Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 63 of 120
Found at i:18191145 original size:13 final size:13
Alignment explanation
Indices: 18191129--18191156 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18191119 AAAAAAAAAG
18191129 AAATGAAAATGAA
1 AAATGAAAATGAA
18191142 AAATGAAAATGAA
1 AAATGAAAATGAA
18191155 AA
1 AA
18191157 GTAATGACGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
AAATGAAAATGAA
Found at i:18192638 original size:88 final size:87
Alignment explanation
Indices: 18192361--18193112 Score: 866
Period size: 88 Copynumber: 8.6 Consensus size: 87
18192351 AACAGATCAA
* * ** * *
18192361 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATC-AAAAGCAAAACCTTGCAT
1 TAAAGATAGCAGATCTTGCCTTCCTGCA-TGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCT
* * *
18192425 CCAACGGTTACAGTGGAGCGGGT
65 CCATCGGTTGCAGTGGAGCAGGT
* * ****
18192448 TAAAGATAGCAGATCTTACCTTCCTGCATTGACAACGAAGCAGATCGAA-AATGAAGCCTTGCCT
1 TAAAGATAGCAGATCTTGCCTTCCTGCA-TGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCT
* *
18192512 CCCTCGGTTGTAGTGGAGCAGGT
65 CCATCGGTTGCAGTGGAGCAGGT
18192535 TAAAGATAGCAGATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCT
1 TAAAGATAGCAGATCTTGCCTTCCTGCAT-GACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCT
* *
18192600 CCATTGGTTGCAGTGGAACAGGT
65 CCATCGGTTGCAGTGGAGCAGGT
* * * *
18192623 TAAATATGGCAGATCTTGCCTTTCTGCATAGACAGTGAAGCAGATCGAAGACCCCAGCCTTGCCT
1 TAAAGATAGCAGATCTTGCCTTCCTGCAT-GACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCT
*
18192688 CCAAT-GGTTGCAGTGGAGCGGGT
65 CC-ATCGGTTGCAGTGGAGCAGGT
* * * * **
18192711 TAAATATAACAGATCTTGCCTTCCTGCATTGACAGCGAAGTAGATCGAA-AACAAAGCCTTGCCT
1 TAAAGATAGCAGATCTTGCCTTCCTGCA-TGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCT
* * * *
18192775 CCATCTGTAGTAGTGGAGCGGGT
65 CCATCGGTTGCAGTGGAGCAGGT
* * *
18192798 TAAAGATAGTAGATCTTGCAC-TCCTGCGCTGATAGCGAAGCAGATCGAAGACCCCAGCCTTGCC
1 TAAAGATAGCAGATCTTGC-CTTCCTGC-ATGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCC
* *
18192862 TCCATCGGTTACAGTGGAGCGGGT
64 TCCATCGGTTGCAGTGGAGCAGGT
* **
18192886 TAAAGATAGCAGATCTTGCCTTCCTACACTGACAGCGAAGCAGATCGAAGATACCAGCCTTGCCT
1 TAAAGATAGCAGATCTTGCCTTCCTGCA-TGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCT
* * * *
18192951 CCCTCAGTTGCAATGGAACAGGT
65 CCATCGGTTGCAGTGGAGCAGGT
* * *
18192974 TAAAGATAGCAGATCTTGCCCTCCTGCGCTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAGATAGCAGATCTTGCCTTCCTGC-ATGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCT
* *
18193039 CCCTCGGTTGCAGTGGAGCACGT
65 CCATCGGTTGCAGTGGAGCAGGT
* * * * *
18193062 TGAAGATAGCAGATCTTGCTTTCCTTCATCGACAGTGAAGTAGATCGAAGA
1 TAAAGATAGCAGATCTTGCCTTCCTGCAT-GACAGCGAAGCAGATCGAAGA
18193113 TTACAAGTCC
Statistics
Matches: 573, Mismatches: 79, Indels: 25
0.85 0.12 0.04
Matches are distributed among these distances:
86 3 0.01
87 188 0.33
88 379 0.66
89 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (87 bp):
TAAAGATAGCAGATCTTGCCTTCCTGCATGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTC
CATCGGTTGCAGTGGAGCAGGT
Found at i:18192902 original size:263 final size:262
Alignment explanation
Indices: 18192361--18193112 Score: 954
Period size: 263 Copynumber: 2.9 Consensus size: 262
18192351 AACAGATCAA
* * ** * *
18192361 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATC-AAAAGCAAAACCTTGCAT
1 TAAAGATAGCAGATCTTGCCTTCCTGCA-TGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCT
* * * *
18192425 CCAACGGTTACAGTGGAGCGGGTTAAAGATAGCAGATCTTACCTTCCTGCATTGACAACGAAGCA
65 CCAATGGTTGCAGTGGAGCGGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCA
**
18192490 GATCGAAAATGAAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTAAAGATAGCAGATCTTGCC
130 GATCGAAAACAAAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTAAAGATAGCAGATCTTGCC
* *
18192555 TTCCTGCATAGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTCCATTGGTTGCAGTGGAACA
195 TTCCTGCATAGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTCCATCGGTTACAGTGGAACA
18192620 GGT
260 GGT
* * * *
18192623 TAAATATGGCAGATCTTGCCTTTCTGCATAGACAGTGAAGCAGATCGAAGACCCCAGCCTTGCCT
1 TAAAGATAGCAGATCTTGCCTTCCTGCAT-GACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCT
* * *
18192688 CCAATGGTTGCAGTGGAGCGGGTTAAATATAACAGATCTTGCCTTCCTGCATTGACAGCGAAGTA
65 CCAATGGTTGCAGTGGAGCGGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCA
* * * * *
18192753 GATCGAAAACAAAGCCTTGCCTCCATCTGTAGTAGTGGAGCGGGTTAAAGATAGTAGATCTTGCA
130 GATCGAAAACAAAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTAAAGATAGCAGATCTTGC-
* * *
18192818 C-TCCTGCGCT-GATAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTCCATCGGTTACAGTGGAG
194 CTTCCTGC-ATAGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTCCATCGGTTACAGTGGAA
*
18192881 CGGGT
258 CAGGT
* **
18192886 TAAAGATAGCAGATCTTGCCTTCCTACACTGACAGCGAAGCAGATCGAAGATACCAGCCTTGCCT
1 TAAAGATAGCAGATCTTGCCTTCCTGCA-TGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCT
* * * * * * **
18192951 CC-CTCAGTTGCAATGGAACAGGTTAAAGATAGCAGATCTTGCCCTCCTGCGCTGACAGCGAAGC
65 CCAAT-GGTTGCAGTGGAGCGGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGC
* * * * *
18193015 AGATCGAAGACACCAGCCTTGCCTCCCTCGGTTGCAGTGGAGCACGTTGAAGATAGCAGATCTTG
129 AGATCGAAAACA-AAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTAAAGATAGCAGATCTTG
* * * * *
18193080 CTTTCCTTCATCGACAGTGAAGTAGATCGAAGA
193 CCTTCCTGCATAGACAGCGAAGCAGATCGAAGA
18193113 TTACAAGTCC
Statistics
Matches: 417, Mismatches: 64, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
261 1 0.00
262 41 0.10
263 305 0.73
264 70 0.17
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (262 bp):
TAAAGATAGCAGATCTTGCCTTCCTGCATGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTC
CAATGGTTGCAGTGGAGCGGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAG
ATCGAAAACAAAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCT
TCCTGCATAGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTCCATCGGTTACAGTGGAACAG
GT
Found at i:18193016 original size:351 final size:351
Alignment explanation
Indices: 18192361--18193110 Score: 1001
Period size: 351 Copynumber: 2.1 Consensus size: 351
18192351 AACAGATCAA
*
18192361 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATC-AAAAGCAAAACCTTGCAT
1 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGTAGATCGAAAAGCAAAACCTTGCAT
*
18192425 CCAACGGTTACAGTGGAGCGGGTTAAAGATAGCAGATCTTACCTTCCTGCATTGACAACGAAGCA
66 CCAACGGTTACAGTGGAGCGGGTTAAAGATAGCAGATCTTACCTTCCTGCACTGACAACGAAGCA
** * **
18192490 GATCGAAAATGAAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTAAAGATAGCAGATCTTGCC
131 GATCGAAAACCAAGCCTTGCCTCCATCGGTTACAGTGGAGCAGGTTAAAGATAGCAGATCTTGCC
* * ** *
18192555 TTCCTGCATAGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTCCATTGGTTGCAGTGGAACA
196 TTCCTACATAGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCATCAGTTGCAATGGAACA
* * * * * *
18192620 GGTTAAATATGGCAGATCTTGCCTTTCTGCATAGACAGTGAAGCAGATCGAAGACCCCAGCCTTG
261 GGTTAAAGATAGCAGATCTTGCCCTCCTGCATAGACAGCGAAGCAGATCGAAGACACCAGCCTTG
**
18192685 CCTCCAAT-GGTTGCAGTGGAGCGGGT
326 CCTCC-ATCGGTTGCAGTGGAGCACGT
* * * *
18192711 TAAATATAACAGATCTTGCCTTCCTGCATTGACAGCGAAGTAGATCGAAAA-CAAAGCCTTGCCT
1 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGTAGATCGAAAAGCAAAACCTTGCAT
* * * * * * * *
18192775 CCATCTG-TAGTAGTGGAGCGGGTTAAAGATAGTAGATCTTGCAC-TCCTGCGCTGATAGCGAAG
66 CCAACGGTTA-CAGTGGAGCGGGTTAAAGATAGCAGATCTTAC-CTTCCTGCACTGACAACGAAG
* * *
18192838 CAGATCGAAGACCCCAGCCTTGCCTCCATCGGTTACAGTGGAGCGGGTTAAAGATAGCAGATCTT
129 CAGATCGAA-AACCAAGCCTTGCCTCCATCGGTTACAGTGGAGCAGGTTAAAGATAGCAGATCTT
* *
18192903 GCCTTCCTACACT-GACAGCGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTCAGTTGCAATGG
193 GCCTTCCTACA-TAGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCATCAGTTGCAATGG
*
18192967 AACAGGTTAAAGATAGCAGATCTTGCCCTCCTGCGCT-GACAGCGAAGCAGATCGAAGACACCAG
257 AACAGGTTAAAGATAGCAGATCTTGCCCTCCTGC-ATAGACAGCGAAGCAGATCGAAGACACCAG
*
18193031 CCTTGCCTCCCTCGGTTGCAGTGGAGCACGT
321 CCTTGCCTCCATCGGTTGCAGTGGAGCACGT
* * * * *
18193062 TGAAGATAGCAGATCTTGCTTTCCTTCATCGACAGTGAAGTAGATCGAA
1 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGTAGATCGAA
18193111 GATTACAAGT
Statistics
Matches: 347, Mismatches: 46, Indels: 13
0.85 0.11 0.03
Matches are distributed among these distances:
349 2 0.01
350 113 0.33
351 230 0.66
352 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (351 bp):
TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGTAGATCGAAAAGCAAAACCTTGCAT
CCAACGGTTACAGTGGAGCGGGTTAAAGATAGCAGATCTTACCTTCCTGCACTGACAACGAAGCA
GATCGAAAACCAAGCCTTGCCTCCATCGGTTACAGTGGAGCAGGTTAAAGATAGCAGATCTTGCC
TTCCTACATAGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCATCAGTTGCAATGGAACA
GGTTAAAGATAGCAGATCTTGCCCTCCTGCATAGACAGCGAAGCAGATCGAAGACACCAGCCTTG
CCTCCATCGGTTGCAGTGGAGCACGT
Found at i:18193080 original size:44 final size:43
Alignment explanation
Indices: 18192856--18193080 Score: 118
Period size: 44 Copynumber: 5.1 Consensus size: 43
18192846 AGACCCCAGC
* * * *
18192856 CTTGCCTCCATCGGTTACAGTGGAGCGGGTTAAAGATAGCAGAT
1 CTTGCCTCCCTCGGTTGCAGTGGAGC-AGTTGAAGATAGCAGAT
* ** * * * * *
18192900 CTTGCCTTCCTAC-ACTGACAGCGAAGCAGATCGAAGATACCAG-C
1 CTTGCCTCCCT-CGGTTG-CAGTGGAGCAG-TTGAAGATAGCAGAT
* * * *
18192944 CTTGCCTCCCTCAGTTGCAATGGAACAGGTTAAAGATAGCAGAT
1 CTTGCCTCCCTCGGTTGCAGTGGAGCA-GTTGAAGATAGCAGAT
* * * * * * *
18192988 CTTGCC-CTCCT-GCGCTGACAGCGAAGCAGATCGAAGACACCAG-C
1 CTTGCCTC-CCTCG-GTTG-CAGTGGAGCAG-TTGAAGATAGCAGAT
18193032 CTTGCCTCCCTCGGTTGCAGTGGAGCACGTTGAAGATAGCAGAT
1 CTTGCCTCCCTCGGTTGCAGTGGAGCA-GTTGAAGATAGCAGAT
18193076 CTTGC
1 CTTGC
18193081 TTTCCTTCAT
Statistics
Matches: 126, Mismatches: 41, Indels: 28
0.65 0.21 0.14
Matches are distributed among these distances:
43 36 0.29
44 55 0.44
45 35 0.28
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (43 bp):
CTTGCCTCCCTCGGTTGCAGTGGAGCAGTTGAAGATAGCAGAT
Found at i:18193760 original size:17 final size:17
Alignment explanation
Indices: 18193734--18193767 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18193724 TTCCCTGGCC
*
18193734 CAAATCAAATAAATAAA
1 CAAATAAAATAAATAAA
18193751 CAAATAAAATAAATAAA
1 CAAATAAAATAAATAAA
18193768 TAAAACCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.18
Consensus pattern (17 bp):
CAAATAAAATAAATAAA
Found at i:18193762 original size:13 final size:13
Alignment explanation
Indices: 18193739--18193772 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
18193729 TGGCCCAAAT
18193739 CAAAT-AAATAAA
1 CAAATAAAATAAA
18193751 CAAATAAAATAAA
1 CAAATAAAATAAA
*
18193764 TAAATAAAA
1 CAAATAAAA
18193773 CCAAGTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (13 bp):
CAAATAAAATAAA
Found at i:18202877 original size:11 final size:11
Alignment explanation
Indices: 18202861--18202886 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18202851 TTGCTTTAAT
18202861 TGCTATCTTTA
1 TGCTATCTTTA
18202872 TGCTATCTTTA
1 TGCTATCTTTA
18202883 TGCT
1 TGCT
18202887 TTATTGATAA
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:0.15, C:0.19, G:0.12, T:0.54
Consensus pattern (11 bp):
TGCTATCTTTA
Found at i:18204627 original size:25 final size:25
Alignment explanation
Indices: 18204539--18204628 Score: 67
Period size: 25 Copynumber: 3.6 Consensus size: 25
18204529 TCATGTACAT
* * *
18204539 GTATGCTCATACGAGCTGTGAATTG
1 GTATGATCATACGAGCTATAAATTG
* * * * *
18204564 GTATGGTCACT-TGAACTATAGATCG
1 GTATGATCA-TACGAGCTATAAATTG
*
18204589 GTATGTTC-TCACGAGCTATAAATTG
1 GTATGATCAT-ACGAGCTATAAATTG
18204614 GTATGATCATACGAG
1 GTATGATCATACGAG
18204629 TTGTAGGTCG
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
23 1 0.02
25 45 0.94
26 2 0.04
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (25 bp):
GTATGATCATACGAGCTATAAATTG
Found at i:18209961 original size:17 final size:17
Alignment explanation
Indices: 18209906--18209960 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
18209896 TCTAATTGCC
18209906 AATTGATACCTTTAACT
1 AATTGATACCTTTAACT
*
18209923 AATTGA-A-CTTCATAGCT
1 AATTGATACCTT--TAACT
*
18209940 AATTTATACCTTTAACT
1 AATTGATACCTTTAACT
18209957 AATT
1 AATT
18209961 TTATGTCCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 3 0.10
16 1 0.03
17 23 0.74
18 1 0.03
19 3 0.10
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.42
Consensus pattern (17 bp):
AATTGATACCTTTAACT
Found at i:18224173 original size:12 final size:12
Alignment explanation
Indices: 18224156--18224183 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
18224146 TTACATGCCC
18224156 GTGTGTTAGGCT
1 GTGTGTTAGGCT
18224168 GTGTGTTAGGCT
1 GTGTGTTAGGCT
18224180 GTGT
1 GTGT
18224184 AAATTCCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.43, T:0.43
Consensus pattern (12 bp):
GTGTGTTAGGCT
Found at i:18227981 original size:29 final size:29
Alignment explanation
Indices: 18227949--18228192 Score: 267
Period size: 29 Copynumber: 8.4 Consensus size: 29
18227939 CTTCGTCACC
18227949 ATCCCTTTTCATAATCGATAGCCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
* *
18227978 ATCCCTTTTAATAATCGATTGCCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
18228007 ATCCCTTTTCATAATCGATAGCCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
* * * * *
18228036 ATCCCTTTTTATATTCGATGGTCGTCA-CT
1 ATCCCTTTTCATAATCGATAGCCG-AAGCT
* * * * * * *
18228065 GTCCCTTTTCATAGTTGATGGTCGTCA-CC
1 ATCCCTTTTCATAATCGATAGCCG-AAGCT
*
18228094 ATCCCTTTTCATAATCGATAGCCAAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
* * *
18228123 ATCCCTTTTCATATTCGATAACTGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
* *
18228152 ATCCCTTTTCATATTCGATACCCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
*
18228181 ATCCTTTTTCAT
1 ATCCCTTTTCAT
18228193 TGGTCAATGA
Statistics
Matches: 184, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
28 1 0.01
29 182 0.99
30 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCCGAAGCT
Found at i:18235796 original size:18 final size:17
Alignment explanation
Indices: 18235763--18235801 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
18235753 TTTTATAAAT
18235763 TGTGAATTATATTTGACA
1 TGTGAATTATATTTGA-A
18235781 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
18235798 TGTG
1 TGTG
18235802 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.44
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:18236062 original size:23 final size:23
Alignment explanation
Indices: 18236027--18236108 Score: 119
Period size: 23 Copynumber: 3.6 Consensus size: 23
18236017 AGTGTTATTG
* *
18236027 ATCAATGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* *
18236050 CTCAGTGGTAGCTACGACTACAT
1 ATCAGTGGTAGCTACGGCTACAT
*
18236073 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
18236096 ATCAGTGGTAGCT
1 ATCAGTGGTAGCT
18236109 TCGTTAGGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (23 bp):
ATCAGTGGTAGCTACGGCTACAT
Found at i:18236139 original size:16 final size:17
Alignment explanation
Indices: 18236118--18236151 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
18236108 TTCGTTAGGG
*
18236118 GCAAAAGT-TTAATTTT
1 GCAAAAGTATGAATTTT
18236134 GCAAAAGTATGAATTTT
1 GCAAAAGTATGAATTTT
18236151 G
1 G
18236152 GACTAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (17 bp):
GCAAAAGTATGAATTTT
Found at i:18237367 original size:219 final size:219
Alignment explanation
Indices: 18236982--18237412 Score: 639
Period size: 219 Copynumber: 2.0 Consensus size: 219
18236972 CATTGAAATG
*
18236982 TTAAGTTATATTCATGATTTACGTACATACTAAGCATTATATGCTTACACAGTCTTCTTTCTCAT
1 TTAAGTTATATTCATGATTTACGAACATACTAAGCATTATATGCTTACACAGTCTTCTTTCTCAT
* * * * *
18237047 TTTTTTTATAATCGGAAGCTCAATCGGTTTGGAAGTTTGTCGAAGATCTATCACACTATCCAGTG
66 GTTTTTTATAATAGGAAGCTCAATCAGTTTGGAAGCTCGTCGAAGATCTATCACACTATCCAGTG
* * * *
18237112 AATATATTGTTAGGTTTTTATGTTTTGGCTAAGGTTATAATGGCATGTATAGGTGGACTTGTGTT
131 AATACATTGGTAGGTTTTTATGTTTTGGCCAAGGTTATAATGGCATGTATAGGTGGACTTATGTT
*
18237177 TAATGGTCTTGTTGATAGGTGGAC
196 TAATGCTCTTGTTGATAGGTGGAC
* * ** * *
18237201 TTAAGTTATATTCATGATTTACGAACTTACTAATCATTATATGCTTACGTAGTTTTCTTTTTCAT
1 TTAAGTTATATTCATGATTTACGAACATACTAAGCATTATATGCTTACACAGTCTTCTTTCTCAT
* * * * *
18237266 GTTTTTTATAATAGGAAGCTCGATTAGTTTTGACGCTCGTCGGAGATCTATCACACTATCCAGTG
66 GTTTTTTATAATAGGAAGCTCAATCAGTTTGGAAGCTCGTCGAAGATCTATCACACTATCCAGTG
*
18237331 AATACATTGGTA-GTTTTTGATGTTTTGGCCAAGGTTATAATGGCTTGTATAGGTGGACTTATGT
131 AATACATTGGTAGGTTTTT-ATGTTTTGGCCAAGGTTATAATGGCATGTATAGGTGGACTTATGT
18237395 TTAATGCTCTTGTTGATA
195 TTAATGCTCTTGTTGATA
18237413 TGGTTAGCAT
Statistics
Matches: 188, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
218 6 0.03
219 182 0.97
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.42
Consensus pattern (219 bp):
TTAAGTTATATTCATGATTTACGAACATACTAAGCATTATATGCTTACACAGTCTTCTTTCTCAT
GTTTTTTATAATAGGAAGCTCAATCAGTTTGGAAGCTCGTCGAAGATCTATCACACTATCCAGTG
AATACATTGGTAGGTTTTTATGTTTTGGCCAAGGTTATAATGGCATGTATAGGTGGACTTATGTT
TAATGCTCTTGTTGATAGGTGGAC
Found at i:18242939 original size:15 final size:15
Alignment explanation
Indices: 18242919--18242952 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18242909 AAAAGTGTCA
18242919 TCTTCTTCAAACTG-T
1 TCTTCTTC-AACTGAT
18242934 TCTTCTTCAACTGAT
1 TCTTCTTCAACTGAT
18242949 TCTT
1 TCTT
18242953 TAAGAGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.18, C:0.26, G:0.06, T:0.50
Consensus pattern (15 bp):
TCTTCTTCAACTGAT
Found at i:18244653 original size:220 final size:220
Alignment explanation
Indices: 18244250--18244674 Score: 649
Period size: 220 Copynumber: 1.9 Consensus size: 220
18244240 ATTGAAATGG
*
18244250 TAAGTTATATTCATAATTTACGAACTTACCAAGCATTATATGCTTACGTAGTTTTCTTTCTCATG
1 TAAGTTATATGCATAATTTACGAACTTACCAAGCATTATATGCTTACGTAGTTTTCTTTCTCATG
* * **
18244315 TTTTTTTAAAATCAGAAGCTCGATAGGTTTGGAAGCTTGTTGGAGATCTATCACACTATCCAACG
66 TTTTTTCAAAATCAGAAGCTCGATAGGTTTGGAAGCTCGTCAGAGATCTATCACACTATCCAACG
*
18244380 AATATATCGATAGTTTTTTATGTTTTGGCCAAGGTTATAATGGCATGTATAGGTGGACTTTTATT
131 AATATATCGATAGTTTTTTATGTTTTGGCCAAGGTTATAATGGCATGTATAGGTGGACTTGTATT
18244445 TAATGATCTTCTTTATAGGTGGAAT
196 TAATGATCTTCTTTATAGGTGGAAT
* * * *
18244470 TAAGTTGTATGCATGATTTATGAACTTACTAAGCATTATATGCTTACGTAGTTTTCTTTCGT-AT
1 TAAGTTATATGCATAATTTACGAACTTACCAAGCATTATATGCTTACGTAGTTTTCTTTC-TCAT
* * *
18244534 -TTTTTTCATAATCGGAAGCTCGATCA-GTTTGGAAGCTCGTCAGAGATCTATCACACTATCCAG
65 GTTTTTTCAAAATCAGAAGCTCGAT-AGGTTTGGAAGCTCGTCAGAGATCTATCACACTATCCAA
* * *
18244597 CGAATATATGGGTAGTTTTTTTATGTTTTGGCCAAGGTTATAGTGGCATGTATAGGTGGACTTGT
129 CGAATATATCGATAG-TTTTTTATGTTTTGGCCAAGGTTATAATGGCATGTATAGGTGGACTTGT
*
18244662 GTTTAATGATCTT
193 ATTTAATGATCTT
18244675 GTTGATATGG
Statistics
Matches: 185, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
219 67 0.36
220 117 0.63
221 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (220 bp):
TAAGTTATATGCATAATTTACGAACTTACCAAGCATTATATGCTTACGTAGTTTTCTTTCTCATG
TTTTTTCAAAATCAGAAGCTCGATAGGTTTGGAAGCTCGTCAGAGATCTATCACACTATCCAACG
AATATATCGATAGTTTTTTATGTTTTGGCCAAGGTTATAATGGCATGTATAGGTGGACTTGTATT
TAATGATCTTCTTTATAGGTGGAAT
Found at i:18249599 original size:107 final size:107
Alignment explanation
Indices: 18249471--18249684 Score: 410
Period size: 107 Copynumber: 2.0 Consensus size: 107
18249461 AAATATCTCA
*
18249471 AAATATATAACTTCTTTTGTTGCTCTATTTCTTTTATGTAAAAATATACTCATTAAGCTTTCATT
1 AAATATATAACTTCTTTTGTTGCTCTATTTCTTTTATGTAAAAATATACTCATTAAGCTTTCAGT
*
18249536 TCATATTTTATTCACTCTGTAATTCAATTTCCATCATTTTTG
66 TCATATTTTATTCACTCTCTAATTCAATTTCCATCATTTTTG
18249578 AAATATATAACTTCTTTTGTTGCTCTATTTCTTTTATGTAAAAATATACTCATTAAGCTTTCAGT
1 AAATATATAACTTCTTTTGTTGCTCTATTTCTTTTATGTAAAAATATACTCATTAAGCTTTCAGT
18249643 TCATATTTTATTCACTCTCTAATTCAATTTCCATCATTTTTG
66 TCATATTTTATTCACTCTCTAATTCAATTTCCATCATTTTTG
18249685 GTGATTTTTC
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 105 1.00
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (107 bp):
AAATATATAACTTCTTTTGTTGCTCTATTTCTTTTATGTAAAAATATACTCATTAAGCTTTCAGT
TCATATTTTATTCACTCTCTAATTCAATTTCCATCATTTTTG
Found at i:18249756 original size:16 final size:16
Alignment explanation
Indices: 18249735--18249766 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18249725 ATTTTGTTGC
*
18249735 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
18249751 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
18249767 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:18250061 original size:51 final size:51
Alignment explanation
Indices: 18249996--18250133 Score: 172
Period size: 51 Copynumber: 2.7 Consensus size: 51
18249986 GGTTCACATT
* * * **
18249996 TAGCCTACACATAGTACTACACATGTGACTATCACTATCCGATACACGTAG
1 TAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGATACACAAAG
* * *
18250047 TAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGGTACGCAAAG
1 TAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGATACACAAAG
18250098 TAGCCTGCACATAGTACTACACACGTGACCATCACT
1 TAGCCTGCACATAGTACTACACACGTGACCATCACT
18250134 TTTACTTTCA
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
50 3 0.04
51 69 0.92
52 3 0.04
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (51 bp):
TAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGATACACAAAG
Found at i:18259380 original size:49 final size:49
Alignment explanation
Indices: 18259303--18259402 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
18259293 TCCTATAGAG
* ** * *
18259303 AACATATGAAAAGCATTAAACATGTTATATTCTTTCCAAAAGGAATTAT
1 AACATATGAAAAGCATTAAAAAAATTATATTATTTCCAAAAAGAATTAT
* *
18259352 AACATATGAAAAGTATTAAAAAAATTATATTATTTCCAAAAATAATTAT
1 AACATATGAAAAGCATTAAAAAAATTATATTATTTCCAAAAAGAATTAT
18259401 AA
1 AA
18259403 ATGTTTCAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (49 bp):
AACATATGAAAAGCATTAAAAAAATTATATTATTTCCAAAAAGAATTAT
Found at i:18261773 original size:42 final size:42
Alignment explanation
Indices: 18261727--18261828 Score: 100
Period size: 42 Copynumber: 2.5 Consensus size: 42
18261717 GTCACACGGT
* **
18261727 CGTGTACCTTAGTCACA-AGGGTGTGTCCCTCAGCCACACAAC
1 CGTGTACCTTACTCACACA-GGCATGTCCCTCAGCCACACAAC
* * * **
18261769 CGTGTATCTCACTCACACAGGCATGTCCCTCAGTCACACGGC
1 CGTGTACCTTACTCACACAGGCATGTCCCTCAGCCACACAAC
*
18261811 CGTGTACCTTGC-CACACA
1 CGTGTACCTTACTCACACA
18261829 CTCTGGGCCT
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
41 6 0.12
42 41 0.85
43 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.22
Consensus pattern (42 bp):
CGTGTACCTTACTCACACAGGCATGTCCCTCAGCCACACAAC
Found at i:18263696 original size:39 final size:39
Alignment explanation
Indices: 18263641--18263742 Score: 141
Period size: 39 Copynumber: 2.6 Consensus size: 39
18263631 AACATGTTTT
*
18263641 TGAGTATTGTGATATATGGTTAAATGTTATGTCATTACA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTCATTACA
* * * *
18263680 TGAGTATTGTGCTATATACTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTCATTACA
* *
18263719 TGTGTAATGTGATATATGCTTAAA
1 TGAGTATTGTGATATATGCTTAAA
18263743 AGTGAATATG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTCATTACA
Found at i:18264957 original size:33 final size:33
Alignment explanation
Indices: 18264915--18264980 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
18264905 GATCCTTAAG
18264915 ATTGTTCGAAAGGGATTTTTTAGGATAAACATT
1 ATTGTTCGAAAGGGATTTTTTAGGATAAACATT
*
18264948 ATTGTTCGAAAGTGATTTTTTAGGATAAACATT
1 ATTGTTCGAAAGGGATTTTTTAGGATAAACATT
18264981 GTTTGGTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (33 bp):
ATTGTTCGAAAGGGATTTTTTAGGATAAACATT
Found at i:18266186 original size:42 final size:42
Alignment explanation
Indices: 18266097--18266198 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 42
18266087 CTCACACGGC
* * *
18266097 CGTGTACCTTAGTCACATGGGCATGTCCTTAAGCCACACAGT
1 CGTGTACCTTAGTCACACGGGCATGCCCTTAAGCCACACAGA
* * **
18266139 TGTGTATCTTAGTCACACGGGCATGCCCCTT-AGCCACATGGA
1 CGTGTACCTTAGTCACACGGGCATG-CCCTTAAGCCACACAGA
*
18266181 CGTGTACCCTA-TCACACG
1 CGTGTACCTTAGTCACACG
18266199 ATCTTGACCT
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 7 0.14
42 38 0.78
43 4 0.08
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (42 bp):
CGTGTACCTTAGTCACACGGGCATGCCCTTAAGCCACACAGA
Found at i:18270923 original size:16 final size:16
Alignment explanation
Indices: 18270892--18270928 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
18270882 ATATGTAGAA
18270892 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
18270908 TATT-TTTAAAAGTTAT
1 TATTATTTAAAA-TTAT
18270924 TATTA
1 TATTA
18270929 AATAAAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:18276593 original size:18 final size:20
Alignment explanation
Indices: 18276552--18276598 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
18276542 ATATGTGTAC
18276552 ATATATAAGGTATATAAATA
1 ATATATAAGGTATATAAATA
18276572 ATATATAA-GTATGA-AAATA
1 ATATATAAGGTAT-ATAAATA
18276591 TATATATA
1 -ATATATA
18276599 CAAATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (20 bp):
ATATATAAGGTATATAAATA
Found at i:18276651 original size:24 final size:23
Alignment explanation
Indices: 18276618--18276663 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
18276608 TTAAAAAAAT
* *
18276618 ATGTACGTATGTATATATGACAAA
1 ATGTAAGTATGTACATAT-ACAAA
18276642 ATGTAAGTATGTACATATACAA
1 ATGTAAGTATGTACATATACAA
18276664 CAAAATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (23 bp):
ATGTAAGTATGTACATATACAAA
Found at i:18276737 original size:18 final size:18
Alignment explanation
Indices: 18276686--18276743 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
18276676 CTAAAATGAC
18276686 ATAAATAGGTAAATCATA
1 ATAAATAGGTAAATCATA
* * *
18276704 A-CAATA-AT-AATAATA
1 ATAAATAGGTAAATCATA
18276719 ATAAATAGGTAAATCATA
1 ATAAATAGGTAAATCATA
*
18276737 ACAAATA
1 ATAAATA
18276744 AAGGATTAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
15 7 0.23
16 5 0.17
17 5 0.17
18 13 0.43
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (18 bp):
ATAAATAGGTAAATCATA
Found at i:18280932 original size:50 final size:50
Alignment explanation
Indices: 18280808--18281184 Score: 406
Period size: 50 Copynumber: 7.6 Consensus size: 50
18280798 GATAATAACA
* * ** * * *
18280808 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCCTGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * ** *
18280857 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *** *
18280907 TGTCC-ATGCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCCCGG
1 TG-CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
18280957 TGCCAACGCCATGTCCCAAACACGATGTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
18281007 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
18281057 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
18281107 TGCCAACGCTATGTCCCAGACATGGTCTTACACT-GG--CTCACATATCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCATCTCGG
* * *
18281155 TGTCGATGCCATGTCCCAGACATGGTCTTA
1 TGCCAACGCCATGTCCCAGACATGGTCTTA
18281185 TATGAGATCG
Statistics
Matches: 280, Mismatches: 43, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
48 36 0.13
49 39 0.14
50 202 0.72
51 3 0.01
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:18284619 original size:43 final size:44
Alignment explanation
Indices: 18284411--18284640 Score: 197
Period size: 43 Copynumber: 5.3 Consensus size: 44
18284401 CTAAGATAAC
**
18284411 TGTATTGGAATCACCATTCATTTGCATTTGCAAAATCTTAGTAT
1 TGTATTGGAATCATTATTCATTTGCATTTGCAAAATCTTAGTAT
* * * * *
18284455 CGTATT-GAA--ATTA-TCA-TT-CCTTTGCAACATTTTAGTTT
1 TGTATTGGAATCATTATTCATTTGCATTTGCAAAATCTTAGTAT
* * *
18284493 TGTATTGGAATCATTATGGT-AATTGTATTGGTTGGAAAATCTTAGTAT
1 TGTATTGGAATCATTAT--TCATTTGCA-T--TTGCAAAATCTTAGTAT
* **
18284541 TGTAATGGAATCACCATTCATTTGCATTTGCAAAATCTTAGTAT
1 TGTATTGGAATCATTATTCATTTGCATTTGCAAAATCTTAGTAT
** * *
18284585 TGTATTGGAAT-ATTATTCATTTGTGTTTGTAAAATCTTAGTAC
1 TGTATTGGAATCATTATTCATTTGCATTTGCAAAATCTTAGTAT
*
18284628 TGTATCGGAATCA
1 TGTATTGGAATCA
18284641 CTATGGTAAT
Statistics
Matches: 145, Mismatches: 28, Indels: 26
0.73 0.14 0.13
Matches are distributed among these distances:
38 21 0.14
39 5 0.03
40 3 0.02
41 6 0.04
43 40 0.28
44 35 0.24
46 3 0.02
47 5 0.03
48 27 0.19
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (44 bp):
TGTATTGGAATCATTATTCATTTGCATTTGCAAAATCTTAGTAT
Found at i:18303346 original size:46 final size:46
Alignment explanation
Indices: 18303276--18303452 Score: 300
Period size: 46 Copynumber: 3.8 Consensus size: 46
18303266 ACAATGCTAT
*
18303276 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
* * * *
18303322 AACTCAGTATGATTTCCGTTACTGAAATACCATACCTACTTCTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
*
18303368 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTCCTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
18303414 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTAC
18303453 GTTCCACACT
Statistics
Matches: 120, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 120 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
Found at i:18310145 original size:34 final size:36
Alignment explanation
Indices: 18310092--18310158 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
18310082 TAACAGAATT
18310092 GATACATAACAACCATACC-ATTTTGGCCATTTAAA
1 GATACATAACAACCATACCAATTTTGGCCATTTAAA
*
18310127 GATACATTAAC-A-CATACCAATTTTGGTCATTT
1 GATACA-TAACAACCATACCAATTTTGGCCATTT
18310159 CAAAACACAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 6 0.21
35 19 0.66
36 4 0.14
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (36 bp):
GATACATAACAACCATACCAATTTTGGCCATTTAAA
Found at i:18311395 original size:25 final size:26
Alignment explanation
Indices: 18311361--18311431 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 26
18311351 CCTATACATA
18311361 TATGCTCACACGAGCTGTG-AATAAG
1 TATGCTCACACGAGCTGTGAAATAAG
* *
18311386 TATGCTCACACGAGCTATGAAAATAGG
1 TATGCTCACACGAGCTGTG-AAATAAG
**
18311413 CCTGCTCACACGAGCTGTG
1 TATGCTCACACGAGCTGTG
18311432 GGTCGAAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 18 0.46
27 21 0.54
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.23
Consensus pattern (26 bp):
TATGCTCACACGAGCTGTGAAATAAG
Found at i:18326245 original size:49 final size:50
Alignment explanation
Indices: 18326155--18326252 Score: 128
Period size: 49 Copynumber: 2.0 Consensus size: 50
18326145 ACCACACAAC
* * *
18326155 CATGCGGGGCCACATGGGCATGTGGGATTACATGGCAAAATTAGGTAGGT
1 CATGCGGGGCCACACGGGCATGTGCGATTACAGGGCAAAATTAGGTAGGT
* *
18326205 CATGTGGGG-CACACGGGCCTGTGCGATTACACGGGC-AAATTAGGTAGG
1 CATGCGGGGCCACACGGGCATGTGCGATTACA-GGGCAAAATTAGGTAGG
18326253 CCGTACAGGC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 31 0.74
50 11 0.26
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.20
Consensus pattern (50 bp):
CATGCGGGGCCACACGGGCATGTGCGATTACAGGGCAAAATTAGGTAGGT
Found at i:18326530 original size:17 final size:18
Alignment explanation
Indices: 18326508--18326541 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18326498 CGTATTTTGT
*
18326508 TATCTGTTTTGA-TATGA
1 TATCTGATTTGACTATGA
18326525 TATCTGATTTGACTATG
1 TATCTGATTTGACTATG
18326542 TAACAGCCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.50
Consensus pattern (18 bp):
TATCTGATTTGACTATGA
Found at i:18327818 original size:27 final size:27
Alignment explanation
Indices: 18327787--18327857 Score: 133
Period size: 27 Copynumber: 2.6 Consensus size: 27
18327777 TTGGTGGTTT
18327787 CTAAGTGCTGATTCCCCCAAGGGGTGG
1 CTAAGTGCTGATTCCCCCAAGGGGTGG
18327814 CTAAGTGCTGATTCCCCCAAGGGGTGG
1 CTAAGTGCTGATTCCCCCAAGGGGTGG
*
18327841 CTAACTGCTGATTCCCC
1 CTAAGTGCTGATTCCCC
18327858 GAATCATTGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (27 bp):
CTAAGTGCTGATTCCCCCAAGGGGTGG
Found at i:18330973 original size:26 final size:29
Alignment explanation
Indices: 18330880--18331006 Score: 84
Period size: 26 Copynumber: 4.3 Consensus size: 29
18330870 TGTAAACATT
*
18330880 ATATATAT-T-AGTGGGTGTTATATATATA
1 ATATATATGTGAGTGGTTG-TATATATATA
** * * *
18330908 ATATATAAATGGGGGAGTTGGTAATATACATAA
1 ATATATATGTGAGTG-GTT-GT-ATATATAT-A
*
18330941 ATATATATGTGCGT-G-TGT-TATATATA
1 ATATATATGTGAGTGGTTGTATATATATA
*
18330967 ATATATATATGAGTGGGTTGTATATATATA
1 ATATATATGTGAGT-GGTTGTATATATATA
18330997 CATATATATG
1 -ATATATATG
18331007 CGTGGGAGAT
Statistics
Matches: 75, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
26 13 0.17
27 6 0.08
28 8 0.11
29 6 0.08
30 11 0.15
31 12 0.16
32 8 0.11
33 11 0.15
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.41
Consensus pattern (29 bp):
ATATATATGTGAGTGGTTGTATATATATA
Found at i:18331077 original size:39 final size:38
Alignment explanation
Indices: 18331022--18331104 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 38
18331012 GAGATTATTC
*
18331022 ATATAT-TATACATATGCATGGCTTTATTTTAATATAAT
1 ATATATATATACATATGCATGGCTTTATTTT-ATACAAT
* * *
18331060 ATATATATATATATATGCATGGTTTTATTTTATACGAT
1 ATATATATATACATATGCATGGCTTTATTTTATACAAT
18331098 ATATATA
1 ATATATA
18331105 ATTATGCGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 18 0.45
39 22 0.55
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.48
Consensus pattern (38 bp):
ATATATATATACATATGCATGGCTTTATTTTATACAAT
Found at i:18331461 original size:17 final size:17
Alignment explanation
Indices: 18331439--18331471 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
18331429 ATTTTTGTAT
18331439 TGTGTTATATT-GTGAAC
1 TGTGTTA-ATTGGTGAAC
18331456 TGTGTTAATTGGTGAA
1 TGTGTTAATTGGTGAA
18331472 TTATATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.24, C:0.03, G:0.27, T:0.45
Consensus pattern (17 bp):
TGTGTTAATTGGTGAAC
Found at i:18331697 original size:7 final size:7
Alignment explanation
Indices: 18331685--18331723 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
18331675 ATCATGCTCT
18331685 ATTGTGA
1 ATTGTGA
18331692 ATTGTGA
1 ATTGTGA
**
18331699 AAGGTGA
1 ATTGTGA
18331706 ATTGTGA
1 ATTGTGA
*
18331713 ATTGCGA
1 ATTGTGA
18331720 ATTG
1 ATTG
18331724 CGAACTGTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.36
Consensus pattern (7 bp):
ATTGTGA
Found at i:18333135 original size:2 final size:2
Alignment explanation
Indices: 18333130--18333155 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18333120 TATGTGTGTA
18333130 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
18333156 GTGGATCGAA
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:18333464 original size:41 final size:41
Alignment explanation
Indices: 18333409--18333569 Score: 277
Period size: 41 Copynumber: 3.9 Consensus size: 41
18333399 ATTGGTGAAT
*
18333409 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATC
1 TGAATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATC
* *
18333450 TGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATA
1 TGAATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATC
*
18333491 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATC
1 TGAATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATC
*
18333532 TGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTG
1 TGAATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTG
18333570 TTCCGAATAT
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 112 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (41 bp):
TGAATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATC
Found at i:18333539 original size:82 final size:82
Alignment explanation
Indices: 18333409--18333569 Score: 322
Period size: 82 Copynumber: 2.0 Consensus size: 82
18333399 ATTGGTGAAT
18333409 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAG
1 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAG
18333474 GCTAAGTGCCGGTGATA
66 GCTAAGTGCCGGTGATA
18333491 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAG
1 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAG
18333556 GCTAAGTGCCGGTG
66 GCTAAGTGCCGGTG
18333570 TTCCGAATAT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (82 bp):
TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAG
GCTAAGTGCCGGTGATA
Found at i:18333835 original size:37 final size:37
Alignment explanation
Indices: 18333794--18333883 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
18333784 TAGTTGGATA
* *
18333794 TATATTTGTATGCATTCGGCATAGTTAGATATAAGTG
1 TATATATGTATGCATTCGGCATAGGTAGATATAAGTG
* * *
18333831 TATATATGTATGCATTTGGCATAGGTGGGTATAAGTG
1 TATATATGTATGCATTCGGCATAGGTAGATATAAGTG
18333868 -A-ATATG--TGCATTCGGC
1 TATATATGTATGCATTCGGC
18333884 CTTTATAGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
33 9 0.19
35 5 0.11
36 1 0.02
37 32 0.68
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.38
Consensus pattern (37 bp):
TATATATGTATGCATTCGGCATAGGTAGATATAAGTG
Found at i:18341528 original size:50 final size:50
Alignment explanation
Indices: 18341416--18341608 Score: 253
Period size: 50 Copynumber: 3.8 Consensus size: 50
18341406 GATAATAACA
* * ** *
18341416 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * * *
18341467 TGCCCATGCCATGTTCAAGACATGGTCTTATGA-GGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTA-CATGGGACCTCTCATCTCGG
*
18341517 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
18341567 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
18341609 TTACCCAAAT
Statistics
Matches: 123, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
49 1 0.01
50 92 0.75
51 29 0.24
52 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:18349655 original size:28 final size:26
Alignment explanation
Indices: 18349610--18349705 Score: 88
Period size: 28 Copynumber: 3.5 Consensus size: 26
18349600 TGTAGAAATT
18349610 GAAAA-AAAAAGAATTGAGAGAAAAA
1 GAAAATAAAAAGAATTGAGAGAAAAA
*
18349635 GAGAAATAAAAAGAATGTGAGCGAGAAAA
1 GA-AAATAAAAAGAAT-TGAGAGA-AAAA
** *
18349664 GAAAATTGAAAGAGTTTGAGAAAGAAAAA
1 GAAAATAAAAAGA-ATTGAG--AGAAAAA
18349693 GAAAA-AAAAAGAA
1 GAAAATAAAAAGAA
18349706 AATGGAAAAC
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
25 2 0.04
26 3 0.05
27 9 0.16
28 24 0.43
29 16 0.29
30 2 0.04
ACGTcount: A:0.66, C:0.01, G:0.23, T:0.10
Consensus pattern (26 bp):
GAAAATAAAAAGAATTGAGAGAAAAA
Found at i:18353781 original size:3 final size:3
Alignment explanation
Indices: 18353773--18353807 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
18353763 AAATGTTTGA
*
18353773 AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
18353808 ATGGAGATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:18355669 original size:24 final size:25
Alignment explanation
Indices: 18355642--18355694 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
18355632 GCTTTTAACG
18355642 TTTACACGTTTT-ATCATTTT-AGCC
1 TTTACACGTTTTAATCATTTTGA-CC
**
18355666 TTTA-ATTTTTTAATCATTTTGACC
1 TTTACACGTTTTAATCATTTTGACC
18355690 TTTAC
1 TTTAC
18355695 CTTTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
23 5 0.21
24 18 0.75
25 1 0.04
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.55
Consensus pattern (25 bp):
TTTACACGTTTTAATCATTTTGACC
Found at i:18355894 original size:14 final size:15
Alignment explanation
Indices: 18355875--18355904 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
18355865 ATTAAAAGAC
18355875 ATAATATTT-TTATA
1 ATAATATTTATTATA
18355889 ATAATATTTATTATA
1 ATAATATTTATTATA
18355904 A
1 A
18355905 AAATGATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATAATATTTATTATA
Found at i:18356588 original size:25 final size:25
Alignment explanation
Indices: 18356559--18356608 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
18356549 CTTATTAATA
18356559 ATATAGATTATAAATTAAAATATATAT
1 ATATA-ATTATAAA-TAAAATATATAT
*
18356586 ATATAATTATATATAAAATATAT
1 ATATAATTATAAATAAAATATAT
18356609 TTAAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 7 0.32
27 5 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
ATATAATTATAAATAAAATATATAT
Found at i:18357677 original size:16 final size:17
Alignment explanation
Indices: 18357656--18357687 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18357646 TTTTAAATTT
18357656 TAATTA-AAAATAATAA
1 TAATTACAAAATAATAA
18357672 TAATTACAAAATAATA
1 TAATTACAAAATAATA
18357688 TGTATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
TAATTACAAAATAATAA
Found at i:18357946 original size:20 final size:19
Alignment explanation
Indices: 18357921--18358005 Score: 73
Period size: 20 Copynumber: 4.3 Consensus size: 19
18357911 AATAAGTTTC
18357921 ACTTAAATTATTTGAATTTT
1 ACTTAAATTATTT-AATTTT
* * *
18357941 ACTTAAATTGTTCAATATAGT
1 ACTTAAATTATTTAAT-T-TT
** *
18357962 AGATAGATTATTTAA-TTT
1 ACTTAAATTATTTAATTTT
18357980 ACTTAAATTATTTAAGTTTT
1 ACTTAAATTATTTAA-TTTT
18358000 ACTTAA
1 ACTTAA
18358006 TAGATAAAAT
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
18 13 0.27
19 4 0.08
20 21 0.43
21 11 0.22
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.49
Consensus pattern (19 bp):
ACTTAAATTATTTAATTTT
Found at i:18362185 original size:43 final size:42
Alignment explanation
Indices: 18362131--18362301 Score: 197
Period size: 43 Copynumber: 4.0 Consensus size: 42
18362121 ACATAGGATT
**
18362131 TCGATATGTGTTTTTGTGTAAGACCATGTCTGGGACGTTGGCA
1 TCGAT-TGTGTTTACGTGTAAGACCATGTCTGGGACGTTGGCA
*
18362174 TCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACATTGGCA
1 TCGA-TTGTGTTTACGTGTAAGACCATGTCTGGGACGTTGGCA
*
18362217 TCGTATT-TGATTT--GTGTAAGACCCTGTCTGGGACAG-TGGCA
1 TCG-ATTGTG-TTTACGTGTAAGACCATGTCTGGGAC-GTTGGCA
* * *
18362258 TCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCA
1 TCGAT-TGTGTTTACGTGTAAGACCATGTCTGGGACGTTGGCA
18362301 T
1 T
18362302 TGTACTAGTC
Statistics
Matches: 110, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
40 2 0.02
41 31 0.28
42 5 0.05
43 70 0.64
44 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (42 bp):
TCGATTGTGTTTACGTGTAAGACCATGTCTGGGACGTTGGCA
Found at i:18362289 original size:84 final size:84
Alignment explanation
Indices: 18362143--18362301 Score: 241
Period size: 84 Copynumber: 1.9 Consensus size: 84
18362133 GATATGTGTT
* * *
18362143 TTTGTGTAAGACCATGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGG
1 TTTGTGTAAGACCATGTCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGG
18362208 ACATTGGCATCGTATTTGA
66 ACATTGGCATCGTATTTGA
*
18362227 TTTGTGTAAGACCCTGTCTGGGACAG-TGGCATCGA-TATGTGATTACATGTAAGACCACGTCTG
1 TTTGTGTAAGACCATGTCTGGGAC-GTTGGCATCGACT-TGTGATTACATGTAAGACCACGTCTG
*
18362290 GGACGTTGGCAT
64 GGACATTGGCAT
18362302 TGTACTAGTC
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
83 1 0.01
84 66 0.97
85 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (84 bp):
TTTGTGTAAGACCATGTCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGG
ACATTGGCATCGTATTTGA
Found at i:18362491 original size:16 final size:17
Alignment explanation
Indices: 18362462--18362493 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
18362452 TGAATTGATG
18362462 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
18362479 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
18362494 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:18365244 original size:15 final size:15
Alignment explanation
Indices: 18365201--18365254 Score: 76
Period size: 15 Copynumber: 3.6 Consensus size: 15
18365191 ATTTAAAATG
18365201 AAAATTTAATTTTA-
1 AAAATTTAATTTTAT
18365215 AATATATTTAA-TTTAT
1 AA-A-ATTTAATTTTAT
18365231 AAAATTTAATTTTAT
1 AAAATTTAATTTTAT
18365246 AAAATTTAA
1 AAAATTTAA
18365255 AATACTTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 8 0.22
15 20 0.56
16 8 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAAATTTAATTTTAT
Found at i:18365339 original size:8 final size:8
Alignment explanation
Indices: 18365304--18365342 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
18365294 TCGTTTTAAT
18365304 AAATTTTA
1 AAATTTTA
*
18365312 AATTTTATA
1 AAATTT-TA
18365321 AAATTTT-
1 AAATTTTA
18365328 AAATTTTA
1 AAATTTTA
18365336 AAATTTT
1 AAATTTT
18365343 GATATTTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 7 0.26
8 13 0.48
9 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
AAATTTTA
Found at i:18365350 original size:15 final size:15
Alignment explanation
Indices: 18365304--18365342 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 15
18365294 TCGTTTTAAT
18365304 AAATTTTAAATTTTATA
1 AAATTTTAAA-TTT-TA
18365321 AAATTTTAAATTTTA
1 AAATTTTAAATTTTA
18365336 AAATTTT
1 AAATTTT
18365343 GATATTTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 9 0.41
16 3 0.14
17 10 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AAATTTTAAATTTTA
Found at i:18365588 original size:2 final size:2
Alignment explanation
Indices: 18365581--18365611 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
18365571 CAACCTTGTA
18365581 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18365612 GTTAGGTCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:18366219 original size:2 final size:2
Alignment explanation
Indices: 18366208--18366244 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
18366198 ATGTGAAAAC
18366208 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
18366245 GGGCAGAGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18368540 original size:12 final size:14
Alignment explanation
Indices: 18368507--18368544 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
18368497 TTTAAATGAT
*
18368507 ATTTTTATTAAATA
1 ATTTTTATTTAATA
18368521 ATTTTTATTTAAT-
1 ATTTTTATTTAATA
18368534 A-TTTTATTTAA
1 ATTTTTATTTAA
18368545 AATATTAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.43
13 1 0.04
14 12 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTTTATTTAATA
Found at i:18368567 original size:18 final size:20
Alignment explanation
Indices: 18368533--18368569 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
18368523 TTTTATTTAA
18368533 TATTTTATTTAAAATATTAG
1 TATTTTATTTAAAATATTAG
18368553 TATTTTA-TT-AAATATTA
1 TATTTTATTTAAAATATTA
18368570 TTATAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TATTTTATTTAAAATATTAG
Found at i:18371964 original size:91 final size:91
Alignment explanation
Indices: 18371786--18371991 Score: 254
Period size: 91 Copynumber: 2.3 Consensus size: 91
18371776 GATTAATCAT
* * *
18371786 CTGCAAACACTGGTTGTTTATCCACAAACTTACTGGCAACTTTTATCTACAAACAGGTTGTGCAT
1 CTGCAAAAACTGGTGGTTTATCCACAAACTTACTGGCAACTTTTATCTACAAACACGTTGTGCAT
* *
18371851 TCACAACCCACTAGCAGTGTATTAAC
66 TCACAACCCAATAGCAGCGTATTAAC
* * * * *
18371877 TTGTAAAAATTGGTGGTTCATCCAGAAACTTACTGGCAA-TTATTATCTACAAACACGTTGTGCA
1 CTGCAAAAACTGGTGGTTTATCCACAAACTTACTGGCAACTT-TTATCTACAAACACGTTGTGCA
** *
18371941 TTCAGTACCTAAT-GTCAGCGTATTAAC
65 TTCACAACCCAATAG-CAGCGTATTAAC
*
18371968 CTGCAAACACTGGTGGTTTATCCA
1 CTGCAAAAACTGGTGGTTTATCCA
18371992 AAAATTGGAG
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
90 3 0.03
91 92 0.97
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (91 bp):
CTGCAAAAACTGGTGGTTTATCCACAAACTTACTGGCAACTTTTATCTACAAACACGTTGTGCAT
TCACAACCCAATAGCAGCGTATTAAC
Found at i:18374884 original size:30 final size:30
Alignment explanation
Indices: 18374848--18374920 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
18374838 AGATTCGATT
*
18374848 TCTTGATTTTCTTGAAAATAAGAATGTGAA
1 TCTTGATTTTCTTGAAAATAAGAAAGTGAA
18374878 TCTTGATTTTCTTGAAAATAAGAAAGTGAA
1 TCTTGATTTTCTTGAAAATAAGAAAGTGAA
18374908 TCTTGATTTTCTT
1 TCTTGATTTTCTT
18374921 TTTCCTTTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (30 bp):
TCTTGATTTTCTTGAAAATAAGAAAGTGAA
Found at i:18388630 original size:17 final size:18
Alignment explanation
Indices: 18388608--18388650 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
18388598 TAATGAACGT
*
18388608 CAAATAATCAATA-AATA
1 CAAATAAGCAATACAATA
18388625 CAAATAAGCAATACAATA
1 CAAATAAGCAATACAATA
*
18388643 CACATAAG
1 CAAATAAG
18388651 AGCAATAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.60, C:0.16, G:0.05, T:0.19
Consensus pattern (18 bp):
CAAATAAGCAATACAATA
Found at i:18389373 original size:23 final size:23
Alignment explanation
Indices: 18389293--18389408 Score: 96
Period size: 23 Copynumber: 5.0 Consensus size: 23
18389283 TAACAAATAC
* * *
18389293 ATGATAAATGT-AAGTAATGTTA
1 ATGATAAATTTAAAATAATATTA
*
18389315 ATGATAAATTTAAAATAATAATA
1 ATGATAAATTTAAAATAATATTA
*
18389338 CATTG-TAAA-TTAAAATAATATTG
1 -A-TGATAAATTTAAAATAATATTA
18389361 ATGATAAATTTAAAAGTAATATTA
1 ATGATAAATTTAAAA-TAATATTA
* *
18389385 A-GCTTAAATATAAAAATAATATTA
1 ATG-ATAAAT-TTAAAATAATATTA
18389409 GATTTAAAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
21 2 0.03
22 15 0.19
23 27 0.35
24 26 0.34
25 7 0.09
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (23 bp):
ATGATAAATTTAAAATAATATTA
Found at i:18389393 original size:46 final size:48
Alignment explanation
Indices: 18389315--18389407 Score: 122
Period size: 46 Copynumber: 2.0 Consensus size: 48
18389305 AGTAATGTTA
*
18389315 ATGATAAATTTAAAATAATAATACATTGTAAAT-T-AAAATAATATTG
1 ATGATAAATTTAAAATAATAATACACTGTAAATATAAAAATAATATTG
*
18389361 ATGATAAATTTAAAAGTAATATTA-AGCT-TAAATATAAAAATAATATT
1 ATGATAAATTTAAAA-TAATAATACA-CTGTAAATATAAAAATAATATT
18389408 AGATTTAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
46 21 0.51
47 9 0.22
48 11 0.27
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (48 bp):
ATGATAAATTTAAAATAATAATACACTGTAAATATAAAAATAATATTG
Found at i:18389415 original size:24 final size:23
Alignment explanation
Indices: 18389319--18389422 Score: 79
Period size: 24 Copynumber: 4.4 Consensus size: 23
18389309 ATGTTAATGA
* * *
18389319 TAAATTTAAAATAATAATACATT
1 TAAATTAAAAATAATATTAGATT
*
18389342 GTAAATT-AAAATAATATT-GATGA
1 -TAAATTAAAAATAATATTAGAT-T
* *
18389365 TAAATTTAAAAGTAATATTA-AGCT
1 TAAA-TTAAAAATAATATTAGA-TT
18389389 TAAATATAAAAATAATATTAGATT
1 TAAAT-TAAAAATAATATTAGATT
18389413 TAAAATTAAA
1 T-AAATTAAA
18389423 TATATAAATT
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
22 6 0.09
23 13 0.20
24 40 0.62
25 5 0.08
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (23 bp):
TAAATTAAAAATAATATTAGATT
Found at i:18390495 original size:17 final size:17
Alignment explanation
Indices: 18390473--18390507 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
18390463 GGTTACTGTT
18390473 TTAGGCTAGGCTTTGTA
1 TTAGGCTAGGCTTTGTA
* *
18390490 TTAGGCTTGGGTTTGTA
1 TTAGGCTAGGCTTTGTA
18390507 T
1 T
18390508 CGGGATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.09, G:0.31, T:0.46
Consensus pattern (17 bp):
TTAGGCTAGGCTTTGTA
Found at i:18390543 original size:17 final size:19
Alignment explanation
Indices: 18390510--18390548 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
18390500 GTTTGTATCG
*
18390510 GGATTATTTATTTGTAATT
1 GGATTATTTATTTGTAAAT
18390529 GGATT-TTTA-TTGTAAAT
1 GGATTATTTATTTGTAAAT
18390546 GGA
1 GGA
18390549 CATTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 4 0.21
19 5 0.26
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (19 bp):
GGATTATTTATTTGTAAAT
Found at i:18398428 original size:50 final size:50
Alignment explanation
Indices: 18398353--18398454 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
18398343 TTCATTAGTT
*
18398353 CTCCTAATTTTTGTCGGAGGCATTTCCGATAAGATTTCAATCTAGAGAGA
1 CTCCTAATTTTTGTCGGAGGCATTTCCAATAAGATTTCAATCTAGAGAGA
18398403 CTCCTAATTTTTGTCGGAGGCATTTCCAATAAGATTTCAATCTAGAGAGA
1 CTCCTAATTTTTGTCGGAGGCATTTCCAATAAGATTTCAATCTAGAGAGA
18398453 CT
1 CT
18398455 AACTTAATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (50 bp):
CTCCTAATTTTTGTCGGAGGCATTTCCAATAAGATTTCAATCTAGAGAGA
Found at i:18403202 original size:24 final size:23
Alignment explanation
Indices: 18403141--18403215 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 23
18403131 GTGCTGACCC
*
18403141 ACAGCTCGTGAGAGCATACCGA-TT
1 ACAGCTCGTGTGAGCATA-C-ATTT
* * *
18403165 ATAGCCCGTATGAGCATACTATTT
1 ACAGCTCGTGTGAGCATAC-ATTT
*
18403189 ACAGCTCGTGTGAGCATACATGT
1 ACAGCTCGTGTGAGCATACATTT
18403212 ACAG
1 ACAG
18403216 GATTTGACGA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
23 9 0.22
24 32 0.78
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (23 bp):
ACAGCTCGTGTGAGCATACATTT
Found at i:18404794 original size:23 final size:25
Alignment explanation
Indices: 18404750--18404796 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
18404740 TATAAGGGGC
*
18404750 AATATGTATTATTTGATTTGATTTT
1 AATATGTATTATTTGATATGATTTT
18404775 AATATGT-TTA-TTGATATGATTT
1 AATATGTATTATTTGATATGATTT
18404797 AAAAAGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.52
24 3 0.14
25 7 0.33
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (25 bp):
AATATGTATTATTTGATATGATTTT
Found at i:18404805 original size:22 final size:23
Alignment explanation
Indices: 18404762--18404805 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
18404752 TATGTATTAT
* * *
18404762 TTGATTTGATTTTAATATGTTTA
1 TTGATATGATTTTAAAAAGTTTA
18404785 TTGATATGA-TTTAAAAAGTTT
1 TTGATATGATTTTAAAAAGTTT
18404806 GAAATTTAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (23 bp):
TTGATATGATTTTAAAAAGTTTA
Found at i:18411610 original size:26 final size:27
Alignment explanation
Indices: 18411553--18411613 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
18411543 TTTTAGCAAT
** *
18411553 GGTAAAATCGTCAAATATTTTATCGAG
1 GGTAAAATCAACAAATAATTTATCGAG
* *
18411580 AGTAAAATCAACAAA-AATTTATCGGG
1 GGTAAAATCAACAAATAATTTATCGAG
18411606 GGTAAAAT
1 GGTAAAAT
18411614 TTGGATAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (27 bp):
GGTAAAATCAACAAATAATTTATCGAG
Found at i:18416159 original size:40 final size:40
Alignment explanation
Indices: 18416104--18416179 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
18416094 AAAAGATAAG
*
18416104 AAAGATTAGCCTAGAGACAAGCCATGAAAATGGACCTTAA
1 AAAGATTAGCCTAGAGACAAGCCACGAAAATGGACCTTAA
**
18416144 AAAGATTAGCCTAGAGACAAGCGGCGAAAATGGACC
1 AAAGATTAGCCTAGAGACAAGCCACGAAAATGGACC
18416180 CTGAAAATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (40 bp):
AAAGATTAGCCTAGAGACAAGCCACGAAAATGGACCTTAA
Found at i:18422923 original size:11 final size:11
Alignment explanation
Indices: 18422896--18422928 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
18422886 ACGATATTTA
*
18422896 ATTTTAGTTTT
1 ATTTTATTTTT
18422907 -TTTTATTTTT
1 ATTTTATTTTT
18422917 ATTTTATTTTT
1 ATTTTATTTTT
18422928 A
1 A
18422929 AGTTGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:18426740 original size:61 final size:61
Alignment explanation
Indices: 18426608--18426724 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 61
18426598 AAAAACAAAC
* * *
18426608 TGCCACCAAAACTAAAAGATCTAGGGAGTTTCACTGTACCTTGTTCGATTGGAAAGAAAAT
1 TGCCACCAAAACTAAAAGATCCAGGGAGTTTCACTATACCATGTTCGATTGGAAAGAAAAT
* *
18426669 TGCCACCAAAATTAGAAGATCCAGGGAGTTTCACTATACCATGTTCGATTGGAAAG
1 TGCCACCAAAACTAAAAGATCCAGGGAGTTTCACTATACCATGTTCGATTGGAAAG
18426725 CATTATGTAG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (61 bp):
TGCCACCAAAACTAAAAGATCCAGGGAGTTTCACTATACCATGTTCGATTGGAAAGAAAAT
Found at i:18435851 original size:323 final size:323
Alignment explanation
Indices: 18435263--18435899 Score: 983
Period size: 323 Copynumber: 2.0 Consensus size: 323
18435253 CTAGCTCTCG
*
18435263 TACCTTCGTTTTTGAAACTGTGAAAGATTTTGAATTTTTCCATTGATGAATCAATGTGATTTTAG
1 TACCTTCGTTTTTGAAACCGTGAAAGATTTTGAATTTTTCCATTGATGAATCAATGTGATTTTAG
* * *
18435328 ATGTTAAATGATGAATTTGAAATATTAGTTGATATGTAAAAGTATTTTGTTAAGTGATTTTGTTG
66 ATGTTAAATGATGAATTTGAAATATTAGTGGATATGTAAAAGTATTTTATTAAGTGATTTTGATG
*
18435393 AATTTTCTGATTAGGGACTAAATTGTTGAAATAGTAAAAGTACAAGGTTTTGATATGAAATTGTT
131 AATTTTCTGATTAGGGACTAAATTGTTGAAATAGTAAAAGTACAAGGTTTCGATATGAAATTGTT
* * *
18435458 CAAAAAACTGGCTGAAATGGAGGCTATGAATATTTGGCTAGTGTGAAATTTCAATAAAAATGGTT
196 CAAAAAACTGGCTGAAATGGAGGCTATGAATATTTGGCTAGTGTAAAATTTAAATAAAAATGATT
* *
18435523 AATTTGCA-TGTTTTACCCTTAGGGCCTAAATTGAATAAAAGTAAAACTTTAGGGGCAATTTTA
261 AATTTGCAGT-TTTTACCCTCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGCAATTTTA
* * * *
18435586 TACCTTCGTTTTTGAAACCGTTAAAGATTTTGAATTTTTCCATTGATGAATTACTGTGCTTTTAG
1 TACCTTCGTTTTTGAAACCGTGAAAGATTTTGAATTTTTCCATTGATGAATCAATGTGATTTTAG
* * * *
18435651 ATGTTTAATGATGAATTTGAAATGTTGGTGGATATTTAAAAGTATTTTATTAAGTGATTTTGATG
66 ATGTTAAATGATGAATTTGAAATATTAGTGGATATGTAAAAGTATTTTATTAAGTGATTTTGATG
* *
18435716 AATTTTTTTATTAGGGACTAAATTGTTGAAATAGTAAAAGTACAAGGTTTCGATATGAAATTGTT
131 AATTTTCTGATTAGGGACTAAATTGTTGAAATAGTAAAAGTACAAGGTTTCGATATGAAATTG-T
* **
18435781 TC-AAAAA-TGAGCTGAAATGGAGGCTGTGAATATTTTTCTAGTGTAAAATTTAAATAAAAATGA
195 TCAAAAAACTG-GCTGAAATGGAGGCTATGAATATTTGGCTAGTGTAAAATTTAAATAAAAATGA
* ** *
18435844 TTAATTTGTAGTTTTTAGGCTCAGGGACTAAATTGAGTAAAAGTAAAACTTTAGGG
259 TTAATTTGCAGTTTTTACCCTCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGG
18435900 ATAATTTTGT
Statistics
Matches: 284, Mismatches: 27, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
322 2 0.01
323 278 0.98
324 4 0.01
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.39
Consensus pattern (323 bp):
TACCTTCGTTTTTGAAACCGTGAAAGATTTTGAATTTTTCCATTGATGAATCAATGTGATTTTAG
ATGTTAAATGATGAATTTGAAATATTAGTGGATATGTAAAAGTATTTTATTAAGTGATTTTGATG
AATTTTCTGATTAGGGACTAAATTGTTGAAATAGTAAAAGTACAAGGTTTCGATATGAAATTGTT
CAAAAAACTGGCTGAAATGGAGGCTATGAATATTTGGCTAGTGTAAAATTTAAATAAAAATGATT
AATTTGCAGTTTTTACCCTCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGCAATTTTA
Found at i:18444087 original size:26 final size:26
Alignment explanation
Indices: 18444058--18444107 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
18444048 AAGAAGGCCA
* *
18444058 ATTTC-CAAGCTCGTGTGAGCATATTC
1 ATTTCACAA-CTCATGTGAACATATTC
18444084 ATTTCACAACTCATGTGAACATAT
1 ATTTCACAACTCATGTGAACATAT
18444108 ATGTACATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (26 bp):
ATTTCACAACTCATGTGAACATATTC
Found at i:18446235 original size:20 final size:21
Alignment explanation
Indices: 18446198--18446236 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
18446188 CCGTAGTATG
*
18446198 AAAATTTTCAAATTTTTCCTA
1 AAAATTTTCAAATGTTTCCTA
*
18446219 AAAATTTT-ATATGTTTCC
1 AAAATTTTCAAATGTTTCC
18446237 AATTTAGTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.49
Consensus pattern (21 bp):
AAAATTTTCAAATGTTTCCTA
Found at i:18457024 original size:14 final size:14
Alignment explanation
Indices: 18457005--18457036 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
18456995 TTAGGTGATT
18457005 ATATGTGTAATAGG
1 ATATGTGTAATAGG
18457019 ATATGTGTAATAGG
1 ATATGTGTAATAGG
18457033 ATAT
1 ATAT
18457037 ATGCTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (14 bp):
ATATGTGTAATAGG
Found at i:18458966 original size:22 final size:22
Alignment explanation
Indices: 18458941--18458982 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
18458931 ATATACACAT
18458941 TTTTTAACTCAAATTCATGCCC
1 TTTTTAACTCAAATTCATGCCC
18458963 TTTTTAACTCAAATTCATGC
1 TTTTTAACTCAAATTCATGC
18458983 AGTTTCGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.43
Consensus pattern (22 bp):
TTTTTAACTCAAATTCATGCCC
Found at i:18484328 original size:20 final size:20
Alignment explanation
Indices: 18484297--18484358 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
18484287 GAAAATAATT
*
18484297 TTAAAATAATTTTAACTTTA
1 TTAAAATCATTTTAACTTTA
* * **
18484317 TTGAAATCATTTTGACTTGG
1 TTAAAATCATTTTAACTTTA
**
18484337 TTAAAATCATTTGCACTTTA
1 TTAAAATCATTTTAACTTTA
18484357 TT
1 TT
18484359 TTAAAATTGT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (20 bp):
TTAAAATCATTTTAACTTTA
Found at i:18491988 original size:24 final size:23
Alignment explanation
Indices: 18491933--18491997 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
18491923 GAAAAGAAAG
*
18491933 AAAAAGTACAAGAAAA-AAGATTGA
1 AAAAAG-A-AAGAAAAGAAAATTGA
18491957 AAAGAAGAAAGAAAAGAAAATTGA
1 AAA-AAGAAAGAAAAGAAAATTGA
18491981 TAAAAAGAAAGGAAAAG
1 -AAAAAGAAA-GAAAAG
18491998 TGAGGAGTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
23 7 0.19
24 17 0.47
25 12 0.33
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (23 bp):
AAAAAGAAAGAAAAGAAAATTGA
Found at i:18505633 original size:17 final size:17
Alignment explanation
Indices: 18505590--18505636 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
18505580 GTTTATTGAT
* *
18505590 TTTTAGTCAATTATTTA
1 TTTTAGTTATTTATTTA
*
18505607 TGTTT-CTTATTTATTTA
1 T-TTTAGTTATTTATTTA
18505624 TTTTAGTTATTTA
1 TTTTAGTTATTTA
18505637 ATTTCTCTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 3 0.12
17 18 0.75
18 3 0.12
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.66
Consensus pattern (17 bp):
TTTTAGTTATTTATTTA
Found at i:18508635 original size:16 final size:16
Alignment explanation
Indices: 18508614--18508644 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
18508604 AAGAAGAAAT
18508614 AAAATGAATGAATGAA
1 AAAATGAATGAATGAA
18508630 AAAATGAATGAATGA
1 AAAATGAATGAATGA
18508645 GTATTGAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.19, T:0.19
Consensus pattern (16 bp):
AAAATGAATGAATGAA
Found at i:18537412 original size:13 final size:13
Alignment explanation
Indices: 18537394--18537418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18537384 GAGGAGTTTT
18537394 AGGTGGTGGTTGA
1 AGGTGGTGGTTGA
18537407 AGGTGGTGGTTG
1 AGGTGGTGGTTG
18537419 TTTGTTAACA
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:0.12, C:0.00, G:0.56, T:0.32
Consensus pattern (13 bp):
AGGTGGTGGTTGA
Found at i:18557171 original size:16 final size:17
Alignment explanation
Indices: 18557150--18557183 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
18557140 AAATATTATG
18557150 AAATAAA-AGCAAACAA
1 AAATAAACAGCAAACAA
*
18557166 AAATAAACATCAAACAA
1 AAATAAACAGCAAACAA
18557183 A
1 A
18557184 CGCCATCTCC
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:0.74, C:0.15, G:0.03, T:0.09
Consensus pattern (17 bp):
AAATAAACAGCAAACAA
Found at i:18567490 original size:17 final size:17
Alignment explanation
Indices: 18567454--18567492 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
18567444 GTCTCAGCCT
* *
18567454 TGTGAGGCACACGGCTG
1 TGTGAGGCACACGACCG
18567471 TGTGAGGCACACGACCG
1 TGTGAGGCACACGACCG
18567488 TGTGA
1 TGTGA
18567493 CCCCTGCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.23, G:0.38, T:0.18
Consensus pattern (17 bp):
TGTGAGGCACACGACCG
Found at i:18579894 original size:40 final size:40
Alignment explanation
Indices: 18579834--18579935 Score: 141
Period size: 40 Copynumber: 2.5 Consensus size: 40
18579824 AATTATTGAA
* * *
18579834 TGAATGCACACATGTGCCCCTAATTGTACTTCAGTACCTC
1 TGAATGCACATACGTGCCCCTAATTGTACTTCAGTACCCC
* ** *
18579874 TGAATGCACATACGTACCCCTGTTTGTACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTAATTGTACTTCAGTACCCC
18579914 TGAATGCACATACGTGCCCCTA
1 TGAATGCACATACGTGCCCCTA
18579936 TTTTTACATT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (40 bp):
TGAATGCACATACGTGCCCCTAATTGTACTTCAGTACCCC
Found at i:18579933 original size:20 final size:20
Alignment explanation
Indices: 18579867--18579934 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
18579857 TTGTACTTCA
*
18579867 GTACCTCTGAATGCACATAC
1 GTACCCCTGAATGCACATAC
** * *
18579887 GTACCCCTGTTTGTAC-TTC
1 GTACCCCTGAATGCACATAC
18579906 GGTACCCCTGAATGCACATAC
1 -GTACCCCTGAATGCACATAC
*
18579927 GTGCCCCT
1 GTACCCCT
18579935 ATTTTTACAT
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 2 0.06
20 32 0.89
21 2 0.06
ACGTcount: A:0.21, C:0.34, G:0.18, T:0.28
Consensus pattern (20 bp):
GTACCCCTGAATGCACATAC
Found at i:18583718 original size:27 final size:27
Alignment explanation
Indices: 18583674--18583782 Score: 139
Period size: 27 Copynumber: 4.1 Consensus size: 27
18583664 TCCGAACGAG
* *
18583674 CTACCCC-TGATTACTGTCTCGGTGGA
1 CTACCCCGTGATTACTGTCCCAGTGGA
**
18583700 CTACCCCGTGATTGTTGTCCCAGTGGA
1 CTACCCCGTGATTACTGTCCCAGTGGA
* *
18583727 CTACCCCGTGATTACTATCCCAGTAGA
1 CTACCCCGTGATTACTGTCCCAGTGGA
* *
18583754 CTACCCCGTGTTTACTGTCCTAGTGGA
1 CTACCCCGTGATTACTGTCCCAGTGGA
18583781 CT
1 CT
18583783 CTATTGGTTG
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
26 7 0.10
27 63 0.90
ACGTcount: A:0.17, C:0.31, G:0.21, T:0.30
Consensus pattern (27 bp):
CTACCCCGTGATTACTGTCCCAGTGGA
Found at i:18586904 original size:50 final size:51
Alignment explanation
Indices: 18586843--18586973 Score: 192
Period size: 50 Copynumber: 2.6 Consensus size: 51
18586833 TATCATTCGA
* * *
18586843 TACACGTAGTAGCCTACACATAGTACTACACACGTGATC-AAACTTTCCAG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTCCAG
* *
18586893 TTCACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTCCAG
* *
18586944 TACGCATAGTAGCCTGCACATAGTACTACA
1 TACACGTAGTAGCCTGCACATAGTACTACA
18586974 TACCGGAAGG
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 36 0.50
51 36 0.50
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (51 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTCCAG
Found at i:18590101 original size:310 final size:310
Alignment explanation
Indices: 18589534--18590142 Score: 1024
Period size: 310 Copynumber: 2.0 Consensus size: 310
18589524 CCTCCAACTC
* *
18589534 AGGGAATTCTGAAATCAATCTCAGCCTACCTCACTAAAATTTAAATATCTCAAAATATACAACTC
1 AGGGAATTCTGAAATCAATCTCACCCTACCTCACTAAAATTCAAATATCTCAAAATATACAACTC
*
18589599 TTTTGCTTGATCTGCTTCTTTTATATAAAAGAAGACTCATTAAGCTTTAATTTCATATCTCATTC
66 TTTTGCTTGATCTGCTTCTTTTATATAAAAGAAGACTCATTAAGCTTTAATTCCATATCTCATTC
** * *
18589664 AACCAATAACTTAATTTCTACAATTTATTGTGATTTTTAAAACTAACATCACTTCCACTGTTCGA
131 AACCAATAACACAATTTCTAAAATTTATTGTGATTTTTAAAACTAACATCACTTCCACTATTCGA
* *
18589729 ATCTGTTCTATTTCAATTTCACTCATTTACATAACATTACAACAATTTATTTTGTAAGCACAGTG
196 ATCTATTCTATTTCAATTTCACTCATTTACATAACATTACAACAATTTATTTTGTAAGCACAGTA
* *
18589794 CGAAACTTCATCACTCCAGTTACTCTTTAGCAAATTTTCCAAGTCAGAAT
261 CAAAACTTCATCACTCCAGTTACTCATTAGCAAATTTTCCAAGTCAGAAT
*
18589844 AGGGGATTCTGAAATCAATC-CGACCCTACCTCACTAAAATTCAAATATCTCAAAATATACAACT
1 AGGGAATTCTGAAATCAATCTC-ACCCTACCTCACTAAAATTCAAATATCTCAAAATATACAACT
* * *
18589908 CTTTTTCTTGATCTGCTTCTTTTATATGAAAGTAGACTCATTAAGCTTTAATTCCATATCTCATT
65 CTTTTGCTTGATCTGCTTCTTTTATATAAAAGAAGACTCATTAAGCTTTAATTCCATATCTCATT
* *
18589973 CAATCAATAACACAATTTCTAAAATTT-TTGGTGATTTTTCAAACTAACATCACTTCCACTATTC
130 CAACCAATAACACAATTTCTAAAATTTATT-GTGATTTTTAAAACTAACATCACTTCCACTATTC
*
18590037 GAATCTATTCTGTTTCAATTTCACTCATTTACATAACATTACAACAATTTATTTTGTAAGCACAG
194 GAATCTATTCTATTTCAATTTCACTCATTTACATAACATTACAACAATTTATTTTGTAAGCACAG
18590102 TACAAAACTTCATCACTCCAGTTACTCATTAGCAAATTTTC
259 TACAAAACTTCATCACTCCAGTTACTCATTAGCAAATTTTC
18590143 ACACTTCAAT
Statistics
Matches: 279, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
309 3 0.01
310 276 0.99
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (310 bp):
AGGGAATTCTGAAATCAATCTCACCCTACCTCACTAAAATTCAAATATCTCAAAATATACAACTC
TTTTGCTTGATCTGCTTCTTTTATATAAAAGAAGACTCATTAAGCTTTAATTCCATATCTCATTC
AACCAATAACACAATTTCTAAAATTTATTGTGATTTTTAAAACTAACATCACTTCCACTATTCGA
ATCTATTCTATTTCAATTTCACTCATTTACATAACATTACAACAATTTATTTTGTAAGCACAGTA
CAAAACTTCATCACTCCAGTTACTCATTAGCAAATTTTCCAAGTCAGAAT
Found at i:18597894 original size:51 final size:51
Alignment explanation
Indices: 18597706--18597896 Score: 201
Period size: 51 Copynumber: 3.8 Consensus size: 51
18597696 TGAAAGTGAA
* * * *
18597706 AGTGATGGTCACGTGTCTAGTACTATGTGCAGGCTACTACGTGTACCAGA-
1 AGTGATAGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT
* * * * *
18597756 A-AGATAGGTCGCATGTGTAGTACTATGTGCAGGCCACTATGCGTACCGGAT
1 AGTGATA-GTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT
* * *
18597807 AGCT--TCGATCACTTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT
1 AG-TGATAG-TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT
* *
18597858 AGTGATAGTCACATGTGTAGTACTATGTGTACGCTACTA
1 AGTGATAGTCACATGTGTAGTACTATGTGCAGGCTACTA
18597897 TGTGAATCAG
Statistics
Matches: 113, Mismatches: 21, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
49 3 0.03
50 39 0.35
51 69 0.61
52 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (51 bp):
AGTGATAGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT
Found at i:18605655 original size:28 final size:27
Alignment explanation
Indices: 18605598--18605657 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 27
18605588 AAAGTCTTTT
18605598 TTTTTTAAATTTACCGAAATAGGCCGG
1 TTTTTTAAATTTACCGAAATAGGCCGG
* *
18605625 TTTTTTAATTATTTACCGGAATGGGCC-G
1 TTTTTTAA--ATTTACCGAAATAGGCCGG
18605653 TTTTT
1 TTTTT
18605658 CCCGAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.28
28 6 0.21
29 15 0.52
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.45
Consensus pattern (27 bp):
TTTTTTAAATTTACCGAAATAGGCCGG
Found at i:18605952 original size:22 final size:22
Alignment explanation
Indices: 18605927--18605995 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
18605917 ACAAATCCTA
*
18605927 TCTCAATTTCATTCAAAAATTC
1 TCTCAATTTCCTTCAAAAATTC
**
18605949 TCTCAAAGTCCTTCAAAAATTC
1 TCTCAATTTCCTTCAAAAATTC
*
18605971 TCTCAATTTCCTTCCAAAATTC
1 TCTCAATTTCCTTCAAAAATTC
18605993 TCT
1 TCT
18605996 TAAACTCTCG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.32, C:0.28, G:0.01, T:0.39
Consensus pattern (22 bp):
TCTCAATTTCCTTCAAAAATTC
Found at i:18606030 original size:52 final size:51
Alignment explanation
Indices: 18605948--18606054 Score: 142
Period size: 52 Copynumber: 2.1 Consensus size: 51
18605938 TTCAAAAATT
* * * *
18605948 CTCTCAAAGTCCTTCAAAAATTCTCTCAATTTCCTTCCAAAATTCTCTTAAA
1 CTCTCAAAGTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTC-TAAA
* * *
18606000 CTCTCGAATTCCTTCCAAAATCCTCACAATTTCCTTCAAAAAATCTCTAAA
1 CTCTCAAAGTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTCTAAA
18606051 CTCT
1 CTCT
18606055 ATATTAAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 8 0.17
52 40 0.83
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.35
Consensus pattern (51 bp):
CTCTCAAAGTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTCTAAA
Found at i:18607419 original size:7 final size:7
Alignment explanation
Indices: 18607407--18607431 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18607397 AGTGGATTGA
18607407 TATTTAG
1 TATTTAG
18607414 TATTTAG
1 TATTTAG
18607421 TATTTAG
1 TATTTAG
18607428 TATT
1 TATT
18607432 ATGTATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:18608747 original size:28 final size:28
Alignment explanation
Indices: 18608668--18609033 Score: 417
Period size: 28 Copynumber: 12.4 Consensus size: 28
18608658 GATATTATTG
*
18608668 ATTTAATTATAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACCTA
*
18608697 ATTCAATTATAAAACCCTAACCTAACCTA
1 ATTTAATTA-AAAACCCTAACCTAACCTA
*
18608726 ATTTAATTAAAAACCCTAACCTAACATA
1 ATTTAATTAAAAACCCTAACCTAACCTA
*
18608754 ATTTAATTAAAAACCCTAACCTAACATA
1 ATTTAATTAAAAACCCTAACCTAACCTA
*
18608782 ATTTAATTAAAAACCCTAAACCCTAATCTA
1 ATTTAATTAAAAACCCT-AA-CCTAACCTA
**
18608812 ATTTAATTTAATTAGCCTAAACCCTAACCTAATTTA
1 ATTTAA-TT-A--A----AAACCCTAACCTAACCTA
* * **
18608848 ATTTAATTAAAAACCCAAACCCAATTTA
1 ATTTAATTAAAAACCCTAACCTAACCTA
*
18608876 ATTTAATTATAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACCTA
*
18608905 ATTCAATTATAAAACCCTAACCTAACCTA
1 ATTTAATTA-AAAACCCTAACCTAACCTA
18608934 ATTTAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACCTA
18608962 ATTTAATTAAAAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCT-AA-CCTAACCTA
** *
18608992 ATTTAATTTAATTAGCCTAAACCCTAACCTA
1 ATTTAA-TTAAAAACCCT-AA-CCTAACCTA
18609023 ATTTAATTAAA
1 ATTTAATTAAA
18609034 TTAAACGACG
Statistics
Matches: 300, Mismatches: 21, Indels: 31
0.85 0.06 0.09
Matches are distributed among these distances:
28 132 0.44
29 60 0.20
30 50 0.17
31 29 0.10
32 2 0.01
34 2 0.01
35 2 0.01
36 14 0.05
37 2 0.01
38 7 0.02
ACGTcount: A:0.45, C:0.23, G:0.01, T:0.31
Consensus pattern (28 bp):
ATTTAATTAAAAACCCTAACCTAACCTA
Found at i:18608921 original size:180 final size:180
Alignment explanation
Indices: 18608668--18609038 Score: 620
Period size: 180 Copynumber: 2.1 Consensus size: 180
18608658 GATATTATTG
* * *
18608668 ATTTAATTATAAACCCTAACCCTAACCTAATTCAATTATAAAACCCTAACCTAACCTAATTTAAT
1 ATTTAATTAAAAACCCAAACCCTAACCTAATTCAATTATAAAACCCTAACCTAACCTAATTCAAT
18608733 TAAAAACCCTAACCTAACATAATTTAATTAAAAACCCTAACCTAACATAATTTAATTAAAAACCC
66 TAAAAACCCTAACCTAACATAATTTAATTAAAAACCCTAACCTAACATAATTTAATTAAAAACCC
*
18608798 TAAACCCTAATCTAATTTAATTTAATTAGCCTAAACCCTAACCTAATTTA
131 TAAACCCTAACCTAATTTAATTTAATTAGCCTAAACCCTAACCTAATTTA
** *
18608848 ATTTAATTAAAAACCCAAACCC-AATTTAATTTAATTAT-AAACCCTAACCCTAACCTAATTCAA
1 ATTTAATTAAAAACCCAAACCCTAACCTAATTCAATTATAAAACCCTAA-CCTAACCTAATTCAA
* *
18608911 TTATAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAAC
65 TTA-AAAACCCTAACCTAACATAATTTAATTAAAAACCCTAACCTAACATAATTTAATTAAAAAC
18608976 CCTAAACCCTAACCTAATTTAATTTAATTAGCCTAAACCCTAACCTAATTTA
129 CCTAAACCCTAACCTAATTTAATTTAATTAGCCTAAACCCTAACCTAATTTA
*
18609028 ATTAAATTAAA
1 ATTTAATTAAA
18609039 CGACGTGGTA
Statistics
Matches: 179, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
178 9 0.05
179 30 0.17
180 140 0.78
ACGTcount: A:0.45, C:0.23, G:0.01, T:0.31
Consensus pattern (180 bp):
ATTTAATTAAAAACCCAAACCCTAACCTAATTCAATTATAAAACCCTAACCTAACCTAATTCAAT
TAAAAACCCTAACCTAACATAATTTAATTAAAAACCCTAACCTAACATAATTTAATTAAAAACCC
TAAACCCTAACCTAATTTAATTTAATTAGCCTAAACCCTAACCTAATTTA
Found at i:18610735 original size:126 final size:124
Alignment explanation
Indices: 18610335--18610742 Score: 631
Period size: 126 Copynumber: 3.2 Consensus size: 124
18610325 CACGAGGGCA
18610335 CGATTTTACACTATTTGCTCAGAAACGTCAAAAAAAAAATTATTTCCTACATGACCAACTGTAGC
1 CGATTTTACACTATTTGCTCAGAAACGTC-AAAAAAAAATTATTTCCTACATGACCAACTGT-GC
* *
18610400 AAAATCGCGTCCACGAGGGCGCGATTTCAAAATTTATTCTCATATAGCATCCTGGTATCAG
64 AAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAG
* *
18610461 CGATTTTACACTATTTGCTCAAAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTTGCG
1 CGATTTTACACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTG-TGCA
18610526 AAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAG
65 AAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAG
* *
18610586 CGATTTTATACTATTTGCTCAGAAAACGTCAAAAAAAAATTATTTCTTACATGACCAACTGTGCT
1 CGATTTTACACTATTTGCTCAG-AAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTGC-
* * **
18610651 AAAATGGCGTCCACGAGGGCACGATTTCACAATTTCTTCTC-TGATAGCATCCTGGTAGAAG
64 AAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAT-ATAGCATCCTGGTATCAG
* *
18610712 CGATTTTATACTATTTTAC-CAGAAACGTCAA
1 CGATTTTACACTA-TTTGCTCAGAAACGTCAA
18610743 CTCGAAATAA
Statistics
Matches: 264, Mismatches: 13, Indels: 11
0.92 0.05 0.04
Matches are distributed among these distances:
125 124 0.47
126 136 0.52
127 4 0.02
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (124 bp):
CGATTTTACACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTGCAA
AATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAG
Found at i:18610822 original size:52 final size:50
Alignment explanation
Indices: 18610745--18610900 Score: 249
Period size: 52 Copynumber: 3.0 Consensus size: 50
18610735 AACGTCAACT
18610745 CGAAATAATTTTTTTGGGACCCCTAAACCCTAAAAAAGCATGCACCCTAAA
1 CGAAATAATTTTTTTGGGACCCCTAAACCCTAAAAAAGC-TGCACCCTAAA
* *
18610796 CGAAATACTTTTTTTCGGCACCCCTAAACCCTAAAAAAGTCTGCACCCTAAA
1 CGAAATAATTTTTTT-GGGACCCCTAAACCCTAAAAAAG-CTGCACCCTAAA
18610848 CGAAATAATTTTTTTTGGGACCCCTAAACCCTAAAAAAGCTTGCACCCTAAA
1 CGAAATAA-TTTTTTTGGGACCCCTAAACCCTAAAAAAGC-TGCACCCTAAA
18610900 C
1 C
18610901 CCTAAAACCC
Statistics
Matches: 97, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
51 15 0.15
52 74 0.76
53 8 0.08
ACGTcount: A:0.37, C:0.28, G:0.11, T:0.25
Consensus pattern (50 bp):
CGAAATAATTTTTTTGGGACCCCTAAACCCTAAAAAAGCTGCACCCTAAA
Found at i:18611183 original size:28 final size:27
Alignment explanation
Indices: 18611124--18611182 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
18611114 GATTTCGGGG
18611124 AAAACGGCCCATTCCGGTAAATAATTAA
1 AAAACGGCCCATTCCGGTAAAT-ATTAA
* *
18611152 AAAACCGGCCTATTTCGGTAAAT-TTAA
1 AAAA-CGGCCCATTCCGGTAAATATTAA
18611179 AAAA
1 AAAA
18611183 AAAGGGCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.29
28 4 0.14
29 16 0.57
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.24
Consensus pattern (27 bp):
AAAACGGCCCATTCCGGTAAATATTAA
Found at i:18616771 original size:33 final size:33
Alignment explanation
Indices: 18616733--18616802 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
18616723 GGAGGCTCAC
18616733 CTTTAGGA-ATAGGAAAACAAAATTCAGTTTTAA
1 CTTTAGGAGA-AGGAAAACAAAATTCAGTTTTAA
* * *
18616766 CTTTAGGAGAAGGAAAACAAAGTTCGGTTTTAC
1 CTTTAGGAGAAGGAAAACAAAATTCAGTTTTAA
18616799 CTTT
1 CTTT
18616803 TCCATTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (33 bp):
CTTTAGGAGAAGGAAAACAAAATTCAGTTTTAA
Found at i:18617704 original size:12 final size:13
Alignment explanation
Indices: 18617680--18617713 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
18617670 TCGTTTTCTC
18617680 TTCTTTCTTCAA-T
1 TTCTTT-TTCAATT
18617693 TTCTTTTTCAATT
1 TTCTTTTTCAATT
18617706 TTCTTTTT
1 TTCTTTTT
18617714 TTCACATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (13 bp):
TTCTTTTTCAATT
Found at i:18619547 original size:7 final size:6
Alignment explanation
Indices: 18619502--18619566 Score: 58
Period size: 6 Copynumber: 10.3 Consensus size: 6
18619492 CTCACTCTCA
* * * * *
18619502 TTTTCT TTTTCA ATTTCT TGTTCT CTTTCT TTTTCT TTTTCA TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
18619550 TTTCTCGTT TTTTCT TT
1 TTT-TC--T TTTTCT TT
18619567 ACAAGATAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
6 38 0.83
7 2 0.04
8 2 0.04
9 4 0.09
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (6 bp):
TTTTCT
Found at i:18622982 original size:24 final size:22
Alignment explanation
Indices: 18622945--18622995 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 22
18622935 AATTATTTAA
18622945 TTTTAAATAGTTAATTATTATGAT
1 TTTTAAATAGTTAA-TATT-TGAT
*
18622969 TTTTAAATTA-TTAATATTTTAT
1 TTTTAAA-TAGTTAATATTTGAT
18622991 TTTTA
1 TTTTA
18622996 TATACTCAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 8 0.32
23 4 0.16
24 11 0.44
25 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (22 bp):
TTTTAAATAGTTAATATTTGAT
Found at i:18625167 original size:18 final size:18
Alignment explanation
Indices: 18625121--18625167 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
18625111 AATCTATGTA
*
18625121 TATATGTATATTTATTTT
1 TATATATATATTTATTTT
* *
18625139 TATGTACATATTTATTTT
1 TATATATATATTTATTTT
18625157 TATATATATAT
1 TATATATATAT
18625168 ACGCATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (18 bp):
TATATATATATTTATTTT
Found at i:18629190 original size:42 final size:42
Alignment explanation
Indices: 18629134--18629225 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
18629124 ATTGATCAAG
18629134 AGTAATATAACTTGATTTTGGACAAAAAATTATAACTATTCA
1 AGTAATATAACTTGATTTTGGACAAAAAATTATAACTATTCA
* **
18629176 AGTATTATAACTTGATTTTTTACAAAAAATTATAACTATTCA
1 AGTAATATAACTTGATTTTGGACAAAAAATTATAACTATTCA
*
18629218 AATAATAT
1 AGTAATAT
18629226 TACCTGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.39
Consensus pattern (42 bp):
AGTAATATAACTTGATTTTGGACAAAAAATTATAACTATTCA
Found at i:18633178 original size:24 final size:24
Alignment explanation
Indices: 18633146--18633194 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
18633136 CTGCCTTGGT
*
18633146 TTACCCTTGCTTTTGTAGACTCTC
1 TTACCCTTGCTTTTGCAGACTCTC
18633170 TTACCCTTGCTTTTGCAGACTCTC
1 TTACCCTTGCTTTTGCAGACTCTC
18633194 T
1 T
18633195 CAACATGACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.31, G:0.12, T:0.45
Consensus pattern (24 bp):
TTACCCTTGCTTTTGCAGACTCTC
Found at i:18634700 original size:11 final size:11
Alignment explanation
Indices: 18634670--18634704 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
18634660 ACTTTATTTT
*
18634670 TTTTGTTCGAG
1 TTTTGTTCGTG
18634681 TTATTGTTCGTG
1 TT-TTGTTCGTG
18634693 TTTTGTTCGTG
1 TTTTGTTCGTG
18634704 T
1 T
18634705 GTTGAAGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.06, C:0.09, G:0.26, T:0.60
Consensus pattern (11 bp):
TTTTGTTCGTG
Found at i:18639758 original size:19 final size:20
Alignment explanation
Indices: 18639713--18639758 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
18639703 TTTTATTATT
18639713 TTAATTCTTGATTAATTATGA
1 TTAATT-TTGATTAATTATGA
* *
18639734 -TGATTTTGTTTAATT-TGA
1 TTAATTTTGATTAATTATGA
18639752 TTAATTT
1 TTAATTT
18639759 CTATATTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
18 3 0.14
19 14 0.67
20 4 0.19
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (20 bp):
TTAATTTTGATTAATTATGA
Found at i:18640157 original size:2 final size:2
Alignment explanation
Indices: 18640150--18640188 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
18640140 TTCAATTTGA
18640150 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18640189 ATTCTATGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18645246 original size:40 final size:40
Alignment explanation
Indices: 18645149--18645315 Score: 129
Period size: 40 Copynumber: 4.2 Consensus size: 40
18645139 TTGAACAACT
*
18645149 TTCAGTAGGTATGGCTTGATAGAACATACTTTTCAGTGGA
1 TTCAGTAGGTATGGCTCGATAGAACATACTTTTCAGTGGA
* * * * * * *
18645189 ATCAATATGTATAGCTCGATGGAGCCTACTTTGT-AGTGGA
1 TTCAGTAGGTATGGCTCGATAGAACATACTTT-TCAGTGGA
* ** * * *
18645229 TTCAGTAGGTATGGCTCGAAAGCGCATACGTTTCAATAGA
1 TTCAGTAGGTATGGCTCGATAGAACATACTTTTCAGTGGA
* * *** * *
18645269 TTCAGTAGCTATGGTTCGATATTGCATACATTTCAGTAGA
1 TTCAGTAGGTATGGCTCGATAGAACATACTTTTCAGTGGA
18645309 TTCAGTA
1 TTCAGTA
18645316 AATACCACTC
Statistics
Matches: 99, Mismatches: 26, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
39 1 0.01
40 97 0.98
41 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (40 bp):
TTCAGTAGGTATGGCTCGATAGAACATACTTTTCAGTGGA
Found at i:18647100 original size:20 final size:19
Alignment explanation
Indices: 18647075--18647189 Score: 88
Period size: 20 Copynumber: 5.8 Consensus size: 19
18647065 TTGTACGGGA
18647075 TTTGCACTTTGGTGCCTCTG
1 TTTGCACTTTGGTGCC-CTG
**
18647095 TTTGCACTTCAGTGCCCCTG
1 TTTGCACTTTGGTG-CCCTG
* *
18647115 TATACACTTTGGTGTCCCTG
1 TTTGCACTTTGGTG-CCCTG
* * *
18647135 TTCGCACTATGGTGCCCTTT
1 TTTGCACTTTGGTGCCC-TG
* *
18647155 TTTGTACATTT-GTGCCCCTA
1 TTTGCAC-TTTGGTG-CCCTG
18647175 TTTGCACTTTGGTGC
1 TTTGCACTTTGGTGC
18647190 TCTTGTTATG
Statistics
Matches: 73, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
19 7 0.10
20 59 0.81
21 7 0.10
ACGTcount: A:0.10, C:0.27, G:0.21, T:0.42
Consensus pattern (19 bp):
TTTGCACTTTGGTGCCCTG
Found at i:18654665 original size:24 final size:24
Alignment explanation
Indices: 18654638--18654684 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
18654628 ATTACCAATG
* *
18654638 AAAACCTCCTCTAATAATAGTAAA
1 AAAACCTCCTATAATAACAGTAAA
18654662 AAAACCTCCTATAATAACAGTAA
1 AAAACCTCCTATAATAACAGTAA
18654685 CATGGTACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.51, C:0.21, G:0.04, T:0.23
Consensus pattern (24 bp):
AAAACCTCCTATAATAACAGTAAA
Done.