Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 21 of 259
Found at i:5667865 original size:26 final size:26
Alignment explanation
Indices: 5667829--5667938 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
5667819 TGATACAAAT
5667829 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5667855 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
5667881 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
5667907 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5667933 TGATAA
1 TGATAA
5667939 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:5682923 original size:16 final size:16
Alignment explanation
Indices: 5682902--5682933 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5682892 TCCAATTGAC
5682902 ATTACATATATAATAA
1 ATTACATATATAATAA
5682918 ATTACATATATAATAA
1 ATTACATATATAATAA
5682934 GGCTAATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTACATATATAATAA
Found at i:5683861 original size:49 final size:49
Alignment explanation
Indices: 5683805--5683903 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
5683795 TGATATTGGG
5683805 TTTAAAGGCTCGAAGTTTACTTGGTTTAATCTTTGTAATATCTCTGGTC
1 TTTAAAGGCTCGAAGTTTACTTGGTTTAATCTTTGTAATATCTCTGGTC
5683854 TTTAAAGGCTCGAAGTTTACTTGGTTTAATCTTTGTAATATCTCTGGTC
1 TTTAAAGGCTCGAAGTTTACTTGGTTTAATCTTTGTAATATCTCTGGTC
5683903 T
1 T
5683904 CATCCGATAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.45
Consensus pattern (49 bp):
TTTAAAGGCTCGAAGTTTACTTGGTTTAATCTTTGTAATATCTCTGGTC
Found at i:5685904 original size:18 final size:18
Alignment explanation
Indices: 5685877--5685969 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
5685867 TACGACCGTT
5685877 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
5685895 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
5685913 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
5685931 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
5685949 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
5685967 TAC
1 TAC
5685970 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:5694241 original size:20 final size:21
Alignment explanation
Indices: 5694218--5694261 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
5694208 AAAACATTAT
5694218 AAACACTAGAAAA-CGTCACA
1 AAACACTAGAAAATCGTCACA
*
5694238 AAACACTAGAAAATTGTCACA
1 AAACACTAGAAAATCGTCACA
5694259 AAA
1 AAA
5694262 AGCAGTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.57, C:0.20, G:0.09, T:0.14
Consensus pattern (21 bp):
AAACACTAGAAAATCGTCACA
Found at i:5694611 original size:72 final size:72
Alignment explanation
Indices: 5694472--5694614 Score: 180
Period size: 72 Copynumber: 2.0 Consensus size: 72
5694462 AAGTATCATA
** * ** * *
5694472 GATTGATTGCCTCTTTTGTGGCATTTAAAAACGTCACGGAAAATGCTATCCAAAATGTGACACAT
1 GATTGATTGCCTCTTTTGTAACATTTAAAAACATCACAAAAAATGCTATCCAAAACGTCACACAT
5694537 TGTTTGT
66 TGTTTGT
* * *
5694544 GATTGATTGCCTCTTTTTTAACATTTAAAAACATCACAAAAAATTCTATTCAAAACGTCACGA-A
1 GATTGATTGCCTCTTTTGTAACATTTAAAAACATCACAAAAAATGCTATCCAAAACGTCAC-ACA
5694608 TTGTTTG
65 TTGTTTG
5694615 ACTATTTTGT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
72 59 0.98
73 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Consensus pattern (72 bp):
GATTGATTGCCTCTTTTGTAACATTTAAAAACATCACAAAAAATGCTATCCAAAACGTCACACAT
TGTTTGT
Found at i:5695540 original size:37 final size:37
Alignment explanation
Indices: 5695479--5695625 Score: 235
Period size: 37 Copynumber: 4.0 Consensus size: 37
5695469 TACGTATGAT
* *
5695479 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
5695514 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
5695551 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
* *
5695588 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
5695625 C
1 C
5695626 GAAGCTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:5695667 original size:52 final size:52
Alignment explanation
Indices: 5695588--5695804 Score: 284
Period size: 52 Copynumber: 4.2 Consensus size: 52
5695578 TAAGTGTAGC
* * *
5695588 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTAT
* *
5695641 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTAT
*
5695693 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCAAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTAT
* * * *
5695739 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTAT
5695791 CACTTTGTCACTTG
1 CACTTT-TCACTTG
5695805 ATCAGAAGTA
Statistics
Matches: 145, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 42 0.29
49 1 0.01
52 87 0.60
53 15 0.10
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTAT
Found at i:5695719 original size:98 final size:98
Alignment explanation
Indices: 5695587--5695810 Score: 385
Period size: 98 Copynumber: 2.3 Consensus size: 98
5695577 ATAAGTGTAG
* * *
5695587 CCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACT
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACT
*
5695652 TGTCACTTGATCAGATAAGTGTAGCCGAAGCTA
66 TGTCACTTGATCAGATAAGTGTAGCCAAAGCTA
* *
5695685 TCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATTACTTATCACTTTCCACT
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACT
*
5695750 TGTCACTTGATCAGATAAGTGTAGCTAAAGCTA
66 TGTCACTTGATCAGATAAGTGTAGCCAAAGCTA
5695783 CCACTTATCACTTTGTCACTTGATCAGA
1 CCACTTATCACTTTGTCACTTGATCAGA
5695811 AGTACTCAAA
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 118 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (98 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACT
TGTCACTTGATCAGATAAGTGTAGCCAAAGCTA
Found at i:5701317 original size:22 final size:22
Alignment explanation
Indices: 5701270--5701328 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 22
5701260 TGTTTTCTTC
* *
5701270 CTTATTGCTCCATTTT-TTGAT
1 CTTATTGTTCTATTTTATTGAT
*
5701291 -TTATTGTTCTATTTTATTTAT
1 CTTATTGTTCTATTTTATTGAT
5701312 CTTATTTGTT-TATTTTA
1 CTTA-TTGTTCTATTTTA
5701329 ATTGTTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 13 0.41
21 4 0.12
22 10 0.31
23 5 0.16
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.66
Consensus pattern (22 bp):
CTTATTGTTCTATTTTATTGAT
Found at i:5701338 original size:22 final size:23
Alignment explanation
Indices: 5701290--5701338 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
5701280 CATTTTTTGA
*
5701290 TTTA-TTGTTCTATTTTATTTAT
1 TTTATTTGTTCTATTTTAATTAT
* *
5701312 CTTATTTGTT-TATTTTAATTGT
1 TTTATTTGTTCTATTTTAATTAT
5701334 TTTAT
1 TTTAT
5701339 CTAACTTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.18, C:0.04, G:0.06, T:0.71
Consensus pattern (23 bp):
TTTATTTGTTCTATTTTAATTAT
Found at i:5703482 original size:24 final size:26
Alignment explanation
Indices: 5703432--5703484 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
5703422 AAAATCTTCG
5703432 CTTTCATTGCTTCTGCTGCCACTTGAT
1 CTTTCATTGCTTCT-CTGCCACTTGAT
*
5703459 CTTTCGTTGCTTCT-T-CCACTTGAT
1 CTTTCATTGCTTCTCTGCCACTTGAT
5703483 CT
1 CT
5703485 CTTGCTAGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 11 0.44
25 1 0.04
27 13 0.52
ACGTcount: A:0.09, C:0.30, G:0.13, T:0.47
Consensus pattern (26 bp):
CTTTCATTGCTTCTCTGCCACTTGAT
Found at i:5705616 original size:24 final size:23
Alignment explanation
Indices: 5705586--5705635 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
5705576 CACGGACCAA
5705586 TTTTTAATAGTAAAAATAGATTAT
1 TTTTTAATAG-AAAAATAGATTAT
* *
5705610 TTTTTAATAGAAAACTAGTTTAT
1 TTTTTAATAGAAAAATAGATTAT
5705633 TTT
1 TTT
5705636 ATTCTCTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (23 bp):
TTTTTAATAGAAAAATAGATTAT
Found at i:5710371 original size:18 final size:19
Alignment explanation
Indices: 5710315--5710371 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
5710305 AAACTTACAA
*
5710315 AAAAATACAAAAAATTATTT
1 AAAAATAAAAAAAATTA-TT
*
5710335 AAAAGTAAAAAAGAATTATT
1 AAAAATAAAAAA-AATTATT
*
5710355 AAAAAT-AGAAAAATTAT
1 AAAAATAAAAAAAATTAT
5710372 AACTTTACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 6 0.19
19 4 0.12
20 17 0.53
21 5 0.16
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (19 bp):
AAAAATAAAAAAAATTATT
Found at i:5710660 original size:20 final size:20
Alignment explanation
Indices: 5710635--5710798 Score: 122
Period size: 20 Copynumber: 8.1 Consensus size: 20
5710625 AGAAATGATC
*
5710635 AAATATATAAAAGTTATAAA
1 AAATATATAAAAATTATAAA
*
5710655 AAATAT-TAAAAACATTATAGA
1 AAATATAT-AAAA-ATTATAAA
* ** *
5710676 AAATATTTAAATTTTATTAA
1 AAATATATAAAAATTATAAA
5710696 AAATATA-AAAAATTATAAA
1 AAATATATAAAAATTATAAA
* *
5710715 AAA-ATCACAAAATTTATAAA
1 AAATAT-ATAAAAATTATAAA
*
5710735 AAAAATCATAAAGAACTTATAAA
1 AAATAT-ATAAA-AA-TTATAAA
*
5710758 AAAT-TGTAAAAATTAT-AA
1 AAATATATAAAAATTATAAA
**
5710776 AAATATATAGTAATATATAAA
1 AAATATATAAAAAT-TATAAA
5710797 AA
1 AA
5710799 TTTATAATTT
Statistics
Matches: 115, Mismatches: 18, Indels: 21
0.75 0.12 0.14
Matches are distributed among these distances:
18 8 0.07
19 24 0.21
20 40 0.35
21 30 0.26
22 3 0.03
23 10 0.09
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (20 bp):
AAATATATAAAAATTATAAA
Found at i:5710704 original size:8 final size:9
Alignment explanation
Indices: 5710693--5710805 Score: 50
Period size: 10 Copynumber: 11.3 Consensus size: 9
5710683 TAAATTTTAT
5710693 TAAAAA-TA
1 TAAAAATTA
5710701 TAAAAAATTA
1 T-AAAAATTA
*
5710711 TAAAAA-AA
1 TAAAAATTA
5710719 TCACAAAATTTA
1 T-A-AAAA-TTA
*
5710731 TAAAAAAAATCA
1 T--AA-AAATTA
5710743 TAAAGAACTTA
1 TAAA-AA-TTA
*
5710754 TAAAAAATTG
1 T-AAAAATTA
5710764 TAAAAATTA
1 TAAAAATTA
5710773 TAAAAATATA
1 TAAAAAT-TA
**
5710783 TAGTAATATA
1 TAAAAAT-TA
5710793 TAAAAATTTA
1 TAAAAA-TTA
5710803 TAA
1 TAA
5710806 TTTTTTAATA
Statistics
Matches: 81, Mismatches: 11, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
8 3 0.04
9 26 0.32
10 33 0.41
11 6 0.07
12 9 0.11
13 4 0.05
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.29
Consensus pattern (9 bp):
TAAAAATTA
Found at i:5710736 original size:10 final size:10
Alignment explanation
Indices: 5710723--5710805 Score: 51
Period size: 10 Copynumber: 8.1 Consensus size: 10
5710713 AAAAAATCAC
5710723 AAAATTTATAAA
1 AAAATTTAT--A
* *
5710735 AAAAATCATA
1 AAAATTTATA
*
5710745 AAGAACTTATA
1 AA-AATTTATA
* *
5710756 AAAAATTGTA
1 AAAATTTATA
5710766 AAAA-TTATA
1 AAAATTTATA
*
5710775 AAAATATATA
1 AAAATTTATA
** *
5710785 GTAATATATA
1 AAAATTTATA
5710795 AAAATTTATA
1 AAAATTTATA
5710805 A
1 A
5710806 TTTTTTAATA
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
9 8 0.14
10 33 0.59
11 8 0.14
12 7 0.12
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (10 bp):
AAAATTTATA
Found at i:5711245 original size:9 final size:9
Alignment explanation
Indices: 5711231--5711286 Score: 53
Period size: 9 Copynumber: 6.0 Consensus size: 9
5711221 ATAGGATACG
5711231 ATAATTTTT
1 ATAATTTTT
5711240 ATAATTTTTTT
1 ATAA--TTTTT
*
5711251 ATAAATTTT
1 ATAATTTTT
5711260 AT-ATTTCTT
1 ATAATTT-TT
5711269 -TACATTTTT
1 ATA-ATTTTT
5711278 ATAATTTTT
1 ATAATTTTT
5711287 TTAAGACTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
8 4 0.10
9 20 0.51
10 6 0.15
11 9 0.23
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (9 bp):
ATAATTTTT
Found at i:5713648 original size:34 final size:35
Alignment explanation
Indices: 5713610--5713679 Score: 124
Period size: 34 Copynumber: 2.0 Consensus size: 35
5713600 AATATTCCAC
*
5713610 ATATGAAATTCCGCATCGTCCTATT-ATTTTTTTA
1 ATATGAAATTCCGCATCGTCCCATTAATTTTTTTA
5713644 ATATGAAATTCCGCATCGTCCCATTAATTTTTTTA
1 ATATGAAATTCCGCATCGTCCCATTAATTTTTTTA
5713679 A
1 A
5713680 CTTTACTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 24 0.71
35 10 0.29
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.44
Consensus pattern (35 bp):
ATATGAAATTCCGCATCGTCCCATTAATTTTTTTA
Found at i:5719613 original size:13 final size:13
Alignment explanation
Indices: 5719595--5719620 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5719585 CATTCAAGCA
5719595 CTCTTTTTATGCT
1 CTCTTTTTATGCT
5719608 CTCTTTTTATGCT
1 CTCTTTTTATGCT
5719621 GCTTTGCCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.23, G:0.08, T:0.62
Consensus pattern (13 bp):
CTCTTTTTATGCT
Found at i:5727270 original size:31 final size:31
Alignment explanation
Indices: 5727232--5727298 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
5727222 GAAAACCCTA
* *
5727232 AAGTTCAGGCTTCAATATA-AGAATAATTGTC
1 AAGTTCAGGCTTCAATATAGA-AACAATTGCC
5727263 AAGTTCAGGCTTCAATATAGAAACAATTGCC
1 AAGTTCAGGCTTCAATATAGAAACAATTGCC
5727294 AAGTT
1 AAGTT
5727299 AAAGGACTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (31 bp):
AAGTTCAGGCTTCAATATAGAAACAATTGCC
Found at i:5728101 original size:96 final size:96
Alignment explanation
Indices: 5727937--5728128 Score: 375
Period size: 96 Copynumber: 2.0 Consensus size: 96
5727927 ATGTTTCCCC
*
5727937 CATTCAGGTCCCTGTTTATATCATTTTGTTTTCTTTTTGGCCAATATGAAAAGGATTAATGGAAT
1 CATTCAGGTCCCTGTTTATATCATTTTGTTTTCTTTTTCGCCAATATGAAAAGGATTAATGGAAT
5728002 TTTCTTTCCTCTCAAGTTGGCAAAGATCACT
66 TTTCTTTCCTCTCAAGTTGGCAAAGATCACT
5728033 CATTCAGGTCCCTGTTTATATCATTTTGTTTTCTTTTTCGCCAATATGAAAAGGATTAATGGAAT
1 CATTCAGGTCCCTGTTTATATCATTTTGTTTTCTTTTTCGCCAATATGAAAAGGATTAATGGAAT
5728098 TTTCTTTCCTCTCAAGTTGGCAAAGATCACT
66 TTTCTTTCCTCTCAAGTTGGCAAAGATCACT
5728129 GATGTGGGGG
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (96 bp):
CATTCAGGTCCCTGTTTATATCATTTTGTTTTCTTTTTCGCCAATATGAAAAGGATTAATGGAAT
TTTCTTTCCTCTCAAGTTGGCAAAGATCACT
Found at i:5729216 original size:148 final size:149
Alignment explanation
Indices: 5729042--5729340 Score: 555
Period size: 149 Copynumber: 2.0 Consensus size: 149
5729032 TATATTATAA
* *
5729042 TAGTATAATGATTTTATCCTTCAGTCTTTATAA-TTTTTTTATCAATTTGATTATTATTAATTTT
1 TAGTATAATGATTTTAGCCTTCAGTCTTTATAATTTTTTTTATCAATTTAATTATTATTAATTTT
5729106 TTTAATTAAATTTAATCCTAAACTTTTCAGAAATAGTCGTATTTGATCATCAATCTTTTAAAAAG
66 TTTAATTAAATTTAATCCTAAACTTTTCAGAAATAGTCGTATTTGATCATCAATCTTTTAAAAAG
*
5729171 ATTCGAATTGTTGTTTTCT
131 ACTCGAATTGTTGTTTTCT
5729190 TAGTATAATGATTTTAGCCTTCAGTCTTTATAATTTTTTTTATCAATTTAATTATTATTAATTTT
1 TAGTATAATGATTTTAGCCTTCAGTCTTTATAATTTTTTTTATCAATTTAATTATTATTAATTTT
*
5729255 TTTAATTAAATTTAATCCTAAATTTTTCAGAAATAGTCGTATTTGATCATCAATCTTTTAAAAAG
66 TTTAATTAAATTTAATCCTAAACTTTTCAGAAATAGTCGTATTTGATCATCAATCTTTTAAAAAG
5729320 ACTCGAATTGTTGTTTTCT
131 ACTCGAATTGTTGTTTTCT
5729339 TA
1 TA
5729341 CCGAAATTAT
Statistics
Matches: 146, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
148 32 0.22
149 114 0.78
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (149 bp):
TAGTATAATGATTTTAGCCTTCAGTCTTTATAATTTTTTTTATCAATTTAATTATTATTAATTTT
TTTAATTAAATTTAATCCTAAACTTTTCAGAAATAGTCGTATTTGATCATCAATCTTTTAAAAAG
ACTCGAATTGTTGTTTTCT
Found at i:5729560 original size:62 final size:62
Alignment explanation
Indices: 5729463--5729581 Score: 220
Period size: 62 Copynumber: 1.9 Consensus size: 62
5729453 TATAAATTTG
* *
5729463 AAATTATTTGTTGGTGTGACACATAAAACAAATAGTGTCATGTTAGCATGAAGTATTTGTAA
1 AAATTATTTGTTAGTGTGACACAAAAAACAAATAGTGTCATGTTAGCATGAAGTATTTGTAA
5729525 AAATTATTTGTTAGTGTGACACAAAAAACAAATAGTGTCATGTTAGCATGAAGTATT
1 AAATTATTTGTTAGTGTGACACAAAAAACAAATAGTGTCATGTTAGCATGAAGTATT
5729582 CATAAACTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.34
Consensus pattern (62 bp):
AAATTATTTGTTAGTGTGACACAAAAAACAAATAGTGTCATGTTAGCATGAAGTATTTGTAA
Found at i:5731063 original size:34 final size:35
Alignment explanation
Indices: 5730990--5731069 Score: 83
Period size: 34 Copynumber: 2.3 Consensus size: 35
5730980 CTCGAACCAT
* * * *
5730990 GAACCCTAAACTCTGAATCTTGAATATTGAACCTA
1 GAACTCTAAACTCTGAATCTTGAACATTAAACCCA
*
5731025 GAACTCTAAACTC-GAATCTCT-AACATTAAACCCC
1 GAACTCTAAACTCTGAATCT-TGAACATTAAACCCA
*
5731059 GAACTCAAAAC
1 GAACTCTAAAC
5731070 ACTAAACTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 25 0.66
35 13 0.34
ACGTcount: A:0.40, C:0.28, G:0.09, T:0.24
Consensus pattern (35 bp):
GAACTCTAAACTCTGAATCTTGAACATTAAACCCA
Found at i:5731148 original size:20 final size:20
Alignment explanation
Indices: 5731119--5731156 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5731109 TCCCAAATCC
5731119 AAACTCGAACCTTGAACCCT
1 AAACTCGAACCTTGAACCCT
*
5731139 AAACTTGAACCTTGAACC
1 AAACTCGAACCTTGAACC
5731157 TTTGGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.32, G:0.11, T:0.21
Consensus pattern (20 bp):
AAACTCGAACCTTGAACCCT
Found at i:5731517 original size:20 final size:20
Alignment explanation
Indices: 5731494--5731536 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
5731484 AAATCCAAAT
*
5731494 TAAAATATTGAAATTCAGGA
1 TAAAATACTGAAATTCAGGA
*
5731514 TAAAATCCTGAAATTCAGGA
1 TAAAATACTGAAATTCAGGA
5731534 TAA
1 TAA
5731537 GAGTACTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (20 bp):
TAAAATACTGAAATTCAGGA
Found at i:5735633 original size:12 final size:12
Alignment explanation
Indices: 5735616--5735640 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5735606 TTTTAAAATT
5735616 ATGAATAATATA
1 ATGAATAATATA
5735628 ATGAATAATATA
1 ATGAATAATATA
5735640 A
1 A
5735641 AACATAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATGAATAATATA
Found at i:5735710 original size:24 final size:24
Alignment explanation
Indices: 5735676--5735770 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 24
5735666 TACGATATAC
*
5735676 ATAACATATAATAAAAAATAATAA
1 ATAATATATAATAAAAAATAATAA
*
5735700 GTAATATATAATAAAAATATAATAA
1 ATAATATATAATAAAAA-ATAATAA
** * *
5735725 ATTTTATATAATAAAATATAATAT
1 ATAATATATAATAAAAAATAATAA
*
5735749 A-AATATAT-ATAGGAAAATAATA
1 ATAATATATAATA-AAAAATAATA
5735771 TATGATAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
22 3 0.05
23 13 0.22
24 22 0.38
25 20 0.34
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (24 bp):
ATAATATATAATAAAAAATAATAA
Found at i:5735712 original size:14 final size:13
Alignment explanation
Indices: 5735623--5735757 Score: 56
Period size: 14 Copynumber: 10.4 Consensus size: 13
5735613 ATTATGAATA
5735623 ATATAATGAATAAT
1 ATATAAT-AATAAT
5735637 ATA-AA-ACATAAAT
1 ATATAATA-AT-AAT
*
5735650 AATATAACAGATAAT
1 -ATATAATA-ATAAT
* *
5735665 ATACGATATACATAAC
1 ATA-TA-ATA-ATAAT
5735681 ATATAATAA-AA-
1 ATATAATAATAAT
5735692 A-ATAATAAGTAAT
1 ATATAATAA-TAAT
5735705 ATATAATAA-AA-
1 ATATAATAATAAT
*
5735716 ATATAATAA-ATT
1 ATATAATAATAAT
* *
5735728 TTAT-ATAATAAA
1 ATATAATAATAAT
5735740 ATATAAT-ATAAAT
1 ATATAATAAT-AAT
5735753 ATATA
1 ATATA
5735758 TAGGAAAATA
Statistics
Matches: 94, Mismatches: 12, Indels: 31
0.69 0.09 0.23
Matches are distributed among these distances:
10 7 0.07
11 16 0.17
12 17 0.18
13 16 0.17
14 19 0.20
15 7 0.07
16 12 0.13
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (13 bp):
ATATAATAATAAT
Found at i:5735757 original size:25 final size:25
Alignment explanation
Indices: 5735681--5735759 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
5735671 TATACATAAC
* *
5735681 ATATAATAAAAAAT-A-ATAAGTAAT
1 ATATAATAAAATATAATATAAAT-AT
* *
5735705 ATATAATAAAAATATAATA-AATTTT
1 ATATAAT-AAAATATAATATAAATAT
5735730 ATATAATAAAATATAATATAAATAT
1 ATATAATAAAATATAATATAAATAT
5735755 ATATA
1 ATATA
5735760 GGAAAATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
24 18 0.39
25 23 0.50
26 4 0.09
27 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (25 bp):
ATATAATAAAATATAATATAAATAT
Found at i:5747881 original size:6 final size:6
Alignment explanation
Indices: 5747870--5747900 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
5747860 ATAAACAAGT
5747870 AAAACA AAAACA AAAACA AAAACA AAAACA A
1 AAAACA AAAACA AAAACA AAAACA AAAACA A
5747901 GTGGGTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:5748196 original size:14 final size:14
Alignment explanation
Indices: 5748173--5748207 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
5748163 ATCCTATAAC
*
5748173 AATCTTTAGGATTT
1 AATCTATAGGATTT
5748187 AATCTATAGGATTT
1 AATCTATAGGATTT
5748201 AATCTAT
1 AATCTAT
5748208 CAATAGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (14 bp):
AATCTATAGGATTT
Found at i:5752086 original size:47 final size:47
Alignment explanation
Indices: 5752034--5752532 Score: 775
Period size: 47 Copynumber: 10.6 Consensus size: 47
5752024 GATAATTGTG
* *
5752034 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
5752081 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
5752128 GTGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
5752177 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
5752224 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCC-ATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
5752270 GTGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCCATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
5752319 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
5752366 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATATGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
5752413 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
5752460 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
5752507 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
5752533 TCCCGAAGGG
Statistics
Matches: 418, Mismatches: 29, Indels: 10
0.91 0.06 0.02
Matches are distributed among these distances:
46 19 0.05
47 311 0.74
48 25 0.06
49 63 0.15
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:5765611 original size:59 final size:59
Alignment explanation
Indices: 5765471--5765611 Score: 178
Period size: 60 Copynumber: 2.4 Consensus size: 59
5765461 TTGAGTGTTA
* * *
5765471 ACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCTTTACAGTAACAGAGTAT
1 ACTGGGCCTT-GCCCATATCAGTATCAATCTGGGCCATAGCCCTATACAGT-ACAGAGTAT
* *
5765532 ACTGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATACAAGT-C-GAGATAT
1 ACTGGGCCTTGCCCATATCAGTATCAATCTGGGCCATAGCCCTATAC-AGTACAGAG-TAT
*
5765591 ATTGGGCCTTGCCCATATCAG
1 ACTGGGCCTTGCCCATATCAG
5765612 CACAGTTGGG
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
58 3 0.04
59 23 0.32
60 33 0.46
61 12 0.17
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (59 bp):
ACTGGGCCTTGCCCATATCAGTATCAATCTGGGCCATAGCCCTATACAGTACAGAGTAT
Found at i:5766252 original size:8 final size:8
Alignment explanation
Indices: 5766238--5766267 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5766228 ACAAATGCCA
5766238 GCTTTTCG
1 GCTTTTCG
*
5766246 ACTTTTCG
1 GCTTTTCG
5766254 GCTTTTCG
1 GCTTTTCG
5766262 GCTTTT
1 GCTTTT
5766268 GCTGATCTAG
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:0.03, C:0.23, G:0.20, T:0.53
Consensus pattern (8 bp):
GCTTTTCG
Found at i:5773885 original size:23 final size:24
Alignment explanation
Indices: 5773859--5773903 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
5773849 ATATCCCCAC
5773859 ATGGAGTGTAG-GGTTGGATGGAG
1 ATGGAGTGTAGAGGTTGGATGGAG
*
5773882 ATGGTGTGTAGAGGTTGGATGG
1 ATGGAGTGTAGAGGTTGGATGG
5773904 GTAGGATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.20, C:0.00, G:0.51, T:0.29
Consensus pattern (24 bp):
ATGGAGTGTAGAGGTTGGATGGAG
Found at i:5786579 original size:21 final size:23
Alignment explanation
Indices: 5786542--5786583 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
5786532 GGGAATAGAA
5786542 TGAAAATACAGAATTAGTTTTAT
1 TGAAAATACAGAATTAGTTTTAT
5786565 TGAAAATA-A-AATTAGTTTT
1 TGAAAATACAGAATTAGTTTT
5786584 GTTTAGGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 1 0.05
23 8 0.42
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.40
Consensus pattern (23 bp):
TGAAAATACAGAATTAGTTTTAT
Found at i:5786868 original size:5 final size:5
Alignment explanation
Indices: 5786858--5786883 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5786848 GCATTGTAGT
5786858 ATTGA ATTGA ATTGA ATTGA ATTGA A
1 ATTGA ATTGA ATTGA ATTGA ATTGA A
5786884 ACAAATTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTGA
Found at i:5787813 original size:17 final size:18
Alignment explanation
Indices: 5787780--5787813 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5787770 TCAAATTTGG
5787780 GTTGATATTGGTATGAAA
1 GTTGATATTGGTATGAAA
*
5787798 GTTGAT-TTGGTTTGAA
1 GTTGATATTGGTATGAA
5787814 TGAAGTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.44
Consensus pattern (18 bp):
GTTGATATTGGTATGAAA
Found at i:5791189 original size:14 final size:16
Alignment explanation
Indices: 5791172--5791203 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5791162 AGAAATCTTC
5791172 ATTTT-ATGA-TACAT
1 ATTTTAATGATTACAT
5791186 ATTTTAATGATTACAT
1 ATTTTAATGATTACAT
5791202 AT
1 AT
5791204 ATATCTCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 4 0.25
16 7 0.44
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTTTAATGATTACAT
Found at i:5795731 original size:41 final size:41
Alignment explanation
Indices: 5795684--5795762 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
5795674 TTAAATTGTG
*
5795684 TAAACTTACTAAGTAATTCATATACTTAGTTTGTTATTATT
1 TAAACTTACTAAGTAATTCATATACTTACTTTGTTATTATT
5795725 TAAACTTACTAAGTAATTCATATACTTACTTTGTTATT
1 TAAACTTACTAAGTAATTCATATACTTACTTTGTTATT
5795763 TTTTTTCTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.48
Consensus pattern (41 bp):
TAAACTTACTAAGTAATTCATATACTTACTTTGTTATTATT
Found at i:5795753 original size:20 final size:20
Alignment explanation
Indices: 5795687--5795754 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
5795677 AATTGTGTAA
5795687 ACTTACTAAGTAATTCATAT
1 ACTTACTAAGTAATTCATAT
* ** * *
5795707 ACTTAGTTTGTTATT-ATTTAA
1 ACTTACTAAGTAATTCA--TAT
5795728 ACTTACTAAGTAATTCATAT
1 ACTTACTAAGTAATTCATAT
5795748 ACTTACT
1 ACTTACT
5795755 TTGTTATTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
19 1 0.03
20 20 0.57
21 13 0.37
22 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (20 bp):
ACTTACTAAGTAATTCATAT
Found at i:5797436 original size:40 final size:40
Alignment explanation
Indices: 5797376--5797467 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 40
5797366 CTCGGTATCA
* *
5797376 CACACTTAGTGCCTCATGTAGCTGAAGCTA-TTCCAACTCG
1 CACACTTAGTGCCTCATGTAGCCGAAGCTATTTCAAAC-CG
*
5797416 CACACTTAGTGCCAT-TTGTAGCCGAAGCTATTTCAAACCG
1 CACACTTAGTGCC-TCATGTAGCCGAAGCTATTTCAAACCG
5797456 CACACTTAGTGC
1 CACACTTAGTGC
5797468 TGAAATTAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
40 40 0.85
41 7 0.15
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.27
Consensus pattern (40 bp):
CACACTTAGTGCCTCATGTAGCCGAAGCTATTTCAAACCG
Found at i:5807571 original size:43 final size:43
Alignment explanation
Indices: 5807523--5807673 Score: 196
Period size: 43 Copynumber: 3.5 Consensus size: 43
5807513 TATCCTAGAT
* *
5807523 ATGGTCTTACATGTTATCACATATCGATGCCAATGTCTCAGAC
1 ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCCAGAC
* * * * *
5807566 ATGGTCTTACACGAAATCATATAACGATGCCAATGTCCCAGAA
1 ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCCAGAC
* * *
5807609 ATGATCTTACATGTAATCACA-ATACAATGCCAATGTCCCAAAC
1 ATGGTCTTACATGTAATCACATAT-CGATGCCAATGTCCCAGAC
5807652 ATGGTCTTACATGTAATCACAT
1 ATGGTCTTACATGTAATCACAT
5807674 CTCGGTCATC
Statistics
Matches: 90, Mismatches: 16, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
42 1 0.01
43 89 0.99
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCCAGAC
Found at i:5810122 original size:48 final size:48
Alignment explanation
Indices: 5810059--5810195 Score: 186
Period size: 48 Copynumber: 2.9 Consensus size: 48
5810049 ATAGTGTCTG
* *
5810059 GTTACCCGTTTGGGTTAAACCTACATGAATAAA-AGATAATAGTACCTA
1 GTTACCCGTTAGGGTTAAACCTACACGAATAAAGA-ATAATAGTACCTA
* *
5810107 GTTACCCGTTAGGGTTAAACCTACACGAATAATGAATAATAGTGCCTA
1 GTTACCCGTTAGGGTTAAACCTACACGAATAAAGAATAATAGTACCTA
* * * *
5810155 ATTACCCATTAGGGTTAAACCTACACGATTAATGAATAATA
1 GTTACCCGTTAGGGTTAAACCTACACGAATAAAGAATAATA
5810196 ATGTTTGGTT
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
48 80 0.99
49 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (48 bp):
GTTACCCGTTAGGGTTAAACCTACACGAATAAAGAATAATAGTACCTA
Found at i:5811363 original size:49 final size:49
Alignment explanation
Indices: 5811306--5811399 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
5811296 GGCCTACTCG
*
5811306 TGTGGGCCCACACGACTGAAATTGGCCTTCACCGTATGGATCACAGGCA
1 TGTGGGCCCACACGACCGAAATTGGCCTTCACCGTATGGATCACAGGCA
* ** *
5811355 TGTGGGCCCACACGGCCGAAATTGGCCTTGGCCGTGTGGATCACA
1 TGTGGGCCCACACGACCGAAATTGGCCTTCACCGTATGGATCACA
5811400 CGGCCTAGCC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.21, C:0.29, G:0.30, T:0.20
Consensus pattern (49 bp):
TGTGGGCCCACACGACCGAAATTGGCCTTCACCGTATGGATCACAGGCA
Found at i:5818068 original size:161 final size:162
Alignment explanation
Indices: 5817799--5818128 Score: 581
Period size: 161 Copynumber: 2.0 Consensus size: 162
5817789 GTGTGATAGT
*
5817799 CACTTGAAAGATTTTAGGAGATATTCCTCAATTTAAAAAAAAACACTATTATATCAACTAACAAT
1 CACTTGAAAGATTTTAGGAGATATTCCTCAATTTAAAAAAAAACACTATTATATCAACTAACAAG
5817864 ATTTAACCACTAATCCTATCCAACTAATCAAAATTTAAATTTAACCCAATTACCAACAACATGGG
66 ATTTAACCACTAATCCTATCCAACTAATCAAAATTTAAATTTAACCCAATTACCAACAACATGGG
*
5817929 CGACACAAACAGGAAGTAGGAAAAATAATTCC
131 CGACACAAACAGGAAGAAGGAAAAATAATTCC
5817961 CACTTGAAAGATTTTAGGAGATATTCCTCAATTT-AAAAAAAACACTATTATATCAACTAACAAG
1 CACTTGAAAGATTTTAGGAGATATTCCTCAATTTAAAAAAAAACACTATTATATCAACTAACAAG
* * * *
5818025 ATTTAACCACTAATCTTATCTAACTAATCAGAATTTGAATTTAACCCAATTACCAACAACATGGG
66 ATTTAACCACTAATCCTATCCAACTAATCAAAATTTAAATTTAACCCAATTACCAACAACATGGG
* *
5818090 CGGCACAAACAGGGAGAAGGAAAAATAATTCC
131 CGACACAAACAGGAAGAAGGAAAAATAATTCC
5818122 CACTTGA
1 CACTTGA
5818129 GCACAACAAA
Statistics
Matches: 160, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
161 126 0.79
162 34 0.21
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.26
Consensus pattern (162 bp):
CACTTGAAAGATTTTAGGAGATATTCCTCAATTTAAAAAAAAACACTATTATATCAACTAACAAG
ATTTAACCACTAATCCTATCCAACTAATCAAAATTTAAATTTAACCCAATTACCAACAACATGGG
CGACACAAACAGGAAGAAGGAAAAATAATTCC
Found at i:5820321 original size:29 final size:29
Alignment explanation
Indices: 5820281--5820339 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
5820271 TTGTAGAAGA
* *
5820281 GGTGGAGAACTTGTTCGTTAAGAGTTTGT
1 GGTGAAGAACTTGTTCGTTAAGAATTTGT
*
5820310 GGTGAAGAACTTGTTCGTTGAGAATTTGT
1 GGTGAAGAACTTGTTCGTTAAGAATTTGT
5820339 G
1 G
5820340 TCAAGTTAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.07, G:0.34, T:0.37
Consensus pattern (29 bp):
GGTGAAGAACTTGTTCGTTAAGAATTTGT
Found at i:5827621 original size:10 final size:10
Alignment explanation
Indices: 5827606--5827632 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
5827596 AAAACATCTC
5827606 AGAATAATAA
1 AGAATAATAA
5827616 AGAATAATAA
1 AGAATAATAA
5827626 AGAATAA
1 AGAATAA
5827633 GAGCTTATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (10 bp):
AGAATAATAA
Found at i:5836188 original size:48 final size:48
Alignment explanation
Indices: 5836133--5836282 Score: 192
Period size: 48 Copynumber: 3.1 Consensus size: 48
5836123 CTGAGCTATC
*
5836133 GACATCGATATGTGATCCCATGTAAGACTATGTCTGGGACATGGCATT
1 GACATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATT
* **
5836181 GACATCGATCTACGATCCCATGTAAGACCATGTCTGGGACATGGCATT
1 GACATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATT
* * * * * * *
5836229 GGCATCAATATGTGATCTCATGTAATACCATATCGGGGATATGGCATT
1 GACATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATT
*
5836277 GGCATC
1 GACATC
5836283 CTACCATGTG
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 88 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (48 bp):
GACATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATT
Found at i:5838604 original size:81 final size:82
Alignment explanation
Indices: 5838465--5838615 Score: 209
Period size: 81 Copynumber: 1.9 Consensus size: 82
5838455 ATCTTGCACA
5838465 CTAAGTGCTAAAGCATAGCCGAAGCTATTATAATCTCACACACAAGTGCCTTTCATAGCCAAAGC
1 CTAAGTGCTAAAGCATAGCCGAAGCTATTATAATCTCACACACAAGTGCCTTTCATAGCCAAAGC
5838530 TATCTCAACCTCACACG
66 TATCTCAACCTCACACG
* * * * * *
5838547 CTAAGTGCTATA-TATAGCCGAAGCTATTATGATTCTCACAC-TAAGTG-CTTTATATAGCCGAA
1 CTAAGTGCTAAAGCATAGCCGAAGCTATTAT-AATCTCACACACAAGTGCCTTT-CATAGCCAAA
5838609 GCTATCT
64 GCTATCT
5838616 TGAAACGCAC
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
80 4 0.07
81 37 0.61
82 20 0.33
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (82 bp):
CTAAGTGCTAAAGCATAGCCGAAGCTATTATAATCTCACACACAAGTGCCTTTCATAGCCAAAGC
TATCTCAACCTCACACG
Found at i:5838627 original size:40 final size:40
Alignment explanation
Indices: 5838460--5838636 Score: 130
Period size: 40 Copynumber: 4.4 Consensus size: 40
5838450 TCAATATCTT
* * *
5838460 GCACACTAAGTGCTAAAGCATAGCCGAAGCTATTAT-AATC
1 GCACACTAAGTGCTATA-TATAGCCGAAGCTATTATGAAAC
* * * * * *
5838500 TCACACACAAGTGCCT-T-TCATAGCCAAAGCTA-TCTCAACC
1 GCACAC-TAAGTG-CTATAT-ATAGCCGAAGCTATTATGAAAC
* **
5838540 TCACACGCTAAGTGCTATATATAGCCGAAGCTATTATGATTC
1 GCACA--CTAAGTGCTATATATAGCCGAAGCTATTATGAAAC
* *
5838582 TCACACTAAGTGCTTTATATAGCCGAAGCTATCT-TGAAAC
1 GCACACTAAGTGCTATATATAGCCGAAGCTAT-TATGAAAC
5838622 GCACACTAAGTGCTA
1 GCACACTAAGTGCTA
5838637 AACATAGTTG
Statistics
Matches: 109, Mismatches: 18, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
39 2 0.02
40 70 0.64
41 24 0.22
42 13 0.12
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.26
Consensus pattern (40 bp):
GCACACTAAGTGCTATATATAGCCGAAGCTATTATGAAAC
Found at i:5844383 original size:24 final size:27
Alignment explanation
Indices: 5844336--5844387 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 27
5844326 AACCGAGGTA
5844336 AGTTCGTATGTTAAATAAGCTTTAATAT
1 AGTTCGTATGTTAAAT-AGCTTTAATAT
5844364 AGTT-GTAT-TTAAAT-GCTTTAATAT
1 AGTTCGTATGTTAAATAGCTTTAATAT
5844388 TGCATGAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 10 0.42
26 6 0.25
27 4 0.17
28 4 0.17
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (27 bp):
AGTTCGTATGTTAAATAGCTTTAATAT
Found at i:5852249 original size:33 final size:31
Alignment explanation
Indices: 5852188--5852249 Score: 72
Period size: 33 Copynumber: 1.9 Consensus size: 31
5852178 AAGTTATAAG
*
5852188 AAATAAAATAAAACAACTAAAAACAATAACAA
1 AAATAAAATAAAACAAC-AAAAAAAATAACAA
5852220 AAATAAAAATAAAACTAA-AAAAATAAATAA
1 AAAT-AAAATAAAAC-AACAAAAA-AAATAA
5852250 GATCAGTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
32 9 0.35
33 15 0.58
34 2 0.08
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (31 bp):
AAATAAAATAAAACAACAAAAAAAATAACAA
Found at i:5853654 original size:16 final size:16
Alignment explanation
Indices: 5853629--5853664 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5853619 ATAATATCGT
*
5853629 AATAATAAATAATAAC
1 AATAAAAAATAATAAC
*
5853645 AATAAAAAATAATAAG
1 AATAAAAAATAATAAC
5853661 AATA
1 AATA
5853665 GAACCTACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (16 bp):
AATAAAAAATAATAAC
Found at i:5853809 original size:15 final size:15
Alignment explanation
Indices: 5853777--5853840 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 15
5853767 AGTTAGTAGG
*
5853777 AATAATGAT-AATAA
1 AATAATAATAAATAA
* *
5853791 AATAATACTAAATAT
1 AATAATAATAAATAA
5853806 AATAATAATAAAATTACTA
1 AATAATAAT-AAA-TA--A
5853825 AAT-ATAATAAATAA
1 AATAATAATAAATAA
5853839 AA
1 AA
5853841 GAAAAAGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 10 0.25
15 12 0.30
16 5 0.12
17 5 0.12
18 5 0.12
19 3 0.08
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (15 bp):
AATAATAATAAATAA
Found at i:5853829 original size:24 final size:25
Alignment explanation
Indices: 5853778--5853834 Score: 89
Period size: 24 Copynumber: 2.3 Consensus size: 25
5853768 GTTAGTAGGA
*
5853778 ATAATGATAATAAAATAATACTAAAT
1 ATAATAATAATAAAAT-ATACTAAAT
5853804 ATAATAATAATAAAAT-TACTAAAT
1 ATAATAATAATAAAATATACTAAAT
5853828 ATAATAA
1 ATAATAA
5853835 ATAAAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 15 0.50
26 15 0.50
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (25 bp):
ATAATAATAATAAAATATACTAAAT
Found at i:5860631 original size:38 final size:39
Alignment explanation
Indices: 5860589--5860664 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 39
5860579 TATGTTACAT
5860589 ATAACCTGAGAATCTACAAC-AAGGCTAGATCTCATTAA
1 ATAACCTGAGAATCTACAACAAAGGCTAGATCTCATTAA
* * **
5860627 ATAACCTGAGGATCTGCAACAAATTCTAGATCTCATTA
1 ATAACCTGAGAATCTACAACAAAGGCTAGATCTCATTA
5860665 TAACATGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 18 0.55
39 15 0.45
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.26
Consensus pattern (39 bp):
ATAACCTGAGAATCTACAACAAAGGCTAGATCTCATTAA
Found at i:5863005 original size:14 final size:14
Alignment explanation
Indices: 5862986--5863018 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5862976 TTATTTGATC
*
5862986 TCTAATTATATATG
1 TCTAATTAAATATG
5863000 TCTAATTAAATATG
1 TCTAATTAAATATG
5863014 TCTAA
1 TCTAA
5863019 AGCTTGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (14 bp):
TCTAATTAAATATG
Found at i:5864497 original size:19 final size:20
Alignment explanation
Indices: 5864453--5864497 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
5864443 TTACGCCAAA
* *
5864453 CTCCCAAACCTCTTTACTTT
1 CTCCCAAAACTCTTTACTCT
*
5864473 CCCCCAAAACT-TTTACTCT
1 CTCCCAAAACTCTTTACTCT
5864492 CTCCCA
1 CTCCCA
5864498 CTTTCCCTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.22, C:0.44, G:0.00, T:0.33
Consensus pattern (20 bp):
CTCCCAAAACTCTTTACTCT
Found at i:5865286 original size:19 final size:19
Alignment explanation
Indices: 5865262--5865351 Score: 79
Period size: 19 Copynumber: 4.9 Consensus size: 19
5865252 ATAATCTTCA
5865262 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5865281 ATGATATG----C---GAT
1 ATGATATGCAATCTTAGAT
5865293 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5865311 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTT---AGAT
*
5865333 ATGATTTTGCAATCTTAGA
1 ATGA-TATGCAATCTTAGA
5865352 GATTTAATTT
Statistics
Matches: 58, Mismatches: 1, Indels: 23
0.71 0.01 0.28
Matches are distributed among these distances:
11 2 0.03
12 8 0.14
15 2 0.03
18 8 0.14
19 17 0.29
20 3 0.05
22 8 0.14
23 10 0.17
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.37
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:5865302 original size:30 final size:31
Alignment explanation
Indices: 5865262--5865319 Score: 109
Period size: 30 Copynumber: 1.9 Consensus size: 31
5865252 ATAATCTTCA
5865262 ATGATATGCAATCTTAGATATGATATGCGAT
1 ATGATATGCAATCTTAGATATGATATGCGAT
5865293 ATGAT-TGCAATCTTAGATATGATATGC
1 ATGATATGCAATCTTAGATATGATATGC
5865320 AATCTTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.36
Consensus pattern (31 bp):
ATGATATGCAATCTTAGATATGATATGCGAT
Found at i:5865318 original size:23 final size:21
Alignment explanation
Indices: 5865290--5865351 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 21
5865280 TATGATATGC
5865290 GATATGATTGCAATCTT---A
1 GATATGATTGCAATCTTAGAA
5865308 GATATGATATGCAATCTTAGAA
1 GATATGAT-TGCAATCTTAGAA
5865330 GATATGATTTTGCAATCTTAGA
1 GATATGA--TTGCAATCTTAGA
5865352 GATTTAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
18 8 0.21
19 9 0.24
22 8 0.21
23 12 0.32
24 1 0.03
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (21 bp):
GATATGATTGCAATCTTAGAA
Found at i:5865361 original size:22 final size:23
Alignment explanation
Indices: 5865317--5865361 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5865307 AGATATGATA
*
5865317 TGCAATCTTAGAAGATATGATTT
1 TGCAATCTTAGAAGATATAATTT
*
5865340 TGCAATCTTAG-AGATTTAATTT
1 TGCAATCTTAGAAGATATAATTT
5865362 GTAGATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (23 bp):
TGCAATCTTAGAAGATATAATTT
Found at i:5871576 original size:44 final size:44
Alignment explanation
Indices: 5871527--5872226 Score: 658
Period size: 44 Copynumber: 15.8 Consensus size: 44
5871517 GATCCAAGAT
* **
5871527 GATTTGGCATCTCTATATTGGCAGAGAGCAGATCGAAGGCAACA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
** * *
5871571 GATTTGGTGTCTTTGTATTGGCAGAGAGCAGATCGAAGATGACA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
* * * *
5871615 GATTTGGCATCTCTGTATTTGGCGGAGAGTAGATCGAAGACATAGCT
1 GATTTGGCATCTCTGTA-TTGGCAGAGAGCAGATCGAAG--ATAACA
** * * * ** *
5871662 GATTCAGCTTCCACGTGT-TTACGTTGA-AGCA-AGTCTAAGAT----
1 GATTTGGCAT-CTC-TGTATT-GGCAGAGAGCAGA-TCGAAGATAACA
* *
5871703 GATTTGGCATCTCTGTATTGGTAGAGAGCAGATCGAAGATAGCA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
*
5871747 GATTTGGCATCTCTGTATTGGTAGAGAGCAGATCGAAGATAACA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
* * *
5871791 GATTTGGCATCTCTGTATTGGTAGAGAGCAGATCAAAGATGACA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
* * * *
5871835 GATTTGGCATCTCTATATTCGGCGGAGAGCAGATCGAAGACATAGCT
1 GATTTGGCATCTCTGTATT-GGCAGAGAGCAGATCGAAG--ATAACA
* * * ** *
5871882 GATTTGGCTTCCACGTGT-TTACGTTGA-AGCA-AGTCTAAGAT----
1 GATTTGGCAT-CTC-TGTATT-GGCAGAGAGCAGA-TCGAAGATAACA
* * *
5871923 GATTTGGCATCTTTGTATTGGCAGAGAGCAGATCAAAGATAGCA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
* * *
5871967 GATTTGGCATCTCTGTATTGGCATAGAGCAGATCAAAGATGACA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
* * *
5872011 GATTTGGCATCTCTGTATTCGGC-GAAGAGCAGATCAAAGACATAGCT
1 GATTTGGCATCTCTGTATT-GGCAG-AGAGCAGATCGAAG--ATAACA
5872058 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
* * *
5872102 GATTTGACATTTCTGTATTGGCAGAGAGCAGATCGAAGATAATA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
5872146 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAGA-A
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA-ACA
* * * *
5872190 GATTTGGCGTCTCTGTTTTGTCAGAGAGCATATCGAA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAA
5872227 AAGAAGAACA
Statistics
Matches: 547, Mismatches: 76, Indels: 66
0.79 0.11 0.10
Matches are distributed among these distances:
39 13 0.02
40 29 0.05
41 18 0.03
44 331 0.61
45 57 0.10
46 18 0.03
47 64 0.12
48 12 0.02
49 5 0.01
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.28
Consensus pattern (44 bp):
GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
Found at i:5871909 original size:220 final size:218
Alignment explanation
Indices: 5871527--5872226 Score: 885
Period size: 220 Copynumber: 3.2 Consensus size: 218
5871517 GATCCAAGAT
* ** ** *
5871527 GATTTGGCATCTCTATATTGGCAGAGAGCAGATCGAAGGCAACAGATTTGGTGTCTTTGTATTGG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTGG
* *
5871592 CAGAGAGCAGATCGAAGATGACAGATTTGGCATCTCTGTATTTGGCGGAGAGTAGATCGAAGACA
66 -AGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTA-TTGGCGGAGAGCAGATCGAAGACA
**
5871657 TAGCTGATTCAGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTCTGTATT
129 TAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTCTGTATT
*
5871722 GGTAGAGAGCAGATCGAAGATAGCA
194 GGCAGAGAGCAGATCGAAGATAGCA
*
5871747 GATTTGGCATCTCTGTATTGGTAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTGG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTGG
*
5871812 TAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTATATTCGGCGGAGAGCAGATCGAAGACA
66 -AGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATT-GGCGGAGAGCAGATCGAAGACA
*
5871877 TAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTTTGTATT
129 TAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTCTGTATT
*
5871942 GGCAGAGAGCAGATCAAAGATAGCA
194 GGCAGAGAGCAGATCGAAGATAGCA
* * *
5871967 GATTTGGCATCTCTGTATTGGCATAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTCG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCTGTATT-G
* * *
5872032 GCGAAGAGCAGATCAAAGACAT-AGCTGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAG
65 GAG-AGAGCAGATCAAAG--ATGA-CAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAG
* * * * * ** *
5872096 --ATAACAGATTTGACATT--TC-TGTATT-GGCAGAGAGC-AGATCGAAGATAATAGATTTGGC
126 ACATAGCTGATTTGGC-TTCCACGTGT-TTACGTTGA-AGCAAG-TCTAAG---AT-GATTTGGC
*
5872154 ATCTCTGTATTGGCAGAGAGCAGATCGAAGATAGAA
183 ATCTCTGTATTGGCAGAGAGCAGATCGAAGATAGCA
* * * *
5872190 GATTTGGCGTCTCTGTTTTGTCAGAGAGCATATCGAA
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAA
5872227 AAGAAGAACA
Statistics
Matches: 425, Mismatches: 41, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
218 8 0.02
219 13 0.03
220 272 0.64
221 18 0.04
222 21 0.05
223 93 0.22
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.28
Consensus pattern (218 bp):
GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTGG
AGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGACATA
GCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGG
CAGAGAGCAGATCGAAGATAGCA
Found at i:5872423 original size:44 final size:44
Alignment explanation
Indices: 5872281--5872559 Score: 165
Period size: 44 Copynumber: 6.2 Consensus size: 44
5872271 GATCCAAGAT
* * *
5872281 GATTTGGCATTCCTATGTTTACAGGGAACAGATCGAAGACATAGCA
1 GATTTGGCATCCCTGTGTTTACAGGGAACAGATTGAAG--ATAGCA
* * * * * ** ***
5872327 GATCTGACA-CTTCTGTGCTTACAGCGAAGCAGATCAAAGATTTTA
1 GATTTGGCATC-CCTGTGTTTACAGGGAA-CAGATTGAAGATAGCA
** *
5872372 -ACATGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCA
1 GATTTGGCATCCCTGTGTTTACAGGGAACAGA-TTGAAGATAGCA
*
5872415 GATTTGGCATCCCTGTGTTTACAGGGAACAGATCGAAGACATAGCA
1 GATTTGGCATCCCTGTGTTTACAGGGAACAGATTGAAG--ATAGCA
* * * * * * **
5872461 GATCTGACATTCCTGTGCTTACAGCGAAGCAGATTGAAAATTTCA
1 GATTTGGCATCCCTGTGTTTACAGGGAA-CAGATTGAAGATAGCA
* * * *
5872506 GCA--TGGCATCCCTGTGTTTATAAGGAATA-AGTTGAAGATAGTA
1 G-ATTTGGCATCCCTGTGTTTACAGGGAACAGA-TTGAAGATAGCA
5872549 GATTTGGCATC
1 GATTTGGCATC
5872560 TCCATATTCG
Statistics
Matches: 173, Mismatches: 47, Indels: 28
0.70 0.19 0.11
Matches are distributed among these distances:
42 3 0.02
43 19 0.11
44 74 0.43
45 10 0.06
46 50 0.29
47 17 0.10
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (44 bp):
GATTTGGCATCCCTGTGTTTACAGGGAACAGATTGAAGATAGCA
Found at i:5872437 original size:134 final size:134
Alignment explanation
Indices: 5872281--5872636 Score: 486
Period size: 134 Copynumber: 2.6 Consensus size: 134
5872271 GATCCAAGAT
*
5872281 GATTTGGCATTCCTATGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGACACTTCTGTGCT
1 GATTTGGCATCCCTATGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGACACTTCTGTGCT
* *
5872346 TACAGCGAAGCAGATCAAAGATTTTAACATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAT
66 TACAGCGAAGCAGATCAAAGATTTCAACATGGCATCCCTGTGTTTATAAGGAACAAGTTGAAGAT
5872411 AGCA
131 AGCA
*
5872415 GATTTGGCATCCCTGTGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGACA-TTCCTGTGC
1 GATTTGGCATCCCTATGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGACACTT-CTGTGC
* * *
5872479 TTACAGCGAAGCAGATTGAAA-ATTTCAGCATGGCATCCCTGTGTTTATAAGGAATAAGTTGAAG
65 TTACAGCGAAGCAGA-TCAAAGATTTCAACATGGCATCCCTGTGTTTATAAGGAACAAGTTGAAG
*
5872543 ATAGTA
129 ATAGCA
** * ** *
5872549 GATTTGGCATCTCCATAT-TCGACAGGGAGCAGATTAAAGACATAGTAGATCTGAC-CTTCATGT
1 GATTTGGCATC-CC-TATGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGACACTTC-TGT
* * *
5872612 GTTTACATCGAAGCAGATCCAAGAT
63 GCTTACAGCGAAGCAGATCAAAGAT
5872637 GACAGATTTG
Statistics
Matches: 196, Mismatches: 19, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
133 2 0.01
134 133 0.68
135 59 0.30
136 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (134 bp):
GATTTGGCATCCCTATGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGACACTTCTGTGCT
TACAGCGAAGCAGATCAAAGATTTCAACATGGCATCCCTGTGTTTATAAGGAACAAGTTGAAGAT
AGCA
Found at i:5872476 original size:46 final size:46
Alignment explanation
Indices: 5872288--5872494 Score: 169
Period size: 44 Copynumber: 4.6 Consensus size: 46
5872278 GATGATTTGG
*
5872288 CATTCCTATGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGA
1 CATTCCTGTGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGA
* * * *** *
5872334 CACTT-CTGTGCTTACAGCGAAGCAGATC-AA-AGATTTTA-A-CATGG
1 CA-TTCCTGTGTTTACAGGGAA-CAGATCGAAGACATAGCAGATC-TGA
* * * * *
5872378 CATCCCTGTGTTTATAGGGAACA-AGTTGAAG--ATAGCAGATTTGG
1 CATTCCTGTGTTTACAGGGAACAGA-TCGAAGACATAGCAGATCTGA
*
5872422 CATCCCTGTGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGA
1 CATTCCTGTGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGA
* *
5872468 CATTCCTGTGCTTACAGCGAAGCAGAT
1 CATTCCTGTGTTTACAGGGAA-CAGAT
5872495 TGAAAATTTC
Statistics
Matches: 124, Mismatches: 24, Indels: 25
0.72 0.14 0.14
Matches are distributed among these distances:
42 1 0.01
43 8 0.06
44 51 0.41
45 5 0.04
46 46 0.37
47 13 0.10
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (46 bp):
CATTCCTGTGTTTACAGGGAACAGATCGAAGACATAGCAGATCTGA
Found at i:5872745 original size:44 final size:45
Alignment explanation
Indices: 5872623--5872821 Score: 258
Period size: 45 Copynumber: 4.5 Consensus size: 45
5872613 TTTACATCGA
* * *
5872623 AGCAGATCCAAGATGACAGATTTGGCATCTTTGTATTAGACGGGG
1 AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
* * *
5872668 AGCAAATCGGAGATAACAGATTTGGCATCTCTGTTTTAGACGGGG
1 AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
* * * *
5872713 AGCAGATTGAAGA-AGCAAATTTGGCGTCTCTGTATTAGACGGGG
1 AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
* *
5872757 AGCAGATCGAAGATAACAGATTTCGCGTCTCTGTATTAGAC-GGG
1 AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
* *
5872801 AGCAGATCAAAGATAGCAGAT
1 AGCAGATCGAAGATAACAGAT
5872822 ATCGCCTTCC
Statistics
Matches: 134, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
44 61 0.46
45 73 0.54
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.25
Consensus pattern (45 bp):
AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
Found at i:5872749 original size:89 final size:88
Alignment explanation
Indices: 5872642--5872807 Score: 260
Period size: 89 Copynumber: 1.9 Consensus size: 88
5872632 AAGATGACAG
* * * *
5872642 ATTTGGCATCTTTGTATTAGACGGGGAGCAAATCGGAGATAACAGATTTGGCATCTCTGTTTTAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGATTTCGCATCTCTGTATTAG
5872707 ACGGGGAGCAGATTGAAGAAGCAA
66 AC-GGGAGCAGATTGAAGAAGCAA
* * *
5872731 ATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAACAGATTTCGCGTCTCTGTATTAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGATTTCGCATCTCTGTATTAG
5872796 ACGGGAGCAGAT
66 ACGGGAGCAGAT
5872808 CAAAGATAGC
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
88 10 0.14
89 60 0.86
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (88 bp):
ATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGATTTCGCATCTCTGTATTAG
ACGGGAGCAGATTGAAGAAGCAA
Found at i:5873195 original size:19 final size:19
Alignment explanation
Indices: 5873171--5873237 Score: 69
Period size: 19 Copynumber: 3.9 Consensus size: 19
5873161 ATAATCTTCA
5873171 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5873190 ATGATATG----C---GAT
1 ATGATATGCAATCTTAGAT
5873202 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
5873220 ATGATATGAAATCTTAGA
1 ATGATATGCAATCTTAGA
5873238 AGATATGATT
Statistics
Matches: 39, Mismatches: 1, Indels: 16
0.70 0.02 0.29
Matches are distributed among these distances:
11 2 0.05
12 8 0.21
15 2 0.05
18 8 0.21
19 19 0.49
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:5873222 original size:18 final size:19
Alignment explanation
Indices: 5873199--5873245 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
5873189 TATGATATGC
*
5873199 GATATGAT-TGCAATCTTA
1 GATATGATATGAAATCTTA
5873217 GATATGATATGAAATCTTA
1 GATATGATATGAAATCTTA
5873236 GA-A-GATATGA
1 GATATGATATGA
5873246 TTTTGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 7 0.26
18 9 0.33
19 11 0.41
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.34
Consensus pattern (19 bp):
GATATGATATGAAATCTTA
Found at i:5873244 original size:22 final size:23
Alignment explanation
Indices: 5873216--5873260 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5873206 TTGCAATCTT
5873216 AGATATGA-TATGAAATCTTAGA
1 AGATATGATTATGAAATCTTAGA
* *
5873238 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGAAATCTTAGA
5873261 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGAAATCTTAGA
Found at i:5874905 original size:3 final size:3
Alignment explanation
Indices: 5874897--5874929 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5874887 CAATAATTAC
5874897 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5874930 AACACAACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5875287 original size:17 final size:17
Alignment explanation
Indices: 5875236--5875287 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
5875226 TGAATGATGT
*
5875236 TATTTATGTTCTTAATTA
1 TATTTAT-TTATTAATTA
* *
5875254 TA-TTATTTAATACTTA
1 TATTTATTTATTAATTA
*
5875270 TATTTATTTATTATTTA
1 TATTTATTTATTAATTA
5875287 T
1 T
5875288 TTTGGAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 9 0.32
17 17 0.61
18 2 0.07
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (17 bp):
TATTTATTTATTAATTA
Found at i:5878028 original size:3 final size:3
Alignment explanation
Indices: 5878020--5878054 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5878010 CTTTCTTTCT
5878020 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
5878055 GCCTTTTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:5880860 original size:9 final size:9
Alignment explanation
Indices: 5880838--5880894 Score: 62
Period size: 9 Copynumber: 6.2 Consensus size: 9
5880828 CAGATTTTCC
5880838 TTTTTCTTT
1 TTTTTCTTT
*
5880847 ATTTTTATTT
1 -TTTTTCTTT
5880857 TTTTGTCTTT
1 TTTT-TCTTT
*
5880867 TCTTTCTTT
1 TTTTTCTTT
*
5880876 CTTTTCTTT
1 TTTTTCTTT
5880885 TTTTT-TTT
1 TTTTTCTTT
5880893 TT
1 TT
5880895 GCTATATGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
8 5 0.12
9 20 0.50
10 15 0.38
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.84
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:5890097 original size:29 final size:30
Alignment explanation
Indices: 5889997--5890124 Score: 92
Period size: 29 Copynumber: 4.4 Consensus size: 30
5889987 TATTTAAAAA
* *
5889997 TATTAAAATATTGATATAA-AATATTATTAAT
1 TATT-AAATATT-ATTTAACAATATAATTAAT
* *
5890028 T-TTAAATATTATTAAAC-ATACTATTTAAT
1 TATTAAATATTATTTAACAATA-TAATTAAT
5890057 TATT---TA-TATTTAACAATATAATTAAT
1 TATTAAATATTATTTAACAATATAATTAAT
** * * *
5890083 TATT-AATATTATTTATTATTTTAATAAAT
1 TATTAAATATTATTTAACAATATAATTAAT
5890112 TATTAAATATTAT
1 TATTAAATATTAT
5890125 AATTTTATTT
Statistics
Matches: 78, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
26 18 0.23
27 5 0.06
28 9 0.12
29 33 0.42
30 12 0.15
31 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (30 bp):
TATTAAATATTATTTAACAATATAATTAAT
Found at i:5890285 original size:23 final size:23
Alignment explanation
Indices: 5890257--5890303 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
5890247 TTTCATAATA
*
5890257 AATATTTT-ATAGTATAAAATATG
1 AATATTTTAATAATAT-AAATATG
5890280 AATATTTTAATAATATAAATATG
1 AATATTTTAATAATATAAATATG
5890303 A
1 A
5890304 GCATTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (23 bp):
AATATTTTAATAATATAAATATG
Found at i:5890309 original size:23 final size:23
Alignment explanation
Indices: 5890260--5890310 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
5890250 CATAATAAAT
* *
5890260 ATTTTATAGTATAAAATATGAAT
1 ATTTTATAATATAAAATATGAAC
*
5890283 ATTTTAATAATAT-AAATATGAGC
1 ATTTT-ATAATATAAAATATGAAC
5890306 ATTTT
1 ATTTT
5890311 TAAAAATCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (23 bp):
ATTTTATAATATAAAATATGAAC
Found at i:5895159 original size:3 final size:3
Alignment explanation
Indices: 5895151--5895181 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
5895141 TACTTTTTTC
*
5895151 TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5895182 TTACTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:5895173 original size:15 final size:15
Alignment explanation
Indices: 5895153--5895182 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5895143 CTTTTTTCTA
5895153 ATAATAATAATAATT
1 ATAATAATAATAATT
5895168 ATAATAATAATAATT
1 ATAATAATAATAATT
5895183 TACTTTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATAATAATAATT
Found at i:5896739 original size:30 final size:30
Alignment explanation
Indices: 5896705--5896763 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
5896695 TATTTTATTA
5896705 TTAATTTTGTTATTATTTTAAAGGTATTTC
1 TTAATTTTGTTATTATTTTAAAGGTATTTC
* *
5896735 TTAATTTTTTTATTATTTTAGAGGTATTT
1 TTAATTTTGTTATTATTTTAAAGGTATTT
5896764 ACTTGTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.63
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGTATTTC
Found at i:5903849 original size:93 final size:93
Alignment explanation
Indices: 5903720--5903891 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
5903710 CGCCCATAAG
* * *
5903720 CGAATTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
5903785 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
5903813 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
5903878 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
5903892 TCAACCATTC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:5903888 original size:46 final size:46
Alignment explanation
Indices: 5903713--5903888 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
5903703 TGTAACCCGC
* * * *
5903713 CCATAAGCGAATTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
5903759 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
5903809 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
5903852 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
5903889 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.56
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:5903907 original size:46 final size:44
Alignment explanation
Indices: 5903764--5903907 Score: 141
Period size: 46 Copynumber: 3.1 Consensus size: 44
5903754 CGCATCCATA
5903764 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT
* * * *
5903811 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCT
5903857 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCA-TCT
5903903 AGTGA
1 AGTGA
5903908 CATGTCACTT
Statistics
Matches: 80, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
44 8 0.10
45 2 0.03
46 33 0.41
47 31 0.39
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCT
Found at i:5905279 original size:18 final size:18
Alignment explanation
Indices: 5905253--5905329 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
5905243 TTTGGCCCAT
5905253 TGCAGTAACAGTAAACAG
1 TGCAGTAACAGTAAACAG
* *
5905271 TGCAATAACAGTACAGTAATAG
1 TGCAGTAACAGT--A--AACAG
*
5905293 TGCAGTAATAGTAAACAG
1 TGCAGTAACAGTAAACAG
* *
5905311 TGCCGTAACAGTAGACAG
1 TGCAGTAACAGTAAACAG
5905329 T
1 T
5905330 ATGTAAGTCC
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
18 31 0.66
20 2 0.04
22 14 0.30
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.21
Consensus pattern (18 bp):
TGCAGTAACAGTAAACAG
Found at i:5906051 original size:114 final size:114
Alignment explanation
Indices: 5905842--5906066 Score: 360
Period size: 114 Copynumber: 2.0 Consensus size: 114
5905832 CTTTTGCACA
* * * * * *
5905842 TGCCCAGGTTTGAACCCAAGACTTCTCAGACATTTTCCAGAACACTTAACCACTGAGGCAGACAT
1 TGCCCAGGCTTGAACCCAAGACTTCTCAGACACTTCCCAGAACACTTAACCACTAACGCAGACAC
*
5905907 ACAGTTATGTCACTTTCTTGTACAATTAAACATTTATGTGCAGCCTCCG
66 ACAGTTATGTCACTTTCTTGCACAATTAAACATTTATGTGCAGCCTCCG
* *
5905956 TGCCTAGGCTTGAACCCAAGACTTCTTAGACACTTCCCAGAACACTTAACCACTAACGCAGACAC
1 TGCCCAGGCTTGAACCCAAGACTTCTCAGACACTTCCCAGAACACTTAACCACTAACGCAGACAC
*
5906021 ACAGTTTTGTCACTTTCTTGCACAATTAAACATTTATGTGCAGCCT
66 ACAGTTATGTCACTTTCTTGCACAATTAAACATTTATGTGCAGCCT
5906067 TCTAATTGTT
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (114 bp):
TGCCCAGGCTTGAACCCAAGACTTCTCAGACACTTCCCAGAACACTTAACCACTAACGCAGACAC
ACAGTTATGTCACTTTCTTGCACAATTAAACATTTATGTGCAGCCTCCG
Found at i:5906676 original size:8 final size:8
Alignment explanation
Indices: 5906656--5906708 Score: 58
Period size: 8 Copynumber: 6.6 Consensus size: 8
5906646 AAATAAGTAA
5906656 TATATTAAT
1 TATATT-AT
5906665 T-TA-TAT
1 TATATTAT
5906671 TAT-TATAT
1 TATAT-TAT
5906679 TATATTAT
1 TATATTAT
5906687 TATATATAT
1 TATAT-TAT
5906696 TATATTAT
1 TATATTAT
5906704 TATAT
1 TATAT
5906709 ATATATGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
6 3 0.08
7 2 0.05
8 24 0.62
9 10 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATATTAT
Found at i:5906696 original size:17 final size:17
Alignment explanation
Indices: 5906668--5906712 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
5906658 TATTAATTTA
5906668 TATTAT-TATATTATAT
1 TATTATATATATTATAT
5906684 TATTATATATATTATAT
1 TATTATATATATTATAT
5906701 TATTATATATAT
1 TATTATATATAT
5906713 ATGTAAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTATATATATTATAT
Found at i:5910684 original size:28 final size:28
Alignment explanation
Indices: 5910652--5910708 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
5910642 TATGGTACTC
5910652 AGTGTACGAAATATTGAGAATGACACTT
1 AGTGTACGAAATATTGAGAATGACACTT
* *
5910680 AGTGTGCGAGATATTGAGAATGACACTT
1 AGTGTACGAAATATTGAGAATGACACTT
5910708 A
1 A
5910709 TTGTGCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.28
Consensus pattern (28 bp):
AGTGTACGAAATATTGAGAATGACACTT
Found at i:5910721 original size:28 final size:28
Alignment explanation
Indices: 5910660--5910721 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
5910650 TCAGTGTACG
*
5910660 AAATATTGAGAATGACACTTAGTGTGCG
1 AAATATTGAGAATGACACTTAGTGTGCA
* *
5910688 AGATATTGAGAATGACACTTATTGTGCA
1 AAATATTGAGAATGACACTTAGTGTGCA
5910716 AAATAT
1 AAATAT
5910722 CGAATGATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.31
Consensus pattern (28 bp):
AAATATTGAGAATGACACTTAGTGTGCA
Found at i:5916339 original size:31 final size:31
Alignment explanation
Indices: 5916304--5916374 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
5916294 AAATACAAAA
5916304 AAGTCACTAAAATA-TTCAAAAGTTTTCATTT
1 AAGTCACTAAAATATTTCAAAA-TTTTCATTT
* * * * *
5916335 AAGTCATTGAACTATTTGAAAATTTTTATTT
1 AAGTCACTAAAATATTTCAAAATTTTCATTT
5916366 AAGTCACTA
1 AAGTCACTA
5916375 GGCTGTTAAG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
31 26 0.81
32 6 0.19
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.41
Consensus pattern (31 bp):
AAGTCACTAAAATATTTCAAAATTTTCATTT
Found at i:5920290 original size:18 final size:18
Alignment explanation
Indices: 5920262--5920305 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
5920252 AATTGAAATG
5920262 ATTTGGACATATGTGGTAA
1 ATTT-GACATATGTGGTAA
5920281 ATTTGACATATGTGGTAA
1 ATTTGACATATGTGGTAA
5920299 ATTTGAC
1 ATTTGAC
5920306 TTAGTGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.39
Consensus pattern (18 bp):
ATTTGACATATGTGGTAA
Found at i:5923689 original size:12 final size:12
Alignment explanation
Indices: 5923672--5923700 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5923662 GGCACTAATC
5923672 CTGTAAGTATTT
1 CTGTAAGTATTT
5923684 CTGTAAGTATTT
1 CTGTAAGTATTT
5923696 CTGTA
1 CTGTA
5923701 TTTGGTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.48
Consensus pattern (12 bp):
CTGTAAGTATTT
Found at i:5926747 original size:18 final size:18
Alignment explanation
Indices: 5926720--5926758 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
5926710 ATCTATATTG
*
5926720 ATCACCAGAGTTTCAAGT
1 ATCACAAGAGTTTCAAGT
5926738 ATCACAAGAGTTTCAAGT
1 ATCACAAGAGTTTCAAGT
5926756 ATC
1 ATC
5926759 TCCTTACTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (18 bp):
ATCACAAGAGTTTCAAGT
Found at i:5931312 original size:17 final size:18
Alignment explanation
Indices: 5931267--5931319 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
5931257 TATATAATTG
*
5931267 ATAAAAATAATAAAATGTA
1 ATAAAAA-ATTAAAATGTA
5931286 CATAATAAAATTAAAATGT-
1 -ATAA-AAAATTAAAATGTA
5931305 ATAAAAAATTAAAAT
1 ATAAAAAATTAAAAT
5931320 AATTTTTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 11 0.35
18 4 0.13
20 13 0.42
21 3 0.10
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (18 bp):
ATAAAAAATTAAAATGTA
Found at i:5932000 original size:13 final size:13
Alignment explanation
Indices: 5931982--5932010 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5931972 CTTGGTTCAA
5931982 TTAGAAATTTATT
1 TTAGAAATTTATT
5931995 TTAGAAATTTATT
1 TTAGAAATTTATT
5932008 TTA
1 TTA
5932011 TAGTTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (13 bp):
TTAGAAATTTATT
Found at i:5932123 original size:29 final size:29
Alignment explanation
Indices: 5932085--5932141 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
5932075 TTATAATTTC
5932085 AACACTTTTAA-AAAAAATAATTTAACTTA
1 AACACTTTTAATAAAAAAT-ATTTAACTTA
* * *
5932114 AACATTTTTAATATAAAATTTTTAACTT
1 AACACTTTTAATAAAAAATATTTAACTT
5932142 TGACTCCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (29 bp):
AACACTTTTAATAAAAAATATTTAACTTA
Found at i:5933096 original size:62 final size:62
Alignment explanation
Indices: 5932999--5933122 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
5932989 ACGGAAGTAT
5932999 TTAAATTTGGTATATTTATTTATTGAGCTAGTTGGTACATAAATTTAAAAATTGTAAATTAA
1 TTAAATTTGGTATATTTATTTATTGAGCTAGTTGGTACATAAATTTAAAAATTGTAAATTAA
5933061 TTAAATTTGGTATATTTATTTATTGAGCTAGTTGGTACATAAATTTAAAAATTGTAAATTAA
1 TTAAATTTGGTATATTTATTTATTGAGCTAGTTGGTACATAAATTTAAAAATTGTAAATTAA
5933123 CTTGATTTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (62 bp):
TTAAATTTGGTATATTTATTTATTGAGCTAGTTGGTACATAAATTTAAAAATTGTAAATTAA
Found at i:5935531 original size:30 final size:32
Alignment explanation
Indices: 5935492--5935551 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
5935482 GGGAAGAAGT
*
5935492 AGCAGTTAATA-A-AAAGAAAAGATTTGGAGA
1 AGCACTTAATATATAAAGAAAAGATTTGGAGA
5935522 AGCACTTAATATTATAAAGAAAAGATTTGG
1 AGCACTTAATA-TATAAAGAAAAGATTTGG
5935552 TTAAATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 10 0.38
32 1 0.04
33 15 0.58
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (32 bp):
AGCACTTAATATATAAAGAAAAGATTTGGAGA
Found at i:5942588 original size:29 final size:29
Alignment explanation
Indices: 5942553--5942626 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
5942543 GTTGTGAGAT
* *
5942553 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
5942582 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
5942611 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
5942627 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:5950952 original size:29 final size:29
Alignment explanation
Indices: 5950917--5950990 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
5950907 GTTGTGAGAT
* *
5950917 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
5950946 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
5950975 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
5950991 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:5964729 original size:14 final size:14
Alignment explanation
Indices: 5964710--5964741 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
5964700 AGGTCATTTA
5964710 GCCCAACCAAACTG
1 GCCCAACCAAACTG
5964724 GCCCAACCAAACTG
1 GCCCAACCAAACTG
5964738 GCCC
1 GCCC
5964742 GGTGATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:5969853 original size:14 final size:14
Alignment explanation
Indices: 5969834--5969865 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
5969824 AGGTCATTTA
5969834 GCCCAACCAAACTG
1 GCCCAACCAAACTG
5969848 GCCCAACCAAACTG
1 GCCCAACCAAACTG
5969862 GCCC
1 GCCC
5969866 GGTGATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:5978106 original size:18 final size:18
Alignment explanation
Indices: 5978083--5978119 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5978073 TTTGCTGAAG
5978083 ACATGTTTTACAACAACA
1 ACATGTTTTACAACAACA
*
5978101 ACATGTTTTACAGCAACA
1 ACATGTTTTACAACAACA
5978119 A
1 A
5978120 GAAACAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (18 bp):
ACATGTTTTACAACAACA
Found at i:5983203 original size:11 final size:11
Alignment explanation
Indices: 5983175--5983217 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
5983165 TTGACCTTTC
5983175 CAAGGTATGGG
1 CAAGGTATGGG
*
5983186 -TAGGTATGGG
1 CAAGGTATGGG
5983196 CAAGGTATGGG
1 CAAGGTATGGG
*
5983207 CAAGGAATGGG
1 CAAGGTATGGG
5983218 TATATTCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.28, C:0.07, G:0.47, T:0.19
Consensus pattern (11 bp):
CAAGGTATGGG
Found at i:5987333 original size:18 final size:18
Alignment explanation
Indices: 5987259--5987333 Score: 78
Period size: 18 Copynumber: 4.2 Consensus size: 18
5987249 CCCAACTACT
*
5987259 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
5987277 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
* * ***
5987295 GTATATGTAAATAGCGTC
1 GTATACGTGAATAGTACC
*
5987313 GTATACATGAATAGTACC
1 GTATACGTGAATAGTACC
5987331 GTA
1 GTA
5987334 AACGGTCGTA
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:5987893 original size:11 final size:11
Alignment explanation
Indices: 5987877--5987920 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
5987867 AGGTATGAGT
5987877 AGGTATGGGAA
1 AGGTATGGGAA
*
5987888 AGGTATGGGCA
1 AGGTATGGGAA
*
5987899 AGGTATGGGCA
1 AGGTATGGGAA
*
5987910 AGGAATGGGAA
1 AGGTATGGGAA
5987921 TATTCTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.45, T:0.16
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:5994011 original size:144 final size:144
Alignment explanation
Indices: 5993855--5994125 Score: 436
Period size: 144 Copynumber: 1.9 Consensus size: 144
5993845 GGATAGATGT
* *
5993855 AATGTAACCAAATTCGTTAGCCTCCCAATTTCATGCGGAATGGATCCATTGAGTTGGTTGT-CAT
1 AATGTAACCAAATTCGTCAGCCTCCCAATTTCATGCGGAATGGATCCATTGAGTAGGTT-TCCAT
* **
5993919 TAAGAACCAGTGATGCAAGATTGGTTAAGTGGTTGACAGAAGATGGGATTGGACCAACAAGCAGA
65 AAAGAACCAACGATGCAAGATTGGTTAAGTGGTTGACAGAAGATGGGATTGGACCAACAAGCAGA
5993984 TTAGAAGATAGCTCC
130 TTAGAAGATAGCTCC
* * * *
5993999 AATGTAATCAAATTTGTCAGTCTCCCAATTTCTTGCGGAATGGATCCATTGAGTAGGTTTCCATA
1 AATGTAACCAAATTCGTCAGCCTCCCAATTTCATGCGGAATGGATCCATTGAGTAGGTTTCCATA
*
5994064 AAGAACCAACGATGCAAGATTGGTTAAGTTGTTGACAGAAGATGGGATTGGACCAACAAGCA
66 AAGAACCAACGATGCAAGATTGGTTAAGTGGTTGACAGAAGATGGGATTGGACCAACAAGCA
5994126 TGTTCCTTGA
Statistics
Matches: 116, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
143 1 0.01
144 115 0.99
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (144 bp):
AATGTAACCAAATTCGTCAGCCTCCCAATTTCATGCGGAATGGATCCATTGAGTAGGTTTCCATA
AAGAACCAACGATGCAAGATTGGTTAAGTGGTTGACAGAAGATGGGATTGGACCAACAAGCAGAT
TAGAAGATAGCTCC
Found at i:5995190 original size:5 final size:5
Alignment explanation
Indices: 5995160--5995189 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
5995150 AATCTTTTTA
*
5995160 CTCCC CTCCC CTCCC CTCCC CTCCC ATCCC
1 CTCCC CTCCC CTCCC CTCCC CTCCC CTCCC
5995190 AACCTCCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.03, C:0.77, G:0.00, T:0.20
Consensus pattern (5 bp):
CTCCC
Found at i:5996577 original size:18 final size:18
Alignment explanation
Indices: 5996556--5996590 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5996546 AATTAATAAT
*
5996556 TTTTTATAATTTATTTAA
1 TTTTGATAATTTATTTAA
*
5996574 TTTTGATATTTTATTTA
1 TTTTGATAATTTATTTA
5996591 TATGAATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTGATAATTTATTTAA
Found at i:6001833 original size:16 final size:18
Alignment explanation
Indices: 6001802--6001838 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
6001792 TTTACAAATG
6001802 CAAAAAACCCTAAAAGCC
1 CAAAAAACCCTAAAAGCC
6001820 CAAAAAA-CCT-AAAGCC
1 CAAAAAACCCTAAAAGCC
6001836 CAA
1 CAA
6001839 TGGCCAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 3 0.16
18 7 0.37
ACGTcount: A:0.57, C:0.32, G:0.05, T:0.05
Consensus pattern (18 bp):
CAAAAAACCCTAAAAGCC
Found at i:6002054 original size:17 final size:16
Alignment explanation
Indices: 6002007--6002063 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
6001997 AGAAGATAGG
**
6002007 AAACAAAAACATCGAA
1 AAACAAAAACAAAGAA
**
6002023 CAAACAAAATGAAAGTAA
1 -AAACAAAAACAAAG-AA
6002041 AAACAAAAACAAAGAA
1 AAACAAAAACAAAGAA
6002057 AAA-AAAA
1 AAACAAAA
6002064 CAATATATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 4 0.12
16 5 0.15
17 22 0.67
18 2 0.06
ACGTcount: A:0.75, C:0.12, G:0.07, T:0.05
Consensus pattern (16 bp):
AAACAAAAACAAAGAA
Found at i:6009697 original size:47 final size:46
Alignment explanation
Indices: 6009642--6009770 Score: 154
Period size: 44 Copynumber: 2.8 Consensus size: 46
6009632 ATGCCATAGG
* *
6009642 TACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTTCGCTCGGAG
1 TACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTTC-CTCGAAA
* * * *
6009689 TATCTATACCATGGCCCAAAGCCAACTCAAGATAAC--CTTCGAAA
1 TACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTTCCTCGAAA
* * *
6009733 TGCCTATACCATGGCCCGAAGCCTACTCAAGGCAACTT
1 TACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTT
6009771 GCACCTGAAG
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
44 34 0.50
45 1 0.01
47 33 0.49
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.20
Consensus pattern (46 bp):
TACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTTCCTCGAAA
Found at i:6009755 original size:44 final size:46
Alignment explanation
Indices: 6009642--6009763 Score: 149
Period size: 47 Copynumber: 2.7 Consensus size: 46
6009632 ATGCCATAGG
* * *
6009642 TACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTTCGCTCGGAG
1 TACCTATACCATGGCCCGAAGCCAACTCAAGATAAC-TCGCTCGAAA
* * *
6009689 TATCTATACCATGGCCCAAAGCCAACTCAAGATAAC-C-TTCGAAA
1 TACCTATACCATGGCCCGAAGCCAACTCAAGATAACTCGCTCGAAA
* *
6009733 TGCCTATACCATGGCCCGAAGCCTACTCAAG
1 TACCTATACCATGGCCCGAAGCCAACTCAAG
6009764 GCAACTTGCA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
44 31 0.48
45 1 0.02
47 33 0.51
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.20
Consensus pattern (46 bp):
TACCTATACCATGGCCCGAAGCCAACTCAAGATAACTCGCTCGAAA
Found at i:6017431 original size:47 final size:46
Alignment explanation
Indices: 6017313--6017489 Score: 189
Period size: 47 Copynumber: 3.8 Consensus size: 46
6017303 CATACCATAG
*
6017313 GTACCTATACCATGGCCCGAAGCCAACTCAAAGTAACCTATCACT-GAA
1 GTACCTATACCATGGCCCGAAGCCAACTCAAGGTAA-CT-TC-CTCGAA
* *
6017361 GTACCTATACCATGGCCCAAAGCCAACTCAAGGTAACTTCGCTCGGA
1 GTACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTTC-CTCGAA
* * * *
6017408 GTATCTATACCATGGCCCGAAGCCAATTCAAGATAACAT-C-CGAA
1 GTACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTTCCTCGAA
* ** * *
6017452 ATGGCTATACCATGGCCCGAAGCCTACTCAAGGCAACT
1 GTACCTATACCATGGCCCGAAGCCAACTCAAGGTAACT
6017490 CGCACCTGAA
Statistics
Matches: 110, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
44 33 0.30
45 1 0.01
46 4 0.04
47 38 0.35
48 34 0.31
ACGTcount: A:0.33, C:0.31, G:0.18, T:0.19
Consensus pattern (46 bp):
GTACCTATACCATGGCCCGAAGCCAACTCAAGGTAACTTCCTCGAA
Found at i:6018850 original size:22 final size:23
Alignment explanation
Indices: 6018820--6018866 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
6018810 CACGTTAGAT
6018820 AACATAATATATAAATAAAAATA
1 AACATAATATATAAATAAAAATA
* *
6018843 AACA-AATATTTATATAAAAATA
1 AACATAATATATAAATAAAAATA
6018865 AA
1 AA
6018867 ATATAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (23 bp):
AACATAATATATAAATAAAAATA
Done.