Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold425
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1118264
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.29
Warning! 137083 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:516245 original size:18 final size:18
Alignment explanation
Indices: 516192--516235 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 18
516182 ATTTCTCATT
516192 GCATAGCATACAAATATCATA
1 GCATAGCATAC-AA-AT-ATA
516213 GCATAGCATACAAATATA
1 GCATAGCATACAAATATA
516231 GCATA
1 GCATA
516236 TCATTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.35
19 2 0.09
20 2 0.09
21 11 0.48
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.23
Consensus pattern (18 bp):
GCATAGCATACAAATATA
Found at i:517573 original size:29 final size:29
Alignment explanation
Indices: 517537--517601 Score: 130
Period size: 29 Copynumber: 2.2 Consensus size: 29
517527 TGACTTGATA
517537 GTTTATATTATTTAGATAACACTGATTTT
1 GTTTATATTATTTAGATAACACTGATTTT
517566 GTTTATATTATTTAGATAACACTGATTTT
1 GTTTATATTATTTAGATAACACTGATTTT
517595 GTTTATA
1 GTTTATA
517602 AATTAAACAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.52
Consensus pattern (29 bp):
GTTTATATTATTTAGATAACACTGATTTT
Found at i:517610 original size:24 final size:27
Alignment explanation
Indices: 517537--517622 Score: 81
Period size: 29 Copynumber: 3.2 Consensus size: 27
517527 TGACTTGATA
*
517537 GTTTATATTATTTAGATAACACTGATTTT
1 GTTTATA-TAATTA-ATAACACTGATTTT
*
517566 GTTTATATTATTTAGATAACACTGATTTT
1 GTTTATA-TAATTA-ATAACACTGATTTT
*
517595 GTTTATA-AATT-A-AACAGTGATTTT
1 GTTTATATAATTAATAACACTGATTTT
517619 -TTTA
1 GTTTA
517623 AACTAATTCA
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
23 4 0.07
24 11 0.20
25 1 0.02
27 3 0.05
29 36 0.65
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (27 bp):
GTTTATATAATTAATAACACTGATTTT
Found at i:518445 original size:167 final size:162
Alignment explanation
Indices: 518094--518515 Score: 587
Period size: 167 Copynumber: 2.6 Consensus size: 162
518084 ACCACATCCC
* * ** * *
518094 TGATTTGAACAAACTTGAATCTACACTACCTAAGGATG-CTACCACTTTAA-TTTGAGTTTTTCT
1 TGATTTGAACAAACTTGAAACTACACTACCTGAGGATGCCT-CCAC-ACAAGTTTAAGCTTTTCT
* *
518157 GGCCCAATAGTTTTTAAGAAGAAGATTTTTAAAGATTTTCTCTATACATTATGGAAAACTTGATC
64 GGCCGAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATACATTATGGAAAACTTGATC
*
518222 CCCAATTATGGCAGCACCCTACCCCCGGAGACCA
129 CCCAATTATGGCACCACCCTACCCCCGGAGACCA
518256 TGATTTGAACAAACTTGAAACTACACTACCTGAGGATGCCTCCACACAAGTTTAAGCTTTTCTGG
1 TGATTTGAACAAACTTGAAACTACACTACCTGAGGATGCCTCCACACAAGTTTAAGCTTTTCTGG
* * * *
518321 CCTGAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTTTCTTTATATTCCTATGTAAAACTTGA
66 CC-GAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATACA-T--TATGGAAAACTTGA
** * * *
518386 TCCCCCTCTTGTGGCACCTCCCTACCCCCGGGGACCA
127 T-CCCCAATTATGGCACCACCCTACCCCCGGAGACCA
* *
518423 TTATTTGAACAAACTTGAAACTACACTACCTGAGGATGCCTCCACACAAGTTTAAGCTTTTCAGG
1 TGATTTGAACAAACTTGAAACTACACTACCTGAGGATGCCTCCACACAAGTTTAAGCTTTTCTGG
518488 CCGAATAGTTTTTGAGAAGAAGATTTTT
66 CCGAATAGTTTTTGAGAAGAAGATTTTT
518516 GAAAAATACC
Statistics
Matches: 233, Mismatches: 20, Indels: 10
0.89 0.08 0.04
Matches are distributed among these distances:
161 2 0.01
162 55 0.24
163 41 0.18
164 1 0.00
166 40 0.17
167 94 0.40
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (162 bp):
TGATTTGAACAAACTTGAAACTACACTACCTGAGGATGCCTCCACACAAGTTTAAGCTTTTCTGG
CCGAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATACATTATGGAAAACTTGATCCC
CAATTATGGCACCACCCTACCCCCGGAGACCA
Found at i:518714 original size:10 final size:10
Alignment explanation
Indices: 518688--518725 Score: 58
Period size: 10 Copynumber: 3.6 Consensus size: 10
518678 AAAGTTTACA
518688 ACAACGACGACG
1 ACAACGAC-A-G
518700 ACAACGACAG
1 ACAACGACAG
518710 ACAACGACAG
1 ACAACGACAG
518720 ACAACG
1 ACAACG
518726 GACAAATTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 17 0.65
11 1 0.04
12 8 0.31
ACGTcount: A:0.47, C:0.32, G:0.21, T:0.00
Consensus pattern (10 bp):
ACAACGACAG
Found at i:521000 original size:60 final size:62
Alignment explanation
Indices: 520862--521029 Score: 193
Period size: 60 Copynumber: 2.7 Consensus size: 62
520852 GAACGCGTAG
*
520862 AAAAAC-AGTAAGGTCTTCCGCT-GAAGACGGAAGACCTTAATAATAGGGAAAAAGAAACAAAGC
1 AAAAACAAG-AAGGTCTTCCGTTGGAA-ACGGAAGACCTTAATAATA-GGAAAAAGAAACAAAGC
* **
520925 AAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAA-A-GAAAAAGAAACCGTAG-
1 AAAAACAAGAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAATAGGAAAAAGAAA-CAAAGC
* * * *
520985 AATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAAAAATA
1 AAAAACAAGAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAATA
521030 AAGAGTTAAA
Statistics
Matches: 92, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
60 48 0.52
61 4 0.04
62 1 0.01
63 35 0.38
64 4 0.04
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.16
Consensus pattern (62 bp):
AAAAACAAGAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAATAGGAAAAAGAAACAAAGC
Found at i:521125 original size:2 final size:2
Alignment explanation
Indices: 521118--521164 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
521108 AGGGACCGGG
521118 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
521160 CT CT C
1 CT CT C
521165 AAATTCTTGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:523545 original size:2 final size:2
Alignment explanation
Indices: 523538--523584 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
523528 CCCTGAATTG
523538 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
523580 GA GA G
1 GA GA G
523585 GAGNNNNNNN
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:523673 original size:2 final size:2
Alignment explanation
Indices: 523666--523695 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
523656 ATCAAAAGAC
523666 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
523696 GCTTTATTTT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:533576 original size:164 final size:161
Alignment explanation
Indices: 533373--533764 Score: 595
Period size: 164 Copynumber: 2.4 Consensus size: 161
533363 GGTAGCTACG
* * * * * *
533373 TCATCTCTTGGGATATAATTGGGGCTGTCCTATAGATGTGCAATAAGATTTTAAAAATCTAAATT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAAT-TAAATT
*
533438 TCATCCAGGGAGTCAAATAGTAGCAGAAAATTGACGTTTATCACTAAAAAAAAACCCATAGATCC
65 TCATCCAGGGAGTCAAAAAGTAGCAGAAAATTGACGTTTATCACTAAAAAAAAA--CATAGATCC
533503 CAGAACTCCTCTTATGATTTAATGGATAGACACA
128 CAGAACTCCTCTTATGATTTAATGGATAGACACA
*
533537 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAGTAAGGTTTTAAAAATTTAAATT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAA-TTAAATT
** *
533602 TCATCCAGGGAGTCAAAAAGTAGCAGAAAATTGACGTTTATCACTTCAAAAAAACATAGATCCTA
65 TCATCCAGGGAGTCAAAAAGTAGCAGAAAATTGACGTTTATCACTAAAAAAAAACATAGATCCCA
*
533667 GAACTCCTTTTATGATTTAATGGATAGACACA
130 GAACTCCTCTTATGATTTAATGGATAGACACA
* * * *
533699 TCATATCTTGGGATATGATAGGAACTGTTCCATAGATGTGCATTACGGTTTTGAAAAATTAAATT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTT-AAAAATTAAATT
533764 T
65 T
533765 AACCCTGAGG
Statistics
Matches: 210, Mismatches: 16, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
162 97 0.46
163 5 0.02
164 107 0.51
165 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (161 bp):
TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTAAATTT
CATCCAGGGAGTCAAAAAGTAGCAGAAAATTGACGTTTATCACTAAAAAAAAACATAGATCCCAG
AACTCCTCTTATGATTTAATGGATAGACACA
Found at i:533960 original size:135 final size:135
Alignment explanation
Indices: 533812--534110 Score: 401
Period size: 134 Copynumber: 2.2 Consensus size: 135
533802 GATGCCCTTT
* *
533812 AAGGATCAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTTCG-AGATATT-CGTGCA
1 AAGGAACAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTT-GAAGATATTAAG-GCA
* * * * *
533875 CTTCCTGTTCGAGGGGGGTCATGACCACCCCCGGGGCCCATGACCTACATACCGTTTGATGCCCC
64 CTTCCTGTTCGA-GGGGGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCC
533940 TTGACA-C
128 TTGACATC
* *
533947 AAGGAACAAGAATATATATGGTTTAA-GGGTGGGGATCTCAACTGTTTTGAAGATATTAAGGGAC
1 AAGGAACAAGAATATATATGG-TTAAGGGGTGGGGATCTCAACCGTTTTGAAGATATTAAGGCAC
* *
534011 TTGCTGTTTGAGGGGGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCCTT
65 TTCCTGTTCGAGGGGGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCCTT
534076 GACATC
130 GACATC
* * *
534082 -AGAAACATGAATATATATGGTTTAGGGGT
1 AAGGAACAAGAATATATATGGTTAAGGGGT
534111 CATGATTATA
Statistics
Matches: 145, Mismatches: 14, Indels: 11
0.85 0.08 0.06
Matches are distributed among these distances:
133 3 0.02
134 76 0.52
135 61 0.42
136 5 0.03
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26
Consensus pattern (135 bp):
AAGGAACAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTTGAAGATATTAAGGCACT
TCCTGTTCGAGGGGGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCCTTG
ACATC
Found at i:536482 original size:12 final size:12
Alignment explanation
Indices: 536464--536510 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
536454 TTGCTAAAAC
536464 GCGGAACGGAAA
1 GCGGAACGGAAA
*
536476 ACGGAACGGAAA
1 GCGGAACGGAAA
536488 GCGGAACGGAAA
1 GCGGAACGGAAA
536500 GCGGAACGGAA
1 GCGGAACGGAA
536511 TGGAAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.43, C:0.17, G:0.40, T:0.00
Consensus pattern (12 bp):
GCGGAACGGAAA
Found at i:536999 original size:16 final size:16
Alignment explanation
Indices: 536978--537011 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
536968 AAGATACCCG
*
536978 GTAATTTTTGAAACTA
1 GTAATTTGTGAAACTA
536994 GTAATTTGTGAAACTA
1 GTAATTTGTGAAACTA
537010 GT
1 GT
537012 TTTTTTAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (16 bp):
GTAATTTGTGAAACTA
Found at i:537668 original size:12 final size:12
Alignment explanation
Indices: 537637--537671 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
537627 CCGTTTTCCC
*
537637 TTCCGTTTCGCT
1 TTCCGTTCCGCT
*
537649 TTCCGTTCCGTT
1 TTCCGTTCCGCT
537661 TTCCGTTCCGC
1 TTCCGTTCCGC
537672 GTTTTAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.37, G:0.17, T:0.46
Consensus pattern (12 bp):
TTCCGTTCCGCT
Found at i:540132 original size:21 final size:21
Alignment explanation
Indices: 540103--540250 Score: 215
Period size: 21 Copynumber: 7.0 Consensus size: 21
540093 TTTTTTTTAT
540103 TTTCTACACTTTAATCTGTAAA
1 TTTC-ACACTTTAATCTGTAAA
540125 TTTCACACTTTAATCTGTAAA
1 TTTCACACTTTAATCTGTAAA
540146 TTTCACACTTTAATCTGTAAA
1 TTTCACACTTTAATCTGTAAA
*
540167 TTTTACACTTTAATCTGTAAA
1 TTTCACACTTTAATCTGTAAA
*
540188 TTTTACACTTTAATCTGTAAA
1 TTTCACACTTTAATCTGTAAA
* * **
540209 ATTCAAACTTTAAAGTGTAAA
1 TTTCACACTTTAATCTGTAAA
* *
540230 ATTCACAGTTTAATCTGTAAA
1 TTTCACACTTTAATCTGTAAA
540251 GGACTATGTG
Statistics
Matches: 116, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
21 112 0.97
22 4 0.03
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.43
Consensus pattern (21 bp):
TTTCACACTTTAATCTGTAAA
Found at i:540792 original size:21 final size:21
Alignment explanation
Indices: 540763--540910 Score: 208
Period size: 21 Copynumber: 7.1 Consensus size: 21
540753 TCCACCTTNG
540763 AATTCACACTTTAATCTGTAA
1 AATTCACACTTTAATCTGTAA
* *
540784 ATTTTACACTTTAATCTGTAA
1 AATTCACACTTTAATCTGTAA
**
540805 AATTCACACTTTAAAGTGTAA
1 AATTCACACTTTAATCTGTAA
**
540826 AATTCACACTTTAAAGTGTAA
1 AATTCACACTTTAATCTGTAA
** *
540847 AATTCACACTTTAAAGTGGAA
1 AATTCACACTTTAATCTGTAA
540868 AATTCACAC-TTAATCTGTAA
1 AATTCACACTTTAATCTGTAA
540888 AATTCACACTTTAATCTGTAA
1 AATTCACACTTTAATCTGTAA
540909 AA
1 AA
540911 ATTAATCTGT
Statistics
Matches: 116, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
20 17 0.15
21 99 0.85
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (21 bp):
AATTCACACTTTAATCTGTAA
Found at i:541549 original size:21 final size:21
Alignment explanation
Indices: 541525--542154 Score: 604
Period size: 21 Copynumber: 30.3 Consensus size: 21
541515 TAACACTTTT
*
541525 AAGTGTAAAAATTACAGATTA
1 AAGTGTAAAATTTACAGATTA
* * *
541546 AAGTGTATATTTTAACAGATCA
1 AAGTGTAAAATTT-ACAGATTA
* * *
541568 AAATGTAAAA--TAGATATTA
1 AAGTGTAAAATTTACAGATTA
541587 AAGTGTAAAATTTACAGATATTA
1 AAGTGTAAAATTTACAG--ATTA
541610 AAGTGTAAAATTTACAGATTA
1 AAGTGTAAAATTTACAGATTA
541631 AAGTGTAAAATTTACAGATTA
1 AAGTGTAAAATTTACAGATTA
* * *
541652 AAGTGTGAATTTTACATATTA
1 AAGTGTAAAATTTACAGATTA
*
541673 AAGTGTAAAATTTACAAATTA
1 AAGTGTAAAATTTACAGATTA
*
541694 AAGTGTAGAATTTACAGATTA
1 AAGTGTAAAATTTACAGATTA
* * *
541715 CAAAT-TACAAA-TTAAAG-TGTG
1 -AAGTGTA-AAATTTACAGAT-TA
* * * *
541736 AATTTTACAGTTT----A--A
1 AAGTGTAAAATTTACAGATTA
* *
541751 -AGTGTAAAATTTATAGATTG
1 AAGTGTAAAATTTACAGATTA
* *
541771 AAGTGTAAATTTTACAGATCA
1 AAGTGTAAAATTTACAGATTA
* *
541792 AAGGGTAAAATTTACAAATTA
1 AAGTGTAAAATTTACAGATTA
* * * *
541813 AAGTCTGAAGTTTACATATTA
1 AAGTGTAAAATTTACAGATTA
541834 AAGTGTAAAATTTACAGATTA
1 AAGTGTAAAATTTACAGATTA
*
541855 AAGTGCAAAATTTACAGATTA
1 AAGTGTAAAATTTACAGATTA
* *
541876 AAGTGTGAATTTTACAGATTA
1 AAGTGTAAAATTTACAGATTA
*
541897 AAGTGTAAACTTTACAGATTA
1 AAGTGTAAAATTTACAGATTA
* * **
541918 AAGTGTGAATTTTACACTTTA
1 AAGTGTAAAATTTACAGATTA
** *
541939 AAGTGTGTATTTTACAGATTA
1 AAGTGTAAAATTTACAGATTA
* *
541960 AAGTGTGAATTTTACAGATTA
1 AAGTGTAAAATTTACAGATTA
541981 AAGTGTAAAATTTACAGATTA
1 AAGTGTAAAATTTACAGATTA
* *
542002 AAGTGTAGATTTTACAGATTA
1 AAGTGTAAAATTTACAGATTA
* *
542023 AAGTGT-GATTTTACAGATTA
1 AAGTGTAAAATTTACAGATTA
*
542043 AAGTGTAAATTTTACAGATTA
1 AAGTGTAAAATTTACAGATTA
* *
542064 AAGTGTGAATTTTACAGATTA
1 AAGTGTAAAATTTACAGATTA
* * *
542085 AAGTGTGAATTTTACAGATTC
1 AAGTGTAAAATTTACAGATTA
542106 AAGTGT-AAATCTTACAGATTA
1 AAGTGTAAAAT-TTACAGATTA
* **
542127 AAGTGTAAAATATACACTTTA
1 AAGTGTAAAATTTACAGATTA
542148 AAGTGTA
1 AAGTGTA
542155 GAAAATGAAA
Statistics
Matches: 511, Mismatches: 77, Indels: 42
0.81 0.12 0.07
Matches are distributed among these distances:
14 8 0.02
18 1 0.00
19 14 0.03
20 29 0.06
21 415 0.81
22 23 0.05
23 21 0.04
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (21 bp):
AAGTGTAAAATTTACAGATTA
Found at i:541671 original size:63 final size:63
Alignment explanation
Indices: 541525--542154 Score: 688
Period size: 63 Copynumber: 10.1 Consensus size: 63
541515 TAACACTTTT
** * * * * * *
541525 AAGTGTAAAAATTACAGATTAAAGTGTATATTTTAACAGATCAAAATGTAAAA--TAGATATTA
1 AAGTGTAAATTTTACAGATTAAAGTGTAAAATTT-ACAGATTAAAGTGTAAAATTTACAGATTA
*
541587 AAGTGTAAAATTTACAGATATTAAAGTGTAAAATTTACAGATTAAAGTGTAAAATTTACAGATTA
1 AAGTGTAAATTTTACAG--ATTAAAGTGTAAAATTTACAGATTAAAGTGTAAAATTTACAGATTA
* * * *
541652 AAGTGTGAATTTTACATATTAAAGTGTAAAATTTACAAATTAAAGTGTAGAATTTACAGATT-
1 AAGTGTAAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTAAAATTTACAGATTA
* * * * * * *
541714 -A---CAAA--TTACAAATTAAAGTGTGAATTTTACAGTTTAAAGTGTAAAATTTATAGATTG
1 AAGTGTAAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTAAAATTTACAGATTA
* * * * * * *
541771 AAGTGTAAATTTTACAGATCAAAGGGTAAAATTTACAAATTAAAGTCTGAAGTTTACATATTA
1 AAGTGTAAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTAAAATTTACAGATTA
* * * *
541834 AAGTGTAAAATTTACAGATTAAAGTGCAAAATTTACAGATTAAAGTGTGAATTTTACAGATTA
1 AAGTGTAAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTAAAATTTACAGATTA
* * * ** ** *
541897 AAGTGTAAACTTTACAGATTAAAGTGTGAATTTTACACTTTAAAGTGTGTATTTTACAGATTA
1 AAGTGTAAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTAAAATTTACAGATTA
* * *
541960 AAGTGTGAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTAGATTTTACAGATTA
1 AAGTGTAAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTAAAATTTACAGATTA
* * * *
542023 AAGTGT-GATTTTACAGATTAAAGTGTAAATTTTACAGATTAAAGTGTGAATTTTACAGATTA
1 AAGTGTAAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTAAAATTTACAGATTA
* * * **
542085 AAGTGTGAATTTTACAGATTCAAGTGT-AAATCTTACAGATTAAAGTGTAAAATATACACTTTA
1 AAGTGTAAATTTTACAGATTAAAGTGTAAAAT-TTACAGATTAAAGTGTAAAATTTACAGATTA
542148 AAGTGTA
1 AAGTGTA
542155 GAAAATGAAA
Statistics
Matches: 484, Mismatches: 71, Indels: 25
0.83 0.12 0.04
Matches are distributed among these distances:
56 44 0.09
58 3 0.01
61 4 0.01
62 77 0.16
63 320 0.66
64 15 0.03
65 21 0.04
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (63 bp):
AAGTGTAAATTTTACAGATTAAAGTGTAAAATTTACAGATTAAAGTGTAAAATTTACAGATTA
Found at i:545546 original size:2 final size:2
Alignment explanation
Indices: 545539--545580 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
545529 TAAAAGCATA
545539 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
545581 NNNNNNNNNN
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:551788 original size:8 final size:7
Alignment explanation
Indices: 551766--551837 Score: 55
Period size: 6 Copynumber: 10.6 Consensus size: 7
551756 TTTCGGGATT
551766 TTTTTTG
1 TTTTTTG
551773 -TTTTTG
1 TTTTTTG
551779 TTTTTCTG
1 TTTTT-TG
551787 TTTGTTTG
1 TTT-TTTG
*
551795 -CTTTTG
1 TTTTTTG
*
551801 TTTTCTG
1 TTTTTTG
551808 TTGTTTTG
1 TT-TTTTG
*
551816 -TTGTTG
1 TTTTTTG
551822 TTTTTT-
1 TTTTTTG
551828 TTTTTT-
1 TTTTTTG
551834 TTTT
1 TTTT
551838 GAAAAACAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
6 24 0.45
7 16 0.30
8 11 0.21
9 2 0.04
ACGTcount: A:0.00, C:0.04, G:0.15, T:0.81
Consensus pattern (7 bp):
TTTTTTG
Found at i:551835 original size:21 final size:20
Alignment explanation
Indices: 551765--551834 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
551755 GTTTCGGGAT
551765 TTTTTTTGTTTTTGTTTTTCTG
1 TTTTTTTG-TTTTGTTTTT-TG
* *
551787 TTTGTTTGCTTTTGTTTTCTG
1 TTTTTTTG-TTTTGTTTTTTG
*
551808 TTGTTTTGTTGTTGTTTTTT-
1 TTTTTTTGTT-TTGTTTTTTG
551828 TTTTTTT
1 TTTTTTT
551835 TTTGAAAAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 8 0.20
21 16 0.40
22 16 0.40
ACGTcount: A:0.00, C:0.04, G:0.16, T:0.80
Consensus pattern (20 bp):
TTTTTTTGTTTTGTTTTTTG
Found at i:552596 original size:21 final size:21
Alignment explanation
Indices: 552535--552605 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
552525 CACACTCGCA
552535 AAACGGTTTACACGAAACGCT
1 AAACGGTTTACACGAAACGCT
** * * * *
552556 TCACGCTTTTCCCGACACGCT
1 AAACGGTTTACACGAAACGCT
*
552577 AAACGGTTTGCACGAAACGCT
1 AAACGGTTTACACGAAACGCT
*
552598 GAACGGTT
1 AAACGGTT
552606 ACCACGGAAC
Statistics
Matches: 37, Mismatches: 13, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AAACGGTTTACACGAAACGCT
Found at i:552611 original size:21 final size:21
Alignment explanation
Indices: 552572--552611 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
552562 TTTTCCCGAC
**
552572 ACGCTAAACGGTTTGCACGAA
1 ACGCTAAACGGTTACCACGAA
*
552593 ACGCTGAACGGTTACCACG
1 ACGCTAAACGGTTACCACG
552612 GAACTTTTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (21 bp):
ACGCTAAACGGTTACCACGAA
Found at i:553374 original size:2 final size:2
Alignment explanation
Indices: 553367--553420 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
553357 AATCAAATTT
* * *
553367 CA CA CA CA CG CA CA CG CA CA CG CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
553409 CA CA CA CA CA CA
1 CA CA CA CA CA CA
553421 TAATTGGAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.44, C:0.50, G:0.06, T:0.00
Consensus pattern (2 bp):
CA
Found at i:557119 original size:21 final size:21
Alignment explanation
Indices: 557090--557142 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
557080 ACTTAAACTT
* * *
557090 AGAGCTCGTGCAATGTATGCG
1 AGAGCTCGTGCAACGTATCCA
*
557111 AGAGTTCGTGCAACGTATCCA
1 AGAGCTCGTGCAACGTATCCA
557132 AGAGCTCGTGC
1 AGAGCTCGTGC
557143 GAATCTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (21 bp):
AGAGCTCGTGCAACGTATCCA
Found at i:559772 original size:54 final size:54
Alignment explanation
Indices: 559682--559845 Score: 283
Period size: 54 Copynumber: 3.0 Consensus size: 54
559672 CAAGAAATGA
* *
559682 TAATTTTGTATAGAAGTTAAACAACGCACTTGTTGCCCTATTACATTCGTAAAG
1 TAATTTTGTATATAAGTTAAACAACGCACTTTTTGCCCTATTACATTCGTAAAG
* * *
559736 TAATTTTGTATATAAGTTAAACAACGAAATTTTTGCCTTATTACATTCGTAAAG
1 TAATTTTGTATATAAGTTAAACAACGCACTTTTTGCCCTATTACATTCGTAAAG
559790 TAATTTTGTATATAAGTTAAACAACGCACTTTTTGCCCTATTACATTCGTAAAG
1 TAATTTTGTATATAAGTTAAACAACGCACTTTTTGCCCTATTACATTCGTAAAG
559844 TA
1 TA
559846 TGCAATTATA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 102 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (54 bp):
TAATTTTGTATATAAGTTAAACAACGCACTTTTTGCCCTATTACATTCGTAAAG
Found at i:560873 original size:8 final size:8
Alignment explanation
Indices: 560860--560889 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
560850 AATGCTTTTT
560860 ATTTATTA
1 ATTTATTA
560868 ATTTATTA
1 ATTTATTA
*
560876 ATTTATTC
1 ATTTATTA
560884 ATTTAT
1 ATTTAT
560890 ATATTCAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (8 bp):
ATTTATTA
Found at i:561488 original size:2 final size:2
Alignment explanation
Indices: 561481--561555 Score: 141
Period size: 2 Copynumber: 37.5 Consensus size: 2
561471 AGATATTATA
*
561481 TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
561523 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
561556 GTGTGTGTGT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:565170 original size:2 final size:2
Alignment explanation
Indices: 565163--565207 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
565153 TCTTATTTCT
565163 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
565205 GA G
1 GA G
565208 TTTAAGAAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:575661 original size:21 final size:21
Alignment explanation
Indices: 575639--575709 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
575629 CTTAGAATAG
* * *
575639 CATAGTATTGGAATTTTATAG
1 CATAGCATTGGAATTTCATAC
* *
575660 CATAGCATTGAAATCTCATAC
1 CATAGCATTGGAATTTCATAC
575681 CATAGCATTGGAATTTCATAC
1 CATAGCATTGGAATTTCATAC
575702 CATAGCAT
1 CATAGCAT
575710 ACAATCTCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (21 bp):
CATAGCATTGGAATTTCATAC
Found at i:575983 original size:21 final size:21
Alignment explanation
Indices: 575954--576034 Score: 81
Period size: 21 Copynumber: 3.9 Consensus size: 21
575944 CATTTCAATT
575954 TCTCATAGCATAGCATACAAA
1 TCTCATAGCATAGCATACAAA
* * **
575975 TCTCGTAGCATTGCATTTAAA
1 TCTCATAGCATAGCATACAAA
* **
575996 TCTCATAGCATATCATGTAAA
1 TCTCATAGCATAGCATACAAA
* *
576017 TCGCATACCATAGCATAC
1 TCTCATAGCATAGCATAC
576035 CATTAAATTG
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (21 bp):
TCTCATAGCATAGCATACAAA
Found at i:578484 original size:21 final size:21
Alignment explanation
Indices: 578458--578530 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
578448 ACTATAGCAA
578458 AGCATAGCATTGTAATCTCAT
1 AGCATAGCATTGTAATCTCAT
* * *
578479 AGCATAGCAATGGAATCTCTT
1 AGCATAGCATTGTAATCTCAT
*
578500 ATCATAGCATTGTAAT-TACAT
1 AGCATAGCATTGTAATCT-CAT
*
578521 ACCATAGCAT
1 AGCATAGCAT
578531 AACAGTTCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 1 0.02
21 42 0.98
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.32
Consensus pattern (21 bp):
AGCATAGCATTGTAATCTCAT
Found at i:579135 original size:21 final size:21
Alignment explanation
Indices: 579115--579193 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
579105 TTACAATTTA
* *
579115 ATGCTATACTATGCGATTT-T
1 ATGCTATGCTATGAGATTTGT
*
579135 AATGATATGCTATGAGATTTGT
1 -ATGCTATGCTATGAGATTTGT
*
579157 ATGGTATGCTATGAGATTTGT
1 ATGCTATGCTATGAGATTTGT
579178 ATGCTATGCTATGAGA
1 ATGCTATGCTATGAGA
579194 AATATAAATG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
21 51 0.98
22 1 0.02
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.41
Consensus pattern (21 bp):
ATGCTATGCTATGAGATTTGT
Found at i:579470 original size:21 final size:21
Alignment explanation
Indices: 579437--579491 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
579427 ATGAGATTGT
* *
579437 ATGCTATGGTATGAGATTTCA
1 ATGCTATGCTATGAGATTCCA
*
579458 ATGTTATGCTATGAGATTCCA
1 ATGCTATGCTATGAGATTCCA
579479 ATGCTATGCTATG
1 ATGCTATGCTATG
579492 CTATGGTGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (21 bp):
ATGCTATGCTATGAGATTCCA
Found at i:581021 original size:11 final size:11
Alignment explanation
Indices: 581005--581030 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
580995 ATGACATCAG
581005 TCAATTTTTTA
1 TCAATTTTTTA
581016 TCAATTTTTTA
1 TCAATTTTTTA
581027 TCAA
1 TCAA
581031 ATGTCTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.58
Consensus pattern (11 bp):
TCAATTTTTTA
Found at i:583302 original size:435 final size:434
Alignment explanation
Indices: 582097--584456 Score: 2438
Period size: 435 Copynumber: 5.4 Consensus size: 434
582087 TTAGTCTCCT
* * * * **
582097 AAAATCCCTCATTACGTCATCAATGGGTGTGGCAATGAGTTTTA-CAAACT-GATATTGTTACGA
1 AAAATCCCTAATTACGTAATAAATGGGCGTGGCAATGAGTTTTACCTGA-TAGATATTGTTACGA
* * * * ** * * *
582160 TCCATAACTTTGTTTTTATAATATATTACAAAAT-TTTGATCGTTTTTAAGGTATGTGTAAAAGA
65 TCAACAACTTTGCTTCTATAATGCATTACAAAATCTTT-ATCGTTTTTAAGTTATCTGTAATAGA
* * * * * * *
582224 TTTTACGAGTGTCTTGGCCCATGATTTAAAGGGCCAGCCCCTTTTTCTTGAGTTCATTCAAAAGG
129 GTTTACGAGTGTCTTGGCCCCTAATTTAAGGGGCCAG-CCCTTTTTCCTGTGTTTATTCAAAAGG
* * * ** * **
582289 TCATACGGATAC-AA-ATATTTTTGTTCTTACATTTATCTAGAATTGTT-TTTTTTTTTAGATAC
193 TCTTAAGAATACTAACAT-TTTTTGTTCTTACAACTATCTAAAATTGTTGTCATTTTTTAGATAC
* * * *
582351 AAATGATTTAATATTTTAGGGGCCAGCCTACTGTAGATTCTTAATGGGGACAGACATTGGTGTTT
257 AAATGATTGAATATTTTAGGGACCAGCC--CTCTAGATCCTTAATGGGGACAGACATTGGTGTTT
* * ** * * * *
582416 TGATTAATGGAATCGATTAGAATCATCAATACAGATATTTTTTTTCTTCCACAATGCTTATCAAA
320 TGATTAATTGAATCGATTAGAATCATCAATGCA-A-ACATTTTCTCTTCTACAATGC-CAACAAA
* * * * * *
582481 TTTTGTCTCCTTTTCTAGATATATTGCGTCAAAATTAAAGTTCTTTGGCCCCTA
382 ATATGTCTCCTTCTCTAGATATATTGCGTCAAAGTTTAAGTAC-TTGGCCCCTA
* * * *
582535 AAAATCCCTAATTACGTAATAAATGTGTGTGGAAATGA-TTTTACCTGATATATATTGTTACGAT
1 AAAATCCCTAATTACGTAATAAATGGGCGTGGCAATGAGTTTTACCTGATAGATATTGTTACGAT
* * * * *
582599 CAACAACTTTGCTACATGTAATATAATGCATAACAAAATCTTGATTGATTTTAAGTTATCTGTAA
66 CAACAACTTTG---C-T-T-CTATAATGCATTACAAAATCTTTATCGTTTTTAAGTTATCTGTAA
** * *
582664 TATTGTTTACGAGTGTCTTGGCCCCTAATTTAAGGGGCCAGCCCTTTTTTCT-TGATTTCATTCG
125 TAGAGTTTACGAGTGTCTTGGCCCCTAATTTAAGGGGCCAGCCCTTTTTCCTGTG-TTT-ATTCA
* * * *
582728 AAAGGTCTTAAGATTACTAACAATTTTTGTTCTTACACAC-ATCTAAAATTTTTGTTCATTTTTG
188 AAAGGTCTTAAGAATACTAACATTTTTTGTTCTTACA-ACTATCTAAAATTGTTG-TCATTTTTT
* * * * * *
582792 AGATACAAATGATTGAATATTTTAGGGGCCAGCCCACTAGATCCTTCATGGAGACAGACTTTAGT
251 AGATACAAATGATTGAATATTTTAGGGACCAGCCCTCTAGATCCTTAATGGGGACAGACATTGGT
* * * *
582857 GTTCTGATTAATTGAATCGATTAGAATCATCGATGCAAACATTTTCTTTTCTACATTGCCAAGCA
316 GTTTTGATTAATTGAATCGATTAGAATCATCAATGCAAACATTTTCTCTTCTACAATGCCAA-CA
* * *
582922 AAATATGTCTCCTTCTCAAGATATATTCCGTCAAAGTTTAAGTACTTCGCCCCTA
380 AAATATGTCTCCTTCTCTAGATATATTGCGTCAAAGTTTAAGTACTTGGCCCCTA
582977 AAAATCCCTAATTACGTAATAAATGGGCGTGGCAATGA-TTTTACCTGATAGATATTGTTACGAT
1 AAAATCCCTAATTACGTAATAAATGGGCGTGGCAATGAGTTTTACCTGATAGATATTGTTACGAT
** * * * * *
583041 CAACATGTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAATTATGTGTAAGACACT
66 CAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTTATCTGTAATAGAGT
* * *
583106 TTACGAGTATCTTGGCCCCTAATTTAAGGGGCCAGCCCTTTTTCCTGTGTTTATTCAAAAGTTCC
131 TTACGAGTGTCTTGGCCCCTAATTTAAGGGGCCAGCCCTTTTTCCTGTGTTTATTCAAAAGGTCT
* * * * *
583171 TACGAATACTAATATTTTTTGTTCTTACAACTATTTCAGATTGTTGATCATTTTTTAGATACAAA
196 TAAGAATACTAACATTTTTTGTTCTTACAACTATCTAAAATTGTTG-TCATTTTTTAGATACAAA
**
583236 TGATTGAATATTTTAGGGACCAGATCTCTAGATCCTTAATGGGGACAGACATTGGTGTTTTGATT
260 TGATTGAATATTTTAGGGACCAGCCCTCTAGATCCTTAATGGGGACAGACATTGGTGTTTTGATT
* * * * * *
583301 AATGGAATCGATTAGAATCATCAAAGCAAACATTATCTCTTCTACAAGGTCAAACAAAATATATC
325 AATTGAATCGATTAGAATCATCAATGCAAACATTTTCTCTTCTACAATG-CCAACAAAATATGTC
* * *
583366 TCCTTCTCTAGATATATTGCGTCAAAGTTGAACTATTTTGGCCCCTA
389 TCCTTCTCTAGATATATTGCGTCAAAGTTTAAGTA-CTTGGCCCCTA
* * *
583413 AAAATCCCTTATTACGTAATAAATGGGCGTGGCAATGAGTTTTGA-TTGATATATATTGTTACGA
1 AAAATCCCTAATTACGTAATAAATGGGCGTGGCAATGAGTTTT-ACCTGATAGATATTGTTACGA
* * * * *
583477 TCAATAACTTTGCTTCTATAATACATTATTAAAA-CTTTATCGTTTTTAAGTTATTTGTATTAGA
65 TCAACAACTTTGCTTCTATAATGCATTA-CAAAATCTTTATCGTTTTTAAGTTATCTGTAATAGA
* * * * * ** * *
583541 GTGTACAAGTGT-TCTGACCCTTAA-TAAAGGGGCCAGCCCCCTTTCATGAT-TTTATTTAAAAG
129 GTTTACGAGTGTCT-TGGCCCCTAATTTAAGGGGCCAGCCCTTTTTCCTG-TGTTTATTCAAAAG
* * * *
583603 GTCTTAAGATTACTAACATTTTTT-TTCTTACACCCATCTAAAATTGTTGTTCATTTTTGAGATA
192 GTCTTAAGAATACTAACATTTTTTGTTCTTACAACTATCTAAAATTGTTG-TCATTTTTTAGATA
* * * *
583667 CAAATGATTGAATATTTTA-GGAGCCAGCCCTCTAGATCCTTCATGTGGACAGACACTGATGTTT
256 CAAATGATTGAATATTTTAGGGA-CCAGCCCTCTAGATCCTTAATGGGGACAGACATTGGTGTTT
** * * * * * *
583731 TGATTAA-TGGGTCGATCAGAATCATCAATACAGATATTGTCTCTTCTACAATGCTTAACAAAAT
320 TGATTAATTGAATCGATTAGAATCATCAATGCAAACATTTTCTCTTCTACAATGC-CAACAAAAT
*
583795 ATGTTTCCTTCTCTAGATATATTGCGTCAAAGTTTAAGTACTCTGGCCCCTA
384 ATGTCTCCTTCTCTAGATATATTGCGTCAAAGTTTAAGTACT-TGGCCCCTA
* * * * * * *
583847 AAAATCTCTTATTACGTAATAAATAGGCTTCGTAATGA-TTTTACCTGATAGATATTGCTACGAA
1 AAAATCCCTAATTACGTAATAAATGGGCGTGGCAATGAGTTTTACCTGATAGATATTGTTACG-A
* * *
583911 T-TACAACTTTAG-TTC-ATAATGAATTACAAAATCTTTATCATTTTTAAGTTATCTGTAATAGA
65 TCAACAACTTT-GCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTTATCTGTAATAGA
* * ** ** *
583973 GTTTACGAGTATCTTGGCCCCAAATAAAAGGGGTAAGTCCCTTTTT-CTG-GATTTCTT-AGATA
129 GTTTACGAGTGTCTTGGCCCCTAATTTAAGGGGCCAG-CCCTTTTTCCTGTG-TTTATTCA-A-A
* * * *
584035 ATGTATTAAGAATACTAACATTTTTTGTTCTTACACCAATCTAAAATTGTTGTACATTTTTTGAG
190 AGGTCTTAAGAATACTAACATTTTTTGTTCTTACAACTATCTAAAATTGTTGT-CATTTTTT-AG
* * *
584100 ATATAAATGATTGAATATTTTAGGGTCCAGCCCTCTAGATTCTTAATGGGGACAGACATTGGTGT
253 ATACAAATGATTGAATATTTTAGGGACCAGCCCTCTAGATCCTTAATGGGGACAGACATTGGTGT
* * * *
584165 TTTGATT-AGTGAAAACGATCAGAATCATCAATGCAAACATTTT-TCTTCTACATTGCCTAACAA
318 TTTGATTAATTG-AATCGATTAGAATCATCAATGCAAACATTTTCTCTTCTACAATGCC-AACAA
* *
584228 AAT-TGTCTCCTTCTTTGGATATATTGCGTCAAAGTTTAAGTACTTTGGCCCCTA
381 AATATGTCTCCTTCTCTAGATATATTGCGTCAAAGTTTAAGTAC-TTGGCCCCTA
** ** * * ** *
584282 AAAATCTTTAATTACGTAATAAATTAGCGTGGTAATGATTTTTGTCTGATAGATATTGTTAGGAT
1 AAAATCCCTAATTACGTAATAAATGGGCGTGGCAATGAGTTTTACCTGATAGATATTGTTACGAT
* * * * *
584347 CAACAACTTTGCTTCTATAATGCATTACAAAACCTTTATCATGTTCAAGTTATTTGTAATAGAGT
66 CAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTTATCTGTAATAGAGT
* * * *
584412 TTACGAGTGTCGTGGCCCTTAA-ATATAGGCGCCAGCCCATTTTTC
131 TTACGAGTGTCTTGGCCCCTAATTTA-AGGGGCCAGCCC-TTTTTC
584457 TTGATTGTAT
Statistics
Matches: 1603, Mismatches: 264, Indels: 110
0.81 0.13 0.06
Matches are distributed among these distances:
431 4 0.00
432 54 0.03
433 49 0.03
434 161 0.10
435 408 0.25
436 310 0.19
437 195 0.12
438 63 0.04
439 1 0.00
442 81 0.05
443 66 0.04
444 85 0.05
445 86 0.05
446 1 0.00
447 39 0.02
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (434 bp):
AAAATCCCTAATTACGTAATAAATGGGCGTGGCAATGAGTTTTACCTGATAGATATTGTTACGAT
CAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTTATCTGTAATAGAGT
TTACGAGTGTCTTGGCCCCTAATTTAAGGGGCCAGCCCTTTTTCCTGTGTTTATTCAAAAGGTCT
TAAGAATACTAACATTTTTTGTTCTTACAACTATCTAAAATTGTTGTCATTTTTTAGATACAAAT
GATTGAATATTTTAGGGACCAGCCCTCTAGATCCTTAATGGGGACAGACATTGGTGTTTTGATTA
ATTGAATCGATTAGAATCATCAATGCAAACATTTTCTCTTCTACAATGCCAACAAAATATGTCTC
CTTCTCTAGATATATTGCGTCAAAGTTTAAGTACTTGGCCCCTA
Found at i:584985 original size:53 final size:53
Alignment explanation
Indices: 584823--584987 Score: 285
Period size: 53 Copynumber: 3.1 Consensus size: 53
584813 GTGGAAAAAA
584823 TAATAAGAAACAGTACGAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCT
1 TAATAAGAAACAGTACGAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCT
* * * *
584876 TAACAAGAAACACTACGAACACAATAAGGTCTTTCGTTGGAAACGGAAGACCT
1 TAATAAGAAACAGTACGAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCT
*
584929 TAATAAGAAACAGTACGAAAACAATAAGGTCTTCCGTTGGAAACGAAAGACCT
1 TAATAAGAAACAGTACGAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCT
584982 TAATAA
1 TAATAA
584988 CTGGACACGA
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 103 1.00
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (53 bp):
TAATAAGAAACAGTACGAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCT
Found at i:585993 original size:177 final size:182
Alignment explanation
Indices: 585646--586360 Score: 755
Period size: 177 Copynumber: 4.0 Consensus size: 182
585636 GGCTGCCAAA
* * *
585646 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAA-TTGTTCTTTTGC
1 AGGGCACCCTCATTGTACGGATAACTTCTCCTACAGTTTTCAAGATAAGAAAGTTGTTCTTTTGC
* ** * * *
585710 AGATTAATTGGGCATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTTATTATTTATTT
66 AGATCAATTGTACATATATCAGAGATGTGCATATTGCTAGGATTTTGATTTCTGATAATTTA--T
* * * *
585775 AAAAAAAAAATACCAGCTCTTGAACTT--T--TTTTGGGCAAAATATTGCATAT
129 ATAAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTGACAAAATATTGCATAT
* * *
585825 A-GG-ACCCGCATTGTACGGATAACTTCTCCTACCGTATTCAAGA-AAGAAAGTTGTTCTTTTGC
1 AGGGCACCCTCATTGTACGGATAACTTCTCCTACAGTTTTCAAGATAAGAAAGTTGTTCTTTTGC
* * * * *
585887 AGATCAATTATACCTATATTAGAGATGTGTATATTGCTAGGATTTTGATTTCTGAT-AGTTA-AT
66 AGATCAATTGTACATATATCAGAGATGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATAT
* * * *
585950 GAAAACAATACCAGCTTTTGACCTTAGTCATTTTTGACAAAATATTGCATAA
131 AAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTGACAAAATATTGCATAT
* *** *
586002 AGGGCACCCTTATTGTACGGATAACAGATCCTACAGTTTTCAAGATAAG-AAG-T-TT-TTTTGA
1 AGGGCACCCTCATTGTACGGATAACTTCTCCTACAGTTTTCAAGATAAGAAAGTTGTTCTTTTGC
* * * *
586063 AGATCAATTGTACATACATCAGAGGTGTGCATATTGCTTA-GATTTTGACTTCTGGTAATTTATA
66 AGATCAATTGTACATATATCAGAGATGTGCATATTGC-TAGGATTTTGATTTCTGATAATTTATA
* * *
586127 T-AAAAAGATACCGGCTTTTGAACTTAGTCTTTTTTGACAAAATATTGCATAT
130 TAAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTGACAAAATATTGCATAT
* * * * * * *
586179 AGGGTATCCTCATTGTACGGATAACTTCTCCAACAGTTTTCAATAT-AGGACGTTGTTCTTTTGT
1 AGGGCACCCTCATTGTACGGATAACTTCTCCTACAGTTTTCAAGATAAGAAAGTTGTTCTTTTGC
* * * * * **
586243 TGATAAATTGTACATATATTAGAGATATGCAAATTGCTAGGATTTTTTTTTTCTGATAATTTAT-
66 AGATCAATTGTACATATATCAGAGATGTGCATATTGCTAGGA-TTTTGATTTCTGATAATTTATA
* ** *
586307 TAAAAAAAAATACCGGCTTTTGAACTCGGTCATTTTTTGGCAAAATATTGCATA
130 T-AAAAAAAATACCAGCTTTTGAACTTAGTCA-TTTTTGACAAAATATTGCATA
586361 GGGTACTCCA
Statistics
Matches: 444, Mismatches: 72, Indels: 36
0.80 0.13 0.07
Matches are distributed among these distances:
173 22 0.05
175 1 0.00
176 61 0.14
177 208 0.47
178 8 0.02
179 41 0.09
180 41 0.09
181 17 0.04
182 25 0.06
183 20 0.05
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (182 bp):
AGGGCACCCTCATTGTACGGATAACTTCTCCTACAGTTTTCAAGATAAGAAAGTTGTTCTTTTGC
AGATCAATTGTACATATATCAGAGATGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATAT
AAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTGACAAAATATTGCATAT
Found at i:596581 original size:21 final size:21
Alignment explanation
Indices: 596557--596610 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
596547 ATCTTAATGA
596557 TATGCTATGAGATTTGTATGC
1 TATGCTATGAGATTTGTATGC
596578 TATGCTATGAGATTTGTATGC
1 TATGCTATGAGATTTGTATGC
596599 TATGCTATGAGA
1 TATGCTATGAGA
596611 AATTGAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (21 bp):
TATGCTATGAGATTTGTATGC
Found at i:596652 original size:10 final size:10
Alignment explanation
Indices: 596634--596667 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
596624 GGCTTCATGA
*
596634 TATGGTATGG
1 TATGGTATGC
*
596644 TATGCTATGC
1 TATGGTATGC
596654 TATGGTATGC
1 TATGGTATGC
596664 TATG
1 TATG
596668 AGATTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.09, G:0.29, T:0.41
Consensus pattern (10 bp):
TATGGTATGC
Found at i:596657 original size:15 final size:15
Alignment explanation
Indices: 596634--596667 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
596624 GGCTTCATGA
*
596634 TATGGTATGGTATGC
1 TATGCTATGGTATGC
596649 TATGCTATGGTATGC
1 TATGCTATGGTATGC
596664 TATG
1 TATG
596668 AGATTTGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.09, G:0.29, T:0.41
Consensus pattern (15 bp):
TATGCTATGGTATGC
Found at i:596833 original size:10 final size:10
Alignment explanation
Indices: 596815--596848 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
596805 AAGAATGTTG
*
596815 TATGCTATGC
1 TATGGTATGC
596825 TATGGTATGC
1 TATGGTATGC
*
596835 TATGGTATGA
1 TATGGTATGC
596845 TATG
1 TATG
596849 ACGAATGCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (10 bp):
TATGGTATGC
Found at i:596834 original size:15 final size:15
Alignment explanation
Indices: 596814--596848 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
596804 AAAGAATGTT
596814 GTATGCTATGCTATG
1 GTATGCTATGCTATG
*
596829 GTATGCTATGGTATG
1 GTATGCTATGCTATG
*
596844 ATATG
1 GTATG
596849 ACGAATGCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.09, G:0.29, T:0.40
Consensus pattern (15 bp):
GTATGCTATGCTATG
Found at i:596899 original size:21 final size:20
Alignment explanation
Indices: 596861--596948 Score: 113
Period size: 21 Copynumber: 4.2 Consensus size: 20
596851 GAATGCGATT
**
596861 CTATGAGATTGTATGCTATG
1 CTATGAGATTCAATGCTATG
*
596881 GTATGAGATTCCAATGCTATG
1 CTATGAGATT-CAATGCTATG
596902 CTATGAGAGTTCAATGCTATG
1 CTATGAGA-TTCAATGCTATG
*
596923 CTATGAGATTTCAATGCTACG
1 CTATGAGA-TTCAATGCTATG
596944 CTATG
1 CTATG
596949 CTATCGTGTA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.15
21 49 0.82
22 2 0.03
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (20 bp):
CTATGAGATTCAATGCTATG
Found at i:596919 original size:42 final size:41
Alignment explanation
Indices: 596831--596948 Score: 128
Period size: 42 Copynumber: 2.8 Consensus size: 41
596821 ATGCTATGGT
* * * * * **
596831 ATGCTATGGTATGATATGACGAATGCGATTCTATGAGATTGT
1 ATGCTATGGTATGAGAT-TCCAATGCTATGCTATGAGATTCA
596873 ATGCTATGGTATGAGATTCCAATGCTATGCTATGAGAGTTCA
1 ATGCTATGGTATGAGATTCCAATGCTATGCTATGAGA-TTCA
* * *
596915 ATGCTATGCTATGAGATTTCAATGCTACGCTATG
1 ATGCTATGGTATGAGATTCCAATGCTATGCTATG
596949 CTATCGTGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 16 0.25
42 49 0.75
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.35
Consensus pattern (41 bp):
ATGCTATGGTATGAGATTCCAATGCTATGCTATGAGATTCA
Found at i:606123 original size:11 final size:10
Alignment explanation
Indices: 606097--606122 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
606087 GTTGTTGTTG
606097 TTTTTTATTT
1 TTTTTTATTT
606107 TTTTTTATTT
1 TTTTTTATTT
606117 TTTTTT
1 TTTTTT
606123 TCAAGGGGGG
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:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:609150 original size:1 final size:1
Alignment explanation
Indices: 609144--609169 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
609134 CATTATTTAT
609144 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
609170 GGGATAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:610398 original size:2 final size:2
Alignment explanation
Indices: 610391--610424 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
610381 ACTCTTTATC
610391 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
610425 TTCATTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:613392 original size:2 final size:2
Alignment explanation
Indices: 613385--613412 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
613375 TACATCGTGT
613385 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
613413 GCGAGTGACA
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):
TA
Found at i:614001 original size:1 final size:1
Alignment explanation
Indices: 613997--614081 Score: 62
Period size: 1 Copynumber: 85.0 Consensus size: 1
613987 CCCCCCCCCC
* * * * * * ** *
613997 AAAAAAAAAAAAAACAAACAAAAAAAAAACAAAACAAAACAAATAAAAAGCAAAAAAAAAATAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
614062 AAAATAAAAACAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAA
614082 CAAACAAACA
Statistics
Matches: 61, Mismatches: 23, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.86, C:0.09, G:0.01, T:0.04
Consensus pattern (1 bp):
A
Found at i:614071 original size:46 final size:47
Alignment explanation
Indices: 614001--614120 Score: 145
Period size: 46 Copynumber: 2.5 Consensus size: 47
613991 CCCCCCAAAA
* * *
614001 AAAAAAAAAACAAACAAAAAAAAAACAAAACAAAACAAATAAA-AAGC
1 AAAAAAAAAATAAACAAAATAAAAACAAAACAAAACAAACAAACAA-C
614048 AAAAAAAAAATAAA-AAAATAAAAACAAAACAAAACAAACAAACAAC
1 AAAAAAAAAATAAACAAAATAAAAACAAAACAAAACAAACAAACAAC
*
614094 AAGAAAAACAAATGTAAATAAAATAAA
1 AA-AAAAA-AAA--TAAACAAAATAAA
614121 TATATACTGA
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
46 29 0.45
47 20 0.31
48 3 0.05
50 4 0.06
51 8 0.12
ACGTcount: A:0.81, C:0.11, G:0.03, T:0.06
Consensus pattern (47 bp):
AAAAAAAAAATAAACAAAATAAAAACAAAACAAAACAAACAAACAAC
Found at i:614077 original size:51 final size:50
Alignment explanation
Indices: 613996--614120 Score: 146
Period size: 51 Copynumber: 2.5 Consensus size: 50
613986 CCCCCCCCCC
* *
613996 CAAAAAAAAAA-AAAACAAACAAAAAAAAAACAAAACAAAACAAATAAAAAG
1 CAAAAAAAAAATAAAA-AAATAAAAAAAAAACAAAAC-AAACAAACAAAAAG
* *
614047 CAAAAAAAAAATAAAAAAATAAAAACAAAACAAAACAAACAAACAACAAG
1 CAAAAAAAAAATAAAAAAATAAAAAAAAAACAAAACAAACAAACAAAAAG
**
614097 -AAAAACAAATGTAAATAAAATAAA
1 CAAAAA-AAAAATAAA-AAAATAAA
614121 TATATACTGA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
49 5 0.08
50 19 0.29
51 37 0.57
52 4 0.06
ACGTcount: A:0.81, C:0.11, G:0.02, T:0.06
Consensus pattern (50 bp):
CAAAAAAAAAATAAAAAAATAAAAAAAAAACAAAACAAACAAACAAAAAG
Found at i:615233 original size:21 final size:22
Alignment explanation
Indices: 615118--615241 Score: 73
Period size: 21 Copynumber: 5.9 Consensus size: 22
615108 CGTGCGATTT
* *
615118 TCGTATCGTATG-ACAAGCGTA
1 TCGTATCGTATGAAGAAACGTA
* ** *
615139 TCGTAACGTGCG-AGAAACGCA
1 TCGTATCGTATGAAGAAACGTA
* * * *
615160 CCGTACCGTAT-AAGAAGCCTA
1 TCGTATCGTATGAAGAAACGTA
* *
615181 TCG-ATCCGTACG-AGAAATGTA
1 TCGTAT-CGTATGAAGAAACGTA
615202 TCGTATCGTAT-AAGAAACGTA
1 TCGTATCGTATGAAGAAACGTA
*
615223 TTGTATCGTATGAA-AAACG
1 TCGTATCGTATGAAGAAACG
615242 CACCGATTAT
Statistics
Matches: 75, Mismatches: 22, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
20 1 0.01
21 70 0.93
22 4 0.05
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (22 bp):
TCGTATCGTATGAAGAAACGTA
Found at i:616684 original size:16 final size:16
Alignment explanation
Indices: 616658--616706 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
616648 AAGGACCTCA
616658 AGAGGTATTCATAATG
1 AGAGGTATTCATAATG
* *
616674 AGCGTTATTCATAATG
1 AGAGGTATTCATAATG
616690 AGAGGTATTCATAATG
1 AGAGGTATTCATAATG
616706 A
1 A
616707 CCCCTACAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (16 bp):
AGAGGTATTCATAATG
Found at i:618353 original size:21 final size:20
Alignment explanation
Indices: 618316--618355 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
618306 ATTAATAATT
* *
618316 TTGATATTAATTTAAATATG
1 TTGATATTAAGTAAAATATG
618336 TTGATAATTAAGTAAAATAT
1 TTGAT-ATTAAGTAAAATAT
618356 AATTTTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (20 bp):
TTGATATTAAGTAAAATATG
Found at i:618790 original size:2 final size:2
Alignment explanation
Indices: 618783--618826 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
618773 AAATAATCTT
618783 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
618825 AG
1 AG
618827 NAATTATTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:619730 original size:21 final size:20
Alignment explanation
Indices: 619681--619765 Score: 89
Period size: 21 Copynumber: 4.1 Consensus size: 20
619671 AAGCGTATAG
*
619681 AAAACGTATCGTATCGTACA
1 AAAACGTATCGTATCGTAGA
* *
619701 AGAAGCGTATCGTATTGTATGA
1 A-AAACGTATCGTATCGTA-GA
* *
619723 AAAACGTACCGTACCGTATGA
1 AAAACGTATCGTATCGTA-GA
*
619744 TAAACGTATCGTATCGTAGA
1 AAAACGTATCGTATCGTAGA
619764 AA
1 AA
619766 CCATATAGCG
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
20 4 0.08
21 46 0.88
22 2 0.04
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (20 bp):
AAAACGTATCGTATCGTAGA
Found at i:624211 original size:1 final size:1
Alignment explanation
Indices: 624207--624279 Score: 110
Period size: 1 Copynumber: 73.0 Consensus size: 1
624197 TTCCTTGTTG
* * *
624207 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTGTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
624272 TGTTTTTT
1 TTTTTTTT
624280 ACTTCAAGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.00, C:0.01, G:0.04, T:0.95
Consensus pattern (1 bp):
T
Found at i:631778 original size:2 final size:2
Alignment explanation
Indices: 631771--631795 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
631761 AAACACGGTA
631771 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
631796 NNNNNNNNNN
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:644539 original size:15 final size:13
Alignment explanation
Indices: 644511--644555 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
644501 TGTATTTTTC
644511 TTTTTTTT-TTTG
1 TTTTTTTTCTTTG
*
644523 TTTTTTGTCTGTTTG
1 TTTTTT-T-TCTTTG
644538 TTTTTTTTCTTTG
1 TTTTTTTTCTTTG
644551 TTTTT
1 TTTTT
644556 GCTTCTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 6 0.21
13 11 0.38
14 2 0.07
15 10 0.34
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.84
Consensus pattern (13 bp):
TTTTTTTTCTTTG
Found at i:646308 original size:3 final size:3
Alignment explanation
Indices: 646300--646355 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
646290 TGTGTATATG
646300 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
646348 TCA TCA TC
1 TCA TCA TC
646356 TNNNNNNNNN
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:660700 original size:6 final size:6
Alignment explanation
Indices: 660689--660732 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
660679 GGCATTGATA
660689 TGTTTT TGTTTTT TGTTTT TGTTTT TGTTTTT TGTTTT T-TTTT T
1 TGTTTT TG-TTTT TGTTTT TGTTTT TG-TTTT TGTTTT TGTTTT T
660733 TTTGGGGGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.14
6 19 0.53
7 12 0.33
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TGTTTT
Found at i:660703 original size:7 final size:7
Alignment explanation
Indices: 660691--660736 Score: 69
Period size: 7 Copynumber: 6.9 Consensus size: 7
660681 CATTGATATG
660691 TTTTTGT
1 TTTTTGT
660698 TTTTTG-
1 TTTTTGT
660704 TTTTTG-
1 TTTTTGT
660710 TTTTTGT
1 TTTTTGT
660717 TTTTTGT
1 TTTTTGT
*
660724 TTTTTTT
1 TTTTTGT
660731 TTTTTG
1 TTTTTG
660737 GGGGGGGGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 12 0.33
7 24 0.67
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (7 bp):
TTTTTGT
Found at i:660733 original size:19 final size:19
Alignment explanation
Indices: 660689--660732 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
660679 GGCATTGATA
660689 TGTTTTTGTTTTTTGTTTT
1 TGTTTTTGTTTTTTGTTTT
660708 TGTTTTTGTTTTTTGTTTT
1 TGTTTTTGTTTTTTGTTTT
660727 T-TTTTT
1 TGTTTTT
660733 TTTGGGGGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (19 bp):
TGTTTTTGTTTTTTGTTTT
Found at i:660734 original size:13 final size:13
Alignment explanation
Indices: 660691--660734 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
660681 CATTGATATG
*
660691 TTTTTGTTTTTTG
1 TTTTTGTTTTTTT
*
660704 TTTTTGTTTTTGT
1 TTTTTGTTTTTTT
660717 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
660730 TTTTT
1 TTTTT
660735 TGGGGGGGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (13 bp):
TTTTTGTTTTTTT
Found at i:665890 original size:50 final size:50
Alignment explanation
Indices: 665815--665948 Score: 178
Period size: 50 Copynumber: 2.7 Consensus size: 50
665805 ATGTACCATC
* *
665815 TTAACGCACTTTGAAAAAAAATTTCAAAGTGGGTTAACTTAGTCCAAAAT
1 TTAACGCACTTTGAAAAAAATTTTCAAAGTGCGTTAACTTAGTCCAAAAT
* * * *
665865 TTAACGCACTTTGAAAAAAATTTTCAAAGTGCGTTGATTTGGTCCTAAAT
1 TTAACGCACTTTGAAAAAAATTTTCAAAGTGCGTTAACTTAGTCCAAAAT
* * **
665915 TTGACGCACTTTGAAATATTTTTTCAAAGTGCGT
1 TTAACGCACTTTGAAAAAAATTTTCAAAGTGCGT
665949 AATTTTTTCA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 74 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (50 bp):
TTAACGCACTTTGAAAAAAATTTTCAAAGTGCGTTAACTTAGTCCAAAAT
Found at i:665955 original size:18 final size:18
Alignment explanation
Indices: 665932--665966 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
665922 ACTTTGAAAT
665932 ATTTTTTCAAAGTGCGTA
1 ATTTTTTCAAAGTGCGTA
665950 ATTTTTTCAAAGTGCGT
1 ATTTTTTCAAAGTGCGT
665967 TGCCACACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (18 bp):
ATTTTTTCAAAGTGCGTA
Found at i:667542 original size:48 final size:48
Alignment explanation
Indices: 667471--667565 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
667461 TCAAGATTAC
667471 AGTTATAGGCATCCTCTATACAATGATTTGCGAAGATTATTTTTATAT
1 AGTTATAGGCATCCTCTATACAATGATTTGCGAAGATTATTTTTATAT
*
667519 AGTTATAGGCATCCTCTATACAATGATTTGTGAAGATTATTTTTATA
1 AGTTATAGGCATCCTCTATACAATGATTTGCGAAGATTATTTTTATA
667566 CGATACTATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.42
Consensus pattern (48 bp):
AGTTATAGGCATCCTCTATACAATGATTTGCGAAGATTATTTTTATAT
Found at i:683656 original size:12 final size:12
Alignment explanation
Indices: 683639--683722 Score: 87
Period size: 12 Copynumber: 6.7 Consensus size: 12
683629 CTTTCCTCTG
*
683639 CGTCTGTCAGTC
1 CGTCTGTCCGTC
683651 CGTCTGTCCATCCGTC
1 CGTCTGT----CCGTC
* *
683667 CGTCCGTCCGTT
1 CGTCTGTCCGTC
683679 CGTCTGTCCGTC
1 CGTCTGTCCGTC
*
683691 CGTCTGTCTGTC
1 CGTCTGTCCGTC
683703 CGTCTGTCCGTC
1 CGTCTGTCCGTC
*
683715 CGCCTGTC
1 CGTCTGTC
683723 TATCCCACTT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
12 50 0.83
16 10 0.17
ACGTcount: A:0.02, C:0.40, G:0.24, T:0.33
Consensus pattern (12 bp):
CGTCTGTCCGTC
Found at i:683670 original size:4 final size:4
Alignment explanation
Indices: 683648--683716 Score: 75
Period size: 4 Copynumber: 17.2 Consensus size: 4
683638 GCGTCTGTCA
* * * * *
683648 GTCC GTCT GTCC ATCC GTCC GTCC GTCC GTTC GTCT GTCC GTCC GTCT
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
* *
683696 GTCT GTCC GTCT GTCC GTCC G
1 GTCC GTCC GTCC GTCC GTCC G
683717 CCTGTCTATC
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.01, C:0.41, G:0.25, T:0.33
Consensus pattern (4 bp):
GTCC
Found at i:684061 original size:2 final size:2
Alignment explanation
Indices: 684054--684103 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
684044 TTCGTACGTT
684054 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
684096 AG AG AG AG
1 AG AG AG AG
684104 TTCATAGTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:706366 original size:89 final size:89
Alignment explanation
Indices: 706215--706382 Score: 302
Period size: 89 Copynumber: 1.9 Consensus size: 89
706205 CGTATCATTA
*
706215 GATTTTCCGGTGTCAACCGTGGAAAATATTCTGTAGTAGAACCTAGGAGTTGATCCGTGAATGTG
1 GATTTTCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAACCTAGGAGTTGATCCGTGAATGTG
706280 TGACTGGGGCATTAACGATTATTT
66 TGACTGGGGCATTAACGATTATTT
*
706304 GATTTTCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAACCGT-GGAGTTGATCTGTGAATGT
1 GATTTTCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAACC-TAGGAGTTGATCCGTGAATGT
706368 GTGACTGGGGCATTA
65 GTGACTGGGGCATTA
706383 TGAAAGAGCA
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
89 75 0.99
90 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.32
Consensus pattern (89 bp):
GATTTTCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAACCTAGGAGTTGATCCGTGAATGTG
TGACTGGGGCATTAACGATTATTT
Found at i:706480 original size:23 final size:23
Alignment explanation
Indices: 706453--706497 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
706443 TGGTTGAGCG
*
706453 TTATGACTTACGATTGTCACGAC
1 TTATGACTTACGATGGTCACGAC
706476 TTATGACTTACGATGGTCACGA
1 TTATGACTTACGATGGTCACGA
706498 TTTTGGTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (23 bp):
TTATGACTTACGATGGTCACGAC
Found at i:708453 original size:11 final size:11
Alignment explanation
Indices: 708436--708469 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
708426 CTACTACACC
708436 ACACGCTCGCT
1 ACACGCTCGCT
*
708447 GCACGCTCGCT
1 ACACGCTCGCT
*
708458 ACCCGCTCGCT
1 ACACGCTCGCT
708469 A
1 A
708470 AACGGTTCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.15, C:0.47, G:0.21, T:0.18
Consensus pattern (11 bp):
ACACGCTCGCT
Found at i:708494 original size:21 final size:21
Alignment explanation
Indices: 708465--708571 Score: 142
Period size: 21 Copynumber: 5.1 Consensus size: 21
708455 GCTACCCGCT
* *
708465 CGCTAAACGGTTCACACGAAA
1 CGCTGAACGGTTTACACGAAA
708486 CGCTGAACGGTTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
* * * *
708507 CGCTGCACGCTTTGCCCGAAA
1 CGCTGAACGGTTTACACGAAA
* *
708528 CGCTAAACGATTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
708549 CGCTGAACGGTTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
708570 CG
1 CG
708572 ATTCTCGCAC
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (21 bp):
CGCTGAACGGTTTACACGAAA
Found at i:710094 original size:21 final size:21
Alignment explanation
Indices: 710044--710108 Score: 103
Period size: 21 Copynumber: 3.0 Consensus size: 21
710034 CACGGTTCTC
*
710044 GCACGCTTTGCCCGAAACGATT
1 GCACGCTTTGCCCGAAACG-CT
710066 GACACGCTTTGCCCGAAACGCT
1 G-CACGCTTTGCCCGAAACGCT
710088 GCACGCTTTGCCCGAAACGCT
1 GCACGCTTTGCCCGAAACGCT
710109 AAACGGTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
21 20 0.49
22 3 0.07
23 18 0.44
ACGTcount: A:0.22, C:0.35, G:0.23, T:0.20
Consensus pattern (21 bp):
GCACGCTTTGCCCGAAACGCT
Found at i:710124 original size:21 final size:21
Alignment explanation
Indices: 710100--710190 Score: 146
Period size: 21 Copynumber: 4.3 Consensus size: 21
710090 ACGCTTTGCC
710100 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
** * *
710121 CGAAACGCTTCACGATTCACA
1 CGAAACGCTAAACGGTTTACA
710142 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
710163 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
710184 CGAAACG
1 CGAAACG
710191 TTTCTCGCAC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (21 bp):
CGAAACGCTAAACGGTTTACA
Found at i:718361 original size:31 final size:31
Alignment explanation
Indices: 718323--718773 Score: 134
Period size: 31 Copynumber: 14.5 Consensus size: 31
718313 ATAATAGAAA
718323 ACAGGGCTGTAATAGACCATCATCAGTTAAT
1 ACAGGGCTGTAATAGACCATCATCAGTTAAT
* *
718354 ACAGGGCTGTAATAGACCATCATTAGTTATT
1 ACAGGGCTGTAATAGACCATCATCAGTTAAT
* * * * *
718385 GCAGGGCTGTAACAGACAGAT-AACA--TATCT
1 ACAGGGCTGTAATAGAC-CATCATCAGTTA-AT
** *** *
718415 ACTTGTAGGTAAGTA-CCCAGTCATAACAG--AGA-
1 ACAGGGCTGTAA-TAGACCA-TCAT--CAGTTA-AT
*
718447 ACAGGGCTGTAATAGACCATCATTAGTTAAT
1 ACAGGGCTGTAATAGACCATCATCAGTTAAT
* * *
718478 ACAGGGCTGTAATACACCATCATAAGATAAT
1 ACAGGGCTGTAATAGACCATCATCAGTTAAT
* * *
718509 ACAGGGCTGTAACAGACAGAAAACAT-A-TCTACAT
1 ACAGGGCTGTAATAGAC---CATCATCAGT-TA-AT
* * * *** * **
718543 ATA--GCTAAGTACTCGGTAAT-AACAGAGAA-
1 ACAGGGCT--GTAATAGACCATCATCAGTTAAT
* *
718572 A-AAGGCTGTAATAGACCATCATCAGTAAAT
1 ACAGGGCTGTAATAGACCATCATCAGTTAAT
*
718602 ACAGGGCTGTAATAGACCATCATTAGTTAAT
1 ACAGGGCTGTAATAGACCATCATCAGTTAAT
* * * * *
718633 GCAGGGCTGTAACAGACAGAT-AACA--TATCT
1 ACAGGGCTGTAATAGAC-CATCATCAGTTA-AT
** *** *
718663 ACTTGTAGGTAAGTA-CCCAGTCATAACAG--AGA-
1 ACAGGGCTGTAA-TAGACCA-TCAT--CAGTTA-AT
*
718695 ACAGGGCTGTAATAGACCATCATTAGTTAAT
1 ACAGGGCTGTAATAGACCATCATCAGTTAAT
* * *
718726 ACAGGGCTGTAATACACCATCATTAGATAAT
1 ACAGGGCTGTAATAGACCATCATCAGTTAAT
*
718757 ACAGGGCTGTAACAGAC
1 ACAGGGCTGTAATAGAC
718774 AGAAAACATA
Statistics
Matches: 297, Mismatches: 85, Indels: 76
0.65 0.19 0.17
Matches are distributed among these distances:
28 8 0.03
29 17 0.06
30 26 0.09
31 198 0.67
32 27 0.09
33 9 0.03
34 12 0.04
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (31 bp):
ACAGGGCTGTAATAGACCATCATCAGTTAAT
Found at i:718475 original size:124 final size:124
Alignment explanation
Indices: 718250--718821 Score: 793
Period size: 124 Copynumber: 4.6 Consensus size: 124
718240 ATCATCTCTA
* * * * * *
718250 AGTTAATGCAGGGCTGTAACAGACAGACAGCATATCTATTAAATCGTAGTTAAGTTCTAAGTAAT
1 AGTTAATGCAGGGCTGTAACAGACAGAAAACATATCTACT---T-GTAGCTAAGTACTCAGTAAT
* * *
718315 AATAGAAAACAGGGCTGTAATAGACCATCATCAGTTAATACAGGGCTGTAATAGACCATCATT
62 AACAGAGAACAGGGCTGTAATAGACCATCATCAGTTAATACAGGGCTGTAATACACCATCATT
* * * * *
718378 AGTTATTGCAGGGCTGTAACAGACAGATAACATATCTACTTGTAGGTAAGTACCCAGTCATAACA
1 AGTTAATGCAGGGCTGTAACAGACAGAAAACATATCTACTTGTAGCTAAGTACTCAGTAATAACA
* *
718443 GAGAACAGGGCTGTAATAGACCATCATTAGTTAATACAGGGCTGTAATACACCATCATA
66 GAGAACAGGGCTGTAATAGACCATCATCAGTTAATACAGGGCTGTAATACACCATCATT
* * * * *
718502 AGATAATACAGGGCTGTAACAGACAGAAAACATATCTACATATAGCTAAGTACTCGGTAATAACA
1 AGTTAATGCAGGGCTGTAACAGACAGAAAACATATCTACTTGTAGCTAAGTACTCAGTAATAACA
* * * *
718567 GAGAAAAAGGCTGTAATAGACCATCATCAGTAAATACAGGGCTGTAATAGACCATCATT
66 GAGAACAGGGCTGTAATAGACCATCATCAGTTAATACAGGGCTGTAATACACCATCATT
* * * *
718626 AGTTAATGCAGGGCTGTAACAGACAGATAACATATCTACTTGTAGGTAAGTACCCAGTCATAACA
1 AGTTAATGCAGGGCTGTAACAGACAGAAAACATATCTACTTGTAGCTAAGTACTCAGTAATAACA
*
718691 GAGAACAGGGCTGTAATAGACCATCATTAGTTAATACAGGGCTGTAATACACCATCATT
66 GAGAACAGGGCTGTAATAGACCATCATCAGTTAATACAGGGCTGTAATACACCATCATT
* * * * *
718750 AGATAATACAGGGCTGTAACAGACAGAAAACATATCTACATATAGCTAAGTACTCGGTAATAACA
1 AGTTAATGCAGGGCTGTAACAGACAGAAAACATATCTACTTGTAGCTAAGTACTCAGTAATAACA
718815 GAGAACA
66 GAGAACA
718822 AGAGGCCCAT
Statistics
Matches: 391, Mismatches: 53, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
124 354 0.91
125 1 0.00
128 36 0.09
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.24
Consensus pattern (124 bp):
AGTTAATGCAGGGCTGTAACAGACAGAAAACATATCTACTTGTAGCTAAGTACTCAGTAATAACA
GAGAACAGGGCTGTAATAGACCATCATCAGTTAATACAGGGCTGTAATACACCATCATT
Found at i:718700 original size:248 final size:248
Alignment explanation
Indices: 718327--718819 Score: 959
Period size: 248 Copynumber: 2.0 Consensus size: 248
718317 TAGAAAACAG
* *
718327 GGCTGTAATAGACCATCATCAGTTAATACAGGGCTGTAATAGACCATCATTAGTTATTGCAGGGC
1 GGCTGTAATAGACCATCATCAGTAAATACAGGGCTGTAATAGACCATCATTAGTTAATGCAGGGC
718392 TGTAACAGACAGATAACATATCTACTTGTAGGTAAGTACCCAGTCATAACAGAGAACAGGGCTGT
66 TGTAACAGACAGATAACATATCTACTTGTAGGTAAGTACCCAGTCATAACAGAGAACAGGGCTGT
718457 AATAGACCATCATTAGTTAATACAGGGCTGTAATACACCATCATAAGATAATACAGGGCTGTAAC
131 AATAGACCATCATTAGTTAATACAGGGCTGTAATACACCATCATAAGATAATACAGGGCTGTAAC
718522 AGACAGAAAACATATCTACATATAGCTAAGTACTCGGTAATAACAGAGAAAAA
196 AGACAGAAAACATATCTACATATAGCTAAGTACTCGGTAATAACAGAGAAAAA
718575 GGCTGTAATAGACCATCATCAGTAAATACAGGGCTGTAATAGACCATCATTAGTTAATGCAGGGC
1 GGCTGTAATAGACCATCATCAGTAAATACAGGGCTGTAATAGACCATCATTAGTTAATGCAGGGC
718640 TGTAACAGACAGATAACATATCTACTTGTAGGTAAGTACCCAGTCATAACAGAGAACAGGGCTGT
66 TGTAACAGACAGATAACATATCTACTTGTAGGTAAGTACCCAGTCATAACAGAGAACAGGGCTGT
*
718705 AATAGACCATCATTAGTTAATACAGGGCTGTAATACACCATCATTAGATAATACAGGGCTGTAAC
131 AATAGACCATCATTAGTTAATACAGGGCTGTAATACACCATCATAAGATAATACAGGGCTGTAAC
718770 AGACAGAAAACATATCTACATATAGCTAAGTACTCGGTAATAACAGAGAA
196 AGACAGAAAACATATCTACATATAGCTAAGTACTCGGTAATAACAGAGAA
718820 CAAGAGGCCC
Statistics
Matches: 242, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
248 242 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (248 bp):
GGCTGTAATAGACCATCATCAGTAAATACAGGGCTGTAATAGACCATCATTAGTTAATGCAGGGC
TGTAACAGACAGATAACATATCTACTTGTAGGTAAGTACCCAGTCATAACAGAGAACAGGGCTGT
AATAGACCATCATTAGTTAATACAGGGCTGTAATACACCATCATAAGATAATACAGGGCTGTAAC
AGACAGAAAACATATCTACATATAGCTAAGTACTCGGTAATAACAGAGAAAAA
Found at i:720808 original size:8 final size:8
Alignment explanation
Indices: 720797--720826 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
720787 TGAAAAGTTT
720797 ACGGACAG
1 ACGGACAG
*
720805 ACGGACGG
1 ACGGACAG
720813 ACGGACAG
1 ACGGACAG
720821 ACGGAC
1 ACGGAC
720827 GACAGACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.33, C:0.27, G:0.40, T:0.00
Consensus pattern (8 bp):
ACGGACAG
Found at i:720818 original size:16 final size:16
Alignment explanation
Indices: 720797--720827 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
720787 TGAAAAGTTT
720797 ACGGACAGACGGACGG
1 ACGGACAGACGGACGG
720813 ACGGACAGACGGACG
1 ACGGACAGACGGACG
720828 ACAGACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.26, G:0.42, T:0.00
Consensus pattern (16 bp):
ACGGACAGACGGACGG
Found at i:721017 original size:31 final size:31
Alignment explanation
Indices: 720979--721053 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
720969 CAGAGAAAAA
*
720979 GGCTGTAATAGACCATCATTAGTTAATACAG
1 GGCTGTAATAGACCATCATTAGATAATACAG
*
721010 GGCTGTAATAAACCATCATTAGATAATACAG
1 GGCTGTAATAGACCATCATTAGATAATACAG
*
721041 GGCTGTAACAGAC
1 GGCTGTAATAGAC
721054 AGAAAACATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Consensus pattern (31 bp):
GGCTGTAATAGACCATCATTAGATAATACAG
Found at i:721111 original size:124 final size:124
Alignment explanation
Indices: 720886--721194 Score: 465
Period size: 124 Copynumber: 2.5 Consensus size: 124
720876 GAGCTAAAAA
* * *
720886 GGCTATAATAGACCATCATTAGTTAATACAGGGCTGTAACAGACAGACAACATATCTTCTTGTAG
1 GGCTATAATAGACCATCATTAGTTAATACAGGGCTGTAACAGACAGACAACATATCTACATATAG
* * * *
720951 GTAAGTACCCAGTCATAACAGAGAAAAAGGCTGTAATAGACCATCATTAGTTAATACAG
66 CTAAGTACCCAGTAATAACAGAGAAAAAGGCTGTAATAGACCATCATCAGTAAATACAG
* * * *
721010 GGCTGTAATAAACCATCATTAGATAATACAGGGCTGTAACAGACAGAAAACATATCTACATATAG
1 GGCTATAATAGACCATCATTAGTTAATACAGGGCTGTAACAGACAGACAACATATCTACATATAG
* * *
721075 CTAAGTACTCGGTAATAACAGAGAAAAAGGCTGTAATAGACCATCATCAGTAAATATAG
66 CTAAGTACCCAGTAATAACAGAGAAAAAGGCTGTAATAGACCATCATCAGTAAATACAG
* * *
721134 GGCTTTTATAGACCATCATTAGTTAATACAGAGCTGTAACAGACAGACAACATATCTACAT
1 GGCTATAATAGACCATCATTAGTTAATACAGGGCTGTAACAGACAGACAACATATCTACAT
721195 TTCCGTCTTT
Statistics
Matches: 165, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
124 165 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (124 bp):
GGCTATAATAGACCATCATTAGTTAATACAGGGCTGTAACAGACAGACAACATATCTACATATAG
CTAAGTACCCAGTAATAACAGAGAAAAAGGCTGTAATAGACCATCATCAGTAAATACAG
Found at i:738191 original size:9 final size:9
Alignment explanation
Indices: 738169--738211 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
738159 ACAATTTGTC
738169 CGTTGTCTGT
1 CGTTGTC-GT
738179 CGTTGTCGT
1 CGTTGTCGT
738188 CG-T-T-GT
1 CGTTGTCGT
738194 CGTTGTCGT
1 CGTTGTCGT
738203 CGTTGTCGT
1 CGTTGTCGT
738212 TGTTAACTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
6 4 0.13
7 2 0.07
8 2 0.07
9 15 0.50
10 7 0.23
ACGTcount: A:0.00, C:0.21, G:0.33, T:0.47
Consensus pattern (9 bp):
CGTTGTCGT
Found at i:738196 original size:15 final size:15
Alignment explanation
Indices: 738176--738214 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
738166 GTCCGTTGTC
738176 TGTCGTTGTCGTCGT
1 TGTCGTTGTCGTCGT
738191 TGTCGTTGTCGTCGT
1 TGTCGTTGTCGTCGT
738206 TGTCGTTGT
1 TGTCGTTGT
738215 TAACTTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.00, C:0.18, G:0.33, T:0.49
Consensus pattern (15 bp):
TGTCGTTGTCGTCGT
Found at i:738553 original size:156 final size:159
Alignment explanation
Indices: 738384--739038 Score: 869
Period size: 167 Copynumber: 4.1 Consensus size: 159
738374 GGTATTTTTC
* *** *
738384 AAAAATCTTCTTCTCAAAAACTATTCA-GCC-GAGAAAGCTTAAACTTGTGTGGAGGCATCCTCA
1 AAAAATCTTCTTCTCAAAAACTATTCAGGCCAGA-AAAGCTCAAACTTAAATGGAAGCATCCTCA
* * * * **
738447 GGTAGTGCAGATTCACGTTTGTTCAAATCATGGTCCCC-GGGGGTAGGGAGGGGCCACAAGAGGG
65 GGAAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCAGGGGGTAGGGTGGGGCCACAATTGGG
738511 GGATCAAGTTTTACATAGGAATATATAGAG
130 GGATCAAGTTTTACATAGGAATATATAGAG
* *
738541 -AAAATCTTCTTCTCAAAAACTA-TCAGGCCAGAAAAGCTCAAACTAAAATGGGAGCATCCTCAG
1 AAAAATCTTCTTCTCAAAAACTATTCAGGCCAGAAAAGCTCAAACTTAAATGGAAGCATCCTCAG
* *
738604 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTTCCC-GGGGGTAGGGTGGGGCCACAATTGGGG
66 GAAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCAGGGGGTAGGGTGGGGCCACAATTGGGG
* *
738668 GATCAAGTTATACATAGGAATAAATGGAGAAAATCTTG
131 GATCAAGTTTTACATAGGAATATAT--AG---A----G
* *
738706 AAAAATCTTCTTCTCAAAAACTATT-AGGCCAGAAAAGCTCAAATTTAAATGGAAGCATTCTCAG
1 AAAAATCTTCTTCTCAAAAACTATTCAGGCCAGAAAAGCTCAAACTTAAATGGAAGCATCCTCAG
*
738770 GAAGTGTAGATTCAAGTTTGTTCAAATCACGGTCCCCAGGGGGTAGGGTGGGGCCACAATTGGGG
66 GAAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCAGGGGGTAGGGTGGGGCCACAATTGGGG
738835 GATCAAGTTTTACATAGGAATATATAGAG
131 GATCAAGTTTTACATAGGAATATATAGAG
* *
738864 AAAATCTTTAAGAATCTTCTTCTCAAAAACTATT-TGGCCAGAAAAGCTCAAATTTAAATGGAAG
1 ---A-----AA-AATCTTCTTCTCAAAAACTATTCAGGCCAGAAAAGCTCAAACTTAAATGGAAG
*
738928 CATTCTCAGGAAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCAGGGGGTAGGGTGGGGCCA
57 CATCCTCAGGAAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCAGGGGGTAGGGTGGGGCCA
738993 CAATTGGGGGATCAAGTTTTACATAGGAATATATAGAG
122 CAATTGGGGGATCAAGTTTTACATAGGAATATATAGAG
739031 -AAAATCTT
1 AAAAATCTT
739039 TCAAAATCTT
Statistics
Matches: 449, Mismatches: 26, Indels: 46
0.86 0.05 0.09
Matches are distributed among these distances:
155 3 0.01
156 130 0.29
157 8 0.02
158 5 0.01
161 2 0.00
162 1 0.00
165 3 0.01
166 93 0.21
167 204 0.45
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.26
Consensus pattern (159 bp):
AAAAATCTTCTTCTCAAAAACTATTCAGGCCAGAAAAGCTCAAACTTAAATGGAAGCATCCTCAG
GAAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCAGGGGGTAGGGTGGGGCCACAATTGGGG
GATCAAGTTTTACATAGGAATATATAGAG
Found at i:738884 original size:167 final size:166
Alignment explanation
Indices: 738541--739207 Score: 885
Period size: 167 Copynumber: 4.0 Consensus size: 166
738531 ATATATAGAG
* * * *
738541 AAAATCTTCTTCTCAAAAACTATCAGGCCAGAAAAGCTCAAACTAAAATGGGAGCATCCTCAGGT
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAACTTAAATGGAAGCATCCTCAGGA
* *
738606 AGTGTAGATTCAAGTTTGTTCAAATCATGGTTCCC-GGGGGTAGGGTGGGGCCACAATTGGGGGA
66 AGTGTAGATTCAAGTTTGTTCAAATCACGGTCCCCAGGGGGTAGGGTGGGGCCACAATTGGGGGA
* * * *
738670 TCAAGTTATACATAGGAATAAATGGAGAAAATCTTGA
131 TCAAGTTTTACATAGGAATATATAGAGAAAATCTT-T
* *
738707 AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTAAATGGAAGCATTCTCAGGA
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAACTTAAATGGAAGCATCCTCAGGA
738772 AGTGTAGATTCAAGTTTGTTCAAATCACGGTCCCCAGGGGGTAGGGTGGGGCCACAATTGGGGGA
66 AGTGTAGATTCAAGTTTGTTCAAATCACGGTCCCCAGGGGGTAGGGTGGGGCCACAATTGGGGGA
738837 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
131 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * *
738873 AAGAATCTTCTTCTCAAAAACTATTTGGCCAGAAAAGCTCAAATTTAAATGGAAGCATTCTCAGG
1 AA-AATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAACTTAAATGGAAGCATCCTCAGG
*
738938 AAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCAGGGGGTAGGGTGGGGCCACAATTGGGGG
65 AAGTGTAGATTCAAGTTTGTTCAAATCACGGTCCCCAGGGGGTAGGGTGGGGCCACAATTGGGGG
739003 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
130 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * * * * *** * * *
739040 CAAAATCTTCTTTTTAAAGACTATTTGGCCAGAAAAGCTTAAACTTGTGTAGAGGCATCCTCGGG
1 -AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAACTTAAATGGAAGCATCCTCAGG
* * * * * * * ***
739105 TAGTGTAAATTCAAGTTTG--CAAAATCACAGTCCCTA-GTGGTAGGGCGGGACCGTGA-TGGCG
65 AAGTGTAGATTCAAGTTTGTTC-AAATCACGGTCCCCAGGGGGTAGGGTGGGGCCACAATTGG-G
** * *
739166 GTTTGAATTTTTACATAGGAATATATAGAGAAAATCTTT
128 GGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
739205 AAA
1 AAA
739208 TATATTCTGG
Statistics
Matches: 455, Mismatches: 41, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
164 6 0.01
165 51 0.11
166 106 0.23
167 290 0.64
168 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (166 bp):
AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAACTTAAATGGAAGCATCCTCAGGA
AGTGTAGATTCAAGTTTGTTCAAATCACGGTCCCCAGGGGGTAGGGTGGGGCCACAATTGGGGGA
TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
Found at i:742957 original size:3 final size:3
Alignment explanation
Indices: 742949--743006 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
742939 TCAAAGCTTT
*
742949 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC TTC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
742997 ATT ATC ATC A
1 ATC ATC ATC A
743007 AATTTTTACA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:744653 original size:68 final size:68
Alignment explanation
Indices: 744517--744679 Score: 184
Period size: 68 Copynumber: 2.4 Consensus size: 68
744507 CAATGCAGAA
** * **
744517 AAATTCTCACAGTATTTCAGTGAGTTTAGATATTTTCAAGCTTCATTTGTGCTACTCTAATTGCA
1 AAATTCTCACAGTATTTCAGTGAGTTTAGATATTTTCAAGCTTCATGAGTGCCACTCTAATTAAA
744582 GAG
66 GAG
* ** * **
744585 AAATTCTCACAGTACTTCAGTGAGTTTAGATATTTTC-ATTTGTCATGAGTGCCACTTTCTTTAA
1 AAATTCTCACAGTATTTCAGTGAGTTTAGATATTTTCAAGCT-TCATGAGTGCCACTCTAATTAA
744649 AGAG
65 AGAG
* * *
744653 AAATTCTCAAAGTTTTTCAGTAAGTTT
1 AAATTCTCACAGTATTTCAGTGAGTTT
744680 TAAATTTTTC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
67 2 0.03
68 77 0.97
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (68 bp):
AAATTCTCACAGTATTTCAGTGAGTTTAGATATTTTCAAGCTTCATGAGTGCCACTCTAATTAAA
GAG
Found at i:745808 original size:110 final size:109
Alignment explanation
Indices: 745609--746195 Score: 518
Period size: 110 Copynumber: 5.2 Consensus size: 109
745599 GAACATGAAG
* * *
745609 GCCTGGGCCAGAAATCTGCCCACAGATCAGTAAGTGGCATATAGGTATAGAAATTGCATGGGCTC
1 GCCTGGGCCAGAAATCTGCCCACTGATCAGTAAGTAGCATATAGGTATAGAAA-TGCGTGGGC-C
* * * * *
745674 -GAAATCTGACAAAAGACCAATAAGTAGCATATCGGTATAGAAAAT
64 AGAAATCTGCCAACAGATCAGTAAGTAGCATATAGGTATAGAAAAT
* * *
745719 GCCTGGGCCAGAAGTCTACCCACTGATCAGTAAGTAGCATATAGGTATAGAGAATGCCTGGGCCA
1 GCCTGGGCCAGAAATCTGCCCACTGATCAGTAAGTAGCATATAGGTATAGA-AATGCGTGGGCCA
* *
745784 GAAATCTGCCAACAGATCATTAAGTAGCATATAGGTATACAAAA-
65 GAAATCTGCCAACAGATCAGTAAGTAGCATATAGGTATAGAAAAT
* * * ** *
745828 GCGTGGGCTCA-AAATCTGACAAAAGACCAG-AATGTAGCATATACCGGTAGGTATAGAAAATGC
1 GCCTGGGC-CAGAAATCTGCCCACTGATCAGTAA-GTAGC--ATA----TAGGTATAG-AAATGC
* ** * * * * *
745891 GTGAGCTTGAAATCTGACAAAAGACCAGTAAGAAGCATATAGGTATAGAGAAT
57 GTGGGCCAGAAATCTGCCAACAGATCAGTAAGTAGCATATAGGTATAGAAAAT
* * * *
745944 GCCTGGGCCAGAAATCTGCCCACTGATCATTAA-TAAGCATGTAGGTATAGAACATGTGTGGGCT
1 GCCTGGGCCAGAAATCTGCCCACTGATCAGTAAGT-AGCATATAGGTATAGAA-ATGCGTGGGCC
* * * *
746008 AGGAATCTGCCCACAGATCAGTAAGTGGCATGTAGGTATAGAAAAT
64 AGAAATCTGCCAACAGATCAGTAAGTAGCATATAGGTATAGAAAAT
*
746054 GAAGGCCTGGGCCAGAAATCTGCCCATTGATCAGTAAGTAGCATATATATATAGGTATAGAAATG
1 ----GCCTGGGCCAGAAATCTGCCCACTGATCAGTAAGTAGC------ATATAGGTATAGAAATG
* * * * * *
746119 TGTGGGCCAGCAGTCTGCCCACAGATCAGAAAGAAGCATATAGGTATAGAAAAT
56 CGTGGGCCAGAAATCTGCCAACAGATCAGTAAGTAGCATATAGGTATAGAAAAT
** *
746173 GTGTGGGCCAGAAATCTCCCCAC
1 GCCTGGGCCAGAAATCTGCCCAC
746196 AGACCGGTAT
Statistics
Matches: 386, Mismatches: 64, Indels: 49
0.77 0.13 0.10
Matches are distributed among these distances:
108 2 0.01
109 27 0.07
110 149 0.39
111 5 0.01
114 36 0.09
115 78 0.20
116 24 0.06
117 2 0.01
119 50 0.13
120 13 0.03
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (109 bp):
GCCTGGGCCAGAAATCTGCCCACTGATCAGTAAGTAGCATATAGGTATAGAAATGCGTGGGCCAG
AAATCTGCCAACAGATCAGTAAGTAGCATATAGGTATAGAAAAT
Found at i:745909 original size:61 final size:60
Alignment explanation
Indices: 745815--745931 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 60
745805 AAGTAGCATA
* *
745815 TAGGTATACAAAAGCGTGGGCTCAAAATCTGACAAAAGACCAG-AATGTAGCATATACCGG
1 TAGGTATACAAAAGCGTGAGCTCAAAATCTGACAAAAGACCAGTAA-GAAGCATATACCGG
* **
745875 TAGGTATAGAAAATGCGTGAGCTTGAAATCTGACAAAAGACCAGTAAGAAGCATATA
1 TAGGTATACAAAA-GCGTGAGCTCAAAATCTGACAAAAGACCAGTAAGAAGCATATA
745932 GGTATAGAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 12 0.24
61 36 0.72
62 2 0.04
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (60 bp):
TAGGTATACAAAAGCGTGAGCTCAAAATCTGACAAAAGACCAGTAAGAAGCATATACCGG
Found at i:745982 original size:55 final size:54
Alignment explanation
Indices: 745609--746198 Score: 459
Period size: 55 Copynumber: 10.5 Consensus size: 54
745599 GAACATGAAG
*
745609 GCCTGGGCCAGAAATCTGCCCACAGATCAGTAAGTGGCATATAGGTATAGAAATT
1 GCCTGGGCCAGAAATCTGCCCACAGATCAGTAAGTAGCATATAGGTATAGAAA-T
* * * * * * *
745664 GCATGGGCTC-GAAATCTGACAAAAGACCAATAAGTAGCATATCGGTATAGAAAAT
1 GCCTGGGC-CAGAAATCTGCCCACAGATCAGTAAGTAGCATATAGGTATAG-AAAT
* * *
745719 GCCTGGGCCAGAAGTCTACCCACTGATCAGTAAGTAGCATATAGGTATAGAGAAT
1 GCCTGGGCCAGAAATCTGCCCACAGATCAGTAAGTAGCATATAGGTATAGA-AAT
* * * *
745774 GCCTGGGCCAGAAATCTGCCAACAGATCATTAAGTAGCATATAGGTATACAAAA
1 GCCTGGGCCAGAAATCTGCCCACAGATCAGTAAGTAGCATATAGGTATAGAAAT
* * * * *
745828 GCGTGGGCTCA-AAATCTGACAAAAGACCAG-AATGTAGCATATACCGGTAGGTATAGAAAAT
1 GCCTGGGC-CAGAAATCTGCCCACAGATCAGTAA-GTAGC--ATA----TAGGTATAG-AAAT
* * ** * * * * *
745889 GCGTGAGCTTGAAATCTGACAAAAGACCAGTAAGAAGCATATAGGTATAGAGAAT
1 GCCTGGGCCAGAAATCTGCCCACAGATCAGTAAGTAGCATATAGGTATAGA-AAT
* * *
745944 GCCTGGGCCAGAAATCTGCCCACTGATCATTAA-TAAGCATGTAGGTATAGAACAT
1 GCCTGGGCCAGAAATCTGCCCACAGATCAGTAAGT-AGCATATAGGTATAGAA-AT
** * * * *
745999 GTGTGGGCTAGGAATCTGCCCACAGATCAGTAAGTGGCATGTAGGTATAGAAAAT
1 GCCTGGGCCAGAAATCTGCCCACAGATCAGTAAGTAGCATATAGGTATAG-AAAT
**
746054 GAAGGCCTGGGCCAGAAATCTGCCCATTGATCAGTAAGTAGCATATATATATAGGTATAGAAAT
1 ----GCCTGGGCCAGAAATCTGCCCACAGATCAGTAAGTAGC------ATATAGGTATAGAAAT
** * * * *
746118 GTGTGGGCCAGCAGTCTGCCCACAGATCAGAAAGAAGCATATAGGTATAGAAAAT
1 GCCTGGGCCAGAAATCTGCCCACAGATCAGTAAGTAGCATATAGGTATAG-AAAT
** *
746173 GTGTGGGCCAGAAATCTCCCCACAGA
1 GCCTGGGCCAGAAATCTGCCCACAGA
746199 CCGGTATAGA
Statistics
Matches: 430, Mismatches: 74, Indels: 62
0.76 0.13 0.11
Matches are distributed among these distances:
53 2 0.00
54 45 0.10
55 251 0.58
56 10 0.02
59 34 0.08
60 38 0.09
61 33 0.08
62 2 0.00
64 4 0.01
65 11 0.03
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (54 bp):
GCCTGGGCCAGAAATCTGCCCACAGATCAGTAAGTAGCATATAGGTATAGAAAT
Found at i:757660 original size:1 final size:1
Alignment explanation
Indices: 757656--757685 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
757646 TAAAAACTGT
757656 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
757686 TTCTGTCCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:770302 original size:21 final size:21
Alignment explanation
Indices: 770278--770370 Score: 134
Period size: 21 Copynumber: 4.4 Consensus size: 21
770268 AAAAAAATTC
770278 TCGCGAATAAACGCGAAACTT
1 TCGCGAATAAACGCGAAACTT
* *
770299 TCGCGAAGAAACGCGTAACTT
1 TCGCGAATAAACGCGAAACTT
**
770320 TCGCG-ATATAACGCGTGACTT
1 TCGCGAATA-AACGCGAAACTT
770341 TCGCGAATAAACGCGAAACTT
1 TCGCGAATAAACGCGAAACTT
770362 TCGCGAATA
1 TCGCGAATA
770371 CAGATTTCCC
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
20 2 0.03
21 59 0.92
22 3 0.05
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCGAATAAACGCGAAACTT
Found at i:770874 original size:6 final size:6
Alignment explanation
Indices: 770859--770935 Score: 79
Period size: 6 Copynumber: 12.5 Consensus size: 6
770849 GACCGTAGTT
*
770859 AAAACAA AAAACA AAAA-A AACAA-A AACAACA ACAACA AAAACAA AAAACA
1 AAAAC-A AAAACA AAAACA AA-AACA AA-AACA AAAACA AAAAC-A AAAACA
770909 AAAAC- AAAACA AATAACA AAAACA AAA
1 AAAACA AAAACA AA-AACA AAAACA AAA
770936 CAACGCTTAC
Statistics
Matches: 63, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
5 8 0.13
6 36 0.57
7 19 0.30
ACGTcount: A:0.82, C:0.17, G:0.00, T:0.01
Consensus pattern (6 bp):
AAAACA
Found at i:770904 original size:28 final size:26
Alignment explanation
Indices: 770861--770939 Score: 92
Period size: 28 Copynumber: 3.0 Consensus size: 26
770851 CCGTAGTTAA
770861 AACAAAAAACAAAAAAAACAAAAACAAC
1 AACAAAAAAC--AAAAAACAAAAACAAC
770889 AACAACAAAAACAAAAAACAAAAACAA-
1 AAC-A-AAAAACAAAAAACAAAAACAAC
*
770916 AACAAATAAC-AAAAAC-AAAACAAC
1 AACAAAAAACAAAAAACAAAAACAAC
770940 GCTTACTTCT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
23 7 0.15
24 6 0.13
25 5 0.11
26 1 0.02
27 3 0.06
28 18 0.38
29 1 0.02
30 6 0.13
ACGTcount: A:0.80, C:0.19, G:0.00, T:0.01
Consensus pattern (26 bp):
AACAAAAAACAAAAAACAAAAACAAC
Found at i:770909 original size:37 final size:40
Alignment explanation
Indices: 770859--770933 Score: 120
Period size: 37 Copynumber: 1.9 Consensus size: 40
770849 GACCGTAGTT
*
770859 AAAACAAAAAAC-AAAA-AAAACAAA-AACAACAACAACA
1 AAAACAAAAAACAAAAACAAAACAAATAACAAAAACAACA
770896 AAAACAAAAAACAAAAACAAAACAAATAACAAAAACAA
1 AAAACAAAAAACAAAAACAAAACAAATAACAAAAACAA
770934 AACAACGCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 12 0.35
38 4 0.12
39 8 0.24
40 10 0.29
ACGTcount: A:0.81, C:0.17, G:0.00, T:0.01
Consensus pattern (40 bp):
AAAACAAAAAACAAAAACAAAACAAATAACAAAAACAACA
Found at i:770919 original size:18 final size:18
Alignment explanation
Indices: 770859--770938 Score: 101
Period size: 18 Copynumber: 4.4 Consensus size: 18
770849 GACCGTAGTT
770859 AAAACAAAAAAC-AAAA-
1 AAAACAAAAAACAAAAAC
*
770875 AAAACAAAAACAACAACAAC
1 AAAAC-AAAA-AACAAAAAC
770895 AAAAACAAAAAACAAAAAC
1 -AAAACAAAAAACAAAAAC
*
770914 AAAACAAATAACAAAAAC
1 AAAACAAAAAACAAAAAC
770932 AAAACAA
1 AAAACAA
770939 CGCTTACTTC
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
16 5 0.09
17 4 0.07
18 27 0.48
19 11 0.20
20 4 0.07
21 5 0.09
ACGTcount: A:0.81, C:0.17, G:0.00, T:0.01
Consensus pattern (18 bp):
AAAACAAAAAACAAAAAC
Found at i:776413 original size:16 final size:16
Alignment explanation
Indices: 776392--776422 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
776382 ATCTATCGTC
776392 GGCGCCTCAAATTAGT
1 GGCGCCTCAAATTAGT
776408 GGCGCCTCAAATTAG
1 GGCGCCTCAAATTAG
776423 CATAAACACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (16 bp):
GGCGCCTCAAATTAGT
Found at i:781043 original size:14 final size:14
Alignment explanation
Indices: 781021--781054 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
781011 GGGATAAGTG
781021 TTTTGTTGTTGTTT
1 TTTTGTTGTTGTTT
*
781035 TTTTTTTGTTGTTT
1 TTTTGTTGTTGTTT
781049 TTTTGT
1 TTTTGT
781055 GGGAGGTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (14 bp):
TTTTGTTGTTGTTT
Found at i:781043 original size:17 final size:16
Alignment explanation
Indices: 781021--781052 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
781011 GGGATAAGTG
781021 TTTTGTTGTTGTTTTTT
1 TTTTGTTGTT-TTTTTT
781038 TTTTGTTGTTTTTTT
1 TTTTGTTGTTTTTTT
781053 GTGGGAGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (16 bp):
TTTTGTTGTTTTTTTT
Found at i:784479 original size:32 final size:32
Alignment explanation
Indices: 784438--784665 Score: 348
Period size: 32 Copynumber: 7.1 Consensus size: 32
784428 GGGTTGTTGA
* *
784438 GAAGCAGAGTGGATTGTAAACCATTGGTTAGG
1 GAAGCAGAGTGGATTGTAAACCCTTGGTTAGC
784470 GAAGCAGAGTGGATTGTAAACCCTTGGTTAGC
1 GAAGCAGAGTGGATTGTAAACCCTTGGTTAGC
* *
784502 GAAGCAGAGTGGATTGTAAATCCTCGGTTAGC
1 GAAGCAGAGTGGATTGTAAACCCTTGGTTAGC
*
784534 GAAGCAGAGTGGATTGTAAACCCTTGGTTTGC
1 GAAGCAGAGTGGATTGTAAACCCTTGGTTAGC
*
784566 AAAGCAGAGTGGATTGTAAACCCTTGGTTAGC
1 GAAGCAGAGTGGATTGTAAACCCTTGGTTAGC
* *
784598 AAAGCAGAGTGGATTGTAAACCCTTGGTTAGT
1 GAAGCAGAGTGGATTGTAAACCCTTGGTTAGC
* * * *
784630 GAAGCGGAGTGGATCGTAAACCTTTGGCTAGC
1 GAAGCAGAGTGGATTGTAAACCCTTGGTTAGC
784662 GAAG
1 GAAG
784666 ATGGGGTTAC
Statistics
Matches: 180, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 180 1.00
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (32 bp):
GAAGCAGAGTGGATTGTAAACCCTTGGTTAGC
Found at i:795465 original size:2 final size:2
Alignment explanation
Indices: 795458--795521 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
795448 ACGCACAAGC
795458 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
795500 AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG
795522 CAAGCGTATA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:796404 original size:2 final size:2
Alignment explanation
Indices: 796397--796457 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
796387 GAGAAAATTC
796397 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
796439 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
796458 TTTTAAAATG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:799699 original size:1 final size:1
Alignment explanation
Indices: 799693--799746 Score: 72
Period size: 1 Copynumber: 54.0 Consensus size: 1
799683 TGTGTGTGTT
* * * *
799693 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGGGGGGGNGGGTGGGGGGTGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
799747 CGGTTAGGGG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.93, T:0.06
Consensus pattern (1 bp):
G
Found at i:799717 original size:19 final size:19
Alignment explanation
Indices: 799693--799746 Score: 83
Period size: 19 Copynumber: 2.9 Consensus size: 19
799683 TGTGTGTGTT
799693 GGGGGGGGGGG-GGGGGGG
1 GGGGGGGGGGGTGGGGGGG
799711 GGGGGGGGGGGTGGGGGGG
1 GGGGGGGGGGGTGGGGGGG
* *
799730 NGGGTGGGGGGTGGGGG
1 GGGGGGGGGGGTGGGGG
799747 CGGTTAGGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
18 11 0.33
19 22 0.67
ACGTcount: A:0.00, C:0.00, G:0.93, T:0.06
Consensus pattern (19 bp):
GGGGGGGGGGGTGGGGGGG
Found at i:808841 original size:74 final size:74
Alignment explanation
Indices: 808720--808869 Score: 273
Period size: 74 Copynumber: 2.0 Consensus size: 74
808710 TTGAAAAAAA
* *
808720 ATCAGTCAAATTTACACTGTAGATTGAAACTCAGTCTCAGTGTAATAAAGACAGACTATATCACG
1 ATCAGTCAAATTTACACTGTAGATAGAAACTCAGTCTCAGTATAATAAAGACAGACTATATCACG
808785 ATCATGATG
66 ATCATGATG
*
808794 ATCAGTCTAATTTACACTGTAGATAGAAACTCAGTCTCAGTATAATAAAGACAGACTATATCACG
1 ATCAGTCAAATTTACACTGTAGATAGAAACTCAGTCTCAGTATAATAAAGACAGACTATATCACG
808859 ATCATGATG
66 ATCATGATG
808868 AT
1 AT
808870 ATTGTATTAC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (74 bp):
ATCAGTCAAATTTACACTGTAGATAGAAACTCAGTCTCAGTATAATAAAGACAGACTATATCACG
ATCATGATG
Found at i:814107 original size:31 final size:30
Alignment explanation
Indices: 814067--814128 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 30
814057 CGCACGTACA
*
814067 CAACCTGAAAAACTGAACATAGCAGAGTTC
1 CAACCTGAAAAACTGAACATAGAAGAGTTC
*
814097 CANACCTGAAAAACTGAACGTAGAAGAGTTC
1 CA-ACCTGAAAAACTGAACATAGAAGAGTTC
814128 C
1 C
814129 CCTTTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 2 0.07
31 27 0.93
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.16
Consensus pattern (30 bp):
CAACCTGAAAAACTGAACATAGAAGAGTTC
Found at i:816880 original size:19 final size:20
Alignment explanation
Indices: 816853--816987 Score: 98
Period size: 19 Copynumber: 6.5 Consensus size: 20
816843 GAATTCAGCG
*
816853 AATTTGTTATAACAGATT-A
1 AATTCGTTATAACAGATTAA
816872 AATTCGTTATAAC-GAATTCCTAA
1 AATTCGTTATAACAG-A-T--TAA
* * *
816895 AATTTGTTATAACAAATT-T
1 AATTCGTTATAACAGATTAA
*
816914 AATTCGTTATAACGGATTCAAA
1 AATTCGTTATAACAGATT--AA
*
816936 AATTCGTTATAAC-GATTTA
1 AATTCGTTATAACAGATTAA
* *
816955 AATTCGTTTTAACAAATTCAA
1 AATTCGTTATAACAGATT-AA
816976 GAATTCGTTATA
1 -AATTCGTTATA
816988 TCAAATTCAA
Statistics
Matches: 91, Mismatches: 13, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
18 1 0.01
19 41 0.45
20 5 0.05
21 5 0.05
22 25 0.27
23 14 0.15
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (20 bp):
AATTCGTTATAACAGATTAA
Found at i:816942 original size:22 final size:22
Alignment explanation
Indices: 816871--817001 Score: 112
Period size: 22 Copynumber: 6.2 Consensus size: 22
816861 ATAACAGATT
* *
816871 AAATTCGTTATAACGAATTCCTA
1 AAATTCGTTATAACAAATT-CAA
*
816894 AAATTTGTTATAACAAATT---
1 AAATTCGTTATAACAAATTCAA
* **
816913 TAATTCGTTATAACGGATTCAA
1 AAATTCGTTATAACAAATTCAA
* *
816935 AAATTCGTTATAAC-GATT--T
1 AAATTCGTTATAACAAATTCAA
*
816954 AAATTCGTTTTAACAAATTCAA
1 AAATTCGTTATAACAAATTCAA
* *
816976 GAATTCGTTATATCAAATTCAA
1 AAATTCGTTATAACAAATTCAA
816998 AAAT
1 AAAT
817002 ATTTTTTGAT
Statistics
Matches: 87, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
19 28 0.32
20 3 0.03
21 4 0.05
22 35 0.40
23 17 0.20
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.37
Consensus pattern (22 bp):
AAATTCGTTATAACAAATTCAA
Found at i:816959 original size:41 final size:42
Alignment explanation
Indices: 816838--816987 Score: 171
Period size: 41 Copynumber: 3.6 Consensus size: 42
816828 AAAATTTGAA
** *
816838 ATAACGAATTCAGCGAATTTGTTATAACAGA-TTAAATTCGTT
1 ATAACGAATTCA-AAAATTCGTTATAACAGATTTAAATTCGTT
* * *
816880 ATAACGAATTCCTAAAATTTGTTATAACAAATTT-AATTCGTT
1 ATAACGAATT-CAAAAATTCGTTATAACAGATTTAAATTCGTT
*
816922 ATAACGGATTCAAAAATTCGTTATAAC-GATTTAAATTCGTT
1 ATAACGAATTCAAAAATTCGTTATAACAGATTTAAATTCGTT
* * *
816963 TTAACAAATTCAAGAATTCGTTATA
1 ATAACGAATTCAAAAATTCGTTATA
816988 TCAAATTCAA
Statistics
Matches: 93, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
40 4 0.04
41 44 0.47
42 42 0.45
43 3 0.03
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (42 bp):
ATAACGAATTCAAAAATTCGTTATAACAGATTTAAATTCGTT
Found at i:816996 original size:63 final size:63
Alignment explanation
Indices: 816871--817001 Score: 151
Period size: 63 Copynumber: 2.1 Consensus size: 63
816861 ATAACAGATT
* * **
816871 AAATTCGTTATAACGAATTCCTAAAATTTGTTATAACAAATTTAATTCGTTATAACGGATTCAA
1 AAATTCGTTATAACGAATT-CTAAAATTCGTTATAACAAATTGAATTCGTTATAACAAATTCAA
* *
816935 AAATTCGTTATAACG-ATT-T-AAATTCGTTTTAACAAATTCAAGAATTCGTTATATCAAATTCA
1 AAATTCGTTATAACGAATTCTAAAATTCGTTATAACAAATT---GAATTCGTTATAACAAATTCA
816997 A
63 A
816998 AAAT
1 AAAT
817002 ATTTTTTGAT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
60 17 0.29
61 1 0.02
63 25 0.43
64 15 0.26
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.37
Consensus pattern (63 bp):
AAATTCGTTATAACGAATTCTAAAATTCGTTATAACAAATTGAATTCGTTATAACAAATTCAA
Found at i:817435 original size:195 final size:194
Alignment explanation
Indices: 817103--817491 Score: 769
Period size: 195 Copynumber: 2.0 Consensus size: 194
817093 AGGTTTGGAA
817103 ATAAACTATGATTTCAGGAAATATCAAATAGTAACGAAAGTTGAATAGAAAACGTAGCGAGAAAT
1 ATAAACTATGATTTCAGGAAATATCAAATAGTAACGAAAGTTGAATAGAAAACGTAGCGAGAAAT
817168 TGTATTTTATATAGTTTGAGATCTACTATTTCTTATTTTAAATTAATAATGAAGGTATAGAGGAT
66 TGTATTTTATATAGTTTGAGATCTACTATTTCTTATTTTAAATTAATAATGAAGGTATAGAGGAT
817233 TGGTATAACTACATGTACGCTTTTATCAACTAAATCAAAATTAAAAAGTATCGAAACGGAAATG
131 TGGTATAACTACATGTACGCTTTTATCAACTAAATCAAAATTAAAAAGTATCGAAACGGAAATG
817297 NATAAACTATGATTTCAGGAAATATCAAATAGTAACGAAAGTTGAATAGAAAACGTAGCGAGAAA
1 -ATAAACTATGATTTCAGGAAATATCAAATAGTAACGAAAGTTGAATAGAAAACGTAGCGAGAAA
817362 TTGTATTTTATATAGTTTGAGATCTACTATTTCTTATTTTAAATTAATAATGAAGGTATAGAGGA
65 TTGTATTTTATATAGTTTGAGATCTACTATTTCTTATTTTAAATTAATAATGAAGGTATAGAGGA
817427 TTGGTATAACTACATGTACGCTTTTATCAACTAAATCAAAATTAAAAAGTATCGAAACGGAAATG
130 TTGGTATAACTACATGTACGCTTTTATCAACTAAATCAAAATTAAAAAGTATCGAAACGGAAATG
817492 TAAGTGCTTT
Statistics
Matches: 194, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
195 194 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.32
Consensus pattern (194 bp):
ATAAACTATGATTTCAGGAAATATCAAATAGTAACGAAAGTTGAATAGAAAACGTAGCGAGAAAT
TGTATTTTATATAGTTTGAGATCTACTATTTCTTATTTTAAATTAATAATGAAGGTATAGAGGAT
TGGTATAACTACATGTACGCTTTTATCAACTAAATCAAAATTAAAAAGTATCGAAACGGAAATG
Found at i:829662 original size:12 final size:12
Alignment explanation
Indices: 829645--829670 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
829635 AAGGGGTGTG
829645 GATGATGATGAA
1 GATGATGATGAA
829657 GATGATGATGAA
1 GATGATGATGAA
829669 GA
1 GA
829671 GGAGGAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (12 bp):
GATGATGATGAA
Found at i:830194 original size:45 final size:45
Alignment explanation
Indices: 830144--830280 Score: 265
Period size: 45 Copynumber: 3.0 Consensus size: 45
830134 ATACAACTGA
*
830144 TAGTGACCAACAGAGGAAGGAAAATGAAACTAGTTCTACCAACAG
1 TAGTGACCAACAGAGGAAGGAAAATGAAACAAGTTCTACCAACAG
830189 TAGTGACCAACAGAGGAAGGAAAATGAAACAAGTTCTACCAACAG
1 TAGTGACCAACAGAGGAAGGAAAATGAAACAAGTTCTACCAACAG
830234 TAGTGACCAACAGAGGAAGGAAAATGAAACAAGTTCTACCAACAG
1 TAGTGACCAACAGAGGAAGGAAAATGAAACAAGTTCTACCAACAG
830279 TA
1 TA
830281 AGTTCGTGTT
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 91 1.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (45 bp):
TAGTGACCAACAGAGGAAGGAAAATGAAACAAGTTCTACCAACAG
Found at i:830979 original size:24 final size:24
Alignment explanation
Indices: 830960--831044 Score: 100
Period size: 24 Copynumber: 3.5 Consensus size: 24
830950 TTTGTGACAT
830960 AAAAACTGAGGAAGTCTGTGAATC
1 AAAAACTGAGGAAGTCTGTGAATC
* * *
830984 AAAAACTGTGGAGGTTTGTGAATC
1 AAAAACTGAGGAAGTCTGTGAATC
* * *
831008 AAAAACT-ATGGAGGTGTATGAATC
1 AAAAACTGA-GGAAGTCTGTGAATC
831032 AAAAACTGAGGAA
1 AAAAACTGAGGAA
831045 CTTTCCAAGT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
24 51 0.98
25 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.26, T:0.22
Consensus pattern (24 bp):
AAAAACTGAGGAAGTCTGTGAATC
Found at i:830998 original size:48 final size:48
Alignment explanation
Indices: 830946--831039 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
830936 TTATGTTACA
*
830946 GAGGTTTGTGACAT-AAAAACTGA-GGAAGTCTGTGAATCAAAAACTGTG
1 GAGGTTTGTGA-ATCAAAAACT-ATGGAAGTCTATGAATCAAAAACTGTG
* *
830994 GAGGTTTGTGAATCAAAAACTATGGAGGTGTATGAATCAAAAACTG
1 GAGGTTTGTGAATCAAAAACTATGGAAGTCTATGAATCAAAAACTG
831040 AGGAACTTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 3 0.07
48 38 0.93
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.26
Consensus pattern (48 bp):
GAGGTTTGTGAATCAAAAACTATGGAAGTCTATGAATCAAAAACTGTG
Found at i:832385 original size:22 final size:22
Alignment explanation
Indices: 832357--832407 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
832347 GGATTTACTA
** *
832357 TCTGGGTTTACTTTGTTTTTTC
1 TCTGGGTTTACTTTGGGTTTAC
832379 TCTGGGTTTACTTTGGGTTTAC
1 TCTGGGTTTACTTTGGGTTTAC
832401 TCTGGGT
1 TCTGGGT
832408 CCACTTTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.06, C:0.14, G:0.25, T:0.55
Consensus pattern (22 bp):
TCTGGGTTTACTTTGGGTTTAC
Found at i:832397 original size:11 final size:11
Alignment explanation
Indices: 832357--832407 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
832347 GGATTTACTA
832357 TCTGGGTTTAC
1 TCTGGGTTTAC
* ** *
832368 TTTGTTTTTTC
1 TCTGGGTTTAC
832379 TCTGGGTTTAC
1 TCTGGGTTTAC
*
832390 TTTGGGTTTAC
1 TCTGGGTTTAC
832401 TCTGGGT
1 TCTGGGT
832408 CCACTTTAGT
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.06, C:0.14, G:0.25, T:0.55
Consensus pattern (11 bp):
TCTGGGTTTAC
Done.