Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 33 of 126
Found at i:9497629 original size:107 final size:108
Alignment explanation
Indices: 9497478--9497692 Score: 252
Period size: 107 Copynumber: 2.0 Consensus size: 108
9497468 ATTATGACCA
* * * * * * *
9497478 AAATACCTCCATACGGTAGAATTACCGAAATATCCCTATAGGGTAAAATGATCGAAATACCCCTA
1 AAATACCCCCATACGGTAGAATGACCGAAATACCCCCACAGGGTAAAATGACCGAAATACCCCCA
* *
9497543 TAA-GAAAAATGACCAAAATACCCCTACAGGGTAAAATGACTG
66 TAAGGAAAAATGACCAAAACACCCCCACAGGGTAAAATGACTG
* ** * *
9497585 AAATACCCCCATAGGGTAGAATGATTGAAATACCCCCACAGGGTAGAATGACCGAAGTACCCCCA
1 AAATACCCCCATACGGTAGAATGACCGAAATACCCCCACAGGGTAAAATGACCGAAATACCCCCA
* * * * *
9497650 TAAGGTAAAATGATCGAAACACCCCCATAGGGTAAAATTACTG
66 TAAGGAAAAATGACCAAAACACCCCCACAGGGTAAAATGACTG
9497693 TTATATCCCT
Statistics
Matches: 88, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
107 56 0.64
108 32 0.36
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (108 bp):
AAATACCCCCATACGGTAGAATGACCGAAATACCCCCACAGGGTAAAATGACCGAAATACCCCCA
TAAGGAAAAATGACCAAAACACCCCCACAGGGTAAAATGACTG
Found at i:9503226 original size:27 final size:26
Alignment explanation
Indices: 9503195--9503247 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
9503185 CTATTATGAA
9503195 CATATAGGAAAATGGAAGCCTTTGTGG
1 CATATAGG-AAATGGAAGCCTTTGTGG
**
9503222 CATATCTGAAATGGAAGCCTTTGTGG
1 CATATAGGAAATGGAAGCCTTTGTGG
9503248 TAAATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.28
Consensus pattern (26 bp):
CATATAGGAAATGGAAGCCTTTGTGG
Found at i:9505442 original size:22 final size:22
Alignment explanation
Indices: 9505410--9505465 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
9505400 TACTTGTCAC
*
9505410 TATGCTACAACACGGAGGGTTG
1 TATGCTGCAACACGGAGGGTTG
*
9505432 TATGCTGCAACATGGAGGGTTG
1 TATGCTGCAACACGGAGGGTTG
* *
9505454 GATGCCGCAACA
1 TATGCTGCAACA
9505466 TAGGGAACAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.21
Consensus pattern (22 bp):
TATGCTGCAACACGGAGGGTTG
Found at i:9518953 original size:19 final size:19
Alignment explanation
Indices: 9518929--9518972 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
9518919 AGGGATCAAA
* *
9518929 TTGAGACAAATCA-GAAATT
1 TTGAGA-AAAACATGAAAAT
9518948 TTGAGAAAAACATGAAAAT
1 TTGAGAAAAACATGAAAAT
9518967 TTGAGA
1 TTGAGA
9518973 TGCAGAGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (19 bp):
TTGAGAAAAACATGAAAAT
Found at i:9520130 original size:40 final size:40
Alignment explanation
Indices: 9520075--9520235 Score: 216
Period size: 40 Copynumber: 4.0 Consensus size: 40
9520065 GAGGTACCAC
9520075 AGTACAAAAAGGGGCACATATGTGCATTTAAGGGTATCGA
1 AGTACAAAAAGGGGCACATATGTGCATTTAAGGGTATCGA
* * * * *
9520115 AGTACAAAAAGGGGCACGTATGAGGATTCAAGGTTATCGA
1 AGTACAAAAAGGGGCACATATGTGCATTTAAGGGTATCGA
* *
9520155 AGTACAAAAAGGGGCACGTATGTGC-TTTCAAGGGTACCGA
1 AGTACAAAAAGGGGCACATATGTGCATTT-AAGGGTATCGA
* * *
9520195 AGTACAAACAGGGGCACATATGGGCATTTAGGGGTATCGA
1 AGTACAAAAAGGGGCACATATGTGCATTTAAGGGTATCGA
9520235 A
1 A
9520236 ATAAGTCTCA
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
39 2 0.02
40 99 0.95
41 3 0.03
ACGTcount: A:0.35, C:0.14, G:0.30, T:0.20
Consensus pattern (40 bp):
AGTACAAAAAGGGGCACATATGTGCATTTAAGGGTATCGA
Found at i:9521013 original size:22 final size:21
Alignment explanation
Indices: 9520984--9521026 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
9520974 GATGACAAAT
* *
9520984 TTTATTTTGTTATTATTTTAC
1 TTTATTTTATTATTAATTTAC
9521005 TTTACTTTTATTATTAATTTAC
1 TTTA-TTTTATTATTAATTTAC
9521027 AATTATACCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTATTTTATTATTAATTTAC
Found at i:9523375 original size:5 final size:5
Alignment explanation
Indices: 9523365--9523389 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
9523355 CTTAGTAATT
9523365 ATTGA ATTGA ATTGA ATTGA ATTGA
1 ATTGA ATTGA ATTGA ATTGA ATTGA
9523390 TAGTTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
ATTGA
Found at i:9524576 original size:20 final size:20
Alignment explanation
Indices: 9524529--9524624 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
9524519 TTGTATGGGA
9524529 TTTGCACTTCGGTGCCTCTG
1 TTTGCACTTCGGTGCCTCTG
* *
9524549 TATACACTTCGGTGCCTCTG
1 TTTGCACTTCGGTGCCTCTG
* *
9524569 TTTGCACTAT-AGTGCCTCTA
1 TTTGCACT-TCGGTGCCTCTG
* *
9524589 CTTGCACATTC-GTGCCTTTG
1 TTTGCAC-TTCGGTGCCTCTG
* *
9524609 TATGCACTTTGGTGCC
1 TTTGCACTTCGGTGCC
9524625 CCTATTATGC
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
19 2 0.03
20 56 0.93
21 2 0.03
ACGTcount: A:0.12, C:0.28, G:0.21, T:0.39
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCTCTG
Found at i:9524623 original size:60 final size:62
Alignment explanation
Indices: 9524530--9524650 Score: 151
Period size: 60 Copynumber: 2.0 Consensus size: 62
9524520 TGTATGGGAT
* *
9524530 TTGCACTTCGGTGCCTCTGTATACACTTCGGTGCCTCTGTT-TGCA-CTAT-AGTGCCTCTAC
1 TTGCACTTCGGTGCCTCTGTATACACTTCGGTGCCCCTATTATGCATCTATGA-TGCCTCTAC
* * *
9524590 TTGCACATTC-GTGCCTTTGTATGCACTTTGGTGCCCCTATTATGCATCTATGATGCCTCTA
1 TTGCAC-TTCGGTGCCTCTGTATACACTTCGGTGCCCCTATTATGCATCTATGATGCCTCTA
9524651 GTGTAGTGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
60 32 0.62
61 7 0.13
62 12 0.23
63 1 0.02
ACGTcount: A:0.15, C:0.28, G:0.19, T:0.38
Consensus pattern (62 bp):
TTGCACTTCGGTGCCTCTGTATACACTTCGGTGCCCCTATTATGCATCTATGATGCCTCTAC
Found at i:9525619 original size:20 final size:20
Alignment explanation
Indices: 9525572--9525625 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
9525562 AATTTTAATC
*
9525572 AAGTATCGATACACATATATA
1 AAGTATCGATAC-CATAAATA
*
9525593 AAGTATCGATACCATAAATT
1 AAGTATCGATACCATAAATA
*
9525613 AATTATCGATACC
1 AAGTATCGATACC
9525626 CCTATTTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (20 bp):
AAGTATCGATACCATAAATA
Found at i:9528365 original size:42 final size:41
Alignment explanation
Indices: 9528309--9528540 Score: 200
Period size: 43 Copynumber: 5.5 Consensus size: 41
9528299 CATTGAATAA
*
9528309 AAAGGGGTTGCTAAGTG-TGGATTCCCCGAATTATTGACTTT
1 AAAGGGGTTGCTAAGTGCT-GATTCCCCGTATTATTGACTTT
* *
9528350 AAAGGTGGTTGCTAAGTGCTGATTCAACCGTATCT-TTGACTGTC
1 AAAGG-GGTTGCTAAGTGCTGATTC-CCCGTAT-TATTGACT-TT
* * * * *
9528394 AACGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATAT
1 AAAGGGGTTGCTAAGTGCTGATTCCCCGTATTATTGACTTT
* * * *
9528435 AAAGGTGGTTGCTAAGTGCTGAATCCACCGTATTTTTTACTGTG
1 AAAGG-GGTTGCTAAGTGCTGATTCC-CCGTATTATTGACT-TT
* * * * *
9528479 AAAGGGGCTGCTATGTGCTGATTCCCCGTATCACTGAATTT
1 AAAGGGGTTGCTAAGTGCTGATTCCCCGTATTATTGACTTT
*
9528520 -AAGTTGGTTGCTAAGTGCTGA
1 AAAG-GGGTTGCTAAGTGCTGA
9528541 ATCCACCGAG
Statistics
Matches: 150, Mismatches: 31, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
40 3 0.02
41 25 0.17
42 54 0.36
43 57 0.38
44 11 0.07
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (41 bp):
AAAGGGGTTGCTAAGTGCTGATTCCCCGTATTATTGACTTT
Found at i:9528455 original size:85 final size:84
Alignment explanation
Indices: 9528309--9528548 Score: 311
Period size: 85 Copynumber: 2.8 Consensus size: 84
9528299 CATTGAATAA
* * * * *
9528309 AAAGGGGTTGCTAAGTG-TGGATTCCCCGAATTATTGACTTTAAAGGTGGTTGCTAAGTGCTGAT
1 AAAGGGGTTGCTATGTGCT-GATTCCCCGTATTACTGA-ATTAAAGGTGGTTGCTAAGTGCTGAA
9528373 TCAACCGTATCTTTGACTGTC
64 TCAACCGTATCTTTGACTGTC
*
9528394 AACGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATATAAAGGTGGTTGCTAAGTGCTGAAT
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAAT-TAAAGGTGGTTGCTAAGTGCTGAAT
* * * *
9528459 CCACCGTATTTTTTACTGTG
65 CAACCGTATCTTTGACTGTC
* * * *
9528479 AAAGGGGCTGCTATGTGCTGATTCCCCGTATCACTGAATTTAAGTTGGTTGCTAAGTGCTGAATC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATTAAAGGTGGTTGCTAAGTGCTGAATC
*
9528544 CACCG
66 AACCG
9528549 AGTAACGAAT
Statistics
Matches: 138, Mismatches: 15, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
84 30 0.22
85 107 0.78
86 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (84 bp):
AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATTAAAGGTGGTTGCTAAGTGCTGAATC
AACCGTATCTTTGACTGTC
Found at i:9535728 original size:14 final size:13
Alignment explanation
Indices: 9535695--9535761 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 13
9535685 TAAACACTAG
9535695 AAAATAAATCACA-A
1 AAAATAAAT-A-ATA
9535709 AAAATAAATAATA
1 AAAATAAATAATA
*
9535722 AAGAATAAAAAATTA
1 AA-AATAAATAA-TA
9535737 ATTAAATAAA-AATA
1 A--AAATAAATAATA
9535751 AAAATAAATAA
1 AAAATAAATAA
9535762 ACCAAATTGC
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
12 8 0.17
13 6 0.13
14 20 0.43
15 5 0.11
16 6 0.13
17 1 0.02
ACGTcount: A:0.75, C:0.03, G:0.01, T:0.21
Consensus pattern (13 bp):
AAAATAAATAATA
Found at i:9541029 original size:40 final size:40
Alignment explanation
Indices: 9540928--9541068 Score: 194
Period size: 40 Copynumber: 3.5 Consensus size: 40
9540918 TAGCGGCGTT
** *
9540928 TATGAGAAAAACGCCACAAAAGGTCAAGCATTAGTGGCGTT
1 TATGAGAAAAACGCCACAAAAGGTCAAGCATTAACGGCG-C
* * *
9540969 TATGAGAAAAATGCCGCAAAAAGTCAAGCATTAACGGCGC
1 TATGAGAAAAACGCCACAAAAGGTCAAGCATTAACGGCGC
9541009 TATGAGAAAAACGCCACAAAAGGTCAAGCATTAACAGG-GC
1 TATGAGAAAAACGCCACAAAAGGTCAAGCATTAAC-GGCGC
*
9541049 TATGAGAAAAATGCCACAAA
1 TATGAGAAAAACGCCACAAA
9541069 GTATCATTTT
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
40 53 0.60
41 36 0.40
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (40 bp):
TATGAGAAAAACGCCACAAAAGGTCAAGCATTAACGGCGC
Found at i:9541177 original size:21 final size:21
Alignment explanation
Indices: 9541153--9541196 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
9541143 CCCTATCTTT
9541153 TCCCTAAAAATT-TTCCCCAAA
1 TCCCT-AAAATTATTCCCCAAA
*
9541174 TCCCTAAATTTATTCCCCAAA
1 TCCCTAAAATTATTCCCCAAA
9541195 TC
1 TC
9541197 AAAATCTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (21 bp):
TCCCTAAAATTATTCCCCAAA
Found at i:9551866 original size:22 final size:22
Alignment explanation
Indices: 9551841--9551884 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
9551831 TGTGCTGCTG
*
9551841 TTTGCAATTTTTGGATT-ATTTA
1 TTTGCAAATTTT-GATTAATTTA
*
9551863 TTTGTAAATTTTGATTAATTTA
1 TTTGCAAATTTTGATTAATTTA
9551885 ATTATATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.59
Consensus pattern (22 bp):
TTTGCAAATTTTGATTAATTTA
Found at i:9553334 original size:21 final size:21
Alignment explanation
Indices: 9553310--9553351 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
9553300 CACTATATGA
9553310 ACTC-GTAATTTTTCTATTTAT
1 ACTCTGTAATTTTTCT-TTTAT
* *
9553331 ACTCTTTTATTTTTCTTTTAT
1 ACTCTGTAATTTTTCTTTTAT
9553352 TTTATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.19, C:0.14, G:0.02, T:0.64
Consensus pattern (21 bp):
ACTCTGTAATTTTTCTTTTAT
Found at i:9557826 original size:9 final size:9
Alignment explanation
Indices: 9557814--9557883 Score: 74
Period size: 9 Copynumber: 8.0 Consensus size: 9
9557804 TATATCATAT
9557814 CATAACTTA
1 CATAACTTA
9557823 CATAACTTA
1 CATAACTTA
9557832 CATAACTTA
1 CATAACTTA
9557841 CATAA--TA
1 CATAACTTA
*
9557848 CATAA-ATA
1 CATAACTTA
* * *
9557856 TATATCATA
1 CATAACTTA
9557865 TCATAACTTA
1 -CATAACTTA
9557875 CATAACTTA
1 CATAACTTA
9557884 ATCATACTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
7 7 0.13
8 5 0.09
9 35 0.66
10 6 0.11
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:9557987 original size:10 final size:10
Alignment explanation
Indices: 9557972--9557996 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9557962 CAATGACATG
9557972 ATTTAAATCA
1 ATTTAAATCA
9557982 ATTTAAATCA
1 ATTTAAATCA
9557992 ATTTA
1 ATTTA
9557997 GTACAAGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTTAAATCA
Found at i:9559456 original size:43 final size:43
Alignment explanation
Indices: 9559408--9559586 Score: 223
Period size: 43 Copynumber: 4.2 Consensus size: 43
9559398 AGAACATGAC
* * *
9559408 CTTTAGCAGCGTTTGTGGGGAAAGTGCTGCTAAAGGTCATGTT
1 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCATGTT
* * * *
9559451 CTTTAGTGGTGTTTGTGGGGAAAGCGCCACTAAAGATCATGTT
1 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCATGTT
* * *
9559494 CTTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCATATT
1 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCATGTT
* * * *
9559537 CTGTAGCGGCGCTTGTGGGGAAAGCGCTGTTAAAGGTCATGTT
1 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCATGTT
*
9559580 CTATAGC
1 CTTTAGC
9559587 AGCATTTTTC
Statistics
Matches: 114, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 114 1.00
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.30
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCATGTT
Found at i:9560993 original size:17 final size:18
Alignment explanation
Indices: 9560971--9561004 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
9560961 AGTTATTTGG
*
9560971 ATTGTGGTTT-GGGTTTC
1 ATTGTGCTTTAGGGTTTC
9560988 ATTGTGCTTTAGGGTTT
1 ATTGTGCTTTAGGGTTT
9561005 TCATGCATGT
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:0.09, C:0.06, G:0.32, T:0.53
Consensus pattern (18 bp):
ATTGTGCTTTAGGGTTTC
Found at i:9561644 original size:21 final size:19
Alignment explanation
Indices: 9561612--9561650 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
9561602 AAAAATTATA
*
9561612 AATAAAAATAAATAATAAT
1 AATAAAAATAAAGAATAAT
9561631 AATAATAACATAAAGAATAA
1 AATAA-AA-ATAAAGAATAA
9561651 CCTACACAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (19 bp):
AATAAAAATAAAGAATAAT
Found at i:9561972 original size:20 final size:20
Alignment explanation
Indices: 9561936--9561974 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9561926 TCAAAGAAAT
*
9561936 ATATAAAATATATTTTAAAA
1 ATATAAAATATAATTTAAAA
9561956 ATATAATAATA-AATTTAAA
1 ATATAA-AATATAATTTAAA
9561975 TTTTATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATAAAATATAATTTAAAA
Found at i:9565950 original size:31 final size:31
Alignment explanation
Indices: 9565915--9565996 Score: 87
Period size: 33 Copynumber: 2.6 Consensus size: 31
9565905 CTAATTTTTA
*
9565915 ATTTTTATTTTTAAAATT-AT-ATATCTTTG
1 ATTTTTATTTATAAAATTAATCATATCTTTG
* *
9565944 ACATTTTAGTTTATATAATTAATCATATCTTTG
1 A-TTTTTA-TTTATAAAATTAATCATATCTTTG
9565977 ATTTTTATTTAAATAAAATT
1 ATTTTTATTT--ATAAAATT
9565997 TAATGAAAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
29 1 0.02
30 5 0.12
31 12 0.29
32 7 0.17
33 17 0.40
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.56
Consensus pattern (31 bp):
ATTTTTATTTATAAAATTAATCATATCTTTG
Found at i:9566094 original size:13 final size:13
Alignment explanation
Indices: 9566078--9566104 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9566068 AAAATTTATC
9566078 TAATAAATAAATA
1 TAATAAATAAATA
9566091 TAATAAATAAATA
1 TAATAAATAAATA
9566104 T
1 T
9566105 TTATGAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAATAAATAAATA
Found at i:9567303 original size:18 final size:20
Alignment explanation
Indices: 9567269--9567307 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
9567259 TGTTTAGTTA
9567269 TTTGTTTTTAGTTTAATTTT
1 TTTGTTTTTAGTTTAATTTT
9567289 TTTG-TTTTA-TTTAATTTT
1 TTTGTTTTTAGTTTAATTTT
9567307 T
1 T
9567308 CACATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 5 0.26
20 4 0.21
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (20 bp):
TTTGTTTTTAGTTTAATTTT
Found at i:9571673 original size:11 final size:11
Alignment explanation
Indices: 9571657--9571683 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
9571647 TTCATCTTTA
9571657 AGTTTTTAAAT
1 AGTTTTTAAAT
9571668 AGTTTTTAAAT
1 AGTTTTTAAAT
9571679 AGTTT
1 AGTTT
9571684 CTTTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (11 bp):
AGTTTTTAAAT
Found at i:9571714 original size:159 final size:159
Alignment explanation
Indices: 9571509--9571903 Score: 763
Period size: 159 Copynumber: 2.5 Consensus size: 159
9571499 TTCATTTTTA
*
9571509 AGTTTTGAAATAGTTTCTTTATATTTTGAAACCATTAATTCAAACTCCAAACCCAATTCATCATA
1 AGTTTTTAAATAGTTTCTTTATATTTTGAAACCATTAATTCAAACTCCAAACCCAATTCATCATA
9571574 GGCATCTTGTAAATCAGCAAAAGAATAAGAATTTAAATTAGATAAGTTAGAAGTTACCTAAGAGT
66 GGCATCTTGTAAATCAGCAAAAGAATAAGAATTTAAATTAGATAAGTTAGAAGTTACCTAAGAGT
9571639 TAATTGTTTTCATCTTTAAGTTTTTAAAT
131 TAATTGTTTTCATCTTTAAGTTTTTAAAT
9571668 AGTTTTTAAATAGTTTCTTTATATTTTGAAACCATTAATTCAAACTCCAAACCCAATTCATCATA
1 AGTTTTTAAATAGTTTCTTTATATTTTGAAACCATTAATTCAAACTCCAAACCCAATTCATCATA
9571733 GGCATCTTGTAAATCAGCAAAAGAATAAGAATTTAAATTAGATAAGTTAGAAGTTACCTAAGAGT
66 GGCATCTTGTAAATCAGCAAAAGAATAAGAATTTAAATTAGATAAGTTAGAAGTTACCTAAGAGT
9571798 TAATTGTTTTCATCTTTAAGTTTTTAAAT
131 TAATTGTTTTCATCTTTAAGTTTTTAAAT
9571827 AGTTTTTAAATAGTTTCTTTATATTTTGAAACCATTAATTCAAACTCCAAACCCAATTCATCATA
1 AGTTTTTAAATAGTTTCTTTATATTTTGAAACCATTAATTCAAACTCCAAACCCAATTCATCATA
**
9571892 GAAATCTTGTAA
66 GGCATCTTGTAA
9571904 TCATTAAAAG
Statistics
Matches: 233, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
159 233 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (159 bp):
AGTTTTTAAATAGTTTCTTTATATTTTGAAACCATTAATTCAAACTCCAAACCCAATTCATCATA
GGCATCTTGTAAATCAGCAAAAGAATAAGAATTTAAATTAGATAAGTTAGAAGTTACCTAAGAGT
TAATTGTTTTCATCTTTAAGTTTTTAAAT
Found at i:9571832 original size:11 final size:11
Alignment explanation
Indices: 9571816--9571842 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
9571806 TTCATCTTTA
9571816 AGTTTTTAAAT
1 AGTTTTTAAAT
9571827 AGTTTTTAAAT
1 AGTTTTTAAAT
9571838 AGTTT
1 AGTTT
9571843 CTTTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (11 bp):
AGTTTTTAAAT
Found at i:9574142 original size:11 final size:11
Alignment explanation
Indices: 9574085--9574152 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 11
9574075 TAGGAATAGA
9574085 AAAATAAAAAT
1 AAAATAAAAAT
9574096 AAATGATAAACAAGT
1 AAA--ATAAA-AA-T
9574111 AAGAATAATAAA-
1 AA-AATAA-AAAT
*
9574123 CAAAT--AAAT
1 AAAATAAAAAT
9574132 AAAATAAAAAT
1 AAAATAAAAAT
9574143 AAAATAAAAA
1 AAAATAAAAA
9574153 CAAAGAATGG
Statistics
Matches: 46, Mismatches: 2, Indels: 18
0.70 0.03 0.27
Matches are distributed among these distances:
8 3 0.07
9 4 0.09
11 20 0.43
12 1 0.02
13 5 0.11
14 8 0.17
15 4 0.09
16 1 0.02
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:9574152 original size:17 final size:18
Alignment explanation
Indices: 9574087--9574151 Score: 50
Period size: 17 Copynumber: 3.7 Consensus size: 18
9574077 GGAATAGAAA
9574087 AATAAAAATAAATGATAAAC
1 AATAAAAATAAA--ATAAAC
*
9574107 AAGTAAGAAT--AATAAAC
1 AA-TAAAAATAAAATAAAC
*
9574124 AA-ATAAATAAAATAAA-
1 AATAAAAATAAAATAAAC
9574140 AAT-AAAATAAAA
1 AATAAAAATAAAA
9574152 ACAAAGAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
15 4 0.11
16 10 0.27
17 14 0.38
19 1 0.03
20 2 0.05
21 6 0.16
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (18 bp):
AATAAAAATAAAATAAAC
Found at i:9574748 original size:20 final size:20
Alignment explanation
Indices: 9574718--9574784 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
9574708 CTTTGTTTCT
*
9574718 CTCACGACCGTGTGAACTCC
1 CTCACGCCCGTGTGAACTCC
*
9574738 CTCACTCCCGTGTGAACTCC
1 CTCACGCCCGTGTGAACTCC
9574758 CTCACGCCCGTGTGAACTCC
1 CTCACGCCCGTGTGAACTCC
*
9574778 CACACGC
1 CTCACGC
9574785 TCGTATGGCT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.18, C:0.45, G:0.18, T:0.19
Consensus pattern (20 bp):
CTCACGCCCGTGTGAACTCC
Found at i:9579171 original size:30 final size:30
Alignment explanation
Indices: 9579114--9579173 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
9579104 GCATATGGTC
** *
9579114 AGCCCGTGTGGTTCACACGGGCGTGTGGCT
1 AGCCCGTGTGGTTCACACAAGCATGTGGCT
*
9579144 AGCCCGTGTGGTTCGCACAAGCATGTGGCT
1 AGCCCGTGTGGTTCACACAAGCATGTGGCT
9579174 GCTGAAAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.13, C:0.27, G:0.37, T:0.23
Consensus pattern (30 bp):
AGCCCGTGTGGTTCACACAAGCATGTGGCT
Found at i:9583595 original size:19 final size:19
Alignment explanation
Indices: 9583573--9583612 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
9583563 TATTCAAAAG
9583573 CACCATTTTTTTATGATTT
1 CACCATTTTTTTATGATTT
9583592 CACCATTTTTTTATGATTT
1 CACCATTTTTTTATGATTT
9583611 CA
1 CA
9583613 GTTTCATACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.05, T:0.55
Consensus pattern (19 bp):
CACCATTTTTTTATGATTT
Found at i:9585638 original size:22 final size:22
Alignment explanation
Indices: 9585604--9585669 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
9585594 ATTTGAAAAA
* *
9585604 TATACTTTAATATTAATATTTT
1 TATATTTTTATATTAATATTTT
9585626 TATATTTTTATATTAAT-TTTT
1 TATATTTTTATATTAATATTTT
*
9585647 TATCTATTTTTATAATAA-ATTTT
1 TA--TATTTTTATATTAATATTTT
9585670 AAATAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
21 6 0.16
22 15 0.39
23 17 0.45
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (22 bp):
TATATTTTTATATTAATATTTT
Found at i:9587468 original size:62 final size:62
Alignment explanation
Indices: 9587342--9587470 Score: 150
Period size: 62 Copynumber: 2.1 Consensus size: 62
9587332 ATCCCTGACT
* * * * * * * *
9587342 GTGTGGTGTTATACCATAAATAGTGAGTTAAACGGCCAAGGCACACGCCCGTGTTCCTGGCC
1 GTGTGGTCTTATACCACAAACAGTGAGTTAAACGACCAAGACACACGCCCGTGTCCCCGCCC
* * * *
9587404 GTGTGGTCTTATACTACAAACAGTGAGTTACACGACCCAGACACACGCCCTTGTCCCCGCCC
1 GTGTGGTCTTATACCACAAACAGTGAGTTAAACGACCAAGACACACGCCCGTGTCCCCGCCC
9587466 GTGTG
1 GTGTG
9587471 ACCCCAAATA
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (62 bp):
GTGTGGTCTTATACCACAAACAGTGAGTTAAACGACCAAGACACACGCCCGTGTCCCCGCCC
Found at i:9588122 original size:28 final size:30
Alignment explanation
Indices: 9588069--9588124 Score: 89
Period size: 28 Copynumber: 1.9 Consensus size: 30
9588059 AGAGTCAAAG
*
9588069 AAGTAAAACAAAGAAAGAAAAGAAGAAAAA
1 AAGTAAAACAAAAAAAGAAAAGAAGAAAAA
9588099 AAGTAAAA-AAAAAAAG-AAAGAAGAAA
1 AAGTAAAACAAAAAAAGAAAAGAAGAAA
9588125 GAAGAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 10 0.40
29 7 0.28
30 8 0.32
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (30 bp):
AAGTAAAACAAAAAAAGAAAAGAAGAAAAA
Found at i:9589175 original size:18 final size:19
Alignment explanation
Indices: 9589141--9589180 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
9589131 TCCAAATTAA
9589141 TAAATTTATTAAACT-AAT
1 TAAATTTATTAAACTAAAT
9589159 TAAATTT-TTAAACCTAAAT
1 TAAATTTATTAAA-CTAAAT
9589178 TAA
1 TAA
9589181 CCTAAGGGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAATTTATTAAACTAAAT
Found at i:9592045 original size:51 final size:51
Alignment explanation
Indices: 9591990--9592187 Score: 222
Period size: 51 Copynumber: 3.9 Consensus size: 51
9591980 ATGTGAAAGT
* *
9591990 GAAAGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCA
1 GAAAGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCG
* *
9592041 GAAA--GATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCG
1 GAAAGTGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCG
* * ** ** * *
9592091 GATAGCTTA-AATCATGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCG
1 GAAAG-TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCG
* * *
9592142 GATAGTGTTGGTCACATGTGTAGTACTATGTGTAGGCTACTATGTG
1 GAAAGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
9592188 ATTCGGTATC
Statistics
Matches: 120, Mismatches: 22, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
49 3 0.03
50 42 0.35
51 74 0.62
53 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (51 bp):
GAAAGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCG
Found at i:9594399 original size:31 final size:32
Alignment explanation
Indices: 9594361--9594434 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 32
9594351 ATACAATAAT
*
9594361 ATAAAATAAAATCCTAAAAA-AT-CAACCAAAA
1 ATAAAATAAAATCCTAAAAATATAAAACC-AAA
* *
9594392 ATAAAAT-AAGTCTTAAAAATATAAAACCAAA
1 ATAAAATAAAATCCTAAAAATATAAAACCAAA
9594423 ATAAAATTAAAA
1 ATAAAA-TAAAA
9594435 ATGTTCTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 10 0.29
31 18 0.51
32 5 0.14
33 2 0.06
ACGTcount: A:0.68, C:0.11, G:0.01, T:0.20
Consensus pattern (32 bp):
ATAAAATAAAATCCTAAAAATATAAAACCAAA
Found at i:9603804 original size:32 final size:32
Alignment explanation
Indices: 9603768--9603842 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 32
9603758 TACAATATAT
*
9603768 ATAAAATAAAATCCTAAAAAAAT-CAACCAAAA
1 ATAAAATAAAATCCTAAAAAAATAAAACC-AAA
* * *
9603800 ATAAAAT-AAGTCTTAAAAATATAAAACCAAA
1 ATAAAATAAAATCCTAAAAAAATAAAACCAAA
9603831 ATAAAATTAAAA
1 ATAAAA-TAAAA
9603843 ATGTTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
31 21 0.60
32 12 0.34
33 2 0.06
ACGTcount: A:0.68, C:0.11, G:0.01, T:0.20
Consensus pattern (32 bp):
ATAAAATAAAATCCTAAAAAAATAAAACCAAA
Found at i:9604094 original size:18 final size:17
Alignment explanation
Indices: 9604052--9604095 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
9604042 GGTCTCCTCC
9604052 TCCTCCTCCTCCTCATCA
1 TCCTCCT-CTCCTCATCA
* *
9604070 TCATCCTCTCCTTCATCG
1 TCCTCCTCTCC-TCATCA
9604088 TCCTCCTC
1 TCCTCCTC
9604096 GTCTAGTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.09, C:0.52, G:0.02, T:0.36
Consensus pattern (17 bp):
TCCTCCTCTCCTCATCA
Found at i:9606776 original size:50 final size:50
Alignment explanation
Indices: 9606670--9606961 Score: 291
Period size: 50 Copynumber: 5.7 Consensus size: 50
9606660 GGAAATAAGA
* *
9606670 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGGGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----CGA-GATGAGAGG
* * *
9606726 TCCCATGTAAGACCATTTTTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* *
9606776 TCCCATGTAAGACCATGTCTGGGACATAGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * * * **
9606826 TCCCCCGTAAGACAATGTCTGGGACATCGCATAGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * * * *
9606876 TCCCATGTAAGACCATATCTGGGATATGACATTGGTA--GTACAAGAAACG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGG
*
9606925 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
9606962 TGTTATTATC
Statistics
Matches: 199, Mismatches: 36, Indels: 9
0.82 0.15 0.04
Matches are distributed among these distances:
48 1 0.01
49 37 0.19
50 124 0.62
51 2 0.01
55 1 0.01
56 34 0.17
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:9608704 original size:16 final size:17
Alignment explanation
Indices: 9608685--9608720 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
9608675 AAAGCACAAA
9608685 AAATAAAATTT-AAAAT
1 AAATAAAATTTAAAAAT
9608701 AAATAAAATTTAAAAAT
1 AAATAAAATTTAAAAAT
9608718 AAA
1 AAA
9608721 GTCAGTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATAAAATTTAAAAAT
Found at i:9610058 original size:10 final size:10
Alignment explanation
Indices: 9610012--9610058 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
9610002 AACATGTTGG
9610012 ATTTTTATTA
1 ATTTTTATTA
9610022 ATTTTATAATTA
1 ATTTT-T-ATTA
**
9610034 ATTTTGGTTA
1 ATTTTTATTA
9610044 ATTTTTATT-
1 ATTTTTATTA
9610053 ATTTTT
1 ATTTTT
9610059 GATAGATTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
9 6 0.19
10 15 0.48
11 1 0.03
12 9 0.29
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (10 bp):
ATTTTTATTA
Found at i:9611369 original size:3 final size:3
Alignment explanation
Indices: 9611363--9611406 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
9611353 TGACATCATC
* * * *
9611363 ATT ATT ATT ATT ATT ATT GTT ATT ATT TTT ATT TTT ATT TTT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
9611407 ATTCATGCGC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (3 bp):
ATT
Found at i:9617357 original size:25 final size:26
Alignment explanation
Indices: 9617329--9617387 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
9617319 CTGAAACACG
*
9617329 GTAAGCTCAT-ACGAGCTGAGAATTA
1 GTAAGCTCATCACGAGCTGAAAATTA
* *
9617354 GTAAGCTC-TCATGAGCTGAAAATTG
1 GTAAGCTCATCACGAGCTGAAAATTA
9617379 GTAAGCTCA
1 GTAAGCTCA
9617388 AACAAGATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 1 0.03
25 28 0.97
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (26 bp):
GTAAGCTCATCACGAGCTGAAAATTA
Found at i:9619203 original size:54 final size:54
Alignment explanation
Indices: 9619127--9619287 Score: 180
Period size: 54 Copynumber: 3.0 Consensus size: 54
9619117 AAGAGAAGAA
* * * * *
9619127 TGGTAAATATGGAAAACCCTGAAAGAATGATATGTATGGCTAACT-TAGAAGGGC
1 TGGTAGATATGGTAAACTCTGAAAGAATGATATGTGTGGCTAACTCT-GAAGGAC
* * *
9619181 TGGTAGATATGGTAAACTCTGAAAGAATAAAATGCGTGGCTAACTCTGAAGGAC
1 TGGTAGATATGGTAAACTCTGAAAGAATGATATGTGTGGCTAACTCTGAAGGAC
* * * * * *
9619235 TGGTTGATATGGTAAACTTTGAGAGAACGATATGTGTGGCGAACTCCGAAGGA
1 TGGTAGATATGGTAAACTCTGAAAGAATGATATGTGTGGCTAACTCTGAAGGA
9619288 ACAGTTTCAT
Statistics
Matches: 89, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
54 88 0.99
55 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (54 bp):
TGGTAGATATGGTAAACTCTGAAAGAATGATATGTGTGGCTAACTCTGAAGGAC
Found at i:9620948 original size:12 final size:13
Alignment explanation
Indices: 9620918--9620952 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
9620908 TTAATCGGCC
9620918 ATCGATTGAATTAG
1 ATCGATT-AATTAG
9620932 ATCGATTAATT-G
1 ATCGATTAATTAG
9620944 ATCGATTAA
1 ATCGATTAA
9620953 CCAAATTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.48
13 4 0.19
14 7 0.33
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (13 bp):
ATCGATTAATTAG
Found at i:9628543 original size:19 final size:19
Alignment explanation
Indices: 9628506--9628545 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
9628496 TAAAATATAA
*
9628506 AATTTTTATTTAAATTTTT
1 AATTTTTATTTAAAATTTT
9628525 AATTTTT-TTTAAAAATTTT
1 AATTTTTATTT-AAAATTTT
9628544 AA
1 AA
9628546 ATTAGCAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTTTTATTTAAAATTTT
Found at i:9628548 original size:20 final size:19
Alignment explanation
Indices: 9628505--9628548 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
9628495 CTAAAATATA
9628505 AAATTTTTATTTAAATTTT
1 AAATTTTTATTTAAATTTT
*
9628524 TAATTTTT-TTTAAAAATTTT
1 AAATTTTTATTT--AAATTTT
9628544 AAATT
1 AAATT
9628549 AGCAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 7 0.33
20 11 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
AAATTTTTATTTAAATTTT
Found at i:9651047 original size:73 final size:73
Alignment explanation
Indices: 9650923--9651084 Score: 245
Period size: 73 Copynumber: 2.2 Consensus size: 73
9650913 TTCACACATC
* *
9650923 GCCTCATTCAATTTCTGACTGACCATCGAATTATGGATGAAAGGTATTATTGGAGTTTAACCGTG
1 GCCTCGTTCAATTTCTGACTGACCATCGAATTATGGATGAAAGGTAGTATTGGAGTTTAACCGTG
9650988 TAACCAAA
66 TAACCAAA
* * * *
9650996 GCCTCGTTCAATTTTTGACTGACTATC-AGATTATGGATGAAAGGTCGTATTGGAGTTTAACTGT
1 GCCTCGTTCAATTTCTGACTGACCATCGA-ATTATGGATGAAAGGTAGTATTGGAGTTTAACCGT
9651060 GTAACCAAA
65 GTAACCAAA
*
9651069 GCCTTGTTCAATTTCT
1 GCCTCGTTCAATTTCT
9651085 TCTAGAACTG
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
72 1 0.01
73 79 0.99
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (73 bp):
GCCTCGTTCAATTTCTGACTGACCATCGAATTATGGATGAAAGGTAGTATTGGAGTTTAACCGTG
TAACCAAA
Found at i:9662217 original size:17 final size:19
Alignment explanation
Indices: 9662196--9662237 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
9662186 TCCAATCAAG
*
9662196 ATATAAAGGAAAAAATGAT
1 ATATACAGGAAAAAATGAT
*
9662215 ATAATACATGAAAAAATGAT
1 AT-ATACAGGAAAAAATGAT
9662235 ATA
1 ATA
9662238 CAGGTTATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.62, C:0.02, G:0.12, T:0.24
Consensus pattern (19 bp):
ATATACAGGAAAAAATGAT
Found at i:9668081 original size:40 final size:40
Alignment explanation
Indices: 9667993--9668082 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
9667983 TGAGTGGATT
* * * *
9667993 CAGGGGTACCGAAGTACAAACAGGGGCCCGTATATGCAAT
1 CAGGGGTACCGAAGTACAAACAGGAGCACATATATGCAAC
** * *
9668033 CAACGGTACCGAAGTACAAACATGAGCACATATGTGCAAC
1 CAGGGGTACCGAAGTACAAACAGGAGCACATATATGCAAC
9668073 CAGGGGTACC
1 CAGGGGTACC
9668083 AATGCATGTA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.34, C:0.24, G:0.27, T:0.14
Consensus pattern (40 bp):
CAGGGGTACCGAAGTACAAACAGGAGCACATATATGCAAC
Found at i:9668126 original size:20 final size:20
Alignment explanation
Indices: 9668101--9668209 Score: 60
Period size: 20 Copynumber: 5.5 Consensus size: 20
9668091 TATGTGAAAT
9668101 TAGGGGCACCGAAGTACAAA
1 TAGGGGCACCGAAGTACAAA
** * *
9668121 TAGGGGCA-CGTATCTGCAAT
1 TAGGGGCACCG-AAGTACAAA
* * *
9668141 TAGGGGTATCGAAGTACAAG
1 TAGGGGCACCGAAGTACAAA
** * *
9668161 TAGGGGCA-CGTATCTGCAAT
1 TAGGGGCACCG-AAGTACAAA
* *
9668181 TAAGGGTACCGAAGTACAAA
1 TAGGGGCACCGAAGTACAAA
*
9668201 CAGGGGCAC
1 TAGGGGCAC
9668210 GTACGTGCAA
Statistics
Matches: 62, Mismatches: 23, Indels: 8
0.67 0.25 0.09
Matches are distributed among these distances:
19 4 0.06
20 54 0.87
21 4 0.06
ACGTcount: A:0.33, C:0.18, G:0.31, T:0.17
Consensus pattern (20 bp):
TAGGGGCACCGAAGTACAAA
Found at i:9668154 original size:40 final size:40
Alignment explanation
Indices: 9668098--9668220 Score: 185
Period size: 40 Copynumber: 3.1 Consensus size: 40
9668088 ATGTATGTGA
*
9668098 AATTAGGGGCACCGAAGTACAAATAGGGGCACGTATCTGC
1 AATTAGGGGTACCGAAGTACAAATAGGGGCACGTATCTGC
* *
9668138 AATTAGGGGTATCGAAGTACAAGTAGGGGCACGTATCTGC
1 AATTAGGGGTACCGAAGTACAAATAGGGGCACGTATCTGC
* *
9668178 AATTAAGGGTACCGAAGTACAAACAGGGGCACGTA-CGTGC
1 AATTAGGGGTACCGAAGTACAAATAGGGGCACGTATC-TGC
9668218 AAT
1 AAT
9668221 CAGCAACAAT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
39 1 0.01
40 74 0.99
ACGTcount: A:0.33, C:0.18, G:0.30, T:0.19
Consensus pattern (40 bp):
AATTAGGGGTACCGAAGTACAAATAGGGGCACGTATCTGC
Found at i:9668188 original size:108 final size:108
Alignment explanation
Indices: 9667994--9668190 Score: 241
Period size: 108 Copynumber: 1.8 Consensus size: 108
9667984 GAGTGGATTC
* * *
9667994 AGGGGTACCGAAGTACAAACAGGGGCCCGTATATGCAATCAACGGTACCGAAGTACAAACATGAG
1 AGGGGCACCGAAGTACAAACAGGGGCACGTATATGCAATCAACGGTACCGAAGTACAAACAGGAG
* *
9668059 CACATATGTGCAACCAGGGGTACCAATGCATGTATGTGAAATT
66 CACATATCTGCAACCAAGGGTACCAATGCATGTATGTGAAATT
* * * ** * ** *
9668102 AGGGGCACCGAAGTACAAATAGGGGCACGTATCTGCAATTAGGGGTATCGAAGTACAAGTAGGGG
1 AGGGGCACCGAAGTACAAACAGGGGCACGTATATGCAATCAACGGTACCGAAGTACAAACAGGAG
* **
9668167 CACGTATCTGCAATTAAGGGTACC
66 CACATATCTGCAACCAAGGGTACC
9668191 GAAGTACAAA
Statistics
Matches: 72, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
108 72 1.00
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (108 bp):
AGGGGCACCGAAGTACAAACAGGGGCACGTATATGCAATCAACGGTACCGAAGTACAAACAGGAG
CACATATCTGCAACCAAGGGTACCAATGCATGTATGTGAAATT
Found at i:9671208 original size:21 final size:21
Alignment explanation
Indices: 9671169--9671211 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
9671159 ACTTGATCTA
9671169 AATAATCAAATTCATTCCATTC
1 AATAATC-AATTCATTCCATTC
9671191 AATAATC-ATTCTATTCCATTC
1 AATAATCAATTC-ATTCCATTC
9671212 TATCCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 9 0.45
22 7 0.35
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (21 bp):
AATAATCAATTCATTCCATTC
Found at i:9725157 original size:20 final size:22
Alignment explanation
Indices: 9725120--9725161 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
9725110 ATTTTTTAAA
*
9725120 AATATTCATATTATTTTAATTT
1 AATATTCATATTAATTTAATTT
9725142 AATATTCA-A-TAATTTAATTT
1 AATATTCATATTAATTTAATTT
9725162 TTTTATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (22 bp):
AATATTCATATTAATTTAATTT
Found at i:9725653 original size:67 final size:66
Alignment explanation
Indices: 9725528--9725655 Score: 202
Period size: 66 Copynumber: 1.9 Consensus size: 66
9725518 ATTTGACAAA
*
9725528 ATTTTTTTCTTTCATTTTCTCTCTTGCCAAACAACACTTTTTTCTTCAAAACACATGGTTGCTGC
1 ATTTTTTTCTCTCATTTTCTCTCTTGCCAAACAACACTTTTTTCTTCAAAACACATGGTTGCTGC
9725593 C
66 C
* * * *
9725594 ATTTTTTTCTCTCATTTTTTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACATATGGTTG
1 ATTTTTTTCTCTCATTTTCTCTCTTGCCAAACAACACTTTT-TTCTTCAAAACACATGGTTG
9725656 GCTCATTTCA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
66 37 0.66
67 19 0.34
ACGTcount: A:0.21, C:0.24, G:0.07, T:0.48
Consensus pattern (66 bp):
ATTTTTTTCTCTCATTTTCTCTCTTGCCAAACAACACTTTTTTCTTCAAAACACATGGTTGCTGC
C
Found at i:9732453 original size:66 final size:66
Alignment explanation
Indices: 9732347--9732473 Score: 202
Period size: 66 Copynumber: 1.9 Consensus size: 66
9732337 AGACCATGTC
* *
9732347 TGGGACATGACGTTGGCATCGAGATGAGAGGTCCCATGTAAGCCCATGTCTGGGACATGGCCTAC
1 TGGGACATGACGTTGGCATCGAGATGAGAGGTCCCATGTAAGACCATGTCCGGGACATGGCCTAC
9732412 A
66 A
* *
9732413 TGGGACATGGCGTTGGCA-CTGAGATGAGAGGTCCTATGTAAGACCATGTCCGGGACATGGC
1 TGGGACATGACGTTGGCATC-GAGATGAGAGGTCCCATGTAAGACCATGTCCGGGACATGGC
9732474 GTTGGCACCG
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
65 1 0.02
66 55 0.98
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.21
Consensus pattern (66 bp):
TGGGACATGACGTTGGCATCGAGATGAGAGGTCCCATGTAAGACCATGTCCGGGACATGGCCTAC
A
Found at i:9732493 original size:50 final size:50
Alignment explanation
Indices: 9732413--9732631 Score: 258
Period size: 50 Copynumber: 4.4 Consensus size: 50
9732403 ATGGCCTACA
* *
9732413 TGGGACATGGCGTTGGCACTGAGATGAGAGGTCCTATGTAAGACCATGTC
1 TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTC
* * * *
9732463 CGGGACATGGCGTTGGCACCGAGATAAGAGGTCCTATGTAAGACGATGTC
1 TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTC
* ** *
9732513 TGGGACATGGCGTTGGCACCGAGATTAGAGGTCCCCCGTAAGACAATGTC
1 TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTC
* * * * * ** *
9732563 TGGGACATAGCATGGGCACTGATATGAGAACATCCCATGTAAGACCATCTC
1 TGGGACATGGCGTTGGCACCGAGATGAG-AGGTCCCATGTAAGACCATGTC
*
9732614 TGGGACATGGCTTTGGCA
1 TGGGACATGGCGTTGGCA
9732632 TGTTATTATC
Statistics
Matches: 143, Mismatches: 25, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
50 112 0.78
51 31 0.22
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.22
Consensus pattern (50 bp):
TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTC
Found at i:9740005 original size:50 final size:50
Alignment explanation
Indices: 9739927--9740269 Score: 447
Period size: 50 Copynumber: 6.8 Consensus size: 50
9739917 ATTTGGGTAA
*
9739927 AGAGGTCCCATGTAAGACCGTGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * *
9739977 AGAGGTCCCATGTAAGCCCATGTTTGGGACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * *
9740027 AGAGGTCCTATATAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
9740077 AGAGGTCCCATGTAAGACCATGT-TCGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCT-GGGACATGGCGTTGGCACCGAGATG
* * *
9740127 AGAAGTCCCATGCAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * * * * *
9740177 AGAGGTCTCC-CGTAAGACCATGTTTGGGACATGGCATGGGCACCAATATG
1 AGAGGTC-CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * *
9740227 AGAACATCTCATGTAAGACCATGTCAGGGACATGTCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
9740270 TGTTATTATC
Statistics
Matches: 256, Mismatches: 32, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
49 1 0.00
50 223 0.87
51 32 0.12
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:9744499 original size:5 final size:6
Alignment explanation
Indices: 9744483--9744508 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
9744473 CAAAGATCTG
9744483 CTTTTT CTTTTT CTTTTT CTTTTT CT
1 CTTTTT CTTTTT CTTTTT CTTTTT CT
9744509 ACCAGCTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:9748721 original size:14 final size:14
Alignment explanation
Indices: 9748702--9748732 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
9748692 ATCTAAACAA
9748702 TAACAACAAAATAG
1 TAACAACAAAATAG
*
9748716 TAACAACATAATAG
1 TAACAACAAAATAG
9748730 TAA
1 TAA
9748733 ATTTGTAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (14 bp):
TAACAACAAAATAG
Found at i:9748779 original size:23 final size:25
Alignment explanation
Indices: 9748742--9748788 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
9748732 AATTTGTAGC
*
9748742 AAAATAGTAAAAAAA-AG-AAAAAG
1 AAAATAGCAAAAAAACAGTAAAAAG
*
9748765 AAAATAGCAACAAAACAGTAAAAA
1 AAAATAGCAAAAAAACAGTAAAAA
9748789 AAACAACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 2 0.10
25 5 0.25
ACGTcount: A:0.74, C:0.06, G:0.11, T:0.09
Consensus pattern (25 bp):
AAAATAGCAAAAAAACAGTAAAAAG
Found at i:9748809 original size:19 final size:19
Alignment explanation
Indices: 9748772--9748828 Score: 96
Period size: 19 Copynumber: 2.9 Consensus size: 19
9748762 AAGAAAATAG
*
9748772 CAACAAAACAGTAAAAAAAA
1 CAACAAAACA-TTAAAAAAA
9748792 CAACAAAACATTAAAAAAA
1 CAACAAAACATTAAAAAAA
9748811 CAACAAAACATTAAAAAA
1 CAACAAAACATTAAAAAA
9748829 TATATTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 26 0.72
20 10 0.28
ACGTcount: A:0.74, C:0.16, G:0.02, T:0.09
Consensus pattern (19 bp):
CAACAAAACATTAAAAAAA
Found at i:9752211 original size:30 final size:32
Alignment explanation
Indices: 9752168--9752226 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
9752158 GAGAAAAAGA
*
9752168 AGAAGATAAGAAAAGGAAA-AA-AAAAGAGGG
1 AGAAGATAAGAAAAAGAAAGAACAAAAGAGGG
9752198 AGAAGA-AATGAAAAAGAAAGAACAAAAGA
1 AGAAGATAA-GAAAAAGAAAGAACAAAAGA
9752227 AAATGGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 2 0.08
30 15 0.60
31 2 0.08
32 6 0.24
ACGTcount: A:0.69, C:0.02, G:0.25, T:0.03
Consensus pattern (32 bp):
AGAAGATAAGAAAAAGAAAGAACAAAAGAGGG
Found at i:9752230 original size:24 final size:24
Alignment explanation
Indices: 9752160--9752287 Score: 68
Period size: 24 Copynumber: 5.2 Consensus size: 24
9752150 AGGAGGAGGA
* *
9752160 GAAAAAG-AAGAAGATAAGAAAAG
1 GAAAAAGAAAGAAGAAAAGAAAAT
* * *
9752183 GAAAAAAAAAGAGGGAGAAG-AAAT
1 GAAAAAGAAAGA-AGAAAAGAAAAT
*
9752207 GAAAAAGAAAGAACAAAAGAAAAT
1 GAAAAAGAAAGAAGAAAAGAAAAT
* *
9752231 GGGAAAATGGGAAAGAA-AAAA-AAGA-
1 --GAAAA--AGAAAGAAGAAAAGAAAAT
* *
9752256 GAAAAGTGGAAGAAAGAAAAGAAAAT
1 GAAAA-AGAAAG-AAGAAAAGAAAAT
9752282 GAAAAA
1 GAAAAA
9752288 AATGTGAAAA
Statistics
Matches: 80, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
22 5 0.06
23 17 0.21
24 26 0.32
25 8 0.10
26 13 0.16
27 4 0.05
28 7 0.09
ACGTcount: A:0.69, C:0.01, G:0.26, T:0.05
Consensus pattern (24 bp):
GAAAAAGAAAGAAGAAAAGAAAAT
Found at i:9752259 original size:23 final size:26
Alignment explanation
Indices: 9752221--9752280 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
9752211 AAGAAAGAAC
*
9752221 AAAAGAAAATGGGAAAA-TGG-GAAAG
1 AAAAGAAAA-GAGAAAAGTGGAGAAAG
9752246 AAAA-AAAAGAGAAAAGTGGAAGAAAG
1 AAAAGAAAAGAGAAAAGTGG-AGAAAG
9752272 AAAAGAAAA
1 AAAAGAAAA
9752281 TGAAAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 6 0.20
24 7 0.23
25 4 0.13
26 9 0.30
27 4 0.13
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (26 bp):
AAAAGAAAAGAGAAAAGTGGAGAAAG
Found at i:9760238 original size:18 final size:18
Alignment explanation
Indices: 9760215--9760278 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
9760205 TATTCATTGC
9760215 AAATATTCAAATATTCAT
1 AAATATTCAAATATTCAT
***
9760233 AAATATTGTTATATATC-T
1 AAATATTCAAATAT-TCAT
*
9760251 ACA-A-TCAAATATTCAT
1 AAATATTCAAATATTCAT
9760267 AAATATTCAAAT
1 AAATATTCAAAT
9760279 TCAAATTATT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
15 2 0.06
16 8 0.24
17 2 0.06
18 20 0.59
19 2 0.06
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (18 bp):
AAATATTCAAATATTCAT
Found at i:9770891 original size:26 final size:25
Alignment explanation
Indices: 9770840--9770891 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
9770830 CAAAAATAAT
* **
9770840 ATCTATTCTAAAAAGAAAAGGGAAA
1 ATCTAATCTAAAAAGAAAAGAAAAA
9770865 ATCTAATCTAAAAATGAAAAGAAAAA
1 ATCTAATCTAAAAA-GAAAAGAAAAA
9770891 A
1 A
9770892 GAAAAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.62, C:0.08, G:0.12, T:0.19
Consensus pattern (25 bp):
ATCTAATCTAAAAAGAAAAGAAAAA
Found at i:9770915 original size:5 final size:5
Alignment explanation
Indices: 9770907--9770958 Score: 104
Period size: 5 Copynumber: 10.4 Consensus size: 5
9770897 AAAGAAAAGA
9770907 AACCT AACCT AACCT AACCT AACCT AACCT AACCT AACCT AACCT AACCT
1 AACCT AACCT AACCT AACCT AACCT AACCT AACCT AACCT AACCT AACCT
9770957 AA
1 AA
9770959 AACTAAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.19
Consensus pattern (5 bp):
AACCT
Found at i:9777138 original size:19 final size:19
Alignment explanation
Indices: 9777114--9777154 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
9777104 AGTGCACATA
9777114 ACAAAAGAGACTCTAAATT
1 ACAAAAGAGACTCTAAATT
*
9777133 ACAAAAGAGACTCTAGATT
1 ACAAAAGAGACTCTAAATT
9777152 ACA
1 ACA
9777155 TTTCCTAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.20
Consensus pattern (19 bp):
ACAAAAGAGACTCTAAATT
Found at i:9779040 original size:13 final size:13
Alignment explanation
Indices: 9779022--9779055 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
9779012 GAAGAATATG
9779022 AAAGGTACATGTC
1 AAAGGTACATGTC
9779035 AAAGGTACATGTC
1 AAAGGTACATGTC
9779048 AAAGGTAC
1 AAAGGTAC
9779056 CTTATTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.21
Consensus pattern (13 bp):
AAAGGTACATGTC
Found at i:9783333 original size:21 final size:20
Alignment explanation
Indices: 9783309--9783392 Score: 60
Period size: 21 Copynumber: 4.0 Consensus size: 20
9783299 AATAGAAGCA
9783309 CATAAGTGCTAAACAGAAACC
1 CATAAG-GCTAAACAGAAACC
* *
9783330 CATAAGGGTTAAACAGAAGCTC
1 CATAA-GGCTAAACAGAAAC-C
* * * *
9783352 GTAAAAGAGCTGAACGGAAACC
1 -CATAAG-GCTAAACAGAAACC
*
9783374 CATAAGGTTAAACAGAAAC
1 CATAAGGCTAAACAGAAAC
9783393 TCAAAAGAAC
Statistics
Matches: 46, Mismatches: 13, Indels: 9
0.68 0.19 0.13
Matches are distributed among these distances:
20 10 0.22
21 20 0.43
22 4 0.09
23 12 0.26
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.14
Consensus pattern (20 bp):
CATAAGGCTAAACAGAAACC
Found at i:9783408 original size:41 final size:42
Alignment explanation
Indices: 9783324--9783432 Score: 139
Period size: 41 Copynumber: 2.5 Consensus size: 42
9783314 GTGCTAAACA
* *
9783324 GAAACCCATAAGGGTTAAACAGAAGCTCGTAAAAGAGCTGAACG
1 GAAACCCATAA-GGTTAAACAGAAACTCG-AAAAGAACTGAACG
9783368 GAAACCCATAAGGTTAAACAGAAACTC-AAAAGAACTGAACG
1 GAAACCCATAAGGTTAAACAGAAACTCGAAAAGAACTGAACG
* * *
9783409 AAAACACATATGAGTTAAACAGAA
1 GAAACCCATAAG-GTTAAACAGAA
9783433 GCTTGTGAGA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
41 22 0.37
42 11 0.19
43 15 0.25
44 11 0.19
ACGTcount: A:0.50, C:0.17, G:0.19, T:0.14
Consensus pattern (42 bp):
GAAACCCATAAGGTTAAACAGAAACTCGAAAAGAACTGAACG
Found at i:9785330 original size:2 final size:2
Alignment explanation
Indices: 9785323--9785352 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9785313 ATATGAACAT
9785323 CA CA CA CA CA 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
9785353 TCTATATAAT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:9789607 original size:253 final size:253
Alignment explanation
Indices: 9789159--9789668 Score: 948
Period size: 253 Copynumber: 2.0 Consensus size: 253
9789149 TATGTTCAAG
* *
9789159 TATGCTAACATGTTTGTGTTGATGCCTAGGCTTGTGCCAAGCTAAAATTTGGATTATGCCATGTT
1 TATGCTAACATGTTTGTGTTGATGCCTAGGCTTGTGCCAAGCTAAAAGTGGGATTATGCCATGTT
*
9789224 AAATTTTAATGTTATGAAGTGAACGATAAGCTGTGTTTTATGTTATACGAACATACTAAGTATTA
66 AAATTTTAATGTTATGAAGTGAACGATAAGCTGTGTTTTATGTTATACGAACATACTAAGCATTA
*
9789289 TATGCTTACATAGTCTCATTTCCCATGTTTTATAGATAATCGGAAGCTCGTTCGGTTTGGAAGCT
131 TATGCTTACATAGTCTCATTTCCCATGTTTTATAGATAATCAGAAGCTCGTTCGGTTTGGAAGCT
* *
9789354 CGTCGGAGACCTATCACACTATCCCGTAACTATTTCGGAAGATTTTGAGGTTTTGAAT
196 CGTCGGAGACCTATCACACTATCCCGCAACTATTTCGAAAGATTTTGAGGTTTTGAAT
9789412 TATGCTAACATGTTTGTGTTGATGCCTAGGCTTGTGCCAAGCTAAAAGTGGGATTATGCCATGTT
1 TATGCTAACATGTTTGTGTTGATGCCTAGGCTTGTGCCAAGCTAAAAGTGGGATTATGCCATGTT
9789477 AAATTTTAATGTTATGAAGTGAACGATAAGCTGTGTTTTATGTTATACGAACATACTAAGCATTA
66 AAATTTTAATGTTATGAAGTGAACGATAAGCTGTGTTTTATGTTATACGAACATACTAAGCATTA
*
9789542 TATGCTTACATAGTCTTATTTCCCATGTTTTATAGATAATCAGAAGCTCGTTCGGTTTGGAAGCT
131 TATGCTTACATAGTCTCATTTCCCATGTTTTATAGATAATCAGAAGCTCGTTCGGTTTGGAAGCT
*
9789607 CGTCGGAGACCTATCACACTATCCCGCGACTATTTCGAAAGATTTTGAGGTTTTGAAT
196 CGTCGGAGACCTATCACACTATCCCGCAACTATTTCGAAAGATTTTGAGGTTTTGAAT
9789665 TATG
1 TATG
9789669 GTTATAATGG
Statistics
Matches: 249, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
253 249 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.37
Consensus pattern (253 bp):
TATGCTAACATGTTTGTGTTGATGCCTAGGCTTGTGCCAAGCTAAAAGTGGGATTATGCCATGTT
AAATTTTAATGTTATGAAGTGAACGATAAGCTGTGTTTTATGTTATACGAACATACTAAGCATTA
TATGCTTACATAGTCTCATTTCCCATGTTTTATAGATAATCAGAAGCTCGTTCGGTTTGGAAGCT
CGTCGGAGACCTATCACACTATCCCGCAACTATTTCGAAAGATTTTGAGGTTTTGAAT
Found at i:9792684 original size:29 final size:29
Alignment explanation
Indices: 9792652--9792731 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 29
9792642 TAAAGGTCAA
9792652 AAAAAATTTTTACCAACTTTTAAGGACCC
1 AAAAAATTTTTACCAACTTTTAAGGACCC
*** *
9792681 AAAAAATTTTTTTGAAGCTTTTAAGGGCCC
1 AAAAAATTTTTACCAA-CTTTTAAGGACCC
9792711 AAAATATATTTTTTACCAACT
1 AAAA-A-A-TTTTTACCAACT
9792732 GTGAAGGGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
29 13 0.32
30 16 0.40
31 1 0.03
32 3 0.08
33 7 0.17
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (29 bp):
AAAAAATTTTTACCAACTTTTAAGGACCC
Found at i:9792686 original size:32 final size:31
Alignment explanation
Indices: 9792649--9792768 Score: 93
Period size: 32 Copynumber: 3.8 Consensus size: 31
9792639 TTTTAAAGGT
9792649 CAAAAAAAATTTTTACCAACTTTTAAGGACC
1 CAAAAAAAATTTTTACCAACTTTTAAGGACC
** * *
9792680 CAAAAAATTTTTTTGA--AGCTTTTAAGGGCC
1 CAAAAAAAATTTTT-ACCAACTTTTAAGGACC
* * * * *
9792710 CAAAATATATTTTTTACCAACTGTGAAGGGATC
1 CAAAA-AAAATTTTTACCAACTTTTAA-GGACC
*
9792743 TAAAAAAAATTTTCT-CCAACTTTTAA
1 CAAAAAAAATTTT-TACCAACTTTTAA
9792769 ATAACCTAAA
Statistics
Matches: 67, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
30 18 0.27
31 19 0.28
32 22 0.33
33 8 0.12
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (31 bp):
CAAAAAAAATTTTTACCAACTTTTAAGGACC
Found at i:9798835 original size:17 final size:18
Alignment explanation
Indices: 9798808--9798843 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
9798798 ATACTCTAAC
*
9798808 AAATGACAAATAATCAAT
1 AAATGACAAATAAACAAT
9798826 AAAT-ACAAATAAACAAT
1 AAATGACAAATAAACAAT
9798843 A
1 A
9798844 CCGTACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.67, C:0.11, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATGACAAATAAACAAT
Found at i:9799599 original size:3 final size:3
Alignment explanation
Indices: 9799586--9799620 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
9799576 ATTGATAAAA
* *
9799586 AAT ACT AAT AAT AAT AAT AGT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9799621 CAAGAGTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:9801058 original size:51 final size:51
Alignment explanation
Indices: 9800960--9801060 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
9800950 ACTCCACTTC
* * *
9800960 AGCTTTAATCTATTCCACTGCAACGCTAGGGAAACAATATTCACTACCTTT
1 AGCTTTAATCTATTCCACTACAACGCAAGGGAAACAAGATTCACTACCTTT
* * * **
9801011 AGCTTTAATCTGTTTCACTACAACGCAAGGGAAATAAGATTTGCTACCTT
1 AGCTTTAATCTATTCCACTACAACGCAAGGGAAACAAGATTCACTACCTT
9801061 CAGTCTTAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (51 bp):
AGCTTTAATCTATTCCACTACAACGCAAGGGAAACAAGATTCACTACCTTT
Found at i:9801153 original size:51 final size:51
Alignment explanation
Indices: 9801072--9801216 Score: 173
Period size: 51 Copynumber: 2.8 Consensus size: 51
9801062 AGTCTTAACG
* * **
9801072 TCAGGGAGATAAGATTTGCTACCTTCAGCTTTAATCTGCTCCGCTGCAACA
1 TCAGGGAGATAAGATTCGCTACCTTTAGCTTTAATCTGCTCCAATGCAACA
* * * * *
9801123 TCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCAATGTAACG
1 TCAGGGAGATAAGATTCGCTACCTTTAGCTTTAATCTGCTCCAATGCAACA
* * * *
9801174 CCAAGGAGATAGGATTCGCTACCTTTAGCTTTAATCCGCTCCA
1 TCAGGGAGATAAGATTCGCTACCTTTAGCTTTAATCTGCTCCA
9801217 CTTCAGCTTT
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 78 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (51 bp):
TCAGGGAGATAAGATTCGCTACCTTTAGCTTTAATCTGCTCCAATGCAACA
Found at i:9801301 original size:51 final size:51
Alignment explanation
Indices: 9801221--9801318 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
9801211 GCTCCACTTC
*
9801221 AGCTTTAATCTATTCCACTGCAACACCAGGGAAACAAGATTTGCTGCTTTT
1 AGCTTTAATCTATTCCACTGCAACACCAGGGAAACAAGATTCGCTGCTTTT
* * * *
9801272 AGCTTTAATCTGTTCTACTGCAACGCCAGGGAAATAAGATTCGCTGC
1 AGCTTTAATCTATTCCACTGCAACACCAGGGAAACAAGATTCGCTGC
9801319 CTTCAGTCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (51 bp):
AGCTTTAATCTATTCCACTGCAACACCAGGGAAACAAGATTCGCTGCTTTT
Found at i:9801313 original size:123 final size:121
Alignment explanation
Indices: 9801094--9801466 Score: 376
Period size: 123 Copynumber: 3.0 Consensus size: 121
9801084 GATTTGCTAC
* * * *
9801094 CTTCAGCTTTAATCTGCTCCGCTGCAACATCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
1 CTTCAGCTTTAATCTGCTCCACTGCAACACCAGGGAAACAAGATTTGCTGCCTTTAGCTTTAATC
* * * * * *
9801159 TGTTCCAATGTAACGCCAAGGAGATAGGATTCGCTACCTTTAGCTTTAATCCGCTCCA
66 TGTT-CTATG-AACGCCAGGGAAATAAGATTCGCTGCCTTTAGCTTTAATCCGTTCCA
** *
9801217 CTTCAGCTTTAATCTATTCCACTGCAACACCAGGGAAACAAGATTTGCTGCTTTTAGCTTTAATC
1 CTTCAGCTTTAATCTGCTCCACTGCAACACCAGGGAAACAAGATTTGCTGCCTTTAGCTTTAATC
* *
9801282 TGTTCTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAG-TCTTAACGCCAAGATTCGCTG
66 TGTTCTA-TG-AACGCCAGGGAAATAAGATTCGCTGCCTTTAGCT-TTAA-TCC--G-TTC-C--
*
9801346 C
121 A
* * * * *
9801347 CTTCAGCTTTAATCTGCTCCACTGCAACGCCAAGGAAATAAGATTTGTTGCCTTCAGCTTTAATC
1 CTTCAGCTTTAATCTGCTCCACTGCAACACCAGGGAAACAAGATTTGCTGCCTTTAGCTTTAATC
* * * * *
9801412 --TACTATG-ACGCTAGGGAAATAAGATTTGCTGCCTTTAACTTTAATCTGTTCCA
66 TGTTCTATGAACGCCAGGGAAATAAGATTCGCTGCCTTTAGCTTTAATCCGTTCCA
9801465 CT
1 CT
9801467 GCAATGCCAA
Statistics
Matches: 207, Mismatches: 33, Indels: 25
0.78 0.12 0.09
Matches are distributed among these distances:
118 2 0.01
120 1 0.00
121 3 0.01
122 4 0.02
123 95 0.46
124 3 0.01
125 31 0.15
126 2 0.01
127 4 0.02
128 5 0.02
130 57 0.28
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (121 bp):
CTTCAGCTTTAATCTGCTCCACTGCAACACCAGGGAAACAAGATTTGCTGCCTTTAGCTTTAATC
TGTTCTATGAACGCCAGGGAAATAAGATTCGCTGCCTTTAGCTTTAATCCGTTCCA
Found at i:9801386 original size:79 final size:79
Alignment explanation
Indices: 9801255--9801403 Score: 226
Period size: 79 Copynumber: 1.9 Consensus size: 79
9801245 ACCAGGGAAA
* * * * * *
9801255 CAAGATTTGCTGCTTTTAGCTTTAATCTGTTCTACTGCAACGCCAGGGAAATAAGATTCGCTGCC
1 CAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACGCCAAGGAAATAAGATTCGCTGCC
9801320 TTCAGTCTTAACGC
66 TTCAGTCTTAACGC
* *
9801334 CAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACGCCAAGGAAATAAGATTTGTTGCC
1 CAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACGCCAAGGAAATAAGATTCGCTGCC
9801399 TTCAG
66 TTCAG
9801404 CTTTAATCTA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 62 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (79 bp):
CAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACGCCAAGGAAATAAGATTCGCTGCC
TTCAGTCTTAACGC
Found at i:9801454 original size:46 final size:47
Alignment explanation
Indices: 9801335--9801749 Score: 275
Period size: 46 Copynumber: 8.6 Consensus size: 47
9801325 TCTTAACGCC
* * * *
9801335 AAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACGCCAAGGAAAT
1 AAGATTTGCTGCCTTCAACTTTAATCTACT--A-TG-AACGCCAGGGAAAT
* * *
9801386 AAGATTTGTTGCCTTCAGCTTTAATCTACTATG-ACGCTAGGGAAAT
1 AAGATTTGCTGCCTTCAACTTTAATCTACTATGAACGCCAGGGAAAT
* * * * *
9801432 AAGATTTGCTGCCTTTAACTTTAATCTGTTCCACTGCAATGCCAAGGAAAT
1 AAGATTTGCTGCCTTCAACTTTAATC--TACTA-TG-AACGCCAGGGAAAT
* * *
9801483 AAGATTTGCTGCCTTTAGCTTTAATCTA-T-TGCGACGCCAGGGAAAT
1 AAGATTTGCTGCCTTCAACTTTAATCTACTATG-AACGCCAGGGAAAT
* * * * * *
9801529 AAGATTCGTTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAAT
1 AAGATTTGCTGCCTTCAACTTTAATC--TACTA-TG-AACGCCAGGGAAAT
* ** *
9801580 AAAATTCACTGCCTTCTACTTTAATCTA-T-TGCAACGCCAGGGAAAT
1 AAGATTTGCTGCCTTCAACTTTAATCTACTATG-AACGCCAGGGAAAT
* * * *
9801626 AAGATTTGCTGCCTTCAACTTTAATTTGCTCCACTGCAATGCCAAGGAAAT
1 AAGATTTGCTGCCTTCAACTTTAATCTACT--A-TG-AACGCCAGGGAAAT
* ** ** * *
9801677 AAGATTCGCTATCTTCTGCTTTAATCTATTGTG-ACGCCAGGGAAAT
1 AAGATTTGCTGCCTTCAACTTTAATCTACTATGAACGCCAGGGAAAT
* * *
9801723 AAGATTCGTTGCCTTCAGCTTTAATCT
1 AAGATTTGCTGCCTTCAACTTTAATCT
9801750 GTTCCACTGC
Statistics
Matches: 292, Mismatches: 57, Indels: 35
0.76 0.15 0.09
Matches are distributed among these distances:
46 143 0.49
47 1 0.00
48 8 0.03
49 5 0.02
51 135 0.46
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (47 bp):
AAGATTTGCTGCCTTCAACTTTAATCTACTATGAACGCCAGGGAAAT
Found at i:9801503 original size:97 final size:97
Alignment explanation
Indices: 9801335--9801926 Score: 774
Period size: 97 Copynumber: 6.1 Consensus size: 97
9801325 TCTTAACGCC
* *
9801335 AAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACGCCAAGGAAATAAGATTTGTTGCCT
1 AAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTTGCTGCCT
* * * *
9801400 TCAGCTTTAATCTACTATGACGCTAGGGAAAT
66 TTAGCTTTAATCTATTGTGACGCCAGGGAAAT
* * * *
9801432 AAGATTTGCTGCCTTTAACTTTAATCTGTTCCACTGCAATGCCAAGGAAATAAGATTTGCTGCCT
1 AAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTTGCTGCCT
*
9801497 TTAGCTTTAATCTATTGCGACGCCAGGGAAAT
66 TTAGCTTTAATCTATTGTGACGCCAGGGAAAT
* * **
9801529 AAGATTCGTTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAAATTCACTGCCT
1 AAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTTGCTGCCT
**
9801594 TCTA-CTTTAATCTATTGCAACGCCAGGGAAAT
66 T-TAGCTTTAATCTATTGTGACGCCAGGGAAAT
* * * * * * **
9801626 AAGATTTGCTGCCTTCAACTTTAATTTGCTCCACTGCAATGCCAAGGAAATAAGATTCGCTATCT
1 AAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTTGCTGCCT
9801691 TCT-GCTTTAATCTATTGTGACGCCAGGGAAAT
66 T-TAGCTTTAATCTATTGTGACGCCAGGGAAAT
* * * * * **
9801723 AAGATTCGTTGCCTTCAGCTTTAATCTGTTCCACTGCAATGCAAAGGAAATAAAATTGGCCACCT
1 AAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTTGCTGCCT
* * *
9801788 TCAGCTTTAATCTATTGTGACACCACGGAAAT
66 TTAGCTTTAATCTATTGTGACGCCAGGGAAAT
* * ** * *
9801820 AGGATTCGTTTTCTTTAGCTTTAATCTGTTCCACTGCAACGCCAAAGAAATAAGATTTGCTGCCT
1 AAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTTGCTGCCT
*
9801885 TTAGCTTTAATCTATTGCGACGCCAGGGAAAT
66 TTAGCTTTAATCTATTGTGACGCCAGGGAAAT
9801917 AAGATTCGCT
1 AAGATTCGCT
9801927 ATGATAACTT
Statistics
Matches: 430, Mismatches: 62, Indels: 6
0.86 0.12 0.01
Matches are distributed among these distances:
97 428 1.00
98 2 0.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (97 bp):
AAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTTGCTGCCT
TTAGCTTTAATCTATTGTGACGCCAGGGAAAT
Found at i:9801700 original size:291 final size:291
Alignment explanation
Indices: 9801335--9801926 Score: 862
Period size: 291 Copynumber: 2.0 Consensus size: 291
9801325 TCTTAACGCC
* * * *
9801335 AAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACGCCAAGGAAATAAGATTTGTTGCCT
1 AAGATTCGCTGCCTTCAACTTTAATCTGCTCCACTGCAACGCCAAGGAAATAAGATTCGCTACCT
* * *
9801400 TCAGCTTTAATCTACTATGACGCTAGGGAAATAAGATTTGCTGCCTTTAACTTTAATCTGTTCCA
66 TCAGCTTTAATCTACTATGACGCCAGGGAAATAAGATTCGCTGCCTTCAACTTTAATCTGTTCCA
* * * ** * * *
9801465 CTGCAATGCCAAGGAAATAAGATTTGCTGCCTTTAGCTTTAATCTATTGCGACGCCAGGGAAATA
131 CTGCAATGCAAAGGAAATAAAATTGGCCACCTTCAGCTTTAATCTATTGCGACACCACGGAAATA
*
9801530 AGATTCGTTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAAATTCACTGCCTT
196 AGATTCGTTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAAGAAATAAAATTCACTGCCTT
9801595 CTA-CTTTAATCTATTGCAACGCCAGGGAAAT
261 -TAGCTTTAATCTATTGCAACGCCAGGGAAAT
* * * *
9801626 AAGATTTGCTGCCTTCAACTTTAATTTGCTCCACTGCAATGCCAAGGAAATAAGATTCGCTATCT
1 AAGATTCGCTGCCTTCAACTTTAATCTGCTCCACTGCAACGCCAAGGAAATAAGATTCGCTACCT
* * * * *
9801691 TCTGCTTTAATCTATTGTGACGCCAGGGAAATAAGATTCGTTGCCTTCAGCTTTAATCTGTTCCA
66 TCAGCTTTAATCTACTATGACGCCAGGGAAATAAGATTCGCTGCCTTCAACTTTAATCTGTTCCA
*
9801756 CTGCAATGCAAAGGAAATAAAATTGGCCACCTTCAGCTTTAATCTATTGTGACACCACGGAAATA
131 CTGCAATGCAAAGGAAATAAAATTGGCCACCTTCAGCTTTAATCTATTGCGACACCACGGAAATA
* ** * * **
9801821 GGATTCGTTTTCTTTAGCTTTAATCTGTTCCACTGCAACGCCAAAGAAATAAGATTTGCTGCCTT
196 AGATTCGTTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAAGAAATAAAATTCACTGCCTT
*
9801886 TAGCTTTAATCTATTGCGACGCCAGGGAAAT
261 TAGCTTTAATCTATTGCAACGCCAGGGAAAT
9801917 AAGATTCGCT
1 AAGATTCGCT
9801927 ATGATAACTT
Statistics
Matches: 265, Mismatches: 35, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
290 2 0.01
291 263 0.99
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (291 bp):
AAGATTCGCTGCCTTCAACTTTAATCTGCTCCACTGCAACGCCAAGGAAATAAGATTCGCTACCT
TCAGCTTTAATCTACTATGACGCCAGGGAAATAAGATTCGCTGCCTTCAACTTTAATCTGTTCCA
CTGCAATGCAAAGGAAATAAAATTGGCCACCTTCAGCTTTAATCTATTGCGACACCACGGAAATA
AGATTCGTTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAAGAAATAAAATTCACTGCCTT
TAGCTTTAATCTATTGCAACGCCAGGGAAAT
Found at i:9802271 original size:24 final size:24
Alignment explanation
Indices: 9802237--9802294 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
9802227 CGGATTGCCC
*
9802237 CCACTGTAATCTTCAAGGTTCAAT
1 CCACTGTAATCTTCAAAGTTCAAT
*
9802261 CTACTGTAATCTTCAAAGTTCAAT
1 CCACTGTAATCTTCAAAGTTCAAT
*
9802285 CCACTATAAT
1 CCACTGTAAT
9802295 TTTGGGACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (24 bp):
CCACTGTAATCTTCAAAGTTCAAT
Found at i:9807692 original size:34 final size:34
Alignment explanation
Indices: 9807651--9807720 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
9807641 AACCACCTTT
9807651 CTTGGCTGACTTACAGTAACTGATCTTGAGTAAC
1 CTTGGCTGACTTACAGTAACTGATCTTGAGTAAC
*
9807685 CTTGGCTGACTTACAGTAATTGATCTTGAGTAAC
1 CTTGGCTGACTTACAGTAACTGATCTTGAGTAAC
9807719 CT
1 CT
9807721 GTGTTATTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (34 bp):
CTTGGCTGACTTACAGTAACTGATCTTGAGTAAC
Found at i:9820521 original size:28 final size:28
Alignment explanation
Indices: 9820476--9820550 Score: 93
Period size: 25 Copynumber: 2.6 Consensus size: 28
9820466 TTTTGAAGAT
9820476 AAGAAGAGAAGAGTAAAAAAATTGGTTGTAG
1 AAGAAGAGAA-A--AAAAAAATTGGTTGTAG
9820507 AAGAAGAG---AAAAAAATTGGTTGTAG
1 AAGAAGAGAAAAAAAAAATTGGTTGTAG
9820532 AAGAAGAGAAAACAAAAAA
1 AAGAAGAGAAAA-AAAAAA
9820551 GAATTCGTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
25 25 0.62
28 1 0.03
29 6 0.15
31 8 0.20
ACGTcount: A:0.59, C:0.01, G:0.25, T:0.15
Consensus pattern (28 bp):
AAGAAGAGAAAAAAAAAATTGGTTGTAG
Found at i:9820524 original size:25 final size:25
Alignment explanation
Indices: 9820482--9820543 Score: 115
Period size: 25 Copynumber: 2.4 Consensus size: 25
9820472 AGATAAGAAG
9820482 AGAAGAGTAAAAAAATTGGTTGTAGA
1 AGAAGAG-AAAAAAATTGGTTGTAGA
9820508 AGAAGAGAAAAAAATTGGTTGTAGA
1 AGAAGAGAAAAAAATTGGTTGTAGA
9820533 AGAAGAGAAAA
1 AGAAGAGAAAA
9820544 CAAAAAAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 29 0.81
26 7 0.19
ACGTcount: A:0.55, C:0.00, G:0.27, T:0.18
Consensus pattern (25 bp):
AGAAGAGAAAAAAATTGGTTGTAGA
Found at i:9823459 original size:15 final size:15
Alignment explanation
Indices: 9823439--9823467 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9823429 TACAAGCTTG
9823439 AAAATTAAGTCAAAT
1 AAAATTAAGTCAAAT
9823454 AAAATTAAGTCAAA
1 AAAATTAAGTCAAA
9823468 CATTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (15 bp):
AAAATTAAGTCAAAT
Found at i:9831814 original size:82 final size:82
Alignment explanation
Indices: 9831677--9831842 Score: 305
Period size: 82 Copynumber: 2.0 Consensus size: 82
9831667 ATCAAAATTA
*
9831677 TAATCACAAATCATGTCATAATTGAATCTTCAATACATTCAAAACATCTAATAATACAAAGAGAC
1 TAATCACAAATCATGTCATAATAGAATCTTCAATACATTCAAAACATCTAATAATACAAAGAGAC
9831742 TTATAATTAATATATAT
66 TTATAATTAATATATAT
*
9831759 TAATCACAAATCATGTCATAATAGAATCTTCAATACATTCAAAACATCTAATAATATAAAGAGAC
1 TAATCACAAATCATGTCATAATAGAATCTTCAATACATTCAAAACATCTAATAATACAAAGAGAC
*
9831824 TTGTAATTAATATATAT
66 TTATAATTAATATATAT
9831841 TA
1 TA
9831843 TCAACTTTCT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (82 bp):
TAATCACAAATCATGTCATAATAGAATCTTCAATACATTCAAAACATCTAATAATACAAAGAGAC
TTATAATTAATATATAT
Found at i:9835952 original size:23 final size:23
Alignment explanation
Indices: 9835926--9835980 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
9835916 ATATTCATTA
*
9835926 TATTTTTTTAAAAATGATTTTTT
1 TATTTTTTAAAAAATGATTTTTT
** *
9835949 TATTTTCAAAAAAATGTTTTTTT
1 TATTTTTTAAAAAATGATTTTTT
*
9835972 TAATTTTTA
1 TATTTTTTA
9835981 CTAGCGTGAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (23 bp):
TATTTTTTAAAAAATGATTTTTT
Found at i:9845116 original size:18 final size:17
Alignment explanation
Indices: 9845088--9845122 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
9845078 ATTATTAATA
*
9845088 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
9845105 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
9845123 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:9845211 original size:66 final size:62
Alignment explanation
Indices: 9845125--9845337 Score: 174
Period size: 66 Copynumber: 3.4 Consensus size: 62
9845115 AAATATATTT
*
9845125 AATATTAATTATTTCAAATTTTCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTA-TT-AAAATTT-TTTTA-AGTATCATATATTATGATTTGAGTAAATTCATATAA
9845190 G
62 G
* * * * **
9845191 AATATTAATTATTAAGAATTTTATTAA--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTAA-AATTTTTTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* * *
9845245 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TAAAATT-T-TTTTA-AGTATCATATATTATGATTTGAGTAAATTCATATAA
9845310 G
62 G
*
9845311 AATATTAATTATTAAGAATTTTATTAA
1 AATATTAATTATTAA-AATTTTTTTAA
9845338 ATTATATATT
Statistics
Matches: 112, Mismatches: 20, Indels: 33
0.68 0.12 0.20
Matches are distributed among these distances:
54 14 0.12
55 7 0.06
56 5 0.04
57 3 0.03
58 1 0.01
59 10 0.09
60 8 0.07
61 10 0.09
62 1 0.01
63 4 0.04
64 11 0.10
65 13 0.12
66 25 0.22
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (62 bp):
AATATTAATTATTAAAATTTTTTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:9845247 original size:15 final size:15
Alignment explanation
Indices: 9845212--9845263 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
9845202 TTAAGAATTT
*
9845212 TATTAAATTAT-ATA
1 TATTTAATTATAATA
9845226 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
9845240 TATTTAATAATAAT-
1 TATTTAATTATAATA
9845254 TATGTTAATT
1 TAT-TTAATT
9845264 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:9845247 original size:120 final size:120
Alignment explanation
Indices: 9845034--9845379 Score: 615
Period size: 120 Copynumber: 2.9 Consensus size: 120
9845024 NNNNNNNNNN
*
9845034 AGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAATAATTTTATTAAA
1 AGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAA
* * * *
9845099 TTATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCTTTTAT
66 TTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTATATTTTAC
9845154 AGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAA
1 AGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAA
9845219 TTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTAC
66 TTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTAC
9845274 AGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAA
1 AGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAA
9845339 TTATATATTTTAATTATAATATATTTAATAATAATTATGTT
66 TTATATATTTTAATTATAATATATTTAATAATAATTATGTT
9845380 TAAATATGAT
Statistics
Matches: 219, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
119 5 0.02
120 212 0.97
121 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAA
TTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTAC
Found at i:9845362 original size:16 final size:16
Alignment explanation
Indices: 9845341--9845382 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
9845331 TTATTAAATT
*
9845341 ATATATTTTAATTATA
1 ATATATTTTAATAATA
9845357 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
9845372 AT-TATGTTTAA
1 ATATAT-TTTAA
9845383 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:9845367 original size:15 final size:15
Alignment explanation
Indices: 9845332--9845373 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
9845322 TTAAGAATTT
*
9845332 TATTAAATTAT-ATA
1 TATTTAATTATAATA
9845346 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
9845360 TATTTAATAATAAT
1 TATTTAATTATAAT
9845374 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:9845493 original size:153 final size:156
Alignment explanation
Indices: 9845316--9845628 Score: 510
Period size: 153 Copynumber: 2.0 Consensus size: 156
9845306 ATAAGAATAT
*
9845316 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATAT-A-TTTAATAATAATTATGT
1 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTA-AA-ATGAGTTTAATAATAATTATGT
* *
9845379 TTAAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAAC
64 TTAAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAAC
*
9845444 AAT-A-A-TTACCAAAACAAATTTCTGC
129 AATAACATTTACCAAAACAAATTTATGC
*
9845469 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATGAGTTTAATAATATTTATGTTT
1 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATGAGTTTAATAATAATTATGTTT
*
9845534 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATCACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
9845599 TAATCATTTACCAAAACAAATTTATGC
131 TAA-CATTTACCAAAACAAATTTATGC
9845626 TAA
1 TAA
9845629 GGGTATTCTA
Statistics
Matches: 148, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
151 2 0.01
152 3 0.02
153 119 0.80
154 1 0.01
156 1 0.01
157 22 0.15
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (156 bp):
TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATGAGTTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAACATTTACCAAAACAAATTTATGC
Found at i:9845776 original size:16 final size:16
Alignment explanation
Indices: 9845751--9845786 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
9845741 GATTTGCTAT
*
9845751 TACACTTCTAATCCAA
1 TACACCTCTAATCCAA
9845767 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
9845783 TACA
1 TACA
9845787 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:9846963 original size:71 final size:71
Alignment explanation
Indices: 9846847--9846990 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 71
9846837 CATGATGAAG
*
9846847 TAAGCTTTCACTCAACTATACCACGCACGTGGTTCTTGCTGAAGTCAATAAAGCACATTCTTTAG
1 TAAGCTTTCACTCAACTATACCACGCACATGGTTCTTGCTGAAGTCAATAAAGCACATTCTTTAG
9846912 CTTATA
66 CTTATA
9846918 TAAGCTTTCACTCAACTATACCACGCACATGGTTCTTGCTGAAGTCAATAAAGCACATTCTTTAG
1 TAAGCTTTCACTCAACTATACCACGCACATGGTTCTTGCTGAAGTCAATAAAGCACATTCTTTAG
9846983 CTTATA
66 CTTATA
9846989 TA
1 TA
9846991 CCTTTTACTC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.33
Consensus pattern (71 bp):
TAAGCTTTCACTCAACTATACCACGCACATGGTTCTTGCTGAAGTCAATAAAGCACATTCTTTAG
CTTATA
Found at i:9863522 original size:24 final size:24
Alignment explanation
Indices: 9863495--9863546 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
9863485 TTAGTAAGTC
*
9863495 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
9863519 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
9863543 AAAT
1 AAAT
9863547 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:9865492 original size:24 final size:24
Alignment explanation
Indices: 9865465--9865516 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
9865455 TTAGTAAGTC
*
9865465 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
9865489 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
9865513 AAAT
1 AAAT
9865517 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:9867663 original size:6 final size:6
Alignment explanation
Indices: 9867654--9867729 Score: 88
Period size: 6 Copynumber: 13.0 Consensus size: 6
9867644 TTTAAATTTC
* *
9867654 ATATTA ATATTA ATATTA ATATTA ATATTA A-ATAA ATATAATT ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATAT--TA ATATTA
9867703 A-A-TA A-ATTA ATATTA ATATTA ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA
9867730 TTAATTTAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
4 4 0.07
5 8 0.13
6 45 0.74
8 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATATTA
Found at i:9867706 original size:15 final size:15
Alignment explanation
Indices: 9867656--9867729 Score: 64
Period size: 19 Copynumber: 4.7 Consensus size: 15
9867646 TAAATTTCAT
9867656 ATTAATATTAATATTAA
1 ATTAATATTAA-A-TAA
9867673 TATTAATATTAAATAA
1 -ATTAATATTAAATAA
9867689 ATATAATTATATTAAATAA
1 AT-T-A--ATATTAAATAA
9867708 ATTAATATT-AAT--
1 ATTAATATTAAATAA
9867720 ATTAATATTA
1 ATTAATATTA
9867730 TTAATTTAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 15
0.77 0.00 0.23
Matches are distributed among these distances:
12 9 0.18
14 3 0.06
15 7 0.14
16 4 0.08
17 3 0.06
18 12 0.24
19 13 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAATATTAAATAA
Found at i:9869104 original size:15 final size:14
Alignment explanation
Indices: 9869082--9869115 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
9869072 TGATAAATCA
*
9869082 AATAAAAATAATAT
1 AATAAAAATAAAAT
9869096 AATATAAAATAAAAT
1 AATA-AAAATAAAAT
9869111 AATAA
1 AATAA
9869116 CACAATAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AATAAAAATAAAAT
Found at i:9873402 original size:22 final size:23
Alignment explanation
Indices: 9873377--9873428 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
9873367 TTAGGCTTAG
9873377 TTTGGGTTTTGGA-TTTTTTT-TA
1 TTTGGGTTTT-GATTTTTTTTATA
9873399 TTTGGG-TTTGATTTTTTTTATA
1 TTTGGGTTTTGATTTTTTTTATA
9873421 TTTGGGTT
1 TTTGGGTT
9873429 GACTTTGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 2 0.07
21 10 0.37
22 14 0.52
23 1 0.04
ACGTcount: A:0.10, C:0.00, G:0.23, T:0.67
Consensus pattern (23 bp):
TTTGGGTTTTGATTTTTTTTATA
Found at i:9883952 original size:19 final size:20
Alignment explanation
Indices: 9883927--9883975 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
9883917 TTCTCTTACA
**
9883927 ATTTTTGATATTTTCTCATT
1 ATTTTTGATATTCCCTCATT
*
9883947 -TTTTTGGTATTCCCTCATT
1 ATTTTTGATATTCCCTCATT
9883966 ATTTTTGATA
1 ATTTTTGATA
9883976 CACCCTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.18, C:0.12, G:0.08, T:0.61
Consensus pattern (20 bp):
ATTTTTGATATTCCCTCATT
Found at i:9885411 original size:16 final size:15
Alignment explanation
Indices: 9885384--9885438 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
9885374 TTTTTCATAA
9885384 ATATATATTATT-TT
1 ATATATATTATTATT
9885398 ATATATATCCTATTATT
1 ATATATAT--TATTATT
*
9885415 -TATATACTTATTATAC
1 ATATATA-TTATTAT-T
9885431 ATATATAT
1 ATATATAT
9885439 AAGTGTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 8 0.24
15 6 0.18
16 11 0.32
17 9 0.26
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATATATTATTATT
Found at i:9886036 original size:110 final size:110
Alignment explanation
Indices: 9885843--9886077 Score: 452
Period size: 110 Copynumber: 2.1 Consensus size: 110
9885833 GAAATTGAGC
*
9885843 CCTAACGTATTAGGTTCTGATTTTCTTTGATGATCTTAAATAACTGAGGATATTCTTTATTCAAA
1 CCTAACGTATTGGGTTCTGATTTTCTTTGATGATCTTAAATAACTGAGGATATTCTTTATTCAAA
9885908 ATGCATGAGTATAAAAATTATTTTTGGGAACTTAACTTGTTGTGT
66 ATGCATGAGTATAAAAATTATTTTTGGGAACTTAACTTGTTGTGT
*
9885953 CCTAACGTATTGGGTTCTGATTTTCTTTGATGATCTTAAATAATTGAGGATATTCTTTATTCAAA
1 CCTAACGTATTGGGTTCTGATTTTCTTTGATGATCTTAAATAACTGAGGATATTCTTTATTCAAA
9886018 ATGCATGAGTATAAAAATTATTTTTGGGAACTTAACTTGTTGTGT
66 ATGCATGAGTATAAAAATTATTTTTGGGAACTTAACTTGTTGTGT
9886063 CCTAACGTATTGGGT
1 CCTAACGTATTGGGT
9886078 GTGGCATGTT
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 123 1.00
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (110 bp):
CCTAACGTATTGGGTTCTGATTTTCTTTGATGATCTTAAATAACTGAGGATATTCTTTATTCAAA
ATGCATGAGTATAAAAATTATTTTTGGGAACTTAACTTGTTGTGT
Found at i:9897321 original size:45 final size:45
Alignment explanation
Indices: 9897244--9897439 Score: 223
Period size: 45 Copynumber: 4.4 Consensus size: 45
9897234 GGTTGAAAAG
* * * * * *
9897244 TAGCAGATCCTGTCTTCCTAAATTGGTAGCGAAGTGGATCGAAGA
1 TAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
*
9897289 TAGCAGATCTTGTCTTCCCATACTGGTGGCGAAATAGATCGAAGA
1 TAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
* *** * * * *
9897334 AAGCAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAATA
1 TAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
* *
9897378 TACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGGAGA
1 TAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
*
9897423 AAGCAGATCTTGTCTTC
1 TAGCAGATCTTGTCTTC
9897440 ATGTATTAAC
Statistics
Matches: 122, Mismatches: 28, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
44 34 0.28
45 88 0.72
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (45 bp):
TAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
Found at i:9897386 original size:44 final size:44
Alignment explanation
Indices: 9897338--9898233 Score: 871
Period size: 44 Copynumber: 20.5 Consensus size: 44
9897328 CGAAGAAAGC
* * * * **
9897338 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAATATACC
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
* ** * ** *
9897382 AGATCTTGTCTTCCCATACTGGTGGC--GAAGTAGATCGGAGA-AAGC
1 AGATCTTGTCTT--CAT-GTATTGACATGAAGTAGATCAAAGATAA-T
* * **
9897427 AGATCTTGTCTTCATGTATTAACATGAAGTAGATCAGAGATAGC
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
* * * *
9897471 AGATCTTATCTTCATATATTGATATGAAGTAGATCGAAGATAAT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
* *
9897515 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
* * * *
9897559 AGATCTTATCTTCATATATTGATATGAAGTAGATCGAAGATAAT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
* *
9897603 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAAT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
* *
9897647 AGATCTTATCTTC----A-T---ATGAAGTAGAACAAAGATAAT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
* * *
9897683 GGATCTTGTCTTCATGTATTGACCTGAAGTAGATCAGAGATAGA-
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATA-AT
* * *
9897727 AAATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAAT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
* *
9897771 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAAT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
* * * * *
9897815 GGATCTTGTCTTCATGTATTAACATGAAGTAGATTAGAGATAGT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
* * *
9897859 AGATCTTGTCTTCATGTATTGACATAAAGTAGATCGAGGATAAT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
* * *
9897903 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
* *** * *** *
9897947 GGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAAT
1 AGATCTTGTCTTCATGTA-TTGACATGAAGTAGATCAAAGATAAT
* *
9897992 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
* *** * *** *
9898036 GGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAAT
1 AGATCTTGTCTTCATGTA-TTGACATGAAGTAGATCAAAGATAAT
* **
9898081 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGC
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
* * * * *
9898125 AGATCTTATCTTTATATATTAATATGAAGTAGATCAAAGATAAT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
* * * * **
9898169 GGATCTTGTCTTCGTGTATTGACAGGAAGTAGATCAAAGACAGC
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
* *
9898213 AGACCTTGTCTTCCTGTATTG
1 AGATCTTGTCTTCATGTATTG
9898234 GCAGCGAGGA
Statistics
Matches: 690, Mismatches: 143, Indels: 38
0.79 0.16 0.04
Matches are distributed among these distances:
36 30 0.04
39 1 0.00
40 2 0.00
41 1 0.00
42 3 0.00
43 4 0.01
44 548 0.79
45 93 0.13
46 3 0.00
47 5 0.01
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (44 bp):
AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
Found at i:9897680 original size:36 final size:36
Alignment explanation
Indices: 9897626--9897697 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
9897616 ATGTATTGAC
* *
9897626 ATGAAGTAGATCAGAGATAATAGATCTTATCTTCAT
1 ATGAAGTAGAACAAAGATAATAGATCTTATCTTCAT
* *
9897662 ATGAAGTAGAACAAAGATAATGGATCTTGTCTTCAT
1 ATGAAGTAGAACAAAGATAATAGATCTTATCTTCAT
9897698 GTATTGACCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (36 bp):
ATGAAGTAGAACAAAGATAATAGATCTTATCTTCAT
Found at i:9897989 original size:45 final size:45
Alignment explanation
Indices: 9897927--9898093 Score: 196
Period size: 45 Copynumber: 3.7 Consensus size: 45
9897917 TGTATTGACA
* *
9897927 TGAAGTAGATCAGAGATAGTGGATCTTGTCTTCCCATACTGGTGG
1 TGAAGTAGATCAGAGATAATAGATCTTGTCTTCCCATACTGGTGG
*** * ***
9897972 TGAAGTAGATC-GAAGATAATAGATCTTGTCTTCATGTA-TTGACA
1 TGAAGTAGATCAG-AGATAATAGATCTTGTCTTCCCATACTGGTGG
* *
9898016 TGAAGTAGATCAGAGATAGTGGATCTTGTCTTCCCATACTGGTGG
1 TGAAGTAGATCAGAGATAATAGATCTTGTCTTCCCATACTGGTGG
9898061 TGAAGTAGATC-GAAGATAATAGATCTTGTCTTC
1 TGAAGTAGATCAG-AGATAATAGATCTTGTCTTC
9898094 ATGTATTGAC
Statistics
Matches: 98, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
44 35 0.36
45 63 0.64
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (45 bp):
TGAAGTAGATCAGAGATAATAGATCTTGTCTTCCCATACTGGTGG
Done.