Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007754.1 Hibiscus syriacus cultivar Beakdansim tig00110020_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: 3698414
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 15
Found at i:3240873 original size:39 final size:39
Alignment explanation
Indices: 3240820--3240937 Score: 164
Period size: 39 Copynumber: 3.0 Consensus size: 39
3240810 AAAGATTTTA
* * * *
3240820 TGTTTCAAGAGAAACTGTATCAAAAGAGATAATATCTTC
1 TGTTTCAAGGGAAACTATATCAAGAGAGATAAAATCTTC
* * *
3240859 TGTTTCGAGGGAAACTATGTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATATCAAGAGAGATAAAATCTTC
*
3240898 TGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATATCAAGAGAGATAAAATCTTC
3240937 T
1 T
3240938 TTAAAACAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 69 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (39 bp):
TGTTTCAAGGGAAACTATATCAAGAGAGATAAAATCTTC
Found at i:3241054 original size:74 final size:76
Alignment explanation
Indices: 3240940--3241100 Score: 220
Period size: 74 Copynumber: 2.1 Consensus size: 76
3240930 AATCTTCTTT
*
3240940 AAAACAATCTTGAGTGAAATGAAATGTCTTATTTTAAGTAAAAAATGTCTCAAGCAAGACAAA-T
1 AAAACAATCTTGAGTGAAATGAAATGTCTTATTTCAAGTAAAAAATGTCTCAAGCAAGACAAAGT
3241004 -TGTTTTAAGA
66 CTGTTTTAAGA
* * * * * *
3241014 AAAATAATCTTGAGTGAAAT-AAATCTTCTTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAAG
1 AAAACAATCTTGAGTGAAATGAAAT-GTCTTATTTCAAGTAAAAAATGTCTCAAGCAAGACAAAG
3241078 TCTGTTTTAAGAA
65 TCTGTTTTAAG-A
3241091 AAAACAATCT
1 AAAACAATCT
3241101 CAAGTGAGAT
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
73 4 0.05
74 51 0.68
75 1 0.01
76 9 0.12
77 10 0.13
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (76 bp):
AAAACAATCTTGAGTGAAATGAAATGTCTTATTTCAAGTAAAAAATGTCTCAAGCAAGACAAAGT
CTGTTTTAAGA
Found at i:3243291 original size:21 final size:21
Alignment explanation
Indices: 3243265--3243309 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3243255 GATTTCTGGG
3243265 CAAGGGGAA-TCGATACCCATT
1 CAAGGGGAACT-GATACCCATT
*
3243286 CAAGGGGAACTGATACCCCTT
1 CAAGGGGAACTGATACCCATT
3243307 CAA
1 CAA
3243310 ACGAACAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (21 bp):
CAAGGGGAACTGATACCCATT
Found at i:3244954 original size:149 final size:149
Alignment explanation
Indices: 3244773--3245087 Score: 551
Period size: 149 Copynumber: 2.1 Consensus size: 149
3244763 GAGTCGAGGG
* *
3244773 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
3244838 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
*
3244903 TATGGCACTACGGTGTAAT
131 TATGGCACTACGGTGCAAT
*
3244922 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
3244987 ACTTGATCTCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
*
3245052 TATGGTACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
3245071 TTTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
3245088 TGCAATTATA
Statistics
Matches: 158, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 157 0.99
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:3248409 original size:21 final size:21
Alignment explanation
Indices: 3248383--3248427 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3248373 GATTTCTGGG
* *
3248383 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3248404 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3248425 CAA
1 CAA
3248428 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:3250078 original size:149 final size:149
Alignment explanation
Indices: 3249891--3250205 Score: 551
Period size: 149 Copynumber: 2.1 Consensus size: 149
3249881 GAGTCGAGGG
* * * *
3249891 TCTACGCGGTCCATCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACGCAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
3249956 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
3250021 TATGGCACTACGGTACAAT
131 TATGGCACTACGGTACAAT
*
3250040 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
3250105 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGATATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
*
3250170 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTACAAT
3250189 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
3250206 TGCAATTATA
Statistics
Matches: 158, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 157 0.99
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTACAAT
Found at i:3250206 original size:23 final size:23
Alignment explanation
Indices: 3250173--3250217 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3250163 ATTATTATAT
*
3250173 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
3250196 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
3250218 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:3258072 original size:6 final size:6
Alignment explanation
Indices: 3257926--3258068 Score: 277
Period size: 6 Copynumber: 23.8 Consensus size: 6
3257916 TCCTAAAATA
3257926 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
3257974 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
*
3258022 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATA TGTAT
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTAT
3258069 ATGTTTTTAG
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 136 1.00
ACGTcount: A:0.17, C:0.00, G:0.32, T:0.50
Consensus pattern (6 bp):
TGTATG
Found at i:3264528 original size:2 final size:2
Alignment explanation
Indices: 3264523--3264556 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3264513 ATATATATAT
*
3264523 AG AG AG AG AG AG AG AG AT AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3264557 TGGACATATG
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:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:3264701 original size:22 final size:22
Alignment explanation
Indices: 3264666--3264712 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3264656 TTAATATACG
* *
3264666 CGTGCTCACTCTAAAATTGTAT
1 CGTGCCCACCCTAAAATTGTAT
* *
3264688 CGTGCCCACCCTAATATTTTAT
1 CGTGCCCACCCTAAAATTGTAT
3264710 CGT
1 CGT
3264713 TTCTACCTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (22 bp):
CGTGCCCACCCTAAAATTGTAT
Found at i:3269580 original size:20 final size:21
Alignment explanation
Indices: 3269555--3269600 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3269545 GATCGCCGAC
*
3269555 ACTTGTTGAT-GCTAACACTA
1 ACTTGTTGATCGCCAACACTA
*
3269575 ACTTGTTGATCGCCGACACTA
1 ACTTGTTGATCGCCAACACTA
3269596 ACTTG
1 ACTTG
3269601 CTCCAAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (21 bp):
ACTTGTTGATCGCCAACACTA
Found at i:3279375 original size:21 final size:23
Alignment explanation
Indices: 3279344--3279385 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3279334 CATTTTATTT
3279344 TTTAACATCAAAA-TTTTCTTAA
1 TTTAACATCAAAACTTTTCTTAA
3279366 TTTAAC-TCAAAACTTTTCTT
1 TTTAACATCAAAACTTTTCTT
3279386 TTATTAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTAACATCAAAACTTTTCTTAA
Found at i:3280295 original size:2 final size:2
Alignment explanation
Indices: 3280288--3280320 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3280278 GTAAAGGATC
3280288 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3280321 GTTTTGATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3280858 original size:22 final size:23
Alignment explanation
Indices: 3280833--3280879 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
3280823 GTTTCGCTAT
3280833 TTATGAAAATAATTT-AAATATA
1 TTATGAAAATAATTTCAAATATA
** *
3280855 TTATGATTATTATTTCAAATATA
1 TTATGAAAATAATTTCAAATATA
3280878 TT
1 TT
3280880 TTATAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
TTATGAAAATAATTTCAAATATA
Found at i:3283991 original size:23 final size:23
Alignment explanation
Indices: 3283955--3284010 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
3283945 ATTATGAATT
*
3283955 ATAAA-ATTATTCTATACTTAGG
1 ATAAAGATTAATCTATACTTAGG
3283977 ATAAAGATTAATCTATACTTAGG
1 ATAAAGATTAATCTATACTTAGG
3284000 ATAAAGATTAA
1 ATAAAGATTAA
3284011 ACCCTTGACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 5 0.16
23 27 0.84
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (23 bp):
ATAAAGATTAATCTATACTTAGG
Found at i:3290932 original size:22 final size:22
Alignment explanation
Indices: 3290904--3290956 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
3290894 CACCACAGCT
3290904 CGTATAATTCCCACTAGGGGCA
1 CGTATAATTCCCACTAGGGGCA
*
3290926 CGTATAATTCCCACTAGGGGCG
1 CGTATAATTCCCACTAGGGGCA
*
3290948 CGTAGAATT
1 CGTATAATT
3290957 TGTCCCGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
CGTATAATTCCCACTAGGGGCA
Found at i:3291027 original size:18 final size:18
Alignment explanation
Indices: 3291004--3291055 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
3290994 ATATAACACA
*
3291004 TATGTCCCGAAGGACCAC
1 TATGTCACGAAGGACCAC
*
3291022 TATGTCACAAAGGACCAC
1 TATGTCACGAAGGACCAC
*
3291040 TATGTCTCGAAGGACC
1 TATGTCACGAAGGACC
3291056 GCGTAGACCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (18 bp):
TATGTCACGAAGGACCAC
Found at i:3298297 original size:3 final size:3
Alignment explanation
Indices: 3298289--3298327 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3298279 CAATAACTTC
3298289 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3298328 CATCATCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3308089 original size:2 final size:2
Alignment explanation
Indices: 3308082--3308110 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3308072 AGAAACAAGG
3308082 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3308111 GCACTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3316841 original size:28 final size:28
Alignment explanation
Indices: 3316804--3316865 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
3316794 GGAATCAAAT
*
3316804 CAAGCAACTAAAGAATCAATCTTTCAGC
1 CAAGTAACTAAAGAATCAATCTTTCAGC
*
3316832 TAAGTAACTAAAGAATCAATCTTTCAGC
1 CAAGTAACTAAAGAATCAATCTTTCAGC
3316860 CAAGTA
1 CAAGTA
3316866 CGGTGGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.44, C:0.21, G:0.11, T:0.24
Consensus pattern (28 bp):
CAAGTAACTAAAGAATCAATCTTTCAGC
Found at i:3319936 original size:21 final size:21
Alignment explanation
Indices: 3319912--3319972 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
3319902 TTCAAAGAAA
3319912 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
3319933 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
3319947 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
3319968 CATTT
1 CATTT
3319973 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:3319946 original size:35 final size:36
Alignment explanation
Indices: 3319861--3320007 Score: 187
Period size: 35 Copynumber: 4.2 Consensus size: 36
3319851 ATCCCATTAT
* *
3319861 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
3319897 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
3319933 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
** *
3319968 CATTTTTTCAAAG--TTAGTTACCAAAC-TTGAAAAC
1 CA-TTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
3320002 CATTTT
1 CATTTT
3320008 AATACTTTCA
Statistics
Matches: 101, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
33 4 0.04
34 10 0.10
35 45 0.45
36 13 0.13
37 29 0.29
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:3319978 original size:72 final size:68
Alignment explanation
Indices: 3319864--3320007 Score: 182
Period size: 72 Copynumber: 2.1 Consensus size: 68
3319854 CCATTATCAT
*
3319864 TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGAAACATTTACCAAACTTTGA
1 TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAG--ACAGTTACCAAAC-TTGA
3319929 AAACCA
63 AAACCA
* * * **
3319935 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCATTTTTTCAAAGTTAGTTACCAAACTTGAA
1 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTA-TTTTTCAAAGACAGTTACCAAACTTGAA
3319999 AACCA
64 AACCA
3320004 TTTT
1 TTTT
3320008 AATACTTTCA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
69 14 0.22
70 10 0.15
71 11 0.17
72 30 0.46
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (68 bp):
TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGACAGTTACCAAACTTGAAAA
CCA
Found at i:3324572 original size:35 final size:35
Alignment explanation
Indices: 3324490--3324634 Score: 211
Period size: 35 Copynumber: 4.1 Consensus size: 35
3324480 CCATTATTAT
* * *
3324490 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTA
1 TTTTCAAAGAAACATTTACCAAACTTT-AAAAACCA
3324525 TTTTTCAAAGAAACATTTACCAAACTTTAAAAACCA
1 -TTTTCAAAGAAACATTTACCAAACTTTAAAAACCA
*
3324561 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTAAAAACCA
* *
3324596 TTTTCAAAGAAACATTTACCAAACTTTGAAAATCA
1 TTTTCAAAGAAACATTTACCAAACTTTAAAAACCA
3324631 TTTT
1 TTTT
3324635 AATACTTTCA
Statistics
Matches: 103, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
35 72 0.70
36 12 0.12
37 19 0.18
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (35 bp):
TTTTCAAAGAAACATTTACCAAACTTTAAAAACCA
Found at i:3324597 original size:21 final size:20
Alignment explanation
Indices: 3324535--3324633 Score: 60
Period size: 20 Copynumber: 5.4 Consensus size: 20
3324525 TTTTTCAAAG
*
3324535 AAACATTTACCAAACTTTAA
1 AAACATTTACCAAACTTTGA
*
3324555 AAACCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
3324570 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
3324590 AAACCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
3324605 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
3324625 AAATCATTT
1 AAA-CATTT
3324634 TAATACTTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 29
0.63 0.05 0.31
Matches are distributed among these distances:
14 10 0.17
15 14 0.24
16 1 0.02
19 2 0.03
20 17 0.29
21 15 0.25
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.30
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:3327706 original size:21 final size:21
Alignment explanation
Indices: 3327667--3327706 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3327657 ACATGTGACA
* *
3327667 ATCATATTAATATCGTAAAGT
1 ATCACATTAATATCATAAAGT
*
3327688 ATCACATTAATTTCATAAA
1 ATCACATTAATATCATAAA
3327707 TTGTTGTATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
ATCACATTAATATCATAAAGT
Found at i:3334589 original size:12 final size:14
Alignment explanation
Indices: 3334568--3334600 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
3334558 AGAAATGAAA
3334568 AAATATATATTTAC
1 AAATATATATTTAC
3334582 AAATATATATTTAC
1 AAATATATATTTAC
3334596 AAATA
1 AAATA
3334601 CAAGTACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATATATATTTAC
Found at i:3347973 original size:7 final size:7
Alignment explanation
Indices: 3347961--3347996 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
3347951 CTAAGGTTGA
3347961 AGATTTT
1 AGATTTT
3347968 AGATTTT
1 AGATTTT
3347975 AGATTTT
1 AGATTTT
3347982 AGATTTT
1 AGATTTT
3347989 AGATTTT
1 AGATTTT
3347996 A
1 A
3347997 AAAATAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.56
Consensus pattern (7 bp):
AGATTTT
Found at i:3349881 original size:21 final size:21
Alignment explanation
Indices: 3349857--3349909 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3349847 TGGTAACCGC
* * * *
3349857 GGAAGCTATGGTGGTGGTCGT
1 GGAAGCTACGGAGGTGGACAT
3349878 GGAAGCTACGGAGGTGGACAT
1 GGAAGCTACGGAGGTGGACAT
*
3349899 GGAAGTTACGG
1 GGAAGCTACGG
3349910 GGGGATCCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.45, T:0.21
Consensus pattern (21 bp):
GGAAGCTACGGAGGTGGACAT
Found at i:3354575 original size:106 final size:105
Alignment explanation
Indices: 3354203--3356024 Score: 3009
Period size: 105 Copynumber: 17.5 Consensus size: 105
3354193 AAATTTCAAC
*
3354203 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
3354268 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT
* ** *
3354308 TTCTCGATTTCAGAGTTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
3354373 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT
* *
3354413 TTCTCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACACAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
* * *
3354478 CAACGTCACGGCGAAGGGACCGCTGGTTGTCAATAAACAAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-AT
* *
3354519 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
* *
3354584 CAACTTCACGGCGAAGGGACCGCTGGTTGTCAATAAACAAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-AT
* * * *
3354625 TTCTCGATTTCAGAGTCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACACAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
* *
3354690 CAACTTCACGGCGAAGGGACCGCTGGTTGTCAATAAACAAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-AT
* *
3354731 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
*
3354796 CAACTTCACGGCGAAGGGACCGCTGGTTGTCAACAAACAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT
*
3354836 TTCTCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
*
3354901 CAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT
3354941 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
*
3355006 CAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT
*
3355046 TTCCCAATTTCAGAGCCAATTTCAACTT--C-AC-----A-ATTGGACTCCAGACAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
3355102 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT
*
3355142 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
*
3355207 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-AT
3355248 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
*
3355313 CAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT
* *
3355353 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGGTATTGGACTCCAGACAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
*
3355418 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT
* *
3355458 TT-TCAATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCTAGACAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
*
3355522 CAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAACAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT
3355562 TT-TCAATTTCAGAGCCAATTTCAACTT--C-AC-----A-ATTGGACTCCAGACAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
3355617 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT
*
3355657 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
*
3355722 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-AT
*
3355763 TTCTCAATTTCAGAGCTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
*
3355828 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-AT
* *
3355869 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAGACAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
*
3355934 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAAT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-CAT
* * ** *
3355975 TTCCCAATTCCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTC
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
3356025 GGAACAATGC
Statistics
Matches: 1624, Mismatches: 70, Indels: 45
0.93 0.04 0.03
Matches are distributed among these distances:
95 64 0.04
96 116 0.07
97 1 0.00
98 2 0.00
99 4 0.00
101 2 0.00
102 3 0.00
103 1 0.00
104 125 0.08
105 655 0.40
106 651 0.40
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT
Found at i:3354609 original size:211 final size:210
Alignment explanation
Indices: 3354203--3356024 Score: 2993
Period size: 211 Copynumber: 8.7 Consensus size: 210
3354193 AAATTTCAAC
* *
3354203 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACGCAAGTT
* **
3354268 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTTCAGAGTTAATTTCAA
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAA
*
3354333 CTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTG
131 CTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
3354398 GTTGTCAACAAACAT
196 GTTGTCAACAAACAT
*
3354413 TTCTCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACACAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACGCAAGTT
* * *
3354478 CAACGTCACGGCGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCAATTTCAGAGCCAATTTCA
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTTCA
* * *
3354543 ACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGGCGAAGGGACCGCT
130 ACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCT
*
3354608 GGTTGTCAATAAACAAT
195 GGTTGTCAACAAAC-AT
* * *
3354625 TTCTCGATTTCAGAGTCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACACAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACGCAAGTT
* *
3354690 CAACTTCACGGCGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCAATTTCAGAGCCAATTTCA
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTTCA
* * *
3354755 ACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGGCGAAGGGACCGCT
130 ACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCT
3354820 GGTTGTCAACAAACAT
195 GGTTGTCAACAAACAT
3354836 TTCTCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACGCAAGTT
*
3354901 CAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTTCAGAGCCAATTTCAA
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAA
3354966 CTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
131 CTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
*
3355031 GTTGTCAATAAACAT
196 GTTGTCAACAAACAT
*
3355046 TTCCCAATTTCAGAGCCAATTTCAACTT---CAC-----A-ATTGGACTCCAGACAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACGCAAGTT
3355102 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAA
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAA
*
3355167 CTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTG
131 CTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
*
3355232 GTTGTCAACAAACAAC
196 GTTGTCAACAAAC-AT
*
3355248 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACGCAAGTT
* *
3355313 CAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTCAGAGCCAATTTCAA
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAA
*
3355378 CTTCACAACGAAGGGTATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
131 CTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
*
3355443 GTTGTCAACAAATAT
196 GTTGTCAACAAACAT
* * *
3355458 TT-TCAATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCTAGACAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACGCAAGTT
*
3355522 CAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAACATTT-TCAATTTCAGAGCCAATTTCAA
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAA
3355586 CTT--C-AC-----A-ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
131 CTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
3355642 GTTGTCAACAAACAT
196 GTTGTCAACAAACAT
* *
3355657 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACGCAAGTT
* *
3355722 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCTAATTTCA
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTTCA
3355787 ACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCT
130 ACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCT
*
3355852 GGTTGTCAACAAACAAC
195 GGTTGTCAACAAAC-AT
*
3355869 TTCTCAATTTCAGAGCCAATTTCAACTTCA-CAGCAAAGGATATTGGACTCCAGACAACGCAAGT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACCA-CGAAGGATATTGGACTCCAGACAACGCAAGT
* * *
3355933 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTCCAGAGCCAATTTC
65 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-CATTTCTCAATTTCAGAGCCAATTTC
** *
3355998 AACTTCACGGCGGAGGATATTGGACTC
129 AACTTCACAACGAAGGATATTGGACTC
3356025 GGAACAATGC
Statistics
Matches: 1523, Mismatches: 62, Indels: 52
0.93 0.04 0.03
Matches are distributed among these distances:
199 65 0.04
200 96 0.06
201 167 0.11
202 53 0.03
204 1 0.00
205 6 0.00
206 1 0.00
207 3 0.00
208 24 0.02
209 100 0.07
210 232 0.15
211 425 0.28
212 350 0.23
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (210 bp):
TTCTCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACGCAAGTT
CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAA
CTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
GTTGTCAACAAACAT
Found at i:3356131 original size:412 final size:417
Alignment explanation
Indices: 3354203--3356024 Score: 2741
Period size: 412 Copynumber: 4.4 Consensus size: 417
3354193 AAATTTCAAC
* *
3354203 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCAC-ACAAAGGATATTGGACTCCAGACAACGCAAGTT
* * **
3354268 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTTCAGAGTTAATTTCAA
65 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAATTTCTCAATTTCAGAGCCAATTTCAA
* *
3354333 CTTCACAACGAAGGATATTGGACTCCAGACA-ACGTAAGTTCAACTTCAC--GACGAAGGGACCG
130 CTTCACAGCGAAGGATATTGGACTCCAGACACAC--AAGTGCAACTTCACTTG-CGAAGGGACCG
*
3354395 CTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGATATTGGA
192 CTGGTTGTCAACAAACA-TTCTCAATTTCAGAGCCAATTTCAAC-TCACAACGAAGGA-ATTGGA
* *
3354460 CTCCAGACAACACAAGTTCAACGTCACGGCGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCA
254 CTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAC-ATTTCTCA
* *
3354525 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTT
318 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* *
3354590 CACGGCGAAGGGACCGCTGGTTGTCAATAAACAAT
383 CACGACGAAGGGACCGCTGGTTGTCAACAAACAAT
* * * *
3354625 TTCTCGATTTCAGAGTCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACACAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCA-CACAAAGGATATTGGACTCCAGACAACGCAAGTT
* *
3354690 CAACTTCACGGCGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCAATTTCAGAGCCAATTTCA
65 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-AATTTCTCAATTTCAGAGCCAATTTCA
* *
3354755 ACTTCACAGCGAAGGATATTGGACTCCAGACA-ACGTAAGTTCAACTTCAC-GGCGAAGGGACCG
129 ACTTCACAGCGAAGGATATTGGACTCCAGACACAC--AAGTGCAACTTCACTTGCGAAGGGACCG
*
3354818 CTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGATATTGGA
192 CTGGTTGTCAACAAACA-TTCTCAATTTCAGAGCCAATTTCAAC-TCACAACGAAGGA-ATTGGA
*
3354883 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAA
254 CTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAA
3354948 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
319 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
*
3355013 ACGACGAAGGGACCGCTGGTTGTCAATAAAC-AT
384 ACGACGAAGGGACCGCTGGTTGTCAACAAACAAT
*
3355046 TTCCCAATTTCAGAGCCAATTTCAACTT--CAC-----A-ATTGGACTCCAGACAACGCAAGTTC
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACACAAAGGATATTGGACTCCAGACAACGCAAGTTC
*
3355103 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAAC
66 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAATTTCTCAATTTCAGAGCCAATTTCAAC
* *
3355168 TTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCAC--GACGAAGGGACCGCT
131 TTCACAGCGAAGGATATTGGACTCCAGAC-ACACAAGTGCAACTTCACTTG-CGAAGGGACCGCT
3355231 GGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
194 GGTTGTCAACAAAC-A-TTCTCAATTTCAGAGCCAATTTCAAC-TCACAACGAAGGA-ATTGGAC
* *
3355296 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAAT
255 TCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAAT
*
3355361 TTCAGAGCCAATTTCAACTTCACAACGAAGGGTATTGGACTCCAGACAACGCAAGTTCAACTTCA
320 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
3355426 CGACGAAGGGACCGCTGGTTGTCAACAAA-TAT
385 CGACGAAGGGACCGCTGGTTGTCAACAAACAAT
*
3355458 TT-TCAATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCTAGACAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCAC-ACAAAGGATATTGGACTCCAGACAACGCAAGTT
* *
3355522 CAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAACATTT-TCAATTTCAGAGCCAATTTCAA
65 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAATTTCTCAATTTCAGAGCCAATTTCAA
* *
3355586 CTT--CA-C-----A-ATTGGACTCCAGACAACGCAAGTTCAACTTCAC--GACGAAGGGACCGC
130 CTTCACAGCGAAGGATATTGGACTCCAGAC-ACACAAGTGCAACTTCACTTG-CGAAGGGACCGC
3355640 TGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
193 TGGTTGTCAACAAACA-TTCTCAATTTCAGAGCCAATTTCAAC-TCACAACGAAGGA-ATTGGAC
* *
3355705 TCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAA
255 TCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAC-ATTTCTCAA
*
3355770 TTTCAGAGCTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
319 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
*
3355835 ACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
384 ACGACGAAGGGACCGCTGGTTGTCAACAAACAAT
3355869 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAGACAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACA-CAAAGGATATTGGACTCCAGACAACGCAAGTT
* *
3355934 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTCCAGAGCCAATTTCA
65 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-AATTTCTCAATTTCAGAGCCAATTTCA
* *
3355999 ACTTCACGGCGGAGGATATTGGACTC
129 ACTTCACAGCGAAGGATATTGGACTC
3356025 GGAACAATGC
Statistics
Matches: 1319, Mismatches: 49, Indels: 63
0.92 0.03 0.04
Matches are distributed among these distances:
409 102 0.08
410 162 0.12
411 126 0.10
412 362 0.27
413 8 0.01
414 25 0.02
416 2 0.00
417 3 0.00
418 3 0.00
419 26 0.02
420 64 0.05
421 27 0.02
422 197 0.15
423 211 0.16
424 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (417 bp):
TTCTCAATTTCAGAGCCAATTTCAACTTCACACAAAGGATATTGGACTCCAGACAACGCAAGTTC
AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAATTTCTCAATTTCAGAGCCAATTTCAAC
TTCACAGCGAAGGATATTGGACTCCAGACACACAAGTGCAACTTCACTTGCGAAGGGACCGCTGG
TTGTCAACAAACATTCTCAATTTCAGAGCCAATTTCAACTCACAACGAAGGAATTGGACTCCAGA
CAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
AGGGACCGCTGGTTGTCAACAAACAAT
Found at i:3357154 original size:21 final size:21
Alignment explanation
Indices: 3357130--3357182 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3357120 TGGTAACCGC
* * * *
3357130 GGAAGCTATGGTGGTGGTCGT
1 GGAAGCTACGGAGGTGGACAT
3357151 GGAAGCTACGGAGGTGGACAT
1 GGAAGCTACGGAGGTGGACAT
*
3357172 GGAAGTTACGG
1 GGAAGCTACGG
3357183 GGGGATCCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.45, T:0.21
Consensus pattern (21 bp):
GGAAGCTACGGAGGTGGACAT
Found at i:3358828 original size:18 final size:18
Alignment explanation
Indices: 3358801--3358844 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
3358791 CACGCTTCTT
*
3358801 ATTTAAACTAATAACATA
1 ATTTATACTAATAACATA
3358819 ATTTATACTAATAACATA
1 ATTTATACTAATAACATA
3358837 ATTTATAC
1 ATTTATAC
3358845 ATGTTAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTTATACTAATAACATA
Found at i:3369877 original size:17 final size:17
Alignment explanation
Indices: 3369855--3369888 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3369845 CTAATAAGGG
3369855 ATAATCTTCTCAATTCC
1 ATAATCTTCTCAATTCC
3369872 ATAATCTTCTCAATTCC
1 ATAATCTTCTCAATTCC
3369889 TTTTCCTATA
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:0.29, C:0.29, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATCTTCTCAATTCC
Found at i:3372307 original size:2 final size:2
Alignment explanation
Indices: 3372287--3372331 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
3372277 AGGTGAGTAT
* *
3372287 TA TA -A TA TT TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3372328 TA TA
1 TA TA
3372332 GGATAATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3374822 original size:112 final size:112
Alignment explanation
Indices: 3374625--3374844 Score: 431
Period size: 112 Copynumber: 2.0 Consensus size: 112
3374615 CCCCATGAAA
3374625 ATGATAATCTTTCTAGTTTGTTCTTGGAGTCGCCCACTCAACTCTAAGGATGAGATTGTCGTAAC
1 ATGATAATCTTTCTAGTTTGTTCTTGGAGTCGCCCACTCAACTCTAAGGATGAGATTGTCGTAAC
*
3374690 CGTATCCGTTCAACTTGTTGATAGCTCTCTGGGCGTCCTCTCTAAGG
66 CATATCCGTTCAACTTGTTGATAGCTCTCTGGGCGTCCTCTCTAAGG
3374737 ATGATAATCTTTCTAGTTTGTTCTTGGAGTCGCCCACTCAACTCTAAGGATGAGATTGTCGTAAC
1 ATGATAATCTTTCTAGTTTGTTCTTGGAGTCGCCCACTCAACTCTAAGGATGAGATTGTCGTAAC
3374802 CATATCCGTTCAACTTGTTGATAGCTCTCTGGGCGTCCTCTCT
66 CATATCCGTTCAACTTGTTGATAGCTCTCTGGGCGTCCTCTCT
3374845 GTTCACAAAG
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 107 1.00
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35
Consensus pattern (112 bp):
ATGATAATCTTTCTAGTTTGTTCTTGGAGTCGCCCACTCAACTCTAAGGATGAGATTGTCGTAAC
CATATCCGTTCAACTTGTTGATAGCTCTCTGGGCGTCCTCTCTAAGG
Found at i:3376023 original size:27 final size:28
Alignment explanation
Indices: 3375990--3376048 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 28
3375980 AGTAATTAAT
*
3375990 ATCCAAAT-GCAATTTAACAATAATCAA
1 ATCCAAATAGCAATTTAACAACAATCAA
3376017 ATCCAAATAGAAGCAATTTAACAACAATCAA
1 ATCCAAAT---AGCAATTTAACAACAATCAA
3376048 A
1 A
3376049 CTTAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 8 0.30
31 19 0.70
ACGTcount: A:0.54, C:0.19, G:0.05, T:0.22
Consensus pattern (28 bp):
ATCCAAATAGCAATTTAACAACAATCAA
Found at i:3376135 original size:31 final size:31
Alignment explanation
Indices: 3376092--3376171 Score: 133
Period size: 31 Copynumber: 2.5 Consensus size: 31
3376082 AATACATAAT
3376092 AATTTAAACAATAATCAAACCCGGATATGAGA
1 AATTT-AACAATAATCAAACCCGGATATGAGA
*
3376124 AATTTAGCAATAATCAAACCCGGATATGAGA
1 AATTTAACAATAATCAAACCCGGATATGAGA
*
3376155 AATTTAACAACAATCAA
1 AATTTAACAATAATCAA
3376172 TCATATATCT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 40 0.89
32 5 0.11
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.23
Consensus pattern (31 bp):
AATTTAACAATAATCAAACCCGGATATGAGA
Found at i:3378970 original size:17 final size:17
Alignment explanation
Indices: 3378948--3378986 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3378938 TCTATTAAAA
3378948 TATTTTATT-GTATTATT
1 TATTTTATTAGTATTA-T
*
3378965 TATTTTATTATTATTAT
1 TATTTTATTAGTATTAT
3378982 TATTT
1 TATTT
3378987 CTTTTATAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
TATTTTATTAGTATTAT
Found at i:3380145 original size:29 final size:29
Alignment explanation
Indices: 3380107--3380166 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
3380097 ATTTTGGCCC
* *
3380107 TTTTATTTAT-TTATTTACTTTTTTTAAT
1 TTTTATTTATCTTATTAACATTTTTTAAT
*
3380135 TTTTATTTTATCTTCTTAACATTTTTTAAT
1 TTTTA-TTTATCTTATTAACATTTTTTAAT
3380165 TT
1 TT
3380167 CAAACCTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 5 0.19
29 5 0.19
30 17 0.63
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (29 bp):
TTTTATTTATCTTATTAACATTTTTTAAT
Found at i:3380212 original size:16 final size:16
Alignment explanation
Indices: 3380182--3380219 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3380172 CTTAGCCTTT
*
3380182 TTTTTCATTTCTTTTA
1 TTTTTCATTTATTTTA
3380198 TATTTT-ATTTATTTTA
1 T-TTTTCATTTATTTTA
3380214 TTTTTC
1 TTTTTC
3380220 CCCTTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
15 4 0.21
16 11 0.58
17 4 0.21
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCATTTATTTTA
Found at i:3380784 original size:2 final size:2
Alignment explanation
Indices: 3380777--3380804 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3380767 GTAAATCTTC
3380777 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
3380805 TCTTTATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3383609 original size:21 final size:21
Alignment explanation
Indices: 3383583--3383625 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
3383573 TCACTTATTT
3383583 TTTCTTTT-AAAATATAACAAA
1 TTTCTTTTCAAAATATAA-AAA
3383604 TTTCTTTTCAAAATATAAAAA
1 TTTCTTTTCAAAATATAAAAA
3383625 T
1 T
3383626 AACAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTCTTTTCAAAATATAAAAA
Found at i:3389164 original size:132 final size:132
Alignment explanation
Indices: 3388927--3389186 Score: 484
Period size: 132 Copynumber: 2.0 Consensus size: 132
3388917 CTTGAATAAA
* **
3388927 CAGACAAGAGAAAACAACTGCACACCAGCTGACGAACTAGCGGCTGCAACTGATAAAATGGCTCT
1 CAGACAAGAGAAAACAACTGCACACCAGCTGAAGAACTAGCGGCTGCAACAAATAAAATGGCTCT
3388992 CACCTGCAATTTTCATCCTCCTCATTATCATTACTATCACTAGCAACTCGTCAAAATTCGTGTTA
66 CACCTGCAATTTTCATCCTCCTCATTATCATTACTATCACTAGCAACTCGTCAAAATTCGTGTTA
3389057 TT
131 TT
*
3389059 CAGACAAGAGAAAACAACTGCACACCAGCTGAAGAACTAGCGGCTGTAACAAATAAAATGGCTCT
1 CAGACAAGAGAAAACAACTGCACACCAGCTGAAGAACTAGCGGCTGCAACAAATAAAATGGCTCT
3389124 CACCTGCAATTTTCATCCTCCTCATTATCATTACTATCACTAGCAACTCGTCAAAATTCGTGT
66 CACCTGCAATTTTCATCCTCCTCATTATCATTACTATCACTAGCAACTCGTCAAAATTCGTGT
3389187 CAGATACATA
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 124 1.00
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (132 bp):
CAGACAAGAGAAAACAACTGCACACCAGCTGAAGAACTAGCGGCTGCAACAAATAAAATGGCTCT
CACCTGCAATTTTCATCCTCCTCATTATCATTACTATCACTAGCAACTCGTCAAAATTCGTGTTA
TT
Found at i:3392649 original size:16 final size:16
Alignment explanation
Indices: 3392630--3392660 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3392620 AACCTACTGG
3392630 ACATATAAACTACCTA
1 ACATATAAACTACCTA
3392646 ACATATAAACTACCT
1 ACATATAAACTACCT
3392661 CTTTTTTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (16 bp):
ACATATAAACTACCTA
Found at i:3396619 original size:22 final size:21
Alignment explanation
Indices: 3396594--3396646 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
3396584 TTTAGATTAT
*
3396594 ATATTAATATCTATAT-TTTAAA
1 ATATTAATAT-TA-ATCGTTAAA
3396616 ATATTTAATATTAATCGTTAAA
1 ATA-TTAATATTAATCGTTAAA
3396638 ATATTAATA
1 ATATTAATA
3396647 CCATATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 8 0.29
22 13 0.46
23 7 0.25
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (21 bp):
ATATTAATATTAATCGTTAAA
Found at i:3409327 original size:2 final size:2
Alignment explanation
Indices: 3409322--3409347 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3409312 AGATTTAATC
3409322 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3409348 ATTGTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3410234 original size:11 final size:11
Alignment explanation
Indices: 3410215--3410281 Score: 55
Period size: 11 Copynumber: 5.7 Consensus size: 11
3410205 TGGTTACTTT
*
3410215 ATATGAATTAA
1 ATATAAATTAA
3410226 ATATAAATTAA
1 ATATAAATTAA
3410237 ATAACAATAAGATT-A
1 AT----ATAA-ATTAA
*
3410252 ATATGAATTAA
1 ATATAAATTAA
3410263 ATATAAATTAA
1 ATATAAATTAA
*
3410274 ATAAAAAT
1 ATATAAAT
3410282 AAGATTAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
10 3 0.07
11 33 0.72
15 7 0.15
16 3 0.07
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (11 bp):
ATATAAATTAA
Found at i:3410256 original size:37 final size:37
Alignment explanation
Indices: 3410215--3410303 Score: 151
Period size: 37 Copynumber: 2.4 Consensus size: 37
3410205 TGGTTACTTT
*
3410215 ATATGAATTAAATATAAATTAAATAACAATAAGATTA
1 ATATGAATTAAATATAAATTAAATAAAAATAAGATTA
3410252 ATATGAATTAAATATAAATTAAATAAAAATAAGATTA
1 ATATGAATTAAATATAAATTAAATAAAAATAAGATTA
*
3410289 ATATGGATTTAAATA
1 ATAT-GAATTAAATA
3410304 ATGAAATATA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
37 40 0.82
38 9 0.18
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.34
Consensus pattern (37 bp):
ATATGAATTAAATATAAATTAAATAAAAATAAGATTA
Found at i:3415246 original size:35 final size:35
Alignment explanation
Indices: 3415200--3415312 Score: 226
Period size: 35 Copynumber: 3.2 Consensus size: 35
3415190 ATCTCTTTAA
3415200 TCAATCAAATGGAAATACTTGGTAACCCATTCAGC
1 TCAATCAAATGGAAATACTTGGTAACCCATTCAGC
3415235 TCAATCAAATGGAAATACTTGGTAACCCATTCAGC
1 TCAATCAAATGGAAATACTTGGTAACCCATTCAGC
3415270 TCAATCAAATGGAAATACTTGGTAACCCATTCAGC
1 TCAATCAAATGGAAATACTTGGTAACCCATTCAGC
3415305 TCAATCAA
1 TCAATCAA
3415313 TTTGATGCGT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 78 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (35 bp):
TCAATCAAATGGAAATACTTGGTAACCCATTCAGC
Found at i:3418939 original size:17 final size:18
Alignment explanation
Indices: 3418917--3418956 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
3418907 AAAGGAAAAG
*
3418917 AAAAATCAAAAT-CAATA
1 AAAAATCAAAATAAAATA
*
3418934 AAAAATTAAAATAAAATA
1 AAAAATCAAAATAAAATA
3418952 AAAAA
1 AAAAA
3418957 CCAACTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAAATCAAAATAAAATA
Found at i:3420804 original size:27 final size:28
Alignment explanation
Indices: 3420741--3420795 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
3420731 TAAACTATTT
3420741 AAACCCCATTAAAAAAAATAGAAGAATC
1 AAACCCCATTAAAAAAAATAGAAGAATC
3420769 AAACCCCATT-AAAAAAATAGAAGAATC
1 AAACCCCATTAAAAAAAATAGAAGAATC
3420796 CTATTCCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.60, C:0.18, G:0.07, T:0.15
Consensus pattern (28 bp):
AAACCCCATTAAAAAAAATAGAAGAATC
Found at i:3426713 original size:12 final size:12
Alignment explanation
Indices: 3426688--3426779 Score: 71
Period size: 12 Copynumber: 7.8 Consensus size: 12
3426678 ACGAAGATAT
* *
3426688 CAGAAATCAAAA
1 CAGAATTCAGAA
3426700 CAGAATTCAGAA
1 CAGAATTCAGAA
3426712 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
3426724 CAGAATCCAGAT
1 CAGAATTCAGAA
*
3426736 CAGAAATCAGAA
1 CAGAATTCAGAA
* **
3426748 CATAATTCAGGT
1 CAGAATTCAGAA
**
3426760 CATTA-TCAGAA
1 CAGAATTCAGAA
3426771 CAGAATTCA
1 CAGAATTCA
3426780 AGTCGGAAAT
Statistics
Matches: 61, Mismatches: 16, Indels: 6
0.73 0.19 0.07
Matches are distributed among these distances:
11 9 0.15
12 50 0.82
13 2 0.03
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:3426715 original size:24 final size:24
Alignment explanation
Indices: 3426688--3426779 Score: 96
Period size: 24 Copynumber: 3.9 Consensus size: 24
3426678 ACGAAGATAT
*
3426688 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * *
3426712 CAGATATCAGAACAGAATCCAGAT
1 CAGAAATCAGAACAGAATTCAGAA
* **
3426736 CAGAAATCAGAACATAATTCAGGT
1 CAGAAATCAGAACAGAATTCAGAA
**
3426760 CA-TTATCAGAACAGAATTCA
1 CAGAAATCAGAACAGAATTCA
3426780 AGTCGGAAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
23 15 0.26
24 42 0.74
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.18
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:3427944 original size:18 final size:18
Alignment explanation
Indices: 3427923--3427958 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3427913 CTGCCATCCG
*
3427923 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
3427941 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
3427959 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:3429283 original size:18 final size:18
Alignment explanation
Indices: 3429260--3429300 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
3429250 CAACGGTATA
3429260 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
*
3429278 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
3429296 CGGGT
1 CGGGT
3429301 TGTGACCGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.20, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:3445125 original size:35 final size:33
Alignment explanation
Indices: 3445036--3445213 Score: 94
Period size: 35 Copynumber: 5.1 Consensus size: 33
3445026 ACAATTATTC
* * *
3445036 TTTTAAATATTTCAAATTAAAAAATATT-TATTA
1 TTTTGAATA-TTCAAATTAAAAGATATTATATAA
* * *
3445069 TCTATTTAATTTTGAATATTAAAAGATAATTATATAA
1 T-T-TTGAATATTCAA-ATTAAAAGAT-ATTATATAA
* *
3445106 TTTTGAATATCTCAAATTAAAAAATATT-TATTA
1 TTTTGAATAT-TCAAATTAAAAGATATTATATAA
* * *
3445139 TCTCTTTAAGT-TTGAATATTAAAAGGTATT-TATATA
1 T-T-TTGAA-TATTCAA-ATTAAAAGATATTATATA-A
*
3445175 TTTTGAATATTTCAAATTAAATGATATTATTATCAA
1 TTTTGAATA-TTCAAATTAAAAGATATTA-TAT-AA
3445211 TTT
1 TTT
3445214 AAATTTGAAT
Statistics
Matches: 110, Mismatches: 19, Indels: 29
0.70 0.12 0.18
Matches are distributed among these distances:
33 7 0.06
34 27 0.25
35 53 0.48
36 17 0.15
37 6 0.05
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (33 bp):
TTTTGAATATTCAAATTAAAAGATATTATATAA
Found at i:3445131 original size:70 final size:69
Alignment explanation
Indices: 3444984--3445230 Score: 290
Period size: 70 Copynumber: 3.6 Consensus size: 69
3444974 ATAATAATAT
* * * * * * *
3444984 AAATTAAAAAATA--T-TTATCT-TTTTAATTTAAATATTAGTAGGACAATTAT-TCTTTTAAAT
1 AAATTAAAAAATATTTATTATCTATTTAAATTTGAATATTA-AAAGATAATTATATATTTTGAAT
3445044 ATTTC
65 ATTTC
*
3445049 AAATTAAAAAATATTTATTATCTATTTAATTTTGAATATTAAAAGATAATTATATAATTTTGAAT
1 AAATTAAAAAATATTTATTATCTATTTAAATTTGAATATTAAAAGATAATTATAT-ATTTTGAAT
*
3445114 ATCTC
65 ATTTC
* * * *
3445119 AAATTAAAAAATATTTATTATCTCTTTAAGTTTGAATATTAAAAGGTATTTATATATTTTGAATA
1 AAATTAAAAAATATTTATTATCTATTTAAATTTGAATATTAAAAGATAATTATATATTTTGAATA
3445184 TTTC
66 TTTC
** *
3445188 AAATTAAATGATA-TTATTATCAATTTAAATTTGAATATTAAAA
1 AAATTAAAAAATATTTATTATCTATTTAAATTTGAATATTAAAA
3445231 TATATCTATT
Statistics
Matches: 157, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
65 13 0.08
67 1 0.01
68 42 0.27
69 39 0.25
70 62 0.39
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.46
Consensus pattern (69 bp):
AAATTAAAAAATATTTATTATCTATTTAAATTTGAATATTAAAAGATAATTATATATTTTGAATA
TTTC
Found at i:3445226 original size:21 final size:21
Alignment explanation
Indices: 3445176--3445227 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
3445166 ATTTATATAT
3445176 TTTGAATATT-TCAAATTAAA
1 TTTGAATATTATCAAATTAAA
*
3445196 --TGATATTATTATCAATTTAAA
1 TTTGA-A-TATTATCAAATTAAA
3445217 TTTGAATATTA
1 TTTGAATATTA
3445228 AAATATATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 9
0.72 0.03 0.25
Matches are distributed among these distances:
18 3 0.12
19 1 0.04
20 4 0.15
21 14 0.54
22 1 0.04
23 3 0.12
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (21 bp):
TTTGAATATTATCAAATTAAA
Found at i:3447805 original size:61 final size:60
Alignment explanation
Indices: 3447740--3447878 Score: 181
Period size: 61 Copynumber: 2.3 Consensus size: 60
3447730 TTCTTGCAAT
* * * *
3447740 TAGGTACTGAATTAGTTAAACTTATTAAT-AATCGAATCTAATAAGTGTATTTACCTACAAA
1 TAGGTCCT-AATTAGTTAAAATCATTAATAAAT-GAATCTAACAAGTGTATTTACCTACAAA
* *
3447801 TAGGTCCATAATTAATTAAAATCATTAATAAATGAATCTAACAAGTGTATTTACCTACAAT
1 TAGGTCC-TAATTAGTTAAAATCATTAATAAATGAATCTAACAAGTGTATTTACCTACAAA
3447862 TAGGTCCTTAATTAGTT
1 TAGGTCC-TAATTAGTT
3447879 CCTTAATTAG
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
61 64 0.94
62 4 0.06
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (60 bp):
TAGGTCCTAATTAGTTAAAATCATTAATAAATGAATCTAACAAGTGTATTTACCTACAAA
Found at i:3447889 original size:12 final size:12
Alignment explanation
Indices: 3447859--3447890 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3447849 ATTTACCTAC
*
3447859 AATTAGGTCCTT
1 AATTAGTTCCTT
3447871 AATTAGTTCCTT
1 AATTAGTTCCTT
3447883 AATTAGTT
1 AATTAGTT
3447891 GAATGATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (12 bp):
AATTAGTTCCTT
Found at i:3448002 original size:60 final size:61
Alignment explanation
Indices: 3447871--3448047 Score: 182
Period size: 60 Copynumber: 2.9 Consensus size: 61
3447861 TTAGGTCCTT
* * * * *
3447871 AATTAGTTCCTTAATTAGTTGAA-TGATTAATAAGTGAACCTAATGAGTGTAG-TTACCTAC
1 AATTAGATCCTTAATTAGTTAAATTGATTAATAATTGAACCTAATAAGTCTAGCTT-CCTAC
* * * * *
3447931 AATCAGGTCCTTAATTAGTT-AATTGATTAATAATTGAACCTAATAAGTTTAGCTTCTTCC
1 AATTAGATCCTTAATTAGTTAAATTGATTAATAATTGAACCTAATAAGTCTAGCTTCCTAC
* * * *
3447991 AGTTAGATCCTTAACTAGTTAAATTGATTAGTAACTT-AACTTAATAAGTCTAGCTTC
1 AATTAGATCCTTAATTAGTTAAATTGATTAATAA-TTGAACCTAATAAGTCTAGCTTC
3448048 ACGTTGAAGA
Statistics
Matches: 99, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
59 2 0.02
60 63 0.64
61 32 0.32
62 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (61 bp):
AATTAGATCCTTAATTAGTTAAATTGATTAATAATTGAACCTAATAAGTCTAGCTTCCTAC
Found at i:3452900 original size:2 final size:2
Alignment explanation
Indices: 3452893--3452922 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3452883 TTTTCTCTAT
3452893 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3452923 CAGATCCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3453846 original size:12 final size:12
Alignment explanation
Indices: 3453829--3453855 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3453819 TCGGACAAGA
3453829 AATGAAAGATGT
1 AATGAAAGATGT
3453841 AATGAAAGATGT
1 AATGAAAGATGT
3453853 AAT
1 AAT
3453856 TGGGGTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (12 bp):
AATGAAAGATGT
Found at i:3455327 original size:29 final size:31
Alignment explanation
Indices: 3455293--3455351 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
3455283 ATAATTATTG
*
3455293 AATTTTCAA-TT-GCTTCAATTATAACATTA
1 AATTTTCAATTTAACTTCAATTATAACATTA
* *
3455322 AATTTTGAATTTAACTTCAATTATATCATT
1 AATTTTCAATTTAACTTCAATTATAACATT
3455352 TTAATGTGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.32
30 2 0.08
31 15 0.60
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.47
Consensus pattern (31 bp):
AATTTTCAATTTAACTTCAATTATAACATTA
Found at i:3464752 original size:13 final size:13
Alignment explanation
Indices: 3464734--3464758 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3464724 GTCGGTTTGA
3464734 AGTGCTCTTATCG
1 AGTGCTCTTATCG
3464747 AGTGCTCTTATC
1 AGTGCTCTTATC
3464759 TTTTTAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (13 bp):
AGTGCTCTTATCG
Found at i:3465204 original size:2 final size:2
Alignment explanation
Indices: 3465197--3465227 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3465187 TATTAAAATA
3465197 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3465228 GTGAATCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3470878 original size:23 final size:23
Alignment explanation
Indices: 3470852--3470904 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
3470842 TATGTAATTT
3470852 CAGCCTTTTATTCTCGATACTTA
1 CAGCCTTTTATTCTCGATACTTA
3470875 CAGCCTTTTATTCTCGATACTTA
1 CAGCCTTTTATTCTCGATACTTA
3470898 CAGCCTT
1 CAGCCTT
3470905 AAATATTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.21, C:0.28, G:0.09, T:0.42
Consensus pattern (23 bp):
CAGCCTTTTATTCTCGATACTTA
Found at i:3473532 original size:20 final size:22
Alignment explanation
Indices: 3473487--3473544 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
3473477 GCATGGGTAG
3473487 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
3473511 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
3473531 TGTATCGATGCACT
1 TGCATCGATGCACT
3473545 TCAAAGGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:3475096 original size:20 final size:20
Alignment explanation
Indices: 3475073--3475150 Score: 88
Period size: 20 Copynumber: 4.0 Consensus size: 20
3475063 GAGGGATTAT
3475073 CAGTGGTCCTTCGGGACAAA
1 CAGTGGTCCTTCGGGACAAA
*
3475093 CAGTGATCCTTCGGGAC--A
1 CAGTGGTCCTTCGGGACAAA
* * ** *
3475111 TAGTGGTTCTTCGAAACAAT
1 CAGTGGTCCTTCGGGACAAA
3475131 CAGTGGTCCTTCGGGACAAA
1 CAGTGGTCCTTCGGGACAAA
3475151 TATTCAGTGC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
18 13 0.30
20 31 0.70
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (20 bp):
CAGTGGTCCTTCGGGACAAA
Found at i:3475135 original size:38 final size:38
Alignment explanation
Indices: 3475074--3475148 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
3475064 AGGGATTATC
**
3475074 AGTGGTCCTTCGGGACAAACAGTGATCCTTCGGGACAT
1 AGTGGTCCTTCGAAACAAACAGTGATCCTTCGGGACAT
* * *
3475112 AGTGGTTCTTCGAAACAATCAGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGAAACAAACAGTGATCCTTCGGGACA
3475149 AATATTCAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (38 bp):
AGTGGTCCTTCGAAACAAACAGTGATCCTTCGGGACAT
Found at i:3475526 original size:4 final size:4
Alignment explanation
Indices: 3475519--3475574 Score: 103
Period size: 4 Copynumber: 13.8 Consensus size: 4
3475509 ATGATATATA
3475519 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
3475567 TAGTG TAT
1 TA-TG TAT
3475575 TTGTTACATA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
4 47 0.92
5 4 0.08
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:3476189 original size:31 final size:31
Alignment explanation
Indices: 3476166--3476245 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
3476156 ATGCTATCTG
3476166 TCCAAAGTGATGATGTGACACATGCTACATA
1 TCCAAAGTGATGATGTGACACATGCTACATA
* * *
3476197 TCCAAAGTGATGGTGTGACATATG-TCACATG
1 TCCAAAGTGATGATGTGACACATGCT-ACATA
* *
3476228 TCCAAATTGATGACGTGA
1 TCCAAAGTGATGATGTGA
3476246 AATATATCAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 1 0.02
31 41 0.98
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.28
Consensus pattern (31 bp):
TCCAAAGTGATGATGTGACACATGCTACATA
Found at i:3476356 original size:30 final size:30
Alignment explanation
Indices: 3476168--3476363 Score: 89
Period size: 31 Copynumber: 6.4 Consensus size: 30
3476158 GCTATCTGTC
* * * *
3476168 CAAAGTGATGATGTGACA-CATGCTACATATC
1 CAAAGTGATGACGTGACATTAT-C-ACATGTT
** * *
3476199 CAAAGTGATGGTGTGACATATGTCACATGTC
1 CAAAGTGATGACGTGACAT-TATCACATGTT
* *
3476230 CAAATTGATGACGTGA-AATAT-ATCATGTAT
1 CAAAGTGATGACGTGACATTATCA-CATGT-T
* * * *
3476260 CCAAAATGATTATGTGACA-CA-CATCATGTGCT
1 -CAAAGTGATGACGTGACATTATCA-CATGT--T
* ** *
3476292 CAAAGTGATGAAGTGGTATTATCACATGTA
1 CAAAGTGATGACGTGACATTATCACATGTT
*
3476322 CAAAGTGATGACGTGACATTGAT-ACGTGTT
1 CAAAGTGATGACGTGACATT-ATCACATGTT
3476352 CAAAGTGATGAC
1 CAAAGTGATGAC
3476364 ATGGAATATG
Statistics
Matches: 127, Mismatches: 27, Indels: 23
0.72 0.15 0.13
Matches are distributed among these distances:
28 1 0.01
29 7 0.06
30 35 0.28
31 72 0.57
32 9 0.07
33 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (30 bp):
CAAAGTGATGACGTGACATTATCACATGTT
Found at i:3481180 original size:4 final size:4
Alignment explanation
Indices: 3481171--3482002 Score: 1650
Period size: 4 Copynumber: 208.5 Consensus size: 4
3481161 ATTTGATTTT
3481171 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3481219 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3481267 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3481315 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3481363 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3481411 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3481459 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3481507 ATAC ATAC ATAC --AC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3481553 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3481601 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3481649 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3481697 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3481745 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3481793 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3481841 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3481889 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3481937 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3481985 ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC AT
3482003 GGGGAACCTT
Statistics
Matches: 826, Mismatches: 0, Indels: 4
1.00 0.00 0.00
Matches are distributed among these distances:
2 2 0.00
4 824 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:3486801 original size:41 final size:41
Alignment explanation
Indices: 3486743--3486825 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
3486733 GAGAACGCTT
*
3486743 AGGCCTTAGTTTAAAGATTTTCTTTAGACTCCAGCTGACAG
1 AGGCCTTAGTTTAAAGATTTTCTTTAGACTCCAGCCGACAG
*
3486784 AGGCCTTAGTTTGAAGATTTTCTTTAGACTCCAGCCGACAG
1 AGGCCTTAGTTTAAAGATTTTCTTTAGACTCCAGCCGACAG
3486825 A
1 A
3486826 AGGGCAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (41 bp):
AGGCCTTAGTTTAAAGATTTTCTTTAGACTCCAGCCGACAG
Found at i:3489315 original size:7 final size:7
Alignment explanation
Indices: 3489300--3489371 Score: 74
Period size: 7 Copynumber: 10.3 Consensus size: 7
3489290 ATTTTTTAAA
*
3489300 TGAATAG
1 TGAACAG
3489307 TGAACAG
1 TGAACAG
3489314 TGAACAG
1 TGAACAG
3489321 TGAACAG
1 TGAACAG
* *
3489328 TGAATAA
1 TGAACAG
3489335 TGAACAG
1 TGAACAG
*
3489342 TGAATA-
1 TGAACAG
3489348 TGGAACAG
1 T-GAACAG
* *
3489356 TAAATAG
1 TGAACAG
3489363 TGAACAG
1 TGAACAG
3489370 TG
1 TG
3489372 TATAATGAAC
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
6 1 0.02
7 50 0.96
8 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.26, T:0.21
Consensus pattern (7 bp):
TGAACAG
Found at i:3489322 original size:14 final size:14
Alignment explanation
Indices: 3489300--3489382 Score: 105
Period size: 14 Copynumber: 5.9 Consensus size: 14
3489290 ATTTTTTAAA
3489300 TGAATAGTGAACAG
1 TGAATAGTGAACAG
*
3489314 TGAACAGTGAACAG
1 TGAATAGTGAACAG
*
3489328 TGAATAATGAACAG
1 TGAATAGTGAACAG
3489342 TGAATA-TGGAACAG
1 TGAATAGT-GAACAG
*
3489356 TAAATAGTGAACAG
1 TGAATAGTGAACAG
* *
3489370 TGTATAATGAACA
1 TGAATAGTGAACA
3489383 ATGACTGCAC
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
13 1 0.02
14 58 0.97
15 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.24, T:0.22
Consensus pattern (14 bp):
TGAATAGTGAACAG
Found at i:3489485 original size:21 final size:21
Alignment explanation
Indices: 3489459--3489506 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
3489449 AAAATATGTA
3489459 TACAGTGCATCGATACACTGC
1 TACAGTGCATCGATACACTGC
3489480 TACAGTGCATCGATACACTGC
1 TACAGTGCATCGATACACTGC
3489501 TACAGT
1 TACAGT
3489507 AATTTATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (21 bp):
TACAGTGCATCGATACACTGC
Found at i:3490018 original size:59 final size:59
Alignment explanation
Indices: 3489955--3490313 Score: 235
Period size: 59 Copynumber: 6.1 Consensus size: 59
3489945 CCTTTTAATA
* * *
3489955 TTAGCACTATCAGTGCTCTATCTGGAAAACCATACACTTAGTATGCTTCCCTTTTCATT
1 TTAGCACTATCAGTGCTCTATCTGGAAAACCATACACTTAGTATGATTTCCTTATCATT
* * ** *
3490014 TTAGCAC-A-CAAAGTGCCCTAT-TCGAAAATCCATAC-CATTAGTATGATTTTGTTACCATT
1 TTAGCACTATC--AGTGCTCTATCTGGAAAA-CCATACAC-TTAGTATGATTTCCTTATCATT
* ** *
3490073 TTAGCACATAAT-A-TG-TCCTATCTGGAAATCCATA-TTTTCAATATGATTTCCTTATCA-T
1 TTAGCAC-T-ATCAGTGCT-CTATCTGGAAAACCATACACTT-AGTATGATTTCCTTATCATT
** * * * * * * *
3490131 TTAGCACCCTTAGTGCTTTATCTGGAAACCCATATACTCAGTATGATTCCCTTACCATT
1 TTAGCACTATCAGTGCTCTATCTGGAAAACCATACACTTAGTATGATTTCCTTATCATT
* * * *
3490190 TTAGCACATAAT-A-TGCCCTATCTGGAAATCCATA-ATTTCAATATGATTTCCTTATCA-T
1 TTAGCAC-T-ATCAGTGCTCTATCTGGAAAACCATACACTT-AGTATGATTTCCTTATCATT
* * *
3490248 TTAGCAC-ACTCAGTGCTCCATATGGAAATA-CATACACTCAGTATGATTTCCTTATCATT
1 TTAGCACTA-TCAGTGCTCTATCTGGAAA-ACCATACACTTAGTATGATTTCCTTATCATT
*
3490307 CTAGCAC
1 TTAGCAC
3490314 ACAAAGTGCC
Statistics
Matches: 230, Mismatches: 44, Indels: 52
0.71 0.13 0.16
Matches are distributed among these distances:
55 1 0.00
56 2 0.01
57 3 0.01
58 93 0.40
59 122 0.53
60 7 0.03
61 1 0.00
62 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (59 bp):
TTAGCACTATCAGTGCTCTATCTGGAAAACCATACACTTAGTATGATTTCCTTATCATT
Found at i:3490164 original size:58 final size:58
Alignment explanation
Indices: 3490090--3490313 Score: 229
Period size: 58 Copynumber: 3.8 Consensus size: 58
3490080 ATAATATGTC
**
3490090 CTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCATTTAGCACCCTTAGTGCT
1 CTATCTGGAAATCCATATACTCAATATGATTTCCTTATCATTTAGCACCCTTAGTGCT
* * * * * * *
3490148 TTATCTGGAAACCCATATACTCAGTATGATTCCCTTACCATTTTAGCA-CATAATA-TGCC
1 CTATCTGGAAATCCATATACTCAATATGATTTCCTTATCA-TTTAGCACCCT--TAGTGCT
* * *
3490207 CTATCTGGAAATCCATA-ATTTCAATATGATTTCCTTATCATTTAGCACACTCAGTGCT
1 CTATCTGGAAATCCATATA-CTCAATATGATTTCCTTATCATTTAGCACCCTTAGTGCT
* * * * *
3490265 CCATATGGAAATACATACACTCAGTATGATTTCCTTATCATTCTAGCAC
1 CTATCTGGAAATCCATATACTCAATATGATTTCCTTATCATT-TAGCAC
3490314 ACAAAGTGCC
Statistics
Matches: 134, Mismatches: 24, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
57 1 0.01
58 81 0.60
59 50 0.37
60 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (58 bp):
CTATCTGGAAATCCATATACTCAATATGATTTCCTTATCATTTAGCACCCTTAGTGCT
Found at i:3490186 original size:117 final size:117
Alignment explanation
Indices: 3490065--3490314 Score: 383
Period size: 117 Copynumber: 2.1 Consensus size: 117
3490055 TATGATTTTG
* *
3490065 TTACCATTTTAGCACATAATATGTCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTCAATATGATTTCCTTATCA
* * ** * * *
3490130 TTTAGCACCCTTAGTGCTTTATCTGGAAACCCATATACTCAGTATGATTCCC
66 TTTAGCACACTCAGTGCTCCATATGGAAACACATACACTCAGTATGATTCCC
3490182 TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTCAATATGATTTCCTTATCA
* *
3490247 TTTAGCACACTCAGTGCTCCATATGGAAATACATACACTCAGTATGATTTCC
66 TTTAGCACACTCAGTGCTCCATATGGAAACACATACACTCAGTATGATTCCC
* *
3490299 TTATCATTCTAGCACA
1 TTACCATTTTAGCACA
3490315 CAAAGTGCCA
Statistics
Matches: 120, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
117 120 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (117 bp):
TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTCAATATGATTTCCTTATCA
TTTAGCACACTCAGTGCTCCATATGGAAACACATACACTCAGTATGATTCCC
Found at i:3499187 original size:21 final size:21
Alignment explanation
Indices: 3499132--3499195 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
3499122 GATTCCCCTG
3499132 TGGGGGGAATCGGTTCCCATTCA
1 TGGGGGGAATCGGTTCCC--TCA
**
3499155 AAGGGGGAATCGGTTCCCTCA
1 TGGGGGGAATCGGTTCCCTCA
* *
3499176 TGGGGGGGATCGATTCCCTC
1 TGGGGGGAATCGGTTCCCTC
3499196 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 19 0.54
23 16 0.46
ACGTcount: A:0.17, C:0.23, G:0.36, T:0.23
Consensus pattern (21 bp):
TGGGGGGAATCGGTTCCCTCA
Found at i:3505679 original size:27 final size:27
Alignment explanation
Indices: 3505649--3505734 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 27
3505639 TACATAAATG
3505649 ATATTATTTATTATTAATAATTTAATA
1 ATATTATTTATTATTAATAATTTAATA
** *
3505676 ATATT-TTTA--AGAAATTAA-TAAATA
1 ATATTATTTATTATTAA-TAATTTAATA
* *
3505700 ATATAATTT-TTATTAATAATTTATTA
1 ATATTATTTATTATTAATAATTTAATA
3505726 TATATTATT
1 -ATATTATT
3505735 AAAATAAGAA
Statistics
Matches: 44, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
24 12 0.27
25 9 0.20
26 11 0.25
27 12 0.27
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (27 bp):
ATATTATTTATTATTAATAATTTAATA
Found at i:3505685 original size:20 final size:20
Alignment explanation
Indices: 3505657--3505696 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3505647 TGATATTATT
* *
3505657 TATTATTAATAATTTAATAA
1 TATTATTAAGAAATTAATAA
*
3505677 TATTTTTAAGAAATTAATAA
1 TATTATTAAGAAATTAATAA
3505697 ATAATATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TATTATTAAGAAATTAATAA
Found at i:3505825 original size:30 final size:30
Alignment explanation
Indices: 3505789--3505847 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
3505779 AGTATATAAT
* *
3505789 AATATTATTATAATATATTATAT-TGTTAAA
1 AATATTAATAT-ATATATTAAATATGTTAAA
*
3505819 AATATTAATATATATTTTAAATATGTTAA
1 AATATTAATATATATATTAAATATGTTAA
3505848 TAATTAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (30 bp):
AATATTAATATATATATTAAATATGTTAAA
Found at i:3505829 original size:18 final size:19
Alignment explanation
Indices: 3505788--3505849 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 19
3505778 AAGTATATAA
*
3505788 TAATATTATTATAATATAT
1 TAATATTATTATAAAATAT
*
3505807 T-ATATTGTTA-AAAATAT
1 TAATATTATTATAAAATAT
* *
3505824 TAATATATATTTTAAATATGT
1 TAATAT-TATTATAAA-ATAT
3505845 TAATA
1 TAATA
3505850 ATTAATATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 7 0.21
18 12 0.35
19 4 0.12
20 3 0.09
21 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TAATATTATTATAAAATAT
Found at i:3505847 original size:21 final size:22
Alignment explanation
Indices: 3505807--3505849 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
3505797 TATAATATAT
3505807 TATATTGTTAAAAATATTAATA
1 TATATTGTTAAAAATATTAATA
* *
3505829 TATATT-TTAAATATGTTAATA
1 TATATTGTTAAAAATATTAATA
3505850 ATTAATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
TATATTGTTAAAAATATTAATA
Found at i:3515017 original size:6 final size:6
Alignment explanation
Indices: 3515003--3515055 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
3514993 CTTGGCAGGT
* * *
3515003 TATATA TACATA TACATA CATATA TATATA TATATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
3515051 TATAT
1 TATAT
3515056 CACACTCTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (6 bp):
TATATA
Found at i:3515021 original size:10 final size:10
Alignment explanation
Indices: 3515003--3515055 Score: 70
Period size: 10 Copynumber: 5.3 Consensus size: 10
3514993 CTTGGCAGGT
3515003 TATATATACA
1 TATATATACA
*
3515013 TATACATACA
1 TATATATACA
*
3515023 TATATATATA
1 TATATATACA
*
3515033 TATATATATA
1 TATATATACA
*
3515043 TATATATATA
1 TATATATACA
3515053 TAT
1 TAT
3515056 CACACTCTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 40 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (10 bp):
TATATATACA
Found at i:3515029 original size:4 final size:4
Alignment explanation
Indices: 3515003--3515055 Score: 79
Period size: 4 Copynumber: 13.2 Consensus size: 4
3514993 CTTGGCAGGT
* * *
3515003 TATA TATA CATA TACA TACA TATA TATA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
3515051 TATA T
1 TATA T
3515056 CACACTCTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (4 bp):
TATA
Found at i:3516148 original size:6 final size:6
Alignment explanation
Indices: 3516137--3516186 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
3516127 TGGTGCTAAT
3516137 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
3516185 TA
1 TA
3516187 CTTTAGGGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:3518483 original size:16 final size:17
Alignment explanation
Indices: 3518464--3518497 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3518454 TAAAAATTTT
3518464 AAAATT-TAAAATATAA
1 AAAATTATAAAATATAA
*
3518480 AAAATTATAAATTATAA
1 AAAATTATAAAATATAA
3518497 A
1 A
3518498 TAATAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATTATAAAATATAA
Found at i:3518498 original size:23 final size:25
Alignment explanation
Indices: 3518455--3518504 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
3518445 TTATTCGATT
*
3518455 AAAAATTTTAAAATTTAAAAT-ATA
1 AAAAATTATAAAATTTAAAATAATA
3518479 AAAAATTAT-AAA-TTATAAATAATA
1 AAAAATTATAAAATTTA-AAATAATA
3518503 AA
1 AA
3518505 TAAAAGTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 3 0.13
23 7 0.30
24 13 0.57
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
AAAAATTATAAAATTTAAAATAATA
Found at i:3523401 original size:18 final size:18
Alignment explanation
Indices: 3523378--3523447 Score: 69
Period size: 18 Copynumber: 4.2 Consensus size: 18
3523368 ACCGGTCATA
3523378 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
3523396 ACCCGACCGGACCCATT-
1 ACCCGACCCGACCCGTTG
*
3523413 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
3523427 ACCCCACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
3523445 ACC
1 ACC
3523448 GTTGACCGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
13 10 0.24
18 31 0.76
ACGTcount: A:0.19, C:0.50, G:0.19, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:3526022 original size:24 final size:24
Alignment explanation
Indices: 3525901--3526015 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
3525891 TCGATTTGAT
3525901 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
3525925 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
3525949 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
3525973 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
* *
3525996 TTTCTTATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
3526016 CTGATTTATG
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
23 3 0.04
24 78 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:3527509 original size:44 final size:44
Alignment explanation
Indices: 3527461--3527549 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
3527451 ACACAGCACC
* *
3527461 ACAAAGAAGCTACTTTCTTGAACCGTTAAAGTACTGGAATATGT
1 ACAAAGAAGCTACTTTATTGAACCGTTAAAGTACTCGAATATGT
*
3527505 ACAAAGCAGCTACTTTATTGAACCGTTAAAGTACTCGAATATGT
1 ACAAAGAAGCTACTTTATTGAACCGTTAAAGTACTCGAATATGT
3527549 A
1 A
3527550 TATGTATGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (44 bp):
ACAAAGAAGCTACTTTATTGAACCGTTAAAGTACTCGAATATGT
Found at i:3529092 original size:21 final size:21
Alignment explanation
Indices: 3529066--3529111 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3529056 GATAATCTTA
*
3529066 TAAATA-ATATTTAGATGATAT
1 TAAATATATATTTAGAT-AAAT
*
3529087 TAAATATATTTTTAGATAAAT
1 TAAATATATATTTAGATAAAT
3529108 TAAA
1 TAAA
3529112 AAATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (21 bp):
TAAATATATATTTAGATAAAT
Found at i:3532075 original size:22 final size:22
Alignment explanation
Indices: 3532047--3532094 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
3532037 CTAACTCAAC
* *
3532047 CCTTAAACTCTATAATTTATAA
1 CCTTAAACTATATAACTTATAA
*
3532069 CCTTAAACTATGTAACTTATAA
1 CCTTAAACTATATAACTTATAA
3532091 CCTT
1 CCTT
3532095 TCTCTAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.40
Consensus pattern (22 bp):
CCTTAAACTATATAACTTATAA
Found at i:3533815 original size:29 final size:29
Alignment explanation
Indices: 3533773--3533830 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3533763 AGCATCGTCA
3533773 TTATTTTTTAATGACTAAGGATCAAATAG
1 TTATTTTTTAATGACTAAGGATCAAATAG
3533802 TTATTTTTTAATGACTAAGGATCAAATAG
1 TTATTTTTTAATGACTAAGGATCAAATAG
3533831 GAAAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (29 bp):
TTATTTTTTAATGACTAAGGATCAAATAG
Found at i:3534207 original size:4 final size:4
Alignment explanation
Indices: 3534198--3534225 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3534188 TAAACCCGAA
3534198 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
3534226 GATGTTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:3539364 original size:21 final size:21
Alignment explanation
Indices: 3539338--3539509 Score: 199
Period size: 21 Copynumber: 8.2 Consensus size: 21
3539328 GTTTCCAGAT
3539338 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
3539359 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
3539380 TCGCAATGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
* *
3539401 TCGCAATGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
* *
3539422 TCGCAAAGCGAA-TAT-GTA-AA
1 TCGCAACGCGAACT-TCG-ACTA
** *
3539442 TCGCAATACGATA-GTCGACTA
1 TCGCAACGCGA-ACTTCGACTA
*
3539463 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
*
3539484 TCGCAACGCAAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
3539505 TCGCA
1 TCGCA
3539510 TTGCGATTTA
Statistics
Matches: 131, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
20 15 0.11
21 116 0.89
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:3548988 original size:19 final size:20
Alignment explanation
Indices: 3548964--3549002 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3548954 AAAAGATTAT
3548964 ATATTTT-TGCAATTTGATC
1 ATATTTTATGCAATTTGATC
*
3548983 ATATTTTATTCAATTTGATC
1 ATATTTTATGCAATTTGATC
3549003 CTTTCAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (20 bp):
ATATTTTATGCAATTTGATC
Found at i:3550059 original size:16 final size:16
Alignment explanation
Indices: 3550038--3550071 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3550028 TTTAGTACTT
*
3550038 GTTCGAATCATTTTAA
1 GTTCGAATCATATTAA
*
3550054 GTTCGAGTCATATTAA
1 GTTCGAATCATATTAA
3550070 GT
1 GT
3550072 CCGAGTCCGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (16 bp):
GTTCGAATCATATTAA
Found at i:3550076 original size:16 final size:16
Alignment explanation
Indices: 3550045--3550078 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3550035 CTTGTTCGAA
* *
3550045 TCATTTTAAGTTCGAG
1 TCATATTAAGTCCGAG
3550061 TCATATTAAGTCCGAG
1 TCATATTAAGTCCGAG
3550077 TC
1 TC
3550079 CGGATCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (16 bp):
TCATATTAAGTCCGAG
Found at i:3554526 original size:248 final size:248
Alignment explanation
Indices: 3554181--3555171 Score: 1558
Period size: 248 Copynumber: 4.0 Consensus size: 248
3554171 TCACTACTTT
3554181 ACAACCACCAGGAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAATAGGA
1 ACAACCACCAGGAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAATAGGA
3554246 GGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGATGACT
66 GGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGATGACT
3554311 CTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCTTCAGGATTGATGAACTATCCGTGG
131 CTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCTTCAGGATTGATGAACTATCCGTGG
3554376 TGGGGTTACCACATATCTTTGGTTTCGAATCAACTCCGAGATAATTAGTCAAG
196 TGGGGTTACCACATATCTTTGGTTTCGAATCAACTCCGAGATAATTAGTCAAG
*
3554429 ACAACCACCAGGAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGTATAGGA
1 ACAACCACCAGGAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAATAGGA
*
3554494 GGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCTATGATTGTTTTGATACAACTTGATGACT
66 GGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGATGACT
* * *
3554559 CTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAG---TTCA-GA--AAT-AAC-A-GC-TGC
131 CTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCTTCAGGATTGATGAACTATCCGTGG
*** * *** * *** * * * * * * ***
3554614 TGCTATTAACATACA-AGAATGGGAGGAC-AAACAAAAGAAT-GGAGGACACATCACTACTTT
196 TGGGGTT-AC-CACATATCTTTGG-TTTCGAATC---A-ACTCCGA-GATA-ATTAGT-CAAG
3554674 ACAACCACCAGGAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAATAGGA
1 ACAACCACCAGGAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAATAGGA
3554739 GGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGATGACT
66 GGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGATGACT
3554804 CTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCTTCAGGATTGATGAACTATCCGTGG
131 CTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCTTCAGGATTGATGAACTATCCGTGG
3554869 TGGGGTTACCACATATCTTTGGTTTCGAATCAACTCCGAGATAATTAGTCAAG
196 TGGGGTTACCACATATCTTTGGTTTCGAATCAACTCCGAGATAATTAGTCAAG
* *
3554922 ACAACCACCAGGAGTTTACTGTCCATTAACCAATCTATTTGTTTGTCTTCTCGTAAAGGATAGGA
1 ACAACCACCAGGAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAATAGGA
3554987 GGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGATGACT
66 GGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGATGACT
3555052 CTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCTTCAGGATTGATGAACTATCCGTGG
131 CTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCTTCAGGATTGATGAACTATCCGTGG
3555117 TGGGGTTACCACATATCTTTGGTTTCGAATCAACTCCGAGATAATTAGTCAAG
196 TGGGGTTACCACATATCTTTGGTTTCGAATCAACTCCGAGATAATTAGTCAAG
3555170 AC
1 AC
3555172 CCTCTTCACT
Statistics
Matches: 668, Mismatches: 52, Indels: 46
0.87 0.07 0.06
Matches are distributed among these distances:
238 6 0.01
239 10 0.01
240 5 0.01
241 3 0.00
242 5 0.01
243 5 0.01
244 6 0.01
245 170 0.25
248 418 0.63
249 6 0.01
250 5 0.01
251 5 0.01
252 3 0.00
253 5 0.01
254 10 0.01
255 6 0.01
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (248 bp):
ACAACCACCAGGAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAATAGGA
GGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGATGACT
CTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCTTCAGGATTGATGAACTATCCGTGG
TGGGGTTACCACATATCTTTGGTTTCGAATCAACTCCGAGATAATTAGTCAAG
Found at i:3554782 original size:245 final size:244
Alignment explanation
Indices: 3553997--3555131 Score: 1354
Period size: 248 Copynumber: 4.6 Consensus size: 244
3553987 CAGTATATCG
*
3553997 AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCTATGATTGTTTTGATACAACTTGAT
1 AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGAT
3554062 GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCA-GA-AAT-AAC-A---GTTG
66 GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCAGGATAATGAACTATCCG-TG
* * * * ***
3554120 CTGCTATTAACATACA-AGAATGGGAGGAC-AACCAAAAGAAT-GGAGGACACATCACTACTTTA
130 CTGCGATT-AC-CACATAGAATGGG-GGACGAATC---A-AATCCGA-GACA-ATCACT-CAAGA
3554182 CAACCACCAGGAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAAT
185 CAACCACCAGGAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAAT
3554242 AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGAT
1 AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGAT
*
3554307 GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCTTCAGGATTGATGAACTATCC
66 GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAG---TTCAGGA-TAATGAACTATCC
* * * *** * *** * * * *
3554372 GTGGTGGGGTTACCACATATCTTTGGTTTCGAATCAACTCCGAGATAATTAGTCAAGACAACCAC
127 GTGCTGCGATTACCACATAGAATGGGGGACGAATCAAATCCGAGACAATCACTCAAGACAACCAC
*
3554437 CAGGAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGTAT
192 CAGGAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAAT
*
3554490 AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCTATGATTGTTTTGATACAACTTGAT
1 AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGAT
*
3554555 GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCA-GA-AAT-AAC-A-GC-TGC
66 GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCAGGATAATGAACTATCCGTGC
* * * * ***
3554614 TGCTATTAACATACA-AGAATGGGAGGAC-AAACAAAAGAAT-GGAGGACACATCACTACTTTAC
131 TGCGATT-AC-CACATAGAATGGG-GGACGAATC---A-AATCCGA-GACA-ATCACT-CAAGAC
3554676 AACCACCAGGAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAAT
186 AACCACCAGGAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAAT
3554735 AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGAT
1 AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGAT
*
3554800 GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCTTCAGGATTGATGAACTATCC
66 GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAG---TTCAGGA-TAATGAACTATCC
* * * *** * *** * * * *
3554865 GTGGTGGGGTTACCACATATCTTTGGTTTCGAATCAACTCCGAGATAATTAGTCAAGACAACCAC
127 GTGCTGCGATTACCACATAGAATGGGGGACGAATCAAATCCGAGACAATCACTCAAGACAACCAC
* *
3554930 CAGGAGTTTACTGTCCATTAACCAATCTATTTGTTTGTCTTCTCGTAAAGGAT
192 CAGGAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAAT
3554983 AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGAT
1 AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGAT
*
3555048 GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCTTCAGGATTGATGAACTATCC
66 GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAG---TTCAGGA-TAATGAACTATCC
* * *
3555113 GTGGTGGGGTTACCACATA
127 GTGCTGCGATTACCACATA
3555132 TCTTTGGTTT
Statistics
Matches: 778, Mismatches: 75, Indels: 71
0.84 0.08 0.08
Matches are distributed among these distances:
238 6 0.01
239 10 0.01
240 5 0.01
241 3 0.00
242 5 0.01
243 5 0.01
244 6 0.01
245 275 0.35
248 383 0.49
249 12 0.02
250 10 0.01
251 10 0.01
252 6 0.01
253 10 0.01
254 19 0.02
255 12 0.02
256 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (244 bp):
AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGAT
GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCAGGATAATGAACTATCCGTGC
TGCGATTACCACATAGAATGGGGGACGAATCAAATCCGAGACAATCACTCAAGACAACCACCAGG
AGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAAT
Found at i:3554923 original size:493 final size:493
Alignment explanation
Indices: 3553997--3555091 Score: 2145
Period size: 493 Copynumber: 2.2 Consensus size: 493
3553987 CAGTATATCG
3553997 AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCTATGATTGTTTTGATACAACTTGAT
1 AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCTATGATTGTTTTGATACAACTTGAT
*
3554062 GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCAGAAATAACAGTTGCTGCTAT
66 GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCAGAAATAACAGCTGCTGCTAT
*
3554127 TAACATACAAGAATGGGAGGACAACCAAAAGAATGGAGGACACATCACTACTTTACAACCACCAG
131 TAACATACAAGAATGGGAGGACAAACAAAAGAATGGAGGACACATCACTACTTTACAACCACCAG
3554192 GAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAATAGGAGGATTCTGTCG
196 GAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAATAGGAGGATTCTGTCG
3554257 CATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGATGACTCTTTTGATTCC
261 CATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGATGACTCTTTTGATTCC
3554322 CCGAGTTCTTTGTACTGTTAGTAGAGTTCTTCAGGATTGATGAACTATCCGTGGTGGGGTTACCA
326 CCGAGTTCTTTGTACTGTTAGTAGAGTTCTTCAGGATTGATGAACTATCCGTGGTGGGGTTACCA
3554387 CATATCTTTGGTTTCGAATCAACTCCGAGATAATTAGTCAAGACAACCACCAGGAGTTTACTGTC
391 CATATCTTTGGTTTCGAATCAACTCCGAGATAATTAGTCAAGACAACCACCAGGAGTTTACTGTC
* *
3554452 CATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGTAT
456 CATTAACCAATCTATTTGTTTGTCTTCTCGTAAAGGAT
3554490 AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCTATGATTGTTTTGATACAACTTGAT
1 AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCTATGATTGTTTTGATACAACTTGAT
3554555 GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCAGAAATAACAGCTGCTGCTAT
66 GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCAGAAATAACAGCTGCTGCTAT
3554620 TAACATACAAGAATGGGAGGACAAACAAAAGAATGGAGGACACATCACTACTTTACAACCACCAG
131 TAACATACAAGAATGGGAGGACAAACAAAAGAATGGAGGACACATCACTACTTTACAACCACCAG
3554685 GAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAATAGGAGGATTCTGTCG
196 GAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAATAGGAGGATTCTGTCG
3554750 CATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGATGACTCTTTTGATTCC
261 CATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGATGACTCTTTTGATTCC
3554815 CCGAGTTCTTTGTACTGTTAGTAGAGTTCTTCAGGATTGATGAACTATCCGTGGTGGGGTTACCA
326 CCGAGTTCTTTGTACTGTTAGTAGAGTTCTTCAGGATTGATGAACTATCCGTGGTGGGGTTACCA
3554880 CATATCTTTGGTTTCGAATCAACTCCGAGATAATTAGTCAAGACAACCACCAGGAGTTTACTGTC
391 CATATCTTTGGTTTCGAATCAACTCCGAGATAATTAGTCAAGACAACCACCAGGAGTTTACTGTC
3554945 CATTAACCAATCTATTTGTTTGTCTTCTCGTAAAGGAT
456 CATTAACCAATCTATTTGTTTGTCTTCTCGTAAAGGAT
*
3554983 AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGAT
1 AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCTATGATTGTTTTGATACAACTTGAT
3555048 GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTC
66 GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTC
3555092 TTCAGGATTG
Statistics
Matches: 597, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
493 597 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (493 bp):
AGGAGGATTCTGTCGCATTTTCGTCCCATTCTTGTATGCCTATGATTGTTTTGATACAACTTGAT
GACTCTTTTGATTCCCCGAGTTCTTTGTACTGTTAGTAGAGTTCAGAAATAACAGCTGCTGCTAT
TAACATACAAGAATGGGAGGACAAACAAAAGAATGGAGGACACATCACTACTTTACAACCACCAG
GAGTTTACTGTCCATTAACTAATCTATTTGTTTGTCTTCTCGTAAAGAATAGGAGGATTCTGTCG
CATTTTCGTCCCATTCTTGTATGCCGATGATTGTTTTGATACAACTTGATGACTCTTTTGATTCC
CCGAGTTCTTTGTACTGTTAGTAGAGTTCTTCAGGATTGATGAACTATCCGTGGTGGGGTTACCA
CATATCTTTGGTTTCGAATCAACTCCGAGATAATTAGTCAAGACAACCACCAGGAGTTTACTGTC
CATTAACCAATCTATTTGTTTGTCTTCTCGTAAAGGAT
Found at i:3557014 original size:2 final size:2
Alignment explanation
Indices: 3557007--3557036 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3556997 AAATTCATAA
3557007 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3557037 TTTACCACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3558078 original size:19 final size:21
Alignment explanation
Indices: 3558054--3558092 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
3558044 AATGTTATTT
3558054 AAAAATATT-ATTTT-TTATC
1 AAAAATATTAATTTTGTTATC
3558073 AAAAATATTAATTTTGTTAT
1 AAAAATATTAATTTTGTTAT
3558093 TTAAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 5 0.28
21 4 0.22
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (21 bp):
AAAAATATTAATTTTGTTATC
Found at i:3558911 original size:31 final size:32
Alignment explanation
Indices: 3558852--3558916 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 32
3558842 ACAACATAAT
*
3558852 ATATGATCACTTTCATTTTTTATTTAATTAAG
1 ATATGATCACTTTCATTTTTAATTTAATTAAG
3558884 ATATGATCACTTTCA-TTTTAATTTAATTAAG
1 ATATGATCACTTTCATTTTTAATTTAATTAAG
3558915 AT
1 AT
3558917 GTGGTCACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 17 0.53
32 15 0.47
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (32 bp):
ATATGATCACTTTCATTTTTAATTTAATTAAG
Found at i:3561791 original size:33 final size:33
Alignment explanation
Indices: 3561754--3561819 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
3561744 GAGAAATACA
3561754 GAGATAAAATTTATTTCAACATATCATAAAAGT
1 GAGATAAAATTTATTTCAACATATCATAAAAGT
*
3561787 GAGATAAAATTTATTTCGACATATCATAAAAGT
1 GAGATAAAATTTATTTCAACATATCATAAAAGT
3561820 TTCAAAGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (33 bp):
GAGATAAAATTTATTTCAACATATCATAAAAGT
Found at i:3564956 original size:26 final size:26
Alignment explanation
Indices: 3564920--3564972 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
3564910 GTTGAGAAGA
3564920 TTGTTTTGGATTACAAAGCTTCCAGG
1 TTGTTTTGGATTACAAAGCTTCCAGG
3564946 TTGTTTTGGATTACAAAGCTTCCAGG
1 TTGTTTTGGATTACAAAGCTTCCAGG
3564972 T
1 T
3564973 AGCTCATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.40
Consensus pattern (26 bp):
TTGTTTTGGATTACAAAGCTTCCAGG
Found at i:3565012 original size:212 final size:213
Alignment explanation
Indices: 3564611--3565032 Score: 634
Period size: 212 Copynumber: 2.0 Consensus size: 213
3564601 GCTAACATCC
* *
3564611 TTCTAAATCTCGCCAGTAAAGTCGTTCTTACTCACCTCCACAAACGTCAAGTTTTTCAACGGTCC
1 TTCTAAATCTCGCCAGTAAAGTCGTTCTTACTCACCTCCACAAACGTCAAGGTTTTCAACAGTCC
* * *
3564676 GAAACAGTAAGATATGGTACCGTTGACAAGATTGTTTTGGATTCGGAATCTTGAAAGTGAAGTGC
66 GAAACAGTAAGATATGGTACCGTTGACAAGATTGTTTTGGATTCGAAAGCTTCAAAGTGAAGTG-
* *
3564741 AGTTTACAAAGCTTCCAGGTAGCTCATTCTTGAACATGTTATTAAACAGTACGAGTCTGAATAGC
130 AGATTACAAAGCTTCCAGGTAGCTCATTCTTGAACATGTTATTAAACACTACGAGTCTGAATAGC
3564806 TTGTTCCCATAGCAATTCT
195 TTGTTCCCATAGCAATTCT
* *
3564825 TTCTAAATCTCGCCAGTAAAGTCGTTCTTACTCGCTTCCACAAACGTC-AGGTTTTCAACAGTCC
1 TTCTAAATCTCGCCAGTAAAGTCGTTCTTACTCACCTCCACAAACGTCAAGGTTTTCAACAGTCC
* * * * ***
3564889 GAAATAGTAAGATATGGTACCGTTGAGAAGATTGTTTTGGATTAC-AAAGCTTCCAGGTTGTTTT
66 GAAACAGTAAGATATGGTACCGTTGACAAGATTGTTTTGGATT-CGAAAGCTTCAAAG-TGAAGT
*
3564953 G-GATTACAAAGCTTCCAGGTAGCTCATTCTTGAACATGTTATTAAACACTATGAGTCTGAATAG
129 GAGATTACAAAGCTTCCAGGTAGCTCATTCTTGAACATGTTATTAAACACTACGAGTCTGAATAG
*
3565017 CTTTTTCCCATAGCAA
194 CTTGTTCCCATAGCAA
3565033 AGATTTGGAG
Statistics
Matches: 188, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
212 75 0.40
213 62 0.33
214 51 0.27
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (213 bp):
TTCTAAATCTCGCCAGTAAAGTCGTTCTTACTCACCTCCACAAACGTCAAGGTTTTCAACAGTCC
GAAACAGTAAGATATGGTACCGTTGACAAGATTGTTTTGGATTCGAAAGCTTCAAAGTGAAGTGA
GATTACAAAGCTTCCAGGTAGCTCATTCTTGAACATGTTATTAAACACTACGAGTCTGAATAGCT
TGTTCCCATAGCAATTCT
Found at i:3567771 original size:58 final size:58
Alignment explanation
Indices: 3567681--3567797 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
3567671 TCTCGAAAAC
* *
3567681 CTATGTATAACAATTGGAAAGTAATTATATCTTGCCTTCTTTGAACATTTTCTAAGAG
1 CTATGTATAACAATTGGAAAGTAATTATATCTTGCCTTCCTTGAACATTTTCCAAGAG
3567739 CTATGTATAACAATTGGAAAGTAATTATATCTTGCCTTCCTTGAACATTTTCCAAGAG
1 CTATGTATAACAATTGGAAAGTAATTATATCTTGCCTTCCTTGAACATTTTCCAAGAG
3567797 C
1 C
3567798 GCTAGCATCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (58 bp):
CTATGTATAACAATTGGAAAGTAATTATATCTTGCCTTCCTTGAACATTTTCCAAGAG
Found at i:3571503 original size:40 final size:40
Alignment explanation
Indices: 3571459--3571538 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
3571449 AATCATTATA
3571459 ATAGTACTGGAGTTCAACATTAATCAATTATGAAAATGTC
1 ATAGTACTGGAGTTCAACATTAATCAATTATGAAAATGTC
*
3571499 ATAGTACTGGAGTTCAACATTAATCAGTTATGAAAATGTC
1 ATAGTACTGGAGTTCAACATTAATCAATTATGAAAATGTC
3571539 CGACTCTTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (40 bp):
ATAGTACTGGAGTTCAACATTAATCAATTATGAAAATGTC
Found at i:3572695 original size:27 final size:27
Alignment explanation
Indices: 3572664--3572724 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 27
3572654 CTTCATGCAT
3572664 AAGTCTCTGATTTTTGTACTTCCATCC
1 AAGTCTCTGATTTTTGTACTTCCATCC
*
3572691 AAGTCTTTTGATTTTTGTACTTCCATCC
1 AAGTC-TCTGATTTTTGTACTTCCATCC
3572719 AAGTCT
1 AAGTCT
3572725 TCTAACCGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 6 0.19
28 26 0.81
ACGTcount: A:0.20, C:0.23, G:0.11, T:0.46
Consensus pattern (27 bp):
AAGTCTCTGATTTTTGTACTTCCATCC
Found at i:3572702 original size:28 final size:28
Alignment explanation
Indices: 3572671--3572725 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
3572661 CATAAGTCTC
3572671 TGATTTTTGTACTTCCATCCAAGTCTTT
1 TGATTTTTGTACTTCCATCCAAGTCTTT
3572699 TGATTTTTGTACTTCCATCCAAGTCTT
1 TGATTTTTGTACTTCCATCCAAGTCTT
3572726 CTAACCGTCA
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:0.18, C:0.22, G:0.11, T:0.49
Consensus pattern (28 bp):
TGATTTTTGTACTTCCATCCAAGTCTTT
Found at i:3573802 original size:36 final size:36
Alignment explanation
Indices: 3573727--3573834 Score: 168
Period size: 35 Copynumber: 3.1 Consensus size: 36
3573717 CTCGAGCCTA
* * *
3573727 CCTTAAAATGTTTAGGGTAATAAAAAAGCACATGA-
1 CCTTAAAATGTTTGGGGGAATAAAAAAGCACATCAT
3573762 CCTTAAAATGTTTGGGGGAATAAAAAAGCACATCAT
1 CCTTAAAATGTTTGGGGGAATAAAAAAGCACATCAT
3573798 CCTTAAAATGTTTGGGGGAAT-AAAAA-CACATCAT
1 CCTTAAAATGTTTGGGGGAATAAAAAAGCACATCAT
3573832 CCT
1 CCT
3573835 CGTTTCTTTC
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
34 11 0.16
35 37 0.54
36 21 0.30
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.26
Consensus pattern (36 bp):
CCTTAAAATGTTTGGGGGAATAAAAAAGCACATCAT
Done.