Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008716.1 Hibiscus syriacus cultivar Beakdansim tig00111769_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5677467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 24
Found at i:5226697 original size:21 final size:21
Alignment explanation
Indices: 5226671--5226749 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
5226661 CGCGTTGCGA
*
5226671 TTCTCTCGTTGCAATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
5226692 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
5226713 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
5226733 TT-TCAT-GTTGCGATTTT
1 TTCTC-TCGTTGCGATTTT
5226750 AAGTTTAGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 30 0.59
21 21 0.41
ACGTcount: A:0.13, C:0.19, G:0.16, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:5227332 original size:20 final size:20
Alignment explanation
Indices: 5227307--5227480 Score: 188
Period size: 20 Copynumber: 8.6 Consensus size: 20
5227297 CTTTAAAAAT
5227307 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5227327 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
5227347 TGTCGTTGCGATTTACAGATA
1 CG-CGTTGCGATTTACGGATA
* *
5227368 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
5227388 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
** *
5227408 CGCGTTGCGATTTTACATATT
1 CGCGTTGCGA-TTTACGGATA
* *
5227429 CTCGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5227449 CGCGTTTCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
5227470 CTCGTTGCGAT
1 CGCGTTGCGAT
5227481 AGTCAGAATC
Statistics
Matches: 124, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
20 74 0.60
21 50 0.40
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:5227368 original size:41 final size:41
Alignment explanation
Indices: 5227309--5227541 Score: 269
Period size: 41 Copynumber: 5.7 Consensus size: 41
5227299 TTAAAAATCG
* *
5227309 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCT
5227350 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCT
* *
5227390 CGTTGCGATTTACGGATACGCGTTGCGATTTTACATATTCT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCT
* * * * *
5227431 CGTTGTGATTTACGGATACGCGTTTCGATTTTACGGATACT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCT
* * *
5227472 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATA--TGTTCG
1 CGTTGCGAT-TTACAGATA-CGCGTTGCGATTT-TACGTATTCT
* * *
5227512 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACAGATACGCGTTGCGATT
5227542 CTGGAAAATC
Statistics
Matches: 166, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
39 1 0.01
40 65 0.39
41 97 0.58
42 3 0.02
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCT
Found at i:5227449 original size:81 final size:82
Alignment explanation
Indices: 5227309--5227541 Score: 285
Period size: 81 Copynumber: 2.9 Consensus size: 82
5227299 TTAAAAATCG
* *
5227309 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACAGATACGCGTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACATATTCTCGTTGCGATTTACAGATACGCGTT
* *
5227374 GCGA-TTTACGTATTCT
66 GCGATTTTACGGATACT
* *
5227390 CGTTGCGATTTACGGATACGCGTTGCGATTTTACATATTCTCGTTGTGATTTACGGATACGCGTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACATATTCTCGTTGCGATTTACAGATACGCGTT
*
5227455 TCGATTTTACGGATACT
66 GCGATTTTACGGATACT
* * * * * * * *
5227472 CGTTGCGATAGT-CAGA-ATCGCGTTGCGA-TTTATATGTTCGCGTTGCGATTTTCATATTCGCG
1 CGTTGCGAT-TTACGGATA-CGCGTTGCGATTTTACATATTCTCGTTGCGATTTACAGATACGCG
5227534 TTGCGATT
64 TTGCGATT
5227542 CTGGAAAATC
Statistics
Matches: 131, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
81 98 0.75
82 32 0.24
83 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (82 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACATATTCTCGTTGCGATTTACAGATACGCGTT
GCGATTTTACGGATACT
Found at i:5227512 original size:20 final size:20
Alignment explanation
Indices: 5227489--5227541 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
5227479 ATAGTCAGAA
*
5227489 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
5227509 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
5227529 TCGCGTTGCGATT
1 TCGCGTTGCGATT
5227542 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:5227594 original size:21 final size:21
Alignment explanation
Indices: 5227509--5227626 Score: 84
Period size: 21 Copynumber: 5.7 Consensus size: 21
5227499 ATTTATATGT
* *
5227509 TCGCGTTGCGATT-TTCATAT
1 TCGCATTGCGATTCTTCATAA
* ** *
5227529 TCGCGTTGCGATTCTGGAAAA
1 TCGCATTGCGATTCTTCATAA
*
5227550 TCGCAATGCGAATT-TGT-ACT-A
1 TCGCATTGCG-ATTCT-TCA-TAA
*
5227571 TCGCATTGTGATTCTTCATAA
1 TCGCATTGCGATTCTTCATAA
*
5227592 TCGCTTTGCGATTCTTCATAA
1 TCGCATTGCGATTCTTCATAA
*
5227613 TCGC-TTTCGATTCT
1 TCGCATTGCGATTCT
5227627 GGGAACTGAT
Statistics
Matches: 78, Mismatches: 13, Indels: 14
0.74 0.12 0.13
Matches are distributed among these distances:
20 27 0.35
21 48 0.62
22 3 0.04
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTCTTCATAA
Found at i:5227625 original size:20 final size:21
Alignment explanation
Indices: 5227570--5227626 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
5227560 AATTTGTACT
* *
5227570 ATCGCATTGTGATTCTTCATA
1 ATCGCTTTGCGATTCTTCATA
5227591 ATCGCTTTGCGATTCTTCATA
1 ATCGCTTTGCGATTCTTCATA
5227612 ATCGCTTT-CGATTCT
1 ATCGCTTTGCGATTCT
5227627 GGGAACTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 7 0.21
21 27 0.79
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (21 bp):
ATCGCTTTGCGATTCTTCATA
Found at i:5229238 original size:32 final size:32
Alignment explanation
Indices: 5229202--5229275 Score: 148
Period size: 32 Copynumber: 2.3 Consensus size: 32
5229192 CATTTTTAGC
5229202 ATTAAATCCCAATGTGAACACTCCATTGTGGG
1 ATTAAATCCCAATGTGAACACTCCATTGTGGG
5229234 ATTAAATCCCAATGTGAACACTCCATTGTGGG
1 ATTAAATCCCAATGTGAACACTCCATTGTGGG
5229266 ATTAAATCCC
1 ATTAAATCCC
5229276 TCCACTGACC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.28
Consensus pattern (32 bp):
ATTAAATCCCAATGTGAACACTCCATTGTGGG
Found at i:5230049 original size:31 final size:31
Alignment explanation
Indices: 5230011--5230071 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
5230001 ATAACGTGGA
*
5230011 CACTTAAAAGTGAAACGGAGAAAACATTAAG
1 CACTTAAAAGTGAAACAGAGAAAACATTAAG
* * *
5230042 CACTTAAAAGTGTAATAGAGAAAATATTAA
1 CACTTAAAAGTGAAACAGAGAAAACATTAA
5230072 ACACATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.21
Consensus pattern (31 bp):
CACTTAAAAGTGAAACAGAGAAAACATTAAG
Found at i:5233609 original size:2 final size:2
Alignment explanation
Indices: 5233604--5233739 Score: 245
Period size: 2 Copynumber: 68.0 Consensus size: 2
5233594 ACACACACAC
* * *
5233604 AT AT AT AC AT AT AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5233646 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5233688 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5233730 AT AT AT AT AT
1 AT AT AT AT AT
5233740 GGACCCGAAT
Statistics
Matches: 128, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 128 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5234434 original size:2 final size:2
Alignment explanation
Indices: 5234427--5234485 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
5234417 CGGGTCCATA
5234427 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5234469 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
5234486 ACCGACTTGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5242108 original size:2 final size:2
Alignment explanation
Indices: 5242101--5242126 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5242091 AATAATACCC
5242101 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5242127 TATTTTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5242393 original size:2 final size:2
Alignment explanation
Indices: 5242384--5242447 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
5242374 TTTTTTAAAA
5242384 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5242425 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
5242448 ATGTGTAAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5242764 original size:22 final size:21
Alignment explanation
Indices: 5242728--5242778 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
5242718 ATTGAATTTT
5242728 TTTTTATAAACTATAATTGATA
1 TTTTTATAAACTAT-ATTGATA
* *
5242750 TTTTTATAAGA-TATATTTATC
1 TTTTTATAA-ACTATATTGATA
5242771 TTTTTATA
1 TTTTTATA
5242779 CTTTTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 13 0.50
22 12 0.46
23 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (21 bp):
TTTTTATAAACTATATTGATA
Found at i:5254896 original size:17 final size:18
Alignment explanation
Indices: 5254874--5254908 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5254864 ATAAAAAAAT
5254874 ATTATTA-TTAATAATAA
1 ATTATTATTTAATAATAA
5254891 ATTATTATTTAATAATAA
1 ATTATTATTTAATAATAA
5254909 TTTTTTCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTATTATTTAATAATAA
Found at i:5255858 original size:20 final size:19
Alignment explanation
Indices: 5255835--5255881 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
5255825 CGATATACCA
5255835 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
5255855 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
5255875 GGTAAAA
1 GGTAAAA
5255882 TTAAAAGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:5256025 original size:20 final size:18
Alignment explanation
Indices: 5256002--5256047 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
5255992 CGATATAACA
5256002 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAA-C
*
5256022 GGTATCAAAATGATAAAAC
1 GGTA-AAAAATGATAAAAC
5256041 GGTAAAA
1 GGTAAAA
5256048 TGATACCGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 5 0.22
20 13 0.57
21 3 0.13
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (18 bp):
GGTAAAAAATGATAAAAC
Found at i:5258365 original size:33 final size:33
Alignment explanation
Indices: 5258323--5258388 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
5258313 AAAAAGATGG
*
5258323 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
5258356 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
5258389 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:5260220 original size:18 final size:19
Alignment explanation
Indices: 5260174--5260235 Score: 101
Period size: 19 Copynumber: 3.4 Consensus size: 19
5260164 AATGTCGAGT
*
5260174 TAATTTTGTATAAGATTTA
1 TAATTTTGTATACGATTTA
5260193 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
5260212 TAA-TTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
5260230 T-ATTTT
1 TAATTTT
5260236 TTATGTGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
17 1 0.02
18 19 0.46
19 21 0.51
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATACGATTTA
Found at i:5260658 original size:197 final size:199
Alignment explanation
Indices: 5260317--5261922 Score: 2861
Period size: 197 Copynumber: 8.1 Consensus size: 199
5260307 TTAAGGGTCA
*
5260317 TGTCGATACTAATATAG-TT-TGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
5260380 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
5260445 TAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
5260509 AATG
196 AATG
5260513 TGTCGACACTAATATAGTTT-TGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
5260577 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
5260641 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGG-TTT-TGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
5260704 AATG
196 AATG
5260708 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
5260773 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
5260838 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
5260903 AA--
196 AATG
* *** *
5260905 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
*
5260969 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
5261034 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
5261099 TAATG
195 TAATG
5261104 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
5261168 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
5261232 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
5261297 AATG
196 AATG
* *** *
5261301 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
*
5261366 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
5261431 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
5261496 TAATG
195 TAATG
5261501 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
5261565 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
5261629 T-ATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
5261693 AATG
196 AATG
* *** *
5261697 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
*
5261762 CATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
5261825 GTAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
5261889 TAATG
195 TAATG
5261894 TGTCGACACTAATATAGTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
5261923 CTAATTTAAA
Statistics
Matches: 1358, Mismatches: 37, Indels: 29
0.95 0.03 0.02
Matches are distributed among these distances:
195 43 0.03
196 250 0.18
197 666 0.49
198 141 0.10
199 118 0.09
200 140 0.10
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:5261473 original size:397 final size:398
Alignment explanation
Indices: 5260317--5261922 Score: 3012
Period size: 397 Copynumber: 4.1 Consensus size: 398
5260307 TTAAGGGTCA
*
5260317 TGTCGATACTAATATAG-TT-TGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
5260380 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
5260445 TAATATGTAATTTTT-AATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
* ***
5260509 AATGTGTCGACACTAATATAGTTT-TGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
* *
5260572 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 CACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
5260637 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGG-TTT-TGAGAGAATAAGTCT
326 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
5260700 AAATAATG
391 AAATAATG
5260708 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
5260773 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
5260838 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
5260903 AA--TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
5260965 CACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
261 CACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
5261030 TAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
325 TAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
5261095 TAAATAATG
390 TAAATAATG
5261104 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
5261168 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
5261232 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
5261297 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
5261362 CACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
261 CACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
5261427 TAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
325 TAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
5261492 TAAATAATG
390 TAAATAATG
5261501 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
5261565 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
5261629 T-ATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
5261693 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
5261758 CACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTAT
261 CACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
5261822 AATGTAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
326 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
5261886 AAATAATG
391 AAATAATG
5261894 TGTCGACACTAATATAGTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
5261923 CTAATTTAAA
Statistics
Matches: 1197, Mismatches: 7, Indels: 20
0.98 0.01 0.02
Matches are distributed among these distances:
391 16 0.01
392 40 0.03
393 251 0.21
394 281 0.23
395 75 0.06
396 235 0.20
397 299 0.25
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (398 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
CACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
AAATAATG
Found at i:5263405 original size:6 final size:6
Alignment explanation
Indices: 5263381--5263460 Score: 70
Period size: 6 Copynumber: 13.3 Consensus size: 6
5263371 ATCGGTCGCA
* * * * * *
5263381 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* * * *
5263429 GAAGAT GATGAA GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
5263461 TGATCCAAAC
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.40, C:0.05, G:0.34, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:5263420 original size:9 final size:9
Alignment explanation
Indices: 5263396--5263464 Score: 84
Period size: 9 Copynumber: 7.7 Consensus size: 9
5263386 TGAAGCTGAC
*
5263396 GATGAAGAT
1 GATGATGAT
*
5263405 GACGATGAT
1 GATGATGAT
5263414 GATGATGAT
1 GATGATGAT
* *
5263423 GACGATGAA
1 GATGATGAT
*
5263432 GATGATGAA
1 GATGATGAT
5263441 GATGATGAT
1 GATGATGAT
*
5263450 GATGAAGAT
1 GATGATGAT
5263459 GATGAT
1 GATGAT
5263465 CCAAACAAGT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.39, C:0.03, G:0.33, T:0.25
Consensus pattern (9 bp):
GATGATGAT
Found at i:5263420 original size:15 final size:15
Alignment explanation
Indices: 5263396--5263464 Score: 93
Period size: 15 Copynumber: 4.6 Consensus size: 15
5263386 TGAAGCTGAC
* * *
5263396 GATGAAGATGACGAT
1 GATGATGATGATGAA
*
5263411 GATGATGATGATGAC
1 GATGATGATGATGAA
*
5263426 GATGAAGATGATGAA
1 GATGATGATGATGAA
5263441 GATGATGATGATGAA
1 GATGATGATGATGAA
5263456 GATGATGAT
1 GATGATGAT
5263465 CCAAACAAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 48 1.00
ACGTcount: A:0.39, C:0.03, G:0.33, T:0.25
Consensus pattern (15 bp):
GATGATGATGATGAA
Found at i:5263461 original size:12 final size:12
Alignment explanation
Indices: 5263381--5263464 Score: 87
Period size: 12 Copynumber: 7.0 Consensus size: 12
5263371 ATCGGTCGCA
* *
5263381 GAAGATGAAGCT
1 GAAGATGATGAT
* *
5263393 GACGATGAAGAT
1 GAAGATGATGAT
*
5263405 GACGATGATGAT
1 GAAGATGATGAT
* *
5263417 GATGATGACGAT
1 GAAGATGATGAT
*
5263429 GAAGATGATGAA
1 GAAGATGATGAT
*
5263441 GATGATGATGAT
1 GAAGATGATGAT
5263453 GAAGATGATGAT
1 GAAGATGATGAT
5263465 CCAAACAAGT
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 61 1.00
ACGTcount: A:0.39, C:0.05, G:0.33, T:0.23
Consensus pattern (12 bp):
GAAGATGATGAT
Found at i:5263464 original size:18 final size:18
Alignment explanation
Indices: 5263381--5263460 Score: 88
Period size: 18 Copynumber: 4.4 Consensus size: 18
5263371 ATCGGTCGCA
* * *
5263381 GAAGATGAAGCTGACGAT
1 GAAGATGACGATGATGAT
5263399 GAAGATGACGATGATGAT
1 GAAGATGACGATGATGAT
* *
5263417 GATGATGACGATGAAGAT
1 GAAGATGACGATGATGAT
* * *
5263435 GATGAAGATGATGATGAT
1 GAAGATGACGATGATGAT
5263453 GAAGATGA
1 GAAGATGA
5263461 TGATCCAAAC
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.40, C:0.05, G:0.34, T:0.21
Consensus pattern (18 bp):
GAAGATGACGATGATGAT
Found at i:5265216 original size:181 final size:181
Alignment explanation
Indices: 5264824--5265306 Score: 896
Period size: 182 Copynumber: 2.7 Consensus size: 181
5264814 CTTTCAACAT
**
5264824 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
5264889 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
5264954 ATGTGTCGATACGATTTAAAAAGTGTCGACATTTTACACATCGGAACCCATA
130 ATGTGTCGATACGATTTAAAAAGTGTCGACATTTTACACATCGGAACCCATA
5265006 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
5265071 GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
66 GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AAA
5265136 ATGTGTCGATACGATTTAAAAAGTGTCGACATTTTACACATCGGAACCCATA
130 ATGTGTCGATACGATTTAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
5265188 ATTATAATGT-ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
5265252 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTT-TAATATTGTGTCGGTACTTTATGTCCATA
5265307 CCATTTAAAA
Statistics
Matches: 295, Mismatches: 4, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
181 116 0.39
182 179 0.61
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (181 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
TGTGTCGATACGATTTAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:5267888 original size:23 final size:23
Alignment explanation
Indices: 5267857--5267919 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
5267847 ATAGGTAAAC
*
5267857 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
5267880 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
5267903 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
5267920 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:5267927 original size:23 final size:23
Alignment explanation
Indices: 5267857--5267929 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
5267847 ATAGGTAAAC
* * **
5267857 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
5267880 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
5267903 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
5267926 ATAT
1 ATAT
5267930 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:5268304 original size:23 final size:23
Alignment explanation
Indices: 5268278--5268340 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
5268268 AATAGGTAAC
*
5268278 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
5268301 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
5268324 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
5268341 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:5268348 original size:23 final size:23
Alignment explanation
Indices: 5268278--5268350 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
5268268 AATAGGTAAC
* * **
5268278 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
5268301 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
5268324 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
5268347 ATAT
1 ATAT
5268351 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:5268770 original size:23 final size:23
Alignment explanation
Indices: 5268707--5268771 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
5268697 ATAGGTAAAC
* *
5268707 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCCCTT
**
5268730 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
5268753 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
5268772 TATCTCGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:5268996 original size:18 final size:18
Alignment explanation
Indices: 5268975--5269011 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5268965 GTAATTGGAG
5268975 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
5268993 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
5269011 T
1 T
5269012 ATATTTCGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:5271290 original size:15 final size:15
Alignment explanation
Indices: 5271270--5271300 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5271260 ATCGATAATA
5271270 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
5271285 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
5271300 T
1 T
5271301 CATCGATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:5275426 original size:15 final size:16
Alignment explanation
Indices: 5275408--5275439 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5275398 ACATACTAAA
5275408 TCGGTT-TCGATTTTT
1 TCGGTTATCGATTTTT
5275423 TCGGTTATCGATTTTT
1 TCGGTTATCGATTTTT
5275439 T
1 T
5275440 GGATCGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.09, C:0.12, G:0.19, T:0.59
Consensus pattern (16 bp):
TCGGTTATCGATTTTT
Found at i:5283900 original size:20 final size:20
Alignment explanation
Indices: 5283875--5283927 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
5283865 TTTTGGTGCA
**
5283875 GAGGGAATCGATCCCCCCTT
1 GAGGGAATCGATCCCCCCAC
*
5283895 GAGGGAACCGATTCCCCCCAC
1 GAGGGAATCGA-TCCCCCCAC
*
5283916 AAGGGAATCGAT
1 GAGGGAATCGAT
5283928 ACCTCCCTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (20 bp):
GAGGGAATCGATCCCCCCAC
Found at i:5283912 original size:21 final size:20
Alignment explanation
Indices: 5283875--5283913 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5283865 TTTTGGTGCA
*
5283875 GAGGGAATCGATCCCCCCTT
1 GAGGGAACCGATCCCCCCTT
5283895 GAGGGAACCGATTCCCCCC
1 GAGGGAACCGA-TCCCCCC
5283914 ACAAGGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCTT
Found at i:5288937 original size:33 final size:33
Alignment explanation
Indices: 5288886--5288950 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
5288876 TGACGTATGA
* *
5288886 TTTTATCATATCTTAATTAACAGGTTAACGTTC
1 TTTTATCATAACTCAATTAACAGGTTAACGTTC
* *
5288919 TTTTATTATAACTCAATTAACATGTTAACGTT
1 TTTTATCATAACTCAATTAACAGGTTAACGTT
5288951 TAGCTAAGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (33 bp):
TTTTATCATAACTCAATTAACAGGTTAACGTTC
Found at i:5290920 original size:137 final size:136
Alignment explanation
Indices: 5290575--5291074 Score: 619
Period size: 137 Copynumber: 3.6 Consensus size: 136
5290565 ATTATTAATC
* * * * * *
5290575 TAATCAATTATTAATTCGATTAATTAAAATGGAAC-CGAAAGCAAAAGCGAGGACCAAACTAAAA
1 TAATCAATTTTTGATTCAAATAATTAAAATGGAACTCG--AGCAAAAGCGAGGACTAAATTAAAA
* *
5290639 ATTCCCCTAAATTAAAGGACTAAGTAT-ACAATTAAGCCTAAAATGGAGGCTCTAATTATGAACC
64 ATTCTCCTAAATTAAAGGACTAAGTATGA-AATTAAGCCTAAAAT-GAGGCTCTAATTATTAACC
*
5290703 AAGTCAATTT
127 TAGTCAATTT
* * * *
5290713 TAAATCAATTATTGATGCAAATAATTAAAATGAAACCTCGAGCAAAAGTGAGGACTAAATTAAAA
1 T-AATCAATTTTTGATTCAAATAATTAAAATGGAA-CTCGAGCAAAAGCGAGGACTAAATTAAAA
* * * *
5290778 ATTCTCCTAAATTAAAGGACTAAATATGAAATTAAGTCTAAAATGAGGCTCTAATTATTAGCGTA
64 ATTCTCCTAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAATGAGGCTCTAATTATTAACCTA
5290843 GTCAATTT
129 GTCAATTT
* * * *
5290851 TAATTAATTTTTTATTCAAATAATTAGAATGGAACATCGAGCAAAAGCAAGGACTAAATTAAAAA
1 TAATCAATTTTTGATTCAAATAATTAAAATGGAAC-TCGAGCAAAAGCGAGGACTAAATTAAAAA
5290916 TTCTCCTAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAATGAGGCTCTAATTATTAACCTAG
65 TTCTCCTAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAATGAGGCTCTAATTATTAACCTAG
5290981 TCAATTT
130 TCAATTT
* * * * * * *
5290988 TAATCAAATTTTGAATCGAATAATTAAAATGGAATCTCGAGCAAGAGTGAGCA-TGGAATTAAAA
1 TAATCAATTTTTGATTCAAATAATTAAAATGGAA-CTCGAGCAAAAGCGAGGACT-AAATTAAAA
* * *
5291052 ATTATCTTAAATTAAGGGACTAA
64 ATTCTCCTAAATTAAAGGACTAA
5291075 TTCTAAAGAG
Statistics
Matches: 314, Mismatches: 41, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
136 2 0.01
137 191 0.61
138 28 0.09
139 89 0.28
140 2 0.01
141 2 0.01
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.29
Consensus pattern (136 bp):
TAATCAATTTTTGATTCAAATAATTAAAATGGAACTCGAGCAAAAGCGAGGACTAAATTAAAAAT
TCTCCTAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAATGAGGCTCTAATTATTAACCTAGT
CAATTT
Found at i:5293075 original size:15 final size:15
Alignment explanation
Indices: 5293055--5293134 Score: 108
Period size: 15 Copynumber: 5.4 Consensus size: 15
5293045 TCAGAAAATA
5293055 AATTACTGGAATTTG
1 AATTACTGGAATTTG
5293070 AATTACTGGAATTTG
1 AATTACTGGAATTTG
* **
5293085 AATTATTGGAAAATG
1 AATTACTGGAATTTG
5293100 AATTACTGGAATTTG
1 AATTACTGGAATTTG
**
5293115 AATT-CTGGAAAATG
1 AATTACTGGAATTTG
5293129 AATTAC
1 AATTAC
5293135 ATTTATGTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 12 0.21
15 44 0.79
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (15 bp):
AATTACTGGAATTTG
Found at i:5293112 original size:45 final size:44
Alignment explanation
Indices: 5293048--5293133 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 44
5293038 TGGTTTTTCA
**
5293048 GAAAATAAATTACTGGAATTTGAATTACTGGAATTTGAATTATTG
1 GAAAATAAATTACTGGAATTTGAATT-CTGGAAAATGAATTATTG
*
5293093 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTA
1 GAAAATAAATTACTGGAATTTGAATTCTGGAAAATGAATTA
5293134 CATTTATGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 13 0.34
45 25 0.66
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.35
Consensus pattern (44 bp):
GAAAATAAATTACTGGAATTTGAATTCTGGAAAATGAATTATTG
Found at i:5293133 original size:29 final size:30
Alignment explanation
Indices: 5293055--5293134 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
5293045 TCAGAAAATA
**
5293055 AATTACTGGAATTTGAATTACTGGAATTTG
1 AATTACTGGAAAATGAATTACTGGAATTTG
*
5293085 AATTATTGGAAAATGAATTACTGGAATTTG
1 AATTACTGGAAAATGAATTACTGGAATTTG
5293115 AATT-CTGGAAAATGAATTAC
1 AATTACTGGAAAATGAATTAC
5293135 ATTTATGTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 15 0.33
30 31 0.67
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (30 bp):
AATTACTGGAAAATGAATTACTGGAATTTG
Found at i:5293146 original size:20 final size:20
Alignment explanation
Indices: 5293117--5293206 Score: 153
Period size: 20 Copynumber: 4.5 Consensus size: 20
5293107 GGAATTTGAA
5293117 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
* *
5293137 TTATGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
5293157 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
5293177 TTCTGGAAAATGAATTATAT
1 TTCTGGAAAATGAATTACAT
5293197 TTCTGGAAAA
1 TTCTGGAAAA
5293207 CGTTTTATGA
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:5293418 original size:30 final size:29
Alignment explanation
Indices: 5293361--5293464 Score: 101
Period size: 29 Copynumber: 3.5 Consensus size: 29
5293351 CTTTACTAAA
*
5293361 ATATTATTGAAATATAT-AAATAATATTAT
1 ATATTATT-AAATATATAAAAAAATATTAT
5293390 -TCATTATTAAATATATAAAAAAATTATTAT
1 AT-ATTATTAAATATATAAAAAAA-TATTAT
5293420 ATATTATTAAA-ATA-AAAATATAATATCT-T
1 ATATTATTAAATATATAAAA-A-AATAT-TAT
5293449 ATATTATTATAATATA
1 ATATTATTA-AATATA
5293465 ATTGATTATT
Statistics
Matches: 65, Mismatches: 1, Indels: 16
0.79 0.01 0.20
Matches are distributed among these distances:
28 13 0.20
29 28 0.43
30 20 0.31
31 4 0.06
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (29 bp):
ATATTATTAAATATATAAAAAAATATTAT
Found at i:5293487 original size:15 final size:16
Alignment explanation
Indices: 5293449--5293506 Score: 52
Period size: 17 Copynumber: 3.8 Consensus size: 16
5293439 ATAATATCTT
5293449 ATATTATTATAATATA
1 ATATTATTATAATATA
*
5293465 ATTGATTATT-TTATATA
1 A-T-ATTATTATAATATA
*
5293482 ATATTA--AAAATAT-
1 ATATTATTATAATATA
5293495 ATATTATTATAA
1 ATATTATTATAA
5293507 ATATTAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 11
0.69 0.08 0.23
Matches are distributed among these distances:
13 6 0.18
14 4 0.12
15 7 0.21
16 2 0.06
17 8 0.24
18 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
ATATTATTATAATATA
Found at i:5293497 original size:16 final size:16
Alignment explanation
Indices: 5293476--5293515 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
5293466 TTGATTATTT
5293476 TATATAATATTAAAAA
1 TATATAATATTAAAAA
* *
5293492 TATATATTATTATAAA
1 TATATAATATTAAAAA
5293508 TAT-TAATA
1 TATATAATA
5293516 AATATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATATAATATTAAAAA
Found at i:5293500 original size:28 final size:26
Alignment explanation
Indices: 5293417--5293522 Score: 82
Period size: 23 Copynumber: 4.2 Consensus size: 26
5293407 AAAAAATTAT
**
5293417 TATATATTATTA-AAATAAAAATATAA
1 TATATATTATTATAAATATTAATA-AA
**
5293443 TATCTTATATTATTAT-AATA-TAATTGA
1 TA---TATATTATTATAAATATTAATAAA
*
5293470 T-TATTTTA-TAT-AATATTAA-AAA
1 TATATATTATTATAAATATTAATAAA
5293492 TATATATTATTATAAATATTAATAAA
1 TATATATTATTATAAATATTAATAAA
5293518 TATAT
1 TATAT
5293523 TTTAATATTT
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
22 9 0.14
23 15 0.23
24 3 0.05
25 8 0.12
26 10 0.16
27 2 0.03
28 3 0.05
29 14 0.22
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (26 bp):
TATATATTATTATAAATATTAATAAA
Found at i:5293520 original size:22 final size:22
Alignment explanation
Indices: 5293490--5293538 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
5293480 TAATATTAAA
*
5293490 AATATATATTATTATAA-ATATT
1 AATAAATA-TATTATAATATATT
* *
5293512 AATAAATATATTTTAATATTTT
1 AATAAATATATTATAATATATT
5293534 AATAA
1 AATAA
5293539 TTAATATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAAATATATTATAATATATT
Found at i:5293775 original size:42 final size:42
Alignment explanation
Indices: 5293716--5293835 Score: 231
Period size: 42 Copynumber: 2.9 Consensus size: 42
5293706 ATGAATTACA
*
5293716 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
5293758 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
5293800 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
5293836 TTCGGGGAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:5299726 original size:15 final size:15
Alignment explanation
Indices: 5299706--5299777 Score: 101
Period size: 15 Copynumber: 4.9 Consensus size: 15
5299696 TTCCGGAAAA
*
5299706 TGAATTACTGGAGTT
1 TGAATTACTGGAATT
5299721 TGAATTACTGGAATT
1 TGAATTACTGGAATT
* **
5299736 TGAATTACTGAAAAA
1 TGAATTACTGGAATT
5299751 TGAATTACTGGAATT
1 TGAATTACTGGAATT
5299766 TGAATT-CTGGAA
1 TGAATTACTGGAA
5299778 AATGAATTGC
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
14 6 0.12
15 44 0.88
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:5299742 original size:30 final size:30
Alignment explanation
Indices: 5299706--5299785 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 30
5299696 TTCCGGAAAA
***
5299706 TGAATTACTGGAGTTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
*
5299736 TGAATTACTGAAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
5299766 TGAATT-CTGGAAAATGAATT
1 TGAATTACTGGAAAATGAATT
5299786 GCATTTCTGG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 13 0.29
30 32 0.71
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:5300032 original size:29 final size:26
Alignment explanation
Indices: 5299999--5300052 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
5299989 TTACTAAAAT
5299999 ATTATTGAAATATATAAATAATATTATTC
1 ATTATT-AAATATATAAA-AAT-TTATTC
5300028 ATTATTAAATATATAAAAATTTATT
1 ATTATTAAATATATAAAAATTTATT
5300053 ATATAGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 5 0.20
27 3 0.12
28 11 0.44
29 6 0.24
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTATTAAATATATAAAAATTTATTC
Found at i:5300051 original size:19 final size:20
Alignment explanation
Indices: 5300029--5300067 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
5300019 ATATTATTCA
5300029 TTATTAAATA-TATAAAAAT
1 TTATTAAATAGTATAAAAAT
* *
5300048 TTATTATATAGTATTAAAAT
1 TTATTAAATAGTATAAAAAT
5300068 AAAAAATATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TTATTAAATAGTATAAAAAT
Found at i:5300053 original size:29 final size:28
Alignment explanation
Indices: 5299997--5300157 Score: 86
Period size: 29 Copynumber: 5.6 Consensus size: 28
5299987 CTTTACTAAA
5299997 ATATTATTGAAATATATAAATAA-TATTAT
1 ATATTATT-AAATATATAAA-AATTATTAT
5300026 -TCATTATTAAATATATAAAAATTTATTAT
1 AT-ATTATTAAATATATAAAAA-TTATTAT
*
5300055 ATAGTATTAAA-ATA-AAAAA-TATCT-T
1 ATATTATTAAATATATAAAAATTAT-TAT
***
5300080 -TATTATTATAATATA-ATTGATTATTTAT
1 ATATTATTA-AATATATAAAAATTA-TTAT
* *
5300108 ATAATATTAAAAATATAATATAATATTATTAT
1 ATATTATT--AAATAT-ATA-AAAATTATTAT
*
5300140 AAATATTAATAAATATAT
1 --ATATTATTAAATATAT
5300158 TTTAAATTTT
Statistics
Matches: 103, Mismatches: 11, Indels: 34
0.70 0.07 0.23
Matches are distributed among these distances:
24 7 0.07
25 6 0.06
26 6 0.06
27 10 0.10
28 17 0.17
29 26 0.25
30 6 0.06
31 4 0.04
32 11 0.11
33 4 0.04
34 6 0.06
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (28 bp):
ATATTATTAAATATATAAAAATTATTAT
Found at i:5300095 original size:26 final size:26
Alignment explanation
Indices: 5300010--5300095 Score: 79
Period size: 26 Copynumber: 3.2 Consensus size: 26
5300000 TTATTGAAAT
*
5300010 ATATAAATAATATTATTCATTATTA-A
1 ATATAAAAAATATTATT-ATTATTATA
*
5300036 ATATATAAAAAT-TTATTATATAGTATTA
1 ATATA-AAAAATATTATTAT-TATTA-TA
*
5300064 AAATAAAAAATATCT-TTATTATTATA
1 ATATAAAAAATAT-TATTATTATTATA
5300090 ATATAA
1 ATATAA
5300096 TTGATTATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
25 2 0.04
26 21 0.43
27 15 0.31
28 10 0.20
29 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (26 bp):
ATATAAAAAATATTATTATTATTATA
Found at i:5300123 original size:30 final size:32
Alignment explanation
Indices: 5300086--5300156 Score: 99
Period size: 32 Copynumber: 2.1 Consensus size: 32
5300076 TCTTTATTAT
5300086 TATAATATAATTGATTATTTATATAATATTAA-AAA
1 TATAATATAA-T-ATTA-TTATA-AATATTAATAAA
5300121 TATAATATAATATTATTATAAATATTAATAAA
1 TATAATATAATATTATTATAAATATTAATAAA
5300153 TATA
1 TATA
5300157 TTTTAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
31 8 0.23
32 12 0.34
33 4 0.11
34 1 0.03
35 10 0.29
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (32 bp):
TATAATATAATATTATTATAAATATTAATAAA
Found at i:5300143 original size:22 final size:21
Alignment explanation
Indices: 5300111--5300172 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
5300101 TATTTATATA
*
5300111 ATATTAAAAATA-TAATATAAT
1 ATATTATAAATATTAATA-AAT
5300132 ATTATTATAAATATTAATAAAT
1 A-TATTATAAATATTAATAAAT
* *
5300154 ATATTTTAAATTTTAATAA
1 ATATTATAAATATTAATAA
5300173 TTAATATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 17 0.47
22 14 0.39
23 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATTATAAATATTAATAAAT
Found at i:5300151 original size:10 final size:10
Alignment explanation
Indices: 5300110--5300155 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
5300100 TTATTTATAT
5300110 AATATTAA-A
1 AATATTAATA
5300119 AATA-TAATA
1 AATATTAATA
5300128 TAATATTATTATA
1 -AATATTA--ATA
5300141 AATATTAATA
1 AATATTAATA
5300151 AATAT
1 AATAT
5300156 ATTTTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 3 0.09
9 5 0.16
10 12 0.38
11 2 0.06
12 7 0.22
13 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AATATTAATA
Found at i:5300163 original size:21 final size:21
Alignment explanation
Indices: 5300118--5300182 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
5300108 ATAATATTAA
*
5300118 AAATA-TAATATAATATTATTAT
1 AAATATTAATA-AATA-TATTTT
5300140 AAATATTAATAAATATATTTT
1 AAATATTAATAAATATATTTT
* *
5300161 AAATTTTAATAATTAATATTTT
1 AAATATTAATAAAT-ATATTTT
5300183 GATGAAATGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 17 0.45
22 16 0.42
23 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATATTAATAAATATATTTT
Found at i:5300412 original size:42 final size:42
Alignment explanation
Indices: 5300353--5300472 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
5300343 ATGAATTACA
*
5300353 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
5300395 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
5300437 TTCCGGAAAACGAATTACGTGAAACAAACACTGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
5300473 TTCGGGGAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:5301304 original size:13 final size:13
Alignment explanation
Indices: 5301286--5301310 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5301276 GAAATTTAAA
5301286 AAACCTAAAAATT
1 AAACCTAAAAATT
5301299 AAACCTAAAAAT
1 AAACCTAAAAAT
5301311 GTAGGTTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (13 bp):
AAACCTAAAAATT
Found at i:5301488 original size:138 final size:137
Alignment explanation
Indices: 5301294--5301967 Score: 676
Period size: 138 Copynumber: 4.9 Consensus size: 137
5301284 AAAAACCTAA
* * * * * *
5301294 AAATTAAACCTAAAAATGTAGG-T-TATATTATTAACCCAAATCATTTTTAATAAATTATTGAGT
1 AAATTAAA-CTTAAAATGGAGGCTCTA-ATTATTAA-CCTAGTCAATTTTAATCAATTATTGAGT
* * * * * * *
5301357 CGAATAATCAAAATGGAACATCGAGCATAAGCAAGGACCAAAATAAGAATTCTCATAGATTAAAA
63 CGAATAATTAAAATGGAAC-TCGAGCAAAAGCGAGGACCAAATTAAAAATTCTCCTAAATTAAAA
5301422 GACTAAATATG
127 GACTAAATATG
* * * * * *
5301433 AAATTAAACTTAAAGTGGATGCTCTAATTATTAACATAATCAATTTTAATCAATTATTGATTCAA
1 AAATTAAACTTAAAATGGAGGCTCTAATTATTAACCTAGTCAATTTTAATCAATTATTGAGTCGA
* * * * * * * * *
5301498 ATAATTAAAATGAAATATCGAGCAAAAACGATGATCAAACTAAAAATTCCCCTTAATTAAAGGGA
66 ATAATTAAAATGGAA-CTCGAGCAAAAGCGAGGACCAAATTAAAAATTCTCCTAAATTAAA-AGA
*
5301563 -GAAGA-ATG
129 CTAA-ATATG
* * ** * * *
5301571 AGATTAAACCTAAAATAAAGGTTCTAATTATTAACTTAGTCAATTTTAATCAATTATTAATGT-G
1 AAATTAAACTTAAAATGGAGGCTCTAATTATTAACCTAGTCAATTTTAATCAATTATTGA-GTCG
* *
5301635 AATAATTAAAATGGAATCTTGAGCAAGAGCGAGGACCAAATTAAAAATT-TCCCTAAATTAAAAG
65 AATAATTAAAATGGAA-CTCGAGCAAAAGCGAGGACCAAATTAAAAATTCT-CCTAAATTAAAAG
* *
5301699 ATTAAGTATG
128 ACTAAATATG
* * *
5301709 AAATTAAGCTTAAAATGGAGGTTCTAATTATTAACCTAGTCAATTTTAATCAATTATTGATTCGA
1 AAATTAAACTTAAAATGGAGGCTCTAATTATTAACCTAGTCAATTTTAATCAATTATTGAGTCGA
* * * * * * * * *
5301774 ATGATTAAAATGGAACCTCAAACAAAAGCGAGGATCATATTGACAATTCTCCTAAATTAAAGGGC
66 ATAATTAAAATGGAA-CTCGAGCAAAAGCGAGGACCAAATTAAAAATTCTCCTAAATTAAAAGAC
*
5301839 TAAGTATG
130 TAAATATG
* * *
5301847 AAATTAAACTTAAAATGGAGGCTCTAATTATTAACCTAGTCAATTTTAACCAATTATTGAATTGA
1 AAATTAAACTTAAAATGGAGGCTCTAATTATTAACCTAGTCAATTTTAATCAATTATTGAGTCGA
* *
5301912 ATAATTAAAATGAAAGCTCGAGCAAAAGCGATGACCAAATTAAAAATTCTCCTAAA
66 ATAATTAAAATGGAA-CTCGAGCAAAAGCGAGGACCAAATTAAAAATTCTCCTAAA
5301968 ATAAGGGACT
Statistics
Matches: 437, Mismatches: 87, Indels: 23
0.80 0.16 0.04
Matches are distributed among these distances:
137 3 0.01
138 410 0.94
139 22 0.05
140 2 0.00
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (137 bp):
AAATTAAACTTAAAATGGAGGCTCTAATTATTAACCTAGTCAATTTTAATCAATTATTGAGTCGA
ATAATTAAAATGGAACTCGAGCAAAAGCGAGGACCAAATTAAAAATTCTCCTAAATTAAAAGACT
AAATATG
Found at i:5301711 original size:276 final size:274
Alignment explanation
Indices: 5301294--5301967 Score: 764
Period size: 276 Copynumber: 2.4 Consensus size: 274
5301284 AAAAACCTAA
** * * * * *
5301294 AAATTAAACCTAAAAATGTAGG-T-TATATTATTAACCCAAATCATTTTTAATAAATTATTGA-G
1 AAATTAAACCT-AAAATAAAGGCTCTA-ATTATTAA-CCTAGTCAATTTTAATCAATTATTAATG
* * * * * *
5301356 TCGAATAATCAAAATGGAACATCGAGCATAAGCAAGGACCAAAATAAGAATTCTCATAGATTAAA
63 T-GAATAATTAAAATGGAAC-TCGAGCA-AAGCGAGGACCAAATTAAAAATTCTCCTAAATTAAA
* *
5301421 AGACTAAATATGAAATTAAACTTAAAGTGGATGCTCTAATTATTAACATAATCAATTTTAATCAA
125 AGACTAAATATGAAATTAAACTTAAAATGGAGGCTCTAATTATTAACATAATCAATTTTAATCAA
* * * *
5301486 TTATTGATTCAAATAATTAAAATGAAATATCGAGCAAAAACGATGATCAAACTAAAAATTCCCCT
190 TTATTGATTCAAATAATTAAAATGAAACATCAAACAAAAACGAGGATCAAACTAAAAATTCCCCT
*
5301551 TAATTAAAGGGAGAAGAATG
255 AAATTAAAGGGAGAAGAATG
* * *
5301571 AGATTAAACCTAAAATAAAGGTTCTAATTATTAACTTAGTCAATTTTAATCAATTATTAATGTGA
1 AAATTAAACCTAAAATAAAGGCTCTAATTATTAACCTAGTCAATTTTAATCAATTATTAATGTGA
*
5301636 ATAATTAAAATGGAATCTTGAGCAAGAGCGAGGACCAAATTAAAAATT-TCCCTAAATTAAAAGA
66 ATAATTAAAATGGAA-CTCGAGCAA-AGCGAGGACCAAATTAAAAATTCT-CCTAAATTAAAAGA
* * * * * *
5301700 TTAAGTATGAAATTAAGCTTAAAATGGAGGTTCTAATTATTAACCTAGTCAATTTTAATCAATTA
128 CTAAATATGAAATTAAACTTAAAATGGAGGCTCTAATTATTAACATAATCAATTTTAATCAATTA
* * * * * * * * * *
5301765 TTGATTCGAATGATTAAAATGGAACCTCAAACAAAAGCGAGGATCATATTGACAATTCTCCTAAA
193 TTGATTCAAATAATTAAAATGAAACATCAAACAAAAACGAGGATCAAACTAAAAATTCCCCTAAA
** *
5301830 TTAAAGGGCTAAGTATG
258 TTAAAGGGAGAAGAATG
* ** *
5301847 AAATTAAACTTAAAATGGAGGCTCTAATTATTAACCTAGTCAATTTTAACCAATTATTGAAT-TG
1 AAATTAAACCTAAAATAAAGGCTCTAATTATTAACCTAGTCAATTTTAATCAATTATT-AATGTG
* *
5301911 AATAATTAAAATGAAAGCTCGAGCAAAAGCGATGACCAAATTAAAAATTCTCCTAAA
65 AATAATTAAAATGGAA-CTCGAGC-AAAGCGAGGACCAAATTAAAAATTCTCCTAAA
5301968 ATAAGGGACT
Statistics
Matches: 335, Mismatches: 53, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
275 2 0.01
276 303 0.90
277 28 0.08
278 2 0.01
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (274 bp):
AAATTAAACCTAAAATAAAGGCTCTAATTATTAACCTAGTCAATTTTAATCAATTATTAATGTGA
ATAATTAAAATGGAACTCGAGCAAAGCGAGGACCAAATTAAAAATTCTCCTAAATTAAAAGACTA
AATATGAAATTAAACTTAAAATGGAGGCTCTAATTATTAACATAATCAATTTTAATCAATTATTG
ATTCAAATAATTAAAATGAAACATCAAACAAAAACGAGGATCAAACTAAAAATTCCCCTAAATTA
AAGGGAGAAGAATG
Found at i:5304359 original size:13 final size:13
Alignment explanation
Indices: 5304330--5304364 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
5304320 ATAACTAATA
*
5304330 ATATTAAAT-ATT
1 ATATTAAATAAAT
5304342 ATATTAAATAAAT
1 ATATTAAATAAAT
5304355 ATATTAAATA
1 ATATTAAATA
5304365 TATTATGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:5305209 original size:21 final size:21
Alignment explanation
Indices: 5305185--5305264 Score: 119
Period size: 21 Copynumber: 3.9 Consensus size: 21
5305175 ATAAAACCCT
*
5305185 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
*
5305206 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
5305227 GCGGGCTAGGAATGTAACCT-
1 GCGGGCTAGGAATGTAACCTG
*
5305247 GC-GGCTCGGAATGTAACC
1 GCGGGCTAGGAATGTAACC
5305265 CTGCGGAGAT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
19 15 0.26
20 2 0.04
21 40 0.70
ACGTcount: A:0.21, C:0.24, G:0.36, T:0.19
Consensus pattern (21 bp):
GCGGGCTAGGAATGTAACCTG
Found at i:5307049 original size:18 final size:18
Alignment explanation
Indices: 5307019--5307134 Score: 51
Period size: 17 Copynumber: 7.1 Consensus size: 18
5307009 CAAAAAAAAT
*
5307019 TAATAAT-TCTAAATAAA
1 TAATAATATATAAATAAA
5307036 TAATAATATATAAAT--A
1 TAATAATATATAAATAAA
* *
5307052 TTAT-TTA-AT-AA-AAA
1 TAATAATATATAAATAAA
* *
5307066 -AATAATATTTACATAAA
1 TAATAATATATAAATAAA
5307083 T-AT-ATAATATAAA-AAA
1 TAATAAT-ATATAAATAAA
*
5307099 TAATAACTATTTAAA-AAA
1 TAATAA-TATATAAATAAA
* *
5307117 TACTAACATA-AAATAAA
1 TAATAATATATAAATAAA
5307134 T
1 T
5307135 TTCTTACCAC
Statistics
Matches: 73, Mismatches: 13, Indels: 26
0.65 0.12 0.23
Matches are distributed among these distances:
13 4 0.05
14 5 0.07
15 3 0.04
16 14 0.19
17 25 0.34
18 21 0.29
19 1 0.01
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.34
Consensus pattern (18 bp):
TAATAATATATAAATAAA
Found at i:5307089 original size:19 final size:18
Alignment explanation
Indices: 5307047--5307116 Score: 58
Period size: 18 Copynumber: 4.0 Consensus size: 18
5307037 AATAATATAT
*
5307047 AAATATTATTTAATAAAA
1 AAATAATATTTAATAAAA
*
5307065 AAATAATATTTACATAAAT
1 AAATAATATTTA-ATAAAA
*
5307084 ATATAATA--TAA-AAAA
1 AAATAATATTTAATAAAA
*
5307099 TAATAACTATTTAA-AAAA
1 AAATAA-TATTTAATAAAA
5307117 TACTAACATA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
15 7 0.17
16 3 0.07
17 2 0.05
18 18 0.43
19 12 0.29
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATAATATTTAATAAAA
Found at i:5307128 original size:15 final size:16
Alignment explanation
Indices: 5307080--5307129 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 16
5307070 ATATTTACAT
5307080 AAATATATAA-TATAAA
1 AAATA-ATAACTATAAA
5307096 AAATAATAACTATTTAAA
1 AAATAATAACTA--TAAA
*
5307114 AAATACTAAC-ATAAA
1 AAATAATAACTATAAA
5307129 A
1 A
5307130 TAAATTTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 9 0.30
16 7 0.23
17 1 0.03
18 13 0.43
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATAATAACTATAAA
Found at i:5312502 original size:15 final size:15
Alignment explanation
Indices: 5312482--5312512 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5312472 CCAAAGGAAG
5312482 GGTATCGATACCAAT
1 GGTATCGATACCAAT
*
5312497 GGTATCGATACTAAT
1 GGTATCGATACCAAT
5312512 G
1 G
5312513 TATAAGTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (15 bp):
GGTATCGATACCAAT
Found at i:5312986 original size:21 final size:21
Alignment explanation
Indices: 5312961--5313001 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5312951 TGTACATGAG
5312961 TACATGCATATG-TATATATGT
1 TACATGCAT-TGTTATATATGT
5312982 TACATGCATTGTTATATATG
1 TACATGCATTGTTATATATG
5313002 AGCTATGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.44
Consensus pattern (21 bp):
TACATGCATTGTTATATATGT
Found at i:5313209 original size:45 final size:45
Alignment explanation
Indices: 5313140--5313257 Score: 114
Period size: 45 Copynumber: 2.6 Consensus size: 45
5313130 TTGACCTATA
* * * * * *
5313140 TGATTAAATGAAAAAGTGAGATAAGCTAAATAACATTAACCTATG
1 TGATTATATGAACATGTGATATAAGCTAAATAACATTAACATAAG
** * *
5313185 TGATTACT-TGAGA-ATGTGATATAAGCTATGTGATATTAACATAAG
1 TGATTA-TATGA-ACATGTGATATAAGCTAAATAACATTAACATAAG
5313230 TGATTATATGAACATGTGATATAAGCTA
1 TGATTATATGAACATGTGATATAAGCTA
5313258 GGTGACAAGG
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
44 2 0.03
45 57 0.95
46 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (45 bp):
TGATTATATGAACATGTGATATAAGCTAAATAACATTAACATAAG
Found at i:5313278 original size:45 final size:45
Alignment explanation
Indices: 5313181--5313284 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 45
5313171 AACATTAACC
* * **
5313181 TATGTGATTACT-TGAGAATGTGATATAAGCTATGTGATATTAACA
1 TATGTGATTA-TATGAGAATGTGATATAAGCTAGGTGACAAGAACA
* * *
5313226 TAAGTGATTATATGA-ACATGTGATATAAGCTAGGTGACAAGGACT
1 TATGTGATTATATGAGA-ATGTGATATAAGCTAGGTGACAAGAACA
5313271 TATGTGATTATATG
1 TATGTGATTATATG
5313285 TCTATGTGAT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
44 2 0.04
45 47 0.96
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.36
Consensus pattern (45 bp):
TATGTGATTATATGAGAATGTGATATAAGCTAGGTGACAAGAACA
Found at i:5313664 original size:6 final size:6
Alignment explanation
Indices: 5313653--5313710 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
5313643 TAATGAACTG
* * * ** *
5313653 TGATAA TGATAA TAATAG TGACAA TGATAA TGATGT TGATAA TGATAT
1 TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA
*
5313701 TGATGA TGAT
1 TGATAA TGAT
5313711 GATAACGATG
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.36
Consensus pattern (6 bp):
TGATAA
Found at i:5313696 original size:18 final size:18
Alignment explanation
Indices: 5313653--5313730 Score: 68
Period size: 18 Copynumber: 4.2 Consensus size: 18
5313643 TAATGAACTG
*
5313653 TGATAATGATAATAATAG-
1 TGATAATGATAATGAT-GT
*
5313671 TGACAATGATAATGATGT
1 TGATAATGATAATGATGT
*
5313689 TGATAATGATATTGATGATGA
1 TGATAATGATA---ATGATGT
* *
5313710 TGATAACGATGATGATGT
1 TGATAATGATAATGATGT
5313728 TGA
1 TGA
5313731 GGATATATAT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
17 1 0.02
18 33 0.67
21 15 0.31
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.35
Consensus pattern (18 bp):
TGATAATGATAATGATGT
Found at i:5313740 original size:2 final size:2
Alignment explanation
Indices: 5313733--5313814 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
5313723 GATGTTGAGG
5313733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5313775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5313815 GCACTTGTGT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5315810 original size:19 final size:18
Alignment explanation
Indices: 5315779--5315814 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5315769 GACCTGAATG
*
5315779 TTGATTTGCTTGTTGACT
1 TTGATTTGATTGTTGACT
5315797 TTGACTTTGATTGTTGAC
1 TTGA-TTTGATTGTTGAC
5315815 CGTTAACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.14, C:0.11, G:0.22, T:0.53
Consensus pattern (18 bp):
TTGATTTGATTGTTGACT
Found at i:5318561 original size:2 final size:2
Alignment explanation
Indices: 5318289--5318548 Score: 115
Period size: 2 Copynumber: 133.0 Consensus size: 2
5318279 TTGAACCAAT
* *
5318289 TA TA -A TA TA TA TA TA TA TA TA TT TA TA TA TA TA AA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
5318331 -A TA -A TA CA T- TA TA TA TA TA AA CTA TA TA -A TT TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * *
5318370 -A TA TA TA TA GTT TA TA CA TA -A TA GTA TA TA -A GTA TA AA T-
1 TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA
* * * *
5318409 TA TA TGG TT TA TA TA TA GTT TA TA T- TA -A TA AA T- TA TA TA -A
1 TA TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
5318449 TT TA TA T- TA -A TA AA CTA TA TA GTT TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA
*
5318491 TA TA TA TA TA T- TA TA GTT TA TA TA TA GTA TA TA -A TA -A TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA
* *
5318532 AA TA TA AA CTA TA TA TA
1 TA TA TA TA -TA TA TA TA
5318549 CTACAAATAT
Statistics
Matches: 191, Mismatches: 37, Indels: 60
0.66 0.13 0.21
Matches are distributed among these distances:
1 18 0.09
2 159 0.83
3 14 0.07
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:5318605 original size:36 final size:37
Alignment explanation
Indices: 5318543--5318612 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 37
5318533 ATATAAACTA
5318543 TATATACTACAAATATATAAACTATATAGTTTATACT
1 TATATACTACAAATATATAAACTATATAGTTTATACT
* * *
5318580 TATATACTAC-TATGTATAAATTATATAGTTTAT
1 TATATACTACAAATATATAAACTATATAGTTTAT
5318613 GTATATAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 20 0.67
37 10 0.33
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (37 bp):
TATATACTACAAATATATAAACTATATAGTTTATACT
Found at i:5318677 original size:30 final size:30
Alignment explanation
Indices: 5318643--5318708 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
5318633 AGGGTTAATT
*
5318643 TATATA-ATTATATATAGTTTA-TATATAAAC
1 TATATAGATTATACATAG--TAGTATATAAAC
*
5318673 TATATAGTTTATACATAGTAGTATATAAAC
1 TATATAGATTATACATAGTAGTATATAAAC
5318703 TATATA
1 TATATA
5318709 TAAAAACTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 2 0.06
30 21 0.66
31 9 0.28
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (30 bp):
TATATAGATTATACATAGTAGTATATAAAC
Found at i:5318732 original size:41 final size:41
Alignment explanation
Indices: 5318682--5318791 Score: 116
Period size: 41 Copynumber: 2.6 Consensus size: 41
5318672 CTATATAGTT
*
5318682 TATACATAGTAGTATATAAACTATATATAAAAACTAAATAAA-
1 TATATATAGTA-TATATAAACTATATATAAAAACT-AATAAAC
* * *
5318724 T-TATATAGTTTACATATGAACTATATATATAAACTAATAAAC
1 TATATATAG--TATATATAAACTATATATAAAAACTAATAAAC
* *
5318766 TATATAAATTATATATAAACTATATA
1 TATATATAGTATATATAAACTATATA
5318792 GTTTATATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
41 27 0.48
42 22 0.39
43 7 0.12
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (41 bp):
TATATATAGTATATATAAACTATATATAAAAACTAATAAAC
Found at i:5318778 original size:9 final size:9
Alignment explanation
Indices: 5318749--5318791 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
5318739 ATGAACTATA
5318749 TATATAAAC
1 TATATAAAC
5318758 TA-ATAAAC
1 TATATAAAC
*
5318766 TATATAAATTA
1 TATATAAA--C
5318777 TATATAAAC
1 TATATAAAC
5318786 TATATA
1 TATATA
5318792 GTTTATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
8 8 0.28
9 13 0.45
11 8 0.28
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (9 bp):
TATATAAAC
Found at i:5318797 original size:20 final size:21
Alignment explanation
Indices: 5318719--5318813 Score: 70
Period size: 20 Copynumber: 4.6 Consensus size: 21
5318709 TAAAAACTAA
* *
5318719 ATAAATTATATAGTTTACA-T
1 ATAAACTATATAGTTTATATT
* * * *
5318739 ATGAACTATATA-TATAAACTA
1 ATAAACTATATAGTTTATA-TT
**
5318760 ATAAACTATATAAATTATA-T
1 ATAAACTATATAGTTTATATT
5318780 ATAAACTATATAGTTTATATTT
1 ATAAACTATATAGTTTATA-TT
*
5318802 ATATACTATATA
1 ATAAACTATATA
5318814 TAATTATAAA
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
19 4 0.07
20 27 0.47
21 11 0.19
22 15 0.26
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (21 bp):
ATAAACTATATAGTTTATATT
Found at i:5318815 original size:17 final size:17
Alignment explanation
Indices: 5318795--5318884 Score: 51
Period size: 17 Copynumber: 5.2 Consensus size: 17
5318785 CTATATAGTT
* *
5318795 TATATTTATATACTATA
1 TATAATTATAAACTATA
*
5318812 TATAATTATAAATTATA
1 TATAATTATAAACTATA
*
5318829 TATACTATGTATAAATTATA
1 TATA--AT-TATAAACTATA
*
5318849 -AGT-ATGTATATA-TATA
1 TA-TAAT-TATAAACTATA
* *
5318865 TATAAGTATAAAGTATA
1 TATAATTATAAACTATA
5318882 TAT
1 TAT
5318885 GCGTAGGACT
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
16 10 0.17
17 35 0.58
19 3 0.05
20 12 0.20
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.46
Consensus pattern (17 bp):
TATAATTATAAACTATA
Found at i:5318815 original size:26 final size:26
Alignment explanation
Indices: 5318768--5318884 Score: 107
Period size: 26 Copynumber: 4.5 Consensus size: 26
5318758 TAATAAACTA
* *
5318768 TATAAATTATATATA-AACTATATAGT
1 TATAAATTATATATACTA-TATATAAT
*
5318794 T-TATATT-TATATACTATATATAAT
1 TATAAATTATATATACTATATATAAT
*
5318818 TATAAATTATATATACTATGTATAAAT
1 TATAAATTATATATACTATATAT-AAT
* * *
5318845 TATAAGTATGTATATA-TATATATAAG
1 TATAAAT-TATATATACTATATATAAT
*
5318871 TATAAAGTATATAT
1 TATAAATTATATAT
5318885 GCGTAGGACT
Statistics
Matches: 74, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
24 14 0.19
25 17 0.23
26 21 0.28
27 15 0.20
28 7 0.09
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (26 bp):
TATAAATTATATATACTATATATAAT
Found at i:5319818 original size:30 final size:28
Alignment explanation
Indices: 5319785--5319904 Score: 80
Period size: 31 Copynumber: 3.9 Consensus size: 28
5319775 AACTAAAATG
5319785 TTTTATTTTTTATTTTGTTTTTGTTTTATGT
1 TTTTATTTTTTATTTT-TTTTTGTTTTA--T
* *
5319816 TTTTATATGTGTTAATTTTTTTTGTTTT-T
1 TTTTAT-T-TTTTATTTTTTTTTGTTTTAT
*
5319845 TTTATATTTTTTTATATATTTTTTGTTTTTAT
1 TTT-TA-TTTTTTAT-TTTTTTTTG-TTTTAT
* * *
5319877 TATTTATTTTATGTTTTTTATTTCTTTT
1 T-TTTATTTTTTATTTTTT-TTTGTTTT
5319905 CGTTTTATGT
Statistics
Matches: 71, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
29 8 0.11
30 19 0.27
31 20 0.28
32 15 0.21
33 9 0.13
ACGTcount: A:0.14, C:0.01, G:0.07, T:0.78
Consensus pattern (28 bp):
TTTTATTTTTTATTTTTTTTTGTTTTAT
Found at i:5319843 original size:38 final size:34
Alignment explanation
Indices: 5319788--5319894 Score: 106
Period size: 38 Copynumber: 2.9 Consensus size: 34
5319778 TAAAATGTTT
*
5319788 TATTTTTTATTTTGTTTTTGTTTTATGTTTTTATA
1 TATTTTTTTTTTTGTTTTT-TTTTATGTTTTTATA
* *
5319823 TGTGTTAATTTTTTTTGTTTTTTTTATATTTTTTTATA
1 TAT-TT--TTTTTTTTGTTTTTTTT-TATGTTTTTATA
*
5319861 TATTTTTTGTTTTTATTATTTATTTTATGTTTTT
1 TATTTTTT-TTTTTGTT-TTT-TTTTATGTTTTT
5319895 TATTTCTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
35 5 0.08
36 9 0.15
37 16 0.27
38 29 0.49
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (34 bp):
TATTTTTTTTTTTGTTTTTTTTTATGTTTTTATA
Found at i:5319847 original size:28 final size:30
Alignment explanation
Indices: 5319815--5319879 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
5319805 TTGTTTTATG
*
5319815 TTTTTATA-TGTGTTA-ATTTTTTTTGTTT
1 TTTTTATATTGTGTTATATATTTTTTGTTT
* *
5319843 TTTTTATATTTTTTTATATATTTTTTGTTT
1 TTTTTATATTGTGTTATATATTTTTTGTTT
*
5319873 TTATTAT
1 TTTTTAT
5319880 TTATTTTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 8 0.26
29 5 0.16
30 18 0.58
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (30 bp):
TTTTTATATTGTGTTATATATTTTTTGTTT
Found at i:5319855 original size:12 final size:12
Alignment explanation
Indices: 5319840--5319895 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
5319830 ATTTTTTTTG
5319840 TTTTTTTTATAT
1 TTTTTTTTATAT
*
5319852 TTTTTTATATAT
1 TTTTTTTTATAT
*
5319864 TTTTTGTTTTTAT
1 TTTTT-TTTATAT
*
5319877 TATTTATTTTATGT
1 T-TTT-TTTTATAT
5319891 TTTTT
1 TTTTT
5319896 ATTTCTTTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
12 17 0.47
13 9 0.25
14 9 0.25
15 1 0.03
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (12 bp):
TTTTTTTTATAT
Found at i:5319873 original size:18 final size:19
Alignment explanation
Indices: 5319844--5319895 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
5319834 TTTTTGTTTT
*
5319844 TTTTATATTTTTTTATATA
1 TTTTATGTTTTTTTATATA
* *
5319863 TTTTTTGTTTTTATTATTTA
1 TTTTATGTTTTT-TTATATA
5319883 TTTTATGTTTTTT
1 TTTTATGTTTTTT
5319896 ATTTCTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (19 bp):
TTTTATGTTTTTTTATATA
Found at i:5319897 original size:18 final size:18
Alignment explanation
Indices: 5319833--5319904 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 18
5319823 TGTGTTAATT
* * *
5319833 TTTTTTGTTTTTTTTATAT
1 TTTTTTATTTATTTTAT-G
* *
5319852 TTTTTTATATATTTTTTG
1 TTTTTTATTTATTTTATG
5319870 TTTTTATTATTTATTTTATG
1 -TTTT-TTATTTATTTTATG
*
5319890 TTTTTTATTTCTTTT
1 TTTTTTATTTATTTT
5319905 CGTTTTATGT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
18 10 0.23
19 21 0.49
20 12 0.28
ACGTcount: A:0.14, C:0.01, G:0.04, T:0.81
Consensus pattern (18 bp):
TTTTTTATTTATTTTATG
Found at i:5319904 original size:9 final size:8
Alignment explanation
Indices: 5319785--5319904 Score: 52
Period size: 9 Copynumber: 14.5 Consensus size: 8
5319775 AACTAAAATG
5319785 TTTTA-TT
1 TTTTATTT
5319792 TTTTATTT
1 TTTTATTT
*
5319800 TGTTT-TTG
1 T-TTTATTT
5319808 TTTTATGTT
1 TTTTAT-TT
*
5319817 TTTATATGT
1 TTT-TATTT
* *
5319826 GTTAATTT
1 TTTTATTT
5319834 TTTT-TGTT
1 TTTTAT-TT
*
5319842 TTTT-TTA
1 TTTTATTT
*
5319849 TATT-TTT
1 TTTTATTT
*
5319856 TTATATATT
1 TTTTAT-TT
*
5319865 TTTTGTTT
1 TTTTATTT
5319873 TTATTATTT
1 TT-TTATTT
5319882 ATTTTATGTT
1 -TTTTAT-TT
5319892 TTTTATTT
1 TTTTATTT
5319900 CTTTT
1 -TTTT
5319905 CGTTTTATGT
Statistics
Matches: 85, Mismatches: 16, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
7 17 0.20
8 26 0.31
9 35 0.41
10 7 0.08
ACGTcount: A:0.14, C:0.01, G:0.07, T:0.78
Consensus pattern (8 bp):
TTTTATTT
Found at i:5320365 original size:21 final size:19
Alignment explanation
Indices: 5320338--5320387 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
5320328 ATAAATAATA
*
5320338 TTTGTTTTTTATTTTTTATT
1 TTTGTTTTTTATTTGTT-TT
*
5320358 TTCTGTTTTCTATTTGTTTT
1 TT-TGTTTTTTATTTGTTTT
5320378 TTTGTTTTTT
1 TTTGTTTTTT
5320388 TATAAGTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 7 0.27
20 6 0.23
21 13 0.50
ACGTcount: A:0.06, C:0.04, G:0.08, T:0.82
Consensus pattern (19 bp):
TTTGTTTTTTATTTGTTTT
Found at i:5320431 original size:12 final size:12
Alignment explanation
Indices: 5320414--5320462 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
5320404 TTTTCCATTT
5320414 TTTGTTTTTTTA
1 TTTGTTTTTTTA
*
5320426 TTTGTTTTTTGTT
1 TTTGTTTTTT-TA
*
5320439 TTTATTTTTTTA
1 TTTGTTTTTTTA
*
5320451 TTAGTTGTTTTT
1 TTTGTT-TTTTT
5320463 TATGTAAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 15 0.50
13 15 0.50
ACGTcount: A:0.08, C:0.00, G:0.10, T:0.82
Consensus pattern (12 bp):
TTTGTTTTTTTA
Found at i:5320446 original size:25 final size:26
Alignment explanation
Indices: 5320412--5320461 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
5320402 TATTTTCCAT
* *
5320412 TTTTTGTTTTTTTATTTGTT-TTTTG
1 TTTTTATTTTTTTATTAGTTGTTTTG
5320437 TTTTTATTTTTTTATTAGTTGTTTT
1 TTTTTATTTTTTTATTAGTTGTTTT
5320462 TTATGTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.08, C:0.00, G:0.10, T:0.82
Consensus pattern (26 bp):
TTTTTATTTTTTTATTAGTTGTTTTG
Found at i:5320450 original size:8 final size:8
Alignment explanation
Indices: 5320411--5320452 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
5320401 TTATTTTCCA
*
5320411 TTTTTTGT
1 TTTTTTAT
5320419 TTTTTTAT
1 TTTTTTAT
5320427 TTGTTTT-T
1 TT-TTTTAT
5320435 TGTTTTTAT
1 T-TTTTTAT
5320444 TTTTTTAT
1 TTTTTTAT
5320452 T
1 T
5320453 AGTTGTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
8 23 0.77
9 7 0.23
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.86
Consensus pattern (8 bp):
TTTTTTAT
Found at i:5320553 original size:87 final size:86
Alignment explanation
Indices: 5320449--5320653 Score: 281
Period size: 85 Copynumber: 2.4 Consensus size: 86
5320439 TTTATTTTTT
* *
5320449 TATTAGTTGTTTTTTATGTAAATGTGAAGGACTT-TGAATTAG-TTGATTCTTATATTGTTTTAT
1 TATTAGTTGATTTTTATGTTAATGTGAAGGA-TTAT-AATTAGCTT-ATTCTTATATTGTTTTAT
*
5320512 GTTTTTATTTGTTGATGTGAAGGA
63 GTTTTTATTTATTGATGTGAAGGA
* * *
5320536 TATTAGTTGATTCTTATGTTAATGTGAAGG-TTATTATTAGCTTATTCTTATATTGTTTTTTGTT
1 TATTAGTTGATTTTTATGTTAATGTGAAGGATTATAATTAGCTTATTCTTATATTGTTTTATGTT
*
5320600 TTTGTTTATTGATGTGAAGGA
66 TTTATTTATTGATGTGAAGGA
*
5320621 TATTAATTGATTTTTAATGTTAATGTGAAGGAT
1 TATTAGTTGATTTTT-ATGTTAATGTGAAGGAT
5320654 ATTGTTTTTT
Statistics
Matches: 105, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
85 59 0.56
86 18 0.17
87 28 0.27
ACGTcount: A:0.25, C:0.02, G:0.20, T:0.53
Consensus pattern (86 bp):
TATTAGTTGATTTTTATGTTAATGTGAAGGATTATAATTAGCTTATTCTTATATTGTTTTATGTT
TTTATTTATTGATGTGAAGGA
Found at i:5320673 original size:32 final size:33
Alignment explanation
Indices: 5320585--5320675 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 33
5320575 GCTTATTCTT
5320585 ATATTGTTTTTTGTTTT-TGTTTATTGATGTGAAGG
1 ATATTGTTTTTTGTTTTATG-TTA-T-ATGTGAAGG
* ** *
5320620 ATATTAATTGATT-TTTAATGTTA-ATGTGAAGG
1 ATATT-GTTTTTTGTTTTATGTTATATGTGAAGG
5320652 ATATTGTTTTTTGTTTTATGTTAT
1 ATATTGTTTTTTGTTTTATGTTAT
5320676 TTATTTGTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
31 4 0.09
32 23 0.52
35 11 0.25
36 6 0.14
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (33 bp):
ATATTGTTTTTTGTTTTATGTTATATGTGAAGG
Found at i:5320704 original size:24 final size:25
Alignment explanation
Indices: 5320655--5320704 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
5320645 GTGAAGGATA
*
5320655 TTGTTTTTTGTTTTATGTTATTTAT
1 TTGTTTTTTGTTTTATGTTATCTAT
5320680 TTGTTTTTTGTTTATAT-TTA-CTAT
1 TTGTTTTTTGTTT-TATGTTATCTAT
5320704 T
1 T
5320705 CTAACAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 16 0.70
26 3 0.13
ACGTcount: A:0.14, C:0.02, G:0.10, T:0.74
Consensus pattern (25 bp):
TTGTTTTTTGTTTTATGTTATCTAT
Found at i:5322622 original size:57 final size:57
Alignment explanation
Indices: 5322549--5322663 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 57
5322539 TATTGTAGGG
*
5322549 TGCTACTGCTTCTACATTTACTGCTTTTTCATTAATTTTCATGAATTTCAGCAAGCA
1 TGCTACTGCTTCTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCA
* * * * * *
5322606 TGCTACTGTTTTTACATTTATTGCTTTTTGATTAATTTTCGTAAATTTTAGCAAGCA
1 TGCTACTGCTTCTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCA
5322663 T
1 T
5322664 ATAAATGAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (57 bp):
TGCTACTGCTTCTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCA
Found at i:5322737 original size:34 final size:30
Alignment explanation
Indices: 5322699--5322767 Score: 95
Period size: 29 Copynumber: 2.2 Consensus size: 30
5322689 TTGATATAAC
5322699 AATTTAAGGAAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--AAAAAT-GTTTTTGGAC-TGAATTG
5322733 AATTT-AAAAAATGTTTTTGGACTGAATTG
1 AATTTAAAAAAATGTTTTTGGACTGAATTG
5322762 AATTTA
1 AATTTA
5322768 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 12 0.35
30 10 0.29
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.41
Consensus pattern (30 bp):
AATTTAAAAAAATGTTTTTGGACTGAATTG
Found at i:5322778 original size:29 final size:30
Alignment explanation
Indices: 5322708--5322767 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
5322698 CAATTTAAGG
5322708 AAAAATGGTTTTTGGACTTGAATTGAATTTA
1 AAAAAT-GTTTTTGGACTTGAATTGAATTTA
5322739 AAAAATGTTTTTGGAC-TGAATTGAATTTA
1 AAAAATGTTTTTGGACTTGAATTGAATTTA
5322768 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 13 0.45
30 10 0.34
31 6 0.21
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (30 bp):
AAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:5322896 original size:22 final size:22
Alignment explanation
Indices: 5322847--5322968 Score: 148
Period size: 22 Copynumber: 5.7 Consensus size: 22
5322837 AGGGTGTCAA
5322847 AGTGCATCCATGCATCCCT-G-C-
1 AGTGCATCCATGCA--CCTGGACT
5322868 AGTGCATCCATGCACCTGGACT
1 AGTGCATCCATGCACCTGGACT
*
5322890 AGTGCATCCATGCACCTGCACT
1 AGTGCATCCATGCACCTGGACT
*
5322912 AGTGCATCCATGCACCTGCACT
1 AGTGCATCCATGCACCTGGACT
*
5322934 AGTGCATCGATGCACCAT-G-C-
1 AGTGCATCCATGCACC-TGGACT
5322954 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
5322969 TCCATGTCGA
Statistics
Matches: 93, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.03
20 15 0.16
21 16 0.17
22 58 0.62
23 1 0.01
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.22
Consensus pattern (22 bp):
AGTGCATCCATGCACCTGGACT
Found at i:5322925 original size:44 final size:41
Alignment explanation
Indices: 5322847--5322968 Score: 172
Period size: 44 Copynumber: 2.8 Consensus size: 41
5322837 AGGGTGTCAA
*
5322847 AGTGCATCCATGCATCCCTGCAGTGCATCCATGCACCTGGACT
1 AGTGCATCCATGCA--CCTGCAGTGCATCCATGCACCTGCACT
5322890 AGTGCATCCATGCACCTGCACTAGTGCATCCATGCACCTGCACT
1 AGTGCATCCATGCACCTG--C-AGTGCATCCATGCACCTGCACT
*
5322934 AGTGCATCGATGCACCATGCAGTGCATCCATGCAC
1 AGTGCATCCATGCACC-TGCAGTGCATCCATGCAC
5322969 TCCATGTCGA
Statistics
Matches: 73, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
41 4 0.05
42 15 0.21
43 16 0.22
44 36 0.49
45 2 0.03
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.22
Consensus pattern (41 bp):
AGTGCATCCATGCACCTGCAGTGCATCCATGCACCTGCACT
Found at i:5323051 original size:20 final size:20
Alignment explanation
Indices: 5322992--5323062 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
5322982 CACTTAGTGA
* * *
5322992 ATCGATGCATCCTGATGCGC
1 ATCGATGCATCATGTTGTGC
*
5323012 ATCGATGCATCAAGGTTGTGC
1 ATCGATGCATC-ATGTTGTGC
*
5323033 ATCGATGCATCTTGTTGTGC
1 ATCGATGCATCATGTTGTGC
*
5323053 ATCCATGCAT
1 ATCGATGCAT
5323063 GAAGGCTGCA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (20 bp):
ATCGATGCATCATGTTGTGC
Found at i:5323643 original size:18 final size:18
Alignment explanation
Indices: 5323620--5323658 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
5323610 ACCACTCTAA
*
5323620 ATCGTTGTGCAATTTTCT
1 ATCGTTGTACAATTTTCT
5323638 ATCGTTGTACAATTTTCT
1 ATCGTTGTACAATTTTCT
5323656 ATC
1 ATC
5323659 TTTCAATCTC
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:0.21, C:0.18, G:0.13, T:0.49
Consensus pattern (18 bp):
ATCGTTGTACAATTTTCT
Found at i:5324397 original size:19 final size:20
Alignment explanation
Indices: 5324373--5324420 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
5324363 AACGATTTTC
*
5324373 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
5324392 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
5324412 TTTTGAAAA
1 TTTTGAAAA
5324421 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:5325699 original size:34 final size:30
Alignment explanation
Indices: 5325661--5325729 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 30
5325651 TTGATATAAC
5325661 AATTTAAGGAAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--AAAAAT-GTTTTTGGAC-TGAATTG
*
5325695 AATTT-ACAAAATGTTTTTGGACTGAATTG
1 AATTTAAAAAAATGTTTTTGGACTGAATTG
5325724 AATTTA
1 AATTTA
5325730 TTCAACGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 12 0.36
30 10 0.30
31 5 0.15
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (30 bp):
AATTTAAAAAAATGTTTTTGGACTGAATTG
Found at i:5325711 original size:30 final size:30
Alignment explanation
Indices: 5325671--5325729 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
5325661 AATTTAAGGA
5325671 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAATGGTTTTTGGAC-TGAATTGAATTTAC
5325702 AAAAT-GTTTTTGGACTGAATTGAATTTA
1 AAAATGGTTTTTGGACTGAATTGAATTTA
5325730 TTCAACGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 13 0.46
30 10 0.36
31 5 0.18
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.42
Consensus pattern (30 bp):
AAAATGGTTTTTGGACTGAATTGAATTTAC
Found at i:5325839 original size:21 final size:21
Alignment explanation
Indices: 5325813--5325865 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
5325803 TGTCAAAGTA
*
5325813 CATCCATGCACCCCTGCAGTG
1 CATCCATGCACCCCTACAGTG
*
5325834 CATCCATGCATCCCTACAGTG
1 CATCCATGCACCCCTACAGTG
*
5325855 CATCAATGCAC
1 CATCCATGCAC
5325866 TCCATTTCGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.40, G:0.15, T:0.21
Consensus pattern (21 bp):
CATCCATGCACCCCTACAGTG
Found at i:5325910 original size:20 final size:20
Alignment explanation
Indices: 5325885--5325959 Score: 89
Period size: 20 Copynumber: 3.7 Consensus size: 20
5325875 AATGCACTTA
5325885 GTGCATCGATGCATCCTGAT
1 GTGCATCGATGCATCCTGAT
** *
5325905 GTGCATCGATGCATCAAGGTT
1 GTGCATCGATGCATC-CTGAT
5325926 GTGCATCGATGCATCCT-ACT
1 GTGCATCGATGCATCCTGA-T
*
5325946 GTGCATCCATGCAT
1 GTGCATCGATGCAT
5325960 GAAGGCTGCA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 29 0.63
21 17 0.37
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGAT
Found at i:5325930 original size:21 final size:20
Alignment explanation
Indices: 5325885--5325940 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
5325875 AATGCACTTA
**
5325885 GTGCATCGATGCATCCTGAT
1 GTGCATCGATGCATCAGGAT
*
5325905 GTGCATCGATGCATCAAGGTT
1 GTGCATCGATGCATC-AGGAT
5325926 GTGCATCGATGCATC
1 GTGCATCGATGCATC
5325941 CTACTGTGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCAGGAT
Found at i:5325930 original size:41 final size:41
Alignment explanation
Indices: 5325885--5325964 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
5325875 AATGCACTTA
*
5325885 GTGCATCGATGCATCCTGA-TGTGCATCGATGCATCAAGGTT
1 GTGCATCGATGCATCCT-ACTGTGCATCCATGCATCAAGGTT
*
5325926 GTGCATCGATGCATCCTACTGTGCATCCATGCATGAAGG
1 GTGCATCGATGCATCCTACTGTGCATCCATGCATCAAGG
5325965 CTGCAACGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 1 0.03
41 35 0.97
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.28
Consensus pattern (41 bp):
GTGCATCGATGCATCCTACTGTGCATCCATGCATCAAGGTT
Found at i:5327598 original size:20 final size:20
Alignment explanation
Indices: 5327573--5327612 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5327563 TGATGTTTTT
5327573 GAGGTTGTAGATTCATATTC
1 GAGGTTGTAGATTCATATTC
5327593 GAGGTTGTAGATTCATATTC
1 GAGGTTGTAGATTCATATTC
5327613 AAGTTTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (20 bp):
GAGGTTGTAGATTCATATTC
Found at i:5327620 original size:20 final size:20
Alignment explanation
Indices: 5327574--5327621 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
5327564 GATGTTTTTG
*
5327574 AGGTTGTAGATTCATATTCG
1 AGGTTGTAGATTCATATTCA
5327594 AGGTTGTAGATTCATATTCA
1 AGGTTGTAGATTCATATTCA
*
5327614 AGTTTGTA
1 AGGTTGTA
5327622 TGATGATTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (20 bp):
AGGTTGTAGATTCATATTCA
Found at i:5329064 original size:14 final size:14
Alignment explanation
Indices: 5329045--5329091 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
5329035 TATATTGGGC
*
5329045 TATTGTCTATGGTT
1 TATTGTTTATGGTT
* *
5329059 TATTGTTTATGATA
1 TATTGTTTATGGTT
*
5329073 TATGGTTTATGGTT
1 TATTGTTTATGGTT
5329087 TATTG
1 TATTG
5329092 GTTAATAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.19, C:0.02, G:0.21, T:0.57
Consensus pattern (14 bp):
TATTGTTTATGGTT
Found at i:5329204 original size:45 final size:45
Alignment explanation
Indices: 5329113--5329247 Score: 227
Period size: 45 Copynumber: 3.0 Consensus size: 45
5329103 GTAACTCTGC
* * *
5329113 AAATAAGCTTACGAGCTTATAGAAT-AATGGTAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
*
5329157 AAATAAGCTTACTAGCTTATGGGATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
5329202 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
5329247 A
1 A
5329248 GAAATTTTAT
Statistics
Matches: 85, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
44 22 0.26
45 63 0.74
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
Found at i:5329677 original size:18 final size:16
Alignment explanation
Indices: 5329635--5329691 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 16
5329625 AAATCCATAT
*
5329635 TAATAT-ATATTTAAA
1 TAATATGATATTTATA
5329650 TAGTATATGATAATTTGATA
1 TA--ATATGAT-ATTT-ATA
*
5329670 TAATATGATATTTTTA
1 TAATATGATATTTATA
5329686 TAATAT
1 TAATAT
5329692 CATTTATCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 2 0.06
16 8 0.23
17 8 0.23
18 9 0.26
19 4 0.11
20 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (16 bp):
TAATATGATATTTATA
Found at i:5329689 original size:16 final size:18
Alignment explanation
Indices: 5329654--5329691 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
5329644 TTTAAATAGT
5329654 ATATGATAATTTGATATA
1 ATATGATAATTTGATATA
*
5329672 ATATGAT-ATTT-TTATA
1 ATATGATAATTTGATATA
5329688 ATAT
1 ATAT
5329692 CATTTATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 4 0.21
18 7 0.37
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (18 bp):
ATATGATAATTTGATATA
Found at i:5331886 original size:9 final size:8
Alignment explanation
Indices: 5331863--5331953 Score: 51
Period size: 8 Copynumber: 10.9 Consensus size: 8
5331853 AGAGTTTATT
*
5331863 AAAACAAG
1 AAAAAAAG
5331871 AAAAAAAG
1 AAAAAAAG
5331879 AAACAAAAGATG
1 -AA-AAAA-A-G
5331891 AAAAAATAG
1 AAAAAA-AG
*
5331900 AAAAATAG
1 AAAAAAAG
5331908 -AAAAAA-
1 AAAAAAAG
* *
5331914 TAAAATAG
1 AAAAAAAG
5331922 AAAAAAAG
1 AAAAAAAG
*
5331930 AAGAAGAAG
1 AA-AAAAAG
* *
5331939 GAAAAAAT
1 AAAAAAAG
5331947 AAAAAAA
1 AAAAAAA
5331954 ACAAGAAAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
7 10 0.16
8 27 0.42
9 14 0.22
10 9 0.14
11 3 0.05
12 1 0.02
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (8 bp):
AAAAAAAG
Found at i:5331903 original size:17 final size:16
Alignment explanation
Indices: 5331883--5331951 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 16
5331873 AAAAAGAAAC
5331883 AAAAGATGAAAAAATA
1 AAAAGATGAAAAAATA
5331899 GAAAA-ATAGAAAAAATA
1 -AAAAGAT-GAAAAAATA
*
5331916 AAATAGA--AAAAAAGA
1 AAA-AGATGAAAAAATA
* *
5331931 AGAAGAAGGAAAAAATA
1 AAAAG-ATGAAAAAATA
5331948 AAAA
1 AAAA
5331952 AAACAAGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
14 2 0.05
15 10 0.24
16 5 0.12
17 24 0.57
18 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (16 bp):
AAAAGATGAAAAAATA
Done.