Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 65 of 210
Found at i:19554131 original size:9 final size:9
Alignment explanation
Indices: 19554119--19554349 Score: 153
Period size: 9 Copynumber: 26.4 Consensus size: 9
19554109 ATTAAGTCAA
19554119 TTATGTAAG
1 TTATGTAAG
*
19554128 TTATGTACG
1 TTATGTAAG
19554137 TGTA--TAAG
1 T-TATGTAAG
19554145 TTATGTAAG
1 TTATGTAAG
19554154 TTATGT-A-
1 TTATGTAAG
*
19554161 TTAAGTAAG
1 TTATGTAAG
* *
19554170 CTATTTAAG
1 TTATGTAAG
*
19554179 TTGTGT-A-
1 TTATGTAAG
19554186 TTATGTAAG
1 TTATGTAAG
19554195 TTATGTAAG
1 TTATGTAAG
**
19554204 TTATCAAAG
1 TTATGTAAG
* *
19554213 TAATGTATG
1 TTATGTAAG
19554222 TTATGTAAG
1 TTATGTAAG
19554231 -T-TGTAAG
1 TTATGTAAG
*
19554238 TTAT-TATG
1 TTATGTAAG
*
19554246 TATTATGTAGG
1 --TTATGTAAG
*
19554257 TTATGTAGG
1 TTATGTAAG
19554266 TTATGTAAG
1 TTATGTAAG
*
19554275 TTTTGT-A-
1 TTATGTAAG
*
19554282 TTATTTAAG
1 TTATGTAAG
*
19554291 TTGTGTAAG
1 TTATGTAAG
*
19554300 TTATGTATG
1 TTATGTAAG
*
19554309 CTATGTAAG
1 TTATGTAAG
* *
19554318 TAATGTGTA-
1 TTATGT-AAG
19554327 TTATGTAAG
1 TTATGTAAG
*
19554336 TTTATATAAG
1 -TTATGTAAG
19554346 TTAT
1 TTAT
19554350 TATGTAACTA
Statistics
Matches: 169, Mismatches: 36, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
7 22 0.13
8 16 0.09
9 113 0.67
10 15 0.09
11 3 0.02
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:19554185 original size:25 final size:25
Alignment explanation
Indices: 19554103--19554207 Score: 117
Period size: 25 Copynumber: 4.2 Consensus size: 25
19554093 TGATATATAT
19554103 TTATGTATTAAGTCAA-TTATGTAAG
1 TTATGTATTAAGT-AAGTTATGTAAG
19554128 TTATGTACGTGT-A-TAAGTTATGTAAG
1 TTATGTA--T-TAAGTAAGTTATGTAAG
* *
19554154 TTATGTATTAAGTAAGCTATTTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
* *
19554179 TTGTGTATTATGTAAGTTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
19554204 TTAT
1 TTAT
19554208 CAAAGTAATG
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
23 1 0.01
24 2 0.03
25 44 0.66
26 17 0.25
27 2 0.03
28 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (25 bp):
TTATGTATTAAGTAAGTTATGTAAG
Found at i:19554203 original size:34 final size:33
Alignment explanation
Indices: 19554118--19554300 Score: 114
Period size: 34 Copynumber: 5.6 Consensus size: 33
19554108 TATTAAGTCA
* * *
19554118 ATTATGTAAGTTATGTACGTGTATAAGTTATGT
1 ATTATGTAAGTTATGTAAGTATTTAAGTTATGT
* *
19554151 AAGTTATGT-A-TTAAGTAAGCTATTTAAGTTGTGT
1 -A-TTATGTAAGTTATGTAAG-TATTTAAGTTATGT
** *
19554185 ATTATGTAAGTTATGTAAGTTATCAAAGTAATGT
1 ATTATGTAAGTTATGTAAG-TATTTAAGTTATGT
19554219 ATGTTATGTAAG-T-TGTAAG---TT-A-TTATGT
1 A--TTATGTAAGTTATGTAAGTATTTAAGTTATGT
* * * *
19554247 ATTATGTAGGTTATGTAGGTTATGTAAGTTTTGT
1 ATTATGTAAGTTATGTAAG-TATTTAAGTTATGT
* *
19554281 ATTATTTAAGTTGTGTAAGT
1 ATTATGTAAGTTATGTAAGT
19554301 TATGTATGCT
Statistics
Matches: 113, Mismatches: 22, Indels: 29
0.69 0.13 0.18
Matches are distributed among these distances:
26 8 0.07
27 1 0.01
28 11 0.10
29 1 0.01
32 7 0.06
33 11 0.10
34 58 0.51
35 7 0.06
36 9 0.08
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (33 bp):
ATTATGTAAGTTATGTAAGTATTTAAGTTATGT
Found at i:19554282 original size:62 final size:63
Alignment explanation
Indices: 19554182--19554308 Score: 152
Period size: 62 Copynumber: 2.0 Consensus size: 63
19554172 ATTTAAGTTG
19554182 TGTATTATGTAAGTTATGTAAGTTATCAAAGTAATGTATGTTATGTAAG-T-TGTAAGTTAT-TA
1 TGTATTATGTAAGTTATGTAAGTTATCAAAGTAATGTA--TTATGTAAGTTGTGTAAGTTATGTA
* * ** ** *
19554244 TGTATTATGTAGGTTATGTAGGTTATGTAAGTTTTGTATTATTTAAGTTGTGTAAGTTATGTA
1 TGTATTATGTAAGTTATGTAAGTTATCAAAGTAATGTATTATGTAAGTTGTGTAAGTTATGTA
19554307 TG
1 TG
19554309 CTATGTAAGT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
60 8 0.15
61 1 0.02
62 42 0.76
63 4 0.07
ACGTcount: A:0.29, C:0.01, G:0.22, T:0.48
Consensus pattern (63 bp):
TGTATTATGTAAGTTATGTAAGTTATCAAAGTAATGTATTATGTAAGTTGTGTAAGTTATGTA
Found at i:19554285 original size:25 final size:25
Alignment explanation
Indices: 19554241--19554442 Score: 65
Period size: 25 Copynumber: 7.7 Consensus size: 25
19554231 TTGTAAGTTA
* *
19554241 TTATGTATTATGTAGGTTATGTAGG
1 TTATGTATTATGTAAGTTATGTAAG
* *
19554266 TTATGTAAGTTTTGT-A-TTATTTAAG
1 TTATGT-A-TTATGTAAGTTATGTAAG
* * *
19554291 TTGTGTAAGTTATGTATGCTATGTAAG
1 TTATGT-A-TTATGTAAGTTATGTAAG
* *
19554318 TAATGTGTATTATGTAAGTTTATATAAG
1 T--TATGTATTATGTAAG-TTATGTAAG
** *
19554346 TTAT-TATGTAACTAA-TGTAT-TATG
1 TTATGTAT-TATGTAAGT-TATGTAAG
* * * * *
19554370 TAAGTTTATT-TGAGAATTTTATATAAG
1 TTA-TGTATTATG-TAAGT-TATGTAAG
*
19554397 TCATGTATTATGTAAGTTAACATGTAAG
1 TTATGTATTATGTAAGTT---ATGTAAG
19554425 TTATGTATTATGTAAGTT
1 TTATGTATTATGTAAGTT
19554443 TAATAAGTAT
Statistics
Matches: 131, Mismatches: 28, Indels: 33
0.68 0.15 0.17
Matches are distributed among these distances:
24 6 0.05
25 37 0.28
26 23 0.18
27 28 0.21
28 32 0.24
29 5 0.04
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (25 bp):
TTATGTATTATGTAAGTTATGTAAG
Found at i:19554290 original size:16 final size:16
Alignment explanation
Indices: 19554244--19554297 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
19554234 TAAGTTATTA
* *
19554244 TGTATTATGTAGGTTA
1 TGTATTATGTAAGTTG
*
19554260 TGTAGGTTATGTAAGTTT
1 TGTA--TTATGTAAGTTG
*
19554278 TGTATTATTTAAGTTG
1 TGTATTATGTAAGTTG
19554294 TGTA
1 TGTA
19554298 AGTTATGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 18 0.56
18 14 0.44
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (16 bp):
TGTATTATGTAAGTTG
Found at i:19554317 original size:43 final size:44
Alignment explanation
Indices: 19554195--19554337 Score: 114
Period size: 44 Copynumber: 3.2 Consensus size: 44
19554185 ATTATGTAAG
* ** * * *
19554195 TTATGTAAGTTATCAAAGTAATGTATGTTATGTAAGT-TGTAAGTTA
1 TTATGTAAGTTGTGTAAGTTATGTAGGCTATGTAAGTATGT--G-TA
* * * *
19554241 TTATGT-A-TTATGTAGGTTATGTAGGTTATGTAAGT-TTTGTA
1 TTATGTAAGTTGTGTAAGTTATGTAGGCTATGTAAGTATGTGTA
* *
19554282 TTATTTAAGTTGTGTAAGTTATGTATGCTATGTAAGTAATGTGTA
1 TTATGTAAGTTGTGTAAGTTATGTAGGCTATGTAAGT-ATGTGTA
19554327 TTATGTAAGTT
1 TTATGTAAGTT
19554338 TATATAAGTT
Statistics
Matches: 80, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
41 7 0.09
42 2 0.03
43 24 0.30
44 25 0.31
45 16 0.20
46 6 0.08
ACGTcount: A:0.29, C:0.01, G:0.22, T:0.48
Consensus pattern (44 bp):
TTATGTAAGTTGTGTAAGTTATGTAGGCTATGTAAGTATGTGTA
Found at i:19554373 original size:38 final size:39
Alignment explanation
Indices: 19554323--19554414 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 39
19554313 GTAAGTAATG
* *
19554323 TGTATTATGTAAGTTTATAT-A-AGTTATTATGTAACTAA
1 TGTATTATGTAAGTTTATATGAGAATT-TTATATAACTAA
* * *
19554361 TGTATTATGTAAGTTTATTTGAGAATTTTATATAAGTCA
1 TGTATTATGTAAGTTTATATGAGAATTTTATATAACTAA
19554400 TGTATTATGTAAGTT
1 TGTATTATGTAAGTT
19554415 AACATGTAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
38 19 0.40
39 25 0.53
40 3 0.06
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (39 bp):
TGTATTATGTAAGTTTATATGAGAATTTTATATAACTAA
Found at i:19555023 original size:13 final size:13
Alignment explanation
Indices: 19555005--19555063 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
19554995 CAAATTTTAG
*
19555005 TAAGTAATGTATT
1 TAAGTAATATATT
19555018 TAAGTAA-ATTATT
1 TAAGTAATA-TATT
19555031 TAAGTAATATATT
1 TAAGTAATATATT
*
19555044 CAAGTAATATATT
1 TAAGTAATATATT
*
19555057 AAAGTAA
1 TAAGTAA
19555064 ATTTTAGTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
13 40 0.98
14 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:19555043 original size:26 final size:27
Alignment explanation
Indices: 19555005--19555074 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 27
19554995 CAAATTTTAG
*
19555005 TAAGTAATGTATTTAAGTAAAT-TATT
1 TAAGTAATATATTTAAGTAAATATATT
*
19555031 TAAGTAATATATTCAAGT-AATATATT
1 TAAGTAATATATTTAAGTAAATATATT
*
19555057 AAAGTAA-AT-TTT-AGTAAA
1 TAAGTAATATATTTAAGTAAA
19555075 AAATATGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
23 3 0.08
24 4 0.11
25 5 0.13
26 26 0.68
ACGTcount: A:0.47, C:0.01, G:0.10, T:0.41
Consensus pattern (27 bp):
TAAGTAATATATTTAAGTAAATATATT
Found at i:19555539 original size:15 final size:15
Alignment explanation
Indices: 19555519--19555550 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19555509 AATTGAAATA
*
19555519 AAATTGTAAATCGAT
1 AAATTGCAAATCGAT
19555534 AAATTGCAAATCGAT
1 AAATTGCAAATCGAT
19555549 AA
1 AA
19555551 TTATAAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.28
Consensus pattern (15 bp):
AAATTGCAAATCGAT
Found at i:19557071 original size:44 final size:44
Alignment explanation
Indices: 19556986--19557072 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
19556976 GAAAAACATT
* * **
19556986 TTTGCGGCATTTTAAGCAAAGCGCCACAAAATATAGGTCAAAAA
1 TTTGCAGCATTTTAAACAAAGCGCCACAAAATATAACTCAAAAA
* * * *
19557030 TTTGCAGCGTTTTAAACTAAGCGCCACTAACTATAACTCAAAA
1 TTTGCAGCATTTTAAACAAAGCGCCACAAAATATAACTCAAAA
19557073 TGCGGTCGCT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (44 bp):
TTTGCAGCATTTTAAACAAAGCGCCACAAAATATAACTCAAAAA
Found at i:19557821 original size:21 final size:21
Alignment explanation
Indices: 19557797--19557849 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
19557787 TATAATTTGT
* *
19557797 AAACCTTAAACCTCAAAAACC
1 AAACCCTAAACCCCAAAAACC
* **
19557818 AAACCCCAAACCCCAAACCCC
1 AAACCCTAAACCCCAAAAACC
19557839 AAACCCTAAAC
1 AAACCCTAAAC
19557850 AGTAAAAGTC
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:0.49, C:0.43, G:0.00, T:0.08
Consensus pattern (21 bp):
AAACCCTAAACCCCAAAAACC
Found at i:19557826 original size:7 final size:7
Alignment explanation
Indices: 19557816--19557849 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
19557806 ACCTCAAAAA
19557816 CCAAACC
1 CCAAACC
19557823 CCAAACC
1 CCAAACC
19557830 CCAAACC
1 CCAAACC
19557837 CCAAACC
1 CCAAACC
*
19557844 CTAAAC
1 CCAAAC
19557850 AGTAAAAGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.44, C:0.53, G:0.00, T:0.03
Consensus pattern (7 bp):
CCAAACC
Found at i:19559222 original size:113 final size:112
Alignment explanation
Indices: 19558934--19559488 Score: 357
Period size: 114 Copynumber: 4.9 Consensus size: 112
19558924 NCGGTAAAAG
* * *** **
19558934 CGCCGCTAATACTATGC-TTCAGCGGCGTTTTCCCATGTGCGCCACTAATT-TCGGTATACATCA
1 CGCCGCTAATACTATACATT-AGCGGCGTTTT-CCTTAAACGCCACTAATTAT-AATATACATCA
* * * *
19558997 TGAACTAAA-TGCTGTGTTTTGGTTAAGATACTTTGCGGCGCGTTCCA-CAAA
63 AG-ACCAAACT-CTGCGTTTTGGTTAAGATATTTTGCGGCGC-TTCCACCAAA
* * * * * * *
19559048 CGCCGCTAATAC--T---TTAGCGGCGTTTTTCATCAAGCGCCACTAATTCTAATACACCTTAAG
1 CGCCGCTAATACTATACATTAGCGGCG-TTTTCCTTAAACGCCACTAATTATAATATACATCAAG
* *
19559108 ACCAAACTTTGCGTTTTGGTTAAGATATTTTGAGGCGCTTACCACCAAA
65 ACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTT-CCACCAAA
* * * *
19559157 CGCTGCT-ATAACTATCCTTTA-CTGGCGTTTTCCTTAAACGCCACTAATTATATTATACATCAA
1 CGCCGCTAAT-ACTATACATTAGC-GGCGTTTTCCTTAAACGCCACTAATTATAATATACATCAA
* * * * ** ***
19559220 GACCAACACGCTGCGTTTTGATTAAGATGTCTTGCGGCG-TTTAACGCTCGG
64 GACCAA-ACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCCAC-C-AAA
* * **
19559271 CACCGCTAATACTATACATTAGCGGCGTTTTCTTTATAAGCGCCACTAATTGCAATATACATCAA
1 CGCCGCTAATACTATACATTAGCGGCGTTTTCCTTA-AA-CGCCACTAATTATAATATACATCAA
* * * * * *
19559336 GACCAAACTCTGCATTTTGGTTAACATCTTTTGCGGCGCTTCCTCTAAG
64 GACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCCACCAAA
* * * ***
19559385 CGCCGCTAATACTATACATTA-CTGGCGTTTGTTCGTAAGCGCCACTAATGCCAA-ATACATCAA
1 CGCCGCTAATACTATACATTAGC-GGCGTTT-TCCTTAAACGCCACTAATTATAATATACATCAA
* * * *
19559448 GACCAGAACGCTGCGTGTTGGTCT-TGAGATTTTGCGGCGCT
64 GACCA-AACTCTGCGTTTTGGT-TAAGATATTTTGCGGCGCT
19559489 GTGTGGTAAA
Statistics
Matches: 347, Mismatches: 70, Indels: 49
0.74 0.15 0.11
Matches are distributed among these distances:
107 2 0.01
108 36 0.10
109 40 0.12
110 7 0.02
111 1 0.00
112 17 0.05
113 78 0.22
114 101 0.29
115 34 0.10
116 31 0.09
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (112 bp):
CGCCGCTAATACTATACATTAGCGGCGTTTTCCTTAAACGCCACTAATTATAATATACATCAAGA
CCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCCACCAAA
Found at i:19559486 original size:228 final size:228
Alignment explanation
Indices: 19559056--19559468 Score: 505
Period size: 229 Copynumber: 1.8 Consensus size: 228
19559046 AACGCCGCTA
* * * * *
19559056 ATACTTTAGCGGCGTTTTTCATCAAGCGCCACTAATTCTAATACACCTTAAGACCAAACTTTGCG
1 ATACATTAGCGGCGTTTTTCATCAAGCGCCACTAATTCTAATACACATCAAGACCAAACTCTGCA
* * * *
19559121 TTTTGGTTAAGATATTTTGAGGCGCTTACCACCAAACGCTGCTATAACTATCCTTTACTGGCGTT
66 TTTTGGTTAACATATTTTGAGGCGCTTACCACCAAACGCCGCTATAACTATACATTACTGGCGTT
* * * * *
19559186 TTCCTTAAACGCCACTAATTATATTATACATCAAGACCAACACGCTGCGTTTTGATTAAGATGTC
131 TTCCGTAAACGCCACTAATGACATAATACATCAAGACCAACACGCTGCGTTTGGATTAAGATGTC
19559251 TTGCGGCGTTTAACGCTCGGCACCGCTAATACT
196 TTGCGGCGTTTAACGCTCGGCACCGCTAATACT
* *
19559284 ATACATTAGCGGCGTTTTCTTTAT-AAGCGCCACTAATTGC-AATATACATCAAGACCAAACTCT
1 ATACATTAGCGGCG-TTT-TTCATCAAGCGCCACTAATT-CTAATACACATCAAGACCAAACTCT
* * * * *
19559347 GCATTTTGGTTAACATCTTTTGCGGCGCTT-CCTCTAAGCGCCGCTA-ATACTATACATTACTGG
63 GCATTTTGGTTAACATATTTTGAGGCGCTTACCACCAAACGCCGCTATA-ACTATACATTACTGG
* * *
19559410 CGTTTGTTCGTAAGCGCCACTAATGCCA-AATACATCAAGACCAGA-ACGCTGCGTGTTGG
127 CGTTT-TCCGTAAACGCCACTAATGACATAATACATCAAGACCA-ACACGCTGCGT-TTGG
19559469 TCTTGAGATT
Statistics
Matches: 154, Mismatches: 24, Indels: 13
0.81 0.13 0.07
Matches are distributed among these distances:
227 1 0.01
228 66 0.43
229 82 0.53
230 5 0.03
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (228 bp):
ATACATTAGCGGCGTTTTTCATCAAGCGCCACTAATTCTAATACACATCAAGACCAAACTCTGCA
TTTTGGTTAACATATTTTGAGGCGCTTACCACCAAACGCCGCTATAACTATACATTACTGGCGTT
TTCCGTAAACGCCACTAATGACATAATACATCAAGACCAACACGCTGCGTTTGGATTAAGATGTC
TTGCGGCGTTTAACGCTCGGCACCGCTAATACT
Found at i:19562780 original size:22 final size:22
Alignment explanation
Indices: 19562747--19562807 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
19562737 GCCCGGCCCG
* *
19562747 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAA-TAAAATTAAAACTAA
19562770 TTTTTAATAAAATTAAAACTAA
1 TTTTTAATAAAATTAAAACTAA
* *
19562792 TTGTTATTAAAATTAA
1 TTTTTAATAAAATTAA
19562808 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAACTAA
Found at i:19562820 original size:16 final size:16
Alignment explanation
Indices: 19562783--19562822 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
19562773 TTAATAAAAT
* *
19562783 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
19562799 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
19562815 TAAAATTA
1 TAAAATTA
19562823 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:19562901 original size:59 final size:61
Alignment explanation
Indices: 19562832--19563011 Score: 265
Period size: 68 Copynumber: 2.9 Consensus size: 61
19562822 ATCAAATTAT
*
19562832 TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC--A--A
19562897 TTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC-A
1 -TAA-T-TATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
*
19562960 -AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
19563012 ACAAACTTGA
Statistics
Matches: 110, Mismatches: 2, Indels: 11
0.89 0.02 0.09
Matches are distributed among these distances:
59 48 0.44
60 1 0.01
61 2 0.02
63 1 0.01
66 3 0.03
67 1 0.01
68 54 0.49
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (61 bp):
TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
Found at i:19562928 original size:9 final size:9
Alignment explanation
Indices: 19562895--19562922 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
19562885 TTTATCAAAT
19562895 TATTAATTG
1 TATTAATTG
19562904 TATTAATTG
1 TATTAATTG
19562913 TATTAATTG
1 TATTAATTG
19562922 T
1 T
19562923 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:19562932 original size:68 final size:68
Alignment explanation
Indices: 19562811--19562981 Score: 319
Period size: 68 Copynumber: 2.5 Consensus size: 68
19562801 AAATTAATTG
*
19562811 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
19562874 TGA
66 TGA
19562877 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
19562942 TGA
66 TGA
19562945 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
19562982 TGTAACAAAA
Statistics
Matches: 102, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
66 26 0.25
68 76 0.75
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:19563118 original size:22 final size:24
Alignment explanation
Indices: 19563078--19563121 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
19563068 AAATAAACTT
19563078 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
19563102 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
19563122 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:19571281 original size:2 final size:2
Alignment explanation
Indices: 19571274--19571299 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19571264 CAAAAAGATA
19571274 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
19571300 TTCCTTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19572675 original size:33 final size:33
Alignment explanation
Indices: 19572633--19572696 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
19572623 AATATTAATA
19572633 TATTAATATAAATCATA-TATTTAAATATTTTGT
1 TATTAATATAAAT-ATAGTATTTAAATATTTTGT
* * *
19572666 TATTTATATAAATATAGTTTTTAATTATTTT
1 TATTAATATAAATATAGTATTTAAATATTTT
19572697 AGTAAATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 24 0.89
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (33 bp):
TATTAATATAAATATAGTATTTAAATATTTTGT
Found at i:19572743 original size:27 final size:25
Alignment explanation
Indices: 19572701--19572760 Score: 59
Period size: 27 Copynumber: 2.3 Consensus size: 25
19572691 TATTTTAGTA
19572701 AATATATATTATTATT-TTTACAAAGT
1 AATA-ATATTATTATTGTTTACAAA-T
**
19572727 AATAATATTAATATATTGTTTTTAAAT
1 AATAATATT-AT-TATTGTTTACAAAT
19572754 AATAATA
1 AATAATA
19572761 CTTTTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 5 0.17
26 6 0.21
27 12 0.41
28 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (25 bp):
AATAATATTATTATTGTTTACAAAT
Found at i:19572826 original size:22 final size:21
Alignment explanation
Indices: 19572797--19572837 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
19572787 TATAAAATTA
19572797 AATATTATAATATTTTATTTT
1 AATATTATAATATTTTATTTT
*
19572818 AATATTTATTATATTTTATT
1 AATA-TTATAATATTTTATT
19572838 CTAAGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
AATATTATAATATTTTATTTT
Found at i:19583234 original size:17 final size:17
Alignment explanation
Indices: 19583212--19583246 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
19583202 CAAGTGGAAG
19583212 TATGATTAATTAATTGT
1 TATGATTAATTAATTGT
*
19583229 TATGATTAATTACTTGT
1 TATGATTAATTAATTGT
19583246 T
1 T
19583247 TTGTAGGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.54
Consensus pattern (17 bp):
TATGATTAATTAATTGT
Found at i:19593359 original size:15 final size:16
Alignment explanation
Indices: 19593334--19593363 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19593324 GAGGATAGTT
19593334 TTTCATATTCTTTTAA
1 TTTCATATTCTTTTAA
19593350 TTTC-TATTCTTTTA
1 TTTCATATTCTTTTA
19593364 GACTTTAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTCATATTCTTTTAA
Found at i:19593396 original size:14 final size:14
Alignment explanation
Indices: 19593377--19593404 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19593367 TTTAGGTTTC
19593377 TTTTCAGTTAATTT
1 TTTTCAGTTAATTT
19593391 TTTTCAGTTAATTT
1 TTTTCAGTTAATTT
19593405 CCTTTAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.64
Consensus pattern (14 bp):
TTTTCAGTTAATTT
Found at i:19596741 original size:25 final size:25
Alignment explanation
Indices: 19596713--19596768 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
19596703 CGGTGGTTCA
* *
19596713 CATGTAATACTCAACAGGTGACTCG
1 CATGTAATAATCAACAAGTGACTCG
19596738 CATGTAATAATCAACAAGTGACTCG
1 CATGTAATAATCAACAAGTGACTCG
19596763 CATGTA
1 CATGTA
19596769 CAATAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (25 bp):
CATGTAATAATCAACAAGTGACTCG
Found at i:19596910 original size:28 final size:28
Alignment explanation
Indices: 19596878--19596934 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
19596868 TAGGGGTTCG
*
19596878 CCTATAGAGG-TCCGCATACAAGGGCTCA
1 CCTATAG-GGTTCCACATACAAGGGCTCA
*
19596906 CCTATAGGGTTCCACATGCAAGGGCTCA
1 CCTATAGGGTTCCACATACAAGGGCTCA
19596934 C
1 C
19596935 ACACAAAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 24 0.92
ACGTcount: A:0.26, C:0.30, G:0.25, T:0.19
Consensus pattern (28 bp):
CCTATAGGGTTCCACATACAAGGGCTCA
Found at i:19596943 original size:15 final size:15
Alignment explanation
Indices: 19596925--19596954 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19596915 TTCCACATGC
19596925 AAGGGCTCACACACA
1 AAGGGCTCACACACA
*
19596940 AAGGGTTCACACACA
1 AAGGGCTCACACACA
19596955 GGGGCTTGCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.30, G:0.20, T:0.10
Consensus pattern (15 bp):
AAGGGCTCACACACA
Found at i:19598954 original size:21 final size:19
Alignment explanation
Indices: 19598908--19598982 Score: 123
Period size: 19 Copynumber: 3.8 Consensus size: 19
19598898 AATCTTCAAG
19598908 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
19598927 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
19598946 GATATATGCAATCTTGGATAT
1 G--ATATGCAATCTTAGATAT
19598967 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
19598983 AGATATGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 34 0.65
21 18 0.35
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:19600718 original size:17 final size:17
Alignment explanation
Indices: 19600698--19600764 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 17
19600688 TTTAGCCAAA
19600698 CATAAGAGTTCGCCAGT
1 CATAAGAGTTCGCCAGT
* *
19600715 CATAGGAGTTTGCCAGT
1 CATAAGAGTTCGCCAGT
* * *
19600732 AAT-AGTGTTCGCCAGG
1 CATAAGAGTTCGCCAGT
* *
19600748 CATCAGAGTTTGCCAGT
1 CATAAGAGTTCGCCAGT
19600765 AATAGTGTTC
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
16 11 0.29
17 27 0.71
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (17 bp):
CATAAGAGTTCGCCAGT
Found at i:19600757 original size:33 final size:32
Alignment explanation
Indices: 19600705--19600793 Score: 115
Period size: 33 Copynumber: 2.7 Consensus size: 32
19600695 AAACATAAGA
*
19600705 GTTCGCCAGTCATAGGAGTTTGCCAGTAATAGT
1 GTTCGCCAGACATA-GAGTTTGCCAGTAATAGT
*
19600738 GTTCGCCAGGCATCAGAGTTTGCCAGTAATAGT
1 GTTCGCCAGACAT-AGAGTTTGCCAGTAATAGT
* *
19600771 GTTCGTCAGACATTGGAGTTTGC
1 GTTCGCCAGACA-TAGAGTTTGC
19600794 TAGACTTAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
33 48 0.96
34 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (32 bp):
GTTCGCCAGACATAGAGTTTGCCAGTAATAGT
Found at i:19604236 original size:37 final size:37
Alignment explanation
Indices: 19604195--19604339 Score: 146
Period size: 37 Copynumber: 3.9 Consensus size: 37
19604185 GATTCCCTGC
*
19604195 AAAAGATGGAGAACAATAGTAAAGATTCTCTGCAAAG
1 AAAAGACGGAGAACAATAGTAAAGATTCTCTGCAAAG
** * * *
19604232 AAAAGACGGAGATTAGTAATAAAGATTCTCTGCAAAAAA
1 AAAAGACGGAGAACAATAGTAAAGATTCTCTGC--AAAG
** * * * *
19604271 AAAAGACATAGATCAACAGTAAAGGTTCTATGCAAAG
1 AAAAGACGGAGAACAATAGTAAAGATTCTCTGCAAAG
* *
19604308 AAAAGACGGAAAACAATAGTAAAGATTTTCTG
1 AAAAGACGGAGAACAATAGTAAAGATTCTCTG
19604340 TAAAAGTTTT
Statistics
Matches: 83, Mismatches: 23, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
37 55 0.66
39 28 0.34
ACGTcount: A:0.50, C:0.11, G:0.19, T:0.20
Consensus pattern (37 bp):
AAAAGACGGAGAACAATAGTAAAGATTCTCTGCAAAG
Found at i:19604294 original size:39 final size:39
Alignment explanation
Indices: 19604203--19604311 Score: 96
Period size: 39 Copynumber: 2.8 Consensus size: 39
19604193 GCAAAAGATG
* * * *
19604203 GAGAACAATAGTAAAGATTCTCTGC--AAAGAAAAGACG
1 GAGATCAACAGTAAAGATTCTCTGCAAAAAAAAAAGACA
* ** *
19604240 GAGATTAGTAATAAAGATTCTCTGCAAAAAAAAAAGACA
1 GAGATCAACAGTAAAGATTCTCTGCAAAAAAAAAAGACA
* * * *
19604279 TAGATCAACAGTAAAGGTTCTATGCAAAGAAAA
1 GAGATCAACAGTAAAGATTCTCTGCAAAAAAAA
19604312 GACGGAAAAC
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
37 21 0.38
39 35 0.62
ACGTcount: A:0.50, C:0.12, G:0.18, T:0.19
Consensus pattern (39 bp):
GAGATCAACAGTAAAGATTCTCTGCAAAAAAAAAAGACA
Found at i:19604659 original size:59 final size:59
Alignment explanation
Indices: 19604593--19604706 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 59
19604583 TCTAACTTTC
* *
19604593 AAAAATTT-AAGTTTTTGTTTTTCAAAAATTTAAATTCAAAATAAATCAAATTTAAATTT
1 AAAAATTTCAAGGTTTT-TTTTTCAAAAATTTAAATTCAAAACAAATCAAATTTAAATTT
* * * *
19604652 AAAAATTTCGAGGTTTTTTTTTCAAAAATTTAAATTTATAACAAATCAATTTTAA
1 AAAAATTTCAAGGTTTTTTTTTCAAAAATTTAAATTCAAAACAAATCAAATTTAA
19604707 GTTTTCAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 42 0.88
60 6 0.12
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (59 bp):
AAAAATTTCAAGGTTTTTTTTTCAAAAATTTAAATTCAAAACAAATCAAATTTAAATTT
Found at i:19609461 original size:9 final size:9
Alignment explanation
Indices: 19609449--19609483 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
19609439 TAATAATACA
19609449 TTTTCTTTC
1 TTTTCTTTC
19609458 TTTTCTTTTC
1 TTTTC-TTTC
19609468 TTTTCTTTC
1 TTTTCTTTC
*
19609477 TTCTCTT
1 TTTTCTT
19609484 CCCCCTCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:19609616 original size:27 final size:27
Alignment explanation
Indices: 19609576--19609649 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 27
19609566 CTAGGTGTGT
* * *
19609576 CGCCTATTATATAGGCACCACCATTGC
1 CGCCTATCAGATAGGCACCACCAGTGC
* *** **
19609603 TGCCTATCAGATAGGGGTCACTGGTGC
1 CGCCTATCAGATAGGCACCACCAGTGC
19609630 CGCCTATCAGATAGGCACCA
1 CGCCTATCAGATAGGCACCA
19609650 TACCTCCATA
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.23
Consensus pattern (27 bp):
CGCCTATCAGATAGGCACCACCAGTGC
Found at i:19610235 original size:18 final size:18
Alignment explanation
Indices: 19610188--19610235 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
19610178 TAAAATTTTA
19610188 ATTTATAATT-TTTTTATG
1 ATTTA-AATTATTTTTATG
*
19610206 ATTTTAAA-TATTTTTATT
1 A-TTTAAATTATTTTTATG
19610224 ATTTAAATTATT
1 ATTTAAATTATT
19610236 GAAGATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 7 0.27
18 15 0.58
19 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTAAATTATTTTTATG
Found at i:19610675 original size:11 final size:11
Alignment explanation
Indices: 19610660--19610699 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
19610650 TGTTTTCTCT
19610660 TTATTTTGCTA
1 TTATTTTGCTA
* *
19610671 CTATTTTACTA
1 TTATTTTGCTA
*
19610682 TTATGTTGCTA
1 TTATTTTGCTA
19610693 TTATTTT
1 TTATTTT
19610700 ATTGTTATAG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.20, C:0.10, G:0.07, T:0.62
Consensus pattern (11 bp):
TTATTTTGCTA
Found at i:19611782 original size:9 final size:9
Alignment explanation
Indices: 19611768--19611798 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
19611758 GTTAAACGAA
19611768 TCGAGTTAT
1 TCGAGTTAT
*
19611777 TCGAGTTAA
1 TCGAGTTAT
19611786 TCGAGTTAT
1 TCGAGTTAT
19611795 TCGA
1 TCGA
19611799 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:19612386 original size:17 final size:17
Alignment explanation
Indices: 19612366--19612448 Score: 64
Period size: 17 Copynumber: 4.8 Consensus size: 17
19612356 ATTTATATCT
19612366 ATTATTTATATTATTAA
1 ATTATTTATATTATTAA
* *
19612383 ATTAAATTTCACATT-TTAT
1 ATT--ATTT-ATATTATTAA
*
19612402 ATTATTTATATTATTGA
1 ATTATTTATATTATTAA
*
19612419 ATTATTTAGTCA-TATTGA
1 ATTATTTA-T-ATTATTAA
19612437 A-TATTTATATTA
1 ATTATTTATATTA
19612449 AAATTGAATT
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
15 1 0.02
16 7 0.13
17 23 0.43
18 8 0.15
19 11 0.20
20 4 0.07
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (17 bp):
ATTATTTATATTATTAA
Found at i:19612796 original size:5 final size:5
Alignment explanation
Indices: 19612786--19612837 Score: 61
Period size: 5 Copynumber: 10.2 Consensus size: 5
19612776 GAACAAATAT
* *
19612786 ATTCG ATTCG ATTCG ATTCG ATTCG AATTCC ATCTC- ACTCG ATTCG ATTCG
1 ATTCG ATTCG ATTCG ATTCG ATTCG -ATTCG AT-TCG ATTCG ATTCG ATTCG
19612837 A
1 A
19612838 GAAAACTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 2 0.05
5 33 0.80
6 6 0.15
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (5 bp):
ATTCG
Found at i:19620015 original size:15 final size:15
Alignment explanation
Indices: 19619995--19620025 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
19619985 TATTTTATCC
19619995 TAATAACTTATTTTG
1 TAATAACTTATTTTG
19620010 TAATAACTTATTTTG
1 TAATAACTTATTTTG
19620025 T
1 T
19620026 TAGGACTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (15 bp):
TAATAACTTATTTTG
Found at i:19629600 original size:46 final size:46
Alignment explanation
Indices: 19629529--19629713 Score: 289
Period size: 46 Copynumber: 4.0 Consensus size: 46
19629519 CATGGAAAAG
* *
19629529 TGTGGAACGTAGGTATGGTAATTCAGTAAAGAAAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGT
* *
19629575 TGTGGAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGT
* *
19629621 TGTGAAACGTAGGTATGGTATTTCAGTAACGAAAACCATACAGAGT
1 TGTGAAACGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGT
* * *
19629667 TGTGAAAAGTAGGTATGGTATTTTAGTGAAGAAAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGT
19629713 T
1 T
19629714 ATAGCATTGT
Statistics
Matches: 128, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 128 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (46 bp):
TGTGAAACGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGT
Found at i:19638123 original size:19 final size:19
Alignment explanation
Indices: 19638099--19638141 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
19638089 TAGTAGTAGT
*
19638099 ATACATAGTACAAATATAC
1 ATACATAGTACAAATACAC
19638118 ATACATAGTACAAATACAC
1 ATACATAGTACAAATACAC
19638137 ATACA
1 ATACA
19638142 CTGCTGTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.53, C:0.19, G:0.05, T:0.23
Consensus pattern (19 bp):
ATACATAGTACAAATACAC
Found at i:19638683 original size:24 final size:24
Alignment explanation
Indices: 19638651--19638705 Score: 92
Period size: 24 Copynumber: 2.2 Consensus size: 24
19638641 CAGACGGATG
*
19638651 GGGGGAAAACTAAGTTAGGGATTT
1 GGGGAAAAACTAAGTTAGGGATTT
19638675 GGGGAAAAACTAAGTTAGGGATTT
1 GGGGAAAAACTAAGTTAGGGATTT
19638699 GGAGGAA
1 GG-GGAA
19638706 TAAGGGTTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.36, C:0.04, G:0.38, T:0.22
Consensus pattern (24 bp):
GGGGAAAAACTAAGTTAGGGATTT
Found at i:19643769 original size:20 final size:20
Alignment explanation
Indices: 19643674--19643769 Score: 61
Period size: 20 Copynumber: 4.8 Consensus size: 20
19643664 CTTGTACGAG
* *
19643674 ATTTACACTTCAGTGCCTCT
1 ATTTGCACTTCAGTGCCCCT
*
19643694 ATTTGCACTTCGGTGCCCCT
1 ATTTGCACTTCAGTGCCCCT
* * * * *
19643714 GTATACACTTCGGTGTCCCT
1 ATTTGCACTTCAGTGCCCCT
* * *
19643734 GTTTGTACATT-TGTGCCCCT
1 ATTTGCAC-TTCAGTGCCCCT
19643754 -TTCTGCACTTCAGTGC
1 ATT-TGCACTTCAGTGC
19643770 TCTTGTTATG
Statistics
Matches: 59, Mismatches: 14, Indels: 6
0.75 0.18 0.08
Matches are distributed among these distances:
19 4 0.07
20 53 0.90
21 2 0.03
ACGTcount: A:0.14, C:0.30, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTTGCACTTCAGTGCCCCT
Found at i:19652737 original size:15 final size:15
Alignment explanation
Indices: 19652719--19652753 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
19652709 GTATTATATA
*
19652719 ATAATGATAATAGTT
1 ATAATGATAATAATT
19652734 ATAATGATAATAATT
1 ATAATGATAATAATT
19652749 ATAAT
1 ATAAT
19652754 AATAGTACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (15 bp):
ATAATGATAATAATT
Found at i:19660056 original size:13 final size:13
Alignment explanation
Indices: 19660038--19660062 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19660028 CTAAATCATA
19660038 ATTTTAGTAAAAT
1 ATTTTAGTAAAAT
19660051 ATTTTAGTAAAA
1 ATTTTAGTAAAA
19660063 CCCCTTTTTG
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTTTAGTAAAAT
Found at i:19661328 original size:29 final size:28
Alignment explanation
Indices: 19661294--19661352 Score: 91
Period size: 29 Copynumber: 2.1 Consensus size: 28
19661284 ACCAAAAATT
*
19661294 TATTTTAAAAATAAAAAATATTTTAAAAA
1 TATTTTAAAAATAAAAAA-ATTTAAAAAA
*
19661323 TATTTTAAAATTAAAAAAATTTAAAAAA
1 TATTTTAAAAATAAAAAAATTTAAAAAA
19661351 TA
1 TA
19661353 AATATTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
TATTTTAAAAATAAAAAAATTTAAAAAA
Found at i:19661333 original size:10 final size:11
Alignment explanation
Indices: 19661307--19661332 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19661297 TTTAAAAATA
19661307 AAAAATATTTT
1 AAAAATATTTT
19661318 AAAAATATTTT
1 AAAAATATTTT
19661329 AAAA
1 AAAA
19661333 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:19661336 original size:17 final size:17
Alignment explanation
Indices: 19661316--19661354 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
19661306 AAAAAATATT
* *
19661316 TTAAAAATATTTTAAAA
1 TTAAAAAAATTTAAAAA
19661333 TTAAAAAAATTTAAAAA
1 TTAAAAAAATTTAAAAA
*
19661350 ATAAA
1 TTAAA
19661355 TATTTATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAAAAATTTAAAAA
Found at i:19662967 original size:109 final size:107
Alignment explanation
Indices: 19662149--19662950 Score: 1066
Period size: 109 Copynumber: 7.4 Consensus size: 107
19662139 AAAAAGATTG
* ** *
19662149 TACTTTTTTCGTATACTGGTACCTTTTATTGACACG-AAAAAGTAAAAAAAACAAAATTTTCCCA
1 TACTTTTTTCGTATACTGATACCTGCTATTGACACGAAAAAAGT---AAAAA-AAAA-TTCCCCA
*
19662213 AAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAA--ATTTTTT
61 AAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTT
* * *
19662258 TACTTTTTTCGTATACTGATACCTTCCATTGACACGAAAAAAGTAAAAAAAAAATTCTCCAAAAA
1 TACTTTTTTCGTATACTGATACCTGCTATTGACACGAAAAAAGT-AAAAAAAAATTCCCCAAAAA
*
19662323 AGGTGGTGCTGGCCATTGGCAGGCCACCACCAAAAGAATTTTTTTTTT
65 AGGTGGTGCCGGCCATTGGCAGGCCACCACC---A-AA-TTTTTTTTT
19662371 TACTTTTTTCGTATACTGATACCTGCTATTGACACGAAAAAA-TAAAAAAAAATTCCCCAAAAAA
1 TACTTTTTTCGTATACTGATACCTGCTATTGACACGAAAAAAGTAAAAAAAAATTCCCCAAAAAA
* * *
19662435 GGTGGTGCCGACCATCGGCAGGCCACCACCAAAAAATTTTCTTTT
66 GGTGGTGCCGGCCATTGGCAGGCCACCACC---AAATTTTTTTTT
* *
19662480 TACTTTTTTCGTATACTCATACCTGATATTGACACGAAAAAAGTAAAAAAAAATTCCCCAAAAAA
1 TACTTTTTTCGTATACTGATACCTGCTATTGACACGAAAAAAGTAAAAAAAAATTCCCC--AAAA
*
19662545 AAGGTGGTGCCGGCCATTGGCAGGCCACCATCAAATTTTTTTTTT
64 AAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAA-TTTTTTTTT
* *
19662590 TACTTTTTTCTTACACTGATACCTGCTATTGACACGAAAAAAGTAAAAAAAAATTTCCCCAAAAA
1 TACTTTTTTCGTATACTGATACCTGCTATTGACACGAAAAAAGTAAAAAAAAA-TTCCCCAAAAA
* * *
19662655 AAGTGGTGCCGGCTATTGGCAGGCCACCATC-AA--TTTTTTT
65 AGGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTT
* *
19662695 TACTTTTTTCGTATACTGATACCAGCTATTGACACGAAAAAAGTAAAAAAAAAATCCCCAAAAAA
1 TACTTTTTTCGTATACTGATACCTGCTATTGACACGAAAAAAGTAAAAAAAAATTCCCCAAAAAA
* * *
19662760 TGTGGTGTCGGCCATTGGCAGGCCACCA-CAATTTTTTTTTT
66 GGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTT
*
19662801 TACTTTTTTCGTAAACTGATACCTGCTATTGACACGAAAAAAGTAAAAAAAAATTTCCCCCAAAA
1 TACTTTTTTCGTATACTGATACCTGCTATTGACACGAAAAAAGTAAAAAAAAA-TT-CCCCAAAA
*
19662866 AAGGTGGTGTCGGCCATTGGCAGGCCACCACCAAATTTTTTTTT
64 AAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTT
* * * *
19662910 TACTTTTTTTGTACT-CTGATGCCGGCCATTGACA-GAAAAAA
1 TACTTTTTTCGTA-TACTGATACCTGCTATTGACACGAAAAAA
19662951 ACTCGAAATT
Statistics
Matches: 629, Mismatches: 44, Indels: 41
0.88 0.06 0.06
Matches are distributed among these distances:
103 1 0.00
104 37 0.06
105 57 0.09
106 97 0.15
107 5 0.01
108 52 0.08
109 159 0.25
110 84 0.13
111 57 0.09
112 34 0.05
113 46 0.07
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.30
Consensus pattern (107 bp):
TACTTTTTTCGTATACTGATACCTGCTATTGACACGAAAAAAGTAAAAAAAAATTCCCCAAAAAA
GGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTT
Found at i:19663620 original size:54 final size:54
Alignment explanation
Indices: 19663535--19663649 Score: 203
Period size: 54 Copynumber: 2.1 Consensus size: 54
19663525 TAAATATCAA
*
19663535 GGTCTCAATGAGCTGGACAGTGAGTCCGTGATGAAAATTTTGTTGCCTAAAGCT
1 GGTCTCAATGAGCTGGACAGTGAATCCGTGATGAAAATTTTGTTGCCTAAAGCT
* *
19663589 GGTCTCAATGAGCTGGACAGTGAATCTGTGATGGAAATTTTGTTGCCTAAAGCT
1 GGTCTCAATGAGCTGGACAGTGAATCCGTGATGAAAATTTTGTTGCCTAAAGCT
19663643 GGTCTCA
1 GGTCTCA
19663650 GTGGCCCAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (54 bp):
GGTCTCAATGAGCTGGACAGTGAATCCGTGATGAAAATTTTGTTGCCTAAAGCT
Found at i:19664548 original size:19 final size:19
Alignment explanation
Indices: 19664516--19664555 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
19664506 TAACTTTCTC
*
19664516 TCTCCCATCCCTCTATCTT
1 TCTCCCATACCTCTATCTT
* *
19664535 TCTCCCATATCTCTTTCTT
1 TCTCCCATACCTCTATCTT
19664554 TC
1 TC
19664556 CCACTCTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.10, C:0.42, G:0.00, T:0.47
Consensus pattern (19 bp):
TCTCCCATACCTCTATCTT
Found at i:19670285 original size:3 final size:3
Alignment explanation
Indices: 19670279--19670310 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
19670269 ACTGATTAGG
19670279 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19670311 CTTTATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19670477 original size:22 final size:22
Alignment explanation
Indices: 19670426--19670478 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
19670416 TCATCTCATT
*
19670426 TATTTATTTATTTGTTTTCTTTA
1 TATTTA-TTATTTGTTTTCTTAA
19670449 T-TGTTATTA-TTGTTTTACTTAA
1 TAT-TTATTATTTGTTTT-CTTAA
19670471 TATTTATT
1 TATTTATT
19670479 CATTCATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 7 0.27
22 14 0.54
23 5 0.19
ACGTcount: A:0.21, C:0.04, G:0.06, T:0.70
Consensus pattern (22 bp):
TATTTATTATTTGTTTTCTTAA
Found at i:19671643 original size:9 final size:9
Alignment explanation
Indices: 19671626--19671671 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
19671616 TGAGTTTTCG
19671626 AATTCGAAT
1 AATTCGAAT
*
19671635 AACTCGAAT
1 AATTCGAAT
19671644 AATTCGAAT
1 AATTCGAAT
19671653 AATTCGAAT
1 AATTCGAAT
19671662 AATTCGAAT
1 AATTCGAAT
19671671 A
1 A
19671672 TCAAACTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:19675963 original size:32 final size:31
Alignment explanation
Indices: 19675898--19675964 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
19675888 ACCTAAAATT
* * *
19675898 ATTAATTCTAATTATTCTAATATTTTATTTA
1 ATTAATTCTAATTATTCTAATATATAATCTA
19675929 ATTAATTCCTAATTATT-TAATTATATAATCTA
1 ATTAATT-CTAATTATTCTAA-TATATAATCTA
19675961 ATTA
1 ATTA
19675965 TGGTTTCCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 10 0.32
32 21 0.68
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (31 bp):
ATTAATTCTAATTATTCTAATATATAATCTA
Found at i:19679798 original size:2 final size:2
Alignment explanation
Indices: 19679791--19679816 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19679781 AACTATCTTA
19679791 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
19679817 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19682576 original size:26 final size:26
Alignment explanation
Indices: 19682546--19682641 Score: 156
Period size: 26 Copynumber: 3.7 Consensus size: 26
19682536 AAGTATACTA
19682546 TACTGGCAGCTTTGCTGCGATACTGT
1 TACTGGCAGCTTTGCTGCGATACTGT
* *
19682572 TACTGGCAGCTTTGCTGCAATACTGA
1 TACTGGCAGCTTTGCTGCGATACTGT
* *
19682598 TACTGGCAGCTTTACTGCGTTACTGT
1 TACTGGCAGCTTTGCTGCGATACTGT
19682624 TACTGGCAGCTTTGCTGC
1 TACTGGCAGCTTTGCTGC
19682642 AATATTGGTG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 63 1.00
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.34
Consensus pattern (26 bp):
TACTGGCAGCTTTGCTGCGATACTGT
Found at i:19682602 original size:52 final size:51
Alignment explanation
Indices: 19682540--19682645 Score: 185
Period size: 52 Copynumber: 2.1 Consensus size: 51
19682530 TGGAGGAAGT
*
19682540 ATACTATACTGGCAGCTTTGCTGCGATACTGTTACTGGCAGCTTTGCTGCA
1 ATACTATACTGGCAGCTTTACTGCGATACTGTTACTGGCAGCTTTGCTGCA
*
19682591 ATACTGATACTGGCAGCTTTACTGCGTTACTGTTACTGGCAGCTTTGCTGCA
1 ATACT-ATACTGGCAGCTTTACTGCGATACTGTTACTGGCAGCTTTGCTGCA
19682643 ATA
1 ATA
19682646 TTGGTGTGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
51 5 0.10
52 47 0.90
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.34
Consensus pattern (51 bp):
ATACTATACTGGCAGCTTTACTGCGATACTGTTACTGGCAGCTTTGCTGCA
Found at i:19683738 original size:35 final size:35
Alignment explanation
Indices: 19683692--19683762 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
19683682 AAAATATCGA
* *
19683692 TACCCTAGTGTCAGTATTGGTACCTACGGACTTGG
1 TACCCTAGTGTCAGTATCGATACCTACGGACTTGG
*
19683727 TACCCTAGTGTCAGTATCGATACTTACGGACTTGG
1 TACCCTAGTGTCAGTATCGATACCTACGGACTTGG
19683762 T
1 T
19683763 TTAAGAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.32
Consensus pattern (35 bp):
TACCCTAGTGTCAGTATCGATACCTACGGACTTGG
Found at i:19690072 original size:21 final size:21
Alignment explanation
Indices: 19690046--19690109 Score: 128
Period size: 21 Copynumber: 3.0 Consensus size: 21
19690036 TTAATAACAC
19690046 ATATAGATCACTTATACACTT
1 ATATAGATCACTTATACACTT
19690067 ATATAGATCACTTATACACTT
1 ATATAGATCACTTATACACTT
19690088 ATATAGATCACTTATACACTT
1 ATATAGATCACTTATACACTT
19690109 A
1 A
19690110 CGTATGTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.38
Consensus pattern (21 bp):
ATATAGATCACTTATACACTT
Found at i:19704518 original size:27 final size:27
Alignment explanation
Indices: 19704476--19704888 Score: 442
Period size: 27 Copynumber: 15.3 Consensus size: 27
19704466 TGTAATGGGC
* *
19704476 GTAAAATGACCGAAATACCCGCGAAGG
1 GTAAAATGATCGAAATACCCTCGAAGG
* *
19704503 GTAAAATG-TCCAAAATACCCCCGAAGG
1 GTAAAATGAT-CGAAATACCCTCGAAGG
*
19704530 GTAAAATGATCGAAATACCCTCGAATG
1 GTAAAATGATCGAAATACCCTCGAAGG
19704557 GTAAAATGATCGAAATACTCC-CGAAGG
1 GTAAAATGATCGAAATAC-CCTCGAAGG
*
19704584 GTAAAATGACCGAAATACCCTCGAAGG
1 GTAAAATGATCGAAATACCCTCGAAGG
**
19704611 GTAAAATGATCGAAATACCCTTAAAGG
1 GTAAAATGATCGAAATACCCTCGAAGG
19704638 GTAAAATGATCGAAATACCCTCG-AGG
1 GTAAAATGATCGAAATACCCTCGAAGG
*
19704664 TGTAAAATGATCGAAATACCCCCGAAGG
1 -GTAAAATGATCGAAATACCCTCGAAGG
* * *
19704692 GTAAAATGATCAAAATA-CCTCAAAGA
1 GTAAAATGATCGAAATACCCTCGAAGG
* *
19704718 GTAAAATGATTGAAATAGCCTCGAAGG
1 GTAAAATGATCGAAATACCCTCGAAGG
* * *
19704745 GTAAAATGATTGAAATAGCCTCTAAGG
1 GTAAAATGATCGAAATACCCTCGAAGG
* *
19704772 GTAAAATG-GCTGAAATACCCTCGAAGT
1 GTAAAATGATC-GAAATACCCTCGAAGG
* * ** *
19704799 GTAAATTGACCGAAATACCCTTAAAAG
1 GTAAAATGATCGAAATACCCTCGAAGG
* * * * *
19704826 GTAAAATGACCAAAATACCTTTGAAGT
1 GTAAAATGATCGAAATACCCTCGAAGG
* * * *
19704853 GTATAATTAACGAAATACCC-CTATAGG
1 GTAAAATGATCGAAATACCCTCGA-AGG
19704880 GTAAAATGA
1 GTAAAATGA
19704889 CCATTATACC
Statistics
Matches: 326, Mismatches: 50, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
26 27 0.08
27 292 0.90
28 7 0.02
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (27 bp):
GTAAAATGATCGAAATACCCTCGAAGG
Found at i:19705112 original size:26 final size:26
Alignment explanation
Indices: 19705083--19705157 Score: 96
Period size: 26 Copynumber: 2.9 Consensus size: 26
19705073 TGCCACATAC
*
19705083 ACTGTTACTGGCAGCATTGCTACATT
1 ACTGTTACTGGCAGCTTTGCTACATT
* *
19705109 ACTGTTACTGGCAGCTTTGCTGCGTT
1 ACTGTTACTGGCAGCTTTGCTACATT
* * *
19705135 ATTATTACTGGCAACTTTGCTAC
1 ACTGTTACTGGCAGCTTTGCTAC
19705158 GATATTGGTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (26 bp):
ACTGTTACTGGCAGCTTTGCTACATT
Found at i:19705331 original size:30 final size:28
Alignment explanation
Indices: 19705282--19705360 Score: 104
Period size: 30 Copynumber: 2.8 Consensus size: 28
19705272 GATTACTGTT
19705282 TTGGGCTAAGGCCCACACTGTTACCGTA
1 TTGGGCTAAGGCCCACACTGTTACCGTA
*
19705310 TTGGGCTAAGGTCCACACACTGTTACTGTA
1 TTGGGCTAAGG-CC-CACACTGTTACCGTA
* **
19705340 ATGGGCTAACACCCACACTGT
1 TTGGGCTAAGGCCCACACTGT
19705361 ACTGCTACTG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
28 19 0.42
29 4 0.09
30 22 0.49
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (28 bp):
TTGGGCTAAGGCCCACACTGTTACCGTA
Found at i:19712287 original size:27 final size:27
Alignment explanation
Indices: 19712257--19712626 Score: 351
Period size: 27 Copynumber: 13.7 Consensus size: 27
19712247 GTAATGGGCC
19712257 TAAAATGATCGAAATACCCTCGAAAGG
1 TAAAATGATCGAAATACCCTCGAAAGG
* *
19712284 TAAAATGA-CCAAATACCCTCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAAGG
* *
19712310 TAAAATGATCGAAATACCCCCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAAGG
* * *
19712337 TAAACTGATCGAAATACCCTTGAAGGG
1 TAAAATGATCGAAATACCCTCGAAAGG
* * *
19712364 TAAAATGACCGAAATACCCCCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAAGG
* * * *
19712391 TAAAATAATTGAAATACCTTTGAAAGG
1 TAAAATGATCGAAATACCCTCGAAAGG
* * * ***
19712418 TAAAATGACCGAAAGACCCTTGGTGGG
1 TAAAATGATCGAAATACCCTCGAAAGG
* *
19712445 TAAAATGATCGAAACACCCTCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAAGG
*
19712472 TAAAATGATCGAAATACCCTCGAATGG
1 TAAAATGATCGAAATACCCTCGAAAGG
19712499 TAAAAT-AGTCGAAATACCCTC-AAAGGG
1 TAAAATGA-TCGAAATACCCTCGAAA-GG
* * *
19712526 TAAAATAATCAAAATACCCCCGAAAGG
1 TAAAATGATCGAAATACCCTCGAAAGG
19712553 TAAAATGA-CTGAAATACCCTCG--AGG
1 TAAAATGATC-GAAATACCCTCGAAAGG
* *
19712578 ATAAACTGA-CTGAAATACCCTTG-AAGG
1 -TAAAATGATC-GAAATACCCTCGAAAGG
* *
19712605 ATAAAATTATTGAAATAACCCT
1 -TAAAATGATCGAAAT-ACCCT
19712627 ATAGGGTAAA
Statistics
Matches: 289, Mismatches: 44, Indels: 19
0.82 0.12 0.05
Matches are distributed among these distances:
25 3 0.01
26 48 0.17
27 229 0.79
28 9 0.03
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (27 bp):
TAAAATGATCGAAATACCCTCGAAAGG
Found at i:19712377 original size:54 final size:54
Alignment explanation
Indices: 19712257--19712642 Score: 397
Period size: 54 Copynumber: 7.2 Consensus size: 54
19712247 GTAATGGGCC
* * *
19712257 TAAAATGATCGAAATACCCTCGAAAGGTAAAATGA-CCAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCGAAGGG
* * * *
19712310 TAAAATGATCGAAATACCCCCGAAGGGTAAACTGATCGAAATACCCTTGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCGAAGGG
* * * * * *
19712364 TAAAATGACCGAAATACCCCCGAAGGGTAAAATAATTGAAATACCTTTGAAAGG
1 TAAAATGACCGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCGAAGGG
* * ** *
19712418 TAAAATGACCGAAAGACCCTTGGTGGGTAAAATGATCGAAACACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCGAAGGG
* * *
19712472 TAAAATGATCGAAATACCCTCGAATGGTAAAAT-AGTCGAAATACCCTCAAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGGTAAAATGA-TCGAAATACCCTCGAAGGG
* * * * * *
19712526 TAAAATAATCAAAATACCCCCGAAAGGTAAAATGA-CTGAAATACCCTCG-AGGA
1 TAAAATGACCGAAATACCCTCGAAGGGTAAAATGATC-GAAATACCCTCGAAGGG
* * * * * *
19712579 TAAACTGACTGAAATACCCTTGAAGGATAAAATTATTGAAATAACCCT--ATAGGG
1 TAAAATGACCGAAATACCCTCGAAGGGTAAAATGATCGAAAT-ACCCTCGA-AGGG
19712633 TAAAATGACC
1 TAAAATGACC
19712643 ATTATACCCT
Statistics
Matches: 275, Mismatches: 50, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
53 67 0.24
54 207 0.75
55 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (54 bp):
TAAAATGACCGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCGAAGGG
Found at i:19712406 original size:81 final size:81
Alignment explanation
Indices: 19712257--19712611 Score: 405
Period size: 81 Copynumber: 4.4 Consensus size: 81
19712247 GTAATGGGCC
* * *
19712257 TAAAATGATCGAAATACCCTCGAAAGGTAAAATGACC-AAATACCCTCGAAGGGTAAAATGATCG
1 TAAAATGATCGAAATACCCTTGAAGGGTAAAATGACCGAAATACCCCCGAAGGGTAAAATGATCG
*
19712321 AAATACCCCCGAAGGG
66 AAATACCCTCGAAGGG
* * *
19712337 TAAACTGATCGAAATACCCTTGAAGGGTAAAATGACCGAAATACCCCCGAAGGGTAAAATAATTG
1 TAAAATGATCGAAATACCCTTGAAGGGTAAAATGACCGAAATACCCCCGAAGGGTAAAATGATCG
* * *
19712402 AAATACCTTTGAAAGG
66 AAATACCCTCGAAGGG
* * ** * * *
19712418 TAAAATGACCGAAAGACCCTTGGTGGGTAAAATGATCGAAACACCCTCGAAGGGTAAAATGATCG
1 TAAAATGATCGAAATACCCTTGAAGGGTAAAATGACCGAAATACCCCCGAAGGGTAAAATGATCG
*
19712483 AAATACCCTCGAATGG
66 AAATACCCTCGAAGGG
** * * * *
19712499 TAAAAT-AGTCGAAATACCCTCAAAGGGTAAAATAATCAAAATACCCCCGAAAGGTAAAATGA-C
1 TAAAATGA-TCGAAATACCCTTGAAGGGTAAAATGACCGAAATACCCCCGAAGGGTAAAATGATC
*
19712562 TGAAATACCCTCG-AGGA
65 -GAAATACCCTCGAAGGG
* *
19712579 TAAACTGA-CTGAAATACCCTTGAAGGATAAAAT
1 TAAAATGATC-GAAATACCCTTGAAGGGTAAAAT
19712612 TATTGAAATA
Statistics
Matches: 230, Mismatches: 40, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
79 1 0.00
80 63 0.27
81 166 0.72
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (81 bp):
TAAAATGATCGAAATACCCTTGAAGGGTAAAATGACCGAAATACCCCCGAAGGGTAAAATGATCG
AAATACCCTCGAAGGG
Found at i:19712885 original size:26 final size:26
Alignment explanation
Indices: 19712834--19712906 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
19712824 TGCCACATAC
* * *
19712834 ACTGTTACTGACAGCATTACTGCGTT
1 ACTGTTACTGGCAGCTTTACTACGTT
*
19712860 ACTGTTACTGGCAGCTTTGCTACGTT
1 ACTGTTACTGGCAGCTTTACTACGTT
* * *
19712886 ATTATTACTAGCAGCTTTACT
1 ACTGTTACTGGCAGCTTTACT
19712907 GTGATATTAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (26 bp):
ACTGTTACTGGCAGCTTTACTACGTT
Found at i:19713087 original size:30 final size:30
Alignment explanation
Indices: 19713025--19713108 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 30
19713015 ATTGCTCTAA
* * *
19713025 TTACTGTTTTGGGCTAAGG-CC-TACATTG
1 TTACTGTATTGGGCTAAGGCCCACACACTG
19713053 TTACTGTATTGGGCTAAGGCCCACACACTG
1 TTACTGTATTGGGCTAAGGCCCACACACTG
* * *
19713083 TTACTGTAATGGGTTAAGACCCACAC
1 TTACTGTATTGGGCTAAGGCCCACAC
19713109 TGTACTGCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
28 18 0.38
29 2 0.04
30 28 0.58
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (30 bp):
TTACTGTATTGGGCTAAGGCCCACACACTG
Found at i:19722548 original size:11 final size:11
Alignment explanation
Indices: 19722532--19722556 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19722522 GACGGCACTC
19722532 CTAAAAGAAGT
1 CTAAAAGAAGT
19722543 CTAAAAGAAGT
1 CTAAAAGAAGT
19722554 CTA
1 CTA
19722557 TGGAACTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.12, G:0.16, T:0.20
Consensus pattern (11 bp):
CTAAAAGAAGT
Found at i:19727440 original size:13 final size:13
Alignment explanation
Indices: 19727422--19727446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19727412 TTCATAATTC
19727422 TTTAATTTTTAAT
1 TTTAATTTTTAAT
19727435 TTTAATTTTTAA
1 TTTAATTTTTAA
19727447 GAAATTATTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTAATTTTTAAT
Found at i:19745685 original size:3 final size:3
Alignment explanation
Indices: 19745677--19745734 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
19745667 TTTAGATTTG
19745677 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
19745725 TTA TTA TTA T
1 TTA TTA TTA T
19745735 CATATTGTCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19747810 original size:22 final size:20
Alignment explanation
Indices: 19747783--19747829 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
19747773 AAATATATAA
* *
19747783 AAATATTTTTTATTAATATTT
1 AAATATTTATAATTAAT-TTT
19747804 ATAATATTTATAATTAATTTT
1 A-AATATTTATAATTAATTTT
19747825 AAATA
1 AAATA
19747830 AAAATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 5 0.22
22 14 0.61
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AAATATTTATAATTAATTTT
Found at i:19748330 original size:25 final size:26
Alignment explanation
Indices: 19748282--19748333 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
19748272 ATCCTATAAA
* * *
19748282 TTCAAAAAAATTATGATTATAAAAAT
1 TTCAAAAAAATAATAAATATAAAAAT
19748308 TTCAAAAAAATAATAAATA-AAAAAT
1 TTCAAAAAAATAATAAATATAAAAAT
19748333 T
1 T
19748334 ACATAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (26 bp):
TTCAAAAAAATAATAAATATAAAAAT
Found at i:19751826 original size:13 final size:12
Alignment explanation
Indices: 19751792--19751817 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19751782 TTTTAGTCGT
19751792 TTGTTTATTTTC
1 TTGTTTATTTTC
19751804 TTGTTTATTTTC
1 TTGTTTATTTTC
19751816 TT
1 TT
19751818 TAGTTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.77
Consensus pattern (12 bp):
TTGTTTATTTTC
Found at i:19759442 original size:46 final size:46
Alignment explanation
Indices: 19759375--19759594 Score: 280
Period size: 46 Copynumber: 4.8 Consensus size: 46
19759365 CTTATTATTA
* * * *
19759375 CTATATTCTCCAGTCCACAACATATGCAGGAGTTGGGAATCTAAAC
1 CTATATTCTCCAGTCTACAACATATGCAGGAGCTGGGAACCTAAAT
** *
19759421 CTATATTCTCCAGTCCGCAACATATGCAGGAGTTGGGAACCTAAAT
1 CTATATTCTCCAGTCTACAACATATGCAGGAGCTGGGAACCTAAAT
* * *
19759467 TTGTATTCTCCAGTCTACAACATATGCAGGAGCTAGGAACCTAAAT
1 CTATATTCTCCAGTCTACAACATATGCAGGAGCTGGGAACCTAAAT
* * * * *
19759513 CTATATTCTCCAGTCTGA-AACATATACAGGAACTAGAAACTTAAAT
1 CTATATTCTCCAGTCT-ACAACATATGCAGGAGCTGGGAACCTAAAT
*
19759559 CTGTATTCTCCAGTCTACAACATATGCAGGAGCTGG
1 CTATATTCTCCAGTCTACAACATATGCAGGAGCTGG
19759595 AACTTGGGCA
Statistics
Matches: 153, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
45 1 0.01
46 151 0.99
47 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (46 bp):
CTATATTCTCCAGTCTACAACATATGCAGGAGCTGGGAACCTAAAT
Found at i:19770236 original size:18 final size:18
Alignment explanation
Indices: 19770203--19770237 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19770193 CCTATTGGTA
19770203 TTTATTTTAATATTTTAT
1 TTTATTTTAATATTTTAT
*
19770221 TTTATTTTAATTTTTTA
1 TTTATTTTAATATTTTA
19770238 GGAAGTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTTAATATTTTAT
Found at i:19770514 original size:26 final size:26
Alignment explanation
Indices: 19770445--19770516 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 26
19770435 CAAGATTCAT
* * * *
19770445 AAATTTTAATTTAGTTATATTTGATA
1 AAATTTTAATTTTGTTTTAATTAATA
*
19770471 AAATTTGAATTTAT-TTTTAATTAATA
1 AAATTTTAATTT-TGTTTTAATTAATA
*
19770497 AAATTTTTATTTTGTTTTAA
1 AAATTTTAATTTTGTTTTAA
19770517 ATTAGAAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
25 1 0.03
26 36 0.97
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (26 bp):
AAATTTTAATTTTGTTTTAATTAATA
Found at i:19770620 original size:19 final size:19
Alignment explanation
Indices: 19770578--19770625 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
19770568 TAAAAAATTG
*
19770578 AATTCAATGTTTTAACATTA
1 AATTCAAT-ATTTAACATTA
* * *
19770598 AATTTAATATTTAATATTT
1 AATTCAATATTTAACATTA
19770617 AATTCAATA
1 AATTCAATA
19770626 ATTCTAATAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (19 bp):
AATTCAATATTTAACATTA
Found at i:19774080 original size:51 final size:49
Alignment explanation
Indices: 19774015--19774142 Score: 150
Period size: 50 Copynumber: 2.6 Consensus size: 49
19774005 AAAGGTAGCA
*
19774015 TGTGTAGTACTATGTGCAGGCTACTA-TGCATACCGGATAGCTTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTACTG-A-ACCGGAAAG-TTCGATCACG
* * *
19774066 TGTGTAGTACTATGTACAGGCTACTACGTGAATCGGAAAGTTTGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTAC-TGAACCGGAAAGTTCGATCACG
** *
19774116 TGTGTAGTTTTATGTGAAGGCTACTAC
1 TGTGTAGTACTATGTGCAGGCTACTAC
19774143 GGGTATCGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
50 32 0.48
51 32 0.48
52 1 0.01
53 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (49 bp):
TGTGTAGTACTATGTGCAGGCTACTACTGAACCGGAAAGTTCGATCACG
Found at i:19774870 original size:66 final size:66
Alignment explanation
Indices: 19774764--19774889 Score: 243
Period size: 66 Copynumber: 1.9 Consensus size: 66
19774754 CATTTCAGAG
*
19774764 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
1 AGCACACTACCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
19774829 T
66 T
19774830 AGCACACTACCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGCACACTACCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
19774890 TAATATAAAC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.27, C:0.37, G:0.18, T:0.18
Consensus pattern (66 bp):
AGCACACTACCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
T
Found at i:19775104 original size:57 final size:60
Alignment explanation
Indices: 19775011--19775158 Score: 205
Period size: 57 Copynumber: 2.5 Consensus size: 60
19775001 ACCCTAATTC
* * * *
19775011 GGATTACCCGTCCGGGCTAAATCCATTTTCCACATATTCTTCGGGAGGGCTATATC-A-A
1 GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAGGGCTATACCGATA
19775069 -GATCACCCGTCCGGGCTAGAT-CTTTTTCACACATATTCTTCGGGAGGGCTATACCAGGATA
1 GGATCACCCGTCCGGGCTAGATCCTTTTTC-CACATATTCTTCGGGAGGGCTATACC--GATA
19775130 GGATCACCCGTCCGGGCTAGATCCTTTTT
1 GGATCACCCGTCCGGGCTAGATCCTTTTT
19775159 ACCGTCAATT
Statistics
Matches: 79, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
56 6 0.08
57 44 0.56
60 1 0.01
61 1 0.01
62 21 0.27
63 6 0.08
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (60 bp):
GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAGGGCTATACCGATA
Found at i:19779725 original size:13 final size:13
Alignment explanation
Indices: 19779707--19779731 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19779697 TTAATTATGT
19779707 GTGTGAAAATTTC
1 GTGTGAAAATTTC
19779720 GTGTGAAAATTT
1 GTGTGAAAATTT
19779732 TATCGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:19787164 original size:3 final size:3
Alignment explanation
Indices: 19787156--19787207 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
19787146 TATTACTTGT
* * *
19787156 TTA TTA TTA CTA TTA TTG TCTA TTA TTA TTA TTA TTA ATA TTA TTCA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT-A
19787203 TTA TT
1 TTA TT
19787208 TTCATGTACA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 36 0.88
4 5 0.12
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:19787174 original size:19 final size:19
Alignment explanation
Indices: 19787143--19787191 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
19787133 TATTTTATGG
*
19787143 TACTATTACTTGTTTATTAT
1 TACTATTA-TTGTCTATTAT
19787163 TACTATTATTGTCTATTAT
1 TACTATTATTGTCTATTAT
*
19787182 TATTATTATT
1 TACTATTATT
19787192 AATATTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (19 bp):
TACTATTATTGTCTATTAT
Found at i:19789467 original size:55 final size:58
Alignment explanation
Indices: 19789354--19789473 Score: 149
Period size: 58 Copynumber: 2.1 Consensus size: 58
19789344 CCCAAAAATC
* *
19789354 GATTGTTTATATGTTTAAATCAATTATTATGGTGAAATATTACTTCTTCTTCTGAATA
1 GATTGTTTATATGTTTAAATCAATTATTATGGTGAAACACTACTTCTTCTTCTGAATA
** * *
19789412 GATTGTTTATATGTTTAAATTGATTATTAT-GTTAGAACACTGCTTC-T-TTC-GAATA
1 GATTGTTTATATGTTTAAATCAATTATTATGGTGA-AACACTACTTCTTCTTCTGAATA
19789467 GATTGTT
1 GATTGTT
19789474 ATGTTAGAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
55 12 0.22
56 3 0.05
57 4 0.07
58 36 0.65
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.48
Consensus pattern (58 bp):
GATTGTTTATATGTTTAAATCAATTATTATGGTGAAACACTACTTCTTCTTCTGAATA
Found at i:19789481 original size:34 final size:34
Alignment explanation
Indices: 19789433--19789509 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 34
19789423 TGTTTAAATT
*
19789433 GATTATTATGTTAGAACACTGCTTCTTTCGAATA
1 GATTATTATGTTAGAACAATGCTTCTTTCGAATA
* * * * *
19789467 GATTGTTATGTTAGAATAATGTTTCTTTTGAATT
1 GATTATTATGTTAGAACAATGCTTCTTTCGAATA
19789501 GATTATTAT
1 GATTATTAT
19789510 ATGACACGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.48
Consensus pattern (34 bp):
GATTATTATGTTAGAACAATGCTTCTTTCGAATA
Found at i:19789587 original size:3 final size:3
Alignment explanation
Indices: 19789579--19789618 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
19789569 CCTATCTTAC
19789579 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
19789619 AAAACTCAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:19791245 original size:3 final size:3
Alignment explanation
Indices: 19791237--19791261 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19791227 CCACACACTG
19791237 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
19791262 TGTCCTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19803821 original size:26 final size:26
Alignment explanation
Indices: 19803792--19803841 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
19803782 AAAGATTGTT
*
19803792 AAAACTCTTTTAAAAG-AAACTCAAGA
1 AAAACTC-TTGAAAAGAAAACTCAAGA
*
19803818 AAAATTCTTGAAAAGAAAACTCAA
1 AAAACTCTTGAAAAGAAAACTCAA
19803842 AGAGAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.56, C:0.14, G:0.08, T:0.22
Consensus pattern (26 bp):
AAAACTCTTGAAAAGAAAACTCAAGA
Found at i:19810143 original size:21 final size:21
Alignment explanation
Indices: 19810117--19810156 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
19810107 GTTCTTAGAT
19810117 AAATTAGTTTAGTAATTTTGA
1 AAATTAGTTTAGTAATTTTGA
19810138 AAATTAGTTTAGTAATTTT
1 AAATTAGTTTAGTAATTTT
19810157 AGATTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (21 bp):
AAATTAGTTTAGTAATTTTGA
Found at i:19810402 original size:5 final size:6
Alignment explanation
Indices: 19810386--19810427 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
19810376 TAATTTAGCC
* *
19810386 ATTTTT ATTTTT ATTTTT ATTTTTT AGTTTA ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT A-TTTTT ATTTTT ATTTTT ATTTT
19810428 CTAATTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (6 bp):
ATTTTT
Found at i:19810409 original size:19 final size:19
Alignment explanation
Indices: 19810387--19810427 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
19810377 AATTTAGCCA
* *
19810387 TTTTTATTTTTATTTTTAT
1 TTTTTAGTTTAATTTTTAT
19810406 TTTTTAGTTTAATTTTTAT
1 TTTTTAGTTTAATTTTTAT
19810425 TTT
1 TTT
19810428 CTAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTAGTTTAATTTTTAT
Found at i:19836265 original size:25 final size:26
Alignment explanation
Indices: 19836230--19836293 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
19836220 TTTCAAATTC
19836230 ATAT-TTTTATAA-TATATATTATA-G
1 ATATATTTTATAATTAT-TATTATAGG
* *
19836254 ATATATTTTATAATTATTTTTCTAGG
1 ATATATTTTATAATTATTATTATAGG
19836280 A-ATATTTTATAATT
1 ATATATTTTATAATT
19836294 TCATAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 4 0.11
25 26 0.74
26 5 0.14
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (26 bp):
ATATATTTTATAATTATTATTATAGG
Found at i:19836271 original size:11 final size:12
Alignment explanation
Indices: 19836230--19836273 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 12
19836220 TTTCAAATTC
19836230 ATAT-TTTTATA
1 ATATATTTTATA
*
19836241 ATATATATTATA
1 ATATATTTTATA
19836253 GATATATTTTATA
1 -ATATATTTTATA
19836266 AT-TATTTT
1 ATATATTTT
19836274 TCTAGGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 10 0.34
12 8 0.28
13 11 0.38
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
ATATATTTTATA
Found at i:19838698 original size:26 final size:26
Alignment explanation
Indices: 19838667--19838717 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
19838657 CATTGAAGTT
* * *
19838667 TGGTTTATCTTTTTACATGCATGAAG
1 TGGTTTATATTTATACACGCATGAAG
19838693 TGGTTTATATTTATACACGCATGAA
1 TGGTTTATATTTATACACGCATGAA
19838718 ATCATAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (26 bp):
TGGTTTATATTTATACACGCATGAAG
Found at i:19846515 original size:2 final size:2
Alignment explanation
Indices: 19846508--19846564 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
19846498 ATCTCATCTC
19846508 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19846550 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
19846565 CCTTCTAATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19850424 original size:30 final size:31
Alignment explanation
Indices: 19850388--19850459 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 31
19850378 GTTATTATAG
*
19850388 TAATTTTTTTAAAATTTTAAAT-TA-AATTAA
1 TAATTTTTTTAAAATTTAAAATATATAA-TAA
**
19850418 TAA-TTTTAAAAAATTTAAAATATATAATAA
1 TAATTTTTTTAAAATTTAAAATATATAATAA
19850448 TAATTTTGTTTA
1 TAATTTT-TTTA
19850460 TTTAATCTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
29 15 0.45
30 11 0.33
31 5 0.15
32 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (31 bp):
TAATTTTTTTAAAATTTAAAATATATAATAA
Found at i:19855845 original size:15 final size:15
Alignment explanation
Indices: 19855821--19855877 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
19855811 ACATAAATTT
19855821 GTTTTATTTTCATTA
1 GTTTTATTTTCATTA
* * *
19855836 GTTTTGTTTTTTATTTT
1 GTTTT-ATTTTCA-TTA
19855853 GTTTTATTTTCATTA
1 GTTTTATTTTCATTA
*
19855868 GTTTTGTTTT
1 GTTTTATTTT
19855878 TTTATTATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
15 16 0.48
16 10 0.30
17 7 0.21
ACGTcount: A:0.12, C:0.04, G:0.11, T:0.74
Consensus pattern (15 bp):
GTTTTATTTTCATTA
Found at i:19855859 original size:32 final size:32
Alignment explanation
Indices: 19855818--19855879 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
19855808 GATACATAAA
19855818 TTTGTTTTATTTTCATTAGTTTTGTTTTTTAT
1 TTTGTTTTATTTTCATTAGTTTTGTTTTTTAT
19855850 TTTGTTTTATTTTCATTAGTTTTGTTTTTT
1 TTTGTTTTATTTTCATTAGTTTTGTTTTTT
19855880 TATTATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.11, C:0.03, G:0.10, T:0.76
Consensus pattern (32 bp):
TTTGTTTTATTTTCATTAGTTTTGTTTTTTAT
Found at i:19855878 original size:16 final size:16
Alignment explanation
Indices: 19855827--19855878 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
19855817 ATTTGTTTTA
19855827 TTTTCATTAGTTTTGT
1 TTTTCATTAGTTTTGT
* * *
19855843 TTTTTATTTTGTTTT-A
1 TTTTCA-TTAGTTTTGT
19855859 TTTTCATTAGTTTTGT
1 TTTTCATTAGTTTTGT
19855875 TTTT
1 TTTT
19855879 TTATTATTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 7 0.25
16 14 0.50
17 7 0.25
ACGTcount: A:0.12, C:0.04, G:0.10, T:0.75
Consensus pattern (16 bp):
TTTTCATTAGTTTTGT
Found at i:19855885 original size:26 final size:29
Alignment explanation
Indices: 19855818--19855888 Score: 76
Period size: 32 Copynumber: 2.4 Consensus size: 29
19855808 GATACATAAA
*
19855818 TTTGTTTTATTTTCATTAGTTTTGTTTTTTAT
1 TTTGTATTATTTTCATTAGTTTTG---TTTAT
*
19855850 TTTGTTTTATTTTCATTAGTTTTG-TT-T
1 TTTGTATTATTTTCATTAGTTTTGTTTAT
19855877 TTT-TATTATTTT
1 TTTGTATTATTTT
19855889 ACTATTTTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
26 8 0.21
27 4 0.11
28 2 0.05
32 24 0.63
ACGTcount: A:0.13, C:0.03, G:0.08, T:0.76
Consensus pattern (29 bp):
TTTGTATTATTTTCATTAGTTTTGTTTAT
Found at i:19860126 original size:94 final size:94
Alignment explanation
Indices: 19859965--19860176 Score: 291
Period size: 94 Copynumber: 2.3 Consensus size: 94
19859955 TAAAACCATA
* * *
19859965 AATCCTATACCCCTAAAGTTACAGTGGGATGAATTGAAGCCATCATGACGAATCTTATCTCCCTG
1 AATCCTATACCCCTAAAGTTGCAGTGGGATGAATTAAAGCCATCATGACGAATATTATCTCCCTG
* *
19860030 AAGTTGCAGTGGAGCAGATTGAAGCCACT
66 AAGATGCAGTGGAGCAGACTGAAGCCACT
* * **
19860059 AATCCTATACCCCTAAAGTTGCAGTGGGATGGATTAAAGTCATCATGGTGAATATTATCTCCCTG
1 AATCCTATACCCCTAAAGTTGCAGTGGGATGAATTAAAGCCATCATGACGAATATTATCTCCCTG
*
19860124 AAGATGCAGTGGAGTAGACTGAAGCCACT
66 AAGATGCAGTGGAGCAGACTGAAGCCACT
* * *
19860153 -AGCCTTATATCCCTGAAGTTGCAG
1 AATCC-TATACCCCTAAAGTTGCAG
19860177 CGGAGCAACT
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
93 3 0.03
94 101 0.97
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (94 bp):
AATCCTATACCCCTAAAGTTGCAGTGGGATGAATTAAAGCCATCATGACGAATATTATCTCCCTG
AAGATGCAGTGGAGCAGACTGAAGCCACT
Found at i:19860376 original size:143 final size:143
Alignment explanation
Indices: 19860113--19860470 Score: 506
Period size: 143 Copynumber: 2.5 Consensus size: 143
19860103 ATGGTGAATA
* * * * * * *
19860113 TTATCTCCCTGAAGATGCAGTGGAGTAGACTGAAGCCACTAGCCTTATATCCCTGAAGTTGCAGC
1 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCCCTGAAGTTGTAGT
*
19860178 GGAGCA-ACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAAATTAAAGCTACAA
66 GGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAATGGAACAAATTAAAGCTACAA
19860242 ATTAT-GACGGATC
131 ATTATGGA-GGATC
* * * *
19860255 TTATCTTCCTAAAGTTGCAGTGGAGCAGATTTAAGCCACTGGCCTTATCTCCCTGAAATTGTAGT
1 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCCCTGAAGTTGTAGT
* *
19860320 GGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAATGGAACAGATTAAAGTTACAA
66 GGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAATGGAACAAATTAAAGCTACAA
19860385 ATTATGGAGGATC
131 ATTATGGAGGATC
* * * * *
19860398 TTATCTTCTTGAAGTTGCAGTGGAGCATATTGAAGCCACCAATCC-TATCTCCCTGAAGTTATAG
1 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-CTAGCCTTATCTCCCTGAAGTTGTAG
19860462 TGGAGCAGA
65 TGGAGCAGA
19860471 TTAAAACGGT
Statistics
Matches: 190, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
142 60 0.32
143 125 0.66
144 5 0.03
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (143 bp):
TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCCCTGAAGTTGTAGT
GGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAATGGAACAAATTAAAGCTACAA
ATTATGGAGGATC
Found at i:19860777 original size:18 final size:20
Alignment explanation
Indices: 19860754--19860796 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
19860744 CTGGGCCCAA
*
19860754 CAAAAT-AA-ATTACAAAGC
1 CAAAATAAACATTACAAACC
19860772 CAAAATAAACATTACAAACC
1 CAAAATAAACATTACAAACC
19860792 CAAAA
1 CAAAA
19860797 ATTAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 2 0.09
20 14 0.64
ACGTcount: A:0.63, C:0.21, G:0.02, T:0.14
Consensus pattern (20 bp):
CAAAATAAACATTACAAACC
Found at i:19860970 original size:16 final size:17
Alignment explanation
Indices: 19860943--19860976 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
19860933 CACACAAAGC
19860943 AGCAATAGAGAAACAAT
1 AGCAATAGAGAAACAAT
*
19860960 AGCAA-AGAGAAATAAT
1 AGCAATAGAGAAACAAT
19860976 A
1 A
19860977 AACAATGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.62, C:0.09, G:0.18, T:0.12
Consensus pattern (17 bp):
AGCAATAGAGAAACAAT
Found at i:19863244 original size:21 final size:21
Alignment explanation
Indices: 19863220--19863259 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
19863210 ATATACATGG
*
19863220 ATTGCTACGTAGATGACAGGT
1 ATTGCCACGTAGATGACAGGT
19863241 ATTGCCACGTAGATGACAG
1 ATTGCCACGTAGATGACAG
19863260 ATCAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (21 bp):
ATTGCCACGTAGATGACAGGT
Found at i:19866806 original size:13 final size:13
Alignment explanation
Indices: 19866774--19866799 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19866764 TTTTACCTTC
19866774 TGTTTTTTTATTT
1 TGTTTTTTTATTT
19866787 TGTTTTTTTATTT
1 TGTTTTTTTATTT
19866800 ATTTTTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (13 bp):
TGTTTTTTTATTT
Found at i:19867580 original size:30 final size:28
Alignment explanation
Indices: 19867518--19867593 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 28
19867508 TTGTTGTTGT
* *
19867518 TATTATAATTATTATTATTACTACTTTC
1 TATTATTATTAATATTATTACTACTTTC
19867546 -ATTATTATTAATATTATTACTA-TTACTGC
1 TATTATTATTAATATTATTACTACTT--T-C
19867575 TATTATTGA-TAATATTATT
1 TATTATT-ATTAATATTATT
19867594 TGCTTATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 2 0.05
27 20 0.49
28 1 0.02
29 1 0.02
30 16 0.39
31 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (28 bp):
TATTATTATTAATATTATTACTACTTTC
Found at i:19867916 original size:29 final size:28
Alignment explanation
Indices: 19867882--19867957 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
19867872 TTCTTTCAAA
* *
19867882 TATTTTAACATCTTTAATTCATTTCAACT
1 TATTTTAATAT-TTTAATTCATTTAAACT
* *
19867911 TATTTTAATATTGTTAATTTATTTAAATT
1 TATTTTAATATT-TTAATTCATTTAAACT
19867940 TATTTTAATATTTTAATT
1 TATTTTAATATTTTAATT
19867958 TACATATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 7 0.17
29 35 0.83
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (28 bp):
TATTTTAATATTTTAATTCATTTAAACT
Found at i:19867972 original size:29 final size:29
Alignment explanation
Indices: 19867910--19867973 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
19867900 TCATTTCAAC
**
19867910 TTATTTTAATATTGTTAATTTATTTAAAT
1 TTATTTTAATATTGTTAATTTACATAAAT
*
19867939 TTATTTTAATATT-TTAATTTACATATAT
1 TTATTTTAATATTGTTAATTTACATAAAT
19867967 TATATTT
1 T-TATTT
19867974 ATTTCTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 13 0.42
29 18 0.58
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (29 bp):
TTATTTTAATATTGTTAATTTACATAAAT
Found at i:19867974 original size:28 final size:29
Alignment explanation
Indices: 19867910--19867974 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
19867900 TCATTTCAAC
**
19867910 TTAT-TTTAATATTGTTAATTTATTTAAA
1 TTATATTTAATATTGTTAATTTACATAAA
*
19867938 TT-TATTTTAATATT-TTAATTTACATATA
1 TTATA-TTTAATATTGTTAATTTACATAAA
19867966 TTATATTTA
1 TTATATTTA
19867975 TTTCTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.03
28 19 0.61
29 11 0.35
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (29 bp):
TTATATTTAATATTGTTAATTTACATAAA
Found at i:19871804 original size:15 final size:17
Alignment explanation
Indices: 19871784--19871815 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
19871774 TGAAAAAGTT
19871784 GAAAAT-AATT-TTTCA
1 GAAAATCAATTCTTTCA
19871799 GAAAATCAATTCTTTCA
1 GAAAATCAATTCTTTCA
19871816 ATCAAACAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (17 bp):
GAAAATCAATTCTTTCA
Found at i:19872236 original size:18 final size:17
Alignment explanation
Indices: 19872213--19872265 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
19872203 ATATATTATG
*
19872213 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATT-ATAT
19872231 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
19872248 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
19872266 TTAATAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Done.