Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 2 of 250
Found at i:355897 original size:27 final size:27
Alignment explanation
Indices: 355867--355925 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
355857 ATTCTAATTC
355867 TAAA-ATATACAAAGAAATATATAAAAA
1 TAAATATATACAAA-AAATATATAAAAA
* * *
355894 TAAATATTTTCAAAAAATATATAATAA
1 TAAATATATACAAAAAATATATAAAAA
355921 TAAAT
1 TAAAT
355926 TTAAATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (27 bp):
TAAATATATACAAAAAATATATAAAAA
Found at i:355898 original size:14 final size:14
Alignment explanation
Indices: 355867--355925 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
355857 ATTCTAATTC
*
355867 TAAA-ATATACAAA
1 TAAATATATAAAAA
*
355880 GAAATATATAAAAA
1 TAAATATATAAAAA
* **
355894 TAAATATTTTCAAA
1 TAAATATATAAAAA
*
355908 -AAATATATAATAA
1 TAAATATATAAAAA
355921 TAAAT
1 TAAAT
355926 TTAAATTTTA
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
13 12 0.35
14 22 0.65
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (14 bp):
TAAATATATAAAAA
Found at i:356313 original size:52 final size:53
Alignment explanation
Indices: 356217--356326 Score: 159
Period size: 52 Copynumber: 2.0 Consensus size: 53
356207 GATTGAGACA
* *
356217 AATTTGATGAGATTTTATTTCTTTATTTCTTTAGGATGGGGTCAATCTTTGATTAT
1 AATTTGATGAGATTTTA--T-TTTATTTCTTTAGGATGGAGTCAATCGTTGATTAT
*
356273 AATTTGATGAGATTTTA-TTTATTTCTTTAGGATTGAGTCAATCGTTGATTAT
1 AATTTGATGAGATTTTATTTTATTTCTTTAGGATGGAGTCAATCGTTGATTAT
356325 AA
1 AA
356327 GGATTCTTCA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
52 34 0.67
56 17 0.33
ACGTcount: A:0.26, C:0.06, G:0.17, T:0.50
Consensus pattern (53 bp):
AATTTGATGAGATTTTATTTTATTTCTTTAGGATGGAGTCAATCGTTGATTAT
Found at i:359223 original size:21 final size:21
Alignment explanation
Indices: 359173--359227 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
359163 CTCTTCCCCT
*
359173 TTTTCTT-TGTTTCTTTATTTC
1 TTTTCTTAT-TTTCTTTATTTA
359194 TTTTCTTATTTTCTTT-TTTA
1 TTTTCTTATTTTCTTTATTTA
*
359214 TTATTTTTATTTTC
1 TT-TTCTTATTTTC
359228 GAAAACGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 5 0.17
21 24 0.80
22 1 0.03
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTTCTTATTTTCTTTATTTA
Found at i:363280 original size:24 final size:23
Alignment explanation
Indices: 363214--363282 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 23
363204 GGATTTTTAT
*
363214 TTTATTTAATATTAA-ATTAATCATA
1 TTTAATTAATATTAATA-TAA--ATA
*
363239 TTTATTTAATATTAATATAAATA
1 TTTAATTAATATTAATATAAATA
363262 TTTAAATTAATTATTATATAT
1 TTT-AATTAA-TATTA-ATAT
363283 TTTTAATATT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 6 0.15
24 5 0.13
25 23 0.59
26 5 0.13
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTAATTAATATTAATATAAATA
Found at i:363284 original size:20 final size:19
Alignment explanation
Indices: 363225--363284 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
363215 TTATTTAATA
* *
363225 TTAAATTAATCATATTTAT
1 TTAAATTAATTATATATAT
*
363244 TTAATATTAA-TATAAATAT
1 TTAA-ATTAATTATATATAT
363263 TTAAATTAATTATTATATAT
1 TTAAATTAATTA-TATATAT
363283 TT
1 TT
363285 TTAATATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
18 5 0.15
19 16 0.47
20 13 0.38
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAAATTAATTATATATAT
Found at i:363310 original size:23 final size:22
Alignment explanation
Indices: 363259--363315 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
363249 ATTAATATAA
* *
363259 ATATTTAAATTAATTATTATAT
1 ATATTTAAATTTATTATTACAT
* *
363281 ATTTTTAATATTTATTTTTACAT
1 ATATTTAA-ATTTATTATTACAT
363304 ATATTTAAATTT
1 ATATTTAAATTT
363316 TACATATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTAAATTTATTATTACAT
Found at i:363467 original size:12 final size:12
Alignment explanation
Indices: 363450--363475 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
363440 ATTTAAAATG
363450 AAAAAATTTGAA
1 AAAAAATTTGAA
363462 AAAAAATTTGAA
1 AAAAAATTTGAA
363474 AA
1 AA
363476 TAATATAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (12 bp):
AAAAAATTTGAA
Found at i:369396 original size:17 final size:17
Alignment explanation
Indices: 369374--369427 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
369364 GCCTAGAATA
369374 GGGCCACACGGGTGTTT
1 GGGCCACACGGGTGTTT
*
369391 GGGCCAC-C---TGTAT
1 GGGCCACACGGGTGTTT
* *
369404 GGACCACATGGGTGTTT
1 GGGCCACACGGGTGTTT
369421 GGGCCAC
1 GGGCCAC
369428 CCGTATGGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
13 10 0.36
16 1 0.04
17 17 0.61
ACGTcount: A:0.15, C:0.26, G:0.37, T:0.22
Consensus pattern (17 bp):
GGGCCACACGGGTGTTT
Found at i:369417 original size:30 final size:30
Alignment explanation
Indices: 369377--369443 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
369367 TAGAATAGGG
*
369377 CCACACGGGTGTTTGGGCCACCTGTATGGA
1 CCACACGGGTGTTTGGGCCACCCGTATGGA
*
369407 CCACATGGGTGTTTGGGCCACCCGTATGGA
1 CCACACGGGTGTTTGGGCCACCCGTATGGA
369437 -CACACGG
1 CCACACGG
369444 CCCCTTACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 6 0.18
30 28 0.82
ACGTcount: A:0.18, C:0.28, G:0.33, T:0.21
Consensus pattern (30 bp):
CCACACGGGTGTTTGGGCCACCCGTATGGA
Found at i:376089 original size:56 final size:56
Alignment explanation
Indices: 375992--376100 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 56
375982 ACATTAGAGT
* * *
375992 CGATATGTGTGTGCAAGTAAGACCATGTTTAATACGTTGGCATCGA-TATGTGACTC
1 CGATATATGTGTGCAAGTAAGACCATGTCTAAGACGTTGGCATC-ATTATGTGACTC
* * *
376048 CGATATATGTGTGCGAGTAAGACCCTGTCTGAGACAG-TGGCATCATTATGTGA
1 CGATATATGTGTGCAAGTAAGACCATGTCTAAGAC-GTTGGCATCATTATGTGA
376101 TTATATGTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
55 1 0.02
56 43 0.96
57 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (56 bp):
CGATATATGTGTGCAAGTAAGACCATGTCTAAGACGTTGGCATCATTATGTGACTC
Found at i:381773 original size:43 final size:43
Alignment explanation
Indices: 381711--381805 Score: 145
Period size: 43 Copynumber: 2.2 Consensus size: 43
381701 CAGTTTAATA
* *
381711 ATTTGCAAACACTAATGGTTTATCCATATCTTACTGGCAGTTT
1 ATTTGCAAACACTAATGGTTTATCCACAACTTACTGGCAGTTT
* *
381754 ATTTGCAAACATTAGTGGTTTATCCACAACTTACTGGCAGTTT
1 ATTTGCAAACACTAATGGTTTATCCACAACTTACTGGCAGTTT
*
381797 AATTGCAAA
1 ATTTGCAAA
381806 TTTTTTTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (43 bp):
ATTTGCAAACACTAATGGTTTATCCACAACTTACTGGCAGTTT
Found at i:384660 original size:28 final size:28
Alignment explanation
Indices: 384629--384735 Score: 99
Period size: 28 Copynumber: 3.7 Consensus size: 28
384619 CATTTTGTTA
384629 TAATTTAGTACCTAAACTTTTTTTTATC
1 TAATTTAGTACCTAAACTTTTTTTTATC
*
384657 TAATTTAGTACCTGAACTTGATATTTTT-TC
1 TAATTTAGTACCTAAACTT--T-TTTTTATC
* * *
384687 TTAACTTGGTACCTAAACTTTTTTGTAGTC
1 -TAATTTAGTACCTAAACTTTTTTTTA-TC
* * *
384717 CAATTTGGTACCTTAACTT
1 TAATTTAGTACCTAAACTT
384736 GGCATTTTTC
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
28 22 0.34
29 17 0.26
30 5 0.08
31 21 0.32
ACGTcount: A:0.26, C:0.16, G:0.09, T:0.49
Consensus pattern (28 bp):
TAATTTAGTACCTAAACTTTTTTTTATC
Found at i:384673 original size:59 final size:57
Alignment explanation
Indices: 384610--384781 Score: 159
Period size: 59 Copynumber: 2.9 Consensus size: 57
384600 AATTAAGGCT
* *
384610 TGAACTTACCATTTTGTTATAATTTAGTACCTAAACTTTTTTTTA-TCTAATTTAGTACC
1 TGAACTTA-CATTTT-TT-TAATTTGGTACCTAAACTTTTTTTTAGTCCAATTTAGTACC
* * * *
384669 TGAACTTGATATTTTTTCTTAACTTGGTACCTAAACTTTTTTGTAGTCCAATTTGGTACC
1 TGAACTT-ACA-TTTTT-TTAATTTGGTACCTAAACTTTTTTTTAGTCCAATTTAGTACC
* * * *
384729 TTAACTTGGCATTTTTCTTAATTTGGTACCT-AAGTTTTTTTTAGGTTCAATTT
1 TGAACTT-ACATTTTT-TTAATTTGGTACCTAAACTTTTTTTTA-GTCCAATTT
384782 GATACCTCAA
Statistics
Matches: 95, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
58 10 0.11
59 59 0.62
60 26 0.27
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.50
Consensus pattern (57 bp):
TGAACTTACATTTTTTTAATTTGGTACCTAAACTTTTTTTTAGTCCAATTTAGTACC
Found at i:384735 original size:60 final size:59
Alignment explanation
Indices: 384636--384788 Score: 184
Period size: 59 Copynumber: 2.6 Consensus size: 59
384626 TTATAATTTA
* * *
384636 GTACCTAAACTTTTTTTTA-TCTAATTTAGTACCTGAACTTGATATTTTTTCTTAACTTG
1 GTACCTAAACTTTTTTTTAGTCCAATTTGGTACCTGAACTTGACA-TTTTTCTTAACTTG
* * * *
384695 GTACCTAAACTTTTTTGTAGTCCAATTTGGTACCTTAACTTGGCATTTTTCTTAATTTG
1 GTACCTAAACTTTTTTTTAGTCCAATTTGGTACCTGAACTTGACATTTTTCTTAACTTG
* * *
384754 GTACCT-AAGTTTTTTTTAGGTTCAATTTGATACCT
1 GTACCTAAACTTTTTTTTA-GTCCAATTTGGTACCT
384789 CAATTTATTA
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
58 10 0.12
59 51 0.63
60 20 0.25
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.49
Consensus pattern (59 bp):
GTACCTAAACTTTTTTTTAGTCCAATTTGGTACCTGAACTTGACATTTTTCTTAACTTG
Found at i:395968 original size:50 final size:49
Alignment explanation
Indices: 395815--396038 Score: 223
Period size: 50 Copynumber: 4.7 Consensus size: 49
395805 GCCACATTAT
* * *
395815 GAGAGCTAGTGTAAGACCATGTCTAGGACATGACATCGACATTGAGA-C
1 GAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACACTGATATC
* * *
395863 GAGTGCTAGTGTAAGA-CATGTCTAGGGCAT-GCATCGGCTA-TGAGT-T-
1 GAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGAC-ACTGA-TATC
* *
395909 --GTG-TAAGTGTAAGACCATGTCTAGGACATGGCATCGACACAGATATGC
1 GAGAGCT-AGTGTAAGACCATGTCTAGGACATGGCATCGACACTGATAT-C
* * *
395957 GAGAACTAGTGTAAGACCATGTCTGGGACATGGCATCGACACGGATATGC
1 GAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACACTGATAT-C
* *
396007 AAGAGCTAGTGTAAGACCATGTCTGGGACATG
1 GAGAGCTAGTGTAAGACCATGTCTAGGACATG
396039 TGTAACATCT
Statistics
Matches: 149, Mismatches: 14, Indels: 24
0.80 0.07 0.13
Matches are distributed among these distances:
43 1 0.01
44 12 0.08
45 15 0.10
46 19 0.13
47 14 0.09
48 15 0.10
50 72 0.48
51 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (49 bp):
GAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACACTGATATC
Found at i:397275 original size:49 final size:50
Alignment explanation
Indices: 397220--397446 Score: 260
Period size: 49 Copynumber: 4.6 Consensus size: 50
397210 ATCTATTGTG
* * * *
397220 AGGTCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGAACCAGATTATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
397270 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * * * **
397320 CGATCACATGTTTAGTACTAAGTACAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
397370 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGCACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
*
397420 -GGTCGCATGTGTAGTACTAAGTGCAGG
1 AGGTCACATGTGTAGTACTAAGTGCAGG
397447 TAACTGAGTA
Statistics
Matches: 146, Mismatches: 29, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
49 65 0.45
50 43 0.29
51 38 0.26
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:397417 original size:101 final size:97
Alignment explanation
Indices: 397223--397446 Score: 279
Period size: 100 Copynumber: 2.3 Consensus size: 97
397213 TATTGTGAGG
* * *
397223 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGAACCAGATTATTGGTCACATGTGTAGTACT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGAACCAGATGATTGGTCACATGTGTAGTACT
*
397288 AAGTGCAGGCTACTATGCGTACCTGATAACTTCGA
66 AAGTGCAGGCTACTATGCG-ACCGGATAA-TT-GA
* * * * * *
397323 TCACATGTTTAGTACTAAGTACAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTAC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGAACCAGATGATT-GGTCACATGTGTAGTAC
*
397388 TAAGTGCAGGCTACTACATGC-ACCGGATAATTGG
65 TAAGTGCAGGCTACT--ATGCGACCGGATAATTGA
*
397422 TCGCATGTGTAGTACTAAGTGCAGG
1 TCACATGTGTAGTACTAAGTGCAGG
397447 TAACTGAGTA
Statistics
Matches: 107, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
99 23 0.21
100 41 0.38
101 39 0.36
103 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (97 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGAACCAGATGATTGGTCACATGTGTAGTACT
AAGTGCAGGCTACTATGCGACCGGATAATTGA
Found at i:399579 original size:12 final size:12
Alignment explanation
Indices: 399564--399593 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
399554 GGTAGTAAAC
399564 ACACGGGCAGAG
1 ACACGGGCAGAG
399576 ACACGGGCAGAG
1 ACACGGGCAGAG
399588 ACACGG
1 ACACGG
399594 CCGTGTGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.27, G:0.40, T:0.00
Consensus pattern (12 bp):
ACACGGGCAGAG
Found at i:401236 original size:47 final size:46
Alignment explanation
Indices: 401180--401547 Score: 267
Period size: 47 Copynumber: 7.8 Consensus size: 46
401170 AGGGTAGAAT
*
401180 GCCGATGCCATGTCCCAGACATGGTCATACACTAGCTCATACATCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTC-TACATCAA
* * *
401227 GTCGATGCCATGTCCCAGACATGGTCTTATACT-GACTATCATA-ATCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-C--TC-TACATC-AA
* * * * *
401276 GCCGACGCCATGTCCCAAACATAGTCTTACACTGGCTCTCACATATCCAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-AC--AT-CAA
* *
401326 GCCGATGCCATGTCCCAGACATGGTCTTACACT-GACACGT-C-TCGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTC-TACATC-AA
** * * *
401372 GTTGATGCCATGTCCCAAACATGGTCTTACACTGGCT-TACATCTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTACA--TC-AA
* *
401420 GCTGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCT-CGTCTCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTAC--ATCAA
*
401465 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CAT-AA
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTACATCAA
401510 TGTGGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGC
1 ----GCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
401548 ACACAAATGA
Statistics
Matches: 262, Mismatches: 32, Indels: 55
0.75 0.09 0.16
Matches are distributed among these distances:
44 1 0.00
45 5 0.02
46 69 0.26
47 77 0.29
48 35 0.13
49 37 0.14
50 36 0.14
51 2 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (46 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTACATCAA
Found at i:401394 original size:46 final size:46
Alignment explanation
Indices: 401183--401499 Score: 221
Period size: 46 Copynumber: 6.7 Consensus size: 46
401173 GTAGAATGCC
* * * * *
401183 GATGCCATGTCCCAGACATGGTCATACACT-AGCTCATACATCAAGTC-
1 GATGCCATGTCCCAGACATGGTCTTACACTGA-CACGT-C-TCGAGGCT
* * * *
401230 GATGCCATGTCCCAGACATGGTCTTATACTGACTATCATAATCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGAC-A-CGT-CTCGAGGCT
* * * * * * * * *
401279 GACGCCATGTCCCAAACATAGTCTTACACTGGCTCTCACATATCCATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACT-G---ACACGTCTCGAGGCT
*
401329 GATGCCATGTCCCAGACATGGTCTTACACTGACACGTCTCGTA-GTT
1 GATGCCATGTCCCAGACATGGTCTTACACTGACACGTCTCG-AGGCT
* * *
401375 GATGCCATGTCCCAAACATGGTCTTACACTGGCTTACATCTCGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGAC--ACGTCTCGAGGCT
* * * * *
401423 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGTCTCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACT-G-ACACGTCTCGAGGCT
401469 GATGCCATGTCCCAGACATGGTCTTACACTG
1 GATGCCATGTCCCAGACATGGTCTTACACTG
401500 GCTCTCATAA
Statistics
Matches: 221, Mismatches: 33, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
46 60 0.27
47 60 0.27
48 30 0.14
49 31 0.14
50 35 0.16
51 3 0.01
52 1 0.00
53 1 0.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (46 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGACACGTCTCGAGGCT
Found at i:401488 original size:94 final size:96
Alignment explanation
Indices: 401177--401544 Score: 364
Period size: 94 Copynumber: 3.9 Consensus size: 96
401167 CATAGGGTAG
* * * * *
401177 AATGCCGATGCCATGTCCCAGACATGGTCATACACTAG--CTCATACATC-AAGTCGATGCCATG
1 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATA-ATCGAGGCCGATGCCATG
* * * *
401239 TCCCAGACATGGTCTTATACTGACTATCATAATC
65 TCCCAGACATGGTCTTACACTG-CTCTCGT-CTC
* * * * * * *
401273 GAGGCCGACGCCATGTCCCAAACATAGTCTTACACTGGCTCTCACATATCCATGCCGATGCCATG
1 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATA-ATCGAGGCCGATGCCATG
* *
401338 TCCCAGACATGGTCTTACACTG-ACACGTCTC
65 TCCCAGACATGGTCTTACACTGCTCTCGTCTC
* ** * *
401369 -GTAGTTGATGCCATGTCCCAAACATGGTCTTACACTGGCT-TACAT-CTCGAGGCTGATG-CAT
1 AAT-GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCT-CATAATCGAGGCCGATGCCAT
401430 GTCCCAGACAT-GTCTTACACTAGCTCTCGTCTC
64 GTCCCAGACATGGTCTTACACT-GCTCTCGTCTC
* *
401463 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCCGATG-CATGT
1 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATCGAGGCCGATGCCATGT
401526 CCCAGACAT-GTCTTACACT
66 CCCAGACATGGTCTTACACT
401545 AGCACACAAA
Statistics
Matches: 225, Mismatches: 37, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
92 10 0.04
93 15 0.07
94 85 0.38
95 4 0.02
96 68 0.30
97 2 0.01
98 8 0.04
99 33 0.15
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (96 bp):
AATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATCGAGGCCGATGCCATGT
CCCAGACATGGTCTTACACTGCTCTCGTCTC
Found at i:401497 original size:140 final size:146
Alignment explanation
Indices: 401177--401499 Score: 412
Period size: 140 Copynumber: 2.3 Consensus size: 146
401167 CATAGGGTAG
* *
401177 AATGCCGATGCCATGTCCCAGACATGGTCATACACT-AGCTCATACATCAAGTCGATGCCATGTC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGAGCACATACATCAAGTCGATGCCATGTC
* *
401241 CCAGACATGGTCTTATACTGACTATCATAATCGAGGCCGACGCCATGTCCCAAACATAGTCTTAC
66 CCAAACATGGTCTTACACTGACTATCATAATCGAGGCCGACGCCATGTCCCAAACATAGTCTTAC
*
401306 ACTGGCTCTCACATATC
131 ACTAGCTCT-ACATATC
* * * *
401323 CATGCCGATGCCATGTCCCAGACATGGTCTTACACTGA-CACGT-C-TCGTAGTTGATGCCATGT
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGAGCACATACATC-AAGTCGATGCCATGT
* * * * *
401385 CCCAAACATGGTCTTACACTGGCT-TACAT-CTCGAGGCTGATG-CATGTCCCAGACAT-GTCTT
65 CCCAAACATGGTCTTACACTGACTAT-CATAATCGAGGCCGACGCCATGTCCCAAACATAGTCTT
* *
401446 ACACTAGCTCT-CGTCTC
129 ACACTAGCTCTACATATC
401463 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTG
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTG
401500 GCTCTCATAA
Statistics
Matches: 157, Mismatches: 17, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
140 40 0.25
142 15 0.10
143 13 0.08
144 13 0.08
145 38 0.24
146 37 0.24
147 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (146 bp):
AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGAGCACATACATCAAGTCGATGCCATGTC
CCAAACATGGTCTTACACTGACTATCATAATCGAGGCCGACGCCATGTCCCAAACATAGTCTTAC
ACTAGCTCTACATATC
Found at i:405412 original size:13 final size:13
Alignment explanation
Indices: 405390--405421 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
405380 TTAGGTGAAG
*
405390 TTTTGGTGACCAA
1 TTTTGATGACCAA
405403 TTTTGATGACCAA
1 TTTTGATGACCAA
405416 TTTTGA
1 TTTTGA
405422 CTAGTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (13 bp):
TTTTGATGACCAA
Found at i:415204 original size:14 final size:13
Alignment explanation
Indices: 415164--415208 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
415154 CATACGAACT
415164 AGAAAGAAAGAAAG
1 AGAAAG-AAGAAAG
415178 A-AAA-AA-AAAG
1 AGAAAGAAGAAAG
415188 AGAAAGAAGAAAGG
1 AGAAAGAAGAAA-G
415202 AGAAAGA
1 AGAAAGA
415209 TGCACAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 5 0.19
11 5 0.19
12 2 0.07
13 6 0.22
14 9 0.33
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AGAAAGAAGAAAG
Found at i:417893 original size:43 final size:43
Alignment explanation
Indices: 417845--417937 Score: 177
Period size: 43 Copynumber: 2.2 Consensus size: 43
417835 TGGAAAGTGA
*
417845 GTAAGTAAGTTGTTCTAAATGACTTCTATATTTGGCCACATAG
1 GTAAGTAAGTTGATCTAAATGACTTCTATATTTGGCCACATAG
417888 GTAAGTAAGTTGATCTAAATGACTTCTATATTTGGCCACATAG
1 GTAAGTAAGTTGATCTAAATGACTTCTATATTTGGCCACATAG
417931 GTAAGTA
1 GTAAGTA
417938 TAAGTGAGGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (43 bp):
GTAAGTAAGTTGATCTAAATGACTTCTATATTTGGCCACATAG
Found at i:417982 original size:35 final size:35
Alignment explanation
Indices: 417942--418151 Score: 180
Period size: 35 Copynumber: 6.1 Consensus size: 35
417932 TAAGTATAAG
* *
417942 TGAGGTTATATTGAACTTGTATGTTCGGCTGCATA
1 TGAGGTTATATTGAACTTGTATATTCGGCTACATA
* ** *
417977 TGAGGTTATATTGAACTTGTGTATTCGATTACATG
1 TGAGGTTATATTGAACTTGTATATTCGGCTACATA
* * *
418012 TGAGCTTATATTGAACTTGTATATT-GGTTACATG
1 TGAGGTTATATTGAACTTGTATATTCGGCTACATA
* *
418046 TGAGATTATATTGAATTTGTATATTCGGC--CATA
1 TGAGGTTATATTGAACTTGTATATTCGGCTACATA
* * * * *
418079 TGAGATGTT-TATTTGAACTTGAACATTAGGTTACATG
1 TGAG--GTTATA-TTGAACTTGTATATTCGGCTACATA
* * *
418116 TGATGATATATTGAACTTATATATTCGGC--CATA
1 TGAGGTTATATTGAACTTGTATATTCGGCTACATA
418149 TGA
1 TGA
418152 AATAATATAA
Statistics
Matches: 140, Mismatches: 28, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
33 13 0.09
34 33 0.24
35 86 0.61
36 2 0.01
37 6 0.04
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (35 bp):
TGAGGTTATATTGAACTTGTATATTCGGCTACATA
Found at i:418095 original size:104 final size:103
Alignment explanation
Indices: 417941--418140 Score: 244
Period size: 104 Copynumber: 1.9 Consensus size: 103
417931 GTAAGTATAA
* * *** *
417941 GTGAGGTTATATTGAACTTGTATGTTCGGCTGCATATGAGGTTATATTGAACTTGTGTATTCGAT
1 GTGAGATTATATTGAACTTGTATATTCGGC-GCATATGAGGTTATATTGAACTTGAACATTAGAT
* *
418006 TACATGTGA-GCTTATATTGAACTTGTATATTGGTTACAT
65 TACATGTGATG-ATATATTGAACTTATATATTGGTTACAT
*
418045 GTGAGATTATATTGAATTTGTATATTCGGC-CATATGAGATGTT-TATTTGAACTTGAACATTAG
1 GTGAGATTATATTGAACTTGTATATTCGGCGCATATGAG--GTTATA-TTGAACTTGAACATTAG
*
418108 GTTACATGTGATGATATATTGAACTTATATATT
63 ATTACATGTGATGATATATTGAACTTATATATT
418141 CGGCCATATG
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
102 8 0.10
103 2 0.02
104 71 0.87
105 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (103 bp):
GTGAGATTATATTGAACTTGTATATTCGGCGCATATGAGGTTATATTGAACTTGAACATTAGATT
ACATGTGATGATATATTGAACTTATATATTGGTTACAT
Found at i:418129 original size:70 final size:70
Alignment explanation
Indices: 418017--418151 Score: 202
Period size: 70 Copynumber: 1.9 Consensus size: 70
418007 ACATGTGAGC
* * * *
418017 TTATATTGAACTTGTATATTGGTTACATGTGAGATTATATTGAATTTGTATATTCGGCCATATGA
1 TTATATTGAACTTGAACATTGGTTACATGTGAGATTATATTGAACTTATATATTCGGCCATATGA
418082 GATGT
66 GATGT
418087 TTAT-TTGAACTTGAACATTAGGTTACATGTGATGA-TATATTGAACTTATATATTCGGCCATAT
1 TTATATTGAACTTGAACATT-GGTTACATGTGA-GATTATATTGAACTTATATATTCGGCCATAT
418150 GA
64 GA
418152 AATAATATAA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
69 13 0.22
70 44 0.75
71 2 0.03
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (70 bp):
TTATATTGAACTTGAACATTGGTTACATGTGAGATTATATTGAACTTATATATTCGGCCATATGA
GATGT
Found at i:418166 original size:70 final size:68
Alignment explanation
Indices: 418018--418166 Score: 183
Period size: 70 Copynumber: 2.1 Consensus size: 68
418008 CATGTGAGCT
* * * * *
418018 TATATTGAACTTGTATATTGGTTACATGTGAGATTATATTGAATTTGTATATTCGGCCATATGAG
1 TATATTGAACTTGAACATTGGTTACATGTGAGATTATATTGAACTTATATATTCGGCCATATGAA
*
418083 ATG
66 ATA
*
418086 TTTATTTGAACTTGAACATTAGGTTACATGTGATGA-TATATTGAACTTATATATTCGGCCATAT
1 TATA-TTGAACTTGAACATT-GGTTACATGTGA-GATTATATTGAACTTATATATTCGGCCATAT
418150 GAAATAA
63 GAAAT-A
*
418157 TATAATGAAC
1 TATATTGAAC
418167 CTTGTGTATT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
68 3 0.04
69 13 0.19
70 47 0.69
71 5 0.07
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (68 bp):
TATATTGAACTTGAACATTGGTTACATGTGAGATTATATTGAACTTATATATTCGGCCATATGAA
ATA
Found at i:420972 original size:17 final size:17
Alignment explanation
Indices: 420934--420979 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
420924 ACGGAAAGTT
420934 AAAGAAAAAGAAAAATG
1 AAAGAAAAAGAAAAATG
*
420951 -GAGAAAAAGGAAAAA-G
1 AAAGAAAAA-GAAAAATG
420967 AAAG-AAAAGAAAA
1 AAAGAAAAAGAAAA
420980 GAATTTGGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 5 0.20
16 12 0.48
17 8 0.32
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (17 bp):
AAAGAAAAAGAAAAATG
Found at i:431126 original size:9 final size:9
Alignment explanation
Indices: 431112--431136 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
431102 TGGGCCATAT
431112 TGAATTTTG
1 TGAATTTTG
431121 TGAATTTTG
1 TGAATTTTG
431130 TGAATTT
1 TGAATTT
431137 ATGAAATAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (9 bp):
TGAATTTTG
Found at i:434439 original size:15 final size:15
Alignment explanation
Indices: 434419--434448 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
434409 AATATATATA
434419 TATATATATATACCC
1 TATATATATATACCC
434434 TATATATATATACCC
1 TATATATATATACCC
434449 ATGATTTAAA
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:0.20, G:0.00, T:0.40
Consensus pattern (15 bp):
TATATATATATACCC
Found at i:437754 original size:27 final size:27
Alignment explanation
Indices: 437716--437769 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
437706 GTAACAATGG
437716 GATGAAGTTATGCACTAAAATAATTAA
1 GATGAAGTTATGCACTAAAATAATTAA
437743 GATGAAGTTATGCACTAAAATAATTAA
1 GATGAAGTTATGCACTAAAATAATTAA
437770 CTCATCCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (27 bp):
GATGAAGTTATGCACTAAAATAATTAA
Found at i:449090 original size:49 final size:47
Alignment explanation
Indices: 449031--449140 Score: 139
Period size: 49 Copynumber: 2.3 Consensus size: 47
449021 ATCAACATAC
*
449031 ATAATTGATTTCCCCGAGAAAATTATGGAGCCAGACATCATCCCAAAAA
1 ATAATTGATTTCCCCGAGAAAATTATGGAGACAGACATCATCCC--AAA
** * * *
449080 ATAATTGATTTCATCGAGGAAATTATGGGGATAGACATCATCCCAAA
1 ATAATTGATTTCCCCGAGAAAATTATGGAGACAGACATCATCCCAAA
*
449127 ATAATTTATTTCCC
1 ATAATTGATTTCCC
449141 TAAGGAAGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
47 14 0.27
49 38 0.73
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (47 bp):
ATAATTGATTTCCCCGAGAAAATTATGGAGACAGACATCATCCCAAA
Found at i:453668 original size:18 final size:16
Alignment explanation
Indices: 453627--453669 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
453617 ATGTGAAATT
*
453627 AGCATGATTAATTTGG
1 AGCATGATAAATTTGG
*
453643 AACATGATAAATGTTGTG
1 AGCATGATAAAT-TTG-G
453661 AGCATGATA
1 AGCATGATA
453670 GTGGATGGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 10 0.45
17 3 0.14
18 9 0.41
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (16 bp):
AGCATGATAAATTTGG
Found at i:454593 original size:66 final size:66
Alignment explanation
Indices: 454451--454577 Score: 200
Period size: 66 Copynumber: 1.9 Consensus size: 66
454441 TTACACTCAA
* * *
454451 ACACTCGTGTGCTAGGTCGTGTGAAAACTAGAGGGTATACTGACTTGTGCCACACGGCCAAGCCA
1 ACACTCGTGTGCCAGGCCGTGTGAAAACTAGAGGGTATACTGACTTGCGCCACACGGCCAAGCCA
454516 T
66 T
* * *
454517 ACACTCGTGTGCCAGGCCGTGTGAAAACTGGAGGGTATACTGGCTTGCGCCACAGGGCCAA
1 ACACTCGTGTGCCAGGCCGTGTGAAAACTAGAGGGTATACTGACTTGCGCCACACGGCCAA
454578 TGTGCTAGGC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.24, C:0.25, G:0.30, T:0.20
Consensus pattern (66 bp):
ACACTCGTGTGCCAGGCCGTGTGAAAACTAGAGGGTATACTGACTTGCGCCACACGGCCAAGCCA
T
Found at i:467247 original size:22 final size:22
Alignment explanation
Indices: 467220--467261 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
467210 ACAAAATGAT
467220 CTGTTGATTATCAAAATATACC
1 CTGTTGATTATCAAAATATACC
* *
467242 CTGTTGATTATTAAGATATA
1 CTGTTGATTATCAAAATATA
467262 TTCAGGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (22 bp):
CTGTTGATTATCAAAATATACC
Found at i:470873 original size:54 final size:54
Alignment explanation
Indices: 470813--470934 Score: 158
Period size: 54 Copynumber: 2.3 Consensus size: 54
470803 GTGTCCTCAC
*
470813 CCATGTAACTCACTGAGATGCCCCACACAC-CT-GTGTGCCAGGTCGTGTGCTAGG
1 CCATGTAACTCACTGAGATG--CCACACACGCTCGTGTGCCAGGCCGTGTGCTAGG
* ** *
470867 CTATGTAACTCTTTGAGTTGCCACACACGCTCGTGTGCCAGGCCGTGTGCTAGG
1 CCATGTAACTCACTGAGATGCCACACACGCTCGTGTGCCAGGCCGTGTGCTAGG
*
470921 CCATGTAATTCACT
1 CCATGTAACTCACT
470935 AACTTGGAAC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
52 8 0.14
53 2 0.04
54 47 0.82
ACGTcount: A:0.20, C:0.30, G:0.25, T:0.26
Consensus pattern (54 bp):
CCATGTAACTCACTGAGATGCCACACACGCTCGTGTGCCAGGCCGTGTGCTAGG
Found at i:474084 original size:4 final size:4
Alignment explanation
Indices: 474054--474115 Score: 65
Period size: 4 Copynumber: 15.0 Consensus size: 4
474044 TTTTCCCTTC
*
474054 TTCT CTTCT TT-T TTCTT TTCTT TTCT TTCT TTCT TTCT TTCT TTCA TTC-
1 TTCT -TTCT TTCT TTC-T TTC-T TTCT TTCT TTCT TTCT TTCT TTCT TTCT
474103 TTCT TCTCT TTCT
1 TTCT T-TCT TTCT
474116 CCTTAGCTTG
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
3 6 0.12
4 29 0.56
5 17 0.33
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.73
Consensus pattern (4 bp):
TTCT
Found at i:479261 original size:54 final size:54
Alignment explanation
Indices: 479179--479310 Score: 219
Period size: 54 Copynumber: 2.4 Consensus size: 54
479169 ATCCTTACAG
479179 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGCATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGCATTGT
* *
479233 CGGGATTACCAGTCCATGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGCATTGT
* * *
479287 CGGGATTATCAATCCAGGTTAAAT
1 CGGGATTACCAGTCCAGGCTAAAT
479311 TTAGACCCTG
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 72 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (54 bp):
CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGCATTGT
Found at i:482028 original size:47 final size:47
Alignment explanation
Indices: 481876--482052 Score: 211
Period size: 47 Copynumber: 3.8 Consensus size: 47
481866 TGTAACCCGC
* * *
481876 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-GTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACAGTTCACAT
*
481922 CTATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-AGTTCACAT
* * * *
481972 -C-TCA-CGAACTCGGACTCAACTCAGCGAGTTCGGACATTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACAGTTCACAT
482016 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
482053 TGTTCAACCA
Statistics
Matches: 110, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
43 3 0.03
44 5 0.05
45 1 0.01
46 36 0.33
47 56 0.51
48 2 0.02
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (47 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACAGTTCACAT
Found at i:482044 original size:94 final size:93
Alignment explanation
Indices: 481884--482054 Score: 279
Period size: 94 Copynumber: 1.8 Consensus size: 93
481874 GCCCATAAGT
* * *
481884 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCTATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
481949 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
481977 GAACTCGGACTCAACTCAGCGAGTTCGGACATTTCACATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGAC-GTTCACATCCATAAGTGAACTCGGACTCAACTCA
482042 ACGAGTTCGGATG
65 ACGAGTTCGGATG
482055 TTCAACCATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
93 27 0.38
94 44 0.62
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:488437 original size:24 final size:24
Alignment explanation
Indices: 488410--488461 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
488400 TACAATGCCA
488410 TATCCCATTTATGGTCTTACATGT
1 TATCCCATTTATGGTCTTACATGT
488434 TATCCCATTTATGGTCTTACATGT
1 TATCCCATTTATGGTCTTACATGT
488458 TATC
1 TATC
488462 ACATATCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (24 bp):
TATCCCATTTATGGTCTTACATGT
Found at i:488590 original size:43 final size:43
Alignment explanation
Indices: 488444--488593 Score: 126
Period size: 43 Copynumber: 3.5 Consensus size: 43
488434 TATCCCATTT
* * * * *
488444 ATGGTCTTACATGTTATCAC-ATATCGATGCCACTGTCCCAGAT
1 ATGGTCTTACACGTAATCACAATAT-AATGCCAATGTCCCAGAC
* * ** *
488487 AGGGTCTTACACGAAAT-TGATTA-ACGATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACAATATA--ATGCCAATGTCCCAGAC
* * *
488530 ATAGTCTTACGCATAATCACAATATAATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACAATATAATGCCAATGTCCCAGAC
*
488573 ATGGTCTTACATGTAATCACA
1 ATGGTCTTACACGTAATCACA
488594 TCTTGATAAC
Statistics
Matches: 80, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
43 76 0.95
44 3 0.04
45 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACACGTAATCACAATATAATGCCAATGTCCCAGAC
Found at i:489188 original size:36 final size:36
Alignment explanation
Indices: 489141--489217 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
489131 TTTCACTAAA
*
489141 AATCACTTTATAAAACAAGATAATCTATCAACAAAT
1 AATCACTTTATAAAAAAAGATAATCTATCAACAAAT
489177 AATCACTTTATAAAAAAAGATAATCTATCAACAAAT
1 AATCACTTTATAAAAAAAGATAATCTATCAACAAAT
489213 AATCA
1 AATCA
489218 TTTTCCATCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.55, C:0.16, G:0.03, T:0.27
Consensus pattern (36 bp):
AATCACTTTATAAAAAAAGATAATCTATCAACAAAT
Found at i:491695 original size:16 final size:16
Alignment explanation
Indices: 491674--491708 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
491664 GTAGAACGGC
491674 AAAAGCTGAAAAGCCG
1 AAAAGCTGAAAAGCCG
*
491690 AAAAGCTGAAAAGTCG
1 AAAAGCTGAAAAGCCG
491706 AAA
1 AAA
491709 GAATGCCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.14, G:0.23, T:0.09
Consensus pattern (16 bp):
AAAAGCTGAAAAGCCG
Found at i:492183 original size:27 final size:27
Alignment explanation
Indices: 492106--492182 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 27
492096 CCCCAAGACA
**
492106 GGTAAAATGACACAAAATACCCCTAAAG
1 GGTAAAATGAC-CATTATACCCCTAAAG
* *
492134 GGTAAAATGACTATTTTACCCCTAATAG
1 GGTAAAATGACCATTATACCCCTAA-AG
* *
492162 GTTAAAATGACCGTTATACCC
1 GGTAAAATGACCATTATACCC
492183 TTAGAGGTAG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 10 0.25
28 30 0.75
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (27 bp):
GGTAAAATGACCATTATACCCCTAAAG
Found at i:492380 original size:27 final size:26
Alignment explanation
Indices: 492310--492383 Score: 103
Period size: 27 Copynumber: 2.8 Consensus size: 26
492300 AGAGGAAGTG
492310 TACTGTACTGGTGGCTTTGCCATATA
1 TACTGTACTGGTGGCTTTGCCATATA
*
492336 TACTGTTAATGGTGGCTTTGCCATATA
1 TACTG-TACTGGTGGCTTTGCCATATA
* *
492363 TACTGATACTAGTAGCTTTGC
1 TACTG-TACTGGTGGCTTTGC
492384 TGTGTTACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 5 0.12
27 37 0.88
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (26 bp):
TACTGTACTGGTGGCTTTGCCATATA
Found at i:497397 original size:3 final size:3
Alignment explanation
Indices: 497389--497418 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
497379 CTCCGTCTTA
497389 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
497419 CTCAAGTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:502298 original size:21 final size:21
Alignment explanation
Indices: 502252--502298 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
502242 TTTATTCATT
502252 CTTTTGGTCAAAATCAAAATG
1 CTTTTGGTCAAAATCAAAATG
* **
502273 ATTTTGGTCAAAATCAGCATG
1 CTTTTGGTCAAAATCAAAATG
502294 CTTTT
1 CTTTT
502299 AGACCACATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (21 bp):
CTTTTGGTCAAAATCAAAATG
Found at i:508893 original size:23 final size:22
Alignment explanation
Indices: 508841--508893 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
508831 TCCACGTCTT
*
508841 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
508863 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
508886 TTTCTTTT
1 TTTCTTTT
508894 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:522948 original size:3 final size:3
Alignment explanation
Indices: 522940--522984 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
522930 AGAGAATTGC
522940 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
522985 AAGCAAAACC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:524794 original size:25 final size:25
Alignment explanation
Indices: 524741--524795 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
524731 ACTTGTCTGG
*
524741 TTTTTAACAATAAAAATTAATAAAT
1 TTTTTAACAATAAAAATTAATAAAC
**
524766 TTTTTAAC-ATAAAATATTAATTTAC
1 TTTTTAACAATAAAA-ATTAATAAAC
524791 TTTTT
1 TTTTT
524796 TATCCAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTTTAACAATAAAAATTAATAAAC
Found at i:525055 original size:21 final size:19
Alignment explanation
Indices: 525023--525070 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
525013 TTAATTAAGA
*
525023 TAAAATTGTAGTGATAATAT
1 TAAAATTATAGTGATAA-AT
*
525043 TAAATATTATAGTGATTAAT
1 TAAA-ATTATAGTGATAAAT
525063 TAAAATTA
1 TAAAATTA
525071 GTTGTGAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 10 0.40
21 11 0.44
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (19 bp):
TAAAATTATAGTGATAAAT
Found at i:525077 original size:20 final size:21
Alignment explanation
Indices: 525023--525077 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
525013 TTAATTAAGA
525023 TAAAATT-GTAGTGATAATAT
1 TAAAATTAGTAGTGATAATAT
*
525043 TAAATATTA-TAGTGATTA-AT
1 TAAA-ATTAGTAGTGATAATAT
*
525063 TAAAATTAGTTGTGA
1 TAAAATTAGTAGTGA
525078 GATGTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 4 0.13
20 15 0.50
21 11 0.37
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.42
Consensus pattern (21 bp):
TAAAATTAGTAGTGATAATAT
Found at i:527672 original size:22 final size:22
Alignment explanation
Indices: 527647--527696 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
527637 ACATGTATTG
*
527647 AGACATTGG-CTCTTATGTCTCA
1 AGACATTGGTC-CTTATGTCACA
* *
527669 AGACTTTGGTCCTTATGTCACG
1 AGACATTGGTCCTTATGTCACA
527691 AGACAT
1 AGACAT
527697 GACCTTAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (22 bp):
AGACATTGGTCCTTATGTCACA
Found at i:533973 original size:29 final size:30
Alignment explanation
Indices: 533908--533978 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
533898 TTAAGAGACA
**
533908 AAAATGTAACATTTAATAACATTAATAATT
1 AAAATGTAATTTTTAATAACATTAATAATT
**
533938 ATTATGTAATTTTTAA-AA-ATTAAATAATT
1 AAAATGTAATTTTTAATAACATT-AATAATT
533967 AAAATGTAATTT
1 AAAATGTAATTT
533979 CAAATAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 3 0.09
29 19 0.56
30 12 0.35
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (30 bp):
AAAATGTAATTTTTAATAACATTAATAATT
Found at i:534224 original size:11 final size:11
Alignment explanation
Indices: 534204--534241 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
534194 TAATTGAACT
534204 TATTTTTTTTA
1 TATTTTTTTTA
*
534215 TATTTCTTTTGA
1 TATTT-TTTTTA
534227 -ATTTTTTTTA
1 TATTTTTTTTA
534237 TATTT
1 TATTT
534242 GTCTAGCTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 5 0.22
11 13 0.57
12 5 0.22
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (11 bp):
TATTTTTTTTA
Found at i:534679 original size:23 final size:22
Alignment explanation
Indices: 534639--534684 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
534629 AGAGATAAAG
*
534639 AAAAATACCTAAATAAATTCTAA
1 AAAAATACATAAATAAATT-TAA
534662 AAAAATACATATAA-AAATTTAA
1 AAAAATACATA-AATAAATTTAA
534684 A
1 A
534685 TAATATTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 15 0.71
24 2 0.10
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAAATACATAAATAAATTTAA
Found at i:541557 original size:28 final size:28
Alignment explanation
Indices: 541473--541569 Score: 97
Period size: 28 Copynumber: 3.4 Consensus size: 28
541463 AATTATTGCA
* *
541473 CTTATCG-TATTATTTTACACTTCGGTG
1 CTTATCGTTATTATTTTGCACTTAGGTG
** * *
541500 CTTATCGTTGCAAAAATTTGCACTTTGGTG
1 CTTATCGTT--ATTATTTTGCACTTAGGTG
*
541530 CTTATCGTTATTATTTTGCACCTAGGTG
1 CTTATCGTTATTATTTTGCACTTAGGTG
*
541558 CTTTTCGTTATT
1 CTTATCGTTATT
541570 TTCACTTTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
27 7 0.12
28 26 0.46
30 23 0.41
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.47
Consensus pattern (28 bp):
CTTATCGTTATTATTTTGCACTTAGGTG
Found at i:546432 original size:10 final size:10
Alignment explanation
Indices: 546417--546476 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
546407 TAATTTTAGG
546417 ATTTAT-TTT
1 ATTTATCTTT
546426 CATTTATCTTT
1 -ATTTATCTTT
546437 ATTTATCTTT
1 ATTTATCTTT
*
546447 AATTATCTTT
1 ATTTATCTTT
546457 ATTTAT-TTGT
1 ATTTATCTT-T
546467 ATTTATCTTT
1 ATTTATCTTT
546477 TAGAATTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:547233 original size:18 final size:18
Alignment explanation
Indices: 547198--547231 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
547188 TATTCCTCAT
547198 TTTAATTTCTGCAATTTA
1 TTTAATTTCTGCAATTTA
547216 TTTAATTT-TGCAATTT
1 TTTAATTTCTGCAATTT
547232 TAATTCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.59
Consensus pattern (18 bp):
TTTAATTTCTGCAATTTA
Found at i:550197 original size:10 final size:10
Alignment explanation
Indices: 550184--550217 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
550174 TTTTATTTTT
550184 TTTAGTTTAG
1 TTTAGTTTAG
550194 TTTAGTTTAG
1 TTTAGTTTAG
550204 TTTAGTTTAG
1 TTTAGTTTAG
550214 TTTA
1 TTTA
550218 TTTTTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.62
Consensus pattern (10 bp):
TTTAGTTTAG
Found at i:550202 original size:15 final size:15
Alignment explanation
Indices: 550184--550217 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
550174 TTTTATTTTT
550184 TTTAGTTTAGTTTAG
1 TTTAGTTTAGTTTAG
550199 TTTAGTTTAGTTTAG
1 TTTAGTTTAGTTTAG
550214 TTTA
1 TTTA
550218 TTTTTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.62
Consensus pattern (15 bp):
TTTAGTTTAGTTTAG
Found at i:550227 original size:15 final size:16
Alignment explanation
Indices: 550189--550235 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
550179 TTTTTTTTAG
*
550189 TTTAGTTTAGTTTA-G
1 TTTAGTTTAGTTTATT
550204 TTTAGTTTAGTTTATT
1 TTTAGTTTAGTTTATT
550220 TTTA-TTTA--TTATT
1 TTTAGTTTAGTTTATT
550233 TTT
1 TTT
550236 TTACTTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 8 0.27
15 18 0.60
16 4 0.13
ACGTcount: A:0.19, C:0.00, G:0.11, T:0.70
Consensus pattern (16 bp):
TTTAGTTTAGTTTATT
Found at i:550236 original size:15 final size:15
Alignment explanation
Indices: 550218--550250 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
550208 GTTTAGTTTA
*
550218 TTTTTATTTATTATT
1 TTTTTACTTATTATT
550233 TTTTTACTTATTATT
1 TTTTTACTTATTATT
550248 TTT
1 TTT
550251 AGATATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTACTTATTATT
Found at i:551159 original size:96 final size:97
Alignment explanation
Indices: 550995--551176 Score: 303
Period size: 96 Copynumber: 1.9 Consensus size: 97
550985 TTTAAGAATG
* * *
550995 TGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTATCTTCGCGTCAAAAGGTTCGAT
1 TGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTATCATCTATCTTCGCATCAAAAGGTTCAAT
*
551060 ATATTCTTAAG-AAAAATAAAAATTAGGAGTA
66 ATATTCCTAAGTAAAAATAAAAATTAGGAGTA
* *
551091 TGTTGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTATCATCTCTCTTCGCATCAAAAGGTTCAAT
1 TGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTATCATCTATCTTCGCATCAAAAGGTTCAAT
551156 ATATTCCTAAGTAAAAATAAA
66 ATATTCCTAAGTAAAAATAAA
551177 TAAATAAAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
96 70 0.89
97 9 0.11
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (97 bp):
TGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTATCATCTATCTTCGCATCAAAAGGTTCAAT
ATATTCCTAAGTAAAAATAAAAATTAGGAGTA
Found at i:553264 original size:10 final size:10
Alignment explanation
Indices: 553249--553308 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
553239 TAATTTTAGG
553249 ATTTAT-TTT
1 ATTTATCTTT
553258 CATTTATCTTT
1 -ATTTATCTTT
553269 ATTTATCTTT
1 ATTTATCTTT
*
553279 AATTATCTTT
1 ATTTATCTTT
553289 ATTTAT-TTGT
1 ATTTATCTT-T
553299 ATTTATCTTT
1 ATTTATCTTT
553309 TAGAATTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:554055 original size:18 final size:18
Alignment explanation
Indices: 554020--554053 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
554010 TATTCCTCAT
*
554020 TTTAATTTCTGCAATTTA
1 TTTAATTTCTACAATTTA
554038 TTTAATTTC-ACAATTT
1 TTTAATTTCTACAATTT
554054 TAATTCACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.12, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTAATTTCTACAATTTA
Found at i:558128 original size:25 final size:24
Alignment explanation
Indices: 558096--558179 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 24
558086 AGCTGTAAAC
558096 GGTAAGCTCCTCCGAGCTAAACAAT
1 GGTAAGCTCCTCCGAGCTAAA-AAT
* * *
558121 GGTAAGCTCCTCCAAAC-AGAATAT
1 GGTAAGCTCCTCCGAGCTA-AAAAT
* *
558145 CAGTAAGCTCTTCCGAGCTAAATAAT
1 -GGTAAGCTCCTCCGAGCTAAA-AAT
558171 GGTAAGCTC
1 GGTAAGCTC
558180 GTATGAGCTG
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
24 3 0.07
25 40 0.87
26 3 0.07
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (24 bp):
GGTAAGCTCCTCCGAGCTAAAAAT
Found at i:572345 original size:12 final size:13
Alignment explanation
Indices: 572323--572351 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
572313 AAGTTTTATT
572323 TTTATTTTATTTA
1 TTTATTTTATTTA
572336 TTTA-TTTATTTA
1 TTTATTTTATTTA
572348 TTTA
1 TTTA
572352 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:576337 original size:12 final size:13
Alignment explanation
Indices: 576315--576343 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
576305 AAGTTTTATT
576315 TTTATTTTATTTA
1 TTTATTTTATTTA
576328 TTTA-TTTATTTA
1 TTTATTTTATTTA
576340 TTTA
1 TTTA
576344 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:577914 original size:56 final size:55
Alignment explanation
Indices: 577816--577977 Score: 191
Period size: 56 Copynumber: 2.9 Consensus size: 55
577806 CGAAGCCAAC
* * * * *
577816 TCGCACATACTTTTCAGGAAAC-TCAAAAAGGTCCGCCTTAGGTCACAAGACTGGT
1 TCGCACATACTTATCAGAAAACATGAACAAGGTCTGCCTTAGGTCA-AAGACTGGT
* *
577871 TGGCACATACTTATCAGAAAACATGAACAAGGTCTGCCTTAGGTCGAGAGACTGGT
1 TCGCACATACTTATCAGAAAACATGAACAAGGTCTGCCTTAGGTC-AAAGACTGGT
* * * *
577927 TCGTACATACTTATTAAAAAACATGAACAAGGTTTGCCTTAGGTCATAAGA
1 TCGCACATACTTATCAGAAAACATGAACAAGGTCTGCCTTAGGTCA-AAGA
577978 TCGGTTCACT
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
55 20 0.22
56 70 0.77
57 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (55 bp):
TCGCACATACTTATCAGAAAACATGAACAAGGTCTGCCTTAGGTCAAAGACTGGT
Found at i:596200 original size:40 final size:40
Alignment explanation
Indices: 596154--596230 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
596144 ACACACCATG
* *
596154 TGGGGATAGAATCGACCCACCCAACCCTTCAAACCAAGTA
1 TGGGGATAGAATCAACCCACCCAACCCTACAAACCAAGTA
* * * *
596194 TGGGGATATAATCAACCCATCCAGCCCTACACACCAA
1 TGGGGATAGAATCAACCCACCCAACCCTACAAACCAA
596231 AAGGTACCGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.35, C:0.34, G:0.16, T:0.16
Consensus pattern (40 bp):
TGGGGATAGAATCAACCCACCCAACCCTACAAACCAAGTA
Found at i:600086 original size:3 final size:3
Alignment explanation
Indices: 600078--600152 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
600068 TTTTTTATAC
* * * * * * * *
600078 ATT ATT ATT AAT ATC ATA ATC ATT ATT ATT ATT ATC GTT ATT AAT GTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
600126 ATT ATT ATC ATT ACT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
600153 CTTACCCCTT
Statistics
Matches: 54, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:609830 original size:23 final size:23
Alignment explanation
Indices: 609781--609831 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
609771 TCTAAAAATT
609781 ATATC-TCTAAGATTACAGAATC
1 ATATCTTCTAAGATTACAGAATC
* *
609803 GTATCTTCTAAAGATTACA-TATC
1 ATATCTTCT-AAGATTACAGAATC
609826 ATATCT
1 ATATCT
609832 AAGATTACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 4 0.17
23 11 0.46
24 9 0.38
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (23 bp):
ATATCTTCTAAGATTACAGAATC
Found at i:612400 original size:18 final size:19
Alignment explanation
Indices: 612379--612421 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
612369 CTATTTTCTG
612379 TTATTGAAAGTTTTGAAA-
1 TTATTGAAAGTTTTGAAAT
**
612397 TTATTGAACTTTTTGAAAT
1 TTATTGAAAGTTTTGAAAT
612416 TTATTG
1 TTATTG
612422 GTGAAAGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (19 bp):
TTATTGAAAGTTTTGAAAT
Found at i:614925 original size:66 final size:65
Alignment explanation
Indices: 614813--614952 Score: 208
Period size: 66 Copynumber: 2.1 Consensus size: 65
614803 GGATCTTCAT
* * * *
614813 CACACCAAATAGACTCATAGAGTCAGACATGTCCCATAAGTGAAGCATAAAACTAACACTCTCCA
1 CACACC-AATAGACTCATACAGTCAAACATATCCCAAAAGTGAAGCATAAAACTAACACTCTCCA
614878 A
65 A
* *
614879 CACACCAATTGACTCATACAGTCAAACATATCCCAAAAAGTGAAGCATAAAGCTAACACTCTCCA
1 CACACCAATAGACTCATACAGTCAAACATATCCC-AAAAGTGAAGCATAAAACTAACACTCTCCA
614944 A
65 A
614945 CACACCAA
1 CACACCAA
614953 ACATGTCCCG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 24 0.36
66 43 0.64
ACGTcount: A:0.44, C:0.29, G:0.10, T:0.17
Consensus pattern (65 bp):
CACACCAATAGACTCATACAGTCAAACATATCCCAAAAGTGAAGCATAAAACTAACACTCTCCAA
Found at i:617367 original size:30 final size:28
Alignment explanation
Indices: 617327--617384 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
617317 TGGAGAACTC
617327 ACAGTAAGTGGCGAGCGCTACCTCAAATGA
1 ACAGTAAGTGGCGA--GCTACCTCAAATGA
* * *
617357 ACAGTGAGTGGTGAGCTACCTCGAATGA
1 ACAGTAAGTGGCGAGCTACCTCAAATGA
617385 GTATAAGCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 13 0.52
30 12 0.48
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (28 bp):
ACAGTAAGTGGCGAGCTACCTCAAATGA
Found at i:620482 original size:36 final size:32
Alignment explanation
Indices: 620400--620465 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
620390 TTTTTATGAC
*
620400 TTAACTAAAACCCTTTACAAATTAATTAAGGT
1 TTAACTAAAAACCTTTACAAATTAATTAAGGT
620432 TTAACTAAAAACCTTTACAAATTAATTAAGGT
1 TTAACTAAAAACCTTTACAAATTAATTAAGGT
620464 TT
1 TT
620466 TATATCTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (32 bp):
TTAACTAAAAACCTTTACAAATTAATTAAGGT
Found at i:627638 original size:19 final size:19
Alignment explanation
Indices: 627614--627654 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
627604 ACACTTTTCA
627614 TTTCACTATAAGAATAT-AC
1 TTTCACTATAA-AATATCAC
*
627633 TTTCACTTTAAAATATCAC
1 TTTCACTATAAAATATCAC
627652 TTT
1 TTT
627655 TTATACACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.44
Consensus pattern (19 bp):
TTTCACTATAAAATATCAC
Found at i:629159 original size:13 final size:13
Alignment explanation
Indices: 629141--629167 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
629131 GGAAATTATT
629141 TTTGCACCTTCTA
1 TTTGCACCTTCTA
629154 TTTGCACCTTCTA
1 TTTGCACCTTCTA
629167 T
1 T
629168 ATCGTGCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.30, G:0.07, T:0.48
Consensus pattern (13 bp):
TTTGCACCTTCTA
Found at i:630191 original size:25 final size:25
Alignment explanation
Indices: 630162--630213 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
630152 TTTTCAATTT
630162 AGCCTCTTATTTATTCCTAATTTTG
1 AGCCTCTTATTTATTCCTAATTTTG
630187 AGCCTCTTATTTATTCCTAATTTTG
1 AGCCTCTTATTTATTCCTAATTTTG
630212 AG
1 AG
630214 TTTATTGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.50
Consensus pattern (25 bp):
AGCCTCTTATTTATTCCTAATTTTG
Found at i:630281 original size:18 final size:18
Alignment explanation
Indices: 630258--630294 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
630248 GCAGAAATCA
630258 CCCTTTTTCCAATTCTAT
1 CCCTTTTTCCAATTCTAT
630276 CCCTTTTTCCAATTCTAT
1 CCCTTTTTCCAATTCTAT
630294 C
1 C
630295 TTTATCTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.35, G:0.00, T:0.49
Consensus pattern (18 bp):
CCCTTTTTCCAATTCTAT
Found at i:633818 original size:116 final size:115
Alignment explanation
Indices: 633607--633830 Score: 403
Period size: 116 Copynumber: 1.9 Consensus size: 115
633597 AACTACTTAT
*
633607 ATTGCCAAAAAGTATTTAGAATTTATATGAATTATATTGCGTATAATGTATGTAAGGTATTTAAA
1 ATTGCCAAAAAATATTTAGAATTTATATGAATTATATTGCGTATAATGTATGTAAGGTATTTAAA
*
633672 ATTAGTGTCTATACGTTCGATCAAAAAGTAAATTGACCATTCTGTTATTA
66 ATTAGTGTCTATACGTTAGATCAAAAAGTAAATTGACCATTCTGTTATTA
*
633722 ATTGCTCAAAAAATATTTAGAATTTATATGAATTATATTGTGTATAATGTATGTAAGGTATTTAA
1 ATTGC-CAAAAAATATTTAGAATTTATATGAATTATATTGCGTATAATGTATGTAAGGTATTTAA
*
633787 AATTAGTGTCTATACGTTAGATCAAAGAGTAAATTGACCATTCT
65 AATTAGTGTCTATACGTTAGATCAAAAAGTAAATTGACCATTCT
633831 ATTAAAAATT
Statistics
Matches: 104, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
115 5 0.05
116 99 0.95
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (115 bp):
ATTGCCAAAAAATATTTAGAATTTATATGAATTATATTGCGTATAATGTATGTAAGGTATTTAAA
ATTAGTGTCTATACGTTAGATCAAAAAGTAAATTGACCATTCTGTTATTA
Found at i:638676 original size:74 final size:74
Alignment explanation
Indices: 638576--638728 Score: 191
Period size: 74 Copynumber: 2.1 Consensus size: 74
638566 CGACTACCTG
* * * * *
638576 TGGGCGCAAATATCGTTGGTAAATCCAACTAGAGCTAGGCTTAC-TATTTATTCGTTGGCTTATC
1 TGGGCGCAAATACCGTTGGTAAATCCAACTAAAGCTAAGCTCACTTA-TTATTCGTCGGCTTATC
638640 CAACTAGCAC
65 CAACTAGCAC
* * * *
638650 TGGGTGCAAATACCTTTGGTATATCCAACTAAAGCTAAGCTCACTTATTATTCGTCGGTTTATCC
1 TGGGCGCAAATACCGTTGGTAAATCCAACTAAAGCTAAGCTCACTTATTATTCGTCGGCTTATCC
* *
638715 GACTAGCGC
66 AACTAGCAC
638724 TGGGC
1 TGGGC
638729 ACAACTTTCG
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
74 64 0.97
75 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (74 bp):
TGGGCGCAAATACCGTTGGTAAATCCAACTAAAGCTAAGCTCACTTATTATTCGTCGGCTTATCC
AACTAGCAC
Found at i:638785 original size:34 final size:35
Alignment explanation
Indices: 638700--638793 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 35
638690 TCACTTATTA
* * *
638700 TTCGTCGGTTTATCCGACTAGCGCTGGGCACAACT
1 TTCGTCAGTTTATCTGACTAGTGCTGGGCACAACT
638735 TTCGTCAGTTTATCTGACTAGTGCTGGGCAC-ACAT
1 TTCGTCAGTTTATCTGACTAGTGCTGGGCACAAC-T
* **
638770 TT-TTTTGTTTATCTGACTAGTGCT
1 TTCGTCAGTTTATCTGACTAGTGCT
638794 AGGTACAAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
34 21 0.40
35 31 0.60
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (35 bp):
TTCGTCAGTTTATCTGACTAGTGCTGGGCACAACT
Found at i:641399 original size:15 final size:15
Alignment explanation
Indices: 641380--641420 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
641370 TTATAATTAA
641380 CTTAATTAACCTAAG
1 CTTAATTAACCTAAG
* *
641395 TTTAATTAAACTTAAG
1 CTTAATT-AACCTAAG
641411 CTTAATTAAC
1 CTTAATTAAC
641421 AATTTTGGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (15 bp):
CTTAATTAACCTAAG
Found at i:646769 original size:17 final size:17
Alignment explanation
Indices: 646746--646787 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
646736 TATCGAAATA
*
646746 AATATTAGATTAAATTT
1 AATATTAAATTAAATTT
*
646763 CATATTAAATTAAATTT
1 AATATTAAATTAAATTT
646780 AATATTAA
1 AATATTAA
646788 GATACTCACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
AATATTAAATTAAATTT
Found at i:649057 original size:39 final size:39
Alignment explanation
Indices: 649003--649081 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
648993 ATTTCCTTAA
649003 ATCTTTACAGGTTTGGAAGGCTGAGTCTGTAGATCCAAT
1 ATCTTTACAGGTTTGGAAGGCTGAGTCTGTAGATCCAAT
*
649042 ATCTTTACAGGTTTGGAAGTCTGAGTCTGTAGATCCAAT
1 ATCTTTACAGGTTTGGAAGGCTGAGTCTGTAGATCCAAT
649081 A
1 A
649082 GGAGTAAGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (39 bp):
ATCTTTACAGGTTTGGAAGGCTGAGTCTGTAGATCCAAT
Found at i:649524 original size:20 final size:20
Alignment explanation
Indices: 649495--649532 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
649485 TTTAACCCTT
649495 CAAAAATCAAA-TCAAATAA
1 CAAAAATCAAATTCAAATAA
649514 CAAATAATCAAATTCAAAT
1 CAAA-AATCAAATTCAAAT
649533 GCTATTCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 7 0.41
21 6 0.35
ACGTcount: A:0.63, C:0.16, G:0.00, T:0.21
Consensus pattern (20 bp):
CAAAAATCAAATTCAAATAA
Found at i:650447 original size:60 final size:63
Alignment explanation
Indices: 650339--650464 Score: 152
Period size: 61 Copynumber: 2.0 Consensus size: 63
650329 ATTTTTAAAC
* * * *
650339 TTTTACAATTAGAATTAAATTGAAAATTTTTGTAAATTTTAAGTGTT-AAATCTATT-AAATT
1 TTTTACAATTAGAATAAAAATGAAAATTTTTGTAAAATTAAAGTGTTAAAATCTATTGAAATT
* * *
650400 TTTTAGAATTAGAA-AAAAATGAAAGTTTTTGTAAACATTAAAG-GTTAAAATTTATTGAAATT
1 TTTTACAATTAGAATAAAAATGAAAATTTTTGTAAA-ATTAAAGTGTTAAAATCTATTGAAATT
650462 TTT
1 TTT
650465 ATATTTAGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
60 21 0.38
61 26 0.47
62 8 0.15
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (63 bp):
TTTTACAATTAGAATAAAAATGAAAATTTTTGTAAAATTAAAGTGTTAAAATCTATTGAAATT
Found at i:650803 original size:6 final size:6
Alignment explanation
Indices: 650794--650827 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
650784 GAGAGAGCCA
650794 TTTCTG TTTCTG TTTCTG TTTCTG TTTCTG TTTC
1 TTTCTG TTTCTG TTTCTG TTTCTG TTTCTG TTTC
650828 AGTGAGCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.15, T:0.68
Consensus pattern (6 bp):
TTTCTG
Found at i:661588 original size:37 final size:37
Alignment explanation
Indices: 661538--661616 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
661528 TTATTACGAA
* * * *
661538 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCAG
*
661575 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCAG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCAG
661612 GTCTT
1 GTCTT
661617 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCAG
Found at i:661861 original size:47 final size:47
Alignment explanation
Indices: 661735--662217 Score: 781
Period size: 47 Copynumber: 10.1 Consensus size: 47
661725 CCCTTCGGGA
* * * * * *
661735 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
661782 CCTGTCACATATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
661831 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
661878 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
661925 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
661972 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
662021 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
662068 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
662117 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
662166 CTTATCAC--ATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
662211 CTTATCA
1 CTTATCA
662218 TCATTTCATA
Statistics
Matches: 414, Mismatches: 16, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
45 44 0.11
47 190 0.46
49 180 0.43
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:661939 original size:96 final size:95
Alignment explanation
Indices: 661735--662217 Score: 803
Period size: 96 Copynumber: 5.1 Consensus size: 95
661725 CCCTTCGGGA
* * * * * * *
661735 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACA-ATATATAC
*
661800 ACTTCCACATTCATCACATCGGCCATTAGGC
65 ACTTTCACATTCATCACATCGGCCATTAGGC
661831 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCAC-ATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACAATATATACA
661895 CTTTCACATTCATCACATCGGCCATTAGGC
66 CTTTCACATTCATCACATCGGCCATTAGGC
661925 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACA-ATATATAC
661990 ACTTTCACATTCATCACATCGGCCATTAGGC
65 ACTTTCACATTCATCACATCGGCCATTAGGC
*
662021 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACA-ATATATAC
662086 ACTTTCACATTCATCACATCGGCCATTAGGC
65 ACTTTCACATTCATCACATCGGCCATTAGGC
*
662117 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC---ATATA
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACAATATATA
662179 CACTTTCACATTCATCACATCGGCCATTAGGC
64 CACTTTCACATTCATCACATCGGCCATTAGGC
662211 CTTATCA
1 CTTATCA
662218 TCATTTCATA
Statistics
Matches: 374, Mismatches: 9, Indels: 10
0.95 0.02 0.03
Matches are distributed among these distances:
94 137 0.37
96 190 0.51
98 47 0.13
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (95 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACAATATATACA
CTTTCACATTCATCACATCGGCCATTAGGC
Found at i:671925 original size:31 final size:29
Alignment explanation
Indices: 671878--671947 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
671868 ACTGCAAAAA
* * *
671878 TAGTCACTTTTATTTGACTCATATTATATTT
1 TAGTCACTTATATTTGA--AATATTACATTT
* *
671909 TAGTCACTTATGTTTGAAATGTTACATTT
1 TAGTCACTTATATTTGAAATATTACATTT
671938 TAGTCACTTA
1 TAGTCACTTA
671948 CGTTATCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.50
Consensus pattern (29 bp):
TAGTCACTTATATTTGAAATATTACATTT
Found at i:674124 original size:24 final size:23
Alignment explanation
Indices: 674084--674132 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
674074 TAGAAAATAT
*
674084 AAAAATAAGATATTTTAATGTAA
1 AAAAATAAGATATTTTAATATAA
674107 AAAAATAA-ATATAATTTAATATAA
1 AAAAATAAGATAT--TTTAATATAA
674131 AA
1 AA
674133 TAATTATACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 8 0.35
24 11 0.48
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAAATAAGATATTTTAATATAA
Found at i:674256 original size:31 final size:31
Alignment explanation
Indices: 674162--674256 Score: 123
Period size: 31 Copynumber: 3.3 Consensus size: 31
674152 ATCAAATTAT
674162 ATATTATTT-TTTATTAAATTATATTTAATA
1 ATATTATTTATTTATTAAATTATATTTAATA
*
674192 ATA--A-TTA--TATTAAAATATATTTAA-A
1 ATATTATTTATTTATTAAATTATATTTAATA
674217 ATATTTATTTATTTATTAAATTATATTTAATA
1 ATA-TTATTTATTTATTAAATTATATTTAATA
674249 ATATTATT
1 ATATTATT
674257 AAAATTTAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
25 4 0.07
26 16 0.29
27 2 0.04
28 2 0.04
29 3 0.05
30 3 0.05
31 21 0.38
32 4 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
ATATTATTTATTTATTAAATTATATTTAATA
Found at i:679319 original size:25 final size:25
Alignment explanation
Indices: 679290--679339 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
679280 AAAACGGGCT
679290 GTTACAACTATGTATATGATCCTCA
1 GTTACAACTATGTATATGATCCTCA
679315 GTTACAACTATGTATATGATCCTCA
1 GTTACAACTATGTATATGATCCTCA
679340 AACTTGAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (25 bp):
GTTACAACTATGTATATGATCCTCA
Found at i:680184 original size:138 final size:138
Alignment explanation
Indices: 679998--680281 Score: 446
Period size: 138 Copynumber: 2.1 Consensus size: 138
679988 CAAAACATAT
*
679998 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTA-CTGAATTTAT
1 ATATAATTAATATATGAATTTGATTCATACAAAATAATAATTGTATATATTTTATC-GAATTTAT
* * *
680062 TAATATAAAAAATTATATTAATTAATTTCAGTCAAAATATTAAAGACAT-GAAAGTTAATATTCT
65 TAATATAAAAAATTATATTAATTAATTTCAGGCAAAATATAAAAGACATGGAAA-TTAATATTAT
*
680126 TTTGGAAAGA
129 TTTAGAAAGA
* * *
680136 TTATAATTAATATATGAATTTGATTCATGCAAAGTAATAATTGTATATATTTTATCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATAATAATTGTATATATTTTATCGAATTTATT
* *
680201 AATATAAACAATTATATTAATTAATTTCAGGCAAAATATAAAAGACATGGAAATTTATATTATTT
66 AATATAAAAAATTATATTAATTAATTTCAGGCAAAATATAAAAGACATGGAAATTAATATTATTT
680266 TAGAAAGA
131 TAGAAAGA
680274 ATATAATT
1 ATATAATT
680282 CTTTTTTCTA
Statistics
Matches: 133, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
138 128 0.96
139 5 0.04
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.41
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATAATAATTGTATATATTTTATCGAATTTATT
AATATAAAAAATTATATTAATTAATTTCAGGCAAAATATAAAAGACATGGAAATTAATATTATTT
TAGAAAGA
Found at i:680382 original size:76 final size:75
Alignment explanation
Indices: 680256--680404 Score: 244
Period size: 76 Copynumber: 2.0 Consensus size: 75
680246 CATGGAAATT
680256 TATATTATTTTAGAAAGAATATAATTCTTTTTTCTAACTTTCCATTTGCCTTCCTCTATTAATAA
1 TATATTATTTTAGAAAGAATATAATTCTTTTTTCTAACTTTCCATTTGCCTT-CTCTATTAATAA
680321 GGGAATAATCC
65 GGGAATAATCC
* * * * *
680332 TATATTCTTTTGGAAAGATTATGATTCTTTTTTCTAACTTTCCATTTGCCTTTTCTATTAATAAG
1 TATATTATTTTAGAAAGAATATAATTCTTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAG
680397 GGAATAAT
66 GGAATAAT
680405 TCTGGTTTTC
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
75 20 0.29
76 48 0.71
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (75 bp):
TATATTATTTTAGAAAGAATATAATTCTTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAG
GGAATAATCC
Found at i:681149 original size:24 final size:24
Alignment explanation
Indices: 681122--681181 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
681112 GAATGTTTTG
*
681122 TATTTTATATAATATTAATATAAA
1 TATTTTATTTAATATTAATATAAA
681146 TATTTTTATTTAA-ATTAATATAAA
1 TA-TTTTATTTAATATTAATATAAA
681170 T-TTTTATTTAAT
1 TATTTTATTTAAT
681182 TAAATTTTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
22 10 0.30
24 14 0.42
25 9 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TATTTTATTTAATATTAATATAAA
Found at i:681175 original size:22 final size:24
Alignment explanation
Indices: 681124--681184 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 24
681114 ATGTTTTGTA
*
681124 TTTTATATAATATTAATATAAATAT
1 TTTTATTTAA-ATTAATATAAATAT
681149 TTTTATTTAAATTAATAT-AA-AT
1 TTTTATTTAAATTAATATAAATAT
681171 TTTTATTT-AATTAA
1 TTTTATTTAAATTAA
681185 ATTTTAGGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
21 6 0.17
22 10 0.29
23 2 0.06
24 8 0.23
25 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTATTTAAATTAATATAAATAT
Found at i:681392 original size:16 final size:16
Alignment explanation
Indices: 681373--681409 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
681363 GGAAAGTGAT
681373 TAAAATAGAAACGATC
1 TAAAATAGAAACGATC
**
681389 TAAAATAGAAATTATC
1 TAAAATAGAAACGATC
681405 TAAAA
1 TAAAA
681410 CATTAGCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.24
Consensus pattern (16 bp):
TAAAATAGAAACGATC
Found at i:684865 original size:19 final size:19
Alignment explanation
Indices: 684826--684865 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
684816 AAAAAAATCA
*
684826 TTTTGGTCCTTTATATAAT
1 TTTTGGTCCTTTATAGAAT
* *
684845 TTTTTGTCCTTTATAGCAT
1 TTTTGGTCCTTTATAGAAT
684864 TT
1 TT
684866 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.60
Consensus pattern (19 bp):
TTTTGGTCCTTTATAGAAT
Found at i:695099 original size:14 final size:14
Alignment explanation
Indices: 695055--695099 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
695045 AAATTATGTT
* *
695055 AATTATTTATTTTT
1 AATTATTTATATTA
*
695069 AATTATTTA-AATA
1 AATTATTTATATTA
695082 AATTATTTATATTA
1 AATTATTTATATTA
695096 AATT
1 AATT
695100 TAACTTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AATTATTTATATTA
Found at i:718451 original size:17 final size:17
Alignment explanation
Indices: 718429--718464 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
718419 TTTAACTAAT
718429 TTAATTTTCTAATTAAA
1 TTAATTTTCTAATTAAA
* *
718446 TTAATTTTTTAATTCAA
1 TTAATTTTCTAATTAAA
718463 TT
1 TT
718465 CTAATTCTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAATTTTCTAATTAAA
Found at i:721995 original size:20 final size:20
Alignment explanation
Indices: 721971--722075 Score: 93
Period size: 20 Copynumber: 5.0 Consensus size: 20
721961 TATAGAATAC
721971 GCCACAAAGGCTAACAGAAT
1 GCCACAAAGGCTAACAGAAT
* * **
721991 CCCACAATGGCTATTTTAGAAT
1 GCCACAAAGGCTA--ACAGAAT
*
722013 GCCACAAAGGCTAATAGAAT
1 GCCACAAAGGCTAACAGAAT
** * *
722033 GCCACAAAAACCATATCATAAT
1 GCCAC-AAAGGC-TAACAGAAT
722055 GCCACAAAGGCTAACAGAAT
1 GCCACAAAGGCTAACAGAAT
722075 G
1 G
722076 AGCCATAAAG
Statistics
Matches: 65, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
20 30 0.46
21 8 0.12
22 27 0.42
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.17
Consensus pattern (20 bp):
GCCACAAAGGCTAACAGAAT
Found at i:722075 original size:42 final size:42
Alignment explanation
Indices: 721971--722075 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
721961 TATAGAATAC
* *** * * *
721971 GCCACAAAGGCTAACAGAATCCCACAATGGCTATTTTAGAAT
1 GCCACAAAGGCTAACAGAATGCCACAAAAACCATATCAGAAT
* *
722013 GCCACAAAGGCTAATAGAATGCCACAAAAACCATATCATAAT
1 GCCACAAAGGCTAACAGAATGCCACAAAAACCATATCAGAAT
722055 GCCACAAAGGCTAACAGAATG
1 GCCACAAAGGCTAACAGAATG
722076 AGCCATAAAG
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.17
Consensus pattern (42 bp):
GCCACAAAGGCTAACAGAATGCCACAAAAACCATATCAGAAT
Found at i:723276 original size:46 final size:46
Alignment explanation
Indices: 723196--723515 Score: 482
Period size: 46 Copynumber: 7.0 Consensus size: 46
723186 TTTGACATGA
* * * * * *
723196 TGCCATAGTGTCTTTCAACTATGGACTTACTCATTTTC-TATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* *** *
723242 TGCCATGGTATCTTTCAACCATAGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
723288 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
723334 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGG-T
*
723381 T-CCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
723426 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
723472 TGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
723516 AGAGCACACT
Statistics
Matches: 256, Mismatches: 15, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
45 5 0.02
46 249 0.97
47 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:728689 original size:15 final size:15
Alignment explanation
Indices: 728671--728727 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
728661 TATCTGTTTT
*
728671 ATTGAGTTTATATTG
1 ATTGAATTTATATTG
* *
728686 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
728701 ATTGAATTTATATTG
1 ATTGAATTTATATTG
728716 ATTGAA-TTATAT
1 ATTGAATTTATAT
728728 AATATATATG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
14 6 0.16
15 31 0.84
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:728705 original size:30 final size:28
Alignment explanation
Indices: 728667--728725 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 28
728657 TGAATATCTG
*
728667 TTTTATTGAGTTTATATTGATTGAAATTA
1 TTTTATTGAATTTATATTGATTG-AATTA
728696 TTTTGATTGAATTTATATTGATTGAATTA
1 TTTT-ATTGAATTTATATTGATTGAATTA
728725 T
1 T
728726 ATAATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.56
Consensus pattern (28 bp):
TTTTATTGAATTTATATTGATTGAATTA
Found at i:729139 original size:23 final size:23
Alignment explanation
Indices: 729113--729185 Score: 91
Period size: 21 Copynumber: 3.3 Consensus size: 23
729103 GCACTTTATC
729113 TGTCGTATTTCAGGCACCTCGTG
1 TGTCGTATTTCAGGCACCTCGTG
729136 TGTCGTA--TCAGGCACCTCGTG
1 TGTCGTATTTCAGGCACCTCGTG
* **
729157 TGTCGT-TTT-AGGCACTTTATG
1 TGTCGTATTTCAGGCACCTCGTG
729178 TGTCGTAT
1 TGTCGTAT
729186 ACTGATCAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
21 35 0.80
22 2 0.05
23 7 0.16
ACGTcount: A:0.14, C:0.22, G:0.26, T:0.38
Consensus pattern (23 bp):
TGTCGTATTTCAGGCACCTCGTG
Found at i:729368 original size:18 final size:19
Alignment explanation
Indices: 729347--729387 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
729337 AATGAAATGA
729347 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
729365 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
729384 GAAA
1 GAAA
729388 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:730605 original size:9 final size:9
Alignment explanation
Indices: 730583--730625 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
730573 AGGTTGAGAA
730583 AATT-ATTT
1 AATTAATTT
730591 AATTAATTT
1 AATTAATTT
*
730600 AGTTAATTT
1 AATTAATTT
* *
730609 AACTAATTA
1 AATTAATTT
730618 AATTAATT
1 AATTAATT
730626 GATTACATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
8 4 0.14
9 25 0.86
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (9 bp):
AATTAATTT
Found at i:732600 original size:62 final size:58
Alignment explanation
Indices: 732491--732645 Score: 140
Period size: 56 Copynumber: 2.7 Consensus size: 58
732481 TAATAGGATT
* * * **
732491 ATTAT-TAAATATAATTTAATAAAAATAAATAATAAATAATTTAATCATATTTTAATATA
1 ATTATATAAATATAATTAAAT-TAAATTAA-AATATTTAATTTAATCATATTTTAATATA
*
732550 ATTAGTACTAAATATAATTAAATTAAATTAAAATATTTAATTTAAT-ATCATTCTTATTATA
1 ATTA-TA-TAAATATAATTAAATTAAATTAAAATATTTAATTTAATCAT-ATT-TTAATATA
** *
732611 ATTAT-T-TTTAT-ATTAAATTATATTAAAATATTTAA
1 ATTATATAAATATAATTAAATTAAATTAAAATATTTAA
732646 AAATTTTAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
56 23 0.28
57 3 0.04
58 1 0.01
59 6 0.07
60 18 0.22
61 17 0.21
62 14 0.17
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (58 bp):
ATTATATAAATATAATTAAATTAAATTAAAATATTTAATTTAATCATATTTTAATATA
Found at i:732996 original size:28 final size:28
Alignment explanation
Indices: 732956--733019 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
732946 ATTACTGTCT
732956 AAATCAAGAAGATAACAAGAAACGCACA
1 AAATCAAGAAGATAACAAGAAACGCACA
*
732984 AAATCAAGGAGATAACAAGAAACGCACA
1 AAATCAAGAAGATAACAAGAAACGCACA
*
733012 AAAACAAG
1 AAATCAAG
733020 TTCTATGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.61, C:0.17, G:0.16, T:0.06
Consensus pattern (28 bp):
AAATCAAGAAGATAACAAGAAACGCACA
Found at i:738390 original size:23 final size:23
Alignment explanation
Indices: 738359--738433 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
738349 TCTACAAACC
738359 TATTATTAAGCAAGTCTAAGGCA
1 TATTATTAAGCAAGTCTAAGGCA
* * * *
738382 TATTCTTAA-CAA-TATTTA--CC
1 TATTATTAAGCAAGT-CTAAGGCA
738402 TATTATTAAGCAAGTCTAAGGCA
1 TATTATTAAGCAAGTCTAAGGCA
*
738425 TATTCTTAA
1 TATTATTAA
738434 CAATATTTAT
Statistics
Matches: 38, Mismatches: 9, Indels: 10
0.67 0.16 0.18
Matches are distributed among these distances:
20 9 0.24
21 6 0.16
22 6 0.16
23 17 0.45
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (23 bp):
TATTATTAAGCAAGTCTAAGGCA
Done.