGAGA
716 TATTCCTCTAACATCTTATCAAAAGAATAATCTTCGAAATTAAATGAGCTAGAGGTTACCTGAGA
*
2451662 ATCCTCTTCGAAAGCCATCAAGCACAAGTTTGCTACTTCTTGTTCATCTTCATCGGAAGCTTCAT
781 ATCCTCCTCGAAAGCCATCAAGCACAAGTTTGCTACTTCTTGTTCATCTTCATCGGAAGCTTCAT
*
2451727 CATCGCTCCATGTAGCCACGTGTTCCTTATGCTTCTTATTGGATTGACCTTTTTTCC
846 CATCGCTCCATGTAGCCACGTGTGCCTTATGCTTCTTATTGGATTGACCTTTTTTCC
2451784 TTAATT
1 TTAATT
2451790 GTGGGCAATC
Statistics
Matches: 892, Mismatches: 16, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
902 892 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (902 bp):
TTAATTTGTATGGAAGAGGTATTACCTATAGTACCTATACCTTCAACGTGACCTTTTGAATTATC
ACCAAAAGTCACCTCTCCTCCATTTTTTTCATTAAGCTCTATGAACCGGCTCTTGTCTCCGGTCA
TATGTCTTGAGCATCCACTATCAAGATACCATGAGTTTGAATTTGTTTCCCGTTCCTTGTAGCAA
TGCTCCTTTCCCTACAAACATAGATTAATTTTTGATTTTTGGTACCCAAATTCTTTTGGGTCCAT
ATTCATTAGTCTCCAAAATTCTAGTCCCTTTGGGTATCCATTTGTGTAGGATATCCTTATCTTTA
GTAGTAATGTGTTCTTTAGGAACCCATATACTTCTAACGATTTTTCCATTAGAGATTCTTCGGGG
ACCTATATGATTGTAGTTTTTAAAACTTTTTCTAACAAAGTTGGATTTTGAACTTTCTCCATTTT
CAAAACTTTTTGTTCCAACTTTATTAAAAGATGCTTTAAGATCATCAATTTCTTTTTGATGATCA
TCGTTGACCTTTAAAAGTAAATTATGCAAATCAGAAAATTTCTTTTCAAACTCATCTAGTTTGAT
TTGTAAATCTTTGATTTTACTTTTAAGATCATTGTTGGTCTTGGATATGAGATTATTTTCGTTAT
TAAATTTTGAAATATCATTTTTGTATTTTAAAAATAATTTCTCATCATCCAAAGCCAACCCAATA
TATTCCTCTAACATCTTATCAAAAGAATAATCTTCGAAATTAAATGAGCTAGAGGTTACCTGAGA
ATCCTCCTCGAAAGCCATCAAGCACAAGTTTGCTACTTCTTGTTCATCTTCATCGGAAGCTTCAT
CATCGCTCCATGTAGCCACGTGTGCCTTATGCTTCTTATTGGATTGACCTTTTTTCC
Found at i:2468394 original size:20 final size:20
Alignment explanation
Indices: 2468369--2468437 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
2468359 CAAAGTGGGT
* *
2468369 AGTATCGATACTTCACTTGC
1 AGTATCGATACTCCACTTGA
2468389 AGTATCGATACTCCACTTGTA
1 AGTATCGATACTCCACTTG-A
2468410 A-TATCGATACTCCACTTGA
1 AGTATCGATACTCCACTTGA
2468429 AGTATCGAT
1 AGTATCGAT
2468438 TCCCCAGGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.04
20 42 0.93
21 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.33
Consensus pattern (20 bp):
AGTATCGATACTCCACTTGA
Found at i:2470305 original size:60 final size:60
Alignment explanation
Indices: 2470221--2470339 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
2470211 GCCTCTGTCG
* * * * *
2470221 TATGAGTACGAGTCGCCACCACCTCCTCTGTACGTGTATAGCTCTCCTCCTCCGCCTCCA
1 TATGAGTACAAGTCGCCACCACCTCCTCCGTACGTGTACAACTCTCCTCCACCGCCTCCA
* *
2470281 TATGAGTACAAGTCTCCACCACCTCCTCCGTACGTGTACAACTCTCCTCCACCTCCTCC
1 TATGAGTACAAGTCGCCACCACCTCCTCCGTACGTGTACAACTCTCCTCCACCGCCTCC
2470340 TCCTCCTTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.18, C:0.42, G:0.13, T:0.26
Consensus pattern (60 bp):
TATGAGTACAAGTCGCCACCACCTCCTCCGTACGTGTACAACTCTCCTCCACCGCCTCCA
Found at i:2470309 original size:30 final size:30
Alignment explanation
Indices: 2470266--2470842 Score: 464
Period size: 30 Copynumber: 19.0 Consensus size: 30
2470256 GTATAGCTCT
* * *
2470266 CCTCCTCCGCCTCCATATGAGTACAAGTCT
1 CCTCCTCCTCCTCCATATGTGTACAAGTCA
* * * * *
2470296 CCACCACCTCCTCCGTACGTGTACAACTCTCCTCCA
1 CCTCCTCCTCCTCCATATGTGTACAA-----GT-CA
* * * *
2470332 CCTCCTCCTCCTCCTTATGTTTATAAATCA
1 CCTCCTCCTCCTCCATATGTGTACAAGTCA
* **
2470362 CCTCCTCCACCTCCATATAAGTACAAGTCA
1 CCTCCTCCTCCTCCATATGTGTACAAGTCA
* * * * *
2470392 TCTCCACCTCCTCCGTATGTTTACAAATCA
1 CCTCCTCCTCCTCCATATGTGTACAAGTCA
* * * *
2470422 CCTCCTCCCCCTCCATACGTCTACAAGTCT
1 CCTCCTCCTCCTCCATATGTGTACAAGTCA
*
2470452 CCTCCTCCTCCTCCATATGAGTACAAGTCA
1 CCTCCTCCTCCTCCATATGTGTACAAGTCA
2470482 CCTCCTCCTCCTCCATATGTGTACAAGTCA
1 CCTCCTCCTCCTCCATATGTGTACAAGTCA
* * *
2470512 -TTGCCT-CTACCTCCATACGTGTACAAGTCT
1 CCT-CCTCCT-CCTCCATATGTGTACAAGTCA
*
2470542 CCTCCTCTTCCTCCATATGT-TCACAAGTCA
1 CCTCCTCCTCCTCCATATGTGT-ACAAGTCA
* *
2470572 CCTCCT-CTACCACCATATGTCTACAAGTCA
1 CCTCCTCCT-CCTCCATATGTGTACAAGTCA
* * * * *
2470602 CCTCCACCCCCTCCATACGTCTACAAGTCT
1 CCTCCTCCTCCTCCATATGTGTACAAGTCA
** * *
2470632 CCTCCTCCAACTCCATATGAGTATAAGTCA
1 CCTCCTCCTCCTCCATATGTGTACAAGTCA
* * *
2470662 CCTCCTCCTCCTCCTTATGTTTATGAA-TCA
1 CCTCCTCCTCCTCCATATGTGTA-CAAGTCA
* ** *
2470692 CCTCCTCCCCCTCCATACATGTACAAATCA
1 CCTCCTCCTCCTCCATATGTGTACAAGTCA
* *
2470722 CCGCCT-CTACCTCCATATGTGTACAAGTCT
1 CCTCCTCCT-CCTCCATATGTGTACAAGTCA
** *
2470752 CCTCCTCCTCCTCCATATAAGTACAAATCA
1 CCTCCTCCTCCTCCATATGTGTACAAGTCA
* * * *
2470782 CCACCTCCACCACCATATGTCTACAAGTCA
1 CCTCCTCCTCCTCCATATGTGTACAAGTCA
* * * *
2470812 CCTTCTCCACCTCCATATGAGTACAAATCA
1 CCTCCTCCTCCTCCATATGTGTACAAGTCA
2470842 C
1 C
2470843 TACCACATGT
Statistics
Matches: 427, Mismatches: 102, Indels: 36
0.76 0.18 0.06
Matches are distributed among these distances:
29 8 0.02
30 388 0.91
31 9 0.02
35 1 0.00
36 21 0.05
ACGTcount: A:0.23, C:0.41, G:0.08, T:0.28
Consensus pattern (30 bp):
CCTCCTCCTCCTCCATATGTGTACAAGTCA
Found at i:2477482 original size:22 final size:21
Alignment explanation
Indices: 2477448--2477490 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
2477438 GGACTTCAGC
2477448 GATGGCAACGGTGAGACGAAAA
1 GATGGCAACGGTG-GACGAAAA
** *
2477470 GATGGCAGGGGTGGCCGAAAA
1 GATGGCAACGGTGGACGAAAA
2477491 TCGATGTGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.35, C:0.14, G:0.42, T:0.09
Consensus pattern (21 bp):
GATGGCAACGGTGGACGAAAA
Found at i:2490285 original size:126 final size:126
Alignment explanation
Indices: 2490053--2490287 Score: 287
Period size: 126 Copynumber: 1.9 Consensus size: 126
2490043 TTTAACGACC
* * * * * *
2490053 TATCCAAATGCGTCGAAGGACCCTCGAAAGCATTCACCACGTGAGCAGCGTCCAATGTCACTACT
1 TATCCAAAGGCGTCGAAGGACCCTCAAAAGCATTAACCACGTGAGCAGCCTCCAAAGCCACTACT
* * * * *
2490118 GAACCCTCATGCATATTATTAATTTCCTGCACCATGATTGTATTTCCCTTGATAACCAACT
66 GAACCCGCATGCATAATATTAATTTCATCCACCATCATTGTATTTCCCTTGATAACCAACT
* *
2490179 TATCCAAAGGCGT-GAAAGGTCCCTCAAAAGCATTAACCTCGTGAGCAGCCTCCAAAGCCACTAC
1 TATCCAAAGGCGTCG-AAGGACCCTCAAAAGCATTAACCACGTGAGCAGCCTCCAAAGCCACTAC
* *
2490243 TGAGCCCGCATGTATAATATTTAA-TTCATCCACCA-CATTTGTATT
65 TGAACCCGCATGCATAATA-TTAATTTCATCCACCATCA-TTGTATT
2490288 ACCGCTCCTC
Statistics
Matches: 91, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
125 2 0.02
126 85 0.93
127 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (126 bp):
TATCCAAAGGCGTCGAAGGACCCTCAAAAGCATTAACCACGTGAGCAGCCTCCAAAGCCACTACT
GAACCCGCATGCATAATATTAATTTCATCCACCATCATTGTATTTCCCTTGATAACCAACT
Found at i:2501896 original size:15 final size:16
Alignment explanation
Indices: 2501871--2501900 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2501861 AAGTTAATCT
2501871 TATTGTTATAAAATTA
1 TATTGTTATAAAATTA
2501887 TATT-TTATAAAATT
1 TATTGTTATAAAATT
2501901 TTAAATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TATTGTTATAAAATTA
Found at i:2507523 original size:9 final size:9
Alignment explanation
Indices: 2507511--2507560 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
2507501 GCTGTCATTA
2507511 TCGTCATCG
1 TCGTCATCG
* *
2507520 TCGTCACCA
1 TCGTCATCG
2507529 TCGTCATCG
1 TCGTCATCG
2507538 TCGTCATCG
1 TCGTCATCG
*
2507547 TCGTCGTCG
1 TCGTCATCG
2507556 TCGTC
1 TCGTC
2507561 CTGAGCAGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.10, C:0.36, G:0.22, T:0.32
Consensus pattern (9 bp):
TCGTCATCG
Found at i:2509656 original size:106 final size:110
Alignment explanation
Indices: 2509440--2509656 Score: 361
Period size: 106 Copynumber: 2.0 Consensus size: 110
2509430 ATTACAAAAA
*
2509440 TTAACTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTACTACTAATAATTTAAATTA
1 TTAACTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATACTACTAATAATTTAAATTA
* *
2509505 GATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTT-AAATGTTACCGTATCAGCAAAGTGTAGAGATAT
*
2509551 TTAATTCTTAATCTAATAATCAT-CATT-AATAAATCAACTAAATA-TACTAATAATTTAAATTA
1 TTAACTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATACTACTAATAATTTAAATTA
2509613 AATTAAAACGTT-AATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
2509657 ATGATTTTCA
Statistics
Matches: 102, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
106 31 0.30
108 29 0.28
109 16 0.16
110 4 0.04
111 22 0.22
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.35
Consensus pattern (110 bp):
TTAACTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATACTACTAATAATTTAAATTA
AATTAAAACGTTAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:2509991 original size:50 final size:50
Alignment explanation
Indices: 2509937--2510044 Score: 164
Period size: 50 Copynumber: 2.2 Consensus size: 50
2509927 AGATACCCAG
* *
2509937 GTATAGCGC-GGATCAGGGGGCTCGCTATACCCACGTGGCGCCATATCACC
1 GTATAGCGCGGGA-CAGGGGGCACGCTATACCCACGTGGCGCCAAATCACC
* *
2509987 GTATATCGCGGGACAGGGGGCACGCTATACCCACGTGGCGCCAAATCAGC
1 GTATAGCGCGGGACAGGGGGCACGCTATACCCACGTGGCGCCAAATCACC
2510037 GTATAGCG
1 GTATAGCG
2510045 TGATTCAGGG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
50 49 0.94
51 3 0.06
ACGTcount: A:0.22, C:0.30, G:0.31, T:0.17
Consensus pattern (50 bp):
GTATAGCGCGGGACAGGGGGCACGCTATACCCACGTGGCGCCAAATCACC
Found at i:2510054 original size:50 final size:50
Alignment explanation
Indices: 2509937--2510062 Score: 159
Period size: 50 Copynumber: 2.5 Consensus size: 50
2509927 AGATACCCAG
* *
2509937 GTATA-GCGCGGATCAGGGGGCTCGCTATACCCACGTGGCGCCATATCACC
1 GTATACGCG-GGATCAGGGGGCACGCTATACCCACGTGGCGCCAAATCACC
*
2509987 GTATATCGCGGGA-CAGGGGGCACGCTATACCCACGTGGCGCCAAATCAGC
1 GTATA-CGCGGGATCAGGGGGCACGCTATACCCACGTGGCGCCAAATCACC
* *
2510037 GTATA-GCGTGATTCAGGGGACACGCT
1 GTATACGCGGGA-TCAGGGGGCACGCT
2510063 TTACTGCTAC
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
48 5 0.07
50 56 0.84
51 3 0.04
52 3 0.04
ACGTcount: A:0.22, C:0.29, G:0.32, T:0.17
Consensus pattern (50 bp):
GTATACGCGGGATCAGGGGGCACGCTATACCCACGTGGCGCCAAATCACC
Found at i:2515680 original size:259 final size:252
Alignment explanation
Indices: 2515380--2515842 Score: 659
Period size: 259 Copynumber: 1.8 Consensus size: 252
2515370 ATAAAATTTC
* * *
2515380 ACCCGACCCGACCCGAAATAGCAAAAGAATATTTTTATTCAAT-AAAACAGTTACTTAATCGGAA
1 ACCCGACCCGACCCAAAATAACAAAAGAATATTTTTATTCAATAAAAACAGTGACTTAATCGGAA
*
2515444 AAAATATATATAG-GG-GTATTA-TGTAATTATTTCTAAATATATAAAGTAAAATTATATACTTT
66 AAAA-ATATATAGAGGAGTATTATTGTAATTATTCCTAAATATATAAAGTAAAA-T-TATA-TTT
* *
2515506 TTGGGTCGGGTTGGATATTTTCACCCTAAA-CCGAACTCGCGGCCCGACCTGAATATCAAATTTA
127 TTGGGTCGGG-T--AT-TTTTCACCCTAAACCCGAACT--CGACCCGACC-GAATATCAAACTT-
*
2515570 AAAAAAACCGACCCTACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATTAATTAAAG
184 AAAAAAACCGACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATTAATTAAAG
2515635 ACCG
249 ACCG
* *
2515639 ACCCGACCCGACCCAAAATAATAAAA-AATTATTTTTATTCAATAAAAACAGTGACTTAATTGGA
1 ACCCGACCCGACCCAAAATAACAAAAGAA-TATTTTTATTCAATAAAAACAGTGACTTAATCGGA
*
2515703 AAAAAATATATAGAGGAGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATTTTTG
65 AAAAAATATATAGAGGAGTATTATTGTAATTATTCCTAAATATATAAAGTAAAATTATATTTTTG
* *
2515768 GGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCGAATATCACACTTAAAAAACCCGA
130 GGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCGAATATCAAACTTAAAAAAACCGA
2515833 CCCGACCCGA
195 CCCGACCCGA
2515843 ATATATGAAT
Statistics
Matches: 186, Mismatches: 12, Indels: 19
0.86 0.06 0.09
Matches are distributed among these distances:
252 19 0.10
253 11 0.06
254 9 0.05
255 13 0.07
256 9 0.05
258 3 0.02
259 58 0.31
260 29 0.16
261 7 0.04
262 28 0.15
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (252 bp):
ACCCGACCCGACCCAAAATAACAAAAGAATATTTTTATTCAATAAAAACAGTGACTTAATCGGAA
AAAAATATATAGAGGAGTATTATTGTAATTATTCCTAAATATATAAAGTAAAATTATATTTTTGG
GTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCGAATATCAAACTTAAAAAAACCGAC
CCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATTAATTAAAGACCG
Found at i:2516611 original size:13 final size:13
Alignment explanation
Indices: 2516590--2516619 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2516580 CTGTTAACCT
*
2516590 TTGACTTTGACCA
1 TTGAATTTGACCA
2516603 TTGAATTTGACCA
1 TTGAATTTGACCA
2516616 TTGA
1 TTGA
2516620 CTTTTTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (13 bp):
TTGAATTTGACCA
Found at i:2517178 original size:30 final size:29
Alignment explanation
Indices: 2517120--2517180 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 29
2517110 GGGACTTTCG
*
2517120 TTCCCGTTCTGACATCTGTATATGATAAAT
1 TTCCCGTTCTGACATC-GTACATGATAAAT
2517150 TTCCCGTTCTGACATC-TACATGGAATAAAT
1 TTCCCGTTCTGACATCGTACAT-G-ATAAAT
2517180 T
1 T
2517181 CTTCTACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 4 0.14
29 1 0.04
30 23 0.82
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (29 bp):
TTCCCGTTCTGACATCGTACATGATAAAT
Found at i:2519564 original size:23 final size:21
Alignment explanation
Indices: 2519510--2519565 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
2519500 TCCTTAAGGA
* *
2519510 GTGGTCTTTCGGGACATATAT
1 GTGGTCATTCGGGACATATAC
*
2519531 GTGGTCATTCGGGACATTTCGAC
1 GTGGTCATTCGGGACATAT--AC
*
2519554 GTGGTCCTTCGG
1 GTGGTCATTCGG
2519566 ACAATCTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 17 0.59
23 12 0.41
ACGTcount: A:0.14, C:0.20, G:0.32, T:0.34
Consensus pattern (21 bp):
GTGGTCATTCGGGACATATAC
Found at i:2522334 original size:20 final size:22
Alignment explanation
Indices: 2522291--2522331 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
2522281 TACTAGTTAA
2522291 ATTTGAGGAACTCTTTAAAAAT
1 ATTTGAGGAACTCTTTAAAAAT
2522313 ATTTG-GGAACTCTTTAAAA
1 ATTTGAGGAACTCTTTAAAA
2522332 TATGCTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
ATTTGAGGAACTCTTTAAAAAT
Found at i:2522910 original size:33 final size:33
Alignment explanation
Indices: 2522861--2522923 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
2522851 GGGTTGATCA
* *
2522861 CTGACCCATTTGACCGACCTGTTTACCGTTGAC
1 CTGACCCATTTGACCGACCCGTTGACCGTTGAC
* *
2522894 CTGACCTATTTTACCGACCCGTTGACCGTT
1 CTGACCCATTTGACCGACCCGTTGACCGTT
2522924 TATCATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.32
Consensus pattern (33 bp):
CTGACCCATTTGACCGACCCGTTGACCGTTGAC
Found at i:2523581 original size:29 final size:29
Alignment explanation
Indices: 2523549--2523719 Score: 144
Period size: 30 Copynumber: 5.8 Consensus size: 29
2523539 GCATAATCCT
* *
2523549 CGTCCTGATTCTGTATGGGATTTATTCTC
1 CGTCCTGAATCTGTATGGGATTTATTCCC
* * *
2523578 CGTCCTGATTCTGCATGGGATTTATTCTC
1 CGTCCTGAATCTGTATGGGATTTATTCCC
* * * *
2523607 CGTCCTGATTCTGCATGGGACCTCATTCCC
1 CGTCCTGAATCTGTATGGGA-TTTATTCCC
* ** *
2523637 CGTTCTGACATCTGTATGGGATAAACTCCC
1 CGTCCTGA-ATCTGTATGGGATTTATTCCC
* **
2523667 CGTTCTGACATCTGTATGGGATAAATTCCC
1 CGTCCTGA-ATCTGTATGGGATTTATTCCC
* *
2523697 CGTTCTGACATCTGTATGAGATT
1 CGTCCTGA-ATCTGTATGGGATT
2523720 ATATCTCCGT
Statistics
Matches: 126, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
29 48 0.38
30 68 0.54
31 10 0.08
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (29 bp):
CGTCCTGAATCTGTATGGGATTTATTCCC
Found at i:2523668 original size:30 final size:30
Alignment explanation
Indices: 2523633--2523714 Score: 155
Period size: 30 Copynumber: 2.7 Consensus size: 30
2523623 GGGACCTCAT
2523633 TCCCCGTTCTGACATCTGTATGGGATAAAC
1 TCCCCGTTCTGACATCTGTATGGGATAAAC
*
2523663 TCCCCGTTCTGACATCTGTATGGGATAAAT
1 TCCCCGTTCTGACATCTGTATGGGATAAAC
2523693 TCCCCGTTCTGACATCTGTATG
1 TCCCCGTTCTGACATCTGTATG
2523715 AGATTATATC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.33
Consensus pattern (30 bp):
TCCCCGTTCTGACATCTGTATGGGATAAAC
Found at i:2526104 original size:13 final size:13
Alignment explanation
Indices: 2526068--2526110 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2526058 ATCGAAAACA
*
2526068 TTTCTTCCTTGTT
1 TTTCTTCTTTGTT
*
2526081 CTTTGTTCTTTGTT
1 -TTTCTTCTTTGTT
*
2526095 TTTCTTCTTTCTT
1 TTTCTTCTTTGTT
2526108 TTT
1 TTT
2526111 ATAAAATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.00, C:0.19, G:0.07, T:0.74
Consensus pattern (13 bp):
TTTCTTCTTTGTT
Found at i:2529279 original size:21 final size:19
Alignment explanation
Indices: 2529250--2529293 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
2529240 ATTTATTTTA
2529250 TTTTTATTTTAGGAAT-TATC
1 TTTTTATTTTA--AATGTATC
2529270 TTTTTAATTTTAAATGTATC
1 TTTTT-ATTTTAAATGTATC
2529290 TTTT
1 TTTT
2529294 AGGATTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.14
20 13 0.59
21 6 0.27
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.64
Consensus pattern (19 bp):
TTTTTATTTTAAATGTATC
Found at i:2536654 original size:13 final size:13
Alignment explanation
Indices: 2536636--2536660 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2536626 ATATGGAGGG
2536636 TTATCTCTATCTT
1 TTATCTCTATCTT
2536649 TTATCTCTATCT
1 TTATCTCTATCT
2536661 ATAGGATAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATCTCTATCTT
Found at i:2540976 original size:29 final size:29
Alignment explanation
Indices: 2540921--2540976 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
2540911 ATCACTTAAT
* *
2540921 CATTTTTAAAGTACAAGTAATATGTTAGA
1 CATTTTTAAAATACAAGTAATACGTTAGA
* * *
2540950 CATTTTTAAAATATAGGTACTACGTTA
1 CATTTTTAAAATACAAGTAATACGTTA
2540977 ATAAATTATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (29 bp):
CATTTTTAAAATACAAGTAATACGTTAGA
Found at i:2543899 original size:23 final size:23
Alignment explanation
Indices: 2543872--2543917 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2543862 AAAGGAGGGA
2543872 GACAAGGCATAAAACACTTAAGG
1 GACAAGGCATAAAACACTTAAGG
*
2543895 GACAAGGCTTAAAACACTTAAGG
1 GACAAGGCATAAAACACTTAAGG
2543918 TTCCAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (23 bp):
GACAAGGCATAAAACACTTAAGG
Found at i:2551875 original size:24 final size:24
Alignment explanation
Indices: 2551847--2551892 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2551837 AAAATATGAG
2551847 AATCATGCCACAAGAGT-AGAGAGA
1 AATCATGCCACAAG-GTCAGAGAGA
*
2551871 AATCATGTCACAAGGTCAGAGA
1 AATCATGCCACAAGGTCAGAGA
2551893 TGCTTATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.15
Consensus pattern (24 bp):
AATCATGCCACAAGGTCAGAGAGA
Found at i:2553305 original size:15 final size:14
Alignment explanation
Indices: 2553279--2553332 Score: 53
Period size: 15 Copynumber: 4.1 Consensus size: 14
2553269 AATAAGTTAA
2553279 TAATAAAATATATT
1 TAATAAAATATATT
*
2553293 TTATAATAATATATT
1 TAATAA-AATATATT
*
2553308 TAAT-AAGT-TA-T
1 TAATAAAATATATT
2553319 T-ATAAAATATATT
1 TAATAAAATATATT
2553332 T
1 T
2553333 TTAAGTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
10 2 0.06
11 5 0.16
12 4 0.12
13 4 0.12
14 6 0.19
15 11 0.34
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
TAATAAAATATATT
Found at i:2553321 original size:25 final size:25
Alignment explanation
Indices: 2553293--2553355 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 25
2553283 AAAATATATT
2553293 TTATAATAATATATTTAATAAGTT-A
1 TTATAATAATATATTT-ATAAGTTAA
*
2553318 TTATAA-AATATATTTTTAAGTTAA
1 TTATAATAATATATTTATAAGTTAA
2553342 TATATATATAATAT
1 T-TATA-ATAATAT
2553356 TATGAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 6 0.18
24 11 0.33
25 10 0.30
26 1 0.03
27 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (25 bp):
TTATAATAATATATTTATAAGTTAA
Found at i:2553343 original size:40 final size:40
Alignment explanation
Indices: 2553269--2553346 Score: 115
Period size: 39 Copynumber: 1.9 Consensus size: 40
2553259 ATTTTTTTAA
2553269 AATAAGTTAATAATAAAATATATTTTATAATAATATATTT
1 AATAAGTTAATAATAAAATATATTTTATAATAATATATTT
*
2553309 AATAAGTT-ATTATAAAATATATTTT-TAAGTTAATATAT
1 AATAAGTTAATAATAAAATATATTTTATAA--TAATATAT
2553347 ATATAATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
38 3 0.09
39 16 0.46
40 16 0.46
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (40 bp):
AATAAGTTAATAATAAAATATATTTTATAATAATATATTT
Found at i:2553345 original size:23 final size:25
Alignment explanation
Indices: 2553294--2553345 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 25
2553284 AAATATATTT
*
2553294 TATAATAATATATTTAATAAGTTAT
1 TATAATAATATATTTAATAAGTTAA
*
2553319 TATAA-AATATATTT-TTAAGTTAA
1 TATAATAATATATTTAATAAGTTAA
2553342 TATA
1 TATA
2553346 TATATAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.44
24 9 0.36
25 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (25 bp):
TATAATAATATATTTAATAAGTTAA
Found at i:2553356 original size:25 final size:25
Alignment explanation
Indices: 2553294--2553356 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 25
2553284 AAATATATTT
*
2553294 TATAATAATATATTTAATAAGTTATTA
1 TATAATAATAT-TTT-ATAAGTTAATA
*
2553321 TAAAAT-ATATTTT-TAAGTTAATA
1 TATAATAATATTTTATAAGTTAATA
2553344 TATATATAATATT
1 TATA-ATAATATT
2553357 ATGAATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 12 0.39
24 2 0.06
25 8 0.26
26 4 0.13
27 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (25 bp):
TATAATAATATTTTATAAGTTAATA
Found at i:2553665 original size:31 final size:31
Alignment explanation
Indices: 2553594--2553669 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
2553584 TTAACTCAGG
* * *
2553594 ATGACCACACCTTAATTAAATAAAAATGAAA
1 ATGACCATATCTTAATTAAATAAAAATAAAA
* *
2553625 GTGATCATATCTTAATTAAAT-AAAATAAAAA
1 ATGACCATATCTTAATTAAATAAAAAT-AAAA
2553656 ATGACCATATCTTA
1 ATGACCATATCTTA
2553670 TGTTTTCTGA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
30 5 0.14
31 32 0.86
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.29
Consensus pattern (31 bp):
ATGACCATATCTTAATTAAATAAAAATAAAA
Found at i:2554138 original size:30 final size:30
Alignment explanation
Indices: 2554104--2554168 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
2554094 CACAAATCAG
*
2554104 TCACTAGCATTAT-AGTTTGTTACAAAATGA
1 TCACTAACATTATCA-TTTGTTACAAAATGA
** *
2554134 TCACTAATGTTATCATTTGTTACAAAATGG
1 TCACTAACATTATCATTTGTTACAAAATGA
2554164 TCACT
1 TCACT
2554169 GGACATTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (30 bp):
TCACTAACATTATCATTTGTTACAAAATGA
Found at i:2555936 original size:30 final size:30
Alignment explanation
Indices: 2555900--2556029 Score: 170
Period size: 30 Copynumber: 4.3 Consensus size: 30
2555890 GTAAACGTCG
*
2555900 AGTGACCATTTTGTAACAATCAATAACATT
1 AGTGACCATTTTGTAACAAACAATAACATT
* * *
2555930 AGTGACCATTTTGTAATAAACGATAATATT
1 AGTGACCATTTTGTAACAAACAATAACATT
*
2555960 AGTGACCATTTTGTAACAAACAATAACGTT
1 AGTGACCATTTTGTAACAAACAATAACATT
* **
2555990 AGTAACCATTTTGTAACAAATGATAACATT
1 AGTGACCATTTTGTAACAAACAATAACATT
* *
2556020 ATTGATCATT
1 AGTGACCATT
2556030 GGCGTAATTT
Statistics
Matches: 85, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 85 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.35
Consensus pattern (30 bp):
AGTGACCATTTTGTAACAAACAATAACATT
Found at i:2555984 original size:60 final size:60
Alignment explanation
Indices: 2555900--2556029 Score: 188
Period size: 60 Copynumber: 2.2 Consensus size: 60
2555890 GTAAACGTCG
* * * *
2555900 AGTGACCATTTTGTAACAATCAATAACATTAGTGACCATTTTGTAATAAACGATAATATT
1 AGTGACCATTTTGTAACAAACAATAACATTAGTAACCATTTTGTAACAAACGATAACATT
* *
2555960 AGTGACCATTTTGTAACAAACAATAACGTTAGTAACCATTTTGTAACAAATGATAACATT
1 AGTGACCATTTTGTAACAAACAATAACATTAGTAACCATTTTGTAACAAACGATAACATT
* *
2556020 ATTGATCATT
1 AGTGACCATT
2556030 GGCGTAATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.35
Consensus pattern (60 bp):
AGTGACCATTTTGTAACAAACAATAACATTAGTAACCATTTTGTAACAAACGATAACATT
Found at i:2558260 original size:46 final size:44
Alignment explanation
Indices: 2558045--2558300 Score: 254
Period size: 44 Copynumber: 5.8 Consensus size: 44
2558035 CCAACTCTGA
2558045 ACTCTCGGTTTTTACTTAAAGTACCTATCTCCGACACTTACTCCG
1 ACTCTCGGTTTTTACTT-AAGTACCTATCTCCGACACTTACTCCG
* * * * * **
2558090 GCTCTCGATTTTTAGTT-A-T--CTATCTCCGGCACTTATTATTG
1 ACTCTCGGTTTTTACTTAAGTACCTATCTCCGACACTTACT-CCG
* * * * *
2558131 -CTCTCGATTTTTACTTAAGCACCTATCTCCGGCGCTTACTCTG
1 ACTCTCGGTTTTTACTTAAGTACCTATCTCCGACACTTACTCCG
* * *
2558174 ATTCTCGGTTTTTACTTGAGTACCTATCTCCGACATTTACTCCG
1 ACTCTCGGTTTTTACTTAAGTACCTATCTCCGACACTTACTCCG
* *
2558218 ACTCTCGGTTTTTACTTAAGTATATCTATCCCCGACACTTACTCCG
1 ACTCTCGGTTTTTACTTAAG--TACCTATCTCCGACACTTACTCCG
* *
2558264 ACTCTTGGTTTTTACTTAAGTACCCT-TCTTCGACACT
1 ACTCTCGGTTTTTACTTAAGTA-CCTATCTCCGACACT
2558301 CGTGACTTGA
Statistics
Matches: 173, Mismatches: 29, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
40 31 0.18
41 2 0.01
42 1 0.01
43 3 0.02
44 80 0.46
45 16 0.09
46 40 0.23
ACGTcount: A:0.19, C:0.29, G:0.12, T:0.40
Consensus pattern (44 bp):
ACTCTCGGTTTTTACTTAAGTACCTATCTCCGACACTTACTCCG
Found at i:2558298 original size:90 final size:88
Alignment explanation
Indices: 2558045--2558287 Score: 226
Period size: 90 Copynumber: 2.8 Consensus size: 88
2558035 CCAACTCTGA
* * * * * *
2558045 ACTCTCGGTTTTTACTTAAAGTACCTATCTCCGACACTTACTCCGGCTCTCGATTTTTAGTT-A-
1 ACTCTCGATTTTTACTT-AAGCACCTATCCCCGACACTTACTCCGACTCTCGGTTTTTACTTAAG
* * * **
2558108 T--CTATCTCCGGCACTTATTATTG
65 TACCTATCTCCGACATTTACT-CCG
* * * * * *
2558131 -CTCTCGATTTTTACTTAAGCACCTATCTCCGGCGCTTACTCTGATTCTCGGTTTTTACTTGAGT
1 ACTCTCGATTTTTACTTAAGCACCTATCCCCGACACTTACTCCGACTCTCGGTTTTTACTTAAGT
2558195 ACCTATCTCCGACATTTACTCCG
66 ACCTATCTCCGACATTTACTCCG
* * * *
2558218 ACTCTCGGTTTTTACTTAAGTATATCTATCCCCGACACTTACTCCGACTCTTGGTTTTTACTTAA
1 ACTCTCGATTTTTACTTAAG--CACCTATCCCCGACACTTACTCCGACTCTCGGTTTTTACTTAA
2558283 GTACC
64 GTACC
2558288 CTTCTTCGAC
Statistics
Matches: 126, Mismatches: 24, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
84 36 0.29
85 16 0.13
86 1 0.01
87 1 0.01
88 33 0.26
90 39 0.31
ACGTcount: A:0.19, C:0.28, G:0.13, T:0.40
Consensus pattern (88 bp):
ACTCTCGATTTTTACTTAAGCACCTATCCCCGACACTTACTCCGACTCTCGGTTTTTACTTAAGT
ACCTATCTCCGACATTTACTCCG
Found at i:2563375 original size:36 final size:37
Alignment explanation
Indices: 2563316--2563416 Score: 116
Period size: 37 Copynumber: 2.8 Consensus size: 37
2563306 CATTTTCGTC
* *
2563316 CTACTAAGATTCAAACTCAT-AAAATAAG-ATAGAATT
1 CTACTATGATTCAAACTCCTAAAAAT-AGTATAGAATT
* * *
2563352 TTGCTATGATTCAAACTCCTAAAAATAGTATAGAGTT
1 CTACTATGATTCAAACTCCTAAAAATAGTATAGAATT
* *
2563389 CTACTATGATTTAAACTCCTAAAGATAG
1 CTACTATGATTCAAACTCCTAAAAATAG
2563417 GATCCACAAG
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
36 18 0.33
37 36 0.67
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.32
Consensus pattern (37 bp):
CTACTATGATTCAAACTCCTAAAAATAGTATAGAATT
Found at i:2563971 original size:3 final size:3
Alignment explanation
Indices: 2563963--2564116 Score: 65
Period size: 3 Copynumber: 55.3 Consensus size: 3
2563953 CTTTACATTT
* * *
2563963 TTA TTA TTA CTA TTA TTA TTA TTA CTA TTA TT- TTCC TT- TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
*
2564006 CTA TTA TT- TTA TTA TTTA TT- TTA -TA TT- TTA -TA TTA TT- TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2564046 -TA TTTA TT- TT- TTA TTA TCT- TTA TT- TT- TTA -TA TTCT TTA TT-
1 TTA -TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TT-A TTA TTA
* *
2564086 TTG TTA TTA TATA TTA TTA TTT TTA -TA TTA T
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA T
2564117 ATATATTTGT
Statistics
Matches: 118, Mismatches: 11, Indels: 44
0.68 0.06 0.25
Matches are distributed among these distances:
2 34 0.29
3 71 0.60
4 13 0.11
ACGTcount: A:0.25, C:0.05, G:0.01, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2564020 original size:39 final size:37
Alignment explanation
Indices: 2563975--2564109 Score: 102
Period size: 37 Copynumber: 3.6 Consensus size: 37
2563965 ATTATTACTA
2563975 TTATTATTATTACTATTATTTTCCTTTTATTCTATTATT
1 TTATTATTATTACTATTATTTT--TTTTATTCTATTATT
* * *
2564014 TTATTATTTATT-TTA-TATTTTATATTATTTTA-TA-T
1 TTATTA-TTATTACTATTATTTT-TTTTATTCTATTATT
* *
2564049 TTATTTTTTATTATCT-TTATTTTTTATATTCT-TTATT
1 TTA-TTATTATTA-CTATTATTTTTTTTATTCTATTATT
* *
2564086 TTGTTATTATATATTATTATTTTT
1 TTATTATTAT-TACTATTATTTTT
2564110 ATATTATATA
Statistics
Matches: 75, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
35 9 0.12
36 19 0.25
37 28 0.37
38 6 0.08
39 8 0.11
40 5 0.07
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (37 bp):
TTATTATTATTACTATTATTTTTTTTATTCTATTATT
Found at i:2564025 original size:7 final size:7
Alignment explanation
Indices: 2564001--2564124 Score: 59
Period size: 7 Copynumber: 17.9 Consensus size: 7
2563991 TATTTTCCTT
2564001 TTATTCTA
1 TTATT-TA
2564009 TTATTTTA
1 TTA-TTTA
2564017 TTATTTA
1 TTATTTA
2564024 TT-TTATA
1 TTATT-TA
2564031 TT-TTATA
1 TTATT-TA
2564038 TTATTT-
1 TTATTTA
2564044 TATATTTA
1 T-TATTTA
*
2564052 TTTTTTA
1 TTATTTA
*
2564059 TTATCT-
1 TTATTTA
2564065 TTATTT-
1 TTATTTA
*
2564071 TT-TATA
1 TTATTTA
*
2564077 TTCTTTA
1 TTATTTA
*
2564084 TTTTGTTA
1 TTAT-TTA
*
2564092 TTATATA
1 TTATTTA
2564099 TTA-TTA
1 TTATTTA
2564105 TT-TTTA
1 TTATTTA
2564111 -TATTATA
1 TTATT-TA
2564118 TATATTT
1 T-TATTT
2564125 GTTAATATAT
Statistics
Matches: 93, Mismatches: 10, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
5 3 0.03
6 21 0.23
7 45 0.48
8 18 0.19
9 6 0.06
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.71
Consensus pattern (7 bp):
TTATTTA
Found at i:2564041 original size:21 final size:21
Alignment explanation
Indices: 2564015--2564124 Score: 81
Period size: 21 Copynumber: 5.4 Consensus size: 21
2564005 TCTATTATTT
2564015 TATTATTTATTTTATATTTTA
1 TATTATTTATTTTATATTTTA
2564036 TATTATTTTATATTTAT-TTTT-
1 TATTA-TTTAT-TTTATATTTTA
* *
2564057 TATTA--T-CTTTATTTTTTA
1 TATTATTTATTTTATATTTTA
* * *
2564075 TATTCTTTATTTTGTTATTATA
1 TATTATTTATTTT-ATATTTTA
*
2564097 TATTA-TTATTTT-TATATTA
1 TATTATTTATTTTATATTTTA
2564116 TATATATTT
1 TAT-TATTT
2564125 GTTAATATAT
Statistics
Matches: 70, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
16 5 0.07
17 4 0.06
18 5 0.07
19 8 0.11
20 3 0.04
21 22 0.31
22 18 0.26
23 5 0.07
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.71
Consensus pattern (21 bp):
TATTATTTATTTTATATTTTA
Found at i:2564042 original size:75 final size:75
Alignment explanation
Indices: 2563978--2564124 Score: 178
Period size: 75 Copynumber: 2.0 Consensus size: 75
2563968 ATTACTATTA
* *
2563978 TTATTATTA-CTATTATTTTCCTTTTATTCTATTATTTTATTATT-TATTTTA-TA-TTTTATAT
1 TTATTATTATCT-TTATTTT--TTATATTCT-TTATTTTATTATTATATATTATTATTTTTATAT
2564039 TATTTTATATTTAT
62 TATTTTATATTTAT
* *
2564053 TTTTTATTATCTTTATTTTTTATATTCTTTATTTTGTTATTATATATTATTATTTTTATATTA-T
1 TTATTATTATCTTTATTTTTTATATTCTTTATTTTATTATTATATATTATTATTTTTATATTATT
*
2564117 ATATATTT
66 TTATATTT
2564125 GTTAATATAT
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
72 12 0.19
73 14 0.22
74 10 0.16
75 25 0.40
76 2 0.03
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (75 bp):
TTATTATTATCTTTATTTTTTATATTCTTTATTTTATTATTATATATTATTATTTTTATATTATT
TTATATTTAT
Found at i:2564056 original size:29 final size:29
Alignment explanation
Indices: 2563959--2564114 Score: 88
Period size: 29 Copynumber: 5.0 Consensus size: 29
2563949 TTTTCTTTAC
2563959 ATTTTTATTAT-TACTATTATTATTATTACTATT
1 ATTTTTATTATCTA-TATTATT-TTA-TA-T-TT
* *
2563992 ATTTTCCTTTTAT-TCTATTATTTTATTATTT
1 ATTTT--TATTATCTATATTATTTTA-TATTT
2564023 ATTTTATATT-T-TATATTATTTTATATTT
1 ATTTT-TATTATCTATATTATTTTATATTT
*
2564051 ATTTTTTATTATCTTTATT-TTTTATATTCTTT
1 A-TTTTTATTATCTATATTATTTTATA---TTT
*
2564083 ATTTTGTTATTATATATTATTATTTTTATATT
1 A-TTT-TTATTATCTA-TATTA-TTTTATATT
2564115 ATATATATTT
Statistics
Matches: 103, Mismatches: 8, Indels: 24
0.76 0.06 0.18
Matches are distributed among these distances:
28 10 0.10
29 24 0.23
30 8 0.08
31 7 0.07
32 9 0.09
33 21 0.20
34 11 0.11
35 6 0.06
36 7 0.07
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (29 bp):
ATTTTTATTATCTATATTATTTTATATTT
Found at i:2564133 original size:21 final size:19
Alignment explanation
Indices: 2564047--2564146 Score: 58
Period size: 19 Copynumber: 5.6 Consensus size: 19
2564037 ATTATTTTAT
*
2564047 ATTTATTT-TTTAT-TATC
1 ATTTATTTGTTAATATATC
*
2564064 -TTTATTT-TTTATAT-TC
1 ATTTATTTGTTAATATATC
*
2564080 -TTTATTTTGTTATTATAT-
1 ATTTA-TTTGTTAATATATC
2564098 ATTATTATTT-TT-ATATTAT-
1 A-T-TTATTTGTTAATA-TATC
*
2564117 ATATATTTGTTAATATATC
1 ATTTATTTGTTAATATATC
2564136 ATTTATTTGTT
1 ATTTATTTGTT
2564147 TTTTTATATA
Statistics
Matches: 67, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
16 18 0.27
17 9 0.13
18 13 0.19
19 20 0.30
20 4 0.06
21 3 0.04
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (19 bp):
ATTTATTTGTTAATATATC
Found at i:2564196 original size:24 final size:24
Alignment explanation
Indices: 2564169--2564226 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
2564159 TTGTATGTCT
2564169 TTATAT-TATTAATTATTTAATTTA
1 TTATATATATTAATT-TTTAATTTA
** *
2564193 TTATATATATTTCTTTTTTATTTA
1 TTATATATATTAATTTTTAATTTA
2564217 TTATATATAT
1 TTATATATAT
2564227 ATATATTTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 24 0.80
25 6 0.20
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
TTATATATATTAATTTTTAATTTA
Found at i:2564323 original size:28 final size:25
Alignment explanation
Indices: 2564250--2564323 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 25
2564240 TTTGTTATTA
*
2564250 TTATTTTGTTTATTTGTTTTATTTAT
1 TTATTTT-TTTATTTGTTTTTTTTAT
*
2564276 TT-TCTTTTTATTT-TTCTTTTTTAT
1 TTATTTTTTTATTTGTT-TTTTTTAT
2564300 ATATATTTTTATTATTTGTTTTTT
1 -T-TATTTTT-TTATTTGTTTTTT
2564324 ACTTACTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 2 0.05
24 14 0.36
25 4 0.10
26 3 0.08
27 4 0.10
28 10 0.26
29 2 0.05
ACGTcount: A:0.15, C:0.03, G:0.04, T:0.78
Consensus pattern (25 bp):
TTATTTTTTTATTTGTTTTTTTTAT
Found at i:2564335 original size:26 final size:25
Alignment explanation
Indices: 2564244--2564337 Score: 68
Period size: 26 Copynumber: 3.6 Consensus size: 25
2564234 TCGTACTTTG
* *
2564244 TTATTATTATTTTGTTTATTTGTTTTAT
1 TTATTACTATTTT-ATTATTTGTTT--T
* *
2564272 TTATTTTCT-TTTTATT-TTTCTTTT
1 TTA-TTACTATTTTATTATTTGTTTT
2564296 TTATATA-TATTTTTATTATTTGTTTT
1 TTAT-TACTA-TTTTATTATTTGTTTT
2564322 TTACTTACTATTTTAT
1 TTA-TTACTATTTTAT
2564338 CTTTGCTTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
23 2 0.04
24 5 0.09
25 7 0.13
26 24 0.45
27 5 0.09
28 7 0.13
29 3 0.06
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.74
Consensus pattern (25 bp):
TTATTACTATTTTATTATTTGTTTT
Found at i:2565480 original size:19 final size:19
Alignment explanation
Indices: 2565456--2565492 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2565446 ATCTTACTAA
2565456 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
2565475 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
2565493 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:2568825 original size:27 final size:28
Alignment explanation
Indices: 2568768--2568827 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
2568758 GGCAAAAACC
*
2568768 AAAAAGAAAAGAAACAAAAAGAACAAAA
1 AAAAAGAAAAGAAACAAAAACAACAAAA
*
2568796 AAAAAG-AAAG-AACAAAAATCAA-AAAG
1 AAAAAGAAAAGAAACAAAAA-CAACAAAA
2568822 AAAAAG
1 AAAAAG
2568828 GGACAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 17 0.59
27 6 0.21
28 6 0.21
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.02
Consensus pattern (28 bp):
AAAAAGAAAAGAAACAAAAACAACAAAA
Found at i:2568833 original size:23 final size:23
Alignment explanation
Indices: 2568752--2568837 Score: 68
Period size: 24 Copynumber: 3.7 Consensus size: 23
2568742 CAATCAGAAC
* *
2568752 AAAAAGG-GCAAAAACCAAAAAG
1 AAAAAGGAACAAAAAACAAAAAG
* *
2568774 -AAAAGAAACAAAAAGAACAAAAAA
1 AAAAAGGAAC-AAAA-AACAAAAAG
* *
2568798 AAAGAAAGAACAAAAATCAAAAAG
1 AAA-AAGGAACAAAAAACAAAAAG
*
2568822 AAAAAGGGACAAAAAA
1 AAAAAGGAACAAAAAA
2568838 GCACATGCAA
Statistics
Matches: 48, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
21 5 0.10
22 1 0.02
23 14 0.29
24 17 0.35
25 6 0.12
26 5 0.10
ACGTcount: A:0.76, C:0.09, G:0.14, T:0.01
Consensus pattern (23 bp):
AAAAAGGAACAAAAAACAAAAAG
Found at i:2569455 original size:22 final size:22
Alignment explanation
Indices: 2569427--2569481 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
2569417 GCTATCCCAT
*
2569427 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAACATCAAATGC
2569449 CAAACCTTTGAACATCAAATGC
1 CAAACCTTTGAACATCAAATGC
2569471 CAAACCTTTGA
1 CAAACCTTTGA
2569482 CAAACACAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAACATCAAATGC
Found at i:2570530 original size:106 final size:106
Alignment explanation
Indices: 2570302--2571886 Score: 2217
Period size: 106 Copynumber: 15.0 Consensus size: 106
2570292 ATATCGTGCC
* * * * * * * *
2570302 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGACAA-CAATAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * *
2570366 AATTTCGGAGCCAATTTCAACTTCACAACGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
2570407 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
2570472 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * *
2570513 ACTTTAGATAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
2570578 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATA-TGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * *
2570618 ACTTTAGA-TACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTT-C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTCC
*
2570681 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTCG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
2570723 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGAACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * *
2570788 AATTTCAGAGCCAATTTCAACTTCACAACAAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
2570829 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGTGACTGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
2570894 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
2570935 ACTCCAGACAACGTAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
2571000 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
2571041 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* **
2571106 AATTTCAGAGCCAATTGCAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
2571147 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACGATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
2571212 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
2571253 ACTCAAGACAACGCAAGTTGAACTTCACGACGAAGGGACCACTGGTTGTCTATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
2571318 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
2571359 ACTCCAGCCAACGCAAGTTCAACTTCACGACGAATGGACCGTTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
2571424 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
2571465 ACTCCAGACAATGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCCATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
2571530 AATTTCATAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
2571571 ACTCAAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * *
2571636 AATTTCAGAGCCAATTTTAACTTCTCAGCGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
2571677 AC-CCAAGACAACACAA-TCTCAACTTTACGACGAAAGGG-CGGCTGATTGTCAA-CAA-AATTT
1 ACTCC-AGACAACGCAAGT-TCAACTTCACGACG-AAGGGACCGCTGGTTGTCAATAAACAATTT
*
2571737 --C-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
63 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * ** * *
2571777 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGATGGTTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
** * * *
2571842 GGTTCCAGAGCAAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
2571883 ACTC
1 ACTC
2571887 GGAATAATGC
Statistics
Matches: 1336, Mismatches: 126, Indels: 35
0.89 0.08 0.02
Matches are distributed among these distances:
99 5 0.00
100 70 0.05
101 5 0.00
102 6 0.00
104 93 0.07
105 76 0.06
106 1076 0.81
107 5 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:2572704 original size:37 final size:37
Alignment explanation
Indices: 2572615--2572718 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
2572605 ACCTTTCGTC
*
2572615 CTACTAGGATTCAAACTCAT-AAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
2572651 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
2572688 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
2572719 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
36 17 0.29
37 41 0.71
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:2573315 original size:21 final size:20
Alignment explanation
Indices: 2573287--2573393 Score: 87
Period size: 21 Copynumber: 5.3 Consensus size: 20
2573277 TTTTCTTTGC
2573287 ATTTTTATTATTACTATTAT
1 ATTTTTATTATTACTATTAT
*
2573307 ATTTATTATTTTTACTATTAT
1 ATTT-TTATTATTACTATTAT
* *
2573328 ATTTTCCTTTTATT-CTACT-T
1 ATTTT--TATTATTACTATTAT
*
2573348 ATTTATATTA-TA-TATGTAT
1 ATTTTTATTATTACTAT-TAT
* *
2573367 ATTTTTATATTTTATTATTAT
1 ATTTTTAT-TATTACTATTAT
2573388 ATTTTT
1 ATTTTT
2573394 TACTTTCTCT
Statistics
Matches: 69, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
17 3 0.04
18 5 0.07
19 8 0.12
20 11 0.16
21 34 0.49
22 8 0.12
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (20 bp):
ATTTTTATTATTACTATTAT
Found at i:2573647 original size:29 final size:27
Alignment explanation
Indices: 2573580--2573634 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
2573570 TCGTCATTTA
* *
2573580 ATTTATTAATT-TATATATATTTACTT
1 ATTTATTTATTATATATATATATACTT
2573606 ATTTATTTATTATATATATATATA-TT
1 ATTTATTTATTATATATATATATACTT
2573632 ATT
1 ATT
2573635 CGTACTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
ATTTATTTATTATATATATATATACTT
Found at i:2573694 original size:26 final size:25
Alignment explanation
Indices: 2573644--2573711 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
2573634 TCGTACTTTG
2573644 TTATTA-TTATTTTGTTTTATTTATT
1 TTATTATTTATTTT-TTTTATTTATT
* *
2573669 TTCTT-TTTCTTTTTTTTATATATATT
1 TTATTATTTATTTTTTTTAT-T-TATT
2573695 TTATTATTTATTTTTTT
1 TTATTATTTATTTTTTT
2573712 ACTTACTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 6 0.17
25 11 0.31
26 8 0.23
27 10 0.29
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (25 bp):
TTATTATTTATTTTTTTTATTTATT
Found at i:2573696 original size:14 final size:12
Alignment explanation
Indices: 2573658--2573712 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
2573648 TATTATTTTG
2573658 TTTTATTTATTT
1 TTTTATTTATTT
2573670 TCTTT-TTCT-TTT
1 T-TTTATT-TATTT
2573682 TTTTATATATATTT
1 TTTTAT-T-TATTT
*
2573696 TATTATTTATTT
1 TTTTATTTATTT
2573708 TTTTA
1 TTTTA
2573713 CTTACTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
11 3 0.09
12 17 0.49
13 7 0.20
14 8 0.23
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTATTTATTT
Found at i:2574574 original size:29 final size:29
Alignment explanation
Indices: 2574540--2574621 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
2574530 TTTACCCCTA
2574540 AAATTTTATAAGTTTAAATTCGCCTCTTG
1 AAATTTTATAAGTTTAAATTCGCCTCTTG
2574569 AAATTTTATAAGTTTAAATTCGCCTCTTG
1 AAATTTTATAAGTTTAAATTCGCCTCTTG
* *
2574598 AAATTTTATAAGTTCACATTCGCC
1 AAATTTTATAAGTTTAAATTCGCC
2574622 CCCCTTAACA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.43
Consensus pattern (29 bp):
AAATTTTATAAGTTTAAATTCGCCTCTTG
Found at i:2577590 original size:21 final size:21
Alignment explanation
Indices: 2577564--2577623 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
2577554 TGTCCGAGTT
*
2577564 GTCCGCAACGACCGCAATAGC
1 GTCCGCGACGACCGCAATAGC
2577585 GTCCGCGACGACCGCAATAGC
1 GTCCGCGACGACCGCAATAGC
*
2577606 G-CCTGCGACGGCCGCAAT
1 GTCC-GCGACGACCGCAAT
2577624 CACGGTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 2 0.06
21 34 0.94
ACGTcount: A:0.23, C:0.38, G:0.28, T:0.10
Consensus pattern (21 bp):
GTCCGCGACGACCGCAATAGC
Found at i:2579866 original size:22 final size:21
Alignment explanation
Indices: 2579819--2579890 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 21
2579809 TATTATTGAA
*
2579819 AATAATTATATTTTCAA-AAG
1 AATAATTATATTTTCAATAAT
2579839 ATATAATTATATCTTTCAATAAT
1 A-ATAATTATAT-TTTCAATAAT
* *
2579862 AATAAATGTCATTTTCAAATAAT
1 AATAATTAT-ATTTTC-AATAAT
2579885 AATAAT
1 AATAAT
2579891 AATAGTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.02
21 10 0.23
22 16 0.37
23 16 0.37
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.42
Consensus pattern (21 bp):
AATAATTATATTTTCAATAAT
Found at i:2590821 original size:22 final size:24
Alignment explanation
Indices: 2590778--2590830 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 24
2590768 GAAATAATGG
*
2590778 TAGTGATCATATGTGTGCATAT-AA
1 TAGTGA-CTTATGTGTGCATATGAA
**
2590802 -AGTGACTTATGTGTTTATATGAA
1 TAGTGACTTATGTGTGCATATGAA
2590825 TAGTGA
1 TAGTGA
2590831 TAAAAGAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
22 12 0.50
23 7 0.29
24 5 0.21
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.40
Consensus pattern (24 bp):
TAGTGACTTATGTGTGCATATGAA
Found at i:2595788 original size:20 final size:20
Alignment explanation
Indices: 2595752--2595789 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2595742 ATCCTATTCC
**
2595752 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
2595772 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
2595790 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:2596736 original size:42 final size:42
Alignment explanation
Indices: 2596636--2596736 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 42
2596626 ATATTCAGAA
* *
2596636 CTTGAATATTTTTC-T-CCTTATCATCTTTTATTTATTTACT
1 CTTGCATATTTTTCTTGCCTTAGCATCTTTTATTTATTTACT
* * *
2596676 CTTGCA-ATTTTTTTTTGCCTTAGCAAT-TTTTATTTGTTTATT
1 CTTGCATA-TTTTTCTTGCCTTAGC-ATCTTTTATTTATTTACT
2596718 CTTGCATATTTTTCTTGCC
1 CTTGCATATTTTTCTTGCC
2596737 ATTACAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
39 1 0.02
40 10 0.20
41 1 0.02
42 35 0.70
43 3 0.06
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.59
Consensus pattern (42 bp):
CTTGCATATTTTTCTTGCCTTAGCATCTTTTATTTATTTACT
Found at i:2599984 original size:2 final size:2
Alignment explanation
Indices: 2599977--2600013 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2599967 AACTAATCAA
2599977 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2600014 ATTTGAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2600062 original size:40 final size:40
Alignment explanation
Indices: 2600007--2600094 Score: 167
Period size: 40 Copynumber: 2.2 Consensus size: 40
2599997 ATATATATAT
*
2600007 ATATATAATTTGAAATTATCTTAGCACTATAAAGGCAAGG
1 ATATATAATTTGAAATTATCTTAACACTATAAAGGCAAGG
2600047 ATATATAATTTGAAATTATCTTAACACTATAAAGGCAAGG
1 ATATATAATTTGAAATTATCTTAACACTATAAAGGCAAGG
2600087 ATATATAA
1 ATATATAA
2600095 AATAATTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.33
Consensus pattern (40 bp):
ATATATAATTTGAAATTATCTTAACACTATAAAGGCAAGG
Found at i:2601977 original size:16 final size:16
Alignment explanation
Indices: 2601921--2601977 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
2601911 TTCTAACTCT
*
2601921 AATAAAAATCAAATAC
1 AATAAAAAACAAATAC
* * *
2601937 AATCAGAAACAAATCC
1 AATAAAAAACAAATAC
**
2601953 AATCTAAAACAAATAC
1 AATAAAAAACAAATAC
2601969 AATAAAAAA
1 AATAAAAAA
2601978 AACAAATGCA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.67, C:0.16, G:0.02, T:0.16
Consensus pattern (16 bp):
AATAAAAAACAAATAC
Found at i:2602898 original size:13 final size:13
Alignment explanation
Indices: 2602882--2602977 Score: 79
Period size: 13 Copynumber: 7.4 Consensus size: 13
2602872 AGTATGCATG
2602882 AACAATATGTAAT
1 AACAATATGTAAT
* * *
2602895 AACAACATGCAGT
1 AACAATATGTAAT
2602908 AACAATATGTAAT
1 AACAATATGTAAT
* *
2602921 AACAGTATG-CAT
1 AACAATATGTAAT
2602933 GAACAATATGTAAT
1 -AACAATATGTAAT
* *
2602947 AACACTATG-CAT
1 AACAATATGTAAT
* *
2602959 GAAAAATATGTATT
1 -AACAATATGTAAT
2602973 AACAA
1 AACAA
2602978 GTTAACCAAA
Statistics
Matches: 62, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
12 4 0.06
13 55 0.89
14 3 0.05
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.26
Consensus pattern (13 bp):
AACAATATGTAAT
Found at i:2602904 original size:26 final size:26
Alignment explanation
Indices: 2602875--2602977 Score: 138
Period size: 26 Copynumber: 4.0 Consensus size: 26
2602865 AGTATACAGT
2602875 ATGCATGAACAATATGTAATAACAAC
1 ATGCATGAACAATATGTAATAACAAC
**
2602901 ATGCA-GTAACAATATGTAATAACAGT
1 ATGCATG-AACAATATGTAATAACAAC
2602927 ATGCATGAACAATATGTAATAAC-AC
1 ATGCATGAACAATATGTAATAACAAC
* *
2602952 TATGCATGAAAAATATGTATTAACAA
1 -ATGCATGAACAATATGTAATAACAA
2602978 GTTAACCAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
25 1 0.01
26 64 0.96
27 2 0.03
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (26 bp):
ATGCATGAACAATATGTAATAACAAC
Found at i:2602908 original size:33 final size:33
Alignment explanation
Indices: 2602818--2602908 Score: 119
Period size: 33 Copynumber: 2.7 Consensus size: 33
2602808 TTATAATAAT
*
2602818 AATATGTATATAACAATATGCAATACACATGAAC
1 AATATGTA-ATAACAATATGCAGTACACATGAAC
* * **
2602852 AATATGTAATAACAGTATACAGTATGCATGAAC
1 AATATGTAATAACAATATGCAGTACACATGAAC
*
2602885 AATATGTAATAACAACATGCAGTA
1 AATATGTAATAACAATATGCAGTA
2602909 ACAATATGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 41 0.84
34 8 0.16
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.26
Consensus pattern (33 bp):
AATATGTAATAACAATATGCAGTACACATGAAC
Found at i:2602930 original size:52 final size:52
Alignment explanation
Indices: 2602870--2602976 Score: 164
Period size: 52 Copynumber: 2.1 Consensus size: 52
2602860 ATAACAGTAT
*
2602870 ACAGTATGCATGAACAATATGTAATAACAAC-ATGCA-GTAACAATATGTAATA
1 ACAGTATGCATGAACAATATGTAATAAC-ACTATGCATG-AAAAATATGTAATA
*
2602922 ACAGTATGCATGAACAATATGTAATAACACTATGCATGAAAAATATGTATTA
1 ACAGTATGCATGAACAATATGTAATAACACTATGCATGAAAAATATGTAATA
2602974 ACA
1 ACA
2602977 AGTTAACCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
51 2 0.04
52 48 0.94
53 1 0.02
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (52 bp):
ACAGTATGCATGAACAATATGTAATAACACTATGCATGAAAAATATGTAATA
Found at i:2605557 original size:17 final size:17
Alignment explanation
Indices: 2605537--2605578 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
2605527 CACTAAACCT
2605537 ATATATTCATGCAGAAC
1 ATATATTCATGCAGAAC
**
2605554 ATATA--CATGCATTAC
1 ATATATTCATGCAGAAC
2605569 ATATATTCAT
1 ATATATTCAT
2605579 TGATTTCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 13 0.62
17 8 0.38
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (17 bp):
ATATATTCATGCAGAAC
Found at i:2605666 original size:15 final size:15
Alignment explanation
Indices: 2605643--2605676 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2605633 ATATTATCAG
*
2605643 AACATATAACCAGTA
1 AACAAATAACCAGTA
*
2605658 AACAAATAATCAGTA
1 AACAAATAACCAGTA
2605673 AACA
1 AACA
2605677 TATCATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.18, G:0.06, T:0.18
Consensus pattern (15 bp):
AACAAATAACCAGTA
Found at i:2605850 original size:107 final size:100
Alignment explanation
Indices: 2605788--2605994 Score: 266
Period size: 93 Copynumber: 2.1 Consensus size: 100
2605778 ATATATCATC
*** *
2605788 AAACATATATATTACACAATTAGTAAACAATCGGTAAGGTTTTTA-GGGTTTTTAAACATATATA
1 AAACATATATATTACACAATTAGTAAACAATCAACAAGGTTTTTAGGGGTTTCTAAACATATATA
* *
2605852 TTAAACAATTTATCATTCGTGC-A--A-T--CAGT
66 TTAAACAATTTCTCATTCGTGCAATTAGTAACAAT
2605881 AAACATATATATTACACAATTAGTAAACAATCAACAAGGTTTTTAGGGGTTTCTAAACATATATA
1 AAACATATATATTACACAATTAGTAAACAATCAACAAGGTTTTTAGGGGTTTCTAAACATATATA
* *
2605946 TTAAATAATTTCTCATTCGTGCAATTAGTAAGCAGT
66 TTAAACAATTTCTCATTCGTGCAATTAGTAA-CAAT
**
2605982 AAACCCATATATT
1 AAACATATATATT
2605995 TAGGGTTTTA
Statistics
Matches: 98, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
93 42 0.43
94 38 0.39
95 1 0.01
97 1 0.01
98 1 0.01
101 15 0.15
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (100 bp):
AAACATATATATTACACAATTAGTAAACAATCAACAAGGTTTTTAGGGGTTTCTAAACATATATA
TTAAACAATTTCTCATTCGTGCAATTAGTAACAAT
Found at i:2605885 original size:93 final size:94
Alignment explanation
Indices: 2605788--2605976 Score: 308
Period size: 94 Copynumber: 2.0 Consensus size: 94
2605778 ATATATCATC
*** *
2605788 AAACATATATATTACACAATTAGTAAACAATCGGTAAGGTTTTTA-GGGTTTTTAAACATATATA
1 AAACATATATATTACACAATTAGTAAACAATCAACAAGGTTTTTAGGGGTTTCTAAACATATATA
2605852 TTAAACAATTTATCATTCGTGCAATCAGT
66 TTAAACAATTTATCATTCGTGCAATCAGT
2605881 AAACATATATATTACACAATTAGTAAACAATCAACAAGGTTTTTAGGGGTTTCTAAACATATATA
1 AAACATATATATTACACAATTAGTAAACAATCAACAAGGTTTTTAGGGGTTTCTAAACATATATA
* * *
2605946 TTAAATAATTTCTCATTCGTGCAATTAGT
66 TTAAACAATTTATCATTCGTGCAATCAGT
2605975 AA
1 AA
2605977 GCAGTAAACC
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
93 42 0.48
94 46 0.52
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (94 bp):
AAACATATATATTACACAATTAGTAAACAATCAACAAGGTTTTTAGGGGTTTCTAAACATATATA
TTAAACAATTTATCATTCGTGCAATCAGT
Found at i:2606107 original size:11 final size:13
Alignment explanation
Indices: 2606045--2606101 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 13
2606035 AAGAAGAAAC
2606045 ACATATATACTAA
1 ACATATATACTAA
*
2606058 ACATATATACTTA
1 ACATATATACTAA
*
2606071 ACA-ATA-A--AC
1 ACATATATACTAA
*
2606080 CCATATATACTAA
1 ACATATATACTAA
2606093 ACATATATA
1 ACATATATA
2606102 TAACATTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 2 0.06
10 3 0.09
11 2 0.06
12 3 0.09
13 24 0.71
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.30
Consensus pattern (13 bp):
ACATATATACTAA
Found at i:2607514 original size:22 final size:22
Alignment explanation
Indices: 2607470--2607514 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2607460 ATATAAATAT
* *
2607470 ATGTTATATTTTTTAAAGTCAA
1 ATGTTATATTTTTGAAAGCCAA
2607492 ATGTTATATTTTTGGAAA-CCAA
1 ATGTTATATTTTT-GAAAGCCAA
2607514 A
1 A
2607515 GTGTAATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (22 bp):
ATGTTATATTTTTGAAAGCCAA
Found at i:2613246 original size:29 final size:29
Alignment explanation
Indices: 2613168--2613246 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
2613158 CAGTGGCCGT
* * ** *
2613168 AGGTCGCCATGCACTCTCAGCGACCTCCT
1 AGGTCGCCATGCACTCCCGGCGACCAACG
* *
2613197 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACTCCCGGCGACCAACG
*
2613226 AGGTCGCCATGCACTCGCGGC
1 AGGTCGCCATGCACTCCCGGC
2613247 AACATCCCCT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.18, C:0.39, G:0.29, T:0.14
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCGGCGACCAACG
Found at i:2613530 original size:29 final size:29
Alignment explanation
Indices: 2613469--2613552 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
2613459 ATGAATCCTT
** * **
2613469 GGTCGCCCCGAGTGCATGGCGACCTCCTT
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
* *
2613498 GGTCGCCGGGCGTGCATGGCGACCTAGGA
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
*
2613527 GGTCGCTGGGAGTGCATGGCGACCTA
1 GGTCGCCGGGAGTGCATGGCGACCTA
2613553 TGGTTGGGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.13, C:0.30, G:0.39, T:0.18
Consensus pattern (29 bp):
GGTCGCCGGGAGTGCATGGCGACCTACGA
Found at i:2619254 original size:77 final size:77
Alignment explanation
Indices: 2619127--2619275 Score: 208
Period size: 77 Copynumber: 1.9 Consensus size: 77
2619117 ATTTGTATTG
* * * * * *
2619127 TTTTTTTTGACACATTTTATCATTCAACGTTTTATTTTGAGTTAGAAAACATCATCGGTGGATGG
1 TTTTTTTTGACACATTTGACCACTCAACGTTTTATTTTGAGTCAAAAAACATCATCAGTGGATGG
2619192 AAATCGTCTTTA
66 AAATCGTCTTTA
* * * *
2619204 TTTTTTTTGACACATTTGACCACTCAACGTTTTATTTTGGGTCAAAAAACATCTTCAGTTGATGT
1 TTTTTTTTGACACATTTGACCACTCAACGTTTTATTTTGAGTCAAAAAACATCATCAGTGGATGG
2619269 AAATCGT
66 AAATCGT
2619276 TAGTCAACTG
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
77 62 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (77 bp):
TTTTTTTTGACACATTTGACCACTCAACGTTTTATTTTGAGTCAAAAAACATCATCAGTGGATGG
AAATCGTCTTTA
Found at i:2626316 original size:21 final size:20
Alignment explanation
Indices: 2626250--2626324 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
2626240 CAAACCTTTA
* *
2626250 AAAATGATCGATCCCTTGAG
1 AAAAGGATCGATCCCTTGTG
* *
2626270 AAAAGGATCGATCCCTTTTC
1 AAAAGGATCGATCCCTTGTG
*
2626290 AAAAGGATCAATCCCTTGGTG
1 AAAAGGATCGATCCCTT-GTG
2626311 AAAAGGATCGATCC
1 AAAAGGATCGATCC
2626325 TCAAAAGAAG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
20 32 0.70
21 14 0.30
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (20 bp):
AAAAGGATCGATCCCTTGTG
Found at i:2627447 original size:175 final size:170
Alignment explanation
Indices: 2627114--2627459 Score: 647
Period size: 175 Copynumber: 2.0 Consensus size: 170
2627104 GTATGTTTTC
2627114 TCTTTCATGGATCGCGATAGGACAACGAGATCATCGGAGTAGTCTCAAATTACCAAAATACGACG
1 TCTTTCATGGATCGCGATAGGACAACGAGATCATCGGAGTAGTCTCAAATTACCAAAATACGACG
2627179 AGTTGGCTTAATGGGCATGTATATGTCATGGTTTAAAAAGAGTCAGTAGTGTATATATGAGTTAT
66 AGTTGGCTTAATGGGCATGTATATGTCATGGTTTAAAAAGAGTCAGTAGTGTATATATGAGTTAT
2627244 TTATTTTTATTTATCGAGTTTCTAAACTAGGGCCCCATTT
131 TTATTTTTATTTATCGAGTTTCTAAACTAGGGCCCCATTT
2627284 TCTTTCATGGATCGCGATAGGACAACGAGATCATCGGAGTAGTCTCAACAAATTACCAAAATACG
1 TCTTTCATGGATCGCGATAGGACAACGAGATCATCGGAGTAGTCT---CAAATTACCAAAATACG
2627349 ACGATGTTGGCTTAATGGGCATGTATATGTCATGGTTTAAAAAGAGTCAGTTAGTGTATATATGA
63 ACGA-GTTGGCTTAATGGGCATGTATATGTCATGGTTTAAAAAGAGTCAG-TAGTGTATATATGA
2627414 GTTATTTATTTTTATTTATCGAGTTTCTAAACTAGGGCCCCATTT
126 GTTATTTATTTTTATTTATCGAGTTTCTAAACTAGGGCCCCATTT
2627459 T
1 T
2627460 TATAAATTGT
Statistics
Matches: 171, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
170 45 0.26
173 21 0.12
174 45 0.26
175 60 0.35
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (170 bp):
TCTTTCATGGATCGCGATAGGACAACGAGATCATCGGAGTAGTCTCAAATTACCAAAATACGACG
AGTTGGCTTAATGGGCATGTATATGTCATGGTTTAAAAAGAGTCAGTAGTGTATATATGAGTTAT
TTATTTTTATTTATCGAGTTTCTAAACTAGGGCCCCATTT
Found at i:2635149 original size:20 final size:20
Alignment explanation
Indices: 2635126--2635169 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
2635116 TAGGGTCAAG
2635126 TATCGATATTCAGAAGATAA
1 TATCGATATTCAGAAGATAA
*
2635146 TATCGATATTCAGAAGATAG
1 TATCGATATTCAGAAGATAA
2635166 TATC
1 TATC
2635170 AATACTGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (20 bp):
TATCGATATTCAGAAGATAA
Found at i:2635272 original size:21 final size:21
Alignment explanation
Indices: 2635246--2635295 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
2635236 ACCAAGGGTA
*
2635246 GAGTATCGTTACTCCTATTGG
1 GAGTATCGTTACTCCTATGGG
*
2635267 GAGTATCGTTACTCTTATGGG
1 GAGTATCGTTACTCCTATGGG
2635288 GAGTATCG
1 GAGTATCG
2635296 ATACCAAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.28, T:0.36
Consensus pattern (21 bp):
GAGTATCGTTACTCCTATGGG
Found at i:2639513 original size:51 final size:51
Alignment explanation
Indices: 2639437--2639538 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
2639427 GTGACAATTT
2639437 TGTAACTTTTAATAATCGAAAAACTCAATAAAACAATGCCATATAATTAAA
1 TGTAACTTTTAATAATCGAAAAACTCAATAAAACAATGCCATATAATTAAA
2639488 TGTAACTTTTAATAATCGAAAAACTCAATAAAACAATGCCATATAATTAAA
1 TGTAACTTTTAATAATCGAAAAACTCAATAAAACAATGCCATATAATTAAA
2639539 ATATCATTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (51 bp):
TGTAACTTTTAATAATCGAAAAACTCAATAAAACAATGCCATATAATTAAA
Found at i:2642566 original size:37 final size:37
Alignment explanation
Indices: 2642516--2642589 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
2642506 TAAAAATCTT
2642516 GATTAATTACTTCCTGGCCTATATGCAAGCAGAAAGC
1 GATTAATTACTTCCTGGCCTATATGCAAGCAGAAAGC
2642553 GATTAATTACTTCCTGGCCTATATGCAAGCAGAAAGC
1 GATTAATTACTTCCTGGCCTATATGCAAGCAGAAAGC
2642590 AAGCTGCAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (37 bp):
GATTAATTACTTCCTGGCCTATATGCAAGCAGAAAGC
Found at i:2643956 original size:409 final size:409
Alignment explanation
Indices: 2643186--2644011 Score: 1573
Period size: 409 Copynumber: 2.0 Consensus size: 409
2643176 ACACAATTAA
*
2643186 TGTCGTTGATCAATAGTCTATCTTATCTTGTGTGTATTTCTATTTAAAACTTTTGTGACTGCATT
1 TGTCATTGATCAATAGTCTATCTTATCTTGTGTGTATTTCTATTTAAAACTTTTGTGACTGCATT
2643251 CCCCTCCATATTTTCCAGTTTTCACATTATAACCACCTATTTGTAGGATCCGACTCCTTGTGAAT
66 CCCCTCCATATTTTCCAGTTTTCACATTATAACCACCTATTTGTAGGATCCGACTCCTTGTGAAT
2643316 ATCATATCTACCAATGGTGGCTAAAAGTGTTTTGAAGTGTACTGAATAGAAAAGTAATGAGAGAA
131 ATCATATCTACCAATGGTGGCTAAAAGTGTTTTGAAGTGTACTGAATAGAAAAGTAATGAGAGAA
2643381 ACTCAAATTTTGTTTTTGTACATGAATTGATTATCTGTTATAATGTTAACCTGGATTTGTGTGCA
196 ACTCAAATTTTGTTTTTGTACATGAATTGATTATCTGTTATAATGTTAACCTGGATTTGTGTGCA
2643446 TTCCGGATAGTTTTTTTTATCTTTATCTTGGAGAGAAATTAAGAATGTATCTGGATTTTCTCTAG
261 TTCCGGATAGTTTTTTTTATCTTTATCTTGGAGAGAAATTAAGAATGTATCTGGATTTTCTCTAG
* * *
2643511 GTTATGTAGTATTCCATAGTTGAAAATTTGACATATACATCATGTAGTGAGAAATAGTTGTAATG
326 GTCATGTAGTATTCCATAGTTGAAAATTTCACATATACATCATGTAGTGAGAAATAGTTATAATG
2643576 CTATTATTATTGTTATAAC
391 CTATTATTATTGTTATAAC
2643595 TGTCATTGATCAATAGTCTTATCTTATCTTGTGTGTATTTCTATTTAAAAC-TTTGTGACTGCAT
1 TGTCATTGATCAATAGTC-TATCTTATCTTGTGTGTATTTCTATTTAAAACTTTTGTGACTGCAT
2643659 TCCCCTCCATATTTTCCAGTTTTCACATTATAACCACCTATTTGTAGGATCCGACTCCTTGTGAA
65 TCCCCTCCATATTTTCCAGTTTTCACATTATAACCACCTATTTGTAGGATCCGACTCCTTGTGAA
*
2643724 TATCATATCTACCAATGGTGGCTAAAAGTGTTTTGAAGTGTAGTGAATAGAAAAGTAATGAGAGA
130 TATCATATCTACCAATGGTGGCTAAAAGTGTTTTGAAGTGTACTGAATAGAAAAGTAATGAGAGA
*
2643789 AACTCAAATTTTGTTTTTGTACATGAATTGATTATCTGTTATAATGTTAACCTGGTTTTGTGTGC
195 AACTCAAATTTTGTTTTTGTACATGAATTGATTATCTGTTATAATGTTAACCTGGATTTGTGTGC
2643854 ATTCCGGATAGTTTTTTTTATCTTTATCTTGGAGAGAAATTAAGAATGTATCTGGATTTTCTCTA
260 ATTCCGGATAGTTTTTTTTATCTTTATCTTGGAGAGAAATTAAGAATGTATCTGGATTTTCTCTA
2643919 GGTCATGTAGTATTCCATAGTTGAAAATTTCACATATACATCATGTAGTGAGAAATAGTTATAAT
325 GGTCATGTAGTATTCCATAGTTGAAAATTTCACATATACATCATGTAGTGAGAAATAGTTATAAT
*
2643984 GCTATTTTTATTGTTATAAC
390 GCTATTATTATTGTTATAAC
2644004 TGTCATTG
1 TGTCATTG
2644012 TTACAATTGT
Statistics
Matches: 409, Mismatches: 7, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
409 377 0.92
410 32 0.08
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (409 bp):
TGTCATTGATCAATAGTCTATCTTATCTTGTGTGTATTTCTATTTAAAACTTTTGTGACTGCATT
CCCCTCCATATTTTCCAGTTTTCACATTATAACCACCTATTTGTAGGATCCGACTCCTTGTGAAT
ATCATATCTACCAATGGTGGCTAAAAGTGTTTTGAAGTGTACTGAATAGAAAAGTAATGAGAGAA
ACTCAAATTTTGTTTTTGTACATGAATTGATTATCTGTTATAATGTTAACCTGGATTTGTGTGCA
TTCCGGATAGTTTTTTTTATCTTTATCTTGGAGAGAAATTAAGAATGTATCTGGATTTTCTCTAG
GTCATGTAGTATTCCATAGTTGAAAATTTCACATATACATCATGTAGTGAGAAATAGTTATAATG
CTATTATTATTGTTATAAC
Done.