Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 141 of 310
Found at i:46030386 original size:199 final size:199
Alignment explanation
Indices: 46030046--46030441 Score: 729
Period size: 199 Copynumber: 2.0 Consensus size: 199
46030036 TTCTGAGTTA
* * *
46030046 GTTACAACGTGTAAAATAGTAGATTCTTCTATCTTCCTATGGGAACCAATACAAGTAGTCATCTT
1 GTTACAACGTGTAAAATAGTAGATTCTTCTATCTACCTATGAGAACCAAAACAAGTAGTCATCTT
*
46030111 TTTTTTCACATCTAGTTGCACTTAAGGAATGGGAATCAAAAGCCAAGCTTAAATTCAGTGAAATC
66 TTTTTTCACATCTAGTTGCACTTAAGGAATGGGAATCAAAAGCCAAGCATAAATTCAGTGAAATC
* * *
46030176 TCTTCAGGGAAATTCAATTATATTCTCCTACAAGTTGCTAACACATACAGCTATCCATACGTTTA
131 ACTTCAGGGAAATTCAATTATATTCTCCTAAAAGTTGCTAACACATACAGCTATCCATACGATTA
46030241 TCAT
196 TCAT
46030245 GTTACAACGTGTAAAATAGTAGATTCTTCTATCTACCTATGAGAACCAAAACAAGTAGTCATCTT
1 GTTACAACGTGTAAAATAGTAGATTCTTCTATCTACCTATGAGAACCAAAACAAGTAGTCATCTT
46030310 TTTTTTCACATCTAGTTGCACTTAAGGAATGGGAATCAAAAGCCAAGCATAAATTCAGTGAAATC
66 TTTTTTCACATCTAGTTGCACTTAAGGAATGGGAATCAAAAGCCAAGCATAAATTCAGTGAAATC
46030375 ACTTCAGGGAAATTCAATTATATTCTCCTAAAAGTTGCTAACACATACAGCTATCCATACGATTA
131 ACTTCAGGGAAATTCAATTATATTCTCCTAAAAGTTGCTAACACATACAGCTATCCATACGATTA
46030440 TC
196 TC
46030442 GTGACAACCT
Statistics
Matches: 190, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
199 190 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (199 bp):
GTTACAACGTGTAAAATAGTAGATTCTTCTATCTACCTATGAGAACCAAAACAAGTAGTCATCTT
TTTTTTCACATCTAGTTGCACTTAAGGAATGGGAATCAAAAGCCAAGCATAAATTCAGTGAAATC
ACTTCAGGGAAATTCAATTATATTCTCCTAAAAGTTGCTAACACATACAGCTATCCATACGATTA
TCAT
Found at i:46038218 original size:44 final size:44
Alignment explanation
Indices: 46038147--46038398 Score: 208
Period size: 44 Copynumber: 5.7 Consensus size: 44
46038137 TCTTTCTAAC
*
46038147 CCACTGCAACTTC-AGAAG-TATAGAATTTGTCGTTTCAATCTACT
1 CCACTGCAACTTCAAGGAGATA-AG-ATTTGTCGTTTCAATCTACT
* * * * * *
46038191 CCATTGCAACTTCAAGGAGATAAAATTTGTAGCTCCAATCTGCT
1 CCACTGCAACTTCAAGGAGATAAGATTTGTCGTTTCAATCTACT
* * **
46038235 CCACTGCAACTTC-TGCGAAATAAGATTCACTAC-TTTCAATCTACT
1 CCACTGCAACTTCAAG-GAGATAAGATT-TGT-CGTTTCAATCTACT
* * * *
46038280 CCACTGCAACTTCAGGGAAATAAGATTT-TCTATTTTCGATCTACT
1 CCACTGCAACTTCAAGGAGATAAGATTTGTC--GTTTCAATCTACT
*** *
46038325 CCACTGCAACTTCAAGGAGATAAGATTTGTAACTTCAATCTGCT
1 CCACTGCAACTTCAAGGAGATAAGATTTGTCGTTTCAATCTACT
* * *
46038369 CCATTGCAACTTTAGGGAGATAAGATTTGT
1 CCACTGCAACTTCAAGGAGATAAGATTTGT
46038399 AATTCGTAGC
Statistics
Matches: 168, Mismatches: 30, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 85 0.51
45 76 0.45
46 4 0.02
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.32
Consensus pattern (44 bp):
CCACTGCAACTTCAAGGAGATAAGATTTGTCGTTTCAATCTACT
Found at i:46038282 original size:45 final size:45
Alignment explanation
Indices: 46038179--46038395 Score: 167
Period size: 45 Copynumber: 4.9 Consensus size: 45
46038169 GAATTTGTCG
* * * **
46038179 TTTCAATCTACTCCATTGCAACTTCAAG-GAGATAAAATT-TGTAGC
1 TTTCAATCTACTCCACTGCAACTTC-AGCGAAATAAGATTCACTA-C
* * *
46038224 -TCCAATCTGCTCCACTGCAACTTCTGCGAAATAAGATTCACTAC
1 TTTCAATCTACTCCACTGCAACTTCAGCGAAATAAGATTCACTAC
* ** *
46038268 TTTCAATCTACTCCACTGCAACTTCAGGGAAATAAGATTTTCTAT
1 TTTCAATCTACTCCACTGCAACTTCAGCGAAATAAGATTCACTAC
* * **
46038313 TTTCGATCTACTCCACTGCAACTTCAAG-GAGATAAGATT-TGTAAC
1 TTTCAATCTACTCCACTGCAACTTC-AGCGAAATAAGATTCACT-AC
* * * * *
46038358 -TTCAATCTGCTCCATTGCAACTTTAGGGAGATAAGATT
1 TTTCAATCTACTCCACTGCAACTTCAGCGAAATAAGATT
46038396 TGTAATTCGT
Statistics
Matches: 143, Mismatches: 23, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
43 3 0.02
44 64 0.45
45 74 0.52
46 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (45 bp):
TTTCAATCTACTCCACTGCAACTTCAGCGAAATAAGATTCACTAC
Found at i:46038288 original size:89 final size:89
Alignment explanation
Indices: 46038179--46038399 Score: 241
Period size: 89 Copynumber: 2.5 Consensus size: 89
46038169 GAATTTGTCG
* *
46038179 TTTCAATCTACTCCATTGCAACTTCAAGGAGATAAAATTTGTAGCTCCAATCTGCTCCACTGCAA
1 TTTCAATCTACTCCATTGCAACTTCAGGGAGATAAAATTTGTAGCTCCAATCTACTCCACTGCAA
*
46038244 CTTC-TGCGAAATAAGATTCACT-AC
66 CTTCAAG-GAAATAAGATT-ACTAAC
* * * * ** * *
46038268 TTTCAATCTACTCCACTGCAACTTCAGGGAAATAAGATTTTCTATTTTCGATCTACTCCACTGCA
1 TTTCAATCTACTCCATTGCAACTTCAGGGAGATAA-AATTTGTAGCTCCAATCTACTCCACTGCA
* **
46038333 ACTTCAAGGAGATAAGATTTGTAAC
65 ACTTCAAGGAAATAAGATTACTAAC
* * *
46038358 -TTCAATCTGCTCCATTGCAACTTTAGGGAGATAAGATTTGTA
1 TTTCAATCTACTCCATTGCAACTTCAGGGAGATAAAATTTGTA
46038400 ATTCGTAGCT
Statistics
Matches: 108, Mismatches: 21, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
88 5 0.05
89 63 0.58
90 39 0.36
91 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.33
Consensus pattern (89 bp):
TTTCAATCTACTCCATTGCAACTTCAGGGAGATAAAATTTGTAGCTCCAATCTACTCCACTGCAA
CTTCAAGGAAATAAGATTACTAAC
Found at i:46038399 original size:44 final size:44
Alignment explanation
Indices: 46038180--46039189 Score: 597
Period size: 44 Copynumber: 22.9 Consensus size: 44
46038170 AATTTGTCGT
* * * * *
46038180 TTCAATCTACTCCATTGCAACTTCAAGGAGATAAAATTTGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
* * * * **
46038224 TCCAATCTGCTCCACTGCAACTTCTGCGAAATAAGATTCACT-AC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-TGTAAC
* * * **
46038268 TTTCAATCTACTCCACTGCAACTTCAGGGAAATAAGATTTTCTATT
1 -TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTTGTAAC
* * *
46038314 TTCGATCTACTCCACTGCAACTTCAAGGAGATAAGATTTGTAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
* *
46038358 TTCAATCTGCTCCATTGCAACTTTAGGGAGATAAGATTTGTAATTCGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT-A-----A-C
* * * * ** * * * *
46038409 TTTAATCTGTTTCATTGCCTCTTCAGAGAAATAAAATTTGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
* * * *
46038453 TTCAATCTGCTCCACTACGACTTCGGGGAGATAAGATTCGTAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
* * *
46038497 TTTAA-CTTGCCCCACTACAACTTCAGGGAGAT---A---G---C
1 TTCAATC-TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
* * ** ** *
46038532 TTTAATCTGTTATACTGCAACTTCAAAGAGATAAGATTTGCTATC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAAC
* * * * * *
46038577 TTCAGTCTGCTCCACTACAACTTTAAGGAGATAAAACTTGTAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
* * * * * * *
46038621 TTCAACCTGCTCCACTACAACTTTAGGGAGATATGGTTTATAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
* * * ** ** *
46038665 TTTAATCTGCTCTACTGCAACTTTAGAAAGATAAGATTCACTATC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-TGTAAC
* * * * * *
46038710 TTCAGTCTACTCCACAGTAACTTTAGGGAGATAAGACTTGTAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
* * * * * *
46038754 TTCAATTTGCTCCACTGAAACTTCAGAGAGATAAGGTTTATAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
* * * * ** ** *
46038798 TTTAATCGGCTCTACTGCAACTTTAGAAAGATAAGATTCACTATC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-TGTAAC
* * * * * *
46038843 TTCAGTCTACTCCACAGTAACTTTAGGGAGATAAGACTTGTAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
* * * * * *
46038887 TTCAATTTGCTCCACTGAAACTTCAGAGAGATAAGGTTTATAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
* * * * * *
46038931 TTTAATCGGCTCTACTGCAACTTCAGAGAGATAAGATTCGCTATC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAAC
** * *
46038976 TTCTGTCTGCTCCACTGCAACTTC-TGGAGATAAGACTTGTAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
* * * *
46039019 TTCAA-CTTGCTCCACTGCAACTTCAGGGTGATAAGGTTTATAGC
1 TTCAATC-TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
* * * * *
46039063 TTTAATCTGCTCCACTGTAACTTTAGAGAGATAAGATTTGCTATC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAAC
* * * ** ***
46039108 TTCAGTATACTCCACTGCAACTTCAGGGAGATCCGATTTGCGGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
* * * * *
46039152 TTTAGTATACTCCACTGCAACTTTAGGGAGATAAGATT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
46039190 CGCCACGATG
Statistics
Matches: 733, Mismatches: 203, Indels: 60
0.74 0.20 0.06
Matches are distributed among these distances:
35 24 0.03
36 1 0.00
38 2 0.00
41 2 0.00
42 1 0.00
43 24 0.03
44 422 0.58
45 220 0.30
46 2 0.00
50 2 0.00
51 33 0.05
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.32
Consensus pattern (44 bp):
TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
Found at i:46038723 original size:89 final size:89
Alignment explanation
Indices: 46038549--46039139 Score: 360
Period size: 89 Copynumber: 6.7 Consensus size: 89
46038539 TGTTATACTG
* * * * * * * *
46038549 CAACTTCAAAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTACAACTTTA-AGGAGATAAAA
1 CAACTTTAGAGAGATAAGATTT-ATAGCTTCAATCTGCTCCACTGCAACTTCAGA-GAGATAAGA
* * *
46038613 CTT--GTAACTTCAACCTGCTCCACTA
64 -TTCACTATCTTCAATCTGCTCCACTA
* * * * * * *
46038638 CAACTTTAGGGAGATATGGTTTATAGCTTTAATCTGCTCTACTGCAACTTTAGAAAGATAAGATT
1 CAACTTTAGAGAGATAAGATTTATAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATT
* *
46038703 CACTATCTTCAGTCTACTCCAC-A
66 CACTATCTTCAATCTGCTCCACTA
* * * * * * * *
46038726 GTAACTTTAGGGAGATAAGACTTGTAACTTCAATTTGCTCCACTGAAACTTCAGAGAGATAAGGT
1 -CAACTTTAGAGAGATAAGATTTATAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
* * * * * *
46038791 TTA-TAGCTTTAATCGGCTCTACTG
65 TCACTATCTTCAATCTGCTCCACTA
* * * * * * * * *
46038815 CAACTTTAGAAAGATAAGATTCACTATCTTCAGTCTACTCCACAGTAACTTTAGGGAGATAAGAC
1 CAACTTTAGAGAGATAAGATTTA-TAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGA-
* * *
46038880 TT--GTAACTTCAATTTGCTCCACTGA
64 TTCACTATCTTCAATCTGCTCCACT-A
* * * * *
46038905 -AACTTCAGAGAGATAAGGTTTATAGCTTTAATCGGCTCTACTGCAACTTCAGAGAGATAAGATT
1 CAACTTTAGAGAGATAAGATTTATAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATT
* ** *
46038969 CGCTATCTTCTGTCTGCTCCACTG
66 CACTATCTTCAATCTGCTCCACTA
* * * * * *
46038993 CAACTTCT-G-GAGATAAGACTTGTAACTTCAA-CTTGCTCCACTGCAACTTCAGGGTGATAAGG
1 CAACTT-TAGAGAGATAAGATTTATAGCTTCAATC-TGCTCCACTGCAACTTCAGAGAGATAAGA
* * * *
46039055 TTTA-TAGCTTTAATCTGCTCCACTG
64 TTCACTATCTTCAATCTGCTCCACTA
* * * * * * *
46039080 TAACTTTAGAGAGATAAGATTTGCTATCTTCAGTATACTCCACTGCAACTTCAGGGAGAT
1 CAACTTTAGAGAGATAAGATTT-ATAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGAT
46039140 CCGATTTGCG
Statistics
Matches: 379, Mismatches: 105, Indels: 36
0.73 0.20 0.07
Matches are distributed among these distances:
86 1 0.00
87 28 0.07
88 146 0.39
89 202 0.53
90 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (89 bp):
CAACTTTAGAGAGATAAGATTTATAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATT
CACTATCTTCAATCTGCTCCACTA
Found at i:46038765 original size:133 final size:133
Alignment explanation
Indices: 46038527--46039139 Score: 849
Period size: 133 Copynumber: 4.6 Consensus size: 133
46038517 CTTCAGGGAG
* * * * *
46038527 ATAGCTTTAATCTGTTATACTGCAACTTCA-AAGAGATAAGATTTGCTATCTTCAGTCTGCTCCA
1 ATAGCTTTAATCTGCTCTACTGCAACTTTAGAA-AGATAAGATTCGCTATCTTCAGTCTACTCCA
* * * * *
46038591 CTA-CAACTTTAAGGAGATAAAACTTGTAACTTCAACCTGCTCCACT-ACAACTTTAGGGAGATA
65 C-AGCAACTTTAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGA-AACTTCAGAGAGATA
*
46038654 TGGTTT
128 AGGTTT
*
46038660 ATAGCTTTAATCTGCTCTACTGCAACTTTAGAAAGATAAGATTCACTATCTTCAGTCTACTCCAC
1 ATAGCTTTAATCTGCTCTACTGCAACTTTAGAAAGATAAGATTCGCTATCTTCAGTCTACTCCAC
* *
46038725 AGTAACTTTAGGGAGATAAGACTTGTAACTTCAATTTGCTCCACTGAAACTTCAGAGAGATAAGG
66 AGCAACTTTAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGAAACTTCAGAGAGATAAGG
46038790 TTT
131 TTT
* *
46038793 ATAGCTTTAATCGGCTCTACTGCAACTTTAGAAAGATAAGATTCACTATCTTCAGTCTACTCCAC
1 ATAGCTTTAATCTGCTCTACTGCAACTTTAGAAAGATAAGATTCGCTATCTTCAGTCTACTCCAC
* *
46038858 AGTAACTTTAGGGAGATAAGACTTGTAACTTCAATTTGCTCCACTGAAACTTCAGAGAGATAAGG
66 AGCAACTTTAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGAAACTTCAGAGAGATAAGG
46038923 TTT
131 TTT
* * * * *
46038926 ATAGCTTTAATCGGCTCTACTGCAACTTCAGAGAGATAAGATTCGCTATCTTCTGTCTGCTCCAC
1 ATAGCTTTAATCTGCTCTACTGCAACTTTAGAAAGATAAGATTCGCTATCTTCAGTCTACTCCAC
* * * *
46038991 TGCAACTTCT--GGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCAACTTCAGGGTGATAAG
66 AGCAACTT-TAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGAAACTTCAGAGAGATAAG
46039054 GTTT
130 GTTT
* * * * *
46039058 ATAGCTTTAATCTGCTCCACTGTAACTTTAGAGAGATAAGATTTGCTATCTTCAGTATACTCCAC
1 ATAGCTTTAATCTGCTCTACTGCAACTTTAGAAAGATAAGATTCGCTATCTTCAGTCTACTCCAC
* *
46039123 TGCAACTTCAGGGAGAT
66 AGCAACTTTAGGGAGAT
46039140 CCGATTTGCG
Statistics
Matches: 439, Mismatches: 35, Indels: 12
0.90 0.07 0.02
Matches are distributed among these distances:
132 119 0.27
133 316 0.72
134 4 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (133 bp):
ATAGCTTTAATCTGCTCTACTGCAACTTTAGAAAGATAAGATTCGCTATCTTCAGTCTACTCCAC
AGCAACTTTAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGAAACTTCAGAGAGATAAGG
TTT
Found at i:46048645 original size:56 final size:56
Alignment explanation
Indices: 46048576--46048688 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
46048566 TTGAGTTCCA
*
46048576 AACTCGTTAAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTG
1 AACTCGTTAAGTTGAGTCCGAGTTCGTGAGATGCAACTAGGCATCCGAACTCGTTG
* *
46048632 AACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGCAACTAGGCATCCGAGCTCGTTG
1 AACTCGTTAAGTTGAGTCCGAGTTCGTGAGATGCAACTAGGCATCCGAACTCGTTG
46048688 A
1 A
46048689 GTTGAGTCCA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (56 bp):
AACTCGTTAAGTTGAGTCCGAGTTCGTGAGATGCAACTAGGCATCCGAACTCGTTG
Found at i:46056727 original size:21 final size:21
Alignment explanation
Indices: 46056703--46056767 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
46056693 AAGTCTAGCT
46056703 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
*
46056724 GAAGC-C-TGAAG-GCT-AACT
1 GAAGCACAT-AAGTGCTAAACG
46056742 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
46056763 GAAGC
1 GAAGC
46056768 TAACTGAAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 8 0.22
19 8 0.22
20 8 0.22
21 13 0.35
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAACG
Found at i:46056744 original size:39 final size:38
Alignment explanation
Indices: 46056685--46056816 Score: 161
Period size: 39 Copynumber: 3.6 Consensus size: 38
46056675 ATCGTGATCT
* *
46056685 GAAGCCCGAAGTCTAGCTGAAGCACATAAGTGCTAAAC
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAAC
*
46056723 GGAAGCCTGAAGGCTAACTGAAGCACATAAGTGCTAAAC
1 -GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAAC
*
46056762 ---G---GAA-GCTAACTGAAGCACATAAGTGTTAAAC
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAAC
46056793 AGAAGCCCGAAGGCTAACTGAAGC
1 -GAAGCCCGAAGGCTAACTGAAGC
46056817 TCATCAAAGC
Statistics
Matches: 81, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
31 26 0.32
32 3 0.04
35 2 0.02
38 3 0.04
39 47 0.58
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.15
Consensus pattern (38 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAAC
Found at i:46056773 original size:31 final size:31
Alignment explanation
Indices: 46056735--46056798 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
46056725 AAGCCTGAAG
*
46056735 GCTAACTGAAGCACATAAGTGCTAAACGGAA
1 GCTAACTGAAGCACATAAGTGCTAAACAGAA
*
46056766 GCTAACTGAAGCACATAAGTGTTAAACAGAA
1 GCTAACTGAAGCACATAAGTGCTAAACAGAA
46056797 GC
1 GC
46056799 CCGAAGGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (31 bp):
GCTAACTGAAGCACATAAGTGCTAAACAGAA
Found at i:46063625 original size:21 final size:22
Alignment explanation
Indices: 46063594--46063644 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
46063584 GTAAATGGAC
*
46063594 TTTGATGTTTTGGACTTATTTA
1 TTTGATTTTTTGGACTTATTTA
**
46063616 TTT-ATTTTTTGGTTTTATTTA
1 TTTGATTTTTTGGACTTATTTA
46063637 TTTGATTT
1 TTTGATTT
46063645 AGTGGGCCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.69
Consensus pattern (22 bp):
TTTGATTTTTTGGACTTATTTA
Found at i:46066620 original size:31 final size:31
Alignment explanation
Indices: 46066577--46066638 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
46066567 ACAAGAAAGA
*
46066577 TTGAATAGAGGAGCGGCTAATCCGGAATGGT
1 TTGAATAAAGGAGCGGCTAATCCGGAATGGT
*
46066608 TTGAATAAAGGAGTGGCTAATCCGGAATGGT
1 TTGAATAAAGGAGCGGCTAATCCGGAATGGT
46066639 GGGATTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.11, G:0.34, T:0.24
Consensus pattern (31 bp):
TTGAATAAAGGAGCGGCTAATCCGGAATGGT
Found at i:46074154 original size:10 final size:10
Alignment explanation
Indices: 46074139--46074164 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
46074129 GAAGGGGTGA
46074139 AAGTGGGACG
1 AAGTGGGACG
46074149 AAGTGGGACG
1 AAGTGGGACG
46074159 AAGTGG
1 AAGTGG
46074165 TTTGCCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.50, T:0.12
Consensus pattern (10 bp):
AAGTGGGACG
Found at i:46075488 original size:17 final size:17
Alignment explanation
Indices: 46075458--46075505 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
46075448 TGCAATGTGG
* *
46075458 TTTCACTTATATTATCA
1 TTTCATTTAAATTATCA
**
46075475 TTTCATTTAAATTATTT
1 TTTCATTTAAATTATCA
46075492 TTTCGATTTAAATT
1 TTTC-ATTTAAATT
46075506 TAATTATTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTCATTTAAATTATCA
Found at i:46075526 original size:21 final size:21
Alignment explanation
Indices: 46075472--46075536 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
46075462 ACTTATATTA
*
46075472 TCATTTC-ATTTAAATTATTTTT
1 TCATTTCAATTT-AATTA-TTTC
*
46075494 TCGATTTAAATTTAATTATTTC
1 TC-ATTTCAATTTAATTATTTC
**
46075516 TCATTTCAATTTTTTTATTTC
1 TCATTTCAATTTAATTATTTC
46075537 AATTTATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 16 0.44
22 7 0.19
23 9 0.25
24 4 0.11
ACGTcount: A:0.26, C:0.11, G:0.02, T:0.62
Consensus pattern (21 bp):
TCATTTCAATTTAATTATTTC
Found at i:46075596 original size:5 final size:5
Alignment explanation
Indices: 46075586--46075632 Score: 58
Period size: 5 Copynumber: 8.6 Consensus size: 5
46075576 CATAATCATA
46075586 ATTTC ATTTC ATGTTC ATTTAAC ATTTC ATTTC ATTTC ATATTC ATT
1 ATTTC ATTTC AT-TTC ATTT--C ATTTC ATTTC ATTTC AT-TTC ATT
46075633 ACAAATTACA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 23 0.61
6 10 0.26
7 5 0.13
ACGTcount: A:0.26, C:0.17, G:0.02, T:0.55
Consensus pattern (5 bp):
ATTTC
Found at i:46075604 original size:11 final size:10
Alignment explanation
Indices: 46075586--46075632 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 10
46075576 CATAATCATA
46075586 ATTTCATTTC
1 ATTTCATTTC
46075596 ATGTTCATTTAAC
1 AT-TTCATTT--C
46075609 ATTTCATTTC
1 ATTTCATTTC
46075619 ATTTCATATTC
1 ATTTCAT-TTC
46075630 ATT
1 ATT
46075633 ACAAATTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
10 10 0.30
11 13 0.39
12 7 0.21
13 3 0.09
ACGTcount: A:0.26, C:0.17, G:0.02, T:0.55
Consensus pattern (10 bp):
ATTTCATTTC
Found at i:46075644 original size:28 final size:28
Alignment explanation
Indices: 46075586--46075644 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
46075576 CATAATCATA
* * *
46075586 ATTTCATTTCATGTTCATTTAACATTTC
1 ATTTCATTTCATATTCATTTAAAATTAC
46075614 ATTTCATTTCATATTCA-TTACAAATTAC
1 ATTTCATTTCATATTCATTTA-AAATTAC
46075642 ATT
1 ATT
46075645 ACATGGCCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 3 0.11
28 24 0.89
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.51
Consensus pattern (28 bp):
ATTTCATTTCATATTCATTTAAAATTAC
Found at i:46078719 original size:29 final size:30
Alignment explanation
Indices: 46078679--46078752 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 30
46078669 AACATATTAA
*
46078679 TAATTAATTAATA-TAAT-TAACTCTAAAAT-
1 TAATTAAATAATATTAATAT-ACT-TAAAATC
46078708 TAATTAAATAATAATTAATATACTTAAAATC
1 TAATTAAATAAT-ATTAATATACTTAAAATC
46078739 TAATTTAAATAATA
1 TAA-TTAAATAATA
46078753 ATTCTATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
29 11 0.28
30 7 0.18
31 11 0.28
32 10 0.26
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (30 bp):
TAATTAAATAATATTAATATACTTAAAATC
Found at i:46094758 original size:54 final size:54
Alignment explanation
Indices: 46094691--46094795 Score: 192
Period size: 54 Copynumber: 1.9 Consensus size: 54
46094681 TTGATTTGAT
*
46094691 TACATATGTTGTCATTATTAGGCTACTAACACTAGCTTCGGATTAGGGTTGTTA
1 TACATATGTTGTCATTATCAGGCTACTAACACTAGCTTCGGATTAGGGTTGTTA
*
46094745 TACATATGTTGTCATTATCGGGCTACTAACACTAGCTTCGGATTAGGGTTG
1 TACATATGTTGTCATTATCAGGCTACTAACACTAGCTTCGGATTAGGGTTG
46094796 CTAACACTAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (54 bp):
TACATATGTTGTCATTATCAGGCTACTAACACTAGCTTCGGATTAGGGTTGTTA
Found at i:46094799 original size:26 final size:26
Alignment explanation
Indices: 46094716--46094834 Score: 86
Period size: 26 Copynumber: 4.5 Consensus size: 26
46094706 TATTAGGCTA
46094716 CTAACACTAGCTTCGGATTAGGGTTG
1 CTAACACTAGCTTCGGATTAGGGTTG
* * * *
46094742 TTATACA-TATG-TT-GTCATTATCGGGCTA
1 CTA-ACACTA-GCTTCG-GATTA--GGGTTG
46094770 CTAACACTAGCTTCGGATTAGGGTTG
1 CTAACACTAGCTTCGGATTAGGGTTG
* **
46094796 CTAACACTAGCTT-GG-TTCGATTCTG
1 CTAACACTAGCTTCGGATTAGGGT-TG
46094821 CTAACACTAGCTTC
1 CTAACACTAGCTTC
46094835 AAAGGATCTA
Statistics
Matches: 72, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
24 4 0.06
25 18 0.25
26 27 0.38
27 8 0.11
28 14 0.19
29 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (26 bp):
CTAACACTAGCTTCGGATTAGGGTTG
Found at i:46094948 original size:25 final size:26
Alignment explanation
Indices: 46094920--46094968 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
46094910 GCTGACATAT
46094920 TCAGG-CTACTAACACTAGCTTCAAA
1 TCAGGACTACTAACACTAGCTTCAAA
* *
46094945 TCAGGATTGCTAACACTAGCTTCA
1 TCAGGACTACTAACACTAGCTTCA
46094969 GACAATCCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.27
Consensus pattern (26 bp):
TCAGGACTACTAACACTAGCTTCAAA
Found at i:46102909 original size:28 final size:27
Alignment explanation
Indices: 46102852--46102922 Score: 106
Period size: 28 Copynumber: 2.6 Consensus size: 27
46102842 GCAATCAAAT
* *
46102852 ATGGTACTTAGTGTACGAATATTGAGA
1 ATGGCACTTAGTGTGCGAATATTGAGA
46102879 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGA-ATATTGAGA
*
46102907 ATGACACTTAGTGTGC
1 ATGGCACTTAGTGTGC
46102923 AAAATATCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 16 0.40
28 24 0.60
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.31
Consensus pattern (27 bp):
ATGGCACTTAGTGTGCGAATATTGAGA
Found at i:46102929 original size:28 final size:28
Alignment explanation
Indices: 46102869--46102929 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
46102859 TTAGTGTACG
* *
46102869 AATATTGAGAATGGCACTTAGTGTGCGA
1 AATATTGAGAATGACACTTAGTGTGCAA
*
46102897 GATATTGAGAATGACACTTAGTGTGCAA
1 AATATTGAGAATGACACTTAGTGTGCAA
46102925 AATAT
1 AATAT
46102930 CAAATGATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.30
Consensus pattern (28 bp):
AATATTGAGAATGACACTTAGTGTGCAA
Found at i:46103110 original size:43 final size:42
Alignment explanation
Indices: 46103041--46103141 Score: 107
Period size: 43 Copynumber: 2.3 Consensus size: 42
46103031 TTTATAATGG
* * * *
46103041 TGATATTCGGGCTTTGAGCCTAGCAAGCTTTAA-GCTGGTGAATAA
1 TGATA-TCGGGCTTCG-GGCTAGCAAGCTATAATGCCGGTG-A-AA
46103086 T-ATTATCGGGCTTCGGGCTAGCAAGCTATAATGCCGGTGAAA
1 TGA-TATCGGGCTTCGGGCTAGCAAGCTATAATGCCGGTGAAA
46103128 TGATATCGGGCTTC
1 TGATATCGGGCTTC
46103142 AAGCCTAGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
42 14 0.29
43 16 0.33
44 16 0.33
45 3 0.06
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (42 bp):
TGATATCGGGCTTCGGGCTAGCAAGCTATAATGCCGGTGAAA
Found at i:46126499 original size:14 final size:14
Alignment explanation
Indices: 46126480--46126538 Score: 68
Period size: 14 Copynumber: 4.3 Consensus size: 14
46126470 TTGCTTACAC
*
46126480 TTAAGGTTAAGTAA
1 TTAAGGTTAATTAA
46126494 TTAAGGTTAATTAA
1 TTAAGGTTAATTAA
**
46126508 GTTAATCTTAATTAA
1 -TTAAGGTTAATTAA
46126523 TTAA--TTAATTAA
1 TTAAGGTTAATTAA
46126535 TTAA
1 TTAA
46126539 CTAGTGAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
12 12 0.29
14 17 0.41
15 12 0.29
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (14 bp):
TTAAGGTTAATTAA
Found at i:46126522 original size:4 final size:4
Alignment explanation
Indices: 46126486--46126538 Score: 52
Period size: 4 Copynumber: 12.0 Consensus size: 4
46126476 ACACTTAAGG
*
46126486 TTAA GTAA TTAA GGTTAA TTAA GTTAA TCTTAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA --TTAA TTAA -TTAA --TTAA TTAA TTAA TTAA TTAA
46126535 TTAA
1 TTAA
46126539 CTAGTGAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
4 30 0.71
5 4 0.10
6 8 0.19
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (4 bp):
TTAA
Found at i:46135164 original size:22 final size:21
Alignment explanation
Indices: 46135130--46135170 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
46135120 GTAGTAAATT
46135130 TTGAATTGATAATTATAGTTAA
1 TTGAATTGATAATTA-AGTTAA
46135152 TTGAA-TGATTAATTAAGTT
1 TTGAATTGA-TAATTAAGTT
46135171 CAAATGGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (21 bp):
TTGAATTGATAATTAAGTTAA
Found at i:46139516 original size:23 final size:23
Alignment explanation
Indices: 46139490--46139534 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
46139480 ATGATATACA
46139490 AAAATGATATCAA-TGAAAAGGTC
1 AAAATGATA-CAACTGAAAAGGTC
*
46139513 AAAATGATAGAACTGAAAAGGT
1 AAAATGATACAACTGAAAAGGT
46139535 TGGCATTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (23 bp):
AAAATGATACAACTGAAAAGGTC
Found at i:46143516 original size:35 final size:35
Alignment explanation
Indices: 46143438--46143516 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
46143428 TAAATTACTT
*
46143438 ATTAT-TTAAGTAAATAGATATTTATTATTTATCA
1 ATTATATTAAGTAAATAGATATTTATTATTAATCA
*
46143472 TTTATTATTAAGTAAA-AGATATTTATTAATTAAAT-A
1 ATTA-TATTAAGTAAATAGATATTTATT-ATT-AATCA
46143508 ATTATATTA
1 ATTATATTA
46143517 TAAGATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
34 3 0.08
35 17 0.45
36 16 0.42
37 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.49
Consensus pattern (35 bp):
ATTATATTAAGTAAATAGATATTTATTATTAATCA
Found at i:46143793 original size:14 final size:14
Alignment explanation
Indices: 46143774--46143806 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
46143764 TTTGGAAGCT
46143774 TTAAGCTTTAATTG
1 TTAAGCTTTAATTG
46143788 TTAAGCTTTAATTG
1 TTAAGCTTTAATTG
46143802 TTAAG
1 TTAAG
46143807 TTAATTAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.48
Consensus pattern (14 bp):
TTAAGCTTTAATTG
Found at i:46144725 original size:47 final size:47
Alignment explanation
Indices: 46144606--46144726 Score: 127
Period size: 47 Copynumber: 2.5 Consensus size: 47
46144596 GACTTCGAGT
* ** *
46144606 CGATGAGGCACCTTATGTGTCGTACTGTTACTGTTACTTCGGTTTAATC
1 CGATGAGGCA-C-TAAGTGTCGTACTGTTACTGTTACTTCGGTCAAAGC
* * **
46144655 CGTTGAGGTACTAAGTACCGTACTGTTACTGTTTACTTCGG-CAAAGC
1 CGATGAGGCACTAAGTGTCGTACTGTTACTG-TTACTTCGGTCAAAGC
*
46144702 CGATGAGGCACTAAGTGTTGTACTG
1 CGATGAGGCACTAAGTGTCGTACTG
46144727 GTGTGTTGGT
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
47 40 0.69
48 10 0.17
49 8 0.14
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (47 bp):
CGATGAGGCACTAAGTGTCGTACTGTTACTGTTACTTCGGTCAAAGC
Found at i:46144881 original size:39 final size:39
Alignment explanation
Indices: 46144795--46144929 Score: 128
Period size: 39 Copynumber: 3.5 Consensus size: 39
46144785 TACTGTACTG
* ** * *
46144795 AATAATTGAT-TTTACTGAATAACTAAATTACTGTATTG
1 AATAATTGATAGTTACTGAATAACTAAATTACTACACTA
* *
46144833 AATAATTGATAGTTATTGAATAACTAAACTACTACACTA
1 AATAATTGATAGTTACTGAATAACTAAATTACTACACTA
* * * ** *
46144872 AATATTTGATAGTTACTAAATGACTAAATTACTGTACTG
1 AATAATTGATAGTTACTGAATAACTAAATTACTACACTA
* *
46144911 AATAACTGATTGTTACTGA
1 AATAATTGATAGTTACTGA
46144930 TTAAATATGA
Statistics
Matches: 77, Mismatches: 19, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
38 10 0.13
39 67 0.87
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (39 bp):
AATAATTGATAGTTACTGAATAACTAAATTACTACACTA
Found at i:46144902 original size:78 final size:77
Alignment explanation
Indices: 46144780--46144925 Score: 193
Period size: 78 Copynumber: 1.9 Consensus size: 77
46144770 TTAATAGGGG
** * * * * *
46144780 TAAACTACTGTACTGAATAATTGATTTTACTGAATAACTAAATTACTGTATTGAATAATTGATAG
1 TAAACTACTACACTAAATAATTGATGTTACTAAATAACTAAATTACTGTACTGAATAACTGATAG
46144845 TTATTGAATAAC
66 TTATTGAATAAC
* * *
46144857 TAAACTACTACACTAAATATTTGATAGTTACTAAATGACTAAATTACTGTACTGAATAACTGATT
1 TAAACTACTACACTAAATAATTGAT-GTTACTAAATAACTAAATTACTGTACTGAATAACTGATA
46144922 GTTA
65 GTTA
46144926 CTGATTAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
77 21 0.36
78 37 0.64
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (77 bp):
TAAACTACTACACTAAATAATTGATGTTACTAAATAACTAAATTACTGTACTGAATAACTGATAG
TTATTGAATAAC
Found at i:46146419 original size:13 final size:13
Alignment explanation
Indices: 46146401--46146427 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
46146391 TCACTCTACC
46146401 TTTTTTTCTTTAT
1 TTTTTTTCTTTAT
46146414 TTTTTTTCTTTAT
1 TTTTTTTCTTTAT
46146427 T
1 T
46146428 CACCCAACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTCTTTAT
Found at i:46151081 original size:21 final size:22
Alignment explanation
Indices: 46151040--46151085 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
46151030 AAATATTATC
46151040 AAAATTTACAAAAAGGAAAATG
1 AAAATTTACAAAAAGGAAAATG
* * *
46151062 AAAATTTATAAAAAGTAAATTG
1 AAAATTTACAAAAAGGAAAATG
46151084 AA
1 AA
46151086 TATCCGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.63, C:0.02, G:0.11, T:0.24
Consensus pattern (22 bp):
AAAATTTACAAAAAGGAAAATG
Found at i:46158027 original size:47 final size:47
Alignment explanation
Indices: 46157976--46158070 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
46157966 AGAAATTCAA
46157976 TGGTTTTATATGGAGTTACTGTTATGCGACTCACTAAATTTATATGT
1 TGGTTTTATATGGAGTTACTGTTATGCGACTCACTAAATTTATATGT
46158023 TGGTTTTATATGGAGTTACTGTTATGCGACTCACTAAATTTATATGT
1 TGGTTTTATATGGAGTTACTGTTATGCGACTCACTAAATTTATATGT
46158070 T
1 T
46158071 TTGATTTATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (47 bp):
TGGTTTTATATGGAGTTACTGTTATGCGACTCACTAAATTTATATGT
Found at i:46158553 original size:219 final size:224
Alignment explanation
Indices: 46158146--46158585 Score: 746
Period size: 219 Copynumber: 2.0 Consensus size: 224
46158136 TTTGCTTTCA
46158146 GACTTGGGTGGCGGGCTTAAATGGTTATGCTGTAATGCTTAATCTCATTTTGGTGCTATGAATCA
1 GACTTGGGTGGCGGGCTTAAATGGTTATGCTGTAATGCTTAATCTCA---T--T-CTATGAATCA
46158211 AATGCTGTTACGTTTTTGAATTGAACTTGATGTTTTGGTTGCATTAGTTAGTATTTGATCCCTAC
60 AATGCTGTTACGTTTTTGAATTGAACTTGATGTTTTGGTTGCATTAGTTAGTATTTGATCCCTAC
*
46158276 ATTTTGTCATTGCATTGAAGCACCTAGCTGGAGCTTTGTCTTGATGGAGTGGTTTTGATAAAAAA
125 ATTTTGTCATTGCATTGAAGCACCTAGCTGGAGCTTTGTCTTGATGGAATGGTTTTGATAAAAAA
46158341 AAAAATTGTATCAAACAAGCTCTCTGGAGCTTTGG
190 AAAAATTGTATCAAACAAGCTCTCTGGAGCTTTGG
46158376 GACTTGGGTGGCGGGC-T-AATGGTTATGCTGTAATGCTTAATCTCA-T-T-TGAATCAAATGCT
1 GACTTGGGTGGCGGGCTTAAATGGTTATGCTGTAATGCTTAATCTCATTCTATGAATCAAATGCT
* *
46158436 GTTATGTTTTTGAATTGAACTTGATGTTTTGGTTGCATTAGTTAGTATTTGATCCCTATATTTTG
66 GTTACGTTTTTGAATTGAACTTGATGTTTTGGTTGCATTAGTTAGTATTTGATCCCTACATTTTG
* *
46158501 TCATTGCATTGAAGCACCTAGCTGGTGCTTTGTCTTGATGGAATGGTTTTGATAAAAAAGAAAAT
131 TCATTGCATTGAAGCACCTAGCTGGAGCTTTGTCTTGATGGAATGGTTTTGATAAAAAAAAAAAT
46158566 TGTATCAAACAAGCTCTCTG
196 TGTATCAAACAAGCTCTCTG
46158586 TTGCAACTTA
Statistics
Matches: 205, Mismatches: 5, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
219 158 0.77
220 1 0.00
222 1 0.00
228 28 0.14
229 1 0.00
230 16 0.08
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (224 bp):
GACTTGGGTGGCGGGCTTAAATGGTTATGCTGTAATGCTTAATCTCATTCTATGAATCAAATGCT
GTTACGTTTTTGAATTGAACTTGATGTTTTGGTTGCATTAGTTAGTATTTGATCCCTACATTTTG
TCATTGCATTGAAGCACCTAGCTGGAGCTTTGTCTTGATGGAATGGTTTTGATAAAAAAAAAAAT
TGTATCAAACAAGCTCTCTGGAGCTTTGG
Found at i:46160851 original size:111 final size:110
Alignment explanation
Indices: 46160611--46160909 Score: 485
Period size: 111 Copynumber: 2.7 Consensus size: 110
46160601 TAATTGTAAA
* *
46160611 ACATTTGAGGCTCTTGTTGTTATGTGTATAGTTTGGAGTGGCAGAG-TAAAATT-TTCCCATTAA
1 ACATTTGAGGCTCTTGTTGTTATGTGTATAATTTGGAATGGCAG-GTTAAAATTCTTCCCATTAA
* *
46160674 TCATATCATCCTGAAGTTCTCATAATTGTGGAGATTTTAAGTTTCC
65 TCATACCATCCTGAAGTTCTCATAATTCTGGAGATTTTAAGTTTCC
* *
46160720 ACATTTGAGGCTCTTTTTGTTAAGTGTATAATTTGGAATGGCAGGTTAAAATTCTTCCCATTAAT
1 ACATTTGAGGCTCTTGTTGTTATGTGTATAATTTGGAATGGCAGGTTAAAATTCTTCCCATTAAT
46160785 CATACCATCCTGAAGTTCTCATAAATTCTGGAGATTTTAAGTTTCC
66 CATACCATCCTGAAGTTCTCAT-AATTCTGGAGATTTTAAGTTTCC
*
46160831 ACATTTGAGGCTCTTGTTGTTATGTGTATAATTTGGAATGGCAGATTAAAATTCTTCCCATTAAT
1 ACATTTGAGGCTCTTGTTGTTATGTGTATAATTTGGAATGGCAGGTTAAAATTCTTCCCATTAAT
*
46160896 AAATACCATCCTGA
66 -CATACCATCCTGA
46160910 TTAAAGTTTC
Statistics
Matches: 176, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
108 1 0.01
109 47 0.27
110 32 0.18
111 84 0.48
112 12 0.07
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (110 bp):
ACATTTGAGGCTCTTGTTGTTATGTGTATAATTTGGAATGGCAGGTTAAAATTCTTCCCATTAAT
CATACCATCCTGAAGTTCTCATAATTCTGGAGATTTTAAGTTTCC
Found at i:46161000 original size:14 final size:14
Alignment explanation
Indices: 46160981--46161009 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
46160971 GAGTAATGTT
46160981 ACATTACTCCTTTA
1 ACATTACTCCTTTA
46160995 ACATTACTCCTTTA
1 ACATTACTCCTTTA
46161009 A
1 A
46161010 TACATGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.41
Consensus pattern (14 bp):
ACATTACTCCTTTA
Found at i:46162183 original size:37 final size:37
Alignment explanation
Indices: 46162133--46162207 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
46162123 GATGCTTGAC
46162133 TATATGGAACTTAACTTGGTTACTTATTCTATTTACT
1 TATATGGAACTTAACTTGGTTACTTATTCTATTTACT
46162170 TATATGGAACTTAACTTGGTTACTTATTCTATTTACT
1 TATATGGAACTTAACTTGGTTACTTATTCTATTTACT
46162207 T
1 T
46162208 CAGTGTGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (37 bp):
TATATGGAACTTAACTTGGTTACTTATTCTATTTACT
Found at i:46162857 original size:27 final size:27
Alignment explanation
Indices: 46162827--46162878 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
46162817 ATAGAATAGC
*
46162827 TGGTAATGAATTTGTGTTATCTGGTCT
1 TGGTAATGAAATTGTGTTATCTGGTCT
*
46162854 TGGTAATGAAATTGTGTTGTCTGGT
1 TGGTAATGAAATTGTGTTATCTGGT
46162879 TTTGATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.06, G:0.29, T:0.46
Consensus pattern (27 bp):
TGGTAATGAAATTGTGTTATCTGGTCT
Found at i:46163331 original size:37 final size:37
Alignment explanation
Indices: 46163281--46163355 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
46163271 GATGCTTGAC
46163281 TATATGGAACTTAACTTGGTTACTTATTCTATTTACT
1 TATATGGAACTTAACTTGGTTACTTATTCTATTTACT
46163318 TATATGGAACTTAACTTGGTTACTTATTCTATTTACT
1 TATATGGAACTTAACTTGGTTACTTATTCTATTTACT
46163355 T
1 T
46163356 CAGTGTGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (37 bp):
TATATGGAACTTAACTTGGTTACTTATTCTATTTACT
Found at i:46164005 original size:27 final size:27
Alignment explanation
Indices: 46163975--46164026 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
46163965 ATAGAATAGC
*
46163975 TGGTAATGAATTTGTGTTATCTGGTCT
1 TGGTAATGAAATTGTGTTATCTGGTCT
*
46164002 TGGTAATGAAATTGTGTTGTCTGGT
1 TGGTAATGAAATTGTGTTATCTGGT
46164027 TTTGATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.06, G:0.29, T:0.46
Consensus pattern (27 bp):
TGGTAATGAAATTGTGTTATCTGGTCT
Found at i:46164544 original size:13 final size:13
Alignment explanation
Indices: 46164526--46164551 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46164516 ATGTTAGTAA
46164526 CAGTCGATGCCTT
1 CAGTCGATGCCTT
46164539 CAGTCGATGCCTT
1 CAGTCGATGCCTT
46164552 AGGTTTTGGA
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:0.15, C:0.31, G:0.23, T:0.31
Consensus pattern (13 bp):
CAGTCGATGCCTT
Found at i:46164877 original size:58 final size:58
Alignment explanation
Indices: 46164787--46164902 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
46164777 TAGACTTACG
46164787 CATTAACAAGGTTCTTTCTTTTACTTTTTACTGTTTTTGTATGTAACTTGGTTAACAA
1 CATTAACAAGGTTCTTTCTTTTACTTTTTACTGTTTTTGTATGTAACTTGGTTAACAA
46164845 CATTAACAAGGTTCTTTCTTTTACTTTTTACTGTTTTTGTATGTAACTTGGTTAACAA
1 CATTAACAAGGTTCTTTCTTTTACTTTTTACTGTTTTTGTATGTAACTTGGTTAACAA
46164903 ATCCAGTTCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.50
Consensus pattern (58 bp):
CATTAACAAGGTTCTTTCTTTTACTTTTTACTGTTTTTGTATGTAACTTGGTTAACAA
Found at i:46171944 original size:35 final size:35
Alignment explanation
Indices: 46171898--46171968 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
46171888 CCTCATCTTC
*
46171898 CTCTATTTGAGCATTTGAGGGTAAAGCCAAATTAT
1 CTCTATTTGAGCATTTGAGGGTAAAACCAAATTAT
46171933 CTCTATTTGAGCATTTGAGGGTAAAACCAAATTAT
1 CTCTATTTGAGCATTTGAGGGTAAAACCAAATTAT
46171968 C
1 C
46171969 ATTGGTATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Consensus pattern (35 bp):
CTCTATTTGAGCATTTGAGGGTAAAACCAAATTAT
Found at i:46180357 original size:41 final size:41
Alignment explanation
Indices: 46180312--46180394 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
46180302 TTGTCAAAAT
* *
46180312 GAGATTTTTAAATTAATTTGGCCATTAATTTTAAAATTTGA
1 GAGATTTTTAAATTAATTTAGCCATCAATTTTAAAATTTGA
46180353 GAGATTTTTAAATTAATTTAGCCATCAATTTTAAAATTTGA
1 GAGATTTTTAAATTAATTTAGCCATCAATTTTAAAATTTGA
46180394 G
1 G
46180395 GCGAAACCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (41 bp):
GAGATTTTTAAATTAATTTAGCCATCAATTTTAAAATTTGA
Found at i:46181369 original size:11 final size:11
Alignment explanation
Indices: 46181355--46181384 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
46181345 TTAGCCTATC
46181355 ATTAATTAGAA
1 ATTAATTAGAA
*
46181366 ATTAATTAGGA
1 ATTAATTAGAA
46181377 ATTAATTA
1 ATTAATTA
46181385 CTAGATTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (11 bp):
ATTAATTAGAA
Found at i:46184040 original size:20 final size:20
Alignment explanation
Indices: 46184015--46184052 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
46184005 CTAGGAACTA
46184015 TGTGTTCTGAGCTCATGAGT
1 TGTGTTCTGAGCTCATGAGT
*
46184035 TGTGTTCTGAGTTCATGA
1 TGTGTTCTGAGCTCATGA
46184053 TGTATGTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.13, G:0.29, T:0.42
Consensus pattern (20 bp):
TGTGTTCTGAGCTCATGAGT
Found at i:46186255 original size:24 final size:25
Alignment explanation
Indices: 46186214--46186268 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
46186204 GCTTATTCGG
46186214 GCTTAATAGCAGAAAGCTCATAAGA
1 GCTTAATAGCAGAAAGCTCATAAGA
* **
46186239 GCTTAA-ATCAGAAAGCTCATGCGA
1 GCTTAATAGCAGAAAGCTCATAAGA
46186263 GCTTAA
1 GCTTAA
46186269 CAGGTAACTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (25 bp):
GCTTAATAGCAGAAAGCTCATAAGA
Found at i:46191503 original size:52 final size:50
Alignment explanation
Indices: 46191432--46191592 Score: 163
Period size: 52 Copynumber: 3.3 Consensus size: 50
46191422 CGACGGAAAA
* *
46191432 GATGTGATATATGCA-CCCGTTTAAGACCATAGCTGGGCTATGGCATCGGT
1 GATGTGATATGTG-ATCCCGTATAAGACCATAGCTGGGCTATGGCATCGGT
* * *
46191482 GCAATGTGATATGTGTTCCCGTATAAGACCAAAGCTGGGATATGGCATCGGT
1 G--ATGTGATATGTGATCCCGTATAAGACCATAGCTGGGCTATGGCATCGGT
* * * *
46191534 G-TGTG--ATGTGAT-CCGTGTAAGACCATAGCAGGGCTATGGCTTCAGT
1 GATGTGATATGTGATCCCGTATAAGACCATAGCTGGGCTATGGCATCGGT
*
46191580 G-TGTGATGTGTGA
1 GATGTGATATGTGA
46191593 CAATGTGAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
46 33 0.35
47 6 0.06
48 5 0.05
49 4 0.04
50 1 0.01
52 44 0.47
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.29
Consensus pattern (50 bp):
GATGTGATATGTGATCCCGTATAAGACCATAGCTGGGCTATGGCATCGGT
Found at i:46191556 original size:46 final size:47
Alignment explanation
Indices: 46191447--46191589 Score: 162
Period size: 46 Copynumber: 3.0 Consensus size: 47
46191437 GATATATGCA
* *
46191447 CCCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATATGTGTT
1 CCCGTATAAGACCATAGCTGGGCTATGGCATCGGTG---TGTG--ATGTGAT
* *
46191499 CCCGTATAAGACCAAAGCTGGGATATGGCATCGGTGTGTGATGTGAT
1 CCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGTGATGTGAT
* * * *
46191546 -CCGTGTAAGACCATAGCAGGGCTATGGCTTCAGTGTGTGATGTG
1 CCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGTGATGTG
46191590 TGACAATGTG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
46 38 0.47
47 6 0.07
49 4 0.05
52 33 0.41
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.28
Consensus pattern (47 bp):
CCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGTGATGTGAT
Found at i:46194530 original size:93 final size:93
Alignment explanation
Indices: 46194371--46194542 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
46194361 GGATGGTTGA
* *
46194371 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGAGAATGTCTGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGAGAACGCCTGAACTCGTTGAGT
46194436 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
46194464 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCTGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGAGAACGCCTGAACTCGTTGAGT
46194529 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
46194543 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGAGAACGCCTGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:46194547 original size:46 final size:45
Alignment explanation
Indices: 46194377--46194549 Score: 181
Period size: 46 Copynumber: 3.8 Consensus size: 45
46194367 TTGAGCATCC
* * *
46194377 GAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGAGAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACGCCT
* * * *
46194423 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAC---GC--CT
46194470 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACGCCT
* *
46194516 GAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
46194550 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 2 0.02
46 59 0.56
47 27 0.26
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.29
Consensus pattern (45 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACGCCT
Found at i:46202004 original size:46 final size:46
Alignment explanation
Indices: 46201954--46202126 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
46201944 TGGTTGAGCA
46201954 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
46202000 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
46202045 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
46202093 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
46202127 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:46202110 original size:93 final size:93
Alignment explanation
Indices: 46201951--46202121 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
46201941 GGATGGTTGA
* *
46201951 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
46202016 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
46202044 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
46202109 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
46202122 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:46212990 original size:50 final size:50
Alignment explanation
Indices: 46212915--46213012 Score: 169
Period size: 50 Copynumber: 2.0 Consensus size: 50
46212905 TTCTAGGTAC
*
46212915 TGAAGTAAAATTAATCTCAGAACAGACCAAATTAAGAATTATACCTTTGT
1 TGAAGTAAAATTAATCTCAGAACAGACCAAATTAAGAATGATACCTTTGT
* *
46212965 TGAAGTTAAATTAATCTCAGAACAGACCAGATTAAGAATGATACCTTT
1 TGAAGTAAAATTAATCTCAGAACAGACCAAATTAAGAATGATACCTTT
46213013 TTTTGCATAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (50 bp):
TGAAGTAAAATTAATCTCAGAACAGACCAAATTAAGAATGATACCTTTGT
Found at i:46225713 original size:73 final size:73
Alignment explanation
Indices: 46225619--46225755 Score: 222
Period size: 73 Copynumber: 1.9 Consensus size: 73
46225609 ATTTGATTAT
* * *
46225619 AAAATTAATAAATTGTTTATAATTTAAAAATTATGCCACCTATATTTAAAAAATT-ACTTCATTT
1 AAAATTAATAAAATGCTTATAATTAAAAAATTATGCCACCTATATTTAAAAAATTAAC-TCATTT
46225683 TTTCAAAAA
65 TTTCAAAAA
*
46225692 AAAATTAATAAAATGCTTATAATTAAAAAATTATGCCACCTATATTTAAACAATTAACTCATTT
1 AAAATTAATAAAATGCTTATAATTAAAAAATTATGCCACCTATATTTAAAAAATTAACTCATTT
46225756 CTATATTCAG
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
73 57 0.97
74 2 0.03
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (73 bp):
AAAATTAATAAAATGCTTATAATTAAAAAATTATGCCACCTATATTTAAAAAATTAACTCATTTT
TTCAAAAA
Found at i:46226263 original size:88 final size:86
Alignment explanation
Indices: 46226087--46226266 Score: 297
Period size: 88 Copynumber: 2.1 Consensus size: 86
46226077 AATCTTTCTT
* * * *
46226087 CATCAATGGCCTTTGCTACGTGGGCATCCCTCATACTAAAAAAGGAGAGGATTCTAACCTGAAAG
1 CATCAATGGCCTTTGCTACATGGGCATCCCTCATACTAAAAAAGGAGAAGATTCTAACATGAAAA
46226152 TATCGAGTGAGTGAAGCTTAA
66 TATCGAGTGAGTGAAGCTTAA
*
46226173 CATCAATGGCCTTTGCTACATGGGCATCCCTCGTACTAAAAAAAGGAGAAGATTTCTAACATGAA
1 CATCAATGGCCTTTGCTACATGGGCATCCCTCATACT-AAAAAAGGAGAAGA-TTCTAACATGAA
46226238 AATATCGAGTGAGTGAAGCTTAA
64 AATATCGAGTGAGTGAAGCTTAA
46226261 CATCAA
1 CATCAA
46226267 AGGTTAAAGT
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
86 35 0.40
87 13 0.15
88 39 0.45
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.24
Consensus pattern (86 bp):
CATCAATGGCCTTTGCTACATGGGCATCCCTCATACTAAAAAAGGAGAAGATTCTAACATGAAAA
TATCGAGTGAGTGAAGCTTAA
Found at i:46228546 original size:11 final size:11
Alignment explanation
Indices: 46228530--46228573 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
46228520 TAGAAGAATG
46228530 GAATTGAAATT
1 GAATTGAAATT
*
46228541 GAATTGAAGAATG
1 GAATTG-A-AATT
46228554 GAATTGAAATT
1 GAATTGAAATT
46228565 GAATTGAAA
1 GAATTGAAA
46228574 AATGAAGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 18 0.62
12 2 0.07
13 9 0.31
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.30
Consensus pattern (11 bp):
GAATTGAAATT
Found at i:46228550 original size:24 final size:24
Alignment explanation
Indices: 46228522--46228577 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
46228512 GAGGGTTGTA
46228522 GAAGAATGGAATTGAAATTGAATT
1 GAAGAATGGAATTGAAATTGAATT
46228546 GAAGAATGGAATTGAAATTGAATT
1 GAAGAATGGAATTGAAATTGAATT
*
46228570 GAAAAATG
1 GAAGAATG
46228578 AAGCTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.25, T:0.27
Consensus pattern (24 bp):
GAAGAATGGAATTGAAATTGAATT
Found at i:46228559 original size:13 final size:13
Alignment explanation
Indices: 46228522--46228561 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
46228512 GAGGGTTGTA
46228522 GAAGAATGGAATT
1 GAAGAATGGAATT
*
46228535 G-A-AATTGAATT
1 GAAGAATGGAATT
46228546 GAAGAATGGAATT
1 GAAGAATGGAATT
46228559 GAA
1 GAA
46228562 ATTGAATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 9 0.39
12 2 0.09
13 12 0.52
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.25
Consensus pattern (13 bp):
GAAGAATGGAATT
Found at i:46228576 original size:13 final size:13
Alignment explanation
Indices: 46228536--46228576 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
46228526 AATGGAATTG
46228536 AAATTGAATTGAA
1 AAATTGAATTGAA
* *
46228549 GAATGGAATTG--
1 AAATTGAATTGAA
46228560 AAATTGAATTGAA
1 AAATTGAATTGAA
46228573 AAAT
1 AAAT
46228577 GAAGCTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
11 9 0.41
13 13 0.59
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (13 bp):
AAATTGAATTGAA
Found at i:46228742 original size:50 final size:50
Alignment explanation
Indices: 46228666--46228774 Score: 193
Period size: 50 Copynumber: 2.2 Consensus size: 50
46228656 GTAAAATGGA
46228666 ATAAAATTGATATATTATGGTAATAAGCTATTAAAATATATTCAGAATTG
1 ATAAAATTGATATATTATGGTAATAAGCTATTAAAATATATTCAGAATTG
* *
46228716 ATAAAATTGATATATTGTGGTTATAAGCTATTAAAATATATTCAGAATTG
1 ATAAAATTGATATATTATGGTAATAAGCTATTAAAATATATTCAGAATTG
46228766 AT-AAATTGA
1 ATAAAATTGA
46228775 AATGAATTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
49 7 0.12
50 50 0.88
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.39
Consensus pattern (50 bp):
ATAAAATTGATATATTATGGTAATAAGCTATTAAAATATATTCAGAATTG
Found at i:46234577 original size:46 final size:46
Alignment explanation
Indices: 46234443--46234587 Score: 173
Period size: 47 Copynumber: 3.1 Consensus size: 46
46234433 CATGGAAACA
* * *
46234443 TGTGATATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGG
1 TGTGATATGTGA--TCCATGTAAGACTATAGCTGGGCTATGGCATCGG
* * * * *
46234491 TGTGATATGTGCTTCTATGTAAGACTATATCTGGGATATGGCATCAG
1 TGTGATATGTG-ATCCATGTAAGACTATAGCTGGGCTATGGCATCGG
* *
46234538 TGTGATATGTGATCCATGTAAGACTATGGCTGGGCTATGGCTTCGG
1 TGTGATATGTGATCCATGTAAGACTATAGCTGGGCTATGGCATCGG
46234584 TGTG
1 TGTG
46234588 TGATATATGA
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
46 32 0.40
47 38 0.47
48 11 0.14
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (46 bp):
TGTGATATGTGATCCATGTAAGACTATAGCTGGGCTATGGCATCGG
Found at i:46239452 original size:17 final size:17
Alignment explanation
Indices: 46239430--46239463 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
46239420 TCAAGTTGTG
46239430 TTTTTAAGTTATCTTTT
1 TTTTTAAGTTATCTTTT
*
46239447 TTTTTAAGTTATGTTTT
1 TTTTTAAGTTATCTTTT
46239464 ATGCATGCTC
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:0.18, C:0.03, G:0.09, T:0.71
Consensus pattern (17 bp):
TTTTTAAGTTATCTTTT
Found at i:46242873 original size:16 final size:16
Alignment explanation
Indices: 46242854--46242884 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46242844 CTTCTTCACT
46242854 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
46242870 TACTTACTTACTTAA
1 TACTCACTTACTTAA
46242885 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:46242890 original size:20 final size:20
Alignment explanation
Indices: 46242851--46242890 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
46242841 AAACTTCTTC
* *
46242851 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
46242871 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
46242891 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:46243211 original size:53 final size:54
Alignment explanation
Indices: 46243076--46243330 Score: 238
Period size: 55 Copynumber: 4.8 Consensus size: 54
46243066 ACACGGGTAC
* * * *
46243076 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
46243125 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * * * * *
46243178 CTCACCAATGCCATGCCTTGGCATCGTCCTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-GAAA
* * * * *
46243233 CTTATCAATGCCATGTCTTGACATGGTCTTGCATGATTTCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * *
46243286 CCTTACCAATTTCCATGCCTTGGCATGCTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
46243331 AAACCCTAAT
Statistics
Matches: 166, Mismatches: 29, Indels: 16
0.79 0.14 0.08
Matches are distributed among these distances:
49 38 0.23
50 1 0.01
52 2 0.01
53 47 0.28
54 10 0.06
55 66 0.40
56 2 0.01
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
Found at i:46243703 original size:30 final size:29
Alignment explanation
Indices: 46243669--46243725 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
46243659 CATTGACTCA
*
46243669 AACTTTTGCAAAATTACATTTTTGCCCCTC
1 AACTTTTACAAAATTACATTTTT-CCCCTC
* *
46243699 AACTTTTACATATTTACATTTTTCCCC
1 AACTTTTACAAAATTACATTTTTCCCC
46243726 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.26, C:0.26, G:0.04, T:0.44
Consensus pattern (29 bp):
AACTTTTACAAAATTACATTTTTCCCCTC
Found at i:46250086 original size:6 final size:6
Alignment explanation
Indices: 46250077--46250103 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
46250067 CTATTTTTGG
46250077 TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT
46250104 GGTTTTGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:46250091 original size:18 final size:18
Alignment explanation
Indices: 46250068--46250103 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
46250058 GGACTTTTAC
*
46250068 TATTTTTGGTTTTATTTT
1 TATTTTTAGTTTTATTTT
*
46250086 TATTTTTATTTTTATTTT
1 TATTTTTAGTTTTATTTT
46250104 GGTTTTGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.81
Consensus pattern (18 bp):
TATTTTTAGTTTTATTTT
Found at i:46251562 original size:44 final size:44
Alignment explanation
Indices: 46251496--46251585 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
46251486 TGTTTTTAAC
* * *
46251496 TTAGTTGCTAGTGAAATGATGGTTAAATGTGTATATGGTTGTGG
1 TTAGTTACTAGTGAAATAATGGTTAAATGTGTATATGGTTATGG
46251540 TTAGTTACTAGTGAAATAATGGTTAAATGTGTATATGGTTATGG
1 TTAGTTACTAGTGAAATAATGGTTAAATGTGTATATGGTTATGG
46251584 TT
1 TT
46251586 GAGGCTATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.28, C:0.02, G:0.28, T:0.42
Consensus pattern (44 bp):
TTAGTTACTAGTGAAATAATGGTTAAATGTGTATATGGTTATGG
Found at i:46259628 original size:47 final size:47
Alignment explanation
Indices: 46259559--46259701 Score: 268
Period size: 47 Copynumber: 3.0 Consensus size: 47
46259549 ATTCAATATA
*
46259559 TCAAATTAAGAAGAATTTGCACTTACCTTATTTTTCCAAGTTTCCTT
1 TCAAATTGAGAAGAATTTGCACTTACCTTATTTTTCCAAGTTTCCTT
*
46259606 TCAAATTGAGAAGAATTTGCACTTACCTTATTTTTCCAAGTTTCTTT
1 TCAAATTGAGAAGAATTTGCACTTACCTTATTTTTCCAAGTTTCCTT
46259653 TCAAATTGAGAAGAATTTGCACTTACCTTATTTTTCCAAGTTTCCTT
1 TCAAATTGAGAAGAATTTGCACTTACCTTATTTTTCCAAGTTTCCTT
46259700 TC
1 TC
46259702 CTTTTCTACT
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 93 1.00
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.43
Consensus pattern (47 bp):
TCAAATTGAGAAGAATTTGCACTTACCTTATTTTTCCAAGTTTCCTT
Found at i:46261295 original size:46 final size:46
Alignment explanation
Indices: 46261235--46261407 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
46261225 TTGAGCATCT
46261235 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
* * * * *
46261281 GAACTCTTTTAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G--TCC
* **
46261328 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
*
46261374 GAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
46261408 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 3 0.03
46 58 0.56
47 26 0.25
48 2 0.02
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
Found at i:46261342 original size:93 final size:93
Alignment explanation
Indices: 46261229--46261400 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
46261219 AGATATTTGA
* ** * *
46261229 GCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCTTTTAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
46261294 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
46261322 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
46261387 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
46261401 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:46265291 original size:26 final size:24
Alignment explanation
Indices: 46265262--46265330 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 24
46265252 TAAATAAAAA
* *
46265262 ATTTTAAAATATAATAAATCAAATAC
1 ATTTAAAAACATAA-AAA-CAAATAC
46265288 ATTTAAAAACATAAAAACAAAT--
1 ATTTAAAAACATAAAAACAAATAC
*
46265310 A-TT-AAAACAAAAAAACAAATA
1 ATTTAAAAACATAAAAACAAATA
46265331 AAAAATGAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 16 0.41
21 2 0.05
22 1 0.03
24 5 0.13
25 3 0.08
26 12 0.31
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.25
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAC
Found at i:46265318 original size:20 final size:20
Alignment explanation
Indices: 46265293--46265330 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
46265283 AATACATTTA
*
46265293 AAAACATAAAAACAAATATT
1 AAAACAAAAAAACAAATATT
46265313 AAAACAAAAAAACAAATA
1 AAAACAAAAAAACAAATA
46265331 AAAAATGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAACAAAAAAACAAATATT
Found at i:46267130 original size:16 final size:15
Alignment explanation
Indices: 46267111--46267144 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
46267101 AATTTTTTAA
46267111 AAATTATAAAAAATAT
1 AAATTATAAAAAAT-T
46267127 AAATTATAAAAAATT
1 AAATTATAAAAAATT
46267142 AAA
1 AAA
46267145 ATTTCATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATTATAAAAAATT
Found at i:46267146 original size:16 final size:15
Alignment explanation
Indices: 46267110--46267147 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 15
46267100 TAATTTTTTA
46267110 AAAATTATAAAAAAT
1 AAAATTATAAAAAAT
46267125 ATAAATTATAAAAAATT
1 A-AAATTATAAAAAA-T
46267142 AAAATT
1 AAAATT
46267148 TCATTCACCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.05
16 18 0.86
17 2 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATTATAAAAAAT
Found at i:46273013 original size:166 final size:166
Alignment explanation
Indices: 46272739--46273060 Score: 545
Period size: 166 Copynumber: 1.9 Consensus size: 166
46272729 CAGAAATGGT
* *
46272739 CATAACTTGATGTTTAATGGTGTGGGAATAAAATCTTCATTTCAGATTACTTTCAGGATCTTATG
1 CATAACTTAATGTTTAATGGTGTGGGAATAAAATCTTCATTTCAGATGACTTTCAGGATCTTATG
* * *
46272804 ACTCTATTGTGTTCTTCTTTTAGGAAATCTTTGAGCATTTTCATGTAATCATTGCGATTGTCTAG
66 ACTCTATTGTGTTCTTCTTTTAGGAAATCTTTCAGCATTTTCATGTAATCATTGCAATTGCCTAG
*
46272869 TTGTCTTCCTTAATTTCTTTTAATTAGGGAACTAGC
131 TTGTCTTCCCTAATTTCTTTTAATTAGGGAACTAGC
* ** *
46272905 CATAACTTAATGTTTAATGGTGTGGGAATAAAATCTTTATTTTTGATGACTTTGAGGATCTTATG
1 CATAACTTAATGTTTAATGGTGTGGGAATAAAATCTTCATTTCAGATGACTTTCAGGATCTTATG
*
46272970 ACTCTGTTGTGTTCTTCTTTTAGGAAATCTTTCAGCATTTTCATGTAATCATTGCAATTGCCTAG
66 ACTCTATTGTGTTCTTCTTTTAGGAAATCTTTCAGCATTTTCATGTAATCATTGCAATTGCCTAG
46273035 TTGTCTTCCCTAATTTCTTTTAATTA
131 TTGTCTTCCCTAATTTCTTTTAATTA
46273061 ATGTTAATTT
Statistics
Matches: 145, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
166 145 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (166 bp):
CATAACTTAATGTTTAATGGTGTGGGAATAAAATCTTCATTTCAGATGACTTTCAGGATCTTATG
ACTCTATTGTGTTCTTCTTTTAGGAAATCTTTCAGCATTTTCATGTAATCATTGCAATTGCCTAG
TTGTCTTCCCTAATTTCTTTTAATTAGGGAACTAGC
Found at i:46278312 original size:29 final size:30
Alignment explanation
Indices: 46278280--46278356 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 30
46278270 AAAAAATTAG
46278280 ATATAAATTTTAAAATTTAATAAGTA-AA-A
1 ATATAAATTTTAAAATTTAA-AAGTATAATA
46278309 ATATTAAATTTTTTAAAA--TAAAAGTATAATA
1 ATA-TAAA--TTTTAAAATTTAAAAGTATAATA
46278340 A-ATAAATTTT-AAATTTA
1 ATATAAATTTTAAAATTTA
46278357 TAAATAGTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
26 3 0.07
27 4 0.10
28 2 0.05
29 12 0.29
30 10 0.24
31 2 0.05
32 8 0.20
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (30 bp):
ATATAAATTTTAAAATTTAAAAGTATAATA
Found at i:46278410 original size:14 final size:14
Alignment explanation
Indices: 46278391--46278432 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
46278381 TATTTTAATC
46278391 ATATTTATATTATA
1 ATATTTATATTATA
*
46278405 ATATTT-TA--ATC
1 ATATTTATATTATA
46278416 ATATTTATATTATA
1 ATATTTATATTATA
46278430 ATA
1 ATA
46278433 GAATGTGGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
11 8 0.35
12 2 0.09
13 2 0.09
14 11 0.48
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATTTATATTATA
Found at i:46278413 original size:25 final size:25
Alignment explanation
Indices: 46278380--46278432 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
46278370 GAGTTATAAT
46278380 ATATTTTAATCATATTTATATTATA
1 ATATTTTAATCATATTTATATTATA
46278405 ATATTTTAATCATATTTATATTATA
1 ATATTTTAATCATATTTATATTATA
46278430 ATA
1 ATA
46278433 GAATGTGGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
ATATTTTAATCATATTTATATTATA
Found at i:46279190 original size:21 final size:21
Alignment explanation
Indices: 46279166--46279208 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
46279156 TATTTATATT
46279166 ATTTCTAAAT-TAAAAAATAAA
1 ATTT-TAAATATAAAAAATAAA
*
46279187 ATTTTAAATATAAAAATTAAA
1 ATTTTAAATATAAAAAATAAA
46279208 A
1 A
46279209 AGATTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTTTAAATATAAAAAATAAA
Found at i:46279372 original size:19 final size:20
Alignment explanation
Indices: 46279316--46279372 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 20
46279306 TATGTATTTA
46279316 TATATATATATATT--AATT
1 TATATATATATATTCAAATT
*
46279334 TATATATTATATGTTGCAAATT
1 TATATA-TATATATT-CAAATT
*
46279356 TTTATATATAT-TTCAAA
1 TATATATATATATTCAAA
46279373 ATATTTTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 6 0.18
19 11 0.33
20 2 0.06
21 5 0.15
22 9 0.27
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (20 bp):
TATATATATATATTCAAATT
Found at i:46283207 original size:21 final size:21
Alignment explanation
Indices: 46283176--46283225 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
46283166 ATTCTTACTC
46283176 AATTCCATAACATATTTCAGAA
1 AATT-CATAACATATTTCAGAA
*
46283198 AATTCATAACATATTTCAGAC
1 AATTCATAACATATTTCAGAA
46283219 AATTCAT
1 AATTCAT
46283226 GCTATTTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.34
Consensus pattern (21 bp):
AATTCATAACATATTTCAGAA
Found at i:46292713 original size:20 final size:20
Alignment explanation
Indices: 46292688--46292810 Score: 99
Period size: 20 Copynumber: 6.0 Consensus size: 20
46292678 ATAGATGCGT
46292688 AACAGAGGCACCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* *
46292708 AACAGAGGCA-TGATTA-TGTA
1 AACAGAGGCACCGA--AGTGCA
* * *
46292728 ATCAGAGGCACTGTAGTGCA
1 AACAGAGGCACCGAAGTGCA
* *
46292748 AACAGAGAGACACCTAAGTGTA
1 AACAGAG-G-CACCGAAGTGCA
* *
46292770 AATAGAGGCACTGAAGTGCGA
1 AACAGAGGCACCGAAGTGC-A
46292791 AA-AGAGGCACCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
46292810 A
1 A
46292811 TCCCATAAAA
Statistics
Matches: 81, Mismatches: 15, Indels: 15
0.73 0.14 0.14
Matches are distributed among these distances:
19 5 0.06
20 54 0.67
21 8 0.10
22 14 0.17
ACGTcount: A:0.40, C:0.18, G:0.28, T:0.14
Consensus pattern (20 bp):
AACAGAGGCACCGAAGTGCA
Found at i:46296096 original size:18 final size:18
Alignment explanation
Indices: 46296070--46296104 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
46296060 GTTTATCTAC
*
46296070 AAGATAAACATTAAATTT
1 AAGACAAACATTAAATTT
46296088 AAGACAAACATTAAATT
1 AAGACAAACATTAAATT
46296105 AAATTTAATA
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:0.57, C:0.09, G:0.06, T:0.29
Consensus pattern (18 bp):
AAGACAAACATTAAATTT
Found at i:46296157 original size:25 final size:27
Alignment explanation
Indices: 46296102--46296157 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
46296092 CAAACATTAA
*
46296102 ATTAAATTTAATATTAAGATAATCACT
1 ATTAAATTTAATATTAAGAAAATCACT
* *
46296129 -TTAATTTTAA-ATTAATAAAAT-ACT
1 ATTAAATTTAATATTAAGAAAATCACT
46296153 ATTAA
1 ATTAA
46296158 GATAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 3 0.12
25 13 0.52
26 9 0.36
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (27 bp):
ATTAAATTTAATATTAAGAAAATCACT
Found at i:46296181 original size:11 final size:13
Alignment explanation
Indices: 46296160--46296197 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
46296150 ACTATTAAGA
46296160 TAAATATT-AAAT
1 TAAATATTAAAAT
46296172 TAAA-ATTAAAAT
1 TAAATATTAAAAT
46296184 TAAACTATTAAAAT
1 TAAA-TATTAAAAT
46296198 AATATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.13
12 12 0.52
14 8 0.35
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAATATTAAAAT
Found at i:46296206 original size:14 final size:14
Alignment explanation
Indices: 46296150--46296197 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 14
46296140 TTAATAAAAT
*
46296150 ACTATTAAGA-TAA
1 ACTATTAAAATTAA
46296163 A-TATT-AAATTAA
1 ACTATTAAAATTAA
46296175 A--ATTAAAATTAA
1 ACTATTAAAATTAA
46296187 ACTATTAAAAT
1 ACTATTAAAAT
46296198 AATATTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 5 0.17
12 16 0.53
13 1 0.03
14 8 0.27
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (14 bp):
ACTATTAAAATTAA
Found at i:46301132 original size:15 final size:15
Alignment explanation
Indices: 46301112--46301143 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
46301102 TATGCATGCA
46301112 AAATATAAAAGACAT
1 AAATATAAAAGACAT
46301127 AAATATAAAAGACAT
1 AAATATAAAAGACAT
46301142 AA
1 AA
46301144 TAGTGAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (15 bp):
AAATATAAAAGACAT
Found at i:46304389 original size:37 final size:37
Alignment explanation
Indices: 46304348--46304513 Score: 120
Period size: 38 Copynumber: 4.4 Consensus size: 37
46304338 TAACCTTTAT
*
46304348 ACTGTTTGCATGGTGTCCCCCCTAGGACCAGTAGATA
1 ACTGTTTACATGGTGTCCCCCCTAGGACCAGTAGATA
* ** * *
46304385 ACTGTTTACACGGTGT-CATCCTAAGAACCAATAGATA
1 ACTGTTTACATGGTGTCCCCCCT-AGGACCAGTAGATA
* ** *
46304422 ACTTTTTACATGGTGTCGCCCCAAAGGACTAGTAGATA
1 ACTGTTTACATGGTGTC-CCCCCTAGGACCAGTAGATA
* * * ** *
46304460 ATTGTTCACACGGTGT-TGCCTTGAAGGACCAGTAGATA
1 ACTGTTTACATGGTGTCCCCCCT--AGGACCAGTAGATA
* *
46304498 ACTGTTCACACGGTGT
1 ACTGTTTACATGGTGT
46304514 TGCCCCAAAG
Statistics
Matches: 99, Mismatches: 25, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
36 6 0.06
37 40 0.40
38 51 0.52
39 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (37 bp):
ACTGTTTACATGGTGTCCCCCCTAGGACCAGTAGATA
Found at i:46304475 original size:38 final size:38
Alignment explanation
Indices: 46304371--46304532 Score: 164
Period size: 38 Copynumber: 4.3 Consensus size: 38
46304361 TGTCCCCCCT
* ** *
46304371 AGGACCAGTAGATAACTGTTTACACGGTGTC-ATCCTA
1 AGGACCAGTAGATAACTGTTCACACGGTGTCGCCCCAA
* * * * *
46304408 AGAACCAATAGATAACTTTTTACATGGTGTCGCCCCAA
1 AGGACCAGTAGATAACTGTTCACACGGTGTCGCCCCAA
* * * ***
46304446 AGGACTAGTAGATAATTGTTCACACGGTGTTGCCTTGA
1 AGGACCAGTAGATAACTGTTCACACGGTGTCGCCCCAA
*
46304484 AGGACCAGTAGATAACTGTTCACACGGTGTTGCCCCAA
1 AGGACCAGTAGATAACTGTTCACACGGTGTCGCCCCAA
*
46304522 AGGACTAGTAG
1 AGGACCAGTAG
46304533 CAAACCGTTC
Statistics
Matches: 100, Mismatches: 24, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
37 27 0.27
38 73 0.73
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (38 bp):
AGGACCAGTAGATAACTGTTCACACGGTGTCGCCCCAA
Found at i:46306295 original size:26 final size:25
Alignment explanation
Indices: 46306249--46306300 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
46306239 ATTAAGTGAT
46306249 TTTAATGAATTTTATTAAAGGTTAA
1 TTTAATGAATTTTATTAAAGGTTAA
*
46306274 TTTAGTGAATTATGTATT-AAGGTTAA
1 TTTAATGAATT-T-TATTAAAGGTTAA
46306300 T
1 T
46306301 AAACTAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 10 0.42
26 10 0.42
27 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (25 bp):
TTTAATGAATTTTATTAAAGGTTAA
Found at i:46309232 original size:20 final size:20
Alignment explanation
Indices: 46309207--46309251 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
46309197 AGGGACTAAA
* *
46309207 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
46309227 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
46309247 ATGAA
1 ATGAA
46309252 CACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:46317786 original size:49 final size:48
Alignment explanation
Indices: 46317729--46317946 Score: 184
Period size: 46 Copynumber: 4.6 Consensus size: 48
46317719 TAAAGTGCCA
46317729 ATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTTCGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATC-TCGAGGCCG
* * *
46317778 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCA-CATAACTG-TGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATC-T--C-GAGGCCG
* * * * * **
46317828 ATGCTATGCCCCAGACATGGTTTTACATTGAC-A-CATCTCGTTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTCGAGGCCG
* * * * *
46317874 ATG-CATGTTCCAGACAT-GTCTTATACTGGCT-TACGTCCCGAGGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTAT-CATCTCGAGGCCG
46317920 ATG-CATGTCCCAGACAT-GTCTTACACT
1 ATGCCATGTCCCAGACATGGTCTTACACT
46317947 AGCACTCGTC
Statistics
Matches: 136, Mismatches: 25, Indels: 19
0.76 0.14 0.11
Matches are distributed among these distances:
44 9 0.07
45 12 0.09
46 42 0.31
48 5 0.04
49 36 0.26
50 31 0.23
51 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.28
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTCGAGGCCG
Found at i:46329066 original size:30 final size:30
Alignment explanation
Indices: 46329032--46329093 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
46329022 TCTTATTTTA
*
46329032 TTGTTAATTTTGTTATTGTTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
46329062 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
46329092 TT
1 TT
46329094 TCTTGTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:46329241 original size:12 final size:12
Alignment explanation
Indices: 46329218--46329251 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
46329208 TATATATTTT
46329218 AAAATT-ATATA
1 AAAATTAATATA
46329229 AAAATTAATATA
1 AAAATTAATATA
46329241 AAAATTAATAT
1 AAAATTAATAT
46329252 GGGCGGGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:46334562 original size:16 final size:15
Alignment explanation
Indices: 46334520--46334562 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
46334510 CTCTTTCAAG
46334520 CATATATCACA-TAA
1 CATATATCACATTAA
46334534 CATATATTC-CATTAA
1 CATATA-TCACATTAA
46334549 TCATATATCACATT
1 -CATATATCACATT
46334563 TCACACAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 8 0.32
15 7 0.28
16 10 0.40
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (15 bp):
CATATATCACATTAA
Found at i:46346311 original size:3 final size:3
Alignment explanation
Indices: 46346303--46346343 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
46346293 AACAGATGTG
46346303 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
46346344 ATTCCATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:46347351 original size:16 final size:15
Alignment explanation
Indices: 46347320--46347348 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
46347310 AGATATAGTA
46347320 AAATATTAAAAAAAC
1 AAATATTAAAAAAAC
46347335 AAATATTAAAAAAA
1 AAATATTAAAAAAA
46347349 ACATAAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATATTAAAAAAAC
Found at i:46348285 original size:50 final size:50
Alignment explanation
Indices: 46348205--46348299 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 50
46348195 CTCTGCCCTA
*
46348205 CTGCCCTGCTGCTATTATTTTTTCGACAACTGCTTTGCTACTTCACGTTC
1 CTGCCCTGCTGCTATTATTTTTTCCACAACTGCTTTGCTACTTCACGTTC
* * * *
46348255 CTGCCCTGTTGTTA-TATTTTTTCCAGCAACTGTTTTGCTGCTTCA
1 CTGCCCTGCTGCTATTATTTTTTCCA-CAACTGCTTTGCTACTTCA
46348300 ATTACTCTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 10 0.26
50 29 0.74
ACGTcount: A:0.14, C:0.27, G:0.15, T:0.44
Consensus pattern (50 bp):
CTGCCCTGCTGCTATTATTTTTTCCACAACTGCTTTGCTACTTCACGTTC
Found at i:46360992 original size:93 final size:93
Alignment explanation
Indices: 46360880--46361094 Score: 376
Period size: 93 Copynumber: 2.3 Consensus size: 93
46360870 GCCCATAAGT
* * *
46360880 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
46360945 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
46360973 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
46361038 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
46361066 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
46361095 TGCCCAAACA
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 116 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:46360994 original size:47 final size:47
Alignment explanation
Indices: 46360926--46361098 Score: 237
Period size: 47 Copynumber: 3.7 Consensus size: 47
46360916 ATCCATAAGT
46360926 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
* * * *
46360973 GAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-TCA-C
* *
46361019 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
46361066 GAACTCGGACTCAACTCAACGAGTTCGGATGCC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCC
46361099 CAAACATCCT
Statistics
Matches: 108, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 28 0.26
47 61 0.56
48 1 0.01
49 2 0.02
50 6 0.06
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:46361047 original size:46 final size:46
Alignment explanation
Indices: 46360872--46361047 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
46360862 TGTAACCCGC
* * *
46360872 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* * *
46360918 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCAT
* * *
46360968 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
46361011 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
46361048 TGCCTAGTTA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 6 0.05
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
Found at i:46374890 original size:21 final size:22
Alignment explanation
Indices: 46374861--46374907 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
46374851 CAGAAGGAGT
*
46374861 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
46374883 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
46374904 GAGT
1 GAGT
46374908 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:46382312 original size:19 final size:20
Alignment explanation
Indices: 46382288--46382349 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 20
46382278 TTCTTCAAAT
46382288 ATAATTATAAAA-ATTAAAA
1 ATAATTATAAAATATTAAAA
46382307 ATAATTAACATAAAAATATTAAAA
1 ATAATT---AT-AAAATATTAAAA
*
46382331 ATTATT-TAAAATATTAAAA
1 ATAATTATAAAATATTAAAA
46382350 TATTGTACCA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
19 18 0.49
20 1 0.03
22 2 0.05
23 4 0.11
24 12 0.32
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
ATAATTATAAAATATTAAAA
Found at i:46386218 original size:26 final size:26
Alignment explanation
Indices: 46386180--46386263 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
46386170 CATGAAATTC
*
46386180 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
46386206 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
*
46386232 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
46386258 TTATCA
1 TTATCA
46386264 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCCA
Found at i:46391153 original size:28 final size:28
Alignment explanation
Indices: 46391078--46391154 Score: 127
Period size: 28 Copynumber: 2.8 Consensus size: 28
46391068 AAATCATTCG
*
46391078 ATATTTCGCACACTAAGTGCCATTCTCA
1 ATATTTCGCACACTAAGTGTCATTCTCA
*
46391106 ATATCTCGCACACTAAGTGTCATTCTCA
1 ATATTTCGCACACTAAGTGTCATTCTCA
*
46391134 ATATTTCTCACACTAAGTGTC
1 ATATTTCGCACACTAAGTGTC
46391155 GTATTTGATG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (28 bp):
ATATTTCGCACACTAAGTGTCATTCTCA
Found at i:46393528 original size:19 final size:18
Alignment explanation
Indices: 46393500--46393542 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
46393490 TGCGAAATAG
*
46393500 AAAG-AAAGAATAAAAGAA
1 AAAGAAAAGAAGAAAA-AA
46393518 AAAGAAAAGAAGAAAAAA
1 AAAGAAAAGAAGAAAAAA
46393536 AAAGAAA
1 AAAGAAA
46393543 CGATAGGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (18 bp):
AAAGAAAAGAAGAAAAAA
Found at i:46393538 original size:13 final size:14
Alignment explanation
Indices: 46393504--46393541 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
46393494 AAATAGAAAG
46393504 AAAGAATAA-AAGAA
1 AAAGAA-AAGAAGAA
46393518 AAAGAAAAGAAGAA
1 AAAGAAAAGAAGAA
46393532 AAA-AAAAGAA
1 AAAGAAAAGAA
46393542 ACGATAGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:46394120 original size:25 final size:26
Alignment explanation
Indices: 46394058--46394123 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 26
46394048 TATATAATAT
46394058 ATATATAATTTTTAAAAAAGTTTAGAA
1 ATATATAA-TTTTAAAAAAGTTTAGAA
** *
46394085 ATA-ATTTTTTTATAAAA-TTCTA-AA
1 ATATATAATTTTAAAAAAGTT-TAGAA
46394109 ATATATAATTTTAAA
1 ATATATAATTTTAAA
46394124 TTTTAAAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
24 7 0.23
25 19 0.61
26 2 0.06
27 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (26 bp):
ATATATAATTTTAAAAAAGTTTAGAA
Found at i:46394159 original size:20 final size:18
Alignment explanation
Indices: 46394141--46394177 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
46394131 AAGTCAAAAT
46394141 AATAT-ATAAAAATTTAA
1 AATATCATAAAAATTTAA
46394158 AATATCATAAAAATTTAA
1 AATATCATAAAAATTTAA
46394176 AA
1 AA
46394178 AAGATATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AATATCATAAAAATTTAA
Found at i:46394179 original size:20 final size:19
Alignment explanation
Indices: 46394136--46394184 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
46394126 TTAAAAAGTC
46394136 AAAATAATATATAAAAATTT
1 AAAA-AATATATAAAAATTT
46394156 --AAAATATCATAAAAATTT
1 AAAAAATAT-ATAAAAATTT
*
46394174 AAAAAAGATAT
1 AAAAAATATAT
46394185 TTGAATTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 5 0.20
18 12 0.48
19 2 0.08
20 6 0.24
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAAAATATATAAAAATTT
Found at i:46394300 original size:20 final size:20
Alignment explanation
Indices: 46394253--46394308 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
46394243 ATTTTATAAA
46394253 AATATTTTTAAAATTTTTAC
1 AATATTTTTAAAATTTTTAC
* * **
46394273 ATTTTTTTTTCAATTTTTAC
1 AATATTTTTAAAATTTTTAC
46394293 AATA-TTTTAAAATTTT
1 AATATTTTTAAAATTTT
46394309 AATAACATTA
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
AATATTTTTAAAATTTTTAC
Found at i:46395052 original size:18 final size:18
Alignment explanation
Indices: 46395029--46395075 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
46395019 TAAATTTTAC
*
46395029 AATTCGAATAACTTAAAT
1 AATTCGAATAACTCAAAT
*
46395047 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCAAAT
*
46395065 AATTCAAATAA
1 AATTCGAATAA
46395076 TAGATTGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (18 bp):
AATTCGAATAACTCAAAT
Done.