Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007704.1 Hibiscus syriacus cultivar Beakdansim tig00109919_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: 612835
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 3
Found at i:291859 original size:83 final size:83
Alignment explanation
Indices: 291720--292274 Score: 821
Period size: 83 Copynumber: 6.7 Consensus size: 83
291710 CATTAACTGA
* *
291720 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
291785 ACCAATCATTGAATTGGG
66 ACCAATCATTGAATTGGG
* * * *
291803 AAGATGAATTTGTTAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGAAGA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
291868 ACCAATCATTGAATTGGG
66 ACCAATCATTGAATTGGG
* * * **
291886 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAAAAGA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
291951 ACCAATCATTGAATTGGG
66 ACCAATCATTGAATTGGG
* * *
291969 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAG-CAG
**
292033 AACCAATCATTGAATTTAG
65 AACCAATCATTGAATTGGG
* *
292052 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAG-CAG
* *
292117 AATCAATCATTGAATTTGG
65 AACCAATCATTGAATTGGG
* *
292136 AAGATGAATTTGCTAATAGCATCTTC-GGAAGTGTTCTTTGAGTTAT-TGATCTGGTTTGGCAAA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
**
292199 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTGGG
* * *
292217 AAGATGAA-TTGCTCATAGCATCTTCTGGAAGTATTCTTTGAGTTATTTGATCTGGTTT
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
292275 GGTAGGAACT
Statistics
Matches: 444, Mismatches: 24, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
80 16 0.04
81 46 0.10
82 26 0.06
83 306 0.69
84 50 0.11
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (83 bp):
AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
ACCAATCATTGAATTGGG
Found at i:294814 original size:21 final size:22
Alignment explanation
Indices: 294785--294838 Score: 92
Period size: 21 Copynumber: 2.5 Consensus size: 22
294775 ACATCACCTC
*
294785 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
294807 TTC-AAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
294828 TTCAAAGATGA
1 TTCAAAGATGA
294839 AAACTTTATG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 20 0.67
22 10 0.33
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:295837 original size:113 final size:112
Alignment explanation
Indices: 295301--296372 Score: 1204
Period size: 111 Copynumber: 9.8 Consensus size: 112
295291 CATTTGAAGA
* * ** * * ** *
295301 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGT-CAGTTAGAG
1 AGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCA-TTGATGGATCAGCA-TTTCCAGAGAAAG
*
295365 TT-AT-ATGAGAAGAACTCATCTGAAGAGAAGAAGAA-AAG--CATAATG
64 TTCATAATGAGAAGAACTCATCTGAAGA-AGGAAGAAGAAGTTCATAATG
* * * * *** *
295410 AGAAGAATTTGTTCAACCTTTT-CCCTGAATTC-T-ACTTGATGAAT-ATTTTTTCCAGAGGAAG
1 AGAAGAACTTGTTCAACCTTTTGCTC-AAATTCATCA-TTGATGGATCAGCATTTCCAGAGAAAG
*
295471 TTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATG
64 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * *
295519 AGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTGATGGATTAACATTTCCAGAGAAAGTT
1 AGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCATTGATGGATCAGCATTTCCAGAGAAAGTT
*
295584 CATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATG
66 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * * * *
295630 AGAAGAACTTGTTTAACCTTTTGCTTAAATTCATCACTGATGGATTATCATTGCCAGAGAAGGTT
1 AGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCATTGATGGATCAGCATTTCCAGAGAAAGTT
*
295695 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
66 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* *
295742 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCATT-GATGGATCAGCATTTCCAGAGAAAGT
295807 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
65 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * *
295855 AGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCA-TTGATGGATCAGCATTTCCAGAGAAAGT
*
295920 TCATAATGAGAAGAACTCATCTG-AGAAGGAAGAAGAAATT-ATAATG
65 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * ** * * * *
295966 AGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTAATGGAT-ATCATTGCCAGAGAAGGT
1 AGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCA-TTGATGGATCAGCATTTCCAGAGAAAGT
*
296030 TCATAATGAGAAGAA--C-TCTGAAGAAGGAAGAAGAAATTCATAATG
65 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* *
296075 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATC-GCA-TTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCATT-GATGGATCAGCATTTCCAGAGAAAGT
*
296138 TCAT-ATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATG
65 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* *
296185 AGAAGAACTTGTTCAACTTTTTGCT----TTCATCATTTGATGGATCAGCTTTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCA-TTGATGGATCAGCATTTCCAGAGAAAGT
** ****
296246 TCATAATGAGAA-CTCTTCATCT-TTCTA-G-A-AA-AAGTTCATAATG
65 TCATAATGAGAAGAAC-TCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * *
296289 AGAAGAATTTGTTCAA-CTTTTGCT-GAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAG
1 AGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCA-TTGATGGATCAGCATTTCCAGAG-AAAG
296351 TTCATAATGAGAAGAACTCATC
64 TTCATAATGAGAAGAACTCATC
296373 AAGAGCTTAT
Statistics
Matches: 844, Mismatches: 88, Indels: 65
0.85 0.09 0.07
Matches are distributed among these distances:
103 7 0.01
104 27 0.03
105 5 0.01
106 77 0.09
107 32 0.04
108 76 0.09
109 118 0.14
110 90 0.11
111 193 0.23
112 69 0.08
113 148 0.18
114 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (112 bp):
AGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCATTGATGGATCAGCATTTCCAGAGAAAGTT
CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
Found at i:295966 original size:336 final size:337
Alignment explanation
Indices: 295301--296372 Score: 1436
Period size: 336 Copynumber: 3.3 Consensus size: 337
295291 CATTTGAAGA
* * * * * *
295301 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGTCAGTTAG-A-
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACCTGATGGATCATCATTGCCAG--AGAAG
**
295364 GTT-AT-ATGAGAAGAACTCATCTGAAG-A-GAAGAAGAAAAGCATAATGAGAAGAATTTGTTCA
64 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
* * * * * *** *
295425 ACCTTTTCCCTGAATTCTA-C-TT-GATGAAT-ATTTTTTCCAGAGGAAGTTCATAATGAGAAGA
129 ACCTTTT-GCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGA
*
295486 ACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATT
193 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATT
*
295550 CATCAC-TGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAA
258 CATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA-AGGAA
295614 GAAGAAGTTCATAATG
322 GAAGAAGTTCATAATG
* *
295630 AGAAGAACTTGTTTAACCTTTTGCTTAAATTCATCA-CTGATGGATTATCATTGCCAGAGAAGGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACCTGATGGATCATCATTGCCAGAGAAGGT
295694 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
295759 CTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACT
131 CTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACT
295824 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCAT
196 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCAT
295889 CACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAA
261 CACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA-AAGGAAGAA
*
295954 GAAATT-ATAATG
325 GAAGTTCATAATG
* * * * *
295966 AGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTAATGGAT-ATCATTGCCAGAGAAGGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACCTGATGGATCATCATTGCCAGAGAAGGT
296030 TCATAATGAGAAGAA--C-TCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
296092 CTTTTGCTCAAATCCATCATTCGATGGATC-GCA-TTCCAGAGAAAGTTCAT-ATGAGAAGAACT
131 CTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACT
* * *
296154 CATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCT----TTCAT
196 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCAT
* * * * ** ***
296215 CATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAA-CTCTTCATCTTTCTA-G-A-A
261 CACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAAC-TCATC-TGAAAGGAAGA
296276 A-AAGTTCATAATG
324 AGAAGTTCATAATG
* * ** * *
296289 AGAAGAATTTGTTCAA-CTTTTGC-TGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAG
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACCTGATGGATCATCATTGCCAGAGAAG-G
296351 TTCATAATGAGAAGAACTCATC
65 TTCATAATGAGAAGAACTCATC
296373 AAGAGCTTAT
Statistics
Matches: 675, Mismatches: 46, Indels: 48
0.88 0.06 0.06
Matches are distributed among these distances:
321 22 0.03
322 37 0.05
323 24 0.04
324 2 0.00
325 4 0.01
326 52 0.08
327 2 0.00
328 18 0.03
329 36 0.05
330 86 0.13
331 25 0.04
332 43 0.06
333 78 0.12
334 7 0.01
335 39 0.06
336 129 0.19
337 70 0.10
338 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (337 bp):
AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACCTGATGGATCATCATTGCCAGAGAAGGT
TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
CTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACT
CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCAT
CACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAGGAAGAAG
AAGTTCATAATG
Found at i:296612 original size:3 final size:3
Alignment explanation
Indices: 296604--296669 Score: 98
Period size: 3 Copynumber: 22.3 Consensus size: 3
296594 ATTTTTTCAT
* * *
296604 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA CTA AT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
296651 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
296670 CAAACGGGCC
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
2 1 0.02
3 56 0.98
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:297902 original size:12 final size:12
Alignment explanation
Indices: 297887--297949 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
297877 TTTTATTATA
297887 TTATTAAATATT
1 TTATTAAATATT
297899 TTATTAAATATT
1 TTATTAAATATT
*
297911 TT-TATAAATATA
1 TTAT-TAAATATT
* *
297923 TAATAAATAGTATT
1 TTATTAA-A-TATT
*
297937 TTTTTAAATATT
1 TTATTAAATATT
297949 T
1 T
297950 ATTTTTAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 1 0.03
12 29 0.73
13 3 0.08
14 7 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
TTATTAAATATT
Found at i:297959 original size:13 final size:12
Alignment explanation
Indices: 297890--297961 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
297880 TATTATATTA
*
297890 TTAAATATTTTA
1 TTAAATATTTTT
297902 TTAAATATTTTT
1 TTAAATATTTTT
* * **
297914 ATAAATATATAA
1 TTAAATATTTTT
*
297926 TAAATAGTATTTTT
1 TTAA-A-TATTTTT
297940 TTAAATATTTATT
1 TTAAATATTT-TT
*
297953 TTTAATATT
1 TTAAATATT
297962 GAAGAAAAAG
Statistics
Matches: 45, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
12 26 0.58
13 12 0.27
14 7 0.16
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (12 bp):
TTAAATATTTTT
Found at i:300584 original size:258 final size:258
Alignment explanation
Indices: 300127--300644 Score: 1020
Period size: 258 Copynumber: 2.0 Consensus size: 258
300117 TTTCTTGTCT
300127 AACTCTTCCAAGAAACTTTGGAGCCAAACCATCTCCTTGCTGACTTCCGTAACAGTGACATATTC
1 AACTCTTCCAAGAAACTTTGGAGCCAAACCATCTCCTTGCTGACTTCCGTAACAGTGACATATTC
300192 TGCTTCAGTTGTGGAGATAGCAACTATCTTCTATAGTTGAGAAACCCAACTCACTGCGGTACCTC
66 TGCTTCAGTTGTGGAGATAGCAACTATCTTCTATAGTTGAGAAACCCAACTCACTGCGGTACCTC
300257 CTATAGTATAGACATACCTTGTAGTGTTTCTTCTGATGTCAACATTTTCCGACTAAGTAACATCT
131 CTATAGTATAGACATACCTTGTAGTGTTTCTTCTGATGTCAACATTTTCCGACTAAGTAACATCT
300322 ACATAGCTTGTCAGTATCGTATCTCCACCTTTGAAACAAAGTGTTTTGTTTGTGATACGCTGC
196 ACATAGCTTGTCAGTATCGTATCTCCACCTTTGAAACAAAGTGTTTTGTTTGTGATACGCTGC
300385 AACTCTTCCAAGAAACTTTGGAGCCAAACCATCTCCTTGCTGACTTCCGTAACAGTGACATATTC
1 AACTCTTCCAAGAAACTTTGGAGCCAAACCATCTCCTTGCTGACTTCCGTAACAGTGACATATTC
300450 TGCTTCAGTTGTGGAGATAGCAACTATCTTCTATAGTTGAGAAACCCAACTCACTGCGGTACCTC
66 TGCTTCAGTTGTGGAGATAGCAACTATCTTCTATAGTTGAGAAACCCAACTCACTGCGGTACCTC
300515 CTATAGTATAGACATACCTTGTAGTGTTTCTTCTGATGTCAACA-TTTCCGACTAAGTAAGCATC
131 CTATAGTATAGACATACCTTGTAGTGTTTCTTCTGATGTCAACATTTTCCGACTAAGTAA-CATC
300579 TACATAGCTTGTCAGTATCGTATCTCCACCTTTGAAACAAAGTGTTTTGTTTGTGATACGCTGC
195 TACATAGCTTGTCAGTATCGTATCTCCACCTTTGAAACAAAGTGTTTTGTTTGTGATACGCTGC
300643 AA
1 AA
300645 ATATCTGAGG
Statistics
Matches: 259, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
257 15 0.06
258 244 0.94
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (258 bp):
AACTCTTCCAAGAAACTTTGGAGCCAAACCATCTCCTTGCTGACTTCCGTAACAGTGACATATTC
TGCTTCAGTTGTGGAGATAGCAACTATCTTCTATAGTTGAGAAACCCAACTCACTGCGGTACCTC
CTATAGTATAGACATACCTTGTAGTGTTTCTTCTGATGTCAACATTTTCCGACTAAGTAACATCT
ACATAGCTTGTCAGTATCGTATCTCCACCTTTGAAACAAAGTGTTTTGTTTGTGATACGCTGC
Found at i:322925 original size:17 final size:17
Alignment explanation
Indices: 322887--322940 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
322877 AAAATTTAAA
**
322887 ATTTAATAAATA-AATT
1 ATTTAATAAATATTTTT
*
322903 AATTAA-AAATCATTTTT
1 ATTTAATAAAT-ATTTTT
322920 ATTTAATAAATATTTTT
1 ATTTAATAAATATTTTT
322937 ATTT
1 ATTT
322941 TGAAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 4 0.13
16 6 0.19
17 17 0.55
18 4 0.13
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTAATAAATATTTTT
Found at i:329531 original size:17 final size:17
Alignment explanation
Indices: 329509--329541 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
329499 AACTGAATGA
329509 ATAACTTATAAAGAAAT
1 ATAACTTATAAAGAAAT
329526 ATAACTTATAAAGAAA
1 ATAACTTATAAAGAAA
329542 GATGCAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (17 bp):
ATAACTTATAAAGAAAT
Found at i:331592 original size:29 final size:29
Alignment explanation
Indices: 331554--331642 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 29
331544 ATATATTTTA
*
331554 TTTTAGTCTTTTAATTTCACTACTTTAATT
1 TTTTA-TCTTTTAATTTCAATACTTTAATT
* *
331584 TTTTATCTTTTTAATTT--TTGCTTTACATT
1 TTTTATC-TTTTAATTTCAATACTTTA-ATT
* *
331613 TTTCAATATTTTAATTTCAATACTTTAATT
1 TTT-TATCTTTTAATTTCAATACTTTAATT
331643 ATTACATTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
28 6 0.12
29 17 0.35
30 19 0.40
31 6 0.12
ACGTcount: A:0.25, C:0.11, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTTATCTTTTAATTTCAATACTTTAATT
Found at i:331630 original size:14 final size:14
Alignment explanation
Indices: 331613--331642 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
331603 GCTTTACATT
*
331613 TTTCAATATTTTAA
1 TTTCAATACTTTAA
331627 TTTCAATACTTTAA
1 TTTCAATACTTTAA
331641 TT
1 TT
331643 ATTACATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTCAATACTTTAA
Found at i:331771 original size:12 final size:11
Alignment explanation
Indices: 331755--331805 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
331745 TTTATTTACA
331755 ATTTTATTATT
1 ATTTTATTATT
*
331766 ACTTTTAATA-T
1 A-TTTTATTATT
331777 ATTTTAATTATT
1 ATTTT-ATTATT
*
331789 ACTTTAATTATT
1 A-TTTTATTATT
331801 ATTTT
1 ATTTT
331806 CATCTTAGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
10 4 0.12
11 9 0.28
12 16 0.50
13 3 0.09
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTTATTATT
Found at i:331780 original size:22 final size:21
Alignment explanation
Indices: 331755--331800 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 21
331745 TTTATTTACA
331755 ATTTT-ATTATTACTTTTAATAT
1 ATTTTAATTATTAC-TTTAAT-T
331777 ATTTTAATTATTACTTTAATT
1 ATTTTAATTATTACTTTAATT
331798 ATT
1 ATT
331801 ATTTTCATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.17
22 11 0.48
23 8 0.35
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTTAATTATTACTTTAATT
Found at i:333589 original size:195 final size:195
Alignment explanation
Indices: 333257--333648 Score: 784
Period size: 195 Copynumber: 2.0 Consensus size: 195
333247 CAGTTAGGTT
333257 AATTTTTCCAAACAAAGCATGGAACTAGAATGCATGATGTTAGGATTTATACCTTAATAAATAGA
1 AATTTTTCCAAACAAAGCATGGAACTAGAATGCATGATGTTAGGATTTATACCTTAATAAATAGA
333322 ATTTTTTTCTTTCCATTAATTGGTACTAACCATTTTATTTTTTCTTATTTTATTTTTTTCATGCA
66 ATTTTTTTCTTTCCATTAATTGGTACTAACCATTTTATTTTTTCTTATTTTATTTTTTTCATGCA
333387 TGTTATTTTTGCTCTAATTTGTTTATATTGATTTCTTTTTGCATTGCATGATCATGGAATAACCA
131 TGTTATTTTTGCTCTAATTTGTTTATATTGATTTCTTTTTGCATTGCATGATCATGGAATAACCA
333452 AATTTTTCCAAACAAAGCATGGAACTAGAATGCATGATGTTAGGATTTATACCTTAATAAATAGA
1 AATTTTTCCAAACAAAGCATGGAACTAGAATGCATGATGTTAGGATTTATACCTTAATAAATAGA
333517 ATTTTTTTCTTTCCATTAATTGGTACTAACCATTTTATTTTTTCTTATTTTATTTTTTTCATGCA
66 ATTTTTTTCTTTCCATTAATTGGTACTAACCATTTTATTTTTTCTTATTTTATTTTTTTCATGCA
333582 TGTTATTTTTGCTCTAATTTGTTTATATTGATTTCTTTTTGCATTGCATGATCATGGAATAACCA
131 TGTTATTTTTGCTCTAATTTGTTTATATTGATTTCTTTTTGCATTGCATGATCATGGAATAACCA
333647 AA
1 AA
333649 AGGTGTTGAC
Statistics
Matches: 197, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
195 197 1.00
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (195 bp):
AATTTTTCCAAACAAAGCATGGAACTAGAATGCATGATGTTAGGATTTATACCTTAATAAATAGA
ATTTTTTTCTTTCCATTAATTGGTACTAACCATTTTATTTTTTCTTATTTTATTTTTTTCATGCA
TGTTATTTTTGCTCTAATTTGTTTATATTGATTTCTTTTTGCATTGCATGATCATGGAATAACCA
Found at i:334220 original size:30 final size:30
Alignment explanation
Indices: 334184--334241 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
334174 AGAATGTCAT
334184 GGAAGAAGTTGCAATCCAGACAAGCAATAC
1 GGAAGAAGTTGCAATCCAGACAAGCAATAC
* *
334214 GGAAGAAGTTGCAGTCTAGACAAGCAAT
1 GGAAGAAGTTGCAATCCAGACAAGCAAT
334242 TTGGCTCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.17, G:0.26, T:0.16
Consensus pattern (30 bp):
GGAAGAAGTTGCAATCCAGACAAGCAATAC
Found at i:334471 original size:14 final size:14
Alignment explanation
Indices: 334448--334495 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
334438 TGCATTTGCA
334448 TTTTGCATTTTTAC
1 TTTTGCATTTTTAC
* *
334462 TTTTGTATTTATA-
1 TTTTGCATTTTTAC
334475 TTTT-CATTTTTAC
1 TTTTGCATTTTTAC
*
334488 ATTTGCAT
1 TTTTGCAT
334496 CTTTGCATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
12 6 0.22
13 7 0.26
14 14 0.52
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (14 bp):
TTTTGCATTTTTAC
Found at i:334831 original size:28 final size:28
Alignment explanation
Indices: 334799--334853 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
334789 CCATGGAGAG
334799 AAACCCTTATAGGATCTTGTTGTGAAAA
1 AAACCCTTATAGGATCTTGTTGTGAAAA
334827 AAACCCTTATAGGATCTTGTTGTGAAA
1 AAACCCTTATAGGATCTTGTTGTGAAA
334854 GATTTGAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (28 bp):
AAACCCTTATAGGATCTTGTTGTGAAAA
Found at i:336942 original size:72 final size:72
Alignment explanation
Indices: 336851--336984 Score: 223
Period size: 72 Copynumber: 1.9 Consensus size: 72
336841 TACAATAAAG
*
336851 CTTGAGTTATCCCCCTAAAGCAATTGGTTAGTAGCCCCAGCTTTATGGATAATATTCAGCTAGTT
1 CTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCAGCTTTATGGATAATATTCAGCTAGTT
336916 TGTTATT
66 TGTTATT
* * **
336923 CTTGAGTTGTCCCCCTAAAGCAATTGGTTAATCGCCCTGGCTTTATGGATAATATTCAGCTA
1 CTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCAGCTTTATGGATAATATTCAGCTA
336985 ACCTATTATA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 57 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (72 bp):
CTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCAGCTTTATGGATAATATTCAGCTAGTT
TGTTATT
Found at i:339810 original size:30 final size:27
Alignment explanation
Indices: 339749--339802 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
339739 ATTACTTCTT
339749 AAGTTTGTGACAACATGAAGAGAATTC
1 AAGTTTGTGACAACATGAAGAGAATTC
339776 AAGTTTGTGACAACATGAAGAGAATTC
1 AAGTTTGTGACAACATGAAGAGAATTC
339803 CTCAAGTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (27 bp):
AAGTTTGTGACAACATGAAGAGAATTC
Found at i:340105 original size:35 final size:35
Alignment explanation
Indices: 340054--340120 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
340044 TTCAACCAGA
340054 AATAGAATATTGGGGCATT-TT-GAAGGCTCATAGT
1 AATAGAATATTGGGGCATTCTTGGAA-GCTCATAGT
*
340088 AATATGAATATTTGGGCATTCTTGGAAGCTCAT
1 AATA-GAATATTGGGGCATTCTTGGAAGCTCAT
340121 CTCAGCAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 4 0.14
35 14 0.48
36 8 0.28
37 3 0.10
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.34
Consensus pattern (35 bp):
AATAGAATATTGGGGCATTCTTGGAAGCTCATAGT
Found at i:341668 original size:22 final size:22
Alignment explanation
Indices: 341634--341709 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
341624 TCTACATTCC
*
341634 TCAAAGATGATAGATTCTCTCT
1 TCAAAAATGATAGATTCTCTCT
*
341656 TCAAAAATTATAGATTCTCT-T
1 TCAAAAATGATAGATTCTCTCT
* * * *
341677 TCCAAATATGATGGATTATCTTT
1 T-CAAAAATGATAGATTCTCTCT
*
341700 TCAAAGATGA
1 TCAAAAATGA
341710 AAGCTTTATT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
21 2 0.04
22 41 0.91
23 2 0.04
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (22 bp):
TCAAAAATGATAGATTCTCTCT
Found at i:342254 original size:113 final size:113
Alignment explanation
Indices: 342056--342506 Score: 525
Period size: 113 Copynumber: 3.9 Consensus size: 113
342046 TAACAAATAT
* * *
342056 TCGAATCCATCACTCAATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATATGA
1 TCGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
* *
342121 AGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTCGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *
342169 TCGAATTCATCACTCGGTGAATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
*
342234 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * *
342282 TCGAATTCATCACTCGATGGATCAACATTTCCA-GAAGAGTTCATAATGAGAAAAATTCATCTGA
1 TCGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
* * *
342346 AAAATG-AGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * * *
342393 TCGACGCTATCA-CAAAAGAAGATAGATCAGCATCAACATTTCCA-GAAGAGTTCATAATGAGAA
1 TCGA--AT-TCATC------A-CTCGAT--GGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
* * * *
342456 GAACTCATCTGAAGAA-TAAGAAGAATTTCATAATGAGAAGAATTTATTCAA
54 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
342507 ACTTGCCTTA
Statistics
Matches: 293, Mismatches: 32, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
111 43 0.15
112 32 0.11
113 135 0.46
114 3 0.01
119 1 0.00
120 4 0.01
122 75 0.26
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (113 bp):
TCGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:346671 original size:13 final size:13
Alignment explanation
Indices: 346643--346683 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
346633 TTTTTAGATG
346643 AAATAATTTTAAAA
1 AAAT-ATTTTAAAA
*
346657 AAAT-TATTAAAA
1 AAATATTTTAAAA
346669 AAATATTTTAAAA
1 AAATATTTTAAAA
346682 AA
1 AA
346684 TTAACGAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.46
13 9 0.38
14 4 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATATTTTAAAA
Found at i:354306 original size:18 final size:17
Alignment explanation
Indices: 354274--354315 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
354264 GAATTATATT
*
354274 AGTAAAATATTAAATAA
1 AGTAAATTATTAAATAA
354291 AGTAAATTACTTAAATAA
1 AGTAAATTA-TTAAATAA
*
354309 ATTAAAT
1 AGTAAAT
354316 ACATAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (17 bp):
AGTAAATTATTAAATAA
Found at i:361355 original size:22 final size:22
Alignment explanation
Indices: 361327--361380 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
361317 ACATCATTAT
361327 TATGCATTATTATAATAAAACA
1 TATGCATTATTATAATAAAACA
*
361349 TATGCATTATTATAATAAAACG
1 TATGCATTATTATAATAAAACA
361371 TATGCATTAT
1 TATGCATTAT
361381 GGAAATGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.39
Consensus pattern (22 bp):
TATGCATTATTATAATAAAACA
Found at i:363430 original size:15 final size:16
Alignment explanation
Indices: 363404--363433 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
363394 ATAATCATTT
363404 TATTATAAATAATTAA
1 TATTATAAATAATTAA
363420 TATTA-AAATAATTA
1 TATTATAAATAATTA
363434 TGACTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTATAAATAATTAA
Found at i:364022 original size:25 final size:25
Alignment explanation
Indices: 363994--364056 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 25
363984 AATATCGATA
*
363994 AAATATAATAAA-ACTAAA-CAAGGAT
1 AAATA-AATAAATAATAAATCAA-GAT
*
364019 AAATAAATAAATAATAAATGAAGAT
1 AAATAAATAAATAATAAATCAAGAT
364044 AAATAAATAAATA
1 AAATAAATAAATA
364057 CATGAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 6 0.18
25 26 0.76
26 2 0.06
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.22
Consensus pattern (25 bp):
AAATAAATAAATAATAAATCAAGAT
Found at i:364026 original size:4 final size:4
Alignment explanation
Indices: 364017--364071 Score: 67
Period size: 4 Copynumber: 13.2 Consensus size: 4
364007 CTAAACAAGG
*
364017 ATAA ATAA ATAA AT-A ATAA ATGAA GATAA ATAA ATAA ATAC ATGAA ATAA
1 ATAA ATAA ATAA ATAA ATAA AT-AA -ATAA ATAA ATAA ATAA AT-AA ATAA
364067 ATAA A
1 ATAA A
364072 AGGAATGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
3 3 0.07
4 33 0.73
5 7 0.16
6 2 0.04
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:364047 original size:21 final size:21
Alignment explanation
Indices: 364019--364071 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
364009 AAACAAGGAT
364019 AAATAAATAAAT-AATAAATG
1 AAATAAATAAATAAATAAATG
*
364039 AAGATAAATAAATAAATACATG
1 AA-ATAAATAAATAAATAAATG
364061 AAATAAATAAA
1 AAATAAATAAA
364072 AGGAATGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 2 0.07
21 19 0.63
22 9 0.30
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.23
Consensus pattern (21 bp):
AAATAAATAAATAAATAAATG
Found at i:364107 original size:2 final size:2
Alignment explanation
Indices: 364100--364151 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
364090 AAATATTATG
* * *
364100 TA TA TA TA TA TA TT TA TA TA TA TA TA TT TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
364142 TA TA TA TA TA
1 TA TA TA TA TA
364152 CATTTAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:364119 original size:14 final size:14
Alignment explanation
Indices: 364100--364157 Score: 107
Period size: 14 Copynumber: 4.1 Consensus size: 14
364090 AAATATTATG
364100 TATATATATATATT
1 TATATATATATATT
364114 TATATATATATATT
1 TATATATATATATT
364128 TATATATATATATT
1 TATATATATATATT
*
364142 TATATATATACATT
1 TATATATATATATT
364156 TA
1 TA
364158 AAAAAGTATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
14 43 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (14 bp):
TATATATATATATT
Found at i:364167 original size:28 final size:28
Alignment explanation
Indices: 364107--364168 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
364097 ATGTATATAT
* * *
364107 ATATATTTATATATATATATTTATATAT
1 ATATATTTATATATATACATTTATAAAA
364135 ATATATTTATATATATACATTTA-AAAA
1 ATATATTTATATATATACATTTATAAAA
364162 AGTATAT
1 A-TATAT
364169 CCAATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 3 0.10
28 27 0.90
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (28 bp):
ATATATTTATATATATACATTTATAAAA
Found at i:364359 original size:12 final size:12
Alignment explanation
Indices: 364342--364366 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
364332 TGTCTAAAAC
364342 ATTTATATATAT
1 ATTTATATATAT
364354 ATTTATATATAT
1 ATTTATATATAT
364366 A
1 A
364367 ATAAAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTATATATAT
Found at i:365604 original size:3 final size:3
Alignment explanation
Indices: 365596--365630 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
365586 AATAAAATAA
365596 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
365631 TAATAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:365635 original size:3 final size:3
Alignment explanation
Indices: 365629--365715 Score: 165
Period size: 3 Copynumber: 29.0 Consensus size: 3
365619 CAACAACAAC
365629 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
365677 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
365716 GATGATGATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:367559 original size:30 final size:30
Alignment explanation
Indices: 367525--367593 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
367515 CTTGGTTCTG
367525 ATACTATTTAACA-TGAGTGGCCAAGTCCCT
1 ATACTATTTAACATTG-GTGGCCAAGTCCCT
**
367555 ATACTATTTGGCATTGGTGGCCAAGTCCCT
1 ATACTATTTAACATTGGTGGCCAAGTCCCT
*
367585 GTACTATTT
1 ATACTATTT
367594 GGTGCTTAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 33 0.94
31 2 0.06
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35
Consensus pattern (30 bp):
ATACTATTTAACATTGGTGGCCAAGTCCCT
Found at i:367947 original size:24 final size:23
Alignment explanation
Indices: 367915--367964 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
367905 TCAAAAGGTG
* *
367915 AAAAAGCTTTATTAAAAAGTTTT
1 AAAAAGCTTTATGAAAAAATTTT
367938 AAAAATGCTTTATGAAAAAATTTT
1 AAAAA-GCTTTATGAAAAAATTTT
367962 AAA
1 AAA
367965 TAACGAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (23 bp):
AAAAAGCTTTATGAAAAAATTTT
Found at i:373396 original size:27 final size:26
Alignment explanation
Indices: 373365--373424 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
373355 AATATAGTCA
*
373365 AACTAAAC-AAGTATAAGTAAATAACAT
1 AACTAAACGAAG-ATAAATAAATAA-AT
373392 AACTAAACGAAGATAAATAAATAAAT
1 AACTAAACGAAGATAAATAAATAAAT
*
373418 AAATAAA
1 AACTAAA
373425 TATATGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 8 0.27
27 19 0.63
28 3 0.10
ACGTcount: A:0.65, C:0.08, G:0.07, T:0.20
Consensus pattern (26 bp):
AACTAAACGAAGATAAATAAATAAAT
Found at i:373413 original size:4 final size:4
Alignment explanation
Indices: 373404--373441 Score: 58
Period size: 4 Copynumber: 9.2 Consensus size: 4
373394 CTAAACGAAG
*
373404 ATAA ATAA ATAA ATAA ATAA ATAT ATGAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA ATAA A
373442 AAGAATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 28 0.90
5 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:373503 original size:18 final size:18
Alignment explanation
Indices: 373480--373536 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 18
373470 GTAAATATAT
*
373480 ATATATATTTTAAAAATA
1 ATATATATATTAAAAATA
** *
373498 ATATATCCAATAAAAATA
1 ATATATATATTAAAAATA
* * *
373516 ATATTTATGTTAAAAAGA
1 ATATATATATTAAAAATA
373534 ATA
1 ATA
373537 AAATATGTAT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (18 bp):
ATATATATATTAAAAATA
Found at i:373712 original size:2 final size:2
Alignment explanation
Indices: 373700--373747 Score: 87
Period size: 2 Copynumber: 23.5 Consensus size: 2
373690 ATACATACAA
373700 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
373743 AT AT A
1 AT AT A
373748 ATAATAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:379259 original size:67 final size:67
Alignment explanation
Indices: 379151--379314 Score: 310
Period size: 67 Copynumber: 2.4 Consensus size: 67
379141 GTTGAGCTTC
379151 TTTTTGTGTATGGCAAATATCTGCCTAACTTCATATGATATACCTTGCAGCAGTAATATATGTTT
1 TTTTTGTGTATGGCAAATATCTGCCTAACTTCATATGATATACCTTGCAGCAGTAATATATGTTT
379216 TT
66 TT
*
379218 TTTTTGTGTATGGCAAATATCTGCCTAACTTCATATGATATACCTTGTAGCAGTAATATATGTTT
1 TTTTTGTGTATGGCAAATATCTGCCTAACTTCATATGATATACCTTGCAGCAGTAATATATGTTT
379283 TT
66 TT
*
379285 TTTTTGTGTATGGCAAATATATGCCTAACT
1 TTTTTGTGTATGGCAAATATCTGCCTAACT
379315 CAAGAATCAA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 95 1.00
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (67 bp):
TTTTTGTGTATGGCAAATATCTGCCTAACTTCATATGATATACCTTGCAGCAGTAATATATGTTT
TT
Found at i:381157 original size:25 final size:25
Alignment explanation
Indices: 381129--381182 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
381119 TATAATATGT
381129 TTTATTC-CTTCTAAAATTTTATAAG
1 TTTATTCTC-TCTAAAATTTTATAAG
*
381154 TTTATTTTCTCTAAAATTTTATAAG
1 TTTATTCTCTCTAAAATTTTATAAG
381179 TTTA
1 TTTA
381183 CCTCTAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.31, C:0.09, G:0.04, T:0.56
Consensus pattern (25 bp):
TTTATTCTCTCTAAAATTTTATAAG
Found at i:381875 original size:333 final size:334
Alignment explanation
Indices: 381112--382067 Score: 1443
Period size: 333 Copynumber: 2.9 Consensus size: 334
381102 GCATTATGCC
*
381112 TTTTATTTATAATATGTTTTATTCCTTCTAAAATTTTATAAGTTTATTTTCTCTAAAATTTTATA
1 TTTTATTTATAATATGTTTTCTTCCTTCTAAAATTTTATAAGTTTATTTTCTCTAAAATTTTATA
* *
381177 AGTTTACCTCTAACATAAAATCTTGAATTAAG------TTTT--TTTT-C-TCTAGCTTGAGATT
66 AGTTTACCTATAACATAAAATCTTGAATTAAGTTTTTTTTTTCATTTTCCTTCTATCTTGAGATT
381232 AATTTGAAAATCCACAAATTTATAATCTAGAAAAAAATAATTGATTTGAGGTTTTTTCGATTTCT
131 AATTTGAAAATCCACAAATTTATAATCTAGAAAAAAATAA-TGATTTGAGGTTTTTTCGATTTCT
** * * *
381297 TTATTTTTTTCCTAGTCCTGTTCTCCTAAATTATTCAGTCTTCCTAATTTGTTTATCTATAAGTT
195 TTA--TTTTTCCCGGTCCTATTCTCCCAAATTCTTCAGTCTTCCTAATTTGTTTATCTATAAGTT
* * *
381362 TTACTTGCAATCTTTTTGTTTCTTCTTCTCTTCGAATATGTTATCAATAATTAAGTAAGGACGAA
258 TTACTTGCAATCTTTTTGTTTCTTCTGCTGTTTGAATATGTTATCAATAATTAAGTAAGGACGAA
381427 TCTTATTATTTTTAT
323 -CTTATTA--TTTAT
* * *
381442 TTTTATTTATAATATGTTTTCCTCATTTTAAAATTTTATAAGTTTATTTTCTCTAAAATTTTATA
1 TTTTATTTATAATATGTTTTCTTCCTTCTAAAATTTTATAAGTTTATTTTCTCTAAAATTTTATA
*
381507 AGTTTACCTTTAACATAAAATCTTGAATTAAGTTTTTTTTTTCATTTTCCTTCTATCTTGAGATT
66 AGTTTACCTATAACATAAAATCTTGAATTAAGTTTTTTTTTTCATTTTCCTTCTATCTTGAGATT
*
381572 AATTTGAAAATCCACAAATTTATAACCTAGAAAAAAATGAATGATTTGAGGTTTTTTCGATTTCT
131 AATTTGAAAATCCACAAATTTATAATCTAGAAAAAAAT-AATGATTTGAGGTTTTTTCGATTTCT
* *
381637 TTATTTTTCCCCGGTCCTCTTCTCCCAAATTCTCCAGTCTTCCTAATTTGTTTATCTATAAGTTT
195 TTATTTTT-CCCGGTCCTATTCTCCCAAATTCTTCAGTCTTCCTAATTTGTTTATCTATAAGTTT
* *
381702 TACTTGCAATCTTTTTGTTTCTTCTGCTGTTTGAATCTGTTATCAATAATTAAGTAAGGACGGA-
259 TACTTGCAATCTTTTTGTTTCTTCTGCTGTTTGAATATGTTATCAATAATTAAGTAAGGACGAAC
381766 TT-TTA-TTAT
324 TTATTATTTAT
* *
381775 TTTTATTTATAATATGTTTTCTTCCTTCTAAAATTTTATGAGTTTACTTTCTCTAAAATTTTATA
1 TTTTATTTATAATATGTTTTCTTCCTTCTAAAATTTTATAAGTTTATTTTCTCTAAAATTTTATA
* *
381840 AGTTTACCTATAACATAAAATCTTGAATTAAGTTTTTTATTTTCATTTTCCTTCTCTATTGAGAT
66 AGTTTACCTATAACATAAAATCTTGAATTAAGTTTTTT-TTTTCATTTTCCTTCTATCTTGAGAT
*
381905 TAAGTTGAAAATCCACAAATTTATAATCTAGAAAAAAATAAATGATTTGAGGTTTTTTCGATTTC
130 TAATTTGAAAATCCACAAATTTATAATCTAGAAAAAAAT-AATGATTTGAGGTTTTTTCGATTTC
* * **
381970 TTTATTTTTCCCGGTTCTATTCTCCCAAATTCTTTAGTCTTCCTAATTTGTTTATCTATAAACTT
194 TTTATTTTTCCCGGTCCTATTCTCCCAAATTCTTCAGTCTTCCTAATTTGTTTATCTATAAGTTT
* * *
382035 CAATTGCAATCTTTTTGTTTCTCCTGCTGTTTG
259 TACTTGCAATCTTTTTGTTTCTTCTGCTGTTTG
382068 TCAAAAATTT
Statistics
Matches: 575, Mismatches: 38, Indels: 23
0.90 0.06 0.04
Matches are distributed among these distances:
330 92 0.16
333 181 0.31
334 95 0.17
336 7 0.01
337 2 0.00
338 9 0.02
339 110 0.19
340 77 0.13
341 2 0.00
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (334 bp):
TTTTATTTATAATATGTTTTCTTCCTTCTAAAATTTTATAAGTTTATTTTCTCTAAAATTTTATA
AGTTTACCTATAACATAAAATCTTGAATTAAGTTTTTTTTTTCATTTTCCTTCTATCTTGAGATT
AATTTGAAAATCCACAAATTTATAATCTAGAAAAAAATAATGATTTGAGGTTTTTTCGATTTCTT
TATTTTTCCCGGTCCTATTCTCCCAAATTCTTCAGTCTTCCTAATTTGTTTATCTATAAGTTTTA
CTTGCAATCTTTTTGTTTCTTCTGCTGTTTGAATATGTTATCAATAATTAAGTAAGGACGAACTT
ATTATTTAT
Found at i:386780 original size:23 final size:23
Alignment explanation
Indices: 386754--386799 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
386744 TATTTGTGTA
386754 AATTTTCATATAGGCTAGATCAG
1 AATTTTCATATAGGCTAGATCAG
*
386777 AATTTTCATATAGGCTATATCAG
1 AATTTTCATATAGGCTAGATCAG
386800 GCTTGTAATG
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:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (23 bp):
AATTTTCATATAGGCTAGATCAG
Found at i:403057 original size:59 final size:59
Alignment explanation
Indices: 402965--403082 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
402955 TGTTATGATA
402965 GCAGGAAAATTAGGGTTTGATCGTGGTGATTTGGGGGAAATTTCGAAGAGAAGATTGGG
1 GCAGGAAAATTAGGGTTTGATCGTGGTGATTTGGGGGAAATTTCGAAGAGAAGATTGGG
403024 GCAGGAAAATTAGGGTTTGATCGTGGTGATTTGGGGGAAATTTCGAAGAGAAGATTGGG
1 GCAGGAAAATTAGGGTTTGATCGTGGTGATTTGGGGGAAATTTCGAAGAGAAGATTGGG
403083 ATGCAACAGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.29, C:0.05, G:0.39, T:0.27
Consensus pattern (59 bp):
GCAGGAAAATTAGGGTTTGATCGTGGTGATTTGGGGGAAATTTCGAAGAGAAGATTGGG
Found at i:406807 original size:20 final size:20
Alignment explanation
Indices: 406784--406833 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
406774 CGATTTCAAA
*
406784 TTCGCAGCATGGATTCTAAT
1 TTCGCAACATGGATTCTAAT
406804 TTCGCAACATGGATTCTAAT
1 TTCGCAACATGGATTCTAAT
406824 TTCGCAACAT
1 TTCGCAACAT
406834 AATTTCCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCGCAACATGGATTCTAAT
Found at i:407529 original size:34 final size:34
Alignment explanation
Indices: 407491--407556 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
407481 GCGATTTTAG
* *
407491 TTTTCGCGTTGCGAATTTT-GTGTTGCGAATTTCA
1 TTTTCGAGTTGCG-ATTTTCATGTTGCGAATTTCA
407525 TTTTCGAGTTGCGATTTTCATGTTGCGAATTT
1 TTTTCGAGTTGCGATTTTCATGTTGCGAATTT
407557 AAGTTTCAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 24 0.83
ACGTcount: A:0.15, C:0.14, G:0.23, T:0.48
Consensus pattern (34 bp):
TTTTCGAGTTGCGATTTTCATGTTGCGAATTTCA
Found at i:409095 original size:42 final size:42
Alignment explanation
Indices: 409041--409188 Score: 179
Period size: 42 Copynumber: 3.5 Consensus size: 42
409031 ACCCCCCACT
* * ** * *
409041 TCGACACCGAGATTCATCACCTCATCGAGCCTCTTCTCCACT
1 TCGACACCGAGATCCATCACCTGATCGAGCCAATTCTACACC
*
409083 TCGACACCGAGATCCATCACCTGATCGAGCCGATTCTACACC
1 TCGACACCGAGATCCATCACCTGATCGAGCCAATTCTACACC
* * * *
409125 TCAATACTGAGAGCCATCACCTGATCGAGCCAATTCTACACC
1 TCGACACCGAGATCCATCACCTGATCGAGCCAATTCTACACC
* *
409167 TCGACACCGAGAGCCATTACCT
1 TCGACACCGAGATCCATCACCT
409189 ATTTCATCAC
Statistics
Matches: 91, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.26, C:0.37, G:0.15, T:0.22
Consensus pattern (42 bp):
TCGACACCGAGATCCATCACCTGATCGAGCCAATTCTACACC
Found at i:409325 original size:21 final size:21
Alignment explanation
Indices: 409284--409334 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
409274 CTTCACCTCC
*
409284 ACATGATGAGTTAGGTGCTTT
1 ACATGATGAGGTAGGTGCTTT
* *
409305 ACATGATGAGGTCGGTTCTTT
1 ACATGATGAGGTAGGTGCTTT
409326 A-AGTGATGA
1 ACA-TGATGA
409335 TAATGATGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.25, C:0.10, G:0.29, T:0.35
Consensus pattern (21 bp):
ACATGATGAGGTAGGTGCTTT
Found at i:409740 original size:21 final size:20
Alignment explanation
Indices: 409702--409770 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
409692 CACCTGTCAT
*
409702 GTTCAAGAG-CCATCCCATC
1 GTTCAAGAGCCCCTCCCATC
409721 GTTCAAGAGGCCCCTCCCATC
1 GTTCAAGA-GCCCCTCCCATC
* * * *
409742 GTTCAGGATACACCTCCCACC
1 GTTCAAGA-GCCCCTCCCATC
409763 GTTCAAGA
1 GTTCAAGA
409771 TCCATATGGC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 8 0.20
20 1 0.02
21 32 0.78
ACGTcount: A:0.25, C:0.38, G:0.17, T:0.20
Consensus pattern (20 bp):
GTTCAAGAGCCCCTCCCATC
Found at i:411594 original size:18 final size:18
Alignment explanation
Indices: 411571--411606 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
411561 AAGGCGGTTG
*
411571 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
411589 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
411607 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:413904 original size:24 final size:24
Alignment explanation
Indices: 413870--413923 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
413860 CTGAAACATA
413870 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
413894 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
413918 ATCAAA
1 ATCAAA
413924 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:414903 original size:20 final size:20
Alignment explanation
Indices: 414868--414925 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
414858 TTGCGAATTT
*
414868 GAAATTCCGTGTTGCGTAAA-A
1 GAAATT-CGAGTTGCG-AAACA
414889 GAAATTCGAGTTGCGAAATCA
1 GAAATTCGAGTTGCGAAA-CA
414910 GAAA-TCGAGTTGCGAA
1 GAAATTCGAGTTGCGAA
414926 TTCAAAATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
19 3 0.09
20 20 0.59
21 11 0.32
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (20 bp):
GAAATTCGAGTTGCGAAACA
Found at i:415763 original size:19 final size:19
Alignment explanation
Indices: 415712--415763 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
415702 TTTTTTAAAA
*
415712 TTTAATAAAAATATTAAATT
1 TTTAATAAAAA-ATAAAATT
* ***
415732 TATAATTGGAAATAAAATT
1 TTTAATAAAAAATAAAATT
415751 TTTAATAAAAAAT
1 TTTAATAAAAAAT
415764 TATTTCTTTA
Statistics
Matches: 23, Mismatches: 9, Indels: 1
0.70 0.27 0.03
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
TTTAATAAAAAATAAAATT
Found at i:421613 original size:23 final size:23
Alignment explanation
Indices: 421587--421655 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
421577 CACCACATCT
* *
421587 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCATCGAAGTGCCA
* * *
421610 CGTAGAATTGCATCGTAGTGCCG
1 CGTAGAAATGCATCGAAGTGCCA
*
421633 CATAGAAATGCATCGAAGTGCCA
1 CGTAGAAATGCATCGAAGTGCCA
421656 TATAAAGTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCATCGAAGTGCCA
Found at i:421903 original size:103 final size:103
Alignment explanation
Indices: 421664--422084 Score: 736
Period size: 103 Copynumber: 4.2 Consensus size: 103
421654 CATATAAAGT
*
421664 TGTCCCTAAGGACCACATATCATTCCTTAAG----A-AT-CATATGCC-AAGATCAAGTATGTGT
1 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
*
421722 CTCAACAGACCTCACACCTATTCCAAAGAATA-ATATA
66 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
421759 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
1 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
421824 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
66 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
421862 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
1 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
*
421927 CTCAACAAACCTCACACCTGTTCCAAAGAATACATATA
66 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
421965 TGTCCCGAAGGACCAC--ATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
1 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
*
422028 CTCAACAGACCTCACACATGTTCCAAAGAATACATATA
66 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
422066 TGTCCCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
422085 GACCCTCTAC
Statistics
Matches: 311, Mismatches: 5, Indels: 12
0.95 0.02 0.04
Matches are distributed among these distances:
95 30 0.10
99 1 0.00
100 2 0.01
101 107 0.34
102 47 0.15
103 124 0.40
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (103 bp):
TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
Found at i:422016 original size:204 final size:197
Alignment explanation
Indices: 421664--422084 Score: 718
Period size: 204 Copynumber: 2.1 Consensus size: 197
421654 CATATAAAGT
*
421664 TGTCCCTAAGGACCACATATCATTCCTTAAGAATCATATGCCAAGATCAAGTATGTGTCTCAACA
1 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATGCCAAGATCAAGTATGTGTCTCAACA
*
421729 GACCTCACACCTATTCCAAAGAATAATATATGTCCCGAAGGACCACATATCATTCCTTAAGAATC
66 AACCTCACACCTATTCCAAAGAATAATATATGTCCCGAAGGACCACA-ATCATTCCTTAAGAATC
*
421794 ATATACATATGCCAAAGATCAAGTATGTGTCTCAACAGACCTCACACCTGTTCCAAAGAATACAT
130 ATATACATATGCCAAAGATCAAGTATGTGTCTCAACAGACCTCACACATGTTCCAAAGAATACAT
421859 ATA
195 ATA
421862 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
1 TGTCCCGAAGGACCACATATCATTCCTTAAG----A-AT-CATATGCC-AAGATCAAGTATGTGT
*
421927 CTCAACAAACCTCACACCTGTTCCAAAGAATACATATATGTCCCGAAGGACCAC-ATCATTCCTT
59 CTCAACAAACCTCACACCTATTCCAAAGAATA-ATATATGTCCCGAAGGACCACAATCATTCCTT
421991 AAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCAACAGACCTCACACATGTTCCAAAG
123 AAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCAACAGACCTCACACATGTTCCAAAG
422056 AATACATATA
188 AATACATATA
422066 TGTCCCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
422085 GACCCTCTAC
Statistics
Matches: 211, Mismatches: 4, Indels: 10
0.94 0.02 0.04
Matches are distributed among these distances:
198 30 0.14
202 1 0.00
203 2 0.01
204 111 0.53
205 46 0.22
206 21 0.10
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (197 bp):
TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATGCCAAGATCAAGTATGTGTCTCAACA
AACCTCACACCTATTCCAAAGAATAATATATGTCCCGAAGGACCACAATCATTCCTTAAGAATCA
TATACATATGCCAAAGATCAAGTATGTGTCTCAACAGACCTCACACATGTTCCAAAGAATACATA
TA
Found at i:422699 original size:21 final size:21
Alignment explanation
Indices: 422673--422728 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
422663 TTATCATTGA
422673 TGCATCGGTGCACAATGAATG
1 TGCATCGGTGCACAATGAATG
422694 TGCATCGGTGCACAATGAATG
1 TGCATCGGTGCACAATGAATG
*
422715 TGCATCGATGCACA
1 TGCATCGGTGCACA
422729 TTGCCCAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (21 bp):
TGCATCGGTGCACAATGAATG
Found at i:428730 original size:23 final size:23
Alignment explanation
Indices: 428704--428758 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
428694 CGTAAATGCA
* *
428704 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACATAGAAATG
* *
428727 CACCGTAGTGCCGCATAGAAATG
1 CACCGAAGTGCCACATAGAAATG
428750 CACCGAAGT
1 CACCGAAGT
428759 TCCATATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.16
Consensus pattern (23 bp):
CACCGAAGTGCCACATAGAAATG
Found at i:429049 original size:95 final size:98
Alignment explanation
Indices: 428802--429079 Score: 435
Period size: 95 Copynumber: 2.8 Consensus size: 98
428792 ATTCTTAAGA
428802 ATATACATAT-CCAAAGATCAAGTATGTGTCTCAACAGACCTCACACCT-TTCCAAAGAATACAT
1 ATATACATATGCCAAAGATCAAGTATGTGTCTCAACAGACCTCACACCTGTTCCAAAGAAT--AT
428865 ATATGTCCCGAAGGACCACATATCATTCCTTAAGAATC
64 ATATGTCCCGAAGGACCAC---TCATTCCTTAAGAATC
428903 ATATACA-ATGCCAAAGAT-AAGTATGTGTCTCAACAGACCTCACACCTGTTCCAAAGAATATAT
1 ATATACATATGCCAAAGATCAAGTATGTGTCTCAACAGACCTCACACCTGTTCCAAAGAATATAT
*
428966 ATAT-CCGAAGGACCACTCATTCCTTAA-AATC
66 ATGTCCCGAAGGACCACTCATTCCTTAAGAATC
*
428997 ATATACATATGCCAAAGATCAAGTATGTGTCTCAACAGACCTCA-ACCTGTTCCAAAGAATACAA
1 ATATACATATGCCAAAGATCAAGTATGTGTCTCAACAGACCTCACACCTGTTCCAAAGAATA-TA
429061 TATGTCCCGAAGGACCACT
65 TATGTCCCGAAGGACCACT
429080 AGACCCTCTA
Statistics
Matches: 168, Mismatches: 3, Indels: 16
0.90 0.02 0.09
Matches are distributed among these distances:
94 11 0.07
95 39 0.23
96 29 0.17
97 13 0.08
98 12 0.07
99 7 0.04
100 31 0.18
101 26 0.15
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (98 bp):
ATATACATATGCCAAAGATCAAGTATGTGTCTCAACAGACCTCACACCTGTTCCAAAGAATATAT
ATGTCCCGAAGGACCACTCATTCCTTAAGAATC
Found at i:435478 original size:21 final size:21
Alignment explanation
Indices: 435452--435493 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
435442 CCATAATGGG
*
435452 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
435473 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
435494 ATATTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:435741 original size:29 final size:30
Alignment explanation
Indices: 435709--435767 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
435699 AAATTTTGAA
*
435709 TAAATTCAATT-AAGTCCAAATACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACATTTTG
435738 TAAATTCAATTCAAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACATTTTG
435768 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (30 bp):
TAAATTCAATTCAAGTCCAAAAACATTTTG
Found at i:444482 original size:32 final size:33
Alignment explanation
Indices: 444411--444528 Score: 93
Period size: 31 Copynumber: 3.6 Consensus size: 33
444401 TTAAAAATTA
* * *
444411 TAAATAACTATT-AAGTTTAT-TAAATTATTAGT
1 TAAATAATTATTAAATTTTATAAAAATTATT-GT
444443 ATAAAATAATTATTAAATTTTA-AAAAATTATTGT
1 -T-AAATAATTATTAAATTTTATAAAAATTATTGT
** * * *
444477 TAAATAACCATTAAATTTTATTAGAA-T-TTAT
1 TAAATAATTATTAAATTTTATAAAAATTATTGT
*
444508 AAAATAATTATTAAATTTTAT
1 TAAATAATTATTAAATTTTAT
444529 CATATTTTAT
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
31 21 0.30
32 18 0.26
33 5 0.07
34 12 0.17
35 14 0.20
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (33 bp):
TAAATAATTATTAAATTTTATAAAAATTATTGT
Found at i:444521 original size:31 final size:31
Alignment explanation
Indices: 444442--444566 Score: 101
Period size: 31 Copynumber: 4.0 Consensus size: 31
444432 AAATTATTAG
444442 TATAAAATAATTATTAAATTTTA-AAAAATTAT
1 TATAAAATAATTATTAAATTTTATAAAAA-T-T
* * ** * *
444474 TGTTAAATAACCATTAAATTTTATTAGAATT
1 TATAAAATAATTATTAAATTTTATAAAAATT
* * *
444505 TATAAAATAATTATTAAATTTTATCATATTT
1 TATAAAATAATTATTAAATTTTATAAAAATT
* * * *
444536 TATAAAACATTTATT-AAGTTTATCAAAATT
1 TATAAAATAATTATTAAATTTTATAAAAATT
444566 T
1 T
444567 TACTCTTACT
Statistics
Matches: 74, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
30 13 0.18
31 38 0.51
32 20 0.27
33 3 0.04
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.46
Consensus pattern (31 bp):
TATAAAATAATTATTAAATTTTATAAAAATT
Found at i:444527 original size:21 final size:21
Alignment explanation
Indices: 444442--444528 Score: 70
Period size: 21 Copynumber: 4.1 Consensus size: 21
444432 AAATTATTAG
444442 TATAAAATAATTATTAAATTT
1 TATAAAATAATTATTAAATTT
* * * **
444463 TAAAAAATTATTGTTAAATAAC
1 TATAAAATAATTATTAAAT-TT
* * *
444485 CATTAAAT-TTTATTAGAA-TT
1 TATAAAATAATTATTA-AATTT
444505 TATAAAATAATTATTAAATTT
1 TATAAAATAATTATTAAATTT
444526 TAT
1 TAT
444529 CATATTTTAT
Statistics
Matches: 47, Mismatches: 15, Indels: 8
0.67 0.21 0.11
Matches are distributed among these distances:
20 8 0.17
21 32 0.68
22 7 0.15
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
TATAAAATAATTATTAAATTT
Found at i:455339 original size:141 final size:146
Alignment explanation
Indices: 455157--455466 Score: 418
Period size: 148 Copynumber: 2.1 Consensus size: 146
455147 CATAATGAAG
*
455157 CACCAAACTAATAAATTCAATGAACACAAAATAAAGCACCAAACTAATAAA-T-TTAATAATGAT
1 CACCAAACTAATAAATTCAATGAACACAAAATAAAGCACCAAAATAATAAATTATTAATAATGAT
* * *
455220 TTTTAAATAATAGCGT-AGACT-TTGCTGCCTT-AAA-AGATA-AAGAATGGACGCAACATAATG
66 TTTTAAATAATAACGTGA-ACTCTT-CTGCCTTGAAAGAGAAAGAAGAATGGACACAACATAATG
* *
455280 AAGAACTGAAGATTAAAA
129 AAGAACTAAAGAATAAAA
* * *
455298 CACCAAACTAATAAATTCAATGAGCACATAATGAAGCACCAAAATAATAAATTTAATTAATAATG
1 CACCAAACTAATAAATTCAATGAACACAAAATAAAGCACCAAAATAATAAA-TT-ATTAATAATG
455363 ATTTTTAAATAATAACGTGAACTCTTCTGCCTTGAAAGAGAAAGAAGAATGGACACAACATAATG
64 ATTTTTAAATAATAACGTGAACTCTTCTGCCTTGAAAGAGAAAGAAGAATGGACACAACATAATG
* *
455428 AAGAATTAAAGAATGAAA
129 AAGAACTAAAGAATAAAA
* *
455446 CACGAAATTAATAAATTCAAT
1 CACCAAACTAATAAATTCAAT
455467 TTACAATACT
Statistics
Matches: 147, Mismatches: 13, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
141 47 0.32
143 1 0.01
145 36 0.24
146 6 0.04
147 4 0.03
148 53 0.36
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.25
Consensus pattern (146 bp):
CACCAAACTAATAAATTCAATGAACACAAAATAAAGCACCAAAATAATAAATTATTAATAATGAT
TTTTAAATAATAACGTGAACTCTTCTGCCTTGAAAGAGAAAGAAGAATGGACACAACATAATGAA
GAACTAAAGAATAAAA
Found at i:455762 original size:19 final size:22
Alignment explanation
Indices: 455738--455779 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
455728 AGTTCTTGCA
455738 AACAAA-AA-ACCAA-AATCAT
1 AACAAACAATACCAACAATCAT
455757 AACAAACAATACCAACAATCAT
1 AACAAACAATACCAACAATCAT
455779 A
1 A
455780 GCAGAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 5 0.25
22 7 0.35
ACGTcount: A:0.64, C:0.24, G:0.00, T:0.12
Consensus pattern (22 bp):
AACAAACAATACCAACAATCAT
Found at i:455789 original size:22 final size:20
Alignment explanation
Indices: 455738--455789 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
455728 AGTTCTTGCA
455738 AACAAAAA-ACCAAAATCAT
1 AACAAAAATACCAAAATCAT
455757 AACAAACAATACCAACAATCAT
1 AACAAA-AATACCAA-AATCAT
*
455779 AGCAGAAAATA
1 AACA-AAAATA
455790 GCACAGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 6 0.21
20 2 0.07
21 5 0.18
22 13 0.46
23 2 0.07
ACGTcount: A:0.63, C:0.21, G:0.04, T:0.12
Consensus pattern (20 bp):
AACAAAAATACCAAAATCAT
Found at i:462846 original size:25 final size:24
Alignment explanation
Indices: 462813--462873 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
462803 ATAATTTTAG
*
462813 AATTTTTAAAATTACATTATAAAAA
1 AATTATTAAAATTACATTAT-AAAA
* * *
462838 AATTATTAAAAATACATTATTAAT
1 AATTATTAAAATTACATTATAAAA
462862 AATTA-TAAAATT
1 AATTATTAAAATT
462874 TTAAAAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 6 0.19
24 7 0.23
25 18 0.58
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (24 bp):
AATTATTAAAATTACATTATAAAA
Found at i:462890 original size:11 final size:11
Alignment explanation
Indices: 462835--462892 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
462825 TACATTATAA
462835 AAAAAT-TATT
1 AAAAATATATT
*
462845 AAAAATACATT
1 AAAAATATATT
**
462856 ATTAATA-ATT
1 AAAAATATATT
462866 ATAAAAT-T-TT
1 A-AAAATATATT
462876 AAAAATATATT
1 AAAAATATATT
462887 AAAAAT
1 AAAAAT
462893 TCTATAATGC
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
9 5 0.13
10 14 0.37
11 19 0.50
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATATT
Found at i:463028 original size:7 final size:7
Alignment explanation
Indices: 463016--463068 Score: 63
Period size: 7 Copynumber: 7.7 Consensus size: 7
463006 GTTAGATTAC
463016 ACCCTAA
1 ACCCTAA
463023 ACCCTAA
1 ACCCTAA
**
463030 ACTATAA
1 ACCCTAA
*
463037 ACCCTTA
1 ACCCTAA
*
463044 ACACTAA
1 ACCCTAA
463051 A-CCTAA
1 ACCCTAA
463057 ACCCTAA
1 ACCCTAA
463064 ACCCT
1 ACCCT
463069 TAATCCAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
6 5 0.14
7 32 0.86
ACGTcount: A:0.43, C:0.38, G:0.00, T:0.19
Consensus pattern (7 bp):
ACCCTAA
Found at i:463058 original size:27 final size:28
Alignment explanation
Indices: 463019--463071 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
463009 AGATTACACC
*
463019 CTAAACCCTAAACTATAAACCCTTAACA
1 CTAAACCCTAAACCATAAACCCTTAACA
*
463047 CTAAA-CCTAAACCCTAAACCCTTAA
1 CTAAACCCTAAACCATAAACCCTTAA
463072 TCCAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (28 bp):
CTAAACCCTAAACCATAAACCCTTAACA
Found at i:463826 original size:20 final size:20
Alignment explanation
Indices: 463801--463839 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
463791 ATCAATAATC
463801 ATACAAATGCAT-TTATTATG
1 ATACAAAT-CATATTATTATG
463821 ATACAAATCATATTATTAT
1 ATACAAATCATATTATTAT
463840 TACATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (20 bp):
ATACAAATCATATTATTATG
Found at i:464596 original size:29 final size:29
Alignment explanation
Indices: 464560--464616 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
464550 AGTGTTGACC
*
464560 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCAACCTT
464589 GTAGGTCGCCATGCACTCCGGGCAACCT
1 GTAGGTCGCCATGCACTCCGGGCAACCT
464617 ACCCTTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.16, C:0.35, G:0.30, T:0.19
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCAACCTT
Found at i:464651 original size:12 final size:12
Alignment explanation
Indices: 464634--464658 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
464624 CTCAAACAGA
464634 GAGAATGAACGT
1 GAGAATGAACGT
464646 GAGAATGAACGT
1 GAGAATGAACGT
464658 G
1 G
464659 TTGCATGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (12 bp):
GAGAATGAACGT
Found at i:464720 original size:29 final size:29
Alignment explanation
Indices: 464687--464742 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
464677 TCCCAACACA
464687 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
464716 TAGGTCGCCATGCCCTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCGACCT
464743 ACCCTCTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.11, C:0.39, G:0.30, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACCTTG
Found at i:464830 original size:33 final size:33
Alignment explanation
Indices: 464758--464830 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
464748 CTCTCGGCTT
* * *
464758 CCCTCGAATTCCCTCGCATAGCTCGCTCGGTTG
1 CCCTCGGATGCCCTCGCATAGCTCGCTCGGATG
*
464791 CCCTCGGATGCCCTCGCATAGCTCGTTCGGATG
1 CCCTCGGATGCCCTCGCATAGCTCGCTCGGATG
*
464824 GCCTCGG
1 CCCTCGG
464831 TCGGATGGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.38, G:0.26, T:0.25
Consensus pattern (33 bp):
CCCTCGGATGCCCTCGCATAGCTCGCTCGGATG
Found at i:465480 original size:22 final size:23
Alignment explanation
Indices: 465453--465516 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
465443 CAAGCTCAAA
465453 ATTGAGCTTAAATCAAGCTTA-T
1 ATTGAGCTTAAATCAAGCTTAGT
* * *
465475 ATTGAGCTTGAATAAAGTTTAGT
1 ATTGAGCTTAAATCAAGCTTAGT
*
465498 -TTCGAGCTTAAATCTAGCT
1 ATT-GAGCTTAAATCAAGCT
465517 GAGTCTCAAG
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (23 bp):
ATTGAGCTTAAATCAAGCTTAGT
Found at i:470156 original size:20 final size:20
Alignment explanation
Indices: 470131--470172 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
470121 AAACATGCAT
*
470131 GGGGGTATCTGTACCCCCTG
1 GGGGGTATATGTACCCCCTG
*
470151 GGGGGTATATGTACCCTCTG
1 GGGGGTATATGTACCCCCTG
470171 GG
1 GG
470173 CAATCTGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.24, G:0.38, T:0.26
Consensus pattern (20 bp):
GGGGGTATATGTACCCCCTG
Found at i:470534 original size:12 final size:12
Alignment explanation
Indices: 470502--470535 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
470492 AGAAAATCAT
*
470502 TTTGAAATCAAA
1 TTTGAAATTAAA
470514 TTTGAAATTAAA
1 TTTGAAATTAAA
470526 TTTGAAATTA
1 TTTGAAATTA
470536 CTACTCCTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (12 bp):
TTTGAAATTAAA
Found at i:477409 original size:21 final size:21
Alignment explanation
Indices: 477383--477445 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
477373 TTTTGGTGCA
*
477383 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCCCT
* **
477404 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCCT
*
477425 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATCCCCCCC
477446 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCCT
Found at i:477453 original size:21 final size:21
Alignment explanation
Indices: 477427--477466 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
477417 CCCCCTTTGA
*
477427 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
477448 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
477467 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:482436 original size:22 final size:23
Alignment explanation
Indices: 482389--482439 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
482379 CAGTTCCCTC
*
482389 AGGGGGAATCGATACCCATTCAA
1 AGGGGGAATCGATACCCATGCAA
*
482412 AGGGGGAATCGGTACCCATGC-A
1 AGGGGGAATCGATACCCATGCAA
482434 AGGGGG
1 AGGGGG
482440 TATAGATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.29, C:0.20, G:0.37, T:0.14
Consensus pattern (23 bp):
AGGGGGAATCGATACCCATGCAA
Found at i:486508 original size:117 final size:116
Alignment explanation
Indices: 486293--486508 Score: 242
Period size: 117 Copynumber: 1.8 Consensus size: 116
486283 ATACTATCAA
* * *
486293 ATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTTCATTTTGATTTTCAAAATCCATTTTC
1 ATTTCATTTTTGAAAGATCTAAATCCTTCTTCAACATTTCATTTTGATTTTCAAAATCCATTTTA
* ** *
486358 GTTTCTAGAAAAAGTTTGTTTAATTTGAAAAATTCTTTTTCAAAGTTTTCAG
66 GTTTCTAGAAAAAGATCATTT-ATTAGAAAAATTCTTTTTCAAAGTTTTCAG
* * * **
486410 ATTTTATTTTTGAAAGATCTAACTCCTT-TCTCAACATTTCATTTTGATTTTCTAAATCTGTTTT
1 ATTTCATTTTTGAAAGATCTAAATCCTTCT-TCAACATTTCATTTTGATTTTCAAAATCCATTTT
486474 AGCTTTC-A-AAAGAAGATCATTT-TTAGCAATAAATT
65 AG-TTTCTAGAAA-AAGATCATTTATTAG-AA-AAATT
486509 TAGAAATCAA
Statistics
Matches: 82, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
115 3 0.04
116 6 0.07
117 69 0.84
118 4 0.05
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.47
Consensus pattern (116 bp):
ATTTCATTTTTGAAAGATCTAAATCCTTCTTCAACATTTCATTTTGATTTTCAAAATCCATTTTA
GTTTCTAGAAAAAGATCATTTATTAGAAAAATTCTTTTTCAAAGTTTTCAG
Found at i:487819 original size:23 final size:23
Alignment explanation
Indices: 487783--487827 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
487773 CCGTTACACA
487783 GGGGGAATCGGTACCCCCTGGAG
1 GGGGGAATCGGTACCCCCTGGAG
* * *
487806 GGGGGTATCTGTACCCTCTGGA
1 GGGGGAATCGGTACCCCCTGGA
487828 CATTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.24, G:0.40, T:0.20
Consensus pattern (23 bp):
GGGGGAATCGGTACCCCCTGGAG
Found at i:489929 original size:2 final size:2
Alignment explanation
Indices: 489922--489946 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
489912 TAGTGAAAAT
489922 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
489947 TACAATTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:500934 original size:83 final size:83
Alignment explanation
Indices: 500795--500949 Score: 292
Period size: 83 Copynumber: 1.9 Consensus size: 83
500785 AGATTATCTA
* *
500795 AACGCACCTTTCATTTCGGATGGGATGGAACACTATGACATGGTAGAGATTCTCTGAATAATAAT
1 AACGCACCTTTCATTTCAGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAAT
500860 GGAAAACGCTTCCTCTGG
66 GGAAAACGCTTCCTCTGG
500878 AACGCACCTTTCATTTCAGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAAT
1 AACGCACCTTTCATTTCAGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAAT
500943 GGAAAAC
66 GGAAAAC
500950 ACTATGACAT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 70 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (83 bp):
AACGCACCTTTCATTTCAGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAAT
GGAAAACGCTTCCTCTGG
Found at i:501852 original size:23 final size:23
Alignment explanation
Indices: 501823--501866 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
501813 CTAAAAAAAC
*
501823 AACAAACCATAAACATTACATTA
1 AACAAACCATAAACATGACATTA
*
501846 AACAAACTATAAACATGACAT
1 AACAAACCATAAACATGACAT
501867 GAAGTATACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.57, C:0.20, G:0.02, T:0.20
Consensus pattern (23 bp):
AACAAACCATAAACATGACATTA
Found at i:502160 original size:21 final size:21
Alignment explanation
Indices: 502130--502197 Score: 86
Period size: 21 Copynumber: 3.2 Consensus size: 21
502120 CTTATCATTG
502130 TCATCCTCCTCTTCCTCGTCA
1 TCATCCTCCTCTTCCTCGTCA
* *
502151 TCATCGTCCT-TATCCTCATCA
1 TCATCCTCCTCT-TCCTCGTCA
502172 TCATCCTCCTCGTT-CTCGTCA
1 TCATCCTCCTC-TTCCTCGTCA
502193 TCATC
1 TCATC
502198 ATCACTCCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 1 0.03
21 37 0.93
22 1 0.03
23 1 0.03
ACGTcount: A:0.13, C:0.43, G:0.06, T:0.38
Consensus pattern (21 bp):
TCATCCTCCTCTTCCTCGTCA
Found at i:503189 original size:17 final size:18
Alignment explanation
Indices: 503161--503194 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
503151 ATATAAATGC
503161 AATTAAATAAAAAATTAA
1 AATTAAATAAAAAATTAA
503179 AATTAAA-AAAAAATTA
1 AATTAAATAAAAAATTA
503195 TCTCCACACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AATTAAATAAAAAATTAA
Found at i:507120 original size:27 final size:26
Alignment explanation
Indices: 507070--507128 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
507060 AAACAAAATA
* * **
507070 ATAATATTGATGCATTTATTTATTTT
1 ATAATATTCATGCATTAAAATATTTT
507096 ATTAATATTCATGCATTAAAATATTTT
1 A-TAATATTCATGCATTAAAATATTTT
507123 ATAATA
1 ATAATA
507129 ACATTTCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (26 bp):
ATAATATTCATGCATTAAAATATTTT
Found at i:517846 original size:2 final size:2
Alignment explanation
Indices: 517841--517892 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
517831 TCGCATACTC
517841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
517883 AT AT AT AT AT
1 AT AT AT AT AT
517893 GACTTTTTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:517929 original size:49 final size:49
Alignment explanation
Indices: 517866--517970 Score: 183
Period size: 49 Copynumber: 2.1 Consensus size: 49
517856 TATATATATA
*
517866 TATATATATATATATATATATATATATGACTTTTTCTAACACCAACCAGAC
1 TATAAATATATATATATATATA-AT-TGACTTTTTCTAACACCAACCAGAC
517917 TATAAATATATATATATATATAATTGACTTTTTCTAACACCAACCAGAC
1 TATAAATATATATATATATATAATTGACTTTTTCTAACACCAACCAGAC
517966 TATAA
1 TATAA
517971 TGGTTAAAAG
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
49 30 0.57
50 2 0.04
51 21 0.40
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.38
Consensus pattern (49 bp):
TATAAATATATATATATATATAATTGACTTTTTCTAACACCAACCAGAC
Found at i:528213 original size:36 final size:36
Alignment explanation
Indices: 528158--528228 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
528148 CTGACGCTCC
*
528158 AATCAATCATTCATCAAATTCCAAAGTTCAATCATA
1 AATCAATCAATCATCAAATTCCAAAGTTCAATCATA
* *
528194 AATCAATCAATCATTAAATTCTAAAGTTCAATCAT
1 AATCAATCAATCATCAAATTCCAAAGTTCAATCAT
528229 GTCCATTGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (36 bp):
AATCAATCAATCATCAAATTCCAAAGTTCAATCATA
Found at i:530700 original size:2 final size:2
Alignment explanation
Indices: 530693--530730 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
530683 GCAATGACAA
*
530693 AT AT AT AT AT AT AT AT AT AT -T AT A- AT AG AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
530731 CCTAATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:530736 original size:18 final size:18
Alignment explanation
Indices: 530703--530737 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
530693 ATATATATAT
*
530703 ATATATATATTATAATAG
1 ATATATATATCATAATAG
*
530721 ATATATATATCCTAATA
1 ATATATATATCATAATA
530738 ATAAATAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
ATATATATATCATAATAG
Found at i:531742 original size:31 final size:31
Alignment explanation
Indices: 531706--531770 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
531696 GAAATACAGT
531706 CCCCAACATTTAGTCCGTTTGCAATATGGTC
1 CCCCAACATTTAGTCCGTTTGCAATATGGTC
*
531737 CCCCAACATTTAGTCTGTTTGCAATATGGTC
1 CCCCAACATTTAGTCCGTTTGCAATATGGTC
531768 CCC
1 CCC
531771 GACCGTTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.32
Consensus pattern (31 bp):
CCCCAACATTTAGTCCGTTTGCAATATGGTC
Found at i:532852 original size:21 final size:19
Alignment explanation
Indices: 532826--532900 Score: 87
Period size: 21 Copynumber: 3.7 Consensus size: 19
532816 CATATTCACA
532826 TTGCGATAGTCCAAGTTTGCG
1 TTGCGATAGTCCAAG-TT-CG
**
532847 TTGCGATTTTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCG
*
532866 TTGGGATAGTCTCCAAGTTCG
1 TTGCGATAG--TCCAAGTTCG
532887 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
532901 AATAGCAATG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
19 13 0.28
20 2 0.04
21 31 0.67
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (19 bp):
TTGCGATAGTCCAAGTTCG
Found at i:533001 original size:6 final size:6
Alignment explanation
Indices: 532990--533014 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
532980 GAAACGTATT
532990 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
533015 GACGAGACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:533908 original size:21 final size:21
Alignment explanation
Indices: 533588--533904 Score: 453
Period size: 21 Copynumber: 15.2 Consensus size: 21
533578 CAAATGCAAT
* *
533588 AACGAAGTTGGAGACTATCAC
1 AACGAACTTGGAGACTATCGC
*
533609 AACGAAGTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
*
533630 AACGAATTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
*
533651 AACGAATTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
*
533672 AACGAAGTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
*
533693 AACGAAGTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
*
533714 AACGAATTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
533735 AACGAACTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
* *
533756 AATGAACGTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
533777 AACGAACTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
* *
533798 AACGCACTTGGAGACTATCGT
1 AACGAACTTGGAGACTATCGC
*
533819 AACGCACTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
*
533840 AACGAATTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
*
533861 AACGAACTTGGA-A-AATCGC
1 AACGAACTTGGAGACTATCGC
533880 AACGCGAACTT-G-GACTATCGC
1 AA--CGAACTTGGAGACTATCGC
533901 AACG
1 AACG
533905 CGAATATGTA
Statistics
Matches: 275, Mismatches: 17, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
19 9 0.03
20 3 0.01
21 263 0.96
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.20
Consensus pattern (21 bp):
AACGAACTTGGAGACTATCGC
Found at i:534653 original size:17 final size:17
Alignment explanation
Indices: 534627--534659 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
534617 TTTTGTTTTT
534627 AATTTATTTAAGTATTTA
1 AATTTATTTAA-TATTTA
534645 AATTT-TTTAATATTT
1 AATTTATTTAATATTT
534660 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:534661 original size:17 final size:19
Alignment explanation
Indices: 534622--534661 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
534612 TAATATTTTG
*
534622 TTTTTAATTTATTTAAGTA
1 TTTTAAATTTATTTAAGTA
534641 -TTTAAATTT-TTTAA-TA
1 TTTTAAATTTATTTAAGTA
534657 TTTTA
1 TTTTA
534662 TTTAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 2 0.11
17 9 0.47
18 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTAAATTTATTTAAGTA
Found at i:537021 original size:22 final size:20
Alignment explanation
Indices: 536995--537046 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
536985 ATCCTATATC
536995 ATAATTTCTAACATATTATTAG
1 ATAATTTCTAACA-ATTATT-G
* *
537017 ATAATTACTAA-AATTATTT
1 ATAATTTCTAACAATTATTG
537036 ATAATTT-TAAC
1 ATAATTTCTAAC
537047 TTTTTTTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 3 0.12
19 6 0.23
20 6 0.23
21 1 0.04
22 10 0.38
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (20 bp):
ATAATTTCTAACAATTATTG
Found at i:538144 original size:2 final size:2
Alignment explanation
Indices: 538137--538170 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
538127 TCCGCTTCAC
*
538137 AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
538171 GCTTTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:540812 original size:36 final size:36
Alignment explanation
Indices: 540771--540840 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
540761 GCCTAACATT
*
540771 ATAAGTTTAGGTGTTTCAATCATGATTATCTTTTGA
1 ATAAGTTTAGGTGCTTCAATCATGATTATCTTTTGA
540807 ATAAGTTTAGGTGCTTCAATCATGATTATCTTTT
1 ATAAGTTTAGGTGCTTCAATCATGATTATCTTTT
540841 TTTAAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.47
Consensus pattern (36 bp):
ATAAGTTTAGGTGCTTCAATCATGATTATCTTTTGA
Found at i:543740 original size:95 final size:96
Alignment explanation
Indices: 543572--543760 Score: 260
Period size: 95 Copynumber: 2.0 Consensus size: 96
543562 TTTTTTTTTC
*
543572 TTTTTTTCTTATTTTTCTTTATTTTTGTGCGGACCATGATCATACATCGGATAATTCGTTCTCTT
1 TTTTTTTCTTATTTTTCTTTATTTTTGTGCGGACCATGATCATACATCGGATAACTCGTTCTCTT
543637 GTACTGACAA-GGATAGAAAAGAGAGATAACT
66 GTACTGACAATGG-TAGAAAAGAGAGATAACT
* * * * *
543668 TTTTTTTCTTTTTCTTTC-TT-TTTTTGTGTGGATCATGATCATACATCGGGTAACTCGTTGTCT
1 TTTTTTTCTTATT-TTTCTTTATTTTTGTGCGGACCATGATCATACATCGGATAACTCGTTCTCT
*
543731 TGT-CTTGACAATGGTAGAAAAGATAGATAA
65 TGTAC-TGACAATGGTAGAAAAGAGAGATAA
543761 AGAGGGGCTC
Statistics
Matches: 83, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
94 1 0.01
95 62 0.75
96 16 0.19
97 4 0.05
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (96 bp):
TTTTTTTCTTATTTTTCTTTATTTTTGTGCGGACCATGATCATACATCGGATAACTCGTTCTCTT
GTACTGACAATGGTAGAAAAGAGAGATAACT
Found at i:547409 original size:5 final size:5
Alignment explanation
Indices: 547399--547432 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
547389 AAAAATAAAC
*
547399 AAATT AAATT AAATT AAATT AAATAA AAATT AAA
1 AAATT AAATT AAATT AAATT AAAT-T AAATT AAA
547433 CAAACGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (5 bp):
AAATT
Found at i:554211 original size:17 final size:17
Alignment explanation
Indices: 554189--554222 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
554179 GGAGTTTTCA
554189 AGCAAAGAAGAAACGAT
1 AGCAAAGAAGAAACGAT
554206 AGCAAAGAAGAAACGAT
1 AGCAAAGAAGAAACGAT
554223 GATGGCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.12, G:0.24, T:0.06
Consensus pattern (17 bp):
AGCAAAGAAGAAACGAT
Found at i:556579 original size:3 final size:3
Alignment explanation
Indices: 556571--556640 Score: 59
Period size: 3 Copynumber: 23.3 Consensus size: 3
556561 CTCTTTACTG
* * * * * *
556571 TCA TCA TCA TCA CCA TCA TCG TCG TCG TCA TCA TCA TCA CCA TCA TCG
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
** *
556619 TTG TCG TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA T
556641 GAGAAGATAC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.24, C:0.34, G:0.09, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:556608 original size:27 final size:27
Alignment explanation
Indices: 556570--556636 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
556560 ACTCTTTACT
556570 GTCATCATCATCACCATCATCGTCGTC
1 GTCATCATCATCACCATCATCGTCGTC
*
556597 GTCATCATCATCACCATCATCGTTGTC
1 GTCATCATCATCACCATCATCGTCGTC
556624 GTCATCATCATCA
1 GTCATCATCATCA
556637 TCATGAGAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.24, C:0.34, G:0.10, T:0.31
Consensus pattern (27 bp):
GTCATCATCATCACCATCATCGTCGTC
Found at i:557015 original size:21 final size:21
Alignment explanation
Indices: 556991--557034 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
556981 TCGCTACAGA
556991 CGGTGGTTGTTGTGAAGGTTC
1 CGGTGGTTGTTGTGAAGGTTC
557012 CGGTGGTTGTTGTGAAGGTTC
1 CGGTGGTTGTTGTGAAGGTTC
557033 CG
1 CG
557035 TCAATGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.11, G:0.43, T:0.36
Consensus pattern (21 bp):
CGGTGGTTGTTGTGAAGGTTC
Found at i:558639 original size:17 final size:18
Alignment explanation
Indices: 558607--558640 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
558597 TAATTAAATA
558607 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
558625 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
558641 ACCTTAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:559982 original size:180 final size:182
Alignment explanation
Indices: 559423--560272 Score: 1071
Period size: 180 Copynumber: 4.7 Consensus size: 182
559413 TGGCGGTTTA
* *** *
559423 TGTCAATACTTTATAA-AACTGTATCGATCCACATTAATATAA-TTGGTAAAAATATGACAAAA-
1 TGTCGATACTTTATAACAA-TGTATCGATCCACAACGATATAACAT-GTAAAAATATGACAAAAC
* * * * * * * * * * *
559485 CGATCTCGAAAAGAAAAAAAACGGTAAAGTGGTATCGGGTATATTGAAAGTGTCGATACTTTAAT
64 CGGTCTC-TAAAGGACAAAACCGGTATAGAGCTACCAGATATATTGAAAGTGTCGATACTTTAAT
* **
559550 ATAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAG
128 ATAAGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
* * *
559605 TGTCGATACTTTATAA-AACTGTATCGATCCACATCAATATAACAGGTAAAAATATGACAAAACC
1 TGTCGATACTTTATAACAA-TGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACC
* * * * *
559669 GGTCTCGAAAAGACAAAA-CTG-ATAAAACGTACCAGATATATTGAAAGTGTCGATACTTTAATA
65 GGTCTCTAAAGGACAAAACCGGTATAGAGC-TACCAGATATATTGAAAGTGTCGATACTTTAATA
* *
559732 TAAGTATCGATACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCTCCTATAAAG
129 TAAGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
* *
559786 TGTCGATACTTTATAACAATGTATTGATCCACAACGATATAACA-GATAAAAATATGACAAAACT
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACATG-TAAAAATATGACAAAACC
* * *
559850 GATATCTAAAGGACAAAACCGGTATAGAGCAACC-GATATATTGAAAGTGT-GATACTTTAATAT
65 GGTCTCTAAAGGACAAAACCGGTATAGAGCTACCAGATATATTGAAAGTGTCGATACTTTAATAT
*
559913 AAGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCCATAAAG
130 AAGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
* * *
559966 TGTCGATACTTTATAACAATGTATCGATCCAAAACGATATAACATGTAAAAATATAATAAAACCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCG
* * * *
560031 GTCTCTAAAGGACAAAATC-ATATAGAGCGACC-GAATATATTTAAA-TGTCGATACTTTAATAT
66 GTCTCTAAAGGACAAAACCGGTATAGAGCTACCAG-ATATATTGAAAGTGTCGATACTTTAATAT
*
560093 AAGTATCGACACTTTGTGAATTT-AAAGAGAAATAGTTTTAGCGCCTATAAAG
130 AAGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
*
560145 TGTCGATACTTTATAACAATGTATCGGTCCACAACGATATAACATGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCG
* * * * * **
560210 GTCTCGT-AATGACAAAACCGGTAAAGCGCTACCGGATATATTTAAAGTGTTTATACTTTAATA
66 GTCTC-TAAAGGACAAAACCGGTATAGAGCTACCAGATATATTGAAAGTGTCGATACTTTAATA
560273 AGTACGCGTA
Statistics
Matches: 591, Mismatches: 63, Indels: 29
0.87 0.09 0.04
Matches are distributed among these distances:
179 118 0.20
180 207 0.35
181 183 0.31
182 72 0.12
183 11 0.02
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.29
Consensus pattern (182 bp):
TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCG
GTCTCTAAAGGACAAAACCGGTATAGAGCTACCAGATATATTGAAAGTGTCGATACTTTAATATA
AGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
Found at i:560268 original size:361 final size:363
Alignment explanation
Indices: 559423--560272 Score: 1150
Period size: 361 Copynumber: 2.4 Consensus size: 363
559413 TGGCGGTTTA
* *** *
559423 TGTCAATACTTTATAA-AACTGTATCGATCCACATTAATATAA-TTGGTAAAAATATGACAAAA-
1 TGTCGATACTTTATAACAA-TGTATCGATCCACAACGATATAACAT-GTAAAAATATGACAAAAC
* * * * * * * *
559485 CGATCTCGAAAAGAAAAAAAACGGTAAAGTGGTATCGGGTATATTGAAAGTGTCGATACTTTAAT
64 CGATCTCGTAAAG-ACAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTTGATACTTTAAT
* *
559550 ATAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACT
128 ATAAGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAAAGCCCATAAAGTGTCGATACT
* * *
559615 TTATAAAACTGTATCGATCCACATCAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAAA
193 TTATAAAACTGTATCGATCCAAAACAATATAACAGGTAAAAATATAACAAAACCGGTCTCGAAAA
*
559680 GACAAAACTGATAAAACGTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGATAC
258 GACAAAACTGATAAAACGTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACAC
*
559745 TTTGTGAATTTAAAAGAGAAACAGTTTTAGCTCCTATAAAG
323 TTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
* *
559786 TGTCGATACTTTATAACAATGTATTGATCCACAACGATATAACA-GATAAAAATATGACAAAACT
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACATG-TAAAAATATGACAAAACC
* * *
559850 GATATC-TAAAGGACAAAACCGGTATAGAGCAACC-GATATATTGAAAGTG-TGATACTTTAATA
65 GATCTCGTAAA-GACAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTTGATACTTTAATA
**
559912 TAAGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCCATAAAGTGTCGATACTT
129 TAAGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAAAGCCCATAAAGTGTCGATACTT
* * * * *
559977 TATAACAA-TGTATCGATCCAAAACGATATAACATGTAAAAATATAATAAAACCGGTCTCTAAAG
194 TATAA-AACTGTATCGATCCAAAACAATATAACAGGTAAAAATATAACAAAACCGGTCTCGAAAA
* * *
560041 GACAAAATCAT-ATAGAGCG-ACC-GAATATATTTAAA-TGTCGATACTTTAATATAAGTATCGA
258 GACAAAA-C-TGATAAAACGTACCAG-ATATATTGAAAGTGTCGATACTTTAATATAAGTATCGA
*
560102 CACTTTGTGAATTT-AAAGAGAAATAGTTTTAGCGCCTATAAAG
320 CACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
*
560145 TGTCGATACTTTATAACAATGTATCGGTCCACAACGATATAACATGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCG
* * * * *
560210 GTCTCGTAATGACAAAACCGGTAAAGCGCTACCGGATATATTTAAAGTGTTTATACTTTAATA
66 ATCTCGTAAAGACAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTTGATACTTTAATA
560273 AGTACGCGTA
Statistics
Matches: 427, Mismatches: 47, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
359 110 0.26
360 58 0.14
361 158 0.37
362 24 0.06
363 69 0.16
364 8 0.02
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.29
Consensus pattern (363 bp):
TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCG
ATCTCGTAAAGACAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTTGATACTTTAATATA
AGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAAAGCCCATAAAGTGTCGATACTTTA
TAAAACTGTATCGATCCAAAACAATATAACAGGTAAAAATATAACAAAACCGGTCTCGAAAAGAC
AAAACTGATAAAACGTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
GTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
Found at i:560800 original size:44 final size:39
Alignment explanation
Indices: 560752--560845 Score: 116
Period size: 39 Copynumber: 2.3 Consensus size: 39
560742 TGATACTTGG
560752 AGATAGAAAATAAATATGATTTGAGACCGATTATATAATATTAT
1 AGATAGAAAATAAATATG----GAGACCGA-TATATAATATTAT
* *
560796 AGATAGAAAATAAATATGGATACCTATATATAATATTAT
1 AGATAGAAAATAAATATGGAGACCGATATATAATATTAT
*
560835 AGGTAGAAAAT
1 AGATAGAAAAT
560846 TATATTTTAG
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
39 23 0.49
40 6 0.13
44 18 0.38
ACGTcount: A:0.50, C:0.04, G:0.14, T:0.32
Consensus pattern (39 bp):
AGATAGAAAATAAATATGGAGACCGATATATAATATTAT
Found at i:561609 original size:177 final size:177
Alignment explanation
Indices: 561281--561609 Score: 462
Period size: 177 Copynumber: 1.9 Consensus size: 177
561271 ATATATTTTC
* *
561281 TAAAAGTATCGACCCCAAAAATATCGAAACCAATAATTATAATGTAATAGATAAATTAACAATGT
1 TAAAAGTATCGACCCCAAAAACATCGAAACCAATAATTATAATATAATAGATAAATTAACAATGT
* * * * ** *
561346 AACCGGTATAAGTATACCGGTTAATTAGAAAACATGTCAACATAATGTATCGACACTTTTTTAAT
66 AACCGGTATAAATATACCGGTTAATAAGAAAACAGGTCAACATAAAGTATCGACACCATTTAAAT
561411 TTGTGTCGATACTTATTGTCCAGAATATAAAGTGTTGATACATTTAT
131 TTGTGTCGATACTTATTGTCCAGAATATAAAGTGTTGATACATTTAT
* * * * *
561458 TAAAAGTATCGA-TCCAATAACATCGAAACCGATAATTATAATATAATAGGTAAATTTACAATGT
1 TAAAAGTATCGACCCCAAAAACATCGAAACCAATAATTATAATATAATAGATAAATTAACAATGT
* * * * *
561522 AACTGGTATAAATATACCGATTTTATAAGAAAATAGGTCAGCATAAAGTATCGACACCATTTAAA
66 AACCGGTATAAATATACCG-GTTAATAAGAAAACAGGTCAACATAAAGTATCGACACCATTTAAA
*
561587 TTTGTGTCGATACTTTTTGTCCA
130 TTTGTGTCGATACTTATTGTCCA
561610 TAATGAATGC
Statistics
Matches: 131, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
176 62 0.47
177 69 0.53
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.33
Consensus pattern (177 bp):
TAAAAGTATCGACCCCAAAAACATCGAAACCAATAATTATAATATAATAGATAAATTAACAATGT
AACCGGTATAAATATACCGGTTAATAAGAAAACAGGTCAACATAAAGTATCGACACCATTTAAAT
TTGTGTCGATACTTATTGTCCAGAATATAAAGTGTTGATACATTTAT
Found at i:561794 original size:200 final size:197
Alignment explanation
Indices: 561447--561958 Score: 613
Period size: 200 Copynumber: 2.6 Consensus size: 197
561437 ATAAAGTGTT
*
561447 GATACATTTATTAAAAGTATCGATCCAATAACATCGAAACCGATAATTATAATATAATAGGTAAA
1 GATACATTTATTAAAAGTATCGATCCAA-AACATCGAAACCGATAATTATAATGTAATAGGTAAA
*** * *
561512 TTTACAATGTAACTGGTATAAATATACCGATTTTATAAGAAAATAGGTCAGCATAAAGTATCGAC
65 TTTACAATGTAACCAATAGAAATATACCGATTTTATAAGAAAATAGGTCAGAATAAAGTATCGAC
*
561577 ACCATTTAAATTTGTGTCGATACTTTTTGTCCATAATGAATGC-CAAACGAGGTGCACGCATAAA
130 ACCATTTAAATTTGTGTCGATACTTTTT-TCCAGAATGAATGCTC-AACGAGGTGCACGCATAAA
561641 ATATC
193 ATATC
* * *
561646 GATAGATTTATTAAAAGTATCGATCCCACAAACATCGAAACCGATAATTACAATGTGATAGGTAA
1 GATACATTTATTAAAAGTATCGAT-CCA-AAACATCGAAACCGATAATTATAATGTAATAGGTAA
* * * *
561711 ATTTACAATGTATCCAATAGAAATATACCGGTTTTATGAGAAAATAGGTCTA-AATAATGTATCG
64 ATTTACAATGTAACCAATAGAAATATACCGATTTTATAAGAAAATAGGTC-AGAATAAAGTATCG
** * * *
561775 ACACTTTTTAAGTTTGTGTCGATACTTTTTTCCAGAATGAATGCTCAATGAGGTGCATGCATAAA
128 ACACCATTTAAATTTGTGTCGATACTTTTTTCCAGAATGAATGCTCAACGAGGTGCACGCATAAA
* *
561840 GTGTC
193 ATATC
* * *
561845 GATACATTGA--AAATTGTATCGATTCAAAAAACATCGAAACCGATAATTATAATGTAATAGGTA
1 GATACATTTATTAAA-AGTATCGA-TC-CAAAACATCGAAACCGATAATTATAATGTAATAGGTA
* * * * * * *
561908 AATTTGCAATATTACCAGTATAAATATACTG--TTTACTTAGAAAATAGGTCA
63 AATTTACAATGTAACCAATAGAAATATACCGATTTTA-TAAGAAAATAGGTCA
561959 ATGTAAGCGC
Statistics
Matches: 270, Mismatches: 35, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
196 5 0.02
197 16 0.06
198 65 0.24
199 66 0.24
200 116 0.43
201 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (197 bp):
GATACATTTATTAAAAGTATCGATCCAAAACATCGAAACCGATAATTATAATGTAATAGGTAAAT
TTACAATGTAACCAATAGAAATATACCGATTTTATAAGAAAATAGGTCAGAATAAAGTATCGACA
CCATTTAAATTTGTGTCGATACTTTTTTCCAGAATGAATGCTCAACGAGGTGCACGCATAAAATA
TC
Found at i:567885 original size:20 final size:20
Alignment explanation
Indices: 567852--567903 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
567842 TGAGTTTCAT
*
567852 AAAAAAAGAAAAAAATAAAAAG
1 AAAAAAAG--AAAAAGAAAAAG
567874 AAAAAAAGAAAAAGAAAAAG
1 AAAAAAAGAAAAAGAAAAAG
*
567894 AAAGAAAGAA
1 AAAAAAAGAA
567904 TCATGAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 20 0.71
22 8 0.29
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (20 bp):
AAAAAAAGAAAAAGAAAAAG
Done.