Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008717.1 Hibiscus syriacus cultivar Beakdansim tig00111772_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: 3453450
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 16
Found at i:3067190 original size:8 final size:8
Alignment explanation
Indices: 3067173--3067276 Score: 55
Period size: 8 Copynumber: 13.6 Consensus size: 8
3067163 AAATTCATAA
3067173 AAAAAG-G
1 AAAAAGAG
3067180 AAAAAGAG
1 AAAAAGAG
*
3067188 AAAAAGAA
1 AAAAAGAG
*
3067196 AAGAAAAAG
1 AA-AAAGAG
*
3067205 AAAGAAAAG
1 AAA-AAGAG
* *
3067214 AAGAATA-
1 AAAAAGAG
*
3067221 AAAGAAGAA
1 AAA-AAGAG
3067230 AAAAAGAAG
1 AAAAAG-AG
3067239 AAAAA-AG
1 AAAAAGAG
3067246 --AAA-AG
1 AAAAAGAG
3067251 AAAAAGAG
1 AAAAAGAG
3067259 --AAA-AG
1 AAAAAGAG
3067264 AAAAAGAG
1 AAAAAGAG
3067272 AAAAA
1 AAAAA
3067277 ATAGAAAAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
5 7 0.09
6 3 0.04
7 16 0.21
8 29 0.38
9 22 0.29
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (8 bp):
AAAAAGAG
Found at i:3067202 original size:11 final size:11
Alignment explanation
Indices: 3067186--3067284 Score: 84
Period size: 11 Copynumber: 9.1 Consensus size: 11
3067176 AAGGAAAAAG
3067186 AGAAAAAGAAA
1 AGAAAAAGAAA
3067197 AGAAAAAG-AA
1 AGAAAAAGAAA
3067207 AG-AAAAGAAGA
1 AGAAAAAGAA-A
*
3067218 A-TAAAAGAAGA
1 AGAAAAAGAA-A
*
3067229 A-AAAAAGAAG
1 AGAAAAAGAAA
3067239 A-AAAAAGAAA
1 AGAAAAAGAAA
3067249 AGAAAAAGAGAAA
1 AG-AAAA-AGAAA
3067262 AGAAAAAGAGAA
1 AGAAAAAGA-AA
*
3067274 A-AAATAGAAA
1 AGAAAAAGAAA
3067284 A
1 A
3067285 ATAAATCAAG
Statistics
Matches: 77, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
9 5 0.06
10 18 0.23
11 36 0.47
12 11 0.14
13 7 0.09
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:3067231 original size:34 final size:31
Alignment explanation
Indices: 3067188--3067277 Score: 103
Period size: 31 Copynumber: 2.8 Consensus size: 31
3067178 GGAAAAAGAG
3067188 AAAAAGAAAAGAAAAAGAAAGAAAAGAAGAATA
1 AAAAAGAAAAGAAAAAGAAA-AAAAGAA-AATA
*
3067221 AAAGAAGAAAA-AAAGAAG-AAAAAAGAAAAGA
1 AAA-AAGAAAAGAAA-AAGAAAAAAAGAAAATA
3067252 AAAAGAGAAAAGAAAAAGAGAAAAAA
1 AAAA-AGAAAAGAAAAAGA-AAAAAA
3067278 TAGAAAAATA
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
30 1 0.02
31 15 0.30
32 10 0.20
33 14 0.28
34 10 0.20
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (31 bp):
AAAAAGAAAAGAAAAAGAAAAAAAGAAAATA
Found at i:3067234 original size:31 final size:29
Alignment explanation
Indices: 3067171--3067265 Score: 85
Period size: 28 Copynumber: 3.3 Consensus size: 29
3067161 ATAAATTCAT
3067171 AAAAA-AAGGAAAAAGAGAA-AA-AGAAAAG
1 AAAAAGAA-GAAAAA-AGAATAAAAGAAAAG
3067199 AAAAAGAAAGAAAAGAAGAATAAAAGAAGAA-
1 AAAAAG-AAGAAAA-AAGAATAAAAGAA-AAG
*
3067230 AAAAAGAAGAAAAAAGAA-AAGA-AAAAG
1 AAAAAGAAGAAAAAAGAATAAAAGAAAAG
3067257 AGAAAAGAA
1 A-AAAAGAA
3067266 AAAGAGAAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 16
0.77 0.01 0.21
Matches are distributed among these distances:
26 2 0.03
27 3 0.05
28 15 0.26
29 14 0.24
30 12 0.21
31 10 0.17
32 2 0.03
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (29 bp):
AAAAAGAAGAAAAAAGAATAAAAGAAAAG
Found at i:3067276 original size:42 final size:41
Alignment explanation
Indices: 3067174--3067285 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 41
3067164 AATTCATAAA
*
3067174 AAAAGGAAAAAGAGAAAAAGAAAAGAAAAAGAAAGAAAAGAAG
1 AAAA-GAAAAAGAGAAAAAGAAGA-AAAAAGAAAGAAAAGAAG
* *
3067217 AATAA-AAGAAGAAAAAAAGAAGAAAAAAGAAAAGAAAA-AGAG
1 AA-AAGAAAAAGAGAAAAAGAAGAAAAAAG-AAAGAAAAGA-AG
3067259 AAAAGAAAAAGAGAAAAA-ATAGAAAAA
1 AAAAGAAAAAGAGAAAAAGA-AGAAAAA
3067286 TAAATCAAGT
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
41 10 0.17
42 45 0.76
43 2 0.03
44 2 0.03
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (41 bp):
AAAAGAAAAAGAGAAAAAGAAGAAAAAAGAAAGAAAAGAAG
Found at i:3069907 original size:93 final size:93
Alignment explanation
Indices: 3069748--3069928 Score: 213
Period size: 93 Copynumber: 1.9 Consensus size: 93
3069738 GCCCCGATTC
* *
3069748 AATGGATCAACTCCTCCATATATGATATTCCCTTCAGAAGAAGCAAAATAAATCCCTCTCATTCA
1 AATGGATCAACTCCTCCATATATGATATTCCCTTCAGAAGAAGCAAAACAAATCCATCTCATTCA
*
3069813 AGATTCAATCTTCCCTGAGTGACAGCGG
66 AGATTCAATATTCCCTGAGTGACAGCGG
* ** ** * **
3069841 AATGGATCAACTCC-CTCATATCTGATATTCCCTTCAG-AGTAAGCGGAACATGTCTATCTTTTT
1 AATGGATCAACTCCTC-CATATATGATATTCCCTTCAGAAG-AAGCAAAACAAATCCATCTCATT
**
3069904 CAAGATTTGATATTCCCTGAGTGAC
64 CAAGATTCAATATTCCCTGAGTGAC
3069929 TGCCCCGATT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
92 3 0.04
93 70 0.96
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (93 bp):
AATGGATCAACTCCTCCATATATGATATTCCCTTCAGAAGAAGCAAAACAAATCCATCTCATTCA
AGATTCAATATTCCCTGAGTGACAGCGG
Found at i:3070030 original size:121 final size:121
Alignment explanation
Indices: 3069814--3070049 Score: 384
Period size: 121 Copynumber: 2.0 Consensus size: 121
3069804 TCTCATTCAA
* * *
3069814 GATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCCTCATATCTGATATTCCCTTCAGA
1 GATTCAATCTTCCCTGAGTGACAGCGGAATGAATCAACTCCCCCAGATCTGATATTCCCTTCAGA
*
3069879 GTAAGCGGAACATGTCTATCTTTTTCAAGATTTGATATTCCCTGAGTGACTGCCCC
66 GTAAGCGGAACAAGTCTATCTTTTTCAAGATTTGATATTCCCTGAGTGACTGCCCC
* *
3069935 GATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACTCCCCCAGATCTGATATTCTCTTCAGA
1 GATTCAATCTTCCCTGAGTGACAGCGGAATGAATCAACTCCCCCAGATCTGATATTCCCTTCAGA
* *
3070000 GTAAGCGGAACAAGTCTCTCTTTTAT-AAGATTTTATATTCCCTGAGTGAC
66 GTAAGCGGAACAAGTCTATCTTTT-TCAAGATTTGATATTCCCTGAGTGAC
3070050 AACGGAAGAA
Statistics
Matches: 106, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
121 105 0.99
122 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (121 bp):
GATTCAATCTTCCCTGAGTGACAGCGGAATGAATCAACTCCCCCAGATCTGATATTCCCTTCAGA
GTAAGCGGAACAAGTCTATCTTTTTCAAGATTTGATATTCCCTGAGTGACTGCCCC
Found at i:3070256 original size:134 final size:134
Alignment explanation
Indices: 3070105--3070625 Score: 541
Period size: 134 Copynumber: 3.9 Consensus size: 134
3070095 GAATGATCAG
* *
3070105 GTCTCTCTTTTCTAAGATTTGATATTCCCTGAGTGACAATGGAACAAGTCTGCCCCGATTCAATC
1 GTCTCTCTTTTCCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCCCGATTCAATC
* * * *
3070170 TTCCCTGAGTGACATCGAAATTGATCAACTCCCCTAGATCTGATATTCCCTTCAGAGTAAG-TGT
66 TTCCCTGAGTGACAGCGAAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGCAG-
3070234 AACAA
130 AACAA
* *
3070239 GTCTCTCTTTTCCAAGATTTGATATTCTCTGAGTGACAGTGGAACAAGTCTGCCCCGATTAAATC
1 GTCTCTCTTTTCCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCCCGATTCAATC
* *
3070304 TTCCTTGAGTGACAGCGGAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGCAGA
66 TTCCCTGAGTGACAGCGAAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGCAGA
*
3070369 ACAT
131 ACAA
* * * ** *
3070373 GTCTCTATTTTCCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCTTGATTCAATT
1 GTCTCTCTTTTCCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCCCGATTCAATC
* * * * * ** **
3070438 TTCCCTGAAG-AACGGC-AGAATGAATCACCTCTCCTCCCAAATCTGATATTTTCTTCAGAAAAA
66 TTCCCTG-AGTGACAGCGA-AATGGATCA--ACTCC-CCCAGATCTGATATTCCCTTCAGAGTAA
*
3070501 GCGGAACAA
126 GCAGAACAA
* * * * * ** * * * *
3070510 ATCCCTCTCATT-GAATATTTGATATTCCCTGAGTGACAGCAGAATAAGTCTACCCTGATTTAAT
1 GTCTCTCT-TTTCCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCCCGATTCAAT
* * * *
3070574 CTTCCCTGAAG-GACAGTGGAATGGATCAACAT-CCACTGATCTGATATTCCCT
65 CTTCCCTG-AGTGACAGCGAAATGGATCAAC-TCCCCCAGATCTGATATTCCCT
3070626 AAGTGACAAC
Statistics
Matches: 324, Mismatches: 54, Indels: 18
0.82 0.14 0.05
Matches are distributed among these distances:
134 210 0.65
135 5 0.02
136 5 0.02
137 102 0.31
138 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (134 bp):
GTCTCTCTTTTCCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGCCCCGATTCAATC
TTCCCTGAGTGACAGCGAAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGCAGA
ACAA
Found at i:3070817 original size:3 final size:3
Alignment explanation
Indices: 3070811--3070851 Score: 64
Period size: 3 Copynumber: 13.0 Consensus size: 3
3070801 AATAATAATA
3070811 ATT ATT ATT ATT ATT AACTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT -A-TT ATT ATT ATT ATT ATT ATT ATT
3070852 CATTTATAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 32 0.89
4 2 0.06
5 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3072093 original size:29 final size:27
Alignment explanation
Indices: 3072029--3072101 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 27
3072019 GCCTTAATAT
*
3072029 ATGTTTTCATTTATTTTAATTCGGCCCC
1 ATGTTTT-ATTTATTTTAATTAGGCCCC
*
3072057 ATGATTTTAATTTATTTTAATATAGTCCCC
1 ATG-TTTT-ATTTATTTTAAT-TAGGCCCC
*
3072087 TTGTTTTATTTATTT
1 ATGTTTTATTTATTT
3072102 CTATTATTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 11 0.28
29 20 0.51
30 8 0.21
ACGTcount: A:0.22, C:0.14, G:0.08, T:0.56
Consensus pattern (27 bp):
ATGTTTTATTTATTTTAATTAGGCCCC
Found at i:3076326 original size:33 final size:34
Alignment explanation
Indices: 3076278--3076356 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 34
3076268 GCATACCAAG
* *
3076278 ATGCCCGCACCAAGACCTACCAAGGGGCACGCCA
1 ATGCCCGCACTAAGACCCACCAAGGGGCACGCCA
* *
3076312 A-GCCCGCACTAAGACCCACCATGGGGCGCGCCA
1 ATGCCCGCACTAAGACCCACCAAGGGGCACGCCA
*
3076345 ATGCCCGAACTA
1 ATGCCCGCACTA
3076357 GAACCAGGCA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 29 0.74
34 10 0.26
ACGTcount: A:0.28, C:0.41, G:0.24, T:0.08
Consensus pattern (34 bp):
ATGCCCGCACTAAGACCCACCAAGGGGCACGCCA
Found at i:3078849 original size:60 final size:60
Alignment explanation
Indices: 3078755--3078877 Score: 201
Period size: 60 Copynumber: 2.0 Consensus size: 60
3078745 TTTAGAAATT
* * *
3078755 AGGGTTTTGTGAATGGTAGAAATGGGTCACGACTCTTGACGAGGGCACAAGCAATAGCGA
1 AGGGTTTTGTGAATGGTAAAAATGGGTCACGACTCTTGACGAGGGCACAAGAAATAGCCA
* *
3078815 AGGGTTTTGTGAATGGTAAAAATGGGTCATGACTCTTGAGGAGGGCACAAGAAATAGCCA
1 AGGGTTTTGTGAATGGTAAAAATGGGTCACGACTCTTGACGAGGGCACAAGAAATAGCCA
3078875 AGG
1 AGG
3078878 AATAGAGTGC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.32, C:0.13, G:0.33, T:0.22
Consensus pattern (60 bp):
AGGGTTTTGTGAATGGTAAAAATGGGTCACGACTCTTGACGAGGGCACAAGAAATAGCCA
Found at i:3080926 original size:13 final size:13
Alignment explanation
Indices: 3080908--3080946 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
3080898 AATAAGATGT
3080908 ATAATATAATTAA
1 ATAATATAATTAA
*
3080921 ATAATATAAAGTAA
1 ATAATAT-AATTAA
*
3080935 ATAATTTAATTA
1 ATAATATAATTA
3080947 TTTATTTACT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
ATAATATAATTAA
Found at i:3084189 original size:19 final size:19
Alignment explanation
Indices: 3084165--3084203 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3084155 CAAAAGAAGG
3084165 CAACCAAATTCAAAAATTA
1 CAACCAAATTCAAAAATTA
3084184 CAACCAAATTCAAAAATTA
1 CAACCAAATTCAAAAATTA
3084203 C
1 C
3084204 TGAACCAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.56, C:0.23, G:0.00, T:0.21
Consensus pattern (19 bp):
CAACCAAATTCAAAAATTA
Found at i:3085976 original size:2 final size:2
Alignment explanation
Indices: 3085965--3086015 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
3085955 GCCCCCAAAA
3085965 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3086006 AT AT AT AT AT
1 AT AT AT AT AT
3086016 TAATTTTGGC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3087624 original size:20 final size:20
Alignment explanation
Indices: 3087582--3087624 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
3087572 CTATTATATT
* * * *
3087582 AATCGAATATTAATTTTTGA
1 AATCGAATATAAAATCTTAA
3087602 AATCGAATATAAAATCTTAA
1 AATCGAATATAAAATCTTAA
3087622 AAT
1 AAT
3087625 TTATTTACTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (20 bp):
AATCGAATATAAAATCTTAA
Found at i:3087736 original size:13 final size:13
Alignment explanation
Indices: 3087720--3087760 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
3087710 TTTTAAGATT
3087720 TTATTTTTGAAAA
1 TTATTTTTGAAAA
3087733 TTATTTTTG-AAA
1 TTATTTTTGAAAA
* *
3087745 TCAATTTTGAAAA
1 TTATTTTTGAAAA
3087758 TTA
1 TTA
3087761 CTACTCCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51
Consensus pattern (13 bp):
TTATTTTTGAAAA
Found at i:3089583 original size:20 final size:20
Alignment explanation
Indices: 3089542--3089584 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3089532 TATAGTTTTC
*
3089542 AAAACAACATAATTAAATCA
1 AAAACAACATAATTAAAACA
*
3089562 AAAACAACA-ATTTAAAAACA
1 AAAACAACATAATT-AAAACA
3089582 AAA
1 AAA
3089585 CGATTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.70, C:0.14, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAACAACATAATTAAAACA
Found at i:3089635 original size:18 final size:19
Alignment explanation
Indices: 3089612--3089649 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3089602 AAATAAAAAA
3089612 TTTTTGAAGAAATTT-TTG
1 TTTTTGAAGAAATTTGTTG
**
3089630 TTTTTGTTGAAATTTGTTG
1 TTTTTGAAGAAATTTGTTG
3089649 T
1 T
3089650 AGATTTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (19 bp):
TTTTTGAAGAAATTTGTTG
Found at i:3096099 original size:20 final size:20
Alignment explanation
Indices: 3096062--3096100 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3096052 ATATTAATCA
* * *
3096062 AATATTAAATTTTGAAATTG
1 AATATAAAATCTTAAAATTG
3096082 AATATAAAATCTTAAAATT
1 AATATAAAATCTTAAAATT
3096101 CATTTACTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTG
Found at i:3097778 original size:30 final size:30
Alignment explanation
Indices: 3097744--3097801 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
3097734 AAAAGATAGG
3097744 GTAAATTATATCTATGATTATTTAATTAGT
1 GTAAATTATATCTATGATTATTTAATTAGT
3097774 GTAAATTATATCTATGATTATTTAATTA
1 GTAAATTATATCTATGATTATTTAATTA
3097802 TTGTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (30 bp):
GTAAATTATATCTATGATTATTTAATTAGT
Found at i:3097817 original size:21 final size:22
Alignment explanation
Indices: 3097794--3097846 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
3097784 TCTATGATTA
* *
3097794 TTTAATTATTGTTTTTTTTTAT
1 TTTAATAATTGTTCTTTTTTAT
*
3097816 TTTAATAATTGTTC-TTTTAAT
1 TTTAATAATTGTTCTTTTTTAT
*
3097837 TTTATTAATT
1 TTTAATAATT
3097847 AGACCACTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (22 bp):
TTTAATAATTGTTCTTTTTTAT
Found at i:3099919 original size:16 final size:17
Alignment explanation
Indices: 3099898--3099935 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
3099888 GACATATAAC
3099898 TTTTTATTTC-TTTTAA
1 TTTTTATTTCATTTTAA
3099914 TTTTTATTTCATTTTAA
1 TTTTTATTTCATTTTAA
3099931 TTTTT
1 TTTTT
3099936 TATAATGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTATTTCATTTTAA
Found at i:3102186 original size:12 final size:12
Alignment explanation
Indices: 3102169--3102198 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3102159 CGTTTGAGGA
3102169 TTTTTTTTTCAT
1 TTTTTTTTTCAT
*
3102181 TTTTTTTTTCGT
1 TTTTTTTTTCAT
3102193 TTTTTT
1 TTTTTT
3102199 AGGTTATCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.03, C:0.07, G:0.03, T:0.87
Consensus pattern (12 bp):
TTTTTTTTTCAT
Found at i:3102716 original size:22 final size:22
Alignment explanation
Indices: 3102690--3102757 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
3102680 TGTAGATGGC
3102690 CAAAAGTCTTAATCATCATGCT
1 CAAAAGTCTTAATCATCATGCT
* * * *
3102712 CAAAAGGCTTACTAAT--TGCC
1 CAAAAGTCTTAATCATCATGCT
* *
3102732 CGAAGGTCTT-ATCATCATGCT
1 CAAAAGTCTTAATCATCATGCT
3102753 CAAAA
1 CAAAA
3102758 TACTTACTAA
Statistics
Matches: 32, Mismatches: 12, Indels: 5
0.65 0.24 0.10
Matches are distributed among these distances:
19 3 0.09
20 10 0.31
21 6 0.19
22 13 0.41
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (22 bp):
CAAAAGTCTTAATCATCATGCT
Found at i:3102746 original size:41 final size:42
Alignment explanation
Indices: 3102695--3102809 Score: 171
Period size: 41 Copynumber: 2.8 Consensus size: 42
3102685 ATGGCCAAAA
*
3102695 GTCTTAATCATCATGCTCAAAAGGCTTACTAATTG-CCCGAAG
1 GTCTT-ATCATCATGCTCAAAAGACTTACTAATTGACCCGAAG
* *
3102737 GTCTTATCATCATGCTCAAAATACTTACTAA-TGACTCGAAG
1 GTCTTATCATCATGCTCAAAAGACTTACTAATTGACCCGAAG
*
3102778 GTCTTAGCATCATGCTCAAAAGACTTACTAAT
1 GTCTTATCATCATGCTCAAAAGACTTACTAAT
3102810 GGCTTGAATG
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
40 2 0.03
41 59 0.89
42 5 0.08
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (42 bp):
GTCTTATCATCATGCTCAAAAGACTTACTAATTGACCCGAAG
Found at i:3108124 original size:29 final size:29
Alignment explanation
Indices: 3108103--3108174 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
3108093 TTGGATCCAT
3108103 ATTTAATTAGAAATTCACTTTGGTCCCAA
1 ATTTAATTAGAAATTCACTTTGGTCCCAA
3108132 ATTTAATTAGAAATTCACTTTGGTCCCAA
1 ATTTAATTAGAAATTCACTTTGGTCCCAA
*
3108161 ATTTAACTA-AAATT
1 ATTTAATTAGAAATT
3108175 TTGATTTAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 5 0.12
29 37 0.88
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (29 bp):
ATTTAATTAGAAATTCACTTTGGTCCCAA
Found at i:3108916 original size:3 final size:3
Alignment explanation
Indices: 3108908--3108994 Score: 165
Period size: 3 Copynumber: 29.0 Consensus size: 3
3108898 TTTGTCCCGT
3108908 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3108956 TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3108995 ATTTCAAATA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3110112 original size:29 final size:29
Alignment explanation
Indices: 3110070--3110136 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
3110060 ACAAGCCTCA
* * *
3110070 GAAAAATTGGGGATCATTTCGTAAGTTTT
1 GAAAAATTGGGGATAAATTCGTAAATTTT
*
3110099 GAAAAGTTGGGGATAAATTCGTAAATTTT
1 GAAAAATTGGGGATAAATTCGTAAATTTT
*
3110128 GTAAAATTG
1 GAAAAATTG
3110137 ATGAAGAACC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (29 bp):
GAAAAATTGGGGATAAATTCGTAAATTTT
Found at i:3114942 original size:64 final size:64
Alignment explanation
Indices: 3114839--3114964 Score: 164
Period size: 64 Copynumber: 2.0 Consensus size: 64
3114829 TTTTGAATGT
* *
3114839 ATTTTGTGTACCGATGCACAAGGCATGCATCAACACACTCCTGAATATTTTGAACATCAAATAC
1 ATTTTGTGTACCGATGCACAAGCCATGCATCAACACACTCCAGAATATTTTGAACATCAAATAC
* ** ** *
3114903 ATTTTGTGTACCGATGCAC-AGACCATGCATCGATGCACTCCAGGTTCTTTTGAACATCAAAT
1 ATTTTGTGTACCGATGCACAAG-CCATGCATCAACACACTCCAGAATATTTTGAACATCAAAT
3114965 GTGATTAGTG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 2 0.04
64 51 0.96
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (64 bp):
ATTTTGTGTACCGATGCACAAGCCATGCATCAACACACTCCAGAATATTTTGAACATCAAATAC
Found at i:3115672 original size:19 final size:20
Alignment explanation
Indices: 3115648--3115693 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3115638 AATTTTATTA
3115648 CCAATTCA-CCCCCTCTTGG
1 CCAATTCACCCCCCTCTTGG
3115667 CCAATTCACCCCCCTCTTGG
1 CCAATTCACCCCCCTCTTGG
3115687 CCAATTC
1 CCAATTC
3115694 GTCGATCGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.17, C:0.48, G:0.09, T:0.26
Consensus pattern (20 bp):
CCAATTCACCCCCCTCTTGG
Found at i:3120544 original size:23 final size:22
Alignment explanation
Indices: 3120516--3120595 Score: 72
Period size: 23 Copynumber: 3.6 Consensus size: 22
3120506 CACTAGACAA
*
3120516 TGCATCGATGCATCCCTTGAATG
1 TGCATCAATGCA-CCCTTGAATG
* * *
3120539 TGCATCAATACA-CCATGAAGG
1 TGCATCAATGCACCCTTGAATG
* *
3120560 TGGACCAATGCACTCCTTGAATG
1 TGCATCAATGCAC-CCTTGAATG
*
3120583 TGCATCGATGCAC
1 TGCATCAATGCAC
3120596 TCTGTTCTGC
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
21 16 0.37
23 27 0.63
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (22 bp):
TGCATCAATGCACCCTTGAATG
Found at i:3121353 original size:48 final size:48
Alignment explanation
Indices: 3121301--3121396 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
3121291 GTGATTTGAG
3121301 TTAAAACCGATCTACCATTTCTTCTCAACCACAAAATCCAAATCCAAA
1 TTAAAACCGATCTACCATTTCTTCTCAACCACAAAATCCAAATCCAAA
3121349 TTAAAACCGATCTACCATTTCTTCTCAACCACAAAATCCAAATCCAAA
1 TTAAAACCGATCTACCATTTCTTCTCAACCACAAAATCCAAATCCAAA
3121397 CGAACCCAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.42, C:0.31, G:0.02, T:0.25
Consensus pattern (48 bp):
TTAAAACCGATCTACCATTTCTTCTCAACCACAAAATCCAAATCCAAA
Found at i:3122983 original size:14 final size:13
Alignment explanation
Indices: 3122960--3122994 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3122950 AAGGGAGTAA
*
3122960 TTTTACAAAATTG
1 TTTTACAAAAATG
*
3122973 TTTTTCAAAAATG
1 TTTTACAAAAATG
3122986 TTTTACAAA
1 TTTTACAAA
3122995 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.46
Consensus pattern (13 bp):
TTTTACAAAAATG
Found at i:3131091 original size:226 final size:215
Alignment explanation
Indices: 3130629--3131404 Score: 702
Period size: 203 Copynumber: 3.6 Consensus size: 215
3130619 TAACAGAACC
** * * * * *
3130629 GGTTAATTGTTGG-AACATTATCAACCATAATAACATAATATGTATCACTTATTTAACGTAATGG
1 GGTTAATTAATGGAAACATTATCAACCATAATAACATAACAAGTAACACTTATTTAATGTAATAG
* * *
3130693 GTAGTGCCTTTTTAAAGCTGATGGGTCCTTAGAAATCCGATGATAACAAAATAGGTCAATTACTT
66 GTA-T-CCTGTTTAAAGCTGATGGGTCCTTAGAAATCCAACGATAACAAAATAGGTCAATTACTT
* * * * *
3130758 AATTTATTATTAACATAATAGGTAGTGCCTAAAATGTTACCAAAGTTTAAGTTGATTGAGTCTTA
129 AATTTATTATCAACATAATAGGTAGTGCCTAAAATATTACCAAAGTTTAAGCTGATGGAGCCTTA
*
3130823 GAAATCTGACGATAAAAAAATA
194 GAAATCAGACGATAAAAAAATA
* * **
3130845 GGTTAATTATTGGAAACATTATCAACCATAATAACATAACAAGTAGCTTTTATTTAATGTAATAG
1 GGTTAATTAATGGAAACATTATCAACCATAATAACATAACAAGTAACACTTATTTAATGTAATAG
* * *
3130910 GTATCATCTGTTTAAAGCTGATGAGG-CCTTATAAATCCAACGATAACAAAATAGGTTAATTAGT
66 GTATC--CTGTTTAAAGCTGATG-GGTCCTTAGAAATCCAACGATAACAAAATAGGTCAATTACT
* *
3130974 TAATTTGTTTTCAATATTATCAACATATTATGTAGTGCCTAAAATATTACCAAAGTTTAAGCTGA
128 TAA------TT---TATTATCAACATAATAGGTAGTGCCTAAAATATTACCAAAGTTTAAGCTGA
*
3131039 TGGAGCCTTAGAAATCAGACGATAACAAAATA
184 TGGAGCCTTAGAAATCAGACGATAAAAAAATA
* * *
3131071 GGTTGATTAATGGAAACATTATCAACCATAATAACATAACAAGTAACGCTTATTTAATGTAAAAG
1 GGTTAATTAATGGAAACATTATCAACCATAATAACATAACAAGTAACACTTATTTAATGTAATAG
* ****** * * * ** ** *
3131136 GTAGCGCCTGTTTAAAGCTGA-AACAAATTAG--GT--TA--ATTACTTAATTTGT---TT--TC
66 GTA--TCCTGTTTAAAGCTGATGGGTCCTTAGAAATCCAACGATAACAAAATAGGTCAATTACTT
* * **
3131189 AA--TATTATCAACATATTAGGTAGCGCCTAAAATATTACCAAAGTTTAAGCTGATTAAGCCTTA
129 AATTTATTATCAACATAATAGGTAGTGCCTAAAATATTACCAAAGTTTAAGCTGATGGAGCCTTA
* *
3131252 GAAATCTGACGATAACAAAATA
194 GAAATCAGACGATAAAAAAATA
* * ** * *
3131274 GGTTCATTATTGGAAATTTTATCAATCATAATAACATAACAAGTATCACTTATTTAATGTAATAG
1 GGTTAATTAATGGAAACATTATCAACCATAATAACATAACAAGTAACACTTATTTAATGTAATAG
* * *** * * *
3131339 GTAGCGTCTGTTTAAAGCTGATGGGACCTTAGAAATTTGATGATAACAAAATATGTTAATTACTT
66 GTATC--CTGTTTAAAGCTGATGGGTCCTTAGAAATCCAACGATAACAAAATAGGTCAATTACTT
3131404 A
129 A
3131405 TTGTTTTCAA
Statistics
Matches: 461, Mismatches: 69, Indels: 61
0.78 0.12 0.10
Matches are distributed among these distances:
201 2 0.00
203 152 0.33
204 5 0.01
206 1 0.00
208 1 0.00
210 10 0.02
213 2 0.00
214 3 0.01
215 3 0.01
216 15 0.03
217 98 0.21
218 2 0.00
219 9 0.02
221 1 0.00
223 3 0.01
225 3 0.01
226 150 0.33
228 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (215 bp):
GGTTAATTAATGGAAACATTATCAACCATAATAACATAACAAGTAACACTTATTTAATGTAATAG
GTATCCTGTTTAAAGCTGATGGGTCCTTAGAAATCCAACGATAACAAAATAGGTCAATTACTTAA
TTTATTATCAACATAATAGGTAGTGCCTAAAATATTACCAAAGTTTAAGCTGATGGAGCCTTAGA
AATCAGACGATAAAAAAATA
Found at i:3131510 original size:20 final size:21
Alignment explanation
Indices: 3131480--3131518 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
3131470 AGGTTTCGAA
3131480 ATTATAAGTATCGATACTTAT
1 ATTATAAGTATCGATACTTAT
3131501 ATTA-AAGTATCGATACTT
1 ATTATAAGTATCGATACTT
3131519 GTACATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (21 bp):
ATTATAAGTATCGATACTTAT
Found at i:3132163 original size:199 final size:198
Alignment explanation
Indices: 3131812--3132357 Score: 675
Period size: 199 Copynumber: 2.7 Consensus size: 198
3131802 TCAAAATTAT
* * * * * *
3131812 AAGTAT-CGATACTTATATGATAGTATCGATACTTGGACATTTATGCCTATTTTCATTATACCGG
1 AAGTATAC-ATACTTATATAAAAGTATTGATACTTGG-TATTTACGCCTATTATCATTATACCGG
* * ** *
3131876 TAGAAACGTTTACCGTGTACATTGTTAATTTATATATTACTTTAAAGTAATATGTTTCGAAATTA
64 TAG--ACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTA
** *
3131941 ATAGTATCGATACTTTATATATGTGTATCGATACATTTTGTGTACAAATATTTCGAGAATCATAC
127 A-AGTATCGATACTTTATATATGTGTATCGATACATTTTGCATACAAATATTTCGAGAAGCATAC
*
3132006 TGGTATAA
191 TGGAATAA
* *
3132014 AAGTATATATACTTATATAAAAGTATTGATACTTGGTATTTACACCTATTATCATTATACCGGTA
1 AAGTATACATACTTATATAAAAGTATTGATACTTGGTATTTACGCCTATTATCATTATACCGGTA
*
3132079 GACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAG
66 GACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATT-AAAG
* * * * * *
3132144 TATTGATACTTTATATATGTGTATCGATACATTTTGCATGCAAATTTTTTGAGAAGCTTATTGGA
130 TATCGATACTTTATATATGTGTATCGATACATTTTGCATACAAATATTTCGAGAAGCATACTGGA
*
3132209 ATAG
195 ATAA
* * * * *
3132213 AAGTATCCATACCTATATAAAAGTATTGATAAATT-GTATTTACGCCTATTATCAATATACCAGT
1 AAGTATACATACTTATATAAAAGTATTGAT-ACTTGGTATTTACGCCTATTATCATTATACCGGT
* * * * * *
3132277 AGACTTTTACCGTTTACATTATAAATTAACCTATTACTTTAAAGAAATAGGATTCAAAATTATAA
65 AGACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTA-AA
3132342 GTATCGATAC-TTATAT
129 GTATCGATACTTTATAT
3132358 GGCAGTATCG
Statistics
Matches: 300, Mismatches: 40, Indels: 12
0.85 0.11 0.03
Matches are distributed among these distances:
198 6 0.02
199 233 0.78
200 4 0.01
201 26 0.09
202 31 0.10
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (198 bp):
AAGTATACATACTTATATAAAAGTATTGATACTTGGTATTTACGCCTATTATCATTATACCGGTA
GACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTAAAGT
ATCGATACTTTATATATGTGTATCGATACATTTTGCATACAAATATTTCGAGAAGCATACTGGAA
TAA
Found at i:3134746 original size:12 final size:12
Alignment explanation
Indices: 3134729--3134753 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3134719 GGATGCATAA
3134729 GCACTTGTTTTC
1 GCACTTGTTTTC
3134741 GCACTTGTTTTC
1 GCACTTGTTTTC
3134753 G
1 G
3134754 AACTAGTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.20, T:0.48
Consensus pattern (12 bp):
GCACTTGTTTTC
Found at i:3136692 original size:25 final size:25
Alignment explanation
Indices: 3136662--3136719 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
3136652 AAAAAGAAAT
*
3136662 GGAAATGATAGAAGAAATGATTTAA
1 GGAAATGATAAAAGAAATGATTTAA
*
3136687 GGAAATGATAAAAGAAATTATTTAA
1 GGAAATGATAAAAGAAATGATTTAA
3136712 GGAAATGA
1 GGAAATGA
3136720 AAAGAATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.24
Consensus pattern (25 bp):
GGAAATGATAAAAGAAATGATTTAA
Found at i:3136693 original size:13 final size:13
Alignment explanation
Indices: 3136662--3136719 Score: 57
Period size: 12 Copynumber: 4.6 Consensus size: 13
3136652 AAAAAGAAAT
**
3136662 GGAAATGATAGAA
1 GGAAATGATTTAA
3136675 -GAAATGATTTAA
1 GGAAATGATTTAA
*
3136687 GGAAATGA-TAAA
1 GGAAATGATTTAA
* *
3136699 AGAAATTATTTAA
1 GGAAATGATTTAA
3136712 GGAAATGA
1 GGAAATGA
3136720 AAAGAATGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
12 19 0.54
13 16 0.46
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.24
Consensus pattern (13 bp):
GGAAATGATTTAA
Found at i:3136738 original size:27 final size:25
Alignment explanation
Indices: 3136662--3136739 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
3136652 AAAAAGAAAT
* * *
3136662 GGAAATGATAGAAGAAATGATTTAA
1 GGAAATGAAAAAAGAAAAGATTTAA
* **
3136687 GGAAATGATAAAAGAAATTATTTAA
1 GGAAATGAAAAAAGAAAAGATTTAA
*
3136712 GGAAATGAAAAGAATGAAAAGGTTTAA
1 GGAAATGAAAA-AA-GAAAAGATTTAA
3136739 G
1 G
3136740 AACAAGGAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 33 0.73
26 2 0.04
27 10 0.22
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (25 bp):
GGAAATGAAAAAAGAAAAGATTTAA
Found at i:3138620 original size:13 final size:13
Alignment explanation
Indices: 3138602--3138626 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3138592 AATTATAACT
3138602 ATATATATATATA
1 ATATATATATATA
3138615 ATATATATATAT
1 ATATATATATAT
3138627 GTGTGTATGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATATATATA
Found at i:3140733 original size:199 final size:199
Alignment explanation
Indices: 3140372--3140873 Score: 767
Period size: 199 Copynumber: 2.5 Consensus size: 199
3140362 ATCCTCCTGA
* *
3140372 ATTTACGCCTATTATCAATATATCAGTAGACTTTTACCGTTTACATTGTTAATTTACCTATTACT
1 ATTTACGCCTATTATCAATATATCGGTAGACTTTTACCATTTACATTGTTAATTTACCTATTACT
* * * *
3140437 TTAAAGTAATAGGTTCTGAAATTCCAAGTATTGATACTTTATATATGTGTATCAATACATTTTGC
66 TTAAAGTAATAGGTTTTGAAATTACAAGTATCGATACTTTATATATGTGCATCAATACATTTTGC
* *
3140502 ATGCAAATTGTTTGAGAAATATACTGGAATAAAAGTA-CCAATACCTACATAAAAGTATTGATAC
131 ATGCAAATTGTTTGAGAAACATACTAGAATAAAAGTATCC-ATACCTACATAAAAGTATTGATAC
3140566 TTGGT
195 TTGGT
*
3140571 ATTTACCCCTATTATCAATATATCGGTAGACTTTTACCATTTACATTGTTAATTTACCTATTACT
1 ATTTACGCCTATTATCAATATATCGGTAGACTTTTACCATTTACATTGTTAATTTACCTATTACT
* *
3140636 TTAAAGTAATAGTTTTTGAAATTACAAGTATCGATACTTTATATATGTGCATCGATACATTTTGC
66 TTAAAGTAATAGGTTTTGAAATTACAAGTATCGATACTTTATATATGTGCATCAATACATTTTGC
* * * * *
3140701 GTGCAAATTGTTTGAGAAGCATACTAGAATAAAAGTATTCATACCTATATAACAGTATTGATACT
131 ATGCAAATTGTTTGAGAAACATACTAGAATAAAAGTATCCATACCTACATAAAAGTATTGATACT
3140766 TGGT
196 TGGT
* * *
3140770 ATTTAAGCC-AGTTATCAATTTACCGGTAGACTTTTACCATTTACATTGTT-ATTTAACCTATTA
1 ATTTACGCCTA-TTATCAATATATCGGTAGACTTTTACCATTTACATTGTTAATTT-ACCTATTA
**
3140833 CTTTAAAGTAATAGGTTTCAAAATTACAAGTATCGATACTT
64 CTTTAAAGTAATAGGTTTTGAAATTACAAGTATCGATACTT
3140874 ACATGACAGT
Statistics
Matches: 277, Mismatches: 23, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
198 5 0.02
199 271 0.98
200 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (199 bp):
ATTTACGCCTATTATCAATATATCGGTAGACTTTTACCATTTACATTGTTAATTTACCTATTACT
TTAAAGTAATAGGTTTTGAAATTACAAGTATCGATACTTTATATATGTGCATCAATACATTTTGC
ATGCAAATTGTTTGAGAAACATACTAGAATAAAAGTATCCATACCTACATAAAAGTATTGATACT
TGGT
Found at i:3141585 original size:33 final size:33
Alignment explanation
Indices: 3141548--3141694 Score: 222
Period size: 33 Copynumber: 4.5 Consensus size: 33
3141538 TGATATGGAG
* * * **
3141548 CAATCAACCAACAACTCATCAAAAAATCATGAC
1 CAATCTACCAACAACTCTTCGAAAAATCCCGAC
*
3141581 CAATCAACCAACAACTCTTCGAAAAATCCCGAC
1 CAATCTACCAACAACTCTTCGAAAAATCCCGAC
3141614 CAATCTACCAACAACTCTTCGAAAAATCCCGAC
1 CAATCTACCAACAACTCTTCGAAAAATCCCGAC
**
3141647 CAATCTACCAACAACTCTTCGAAAAATCGTGAC
1 CAATCTACCAACAACTCTTCGAAAAATCCCGAC
3141680 CAATCTACCAACAAC
1 CAATCTACCAACAAC
3141695 GCTTTAGAGA
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 107 1.00
ACGTcount: A:0.44, C:0.34, G:0.05, T:0.17
Consensus pattern (33 bp):
CAATCTACCAACAACTCTTCGAAAAATCCCGAC
Found at i:3142492 original size:12 final size:12
Alignment explanation
Indices: 3142475--3142523 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
3142465 GTAGTGGAGC
3142475 TCAAATTGAAAT
1 TCAAATTGAAAT
3142487 TCAAATTGAAAT
1 TCAAATTGAAAT
*
3142499 TCAAGTTGAAAT
1 TCAAATTGAAAT
* *
3142511 TGAAACTGAAAT
1 TCAAATTGAAAT
3142523 T
1 T
3142524 TAATTACTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (12 bp):
TCAAATTGAAAT
Found at i:3142513 original size:6 final size:6
Alignment explanation
Indices: 3142477--3142523 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
3142467 AGTGGAGCTC
* * * *
3142477 AAATTG AAATTC AAATTG AAATTC AAGTTG AAATTG AAACTG AAATT
1 AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATT
3142524 TAATTACTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (6 bp):
AAATTG
Found at i:3142703 original size:72 final size:74
Alignment explanation
Indices: 3142607--3142750 Score: 211
Period size: 72 Copynumber: 2.0 Consensus size: 74
3142597 AAAAATATAA
* * * * *
3142607 CTTTAAAGAAATCAGTAGGTAGTTTAACGTAATAGGTAGTACCTA-TTTTTTAAC-GTTTACATT
1 CTTTAAACAAACCAGTAGCTAGTTTAACGTAATAGGTAGCACCTATTTTTTTAACTGTGTACATT
3142670 ATTATTAAC
66 ATTATTAAC
* *
3142679 CTTTAAACAAACCAGTAGCTAGTTTAACGTAATAGGTAGCGCCTATTTTTTTTACTGTGTACATT
1 CTTTAAACAAACCAGTAGCTAGTTTAACGTAATAGGTAGCACCTATTTTTTTAACTGTGTACATT
3142744 ATTATTA
66 ATTATTA
3142751 TCTGTTAAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
72 40 0.63
73 8 0.13
74 15 0.24
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (74 bp):
CTTTAAACAAACCAGTAGCTAGTTTAACGTAATAGGTAGCACCTATTTTTTTAACTGTGTACATT
ATTATTAAC
Found at i:3143232 original size:45 final size:45
Alignment explanation
Indices: 3143183--3143271 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
3143173 TTGATATACA
*
3143183 ATTATTGTTTAATATGTTTGAGTATATTAAAATTGAAAATAATGT
1 ATTATTGTTTAATATGTTTGAGTACATTAAAATTGAAAATAATGT
*
3143228 ATTATTGTTTGATATGTTTGAGTACATTAAAATTGAAAATAATG
1 ATTATTGTTTAATATGTTTGAGTACATTAAAATTGAAAATAATG
3143272 CATTTGTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.39, C:0.01, G:0.15, T:0.45
Consensus pattern (45 bp):
ATTATTGTTTAATATGTTTGAGTACATTAAAATTGAAAATAATGT
Found at i:3144482 original size:18 final size:18
Alignment explanation
Indices: 3144449--3144506 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
3144439 TGATTTGATC
**
3144449 AGAAGACCTTACTTGAGA
1 AGAAGACCTTGGTTGAGA
3144467 AGAAGACCTTGGTTGAGA
1 AGAAGACCTTGGTTGAGA
* ***
3144485 ATAAGGTTTTGGTTGAGA
1 AGAAGACCTTGGTTGAGA
3144503 AGAA
1 AGAA
3144507 CTGCATATCA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.36, C:0.09, G:0.29, T:0.26
Consensus pattern (18 bp):
AGAAGACCTTGGTTGAGA
Found at i:3144879 original size:198 final size:198
Alignment explanation
Indices: 3144631--3145645 Score: 1518
Period size: 198 Copynumber: 5.1 Consensus size: 198
3144621 TTCTATCCAT
**
3144631 ACTTTTACCGTTTACATTGTTAATTT-CCTATTACTTTAAAGTAATAGGTTTTGAAATTTCAAGT
1 ACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCAAGT
* * *
3144695 ATCGATACTTTATAGATATGTATTGATACATTTTGCATGCAAATTGTTTGATAAGCATACT-AAA
66 ATCGATACTTTATAGATATGTATCGATACATTTTGCATGCAAATTGTTTGAGAAGCATACTGGAA
* *
3144759 TAAAAGTATTGATACCTATATACAAGTATCGATACTTGGTATTTACACCTATTATCAATATATCG
131 TAAAAGTATCGATACCTATATACAAGTATCGATACTTGGTATTTACGCCTATTATCAATATA-CG
*
3144824 GTTG
195 GTAG
**
3144828 ACTTTTATTGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCAAGT
1 ACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCAAGT
* *
3144893 ATCGATACTTTATAGATATGTATCAATACATTTTG-AGTGCAAATTGTTCGAGAAGCATACTGGA
66 ATCGATACTTTATAGATATGTATCGATACATTTTGCA-TGCAAATTGTTTGAGAAGCATACTGGA
* * * *
3144957 ATAAAAGTATCGATACATATATACAAGTATCGATATTTGGTATTTACACATATTATCAATATACT
130 ATAAAAGTATCGATACCTATATACAAGTATCGATACTTGGTATTTACGCCTATTATCAATATAC-
3145022 GGTAG
194 GGTAG
**
3145027 ACTTTTACCGTTTACATTGTTAATTT-CCTATTACTTTAAAGTAATAGGTTTTGAAATTTCAAGT
1 ACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCAAGT
*
3145091 ATCGATACTTTATAGATATGTATCGATACATTTTGCATGCAAATTGTTTGAGAAGCATATTGGAA
66 ATCGATACTTTATAGATATGTATCGATACATTTTGCATGCAAATTGTTTGAGAAGCATACTGGAA
* * * *
3145156 TAAAAGTATTGATACCTATATACAAGTATCGATACTTGGTATTTATGCCTATTATCAATACAACT
131 TAAAAGTATCGATACCTATATACAAGTATCGATACTTGGTATTTACGCCTATTATCAATA-TACG
*
3145221 GTTG
195 GTAG
*
3145225 ACTTTTATCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCAAGT
1 ACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCAAGT
* * * * * * *
3145290 ATCAATACTTTATAGATGTGTATCAATACATTTTGCGTGCAAATTGTTCGAGAAACATACTAGAA
66 ATCGATACTTTATAGATATGTATCGATACATTTTGCATGCAAATTGTTTGAGAAGCATACTGGAA
* * *
3145355 TAAAAGTATCGATACCTACATACAAGTATCTATACTTGGTATTTACGCCTATTATCAATATACCA
131 TAAAAGTATCGATACCTATATACAAGTATCGATACTTGGTATTTACGCCTATTATCAATATA-CG
3145420 GTAG
195 GTAG
*
3145424 ACTTTTACC-TTTACCTTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCAAGT
1 ACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCAAGT
* * * *
3145488 ATCGCTACTTTATAGATTTGTTTCGATACATTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAA
66 ATCGATACTTTATAGATATGTATCGATACATTTTGCATGCAAATTGTTTGAGAAGCATACTGGAA
* * * **
3145553 TAGAAGTATCGATACATATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCAATATAATT
131 TAAAAGTATCGATACCTATATACAAGTATCGATACTTGGTATTTACGCCTATTATCAATAT-ACG
*
3145618 GTAC
195 GTAG
*
3145622 ACTTTTACCGTTTACATTATTAAT
1 ACTTTTACCGTTTACATTGTTAAT
3145646 CTACGATTTT
Statistics
Matches: 740, Mismatches: 68, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
197 25 0.03
198 450 0.61
199 265 0.36
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (198 bp):
ACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCAAGT
ATCGATACTTTATAGATATGTATCGATACATTTTGCATGCAAATTGTTTGAGAAGCATACTGGAA
TAAAAGTATCGATACCTATATACAAGTATCGATACTTGGTATTTACGCCTATTATCAATATACGG
TAG
Found at i:3145363 original size:397 final size:397
Alignment explanation
Indices: 3144631--3145645 Score: 1656
Period size: 397 Copynumber: 2.6 Consensus size: 397
3144621 TTCTATCCAT
3144631 ACTTTTACCGTTTACATTGTTAATTTCCTATTACTTTAAAGTAATAGGTTTTGAAATTTCAAGTA
1 ACTTTTACCGTTTACATTGTTAATTTCCTATTACTTTAAAGTAATAGGTTTTGAAATTTCAAGTA
* * *
3144696 TCGATACTTTATAGATATGTATTGATACATTTTGCATGCAAATTGTTTGATAAGCATACT-AAAT
66 TCGATACTTTATAGATATGTATCGATACATTTTGCATGCAAATTGTTTGAGAAGCATACTGGAAT
* * *
3144760 AAAAGTATTGATACCTATATACAAGTATCGATACTTGGTATTTACACCTATTATCAATATATCGG
131 AAAAGTATTGATACCTATATACAAGTATCGATACTTGGTATTTACGCCTATTATCAATATAACTG
*
3144825 TTGACTTTTATTGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCA
196 TTGACTTTTATCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCA
* * *
3144890 AGTATCGATACTTTATAGATATGTATCAATACATTTTGAGTGCAAATTGTTCGAGAAGCATACTG
261 AGTATCAATACTTTATAGATATGTATCAATACATTTTGAGTGCAAATTGTTCGAGAAACATACTA
* *
3144955 GAATAAAAGTATCGATACATATATACAAGTATCGATATTTGGTATTTACACATATTATCAATATA
326 GAATAAAAGTATCGATACATACATACAAGTATCGATACTTGGTATTTACACATATTATCAATATA
**
3145020 CTGGTAG
391 CCAGTAG
3145027 ACTTTTACCGTTTACATTGTTAATTTCCTATTACTTTAAAGTAATAGGTTTTGAAATTTCAAGTA
1 ACTTTTACCGTTTACATTGTTAATTTCCTATTACTTTAAAGTAATAGGTTTTGAAATTTCAAGTA
*
3145092 TCGATACTTTATAGATATGTATCGATACATTTTGCATGCAAATTGTTTGAGAAGCATATTGGAAT
66 TCGATACTTTATAGATATGTATCGATACATTTTGCATGCAAATTGTTTGAGAAGCATACTGGAAT
* *
3145157 AAAAGTATTGATACCTATATACAAGTATCGATACTTGGTATTTATGCCTATTATCAATACAACTG
131 AAAAGTATTGATACCTATATACAAGTATCGATACTTGGTATTTACGCCTATTATCAATATAACTG
3145222 TTGACTTTTATCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCA
196 TTGACTTTTATCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCA
* *
3145287 AGTATCAATACTTTATAGATGTGTATCAATACATTTTGCGTGCAAATTGTTCGAGAAACATACTA
261 AGTATCAATACTTTATAGATATGTATCAATACATTTTGAGTGCAAATTGTTCGAGAAACATACTA
* * * *
3145352 GAATAAAAGTATCGATACCTACATACAAGTATCTATACTTGGTATTTACGCCTATTATCAATATA
326 GAATAAAAGTATCGATACATACATACAAGTATCGATACTTGGTATTTACACATATTATCAATATA
3145417 CCAGTAG
391 CCAGTAG
* **
3145424 ACTTTTACC-TTTACCTTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCAAGT
1 ACTTTTACCGTTTACATTGTTAATTT-CCTATTACTTTAAAGTAATAGGTTTTGAAATTTCAAGT
* * * *
3145488 ATCGCTACTTTATAGATTTGTTTCGATACATTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAA
65 ATCGATACTTTATAGATATGTATCGATACATTTTGCATGCAAATTGTTTGAGAAGCATACTGGAA
* * * * *
3145553 TAGAAGTATCGATACATATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCAATATAATT
130 TAAAAGTATTGATACCTATATACAAGTATCGATACTTGGTATTTACGCCTATTATCAATATAACT
** * *
3145618 GTACACTTTTACCGTTTACATTATTAAT
195 GTTGACTTTTATCGTTTACATTGTTAAT
3145646 CTACGATTTT
Statistics
Matches: 575, Mismatches: 42, Indels: 3
0.93 0.07 0.00
Matches are distributed among these distances:
396 137 0.24
397 438 0.76
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (397 bp):
ACTTTTACCGTTTACATTGTTAATTTCCTATTACTTTAAAGTAATAGGTTTTGAAATTTCAAGTA
TCGATACTTTATAGATATGTATCGATACATTTTGCATGCAAATTGTTTGAGAAGCATACTGGAAT
AAAAGTATTGATACCTATATACAAGTATCGATACTTGGTATTTACGCCTATTATCAATATAACTG
TTGACTTTTATCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCA
AGTATCAATACTTTATAGATATGTATCAATACATTTTGAGTGCAAATTGTTCGAGAAACATACTA
GAATAAAAGTATCGATACATACATACAAGTATCGATACTTGGTATTTACACATATTATCAATATA
CCAGTAG
Found at i:3147348 original size:12 final size:12
Alignment explanation
Indices: 3147330--3147367 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
3147320 CCCCTACTAC
3147330 CTTCTCTTCTTT
1 CTTCTCTTCTTT
* *
3147342 GTTCTCTTCTTC
1 CTTCTCTTCTTT
3147354 CTTCTCTTCTTT
1 CTTCTCTTCTTT
3147366 CT
1 CT
3147368 CTTCTTCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.63
Consensus pattern (12 bp):
CTTCTCTTCTTT
Found at i:3147367 original size:21 final size:23
Alignment explanation
Indices: 3147329--3147383 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 23
3147319 CCCCCTACTA
3147329 CCTTCTCTTCTTTGTTCTCTTCTT
1 CCTTCTCTTC-TTGTTCTCTTCTT
3147353 CCTTCTCTTC-T-TTCTCTTCTT
1 CCTTCTCTTCTTGTTCTCTTCTT
*
3147374 CATTCTCTTC
1 CCTTCTCTTC
3147384 CTCCTTGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 19 0.63
22 1 0.03
24 10 0.33
ACGTcount: A:0.02, C:0.36, G:0.02, T:0.60
Consensus pattern (23 bp):
CCTTCTCTTCTTGTTCTCTTCTT
Found at i:3147373 original size:12 final size:12
Alignment explanation
Indices: 3147331--3147383 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
3147321 CCCTACTACC
3147331 TTCTCTTCTT-T
1 TTCTCTTCTTCT
3147342 GTTCTCTTCTTC-
1 -TTCTCTTCTTCT
*
3147354 CT-TC-TCTTCT
1 TTCTCTTCTTCT
*
3147364 TTCTCTTCTTCA
1 TTCTCTTCTTCT
3147376 TTCTCTTC
1 TTCTCTTC
3147384 CTCCTTGCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
9 5 0.15
10 3 0.09
11 3 0.09
12 23 0.68
ACGTcount: A:0.02, C:0.34, G:0.02, T:0.62
Consensus pattern (12 bp):
TTCTCTTCTTCT
Found at i:3149782 original size:177 final size:177
Alignment explanation
Indices: 3149464--3149915 Score: 565
Period size: 177 Copynumber: 2.6 Consensus size: 177
3149454 TTTTTCATTT
* * * * * *
3149464 TTTTAAATTCCTAAAGT-ACTGATA-TTATGGTACATATACTTGTAAAAGTA-C--TGATACTTT
1 TTTTAAATTCCTAAAGTAAC-GACACTT-CGGTACATATACTTATAAAAGTATCAATAAAAATTT
* * * * * * *
3149524 CAACAAATCTGGTATCGCTTTACAGGTTTTGTCAAATTTCAACCTATTATATTGTCATGTATTGA
64 CAACAATTATGGTAGCTCTTTACCGGTTTTGTCAAATTTCAACATATTATATTGTCATGTATCGA
* * *
3149589 TATATGTGTCTAAGGTATCGATACTTTATAGGCACTATTATTGCAATTC
129 TACATGTGTCTAAGGTATCAATACTTTATAGCCACTATTATTGCAATTC
*
3149638 TTTTAAATTCCTAAAGTACCGACACTTCGGTACATATACTTATAAAAGTATCAATAAAAAATTT-
1 TTTTAAATTCCTAAAGTAACGACACTTCGGTACATATACTTATAAAAGTATCAAT-AAAAATTTC
* *
3149702 AACCATTATGGTAGCTCTTTACCGGTTTTGTCAAATTTCAACATGTTATATTGTCATGTATCGAT
65 AACAATTATGGTAGCTCTTTACCGGTTTTGTCAAATTTCAACATATTATATTGTCATGTATCGAT
* *
3149767 ACATGTGTGTAAGGTATCAATACTTTATAGCCTCTATTATTGCAATTC
130 ACATGTGTCTAAGGTATCAATACTTTATAGCCACTATTATTGCAATTC
* * * * *
3149815 TTTTAAATTCCTAAAGTAACGATACTTTGGTATATATACTTATAAATGTATCAATACAAATTTCA
1 TTTTAAATTCCTAAAGTAACGACACTTCGGTACATATACTTATAAAAGTATCAATAAAAATTTCA
* * **
3149880 ACAATTTTGGTAGCTCATTACCAATTTTGTCAAATT
66 ACAATTATGGTAGCTCTTTACCGGTTTTGTCAAATT
3149916 GAAATCGATT
Statistics
Matches: 239, Mismatches: 32, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
174 41 0.17
175 4 0.02
176 7 0.03
177 182 0.76
178 5 0.02
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (177 bp):
TTTTAAATTCCTAAAGTAACGACACTTCGGTACATATACTTATAAAAGTATCAATAAAAATTTCA
ACAATTATGGTAGCTCTTTACCGGTTTTGTCAAATTTCAACATATTATATTGTCATGTATCGATA
CATGTGTCTAAGGTATCAATACTTTATAGCCACTATTATTGCAATTC
Found at i:3149926 original size:20 final size:20
Alignment explanation
Indices: 3149903--3149996 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 20
3149893 CTCATTACCA
3149903 ATTTTGTCAAATTGAAATCG
1 ATTTTGTCAAATTGAAATCG
* **
3149923 ATTTTGTCAATTTCCAATCG
1 ATTTTGTCAAATTGAAATCG
* * ** * *
3149943 GTTTTGTTAAATTCGTTACCT
1 ATTTTGTCAAATT-GAAATCG
*
3149964 ATTTTGTCAAATTGAAACTGG
1 ATTTTGTCAAATTGAAA-TCG
3149985 A-TTTGTCAAATT
1 ATTTTGTCAAATT
3149997 TCAGCCTATT
Statistics
Matches: 54, Mismatches: 18, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
20 40 0.74
21 14 0.26
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.45
Consensus pattern (20 bp):
ATTTTGTCAAATTGAAATCG
Found at i:3152759 original size:44 final size:44
Alignment explanation
Indices: 3152711--3152803 Score: 186
Period size: 44 Copynumber: 2.1 Consensus size: 44
3152701 TTCGAACTTC
3152711 TTATTCATATTTTTATTTTTATTTTTATTTAAGGTTGAATATTA
1 TTATTCATATTTTTATTTTTATTTTTATTTAAGGTTGAATATTA
3152755 TTATTCATATTTTTATTTTTATTTTTATTTAAGGTTGAATATTA
1 TTATTCATATTTTTATTTTTATTTTTATTTAAGGTTGAATATTA
3152799 TTATT
1 TTATT
3152804 TACGTATTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (44 bp):
TTATTCATATTTTTATTTTTATTTTTATTTAAGGTTGAATATTA
Found at i:3155865 original size:19 final size:19
Alignment explanation
Indices: 3155843--3155879 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3155833 TAGGGATTTA
*
3155843 TTTAATTTTAAAAAATATT
1 TTTAAATTTAAAAAATATT
*
3155862 TTTAAATTTAAAATATAT
1 TTTAAATTTAAAAAATAT
3155880 AATATACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTAAATTTAAAAAATATT
Found at i:3155893 original size:19 final size:20
Alignment explanation
Indices: 3155871--3155912 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
3155861 TTTTAAATTT
3155871 AAAATATATA-ATA-TACAAA
1 AAAATATA-ACATATTACAAA
3155890 AAAATATAACATATTACAAA
1 AAAATATAACATATTACAAA
3155910 AAA
1 AAA
3155913 TATCACTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.05
19 11 0.52
20 9 0.43
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAATATAACATATTACAAA
Found at i:3156191 original size:40 final size:41
Alignment explanation
Indices: 3156121--3156213 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 41
3156111 AAATAACCAA
3156121 CAAATTCGCAACGCGAACTCCAATTTCGCAACAC-AGTTTC
1 CAAATTCGCAACGCGAACTCCAATTTCGCAACACGAGTTTC
* * * * * *
3156161 CAAATTCGCAACTCGAATTTC-TTTTCCGCAACGCGATTTTC
1 CAAATTCGCAACGCGAACTCCAATTT-CGCAACACGAGTTTC
3156202 CAAATTCGCAAC
1 CAAATTCGCAAC
3156214 ACAGAAGTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 3 0.07
40 25 0.56
41 17 0.38
ACGTcount: A:0.30, C:0.31, G:0.12, T:0.27
Consensus pattern (41 bp):
CAAATTCGCAACGCGAACTCCAATTTCGCAACACGAGTTTC
Found at i:3156721 original size:20 final size:20
Alignment explanation
Indices: 3156658--3156726 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
3156648 TTTGAAACTT
* *
3156658 AAATTTGCAACACGAAAATG
1 AAATTCGCAACGCGAAAATG
*
3156678 AAATTCGCAA--C-ACAA--
1 AAATTCGCAACGCGAAAATG
3156693 AAA-TCGCAACGCGAAAATG
1 AAATTCGCAACGCGAAAATG
3156712 AAATTCGCAACGCGA
1 AAATTCGCAACGCGA
3156727 TTTTAGTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 6 0.15
15 3 0.08
16 1 0.03
17 6 0.15
18 1 0.03
19 3 0.08
20 20 0.50
ACGTcount: A:0.48, C:0.22, G:0.16, T:0.14
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATG
Found at i:3156746 original size:20 final size:21
Alignment explanation
Indices: 3156726--3156776 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
3156716 TCGCAACGCG
*
3156726 ATTTTAGTTTTCGCGTTGCGA
1 ATTTAAGTTTTCGCGTTGCGA
* *
3156747 ATTTCA-TTTTCGTGTTGCGA
1 ATTTAAGTTTTCGCGTTGCGA
3156767 ATTTAAGTTT
1 ATTTAAGTTT
3156777 CAAAAACTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.18, C:0.12, G:0.20, T:0.51
Consensus pattern (21 bp):
ATTTAAGTTTTCGCGTTGCGA
Found at i:3160845 original size:21 final size:22
Alignment explanation
Indices: 3160750--3160853 Score: 97
Period size: 21 Copynumber: 4.7 Consensus size: 22
3160740 GTACCATCAT
* *
3160750 GGGGTATCGATACCCATTCAAGGG
1 GGGGTATCGATACCTATTCAA--A
* *
3160774 GGGGTATCAATACCTATT-GAA
1 GGGGTATCGATACCTATTCAAA
*
3160795 GAGGTATCGATACCTATTCAAA
1 GGGGTATCGATACCTATTCAAA
*
3160817 GGGGGTATCGATACC-ATTCTCAA
1 -GGGGTATCGATACCTATTC-AAA
3160840 -GGGTATCGATACCT
1 GGGGTATCGATACCT
3160854 TATGCACAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
21 29 0.43
22 6 0.09
23 16 0.24
24 16 0.24
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (22 bp):
GGGGTATCGATACCTATTCAAA
Found at i:3160845 original size:44 final size:44
Alignment explanation
Indices: 3160751--3160853 Score: 129
Period size: 44 Copynumber: 2.3 Consensus size: 44
3160741 TACCATCATG
* * *
3160751 GGGTATCGATACCCATTCAAGGGGGGGTATCAATACCTATTGAA
1 GGGTATCGATACCTATTCAAGAGGGGGTATCAATACCTATTCAA
*
3160795 GAGGTATCGATACCTATTCAA-AGGGGGTATCGATACC-ATTCTCAA
1 G-GGTATCGATACCTATTCAAGAGGGGGTATCAATACCTA-T-TCAA
3160840 GGGTATCGATACCT
1 GGGTATCGATACCT
3160854 TATGCACAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
43 1 0.02
44 29 0.56
45 22 0.42
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (44 bp):
GGGTATCGATACCTATTCAAGAGGGGGTATCAATACCTATTCAA
Found at i:3164682 original size:22 final size:21
Alignment explanation
Indices: 3164640--3164679 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3164630 GAGTTTATTT
*
3164640 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3164661 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3164680 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3166633 original size:20 final size:19
Alignment explanation
Indices: 3166608--3166681 Score: 87
Period size: 19 Copynumber: 3.7 Consensus size: 19
3166598 ATATGCCTTA
*
3166608 GGGTATCGGTACCATCTGAG
1 GGGTATCGATACCAT-TGAG
3166628 GGGTATCGATACCATTGCATGG
1 GGGTATCGATACCATTG-A--G
3166650 GGGTATCGATACC-TATGAG
1 GGGTATCGATACCAT-TGAG
3166669 GGGTATCGATACC
1 GGGTATCGATACC
3166682 TTTCGAGCAT
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
19 16 0.33
20 15 0.31
21 2 0.04
22 16 0.33
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (19 bp):
GGGTATCGATACCATTGAG
Found at i:3166763 original size:20 final size:21
Alignment explanation
Indices: 3166722--3166776 Score: 94
Period size: 20 Copynumber: 2.7 Consensus size: 21
3166712 AAGTGTTACA
*
3166722 GGGGTATCGGTACCCTATAAG
1 GGGGTATCGATACCCTATAAG
3166743 GGGGTATCGATACCCTA-AAG
1 GGGGTATCGATACCCTATAAG
3166763 GGGGTATCGATACC
1 GGGGTATCGATACC
3166777 ATACTAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.22
Consensus pattern (21 bp):
GGGGTATCGATACCCTATAAG
Found at i:3168075 original size:42 final size:42
Alignment explanation
Indices: 3167991--3168088 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
3167981 CCCCCCACTT
* * * *
3167991 CGAGAGCCATCACCTGATCGAGCCAATTCTATAGCTCTACAC
1 CGAGAACCATCACCTGATCGAGCCAATTATATACCTCGACAC
* *
3168033 CGAGAATCATCACCTGATCGAGCCGATTAT-TCACCTCGACAC
1 CGAGAACCATCACCTGATCGAGCCAATTATAT-ACCTCGACAC
*
3168075 CGAGAGCCATCACC
1 CGAGAACCATCACC
3168089 CATTCCATCA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.02
42 46 0.98
ACGTcount: A:0.29, C:0.35, G:0.17, T:0.19
Consensus pattern (42 bp):
CGAGAACCATCACCTGATCGAGCCAATTATATACCTCGACAC
Found at i:3168239 original size:21 final size:21
Alignment explanation
Indices: 3168204--3168256 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3168194 GTTAGGGGAG
* * *
3168204 TTACGTAATGAGGTCAGTGCT
1 TTACGTGACGAGGTCAGTACT
* *
3168225 TTGCGTGACGAGGTCGGTACT
1 TTACGTGACGAGGTCAGTACT
3168246 TTACGTGACGA
1 TTACGTGACGA
3168257 TAATGGTGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (21 bp):
TTACGTGACGAGGTCAGTACT
Found at i:3168518 original size:4 final size:4
Alignment explanation
Indices: 3168509--3168550 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
3168499 TTTTTTGGTA
* * *
3168509 TTAT TTAT TTAT TTAT TTAC TTAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
3168551 TTAGCGGCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:3168721 original size:21 final size:21
Alignment explanation
Indices: 3168695--3168766 Score: 126
Period size: 21 Copynumber: 3.4 Consensus size: 21
3168685 ATTCACCTGT
3168695 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
3168716 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* *
3168737 CATCGTTCAAGAGGCCCTTTC
1 CATCGTTCAAGAGGCCCCTCC
3168758 CATCGTTCA
1 CATCGTTCA
3168767 GGATCCACAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.19, C:0.39, G:0.18, T:0.24
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:3170301 original size:20 final size:20
Alignment explanation
Indices: 3170278--3170321 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
3170268 TAGAAAATCG
3170278 AATTCGCAACGAGAAAGTCA
1 AATTCGCAACGAGAAAGTCA
3170298 AATTCGCAACGAGAAAGTCA
1 AATTCGCAACGAGAAAGTCA
3170318 AATT
1 AATT
3170322 TACGTTGCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (20 bp):
AATTCGCAACGAGAAAGTCA
Found at i:3172738 original size:12 final size:12
Alignment explanation
Indices: 3172721--3172745 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3172711 TCTTCGGGGA
3172721 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3172733 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3172745 C
1 C
3172746 AGGGTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3173815 original size:18 final size:19
Alignment explanation
Indices: 3173794--3173950 Score: 84
Period size: 20 Copynumber: 7.8 Consensus size: 19
3173784 AGAGGATGGA
3173794 TGAGTTGCG-ATTTGAAAT
1 TGAGTTGCGAATTTGAAAT
3173812 TGAGTTGCGAATTTGAAAT
1 TGAGTTGCGAATTTGAAAT
* *
3173831 TCCGTGTTGCAAATTTGGAAAAT
1 T--GAGTTGCGAATTT-G-AAAT
* * *
3173854 CGCGTTGCG-ATTCCAGAAAT
1 TGAGTTGCGAATT--TGAAAT
*
3173874 TGAGTTGTGAATTTGGGAAAT
1 TGAGTTGCGAATTT--GAAAT
* *
3173895 TCGCGTTGCGAATTTGAAAAC
1 T-GAGTTGCGAATTTG-AAAT
* * * *
3173916 TGTGTTGCGAAATTGGAGT
1 TGAGTTGCGAATTTGAAAT
*
3173935 TCGCGTTGCGAATTTG
1 T-GAGTTGCGAATTTG
3173951 TTGGTTATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
18 9 0.08
19 12 0.11
20 38 0.36
21 31 0.29
22 12 0.11
23 4 0.04
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.34
Consensus pattern (19 bp):
TGAGTTGCGAATTTGAAAT
Found at i:3173845 original size:21 final size:19
Alignment explanation
Indices: 3173794--3173847 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 19
3173784 AGAGGATGGA
*
3173794 TGAGTTGC-GATTTGAAAT
1 TGAGTTGCAAATTTGAAAT
*
3173812 TGAGTTGCGAATTTGAAAT
1 TGAGTTGCAAATTTGAAAT
*
3173831 TCCGTGTTGCAAATTTG
1 T--GAGTTGCAAATTTG
3173848 GAAAATCGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.27
19 10 0.33
21 12 0.40
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (19 bp):
TGAGTTGCAAATTTGAAAT
Found at i:3173861 original size:42 final size:41
Alignment explanation
Indices: 3173803--3173950 Score: 121
Period size: 42 Copynumber: 3.6 Consensus size: 41
3173793 ATGAGTTGCG
*
3173803 ATTT-GAAATT-GAGTTGCGAATTTGAAATTCCGTGTTGCAA
1 ATTTGGAAATTCGCGTTGCGAATTTGAAATT-CGTGTTGCAA
* * * **
3173843 ATTTGGAAAATCGCGTTGCG-ATTCCAGAAATT-GAGTTGTGA
1 ATTTGGAAATTCGCGTTGCGAATT--TGAAATTCGTGTTGCAA
*
3173884 ATTTGGGAAATTCGCGTTGCGAATTTGAAA-ACTGTGTTGCGAA
1 ATTT-GGAAATTCGCGTTGCGAATTTGAAATTC-GTGTTGC-AA
*
3173927 A-TTGG-AGTTCGCGTTGCGAATTTG
1 ATTTGGAAATTCGCGTTGCGAATTTG
3173951 TTGGTTATTT
Statistics
Matches: 86, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
40 22 0.26
41 24 0.28
42 29 0.34
43 11 0.13
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.34
Consensus pattern (41 bp):
ATTTGGAAATTCGCGTTGCGAATTTGAAATTCGTGTTGCAA
Found at i:3174337 original size:7 final size:7
Alignment explanation
Indices: 3174325--3174354 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
3174315 TTTAAATATT
3174325 ATTTTAA
1 ATTTTAA
3174332 ATTTTAA
1 ATTTTAA
3174339 ATTTTAA
1 ATTTTAA
3174346 ATTTTAA
1 ATTTTAA
3174353 AT
1 AT
3174355 ATACAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTTTAA
Found at i:3176366 original size:6 final size:6
Alignment explanation
Indices: 3176355--3176382 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3176345 ATAAGTATTT
3176355 GCATCA GCATCA GCATCA GCATCA GCAT
1 GCATCA GCATCA GCATCA GCATCA GCAT
3176383 ATCCATCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (6 bp):
GCATCA
Found at i:3183443 original size:14 final size:14
Alignment explanation
Indices: 3183424--3183453 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3183414 TCATCTATTA
3183424 CTTTAGTTCTTTAC
1 CTTTAGTTCTTTAC
3183438 CTTTAGTTCTTTAC
1 CTTTAGTTCTTTAC
3183452 CT
1 CT
3183454 GTTTGCAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.23, G:0.07, T:0.57
Consensus pattern (14 bp):
CTTTAGTTCTTTAC
Found at i:3185958 original size:318 final size:317
Alignment explanation
Indices: 3185382--3186012 Score: 1199
Period size: 318 Copynumber: 2.0 Consensus size: 317
3185372 ATGTTTAAAC
*
3185382 AATGAGAAGTAGAGAGTTGATAGTGTCCCCTTTTTTACTATCCAAATAAAATTGATAAAAAATTA
1 AATGAGAAGTAGAGAGTTGATAGTGTCCCCTTTTTTACTATCCAAATAAAATTAATAAAAAATTA
3185447 TAACAAATGAAATGATAGAGAACTTCAATCAAGCAAGCTTTTTTATGTCCGTAGCCTTGCAAGAA
66 TAACAAATGAAATGATAGAGAACTTCAATCAAGCAAGCTTTTTTATGTCCGTAGCCTTGCAAGAA
3185512 AGCACACTTAGGCACACCAAGTGTGCATCTGATCAAATAAACCTAGCTAAAAGGTGTTTGAGGCG
131 AGCACACTTAGGCACACCAAGTGTGCATCTGATCAAATAAACCTAGCTAAAAGGTGTTTGAGGCG
*
3185577 CTTTTGTTGTCTATTGCAAAGGCACGGCTCCTAGGCCAAAGCCTTGACAACAATGGTTTAAAAAA
196 CTTTTGTTGTCTACTGCAAAGGCACGGCTCCTAGGCCAAAGCCTTGACAACAATGGTTTAAAAAA
3185642 TCAAATTCCAAACCCTGTTCTCACCATATTCTTCTGATTTCTCTTATCCATCAGAAG
261 TCAAATTCCAAACCCTGTTCTCACCATATTCTTCTGATTTCTCTTATCCATCAGAAG
3185699 AATGAGAAGTAGAGAGTTGATAGTGTCCCCTTTTTTTACTATCCAAATAAAATTAATAAAAAATT
1 AATGAGAAGTAGAGAGTTGATAGTGTCCCC-TTTTTTACTATCCAAATAAAATTAATAAAAAATT
*
3185764 ATAACAAATGAAATGATAGAGAACTTCAATCAAGCAAGCTTTTTTATGTCTGTAGCCTTGCAAGA
65 ATAACAAATGAAATGATAGAGAACTTCAATCAAGCAAGCTTTTTTATGTCCGTAGCCTTGCAAGA
* *
3185829 AAGCGCACTTAGGCACACCAAGTGTGCATCTGATCAAATACACCTAGCTAAAAGGTGTTTGAGGC
130 AAGCACACTTAGGCACACCAAGTGTGCATCTGATCAAATAAACCTAGCTAAAAGGTGTTTGAGGC
3185894 GCTTTTGTTGTCTACTGCAAAGGCACGGCTCCTAGGCCAAAGCCTTGACAACAATGGTTTAAAAA
195 GCTTTTGTTGTCTACTGCAAAGGCACGGCTCCTAGGCCAAAGCCTTGACAACAATGGTTTAAAAA
*
3185959 ATCAAATTCCAAACCCTGTTCTCACCATTTTCTTCTGATTTCTCTTATCCATCA
260 ATCAAATTCCAAACCCTGTTCTCACCATATTCTTCTGATTTCTCTTATCCATCA
3186013 CATCAGCAGA
Statistics
Matches: 307, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
317 30 0.10
318 277 0.90
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Consensus pattern (317 bp):
AATGAGAAGTAGAGAGTTGATAGTGTCCCCTTTTTTACTATCCAAATAAAATTAATAAAAAATTA
TAACAAATGAAATGATAGAGAACTTCAATCAAGCAAGCTTTTTTATGTCCGTAGCCTTGCAAGAA
AGCACACTTAGGCACACCAAGTGTGCATCTGATCAAATAAACCTAGCTAAAAGGTGTTTGAGGCG
CTTTTGTTGTCTACTGCAAAGGCACGGCTCCTAGGCCAAAGCCTTGACAACAATGGTTTAAAAAA
TCAAATTCCAAACCCTGTTCTCACCATATTCTTCTGATTTCTCTTATCCATCAGAAG
Found at i:3187684 original size:12 final size:13
Alignment explanation
Indices: 3187646--3187700 Score: 78
Period size: 13 Copynumber: 4.4 Consensus size: 13
3187636 CATATATTCA
3187646 AATCTCTAAATTT
1 AATCTCTAAATTT
3187659 AATCTCTAAATTT
1 AATCTCTAAATTT
3187672 AATCTCT-AATTT
1 AATCTCTAAATTT
* *
3187684 ATTAT-TAAATTT
1 AATCTCTAAATTT
3187696 AATCT
1 AATCT
3187701 AAATTTAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
11 1 0.03
12 16 0.43
13 20 0.54
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (13 bp):
AATCTCTAAATTT
Found at i:3187697 original size:24 final size:24
Alignment explanation
Indices: 3187646--3187716 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 24
3187636 CATATATTCA
*
3187646 AATCTCTAAATTTAATCTCTAAATTT
1 AATCTCT-AATTTAATAT-TAAATTT
*
3187672 AATCTCTAATTTATTATTAAATTT
1 AATCTCTAATTTAATATTAAATTT
* *
3187696 AATCT-AAATTTAGTATTAAAT
1 AATCTCTAATTTAATATTAAAT
3187717 ACAATTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
23 14 0.34
24 12 0.29
25 8 0.20
26 7 0.17
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.48
Consensus pattern (24 bp):
AATCTCTAATTTAATATTAAATTT
Found at i:3187705 original size:11 final size:11
Alignment explanation
Indices: 3187650--3187707 Score: 55
Period size: 12 Copynumber: 4.9 Consensus size: 11
3187640 TATTCAAATC
3187650 TCTAAATTTAA
1 TCTAAATTTAA
3187661 TCTCTAAATTTAA
1 --TCTAAATTTAA
*
3187674 TCTCTAATTTATTA
1 TCT-AAATTTA--A
3187688 T-TAAATTTAA
1 TCTAAATTTAA
3187698 TCTAAATTTA
1 TCTAAATTTA
3187708 GTATTAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 2 0.05
11 11 0.28
12 12 0.31
13 12 0.31
14 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (11 bp):
TCTAAATTTAA
Found at i:3189531 original size:3 final size:3
Alignment explanation
Indices: 3189518--3189559 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
3189508 CTATAAAAAA
3189518 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3189560 ACATATATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3190545 original size:30 final size:30
Alignment explanation
Indices: 3190502--3190653 Score: 157
Period size: 30 Copynumber: 5.1 Consensus size: 30
3190492 GTAATAACTA
3190502 TTTAG-CCCTTTAAGTTTCTATTTTTTCTAT
1 TTTAGTCCC-TTAAGTTTCTATTTTTTCTAT
*
3190532 TTTAGTCCCTTAAGTTTCTATTTTTGCTAT
1 TTTAGTCCCTTAAGTTTCTATTTTTTCTAT
* * * *
3190562 ATTAGTCCTTTAAATGTCTATTTTTGT-TAT
1 TTTAGTCCCTTAAGTTTCTATTTTT-TCTAT
* * * * *
3190592 TTTAATCCTTTAAGTTTATGTTTTTGCTAT
1 TTTAGTCCCTTAAGTTTCTATTTTTTCTAT
* *
3190622 TTTAGCCCCTTAAGTTTC-AGTTTTTCTAT
1 TTTAGTCCCTTAAGTTTCTATTTTTTCTAT
3190651 TTT
1 TTT
3190654 GTACCTTTAA
Statistics
Matches: 99, Mismatches: 20, Indels: 7
0.79 0.16 0.06
Matches are distributed among these distances:
29 11 0.11
30 85 0.86
31 3 0.03
ACGTcount: A:0.18, C:0.14, G:0.09, T:0.58
Consensus pattern (30 bp):
TTTAGTCCCTTAAGTTTCTATTTTTTCTAT
Found at i:3190582 original size:60 final size:59
Alignment explanation
Indices: 3190499--3190653 Score: 188
Period size: 60 Copynumber: 2.6 Consensus size: 59
3190489 TTTGTAATAA
* *
3190499 CTATTTAGCCCTTTAAGTTTCTATTTTTTCTATTTTAGTCCCTTAAGTTTCTATTTTTG
1 CTATTTAGCCCTTTAAGTTTCTATTTTTTCTATTTTAATCCCTTAAGTTTATATTTTTG
* * * * *
3190558 CTATATTAGTCCTTTAAATGTCTATTTTTGT-TATTTTAATCCTTTAAGTTTATGTTTTTG
1 CTAT-TTAGCCCTTTAAGTTTCTATTTTT-TCTATTTTAATCCCTTAAGTTTATATTTTTG
* *
3190618 CTATTTTAGCCCCTTAAGTTTC-AGTTTTTCTATTTT
1 CTA-TTTAGCCCTTTAAGTTTCTATTTTTTCTATTTT
3190654 GTACCTTTAA
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
58 1 0.01
59 15 0.19
60 62 0.77
61 2 0.03
ACGTcount: A:0.19, C:0.15, G:0.09, T:0.57
Consensus pattern (59 bp):
CTATTTAGCCCTTTAAGTTTCTATTTTTTCTATTTTAATCCCTTAAGTTTATATTTTTG
Found at i:3190702 original size:30 final size:28
Alignment explanation
Indices: 3190498--3190704 Score: 108
Period size: 30 Copynumber: 7.0 Consensus size: 28
3190488 ATTTGTAATA
* * *
3190498 ACTATTTAGCCCTTTAAGTTTCTATTTTT
1 ACTATTTTGTCCTTTAAGTTTCT-GTTTT
* * *
3190527 TCTATTTTAGTCCCTTAAGTTTCTATTTTT
1 ACTATTTT-GTCCTTTAAGTTTCT-GTTTT
* * * * *
3190557 GCTATATTAGTCCTTTAAATGTCTATTTTT
1 ACTAT-TTTGTCCTTTAAGTTTCT-GTTTT
** * *
3190587 GTTATTTTAATCCTTTAAGTTTATGTTTTT
1 ACTATTTT-GTCCTTTAAGTTTCTG-TTTT
* * * *
3190617 GCTATTTTAGCCCCTTAAGTTTCAGTTTT
1 ACTATTTT-GTCCTTTAAGTTTCTGTTTT
* * *
3190646 TCTATTTTGTACCTTTAAATTCCTGTTTGT
1 ACTATTTTGT-CCTTTAAGTTTCTGTTT-T
*
3190676 ACTATTTTGGTCCTTTTAGTTTCTGTTTT
1 ACTATTTT-GTCCTTTAAGTTTCTGTTTT
3190705 CCCATTATGG
Statistics
Matches: 139, Mismatches: 32, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
28 1 0.01
29 33 0.24
30 101 0.73
31 4 0.03
ACGTcount: A:0.18, C:0.15, G:0.10, T:0.57
Consensus pattern (28 bp):
ACTATTTTGTCCTTTAAGTTTCTGTTTT
Found at i:3193139 original size:7 final size:7
Alignment explanation
Indices: 3193106--3193147 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
3193096 GGATCAATAT
3193106 TTTTGCA
1 TTTTGCA
3193113 -TTTGCA
1 TTTTGCA
*
3193119 -TGTGCA
1 TTTTGCA
3193125 TATTTGCA
1 T-TTTGCA
3193133 TTTTGCA
1 TTTTGCA
3193140 TTTTGCA
1 TTTTGCA
3193147 T
1 T
3193148 CTACATTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 11 0.35
7 14 0.45
8 6 0.19
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.52
Consensus pattern (7 bp):
TTTTGCA
Found at i:3194515 original size:16 final size:17
Alignment explanation
Indices: 3194488--3194611 Score: 67
Period size: 16 Copynumber: 6.9 Consensus size: 17
3194478 AAGATCACAT
3194488 CAAAGCAAAGAAAAAAA
1 CAAAGCAAAGAAAAAAA
3194505 CAAAG-AAAGAAAAAAA
1 CAAAGCAAAGAAAAAAA
* *
3194521 GGAAAACAAAGAAAAAAGA
1 -CAAAGCAAAGAAAAAA-A
3194540 GCAAAGGAAAACAAAGGAAAAAAA
1 -CAAA-G----CAAA-GAAAAAAA
* *
3194564 CAAAGAGCATAGATAAAAA
1 C-AA-AGCAAAGAAAAAAA
* *
3194583 -AAAGCAAAGAGAAGAA
1 CAAAGCAAAGAAAAAAA
3194599 -AAAGCAAA-AAAAA
1 CAAAGCAAAGAAAAA
3194612 GAAGACAATA
Statistics
Matches: 85, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
15 3 0.04
16 30 0.35
17 10 0.12
18 10 0.12
19 12 0.14
20 3 0.04
23 1 0.01
24 8 0.09
25 8 0.09
ACGTcount: A:0.73, C:0.08, G:0.17, T:0.02
Consensus pattern (17 bp):
CAAAGCAAAGAAAAAAA
Found at i:3194531 original size:18 final size:16
Alignment explanation
Indices: 3194493--3194537 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
3194483 CACATCAAAG
*
3194493 CAAAGAAAAAAACAAA
1 CAAAGAAAAAAAAAAA
*
3194509 GAAAGAAAAAAAGGAAAA
1 CAAAGAAAAAAA--AAAA
3194527 CAAAGAAAAAA
1 CAAAGAAAAAA
3194538 GAGCAAAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.46
18 13 0.54
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (16 bp):
CAAAGAAAAAAAAAAA
Found at i:3194538 original size:25 final size:24
Alignment explanation
Indices: 3194501--3194562 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
3194491 AGCAAAGAAA
*
3194501 AAAACAAAG-AAAGA-AAAAAAGG
1 AAAACAAAGAAAAAAGAAAAAAGG
**
3194523 AAAACAAAGAAAAAAGAGCAAAGG
1 AAAACAAAGAAAAAAGAAAAAAGG
3194547 AAAACAAAGGAAAAAA
1 AAAACAAA-GAAAAAA
3194563 ACAAAGAGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.26
23 4 0.12
24 14 0.41
25 7 0.21
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (24 bp):
AAAACAAAGAAAAAAGAAAAAAGG
Found at i:3195931 original size:35 final size:35
Alignment explanation
Indices: 3195884--3195978 Score: 122
Period size: 35 Copynumber: 2.7 Consensus size: 35
3195874 GGAAATTTTT
*
3195884 TTTTGTCTCGCTTGAGACAGTTTTCTA-AAAACAAA
1 TTTTGTCTCGCTTGAGACA-ATTTCTACAAAACAAA
*
3195919 TTTTGTCACGCTTGAGACAATTTCTATCAAAACAAA
1 TTTTGTCTCGCTTGAGACAATTTCTA-CAAAACAAA
* *
3195955 TTTCGTCTCACTTGAGAC-ATTTCT
1 TTTTGTCTCGCTTGAGACAATTTCT
3195979 TCTTTAAAAC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
34 6 0.11
35 24 0.45
36 23 0.43
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (35 bp):
TTTTGTCTCGCTTGAGACAATTTCTACAAAACAAA
Found at i:3195969 original size:36 final size:34
Alignment explanation
Indices: 3195888--3195978 Score: 112
Period size: 36 Copynumber: 2.6 Consensus size: 34
3195878 ATTTTTTTTT
* *
3195888 GTCTCGCTTGAGACAGTTTTCTAAAAACAAATTTT
1 GTCTCGCTTGAGACA-ATTTCTAAAAACAAATTTC
*
3195923 GTCACGCTTGAGACAATTTCTATCAAAACAAATTTC
1 GTCTCGCTTGAGACAATTTCTA--AAAACAAATTTC
*
3195959 GTCTCACTTGAGAC-ATTTCT
1 GTCTCGCTTGAGACAATTTCT
3195979 TCTTTAAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
34 6 0.12
35 20 0.41
36 23 0.47
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (34 bp):
GTCTCGCTTGAGACAATTTCTAAAAACAAATTTC
Found at i:3196100 original size:66 final size:64
Alignment explanation
Indices: 3196028--3196185 Score: 210
Period size: 66 Copynumber: 2.4 Consensus size: 64
3196018 AAAATTTATA
* **
3196028 ATCTTTGAGTCTGTTTCTCTTGAAACAAGTTTTGTCTCACTTGAGACAGTTTCTCTTGAAACACC
1 ATCTTTGAGTCTGTTTCCCTTGAAACAA-TTTTGTCTCACTTGAGACAACTTCTCTTGAAACA-C
3196093 C
64 C
* * *
3196094 ATCTTTGAGATC-GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAACTTCTCTTGAAGCAT
1 ATCTTTGAG-TCTGTTTCCCTTGAAAC-AATTTTGTCTCACTTGAGACAACTTCTCTTGAAACAC
3196158 C
64 C
*
3196159 ATCTTTGAGTCTGTTTCCCTTAAAACA
1 ATCTTTGAGTCTGTTTCCCTTGAAACA
3196186 TTATCCCTAA
Statistics
Matches: 82, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
64 3 0.04
65 23 0.28
66 52 0.63
67 4 0.05
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (64 bp):
ATCTTTGAGTCTGTTTCCCTTGAAACAATTTTGTCTCACTTGAGACAACTTCTCTTGAAACACC
Found at i:3196506 original size:135 final size:130
Alignment explanation
Indices: 3196188--3196542 Score: 388
Period size: 131 Copynumber: 2.7 Consensus size: 130
3196178 TTAAAACATT
* * * * *
3196188 ATCCCTAAAGATGGTTTACCGTCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCT
1 ATCCCTAAAGATGGTAT-GCATCCTCATCACGTAGGAATCGTGTCATCCACCGACCAGACCTCCT
* * * * * * ** *
3196253 CATCACGTAAGAGTCGAGTCACCCTTAGATAACCAGTCGTTCTCATCACGTAGGAACCGTGTTAT
65 CATCACGTAGGAGCCGAGTCACCCCTAGATAACCAATCGTCCACATCACGTAAAAACCGTGCTAT
3196318 C
130 C
* ** * * *
3196319 ATCCCTAAAAATGGCCTGCTATCTTCATCACGTAGGAATCGTGTCATCCACCGACCATACCTTCT
1 ATCCCTAAAGATGGTATGC-ATCCTCATCACGTAGGAATCGTGTCATCCACCGACCAGACCTCCT
* * *
3196384 CATCACGTAGGAGCCGTGTCACCCCTAGATAACCAATCGTCCACATTATGTATAAAACCGTGCTA
65 CATCACGTAGGAGCCGAGTCACCCCTAGATAACCAATCGTCCACATCACGTA-AAAACCGTGCTA
3196449 TC
129 TC
* * *
3196451 ACCCTCCCTAAAGATGGTATGTCATCCTCATCGCGTAGGAATTGTGTCATCCACCGACCAGATCT
1 A---TCCCTAAAGATGGTATG-CATCCTCATCACGTAGGAATCGTGTCATCCACCGACCAGACCT
*
3196516 CCTTATCACGTAGGAGCCGCA-TCACCC
62 CCTCATCACGTAGGAGCCG-AGTCACCC
3196543 TTAAAGACCA
Statistics
Matches: 184, Mismatches: 33, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
130 1 0.01
131 96 0.52
132 12 0.07
135 74 0.40
136 1 0.01
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (130 bp):
ATCCCTAAAGATGGTATGCATCCTCATCACGTAGGAATCGTGTCATCCACCGACCAGACCTCCTC
ATCACGTAGGAGCCGAGTCACCCCTAGATAACCAATCGTCCACATCACGTAAAAACCGTGCTATC
Found at i:3198283 original size:30 final size:30
Alignment explanation
Indices: 3198249--3198598 Score: 230
Period size: 30 Copynumber: 11.6 Consensus size: 30
3198239 TTGTAATTAT
*
3198249 TTTTAGCCCTTTAAGTTTATGA-TTTTGCTA
1 TTTTAGTCCTTTAAGTTTAT-ATTTTTGCTA
* * *
3198279 TTTTAGTCCTTTAAATGTCT-TTATTTGCTA
1 TTTTAGTCCTTTAAGTTTATATT-TTTGCTA
* * *
3198309 -TTTAGTCCATTT-AGTTTCTGTTTTTACTA
1 TTTTAGTCC-TTTAAGTTTATATTTTTGCTA
* * * *
3198338 TTTTAGTCCTTTAAATGTACATTTTTGTTA
1 TTTTAGTCCTTTAAGTTTATATTTTTGCTA
**
3198368 TTTTAGTTCC-TTAAGTTTATATTTTTTTATTA
1 TTTTAG-TCCTTTAAGTTTATA--TTTTTGCTA
* *
3198400 TTTTAGTCCTTTAAATGTCTAT-TTTTTTCTA
1 TTTTAGTCCTTT-AA-GTTTATATTTTTGCTA
* *
3198431 TTTTAGTCCCTTAAGTTTTTATTTTTGCTA
1 TTTTAGTCCTTTAAGTTTATATTTTTGCTA
* * * * * *
3198461 GTTTAGTCCTTTAAATGTCTGTTTTTGTTA
1 TTTTAGTCCTTTAAGTTTATATTTTTGCTA
* * *
3198491 TTTTAGTCCATTAAGTTTCTATTTTTACTA
1 TTTTAGTCCTTTAAGTTTATATTTTTGCTA
* * *
3198521 TTTTTGTCCCTTAAGTTT-TGATTTTTTCTA
1 TTTTAGTCCTTTAAGTTTAT-ATTTTTGCTA
* * * * *
3198551 TTTTGGACCTTTAAATTCT-TATTTGTACTA
1 TTTTAGTCCTTTAAGTT-TATATTTTTGCTA
* *
3198581 TTTTGGTCCTTTCAGTTT
1 TTTTAGTCCTTTAAGTTT
3198599 CTGTTTTTCC
Statistics
Matches: 254, Mismatches: 51, Indels: 31
0.76 0.15 0.09
Matches are distributed among these distances:
29 29 0.11
30 176 0.69
31 26 0.10
32 16 0.06
33 2 0.01
34 5 0.02
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.59
Consensus pattern (30 bp):
TTTTAGTCCTTTAAGTTTATATTTTTGCTA
Found at i:3198401 original size:32 final size:31
Alignment explanation
Indices: 3198359--3198456 Score: 108
Period size: 31 Copynumber: 3.1 Consensus size: 31
3198349 TAAATGTACA
*
3198359 TTTTTGTTATTTTAGTTCCTTAAGTTTATAT
1 TTTTTTTTATTTTAGTTCCTTAAGTTTATAT
* * *
3198390 TTTTTTATTATTTTAG-TCCTTTAAATGTCTAT
1 TTTTTT-TTATTTTAGTTCC-TTAAGTTTATAT
* * *
3198422 TTTTTTCTATTTTAGTCCCTTAAGTTTTTAT
1 TTTTTTTTATTTTAGTTCCTTAAGTTTATAT
3198453 TTTT
1 TTTT
3198457 GCTAGTTTAG
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
31 29 0.53
32 26 0.47
ACGTcount: A:0.18, C:0.09, G:0.07, T:0.65
Consensus pattern (31 bp):
TTTTTTTTATTTTAGTTCCTTAAGTTTATAT
Found at i:3198448 original size:123 final size:121
Alignment explanation
Indices: 3198277--3198516 Score: 340
Period size: 123 Copynumber: 2.0 Consensus size: 121
3198267 ATGATTTTGC
* * *
3198277 TATTTTAGTCCTTTAAATGTCTTTATTTGCTATTTAGTCCATTTAGTTTCTGTTTTTACTATTTT
1 TATTTTAGTCCTTTAAATGTCTTTATTTGCTATTTAGTCCATTAAGTTTCTATTTTTACTAGTTT
3198342 AGTCCTTTAAATGTAC-ATTTTTGTTATTTTAGTTCC-TTAAGTTTATATTTTTTTAT
66 AGTCCTTTAAATGT-CTATTTTTGTTATTTTAG-TCCATTAAGTTTATATTTTTTTAT
* * * * *
3198398 TATTTTAGTCCTTTAAATGTCTATTTTTTTCTATTTTAGTCCCTTAAGTTTTTATTTTTGCTAGT
1 TATTTTAGTCCTTTAAATGTCT-TTATTTGCTA-TTTAGTCCATTAAGTTTCTATTTTTACTAGT
* *
3198463 TTAGTCCTTTAAATGTCTGTTTTTGTTATTTTAGTCCATTAAGTTTCTATTTTT
64 TTAGTCCTTTAAATGTCTATTTTTGTTATTTTAGTCCATTAAGTTTATATTTTT
3198517 ACTATTTTTG
Statistics
Matches: 105, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
121 22 0.21
122 12 0.11
123 71 0.68
ACGTcount: A:0.20, C:0.11, G:0.10, T:0.60
Consensus pattern (121 bp):
TATTTTAGTCCTTTAAATGTCTTTATTTGCTATTTAGTCCATTAAGTTTCTATTTTTACTAGTTT
AGTCCTTTAAATGTCTATTTTTGTTATTTTAGTCCATTAAGTTTATATTTTTTTAT
Found at i:3198486 original size:153 final size:153
Alignment explanation
Indices: 3198271--3198552 Score: 342
Period size: 153 Copynumber: 1.8 Consensus size: 153
3198261 AAGTTTATGA
* * *
3198271 TTTTGCTATTTTAGTCCTTTAAATGTCTTTATTTGCTATTTAGTCCATTTAGTTTCTGTTTTTAC
1 TTTTGCTATTTTAGTCCCTTAAATGTCTTTATTTGCTATTTAGTCCATTTAATGTCTGTTTTTAC
* ** *
3198336 TATTTTAGTCCTTTAAATGTAC-ATTTTTGTTATTTTAGTTCCTTAAGTTTAT-ATTTTTT-TAT
66 TATTTTAGTCCATTAAAT-TACTATTTTTACTATTTTAGTCCCTTAAGTTT-TGATTTTTTCTAT
3198398 TATTTTAGTCCTTTAAATGTCTATT
129 TATTTTAGTCCTTTAAATGTCTATT
* *
3198423 TTTTTCTATTTTAGTCCCTT-AA-GTTTTTATTTTTGCTAGTTTAGTCC-TTTAAATGTCTGTTT
1 TTTTGCTATTTTAGTCCCTTAAATGTCTTTA--TTTGCTA-TTTAGTCCATTT-AATGTCTGTTT
** * * *
3198485 TTGTTATTTTAGTCCATTAAGTTTCTATTTTTACTATTTTTGTCCCTTAAGTTTTGATTTTTTCT
62 TTACTATTTTAGTCCATTAAATTACTATTTTTACTATTTTAGTCCCTTAAGTTTTGATTTTTTCT
3198550 ATT
127 ATT
3198553 TTGGACCTTT
Statistics
Matches: 109, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
150 6 0.06
151 2 0.02
152 31 0.28
153 66 0.61
154 4 0.04
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.60
Consensus pattern (153 bp):
TTTTGCTATTTTAGTCCCTTAAATGTCTTTATTTGCTATTTAGTCCATTTAATGTCTGTTTTTAC
TATTTTAGTCCATTAAATTACTATTTTTACTATTTTAGTCCCTTAAGTTTTGATTTTTTCTATTA
TTTTAGTCCTTTAAATGTCTATT
Found at i:3198514 original size:60 final size:60
Alignment explanation
Indices: 3198249--3198534 Score: 321
Period size: 60 Copynumber: 4.7 Consensus size: 60
3198239 TTGTAATTAT
* * * *
3198249 TTTTAGCCCTTTAAGTTTATGA-TTTTGCTATTTTAGTCCTTTAAATGTCT-TTATTTGCTA
1 TTTTAGTCCATTAAGTTTAT-ATTTTTACTATTTTAGTCCTTTAAATGTCTATT-TTTGTTA
* * *
3198309 -TTTAGTCCATTTAGTTTCTGTTTTTACTATTTTAGTCCTTTAAATGTAC-ATTTTTGTTA
1 TTTTAGTCCATTAAGTTTATATTTTTACTATTTTAGTCCTTTAAATGT-CTATTTTTGTTA
* *
3198368 TTTTAGTTCC-TTAAGTTTATATTTTTTTATTATTTTAGTCCTTTAAATGTCTATTTTTTTCTA
1 TTTTAG-TCCATTAAGTTTATA--TTTTTACTATTTTAGTCCTTTAAATGTCTATTTTTGT-TA
* * * * *
3198431 TTTTAGTCCCTTAAGTTTTTATTTTTGCTAGTTTAGTCCTTTAAATGTCTGTTTTTGTTA
1 TTTTAGTCCATTAAGTTTATATTTTTACTATTTTAGTCCTTTAAATGTCTATTTTTGTTA
* * *
3198491 TTTTAGTCCATTAAGTTTCTATTTTTACTATTTTTGTCCCTTAA
1 TTTTAGTCCATTAAGTTTATATTTTTACTATTTTAGTCCTTTAA
3198535 GTTTTGATTT
Statistics
Matches: 192, Mismatches: 24, Indels: 20
0.81 0.10 0.08
Matches are distributed among these distances:
59 46 0.24
60 56 0.29
61 36 0.19
62 36 0.19
63 18 0.09
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.58
Consensus pattern (60 bp):
TTTTAGTCCATTAAGTTTATATTTTTACTATTTTAGTCCTTTAAATGTCTATTTTTGTTA
Found at i:3198539 original size:90 final size:89
Alignment explanation
Indices: 3198249--3198606 Score: 332
Period size: 90 Copynumber: 4.0 Consensus size: 89
3198239 TTGTAATTAT
*
3198249 TTTTAG-CCCTTTAAGTTTATGA-TTTTGCTATTTTAGTCCTTTAAATGTCTTTATTTGCTA-TT
1 TTTTAGTCCC-TTAAGTTT-TGATTTTTGCTATTTTAGTCCTTTAAATGTCTTT-TTTGTTATTT
* *
3198311 TAGTCCATTTAGTTTCTGTTTTTACTA
63 TAGTCCATTAAGTTTCTATTTTTACTA
* * * ** * * *
3198338 TTTTAGTCCTTTAAATGTACATTTTTGTTATTTTAGTTCC-TTAAGTTTATAT-TTTTTTATTAT
1 TTTTAGTCCCTTAAGTTTTGATTTTTGCTATTTTAG-TCCTTTAA----ATGTCTTTTTTGTTAT
* * * *
3198401 TTTAGTCCTTTAAATGTCTATTTTTTTCTA
61 TTTAGTCCATTAAGTTTCTA-TTTTTACTA
* *
3198431 TTTTAGTCCCTTAAGTTTTTATTTTTGCTAGTTTAGTCCTTTAAATGTCTGTTTTTGTTATTTTA
1 TTTTAGTCCCTTAAGTTTTGATTTTTGCTATTTTAGTCCTTTAAATGTCT-TTTTTGTTATTTTA
3198496 GTCCATTAAGTTTCTATTTTTACTA
65 GTCCATTAAGTTTCTATTTTTACTA
* * * * *
3198521 TTTTTGTCCCTTAAGTTTTGATTTTTTCTATTTTGGACCTTTAAAT-TCTTATTTGTACTATTTT
1 TTTTAGTCCCTTAAGTTTTGATTTTTGCTATTTTAGTCCTTTAAATGTCTTTTTTGT--TATTTT
* * * *
3198585 GGTCCTTTCAGTTTCTGTTTTT
64 AGTCCATTAAGTTTCTATTTTT
3198607 CCCATTCTGG
Statistics
Matches: 216, Mismatches: 39, Indels: 27
0.77 0.14 0.10
Matches are distributed among these distances:
88 7 0.03
89 35 0.16
90 78 0.36
91 31 0.14
92 21 0.10
93 44 0.20
ACGTcount: A:0.18, C:0.12, G:0.10, T:0.59
Consensus pattern (89 bp):
TTTTAGTCCCTTAAGTTTTGATTTTTGCTATTTTAGTCCTTTAAATGTCTTTTTTGTTATTTTAG
TCCATTAAGTTTCTATTTTTACTA
Found at i:3198546 original size:60 final size:61
Alignment explanation
Indices: 3198249--3198592 Score: 271
Period size: 60 Copynumber: 5.7 Consensus size: 61
3198239 TTGTAATTAT
* * * * *
3198249 TTTTAGCCCTTTAAGTTTATGA-TTTTGCTATTTTAGTCCTTTAAATGTCTT--TATTTG-CTA
1 TTTTAGTCCATTAAGTTTCT-ATTTTTACTATTTTAGTCCTTTAAAT-T-TTGATTTTTGTCTA
* * * **
3198309 -TTTAGTCCATTTAGTTTCTGTTTTTACTATTTTAGTCCTTTAAATGTACATTTTTGT-TA
1 TTTTAGTCCATTAAGTTTCTATTTTTACTATTTTAGTCCTTTAAATTTTGATTTTTGTCTA
* * * *
3198368 TTTTAGTTCC-TTAAGTTTATATTTTTTTATTATTTTAGTCCTTTAAATGTCT-ATTTTTTTCTA
1 TTTTAG-TCCATTAAGTTTCTA--TTTTTACTATTTTAGTCCTTTAAAT-TTTGATTTTTGTCTA
* * * * *
3198431 TTTTAGTCCCTTAAGTTTTTATTTTTGCTAGTTTAGTCCTTTAAATGTCTG-TTTTTGT-TA
1 TTTTAGTCCATTAAGTTTCTATTTTTACTATTTTAGTCCTTTAAAT-TTTGATTTTTGTCTA
* * *
3198491 TTTTAGTCCATTAAGTTTCTATTTTTACTATTTTTGTCCCTTAAGTTTTGATTTTT-TCTA
1 TTTTAGTCCATTAAGTTTCTATTTTTACTATTTTAGTCCTTTAAATTTTGATTTTTGTCTA
* * * * * *
3198551 TTTTGGACCTTTAA-ATTCTTATTTGTACTATTTTGGTCCTTT
1 TTTTAGTCCATTAAGTTTC-TATTTTTACTATTTTAGTCCTTT
3198593 CAGTTTCTGT
Statistics
Matches: 232, Mismatches: 37, Indels: 30
0.78 0.12 0.10
Matches are distributed among these distances:
57 1 0.00
59 52 0.22
60 92 0.40
61 35 0.15
62 34 0.15
63 18 0.08
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.59
Consensus pattern (61 bp):
TTTTAGTCCATTAAGTTTCTATTTTTACTATTTTAGTCCTTTAAATTTTGATTTTTGTCTA
Found at i:3199627 original size:22 final size:22
Alignment explanation
Indices: 3199599--3199647 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
3199589 ATTGAAGTTT
3199599 AAATCGTTATATCATTCATTTC
1 AAATCGTTATATCATTCATTTC
*
3199621 AAATCGTTATATCATTCGTTTC
1 AAATCGTTATATCATTCATTTC
3199643 AAATC
1 AAATC
3199648 ATTAACTCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (22 bp):
AAATCGTTATATCATTCATTTC
Found at i:3200798 original size:15 final size:16
Alignment explanation
Indices: 3200767--3200800 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3200757 TATTTAATGA
3200767 TTAAAATATTATTTAT
1 TTAAAATATTATTTAT
*
3200783 TTAATATATT-TTTAT
1 TTAAAATATTATTTAT
3200798 TTA
1 TTA
3200801 TTCAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTAAAATATTATTTAT
Found at i:3201337 original size:29 final size:29
Alignment explanation
Indices: 3201258--3201339 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
3201248 AACATTCTAG
*
3201258 TTATAATCAAGTCATTAAATCTATCAATTA
1 TTATAATCAAGTCACTAAAT-TATCAATTA
* * * * * *
3201288 TAACAAGCAAGTTACTCAATTATCGATTA
1 TTATAATCAAGTCACTAAATTATCAATTA
*
3201317 TTATAATCAGGTCACTAAATTAT
1 TTATAATCAAGTCACTAAATTAT
3201340 AATAAGAAGG
Statistics
Matches: 39, Mismatches: 13, Indels: 1
0.74 0.25 0.02
Matches are distributed among these distances:
29 25 0.64
30 14 0.36
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (29 bp):
TTATAATCAAGTCACTAAATTATCAATTA
Found at i:3204753 original size:3 final size:3
Alignment explanation
Indices: 3204747--3204883 Score: 56
Period size: 3 Copynumber: 45.7 Consensus size: 3
3204737 ATATTACGTT
*
3204747 TTA TTA TATA TATA TTA CTA TTA TTA TTA TTA TTA -TA TGTA TATA TATA
1 TTA TTA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA T-TA
* * * *
3204796 TATA TTTA TT- TCA TT- TTA -TA CTC TT- TTA TTA TTT TTA TT- TT-
1 T-TA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* ** * *
3204837 TTA TTA TTA TTC TT- TATA TTA TCC TTA TTA TTT TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3204882 TT
1 TT
3204884 TTTTTTACTT
Statistics
Matches: 105, Mismatches: 18, Indels: 22
0.72 0.12 0.15
Matches are distributed among these distances:
2 14 0.13
3 67 0.64
4 23 0.22
5 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3204760 original size:21 final size:19
Alignment explanation
Indices: 3204733--3204801 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 19
3204723 AAATCTTTTT
*
3204733 TTATATATTACGTTTTATTA
1 TTATATATTAC-TATTATTA
3204753 TATATATATTACTATTATTA
1 T-TATATATTACTATTATTA
3204773 TTAT-TATTA-TATGTATATA
1 TTATATATTACTAT-TAT-TA
3204792 TATATATATT
1 T-TATATATT
3204802 TATTTCATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
17 3 0.07
18 8 0.19
19 6 0.14
20 12 0.28
21 14 0.33
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (19 bp):
TTATATATTACTATTATTA
Found at i:3204773 original size:23 final size:20
Alignment explanation
Indices: 3204733--3204784 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 20
3204723 AAATCTTTTT
*
3204733 TTATATATTACGTTTTATTA
1 TTATATATTACATTTTATTA
3204753 TATATATATTACTATTATTATTA
1 T-TATATATTAC-ATT-TTATTA
3204776 TTATTATAT
1 TTA-TATAT
3204785 GTATATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 1 0.04
21 10 0.37
22 4 0.15
23 12 0.44
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (20 bp):
TTATATATTACATTTTATTA
Found at i:3204840 original size:13 final size:13
Alignment explanation
Indices: 3204819--3204887 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
3204809 TTTTATACTC
*
3204819 TTTTATTATTTTTA
1 TTTT-TTATTATTA
3204833 TTTTTTATTATTA
1 TTTTTTATTATTA
*
3204846 TTCTTTA-TATTA
1 TTTTTTATTATTA
**
3204858 -TCCTTATTATT-
1 TTTTTTATTATTA
* *
3204869 TTTATTATTACTA
1 TTTTTTATTATTA
3204882 TTTTTT
1 TTTTTT
3204888 TTACTTATCT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
11 5 0.11
12 17 0.38
13 19 0.42
14 4 0.09
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTATTATTA
Found at i:3205376 original size:21 final size:20
Alignment explanation
Indices: 3205335--3205383 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
3205325 TTTTTTCATA
* **
3205335 TTTTATTATTTTATTGCTAT
1 TTTTTTTATTTTATTAATAT
3205355 TTTTTTTATTTTATTTAATAT
1 TTTTTTTATTTTA-TTAATAT
3205376 TTGTTTTT
1 TT-TTTTT
3205384 GTATTTGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 12 0.50
21 7 0.29
22 5 0.21
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (20 bp):
TTTTTTTATTTTATTAATAT
Found at i:3205469 original size:26 final size:27
Alignment explanation
Indices: 3205440--3205514 Score: 86
Period size: 26 Copynumber: 2.9 Consensus size: 27
3205430 AATTAATTAG
3205440 TTTA-TTGTTTATTTGTTTATTTTTAT
1 TTTATTTGTTTATTTGTTTATTTTTAT
* *
3205466 TTTATTTGTTTATTAT-CTTA-TCTTAT
1 TTTATTTGTTTATT-TGTTTATTTTTAT
*
3205492 TTTATTTGTTTA-TTGTTTGTTTT
1 TTTATTTGTTTATTTGTTTATTTT
3205515 ATCTTTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
24 1 0.03
25 3 0.08
26 23 0.57
27 12 0.30
28 1 0.03
ACGTcount: A:0.15, C:0.03, G:0.08, T:0.75
Consensus pattern (27 bp):
TTTATTTGTTTATTTGTTTATTTTTAT
Found at i:3205471 original size:19 final size:21
Alignment explanation
Indices: 3205447--3205493 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
3205437 TAGTTTATTG
3205447 TTTATTTGTTTATT-T-TTAT
1 TTTATTTGTTTATTATCTTAT
3205466 TTTATTTGTTTATTATCTTAT
1 TTTATTTGTTTATTATCTTAT
*
3205487 CTTATTT
1 TTTATTT
3205494 TATTTGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 14 0.56
20 1 0.04
21 10 0.40
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (21 bp):
TTTATTTGTTTATTATCTTAT
Found at i:3209209 original size:39 final size:39
Alignment explanation
Indices: 3209155--3209233 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
3209145 CACCCGGAGT
* *
3209155 ATTACCCGGGGACTCATCCGCTACTAAAGGGAAAGCTGC
1 ATTACCCGGGGACTCATCCGCTACCAAAGCGAAAGCTGC
* *
3209194 ATTACCTGGGGACTCATCCGCTACCAAAGCGAAAGTTGC
1 ATTACCCGGGGACTCATCCGCTACCAAAGCGAAAGCTGC
3209233 A
1 A
3209234 CCTACTGTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.19
Consensus pattern (39 bp):
ATTACCCGGGGACTCATCCGCTACCAAAGCGAAAGCTGC
Found at i:3218240 original size:23 final size:23
Alignment explanation
Indices: 3218211--3218267 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
3218201 TATATTTTAA
* *
3218211 TAAATAAAATCTTACTATAACTC
1 TAAATAAAATCATACTAAAACTC
* *
3218234 TAAATAAAACCATACTAAAATTC
1 TAAATAAAATCATACTAAAACTC
3218257 TAAATAAAATC
1 TAAATAAAATC
3218268 CTAGTCCTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAATAAAATCATACTAAAACTC
Found at i:3220202 original size:16 final size:16
Alignment explanation
Indices: 3220178--3220212 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3220168 ACATAAAATT
3220178 AAAAATTAATGGTTAG
1 AAAAATTAATGGTTAG
* *
3220194 AAAAGTTAATTGTTAG
1 AAAAATTAATGGTTAG
3220210 AAA
1 AAA
3220213 TTAGTAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.31
Consensus pattern (16 bp):
AAAAATTAATGGTTAG
Found at i:3225030 original size:61 final size:60
Alignment explanation
Indices: 3224916--3225031 Score: 223
Period size: 61 Copynumber: 1.9 Consensus size: 60
3224906 CGTAAGTGTC
3224916 TTGTTAGTGTCGCCCATTCTGAAATCAAACACTCAAAAGAAAATTTTAAAGTAAATAATG
1 TTGTTAGTGTCGCCCATTCTGAAATCAAACACTCAAAAGAAAATTTTAAAGTAAATAATG
3224976 TTGTTAGTGTCGCCCATTCTGAAATCATAACACTCAAAAGAAAATTTTAAAGTAAA
1 TTGTTAGTGTCGCCCATTCTGAAATCA-AACACTCAAAAGAAAATTTTAAAGTAAA
3225032 ATAAAAATAA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 27 0.49
61 28 0.51
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (60 bp):
TTGTTAGTGTCGCCCATTCTGAAATCAAACACTCAAAAGAAAATTTTAAAGTAAATAATG
Found at i:3225901 original size:15 final size:15
Alignment explanation
Indices: 3225883--3225931 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 15
3225873 AAATTTTGGC
3225883 TTTTTTGGCTCTTTTT
1 TTTTTTGGC-CTTTTT
*
3225899 TTTTTTTGCC---TT
1 TTTTTTGGCCTTTTT
3225911 TTTTTT-GCCTTTTT
1 TTTTTTGGCCTTTTT
3225925 TTTTTTG
1 TTTTTTG
3225932 AAAAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
11 3 0.11
12 8 0.29
14 8 0.29
15 1 0.04
16 8 0.29
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (15 bp):
TTTTTTGGCCTTTTT
Found at i:3225903 original size:17 final size:15
Alignment explanation
Indices: 3225883--3225916 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3225873 AAATTTTGGC
*
3225883 TTTTTTGGCTCTTTTT
1 TTTTTTTGC-CTTTTT
3225899 TTTTTTTGCCTTTTT
1 TTTTTTTGCCTTTTT
3225914 TTT
1 TTT
3225917 GCCTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (15 bp):
TTTTTTTGCCTTTTT
Found at i:3225912 original size:11 final size:11
Alignment explanation
Indices: 3225898--3225927 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
3225888 TGGCTCTTTT
3225898 TTTTTTTTGCC
1 TTTTTTTTGCC
3225909 TTTTTTTTGCC
1 TTTTTTTTGCC
3225920 TTTTTTTT
1 TTTTTTTT
3225928 TTTGAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (11 bp):
TTTTTTTTGCC
Found at i:3225930 original size:17 final size:17
Alignment explanation
Indices: 3225883--3225916 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3225873 AAATTTTGGC
*
3225883 TTTTTTGGCTCTTTTTT
1 TTTTTTGCCTCTTTTTT
3225900 TTTTTTGCCT-TTTTTT
1 TTTTTTGCCTCTTTTTT
3225916 T
1 T
3225917 GCCTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (17 bp):
TTTTTTGCCTCTTTTTT
Done.