Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397291.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_182.0, 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: 632866
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.29
Warning! 95618 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:351560 original size:22 final size:22
Alignment explanation
Indices: 351505--351562 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
351495 CATTACGTTT
351505 TTGATTTTTAGGCATTGCGTGA
1 TTGATTTTTAGGCATTGCGTGA
* * * *
351527 CT-AGGTTATAGGCATTGTGTGA
1 TTGA-TTTTTAGGCATTGCGTGA
351549 TTGATTTTTAGGCA
1 TTGATTTTTAGGCA
351563 ATGCATAGGT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.21, C:0.09, G:0.28, T:0.43
Consensus pattern (22 bp):
TTGATTTTTAGGCATTGCGTGA
Found at i:351683 original size:22 final size:22
Alignment explanation
Indices: 351624--351696 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
351614 AATGCCTATC
*
351624 AACTAGGCACACAATACCTTAA
1 AACTAGTCACACAATACCTTAA
* ** *
351646 AATTAGTCACGTAATA-TTTGAA
1 AACTAGTCACACAATACCTT-AA
**
351668 AACTAGTCACACAATACCCAAA
1 AACTAGTCACACAATACCTTAA
351690 AACTAGT
1 AACTAGT
351697 TATGTAAAAC
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
21 2 0.05
22 36 0.95
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.23
Consensus pattern (22 bp):
AACTAGTCACACAATACCTTAA
Found at i:351714 original size:44 final size:44
Alignment explanation
Indices: 351624--351716 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 44
351614 AATGCCTATC
** * * * *
351624 AACTAGGCACACAATACCTTAAAATTAGTCACGTAATATTTGAA
1 AACTAGGCACACAATACCCAAAAACTAGTCACGTAAAACTTAAA
* * *
351668 AACTAGTCACACAATACCCAAAAACTAGTTATGTAAAACTTAAA
1 AACTAGGCACACAATACCCAAAAACTAGTCACGTAAAACTTAAA
351712 AACTA
1 AACTA
351717 CCAAAACTAC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (44 bp):
AACTAGGCACACAATACCCAAAAACTAGTCACGTAAAACTTAAA
Found at i:352786 original size:22 final size:22
Alignment explanation
Indices: 352734--352787 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
352724 TGCATTTTTG
352734 GTTTTTAGGCATTGCGTGACTA
1 GTTTTTAGGCATTGCGTGACTA
* * *
352756 GGTTGTAGGCATTGCGTGA-TT
1 GTTTTTAGGCATTGCGTGACTA
352777 GATTTTTAGGC
1 G-TTTTTAGGC
352788 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.17, C:0.11, G:0.31, T:0.41
Consensus pattern (22 bp):
GTTTTTAGGCATTGCGTGACTA
Found at i:370028 original size:23 final size:22
Alignment explanation
Indices: 369904--370028 Score: 92
Period size: 23 Copynumber: 5.5 Consensus size: 22
369894 TTCCCATGCA
* **
369904 ACACGCCACGGTGAGAATATGCA
1 ACACGCCATGG-GAGAATATGTG
*
369927 ACACGCCATGGAAGGAATATGTG
1 ACACGCCATGGGA-GAATATGTG
*
369950 ACATGCCAT-GGAGGAAATATGTG
1 ACACGCCATGGGA-G-AATATGTG
* *
369973 ACACGACACTAAGG-GAATATGTG
1 ACACGCCA-T-GGGAGAATATGTG
*
369996 ACATGCCATGGTGAGAATATGTG
1 ACACGCCATGG-GAGAATATGTG
*
370019 ACACGACATG
1 ACACGCCATG
370029 TTNNNNNNNN
Statistics
Matches: 82, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
21 1 0.01
22 7 0.09
23 70 0.85
24 2 0.02
26 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.18
Consensus pattern (22 bp):
ACACGCCATGGGAGAATATGTG
Found at i:370242 original size:23 final size:23
Alignment explanation
Indices: 370210--370362 Score: 114
Period size: 23 Copynumber: 6.7 Consensus size: 23
370200 NNNNCGACAT
*
370210 GGTGAGAATATGTGACATGCCAA
1 GGTGAGAATATGTGACATGCCAC
* *
370233 GTTGAGAATATGTGACACGCCAC
1 GGTGAGAATATGTGACATGCCAC
* * *
370256 GATGAGAATGTGTG--ATGCCAT
1 GGTGAGAATATGTGACATGCCAC
* * * *
370277 GGAGGGAATATATGACACGCCAC
1 GGTGAGAATATGTGACATGCCAC
* **
370300 GGTGAGAATATGTGAGATATCA-
1 GGTGAGAATATGTGACATGCCAC
* *
370322 GGTTGAGTATATGTGACATGCCAT
1 GG-TGAGAATATGTGACATGCCAC
* * *
370346 GGAGGGAATTTGTGACA
1 GGTGAGAATATGTGACA
370363 CGACATGNNN
Statistics
Matches: 97, Mismatches: 29, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
21 14 0.14
22 2 0.02
23 79 0.81
24 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.24
Consensus pattern (23 bp):
GGTGAGAATATGTGACATGCCAC
Found at i:370333 original size:44 final size:44
Alignment explanation
Indices: 370210--370334 Score: 101
Period size: 44 Copynumber: 2.8 Consensus size: 44
370200 NNNNCGACAT
* ** * *
370210 GGTGAGAATATGTGACATGCCAAGTTGAGAATATGTGACACGCCAC
1 GGTGAGAATATGTGAGATATCAGGTTGAG--TATATGACACGCCAC
* * ** * *
370256 GATGAGAATGTGTGATGCCATGGAGG--GAATATATGACACGCCAC
1 GGTGAGAATATGTGA-GATAT-CAGGTTGAGTATATGACACGCCAC
370300 GGTGAGAATATGTGAGATATCAGGTTGAGTATATG
1 GGTGAGAATATGTGAGATATCAGGTTGAGTATATG
370335 TGACATGCCA
Statistics
Matches: 58, Mismatches: 17, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
42 3 0.05
43 3 0.05
44 35 0.60
46 15 0.26
48 2 0.03
ACGTcount: A:0.32, C:0.13, G:0.31, T:0.24
Consensus pattern (44 bp):
GGTGAGAATATGTGAGATATCAGGTTGAGTATATGACACGCCAC
Found at i:371303 original size:23 final size:23
Alignment explanation
Indices: 371276--371440 Score: 79
Period size: 23 Copynumber: 7.2 Consensus size: 23
371266 NNNNNNNAGG
*
371276 AATATGCGACATGCCATGGAGGA
1 AATATGTGACATGCCATGGAGGA
* * * *
371299 AATATGTGACAAGACACT-AAGGG
1 AATATGTGACATGCCA-TGGAGGA
*
371322 AATATGTGACATGCCATGG-TGA
1 AATATGTGACATGCCATGGAGGA
*** ** *
371344 GAATATGTGACACAACATGTTGGG
1 -AATATGTGACATGCCATGGAGGA
***
371368 AATATGTGACACAACATGGA-GA
1 AATATGTGACATGCCATGGAGGA
* *
371390 GAATATATGACACGCCATGGTTA-G-
1 -AATATGTGACATGCCATGG--AGGA
* *
371414 AATATGTGAGATGCCATGGAGGG
1 AATATGTGACATGCCATGGAGGA
371437 AATA
1 AATA
371441 NNNNNNNNNN
Statistics
Matches: 108, Mismatches: 25, Indels: 18
0.72 0.17 0.12
Matches are distributed among these distances:
21 1 0.01
22 4 0.04
23 99 0.92
24 2 0.02
25 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (23 bp):
AATATGTGACATGCCATGGAGGA
Found at i:371369 original size:46 final size:46
Alignment explanation
Indices: 371274--371440 Score: 153
Period size: 46 Copynumber: 3.6 Consensus size: 46
371264 NNNNNNNNNA
* **
371274 GGAATATGCGACATGCCATGGAG-GAAATATGTGACA-AGACACT-AAG
1 GGAATATGTGACATGCCATGGAGAG-AATATGTGACACA-ACA-TGTTG
*
371320 GGAATATGTGACATGCCATGGTGAGAATATGTGACACAACATGTTG
1 GGAATATGTGACATGCCATGGAGAGAATATGTGACACAACATGTTG
*** * **
371366 GGAATATGTGACACAACATGGAGAGAATATATGACACGCCATGGTT-
1 GGAATATGTGACATGCCATGGAGAGAATATGTGACACAACAT-GTTG
* * *
371412 AGAATATGTGAGATGCCATGGAGGGAATA
1 GGAATATGTGACATGCCATGGAGAGAATA
371441 NNNNNNNNNN
Statistics
Matches: 100, Mismatches: 17, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
45 1 0.01
46 94 0.94
47 5 0.05
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.22
Consensus pattern (46 bp):
GGAATATGTGACATGCCATGGAGAGAATATGTGACACAACATGTTG
Found at i:371438 original size:69 final size:69
Alignment explanation
Indices: 371275--371440 Score: 183
Period size: 69 Copynumber: 2.4 Consensus size: 69
371265 NNNNNNNNAG
* * * * *
371275 GAATATGCGACATGCCATGGAGGAAATATGTGACAAGACACTAAGGGAATATGTGACATGCCATG
1 GAATATGTGACATGCCATGGAGGGAATATGTGACAAGACACTAAGAGAATATATGACACGCCATG
371340 GTGA
66 GTGA
*** ** *
371344 GAATATGTGACACAACATGTTGGGAATATGTGACACA-ACA-TGGAGAGAATATATGACACGCCA
1 GAATATGTGACATGCCATGGAGGGAATATGTGACA-AGACACT-AAGAGAATATATGACACGCCA
*
371407 TGGTTA
64 TGGTGA
*
371413 GAATATGTGAGATGCCATGGAGGGAATA
1 GAATATGTGACATGCCATGGAGGGAATA
371441 NNNNNNNNNN
Statistics
Matches: 77, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
68 1 0.01
69 75 0.97
70 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (69 bp):
GAATATGTGACATGCCATGGAGGGAATATGTGACAAGACACTAAGAGAATATATGACACGCCATG
GTGA
Found at i:374742 original size:23 final size:23
Alignment explanation
Indices: 374710--374754 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
374700 TTTCCCACAT
* **
374710 AACACTCCATGGTGAGAATATGC
1 AACACACCATGGAAAGAATATGC
374733 AACACACCATGGAAAGAATATG
1 AACACACCATGGAAAGAATATG
374755 NNNNNNNNNN
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (23 bp):
AACACACCATGGAAAGAATATGC
Found at i:374820 original size:23 final size:23
Alignment explanation
Indices: 374794--375189 Score: 163
Period size: 23 Copynumber: 17.3 Consensus size: 23
374784 GACACTAAAG
*
374794 GAATATGTGACATGCCATGGTGA
1 GAATATGTGACACGCCATGGTGA
* *
374817 GAATATGTGACACGACAT-GTAGG
1 GAATATGTGACACGCCATGGT-GA
** *
374840 GAATATGTGACATACCATGGAGA
1 GAATATGTGACACGCCATGGTGA
* *
374863 GAATATATGACACGCCATGGTTA
1 GAATATGTGACACGCCATGGTGA
********** * *
374886 GAANNNNNNNNNNGCCATGGAGG
1 GAATATGTGACACGCCATGGTGA
* * *
374909 GATTAAGTGACACGCCATGTTGA
1 GAATATGTGACACGCCATGGTGA
* * *
374932 TAATATGCGACACACCATGGTGA
1 GAATATGTGACACGCCATGGTGA
374955 GAATATGTGACACAG-CATGGTGA
1 GAATATGTGACAC-GCCATGGTGA
* * *
374978 GAATATATGAGACGACATGGTGA
1 GAATATGTGACACGCCATGGTGA
* * * *********
375001 GGATGTGTGACATGNNNNNNNNN
1 GAATATGTGACACGCCATGGTGA
* * *
375024 NAATATGTGAGACGACATGGTGA
1 GAATATGTGACACGCCATGGTGA
* * *
375047 GACTATGTGACACGCCAAGTTGA
1 GAATATGTGACACGCCATGGTGA
* **
375070 GAATATGTGACATGCCACAGTGA
1 GAATATGTGACACGCCATGGTGA
* *
375093 GAATATGTGACA--CCATGGAGG
1 GAATATGTGACACGCCATGGTGA
* * ** *
375114 GAATATGTGAGATGATATAGTGA
1 GAATATGTGACACGCCATGGTGA
** *
375137 GAATATGTGACACATCA-GGTTAA
1 GAATATGTGACACGCCATGG-TGA
* * *
375160 GTATATGTGACACGCCATGGAGG
1 GAATATGTGACACGCCATGGTGA
375183 GAATATG
1 GAATATG
375190 NNNNNNNNNN
Statistics
Matches: 251, Mismatches: 114, Indels: 16
0.66 0.30 0.04
Matches are distributed among these distances:
21 16 0.06
22 4 0.02
23 228 0.91
24 3 0.01
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.22
Consensus pattern (23 bp):
GAATATGTGACACGCCATGGTGA
Found at i:374822 original size:46 final size:46
Alignment explanation
Indices: 374772--374881 Score: 150
Period size: 46 Copynumber: 2.4 Consensus size: 46
374762 NNNNNNAGGA
* *
374772 AATATGTGACACGACACT-AAAGGAATATGTGACATGCCATGGTGAG
1 AATATGTGACACGACA-TGAAAGGAATATGTGACATACCATGGAGAG
* *
374818 AATATGTGACACGACATGTAGGGAATATGTGACATACCATGGAGAG
1 AATATGTGACACGACATGAAAGGAATATGTGACATACCATGGAGAG
* *
374864 AATATATGACACGCCATG
1 AATATGTGACACGACATG
374882 GTTAGAANNN
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 1 0.02
46 56 0.98
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.22
Consensus pattern (46 bp):
AATATGTGACACGACATGAAAGGAATATGTGACATACCATGGAGAG
Found at i:375075 original size:46 final size:45
Alignment explanation
Indices: 375025--375149 Score: 135
Period size: 44 Copynumber: 2.8 Consensus size: 45
375015 NNNNNNNNNN
* * * **
375025 AATATGTGAGACGACATGGTGAGACTATGTGACACGCCAAGTTGAG
1 AATATGTGAGATGACATAGTGAGAATATGTGACAC-CCAAGGAGAG
* * * * *
375071 AATATGTGACATGCCACAGTGAGAATATGTGACA-CCATGGAGGG
1 AATATGTGAGATGACATAGTGAGAATATGTGACACCCAAGGAGAG
*
375115 AATATGTGAGATGATATAGTGAGAATATGTGACAC
1 AATATGTGAGATGACATAGTGAGAATATGTGACAC
375150 ATCAGGTTAA
Statistics
Matches: 64, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
44 36 0.56
46 28 0.44
ACGTcount: A:0.35, C:0.13, G:0.29, T:0.23
Consensus pattern (45 bp):
AATATGTGAGATGACATAGTGAGAATATGTGACACCCAAGGAGAG
Found at i:375624 original size:17 final size:18
Alignment explanation
Indices: 375589--375625 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
375579 TTCGTAGGAA
*
375589 ATTTGATGAAAAATGCTC
1 ATTTGATGAAAAATCCTC
375607 ATTTGATG-AAAATCCTC
1 ATTTGATGAAAAATCCTC
375624 AT
1 AT
375626 AAGTATAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (18 bp):
ATTTGATGAAAAATCCTC
Found at i:377066 original size:23 final size:23
Alignment explanation
Indices: 377040--377526 Score: 291
Period size: 23 Copynumber: 21.4 Consensus size: 23
377030 GAAACTAAAG
* *
377040 GAATATGTGACATGCCATGGTAA
1 GAATATGTGACACGCCATGGTGA
** *
377063 GAATATGTGACACGATAT-GTAA
1 GAATATGTGACACGCCATGGTGA
* *
377085 GGAATATGTGACACACCATGGAGA
1 -GAATATGTGACACGCCATGGTGA
* * *
377109 GAATATATGACACACCATGGTTA
1 GAATATGTGACACGCCATGGTGA
* * *
377132 GAATATGTGAGACGCCATGGAGG
1 GAATATGTGACACGCCATGGTGA
* * *
377155 GATTAAGTGACACGCCATGTTGA
1 GAATATGTGACACGCCATGGTGA
* ** *
377178 CAATATGCAACACACCATGGTGA
1 GAATATGTGACACGCCATGGTGA
* * *
377201 GAATATGTGAGATGACATGGTGA
1 GAATATGTGACACGCCATGGTGA
* *
377224 GAATATGTGAGACGACATGGTGA
1 GAATATGTGACACGCCATGGTGA
* **
377247 GAATATGTGAGACAACATGGTGA
1 GAATATGTGACACGCCATGGTGA
* * * * * *
377270 GGATGTATAACATGCCATGG-AA
1 GAATATGTGACACGCCATGGTGA
* *
377292 GGAATATGTGAGACGACATGGTGA
1 -GAATATGTGACACGCCATGGTGA
* *
377316 G-A-ATGTGACACGCCAAGTTGA
1 GAATATGTGACACGCCATGGTGA
* *
377337 GAATATGTGACAGGCCACGGTGA
1 GAATATGTGACACGCCATGGTGA
* *
377360 GAATATGTGACA--CCATGGAGG
1 GAATATGTGACACGCCATGGTGA
* * * *
377381 GAATATGTGAGAGGACATAGTGA
1 GAATATGTGACACGCCATGGTGA
** *
377404 GAATATGTGACACATCA-GGTTAA
1 GAATATGTGACACGCCATGG-TGA
* * * * *
377427 GTATATCTGACACACCATGGAGG
1 GAATATGTGACACGCCATGGTGA
*
377450 GAATATGTGACAC-CACATAAG-G-
1 GAATATGTGACACGC-CAT-GGTGA
*
377472 GAATATGTGACAC-CACATAAG-G-
1 GAATATGTGACACGC-CAT-GGTGA
*
377494 GAATATGTGACAC-CACATGCTGA
1 GAATATGTGACACGC-CATGGTGA
377517 GAATATGTGA
1 GAATATGTGA
377527 AATGACTGAT
Statistics
Matches: 362, Mismatches: 88, Indels: 28
0.76 0.18 0.06
Matches are distributed among these distances:
21 33 0.09
22 50 0.14
23 273 0.75
24 6 0.02
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (23 bp):
GAATATGTGACACGCCATGGTGA
Found at i:377087 original size:46 final size:45
Alignment explanation
Indices: 376991--377121 Score: 147
Period size: 46 Copynumber: 2.8 Consensus size: 45
376981 CACAGCACGG
* * *
376991 AAGGAATATGCGACATGTCATGGAGGAAATATGTGACACGAAACTA
1 AAGGAATATGTGACATGCCATGGAAG-AATATGTGACACGAAACTA
* *
377037 AAGGAATATGTGACATGCCATGGTAAGAATATGTGACACGATA-TGT
1 AAGGAATATGTGACATGCCATGG-AAGAATATGTGACACGAAACT-A
** *
377083 AAGGAATATGTGACACACCATGGAGAGAATATATGACAC
1 AAGGAATATGTGACATGCCATGGA-AGAATATGTGACAC
377122 ACCATGGTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
45 2 0.03
46 70 0.95
47 2 0.03
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.21
Consensus pattern (45 bp):
AAGGAATATGTGACATGCCATGGAAGAATATGTGACACGAAACTA
Found at i:377212 original size:10 final size:10
Alignment explanation
Indices: 377197--377258 Score: 52
Period size: 10 Copynumber: 5.6 Consensus size: 10
377187 ACACACCATG
377197 GTGAGAATAT
1 GTGAGAATAT
*
377207 GTGAGATGACAT
1 GTGAGA--ATAT
377219 GGTGAGAATAT
1 -GTGAGAATAT
*
377230 GTGAGACGACAT
1 GTGAGA--ATAT
377242 GGTGAGAATAT
1 -GTGAGAATAT
377253 GTGAGA
1 GTGAGA
377259 CAACATGGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
10 18 0.43
11 6 0.14
12 6 0.14
13 12 0.29
ACGTcount: A:0.35, C:0.05, G:0.35, T:0.24
Consensus pattern (10 bp):
GTGAGAATAT
Found at i:377225 original size:13 final size:12
Alignment explanation
Indices: 377193--377270 Score: 51
Period size: 10 Copynumber: 6.8 Consensus size: 12
377183 TGCAACACAC
377193 CATGGTGAGA-A
1 CATGGTGAGAGA
*
377204 TAT-GTGAGATGA
1 CATGGTGAGA-GA
377216 CATGGTGAGA-A
1 CATGGTGAGAGA
*
377227 TAT-GTGAGACGA
1 CATGGTGAGA-GA
377239 CATGGTGAGA-A
1 CATGGTGAGAGA
* *
377250 TAT-GTGAGACAA
1 CATGGTGAGA-GA
377262 CATGGTGAG
1 CATGGTGAG
377271 GATGTATAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
10 18 0.35
11 8 0.15
12 9 0.17
13 17 0.33
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.23
Consensus pattern (12 bp):
CATGGTGAGAGA
Found at i:377474 original size:22 final size:22
Alignment explanation
Indices: 377447--377511 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
377437 CACACCATGG
377447 AGGGAATATGTGACACCACATA
1 AGGGAATATGTGACACCACATA
377469 AGGGAATATGTGACACCACATA
1 AGGGAATATGTGACACCACATA
377491 AGGGAATATGTGACACCACAT
1 AGGGAATATGTGACACCACAT
377512 GCTGAGAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.18
Consensus pattern (22 bp):
AGGGAATATGTGACACCACATA
Found at i:385138 original size:81 final size:80
Alignment explanation
Indices: 385021--385225 Score: 189
Period size: 81 Copynumber: 2.5 Consensus size: 80
385011 NNNNNNNNNG
* * **
385021 GGAACTTCTAAACAGTTGATGCT-AAAGGAGAACATGTACCTCATGCTTATGCAGTTGTTAATGA
1 GGAACTT-TAAACAGTTGATGTTGAAA-GAGACCATGTACCTCATGCCAATGCAGTTGTTAATGA
*** *
385085 AGTTGT-GAGAGGGGATA
64 AACCGTAGA-AGGGAATA
* * * * *
385102 GGAACCTTTAAACAGTTGATGTTGAAAAAGACCATGTATCTTATGCCAATGCGGTTGTTGATGAA
1 GGAA-CTTTAAACAGTTGATGTTGAAAGAGACCATGTACCTCATGCCAATGCAGTTGTTAATGAA
*
385167 ACCGTAGAAGGGAATT
65 ACCGTAGAAGGGAATA
* * * *
385183 GGAAAATTTCATCAATTGATGTTGAAAGAGACCATGTACCTCA
1 GG-AACTTTAAACAGTTGATGTTGAAAGAGACCATGTACCTCA
385226 AAACGCTCCT
Statistics
Matches: 99, Mismatches: 21, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
81 89 0.90
82 10 0.10
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (80 bp):
GGAACTTTAAACAGTTGATGTTGAAAGAGACCATGTACCTCATGCCAATGCAGTTGTTAATGAAA
CCGTAGAAGGGAATA
Found at i:391951 original size:26 final size:25
Alignment explanation
Indices: 391922--391970 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
391912 GCAACATTTT
*
391922 TTTTGAACATGGTGTATAACAAAACA
1 TTTTCAACATGGTGTATAA-AAAACA
*
391948 TTTTCAACATGGTGTGTAAAAAA
1 TTTTCAACATGGTGTATAAAAAA
391971 TGTGTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (25 bp):
TTTTCAACATGGTGTATAAAAAACA
Found at i:395252 original size:41 final size:41
Alignment explanation
Indices: 395197--395274 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
395187 TATATGTCAT
* * * *
395197 TTACATGTTTTTACATGCCATTTTGTTTTACTTATATGTTG
1 TTACATCTTCTTACATGCCATTTCGTTTTACTCATATGTTG
395238 TTACATCTTCTTACATGCCATTTCGTTTTACTCATAT
1 TTACATCTTCTTACATGCCATTTCGTTTTACTCATAT
395275 AGTGTGACAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.53
Consensus pattern (41 bp):
TTACATCTTCTTACATGCCATTTCGTTTTACTCATATGTTG
Found at i:395414 original size:40 final size:40
Alignment explanation
Indices: 395370--395448 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
395360 TAAGTATTAT
*
395370 ATTGTTACACACTATG-CTTGTTAAATGTCATTTACATCTC
1 ATTGTTACACACTA-GACTTCTTAAATGTCATTTACATCTC
****
395410 ATTGTTACGTGTTAGACTTCTTAAATGTCATTTACATCT
1 ATTGTTACACACTAGACTTCTTAAATGTCATTTACATCT
395449 TGTGATATGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
39 1 0.03
40 32 0.97
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (40 bp):
ATTGTTACACACTAGACTTCTTAAATGTCATTTACATCTC
Found at i:397273 original size:31 final size:31
Alignment explanation
Indices: 397235--397300 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
397225 NNNNNNACAT
*
397235 GCCATTTCGTTTTACTTATATAGTGTAACAC
1 GCCATTTCGTTTTACTCATATAGTGTAACAC
397266 GCCATTTCGTTTTACTCATATAGTGTAACAC
1 GCCATTTCGTTTTACTCATATAGTGTAACAC
397297 GCCA
1 GCCA
397301 GTNNNNNNNN
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.38
Consensus pattern (31 bp):
GCCATTTCGTTTTACTCATATAGTGTAACAC
Found at i:397424 original size:40 final size:40
Alignment explanation
Indices: 397380--397458 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
397370 TTCAGTATTA
*
397380 TATTGTTACACACTATG-CTTGTTAAATGTCATTTACATCT
1 TATTGTTACACACTA-GACTTCTTAAATGTCATTTACATCT
***
397420 TATTGTTACATGTTAGACTTCTTAAATGTCATTTACATC
1 TATTGTTACACACTAGACTTCTTAAATGTCATTTACATC
397459 NNNNNNNNNN
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.03
40 33 0.97
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (40 bp):
TATTGTTACACACTAGACTTCTTAAATGTCATTTACATCT
Found at i:400138 original size:41 final size:41
Alignment explanation
Indices: 400077--400154 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
400067 TATATGTCAT
* * * *
400077 TTACATGTTTTTACATGCCATTTTGTTTTACTCATATGTTG
1 TTACATCTTTTAACACGCCATTTCGTTTTACTCATATGTTG
400118 TTACATCTTTTAACACGCCATTTCGTTTTACTCATAT
1 TTACATCTTTTAACACGCCATTTCGTTTTACTCATAT
400155 AATGTGACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.22, C:0.19, G:0.09, T:0.50
Consensus pattern (41 bp):
TTACATCTTTTAACACGCCATTTCGTTTTACTCATATGTTG
Found at i:400293 original size:40 final size:40
Alignment explanation
Indices: 400249--400329 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
400239 TTCAGTATTA
* ** * *
400249 TATTGTTACACACTATTCTTGTTAGATGTCATTTACATCT
1 TATTGCTACACACTAGACTTCTTAAATGTCATTTACATCT
**
400289 TATTGCTACATGCTAGACTTCTTAAATGTCATTTACATCT
1 TATTGCTACACACTAGACTTCTTAAATGTCATTTACATCT
400329 T
1 T
400330 GTGACATGGN
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.46
Consensus pattern (40 bp):
TATTGCTACACACTAGACTTCTTAAATGTCATTTACATCT
Found at i:400440 original size:71 final size:69
Alignment explanation
Indices: 400357--400622 Score: 262
Period size: 69 Copynumber: 3.8 Consensus size: 69
400347 NNAACTATTG
** * * * * **
400357 TATTGTTACATGCCACACTAGTTAGATGTCATTTACATCTTGTTCTGACACGCCATTTGATTGCA
1 TATTGTTACATGCCAGGCTTGTTAGATGTCATTTACATCTTATTGTGACACGCCATTTCA--AAA
400422 GTCTTA
64 GTCTTA
* * * * *
400428 TATTGTTACATGCCAGGCTTGTTAGATATCGTTTACATCTTATTGTAACATGCCATTTCAAAAAT
1 TATTGTTACATGCCAGGCTTGTTAGATGTCATTTACATCTTATTGTGACACGCCATTTCAAAAGT
400493 CTTA
66 CTTA
** * * ** * *
400497 TATTGTTACAAACCATGCTTGTTAAATGTTGTTTTCATCTTATTGTGACACACCATTTCAAAAGT
1 TATTGTTACATGCCAGGCTTGTTAGATGTCATTTACATCTTATTGTGACACGCCATTTCAAAAGT
400562 CTTA
66 CTTA
* ** * * * *
400566 TATTGTTACACGGTAGGCTTCTTGGATGTCATTTACATCTTGTTGTGACACTCCATT
1 TATTGTTACATGCCAGGCTTGTTAGATGTCATTTACATCTTATTGTGACACGCCATT
400623 GCATTGCAGC
Statistics
Matches: 158, Mismatches: 37, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
69 108 0.68
71 50 0.32
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (69 bp):
TATTGTTACATGCCAGGCTTGTTAGATGTCATTTACATCTTATTGTGACACGCCATTTCAAAAGT
CTTA
Found at i:403581 original size:171 final size:171
Alignment explanation
Indices: 403266--404323 Score: 1126
Period size: 171 Copynumber: 6.2 Consensus size: 171
403256 NNNNNNNAGT
* *
403266 GAGTAATAAGACTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTCTC-ACGGATAGCTT
1 GAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTC-CAACGAATAGCTT
* ** *
403330 TTGCTTCACGTTTCCCAAGGTAGACATTCAATTAGAGTATATTTTAACCAAAAATGTAAAAAAAT
65 TTGCTTCACGTTTCCCAAGGTAGACATTCAATTATAACATATTTTAACCAAAAATATAAAAAAAT
* * *
403395 CCAACTTAGAATCAATTATGAGAATATAAAACCATTCAAAGC
130 CTAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAGC
* * * * *
403437 AAGCAATAAGGCTTTCTAAGGCTTGAGTGACTATAAATGGACTTTT-TCCTCCAATGGATAGCTT
1 GAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCT-CTCCAACGAATAGCTT
* * ** * *
403501 TTACTTCACTTTTTTCAAGGCAGACATTCAATTATAGCATATTTTAACCAAAAATATAAAAAAAT
65 TTGCTTCACGTTTCCCAAGGTAGACATTCAATTATAACATATTTTAACCAAAAATATAAAAAAAT
* *
403566 CTAATTTAAAATCAATTTTGAGAATATAAAACCATTTAAAGC
130 CTAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAGC
* * * * *
403608 GAGTAATAAAGCTTTCAAAGGCTTGAGTGACTATATATGGACTTTTCTCTCCCACGGATGGCTTT
1 GAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTCCAACGAATAGCTTT
* * ** * * ** ** * * *
403673 TGCATCACGGTTATCAAGGCAGCCATTCAACCATAGTATATTTTAGCCAAAAATGTAAAAAAATA
66 TGCTTCACGTTTCCCAAGGTAGACATTCAATTATAACATATTTTAACCAAAAATATAAAAAAATC
* * *
403738 AAACTTAAAATGAATTATGAGAATATAAAGCCATTTAAA-C
131 TAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAGC
* * * ** *
403778 TAAGTTATAAAGCTTTCAAAGGCTTGAGTGACTAGGAATGGACTTTTCTCAT-CAATGAAT-GTC
1 -GAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTC-TCCAACGAATAG-C
* * * * * ** * * *
403841 TTTTGCTTTATGTTTCCTAAGGAAAATTTTCAATTATAACATATTTTAACTAAAAATGTAAGAAA
63 TTTTGCTTCACGTTTCCCAAGGTAGACATTCAATTATAACATATTTTAACCAAAAATATAAAAAA
* * * ** *
403906 TTCCAACTTAAAATCAATTATAAGAATATAAAATTATTTAAAGT
128 ATCTAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAGC
* * * * * * *
403950 GACTAATAACGCTTTTACAGGCTTGAGTGACTATAAATGTACTTTTCTCTCTAATGAATAGCTTT
1 GAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTCCAACGAATAGCTTT
* * *
404015 TGCTTCAGGTTTCCCAAGGTTGACATTCAATTATAACATATTTTAACC-AAAATATCAAAAAAT-
66 TGCTTCACGTTTCCCAAGGTAGACATTCAATTATAACATATTTTAACCAAAAATATAAAAAAATC
* * **
404078 TCAAATTAAAATTAATTATGAGAATATAAAACTTTTTAAAGC
131 T-AACTTAAAATCAATTATGAGAATATAAAACCATTTAAAGC
* * * *
404120 GAGTGATAAGGCTTTCAATGGCTTGAGTGACTATAAATGG-CTTTTCT-TACTAACGAATGGCTT
1 GAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCT-CCAACGAATAGCTT
* * * * * *
404183 TTGCTTCATGTTTCTCAAGGTAGACAATCAACTATAACATGTTTTAACCAAAAATATAAAAAATT
65 TTGCTTCACGTTTCCCAAGGTAGACATTCAATTATAACATATTTTAACCAAAAATATAAAAAAAT
* * *
404248 CTAACTTAAAACCAATTATGAGATTATAAAACCATTTAAAGT
130 CTAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAGC
* * * *
404290 GAGTAATAAGACATTCAAAGGTTTGAGTGCCTAT
1 GAGTAATAAGGCTTTCAAAGGCTTGAGTGACTAT
404324 TGTTGGTCCC
Statistics
Matches: 735, Mismatches: 139, Indels: 27
0.82 0.15 0.03
Matches are distributed among these distances:
168 1 0.00
169 62 0.08
170 157 0.21
171 512 0.70
172 3 0.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (171 bp):
GAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTCCAACGAATAGCTTT
TGCTTCACGTTTCCCAAGGTAGACATTCAATTATAACATATTTTAACCAAAAATATAAAAAAATC
TAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAGC
Found at i:404679 original size:35 final size:35
Alignment explanation
Indices: 404625--404717 Score: 114
Period size: 35 Copynumber: 2.7 Consensus size: 35
404615 TTACAAAGAC
* * * *
404625 TTTTCATAGGCTCAGCCACAACTTTCAACAATGGT
1 TTTTCAAAGGATCAACCACAACCTTCAACAATGGT
404660 TTTTCAAAGGATCAACCACAACCTTCAACAATGGT
1 TTTTCAAAGGATCAACCACAACCTTCAACAATGGT
*** *
404695 TTTTCCTGGGATCAACCAAAACC
1 TTTTCAAAGGATCAACCACAACC
404718 CAAAAACTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (35 bp):
TTTTCAAAGGATCAACCACAACCTTCAACAATGGT
Found at i:406168 original size:26 final size:26
Alignment explanation
Indices: 406132--406181 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
406122 AGTTTTCCTA
*
406132 GAATGCTCCTAACA-TTTCTAAGAATT
1 GAATGCCCCTAA-AGTTTCTAAGAATT
406158 GAATGCCCCTAAAGTTTCTAAGAA
1 GAATGCCCCTAAAGTTTCTAAGAA
406182 CTTCTACCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (26 bp):
GAATGCCCCTAAAGTTTCTAAGAATT
Found at i:412443 original size:60 final size:60
Alignment explanation
Indices: 412367--412482 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 60
412357 ACCATCACCT
* *
412367 ACTCGTGGGAATTGCCCACGCCACC-ATGTATAAATTAGGGCTTCAGGTTCCC-CTTTACCA
1 ACTCGTGGGAACTGCCCACGCCACCTA-ATATAAATTAGGGCTTCAGG-TCCCTCTTTACCA
* * *
412427 ACTCGTGGGAACTGCCCATGGCACCTAATATGAATTAGGGCTTCAGGTCCCTCTTT
1 ACTCGTGGGAACTGCCCACGCCACCTAATATAAATTAGGGCTTCAGGTCCCTCTTT
412483 TTCCTACTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 4 0.08
60 44 0.90
61 1 0.02
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (60 bp):
ACTCGTGGGAACTGCCCACGCCACCTAATATAAATTAGGGCTTCAGGTCCCTCTTTACCA
Found at i:414205 original size:171 final size:171
Alignment explanation
Indices: 413888--417735 Score: 1893
Period size: 171 Copynumber: 22.1 Consensus size: 171
413878 NNNNNNNNNN
* * * *
413888 AAAGCCTTATTACTCGCTTTAAATGGTTTTATATTCTCGTAATAGATTTTAAGTAAGATTTTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAGA-TTTTTT
* * ** * * *** * *
413953 TACATATTTGTTTAAAATATGCTATAACCGAATGACTGCTTGGGGAAACATAAAGCAAAAGCCAT
65 TACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCAAGAAACGTGAAGCAAAAGCCAT
* * *
414018 CTATGGGAGAGAAAAGTCCATTTATAGGCACTCAAGCCTTTG
130 CCATTGGAGAGAAAAGTCCATTTATAGTCACTCAAGCCTTTG
* * *
414060 AAAACCTTATTACTCCCTTTAAATAGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTT
* * * * ***
414125 ACATTTTTGGTTAAAGTATGCTATAATGGAATGTTTACCTTGGGAAACGT-AAGGCAAAAGCCAT
66 ACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCAAGAAACGTGAA-GCAAAAGCCAT
* *
414189 CCCTTGGAGAGAAAAGTCCATATATAGTCACTCAAGCCTTTG
130 CCATTGGAGAGAAAAGTCCATTTATAGTCACTCAAGCCTTTG
* * * *
414231 AAAGCTTTATAACTTACTTTAAATAGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTT
* * * * ** *
414296 ATATTTTTTGTTAAAATATGGTATAATTGAATGTCTGCCTCAAGAAAAGTGAAGTGAAAGCCTTC
66 ACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCAAGAAACGTGAAGCAAAAGCCATC
* **
414361 CATTGGAG-GAAAAAGTCCATTTATAGTCACTCAAGTCTTAA
131 CATTGGAGAG-AAAAGTCCATTTATAGTCACTCAAGCCTTTG
* * * * * *
414402 AAAGCCTTATTACTCGCTTTAAATGATTTTATATTCTCGTAATGGATTCTAAGTTGGATTTTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTT
* * * * * * * *
414467 ATATTTTTTTGTTAAAATATGCTATAATTAAATGTCTGTCTCATGAAATGTGAAGTACAAGCCAT
66 ACA-TTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCAAGAAACGTGAAGCAAAAGCCAT
* *
414532 CCATTGGAG-GAAAAAGTCTATTTATAGTCACTCAAGCCTTAG
130 CCATTGGAGAG-AAAAGTCCATTTATAGTCACTCAAGCCTTTG
* * * * * *
414574 AAAGCCTTATTACACACTCTAGATGGCTTTATATTCTCATAATTAATTTTAATTTAGA-TTTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTT
** * *
414638 ACATTTTTGGTTAAAATATTTTATAATTGAATGAT-TGCCTCAAGAAACATGAAGCAAAAGCAAT
66 ACATTTTTGGTTAAAATATGCTATAATTGAATG-TCTGCCTCAAGAAACGTGAAGCAAAAGCCAT
* **
414702 CCATGGGAGAGAAAAGTCCATTTATAGTCACTCAAGCCTCGG
130 CCATTGGAGAGAAAAGTCCATTTATAGTCACTCAAGCCTTTG
* * * *
414744 AAAGCCTTATTACTCGCTTTAAATGGTTTTATATTCTCGTAATGGATTCTAAGTTAGATTTTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTT
* ** * ** * ** * *
414809 ATATTTTTATTTAAAATATGCTATGAGGGAATGTTTGCCTCTGGAAACGTGAGGCAAAAGCCATT
66 ACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCAAGAAACGTGAAGCAAAAGCCATC
* * *
414874 CATTAGAGAGAAAAGTCTATTTATAGTCACTCAACCCTTTG
131 CATTGGAGAGAAAAGTCCATTTATAGTCACTCAAGCCTTTG
*
414915 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTGGATTTTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTT
* * * ** * * * *
414980 ACATTTTTGATTAAAATATGTTATAATTGAATGACTATCACAAGAAACATCAAGAAAAAGCCATC
66 ACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCAAGAAACGTGAAGCAAAAGCCATC
** * * *
415045 CAAAGGAGAGAAAAGCCCATTTATAG-CTACACAAACCTTTG
131 CATTGGAGAGAAAAGTCCATTTATAGTC-ACTCAAGCCTTTG
** * *
415086 AAAGTTTTATTACTCAGTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTGGATTTTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAGA-TTTTTT
* * * *
415151 TACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCTTCAAGAAATGTGAAGTAAAAGCCTT
65 TACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCAAGAAACGTGAAGCAAAAGCCAT
** ** * * *
415216 CCATCAGAG-GAAAAAGTCTGTTTATAGTCATTCAAACCTTAG
130 CCATTGGAGAG-AAAAGTCCATTTATAGTCACTCAAGCCTTTG
* ** * * * ** * *
415258 AAAGCTTTATTACTTGCTTGAAATGGTTTAATATTCTCGTAAGGGATTCTAAGTTGGATTTTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTT
* * * *
415323 ACATTTTTGGTTAAAATATGCTATAATCGAATGACTGCCT-AGGGAAACATGAAGCAAAAGCCAT
66 ACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCA-AGAAACGTGAAGCAAAAGCCAT
* * * *****************
415387 CTATGGGAGAGAAAAGTCAATTTATNNNNNNNNNNNNNNNNNNNNNN
130 CCATTGGAGAGAAAAGTCCATTTAT-----AGTCACTCAAGCCTTTG
****************************** * ** * ****
415434 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAAAAGC-CATCCATTGAAGAGAAAAGTCT--ATTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCAT-AATTG-A-TTTTAAGT-TAGATTT
* * ** * * * * * ** * *
415496 ATAGTCACTCAAGCCTTTGAAAGCCT-GATTACTCTCTTTAGATGGTTTTATAGTCT-CAT-AAT
62 -T-TTTA--C-A-TTTTTG---G-TTAAAATA-T-GCTATA-A---TTGAAT-GTCTGCCTCAAG
** ** * ** ****** ** *** * * * * * *
415558 TGATTTTAATTTAGATTTTTTTATATTTTTG-GTTAAAA-T--ATGTTATAATTGAATGATTGCA
110 AAACGTGAA-GCA-AAAGCCATCCATTGGAGAG--AAAAGTCCAT-TTAT-AGTCACTCA-AGCC
*
415619 TTAGG
168 TT-TG
* ******** ** *
415624 AAA-CATTA--AGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNAA--GCCTTAT-TACTCACTTTA
1 AAAGCCTTATTA-C--------------------TCACTTTAAATGGTTTTATATTCTCA---T-
* * *** *
415683 AATGGTTTTATATTCTCATAATTGATTTTAAGTTTGATGTTTTTACATTTTTTACTAAAATATGT
41 AA-----TT-GATT-T--TAA--G---TT-A----GATTTTTTTACATTTTTGGTTAAAATATGC
* * * * * * * *
415748 TATAATTGAATGACTGTCACAAGAAATGTCAAGCAAAAGCCAATCCA--AGAGGAGAAGTAGCCC
87 TATAATTGAATGTCTGCCTCAAGAAACGTGAAGCAAAAGCC-ATCCATTGGA-GAGAA-AAGTCC
415811 ATTTATAGTCACT-AA-CCTTTG
149 ATTTATAGTCACTCAAGCCTTTG
* *
415832 AAATCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATCTTTTCAAGTTGGATTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGA--TTTT-AAGTTAGATTTT
* * * * *
415897 TTTACATTTTTTGTTAAAATATGCTATAATTGAATGTCTGCTTCAAGAAATGTAAAGTAAAAGCC
63 TTTACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCAAGAAACGTGAAGCAAAAGCC
* * * * * * **
415962 TTCCATTAGAG-GAAAAACTCCGTTTATAGTCATTCAAGTCTTAA
128 ATCCATTGGAGAG-AAAAGTCCATTTATAGTCACTCAAGCCTTTG
* ** * ** * *
416006 AAAGCTTTATTACTTGCTTTAAATGGTTTAATATTCTTGT-ATTAGATTCTAAGTTGGATTTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATT-GATTTTAAGTTAGATTTTTT
* * * * * * * *
416070 TACATTTTTAGTTAAAATATACTATAATCGAATGACTGCCT-AGGGAAACATGAAGAAAAAGCTA
65 TACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCA-AGAAACGTGAAGCAAAAGCCA
* * * * * *
416134 TCTATGGGGGAGAAAAGTCAATTTATAGGCA--CAGAGCTTTTG
129 TCCATTGGAGAGAAAAGTCCATTTATAGTCACTCA-AGCCTTTG
* * **********
416176 AAAGCCTTATTACTCGCTCTAAATGGTTTTATATTCTCATAATTNNNNNNNNNNT-GAATTTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAG-ATTTTTT
** * * *** *
416240 TACATTTTTGGTTAATGTATGCTATAATGGAATGTTTGCCTTGGGAAACGTGAGGCAAAAGCCAT
65 TACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCAAGAAACGTGAAGCAAAAGCCAT
* *************
416305 CCATTGGAGAGAAAAGTCTATTTATAGNNNNNNNNNNNNNTG
130 CCATTGGAGAGAAAAGTCCATTTATAGTCACTCAAGCCTTTG
* * * *
416347 AAAGCCTTATTACTCGCTTTAAATGATTTTATATTCTCATAATTGATTTTAATTTGGA-TTTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTT
* * * * * * * *
416411 AAACTTTTT-GTTAAAATATGTTATAATTGAAAGACTG--TGATGGGAAACATCAAGCAAAAGCC
66 ACA-TTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCA--AGAAACGTGAAGCAAAAGCC
** * * * *
416473 ATCCAAAGGAGAGAAAAGCCCATTTGTAGTTACAT-AAACCTTTG
128 ATCCATTGGAGAGAAAAGTCCATTTATAGTCAC-TCAAGCCTTTG
* * * * *
416517 AAAGTCTTATTATTCACTTTAAATGGTTTTATATTCTCATAATTCATTTTAAGTTGGATTTTTTC
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTT
* * ** * * *
416582 AAATTTTTTGTTAAAATATGCTATAATTGAATGTCTGCCTCAAGAAATATGAAGTAATAGCCTTC
66 ACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCAAGAAACGTGAAGCAAAAGCCATC
* * *
416647 CATTAGAG-GAAAAAGTTCATTTATAGTCACTCAAGCCTTAG
131 CATTGGAGAG-AAAAGTCCATTTATAGTCACTCAAGCCTTTG
* * * * *
416688 AAAGCTTTATTACTCGCTTTAAATGGTTTTATATTCTCGTAATGGATTCTAAGTT-GAATTTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAG-ATTTTTT
* * * * **
416752 TATATTTTTGGTTCAAATATGCTATAATCGAATGACTGCCT-AAGGAAATATGAAGCAAAAGCC-
65 TACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCAA-GAAACGTGAAGCAAAAGCCA
* * * *
416815 -CTATAT-GAGAGAAAAGGTCAACTTATAAG-CAATCAAGCCTTTG
129 TCCAT-TGGAGAGAAAA-GTCCATTTAT-AGTCACTCAAGCCTTTG
* *
416858 AAAGCCTTATTACTCGCTTTAAATAGTTTTATATTCTCATAATTGATTTTAA-TTAAGATTTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTT-AGATTTTTT
* * * * * * * * * *
416922 TATATTTTTAGTTAAAATATGTTATAATTTAATGAT-TGCATTAGGAAACATGAAGTAAAAACCA
65 TACATTTTTGGTTAAAATATGCTATAATTGAATG-TCTGCCTCAAGAAACGTGAAGCAAAAGCCA
* *
416986 TCCA-TGGAAGAGAAATGTCCATTTATAGTCACTCAACCCTTTG
129 TCCATTGG-AGAGAAAAGTCCATTTATAGTCACTCAAGCCTTTG
* ********** * * *
417029 AAAGTCTTATTACTCACTTTNNNNNNNNNNATAATCTCATAATTAATTTTAAGTTAGAATTTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTT
** * * * * * *
417094 ACATTTTTGAATAAAATATGTTATAATTGAATGACTGTCACAAGAAACGTCAAGCAAAAGCCATT
66 ACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCAAGAAACGTGAAGCAAAAGCCATC
** * *
417159 CAAAGAAGAGAAAAG-CCTATTTATAG-CTACAT-AAACCTTTG
131 CATTGGAGAGAAAAGTCC-ATTTATAGTC-AC-TCAAGCCTTTG
* ********** *
417200 AAAGTCTTATTACTCACTTTAAANNNNNNNNNNTTCTCATAATTGATTTTAAGTTAGCTTTTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTT
* * * * ** * * *
417265 ACATTTTTAGTTAAAATATGCTATAATTGAATGTTTGCCTTAGGAAGTGCGAAGTAAAAGCCTTC
66 ACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCAAGAAACGTGAAGCAAAAGCCATC
* * * *
417330 CATTAGAG-GAAACAGTCCGTTTATAGTCATTCAAGCCTTAG
131 CATTGGAGAGAAA-AGTCCATTTATAGTCACTCAAGCCTTTG
* ** * * * * * *
417371 AAAGCTTTATTACTTGCTTTAAATGGTTTAATATTCTCCTAATGGATTCTAAGTTGGATTCTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTT
* * * * *
417436 ACATTTTTGGTTAAAATATGCTATGATCGAATGACTGCCT-AGGGAAACATGAAGCAAAAGCCAT
66 ACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCA-AGAAACGTGAAGCAAAAGCCAT
* * * *
417500 CTATAGGAGAGAAAAGTCAATTTATAGGCACTCAAGCCTTTG
130 CCATTGGAGAGAAAAGTCCATTTATAGTCACTCAAGCCTTTG
* ********** *
417542 AAAGCCTTATTACTCGCTTTANNNNNNNNNNTATTCTCATAATTGATTTTAAGTTAGATATTTTT
1 AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTT
* ** * * ** * *
417607 ATATTTTTGGTTAACGTATGCTATAATGGAATGTTTGCCT-TGGAAAACGTGAGGCAAAAGTCAT
66 ACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCAAG-AAACGTGAAGCAAAAGCCAT
* * *
417671 CTATTGGAGAAAAAAGTCCATTTATAGTCACTCAAACCTTTG
130 CCATTGGAGAGAAAAGTCCATTTATAGTCACTCAAGCCTTTG
*
417713 AAAGCCTTATTACTCGCTTTAAA
1 AAAGCCTTATTACTCACTTTAAA
417736 NNNNNNNNNN
Statistics
Matches: 2762, Mismatches: 749, Indels: 331
0.72 0.19 0.09
Matches are distributed among these distances:
168 1 0.00
169 15 0.01
170 532 0.19
171 1542 0.56
172 373 0.14
173 72 0.03
174 41 0.01
175 2 0.00
176 5 0.00
177 5 0.00
178 7 0.00
179 3 0.00
181 2 0.00
182 2 0.00
183 7 0.00
184 3 0.00
185 2 0.00
186 4 0.00
187 2 0.00
188 4 0.00
189 3 0.00
190 3 0.00
191 6 0.00
192 17 0.01
193 15 0.01
194 4 0.00
205 1 0.00
206 3 0.00
208 12 0.00
209 9 0.00
210 3 0.00
211 8 0.00
212 12 0.00
213 11 0.00
214 5 0.00
215 1 0.00
216 5 0.00
217 3 0.00
218 4 0.00
220 1 0.00
221 4 0.00
222 1 0.00
223 1 0.00
225 2 0.00
226 1 0.00
227 3 0.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.37
Consensus pattern (171 bp):
AAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTT
ACATTTTTGGTTAAAATATGCTATAATTGAATGTCTGCCTCAAGAAACGTGAAGCAAAAGCCATC
CATTGGAGAGAAAAGTCCATTTATAGTCACTCAAGCCTTTG
Found at i:415258 original size:684 final size:683
Alignment explanation
Indices: 413888--417735 Score: 3486
Period size: 684 Copynumber: 5.5 Consensus size: 683
413878 NNNNNNNNNN
* * * **
413888 AAAGCCTTATTACTCGCTTTAAATGGTTTTATATTCTCGTAAT-AGATTTTAAGTAAGATTTTTT
1 AAAGCTTTATTACTCGCTTTAAATGGTTTAATATTCTCGTAATGA-ATTCTAAGTTGGA-TTTTT
* * * * * *
413952 TTACATATTTGTTTAAAATATGCTATAACCGAATGACTGCTTGGGGAAACATAAAGCAAAAGCCA
64 TTACATTTTTGGTTAAAATATGCTATAATCGAATGACTGCCTAGGGAAACATGAAGCAAAAGCCA
* * *
414017 TCTATGGGAGAGAAAAGTCCATTTATAGGCACTCAAGCCTTTGAAAACCTTATTACTCCCTTTAA
129 TCTATGGGAGAGAAAAGTCAATTTATAGGCACTCAAGCCTTTGAAAGCCTTATTACTCGCTTTAA
* * *
414082 ATAGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTTACATTTTTGGTTAAAGTATGCT
194 ATGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTTATATTTTTAGTTAAAGTATGCT
* * * *
414147 ATAATGGAATGTTTACCTTGGGAAACGTAAGGCAAAAGCCATCCCTTGGAGAGAAAAGTCCATAT
259 ATAATGGAATGTTTGCCTTGGGAAACGTGAGGCAAAAGCCATCCATTGGAGAGAAAAGTCCATTT
* * * * *
414212 ATAGTCACTCAAGCCTTTGAAAGCTTTATAACTTACTTTAAATAGTTTTATATTCTCATAATTGA
324 ATAGTCACTCAACCCTTTGAAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGA
* * * * *
414277 TTTTAAGTTAGATTTTTTTATATTTTTTG-TTAAAATATGGTATAATTGAATGTCTGCCTCAAGA
389 TTTTAAGTTAGATTTTTTTACA-TTTTTGATTAAAATATGTTATAATTGAATGACTGTCACAAGA
* ** * ** * * ** **
414341 AA-AGTGAAGTGAAAGCCTTCCATTGGAG-GAAAAAGTCCATTTATAGTCACTCAAGTCTTAAAA
453 AACA-TCAAGCAAAAGCCATCCAAAGGAGAG-AAAAGCCCATTTATAGT-ACACAAACCTTTGAA
* * * * * * *
414404 AGCCTTATTACTCGCTTTAAATGATTTTATATTCTCGTAATGGATTCTAAGTTGGATTTTTTTAT
515 AGTCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTGGATTTTTTTAC
* * * *
414469 ATTTTTTTGTTAAAATATGCTATAATTAAATGTCTG-TCTCATGAAATGTGAAGTACAAGCCATC
580 A-TTTTTTGTTAAAATATGCTATAATTGAATGTCTGCT-TCAAGAAATGTGAAGTAAAAGCCTTC
* * *
414533 CATTGGAGGAAAAAGTCTATTTATAGTCACTCAAGCCTTAG
643 CATTAGAGGAAAAAGTCTGTTTATAGTCATTCAAGCCTTAG
* * * * * * * * * *
414574 AAAGCCTTATTACACACTCTAGATGGCTTT-ATATTCTCATAATTAATTTTAATTTAGA-TTTTT
1 AAAGCTTTATTACTCGCTTTAAATGG-TTTAATATTCTCGTAATGAATTCTAAGTTGGATTTTTT
** * * * *
414637 TACATTTTTGGTTAAAATATTTTATAATTGAATGATTGCCTCA-AGAAACATGAAGCAAAAGCAA
65 TACATTTTTGGTTAAAATATGCTATAATCGAATGACTGCCT-AGGGAAACATGAAGCAAAAGCCA
* * * **
414701 TCCATGGGAGAGAAAAGTCCATTTATAGTCACTCAAGCCTCGGAAAGCCTTATTACTCGCTTTAA
129 TCTATGGGAGAGAAAAGTCAATTTATAGGCACTCAAGCCTTTGAAAGCCTTATTACTCGCTTTAA
* * * * *
414766 ATGGTTTTATATTCTCGTAATGGATTCTAAGTTAGATTTTTTTATATTTTTATTTAAAATATGCT
194 ATGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTTATATTTTTAGTTAAAGTATGCT
* * * * *
414831 ATGAGGGAATGTTTGCCTCT-GGAAACGTGAGGCAAAAGCCATTCATTAGAGAGAAAAGTCTATT
259 ATAATGGAATGTTTGCCT-TGGGAAACGTGAGGCAAAAGCCATCCATTGGAGAGAAAAGTCCATT
414895 TATAGTCACTCAACCCTTTGAAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTG
323 TATAGTCACTCAACCCTTTGAAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTG
* *
414960 ATTTTAAGTTGGATTTTTTTACATTTTTGATTAAAATATGTTATAATTGAATGACTATCACAAGA
388 ATTTTAAGTTAGATTTTTTTACATTTTTGATTAAAATATGTTATAATTGAATGACTGTCACAAGA
*
415025 AACATCAAGAAAAAGCCATCCAAAGGAGAGAAAAGCCCATTTATAGCTACACAAACCTTTGAAAG
453 AACATCAAGCAAAAGCCATCCAAAGGAGAGAAAAGCCCATTTATAG-TACACAAACCTTTGAAAG
* *
415090 TTTTATTACTCAGTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTGGATTTTTTTTACA
517 TCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTGGA-TTTTTTTACA
*
415155 TTTTTGGTTAAAATATGCTATAATTGAATGTCTGCTTCAAGAAATGTGAAGTAAAAGCCTTCCAT
581 TTTTTTGTTAAAATATGCTATAATTGAATGTCTGCTTCAAGAAATGTGAAGTAAAAGCCTTCCAT
* *
415220 CAGAGGAAAAAGTCTGTTTATAGTCATTCAAACCTTAG
646 TAGAGGAAAAAGTCTGTTTATAGTCATTCAAGCCTTAG
* * * *
415258 AAAGCTTTATTACTTGCTTGAAATGGTTTAATATTCTCGTAAGGGATTCTAAGTTGGATTTTTTT
1 AAAGCTTTATTACTCGCTTTAAATGGTTTAATATTCTCGTAATGAATTCTAAGTTGGATTTTTTT
415323 ACATTTTTGGTTAAAATATGCTATAATCGAATGACTGCCTAGGGAAACATGAAGCAAAAGCCATC
66 ACATTTTTGGTTAAAATATGCTATAATCGAATGACTGCCTAGGGAAACATGAAGCAAAAGCCATC
*****
415388 TATGGGAGAGAAAAGTCAATTTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
131 TATGGGAGAGAAAAGTCAATTTAT------------------------------------AGGCA
************ * * ** * * * * *
415453 NNNNNNNNNNCAAAAGCCATCCATTGA--AG--AGAAAAGTCTATTTATAGTCAC-TCAA--GCC
160 CTCAAGCCTTTGAAAGCC-T-TATT-ACTCGCTTTAAATG-GT-TTTATATTCTCAT-AATTG-A
* * * * * *
415511 TTTGAAAGCCT-GATTACTCTCTTTAGATGGTTTTATAGTCTCATAA-T-TGATTTTAATTTAGA
218 TTT-TAAG-TTAGATT--T-T-TTT--AT-ATTTT-TAGT-T-A-AAGTATG-CTATAA--TGGA
* * *** * * ** *** * * * *
415573 TTTTTTTATATTTTTGGTTAAA-AT-ATGTTATAATTGAATGATTGCATTAGGAAACATTAAG-C
267 --ATGTT-T-GCCTTGG-GAAACGTGA-GGCA-AA---AGCCA-TCCATT-GGAGAGA-AAAGTC
*************************
415635 NNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTC
319 ---CATTTATAGTCACTCAACCCTTTGAAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTC
* * * *
415700 ATAATTGATTTTAAGTTTGATGTTTTTACATTTTTTACTAAAATATGTTATAATTGAATGACTGT
381 ATAATTGATTTTAAGTTAGATTTTTTTACATTTTTGATTAAAATATGTTATAATTGAATGACTGT
** ** *
415765 CACAAGAAATGTCAAGCAAAAGCCAATCCAAGAGGAGA-AGTAGCCCATTTATAGT-CACTAACC
446 CACAAGAAACATCAAGCAAAAGCC-ATCCAA-AGGAGAGAAAAGCCCATTTATAGTACACAAACC
415828 TTTGAAA-TCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATCTTTTCAAGTTGG
509 TTTGAAAGT-CTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGA--TTTT-AAGTTGG
*
415892 ATTTTTTTACATTTTTTGTTAAAATATGCTATAATTGAATGTCTGCTTCAAGAAATGTAAAGTAA
570 ATTTTTTTACATTTTTTGTTAAAATATGCTATAATTGAATGTCTGCTTCAAGAAATGTGAAGTAA
* * * *
415957 AAGCCTTCCATTAGAGGAAAAACTCCGTTTATAGTCATTCAAGTCTTAA
635 AAGCCTTCCATTAGAGGAAAAAGTCTGTTTATAGTCATTCAAGCCTTAG
* * *
416006 AAAGCTTTATTACTTGCTTTAAATGGTTTAATATTCTTGT-ATTAGATTCTAAGTTGGATTTTTT
1 AAAGCTTTATTACTCGCTTTAAATGGTTTAATATTCTCGTAATGA-ATTCTAAGTTGGATTTTTT
* * * *
416070 TACATTTTTAGTTAAAATATACTATAATCGAATGACTGCCTAGGGAAACATGAAGAAAAAGCTAT
65 TACATTTTTGGTTAAAATATGCTATAATCGAATGACTGCCTAGGGAAACATGAAGCAAAAGCCAT
* * *
416135 CTATGGGGGAGAAAAGTCAATTTATAGGCA--CAGAGCTTTTGAAAGCCTTATTACTCGCTCTAA
130 CTATGGGAGAGAAAAGTCAATTTATAGGCACTCA-AGCCTTTGAAAGCCTTATTACTCGCTTTAA
********** * * *
416198 ATGGTTTTATATTCTCATAATTNNNNNNNNNNT-GAATTTTTTTACATTTTTGGTTAATGTATGC
194 ATGGTTTTATATTCTCATAATTGATTTTAAGTTAG-ATTTTTTTATATTTTTAGTTAAAGTATGC
*
416262 TATAATGGAATGTTTGCCTTGGGAAACGTGAGGCAAAAGCCATCCATTGGAGAGAAAAGTCTATT
258 TATAATGGAATGTTTGCCTTGGGAAACGTGAGGCAAAAGCCATCCATTGGAGAGAAAAGTCCATT
************* * *
416327 TATAGNNNNNNNNNNNNNTGAAAGCCTTATTACTCGCTTTAAATGATTTTATATTCTCATAATTG
323 TATAGTCACTCAACCCTTTGAAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTG
* * * * * ***
416392 ATTTTAATTTGGA-TTTTTTAAACTTTTTG-TTAAAATATGTTATAATTGAAAGACTGTGATGGG
388 ATTTTAAGTTAGATTTTTTTACA-TTTTTGATTAAAATATGTTATAATTGAATGACTGTCACAAG
* *
416455 AAACATCAAGCAAAAGCCATCCAAAGGAGAGAAAAGCCCATTTGTAGTTACATAAACCTTTGAAA
452 AAACATCAAGCAAAAGCCATCCAAAGGAGAGAAAAGCCCATTTATAG-TACACAAACCTTTGAAA
* * * *
416520 GTCTTATTATTCACTTTAAATGGTTTTATATTCTCATAATTCATTTTAAGTTGGATTTTTTCAAA
516 GTCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTGGATTTTTTTACA
* * *
416585 TTTTTTGTTAAAATATGCTATAATTGAATGTCTGCCTCAAGAAATATGAAGTAATAGCCTTCCAT
581 TTTTTTGTTAAAATATGCTATAATTGAATGTCTGCTTCAAGAAATGTGAAGTAAAAGCCTTCCAT
* *
416650 TAGAGGAAAAAGT-TCATTTATAGTCACTCAAGCCTTAG
646 TAGAGGAAAAAGTCT-GTTTATAGTCATTCAAGCCTTAG
* * *
416688 AAAGCTTTATTACTCGCTTTAAATGGTTTTATATTCTCGTAATGGATTCTAAGTTGAATTTTTTT
1 AAAGCTTTATTACTCGCTTTAAATGGTTTAATATTCTCGTAATGAATTCTAAGTTGGATTTTTTT
* * * *
416753 ATATTTTTGGTTCAAATATGCTATAATCGAATGACTGCCTAAGGAAATATGAAGCAAAAGCC--C
66 ACATTTTTGGTTAAAATATGCTATAATCGAATGACTGCCTAGGGAAACATGAAGCAAAAGCCATC
** * * *
416816 TATATGAGAGAAAAGGTCAACTTATAAGCAATCAAGCCTTTGAAAGCCTTATTACTCGCTTTAAA
131 TATGGGAGAGAAAA-GTCAATTTATAGGCACTCAAGCCTTTGAAAGCCTTATTACTCGCTTTAAA
* * *
416881 TAGTTTTATATTCTCATAATTGATTTTAA-TTAAGATTTTTTTATATTTTTAGTTAAAATATGTT
195 TGGTTTTATATTCTCATAATTGATTTTAAGTT-AGATTTTTTTATATTTTTAGTTAAAGTATGCT
** * * * * * * * *
416945 ATAATTTAATGATTGCATTAGGAAACATGAAGTAAAAACCATCCA-TGGAAGAGAAATGTCCATT
259 ATAATGGAATGTTTGCCTTGGGAAACGTGAGGCAAAAGCCATCCATTGG-AGAGAAAAGTCCATT
* ********** * *
417009 TATAGTCACTCAACCCTTTGAAAGTCTTATTACTCACTTTNNNNNNNNNNATAATCTCATAATTA
323 TATAGTCACTCAACCCTTTGAAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTG
* *
417074 ATTTTAAGTTAGAATTTTTTACATTTTTGAATAAAATATGTTATAATTGAATGACTGTCACAAGA
388 ATTTTAAGTTAGATTTTTTTACATTTTTGATTAAAATATGTTATAATTGAATGACTGTCACAAGA
* * * * *
417139 AACGTCAAGCAAAAGCCATTCAAAGAAGAGAAAAGCCTATTTATAGCTACATAAACCTTTGAAAG
453 AACATCAAGCAAAAGCCATCCAAAGGAGAGAAAAGCCCATTTATAG-TACACAAACCTTTGAAAG
********** * *
417204 TCTTATTACTCACTTTAAANNNNNNNNNNTTCTCATAATTGATTTTAAGTTAGCTTTTTTTACAT
517 TCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTGGATTTTTTTACAT
* * * * *
417269 TTTTAGTTAAAATATGCTATAATTGAATGTTTGCCTT-AGGAAGTGCGAAGTAAAAGCCTTCCAT
582 TTTTTGTTAAAATATGCTATAATTGAATGTCTG-CTTCAAGAAATGTGAAGTAAAAGCCTTCCAT
* *
417333 TAGAGGAAACAGTCCGTTTATAGTCATTCAAGCCTTAG
646 TAGAGGAAAAAGTCTGTTTATAGTCATTCAAGCCTTAG
* * * *
417371 AAAGCTTTATTACTTGCTTTAAATGGTTTAATATTCTCCTAATGGATTCTAAGTTGGATTCTTTT
1 AAAGCTTTATTACTCGCTTTAAATGGTTTAATATTCTCGTAATGAATTCTAAGTTGGATTTTTTT
*
417436 ACATTTTTGGTTAAAATATGCTATGATCGAATGACTGCCTAGGGAAACATGAAGCAAAAGCCATC
66 ACATTTTTGGTTAAAATATGCTATAATCGAATGACTGCCTAGGGAAACATGAAGCAAAAGCCATC
* ***
417501 TATAGGAGAGAAAAGTCAATTTATAGGCACTCAAGCCTTTGAAAGCCTTATTACTCGCTTTANNN
131 TATGGGAGAGAAAAGTCAATTTATAGGCACTCAAGCCTTTGAAAGCCTTATTACTCGCTTTAAAT
******* * * *
417566 NNNNNNNTATTCTCATAATTGATTTTAAGTTAGATATTTTTATATTTTTGGTTAACGTATGCTAT
196 GGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTTATATTTTTAGTTAAAGTATGCTAT
* * * *
417631 AATGGAATGTTTGCCTTGGAAAACGTGAGGCAAAAGTCATCTATTGGAGAAAAAAGTCCATTTAT
261 AATGGAATGTTTGCCTTGGGAAACGTGAGGCAAAAGCCATCCATTGGAGAGAAAAGTCCATTTAT
* *
417696 AGTCACTCAAACCTTTGAAAGCCTTATTACTCGCTTTAAA
326 AGTCACTCAACCCTTTGAAAGCCTTATTACTCACTTTAAA
417736 NNNNNNNNNN
Statistics
Matches: 2547, Mismatches: 484, Indels: 264
0.77 0.15 0.08
Matches are distributed among these distances:
680 12 0.00
681 17 0.01
682 402 0.16
683 385 0.15
684 791 0.31
685 241 0.09
686 46 0.02
687 7 0.00
688 6 0.00
689 5 0.00
690 2 0.00
693 5 0.00
694 7 0.00
695 2 0.00
696 3 0.00
698 3 0.00
699 1 0.00
700 6 0.00
701 3 0.00
702 3 0.00
703 4 0.00
704 1 0.00
706 3 0.00
707 1 0.00
708 2 0.00
709 5 0.00
710 16 0.01
711 8 0.00
712 4 0.00
720 5 0.00
721 10 0.00
722 20 0.01
723 4 0.00
724 2 0.00
725 1 0.00
726 3 0.00
728 2 0.00
729 4 0.00
730 3 0.00
731 3 0.00
732 5 0.00
733 2 0.00
734 2 0.00
736 3 0.00
737 3 0.00
738 5 0.00
739 5 0.00
742 2 0.00
743 5 0.00
744 5 0.00
745 4 0.00
746 53 0.02
747 120 0.05
748 271 0.11
749 14 0.01
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.37
Consensus pattern (683 bp):
AAAGCTTTATTACTCGCTTTAAATGGTTTAATATTCTCGTAATGAATTCTAAGTTGGATTTTTTT
ACATTTTTGGTTAAAATATGCTATAATCGAATGACTGCCTAGGGAAACATGAAGCAAAAGCCATC
TATGGGAGAGAAAAGTCAATTTATAGGCACTCAAGCCTTTGAAAGCCTTATTACTCGCTTTAAAT
GGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTTATATTTTTAGTTAAAGTATGCTAT
AATGGAATGTTTGCCTTGGGAAACGTGAGGCAAAAGCCATCCATTGGAGAGAAAAGTCCATTTAT
AGTCACTCAACCCTTTGAAAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATT
TTAAGTTAGATTTTTTTACATTTTTGATTAAAATATGTTATAATTGAATGACTGTCACAAGAAAC
ATCAAGCAAAAGCCATCCAAAGGAGAGAAAAGCCCATTTATAGTACACAAACCTTTGAAAGTCTT
ATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTGGATTTTTTTACATTTTT
TGTTAAAATATGCTATAATTGAATGTCTGCTTCAAGAAATGTGAAGTAAAAGCCTTCCATTAGAG
GAAAAAGTCTGTTTATAGTCATTCAAGCCTTAG
Found at i:417493 original size:342 final size:339
Alignment explanation
Indices: 415663--417735 Score: 1753
Period size: 341 Copynumber: 6.1 Consensus size: 339
415653 NNNNNNNNNN
* * * *
415663 AAGCCTTATTACTCACTTTAAATGGTTTTATATTCTCATAATTGATTTTAAGTTTGATGTTTTTA
1 AAGCTTTATTACTCGCTTTAAATGGTTTTATATTCTCATAATTGATTCTAAGTTGGAT-TTTTTA
*** * * * **
415728 CATTTTTTACTAAAATATGTTATAATTGAATGACTGTCAC-A-AGAAATGTCAAGCAAAAGCCAA
65 CATTTTTGGTTAAAATATGCTATAATCGAATGACTG-C-CTAGGGAAACATCAAGCAAAAGCC-A
** * *
415791 TCCAAGAGGAGA-AGTAGCCCATTTATAGTCAC-T-AACCTTTGAAATCCTTATTACTCACTTTA
127 T-CAA-AGGAGAGAAAAGCCAATTTATAG-CACATAAACCTTTGAAAGCCTTATTACTCACTTTA
* *
415853 AATGGTTTTATATTCTCATAATTGATCTTTTCAAGTTGGATTTTTTTACATTTTTTGTTAAAATA
189 AATGGTTTTATATTCTCATAATTGA--TTTT-AAGTTAGATTTTTTTACATTTTTAGTTAAAATA
* * * * * *
415918 TGCTATAATTGAATGTCTG-CTTCAAGAAATGTAAAGTAAAAGCCTTCCATTAGAGGAAAAACTC
251 TGCTATAATTGAATGTTTGCCTT-AGGAAACGTGAAGTAAAAGCCATCCATTAGAGGAAAAAGTC
* * * *
415982 CGTTTATAGTCATTCAAGTCTTAAA
315 CATTTATAGTCACTCAAGCCTTAGA
* * **
416007 AAGCTTTATTACTTGCTTTAAATGGTTTAATATTCTTGT-ATTAGATTCTAAGTTGGATTTTTTT
1 AAGCTTTATTACTCGCTTTAAATGGTTTTATATTCTCATAATT-GATTCTAAGTTGGA-TTTTTT
* * * * *
416071 ACATTTTTAGTTAAAATATACTATAATCGAATGACTGCCTAGGGAAACATGAAGAAAAAGCTATC
64 ACATTTTTGGTTAAAATATGCTATAATCGAATGACTGCCTAGGGAAACATCAAGCAAAAGCCATC
** * * * * * * *
416136 TATGGGGGAGAAAAGTCAATTTATAGGCACA-GAGCTTTTGAAAGCCTTATTACTCGCTCTAAAT
129 -AAAGGAGAGAAAAGCCAATTTATA-GCACATAAACCTTTGAAAGCCTTATTACTCACTTTAAAT
********** * **
416200 GGTTTTATATTCTCATAATTNNNNNNNNNNT-GAATTTTTTTACATTTTTGGTTAATGTATGCTA
192 GGTTTTATATTCTCATAATTGATTTTAAGTTAG-ATTTTTTTACATTTTTAGTTAAAATATGCTA
* * * * * *
416264 TAATGGAATGTTTGCCTTGGGAAACGTGAGGCAAAAGCCATCCATTGGA-GAGAAAAGTCTATTT
256 TAATTGAATGTTTGCCTTAGGAAACGTGAAGTAAAAGCCATCCATTAGAGGA-AAAAGTCCATTT
************
416328 ATAGNNNNNNNNNNNNNT-GA
320 ATAG-TCACTCAAGCCTTAGA
* * * * *
416348 AAGCCTTATTACTCGCTTTAAATGATTTTATATTCTCATAATTGATTTTAATTTGGATTTTTTAA
1 AAGCTTTATTACTCGCTTTAAATGGTTTTATATTCTCATAATTGATTCTAAGTTGGATTTTTTAC
* * *
416413 ACTTTTT-GTTAAAATATGTTATAATTGAAAGACTG--TGATGGGAAACATCAAGCAAAAGCCAT
66 A-TTTTTGGTTAAAATATGCTATAATCGAATGACTGCCT-A-GGGAAACATCAAGCAAAAGCCAT
* * * * *
416475 CCAAAGGAGAGAAAAGCCCATTTGTAGTTACATAAACCTTTGAAAGTCTTATTATTCACTTTAAA
128 -CAAAGGAGAGAAAAGCCAATTTATAG-CACATAAACCTTTGAAAGCCTTATTACTCACTTTAAA
* * * * *
416540 TGGTTTTATATTCTCATAATTCATTTTAAGTTGGATTTTTTCAAATTTTTTGTTAAAATATGCTA
191 TGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTTACATTTTTAGTTAAAATATGCTA
* * * ** * * *
416605 TAATTGAATGTCTGCCTCAAGAAATATGAAGTAATAGCCTTCCATTAGAGGAAAAAGTTCATTTA
256 TAATTGAATGTTTGCCTTAGGAAACGTGAAGTAAAAGCCATCCATTAGAGGAAAAAGTCCATTTA
416670 TAGTCACTCAAGCCTTAGA
321 TAGTCACTCAAGCCTTAGA
* * *
416689 AAGCTTTATTACTCGCTTTAAATGGTTTTATATTCTCGTAATGGATTCTAAGTTGAATTTTTTTA
1 AAGCTTTATTACTCGCTTTAAATGGTTTTATATTCTCATAATTGATTCTAAGTTGGA-TTTTTTA
* * * * * *
416754 TATTTTTGGTTCAAATATGCTATAATCGAATGACTGCCTAAGGAAATATGAAGCAAAAGCCCT-A
65 CATTTTTGGTTAAAATATGCTATAATCGAATGACTGCCTAGGGAAACATCAAGCAAAAGCCATCA
* * * * * *
416818 TATGAGAGAAAAGGTCAACTTATAAGCA-ATCAAGCCTTTGAAAGCCTTATTACTCGCTTTAAAT
130 AAGGAGAGAAAA-GCCAATTTAT-AGCACAT-AAACCTTTGAAAGCCTTATTACTCACTTTAAAT
* * *
416882 AGTTTTATATTCTCATAATTGATTTTAA-TTAAGATTTTTTTATATTTTTAGTTAAAATATGTTA
192 GGTTTTATATTCTCATAATTGATTTTAAGTT-AGATTTTTTTACATTTTTAGTTAAAATATGCTA
* * * * * * * *
416946 TAATTTAATGATTGCATTAGGAAACATGAAGTAAAAACCATCCA-TGGAAGAGAAATGTCCATTT
256 TAATTGAATGTTTGCCTTAGGAAACGTGAAGTAAAAGCCATCCATTAGAGGA-AAAAGTCCATTT
* *
417010 ATAGTCACTCAACCCTTTGA
320 ATAGTCACTCAAGCCTTAGA
* ********** * * * *
417030 AAG-TCTTATTACTCACTTTNNNNNNNNNNATAATCTCATAATTAATTTTAAGTTAGAATTTTTT
1 AAGCT-TTATTACTCGCTTTAAATGGTTTTATATTCTCATAATTGATTCTAAGTT-GGATTTTTT
** * * * *
417094 ACATTTTTGAATAAAATATGTTATAATTGAATGACTGTCAC-A-AGAAACGTCAAGCAAAAGCCA
64 ACATTTTTGGTTAAAATATGCTATAATCGAATGACTG-C-CTAGGGAAACATCAAGCAAAAGCCA
* * *
417157 TTCAAAGAAGAGAAAAGCCTATTTATAGCTACATAAACCTTTGAAAGTCTTATTACTCACTTTAA
127 -TCAAAGGAGAGAAAAGCCAATTTATAGC-ACATAAACCTTTGAAAGCCTTATTACTCACTTTAA
********** *
417222 ANNNNNNNNNNTTCTCATAATTGATTTTAAGTTAGCTTTTTTTACATTTTTAGTTAAAATATGCT
190 ATGGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTTACATTTTTAGTTAAAATATGCT
** * * * *
417287 ATAATTGAATGTTTGCCTTAGGAAGTGCGAAGTAAAAGCCTTCCATTAGAGGAAACAGTCCGTTT
255 ATAATTGAATGTTTGCCTTAGGAAACGTGAAGTAAAAGCCATCCATTAGAGGAAAAAGTCCATTT
*
417352 ATAGTCATTCAAGCCTTAGA
320 ATAGTCACTCAAGCCTTAGA
* * * *
417372 AAGCTTTATTACTTGCTTTAAATGGTTTAATATTCTCCTAATGGATTCTAAGTTGGATTCTTTTA
1 AAGCTTTATTACTCGCTTTAAATGGTTTTATATTCTCATAATTGATTCTAAGTTGGATT-TTTTA
* *
417437 CATTTTTGGTTAAAATATGCTATGATCGAATGACTGCCTAGGGAAACATGAAGCAAAAGCCATCT
65 CATTTTTGGTTAAAATATGCTATAATCGAATGACTGCCTAGGGAAACATCAAGCAAAAGCCATC-
* * * * ***
417502 ATAGGAGAGAAAAGTCAATTTATAGGCAC-TCAAGCCTTTGAAAGCCTTATTACTCGCTTTANNN
129 AAAGGAGAGAAAAGCCAATTTATA-GCACAT-AAACCTTTGAAAGCCTTATTACTCACTTTAAAT
******* * * * **
417566 NNNNNNNTATTCTCATAATTGATTTTAAGTTAGATATTTTTATATTTTTGGTTAACGTATGCTAT
192 GGTTTTATATTCTCATAATTGATTTTAAGTTAGATTTTTTTACATTTTTAGTTAAAATATGCTAT
* * * * * * *
417631 AATGGAATGTTTGCCTT-GGAAAACGTGAGGCAAAAGTCATCTATTGGAGAAAAAAGTCCATTTA
257 AATTGAATGTTTGCCTTAGG-AAACGTGAAGTAAAAGCCATCCATTAGAGGAAAAAGTCCATTTA
* *
417695 TAGTCACTCAAACCTTTGA
321 TAGTCACTCAAGCCTTAGA
*
417714 AAGCCTTATTACTCGCTTTAAA
1 AAGCTTTATTACTCGCTTTAAA
417736 NNNNNNNNNN
Statistics
Matches: 1360, Mismatches: 319, Indels: 102
0.76 0.18 0.06
Matches are distributed among these distances:
338 1 0.00
339 2 0.00
340 99 0.07
341 565 0.42
342 502 0.37
343 46 0.03
344 144 0.11
345 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.37
Consensus pattern (339 bp):
AAGCTTTATTACTCGCTTTAAATGGTTTTATATTCTCATAATTGATTCTAAGTTGGATTTTTTAC
ATTTTTGGTTAAAATATGCTATAATCGAATGACTGCCTAGGGAAACATCAAGCAAAAGCCATCAA
AGGAGAGAAAAGCCAATTTATAGCACATAAACCTTTGAAAGCCTTATTACTCACTTTAAATGGTT
TTATATTCTCATAATTGATTTTAAGTTAGATTTTTTTACATTTTTAGTTAAAATATGCTATAATT
GAATGTTTGCCTTAGGAAACGTGAAGTAAAAGCCATCCATTAGAGGAAAAAGTCCATTTATAGTC
ACTCAAGCCTTAGA
Found at i:420133 original size:170 final size:161
Alignment explanation
Indices: 419911--420241 Score: 327
Period size: 170 Copynumber: 2.0 Consensus size: 161
419901 CGAGAATATT
* *
419911 AAACTATTTAAAGCAAGTAATAAAGCTTTCTAAGGCTTGAATGACTATAAAT-GGACTTT-T-TC
1 AAACCATTTAAAGCAAGTAATAAAGCTTTCAAAGGCTTGAATGACTATAAATGGGACTTTCTCTC
*
419973 CTCTAATGGAA-GGCTTTTACTTCACATTTCCTGAGGCAGACATTCAATTATAACATATTTTAAT
66 CT-T--T-GAATGGCTTTTACTTCACATTTCCTGAGACAGACATTCAATTATAACATATTTTAAT
*
420037 CAAAAATGT-CAAAAATCCAACTTAAAATCAATTA
127 CAAAAATGTAAAAAAATCCAACTTAAAATCAATTA
* *
420071 NNNNNNNNNNAAACCATTTAAAGTAAGTAAT-AAGACTTTCAAAGG-TT-TATGTAGCTATAAAT
1 ----------AAACCATTTAAAGCAAGTAATAAAG-CTTTCAAAGGCTTGAATG-A-CTATAAAT
* * * * * *
420133 GGGCCTTTCTCTCCTTTGAATGGCTTTTACTTGACGTTTCTTGTGACAGTCATTCAATTATAACA
53 GGGACTTTCTCTCCTTTGAATGGCTTTTACTTCACATTTCCTGAGACAGACATTCAATTATAACA
* *
420198 TATTTTAATTAAAAATGTAAAAAAATCTAACTTAAAATCAATTA
118 TATTTTAATCAAAAATGTAAAAAAATCCAACTTAAAATCAATTA
420242 TGAGAATATN
Statistics
Matches: 139, Mismatches: 14, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
168 3 0.02
169 9 0.06
170 92 0.66
171 29 0.21
172 2 0.01
173 4 0.03
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.34
Consensus pattern (161 bp):
AAACCATTTAAAGCAAGTAATAAAGCTTTCAAAGGCTTGAATGACTATAAATGGGACTTTCTCTC
CTTTGAATGGCTTTTACTTCACATTTCCTGAGACAGACATTCAATTATAACATATTTTAATCAAA
AATGTAAAAAAATCCAACTTAAAATCAATTA
Found at i:420468 original size:171 final size:171
Alignment explanation
Indices: 419500--420683 Score: 646
Period size: 171 Copynumber: 6.9 Consensus size: 171
419490 CTATAACAGT
* * ********
419500 CATTCAATTATAACATATTTTAATCAAAAATTTAAAAAAATCCAACTTAAAAT-AANNNNNNNNN
1 CATTCAATTATAACATATTTTAACCAAAAATGTAAAAAAATCCAACTTAAAATCAA-TTATGAGA
* *
419564 NTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTC-AAGGCTTGAGTGACTATAAATAGACTTT
65 ATATAAAACTATTTAAAGTGAGTAATAAGGC-TTTCAAAGGCTTGAGTGACTATAAATGGACTTT
********** * * * * * *
419628 NNNNNNNNNNGGATGGCTTTTGCCTCACGTTTCCCAAGGAAAA
129 TTTCTCCAATGAATGGCTTTTACTTCACGTTTCTCGAGGCAAA
* * * * *
419671 CATTCCATTATAGCATACTTTAACCAAAAAAGTAAAAAAATCCAACTTAAAATCAATTATGAGAN
1 CATTCAATTATAACATATTTTAACCAAAAATGTAAAAAAATCCAACTTAAAATCAATTATGAGAA
********* * * * * *
419736 NNNNNNNNNATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTTAGTGCCTATAAATTGACTTTTC
66 TATAAAACTATTTAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTT
* * * * **
419801 TCTCCTAT-AGATGGCTTTTGCTTCATGTTT-TCCTAGGCAGT
131 TCTCCAATGA-ATGGCTTTTACTTCACGTTTCT-CGAGGCAAA
** * * * * * *
419842 CATTTGATTATAGCATATTTTAACCAAAAATGTAAAAAAATCAAACTTAGAATCCACTACGAGAA
1 CATTCAATTATAACATATTTTAACCAAAAATGTAAAAAAATCCAACTTAAAATCAATTATGAGAA
* ** * * *
419907 TATTAAACTATTTAAAGCAAGTAATAAAGCTTTCTAAGGCTTGAATGACTATAAATGGACTTTTT
66 TATAAAACTATTTAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTT
* * * *
419972 CCTCTAATGGAA-GGCTTTTACTTCACATTTC-CTGAGGCAGA
131 TCTCCAAT-GAATGGCTTTTACTTCACGTTTCTC-GAGGCAAA
* * ******
420013 CATTCAATTATAACATATTTTAATCAAAAATGT-CAAAAATCCAACTTAAAATCAATTANNNNNN
1 CATTCAATTATAACATATTTTAACCAAAAATGTAAAAAAATCCAACTTAAAATCAATTATGAGAA
**** * * * * * *
420077 NNNNAAACCATTTAAAGTAAGTAATAAGACTTTCAAAGG-TTTA-TGTAGCTATAAATGGGCCTT
66 TATAAAACTATTTAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTG-A-CTATAAATGGACTTT
* ** * * * * **
420140 TCTCTCCTTTGAATGGCTTTTACTTGACGTTTCTTGTGACAGT
129 TTTCTCCAATGAATGGCTTTTACTTCACGTTTCTCGAGGCAAA
** *
420183 CATTCAATTATAACATATTTTAATTAAAAATGTAAAAAAATCTAACTTAAAATCAATTATGAGAA
1 CATTCAATTATAACATATTTTAACCAAAAATGTAAAAAAATCCAACTTAAAATCAATTATGAGAA
********************************* * * *
420248 TATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGGTTAAGTGACTATATATGGACTTTTT
66 TATAAAACTATTTAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTT
*
420313 TCTCCAATGAATGGCTTTTACCTCACGTTTCTCGAGGCAAA
131 TCTCCAATGAATGGCTTTTACTTCACGTTTCTCGAGGCAAA
* * * * * *
420354 CATTCCATTATAGCATATTTTAACCAAAAATATAAAAAAATCCAACTTAGAATCCATTACGAGAA
1 CATTCAATTATAACATATTTTAACCAAAAATGTAAAAAAATCCAACTTAAAATCAATTATGAGAA
* * ****
420419 TATAAAACCATTTAAAGTGAGTAATAAGGCTTTCCAAGGCTTGAGTGACTATAAATGGACNNNNN
66 TATAAAACTATTTAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGAC-TTTT
***** * * * * *
420484 NNNNNC-ATGGATGGCTTTTGCTTCATGTTTC-CTGATGCAAT
130 TTCTCCAATGAATGGCTTTTACTTCACGTTTCTC-GAGGCAAA
* *
420525 CATTCAATTATAAAATATTTTAACCAAAAATGTAAAAAAATCCAAATTAAAATCAATTATGAGAA
1 CATTCAATTATAACATATTTTAACCAAAAATGTAAAAAAATCCAACTTAAAATCAATTATGAGAA
* * * * * * *
420590 TATAAAACTATGTAGAGTGTGTAATATGGCTTTCTAAGGCTTGAATGACTATAAATAGACTTTTT
66 TATAAAACTATTTAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTT
* *
420655 CCTCCAATGGATGG-TTTGTACTTCACGTT
131 TCTCCAATGAATGGCTTT-TACTTCACGTT
420684 NNNNNNNNNN
Statistics
Matches: 731, Mismatches: 263, Indels: 38
0.71 0.25 0.04
Matches are distributed among these distances:
168 2 0.00
169 7 0.01
170 132 0.18
171 579 0.79
172 8 0.01
173 3 0.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.31
Consensus pattern (171 bp):
CATTCAATTATAACATATTTTAACCAAAAATGTAAAAAAATCCAACTTAAAATCAATTATGAGAA
TATAAAACTATTTAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTT
TCTCCAATGAATGGCTTTTACTTCACGTTTCTCGAGGCAAA
Found at i:430868 original size:17 final size:17
Alignment explanation
Indices: 430846--430911 Score: 62
Period size: 17 Copynumber: 3.7 Consensus size: 17
430836 TTTTCTTTTT
430846 ACTATTTATATTATTTA
1 ACTATTTATATTATTTA
430863 ACTATTTATA-TATTTAA
1 ACTATTTATATTATTT-A
* * *
430880 AATCTTGTATATGGTAATTA
1 ACTATT-TATAT--TATTTA
430900 ACTATTTATATT
1 ACTATTTATATT
430912 TTATGNNNNN
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
16 5 0.13
17 16 0.41
18 4 0.10
19 5 0.13
20 5 0.13
21 4 0.10
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.53
Consensus pattern (17 bp):
ACTATTTATATTATTTA
Found at i:467908 original size:22 final size:23
Alignment explanation
Indices: 467874--467920 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
467864 ATATAGAGTT
467874 ATTTAGACTTAGTT-TTGATAGTA
1 ATTTAGACTTAGTTCTTG-TAGTA
467897 ATTTAG-CTTAGTTCTTGTAGTA
1 ATTTAGACTTAGTTCTTGTAGTA
467919 AT
1 AT
467921 GCATAGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.49
Consensus pattern (23 bp):
ATTTAGACTTAGTTCTTGTAGTA
Found at i:480089 original size:38 final size:38
Alignment explanation
Indices: 480033--480110 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
480023 CCCTAATCTT
* *
480033 CTTTGAACTGGGTCAAGTGATAAACATAAAAGTTTTAG
1 CTTTAAACTGGGTAAAGTGATAAACATAAAAGTTTTAG
480071 CTTTAAACTGGGTAAAGTGATAAACATAAAAGTTTTAG
1 CTTTAAACTGGGTAAAGTGATAAACATAAAAGTTTTAG
480109 CT
1 CT
480111 CTATCTCTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.32
Consensus pattern (38 bp):
CTTTAAACTGGGTAAAGTGATAAACATAAAAGTTTTAG
Found at i:484190 original size:15 final size:16
Alignment explanation
Indices: 484157--484190 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
484147 TTAATTTAAG
484157 TTATTTTAGTTAAATT
1 TTATTTTAGTTAAATT
*
484173 TTATTTTA-TTATATT
1 TTATTTTAGTTAAATT
484188 TTA
1 TTA
484191 AATTACTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTATTTTAGTTAAATT
Found at i:484622 original size:38 final size:38
Alignment explanation
Indices: 484571--484645 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
484561 NNNATAGAGG
*
484571 TAAAACTTTTATGTTTATCACTTTACCCAGTTCAAAGC
1 TAAAACTTTTATGTTTATCACTTGACCCAGTTCAAAGC
*
484609 TAAAACTTTTATGTTTATCACTTGACTCAGTTCAAAG
1 TAAAACTTTTATGTTTATCACTTGACCCAGTTCAAAG
484646 AAGATTAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (38 bp):
TAAAACTTTTATGTTTATCACTTGACCCAGTTCAAAGC
Found at i:508972 original size:49 final size:49
Alignment explanation
Indices: 508915--509013 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
508905 AAGATGTCCT
508915 GACCAAAAAAAGGAAAATTGGAAGATTTTGAGACAATTGCACTTACTGG
1 GACCAAAAAAAGGAAAATTGGAAGATTTTGAGACAATTGCACTTACTGG
* *
508964 GACCAAAAAAAGGGAAATTGGAAGATTTTGAGACAATTGTACTTACTGG
1 GACCAAAAAAAGGAAAATTGGAAGATTTTGAGACAATTGCACTTACTGG
509013 G
1 G
509014 TAGTGCATTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.23
Consensus pattern (49 bp):
GACCAAAAAAAGGAAAATTGGAAGATTTTGAGACAATTGCACTTACTGG
Found at i:518882 original size:13 final size:13
Alignment explanation
Indices: 518864--518888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
518854 GAGTTTCTTA
518864 TCATTTTGTGCTG
1 TCATTTTGTGCTG
518877 TCATTTTGTGCT
1 TCATTTTGTGCT
518889 TAGCAGACTT
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:0.08, C:0.16, G:0.20, T:0.56
Consensus pattern (13 bp):
TCATTTTGTGCTG
Found at i:524899 original size:22 final size:21
Alignment explanation
Indices: 524874--524934 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
524864 GGATATGTTC
* *
524874 ATGCAATTCATGACAAAGCCTA
1 ATGC-ATTTATGACAAAGACTA
* *
524896 ATGCATTTATAACAAAGACTG
1 ATGCATTTATGACAAAGACTA
524917 ATGCATTTATGACAAAGA
1 ATGCATTTATGACAAAGA
524935 TTGATGCGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 30 0.88
22 4 0.12
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (21 bp):
ATGCATTTATGACAAAGACTA
Found at i:524939 original size:21 final size:21
Alignment explanation
Indices: 524886--524941 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
524876 GCAATTCATG
* *
524886 ACAAAGCCTAATGCATTTATA
1 ACAAAGACTGATGCATTTATA
*
524907 ACAAAGACTGATGCATTTATG
1 ACAAAGACTGATGCATTTATA
*
524928 ACAAAGATTGATGC
1 ACAAAGACTGATGC
524942 GTCCATTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (21 bp):
ACAAAGACTGATGCATTTATA
Found at i:535255 original size:13 final size:13
Alignment explanation
Indices: 535237--535261 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
535227 AAGTCGGCTA
535237 AGCACAAAATGAC
1 AGCACAAAATGAC
535250 AGCACAAAATGA
1 AGCACAAAATGA
535262 TAACAAACTC
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:0.56, C:0.20, G:0.16, T:0.08
Consensus pattern (13 bp):
AGCACAAAATGAC
Found at i:539717 original size:35 final size:36
Alignment explanation
Indices: 539657--539730 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 36
539647 CAAGTTAGTA
***
539657 GGCCTAATTGATTAAATTGTTTAATTAAATT-ATTG
1 GGCCTAATTGATTAAATTAAATAATTAAATTAATTG
*
539692 GGCCTAATTGATTAAATTAAATAATTAAGTTAATTG
1 GGCCTAATTGATTAAATTAAATAATTAAATTAATTG
539728 GGC
1 GGC
539731 TTCTTAAGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
35 27 0.79
36 7 0.21
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (36 bp):
GGCCTAATTGATTAAATTAAATAATTAAATTAATTG
Found at i:553590 original size:35 final size:35
Alignment explanation
Indices: 553562--553779 Score: 145
Period size: 35 Copynumber: 6.3 Consensus size: 35
553552 AATTGTTAAT
553562 TTTAATCAATAAGGCCCAATAACTTAATTAAACAA
1 TTTAATCAATAAGGCCCAATAACTTAATTAAACAA
* **********
553597 TTTAATCAATTAGGCCCAATAACTTGNNNNNNNNNN
1 TTTAATCAATAAGGCCCAATAACTT-AATTAAACAA
*
553633 TTTAATCAATTAGGCCCAATAACTTAATTAAACAA
1 TTTAATCAATAAGGCCCAATAACTTAATTAAACAA
* ** * ***
553668 TTTAATCAATTAGGCTTAATAAGTTAATTATTTAA
1 TTTAATCAATAAGGCCCAATAACTTAATTAAACAA
* * * * * *
553703 TTTAATTAATTAGACTCAATGACTTAATTAAATAA
1 TTTAATCAATAAGGCCCAATAACTTAATTAAACAA
* * *
553738 TTTAATGAATTAGG--C-ATAACTTAATTAAATAA
1 TTTAATCAATAAGGCCCAATAACTTAATTAAACAA
553770 TTTTAATCAA
1 -TTTAATCAA
553780 ATGCTTGAGA
Statistics
Matches: 143, Mismatches: 38, Indels: 6
0.76 0.20 0.03
Matches are distributed among these distances:
32 16 0.11
33 9 0.06
35 93 0.65
36 25 0.17
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.35
Consensus pattern (35 bp):
TTTAATCAATAAGGCCCAATAACTTAATTAAACAA
Found at i:554115 original size:36 final size:36
Alignment explanation
Indices: 554074--554318 Score: 199
Period size: 36 Copynumber: 6.9 Consensus size: 36
554064 NNNATTAAAC
554074 AATTTAATCAATTAGGCCCAATAACTTGATTAAAAA
1 AATTTAATCAATTAGGCCCAATAACTTGATTAAAAA
* * ****
554110 AATTTAATCAATTAGGCCTAATAACTTAATT-GTTT
1 AATTTAATCAATTAGGCCCAATAACTTGATTAAAAA
* * * * *
554145 AATTTAATCAATGAGGTCCAATAATTTAATT-AAAC
1 AATTTAATCAATTAGGCCCAATAACTTGATTAAAAA
********** *
554180 AATTTAATCAATTAGNNNNNNNNNNTTGATTAAACA
1 AATTTAATCAATTAGGCCCAATAACTTGATTAAAAA
* *
554216 AATTTAATCAATTACGCCCAATAACTTGATT-AAAC
1 AATTTAATCAATTAGGCCCAATAACTTGATTAAAAA
* *
554251 AATTTAATCAATTAGGCTCAATAACTTGATTAAACA
1 AATTTAATCAATTAGGCCCAATAACTTGATTAAAAA
** * *
554287 AACATAATCTATTAGGCCCAATAACTTAATTA
1 AATTTAATCAATTAGGCCCAATAACTTGATTA
554319 TTTAATTGAA
Statistics
Matches: 157, Mismatches: 50, Indels: 4
0.74 0.24 0.02
Matches are distributed among these distances:
35 77 0.49
36 80 0.51
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.33
Consensus pattern (36 bp):
AATTTAATCAATTAGGCCCAATAACTTGATTAAAAA
Found at i:554156 original size:35 final size:34
Alignment explanation
Indices: 554067--554384 Score: 192
Period size: 35 Copynumber: 9.1 Consensus size: 34
554057 NNNNNNNNNN
* *
554067 ATTAAACAATTTAATCAATTAGGCCCAATAACTTG
1 ATTAAAAAATTTAATCAATTAGG-CCAATAACTTA
554102 ATTAAAAAAATTTAATCAATTAGGCCTAATAACTTA
1 ATT-AAAAAATTTAATCAATTAGGCC-AATAACTTA
**** * *
554138 ATTGTTTAATTTAATCAATGAGGTCCAATAATTTA
1 ATTAAAAAATTTAATCAATTAGG-CCAATAACTTA
* ********* *
554173 ATTAAACAATTTAATCAATTAGNNNNNNNNNNTTG
1 ATTAAAAAATTTAATCAATTAG-GCCAATAACTTA
* *
554208 ATTAAACAAATTTAATCAATTACGCCCAATAACTTG
1 ATTAAA-AAATTTAATCAATTA-GGCCAATAACTTA
* *
554244 ATTAAACAATTTAATCAATTAGGCTCAATAACTTG
1 ATTAAAAAATTTAATCAATTAGGC-CAATAACTTA
** *
554279 ATTAAACAAACATAATCTATTAGGCCCAATAACTTA
1 ATTAAA-AAATTTAATCAATTAGG-CCAATAACTTA
*** * * *
554315 ATTATTTAATTGAATTAATT-GGACCCAATGACTTA
1 ATTAAAAAATTTAATCAATTAGG--CCAATAACTTA
* * *
554350 ATTAGATAATTTAATGAATTAGG-C-ATAACTTA
1 ATTAAAAAATTTAATCAATTAGGCCAATAACTTA
554382 ATT
1 ATT
554385 NNNNNNNNNN
Statistics
Matches: 218, Mismatches: 54, Indels: 25
0.73 0.18 0.08
Matches are distributed among these distances:
32 10 0.05
33 1 0.00
34 4 0.02
35 118 0.54
36 83 0.38
37 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.34
Consensus pattern (34 bp):
ATTAAAAAATTTAATCAATTAGGCCAATAACTTA
Found at i:554280 original size:71 final size:70
Alignment explanation
Indices: 554067--554318 Score: 238
Period size: 71 Copynumber: 3.6 Consensus size: 70
554057 NNNNNNNNNN
* *
554067 ATTAAAC-AATTTAATCAATTAGGCCCAATAACTTGATTAAAAAAATTTAATCAATTAGGCCTAA
1 ATTAAACAAATTTAATCAATTAGGCCCAATAACTTAATT-AAACAATTTAATCAATTAGGCC-AA
*
554131 TAACTTA
64 TAACTTG
**** * * * ******
554138 ATT-GTTTAATTTAATCAATGAGGTCCAATAATTTAATTAAACAATTTAATCAATTAGNNNNNNN
1 ATTAAACAAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAG-GCCAAT
***
554202 NNNTTG
65 AACTTG
* *
554208 ATTAAACAAATTTAATCAATTACGCCCAATAACTTGATTAAACAATTTAATCAATTAGGCTCAAT
1 ATTAAACAAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAGGC-CAAT
554273 AACTTG
65 AACTTG
** *
554279 ATTAAACAAACATAATCTATTAGGCCCAATAACTTAATTA
1 ATTAAACAAATTTAATCAATTAGGCCCAATAACTTAATTA
554319 TTTAATTGAA
Statistics
Matches: 136, Mismatches: 41, Indels: 8
0.74 0.22 0.04
Matches are distributed among these distances:
70 23 0.17
71 113 0.83
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.33
Consensus pattern (70 bp):
ATTAAACAAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAGGCCAATA
ACTTG
Found at i:557363 original size:25 final size:24
Alignment explanation
Indices: 557335--557386 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
557325 TTATTGCCAT
*
557335 GTGGCACCATAATGTCATCATGTCA
1 GTGGCACCACAATGTCATCAT-TCA
* *
557360 GTGGCACTACCATGTCATCATTCA
1 GTGGCACCACAATGTCATCATTCA
557384 GTG
1 GTG
557387 TCACGTGGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (24 bp):
GTGGCACCACAATGTCATCATTCA
Found at i:566827 original size:21 final size:20
Alignment explanation
Indices: 566801--566842 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
566791 TAATTTAAAA
566801 TAAAATAACATAAAATTTAAC
1 TAAAATAACAT-AAATTTAAC
*
566822 TAAAATAACCTAAA-TTAAC
1 TAAAATAACATAAATTTAAC
566841 TA
1 TA
566843 CTCAACATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 3 0.15
21 10 0.50
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAATAACATAAATTTAAC
Found at i:581391 original size:16 final size:15
Alignment explanation
Indices: 581365--581397 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
581355 ACACAATCAC
581365 ATACAATTCACATAT
1 ATACAATTCACATAT
581380 ATACATATTCACATAT
1 ATACA-ATTCACATAT
581396 AT
1 AT
581398 TGTTGTGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (15 bp):
ATACAATTCACATAT
Found at i:592729 original size:20 final size:19
Alignment explanation
Indices: 592704--592758 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
592694 TTTTTGTTTA
592704 AATGTTTATTTTAAGTTAAT
1 AATGTTTATTTTAA-TTAAT
*
592724 AATG-TTAGTTTTATATTATT
1 AATGTTTA-TTTTA-ATTAAT
*
592744 TATGTTTATTTTAAT
1 AATGTTTATTTTAAT
592759 GTTTTTGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 5 0.17
20 21 0.70
21 4 0.13
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (19 bp):
AATGTTTATTTTAATTAAT
Found at i:593720 original size:18 final size:18
Alignment explanation
Indices: 593672--593721 Score: 77
Period size: 17 Copynumber: 2.8 Consensus size: 18
593662 GGGATATAGC
593672 ATTTTGGTTAAGATAGAT
1 ATTTTGGTTAAGATAGAT
593690 ATTTT--TATAAGATAGAT
1 ATTTTGGT-TAAGATAGAT
593707 ATTTTGGTTAAGATA
1 ATTTTGGTTAAGATA
593722 CTTTGCTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.03
17 15 0.52
18 12 0.41
19 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (18 bp):
ATTTTGGTTAAGATAGAT
Found at i:595199 original size:16 final size:16
Alignment explanation
Indices: 595175--595217 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
595165 ACATAAAATT
*
595175 AAAATAACTCACT-TA
1 AAAATAACTAACTATA
595190 AAAATAAACTAACTATA
1 AAAAT-AACTAACTATA
*
595207 AAAACAACTAA
1 AAAATAACTAA
595218 AAATAAGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 13 0.54
17 6 0.25
ACGTcount: A:0.63, C:0.16, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATAACTAACTATA
Found at i:596049 original size:16 final size:15
Alignment explanation
Indices: 596028--596062 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
596018 CTAGACAACA
596028 ATATATGTGAATATGT
1 ATATATGTGAAT-TGT
596044 ATATATGTGAATTGT
1 ATATATGTGAATTGT
596059 ATAT
1 ATAT
596063 GATTCTGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (15 bp):
ATATATGTGAATTGT
Found at i:598113 original size:21 final size:19
Alignment explanation
Indices: 598087--598127 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
598077 AATTTAAAAC
598087 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
598108 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
598127 A
1 A
598128 CTCAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:605164 original size:21 final size:21
Alignment explanation
Indices: 605104--605165 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
605094 TTGAATGGAG
* * *
605104 GCATCGGTCCTTGTCATAAAT
1 GCATCAGTCTTTGTCATGAAT
*
605125 GCATCAGTCTTTGTTATGAAT
1 GCATCAGTCTTTGTCATGAAT
*
605146 GTATCAGTCTTTGTCATGAA
1 GCATCAGTCTTTGTCATGAA
605166 CTACATTAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (21 bp):
GCATCAGTCTTTGTCATGAAT
Found at i:616419 original size:20 final size:21
Alignment explanation
Indices: 616394--616436 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
616384 TTGTTTTCGC
*
616394 AATT-AATAGAAAAATAAAAA
1 AATTAAATAAAAAAATAAAAA
616414 AATTAAATAAAAAAATAAAAA
1 AATTAAATAAAAAAATAAAAA
616435 AA
1 AA
616437 AAGAGTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (21 bp):
AATTAAATAAAAAAATAAAAA
Found at i:616423 original size:13 final size:12
Alignment explanation
Indices: 616405--616438 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
616395 ATTAATAGAA
616405 AAATAAAAAAATT
1 AAATAAAAAAA-T
616418 AAATAAAAAAAT
1 AAATAAAAAAAT
616430 AAA-AAAAAA
1 AAATAAAAAA
616439 GAGTCAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 6 0.29
12 4 0.19
13 11 0.52
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATAAAAAAAT
Found at i:621764 original size:23 final size:23
Alignment explanation
Indices: 621734--621778 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
621724 CCACATGGAA
621734 TAAAAATAAGAGAAAGCAAAGTT
1 TAAAAATAAGAGAAAGCAAAGTT
*
621757 TAAAAATAAGAGAAATCAAAGT
1 TAAAAATAAGAGAAAGCAAAGT
621779 CAAAATGCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.62, C:0.04, G:0.16, T:0.18
Consensus pattern (23 bp):
TAAAAATAAGAGAAAGCAAAGTT
Found at i:631098 original size:18 final size:19
Alignment explanation
Indices: 631058--631105 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
631048 GTAATATTTT
631058 AATATTATTTTATTCACAAA
1 AATATTATTTTATT-ACAAA
*
631078 AATATTATTTTATT-TAAA
1 AATATTATTTTATTACAAA
631096 AATATT-TTTT
1 AATATTATTTT
631106 CTTCCCATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 9 0.33
20 14 0.52
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTATTTTATTACAAA
Done.