Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 69 of 276
Found at i:21346653 original size:32 final size:32
Alignment explanation
Indices: 21346617--21346679 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
21346607 AGTTTAATTT
* *
21346617 AAATATTTAAATATTATAATTCAAACATTTTG
1 AAATAATTAAAAATTATAATTCAAACATTTTG
* *
21346649 AAATAATTAAAAATTTTAATTCAAACCTTTT
1 AAATAATTAAAAATTATAATTCAAACATTTT
21346680 TACATATGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.43
Consensus pattern (32 bp):
AAATAATTAAAAATTATAATTCAAACATTTTG
Found at i:21347424 original size:26 final size:25
Alignment explanation
Indices: 21347395--21347452 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
21347385 TTAGCATCAC
*
21347395 TAATT-TTAGTTAATTGTGATTAAGGT
1 TAATTATTAGTTAA-T-TAATTAAGGT
21347421 TAATTAATTAGTTAATTAATTAAGGT
1 TAATT-ATTAGTTAATTAATTAAGGT
21347447 TAATTA
1 TAATTA
21347453 AATTTTAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 1 0.03
26 19 0.66
27 1 0.03
28 8 0.28
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (25 bp):
TAATTATTAGTTAATTAATTAAGGT
Found at i:21347448 original size:14 final size:14
Alignment explanation
Indices: 21347413--21347453 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
21347403 GTTAATTGTG
21347413 ATTAAGGTTAATTA
1 ATTAAGGTTAATTA
21347427 ATT-A-GTTAATTA
1 ATTAAGGTTAATTA
21347439 ATTAAGGTTAATTA
1 ATTAAGGTTAATTA
21347453 A
1 A
21347454 ATTTTAATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 11 0.44
13 2 0.08
14 12 0.48
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (14 bp):
ATTAAGGTTAATTA
Found at i:21347756 original size:21 final size:21
Alignment explanation
Indices: 21347730--21347793 Score: 128
Period size: 21 Copynumber: 3.0 Consensus size: 21
21347720 GTAGATGGTA
21347730 TTTGTAATCAATTAATTTAAG
1 TTTGTAATCAATTAATTTAAG
21347751 TTTGTAATCAATTAATTTAAG
1 TTTGTAATCAATTAATTTAAG
21347772 TTTGTAATCAATTAATTTAAG
1 TTTGTAATCAATTAATTTAAG
21347793 T
1 T
21347794 GTAATCCTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (21 bp):
TTTGTAATCAATTAATTTAAG
Found at i:21356348 original size:27 final size:27
Alignment explanation
Indices: 21356329--21356485 Score: 215
Period size: 27 Copynumber: 5.8 Consensus size: 27
21356319 ATTACCAAAG
*
21356329 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* * **
21356356 TACCCTCGGTTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCATTT
*
21356383 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* * *
21356410 TACCCTCAATTTACAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
*
21356437 TACCCTCGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCATTT
*
21356464 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
21356486 TAAAATACCC
Statistics
Matches: 115, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 115 1.00
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCATTT
Found at i:21356377 original size:54 final size:54
Alignment explanation
Indices: 21356318--21356514 Score: 205
Period size: 54 Copynumber: 3.6 Consensus size: 54
21356308 CAATTTGTAA
* * * *
21356318 AATTACCAAAGTACCCTCGATTTACAGAATTACCGTTTTACCCTCGGTTTATAG
1 AATTACCAAATTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAG
**** * *
21356372 AATTACTGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCAATTTACAG
1 AATTACCAAATTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAG
* *** * *
21356426 AATTATCGTTTTACCCTCGATTTACAGAATTACTATTTTACCCTCGATTTACAA
1 AATTACCAAATTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAG
* * * * *
21356480 AATTACTAAAATACCCTTGGTTTACAAAATTACCA
1 AATTACCAAATTACCCTCGATTTACAGAATTACCA
21356515 AAATACCCCT
Statistics
Matches: 117, Mismatches: 26, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 117 1.00
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (54 bp):
AATTACCAAATTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAG
Found at i:21356504 original size:81 final size:81
Alignment explanation
Indices: 21356316--21356513 Score: 261
Period size: 81 Copynumber: 2.4 Consensus size: 81
21356306 CTCAATTTGT
* * * *
21356316 AAAATTACCAAAGTACCCTCGATTTACAGAATTACCGTTTTACCCTCGGTTTATAGAATTACTGT
1 AAAATTACCAAAATACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACTAT
*
21356381 TTTACCCTCGATTTAT
66 TTTACCCTCGATTTAC
* *** * *
21356397 AGAATTACCATTTTACCCTCAATTTACAGAATTATCGTTTTACCCTCGATTTACAGAATTACTAT
1 AAAATTACCAAAATACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACTAT
21356462 TTTACCCTCGATTTAC
66 TTTACCCTCGATTTAC
* * * *
21356478 AAAATTACTAAAATACCCTTGGTTTACAAAATTACC
1 AAAATTACCAAAATACCCTCGATTTACAGAATTACC
21356514 AAAATACCCC
Statistics
Matches: 97, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
81 97 1.00
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (81 bp):
AAAATTACCAAAATACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACTAT
TTTACCCTCGATTTAC
Found at i:21356522 original size:54 final size:55
Alignment explanation
Indices: 21356437--21356687 Score: 181
Period size: 54 Copynumber: 4.6 Consensus size: 55
21356427 ATTATCGTTT
* * * *** * *
21356437 TACCCTCGATTTACAGAATTACTATTTTACCCTCGA-TTTACAAAATTACTAAAA
1 TACCCTTGGTTTACAAAATTACTAAAATACCCTCGACTTTGCAAAATTACCAAAA
* * * *
21356491 TACCCTTGGTTTACAAAATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACTAAAATACCCTCGACTTTGCAAAATTACCAAAA
** * * * * *
21356545 TACCAC-TGGTTTATGAAATTATTGAAATACCTTC-AATTTGTAAAATTACCAAAA
1 TACC-CTTGGTTTACAAAATTACTAAAATACCCTCGACTTTGCAAAATTACCAAAA
* * * * *
21356599 TACCCCTGATTTACAAAATTACAAAAATACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTTGGTTTACAAAATTACTAAAATACCCTCGACTTTGC--AAAATTACCA-AAA
* * *
21356655 TACCATTAGTTTACAAAATTACTGAAATACCCT
1 TACCCTTGGTTTACAAAATTACTAAAATACCCT
21356688 TGGTTTGTAG
Statistics
Matches: 154, Mismatches: 35, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
53 3 0.02
54 107 0.69
55 7 0.05
56 37 0.24
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.33
Consensus pattern (55 bp):
TACCCTTGGTTTACAAAATTACTAAAATACCCTCGACTTTGCAAAATTACCAAAA
Found at i:21356693 original size:27 final size:27
Alignment explanation
Indices: 21356437--21356693 Score: 162
Period size: 27 Copynumber: 9.4 Consensus size: 27
21356427 ATTATCGTTT
* * * ***
21356437 TACCCTCGATTTACAGAATTACTATTT
1 TACCCTTGGTTTACAAAATTACTAAAA
* *
21356464 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
*
21356491 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
* * ** *
21356518 TACCCCTAGTTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
** * *
21356545 TACCAC-TGGTTTATGAAATTATTGAAA
1 TACC-CTTGGTTTACAAAATTACTAAAA
** ** *
21356572 TA-CCTTCAATTTGTAAAATTACCAAAA
1 TACCCTT-GGTTTACAAAATTACTAAAA
* * *
21356599 TACCCCTGATTTACAAAATTACAAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
*
21356626 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTTG-GTTTAC--AAAATTACTA-AAA
* * *
21356655 TACCATTAGTTTACAAAATTACTGAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
21356682 TACCCTTGGTTT
1 TACCCTTGGTTT
21356694 GTAGATTTAC
Statistics
Matches: 182, Mismatches: 38, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
25 1 0.01
26 2 0.01
27 150 0.82
28 12 0.07
29 17 0.09
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.33
Consensus pattern (27 bp):
TACCCTTGGTTTACAAAATTACTAAAA
Found at i:21356806 original size:27 final size:27
Alignment explanation
Indices: 21356745--21356811 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
21356735 ATACCTCTAA
*
21356745 TAGG-TAAAAAGACCGTAAAGCCCCTG
1 TAGGATAAAATGACCGTAAAGCCCCTG
* *
21356771 TAGGGTAAAGTGACCGTAATA-CCCCTG
1 TAGGATAAAATGACCGTAA-AGCCCCTG
*
21356798 TATGATAAAATGAC
1 TAGGATAAAATGAC
21356812 GAATATGCCC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 4 0.12
27 29 0.85
28 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.21
Consensus pattern (27 bp):
TAGGATAAAATGACCGTAAAGCCCCTG
Found at i:21358623 original size:100 final size:100
Alignment explanation
Indices: 21358431--21358623 Score: 221
Period size: 100 Copynumber: 1.9 Consensus size: 100
21358421 TTATAGAGAA
*
21358431 TCAAAGATAATATCACAAATGTGCATACCTATATGGCCAAATATGCAAGATCAAATTTAACATCA
1 TCAAAGATAATATCACAAATGTGCATACCTATATGGCCAAATATGCAAGATCAAATATAACATCA
* * *
21358496 CCTAAGTACTTACTCATATGGCTGAATATACAAAT
66 CATAAGTACATACTCATATGGCCGAATATACAAAT
* *** * * *
21358531 TCAAATATAATATCACTTTTGTGCATACCT-TCATGGTCAAATATTCAAGATTC-AATATAACGT
1 TCAAAGATAATATCACAAATGTGCATACCTAT-ATGGCCAAATATGCAAGA-TCAAATATAACAT
* *
21358594 CACATATGTACATAC-CTATGTGGCCGAATA
64 CACATAAGTACATACTC-ATATGGCCGAATA
21358624 AATACAAGAT
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
99 2 0.03
100 73 0.95
101 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (100 bp):
TCAAAGATAATATCACAAATGTGCATACCTATATGGCCAAATATGCAAGATCAAATATAACATCA
CATAAGTACATACTCATATGGCCGAATATACAAAT
Found at i:21359775 original size:23 final size:22
Alignment explanation
Indices: 21359749--21359802 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
21359739 TTAATTTATG
*
21359749 TTATAATATATAC-ATATTATTA
1 TTATAATATA-ACTATAATATTA
* *
21359771 CTTATATTATAACTTTAATATTA
1 -TTATAATATAACTATAATATTA
21359794 TTATAATAT
1 TTATAATAT
21359803 TATTTCCACC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATAATATAACTATAATATTA
Found at i:21360390 original size:30 final size:31
Alignment explanation
Indices: 21360356--21360438 Score: 127
Period size: 31 Copynumber: 2.7 Consensus size: 31
21360346 CGCTTACAGT
*
21360356 AAAGGCTTCAG-CCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
21360386 AAAGGCTTCGGCCCAAG-GATATGATTTATGA
1 AAAGGCTTCGGCCC-AGTGATATGATTTATGA
21360417 AAAGGCTTCGGCCCAGTG-TATG
1 AAAGGCTTCGGCCCAGTGATATG
21360439 TCGAGACTGA
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
30 16 0.33
31 31 0.63
32 2 0.04
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:21362833 original size:27 final size:27
Alignment explanation
Indices: 21362803--21362959 Score: 199
Period size: 27 Copynumber: 5.8 Consensus size: 27
21362793 ATTTCCAAAG
*
21362803 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
21362830 TACCCTC-AGTTTACAAAATTACCGTTT
1 TACCCTCGA-TTTACAGAATTACCGTTT
* * *
21362857 TACCTTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
21362884 TACCCTCAATTTACAGAATTATCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
21362911 TACCCTCAATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
21362938 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
21362960 TAAAATACCC
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
26 1 0.01
27 110 0.98
28 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:21362912 original size:81 final size:81
Alignment explanation
Indices: 21362803--21362959 Score: 224
Period size: 81 Copynumber: 1.9 Consensus size: 81
21362793 ATTTCCAAAG
* * * * *
21362803 TACCCTCGATTTATAGAATTACCGTTTTACCCTCAGTTTACAAAATTACCGTTTTACCTTCGATT
1 TACCCTCAATTTACAGAATTACCATTTTACCCTCAATTTACAAAATTACCGTTTTACCCTCGATT
* *
21362868 TATAGAATTACCATTT
66 TACAAAATTACCATTT
* * *
21362884 TACCCTCAATTTACAGAATTATCATTTTACCCTCAATTTATAGAATTACCGTTTTACCCTCGATT
1 TACCCTCAATTTACAGAATTACCATTTTACCCTCAATTTACAAAATTACCGTTTTACCCTCGATT
21362949 TACAAAATTAC
66 TACAAAATTAC
21362960 TAAAATACCC
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (81 bp):
TACCCTCAATTTACAGAATTACCATTTTACCCTCAATTTACAAAATTACCGTTTTACCCTCGATT
TACAAAATTACCATTT
Found at i:21362958 original size:54 final size:53
Alignment explanation
Indices: 21362803--21362959 Score: 233
Period size: 54 Copynumber: 2.9 Consensus size: 53
21362793 ATTTCCAAAG
*
21362803 TACCCTCGATTTATAGAATTACCGTTTTACCCTCAGTTTACAAAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTTTACCCTCA-TTTACAAAATTACCATTT
* * * *
21362857 TACCTTCGATTTATAGAATTACCATTTTACCCTCAATTTACAGAATTATCATTT
1 TACCCTCGATTTATAGAATTACCGTTTTACCCTC-ATTTACAAAATTACCATTT
*
21362911 TACCCTCAATTTATAGAATTACCGTTTTACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTATAGAATTACCGTTTTACCCTC-ATTTACAAAATTAC
21362960 TAAAATACCC
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
54 90 0.99
55 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (53 bp):
TACCCTCGATTTATAGAATTACCGTTTTACCCTCATTTACAAAATTACCATTT
Found at i:21362968 original size:27 final size:27
Alignment explanation
Indices: 21362790--21363093 Score: 130
Period size: 27 Copynumber: 11.3 Consensus size: 27
21362780 CTCAATTTGT
* * *
21362790 AAAATTTCCAAAGTACCCTCGATTTAT
1 AAAATTACCAAAATACCCTCGATTTAC
* ****
21362817 AGAATTACCGTTTTACCCTC-AGTTTAC
1 AAAATTACCAAAATACCCTCGA-TTTAC
**** * *
21362844 AAAATTACCGTTTTACCTTCGATTTAT
1 AAAATTACCAAAATACCCTCGATTTAC
* *** *
21362871 AGAATTACCATTTTACCCTCAATTTAC
1 AAAATTACCAAAATACCCTCGATTTAC
* * *** * *
21362898 AGAATTATCATTTTACCCTCAATTTAT
1 AAAATTACCAAAATACCCTCGATTTAC
* ****
21362925 AGAATTACCGTTTTACCCTCGATTTAC
1 AAAATTACCAAAATACCCTCGATTTAC
* * *
21362952 AAAATTACTAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCTCGATTTAC
* **
21362979 AAAATTACCAAAATACCC-CTAGTTTGT
1 AAAATTACCAAAATACCCTCGA-TTTAC
* **
21363006 AAAATTACCAAAATACCACT-GGTTTGT
1 AAAATTACCAAAATACC-CTCGATTTAC
* * * **
21363033 GAAATTACCGAAATACCCTCAATTTGT
1 AAAATTACCAAAATACCCTCGATTTAC
*
21363060 AGAATTACCAAAATATCCCT-GATTTAC
1 AAAATTACCAAAATA-CCCTCGATTTAC
21363087 AAAATTA
1 AAAATTA
21363094 TAGAAATACC
Statistics
Matches: 222, Mismatches: 48, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
26 3 0.01
27 213 0.96
28 6 0.03
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTCGATTTAC
Found at i:21362969 original size:81 final size:81
Alignment explanation
Indices: 21362790--21362988 Score: 218
Period size: 81 Copynumber: 2.5 Consensus size: 81
21362780 CTCAATTTGT
* * * * * *
21362790 AAAATTTCCAAAGTACCCTCGATTTATAGAATTACCGTTTTACCCTCAGTTTACAAAATTACCGT
1 AAAATTACCAAAATACCCTCAATTTACAGAATTACCATTTTACCCTCAATTTACAAAATTACCGT
* *
21362855 TTTACCTTCGATTTAT
66 TTTACCCTCGATTTAC
* *** * * *
21362871 AGAATTACCATTTTACCCTCAATTTACAGAATTATCATTTTACCCTCAATTTATAGAATTACCGT
1 AAAATTACCAAAATACCCTCAATTTACAGAATTACCATTTTACCCTCAATTTACAAAATTACCGT
21362936 TTTACCCTCGATTTAC
66 TTTACCCTCGATTTAC
* *** *
21362952 AAAATTACTAAAATACCCTTGGTTTACAAAATTACCA
1 AAAATTACCAAAATACCCTCAATTTACAGAATTACCA
21362989 AAATACCCCT
Statistics
Matches: 94, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
81 94 1.00
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (81 bp):
AAAATTACCAAAATACCCTCAATTTACAGAATTACCATTTTACCCTCAATTTACAAAATTACCGT
TTTACCCTCGATTTAC
Found at i:21362996 original size:54 final size:54
Alignment explanation
Indices: 21362938--21363161 Score: 163
Period size: 54 Copynumber: 4.1 Consensus size: 54
21362928 ATTACCGTTT
* *
21362938 TACCCTCGA-TTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTCGACTTTGCAAAATTACCAAAATACCC-TGGTTTACAAAATTACCAAAA
* * * *** *
21362992 TACCC-CTAGTTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAA
1 TACCCTCGACTTTGCAAAATTACCAAAATACC-CTGGTTTACAAAATTACCAAAA
* * * * *
21363046 TACCCTC-AATTTGTAGAATTACCAAAATATCCCTGATTTACAAAATTA-TAGAAA
1 TACCCTCGACTTTGCAAAATTACCAAAATA-CCCTGGTTTACAAAATTACCA-AAA
* * * **
21363100 TACCCTTGACTTT-CTAAAAATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAA
1 TACCCTCGACTTTGC--AAAATTACCA-AAATACC-CTGGTTTACAAAATTACCAAAA
21363156 TACCCT
1 TACCCT
21363162 TAGTTTGTAG
Statistics
Matches: 135, Mismatches: 24, Indels: 20
0.75 0.13 0.11
Matches are distributed among these distances:
53 2 0.01
54 87 0.64
55 11 0.08
56 34 0.25
57 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.31
Consensus pattern (54 bp):
TACCCTCGACTTTGCAAAATTACCAAAATACCCTGGTTTACAAAATTACCAAAA
Found at i:21362996 original size:81 final size:81
Alignment explanation
Indices: 21362830--21363093 Score: 174
Period size: 81 Copynumber: 3.3 Consensus size: 81
21362820 ATTACCGTTT
* * * * ***
21362830 TACCCTCAGTTTACAAAATTACCGTTTTACCTTCGATTTATAGAATTACCATTTTACCCTCAATT
1 TACCCTCAATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCAAAATACCCTCAATT
* * ***
21362895 TACAGAATTATCATTT
66 TACAAAATTACCAAAA
* * * ***
21362911 TACCCTCAATTTATAGAATTACCGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGGTT
1 TACCCTCAATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCAAAATACCCTCAATT
21362976 TACAAAATTACCAAAA
66 TACAAAATTACCAAAA
* ** **** * *** *
21362992 TACCC-CTAGTTTGTAAAATTACCAAAATACCACT-GGTTTGTGAAATTACCGAAATACCCTCAA
1 TACCCTC-AATTTACAAAATTACCGTTTTACC-CTCGATTTACAAAATTACCAAAATACCCTCAA
** *
21363055 TTTGTAGAATTACCAAAA
64 TTTACAAAATTACCAAAA
*
21363073 TATCCCT-GATTTACAAAATTA
1 TA-CCCTCAATTTACAAAATTA
21363094 TAGAAATACC
Statistics
Matches: 138, Mismatches: 41, Indels: 8
0.74 0.22 0.04
Matches are distributed among these distances:
80 1 0.01
81 132 0.96
82 5 0.04
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.35
Consensus pattern (81 bp):
TACCCTCAATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCAAAATACCCTCAATT
TACAAAATTACCAAAA
Found at i:21363167 original size:27 final size:27
Alignment explanation
Indices: 21362947--21363167 Score: 137
Period size: 27 Copynumber: 8.1 Consensus size: 27
21362937 TTACCCTCGA
* *
21362947 TTTACAAAATTACTAAAATACCCTTGG
1 TTTACAAAATTACCAAAATACCCTTAG
*
21362974 TTTACAAAATTACCAAAATACCCCTAG
1 TTTACAAAATTACCAAAATACCCTTAG
** *
21363001 TTTGTAAAATTACCAAAATACCAC-TGG
1 TTTACAAAATTACCAAAATACC-CTTAG
*** * * *
21363028 TTTGTGAAATTACCGAAATACCCTCAA
1 TTTACAAAATTACCAAAATACCCTTAG
** * *
21363055 TTTGTAGAATTACCAAAATATCCCTGA-
1 TTTACAAAATTACCAAAATA-CCCTTAG
* *
21363082 TTTACAAAATTA-TAGAAATACCCTTGAC
1 TTTACAAAATTACCA-AAATACCCTT-AG
* * *
21363110 TTT-CTAAAAATTA-TAGAAATACCATTGG
1 TTTAC--AAAATTACCA-AAATACCCTTAG
**
21363138 TTTACAAAATTACTGAAATACCCTTAG
1 TTTACAAAATTACCAAAATACCCTTAG
21363165 TTT
1 TTT
21363168 GTAGATTTAC
Statistics
Matches: 158, Mismatches: 26, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
26 6 0.04
27 119 0.75
28 13 0.08
29 20 0.13
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.33
Consensus pattern (27 bp):
TTTACAAAATTACCAAAATACCCTTAG
Found at i:21364138 original size:25 final size:25
Alignment explanation
Indices: 21364110--21364164 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
21364100 GGCTATACCT
21364110 CAGTTTACCGAA-AAGGGCTTTGCCC
1 CAGTTTACC-AAGAAGGGCTTTGCCC
*
21364135 CAGTTTATCAAGAAGGGCTTTGCCC
1 CAGTTTACCAAGAAGGGCTTTGCCC
21364160 CAGTT
1 CAGTT
21364165 ATTAAAAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 2 0.07
25 26 0.93
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (25 bp):
CAGTTTACCAAGAAGGGCTTTGCCC
Found at i:21364177 original size:24 final size:23
Alignment explanation
Indices: 21364120--21364191 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 23
21364110 CAGTTTACCG
21364120 AAAAGGGCTTTGCCCCAGTTTATC
1 AAAAGGGCTTTGCCCCAG-TTATC
*
21364144 AAGAAGGGCTTTGCCCCAGTTATT
1 AA-AAGGGCTTTGCCCCAGTTATC
**
21364168 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAG-GGCTTTGCC-CCAGTTAT
21364192 ATGATAAAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
23 3 0.07
24 15 0.36
25 24 0.57
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (23 bp):
AAAAGGGCTTTGCCCCAGTTATC
Found at i:21364436 original size:31 final size:30
Alignment explanation
Indices: 21364384--21364466 Score: 132
Period size: 31 Copynumber: 2.7 Consensus size: 30
21364374 CGCTTACAGT
21364384 AAAGGCTTCGG-CCAGTCATATGATTTATGA
1 AAAGGCTTCGGCCCAGT-ATATGATTTATGA
*
21364414 AAAGGCTTTGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGT-ATATGATTTATGA
21364445 AAAGGCTTCGGCCCAGTATATG
1 AAAGGCTTCGGCCCAGTATATG
21364467 TCGAGACTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
30 15 0.31
31 34 0.69
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (30 bp):
AAAGGCTTCGGCCCAGTATATGATTTATGA
Found at i:21366852 original size:32 final size:32
Alignment explanation
Indices: 21366816--21366880 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
21366806 CGTATGCATT
21366816 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
21366848 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
21366880 T
1 T
21366881 GGTAAGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGGCA
Found at i:21368390 original size:26 final size:26
Alignment explanation
Indices: 21368361--21368413 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
21368351 TTTACAGTTT
21368361 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* * *
21368387 TACCTCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
21368413 T
1 T
21368414 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:21370077 original size:13 final size:13
Alignment explanation
Indices: 21370059--21370084 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21370049 AGGATTTGTT
21370059 TTATCTAAACTAA
1 TTATCTAAACTAA
21370072 TTATCTAAACTAA
1 TTATCTAAACTAA
21370085 GAATGCACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:21372880 original size:17 final size:19
Alignment explanation
Indices: 21372858--21372906 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
21372848 CTAATAGATA
21372858 AATATTAAATTA-CA-TTT
1 AATATTAAATTATCACTTT
*
21372875 AATATTAAGATAATCACTTT
1 AATATTAA-ATTATCACTTT
21372895 AATATTAAATTA
1 AATATTAAATTA
21372907 ATAAAATACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 8 0.30
18 3 0.11
19 5 0.19
20 11 0.41
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (19 bp):
AATATTAAATTATCACTTT
Found at i:21377448 original size:22 final size:21
Alignment explanation
Indices: 21377418--21377464 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
21377408 TACAAATTAA
21377418 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
21377440 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
21377461 ATCT
1 ATCT
21377465 AAGATTGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:21377470 original size:19 final size:19
Alignment explanation
Indices: 21377435--21377513 Score: 117
Period size: 19 Copynumber: 4.2 Consensus size: 19
21377425 AGATTACAAG
21377435 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
21377456 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
*
21377475 GTCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
21377492 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
21377511 ATC
1 ATC
21377514 CTTAAAGATT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
17 16 0.30
19 29 0.54
20 1 0.02
21 8 0.15
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:21377498 original size:36 final size:39
Alignment explanation
Indices: 21377436--21377510 Score: 120
Period size: 36 Copynumber: 2.0 Consensus size: 39
21377426 GATTACAAGA
21377436 TCATATCTTCAAGATTGCATATCATATCTAAGATTGCATG
1 TCATATCTTCAAGATTG-ATATCATATCTAAGATTGCATG
21377476 TCATATC-T-AAGATTG-TATCATATCTAAGATTGCAT
1 TCATATCTTCAAGATTGATATCATATCTAAGATTGCAT
21377511 ATCCTTAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
36 20 0.57
38 7 0.20
39 1 0.03
40 7 0.20
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (39 bp):
TCATATCTTCAAGATTGATATCATATCTAAGATTGCATG
Found at i:21377513 original size:14 final size:15
Alignment explanation
Indices: 21377474--21377513 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
21377464 TAAGATTGCA
21377474 TGTCATATCTAAGAT
1 TGTCATATCTAAGAT
21377489 TGTATCATATCTAAGAT
1 TG--TCATATCTAAGAT
21377506 TG-CATATC
1 TGTCATATC
21377514 CTTAAAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.26
15 2 0.09
17 15 0.65
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (15 bp):
TGTCATATCTAAGAT
Found at i:21384297 original size:46 final size:46
Alignment explanation
Indices: 21384245--21384518 Score: 478
Period size: 46 Copynumber: 6.0 Consensus size: 46
21384235 AGTGTGCTCT
21384245 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
21384291 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
21384337 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
21384383 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
21384429 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
21384475 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
21384519 TCACGTCAAA
Statistics
Matches: 221, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
45 1 0.00
46 220 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:21392225 original size:23 final size:25
Alignment explanation
Indices: 21392180--21392226 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
21392170 AATAAATATA
*
21392180 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
21392205 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
21392227 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:21395092 original size:5 final size:5
Alignment explanation
Indices: 21395082--21395151 Score: 56
Period size: 5 Copynumber: 13.6 Consensus size: 5
21395072 TCCTCCTATC
*
21395082 TTTAT TTTAT TTTA- TTTAT TTTATT TTTCT TTTGATT TTTAT TTTCAT
1 TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTT-A-T TTTAT TTT-AT
*
21395130 TTCAAT TTTA- -TTAT TTTAT TTT
1 TT-TAT TTTAT TTTAT TTTAT TTT
21395152 GAAAGAATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
3 3 0.06
4 4 0.08
5 29 0.55
6 13 0.25
7 4 0.08
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:21395121 original size:12 final size:11
Alignment explanation
Indices: 21395082--21395151 Score: 56
Period size: 12 Copynumber: 6.3 Consensus size: 11
21395072 TCCTCCTATC
21395082 TTTA-TTTTAT
1 TTTATTTTTAT
21395092 TTTA--TTTAT
1 TTTATTTTTAT
*
21395101 TTTATTTTTCT
1 TTTATTTTTAT
21395112 TTTGATTTTTAT
1 TTT-ATTTTTAT
**
21395124 TTTCATTTCAAT
1 TTT-ATTTTTAT
21395136 TTTATTATTTTAT
1 TTTA-T-TTTTAT
21395149 TTT
1 TTT
21395152 GAAAGAATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
9 9 0.19
10 4 0.08
11 8 0.17
12 20 0.42
13 7 0.15
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:21395126 original size:17 final size:17
Alignment explanation
Indices: 21395085--21395141 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
21395075 TCCTATCTTT
21395085 ATTTTATTTT-ATTT--
1 ATTTTATTTTCATTTCA
* *
21395099 ATTTTATTTTTCTTTTGA
1 ATTTTA-TTTTCATTTCA
*
21395117 TTTTTATTTTCATTTCA
1 ATTTTATTTTCATTTCA
21395134 ATTTTATT
1 ATTTTATT
21395142 ATTTTATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
14 6 0.18
15 4 0.12
16 3 0.09
17 16 0.47
18 5 0.15
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (17 bp):
ATTTTATTTTCATTTCA
Found at i:21400735 original size:24 final size:24
Alignment explanation
Indices: 21400703--21400753 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
21400693 AAGTCTGTCA
**
21400703 GGATAGGATTTAGGAGTTGATAAG
1 GGATAGGATTTAGGAGCAGATAAG
21400727 GGATAGGATTTAGGAGCAGATAAG
1 GGATAGGATTTAGGAGCAGATAAG
21400751 GGA
1 GGA
21400754 GGAAATCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.02, G:0.39, T:0.24
Consensus pattern (24 bp):
GGATAGGATTTAGGAGCAGATAAG
Found at i:21402230 original size:27 final size:26
Alignment explanation
Indices: 21402172--21402285 Score: 120
Period size: 27 Copynumber: 4.2 Consensus size: 26
21402162 AGGAAGCGTC
* *
21402172 CTGGTGGCTATGCCACAAATTATCTGAT
1 CTGGTGGCTCTGCCAC--ATTATCTGTT
21402200 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
* *
21402227 CTGGTGGTTCTGCCACGATTATTTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGT-T
* *
21402255 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
*
21402281 TTGGT
1 CTGGT
21402286 AGCCATGCTG
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
26 7 0.09
27 36 0.49
28 31 0.42
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:21402257 original size:55 final size:54
Alignment explanation
Indices: 21402172--21402285 Score: 140
Period size: 55 Copynumber: 2.1 Consensus size: 54
21402162 AGGAAGCGTC
*
21402172 CTGGTGGCTATGCCACAAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAAATTATCTGATCTGGTGACTCTGCCACAT-TATCTGTT
* * * * *
21402227 CTGGTGGTTCTGCCAC-GATTATTTGTATCTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTATGCCACAAATTATCTG-ATCTGGTGACTCTGCCACATTATCTGTT
*
21402281 TTGGT
1 CTGGT
21402286 AGCCATGCTG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
54 19 0.37
55 32 0.63
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAAATTATCTGATCTGGTGACTCTGCCACATTATCTGTT
Found at i:21403360 original size:16 final size:16
Alignment explanation
Indices: 21403339--21403372 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
21403329 AGGGTCCTTG
21403339 TCTCAAAGAGCATCTT
1 TCTCAAAGAGCATCTT
21403355 TCTCAAAGAGCATCTT
1 TCTCAAAGAGCATCTT
21403371 TC
1 TC
21403373 CTCGTCACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (16 bp):
TCTCAAAGAGCATCTT
Found at i:21415538 original size:12 final size:12
Alignment explanation
Indices: 21415521--21415559 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
21415511 ATATATACAT
21415521 ATCAATTTCATA
1 ATCAATTTCATA
21415533 ATCAA--TCAT-
1 ATCAATTTCATA
21415542 ATCAATTTCATA
1 ATCAATTTCATA
21415554 ATCAAT
1 ATCAAT
21415560 CATAACATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
9 5 0.21
10 4 0.17
11 4 0.17
12 11 0.46
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (12 bp):
ATCAATTTCATA
Found at i:21415542 original size:21 final size:21
Alignment explanation
Indices: 21415518--21415563 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
21415508 TCAATATATA
21415518 CATATCAATTTCATAATCAAT
1 CATATCAATTTCATAATCAAT
21415539 CATATCAATTTCATAATCAAT
1 CATATCAATTTCATAATCAAT
21415560 CATA
1 CATA
21415564 ACATCCACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (21 bp):
CATATCAATTTCATAATCAAT
Found at i:21417409 original size:9 final size:9
Alignment explanation
Indices: 21417395--21417427 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
21417385 GTTAAACAAA
21417395 TCGAGTTAT
1 TCGAGTTAT
*
21417404 TCGAGTTAA
1 TCGAGTTAT
21417413 TCGAGTTAT
1 TCGAGTTAT
21417422 TCGAGT
1 TCGAGT
21417428 CAACTCGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:21417416 original size:18 final size:18
Alignment explanation
Indices: 21417393--21417427 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
21417383 GAGTTAAACA
21417393 AATCGAGTTATTCGAGTT
1 AATCGAGTTATTCGAGTT
21417411 AATCGAGTTATTCGAGT
1 AATCGAGTTATTCGAGT
21417428 CAACTCGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:21417494 original size:9 final size:9
Alignment explanation
Indices: 21417477--21417513 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
21417467 TGAGTTTTCG
21417477 AATTCGAAT
1 AATTCGAAT
*
21417486 AACTCGAAT
1 AATTCGAAT
21417495 AATTCGAAT
1 AATTCGAAT
21417504 AATTCGAAT
1 AATTCGAAT
21417513 A
1 A
21417514 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:21417901 original size:16 final size:16
Alignment explanation
Indices: 21417869--21417898 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
21417859 CTATTTACTT
21417869 TCCCTCAAAACTTTTA
1 TCCCTCAAAACTTTTA
21417885 TCCC-CAAAACTTTT
1 TCCCTCAAAACTTTT
21417899 TATTTTCCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (16 bp):
TCCCTCAAAACTTTTA
Found at i:21422186 original size:22 final size:22
Alignment explanation
Indices: 21422158--21422202 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
21422148 TTAATAAAAA
21422158 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
21422180 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
21422202 A
1 A
21422203 CACTCCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:21425541 original size:22 final size:22
Alignment explanation
Indices: 21425516--21425560 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
21425506 TTTAATAAAA
21425516 AAAATATCTAAAAAATATTCCT
1 AAAATATCTAAAAAATATTCCT
* * *
21425538 AAAATATTTACAGAATATTCCT
1 AAAATATCTAAAAAATATTCCT
21425560 A
1 A
21425561 CAGTAATCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTAAAAAATATTCCT
Found at i:21431399 original size:12 final size:12
Alignment explanation
Indices: 21431384--21431410 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
21431374 AAATTATTTT
21431384 ATTAAAATTCAA
1 ATTAAAATTCAA
21431396 ATTAAAATTCAA
1 ATTAAAATTCAA
21431408 ATT
1 ATT
21431411 TTGCATTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (12 bp):
ATTAAAATTCAA
Found at i:21451270 original size:41 final size:39
Alignment explanation
Indices: 21451108--21451348 Score: 283
Period size: 40 Copynumber: 6.0 Consensus size: 39
21451098 AAAATCGAAT
* * *
21451108 AGATCTAGCATTAGTGGGGTTTTTAACAAAGCGCCGCTAA
1 AGATCGAGCATTAGCGGCGTTTTTAA-AAAGCGCCGCTAA
21451148 AGATCGAGCATTAGCGGCGTTTTTAACAAAGCGCCGCTAA
1 AGATCGAGCATTAGCGGCGTTTTTAA-AAAGCGCCGCTAA
* * *
21451188 AGATCAAGCATTAGCGGTGCTTTGTT--AAA-CACCGCTAA
1 AGATCGAGCATTAGCGGCG-TTT-TTAAAAAGCGCCGCTAA
*
21451226 AGATCTGAGCATTAGCGGCGTTTTTAGGAAAGCGCCGCTAA
1 AGATC-GAGCATTAGCGGCGTTTTTA-AAAAGCGCCGCTAA
**
21451267 AGATCTGAGCATTAGCGGCGTTTTTAAGAAAGCGCTACTAA
1 AGATC-GAGCATTAGCGGCGTTTTTAA-AAAGCGCCGCTAA
21451308 AGATCGAGCATTAGCGGCGCTTTTTTAAAAA-CGCCGCTAA
1 AGATCGAGCATTAGCGGCG--TTTTTAAAAAGCGCCGCTAA
21451348 A
1 A
21451349 AGATTAAGCA
Statistics
Matches: 177, Mismatches: 14, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
37 2 0.01
38 16 0.09
39 15 0.08
40 79 0.45
41 56 0.32
42 9 0.05
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (39 bp):
AGATCGAGCATTAGCGGCGTTTTTAAAAAGCGCCGCTAA
Found at i:21451330 original size:120 final size:118
Alignment explanation
Indices: 21451108--21451336 Score: 350
Period size: 120 Copynumber: 1.9 Consensus size: 118
21451098 AAAATCGAAT
* *
21451108 AGATCTAGCATTAGTGGGGTTTTTAACAAAGCGCCGCTAAAGATCGAGCATTAGCGGCGTTTTTA
1 AGATCTAGCATTAGCGGCGTTTTTAACAAAGCGCCGCTAAAGATCGAGCATTAGCGGCGTTTTTA
* *
21451173 ACAAAGCGCCGCTAAAGATCAAGCATTAGCGGTGCTTTGTTAAACACCGCTAA
66 ACAAAGCGCCACTAAAGATCAAGCATTAGCGGCGCTTTGTTAAACACCGCTAA
**
21451226 AGATCTGAGCATTAGCGGCGTTTTTAGGAAAGCGCCGCTAAAGATCTGAGCATTAGCGGCGTTTT
1 AGATCT-AGCATTAGCGGCGTTTTTAACAAAGCGCCGCTAAAGATC-GAGCATTAGCGGCGTTTT
* * * *
21451291 TAAGAAAGCGCTACTAAAGATCGAGCATTAGCGGCGCTTTTTTAAA
64 TAACAAAGCGCCACTAAAGATCAAGCATTAGCGGCGCTTTGTTAAA
21451337 AACGCCGCTA
Statistics
Matches: 99, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
118 6 0.06
119 35 0.35
120 58 0.59
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (118 bp):
AGATCTAGCATTAGCGGCGTTTTTAACAAAGCGCCGCTAAAGATCGAGCATTAGCGGCGTTTTTA
ACAAAGCGCCACTAAAGATCAAGCATTAGCGGCGCTTTGTTAAACACCGCTAA
Found at i:21452014 original size:29 final size:29
Alignment explanation
Indices: 21451928--21452019 Score: 69
Period size: 29 Copynumber: 3.2 Consensus size: 29
21451918 TAGGGATTAT
* * * * *
21451928 GTTTACGGCTTATGGTTTAA-GGGTTGGG
1 GTTTAAGGGTTATGGGTTAATGGTTTAGG
* * * * *
21451956 GTTTAAAGGTTATGGGCTAGTGATTAAGG
1 GTTTAAGGGTTATGGGTTAATGGTTTAGG
*
21451985 GTTTATGGGTTATGGGTTAATGGTTTAGG
1 GTTTAAGGGTTATGGGTTAATGGTTTAGG
*
21452014 GGTTAA
1 GTTTAA
21452020 TGCTTAGGGG
Statistics
Matches: 45, Mismatches: 18, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
28 14 0.31
29 31 0.69
ACGTcount: A:0.21, C:0.03, G:0.37, T:0.39
Consensus pattern (29 bp):
GTTTAAGGGTTATGGGTTAATGGTTTAGG
Found at i:21452026 original size:14 final size:15
Alignment explanation
Indices: 21451983--21452031 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
21451973 TAGTGATTAA
* * *
21451983 GGGTTTATGGGTTAT
1 GGGTTAATGGCTTAG
*
21451998 GGGTTAATGGTTTAG
1 GGGTTAATGGCTTAG
21452013 GGGTTAAT-GCTTAG
1 GGGTTAATGGCTTAG
21452027 GGGTT
1 GGGTT
21452032 TTTATTTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 10 0.33
15 20 0.67
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (15 bp):
GGGTTAATGGCTTAG
Found at i:21452312 original size:207 final size:203
Alignment explanation
Indices: 21452083--21452542 Score: 787
Period size: 207 Copynumber: 2.2 Consensus size: 203
21452073 ACTTTAGTAG
* *
21452083 GGGATATAGTTTAATTGTTTAAGGTTTAGAGTATTGATTAATTAGTGTTATTATTTTGTGGTTTA
1 GGGATATAGTTTAATGGTTTAAGGTTTAGAGTTTTGATTAATTAGTGTTATTATTTTGTGGTTTA
21452148 AGGATCAAGGGATATAGTTTAGGGGTATGATTAATTCATACATTTTGTGGTTAAGGCTTAAAGGT
66 AGGATCAAGGGATATAGTTTAGGGGTATGATTAATTCATACATTTTGTGGTTAAGGCTTAAAGGT
21452213 TATTATTTTATGGTTTATGGTTAGGGGATATAGTTTAGGGTTTA-ATGGATATATATACTTTAGG
131 TATTATTTTATGGTTTATGGTTAGGGGATATAGTTTAGGGTTTAGA-GG----ATATACTTTAGG
21452277 GTTTAAGGTTATA
191 GTTTAAGGTTATA
*
21452290 GGGATATAGTTTAATGGTTTAAGGTTTACAGTTTTGATTAATTAGTGTTATTATTTTGTGGTTTA
1 GGGATATAGTTTAATGGTTTAAGGTTTAGAGTTTTGATTAATTAGTGTTATTATTTTGTGGTTTA
* **
21452355 AGGATCAAGGGATATAGTTTAGGGTTATGATTAATTCATACATTTTGTGGTTAAGGCTTAGGGGT
66 AGGATCAAGGGATATAGTTTAGGGGTATGATTAATTCATACATTTTGTGGTTAAGGCTTAAAGGT
* *
21452420 TATTGTTTTGTGGTTTATGGTTAGGGGATATAGTTTAGGGTTTAGAGGATATACTTTAGGGTTTA
131 TATTATTTTATGGTTTATGGTTAGGGGATATAGTTTAGGGTTTAGAGGATATACTTTAGGGTTTA
21452485 AGGTTATA
196 AGGTTATA
*
21452493 GAGATATAGTTTAATGGTTTAAGGTTTAGAGTTTTGATTAATTAGTGTTA
1 GGGATATAGTTTAATGGTTTAAGGTTTAGAGTTTTGATTAATTAGTGTTA
21452543 ATAATATTAA
Statistics
Matches: 242, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
203 73 0.30
207 168 0.69
208 1 0.00
ACGTcount: A:0.27, C:0.02, G:0.26, T:0.45
Consensus pattern (203 bp):
GGGATATAGTTTAATGGTTTAAGGTTTAGAGTTTTGATTAATTAGTGTTATTATTTTGTGGTTTA
AGGATCAAGGGATATAGTTTAGGGGTATGATTAATTCATACATTTTGTGGTTAAGGCTTAAAGGT
TATTATTTTATGGTTTATGGTTAGGGGATATAGTTTAGGGTTTAGAGGATATACTTTAGGGTTTA
AGGTTATA
Found at i:21452443 original size:28 final size:29
Alignment explanation
Indices: 21452397--21452463 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
21452387 AATTCATACA
* *
21452397 TTTTGTGG-TTAAGGCTTAGGGGTTATTG
1 TTTTGTGGTTTAAGGCTTAGGGGATATAG
*
21452425 TTTTGTGGTTTATGG-TTAGGGGATATAG
1 TTTTGTGGTTTAAGGCTTAGGGGATATAG
*
21452453 TTTAG-GGTTTA
1 TTTTGTGGTTTA
21452464 GAGGATATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 6 0.18
28 23 0.68
29 5 0.15
ACGTcount: A:0.16, C:0.01, G:0.34, T:0.48
Consensus pattern (29 bp):
TTTTGTGGTTTAAGGCTTAGGGGATATAG
Found at i:21452469 original size:21 final size:21
Alignment explanation
Indices: 21452432--21452493 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
21452422 TTGTTTTGTG
* *
21452432 GTTTATGG-TTAGGGGATATA
1 GTTTAGGGTTTAGAGGATATA
21452452 GTTTAGGGTTTAGAGGATATA
1 GTTTAGGGTTTAGAGGATATA
* *
21452473 CTTTAGGGTTTA-AGGTTATA
1 GTTTAGGGTTTAGAGGATATA
21452493 G
1 G
21452494 AGATATAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
20 14 0.39
21 22 0.61
ACGTcount: A:0.26, C:0.02, G:0.32, T:0.40
Consensus pattern (21 bp):
GTTTAGGGTTTAGAGGATATA
Found at i:21452489 original size:28 final size:29
Alignment explanation
Indices: 21452452--21452523 Score: 94
Period size: 28 Copynumber: 2.5 Consensus size: 29
21452442 AGGGGATATA
*
21452452 GTTTAGGGTTTAGAGGATATACTTT-AGG
1 GTTTAAGGTTTAGAGGATATACTTTAAGG
* *
21452480 GTTTAAGGTTATAGA-GATATAGTTTAATG
1 GTTTAAGGTT-TAGAGGATATACTTTAAGG
21452509 GTTTAAGGTTTAGAG
1 GTTTAAGGTTTAGAG
21452524 TTTTGATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
28 22 0.58
29 16 0.42
ACGTcount: A:0.29, C:0.01, G:0.29, T:0.40
Consensus pattern (29 bp):
GTTTAAGGTTTAGAGGATATACTTTAAGG
Found at i:21453212 original size:6 final size:6
Alignment explanation
Indices: 21453201--21453236 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
21453191 TGACTTTCTC
*
21453201 CCCTCT CCCTCT CCCTCT TCCTCT CCCTCT CCCTCT
1 CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT
21453237 TTCTGTCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (6 bp):
CCCTCT
Found at i:21453225 original size:18 final size:18
Alignment explanation
Indices: 21453202--21453237 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21453192 GACTTTCTCC
21453202 CCTCTCCCTCTCCCTCTT
1 CCTCTCCCTCTCCCTCTT
21453220 CCTCTCCCTCTCCCTCTT
1 CCTCTCCCTCTCCCTCTT
21453238 TCTGTCTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (18 bp):
CCTCTCCCTCTCCCTCTT
Found at i:21455087 original size:14 final size:13
Alignment explanation
Indices: 21455064--21455093 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
21455054 ATTACTATAA
21455064 TAATTATATGAAG
1 TAATTATATGAAG
21455077 TAATATATATGAAG
1 TAAT-TATATGAAG
21455091 TAA
1 TAA
21455094 AATTATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (13 bp):
TAATTATATGAAG
Found at i:21455472 original size:183 final size:183
Alignment explanation
Indices: 21455164--21455532 Score: 702
Period size: 183 Copynumber: 2.0 Consensus size: 183
21455154 GATATAGTTC
21455164 CATGTGTCTGTACTAGTGAATTAATGTTGTATGTATTTCAGTTACTGCTTCCTACTCCTCCTGCA
1 CATGTGTCTGTACTAGTGAATTAATGTTGTATGTATTTCAGTTACTGCTTCCTACTCCTCCTGCA
*
21455229 ACTATTGTTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
66 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
21455294 GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
131 GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
* *
21455347 CATGTGTCTGTATTAGTGAATTAATGTTGTATGTATTTCAGTTACTGCTTCCTGCTCCTCCTGCA
1 CATGTGTCTGTACTAGTGAATTAATGTTGTATGTATTTCAGTTACTGCTTCCTACTCCTCCTGCA
*
21455412 ACTATTGGTTCAACTGAAGCTGTCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
66 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
21455477 GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
131 GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
21455530 CAT
1 CAT
21455533 CTGTTCTAGG
Statistics
Matches: 182, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
183 182 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (183 bp):
CATGTGTCTGTACTAGTGAATTAATGTTGTATGTATTTCAGTTACTGCTTCCTACTCCTCCTGCA
ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
Found at i:21457060 original size:18 final size:17
Alignment explanation
Indices: 21457024--21457063 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
21457014 GTAAAAAAAT
21457024 ATAATTTTATTGTTTTA
1 ATAATTTTATTGTTTTA
21457041 ATAA-TTTATAT-TTTT-
1 ATAATTTTAT-TGTTTTA
21457056 ATAATTTT
1 ATAATTTT
21457064 TAAAAGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.19
16 12 0.57
17 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
ATAATTTTATTGTTTTA
Found at i:21457288 original size:54 final size:54
Alignment explanation
Indices: 21457218--21457325 Score: 180
Period size: 54 Copynumber: 2.0 Consensus size: 54
21457208 TTTTTTTTTT
* * *
21457218 TTTTTTTTTAAAAAAACGAATAATTGGATTTTTTGATAGATCTTTTTACAAGCC
1 TTTTTTTTGAAAAAAACGAATAATTCGATTCTTTGATAGATCTTTTTACAAGCC
*
21457272 TTTTTTTTGAACAAAACGAATAATTCGATTCTTTGATAGATCTTTTTACAAGCC
1 TTTTTTTTGAAAAAAACGAATAATTCGATTCTTTGATAGATCTTTTTACAAGCC
21457326 ATGAAAACAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.44
Consensus pattern (54 bp):
TTTTTTTTGAAAAAAACGAATAATTCGATTCTTTGATAGATCTTTTTACAAGCC
Found at i:21457724 original size:15 final size:15
Alignment explanation
Indices: 21457704--21457737 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
21457694 ATTGAAGAAC
* *
21457704 TTTGCTTGTATTTGG
1 TTTGCTTCTATTTCG
21457719 TTTGCTTCTATTTCG
1 TTTGCTTCTATTTCG
21457734 TTTG
1 TTTG
21457738 AAACATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.21, T:0.62
Consensus pattern (15 bp):
TTTGCTTCTATTTCG
Found at i:21459311 original size:18 final size:18
Alignment explanation
Indices: 21459283--21459322 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
21459273 TCAGCTTCTA
21459283 ATTTTTATTTCTCAATCAT
1 ATTTTTATTTCTCAATC-T
21459302 ATTTTT-TTTCTCAATCT
1 ATTTTTATTTCTCAATCT
21459319 ATTT
1 ATTT
21459323 GATTGATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.24
18 10 0.48
19 6 0.29
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTTATTTCTCAATCT
Found at i:21462422 original size:40 final size:40
Alignment explanation
Indices: 21462363--21462443 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
21462353 GGTTATTGAC
21462363 TTAGGTCACACAGCCGACCACACGCCCATGTGCCAGCCAG
1 TTAGGTCACACAGCCGACCACACGCCCATGTGCCAGCCAG
*
21462403 TTAGGTCACACAGCTGACCACACGCCCATGTGCCAGCCAG
1 TTAGGTCACACAGCCGACCACACGCCCATGTGCCAGCCAG
21462443 T
1 T
21462444 ATGCCACACA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.38, G:0.22, T:0.15
Consensus pattern (40 bp):
TTAGGTCACACAGCCGACCACACGCCCATGTGCCAGCCAG
Found at i:21462890 original size:19 final size:20
Alignment explanation
Indices: 21462858--21462903 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
21462848 CGAAAAATGA
21462858 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
21462878 TTTCTGG-AAATGATTTACT
1 TTTCTGGAAAATGATTTACT
21462897 TTTCTGG
1 TTTCTGG
21462904 TGTTTGGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:21467249 original size:43 final size:43
Alignment explanation
Indices: 21467200--21467346 Score: 136
Period size: 43 Copynumber: 3.4 Consensus size: 43
21467190 CCAGATATCA
* * * *
21467200 TCTTACATGTTATCACATAACGATGCCACTGTCCCAGACAGGG
1 TCTTACACGTAATCACATAACGATGCCAATGTCCCAGACATGG
* * * *
21467243 TCTTACACGAAATCGA-TTAACGATGTCAATGTCCTAGACATGG
1 TCTTACACGTAATC-ACATAACGATGCCAATGTCCCAGACATGG
* * * *
21467286 TCTTACACATAATCTCA-ATACAATACCAATGTCCCAGACATGG
1 TCTTACACGTAATCACATA-ACGATGCCAATGTCCCAGACATGG
* *
21467329 TTTTACATGTAATCACAT
1 TCTTACACGTAATCACAT
21467347 CTCGATAACC
Statistics
Matches: 80, Mismatches: 20, Indels: 7
0.75 0.19 0.07
Matches are distributed among these distances:
42 1 0.01
43 78 0.98
44 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (43 bp):
TCTTACACGTAATCACATAACGATGCCAATGTCCCAGACATGG
Found at i:21476399 original size:196 final size:195
Alignment explanation
Indices: 21476059--21476429 Score: 643
Period size: 196 Copynumber: 1.9 Consensus size: 195
21476049 ACGTAGCTGG
* *
21476059 CTCCCAAGTTAAACGGTCAGGCTGAGTGCCCTCCTTAACTGTCAACCACCACTGATATGCTTCGT
1 CTCCCAAGTCAAACGGTCAGGCTGAGTGCCCTCATTAACTGTCAACCACCACTGATATGCTTCGT
** * ** *
21476124 CGCGAAGAAAAGAGATTGCACCCTTTAATTTCTGCTCAGTGGTACAGTCCAGATTATCCATAATC
66 CGCGAAGAAAAGAGATTAAACCCTTTAATTTCTACTCAGCAGTACAGTCCAGACTATCCATAATC
* *
21476189 CTCTCGGTGGCCTCCAACTAGTACTCAGCCACATTAGGGGTGACTCTGAAATGTAGTCTTCAAGA
131 CTCTCGGAGGCCTCCAA-TAGTACTCAGCCACATTAGAGGTGACTCTGAAATGTAGTCTTCAAGA
21476254 A
195 A
21476255 CTCCCAAGTCAAACGGTCAGGCTGAGTGCCCTCATTAACTGTCAACCACCACTGATATGCTTCGT
1 CTCCCAAGTCAAACGGTCAGGCTGAGTGCCCTCATTAACTGTCAACCACCACTGATATGCTTCGT
21476320 CGCGAAGAAAAGAGATTAAACCCTTTAATTTCTACTCAGCAGTACAGTCCAGACTATCCATAATC
66 CGCGAAGAAAAGAGATTAAACCCTTTAATTTCTACTCAGCAGTACAGTCCAGACTATCCATAATC
21476385 CTCTCGGAGGCCTCCAATAGTACTCAGCCACATTAGAGGTGACTC
131 CTCTCGGAGGCCTCCAATAGTACTCAGCCACATTAGAGGTGACTC
21476430 ATGTGACACC
Statistics
Matches: 165, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
195 27 0.16
196 138 0.84
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (195 bp):
CTCCCAAGTCAAACGGTCAGGCTGAGTGCCCTCATTAACTGTCAACCACCACTGATATGCTTCGT
CGCGAAGAAAAGAGATTAAACCCTTTAATTTCTACTCAGCAGTACAGTCCAGACTATCCATAATC
CTCTCGGAGGCCTCCAATAGTACTCAGCCACATTAGAGGTGACTCTGAAATGTAGTCTTCAAGAA
Found at i:21476852 original size:24 final size:24
Alignment explanation
Indices: 21476825--21476872 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
21476815 TTCAAGAGCT
*
21476825 GTTTTTAGAACTTTCAGTTTTCTA
1 GTTTTCAGAACTTTCAGTTTTCTA
* *
21476849 GTTTTCAGAAGTTTTAGTTTTCTA
1 GTTTTCAGAACTTTCAGTTTTCTA
21476873 ACTATCTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (24 bp):
GTTTTCAGAACTTTCAGTTTTCTA
Found at i:21479065 original size:10 final size:10
Alignment explanation
Indices: 21479046--21479094 Score: 73
Period size: 10 Copynumber: 4.9 Consensus size: 10
21479036 TTAAATTCTA
21479046 AAAGATAAAT
1 AAAGATAAAT
21479056 ACAA-ATAAAT
1 A-AAGATAAAT
21479066 AAAGATAAAT
1 AAAGATAAAT
*
21479076 AAGGATAAAT
1 AAAGATAAAT
21479086 AAAGATAAA
1 AAAGATAAA
21479095 AGCTAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.69, C:0.02, G:0.10, T:0.18
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:21483687 original size:30 final size:30
Alignment explanation
Indices: 21483631--21483698 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
21483621 CACCCTTAAA
* * *
21483631 ATATTTGCACTATTAGTCCTTCAATTTTTC
1 ATATTTACACTATTAATCCCTCAATTTTTC
* *
21483661 ATATTTACACT-TTAATCCCTCAAATTTTG
1 ATATTTACACTATTAATCCCTCAATTTTTC
21483690 AGTATTTAC
1 A-TATTTAC
21483699 TATTGGGCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (30 bp):
ATATTTACACTATTAATCCCTCAATTTTTC
Found at i:21484841 original size:18 final size:19
Alignment explanation
Indices: 21484803--21484841 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
21484793 TGTTTCAAGC
*
21484803 TTTCAATCTCATATCTCAA
1 TTTCAATCTCACATCTCAA
*
21484822 TTTCAAT-TCACATTTCAA
1 TTTCAATCTCACATCTCAA
21484840 TT
1 TT
21484842 CTTAATTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCACATCTCAA
Found at i:21485175 original size:24 final size:23
Alignment explanation
Indices: 21485142--21485186 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
21485132 ACACGGATCC
*
21485142 CAACCCAAACACACCAGTAATATA
1 CAACCAAAACACACCAG-AATATA
21485166 CAACCAAAACACACCAGAATA
1 CAACCAAAACACACCAGAATA
21485187 ATCATGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.53, C:0.33, G:0.04, T:0.09
Consensus pattern (23 bp):
CAACCAAAACACACCAGAATATA
Found at i:21486708 original size:53 final size:52
Alignment explanation
Indices: 21486627--21486786 Score: 196
Period size: 52 Copynumber: 3.1 Consensus size: 52
21486617 CGGATCACAT
** * *
21486627 ATCATACCGATGCCATATACTAGATATGGTCTTATACAGAATCACATTATCAC
1 ATCATACCGATGCCATAGCCTAGCTATGGTCTTATACGGAATCACA-TATCAC
* * *
21486680 ATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAA-CACAAATCAC
1 ATCATACCGATGCCATAGCCTAGCTATGGTCTTATAC-GGAATCACATATCAC
** * *
21486732 ATGGTACCGATGCCATAGCCTGGCTATGGTCTTATACGGAATCATATATCAC
1 ATCATACCGATGCCATAGCCTAGCTATGGTCTTATACGGAATCACATATCAC
21486784 ATC
1 ATC
21486787 TTTTCCATCA
Statistics
Matches: 90, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
51 4 0.04
52 47 0.52
53 36 0.40
54 3 0.03
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (52 bp):
ATCATACCGATGCCATAGCCTAGCTATGGTCTTATACGGAATCACATATCAC
Found at i:21486709 original size:99 final size:101
Alignment explanation
Indices: 21486593--21486786 Score: 232
Period size: 105 Copynumber: 1.9 Consensus size: 101
21486583 CACACAGAAA
* * * *
21486593 CCATAGCCCTGCCATGGTCTTACAC-GGATCACATAT-CA-TACCGATGCCATATACTAGATATG
1 CCATAGCCCAGCCATGGTCTTACACGGGAACACAAATACAGTACCGATGCCATAGACTAGATATG
21486655 GTCTTATACAGAATCACATTATCACATCACACCGATG
66 GTCTTATACAGAATCACA-TATCACATCACACCGATG
* * * * *
21486692 CCATAGCCCAGCTATGGTCTTATACGGGAACACAAATCACATGGTACCGATGCCATAGCCTGGCT
1 CCATAGCCCAGCCATGGTCTTACACGGGAACACAAAT-ACA--GTACCGATGCCATAGACTAGAT
* *
21486757 ATGGTCTTATACGGAATCATATATCACATC
63 ATGGTCTTATACAGAATCACATATCACATC
21486787 TTTTCCATCA
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
99 22 0.28
100 9 0.12
102 2 0.03
104 9 0.12
105 36 0.46
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (101 bp):
CCATAGCCCAGCCATGGTCTTACACGGGAACACAAATACAGTACCGATGCCATAGACTAGATATG
GTCTTATACAGAATCACATATCACATCACACCGATG
Found at i:21491944 original size:44 final size:44
Alignment explanation
Indices: 21491895--21491982 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
21491885 TGATCTTTTC
21491895 GGTGCTGAAGTGGCTCAACTAAATTCCTCTTTAAATTTCTTCAT
1 GGTGCTGAAGTGGCTCAACTAAATTCCTCTTTAAATTTCTTCAT
* **
21491939 GGTGCTGAAGTGGCTCGACTAAATTCCTCTTTAGTTTTCTTCAT
1 GGTGCTGAAGTGGCTCAACTAAATTCCTCTTTAAATTTCTTCAT
21491983 TGGTAAAGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (44 bp):
GGTGCTGAAGTGGCTCAACTAAATTCCTCTTTAAATTTCTTCAT
Found at i:21493262 original size:20 final size:20
Alignment explanation
Indices: 21493230--21493281 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
21493220 AGGGGCACAC
*
21493230 GCCCGTATGGCCTGGAACAT
1 GCCCGTGTGGCCTGGAACAT
*
21493250 GCCTGTGTGGCCTGGAACAT
1 GCCCGTGTGGCCTGGAACAT
21493270 GCCCGTGTGGCC
1 GCCCGTGTGGCC
21493282 AGCCTATGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.13, C:0.31, G:0.35, T:0.21
Consensus pattern (20 bp):
GCCCGTGTGGCCTGGAACAT
Found at i:21494164 original size:52 final size:50
Alignment explanation
Indices: 21494007--21494166 Score: 165
Period size: 52 Copynumber: 3.3 Consensus size: 50
21493997 TTTCACATTG
* * * * *
21494007 TCACACATCACA-CACCGAAGCCATAGCCCTGCTATGGTCTTACACGG-A
1 TCACATATCACATTACCGATGCCATAGCCCAGCTATGGTCTTACGCGGAA
21494055 TCACATAT--CA-TACCGATGCCATAGCCCAGCTATGGTCTTATACG-GGAA
1 TCACATATCACATTACCGATGCCATAGCCCAGCTATGGTC-T-TACGCGGAA
21494103 -CACGA-ATCACATGGTACCGATGCCATAGCCCAGCTATGGTCTTACGCGGAA
1 TCAC-ATATCACAT--TACCGATGCCATAGCCCAGCTATGGTCTTACGCGGAA
*
21494154 TCATATATCACAT
1 TCACATATCACAT
21494167 CTTTTCCATC
Statistics
Matches: 94, Mismatches: 6, Indels: 20
0.78 0.05 0.17
Matches are distributed among these distances:
46 26 0.28
47 8 0.09
48 12 0.13
49 2 0.02
50 4 0.04
51 6 0.06
52 36 0.38
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (50 bp):
TCACATATCACATTACCGATGCCATAGCCCAGCTATGGTCTTACGCGGAA
Found at i:21495905 original size:46 final size:46
Alignment explanation
Indices: 21495603--21495898 Score: 439
Period size: 46 Copynumber: 6.4 Consensus size: 46
21495593 TGCCATAGCG
* * ** *
21495603 TCTTTCTACTATGGTCTTATTCATTTCCCCGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTT-CATGTCACGTTGCCATGGTA
* *
21495650 TCTTTAAACCATGGTCTTATTCATTTCATGTCACATTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
21495696 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
* *
21495742 TCTTTCAACCATGGTCTTATTCCTTTCATGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
* * *
21495788 TATTTAAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGATA
1 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
* * *
21495834 TCTTTCAACCATGGTCTTATACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
*
21495880 TCTTTCAATCATGGTCTTA
1 TCTTTCAACCATGGTCTTA
21495899 CACATTTGAA
Statistics
Matches: 226, Mismatches: 23, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
46 203 0.90
47 23 0.10
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.43
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
Found at i:21495944 original size:45 final size:45
Alignment explanation
Indices: 21495895--21495995 Score: 139
Period size: 45 Copynumber: 2.2 Consensus size: 45
21495885 CAATCATGGT
*
21495895 CTTACACATTTGAATCGCGATGCCATAGCGTCTTTCAGCTATAGC
1 CTTACTCATTTGAATCGCGATGCCATAGCGTCTTTCAGCTATAGC
* * * * * *
21495940 CTTACTCGTCTGAATCGTGATGCCATAGCTTCTTTCAGCTATGGT
1 CTTACTCATTTGAATCGCGATGCCATAGCGTCTTTCAGCTATAGC
21495985 CTTACTCATTT
1 CTTACTCATTT
21495996 CTGGTATGAT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.37
Consensus pattern (45 bp):
CTTACTCATTTGAATCGCGATGCCATAGCGTCTTTCAGCTATAGC
Found at i:21500036 original size:32 final size:34
Alignment explanation
Indices: 21500000--21500062 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
21499990 TAACAGTGGT
*
21500000 ACTGGGCCAGAG-CCCTT-TTCAGATTACAATAA
1 ACTGGGCCAGAGCCCCTTATTCAGATAACAATAA
**
21500032 ACTGGGCCTTAGCCCCTTATTCAGATAACAA
1 ACTGGGCCAGAGCCCCTTATTCAGATAACAA
21500063 CATGGCCCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 10 0.38
33 5 0.19
34 11 0.42
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25
Consensus pattern (34 bp):
ACTGGGCCAGAGCCCCTTATTCAGATAACAATAA
Found at i:21500086 original size:137 final size:137
Alignment explanation
Indices: 21499840--21500126 Score: 529
Period size: 137 Copynumber: 2.1 Consensus size: 137
21499830 GATTGGGCCT
**
21499840 AAGCCCATTCAGGTAACAGTGGTACTAGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTAGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
**
21499905 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAACATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
21499970 CATATGC
131 CATATGC
*
21499977 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTAGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
21500042 AGCCCCTTATTCAGATAACAACATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAACATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
21500107 CATATGC
131 CATATGC
21500114 AAGCCCATTTGGG
1 AAGCCCATTTGGG
21500127 GAGACTACTC
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 145 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTAGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAACATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:21501942 original size:26 final size:26
Alignment explanation
Indices: 21501906--21502015 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
21501896 CATGAAATTC
21501906 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
21501932 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
21501958 TTATCATGGAAA-ATTTACCTAACCTA
1 TTATCAT-GAAACATTTACCTAACCCA
* *
21501984 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
21502010 TTATCA
1 TTATCA
21502016 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
25 3 0.04
26 73 0.91
27 4 0.05
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:21502026 original size:10 final size:10
Alignment explanation
Indices: 21502011--21502058 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
21502001 CCTAACCTAT
21502011 TATCAATTTG
1 TATCAATTTG
21502021 TATCAATTTG
1 TATCAATTTG
*
21502031 TA-CCA--T-
1 TATCAATTTG
21502037 TATCAATTTG
1 TATCAATTTG
21502047 TATCAATTTG
1 TATCAATTTG
21502057 TA
1 TA
21502059 CCATAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
6 2 0.06
7 3 0.09
9 3 0.09
10 24 0.75
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.48
Consensus pattern (10 bp):
TATCAATTTG
Found at i:21502038 original size:26 final size:26
Alignment explanation
Indices: 21502009--21502062 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
21501999 TACCTAACCT
21502009 ATTATCAATTTGTATCAATTTGTACC
1 ATTATCAATTTGTATCAATTTGTACC
21502035 ATTATCAATTTGTATCAATTTGTACC
1 ATTATCAATTTGTATCAATTTGTACC
21502061 AT
1 AT
21502063 AAATTATGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.46
Consensus pattern (26 bp):
ATTATCAATTTGTATCAATTTGTACC
Found at i:21509808 original size:26 final size:26
Alignment explanation
Indices: 21509770--21509830 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
21509760 ATTTGATGAG
* *
21509770 AATAGTTTATTAAA-TACAAATAAAAC
1 AATATTTTATTAAAGTA-AAACAAAAC
* *
21509796 AATATTTTTTTAAAGTAAAACAAAAT
1 AATATTTTATTAAAGTAAAACAAAAC
21509822 AATATTTTA
1 AATATTTTA
21509831 AAATTTATTG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 27 0.93
27 2 0.07
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (26 bp):
AATATTTTATTAAAGTAAAACAAAAC
Found at i:21518871 original size:6 final size:6
Alignment explanation
Indices: 21518860--21518887 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
21518850 GAAGGATGAG
21518860 ATGGAA ATGGAA ATGGAA ATGGAA ATGG
1 ATGGAA ATGGAA ATGGAA ATGGAA ATGG
21518888 GGGGACAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.36, T:0.18
Consensus pattern (6 bp):
ATGGAA
Found at i:21519610 original size:20 final size:20
Alignment explanation
Indices: 21519563--21519611 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
21519553 TTTAAAATTA
21519563 TATTTAAAAATTATTATTTT
1 TATTTAAAAATTATTATTTT
*
21519583 TGAATTAAAAA-TATTAATTTT
1 T-ATTTAAAAATTATT-ATTTT
21519604 TATTTAAA
1 TATTTAAA
21519612 TTTAAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TATTTAAAAATTATTATTTT
Found at i:21522424 original size:25 final size:26
Alignment explanation
Indices: 21522373--21522424 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
21522363 GGGGTGAAAG
* *
21522373 AAAATAATTTTAAATATTTTATATTA
1 AAAATAATTTTAAAAAGTTTATATTA
*
21522399 AAAATATTTTTAAAAAGTTTAT-TTA
1 AAAATAATTTTAAAAAGTTTATATTA
21522424 A
1 A
21522425 CAATGAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
AAAATAATTTTAAAAAGTTTATATTA
Found at i:21522563 original size:13 final size:13
Alignment explanation
Indices: 21522545--21522569 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21522535 TATGAAAAAA
21522545 ATAAAAATATTAC
1 ATAAAAATATTAC
21522558 ATAAAAATATTA
1 ATAAAAATATTA
21522570 ATTATAATTT
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:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAAAAATATTAC
Found at i:21529612 original size:20 final size:20
Alignment explanation
Indices: 21529587--21529633 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
21529577 GTTTTGATAT
21529587 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
*
21529607 ACATGATATGTATGATATTC
1 ACATGATATGTATGATATGC
21529627 ACATGAT
1 ACATGAT
21529634 GTATTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:21529741 original size:25 final size:24
Alignment explanation
Indices: 21529680--21529786 Score: 144
Period size: 25 Copynumber: 4.4 Consensus size: 24
21529670 GAGAAAGTGC
* * **
21529680 AAAAAGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTA-TT
21529705 AAAAGGGCTTTGCCCCAGTTTATT
1 AAAAGGGCTTTGCCCCAGTTTATT
21529729 AAAAGGGCTTTTGCCCCAGTTTATT
1 AAAAGGGC-TTTGCCCCAGTTTATT
21529754 AAAAGGGCTTTGCCCCAG-TTATT
1 AAAAGGGCTTTGCCCCAGTTTATT
21529777 AAAAGAGGCT
1 AAAAG-GGCT
21529787 AGGCCTCCAA
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
23 10 0.13
24 22 0.29
25 44 0.58
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATT
Found at i:21529765 original size:49 final size:50
Alignment explanation
Indices: 21529690--21529786 Score: 153
Period size: 49 Copynumber: 2.0 Consensus size: 50
21529680 AAAAAGGCTA
21529690 TGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATTAAAAG-GGCTTT
1 TGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAG-TTATTAAAAGAGGCTTT
**
21529740 TGCCCCAGTTTA-TTAAAAGGGCTTTGCCCCAGTTATTAAAAGAGGCT
1 TGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTATTAAAAGAGGCT
21529787 AGGCCTCCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
48 10 0.23
49 22 0.50
50 12 0.27
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (50 bp):
TGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTATTAAAAGAGGCTTT
Found at i:21537877 original size:24 final size:24
Alignment explanation
Indices: 21537786--21537893 Score: 128
Period size: 25 Copynumber: 4.4 Consensus size: 24
21537776 AGAAAGTGCA
* * *
21537786 AAAATGGCTATGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTATC
*
21537810 GAAAAGGGCTTTTGCCCCAGTTTATT
1 -AAAAGGGC-TTTGCCCCAGTTTATC
21537836 AAAAGGGCTTTTGCCCCAGTTTATC
1 AAAAGGGC-TTTGCCCCAGTTTATC
*
21537861 AAAAGGGCTTTGCCCCAG-TTATT
1 AAAAGGGCTTTGCCCCAGTTTATC
21537884 AAAAGAGGCT
1 AAAAG-GGCT
21537894 AGGCCTCCAG
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
23 9 0.12
24 14 0.19
25 39 0.52
26 13 0.17
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATC
Found at i:21537904 original size:49 final size:50
Alignment explanation
Indices: 21537786--21537905 Score: 156
Period size: 49 Copynumber: 2.4 Consensus size: 50
21537776 AGAAAGTGCA
*
21537786 AAAATGGCTATGCCCCAGTTTACCGAAAAGGGCTTTTGCCCCAGTTTATT
1 AAAAGGGCTATGCCCCAGTTTACCGAAAAGGGCTTTTGCCCCAGTTTATT
* *
21537836 AAAAGGGCTTTTGCCCCAGTTTATC-AAAAGGGC-TTTGCCCCAG-TTATT
1 AAAAGGGC-TATGCCCCAGTTTACCGAAAAGGGCTTTTGCCCCAGTTTATT
*
21537884 AAAAGAGGCTAGGCCTCCAGTT
1 AAAAG-GGCTATGCC-CCAGTT
21537906 ATATGATAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
48 14 0.23
49 19 0.31
50 15 0.24
51 14 0.23
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (50 bp):
AAAAGGGCTATGCCCCAGTTTACCGAAAAGGGCTTTTGCCCCAGTTTATT
Found at i:21538140 original size:31 final size:31
Alignment explanation
Indices: 21538102--21538165 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
21538092 CATTTACAGT
21538102 AAAGGCTTCGACCCAGTAATATGAAATATGA
1 AAAGGCTTCGACCCAGTAATATGAAATATGA
* * **
21538133 AAAGGCTTCGGCCTAGTGTTATGAAATATGA
1 AAAGGCTTCGACCCAGTAATATGAAATATGA
21538164 AA
1 AA
21538166 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGACCCAGTAATATGAAATATGA
Found at i:21545107 original size:13 final size:13
Alignment explanation
Indices: 21545089--21545117 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
21545079 CATTGAGATG
21545089 AACTATAAATATT
1 AACTATAAATATT
21545102 AACTATAAATATT
1 AACTATAAATATT
21545115 AAC
1 AAC
21545118 GGTTAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (13 bp):
AACTATAAATATT
Found at i:21552288 original size:13 final size:14
Alignment explanation
Indices: 21552262--21552292 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
21552252 TTAAAAATAA
21552262 ATTTTAAATATTTT
1 ATTTTAAATATTTT
21552276 ATTTTAAAT-TTTT
1 ATTTTAAATATTTT
21552289 ATTT
1 ATTT
21552293 GTCACATATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTAAATATTTT
Found at i:21557135 original size:18 final size:18
Alignment explanation
Indices: 21557112--21557147 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
21557102 AAAAGTTGAT
*
21557112 AAGTTTTCTTTTTGTTAG
1 AAGTTTCCTTTTTGTTAG
21557130 AAGTTTCCTTTTTGTTAG
1 AAGTTTCCTTTTTGTTAG
21557148 TTCTTAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.17, T:0.58
Consensus pattern (18 bp):
AAGTTTCCTTTTTGTTAG
Found at i:21559458 original size:16 final size:16
Alignment explanation
Indices: 21559437--21559467 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21559427 TTAGGTTAGG
21559437 TTTTCTTTTCATTTTC
1 TTTTCTTTTCATTTTC
21559453 TTTTCTTTTCATTTT
1 TTTTCTTTTCATTTT
21559468 TAGATTAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCTTTTCATTTTC
Found at i:21559501 original size:25 final size:26
Alignment explanation
Indices: 21559456--21559511 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
21559446 CATTTTCTTT
*
21559456 TCTTTTCATTTTTAGATTAGATTTTC
1 TCTTTTCATTTTTAGAGTAGATTTTC
*
21559482 TCTTTTC-TTTTTATAGTAGATTTTC
1 TCTTTTCATTTTTAGAGTAGATTTTC
21559507 T-TTTT
1 TCTTTT
21559512 GTTGTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 4 0.14
25 17 0.61
26 7 0.25
ACGTcount: A:0.16, C:0.11, G:0.07, T:0.66
Consensus pattern (26 bp):
TCTTTTCATTTTTAGAGTAGATTTTC
Found at i:21560584 original size:46 final size:46
Alignment explanation
Indices: 21560531--21560741 Score: 298
Period size: 46 Copynumber: 4.6 Consensus size: 46
21560521 TGCCGTAGTG
* * *
21560531 TCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACA-TTTCGTATCATGTTGCCATGGTA
* ** * * * *
21560577 TCTTTCAACCATAGTCTTATTCATTTCATGTCACGTTGCCATGGTG
1 TCTTTCAACCATGGTCTTACACATTTCGTATCATGTTGCCATGGTA
21560623 TCTTTCAACCATGGTCTTACACATTTCGTATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCGTATCATGTTGCCATGGTA
*
21560669 TCTTTCAACCATGGTCTTACACATTTCGTATCATGTTGTCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCGTATCATGTTGCCATGGTA
*
21560715 TATTTCAACCATGGTCTTACACATTTC
1 TCTTTCAACCATGGTCTTACACATTTC
21560742 ATTTCAGAAA
Statistics
Matches: 150, Mismatches: 14, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
45 4 0.03
46 146 0.97
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACACATTTCGTATCATGTTGCCATGGTA
Found at i:21561509 original size:22 final size:20
Alignment explanation
Indices: 21561479--21561526 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
21561469 CGAAATTTTA
*
21561479 ATTAGTATTATGAGATAAAATT
1 ATTATTATTATGAGA-AAAA-T
*
21561501 ATTATTATTATTAGAAAAAT
1 ATTATTATTATGAGAAAAAT
21561521 ATTATT
1 ATTATT
21561527 GCATGTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.29
21 4 0.17
22 13 0.54
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (20 bp):
ATTATTATTATGAGAAAAAT
Found at i:21561625 original size:3 final size:3
Alignment explanation
Indices: 21561617--21561647 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
21561607 TATTTATAAA
*
21561617 ATT ATT ATT ATT ATA ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
21561648 GATAGGGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:21561634 original size:15 final size:15
Alignment explanation
Indices: 21561616--21561645 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21561606 ATATTTATAA
21561616 AATTATTATTATTAT
1 AATTATTATTATTAT
21561631 AATTATTATTATTAT
1 AATTATTATTATTAT
21561646 TAGATAGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTATTATTATTAT
Found at i:21564093 original size:28 final size:27
Alignment explanation
Indices: 21564060--21564112 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
21564050 ATACTGTAAG
* *
21564060 GGGCTATGGCCCAGATTAATATTGATAT
1 GGGCTAAGGCCCAG-TTAACATTGATAT
21564088 GGGCTAAGGCCCAGTTAACATTGAT
1 GGGCTAAGGCCCAGTTAACATTGAT
21564113 TTCTGAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (27 bp):
GGGCTAAGGCCCAGTTAACATTGATAT
Found at i:21566010 original size:8 final size:8
Alignment explanation
Indices: 21565987--21566016 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
21565977 TATATATATT
21565987 AAATAATA
1 AAATAATA
21565995 ATAATAATA
1 A-AATAATA
21566004 AAATAATA
1 AAATAATA
21566012 AAATA
1 AAATA
21566017 TCATATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
AAATAATA
Found at i:21578662 original size:21 final size:21
Alignment explanation
Indices: 21578638--21578711 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
21578628 ACTCATATGA
21578638 GTTTCAGTTTAACCCTTTTGG
1 GTTTCAGTTTAACCCTTTTGG
* * * *
21578659 GTTTCAATTTAGCTCTTTTGA
1 GTTTCAGTTTAACCCTTTTGG
*
21578680 GATTCAGTTTAA-CCTTTATGG
1 GTTTCAGTTTAACCCTTT-TGG
21578701 GTTTCAGTTTA
1 GTTTCAGTTTA
21578712 GCTCTTCTAA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 4 0.10
21 38 0.90
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.49
Consensus pattern (21 bp):
GTTTCAGTTTAACCCTTTTGG
Found at i:21578687 original size:42 final size:42
Alignment explanation
Indices: 21578633--21578814 Score: 179
Period size: 42 Copynumber: 4.3 Consensus size: 42
21578623 GGTTAACTCA
*
21578633 TATGAGTTTCAGTTTAACCCTTT-TGGGTTTCAATTTAGCTCT
1 TATGAGATTCAGTTTAA-CCTTTATGGGTTTCAATTTAGCTCT
* *
21578675 TTTGAGATTCAGTTTAACCTTTATGGGTTTCAGTTTAGCTCT
1 TATGAGATTCAGTTTAACCTTTATGGGTTTCAATTTAGCTCT
* * * * * * * *
21578717 TCTAAGCTTCAGTTCAACCCTTATGAGTTTCTATTCAGCTCT
1 TATGAGATTCAGTTTAACCTTTATGGGTTTCAATTTAGCTCT
* * ** *
21578759 TATGAGCTTTCA-TTTAACCTTTACGGGTTTCCGTTTAGCACT
1 TATGAG-ATTCAGTTTAACCTTTATGGGTTTCAATTTAGCTCT
*
21578801 TATGTGATTCAGTT
1 TATGAGATTCAGTT
21578815 AGCCTTTTGG
Statistics
Matches: 112, Mismatches: 25, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
41 9 0.08
42 99 0.88
43 4 0.04
ACGTcount: A:0.20, C:0.19, G:0.16, T:0.45
Consensus pattern (42 bp):
TATGAGATTCAGTTTAACCTTTATGGGTTTCAATTTAGCTCT
Found at i:21578781 original size:84 final size:84
Alignment explanation
Indices: 21578640--21578797 Score: 219
Period size: 84 Copynumber: 1.9 Consensus size: 84
21578630 TCATATGAGT
* * * * * *
21578640 TTCAGTTTAACCCTTTTGGGTTTCAATTTAGCTCTTTTGAGATTCAGTTTAACCTTTATGGGTTT
1 TTCAGTTCAACCCTTATGAGTTTCAATTCAGCTCTTATGAGATTCAGTTTAACCTTTACGGGTTT
21578705 CAGTTTAGCTCTTCTAAGC
66 CAGTTTAGCTCTTCTAAGC
* *
21578724 TTCAGTTCAACCCTTATGAGTTTCTATTCAGCTCTTATGAGCTTTCA-TTTAACCTTTACGGGTT
1 TTCAGTTCAACCCTTATGAGTTTCAATTCAGCTCTTATGAG-ATTCAGTTTAACCTTTACGGGTT
*
21578788 TCCGTTTAGC
65 TCAGTTTAGC
21578798 ACTTATGTGA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
84 60 0.94
85 4 0.06
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.45
Consensus pattern (84 bp):
TTCAGTTCAACCCTTATGAGTTTCAATTCAGCTCTTATGAGATTCAGTTTAACCTTTACGGGTTT
CAGTTTAGCTCTTCTAAGC
Found at i:21580247 original size:29 final size:30
Alignment explanation
Indices: 21580189--21580253 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
21580179 GACGAAAAAC
*
21580189 CTAATTAGAATGATGTTAATAGTTTAAAGA
1 CTAATTACAATGATGTTAATAGTTTAAAGA
* *
21580219 CTTAATTACAAT-ATTTTAA-AGTTTGAAGA
1 C-TAATTACAATGATGTTAATAGTTTAAAGA
21580248 CTAATT
1 CTAATT
21580254 TAGAGTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 5 0.16
29 10 0.32
30 7 0.23
31 9 0.29
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (30 bp):
CTAATTACAATGATGTTAATAGTTTAAAGA
Found at i:21586196 original size:32 final size:33
Alignment explanation
Indices: 21586135--21586197 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
21586125 CAAACAAATC
* *
21586135 TTTTTTATTATATAAAAGTATATCAAATAACTT
1 TTTTTTATTAAATAAAAGTAGATCAAATAACTT
21586168 TTTTTTATTAAATAAAAG-AGA-CATAATAAC
1 TTTTTTATTAAATAAAAGTAGATCA-AATAAC
21586198 AAATTGGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 2 0.07
32 8 0.30
33 17 0.63
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (33 bp):
TTTTTTATTAAATAAAAGTAGATCAAATAACTT
Found at i:21588049 original size:58 final size:58
Alignment explanation
Indices: 21587959--21588076 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
21587949 AATAAAGGTT
*
21587959 AGTTTTTTTTTTTTTTTTTTTCTTTTTTTGTTTGAGGTGCTCGTAGAGGTATTTGTTA
1 AGTTTTTTTTTTTTTTTTGTTCTTTTTTTGTTTGAGGTGCTCGTAGAGGTATTTGTTA
21588017 AGTTTTTTTTTTTTTTTTGTTCTTTTTTTGTTTGAGGTGCTCGTAGAGGTATTTGTTA
1 AGTTTTTTTTTTTTTTTTGTTCTTTTTTTGTTTGAGGTGCTCGTAGAGGTATTTGTTA
21588075 AG
1 AG
21588077 GTTCTCTTGT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.11, C:0.05, G:0.20, T:0.64
Consensus pattern (58 bp):
AGTTTTTTTTTTTTTTTTGTTCTTTTTTTGTTTGAGGTGCTCGTAGAGGTATTTGTTA
Found at i:21589376 original size:17 final size:17
Alignment explanation
Indices: 21589354--21589386 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
21589344 TTTCTCTTTT
21589354 TACTTTGCATCTTGTTC
1 TACTTTGCATCTTGTTC
21589371 TACTTTGCATCTTGTT
1 TACTTTGCATCTTGTT
21589387 TGTTCTGTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.21, G:0.12, T:0.55
Consensus pattern (17 bp):
TACTTTGCATCTTGTTC
Found at i:21591817 original size:21 final size:21
Alignment explanation
Indices: 21591792--21591860 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
21591782 TATAGTGATT
21591792 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
21591813 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
21591833 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
21591853 ATTATTAT
1 ATTATTAT
21591861 TATTACCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:21592902 original size:31 final size:31
Alignment explanation
Indices: 21592849--21592916 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
21592839 GTATGAACTA
* *
21592849 AATTATGAATTGAGTTAGTATG-AGAAAAAT
1 AATTATGAATTAAGATAGTATGAAGAAAAAT
*
21592879 GAATTATGAATTTAAGATA-TATGAAGTAAAAT
1 -AATTATGAA-TTAAGATAGTATGAAGAAAAAT
21592911 AATTAT
1 AATTAT
21592917 ATATAAAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 19 0.59
32 13 0.41
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (31 bp):
AATTATGAATTAAGATAGTATGAAGAAAAAT
Found at i:21596219 original size:23 final size:23
Alignment explanation
Indices: 21596137--21596223 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
21596127 CCTGATCAGT
*
21596137 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* * *
21596159 A-ACGACACACGAGGTGCTTG--
1 ATACGACACACAAAGTGCCTGAA
* *
21596179 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
21596202 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
21596224 TCGATAAAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
20 1 0.02
21 32 0.60
22 1 0.02
23 19 0.36
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:21596622 original size:15 final size:15
Alignment explanation
Indices: 21596596--21596652 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
21596586 CATATATATT
21596596 ATATAA-TTCAATCA
1 ATATAATTTCAATCA
21596610 ATATAATTTCAATCA
1 ATATAATTTCAATCA
*
21596625 AAATAATTTCAATCA
1 ATATAATTTCAATCA
*
21596640 ATATAAATTCAAT
1 ATATAATTTCAAT
21596653 AAATTCATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 6 0.15
15 33 0.85
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATAATTTCAATCA
Done.