Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009070.1 Hibiscus syriacus cultivar Beakdansim tig00112498_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2268343
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1822494 original size:183 final size:183
Alignment explanation
Indices: 1822186--1822696 Score: 932
Period size: 183 Copynumber: 2.8 Consensus size: 183
1822176 CTTTATGTCC
* *
1822186 AAAAAGTGTCGACATTTACATATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATACA
1 AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATA
*
1822251 ACTGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATA
66 ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATA
1822316 TTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTATCGATACCATTTA
131 TTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTATCGATACCATTTA
1822369 AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATA
1 AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATA
* *
1822434 ACCGGTATAAATATACCGGTTTTATGAGTGAATAGGTCTACAACCTATATCAACACTTTCTAATA
66 ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATA
* * *
1822499 TTATGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTT
131 TTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTATCGATACCATTTA
*
1822552 AAAAAGTGTCGACATTTATACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATA
1 AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATA
1822617 ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATA
66 ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATA
*
1822682 TTGTATCGGTACTTT
131 TTGTGTCGGTACTTT
1822697 TAAGTAACGC
Statistics
Matches: 315, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 315 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (183 bp):
AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATA
ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATA
TTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTATCGATACCATTTA
Found at i:1822647 original size:517 final size:517
Alignment explanation
Indices: 1821669--1822696 Score: 1921
Period size: 517 Copynumber: 2.0 Consensus size: 517
1821659 ATACCATTTA
*
1821669 AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATA
1 AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATACA
*
1821734 ACCGGTATAAATATACCGGTTTTATGAGCGAATAGTTATACAACCTATATCGACACTTTCTAATA
66 ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTATACAACCTATATCGACACTTTCTAATA
*
1821799 TTGTGTAGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGA
131 TTGTGTAGGTACTTTATGTCCAGATTGGAAGAAAAATGTATCGATACCATTTAAAAAAGTGTCGA
*
1821864 CATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACTGGTATAAAT
196 CATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAAT
* *
1821929 ATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATTGTGTCGGTAC
261 ATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCAACACTTTCTAATATTATGTCGGTAC
1821994 TTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACATTTACACATC
326 TTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACATTTACACATC
*
1822059 GGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTT
391 GGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTA
*
1822124 TGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATTGTGTCGGTACTTTATGTCC
456 TGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATTGTATCGGTACTTTATGTCC
*
1822186 AAAAAGTGTCGACATTTACATATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATACA
1 AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATACA
* *
1822251 ACTGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATA
66 ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTATACAACCTATATCGACACTTTCTAATA
*
1822316 TTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTATCGATACCATTTAAAAAAGTGTCGA
131 TTGTGTAGGTACTTTATGTCCAGATTGGAAGAAAAATGTATCGATACCATTTAAAAAAGTGTCGA
1822381 CATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAAT
196 CATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAAT
*
1822446 ATACCGGTTTTATGAGTGAATAGGTCTACAACCTATATCAACACTTTCTAATATTATGTCGGTAC
261 ATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCAACACTTTCTAATATTATGTCGGTAC
* *
1822511 TTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTTAAAAAGTGTCGACATTTATACATC
326 TTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACATTTACACATC
1822576 GGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTA
391 GGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTA
1822641 TGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATTGTATCGGTACTTT
456 TGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATTGTATCGGTACTTT
1822697 TAAGTAACGC
Statistics
Matches: 496, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
517 496 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (517 bp):
AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATACA
ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTATACAACCTATATCGACACTTTCTAATA
TTGTGTAGGTACTTTATGTCCAGATTGGAAGAAAAATGTATCGATACCATTTAAAAAAGTGTCGA
CATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAAT
ATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCAACACTTTCTAATATTATGTCGGTAC
TTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACATTTACACATC
GGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTA
TGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATTGTATCGGTACTTTATGTCC
Found at i:1825174 original size:25 final size:25
Alignment explanation
Indices: 1825146--1825210 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
1825136 TTATCATTAA
1825146 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
1825171 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
1825196 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
1825211 TCTTTTGAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:1825587 original size:23 final size:23
Alignment explanation
Indices: 1825556--1825628 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1825546 ATAGGTAAAA
*
1825556 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1825579 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1825602 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1825625 ATAT
1 ATAT
1825629 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1826077 original size:23 final size:23
Alignment explanation
Indices: 1826046--1826118 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1826036 ATAGGTAAAA
*
1826046 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1826069 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1826092 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1826115 ATAT
1 ATAT
1826119 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1826130 original size:490 final size:489
Alignment explanation
Indices: 1825210--1826519 Score: 2534
Period size: 490 Copynumber: 2.7 Consensus size: 489
1825200 AGGTATATAC
1825210 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
*
1825275 GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATA
66 GTTAC-GTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
1825340 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
130 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
1825405 ATTTTTTGTGTAAATGAAATTCTTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
195 ATTTTTTGTGTAAATGAAATTCTTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
1825470 AAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACA
260 AAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACA
1825535 CTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGT
325 CTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGT
1825600 TTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTTATAAAAGTGTCCAT
390 TTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTTATAAAAGTGTCCAT
1825665 ACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
455 ACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
1825700 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1825765 GTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACG-TATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
1825830 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
130 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
1825895 ATTTTTTGTGTAAATGAAATTCTTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
195 ATTTTTTGTGTAAATGAAATTCTTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
1825960 AAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACA
260 AAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACA
1826025 CTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGT
325 CTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGT
*
1826090 TTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATTCTTTTTTATAAAAGTGTCCAT
390 TTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTTATAAAAGTGTCCAT
1826155 ACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
455 ACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
1826190 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
* *
1826255 GTTACG-GTATA-TATTATTAAATTAAAAAAAATAAACATATATATTACATATTTATTATTATCT
66 GTTACGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCT
1826318 TTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAA
131 TTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAA
1826383 TTTTTTGTGTAAATGAAATTCTTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAA
196 TTTTTTGTGTAAATGAAATTCTTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAA
*
1826448 AAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACA
260 AAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACA
1826513 CTTTCAA
325 CTTTCAA
1826520 CATATTATAA
Statistics
Matches: 813, Mismatches: 5, Indels: 6
0.99 0.01 0.01
Matches are distributed among these distances:
487 176 0.22
488 79 0.10
489 1 0.00
490 557 0.69
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (489 bp):
ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
GTTACGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCT
TTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAA
TTTTTTGTGTAAATGAAATTCTTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAA
AATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACAC
TTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTT
TATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTTATAAAAGTGTCCATA
CTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
Found at i:1827201 original size:2 final size:2
Alignment explanation
Indices: 1827196--1827223 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1827186 TTCATTAACA
1827196 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1827224 TACATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1832854 original size:21 final size:21
Alignment explanation
Indices: 1832821--1832871 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1832811 ATTATGACTA
1832821 TCGCAATGCGATTTT-CCAATT
1 TCGCAATGCGATTTTCCCAA-T
* *
1832842 TCGCATTGTGATTTTCCCAAT
1 TCGCAATGCGATTTTCCCAAT
1832863 TCGCAATGC
1 TCGCAATGC
1832872 AAATAAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCCAAT
Found at i:1832927 original size:41 final size:41
Alignment explanation
Indices: 1832900--1833037 Score: 152
Period size: 41 Copynumber: 3.4 Consensus size: 41
1832890 GCGAATTTGG
*
1832900 AAAATCGCAACGCGGTACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
1832941 AAAATCGCAACGCGATACTGACTTTCGCAACTCGATACT-T
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
** * * * *
1832981 AATTTCGCAACTCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
1833022 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
1833038 TTTCAAAACG
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 32 0.42
41 45 0.58
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1832928 original size:20 final size:20
Alignment explanation
Indices: 1832903--1833017 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
1832893 AATTTGGAAA
*
1832903 ATCGCAACGCGGTACTGACT
1 ATCGCAACGCGATACTGACT
* *
1832923 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
1832944 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
1832964 TTCGCAACTCGATACTTAAT
1 ATCGCAACGCGATACTGACT
* * *
1832984 TTCGCAACTCAATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1833004 TTCGCAACGAGATA
1 ATCGCAACGCGATA
1833018 ATACATAATC
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.03
20 58 0.75
21 15 0.19
22 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1833232 original size:22 final size:22
Alignment explanation
Indices: 1833204--1833247 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1833194 CACTCTCTCA
1833204 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1833226 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1833248 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1833759 original size:25 final size:24
Alignment explanation
Indices: 1833705--1833759 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1833695 TGTTTATTAT
* *
1833705 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1833729 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1833755 TGTTT
1 TGTTT
1833760 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1834909 original size:18 final size:18
Alignment explanation
Indices: 1834888--1834935 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1834878 TCCACTTCGG
1834888 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
1834906 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1834924 GAGCCATCACCT
1 GAGCCATCACCT
1834936 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1835501 original size:20 final size:20
Alignment explanation
Indices: 1835476--1835521 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1835466 TAGTTTACTT
1835476 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
1835496 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
1835516 TCGCAA
1 TCGCAA
1835522 TGCGAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1835537 original size:19 final size:19
Alignment explanation
Indices: 1835515--1835597 Score: 86
Period size: 19 Copynumber: 4.6 Consensus size: 19
1835505 GGAAATGGCT
1835515 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATAAAA
*
1835534 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATAAAA
* *
1835548 ATCGCAATGTGAAATTAAA
1 ATCGCAATGCGAAATAAAA
* *
1835567 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATAAAA
1835586 ATCGCAATGCGA
1 ATCGCAATGCGA
1835598 TTTGTATTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 1 0.02
17 2 0.04
18 1 0.02
19 37 0.71
ACGTcount: A:0.47, C:0.19, G:0.18, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATAAAA
Found at i:1835609 original size:19 final size:19
Alignment explanation
Indices: 1835587--1835669 Score: 79
Period size: 19 Copynumber: 4.6 Consensus size: 19
1835577 GAAATGAAAA
*
1835587 TCGCAATGCGATTTGT-ATT
1 TCGCATTGCGATTT-TCATT
*
1835606 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1835625 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
1835641 TCG--TTGCGTTTTTCATT
1 TCGCATTGCGATTTTCATT
1835658 TCGCATTGCGAT
1 TCGCATTGCGAT
1835670 GGCCATTTCC
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
14 5 0.10
15 3 0.06
16 4 0.08
17 4 0.08
18 4 0.08
19 31 0.61
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1835688 original size:20 final size:20
Alignment explanation
Indices: 1835653--1835728 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
1835643 GTTGCGTTTT
* *
1835653 TCATTT-CGCATTGCGATGG
1 TCATTTCCGCGTTGCGATAG
*
1835672 CCATTTCCGCGTTGCGATAG
1 TCATTTCCGCGTTGCGATAG
*
1835692 TCATTTCCGCGTTACGATAG
1 TCATTTCCGCGTTGCGATAG
*
1835712 TCATTTTCGCGTTGCGA
1 TCATTTCCGCGTTGCGA
1835729 AAGTAAGTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 5 0.10
20 44 0.90
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.36
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATAG
Found at i:1835739 original size:20 final size:19
Alignment explanation
Indices: 1835674--1835754 Score: 72
Period size: 20 Copynumber: 4.1 Consensus size: 19
1835664 TGCGATGGCC
* *
1835674 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGAAAGTA
* *
1835694 ATTTCCGCGTTACGATAGTCA
1 ATTT-CGCGTTGCGAAAGT-A
*
1835715 TTTTCGCGTTGCGAAAGTA
1 ATTTCGCGTTGCGAAAGTA
*
1835734 AGTTTCGTGTTGCGAAAGTA
1 A-TTTCGCGTTGCGAAAGTA
1835754 A
1 A
1835755 ACTATTCTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.02
20 48 0.92
21 3 0.06
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (19 bp):
ATTTCGCGTTGCGAAAGTA
Found at i:1836127 original size:21 final size:20
Alignment explanation
Indices: 1836103--1836172 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
1836093 CTGTCATTCG
1836103 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
1836124 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
1836145 TCAAGAGTCCCCCCCCACCGT
1 TCAAGAGT-CCCCTCCATCGT
1836166 TCAAGAG
1 TCAAGAG
1836173 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
21 32 0.86
22 5 0.14
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:1836205 original size:42 final size:42
Alignment explanation
Indices: 1836103--1836184 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
1836093 CTGTCATTCG
* * *
1836103 TCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATCCC
* *
1836145 TCAAGAGTCCCCCCCCACCGTTCAAGAGGCCACTGTCATC
1 TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATC
1836185 GTTGAAGAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.41, G:0.16, T:0.20
Consensus pattern (42 bp):
TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATCCC
Found at i:1837101 original size:20 final size:21
Alignment explanation
Indices: 1837057--1837104 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1837047 ATAGTCAGTA
*
1837057 TCGCATTACGATTTTCCAAAT
1 TCGCATTACGATTTTACAAAT
**
1837078 TCGCATTACGA-TTTACTTAT
1 TCGCATTACGATTTTACAAAT
1837098 TCGCATT
1 TCGCATT
1837105 GCGAATTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (21 bp):
TCGCATTACGATTTTACAAAT
Found at i:1837324 original size:12 final size:12
Alignment explanation
Indices: 1837305--1837338 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1837295 CTCTCCGACG
1837305 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1837317 ATATCCGTTCCT
1 ACATCCGTTCCT
1837329 ACATCC-TTCC
1 ACATCCGTTCC
1837339 CCATCTGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1838139 original size:12 final size:12
Alignment explanation
Indices: 1838122--1838158 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1838112 ATATAATCCT
1838122 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1838134 GAAGAAGAAAAA
1 GAAGAAGAAAAA
*
1838146 GAAAAAGAAAAA
1 GAAGAAGAAAAA
1838158 G
1 G
1838159 TCCCCGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1838141 original size:6 final size:6
Alignment explanation
Indices: 1838126--1838158 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1838116 AATCCTGAAG
*
1838126 AAGAAA AAGAAG AAGAAA AAGAAA AAGAAA AAG
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAG
1838159 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:1840472 original size:19 final size:19
Alignment explanation
Indices: 1840450--1840580 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
1840440 GGAAATTACT
1840450 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1840469 ATCGCAA--C--TA-GAGA
1 ATCGCAATGCGAAATGAAA
1840483 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1840502 ATCGCAA--CG---TGAAT
1 ATCGCAATGCGAAATGAAA
* *
1840516 TTCGCAATGCTAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1840535 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1840549 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1840568 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1840581 TTTAGTTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 29 0.35
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 41 0.50
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1840557 original size:66 final size:66
Alignment explanation
Indices: 1840451--1840583 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
1840441 GAAATTACTA
* *
1840451 TCGCAATGCGAAATGAAAATCGCAACTAGAGAATCGCAATGCGAAATGAAAATCGCAACGTGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1840516 T
66 T
* *
1840517 TCGCAATGCTAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1840582 T
66 T
1840583 T
1 T
1840584 AGTTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1840576 original size:33 final size:33
Alignment explanation
Indices: 1840450--1840576 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
1840440 GGAAATTACT
*
1840450 ATCGCAATGCGAAATGAAAATCGCAACTAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1840483 ATCGCAATGCGAAATGAAAATCGCAACGTGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1840515 TTTCGCAATGCTAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1840549 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1840577 CGAATTTAGT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1840611 original size:19 final size:19
Alignment explanation
Indices: 1840576--1840652 Score: 94
Period size: 19 Copynumber: 4.3 Consensus size: 19
1840566 AAATCGCAAC
*
1840576 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
1840595 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
1840614 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
1840628 GCGATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
1840647 GCGATT
1 GCGATT
1840653 CTCTCATTGC
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
14 12 0.24
16 1 0.02
17 1 0.02
18 1 0.02
19 36 0.71
ACGTcount: A:0.12, C:0.17, G:0.26, T:0.45
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:1840633 original size:33 final size:33
Alignment explanation
Indices: 1840591--1840717 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
1840581 TTTAGTTTCG
* *
1840591 CGTTGCGATTTT-AGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCGTTGCGATTCTCT
1840624 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
1840657 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
1840690 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
1840718 AGTACTTTTT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
33 87 0.99
34 1 0.01
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:1840683 original size:19 final size:19
Alignment explanation
Indices: 1840586--1840717 Score: 98
Period size: 19 Copynumber: 7.7 Consensus size: 19
1840576 GCGAATTTAG
1840586 TTTCGCGTTGCGATTTT-A
1 TTTCGCGTTGCGATTTTCA
1840604 GTTTCGCGTTGCGA-TTT--
1 -TTTCGCGTTGCGATTTTCA
*
1840621 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
1840638 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
* *
1840654 --TCTCATTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
1840671 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
1840687 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
1840704 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1840718 AGTACTTTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 30
0.70 0.07 0.23
Matches are distributed among these distances:
14 27 0.30
15 3 0.03
16 8 0.09
17 8 0.09
18 3 0.03
19 40 0.45
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:1840695 original size:14 final size:14
Alignment explanation
Indices: 1840643--1840699 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1840633 TTTCATTTCG
1840643 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
1840657 CATTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1840676 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1840690 CGTTGCGATT
1 CGTTGCGATT
1840700 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1840843 original size:14 final size:14
Alignment explanation
Indices: 1840824--1840860 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1840814 CATCAATTAA
1840824 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1840838 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1840852 ACAAATCAA
1 ACAAATCAA
1840861 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1842658 original size:93 final size:91
Alignment explanation
Indices: 1842548--1842732 Score: 293
Period size: 91 Copynumber: 2.0 Consensus size: 91
1842538 ATTTCAAACT
*
1842548 TTCAACCAAAAGACAAAAC-AAAA-ACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGTTTA
1842611 GCAGAATTGGCAGCAACCGAATAAATTTAC
62 GCAGAATTGGCAGCAACCGAATAAATTTAC
*
1842641 TTCAACCAAAAGTCAAAACAAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAG
1 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAG
*
1842706 TATTGGCAGCAACCGAATAAATTTAC
66 AATTGGCAGCAACCGAATAAATTTAC
1842732 T
1 T
1842733 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 42 0.48
93 18 0.21
94 4 0.05
95 23 0.26
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (91 bp):
TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAG
AATTGGCAGCAACCGAATAAATTTAC
Found at i:1844486 original size:14 final size:14
Alignment explanation
Indices: 1844467--1844523 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1844457 CGGAAATGAC
1844467 TATCGCAACGAGAG
1 TATCGCAACGAGAG
*
1844481 TATCGCAACGCGAAATGAC
1 TATCGCAA--CG--A-GAG
1844500 TATCGCAACGAGAG
1 TATCGCAACGAGAG
*
1844514 AATCGCAACG
1 TATCGCAACG
1844524 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.37, C:0.25, G:0.25, T:0.14
Consensus pattern (14 bp):
TATCGCAACGAGAG
Found at i:1844501 original size:33 final size:33
Alignment explanation
Indices: 1844444--1844606 Score: 254
Period size: 33 Copynumber: 4.9 Consensus size: 33
1844434 ACGAGATAAT
**
1844444 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGAAAATCGCAACGA
* **
1844478 GAGTATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
*
1844511 GAGAATCGCAACGCGAAATTAAAATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
*
1844544 GAGAATCGCAACGCGAAATGAAAATCGCAACAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1844577 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
1844607 TGCGATTTTG
Statistics
Matches: 122, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
33 109 0.89
34 13 0.11
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:1844538 original size:19 final size:19
Alignment explanation
Indices: 1844419--1844611 Score: 102
Period size: 19 Copynumber: 11.1 Consensus size: 19
1844409 TCTTTTGGTT
* *
1844419 GAAATGAAAATTGCAACGA
1 GAAATGAAAATCGCAACGC
*
1844438 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1844458 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
**
1844476 G--A-GAGTATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
1844492 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1844509 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1844525 GAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1844542 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1844558 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1844575 --AA-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1844591 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1844610 GA
1 GA
1844612 TTTTGGTTTC
Statistics
Matches: 135, Mismatches: 17, Indels: 44
0.69 0.09 0.22
Matches are distributed among these distances:
14 38 0.28
15 5 0.04
16 7 0.05
17 6 0.04
18 6 0.04
19 45 0.33
20 26 0.19
21 2 0.01
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1844552 original size:14 final size:14
Alignment explanation
Indices: 1844533--1844589 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1844523 GCGAAATTAA
1844533 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1844547 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1844566 AATCGCAACAAGAG
1 AATCGCAACGAGAG
1844580 AATCGCAACG
1 AATCGCAACG
1844590 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1845718 original size:20 final size:20
Alignment explanation
Indices: 1845628--1845722 Score: 86
Period size: 20 Copynumber: 4.7 Consensus size: 20
1845618 GATTATGTAT
* *
1845628 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
1845648 TATTGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
1845668 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
1845689 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
1845709 TA-CTGCGTTGCGAT
1 TATC-GCGTTGCGAT
1845723 TTTCCAAATT
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
19 4 0.07
20 41 0.67
21 14 0.23
22 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:1845741 original size:41 final size:41
Alignment explanation
Indices: 1845655--1845743 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 41
1845645 CAGTATTGAG
* ** * *
1845655 TTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCG
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAATATCGCA
1845696 TTGCGATAGTCAGTA-CTGCGTTGCGATTTTCCAAAT-TCGCA
1 TTGCGATAGTCAGTATC-GCGTTGCGATTTT-CAAATATCGCA
1845737 TTGCGAT
1 TTGCGAT
1845744 TTTCCAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 1 0.02
41 38 0.93
42 2 0.05
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAATATCGCA
Found at i:1845742 original size:21 final size:21
Alignment explanation
Indices: 1845716--1845783 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
1845706 CAGTACTGCG
1845716 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
1845737 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
* **
1845758 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCAAATTCGCA
1845778 TTGCGA
1 TTGCGA
1845784 ATTGGGAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 17 0.39
21 27 0.61
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCA
Found at i:1845825 original size:21 final size:22
Alignment explanation
Indices: 1845773--1845825 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
1845763 ATTTACTTAT
*
1845773 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGAGAAAA
*
1845794 TCGC-TACGCGAAATT-AGAAAA
1 TCGCAT-TGCGAAATTGAGAAAA
1845815 TCGCATTGCGA
1 TCGCATTGCGA
1845826 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 1 0.04
21 20 0.77
22 5 0.19
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGAGAAAA
Found at i:1853020 original size:16 final size:16
Alignment explanation
Indices: 1852983--1853021 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1852973 AGCCTATTCG
*
1852983 AACTCGAGTATTGTGG
1 AACTCGAGTATTGTGA
*
1852999 AGCTCGAGTATTGTGA
1 AACTCGAGTATTGTGA
1853015 AACTCGA
1 AACTCGA
1853022 CTCAACTCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (16 bp):
AACTCGAGTATTGTGA
Found at i:1853998 original size:20 final size:20
Alignment explanation
Indices: 1853926--1854002 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
1853916 AATAAGTAAA
* * *
1853926 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATTCTGACTT
*
1853946 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
1853966 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
1853986 TCGCAACGAGATTCTGA
1 TCGCAACGCGATTCTGA
1854003 AAATCGCAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:1854009 original size:20 final size:20
Alignment explanation
Indices: 1853966--1854011 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1853956 ATACTGACTT
* ***
1853966 TCGCAACGCGATTCTGACTT
1 TCGCAACGAGATTCTGAAAA
1853986 TCGCAACGAGATTCTGAAAA
1 TCGCAACGAGATTCTGAAAA
1854006 TCGCAA
1 TCGCAA
1854012 TCATCTTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGCAACGAGATTCTGAAAA
Found at i:1854010 original size:40 final size:40
Alignment explanation
Indices: 1853923--1854011 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
1853913 GCGAATAAGT
* *
1853923 AAATCGCAATGCGATACTGACTATCGCAACGCGATACTGA
1 AAATCGCAACGCGATACTGACTATCGCAACGAGATACTGA
*** * * *
1853963 CTTTCGCAACGCGATTCTGACTTTCGCAACGAGATTCTGA
1 AAATCGCAACGCGATACTGACTATCGCAACGAGATACTGA
1854003 AAATCGCAA
1 AAATCGCAA
1854012 TCATCTTCAA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (40 bp):
AAATCGCAACGCGATACTGACTATCGCAACGAGATACTGA
Found at i:1854250 original size:20 final size:20
Alignment explanation
Indices: 1854225--1854300 Score: 134
Period size: 20 Copynumber: 3.8 Consensus size: 20
1854215 AAACGGGGAA
*
1854225 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGGCT
1854245 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1854265 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
1854285 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
1854301 CGCAATGCGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:1854311 original size:34 final size:34
Alignment explanation
Indices: 1854206--1854312 Score: 106
Period size: 40 Copynumber: 3.0 Consensus size: 34
1854196 GACATTCATT
* * *
1854206 TGACTATCGAAACGGGGAAATCGCAACGCGAAAA
1 TGACTATCGCAACGAGAAAATCGCAACGCGAAAA
*
1854240 TGACTATCGCAACGCGAAAATGGCTATCGCAACGCGAAAA
1 TGACTATCGCAACGAG-AAA-----ATCGCAACGCGAAAA
* *
1854280 TGGCTATCGCAACGAGAAAATCGCAATGCGAAA
1 TGACTATCGCAACGAGAAAATCGCAACGCGAAA
1854313 TGAAAATCGC
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
34 27 0.44
35 2 0.03
39 3 0.05
40 29 0.48
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.14
Consensus pattern (34 bp):
TGACTATCGCAACGAGAAAATCGCAACGCGAAAA
Found at i:1854343 original size:33 final size:33
Alignment explanation
Indices: 1854306--1854376 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
1854296 AAAATCGCAA
*
1854306 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
** ** **
1854339 TGCGATTTTTATTTCGCATTGCGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
1854372 TGCGA
1 TGCGA
1854377 TAGTCAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
Found at i:1855822 original size:20 final size:20
Alignment explanation
Indices: 1855774--1855816 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1855764 AATAGTTTCT
* *
1855774 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
1855794 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
1855814 GAA
1 GAA
1855817 TTTGACTGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.21, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:1856357 original size:20 final size:20
Alignment explanation
Indices: 1856327--1856379 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1856317 GATTATGTAT
*
1856327 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1856347 TATTGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
1856367 TATCGCGTTGCGA
1 TATCGCGTTGCGA
1856380 TTTTTCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1863857 original size:2 final size:2
Alignment explanation
Indices: 1863850--1863874 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1863840 TCAACCTCTG
1863850 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1863875 GGGCGGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1881748 original size:21 final size:22
Alignment explanation
Indices: 1881725--1881767 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1881715 AAGGTAAAGG
*
1881725 AAACATGTCATAAAGACAGAGAA
1 AAACATATCATAAAGACAGAG-A
*
1881748 AAACGTATCATAAAGACAGA
1 AAACATATCATAAAGACAGA
1881768 ATTATTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.56, C:0.14, G:0.16, T:0.14
Consensus pattern (22 bp):
AAACATATCATAAAGACAGAGA
Found at i:1891872 original size:2 final size:2
Alignment explanation
Indices: 1891856--1891900 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
1891846 ATTAATTAAT
*
1891856 TA TA -A TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
1891898 TA T
1 TA T
1891901 TATTGTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1892469 original size:40 final size:42
Alignment explanation
Indices: 1892406--1892513 Score: 109
Period size: 41 Copynumber: 2.6 Consensus size: 42
1892396 TGATCGCTAA
* ** *
1892406 TTCGCAACGCGATCTCCATTATCGCAAAT-C-AGTTTCCAGA-
1 TTCGCAACGCGATATTGACTATCGCAAATGCGAGTTTCCA-AT
*
1892446 TTCGCAACGCGAT-TATGACTATCGC-AATGCGATTTTCCAAT
1 TTCGCAACGCGATAT-TGACTATCGCAAATGCGAGTTTCCAAT
*
1892487 TTCGCAACGCGATATTGACTTTCGCAA
1 TTCGCAACGCGATATTGACTATCGCAA
1892514 CGCGATACTG
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
39 4 0.07
40 22 0.39
41 29 0.51
42 2 0.04
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.30
Consensus pattern (42 bp):
TTCGCAACGCGATATTGACTATCGCAAATGCGAGTTTCCAAT
Found at i:1892599 original size:20 final size:20
Alignment explanation
Indices: 1892446--1892595 Score: 160
Period size: 20 Copynumber: 7.5 Consensus size: 20
1892436 AGTTTCCAGA
*
1892446 TTCGCAACGCGATTATGACT
1 TTCGCAACGCGATTCTGACT
* * * * *
1892466 ATCGCAATGCGATTTTCCAAT
1 TTCGCAACGCGATTCT-GACT
1892487 TTCGCAACGCGATAT-TGACT
1 TTCGCAACGCGAT-TCTGACT
*
1892507 TTCGCAACGCGATACTGACT
1 TTCGCAACGCGATTCTGACT
*
1892527 TTCGCGTA-GCGATTCTGACT
1 TTCGC-AACGCGATTCTGACT
1892547 TTCGCAACGCGATTCTGACT
1 TTCGCAACGCGATTCTGACT
* *
1892567 TTCGCAACGAGATTTTGACT
1 TTCGCAACGCGATTCTGACT
*
1892587 ATCGCAACG
1 TTCGCAACG
1892596 AGATAATACA
Statistics
Matches: 109, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.01
20 92 0.84
21 15 0.14
22 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (20 bp):
TTCGCAACGCGATTCTGACT
Found at i:1893169 original size:34 final size:34
Alignment explanation
Indices: 1893126--1893225 Score: 101
Period size: 40 Copynumber: 2.8 Consensus size: 34
1893116 GACATTCATT
1893126 TGACTATCGCAACGGGGAAATCGCAACGCGAAAA
1 TGACTATCGCAACGGGGAAATCGCAACGCGAAAA
**
1893160 TGACTATCGCAACGTGAAAATGGCTATCGCAACGCGAAAA
1 TGACTATCGCAACG-G-----GGAAATCGCAACGCGAAAA
* * *
1893200 TGGCTATCGCAACGAGAAAATCGCAA
1 TGACTATCGCAACGGGGAAATCGCAA
1893226 TGTGAAATGA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
34 22 0.42
35 1 0.02
40 30 0.57
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (34 bp):
TGACTATCGCAACGGGGAAATCGCAACGCGAAAA
Found at i:1893170 original size:20 final size:20
Alignment explanation
Indices: 1893145--1893220 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
1893135 CAACGGGGAA
*
1893145 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGGCT
*
1893165 ATCGCAACGTGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1893185 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
1893205 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
1893221 CGCAATGTGA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:1893281 original size:19 final size:19
Alignment explanation
Indices: 1893239--1893303 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
1893229 GAAATGAAAA
1893239 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1893255 TCG-A-TGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1893272 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1893291 TCGTATTGCGATT
1 TCGCATTGCGATT
1893304 CTCTCGTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
14 10 0.23
15 1 0.02
16 3 0.07
17 3 0.07
18 1 0.02
19 25 0.58
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1894947 original size:41 final size:42
Alignment explanation
Indices: 1894893--1894984 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
1894883 CCTCTTCAAC
* *
1894893 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
1894934 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
1894976 GATGACAGG
1 GATGACAGG
1894985 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 20 0.44
42 25 0.56
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:1894949 original size:21 final size:21
Alignment explanation
Indices: 1894920--1894980 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1894910 GAACGGTGGG
*
1894920 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
1894941 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
1894962 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
1894981 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:1895347 original size:20 final size:20
Alignment explanation
Indices: 1895322--1895374 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1895312 GAAGAATAGT
*
1895322 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
1895342 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* *
1895362 TGACTATCGCAAC
1 TTACTTTCGCAAC
1895375 GCAAAAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:1895375 original size:20 final size:20
Alignment explanation
Indices: 1895328--1895414 Score: 86
Period size: 20 Copynumber: 4.4 Consensus size: 20
1895318 TAGTTTACTT
* * * *
1895328 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAAATGACTA
1895348 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
1895368 TCGCAACGCAAAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
1895388 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
1895407 TCGCAACG
1 TCGCAACG
1895415 ACAAAATCGC
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
19 13 0.24
20 42 0.76
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:1895409 original size:19 final size:19
Alignment explanation
Indices: 1895387--1895452 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
1895377 AAAAATGGCT
1895387 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1895406 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
1895420 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1895439 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
1895453 CACAAATCGC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1895459 original size:19 final size:19
Alignment explanation
Indices: 1895387--1895462 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
1895377 AAAAATGGCT
*
1895387 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
1895406 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATCAAA
*
1895420 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
1895439 ATCGCAATGCGAAA-CACAA
1 ATCGCAATGCGAAATCA-AA
1895458 ATCGC
1 ATCGC
1895463 GTTGCGATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
14 10 0.21
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 31 0.65
ACGTcount: A:0.46, C:0.22, G:0.18, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATCAAA
Found at i:1895508 original size:20 final size:19
Alignment explanation
Indices: 1895459--1895528 Score: 77
Period size: 20 Copynumber: 3.6 Consensus size: 19
1895449 GAAACACAAA
**
1895459 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATT
* *
1895478 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATAGTCATT
1895497 TCCGCGTTGCGATAGTCATTT
1 T-CGCGTTGCGATAGTCA-TT
*
1895518 TCGTGTTGCGA
1 TCGCGTTGCGA
1895529 AAGTAAACTA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 16 0.38
20 23 0.55
21 3 0.07
ACGTcount: A:0.14, C:0.23, G:0.24, T:0.39
Consensus pattern (19 bp):
TCGCGTTGCGATAGTCATT
Found at i:1896092 original size:18 final size:18
Alignment explanation
Indices: 1896069--1896116 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1896059 CGGGTCGATC
1896069 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
1896087 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
1896105 AGGTGATGGCTC
1 AGGTGATGGCTC
1896117 CCAAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:1897490 original size:20 final size:20
Alignment explanation
Indices: 1897437--1897479 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1897427 AATAGTTTCT
* *
1897437 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
1897457 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
1897477 GAA
1 GAA
1897480 TTTGACTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.21, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:1897784 original size:22 final size:22
Alignment explanation
Indices: 1897758--1897801 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1897748 GATGGAGATA
1897758 GACGGATTTCGCCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* *
1897780 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
1897802 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:1898000 original size:21 final size:21
Alignment explanation
Indices: 1897968--1898104 Score: 115
Period size: 20 Copynumber: 6.7 Consensus size: 21
1897958 CGATTTGAAA
*
1897968 ATCGCATTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
* * *
1897989 ATCTCGTTGCGA--AAGTCAGT
1 ATCGCGTTGCGATTATGT-ATT
*
1898009 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTATGTATT
* *
1898030 ATCGCGTTGCGA--AAGTCAGT
1 ATCGCGTTGCGATTATGT-ATT
*
1898050 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTATGTATT
*
1898071 ATCGCGTTGCGA-TA-GTCAGT
1 ATCGCGTTGCGATTATGT-ATT
*
1898091 ATCGCATTGCGATT
1 ATCGCGTTGCGATT
1898105 TTCCAAATTC
Statistics
Matches: 91, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
19 7 0.08
20 41 0.45
21 39 0.43
22 4 0.04
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:1898122 original size:82 final size:82
Alignment explanation
Indices: 1897968--1898123 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 82
1897958 CGATTTGAAA
* * ** *
1897968 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATC
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTCAAATATC
*
1898033 GCGTTGCGAAAGTCAGT
66 GCATTGCGAAAGTCAGT
* * *
1898050 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT-T
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTT-CAAATAT
1898114 CGCATTGCGA
65 CGCATTGCGA
1898124 TTTACTTATT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
82 62 0.97
83 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (82 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTCAAATATC
GCATTGCGAAAGTCAGT
Found at i:1898124 original size:41 final size:41
Alignment explanation
Indices: 1897968--1898106 Score: 233
Period size: 41 Copynumber: 3.4 Consensus size: 41
1897958 CGATTTGAAA
* * *
1897968 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
1898009 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
1898050 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
1898091 ATCGCATTGCGATTTT
1 ATCGCGTTGCGATTTT
1898107 CCAAATTCGC
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.38
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:1898136 original size:20 final size:21
Alignment explanation
Indices: 1898092--1898143 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1898082 ATAGTCAGTA
*
1898092 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1898113 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1898133 TCGCATTGCGA
1 TCGCATTGCGA
1898144 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1898185 original size:21 final size:22
Alignment explanation
Indices: 1898133--1898185 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1898123 ATTTACTTAT
1898133 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
1898154 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
1898175 TCGCATTGCGA
1 TCGCATTGCGA
1898186 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1900647 original size:18 final size:18
Alignment explanation
Indices: 1900624--1900697 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
1900614 GCAACCAACC
1900624 AAAATATTTATTATATAA
1 AAAATATTTATTATATAA
* * *
1900642 AAAATATATATTAAATTA
1 AAAATATTTATTATATAA
**
1900660 ATTATATTTATT-TATAA
1 AAAATATTTATTATATAA
* *
1900677 AAGTATATTAATTATACTAA
1 AA-AATATTTATTATA-TAA
1900697 A
1 A
1900698 TATTATTATA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
17 4 0.09
18 33 0.77
19 2 0.05
20 4 0.09
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (18 bp):
AAAATATTTATTATATAA
Found at i:1902495 original size:2 final size:2
Alignment explanation
Indices: 1902488--1902573 Score: 67
Period size: 2 Copynumber: 44.0 Consensus size: 2
1902478 AACAATAATG
* *
1902488 TA TA TA TA TA TA TA TA TA TA TGA TA -A TA TGA TA -A AA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA T-A TA TA TA TA TA TA
*
1902530 TA AA TCA GT- TA TA T- TA -A TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA T-A -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1902570 TA TA
1 TA TA
1902574 AAATTATGAG
Statistics
Matches: 69, Mismatches: 5, Indels: 20
0.73 0.05 0.21
Matches are distributed among these distances:
1 6 0.09
2 57 0.83
3 5 0.07
4 1 0.01
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1903618 original size:17 final size:19
Alignment explanation
Indices: 1903572--1903611 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
1903562 TAAAAAGTTT
*
1903572 ATATTTTTATTTATTTTTA
1 ATATTTTTATTTATTTCTA
1903591 ATAATTATTTATTTATTTCTA
1 AT-ATT-TTTATTTATTTCTA
1903612 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 3 0.17
21 13 0.72
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
ATATTTTTATTTATTTCTA
Found at i:1907975 original size:24 final size:25
Alignment explanation
Indices: 1907932--1907978 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1907922 ATTTTAGGTT
1907932 AGAGATAAAATTATAAAATTTTAAG
1 AGAGATAAAATTATAAAATTTTAAG
* *
1907957 AGAGAT-AATTTATATAATTTTA
1 AGAGATAAAATTATAAAATTTTA
1907979 GGACAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (25 bp):
AGAGATAAAATTATAAAATTTTAAG
Found at i:1923619 original size:15 final size:15
Alignment explanation
Indices: 1923599--1923636 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
1923589 TTAGACCCTT
1923599 GAGAGCATTCTTTCA
1 GAGAGCATTCTTTCA
1923614 GAGAGCATTCTTTCA
1 GAGAGCATTCTTTCA
1923629 GAGAGCAT
1 GAGAGCAT
1923637 ACTACTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (15 bp):
GAGAGCATTCTTTCA
Found at i:1941002 original size:84 final size:84
Alignment explanation
Indices: 1940886--1941050 Score: 312
Period size: 84 Copynumber: 2.0 Consensus size: 84
1940876 AAATCTCCAA
*
1940886 CAGAAATATGCACCAAACCATACTGAAAGAACAAATAAATATATATAATTTTCACTTCAATTGGA
1 CAGAAATATGCACCAAACCATACTGAAAGAACAAATAAATATATATAATTTTAACTTCAATTGGA
1940951 AATAAGAAAAAACAACCAG
66 AATAAGAAAAAACAACCAG
*
1940970 CAGAAATATGCACCAAACCATACTGAATGAACAAATAAATATATATAATTTTAACTTCAATTGGA
1 CAGAAATATGCACCAAACCATACTGAAAGAACAAATAAATATATATAATTTTAACTTCAATTGGA
1941035 AATAAGAAAAAACAAC
66 AATAAGAAAAAACAAC
1941051 GCATAAATTT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.22
Consensus pattern (84 bp):
CAGAAATATGCACCAAACCATACTGAAAGAACAAATAAATATATATAATTTTAACTTCAATTGGA
AATAAGAAAAAACAACCAG
Found at i:1941524 original size:12 final size:13
Alignment explanation
Indices: 1941501--1941529 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1941491 GCCCCTTTGC
1941501 CTCTGCGCTCTCT
1 CTCTGCGCTCTCT
1941514 CTCTG-GCTCTCT
1 CTCTGCGCTCTCT
1941526 CTCT
1 CTCT
1941530 CTGGATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.00, C:0.45, G:0.14, T:0.41
Consensus pattern (13 bp):
CTCTGCGCTCTCT
Found at i:1945115 original size:17 final size:19
Alignment explanation
Indices: 1945094--1945135 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
1945084 TTTAAATAGA
1945094 AATAAACTT-TATAA-AAT
1 AATAAACTTATATAATAAT
*
1945111 CATAAACTTATATAATAAT
1 AATAAACTTATATAATAAT
1945130 AATAAA
1 AATAAA
1945136 GAAATCATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 8 0.38
18 5 0.24
19 8 0.38
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
AATAAACTTATATAATAAT
Found at i:1946946 original size:23 final size:23
Alignment explanation
Indices: 1946830--1946936 Score: 196
Period size: 23 Copynumber: 4.7 Consensus size: 23
1946820 CTCGTATAAA
1946830 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1946853 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1946876 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1946899 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1946922 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
1946937 TATAAGATTG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 81 1.00
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1953648 original size:23 final size:23
Alignment explanation
Indices: 1953591--1953651 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1953581 CTCGTATAAA
*
1953591 TACACCGAAGTACCACGTAGAAT
1 TACACCGAAGTGCCACGTAGAAT
* *
1953614 TGCACCGAAGTGCCGCGTAGAAT
1 TACACCGAAGTGCCACGTAGAAT
*
1953637 TACACCGTAGTGCCA
1 TACACCGAAGTGCCA
1953652 TATAAGATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.31, C:0.28, G:0.23, T:0.18
Consensus pattern (23 bp):
TACACCGAAGTGCCACGTAGAAT
Found at i:1954450 original size:64 final size:63
Alignment explanation
Indices: 1954292--1954450 Score: 165
Period size: 63 Copynumber: 2.5 Consensus size: 63
1954282 CCTTGACGGG
* * *** *** * *
1954292 TGCATCGATGCACTATCTATGCATCGATACAGAAATCATATTCGATGTTTGTATTTAAGGGGG
1 TGCATCGATGCACTACCTGTGCATCGATACACTGATGGCATTCGATGTTTGTATTTAAAGGGA
* * * *
1954355 TGTATCGATGCACTACTTGTGCATCGATACACTGATGGCATTCGATGTTTTTATTTTAAAGGTA
1 TGCATCGATGCACTACCTGTGCATCGATACACTGATGGCATTCGATGTTTGTA-TTTAAAGGGA
* *
1954419 TGCATCGATGCACTTCCTGTGCATCGGTACAC
1 TGCATCGATGCACTACCTGTGCATCGATACAC
1954451 ATTGAATGTA
Statistics
Matches: 77, Mismatches: 18, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
63 42 0.55
64 35 0.45
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (63 bp):
TGCATCGATGCACTACCTGTGCATCGATACACTGATGGCATTCGATGTTTGTATTTAAAGGGA
Found at i:1959844 original size:19 final size:19
Alignment explanation
Indices: 1959806--1959856 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
1959796 GCAATTACTT
*
1959806 TTATATTTTTTAAGACATA
1 TTATATTTTTTAAGAAATA
*
1959825 TTATGATTTTTTAAAAATATAA
1 TTAT-ATTTTTTAAGAA-AT-A
1959847 TTATATTTTT
1 TTATATTTTT
1959857 GTTTGAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 4 0.15
20 10 0.37
21 8 0.30
22 5 0.19
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (19 bp):
TTATATTTTTTAAGAAATA
Found at i:1961554 original size:112 final size:112
Alignment explanation
Indices: 1961352--1961917 Score: 925
Period size: 112 Copynumber: 5.1 Consensus size: 112
1961342 TTGTCGGTTT
* * *
1961352 GTGTCGATATTTTATAAAAATGTATTGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
1961417 GGTCTATAAATTACAAAACATGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
1961464 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1961529 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
1961576 GTGTTGATACTTTAT-AAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
1961640 GGTCTAT-AATGACAAAACAGGTAAAGCGCTACCAGATATATTG-AA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1961685 GTGTCGATACTTTAT--AAATGTATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
1961748 GGTATATAAATGAC-AAATAGGT--AGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1961792 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAAAAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
1961856 GGTCTATAAATGACAAAACAGGTAAAGCGCTATCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1961903 GTGTCAATACTTTAT
1 GTGTCGATACTTTAT
1961918 TATAAGTATC
Statistics
Matches: 425, Mismatches: 22, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
106 18 0.04
107 17 0.04
108 88 0.21
109 58 0.14
110 35 0.08
111 88 0.21
112 121 0.28
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:1962088 original size:173 final size:175
Alignment explanation
Indices: 1961788--1962180 Score: 542
Period size: 173 Copynumber: 2.2 Consensus size: 175
1961778 CGGATATATT
*
1961788 GAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAAAAGGTAAAAAATGACAAA
1 GAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT-A-AACAT---A-GTAAAAAATGACAAA
* * * * *
1961853 ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTATCGGATATGTTGATAGTGTCAATACTTTAT
60 ACCGGTCTAGAAATGACAAAACAGGTAAAGAGCTACCAGATATGTTGAAAGTGTCAATACTTTAT
* *
1961918 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGGTATAGCGCTAA
125 TATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGGTATAGCGCCAA
* * *
1961969 -TAAGTGTCGATACTCTAT-AAAATGTATCGATCCATAAACAT-GTAAAAATATGACAAAATCGG
1 GAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAACATAGTAAAAA-ATGACAAAACCGG
* ** *
1962031 TCTCGAAATGACAAAATCA-GTAAAGATTTACCAGATATGTTGAAAGTGTCGATACTTTATTATA
65 TCTAGAAATGACAAAA-CAGGTAAAGAGCTACCAGATATGTTGAAAGTGTCAATACTTTATTATA
*
1962095 AGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAA
129 AGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGGTATAGCGCCAA
1962142 GAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAA
1 GAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAA
1962181 CAATATAACA
Statistics
Matches: 190, Mismatches: 18, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
172 7 0.04
173 108 0.57
174 18 0.09
175 19 0.10
177 4 0.02
178 1 0.01
179 17 0.09
180 16 0.08
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (175 bp):
GAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAACATAGTAAAAAATGACAAAACCGGT
CTAGAAATGACAAAACAGGTAAAGAGCTACCAGATATGTTGAAAGTGTCAATACTTTATTATAAG
TATCGACACTTTTGGAATTTAAAAGAAAAGAAGGTATAGCGCCAA
Found at i:1965706 original size:15 final size:15
Alignment explanation
Indices: 1965654--1965707 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
1965644 GCACAGACAT
1965654 CACATGCTCCACCAG
1 CACATGCTCCACCAG
* **
1965669 CGCATGCTCCACTTG
1 CACATGCTCCACCAG
* *
1965684 CACTTGCTCCACCAC
1 CACATGCTCCACCAG
1965699 CACATGCTC
1 CACATGCTC
1965708 AATCAATGTG
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.20, C:0.46, G:0.13, T:0.20
Consensus pattern (15 bp):
CACATGCTCCACCAG
Found at i:1968389 original size:9 final size:9
Alignment explanation
Indices: 1968377--1968406 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1968367 TTTAAAGGTT
1968377 TTTTTTTTA
1 TTTTTTTTA
1968386 TTTTTTTTA
1 TTTTTTTTA
*
1968395 TTTTTTGTA
1 TTTTTTTTA
1968404 TTT
1 TTT
1968407 GATACGTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:1972525 original size:45 final size:42
Alignment explanation
Indices: 1972456--1972544 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 42
1972446 TCCTCATTAC
* * *
1972456 GTAAAATATGATTTACGCATGACATAGCCTTTAACCTACTACTT
1 GTAAAATATGATTTACGAACGACATAG-C-TTAACCTAATACTT
*
1972500 GTAAAATATTGATTTACTAACGACATAGCTTAACCTAATACTT
1 GTAAAATA-TGATTTACGAACGACATAGCTTAACCTAATACTT
1972543 GT
1 GT
1972545 TGGATTAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 15 0.38
44 9 0.22
45 16 0.40
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (42 bp):
GTAAAATATGATTTACGAACGACATAGCTTAACCTAATACTT
Found at i:1994261 original size:9 final size:9
Alignment explanation
Indices: 1994247--1994280 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1994237 TAAGTAAAAT
1994247 ATTAAATAA
1 ATTAAATAA
1994256 ATTAAAT-A
1 ATTAAATAA
*
1994264 CTTAAATAA
1 ATTAAATAA
1994273 ATTAAATA
1 ATTAAATA
1994281 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:1994279 original size:17 final size:17
Alignment explanation
Indices: 1994243--1994281 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1994233 TAATTAAGTA
1994243 AAATA-TTAAATAAATT
1 AAATACTTAAATAAATT
1994259 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
1994276 AAATAC
1 AAATAC
1994282 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACTTAAATAAATT
Found at i:1998882 original size:69 final size:63
Alignment explanation
Indices: 1998756--1998887 Score: 201
Period size: 69 Copynumber: 2.0 Consensus size: 63
1998746 TTAACTGCAA
*
1998756 CAAAGCTTTGGAGACAAGGGACCACTTGTTCTTAAGAGTTCCCCTTGGCTTCTTCTTTATGGG
1 CAAAGCTTTGGAGACAAGGGACCACTTGTTCTTAAGAGTGCCCCTTGGCTTCTTCTTTATGGG
1998819 CAAAGCTTTGGAGACAAGGGACCACTTGTTCTTGTTCTTAAGAGTGCCCCTTGGCTTCTTCTTTA
1 CAAAGCTTTGGAGACAAGGGACCA------CTTGTTCTTAAGAGTGCCCCTTGGCTTCTTCTTTA
1998884 TGGG
60 TGGG
1998888 AGGCCATTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
63 24 0.39
69 38 0.61
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (63 bp):
CAAAGCTTTGGAGACAAGGGACCACTTGTTCTTAAGAGTGCCCCTTGGCTTCTTCTTTATGGG
Found at i:2007759 original size:2 final size:2
Alignment explanation
Indices: 2007752--2007793 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2007742 ATTCATTCAA
2007752 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2007794 TATGAAACTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2009188 original size:6 final size:6
Alignment explanation
Indices: 2009177--2009202 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2009167 GAAGGAATTG
2009177 GGGACT GGGACT GGGACT GGGACT GG
1 GGGACT GGGACT GGGACT GGGACT GG
2009203 ACTCAAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.54, T:0.15
Consensus pattern (6 bp):
GGGACT
Found at i:2012360 original size:4 final size:4
Alignment explanation
Indices: 2012351--2012388 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
2012341 TATACATAAA
* *
2012351 ATGT ATGT ATGC ATGT ATGC ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
2012389 AGGATACACA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (4 bp):
ATGT
Found at i:2013259 original size:25 final size:26
Alignment explanation
Indices: 2013217--2013271 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
2013207 TTGATAATTT
*
2013217 ATTT-TTATCTTTTAAAATTTTACAA
1 ATTTATTATCTTTTAAAATATTACAA
* *
2013242 ATTTATTAT-TTTTTAAATATTATAA
1 ATTTATTATCTTTTAAAATATTACAA
2013267 ATTTA
1 ATTTA
2013272 CTCTCTAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (26 bp):
ATTTATTATCTTTTAAAATATTACAA
Found at i:2014129 original size:16 final size:16
Alignment explanation
Indices: 2014108--2014140 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2014098 TGGCTTTATG
2014108 ATTTTCAATTGTTTTA
1 ATTTTCAATTGTTTTA
2014124 ATTTTCAATTGTTTTA
1 ATTTTCAATTGTTTTA
2014140 A
1 A
2014141 GTTTATTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
ATTTTCAATTGTTTTA
Found at i:2021071 original size:28 final size:28
Alignment explanation
Indices: 2021039--2021095 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
2021029 CACCAAGGGT
2021039 GCATACCAGGTTAACCAAAAGAGAACAA
1 GCATACCAGGTTAACCAAAAGAGAACAA
2021067 GCATACCAGGTTAACCAAAAGAGAACAA
1 GCATACCAGGTTAACCAAAAGAGAACAA
2021095 G
1 G
2021096 TAAAAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.11
Consensus pattern (28 bp):
GCATACCAGGTTAACCAAAAGAGAACAA
Found at i:2026422 original size:72 final size:72
Alignment explanation
Indices: 2026305--2026447 Score: 250
Period size: 72 Copynumber: 2.0 Consensus size: 72
2026295 TTTTACCATT
* *
2026305 GCCTTGTCTAAACAAGGCTTATTTAATTTCCTCATCCTCCACCTCCTTAATAAGCATAGCTCCAG
1 GCCTTATCTAAACAAGGCTTATTTAATTTCCTCATCCTCCACCTCCTTAATAAGCATAACTCCAG
2026370 CATCAAA
66 CATCAAA
*
2026377 GCCTTATCTAAACAAGGCTTCTTTAATTTCCTCATCCTCCACCTCCTTAATAAGCATAACTCCAG
1 GCCTTATCTAAACAAGGCTTATTTAATTTCCTCATCCTCCACCTCCTTAATAAGCATAACTCCAG
*
2026442 CGTCAA
66 CATCAA
2026448 TAGGTAGAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (72 bp):
GCCTTATCTAAACAAGGCTTATTTAATTTCCTCATCCTCCACCTCCTTAATAAGCATAACTCCAG
CATCAAA
Found at i:2027677 original size:21 final size:21
Alignment explanation
Indices: 2027662--2027704 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2027652 GCTCAGCTTC
2027662 TCCACCGCATCACTCAACTCT
1 TCCACCGCATCACTCAACTCT
2027683 TCCACCGCATCACTCAACTCT
1 TCCACCGCATCACTCAACTCT
2027704 T
1 T
2027705 TCTACTCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.47, G:0.05, T:0.26
Consensus pattern (21 bp):
TCCACCGCATCACTCAACTCT
Found at i:2031319 original size:28 final size:30
Alignment explanation
Indices: 2031259--2031319 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 30
2031249 CATGTACTAT
* *
2031259 ATGTCTAAAGTGATGATGTGGCACATTCTAC
1 ATGTCTAAAGTGATGATGTAG-ACATGCTAC
*
2031290 ATGTTTAAAGTGATGATGTAG-CATGC-AC
1 ATGTCTAAAGTGATGATGTAGACATGCTAC
2031318 AT
1 AT
2031320 AGGTCTTGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 4 0.15
29 4 0.15
31 19 0.70
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (30 bp):
ATGTCTAAAGTGATGATGTAGACATGCTAC
Found at i:2067748 original size:56 final size:55
Alignment explanation
Indices: 2067687--2067794 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 55
2067677 ATATCTATAT
* *
2067687 GATATTGTTTGGTATAATCATCGGTATCCGATTTATTAATCGATTATTATTTTTGA
1 GATATTGTTTGGTAAAATCATCGATATCCGATTTATTAATCGATTATT-TTTTTGA
* * * *
2067743 GATATTGTTTGGTAAAATCTTCTATTTCCGATTTATTAGTCGATTATTTTTT
1 GATATTGTTTGGTAAAATCATCGATATCCGATTTATTAATCGATTATTTTTT
2067795 CTATGATTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
55 4 0.09
56 42 0.91
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.51
Consensus pattern (55 bp):
GATATTGTTTGGTAAAATCATCGATATCCGATTTATTAATCGATTATTTTTTTGA
Found at i:2072637 original size:45 final size:45
Alignment explanation
Indices: 2072538--2072671 Score: 243
Period size: 45 Copynumber: 3.0 Consensus size: 45
2072528 TTGTAAAAAA
2072538 CCGTCTAATATTTACTTTCCAAAACAATAACATAG-TTTTAATCC
1 CCGTCTAATATTTACTTTCCAAAACAATAACATAGTTTTTAATCC
2072582 CCGTCTAATATTTACTTTCCAAAACAATAACATAGTTTTTAATCC
1 CCGTCTAATATTTACTTTCCAAAACAATAACATAGTTTTTAATCC
*
2072627 CCGTCTAATATTTACTTTCCCAAACAATAACATAGTTTTTTAATC
1 CCGTCTAATATTTACTTTCCAAAACAATAACATAG-TTTTTAATC
2072672 ACTTGCTTTT
Statistics
Matches: 87, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
44 35 0.40
45 43 0.49
46 9 0.10
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.38
Consensus pattern (45 bp):
CCGTCTAATATTTACTTTCCAAAACAATAACATAGTTTTTAATCC
Found at i:2079284 original size:26 final size:25
Alignment explanation
Indices: 2079222--2079284 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 25
2079212 GAATAAAGTG
*
2079222 AAAATTGTATATTATTTTTAAATAT
1 AAAATTGTATAATATTTTTAAATAT
*
2079247 AAAATGTGTATAATACTTTTTAAAATTT
1 AAAAT-TGTATAATA-TTTTT-AAATAT
2079275 AAAATT-TATA
1 AAAATTGTATA
2079285 TTATAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 5 0.15
26 12 0.36
27 6 0.18
28 10 0.30
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (25 bp):
AAAATTGTATAATATTTTTAAATAT
Found at i:2082374 original size:21 final size:21
Alignment explanation
Indices: 2082348--2082483 Score: 161
Period size: 21 Copynumber: 6.5 Consensus size: 21
2082338 GTTTCCAGAT
**
2082348 TCGCAATGCGATTTTGGACTA
1 TCGCAATGCGAACTTGGACTA
2082369 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
2082390 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
2082410 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
2082431 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
2082452 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
*
2082473 TCGCATTGCGA
1 TCGCAATGCGA
2082484 TTTACATATT
Statistics
Matches: 99, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
20 16 0.16
21 83 0.84
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:2082518 original size:21 final size:21
Alignment explanation
Indices: 2082473--2082560 Score: 97
Period size: 21 Copynumber: 4.2 Consensus size: 21
2082463 ACTTCGACTA
* * *
2082473 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGTCCAAAT
* *
2082493 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAAT
*
2082514 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAT
* *
2082535 CCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAT
2082556 TCGCA
1 TCGCA
2082561 ACGATTGGTG
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
20 12 0.21
21 45 0.79
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.27
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAT
Found at i:2083300 original size:21 final size:20
Alignment explanation
Indices: 2083276--2083349 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
2083266 TAGTCTATAT
2083276 TCGCATTGCGAACTTCAACTA
1 TCGCATTGCGAACTTCAA-TA
*
2083297 TCGCATTGCG-ATTTACAAGT-
1 TCGCATTGCGAACTT-CAA-TA
* * *
2083317 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGA-ACTTCAATA
2083338 TCGCATTGCGAA
1 TCGCATTGCGAA
2083350 TCTGGAAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
20 14 0.32
21 28 0.64
22 2 0.05
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (20 bp):
TCGCATTGCGAACTTCAATA
Found at i:2083322 original size:20 final size:19
Alignment explanation
Indices: 2083275--2083328 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2083265 ATAGTCTATA
*
2083275 TTCGCATTGCGAACTTCAAC
1 TTCGCATTGCG-ATTTCAAC
*
2083295 TATCGCATTGCGATTTACAAG
1 T-TCGCATTGCGATTT-CAAC
2083316 TTCGCATTGCGAT
1 TTCGCATTGCGAT
2083329 AGTCCAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (19 bp):
TTCGCATTGCGATTTCAAC
Found at i:2085909 original size:2 final size:2
Alignment explanation
Indices: 2085904--2085933 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2085894 TTTTTCCCAT
2085904 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2085934 CTTCGACTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2087821 original size:4 final size:4
Alignment explanation
Indices: 2087812--2087930 Score: 238
Period size: 4 Copynumber: 29.8 Consensus size: 4
2087802 CAAAAAGCAT
2087812 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
2087860 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
2087908 TACA TACA TACA TACA TACA TAC
1 TACA TACA TACA TACA TACA TAC
2087931 TGAATTCATG
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 115 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:2102091 original size:48 final size:50
Alignment explanation
Indices: 2102020--2102124 Score: 160
Period size: 48 Copynumber: 2.1 Consensus size: 50
2102010 AGAAATTAAG
*
2102020 AACCAATAAATCGATGACAATAATTG-T-AACTTTCTGGCTTTTCATGAA
1 AACCAATAAATCGATGACAATAATTGTTCAACTTTCTGGCTTTTCAAGAA
*
2102068 AACCAATAAATTGATGACAATAATTGTTGCAACTTTCTGGCTTTTCAAGAA
1 AACCAATAAATCGATGACAATAATTGTT-CAACTTTCTGGCTTTTCAAGAA
2102119 ACACCA
1 A-ACCA
2102125 GCAGCAACAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
48 25 0.49
49 1 0.02
51 21 0.41
52 4 0.08
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.31
Consensus pattern (50 bp):
AACCAATAAATCGATGACAATAATTGTTCAACTTTCTGGCTTTTCAAGAA
Found at i:2103331 original size:43 final size:43
Alignment explanation
Indices: 2103278--2103364 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
2103268 GAAAACCTTC
* * *
2103278 TTGTAGTCTATCATTCAAGTAATCCTATTTGAACGAAAAGAAA
1 TTGTAATCTATCAGTCAAGTAATCCTATTTGAACCAAAAGAAA
2103321 TTGTAATCTATCAGTCAAGTAATCCTATTTGAACCAAAAGAAA
1 TTGTAATCTATCAGTCAAGTAATCCTATTTGAACCAAAAGAAA
2103364 T
1 T
2103365 CCATAAGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (43 bp):
TTGTAATCTATCAGTCAAGTAATCCTATTTGAACCAAAAGAAA
Found at i:2120474 original size:12 final size:12
Alignment explanation
Indices: 2120457--2120481 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2120447 CGACTAAAGA
2120457 CCTCAATAGCGG
1 CCTCAATAGCGG
2120469 CCTCAATAGCGG
1 CCTCAATAGCGG
2120481 C
1 C
2120482 GACAACGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CCTCAATAGCGG
Found at i:2126847 original size:22 final size:20
Alignment explanation
Indices: 2126826--2126864 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2126816 ATTCCCTCTT
*
2126826 TTTGAGACCTTGAAACATTC
1 TTTGAGACATTGAAACATTC
*
2126846 TTTGTGACATTGAAACATT
1 TTTGAGACATTGAAACATT
2126865 ACATTTATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
TTTGAGACATTGAAACATTC
Found at i:2128699 original size:16 final size:16
Alignment explanation
Indices: 2128675--2128705 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2128665 TAGATCAAGA
*
2128675 AATATATACATACATC
1 AATACATACATACATC
2128691 AATACATACATACAT
1 AATACATACATACAT
2128706 GTTATATAAG
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:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (16 bp):
AATACATACATACATC
Found at i:2129306 original size:36 final size:36
Alignment explanation
Indices: 2129264--2129355 Score: 139
Period size: 36 Copynumber: 2.6 Consensus size: 36
2129254 CAAAATAAAC
* *
2129264 TGTCTCGCTTGAGACAATTTATCTAAAAACAATTTT
1 TGTCTCGCTTGAGACAATTTATCTAAAAAAAATTAT
* *
2129300 TGTCTCGTTTGAGACAATTTCTCTAAAAAAAATTAT
1 TGTCTCGCTTGAGACAATTTATCTAAAAAAAATTAT
*
2129336 TGTCTCACTTGAGACAATTT
1 TGTCTCGCTTGAGACAATTT
2129356 TCCAAATTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (36 bp):
TGTCTCGCTTGAGACAATTTATCTAAAAAAAATTAT
Found at i:2129429 original size:30 final size:31
Alignment explanation
Indices: 2129393--2129451 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2129383 AACAAACATC
**
2129393 ATCTTTGAGT-CGTTTCTTTTGAAACAAAGG
1 ATCTTTGAGTACGTTTCACTTGAAACAAAGG
*
2129423 ATCTTTGAGTATGTTTCACTTGAAACAAA
1 ATCTTTGAGTACGTTTCACTTGAAACAAA
2129452 ATAAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.39
Consensus pattern (31 bp):
ATCTTTGAGTACGTTTCACTTGAAACAAAGG
Found at i:2129829 original size:36 final size:35
Alignment explanation
Indices: 2129778--2129874 Score: 108
Period size: 36 Copynumber: 2.7 Consensus size: 35
2129768 TTTAAGAAAA
* **
2129778 ATCTTTGAGTCTGTTT-CTTTAGAAACAAAATTAAT
1 ATCTTTGAGTCTGTTTCCCTT-GAAACAAAACAAAT
*
2129813 CATCTTTGAGTTTGTTTCCCTTGAAACAAAACAAAT
1 -ATCTTTGAGTCTGTTTCCCTTGAAACAAAACAAAT
*
2129849 ATCTTTGAGATC-ATTTCCCTTGAAAC
1 ATCTTTGAG-TCTGTTTCCCTTGAAAC
2129875 GAATTTTGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
35 22 0.42
36 28 0.53
37 3 0.06
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (35 bp):
ATCTTTGAGTCTGTTTCCCTTGAAACAAAACAAAT
Found at i:2129866 original size:35 final size:36
Alignment explanation
Indices: 2129799--2129874 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
2129789 TGTTTCTTTA
** * **
2129799 GAAACAAAATTAATCATCTTTGAGTTTGTTTCCCTT
1 GAAACAAAACAAATCATCTTTGAGATCATTTCCCTT
2129835 GAAACAAAACAAAT-ATCTTTGAGATCATTTCCCTT
1 GAAACAAAACAAATCATCTTTGAGATCATTTCCCTT
2129870 GAAAC
1 GAAAC
2129875 GAATTTTGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (36 bp):
GAAACAAAACAAATCATCTTTGAGATCATTTCCCTT
Done.