Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 167 of 172
Found at i:54683968 original size:72 final size:72
Alignment explanation
Indices: 54683851--54684373 Score: 949
Period size: 72 Copynumber: 7.2 Consensus size: 72
54683841 AAAGCAGATT
54683851 AATTTTGAAAACAGAAATTGGAATTACCTCAACGTGTCTTGAGGCTTAACTCATTTCTCGCAATA
1 AATTTTGAAAACAGAAATTGGAATTACCTCAACGTGTCTTGAGGCTTAACTCATTTCTCGCAATA
54683916 TGAGTTG
66 TGAGTTG
54683923 AATTTTGAAAACAGAAATTGGAATTACCTCAACGTGTCTTGAGGCTTAACTCATTTCTCGCAATA
1 AATTTTGAAAACAGAAATTGGAATTACCTCAACGTGTCTTGAGGCTTAACTCATTTCTCGCAATA
54683988 TGAGTTG
66 TGAGTTG
54683995 AATTTTGAAAACAGAAATTGGAATTACCTCAACGTGTCTTGAGGCTTAACTCATTTCTCGCAATA
1 AATTTTGAAAACAGAAATTGGAATTACCTCAACGTGTCTTGAGGCTTAACTCATTTCTCGCAATA
54684060 TGAGTTG
66 TGAGTTG
54684067 AATTTTGAAAACAGAAATTGGAATTACCTCAACGTGTCTTGAGGCTTAACTCATTTCTCGCAATA
1 AATTTTGAAAACAGAAATTGGAATTACCTCAACGTGTCTTGAGGCTTAACTCATTTCTCGCAATA
54684132 TGAGTTG
66 TGAGTTG
54684139 AATTTTGAAAACAGAAATTGGAATTACCTCAACGTGTCTTGAGGCTTAACTCATTTCTCGCAATA
1 AATTTTGAAAACAGAAATTGGAATTACCTCAACGTGTCTTGAGGCTTAACTCATTTCTCGCAATA
54684204 TGAGTTG
66 TGAGTTG
* * * * * *
54684211 AATTTTGAAAAGCAAAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTTGCAAT
1 AATTTTGAAAA-CAGAAATTGGAATTACCTCAACGTGTCTTGAGGCTTAACTCATTTCTCGCAAT
54684276 ATGAGTTG
65 ATGAGTTG
* *
54684284 AATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATA
1 AATTTTGAAAACAGAAATTGGAATTACCTCAACGTGTCTTGAGGCTTAACTCATTTCTCGCAATA
54684349 TGAGTTG
66 TGAGTTG
54684356 AATTTTTG-AAACAGAAAT
1 AA-TTTTGAAAACAGAAAT
54684374 AAAAGCATCA
Statistics
Matches: 439, Mismatches: 10, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
72 368 0.84
73 71 0.16
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (72 bp):
AATTTTGAAAACAGAAATTGGAATTACCTCAACGTGTCTTGAGGCTTAACTCATTTCTCGCAATA
TGAGTTG
Found at i:54686588 original size:17 final size:15
Alignment explanation
Indices: 54686574--54686618 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 15
54686564 TTTCTTGTCC
54686574 TTTTTTTCTTTTTGT
1 TTTTTTTCTTTTTGT
*
54686589 TTTTTTTTTGTTTTGTT
1 TTTTTTTCT-TTTTG-T
54686606 TTCTTTTTCTTTT
1 TT-TTTTTCTTTT
54686619 CATGACTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 8 0.32
16 5 0.20
17 6 0.24
18 6 0.24
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.87
Consensus pattern (15 bp):
TTTTTTTCTTTTTGT
Found at i:54686591 original size:11 final size:11
Alignment explanation
Indices: 54686577--54686618 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
54686567 CTTGTCCTTT
54686577 TTTTCTTTTTG
1 TTTTCTTTTTG
*
54686588 TTTTTTTTTTG
1 TTTTCTTTTTG
*
54686599 TTTTGTTTTCT-
1 TTTTCTTTT-TG
54686610 TTTTCTTTT
1 TTTTCTTTT
54686619 CATGACTGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 26 0.96
12 1 0.04
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (11 bp):
TTTTCTTTTTG
Found at i:54686593 original size:16 final size:16
Alignment explanation
Indices: 54686574--54686618 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
54686564 TTTCTTGTCC
54686574 TTTTTTTCTTTTTGTT
1 TTTTTTTCTTTTTGTT
54686590 TTTTTTT-TGTTTTGTT
1 TTTTTTTCT-TTTTGTT
54686606 TTCTTTTTCTTTT
1 TT-TTTTTCTTTT
54686619 CATGACTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.04
16 16 0.62
17 8 0.31
18 1 0.04
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.87
Consensus pattern (16 bp):
TTTTTTTCTTTTTGTT
Found at i:54686613 original size:27 final size:28
Alignment explanation
Indices: 54686546--54686618 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
54686536 CTTTCTGGCA
*
54686546 TTTGATTT-TTTTTATTTTTTTCTTGTCC
1 TTTGTTTTCTTTTTATTTTTTTCTTGT-C
* *
54686574 TTT-TTTTCTTTTTGTTTTTTTTTTGT-
1 TTTGTTTTCTTTTTATTTTTTTCTTGTC
*
54686600 TTTGTTTTCTTTTTCTTTT
1 TTTGTTTTCTTTTTATTTT
54686619 CATGACTGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 3 0.08
27 17 0.44
28 19 0.49
ACGTcount: A:0.03, C:0.08, G:0.07, T:0.82
Consensus pattern (28 bp):
TTTGTTTTCTTTTTATTTTTTTCTTGTC
Found at i:54691435 original size:15 final size:15
Alignment explanation
Indices: 54691415--54691544 Score: 149
Period size: 15 Copynumber: 8.5 Consensus size: 15
54691405 TTTTTGGTTT
54691415 TTTTTTTGCTGGAAA
1 TTTTTTTGCTGGAAA
54691430 -TTTTTTGCTGG-AA
1 TTTTTTTGCTGGAAA
*
54691443 TTTTCTTTGCTGGAAT
1 TTTT-TTTGCTGGAAA
54691459 TTTTTTTGCTGGAAA
1 TTTTTTTGCTGGAAA
*
54691474 TTTTTTTGCTGCTGGAA
1 TTTTTTTGCTG--GAAA
*
54691491 TTTTTTTGCTTGAAA
1 TTTTTTTGCTGGAAA
54691506 TTTTTTGCTGCTGG-AA
1 TTTTTT--TGCTGGAAA
*
54691522 TTTTTTTGCTAGAAAA
1 TTTTTTTGCT-GGAAA
54691538 TTTTTTT
1 TTTTTTT
54691545 TGCTTCCCGC
Statistics
Matches: 99, Mismatches: 7, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
13 2 0.02
14 18 0.18
15 39 0.39
16 22 0.22
17 18 0.18
ACGTcount: A:0.17, C:0.08, G:0.18, T:0.56
Consensus pattern (15 bp):
TTTTTTTGCTGGAAA
Found at i:54691439 original size:44 final size:44
Alignment explanation
Indices: 54691390--54691484 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 44
54691380 CTTGCTTAGA
** **
54691390 TTGCTGAATGTTCCTTTTTTGGTTTTTTTTTTGCTGGAAA-TTTT
1 TTGCTGAAT-TTCCTTTGCTGGAATTTTTTTTGCTGGAAATTTTT
*
54691434 TTGCTGGAATTTTCTTTGCTGGAATTTTTTTTGCTGGAAATTTTT
1 TTGCT-GAATTTCCTTTGCTGGAATTTTTTTTGCTGGAAATTTTT
54691479 TTGCTG
1 TTGCTG
54691485 CTGGAATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
44 31 0.70
45 13 0.30
ACGTcount: A:0.13, C:0.09, G:0.20, T:0.58
Consensus pattern (44 bp):
TTGCTGAATTTCCTTTGCTGGAATTTTTTTTGCTGGAAATTTTT
Found at i:54691476 original size:31 final size:30
Alignment explanation
Indices: 54691414--54691548 Score: 173
Period size: 31 Copynumber: 4.4 Consensus size: 30
54691404 TTTTTTGGTT
*
54691414 TTTTTTTTGCTGGAAATTTTTTGCTGG-AA
1 TTTTTTTTGCTGGAATTTTTTTGCTGGAAA
*
54691443 TTTTCTTTGCTGGAATTTTTTTTGCTGGAAA
1 TTTTTTTTGCTGGAA-TTTTTTTGCTGGAAA
*
54691474 TTTTTTTGCTGCTGGAATTTTTTTGCTTGAAA
1 TTTTTTT--TGCTGGAATTTTTTTGCTGGAAA
* *
54691506 TTTTTTGCTGCTGGAATTTTTTTGCTAGAAAA
1 TTTTTT-TTGCTGGAATTTTTTTGCT-GGAAA
54691538 TTTTTTTTGCT
1 TTTTTTTTGCT
54691549 TCCCGCCCCT
Statistics
Matches: 92, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
29 14 0.15
30 11 0.12
31 30 0.33
32 29 0.32
33 8 0.09
ACGTcount: A:0.16, C:0.09, G:0.19, T:0.56
Consensus pattern (30 bp):
TTTTTTTTGCTGGAATTTTTTTGCTGGAAA
Found at i:54691543 original size:48 final size:45
Alignment explanation
Indices: 54691414--54691549 Score: 141
Period size: 48 Copynumber: 2.9 Consensus size: 45
54691404 TTTTTTGGTT
* * * *
54691414 TTTTTTTTGCTGGAAATTTTTTGCTGGAATTTTCTTTGC-TGGAA
1 TTTTTTCTGCTGGAATTTTTTTGCTGGAATTTTTTTTGCTTGAAA
*
54691458 TTTTTTTTGCTGGAAATTTTTTTGCTGCTGGAA-TTTTTTTGCTTGAAA
1 TTTTTTCTGCTGG-AA-TTTTTT--TGCTGGAATTTTTTTTGCTTGAAA
*
54691506 TTTTTTGCTGCTGGAATTTTTTTGCTAGAAAATTTTTTTTGCTT
1 TTTTTT-CTGCTGGAATTTTTTTGCT-G-GAATTTTTTTTGCTT
54691550 CCCGCCCCTT
Statistics
Matches: 78, Mismatches: 5, Indels: 14
0.80 0.05 0.14
Matches are distributed among these distances:
44 13 0.17
45 6 0.08
46 6 0.08
47 16 0.21
48 31 0.40
49 6 0.08
ACGTcount: A:0.16, C:0.09, G:0.18, T:0.57
Consensus pattern (45 bp):
TTTTTTCTGCTGGAATTTTTTTGCTGGAATTTTTTTTGCTTGAAA
Found at i:54695855 original size:130 final size:131
Alignment explanation
Indices: 54695586--54695939 Score: 421
Period size: 130 Copynumber: 2.7 Consensus size: 131
54695576 ATTCGATTGC
* ** * * * * * *
54695586 TTTGAGCAAATGAGAAATCACAACCCAGCACGATAGGGTATGATTCCCGAATTGTCAAACACCGA
1 TTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCCGAATTGTCAAATATCGA
** * * *
54695651 GTATTACCTTCGTTTTAAAAGATTTTTAGAAGACCTGAGTGAAATTTTGAAGGGATATTTGATTA
66 ACATCACCTTCGTTTTAAAAGATTTTTAAAAGACATGAGTGAAATTTTGAAGGGATATTTGATTA
54695716 T
131 T
* *
54695717 TTTAAGCAAACGAGAAATTGCGACCCAACACGTTAGGGCACGATTCCACGAATTGTCAAATATCG
1 TTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCC-CGAATTGTCAAATATCG
* ** *
54695782 AACATCGCCTTC-TTTTAAGTGA-TTTTAAAATACATGAGTGAAATTTTGAAGGGATATTTGATT
65 AACATCACCTTCGTTTTAAAAGATTTTTAAAAGACATGAGTGAAATTTTGAAGGGATATTTGATT
54695845 AT
130 AT
* *
54695847 TTTGAGCAAACGAAAAATTGCAACTCAACACGTTAGGGCACGATTCCGCGAATTGTCAAATATC-
1 TTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCC-CGAATTGTCAAATATCG
*
54695911 AA-ATCTCGTCTTCGTTTT-AAAGAATTTTT
65 AACATCAC--CTTCGTTTTAAAAG-ATTTTT
54695940 GGATGAATGA
Statistics
Matches: 189, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
128 4 0.02
129 2 0.01
130 105 0.56
131 51 0.27
132 27 0.14
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (131 bp):
TTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCCGAATTGTCAAATATCGA
ACATCACCTTCGTTTTAAAAGATTTTTAAAAGACATGAGTGAAATTTTGAAGGGATATTTGATTA
T
Found at i:54702179 original size:126 final size:126
Alignment explanation
Indices: 54701961--54702196 Score: 357
Period size: 126 Copynumber: 1.9 Consensus size: 126
54701951 TTCGTGAGCG
* *
54701961 GGATCTTAATCATTGCCCAATGATCAAATTTCCAAGAATCCCTAGAAGCTTAATAAAAATAAACT
1 GGATCTTAATCATTGCCCAATGATCAAATTTCCAAGAATCCCAAGAAGCTTAACAAAAATAAACT
* *
54702026 TATCTGGCACTCAAATTGATGAAGTGTCCTTACCTTTGGACTCTCGATCCCTTCGTGAATT
66 TATCTGGCACTCAAATTGAAGAAGTGTCCTTACCTTTCGACTCTCGATCCCTTCGTGAATT
* * * * *
54702087 GGATCTTAGTTATTGCCCAATGGTCAAGTTTCC-AGAAATCCCAAGAAGCTTAACAAAATTAAAC
1 GGATCTTAATCATTGCCCAATGATCAAATTTCCAAG-AATCCCAAGAAGCTTAACAAAAATAAAC
* *
54702151 TTATCTGGCACTCAAATTGAAGAGGTGTCCTTGCCTTTCGACTCTC
65 TTATCTGGCACTCAAATTGAAGAAGTGTCCTTACCTTTCGACTCTC
54702197 TATGTAATCT
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
125 2 0.02
126 96 0.98
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (126 bp):
GGATCTTAATCATTGCCCAATGATCAAATTTCCAAGAATCCCAAGAAGCTTAACAAAAATAAACT
TATCTGGCACTCAAATTGAAGAAGTGTCCTTACCTTTCGACTCTCGATCCCTTCGTGAATT
Found at i:54703473 original size:15 final size:15
Alignment explanation
Indices: 54703453--54703484 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
54703443 ATCCTTCACG
54703453 ATGAAGAAGAAGATT
1 ATGAAGAAGAAGATT
*
54703468 ATGAAGGAGAAGATT
1 ATGAAGAAGAAGATT
54703483 AT
1 AT
54703485 CACGTAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.28, T:0.22
Consensus pattern (15 bp):
ATGAAGAAGAAGATT
Found at i:54707013 original size:21 final size:21
Alignment explanation
Indices: 54706987--54707027 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
54706977 ATCTGCTCAA
* *
54706987 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
*
54707008 ACTCCATCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
54707028 TTGCCCGTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:54718274 original size:32 final size:31
Alignment explanation
Indices: 54718238--54718298 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
54718228 GATTTTTGAA
*
54718238 AAAGAATTATAACTATTTAAATAAT-ATTATTT
1 AAAGAATTATAA-TA-TTAAAAAATAATTATTT
*
54718270 AAAGAGTTATAATATTAAAAAATAATTAT
1 AAAGAATTATAATATTAAAAAATAATTAT
54718299 GTGTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 7 0.27
32 11 0.42
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (31 bp):
AAAGAATTATAATATTAAAAAATAATTATTT
Found at i:54719867 original size:21 final size:21
Alignment explanation
Indices: 54719841--54719895 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
54719831 ATGAGTTTTT
* *
54719841 TTGTTTCATGACTTTTAAACA
1 TTGTTTCATAAATTTTAAACA
*
54719862 TTGTTTGATAAATTTTAAAC-
1 TTGTTTCATAAATTTTAAACA
*
54719882 TGAGTTTCATAAAT
1 T-TGTTTCATAAAT
54719896 ATTTCTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (21 bp):
TTGTTTCATAAATTTTAAACA
Found at i:54719979 original size:28 final size:25
Alignment explanation
Indices: 54719947--54720011 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
54719937 TGTCACTATT
*
54719947 TTAAATATAAAATATATAATTTTATA
1 TTAAATATAAAATAT-TAATTATATA
* *
54719973 TCGTAAAAATTAAA-ATTAATTATATA
1 T--TAAATATAAAATATTAATTATATA
54719999 TTAAATA-AAAATA
1 TTAAATATAAAATA
54720012 AAATTCAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
23 3 0.10
24 6 0.19
26 11 0.35
27 2 0.06
28 9 0.29
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
TTAAATATAAAATATTAATTATATA
Found at i:54725379 original size:21 final size:20
Alignment explanation
Indices: 54725355--54725414 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
54725345 GGTCTCATTT
*
54725355 TCATCTCTTTTTGTCATATTA
1 TCATCTCATTTT-TCATATTA
*
54725376 TCATC-CATTTTTCAGTTTTA
1 TCATCTCATTTTTCA-TATTA
*
54725396 TCATTTCATTTTTCATATT
1 TCATCTCATTTTTCATATT
54725415 CCCATACTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 3 0.09
20 16 0.48
21 14 0.42
ACGTcount: A:0.20, C:0.18, G:0.03, T:0.58
Consensus pattern (20 bp):
TCATCTCATTTTTCATATTA
Found at i:54727479 original size:798 final size:798
Alignment explanation
Indices: 54725874--54729140 Score: 6376
Period size: 798 Copynumber: 4.1 Consensus size: 798
54725864 ACCAAAATTC
* * * * * * *
54725874 AGATATTAA-ACTTCGTACTT-AATTCTTATTGACAGTTAACTTGTTATTGGCTGGTTTTTTTTA
1 AGATATTAAGA-TTCATACTTGAATTCTTTTTGGCAGTTGACTTGTTATTAGTTGG---TTTTGA
*
54725937 ATTCACAGGACCATTGGTGGACTCGGTTCAGCTTCATTGTTTAGTTCCGGCATCGGTGTCATCTG
62 A-TCATAGGACCATTGGTGGACTCGGTTCAGCTTCATTGTTTAGTTCCGGCATCGGTGTCATCTG
54726002 GTCTCTCAATACTTGCTGCATTTTCCTTCAATGATATCTTGATTCATAGAAAGATTGGTTATTTG
126 GTCTCTCAATACTTGCTGCATTTTCCTTCAATGATATCTTGATTCATAGAAAGATTGGTTATTTG
54726067 TGAGATTGGTTTTTCTTATATCCTTTGCTTCTGTGTTGATGTAAGATTAGGAATGACAGATCTTT
191 TGAGATTGGTTTTTCTTATATCCTTTGCTTCTGTGTTGATGTAAGATTAGGAATGACAGATCTTT
54726132 GAGAATGCCACTTCTGAATTGGAGCTTTAGCCATACAAGGAGGAACACCTGACCTGTAAGACCCT
256 GAGAATGCCACTTCTGAATTGGAGCTTTAGCCATACAAGGAGGAACACCTGACCTGTAAGACCCT
54726197 CAATTTGTTTTACTGAATGCTTACTTTATGTAAGTGTTCGAACTGATATTTGGTGACAATGCAAG
321 CAATTTGTTTTACTGAATGCTTACTTTATGTAAGTGTTCGAACTGATATTTGGTGACAATGCAAG
54726262 ATGTCAACAGATTTGTCAACACAAATCCAAAGTAATCTTTTGAGGCCCTTTCTGGGTTCTGGCAA
386 ATGTCAACAGATTTGTCAACACAAATCCAAAGTAATCTTTTGAGGCCCTTTCTGGGTTCTGGCAA
54726327 TTCAGTCTTGGTGGATAAGTAAGTTACCTATGACTTTTGACTTATTATTATGATTTTAGGTTCAT
451 TTCAGTCTTGGTGGATAAGTAAGTTACCTATGACTTTTGACTTATTATTATGATTTTAGGTTCAT
54726392 ATAATGAATTTCAGCATCCTCACCTTTTTTTTTTCACATATTTATCAATGGGATTATATAAATCC
516 ATAATGAATTTCAGCATCCTCACCTTTTTTTTTTCACATATTTATCAATGGGATTATATAAATCC
54726457 AGAATTTACAAGAGGTCTCAAAACTTTGGTATGAACAAATGGAGCTGGAGGCAACCTTTGACAGT
581 AGAATTTACAAGAGGTCTCAAAACTTTGGTATGAACAAATGGAGCTGGAGGCAACCTTTGACAGT
54726522 TTTCATTCTCAAGCTAGATTGAGTTAGTTTCATGGTAGAGCCGTTGGAGTTGATATTTTCTTATC
646 TTTCATTCTCAAGCTAGATTGAGTTAGTTTCATGGTAGAGCCGTTGGAGTTGATATTTTCTTATC
54726587 TTGGATTTTAATTATCATATCAGTTTGGGCTGAAATTTCTTTGTATGTTACTTACTGCCTCTTAT
711 TTGGATTTTAATTATCATATCAGTTTGGGCTGAAATTTCTTTGTATGTTACTTACTGCCTCTTAT
54726652 GTTGTTTGAGCATTGCGGTGAGT
776 GTTGTTTGAGCATTGCGGTGAGT
54726675 AGATATTAAGATTCATACTTGAATTCTTTTTGGCAGTTGACTTGTTATTAGTTGGTTTTGAATCA
1 AGATATTAAGATTCATACTTGAATTCTTTTTGGCAGTTGACTTGTTATTAGTTGGTTTTGAATCA
54726740 TAGGACCATTGGTGGACTCGGTTCAGCTTCATTGTTTAGTTCCGGCATCGGTGTCATCTGGTCTC
66 TAGGACCATTGGTGGACTCGGTTCAGCTTCATTGTTTAGTTCCGGCATCGGTGTCATCTGGTCTC
54726805 TCAATACTTGCTGCATTTTCCTTCAATGATATCTTGATTCATAGAAAGATTGGTTATTTGTGAGA
131 TCAATACTTGCTGCATTTTCCTTCAATGATATCTTGATTCATAGAAAGATTGGTTATTTGTGAGA
54726870 TTGGTTTTTCTTATATCCTTTGCTTCTGTGTTGATGTAAGATTAGGAATGACAGATCTTTGAGAA
196 TTGGTTTTTCTTATATCCTTTGCTTCTGTGTTGATGTAAGATTAGGAATGACAGATCTTTGAGAA
54726935 TGCCACTTCTGAATTGGAGCTTTAGCCATACAAGGAGGAACACCTGACCTGTAAGACCCTCAATT
261 TGCCACTTCTGAATTGGAGCTTTAGCCATACAAGGAGGAACACCTGACCTGTAAGACCCTCAATT
54727000 TGTTTTACTGAATGCTTACTTTATGTAAGTGTTCGAACTGATATTTGGTGACAATGCAAGATGTC
326 TGTTTTACTGAATGCTTACTTTATGTAAGTGTTCGAACTGATATTTGGTGACAATGCAAGATGTC
54727065 AACAGATTTGTCAACACAAATCCAAAGTAATCTTTTGAGGCCCTTTCTGGGTTCTGGCAATTCAG
391 AACAGATTTGTCAACACAAATCCAAAGTAATCTTTTGAGGCCCTTTCTGGGTTCTGGCAATTCAG
54727130 TCTTGGTGGATAAGTAAGTTACCTATGACTTTTGACTTATTATTATGATTTTAGGTTCATATAAT
456 TCTTGGTGGATAAGTAAGTTACCTATGACTTTTGACTTATTATTATGATTTTAGGTTCATATAAT
54727195 GAATTTCAGCATCCTCACCTTTTTTTTTTCACATATTTATCAATGGGATTATATAAATCCAGAAT
521 GAATTTCAGCATCCTCACCTTTTTTTTTTCACATATTTATCAATGGGATTATATAAATCCAGAAT
54727260 TTACAAGAGGTCTCAAAACTTTGGTATGAACAAATGGAGCTGGAGGCAACCTTTGACAGTTTTCA
586 TTACAAGAGGTCTCAAAACTTTGGTATGAACAAATGGAGCTGGAGGCAACCTTTGACAGTTTTCA
54727325 TTCTCAAGCTAGATTGAGTTAGTTTCATGGTAGAGCCGTTGGAGTTGATATTTTCTTATCTTGGA
651 TTCTCAAGCTAGATTGAGTTAGTTTCATGGTAGAGCCGTTGGAGTTGATATTTTCTTATCTTGGA
54727390 TTTTAATTATCATATCAGTTTGGGCTGAAATTTCTTTGTATGTTACTTACTGCCTCTTATGTTGT
716 TTTTAATTATCATATCAGTTTGGGCTGAAATTTCTTTGTATGTTACTTACTGCCTCTTATGTTGT
54727455 TTGAGCATTGCGGTGAGT
781 TTGAGCATTGCGGTGAGT
54727473 AGATATTAAGATTCATACTTGAATTCTTTTTGGCAGTTGACTTGTTATTAGTTGGTTTTGAATCA
1 AGATATTAAGATTCATACTTGAATTCTTTTTGGCAGTTGACTTGTTATTAGTTGGTTTTGAATCA
54727538 TAGGACCATTGGTGGACTCGGTTCAGCTTCATTGTTTAGTTCCGGCATCGGTGTCATCTGGTCTC
66 TAGGACCATTGGTGGACTCGGTTCAGCTTCATTGTTTAGTTCCGGCATCGGTGTCATCTGGTCTC
54727603 TCAATACTTGCTGCATTTTCCTTCAATGATATCTTGATTCATAGAAAGATTGGTTATTTGTGAGA
131 TCAATACTTGCTGCATTTTCCTTCAATGATATCTTGATTCATAGAAAGATTGGTTATTTGTGAGA
54727668 TTGGTTTTTCTTATATCCTTTGCTTCTGTGTTGATGTAAGATTAGGAATGACAGATCTTTGAGAA
196 TTGGTTTTTCTTATATCCTTTGCTTCTGTGTTGATGTAAGATTAGGAATGACAGATCTTTGAGAA
54727733 TGCCACTTCTGAATTGGAGCTTTAGCCATACAAGGAGGAACACCTGACCTGTAAGACCCTCAATT
261 TGCCACTTCTGAATTGGAGCTTTAGCCATACAAGGAGGAACACCTGACCTGTAAGACCCTCAATT
*
54727798 TGTTTTACTGAATGCTTACTTTATGCAAGTGTTCGAACTGATATTTGGTGACAATGCAAGATGTC
326 TGTTTTACTGAATGCTTACTTTATGTAAGTGTTCGAACTGATATTTGGTGACAATGCAAGATGTC
54727863 AACAGATTTGTCAACACAAATCCAAAGTAATCTTTTGAGGCCCTTTCTGGGTTCTGGCAATTCAG
391 AACAGATTTGTCAACACAAATCCAAAGTAATCTTTTGAGGCCCTTTCTGGGTTCTGGCAATTCAG
54727928 TCTTGGTGGATAAGTAAGTTACCTATGACTTTTGACTTATTATTATGATTTTAGGTTCATATAAT
456 TCTTGGTGGATAAGTAAGTTACCTATGACTTTTGACTTATTATTATGATTTTAGGTTCATATAAT
54727993 GAATTTCAGCATCCTCACCTTTTTTTTTTCACATATTTATCAATGGGATTATATAAATCCAGAAT
521 GAATTTCAGCATCCTCACCTTTTTTTTTTCACATATTTATCAATGGGATTATATAAATCCAGAAT
54728058 TTACAAGAGGTCTCAAAACTTTGGTATGAACAAATGGAGCTGGAGGCAACCTTTGACAGTTTTCA
586 TTACAAGAGGTCTCAAAACTTTGGTATGAACAAATGGAGCTGGAGGCAACCTTTGACAGTTTTCA
54728123 TTCTCAAGCTAGATTGAGTTAGTTTCATGGTAGAGCCGTTGGAGTTGATATTTTCTTATCTTGGA
651 TTCTCAAGCTAGATTGAGTTAGTTTCATGGTAGAGCCGTTGGAGTTGATATTTTCTTATCTTGGA
54728188 TTTTAATTATCATATCAGTTTGGGCTGAAATTTCTTTGTATGTTACTTACTGCCTCTTATGTTGT
716 TTTTAATTATCATATCAGTTTGGGCTGAAATTTCTTTGTATGTTACTTACTGCCTCTTATGTTGT
54728253 TTGAGCATTGCGGTGAGT
781 TTGAGCATTGCGGTGAGT
54728271 AGATATTAAGATTCATACTTGAATTCTTTTTGGCAGTTGACTTGTTATTAGTTGGTTTTGAATCA
1 AGATATTAAGATTCATACTTGAATTCTTTTTGGCAGTTGACTTGTTATTAGTTGGTTTTGAATCA
54728336 TAGGACCATTGGTGGACTCGGTTCAGCTTCATTGTTTAGTTCCGGCATCGGTGTCATCTGGTCTC
66 TAGGACCATTGGTGGACTCGGTTCAGCTTCATTGTTTAGTTCCGGCATCGGTGTCATCTGGTCTC
54728401 TCAATACTTGCTGCATTTTCCTTCAATGATATCTTGATTCATAGAAAGATTGGTTATTTGTGAGA
131 TCAATACTTGCTGCATTTTCCTTCAATGATATCTTGATTCATAGAAAGATTGGTTATTTGTGAGA
54728466 TTGGTTTTTCTTATATCCTTTGCTTCTGTGTTGATGTAAGATTAGGAATGACAGATCTTTGAGAA
196 TTGGTTTTTCTTATATCCTTTGCTTCTGTGTTGATGTAAGATTAGGAATGACAGATCTTTGAGAA
54728531 TGCCACTTCTGAATTGGAGCTTTAGCCATACAAGGAGGAACACCTGACCTGTAAGACCCTCAATT
261 TGCCACTTCTGAATTGGAGCTTTAGCCATACAAGGAGGAACACCTGACCTGTAAGACCCTCAATT
54728596 TGTTTTACTGAATGCTTACTTTATGTAAGTGTTCGAACTGATATTTGGTGACAATGCAAGATGTC
326 TGTTTTACTGAATGCTTACTTTATGTAAGTGTTCGAACTGATATTTGGTGACAATGCAAGATGTC
54728661 AACAGATTTGTCAACACAAATCCAAAGTAATCTTTTGAGGCCCTTTCTGGGTTCTGGCAATTCAG
391 AACAGATTTGTCAACACAAATCCAAAGTAATCTTTTGAGGCCCTTTCTGGGTTCTGGCAATTCAG
54728726 TCTTGGTGGATAAGTAAGTTACCTATGACTTTTGACTTATTATTATGATTTTAGGTTCATATAAT
456 TCTTGGTGGATAAGTAAGTTACCTATGACTTTTGACTTATTATTATGATTTTAGGTTCATATAAT
54728791 GAATTTCAGCATCCTCACCTTTTTTTTTTCACATATTTATCAATGGGATTATATAAATCCAGAAT
521 GAATTTCAGCATCCTCACCTTTTTTTTTTCACATATTTATCAATGGGATTATATAAATCCAGAAT
54728856 TTACAAGAGGTCTCAAAACTTTGGTATGAACAAATGGAGCTGGAGGCAACCTTTGACAGTTTTCA
586 TTACAAGAGGTCTCAAAACTTTGGTATGAACAAATGGAGCTGGAGGCAACCTTTGACAGTTTTCA
54728921 TTCTCAAGCTAGATTGAGTTAGTTTCATGGTAGAGCCGTTGGAGTTGATATTTTCTTATCTTGGA
651 TTCTCAAGCTAGATTGAGTTAGTTTCATGGTAGAGCCGTTGGAGTTGATATTTTCTTATCTTGGA
54728986 TTTTAATTATCATATCAGTTTGGGCTGAAATTTCTTTGTATATGTTACTTACTGCCTCTTATGTT
716 TTTTAATTATCATATCAGTTTGGGCTGAAATTTCTTTG--TATGTTACTTACTGCCTCTTATGTT
54729051 GTTTGAGCATTGCGGTGAGT
779 GTTTGAGCATTGCGGTGAGT
54729071 AGATATTAAGATTCATACTTGAATTCTTTTTGGCAGTTGACTTGTTATTAGTTGGTTTTGAATCA
1 AGATATTAAGATTCATACTTGAATTCTTTTTGGCAGTTGACTTGTTATTAGTTGGTTTTGAATCA
54729136 TAGGA
66 TAGGA
54729141 TAAGTGGAGC
Statistics
Matches: 2452, Mismatches: 10, Indels: 9
0.99 0.00 0.00
Matches are distributed among these distances:
798 2284 0.93
799 6 0.00
800 115 0.05
801 17 0.01
802 30 0.01
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.39
Consensus pattern (798 bp):
AGATATTAAGATTCATACTTGAATTCTTTTTGGCAGTTGACTTGTTATTAGTTGGTTTTGAATCA
TAGGACCATTGGTGGACTCGGTTCAGCTTCATTGTTTAGTTCCGGCATCGGTGTCATCTGGTCTC
TCAATACTTGCTGCATTTTCCTTCAATGATATCTTGATTCATAGAAAGATTGGTTATTTGTGAGA
TTGGTTTTTCTTATATCCTTTGCTTCTGTGTTGATGTAAGATTAGGAATGACAGATCTTTGAGAA
TGCCACTTCTGAATTGGAGCTTTAGCCATACAAGGAGGAACACCTGACCTGTAAGACCCTCAATT
TGTTTTACTGAATGCTTACTTTATGTAAGTGTTCGAACTGATATTTGGTGACAATGCAAGATGTC
AACAGATTTGTCAACACAAATCCAAAGTAATCTTTTGAGGCCCTTTCTGGGTTCTGGCAATTCAG
TCTTGGTGGATAAGTAAGTTACCTATGACTTTTGACTTATTATTATGATTTTAGGTTCATATAAT
GAATTTCAGCATCCTCACCTTTTTTTTTTCACATATTTATCAATGGGATTATATAAATCCAGAAT
TTACAAGAGGTCTCAAAACTTTGGTATGAACAAATGGAGCTGGAGGCAACCTTTGACAGTTTTCA
TTCTCAAGCTAGATTGAGTTAGTTTCATGGTAGAGCCGTTGGAGTTGATATTTTCTTATCTTGGA
TTTTAATTATCATATCAGTTTGGGCTGAAATTTCTTTGTATGTTACTTACTGCCTCTTATGTTGT
TTGAGCATTGCGGTGAGT
Found at i:54732168 original size:28 final size:28
Alignment explanation
Indices: 54732136--54732190 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
54732126 TATGAGTATG
*
54732136 TGTATGTATAT-TCTTTTAAAATTCATTA
1 TGTATGTATATAT-TTTTAAAACTCATTA
54732164 TGTATGTATATATTTTTAAAACTCATT
1 TGTATGTATATATTTTTAAAACTCATT
54732191 TGCATATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (28 bp):
TGTATGTATATATTTTTAAAACTCATTA
Found at i:54737571 original size:82 final size:82
Alignment explanation
Indices: 54737470--54737632 Score: 290
Period size: 82 Copynumber: 2.0 Consensus size: 82
54737460 GAAGCAAGCC
* *
54737470 ATGAATGAAGAAATGCAGTCTCTTCATAAAAATAGGACTTGGGAATCGGTGACACTACCCAAGGG
1 ATGAATGAAGAAATGCAGTCTCTTCATAAAAATAAGACCTGGGAATCGGTGACACTACCCAAGGG
54737535 AAAGAAGGCAATTGGAA
66 AAAGAAGGCAATTGGAA
* *
54737552 ATGAATGAAGAAATGCAGTCTCTTCATAAAAATAAGACCTGGGAGTTGGTGACACTACCCAAGGG
1 ATGAATGAAGAAATGCAGTCTCTTCATAAAAATAAGACCTGGGAATCGGTGACACTACCCAAGGG
54737617 AAAGAAGGCAATTGGA
66 AAAGAAGGCAATTGGA
54737633 TGCAAATGGG
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.20
Consensus pattern (82 bp):
ATGAATGAAGAAATGCAGTCTCTTCATAAAAATAAGACCTGGGAATCGGTGACACTACCCAAGGG
AAAGAAGGCAATTGGAA
Found at i:54746871 original size:431 final size:429
Alignment explanation
Indices: 54744121--54748639 Score: 7197
Period size: 428 Copynumber: 10.6 Consensus size: 429
54744111 TACTCTTTTT
* * * *
54744121 TATTCATATAATAACATTTTATTTAAATTTTTTTAAAAATAAAAAT-AAAGATTTTATTTTATTT
1 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
*
54744185 AGATAAGTGGCATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
66 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
54744250 AATTTTTA-TTTTTTATAGTATTATAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGAT
131 AATTTTTATTTTTTTATAGTATTATAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGAT
* * *
54744314 GCTTAAAAGTAATAGGCTTATTTTTTCTGTATAGGACTTTGTTAATTTAAGGAAAATTAACTTCA
196 GCTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTCA
* * ** *
54744379 ATGGGTGCATGAGTTTAACCAAGATACCTAATC-TTCTAAGAGCCATCAACCTTGAATACCTTTA
261 ATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTC-AAGAGCCATCAACCTTGAATACCTTTA
* *
54744443 TTGCAGTGACTGTAAAAGTTTGGTTGAACTTTGGAATGGAGATGATTGTGTGGTAAGTATTTTCA
325 TTGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCA
*
54744508 TA----TTTTTAAAAAAAAAATTATATTTTGATGTATAAA
390 TACTTTTTTTTGAAAAAAAAATTATATTTTGATGTATAAA
* *
54744544 TATTCATATGATAATATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATGTTATTT
1 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
* * * *
54744609 AGATAAGTGATATCTTTTGATTTATTAATTGTGGGTGAATTTTCACACCCTATACATTAAATATA
66 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
* * *
54744674 AATTCTTATTTTTTTATATTATTATAATTATTTCTTTCTTTTCCTTTTTTTACTAAATAGTTGAT
131 AATTTTTATTTTTTTATAGTATTATAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGAT
* *
54744739 GCTTAAAAGTAATACGCTTATTTTTTCTGTACAAGATTTTGTTAATTTAAGGGAAATTAACTTCA
196 GCTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTCA
* * * * *
54744804 ATGGATGTGTGAGTTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAATCTTAAATACCTTTAT
261 ATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTAT
*
54744869 TGCAGTGACTGTAAAAGTTT-GATTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCG
326 TGCAGTGACTGTAAAAGTTTAG-TTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCA
54744933 TAC---TTTTT--AAAAAAAATTATATTTTGATGTATAAA
390 TACTTTTTTTTGAAAAAAAAATTATATTTTGATGTATAAA
*
54744968 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAGTAAATATAAAAGATTTTATTTTATTT
1 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
** * * *
54745033 ATTTAAGTGACATTGTTTGATTTATTAATTGTGTGTGAATTTTTACACCCTATACATCAAATATA
66 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
* *
54745098 AATTTTTATTTTTTTTTATAGTATTATAATTATATCTTTCCTTTCCATTTTTTACTAAATAGTTG
131 AATTTTTA--TTTTTTTATAGTATTATAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTG
* *
54745163 ATGCTTAAAAGTAATACGTTTATTTTTTCTGTACAGGATTTTGTTAATTTAAGGGAAATTAACTT
194 ATGCTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTT
* * * *
54745228 TAATGGGTGCGTGAGTTTAAGGAAGATACCTAATCTTTCAAGAGCTATCAACCTTGAATACCTTT
259 CAATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTT
* * *
54745293 ATTGCAGTGACTGTAAAAGTTTGGTTGAAATTTGGAATGAAGATGATTGTGTGGTATGTATTTTC
324 ATTGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTC
*
54745358 GTACTTTTTTTTGAAAAAAAAATTATATTTTGATGTATAAA
389 ATACTTTTTTTTGAAAAAAAAATTATATTTTGATGTATAAA
* *
54745399 TATTCATATGATAACATTTTATTTAAAGTTTTCAAAAAATAAATATAAAAGAATTTATTTTATTT
1 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
54745464 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
66 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
* *
54745529 AA-TTTTATTTTTTTATAGTTTTATAATTATTTATTTCCTTTCCTTTTTTTACTAAATAGTTGAT
131 AATTTTTATTTTTTTATAGTATTATAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGAT
* * * *
54745593 GCTTAAAAGTAATAGGCTTATTTTTTTTGTACAGGATTTTGTTAATTTAAGGAAAATTAACTTCA
196 GCTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTCA
* * * *
54745658 ATGGGTGTGTGAGTTTAACGAAGATACTTAATTTTTCAAGAGCCATCAACCTTGAATACCTTTAT
261 ATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTAT
* * *
54745723 TGCAGTGACTGTAAAAGTTTGGTTGAACTTTGGAACGGAGATGATTGTGTGGTAAGTATTTTCA-
326 TGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCAT
*
54745787 AATTTTTTTTG-AAAAAAAATTATATTTTGATGTATAAA
391 ACTTTTTTTTGAAAAAAAAATTATATTTTGATGTATAAA
*
54745825 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATGTTATTT
1 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
* * * * *
54745890 AGATAAGTGACATCTTTTGATTTATTAATTGTGAGTGAATTTTCACACCTTATACATTAAATATA
66 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
*
54745955 AATTTTTA-TTTTTTATAGTATTATAATTATTTCTTT-CTTTCCCTTTTTTTATTAAATAGTTGA
131 AATTTTTATTTTTTTATAGTATTATAATTATTTCTTTCCTTT-CCTTTTTTTACTAAATAGTTGA
54746018 TGCTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTC
195 TGCTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTC
54746083 AATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTA
260 AATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTA
54746148 TTGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCA
325 TTGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCA
* *
54746213 AATTTTTTTTTGAAAAAAAAATTATATTTTGATGTATAAA
390 TACTTTTTTTTGAAAAAAAAATTATATTTTGATGTATAAA
*
54746253 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGAATTTATTTTATTT
1 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
* *
54746318 AGATAAGTGGCATCGTTTGATTTTTTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
66 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
54746383 AATTTTTATTTTTTTATAGTATTATAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGAT
131 AATTTTTATTTTTTTATAGTATTATAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGAT
*
54746448 GCTTAAAAGTAATATGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTCA
196 GCTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTCA
54746513 ATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTAT
261 ATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTAT
*
54746578 TGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCAA
326 TGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCAT
54746643 ACTTTTTTTTTTGAAAAAAAAATTATATTTTGATGTATAAA
391 AC--TTTTTTTTGAAAAAAAAATTATATTTTGATGTATAAA
*
54746684 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGAATTTATTTTATTT
1 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
* *
54746749 AGATAAGTGGCATCGTTTGATTTTTTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
66 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
54746814 AATTTTTATTTTTTTATAGTATTATAATTATTTCTTT-CTTTCCCTTTTTTTACTAAATAGTTGA
131 AATTTTTATTTTTTTATAGTATTATAATTATTTCTTTCCTTT-CCTTTTTTTACTAAATAGTTGA
*
54746878 TGCTTAAAAGTAATATGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTC
195 TGCTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTC
54746943 AATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTA
260 AATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTA
54747008 TTGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCA
325 TTGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCA
54747073 TACTTTTTTTTTTG-AAAAAAAATTATATTTTGATGTATAAA
390 TAC--TTTTTTTTGAAAAAAAAATTATATTTTGATGTATAAA
* * *
54747114 TATTCATATGATAACATTTTATTTAAAGCTTTCAAAAAA-AAATATAAAAGATTTTATGTTATTT
1 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
* * ** * * *
54747178 AGATAAGTGACATCTTTTGATTTATTAAATGTAAGTGAATTTTCACACCTTATACATTAAATATA
66 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
* *
54747243 AGTTTTTA-TTTTTTATGGTATTATAATTATTTCTTT-CTTTCCCTTTTTTTACTAAATAGTTGA
131 AATTTTTATTTTTTTATAGTATTATAATTATTTCTTTCCTTT-CCTTTTTTTACTAAATAGTTGA
*
54747306 TGCTTAAAAGTAATATGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTC
195 TGCTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTC
54747371 AATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTA
260 AATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTA
54747436 TTGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCA
325 TTGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCA
*
54747501 AACTTTTTTTTTTGAAAAAAAAATTATATTTTGATGTATAAA
390 TAC--TTTTTTTTGAAAAAAAAATTATATTTTGATGTATAAA
*
54747543 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGAATTTATTTTATTT
1 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
* *
54747608 AGATAAGTGGCATCGTTTGATTTTTTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
66 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
54747673 AATTTTTATTTTTTTATAGTATTATAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGAT
131 AATTTTTATTTTTTTATAGTATTATAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGAT
*
54747738 GCTTAAAAGTAATATGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTCA
196 GCTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTCA
* * *
54747803 ATGGGTGCTTGAATTTAAGGAAGATACTTAATCTTCCAAGAGCCATCAACCTCGAATACCTTTAT
261 ATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTAT
* *
54747868 TGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGAAGATGATTGTGTGGTGTGTATTTTCAT
326 TGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCAT
54747933 ACCTTTTTTTTG--AAAAAAATTATATTTTGATGTATAAA
391 A-CTTTTTTTTGAAAAAAAAATTATATTTTGATGTATAAA
* *
54747971 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGAATTTACTTTATTT
1 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
* * *
54748036 AGATAAGTGGCATCGTTTGATTTATTAATTGTGTGTGAATTTTCACACCCTATACATCAAATATA
66 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
* * * * *
54748101 AATTTTTA-TTTTTTATGGTATTATAAATATTTCTTTCCTTTCCATTTTTTGCTAAATAATTGAT
131 AATTTTTATTTTTTTATAGTATTATAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGAT
* * *
54748165 GCTTAAAAGTAATACACTTATTTTTTCTGTACAGGATTTTTTTAATTTAAGGGAAATTAACTTCA
196 GCTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTCA
* * *
54748230 ATGGGTGCGTGAGA-TTAAGGAAGGTAAC-TAATCTTTCAAGAGCCATCAACTTGTGAA-ATCTT
261 ATGGGTGCGTGA-ATTTAAGGAAGAT-ACTTAATCTTTCAAGAGCCATCAACCT-TGAATA-CCT
** * * * * * * *
54748292 TTATTGCTCTAACTGTAGAAGTTTGGTTGAACCTTGAAATGGAGATGATTGTATGGTATGCATTT
322 TTATTGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTT
** *
54748357 TCATAC-TTTTTTAAAAAAAAAAATTATATTTTGATTTATAAA
387 TCATACTTTTTTTTGAAAAAAAAATTATATTTTGATGTATAAA
* * * *
54748399 TATTCATATAATAACATTTTTTTTAAAGTTTATAAAAAATATATATAAAAGATTTTATTTTATTT
1 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
* * * * ***
54748464 AGAAAAGTGACATCATTTGATTTATTAATTATGGGTGAATTTTCACACTGGATACATCAAATATA
66 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
* *
54748529 AATTTTTA-TTTTTTATTA-TATTATAATTATTTATTTCCTTT--TTATTTTTACT--A-AGCTG
131 AATTTTTATTTTTTTA-TAGTATTATAATTATTTCTTTCCTTTCCTT-TTTTTACTAAATAGTTG
* * * *
54748587 ATGCTTGAAAGTAATACAAC-TATTTTTTCTGTACAGGGCTTTTGTTAATTTAA
194 ATGCTTAAAAGTAATAC-GCTTATTTTTTCTGTATA-GGATTTTGTTAATTTAA
54748640 CATCCTTGTA
Statistics
Matches: 3845, Mismatches: 214, Indels: 72
0.93 0.05 0.02
Matches are distributed among these distances:
423 41 0.01
424 272 0.07
425 251 0.07
426 634 0.16
427 190 0.05
428 1054 0.27
429 401 0.10
430 172 0.04
431 825 0.21
432 5 0.00
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (429 bp):
TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
AATTTTTATTTTTTTATAGTATTATAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGAT
GCTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTCA
ATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTAT
TGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCAT
ACTTTTTTTTGAAAAAAAAATTATATTTTGATGTATAAA
Found at i:54747447 original size:859 final size:856
Alignment explanation
Indices: 54744121--54748639 Score: 7214
Period size: 859 Copynumber: 5.3 Consensus size: 856
54744111 TACTCTTTTT
* * * *
54744121 TATTCATATAATAACATTTTATTTAAATTTTTTTAAAAATAAAAAT-AAAGATTTTATTTTATTT
1 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
*
54744185 AGATAAGTGGCATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
66 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
54744250 AATTTTTATTTTTTATAGTATTATAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGATG
131 AATTTTTATTTTTTATAGTATTATAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGATG
* * *
54744315 CTTAAAAGTAATAGGCTTATTTTTTCTGTATAGGACTTTGTTAATTTAAGGAAAATTAACTTCAA
196 CTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTCAA
* * ** *
54744380 TGGGTGCATGAGTTTAACCAAGATACCTAATC-TTCTAAGAGCCATCAACCTTGAATACCTTTAT
261 TGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTC-AAGAGCCATCAACCTTGAATACCTTTAT
* *
54744444 TGCAGTGACTGTAAAAGTTTGGTTGAACTTTGGAATGGAGATGATTGTGTGGTAAGTATTTTCAT
325 TGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCAT
** *
54744509 A---TTTTTAAAAAAAAAATTATATTTTGATGTATAAATATTCATATGATAATATTTTATTTAAA
390 ACTTTTTTTTGAAAAAAAATTATATTTTGATGTATAAATATTCATATGATAACATTTTATTTAAA
* * *
54744571 GTTTTTAAAAAATAAATATAAAAGATTTTATGTTATTTAGATAAGTGATATCTTTTGATTTATTA
455 GTTTTTAAAAAATAAATATAAAAGAATTTATGTTATTTAGATAAGTGACATCGTTTGATTTATTA
* * *
54744636 ATTGTGGGTGAATTTTCACACCCTATACATTAAATATAAATTCTTATTTTTTTATATTATTATAA
520 ATTGTGGGTGAATTTTCACACCCTATACATCAAATATAAATTTTTATTTTTTTATAGTATTATAA
*
54744701 TTATTTCTTTCTTTTCCTTTTTTTACTAAATAGTTGATGCTTAAAAGTAATACGCTTATTTTTTC
585 TTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGATGCTTAAAAGTAATACGCTTATTTTTTC
* * * *
54744766 TGTACAAGATTTTGTTAATTTAAGGGAAATTAACTTCAATGGATGTGTGAGTTTAAGGAAGATAC
650 TGTACAGGATTTTGTTAATTTAAGGGAAATTAACTTCAATGGGTGCGTGAATTTAAGGAAGATAC
* *
54744831 TTAATCTTTCAAGAGCCATCAATCTTAAATACCTTTATTGCAGTGACTGTAAAAGTTT-GATTGA
715 TTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTATTGCAGTGACTGTAAAAGTTTAG-TTGA
**
54744895 ACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCGTAC---TTTTT--AAAAAAAATTATAT
779 ACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCAAACTTTTTTTTGAAAAAAAAATTATAT
54744955 TTTGATGTATAAA
844 TTTGATGTATAAA
*
54744968 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAGTAAATATAAAAGATTTTATTTTATTT
1 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
** * * *
54745033 ATTTAAGTGACATTGTTTGATTTATTAATTGTGTGTGAATTTTTACACCCTATACATCAAATATA
66 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
* *
54745098 AATTTTTATTTTTTTTTATAGTATTATAATTATATCTTTCCTTTCCATTTTTTACTAAATAGTTG
131 AATTTTTA---TTTTTTATAGTATTATAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTG
* *
54745163 ATGCTTAAAAGTAATACGTTTATTTTTTCTGTACAGGATTTTGTTAATTTAAGGGAAATTAACTT
193 ATGCTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTT
* * * *
54745228 TAATGGGTGCGTGAGTTTAAGGAAGATACCTAATCTTTCAAGAGCTATCAACCTTGAATACCTTT
258 CAATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTT
* * *
54745293 ATTGCAGTGACTGTAAAAGTTTGGTTGAAATTTGGAATGAAGATGATTGTGTGGTATGTATTTTC
323 ATTGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTC
*
54745358 GTACTTTTTTTTGAAAAAAAAATTATATTTTGATGTATAAATATTCATATGATAACATTTTATTT
388 ATACTTTTTTTTG-AAAAAAAATTATATTTTGATGTATAAATATTCATATGATAACATTTTATTT
* *
54745423 AAAGTTTTCAAAAAATAAATATAAAAGAATTTATTTTATTTAGATAAGTGACATCGTTTGATTTA
452 AAAGTTTTTAAAAAATAAATATAAAAGAATTTATGTTATTTAGATAAGTGACATCGTTTGATTTA
* *
54745488 TTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATAAA-TTTTATTTTTTTATAGTTTTA
517 TTAATTGTGGGTGAATTTTCACACCCTATACATCAAATATAAATTTTTATTTTTTTATAGTATTA
* *
54745552 TAATTATTTATTTCCTTTCCTTTTTTTACTAAATAGTTGATGCTTAAAAGTAATAGGCTTATTTT
582 TAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGATGCTTAAAAGTAATACGCTTATTTT
* * * * *
54745617 TTTTGTACAGGATTTTGTTAATTTAAGGAAAATTAACTTCAATGGGTGTGTGAGTTTAACGAAGA
647 TTCTGTACAGGATTTTGTTAATTTAAGGGAAATTAACTTCAATGGGTGCGTGAATTTAAGGAAGA
* *
54745682 TACTTAATTTTTCAAGAGCCATCAACCTTGAATACCTTTATTGCAGTGACTGTAAAAGTTTGGTT
712 TACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTATTGCAGTGACTGTAAAAGTTTAGTT
* *
54745747 GAACTTTGGAACGGAGATGATTGTGTGGTAAGTATTTTCAAA-TTTTTTTTG-AAAAAAAATTAT
777 GAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCAAACTTTTTTTTGAAAAAAAAATTAT
54745810 ATTTTGATGTATAAA
842 ATTTTGATGTATAAA
*
54745825 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATGTTATTT
1 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
* * * * *
54745890 AGATAAGTGACATCTTTTGATTTATTAATTGTGAGTGAATTTTCACACCTTATACATTAAATATA
66 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
*
54745955 AATTTTTATTTTTTATAGTATTATAATTATTTCTTT-CTTTCCCTTTTTTTATTAAATAGTTGAT
131 AATTTTTATTTTTTATAGTATTATAATTATTTCTTTCCTTT-CCTTTTTTTACTAAATAGTTGAT
54746019 GCTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTCA
195 GCTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTCA
54746084 ATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTAT
260 ATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTAT
*
54746149 TGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCAA
325 TGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCAT
*
54746214 ATTTTTTTTTGAAAAAAAAATTATATTTTGATGTATAAATATTCATATGATAACATTTTATTTAA
390 ACTTTTTTTTG-AAAAAAAATTATATTTTGATGTATAAATATTCATATGATAACATTTTATTTAA
* * *
54746279 AGTTTTTAAAAAATAAATATAAAAGAATTTATTTTATTTAGATAAGTGGCATCGTTTGATTTTTT
454 AGTTTTTAAAAAATAAATATAAAAGAATTTATGTTATTTAGATAAGTGACATCGTTTGATTTATT
*
54746344 AATTGTGGGTGAATTTTAACACCCTATACATCAAATATAAATTTTTATTTTTTTATAGTATTATA
519 AATTGTGGGTGAATTTTCACACCCTATACATCAAATATAAATTTTTATTTTTTTATAGTATTATA
*
54746409 ATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGATGCTTAAAAGTAATATGCTTATTTTTT
584 ATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGATGCTTAAAAGTAATACGCTTATTTTTT
*
54746474 CTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTCAATGGGTGCGTGAATTTAAGGAAGATA
649 CTGTACAGGATTTTGTTAATTTAAGGGAAATTAACTTCAATGGGTGCGTGAATTTAAGGAAGATA
54746539 CTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTATTGCAGTGACTGTAAAAGTTTAGTTGA
714 CTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTATTGCAGTGACTGTAAAAGTTTAGTTGA
54746604 ACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCAAACTTTTTTTTTTGAAAAAAAAATTAT
779 ACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCAAAC--TTTTTTTTGAAAAAAAAATTAT
54746669 ATTTTGATGTATAAA
842 ATTTTGATGTATAAA
*
54746684 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGAATTTATTTTATTT
1 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
* *
54746749 AGATAAGTGGCATCGTTTGATTTTTTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
66 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
54746814 AATTTTTATTTTTTTATAGTATTATAATTATTTCTTT-CTTTCCCTTTTTTTACTAAATAGTTGA
131 AATTTTTA-TTTTTTATAGTATTATAATTATTTCTTTCCTTT-CCTTTTTTTACTAAATAGTTGA
*
54746878 TGCTTAAAAGTAATATGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTC
194 TGCTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTC
54746943 AATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTA
259 AATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTA
54747008 TTGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCA
324 TTGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCA
54747073 TACTTTTTTTTTTGAAAAAAAATTATATTTTGATGTATAAATATTCATATGATAACATTTTATTT
389 TAC--TTTTTTTTGAAAAAAAATTATATTTTGATGTATAAATATTCATATGATAACATTTTATTT
* * * *
54747138 AAAGCTTTCAAAAAA-AAATATAAAAGATTTTATGTTATTTAGATAAGTGACATCTTTTGATTTA
452 AAAGTTTTTAAAAAATAAATATAAAAGAATTTATGTTATTTAGATAAGTGACATCGTTTGATTTA
* ** * * * *
54747202 TTAAATGTAAGTGAATTTTCACACCTTATACATTAAATATAAGTTTTTA-TTTTTTATGGTATTA
517 TTAATTGTGGGTGAATTTTCACACCCTATACATCAAATATAAATTTTTATTTTTTTATAGTATTA
*
54747266 TAATTATTTCTTT-CTTTCCCTTTTTTTACTAAATAGTTGATGCTTAAAAGTAATATGCTTATTT
582 TAATTATTTCTTTCCTTT-CCTTTTTTTACTAAATAGTTGATGCTTAAAAGTAATACGCTTATTT
*
54747330 TTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTCAATGGGTGCGTGAATTTAAGGAAG
646 TTTCTGTACAGGATTTTGTTAATTTAAGGGAAATTAACTTCAATGGGTGCGTGAATTTAAGGAAG
54747395 ATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTATTGCAGTGACTGTAAAAGTTTAGT
711 ATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTATTGCAGTGACTGTAAAAGTTTAGT
54747460 TGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCAAACTTTTTTTTTTGAAAAAAAAAT
776 TGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCAAAC--TTTTTTTTGAAAAAAAAAT
54747525 TATATTTTGATGTATAAA
839 TATATTTTGATGTATAAA
*
54747543 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGAATTTATTTTATTT
1 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
* *
54747608 AGATAAGTGGCATCGTTTGATTTTTTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
66 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
54747673 AATTTTTATTTTTTTATAGTATTATAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGAT
131 AATTTTTA-TTTTTTATAGTATTATAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGAT
*
54747738 GCTTAAAAGTAATATGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTCA
195 GCTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTCA
* * *
54747803 ATGGGTGCTTGAATTTAAGGAAGATACTTAATCTTCCAAGAGCCATCAACCTCGAATACCTTTAT
260 ATGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTAT
* *
54747868 TGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGAAGATGATTGTGTGGTGTGTATTTTCAT
325 TGCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCAT
54747933 ACCTTTTTTTTG-AAAAAAATTATATTTTGATGTATAAATATTCATATGATAACATTTTATTTAA
390 A-CTTTTTTTTGAAAAAAAATTATATTTTGATGTATAAATATTCATATGATAACATTTTATTTAA
*
54747997 AGTTTTTAAAAAATAAATATAAAAGAATTTACT-TTATTTAGATAAGTGGCATCGTTTGATTTAT
454 AGTTTTTAAAAAATAAATATAAAAGAATTTA-TGTTATTTAGATAAGTGACATCGTTTGATTTAT
* *
54748061 TAATTGTGTGTGAATTTTCACACCCTATACATCAAATATAAATTTTTA-TTTTTTATGGTATTAT
518 TAATTGTGGGTGAATTTTCACACCCTATACATCAAATATAAATTTTTATTTTTTTATAGTATTAT
* * * * *
54748125 AAATATTTCTTTCCTTTCCATTTTTTGCTAAATAATTGATGCTTAAAAGTAATACACTTATTTTT
583 AATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGATGCTTAAAAGTAATACGCTTATTTTT
* *
54748190 TCTGTACAGGATTTTTTTAATTTAAGGGAAATTAACTTCAATGGGTGCGTGAGA-TTAAGGAAGG
648 TCTGTACAGGATTTTGTTAATTTAAGGGAAATTAACTTCAATGGGTGCGTGA-ATTTAAGGAAGA
* * ** * * *
54748254 TAAC-TAATCTTTCAAGAGCCATCAACTTGTGAA-ATCTTTTATTGCTCTAACTGTAGAAGTTTG
712 T-ACTTAATCTTTCAAGAGCCATCAACCT-TGAATA-CCTTTATTGCAGTGACTGTAAAAGTTTA
* * * * * **
54748317 GTTGAACCTTGAAATGGAGATGATTGTATGGTATGCATTTTCATAC-TTTTTTAAAAAAAAAAAT
774 GTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCAAACTTTTTTTTGAAAAAAAAAT
*
54748381 TATATTTTGATTTATAAA
839 TATATTTTGATGTATAAA
* * * *
54748399 TATTCATATAATAACATTTTTTTTAAAGTTTATAAAAAATATATATAAAAGATTTTATTTTATTT
1 TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
* * * * ***
54748464 AGAAAAGTGACATCATTTGATTTATTAATTATGGGTGAATTTTCACACTGGATACATCAAATATA
66 AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
* *
54748529 AATTTTTATTTTTTATTA-TATTATAATTATTTATTTCCTTT--TTATTTTTACT--A-AGCTGA
131 AATTTTTATTTTTTA-TAGTATTATAATTATTTCTTTCCTTTCCTT-TTTTTACTAAATAGTTGA
* * * *
54748588 TGCTTGAAAGTAATACAAC-TATTTTTTCTGTACAGGGCTTTTGTTAATTTAA
194 TGCTTAAAAGTAATAC-GCTTATTTTTTCTGTATA-GGATTTTGTTAATTTAA
54748640 CATCCTTGTA
Statistics
Matches: 3450, Mismatches: 185, Indels: 69
0.93 0.05 0.02
Matches are distributed among these distances:
847 41 0.01
848 85 0.02
851 265 0.08
852 21 0.01
853 6 0.00
854 650 0.19
855 426 0.12
856 164 0.05
857 218 0.06
858 263 0.08
859 898 0.26
860 340 0.10
861 64 0.02
862 9 0.00
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (856 bp):
TATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAAGATTTTATTTTATTT
AGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTAACACCCTATACATCAAATATA
AATTTTTATTTTTTATAGTATTATAATTATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGATG
CTTAAAAGTAATACGCTTATTTTTTCTGTATAGGATTTTGTTAATTTAAGGGAAATTAACTTCAA
TGGGTGCGTGAATTTAAGGAAGATACTTAATCTTTCAAGAGCCATCAACCTTGAATACCTTTATT
GCAGTGACTGTAAAAGTTTAGTTGAACTTTGGAATGGAGATGATTGTGTGGTATGTATTTTCATA
CTTTTTTTTGAAAAAAAATTATATTTTGATGTATAAATATTCATATGATAACATTTTATTTAAAG
TTTTTAAAAAATAAATATAAAAGAATTTATGTTATTTAGATAAGTGACATCGTTTGATTTATTAA
TTGTGGGTGAATTTTCACACCCTATACATCAAATATAAATTTTTATTTTTTTATAGTATTATAAT
TATTTCTTTCCTTTCCTTTTTTTACTAAATAGTTGATGCTTAAAAGTAATACGCTTATTTTTTCT
GTACAGGATTTTGTTAATTTAAGGGAAATTAACTTCAATGGGTGCGTGAATTTAAGGAAGATACT
TAATCTTTCAAGAGCCATCAACCTTGAATACCTTTATTGCAGTGACTGTAAAAGTTTAGTTGAAC
TTTGGAATGGAGATGATTGTGTGGTATGTATTTTCAAACTTTTTTTTGAAAAAAAAATTATATTT
TGATGTATAAA
Found at i:54754493 original size:19 final size:19
Alignment explanation
Indices: 54754469--54754508 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
54754459 TCATAATTAA
54754469 AATAAGCAAATTGGTCAGC
1 AATAAGCAAATTGGTCAGC
54754488 AATAAGCAAATTGGTCAGC
1 AATAAGCAAATTGGTCAGC
54754507 AA
1 AA
54754509 GTGCCTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (19 bp):
AATAAGCAAATTGGTCAGC
Found at i:54757455 original size:15 final size:16
Alignment explanation
Indices: 54757419--54757448 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54757409 ACATATCATT
54757419 TATTTCATTATATCAA
1 TATTTCATTATATCAA
54757435 TATTTCA-TATATCA
1 TATTTCATTATATCA
54757449 TAGTTTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTCATTATATCAA
Found at i:54758444 original size:49 final size:49
Alignment explanation
Indices: 54758372--54758553 Score: 213
Period size: 49 Copynumber: 3.7 Consensus size: 49
54758362 CTGGTACGCA
**
54758372 TAGTAGCCTGCACTTAGTACTACACATGTGACCAACAATCTAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAACAATCCGGTACACG
* * * * * * *
54758421 TAGTAACCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAACA---ATCCGGTACACG
* * **
54758472 TAGTAGCCTGTACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAACAATCCGGTACACG
54758521 TAGTAGCCTGCACTTAGTACTACACATGTGACC
1 TAGTAGCCTGCACTTAGTACTACACATGTGACC
54758554 TCACAATAGC
Statistics
Matches: 108, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
48 3 0.03
49 69 0.64
51 35 0.32
52 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCAACAATCCGGTACACG
Found at i:54758537 original size:100 final size:100
Alignment explanation
Indices: 54758364--54758551 Score: 304
Period size: 100 Copynumber: 1.9 Consensus size: 100
54758354 GGAGCTATCT
* *
54758364 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAACAATCTAGTACACGTAGTAACC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCCAGTACACGTAGTAACC
54758429 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
66 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
* ** * *
54758464 GGTACGCATAGTAGCCTGTACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCCAGTACACGTAGTAACC
*
54758529 TGCACTTAGTACTACACATGTGA
66 TGCACTTAGTACTACACACGTGA
54758552 CCTCACAATA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 80 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCCAGTACACGTAGTAACC
TGCACTTAGTACTACACACGTGATCACAGTTTTCG
Found at i:54764659 original size:18 final size:18
Alignment explanation
Indices: 54764636--54764758 Score: 151
Period size: 18 Copynumber: 6.8 Consensus size: 18
54764626 CGTTTACAGT
54764636 ACTATTCACGTATACGAC
1 ACTATTCACGTATACGAC
* *
54764654 ACTATTCACGTATA-TAGT
1 ACTATTCACGTATACGA-C
*
54764672 ACTATTCACATATACGAC
1 ACTATTCACGTATACGAC
*
54764690 ACTATTCACGTATAC-AGT
1 ACTATTCACGTATACGA-C
54764708 ACTATTCACGTATACGAC
1 ACTATTCACGTATACGAC
**
54764726 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGAC
*
54764744 ACTGTTCACGTATAC
1 ACTATTCACGTATAC
54764759 AGTAGTTGGG
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
17 2 0.02
18 86 0.96
19 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (18 bp):
ACTATTCACGTATACGAC
Found at i:54764680 original size:36 final size:36
Alignment explanation
Indices: 54764630--54764758 Score: 222
Period size: 36 Copynumber: 3.6 Consensus size: 36
54764620 TACGATCGTT
54764630 TACAGTACTATTCACGTATACGACACTATTCACGTA
1 TACAGTACTATTCACGTATACGACACTATTCACGTA
* *
54764666 TATAGTACTATTCACATATACGACACTATTCACGTA
1 TACAGTACTATTCACGTATACGACACTATTCACGTA
54764702 TACAGTACTATTCACGTATACGACACTATTCACGTA
1 TACAGTACTATTCACGTATACGACACTATTCACGTA
* *
54764738 TACGGTACTGTTCACGTATAC
1 TACAGTACTATTCACGTATAC
54764759 AGTAGTTGGG
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 87 1.00
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.32
Consensus pattern (36 bp):
TACAGTACTATTCACGTATACGACACTATTCACGTA
Found at i:54772657 original size:25 final size:25
Alignment explanation
Indices: 54772623--54772679 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
54772613 AATATTAATG
54772623 CAGAATTTGACAGTTGCTCGTATCT
1 CAGAATTTGACAGTTGCTCGTATCT
54772648 CAGAATTTGACAGTTGCTCGTATCT
1 CAGAATTTGACAGTTGCTCGTATCT
54772673 CAGAATT
1 CAGAATT
54772680 CATGGAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (25 bp):
CAGAATTTGACAGTTGCTCGTATCT
Found at i:54782240 original size:24 final size:24
Alignment explanation
Indices: 54782196--54782242 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
54782186 CGGTAATGTT
*
54782196 AATTTAAATAAAATTTCAATTTAA
1 AATTTAAATAAAATTTAAATTTAA
54782220 AATTGTAAATAAAA-TTAAATTTA
1 AATT-TAAATAAAATTTAAATTTA
54782243 TGGTACATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
AATTTAAATAAAATTTAAATTTAA
Found at i:54785680 original size:36 final size:36
Alignment explanation
Indices: 54785629--54785739 Score: 195
Period size: 36 Copynumber: 3.1 Consensus size: 36
54785619 TATAATGGTC
* * *
54785629 TTGGTGCTGGAAATTTAAATGCGAATTTGACTGGTT
1 TTGGTGCTGGGAATTTAAATGCAAATTTGACTGGGT
54785665 TTGGTGCTGGGAATTTAAATGCAAATTTGACTGGGT
1 TTGGTGCTGGGAATTTAAATGCAAATTTGACTGGGT
54785701 TTGGTGCTGGGAATTTAAATGCAAATTTGACTGGGT
1 TTGGTGCTGGGAATTTAAATGCAAATTTGACTGGGT
54785737 TTG
1 TTG
54785740 CACCTATTAG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 72 1.00
ACGTcount: A:0.24, C:0.08, G:0.30, T:0.38
Consensus pattern (36 bp):
TTGGTGCTGGGAATTTAAATGCAAATTTGACTGGGT
Found at i:54786473 original size:36 final size:36
Alignment explanation
Indices: 54786424--54786498 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
54786414 GAACTTTAGA
54786424 ATAAGACTACTAAAGGTGATGTGTTTTCCTTGTGGC
1 ATAAGACTACTAAAGGTGATGTGTTTTCCTTGTGGC
*
54786460 ATAAGACTGCTAAAGGTGATGTGTTTTCCTTGTGGC
1 ATAAGACTACTAAAGGTGATGTGTTTTCCTTGTGGC
54786496 ATA
1 ATA
54786499 GACGTCTTGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (36 bp):
ATAAGACTACTAAAGGTGATGTGTTTTCCTTGTGGC
Found at i:54789966 original size:52 final size:52
Alignment explanation
Indices: 54789899--54790007 Score: 209
Period size: 52 Copynumber: 2.1 Consensus size: 52
54789889 GCAACAGATC
*
54789899 TTATAAAAGAGGAGGGGTTGCACCACATTGAAGCATATTACCCCAATATAAT
1 TTATTAAAGAGGAGGGGTTGCACCACATTGAAGCATATTACCCCAATATAAT
54789951 TTATTAAAGAGGAGGGGTTGCACCACATTGAAGCATATTACCCCAATATAAT
1 TTATTAAAGAGGAGGGGTTGCACCACATTGAAGCATATTACCCCAATATAAT
54790003 TTATT
1 TTATT
54790008 GGTCGTCCAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (52 bp):
TTATTAAAGAGGAGGGGTTGCACCACATTGAAGCATATTACCCCAATATAAT
Found at i:54790933 original size:35 final size:35
Alignment explanation
Indices: 54790889--54790957 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
54790879 CTCTAAAACG
54790889 AAAAAAAACAAAAAAGAATAGGAATCAGCTAGCAA
1 AAAAAAAACAAAAAAGAATAGGAATCAGCTAGCAA
*
54790924 AAAAAAAACAAAAAAGAATAGGTATCAGCTAGCA
1 AAAAAAAACAAAAAAGAATAGGAATCAGCTAGCA
54790958 TTATTGGCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.64, C:0.12, G:0.14, T:0.10
Consensus pattern (35 bp):
AAAAAAAACAAAAAAGAATAGGAATCAGCTAGCAA
Found at i:54794912 original size:17 final size:19
Alignment explanation
Indices: 54794892--54794930 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
54794882 AAGTGAATTG
54794892 AAATTACG-AAATT-AAAT
1 AAATTACGAAAATTAAAAT
54794909 AAATTACGAAAATTAAAAT
1 AAATTACGAAAATTAAAAT
54794928 AAA
1 AAA
54794931 AATATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.40
18 5 0.25
19 7 0.35
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
AAATTACGAAAATTAAAAT
Found at i:54795672 original size:10 final size:10
Alignment explanation
Indices: 54795645--54795682 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
54795635 TGAAATTCTA
*
54795645 AAAGATAAAT
1 AAAGATAATT
54795655 ACAA-ATAATT
1 A-AAGATAATT
54795665 AAAGATAATT
1 AAAGATAATT
54795675 AAAGATAA
1 AAAGATAA
54795683 ATGAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAGATAATT
Found at i:54797354 original size:25 final size:25
Alignment explanation
Indices: 54797320--54797368 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
54797310 AATATCCTAA
54797320 TAATAAAT-AATAAAATAAAATAAAG
1 TAATAAATAAAT-AAATAAAATAAAG
54797345 TAATAAATAAATAAATAAAATAAA
1 TAATAAATAAATAAATAAAATAAA
54797369 AGTTGGGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (25 bp):
TAATAAATAAATAAATAAAATAAAG
Found at i:54801080 original size:10 final size:10
Alignment explanation
Indices: 54801061--54801110 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
54801051 TGAAATTCTA
54801061 AAAGATAAAT
1 AAAGATAAAT
54801071 ACAA-ATAAAT
1 A-AAGATAAAT
*
54801081 AAAGATAATT
1 AAAGATAAAT
54801091 AAAGATAAAT
1 AAAGATAAAT
54801101 GAAA-ATAAAT
1 -AAAGATAAAT
54801111 CCTAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:54804342 original size:167 final size:167
Alignment explanation
Indices: 54804063--54804396 Score: 641
Period size: 167 Copynumber: 2.0 Consensus size: 167
54804053 CCAAACACCT
*
54804063 TCAAATGGGAAACGGATGGTTTGAGCCCATACCATGCCTCAAAGGGTGTTTTGTCCTTTACAGCT
1 TCAAATGGGAAACGGATGGTTTGAGCCCATACCATGCCTCAAAAGGTGTTTTGTCCTTTACAGCT
*
54804128 CTTGTAGGAAGCTTGTTCAATAGGTAAACTGAGGTGTTGAGAGCTTCTGCCCAAAATTTGCTTGG
66 CTTGTAGGAAGCTTGTTCAATAGGTAAACTGAGGTGTTGACAGCTTCTGCCCAAAATTTGCTTGG
54804193 AAGCTTGCTTTGAAACAACAAACATCTGGCCATATTC
131 AAGCTTGCTTTGAAACAACAAACATCTGGCCATATTC
54804230 TCAAATGGGAAACGGATGGTTTGAGCCCATACCATGCCTCAAAAGGTGTTTTGTCCTTTACAGCT
1 TCAAATGGGAAACGGATGGTTTGAGCCCATACCATGCCTCAAAAGGTGTTTTGTCCTTTACAGCT
54804295 CTTGTAGGAAGCTTGTTCAATAGGTAAACTGAGGTGTTGACAGCTTCTGCCCAAAATTTGCTTGG
66 CTTGTAGGAAGCTTGTTCAATAGGTAAACTGAGGTGTTGACAGCTTCTGCCCAAAATTTGCTTGG
*
54804360 AAGCTTGCTTTGAAACAACAGACATCTGGCCATATTC
131 AAGCTTGCTTTGAAACAACAAACATCTGGCCATATTC
54804397 ATCACTGTTC
Statistics
Matches: 164, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
167 164 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (167 bp):
TCAAATGGGAAACGGATGGTTTGAGCCCATACCATGCCTCAAAAGGTGTTTTGTCCTTTACAGCT
CTTGTAGGAAGCTTGTTCAATAGGTAAACTGAGGTGTTGACAGCTTCTGCCCAAAATTTGCTTGG
AAGCTTGCTTTGAAACAACAAACATCTGGCCATATTC
Found at i:54812188 original size:39 final size:39
Alignment explanation
Indices: 54812133--54812222 Score: 126
Period size: 39 Copynumber: 2.3 Consensus size: 39
54812123 ATTTTATGTG
* * *
54812133 GATGAAGATCAGATTGATGAGACGAGCAATGATGTATCA
1 GATGAAGATCAAATTGAAGAGACGAGCAATGATGCATCA
* *
54812172 GATGAAAATCAAATTGAAGAGACGAGCAGTGATGCATCA
1 GATGAAGATCAAATTGAAGAGACGAGCAATGATGCATCA
*
54812211 CATGAAGATCAA
1 GATGAAGATCAA
54812223 GAAATGTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.42, C:0.12, G:0.26, T:0.20
Consensus pattern (39 bp):
GATGAAGATCAAATTGAAGAGACGAGCAATGATGCATCA
Found at i:54814293 original size:18 final size:19
Alignment explanation
Indices: 54814270--54814368 Score: 62
Period size: 19 Copynumber: 5.2 Consensus size: 19
54814260 TTTTTTTTAT
54814270 AAAAATCGTAGA-AAAT-TA
1 AAAAAT-GTAGAGAAATATA
*
54814288 AAAAATGTATAGAAATATA
1 AAAAATGTAGAGAAATATA
* * *
54814307 AAAAATTTATA-AAATTTTA
1 AAAAATGTAGAGAAA-TATA
* *
54814326 TATAATCGTA-AGAAAATTATA
1 AAAAAT-GTAGAG-AAA-TATA
*
54814347 AAAAATATAGAGAAATATA
1 AAAAATGTAGAGAAATATA
54814366 AAA
1 AAA
54814369 TTTGTAAAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
17 4 0.06
18 13 0.20
19 27 0.42
20 7 0.11
21 13 0.20
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (19 bp):
AAAAATGTAGAGAAATATA
Found at i:54814300 original size:19 final size:19
Alignment explanation
Indices: 54814282--54814368 Score: 63
Period size: 19 Copynumber: 4.5 Consensus size: 19
54814272 AAATCGTAGA
54814282 AAAT-TAAAAAATGTATAG
1 AAATATAAAAAATGTATAG
*
54814300 AAATATAAAAAATTTATA-
1 AAATATAAAAAATGTATAG
* * *
54814318 AAATTTTATATAATCGTA-AG
1 AAA-TATAAAAAAT-GTATAG
* *
54814338 AAAATTATAAAAAATATAGAG
1 -AAA-TATAAAAAATGTATAG
54814359 AAATATAAAA
1 AAATATAAAA
54814369 TTTGTAAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
18 7 0.13
19 27 0.50
20 7 0.13
21 13 0.24
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (19 bp):
AAATATAAAAAATGTATAG
Found at i:54814609 original size:9 final size:9
Alignment explanation
Indices: 54814573--54814723 Score: 73
Period size: 10 Copynumber: 16.4 Consensus size: 9
54814563 TTTTGATACA
54814573 TTTTATAATT
1 TTTTATAA-T
*
54814583 TTTTATGA-
1 TTTTATAAT
54814591 TTTT-T-A-
1 TTTTATAAT
54814597 TTTTATAATT
1 TTTTATAA-T
*
54814607 TTTTACAAT
1 TTTTATAAT
* *
54814616 TTCTATAAAAA
1 TT-T-TATAAT
*
54814627 TTTTCTAAT
1 TTTTATAAT
54814636 TTTTAATAAT
1 TTTT-ATAAT
*
54814646 TTTTATATGT
1 TTTTATA-AT
*
54814656 TTTTATCAAAA
1 TTTTAT--AAT
*
54814667 CTTTATAAT
1 TTTTATAAT
*
54814676 TTTTATAAC
1 TTTTATAAT
*
54814685 TTTTATTGA-
1 TTTTA-TAAT
54814694 TTTT-T-AT
1 TTTTATAAT
54814701 TTTTATAATT
1 TTTTATAA-T
54814711 TTTTATAAT
1 TTTTATAAT
54814720 TTTT
1 TTTT
54814724 TTGTCACATA
Statistics
Matches: 110, Mismatches: 16, Indels: 31
0.70 0.10 0.20
Matches are distributed among these distances:
6 6 0.05
7 7 0.06
8 6 0.05
9 37 0.34
10 42 0.38
11 11 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:54814617 original size:24 final size:24
Alignment explanation
Indices: 54814572--54814617 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
54814562 TTTTTGATAC
**
54814572 ATTTTATAATTTTTTATGATTTTT
1 ATTTTATAATTTTTTACAATTTTT
54814596 ATTTTATAATTTTTTACAATTT
1 ATTTTATAATTTTTTACAATTT
54814618 CTATAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (24 bp):
ATTTTATAATTTTTTACAATTTTT
Found at i:54814721 original size:25 final size:25
Alignment explanation
Indices: 54814674--54814723 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
54814664 AAACTTTATA
*
54814674 ATTTTTATAACTTTTATTGATTTTT
1 ATTTTTATAACTTTTATTAATTTTT
*
54814699 ATTTTTATAA-TTTTTTATAATTTTT
1 ATTTTTATAACTTTTAT-TAATTTTT
54814724 TTGTCACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (25 bp):
ATTTTTATAACTTTTATTAATTTTT
Found at i:54817371 original size:28 final size:28
Alignment explanation
Indices: 54817331--54817386 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
54817321 TACTTTTAGA
54817331 GGACTGAATCAATCCAAGGAATCATGTT
1 GGACTGAATCAATCCAAGGAATCATGTT
54817359 GGACTGAATCAATCCAAGGAATCATGTT
1 GGACTGAATCAATCCAAGGAATCATGTT
54817387 AGACATTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (28 bp):
GGACTGAATCAATCCAAGGAATCATGTT
Found at i:54826276 original size:12 final size:12
Alignment explanation
Indices: 54826259--54826285 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
54826249 TTATGCACTT
54826259 TGTTTTATTTGG
1 TGTTTTATTTGG
54826271 TGTTTTATTTGG
1 TGTTTTATTTGG
54826283 TGT
1 TGT
54826286 GGTTATCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.26, T:0.67
Consensus pattern (12 bp):
TGTTTTATTTGG
Found at i:54834817 original size:15 final size:15
Alignment explanation
Indices: 54834797--54834825 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54834787 GAAGTGGACT
54834797 TGTCTTCCAACTCAG
1 TGTCTTCCAACTCAG
54834812 TGTCTTCCAACTCA
1 TGTCTTCCAACTCA
54834826 AGGGCAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.34, G:0.10, T:0.34
Consensus pattern (15 bp):
TGTCTTCCAACTCAG
Found at i:54835657 original size:15 final size:15
Alignment explanation
Indices: 54835616--54835658 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
54835606 CTCATTTTCG
*
54835616 ATGAAGAAGAACATT
1 ATGAAGAAGAAGATT
54835631 ATGAAGAAGAAGATT
1 ATGAAGAAGAAGATT
* *
54835646 GTGAAGGAGAAGA
1 ATGAAGAAGAAGA
54835659 CCTTCTCATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.51, C:0.02, G:0.30, T:0.16
Consensus pattern (15 bp):
ATGAAGAAGAAGATT
Found at i:54841514 original size:46 final size:45
Alignment explanation
Indices: 54841462--54841629 Score: 171
Period size: 46 Copynumber: 3.6 Consensus size: 45
54841452 TGGTTGAGCA
*
54841462 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TAAGGATGCGAATG
* * * *
54841508 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTAAGGATGCGAA-T--G
* *
54841553 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTAAAGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-AAGGATGCGAATG
* *
54841601 CCCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
54841630 GTTTATGGGC
Statistics
Matches: 101, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 1 0.01
45 1 0.01
46 56 0.55
47 27 0.27
48 2 0.02
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTAAGGATGCGAATG
Found at i:54841618 original size:93 final size:93
Alignment explanation
Indices: 54841459--54841631 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
54841449 GGATGGTTGA
* * * **
54841459 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTAAAGGATGCGAACGCCCGAACTCGTTGAGT
54841524 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
54841552 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTAAAGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTAAAGGATGCGAACGCCCGAACTCGTTGAGT
54841617 TGAGTCCGAGTTCGT
66 TGAGTCCGAGTTCGT
54841632 TTATGGGCAT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTAAAGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:54845886 original size:5 final size:5
Alignment explanation
Indices: 54845876--54845907 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
54845866 TTGTGTGTTC
54845876 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
54845908 TCACAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:54845890 original size:9 final size:9
Alignment explanation
Indices: 54845876--54845906 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
54845866 TTGTGTGTTC
54845876 TTTATTTTA
1 TTTATTTTA
54845885 TTTATTTTA
1 TTTATTTTA
54845894 TTTTATTTTA
1 -TTTATTTTA
54845904 TTT
1 TTT
54845907 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:54851653 original size:48 final size:49
Alignment explanation
Indices: 54851559--54851660 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 49
54851549 ATACCAAAGA
* * *
54851559 TCTTTTGCCTTAATCAGACAATTAATCCATACTCTTTGACTTCTTCTTCTTC
1 TCTTTTGCCTCAATCAGAC-A--AATCCATACTCTTGGACTTCTTCTCCTTC
54851611 TCTTTTGCCTCAATCAGAC-AATCCATACTCTATGGA-TTCTTCTCCTTC
1 TCTTTTGCCTCAATCAGACAAATCCATACTCT-TGGACTTCTTCTCCTTC
54851659 TC
1 TC
54851661 GTCAAATGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
48 25 0.54
49 3 0.07
52 18 0.39
ACGTcount: A:0.21, C:0.29, G:0.07, T:0.43
Consensus pattern (49 bp):
TCTTTTGCCTCAATCAGACAAATCCATACTCTTGGACTTCTTCTCCTTC
Found at i:54852212 original size:54 final size:54
Alignment explanation
Indices: 54852130--54852290 Score: 313
Period size: 54 Copynumber: 3.0 Consensus size: 54
54852120 AGTTGGTTTC
54852130 ATGATAGAGCCATTTGACTTGATTATCAAGTCAGTTTGGGTGAAACTTTAATCT
1 ATGATAGAGCCATTTGACTTGATTATCAAGTCAGTTTGGGTGAAACTTTAATCT
54852184 ATGATAGAGCCATTTGACTTGATTATCAAGTCAGTTTGGGTGAAACTTTAATCT
1 ATGATAGAGCCATTTGACTTGATTATCAAGTCAGTTTGGGTGAAACTTTAATCT
*
54852238 ATGATAGAGCCATTTGACTTGATTATCAAGTCAGTTTGCGTGAAACTTTAATC
1 ATGATAGAGCCATTTGACTTGATTATCAAGTCAGTTTGGGTGAAACTTTAATC
54852291 AATTTTCGGC
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 106 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.37
Consensus pattern (54 bp):
ATGATAGAGCCATTTGACTTGATTATCAAGTCAGTTTGGGTGAAACTTTAATCT
Found at i:54855256 original size:10 final size:10
Alignment explanation
Indices: 54855241--54855275 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
54855231 ATTTATAGCA
54855241 AATGTTTAAT
1 AATGTTTAAT
54855251 AATGTTTAAT
1 AATGTTTAAT
*
54855261 AATCTTTAAT
1 AATGTTTAAT
54855271 -ATGTT
1 AATGTT
54855276 GGCGTGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 4 0.17
10 19 0.83
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (10 bp):
AATGTTTAAT
Found at i:54857853 original size:21 final size:21
Alignment explanation
Indices: 54857827--54857867 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54857817 ATCTGCTCAA
* *
54857827 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
54857848 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
54857868 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:54862454 original size:46 final size:46
Alignment explanation
Indices: 54862387--54862479 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
54862377 ATTTCTATTT
54862387 AGTTGCTCTAATTTTTTTATTAGTTTATTATAAAAAAGATAAAAAC
1 AGTTGCTCTAATTTTTTTATTAGTTTATTATAAAAAAGATAAAAAC
54862433 AGTTGCTCTAATTTTTTTATTAGTTTATTATAAAAAAGATAAAAAC
1 AGTTGCTCTAATTTTTTTATTAGTTTATTATAAAAAAGATAAAAAC
54862479 A
1 A
54862480 ATGTCATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (46 bp):
AGTTGCTCTAATTTTTTTATTAGTTTATTATAAAAAAGATAAAAAC
Found at i:54863371 original size:15 final size:15
Alignment explanation
Indices: 54863336--54863365 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54863326 CTTAATCCTT
*
54863336 TATAAATTATAAAGA
1 TATAAATTATAAAAA
54863351 TATAAATTATAAAAA
1 TATAAATTATAAAAA
54863366 ATTAAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
TATAAATTATAAAAA
Found at i:54865963 original size:11 final size:12
Alignment explanation
Indices: 54865947--54865975 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
54865937 CACCATGTTC
54865947 TATCTTTCCA-T
1 TATCTTTCCATT
54865958 TATCTTTCCATT
1 TATCTTTCCATT
54865970 TATCTT
1 TATCTT
54865976 CTTTATTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
TATCTTTCCATT
Found at i:54879735 original size:19 final size:19
Alignment explanation
Indices: 54879691--54879739 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
54879681 TTAGAGGGGC
*
54879691 TAAAATATAATTTTACTTT
1 TAAAATTTAATTTTACTTT
**
54879710 TATAAATTTAATTTTTTTTT
1 TA-AAATTTAATTTTACTTT
54879730 TAAAATTTAA
1 TAAAATTTAA
54879740 GAGCTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TAAAATTTAATTTTACTTT
Found at i:54886862 original size:18 final size:18
Alignment explanation
Indices: 54886766--54886858 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
54886756 CAATCCCAAC
*
54886766 TACTGTATACGTGAACAG
1 TACTGTATACGTGAATAG
*
54886784 TATTGTATACGTGAATAG
1 TACTGTATACGTGAATAG
* * *
54886802 TGCTATATACATGAATAG
1 TACTGTATACGTGAATAG
54886820 TACTGTATACGTGAATAG
1 TACTGTATACGTGAATAG
* *
54886838 TGCCGTATACGTGAATAG
1 TACTGTATACGTGAATAG
54886856 TAC
1 TAC
54886859 CGTAAACGGT
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (18 bp):
TACTGTATACGTGAATAG
Found at i:54891180 original size:3 final size:3
Alignment explanation
Indices: 54891172--54891550 Score: 129
Period size: 3 Copynumber: 125.7 Consensus size: 3
54891162 TAAAACATAT
* * * *
54891172 ATA ATA AT- ATG ATA ATA ATA ATA ACA ATA GTA ATAA ATAA ATA ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A AT-A ATA ATA
* * * * *
54891218 ATA ATA AAA ATA ATA GTA A-A GAAA ATA A-A GATA AAA AAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA
* * * * * *
54891263 ATG GTA ATA ATA ATA AAA ATA A-A AGTA ATA ATA AT- ATG TTA AGTT
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA A-TA
* * * * * *
54891308 ATA ATA GT- AGA ATA ATA ATA ATA GTG ACA ATA ATA AT- ATA TTA GATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * * * * *
54891355 ATA ATA ATA GTA ATA ATT ATA ATG GTA ATA ATT ATA ATT ATA ATTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
* * * * * *
54891401 ATA CTA ATA CTA ACA ATA A-A TGTA ATA GTA A-A AT- ATC ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
54891444 ATA ATA GCT- ATA ATA ATA AT- ATT TTAA ATA A-G ATA ATG ATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
* * * * *
54891488 GATA GA-A AGTG GTA GTA GTG ATA ATA CATTA ATA ATA ATA ATA ATA
1 -ATA -ATA A-TA ATA ATA ATA ATA ATA -A-TA ATA ATA ATA ATA ATA
54891534 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
54891551 TAATTTGAAA
Statistics
Matches: 273, Mismatches: 75, Indels: 56
0.68 0.19 0.14
Matches are distributed among these distances:
2 20 0.07
3 223 0.82
4 28 0.10
5 2 0.01
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:54891205 original size:29 final size:28
Alignment explanation
Indices: 54891165--54891232 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
54891155 CAATTAGTAA
*
54891165 AACATATATAAT-AATATGATAATAATAAT
1 AACA-ATATAATAAATA-AATAATAATAAT
*
54891194 AACAATAGTAATAAATAAATAATGATAAT
1 AACAATA-TAATAAATAAATAATAATAAT
54891223 AA-AA-ATAATA
1 AACAATATAATA
54891233 GTAAAGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
26 5 0.14
27 1 0.03
28 5 0.14
29 20 0.57
30 4 0.11
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.29
Consensus pattern (28 bp):
AACAATATAATAAATAAATAATAATAAT
Found at i:54892375 original size:9 final size:9
Alignment explanation
Indices: 54892361--54892392 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
54892351 AATGTCTCCA
54892361 AAAAAAACC
1 AAAAAAACC
54892370 AAAAAAACC
1 AAAAAAACC
54892379 AAAAAAACC
1 AAAAAAACC
54892388 AAAAA
1 AAAAA
54892393 GATTAAAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACC
Found at i:54894552 original size:15 final size:15
Alignment explanation
Indices: 54894532--54894565 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
54894522 ATATGATAAA
54894532 TAAAAT-AATAACATT
1 TAAAATAAAT-ACATT
54894547 TAAAATAAATACATT
1 TAAAATAAATACATT
54894562 TAAA
1 TAAA
54894566 TGCTATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.83
16 3 0.17
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAATAAATACATT
Found at i:54904449 original size:44 final size:43
Alignment explanation
Indices: 54904386--54904472 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 43
54904376 TCCTAATTGG
54904386 GAAAATAGTTCCCTTATTCTAATAAACTTACTAAAACATAAAAA
1 GAAAATAGTTCCCTTATTCTAATAAAC-TACTAAAACATAAAAA
* *
54904430 GAAAATAGTTCCCTTATTCTAGTAAACTACTAAAAGATAAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAA
54904473 TATTTCTAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 15 0.37
44 26 0.63
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (43 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAA
Found at i:54909192 original size:44 final size:43
Alignment explanation
Indices: 54909122--54909208 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 43
54909112 TCCTAATTGG
54909122 GAAAATAGTTCCCTTATTCCAATAAACTTACTAAAACATAAAAA
1 GAAAATAGTTCCCTTATTCCAATAAAC-TACTAAAACATAAAAA
* * *
54909166 GAAAATAGTTCCCTTATTCTAGTAAACTACTAAAAGATAAAAA
1 GAAAATAGTTCCCTTATTCCAATAAACTACTAAAACATAAAAA
54909209 TATTTCTAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 15 0.38
44 25 0.62
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (43 bp):
GAAAATAGTTCCCTTATTCCAATAAACTACTAAAACATAAAAA
Found at i:54915032 original size:15 final size:15
Alignment explanation
Indices: 54915012--54915041 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54915002 GACCATGATT
54915012 TATGGCAAAGATAAA
1 TATGGCAAAGATAAA
*
54915027 TATGGCAGAGATAAA
1 TATGGCAAAGATAAA
54915042 CTCTTATTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.23, T:0.20
Consensus pattern (15 bp):
TATGGCAAAGATAAA
Found at i:54922354 original size:189 final size:189
Alignment explanation
Indices: 54922128--54922764 Score: 965
Period size: 189 Copynumber: 3.4 Consensus size: 189
54922118 CAATATTTCA
* *
54922128 AAGTTGGAATTCCTTCATCAATTGGATCTTAGTGATTGCCCAATGATTAAATTTCCAGAAATCCC
1 AAGTTGGAATCCCTTCGTCAATTGGATCTTAGTGATTGCCCAATGATTAAATTTCCAGAAATCCC
54922193 AAGAAGCTTAACAGAATTAAACTTATCTGGCACTCAAATTGAAGAAGTGTCCTTGCCTTTCGACT
66 AAGAAGCTTAACAGAATTAAACTTATCTGGCACTCAAATTGAAGAAGTGTCCTTGCCTTTCGACT
*
54922258 CCCTATGTAATCTTCGGAATTTAAATATGAAGGGCTCAAGGGTAAAAAATGTGTCGATC
131 CCCTATGTAATCTTCGGAATTTAAATATGAAGGGCTCAAGGGTAAAAAATGTATCGATC
*
54922317 AAGTTGGAATCCCTTCGTCAATTAGATCTTAGTGATTGCCCAATGATTAAATTTCCAGAAATCCC
1 AAGTTGGAATCCCTTCGTCAATTGGATCTTAGTGATTGCCCAATGATTAAATTTCCAGAAATCCC
* *
54922382 AGGAAGCTTAACAGAATTAAACTTATCTGGCACTCAAATTGAAGAAGTGTTCTTGCCTTTCGACT
66 AAGAAGCTTAACAGAATTAAACTTATCTGGCACTCAAATTGAAGAAGTGTCCTTGCCTTTCGACT
* * *
54922447 CCCTAAGTAATCTTCGAAATTTAAATATGAGGGGCTCAAGGGTAAAAAATGTATCGATC
131 CCCTATGTAATCTTCGGAATTTAAATATGAAGGGCTCAAGGGTAAAAAATGTATCGATC
* * * * *
54922506 AAGTTGGAATCCCTTCGTAAACTGAATCTTAGTAATTGCCCAATGATCAAATTTCCAGAAATCCC
1 AAGTTGGAATCCCTTCGTCAATTGGATCTTAGTGATTGCCCAATGATTAAATTTCCAGAAATCCC
* * *
54922571 AAGAAGCTTAATAGAATTAAACTTATCTGGCACTCAAATTGAAGAAGTGTCATTGCCTTTGGACT
66 AAGAAGCTTAACAGAATTAAACTTATCTGGCACTCAAATTGAAGAAGTGTCCTTGCCTTTCGACT
* * * * * *
54922636 CTCTATGTAATCTTCGGGACTTAGATATG-AGTGGCTC-TGCGGTAAAAAATGTATCGACC
131 CCCTATGTAATCTTCGGAATTTAAATATGAAG-GGCTCAAG-GGTAAAAAATGTATCGATC
* * * * * *
54922695 AAGTTGGAATCTCTTCGT-TATCTGGATCTTAGTGGTTGCCCAATGGTTGAATTTCCAGAAATTC
1 AAGTTGGAATCCCTTCGTCAAT-TGGATCTTAGTGATTGCCCAATGATTAAATTTCCAGAAATCC
54922759 CAAGAA
65 CAAGAA
54922765 TTACATGGGA
Statistics
Matches: 406, Mismatches: 39, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
188 3 0.01
189 403 0.99
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (189 bp):
AAGTTGGAATCCCTTCGTCAATTGGATCTTAGTGATTGCCCAATGATTAAATTTCCAGAAATCCC
AAGAAGCTTAACAGAATTAAACTTATCTGGCACTCAAATTGAAGAAGTGTCCTTGCCTTTCGACT
CCCTATGTAATCTTCGGAATTTAAATATGAAGGGCTCAAGGGTAAAAAATGTATCGATC
Found at i:54923245 original size:3 final size:3
Alignment explanation
Indices: 54923237--54923271 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
54923227 CAAATCAGTT
*
54923237 TGA TGA TGA TAA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
54923272 TGTTTCGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:54927285 original size:555 final size:555
Alignment explanation
Indices: 54926235--54927347 Score: 2129
Period size: 555 Copynumber: 2.0 Consensus size: 555
54926225 TTGCAAACCC
54926235 TTTCTACATGACCCATCTTCTTGCAAAATCTGCACTGCACATCAGGCCTGAACCAACATACTTTA
1 TTTCTACATGACCCATCTTCTTGCAAAATCTGCACTGCACATCAGGCCTGAACCAACATACTTTA
54926300 CCCGGGTGACTTGCCCTTCTGCAGTGTGGACAGGGTGGATATCTTCCTGCACCATCTGCTTTAGG
66 CCCGGGTGACTTGCCCTTCTGCAGTGTGGACAGGGTGGATATCTTCCTGCACCATCTGCTTTAGG
* *
54926365 CTCGTTTGACCAGGTATTCTTGCCTTTGTAGGCAGAGGTGCTCGAGGCAGACTTGGCTTCGGCTT
131 CTCGTTTGACCAGGTATTCTTGCCTTCGTAGGCAGAGGTGCTCGAGGCAGACTTGGCTTCGACTT
54926430 GAAAGGCACCTTCTTGGTGCTCCTCCGATCTGCTGGCCCTCCTTTGCTCTTGTGCATACAGAGCA
196 GAAAGGCACCTTCTTGGTGCTCCTCCGATCTGCTGGCCCTCCTTTGCTCTTGTGCATACAGAGCA
* *
54926495 TTGATCAGCTCTGTTAAAGAGATGCTGGTCAGGTCCCTTGAGTCCTCTAAAGAGGATATTTTTGC
261 TTGATCAGCTCTGTTAAAGAGATGCTGGTCAAGTCCCTTGAATCCTCTAAAGAGGATATTTTTGC
54926560 TTCATACCTTTCTGGTAAGGTAGAGAGCACTTTCTCCACAATCCTTGCTTCACTAAAATGCTCAC
326 TTCATACCTTTCTGGTAAGGTAGAGAGCACTTTCTCCACAATCCTTGCTTCACTAAAATGCTCAC
54926625 CAAGGAGCCTTATGCTATTTACTACAGCCGTAATTCTGTCTGAATACTTCTTGACAGTTTCCTCT
391 CAAGGAGCCTTATGCTATTTACTACAGCCGTAATTCTGTCTGAATACTTCTTGACAGTTTCCTCT
*
54926690 TCCTTCATCTTTAAGTTCTCGAACTCCCTTCTCAGGTTCAACAACTGCTGTTGTCTTGTCCTTTC
456 TCCTTCATCTTTAAGTTCTCGAACTCCCTTCTCAGGTTCAACAACTGCTGTTGTCTTGTCCTCTC
54926755 AGTACCTTGGAACTCCTCCTTGAGTTTGTCCCAGG
521 AGTACCTTGGAACTCCTCCTTGAGTTTGTCCCAGG
54926790 TTTCTACATGACCCATCTTCTTGCAAAATCTGCACTGCACATCAGGCCTGAACCAACATACTTTA
1 TTTCTACATGACCCATCTTCTTGCAAAATCTGCACTGCACATCAGGCCTGAACCAACATACTTTA
54926855 CCCGGGTGACTTGCCCTTCTGCAGTGTGGACAGGGTGGATATCTTCCTGCACCATCTGCTTTAGG
66 CCCGGGTGACTTGCCCTTCTGCAGTGTGGACAGGGTGGATATCTTCCTGCACCATCTGCTTTAGG
* *
54926920 CTCGTTTGACTAGGTATTCTTGCCTTCGTAGGTAGAGGTGCTCGAGGCAGACTTGGCTTCGACTT
131 CTCGTTTGACCAGGTATTCTTGCCTTCGTAGGCAGAGGTGCTCGAGGCAGACTTGGCTTCGACTT
54926985 GAAAGGCACCTTCTTGGTGCTCCTCCTG-TCTGCTGGCCCTCCTTTGCTCTTGTGCATACAGAGC
196 GAAAGGCACCTTCTTGGTGCTCCTCC-GATCTGCTGGCCCTCCTTTGCTCTTGTGCATACAGAGC
* *
54927049 ATTGATCAGCTCTGTTAAAGAGATGCTGGTTAAGTCCCTTGAATCCTCTAAGGAGGATATTTTTG
260 ATTGATCAGCTCTGTTAAAGAGATGCTGGTCAAGTCCCTTGAATCCTCTAAAGAGGATATTTTTG
54927114 CTTCATACCTTTCTGGTAAGGTAGAGAGCACTTTCTCCACAATCCTTGCTTCACTAAAATGCTCA
325 CTTCATACCTTTCTGGTAAGGTAGAGAGCACTTTCTCCACAATCCTTGCTTCACTAAAATGCTCA
54927179 CCAAGGAGCCTTATGCTATTTACTACAGCCGTAATTCTGTCTGAATACTTCTTGACAGTTTCCTC
390 CCAAGGAGCCTTATGCTATTTACTACAGCCGTAATTCTGTCTGAATACTTCTTGACAGTTTCCTC
54927244 TTCCTTCATCTTTAAGTTCTCGAACTCCCTTCTCAGGTTCAACAACTGCTGTTGTCTTGTCCTCT
455 TTCCTTCATCTTTAAGTTCTCGAACTCCCTTCTCAGGTTCAACAACTGCTGTTGTCTTGTCCTCT
54927309 CAGTACCTTGGAACTCCTCCTTGAGTTTGTCCCAGG
520 CAGTACCTTGGAACTCCTCCTTGAGTTTGTCCCAGG
54927345 TTT
1 TTT
54927348 GTTTTGGTGT
Statistics
Matches: 548, Mismatches: 9, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
555 547 1.00
556 1 0.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (555 bp):
TTTCTACATGACCCATCTTCTTGCAAAATCTGCACTGCACATCAGGCCTGAACCAACATACTTTA
CCCGGGTGACTTGCCCTTCTGCAGTGTGGACAGGGTGGATATCTTCCTGCACCATCTGCTTTAGG
CTCGTTTGACCAGGTATTCTTGCCTTCGTAGGCAGAGGTGCTCGAGGCAGACTTGGCTTCGACTT
GAAAGGCACCTTCTTGGTGCTCCTCCGATCTGCTGGCCCTCCTTTGCTCTTGTGCATACAGAGCA
TTGATCAGCTCTGTTAAAGAGATGCTGGTCAAGTCCCTTGAATCCTCTAAAGAGGATATTTTTGC
TTCATACCTTTCTGGTAAGGTAGAGAGCACTTTCTCCACAATCCTTGCTTCACTAAAATGCTCAC
CAAGGAGCCTTATGCTATTTACTACAGCCGTAATTCTGTCTGAATACTTCTTGACAGTTTCCTCT
TCCTTCATCTTTAAGTTCTCGAACTCCCTTCTCAGGTTCAACAACTGCTGTTGTCTTGTCCTCTC
AGTACCTTGGAACTCCTCCTTGAGTTTGTCCCAGG
Found at i:54935552 original size:30 final size:30
Alignment explanation
Indices: 54935518--54935587 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
54935508 GCCCCCTCTA
54935518 AAATTATAAAAATTCAATTTAATCATTTAC
1 AAATTATAAAAATTCAATTTAATCATTTAC
54935548 AAATTATAAAAATTCAATTTAATCATTTAC
1 AAATTATAAAAATTCAATTTAATCATTTAC
54935578 AAATTATAAA
1 AAATTATAAA
54935588 GATATAAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.39
Consensus pattern (30 bp):
AAATTATAAAAATTCAATTTAATCATTTAC
Found at i:54936357 original size:16 final size:16
Alignment explanation
Indices: 54936336--54936369 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
54936326 TTGAAATCTT
*
54936336 AAGCTTTAAAATGGGA
1 AAGCTTGAAAATGGGA
54936352 AAGCTTGAAAATGGGA
1 AAGCTTGAAAATGGGA
54936368 AA
1 AA
54936370 CACTTTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.26, T:0.21
Consensus pattern (16 bp):
AAGCTTGAAAATGGGA
Found at i:54941009 original size:20 final size:21
Alignment explanation
Indices: 54940960--54941011 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
54940950 TTATGCCACA
54940960 TCAA-TATTCTTATCCTGAATT
1 TCAAGTATT-TTATCCTGAATT
54940981 TCAAG-ATTTTATCCTGAATT
1 TCAAGTATTTTATCCTGAATT
*
54941001 T-TAGTATTTTA
1 TCAAGTATTTTA
54941012 ATTTTGGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 19 0.68
21 7 0.25
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (21 bp):
TCAAGTATTTTATCCTGAATT
Found at i:54943143 original size:189 final size:189
Alignment explanation
Indices: 54942930--54943566 Score: 918
Period size: 189 Copynumber: 3.4 Consensus size: 189
54942920 CAATATTTCA
* *
54942930 AAGTTGGAATTCCTTCATCAATTGGATCTTAGTGATTGCCCAATGATTAAATTTCCAGAAATCCC
1 AAGTTGGAATCCCTTCATCAATTGGATCTTAGTGATTGCCCAATGATCAAATTTCCAGAAATCCC
* *
54942995 AAGAAGCTTAACAGAATTAAACTTATCTGGCACCCAAATTGAAGAAGTGTCCTTACCTTTCGACT
66 AAGAAGCTTAACAGAATTAAACTTATCTGGCACTCAAATTGAAGAAGTGTCCTTGCCTTTCGACT
*
54943060 CCCTAGGTAATCTTCGGAATTTAAATATGAGGGGCTCAAGGGTAAAAAATGTATCGATC
131 CCCTATGTAATCTTCGGAATTTAAATATGAGGGGCTCAAGGGTAAAAAATGTATCGATC
*
54943119 AAGTTGGAATCCCTTCATCAATTGGATCTTAGTGATTGCCCAATGATTAAATTTCCAGAAATCCC
1 AAGTTGGAATCCCTTCATCAATTGGATCTTAGTGATTGCCCAATGATCAAATTTCCAGAAATCCC
* *
54943184 AAGAAGCTTAACAGAATTAAACTTATCTGGAACTCAAATTGAAGAAGTGTTCTTGCCTTTCGACT
66 AAGAAGCTTAACAGAATTAAACTTATCTGGCACTCAAATTGAAGAAGTGTCCTTGCCTTTCGACT
* *
54943249 CCCTATGTAATCTTCGAAATTTAAATATGAGGGGCTCAAGGGTAAAAAATGTATCAATC
131 CCCTATGTAATCTTCGGAATTTAAATATGAGGGGCTCAAGGGTAAAAAATGTATCGATC
* * * * *
54943308 AAGTTGGAATCCCTTCGTAAACTGAATCTTAATGATTGCCCAATGATCAAATTTCCAGAAATCCC
1 AAGTTGGAATCCCTTCATCAATTGGATCTTAGTGATTGCCCAATGATCAAATTTCCAGAAATCCC
* * * * *
54943373 AAAAAGCTTAATAGAATTAAACTTATCTGGCACTCAAATTGAAGAAGTATCATTGCCTTTGGACT
66 AAGAAGCTTAACAGAATTAAACTTATCTGGCACTCAAATTGAAGAAGTGTCCTTGCCTTTCGACT
** * * * * * *
54943438 CTTTATGTAATCTTCGGGACTTAGATATGAGTGGCTC-TGCGGTTAAAAATGTATCGATC
131 CCCTATGTAATCTTCGGAATTTAAATATGAGGGGCTCAAG-GGTAAAAAATGTATCGATC
* * * * * * * *
54943497 AAGTTGGAATCTCTTCGT-TATCTAGATCTTAGTGGTTGCCCAATGGTCGAATTTCCAGAAATTC
1 AAGTTGGAATCCCTTCATCAAT-TGGATCTTAGTGATTGCCCAATGATCAAATTTCCAGAAATCC
54943561 CAAGAA
65 CAAGAA
54943567 TTATATGGGA
Statistics
Matches: 404, Mismatches: 42, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
188 2 0.00
189 402 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (189 bp):
AAGTTGGAATCCCTTCATCAATTGGATCTTAGTGATTGCCCAATGATCAAATTTCCAGAAATCCC
AAGAAGCTTAACAGAATTAAACTTATCTGGCACTCAAATTGAAGAAGTGTCCTTGCCTTTCGACT
CCCTATGTAATCTTCGGAATTTAAATATGAGGGGCTCAAGGGTAAAAAATGTATCGATC
Found at i:54946612 original size:39 final size:39
Alignment explanation
Indices: 54946558--54946853 Score: 477
Period size: 39 Copynumber: 7.5 Consensus size: 39
54946548 TAATGGAGAA
54946558 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
54946597 TTATATCCGGGCTAAGTCCAGAAGGAATTCGTGCTAGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
54946636 TTATATCCGGGCTAAGTCTCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
54946675 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
54946714 TTATATCCGGGCTAAGCCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
54946753 TTATATCCGGGCTAAGCCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
54946792 TTATATCCGGGCTAAAGTCCCGCAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTG
54946831 TTATATCCGGGCTTAAAGTCCCG
1 TTATATCCGGGC-T-AAGTCCCG
54946854 CATGCTTTGT
Statistics
Matches: 242, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
39 221 0.91
40 21 0.09
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.28
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:54949777 original size:21 final size:21
Alignment explanation
Indices: 54949751--54949791 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54949741 ATCTGCTCAA
* *
54949751 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
54949772 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
54949792 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:54949790 original size:118 final size:118
Alignment explanation
Indices: 54949582--54949816 Score: 409
Period size: 118 Copynumber: 2.0 Consensus size: 118
54949572 TAATCCTCCA
54949582 TTGTGGCTGGAGAATTAGACTTATTAACTGGGCAAATCCCCACCTGCTCAAACTCCACCTGTTTT
1 TTGTGGCTGGAGAATTAGACTTATTAACTGGGCAAATCCCCACCTGCTCAAACTCCACCTGTTTT
* *
54949647 GGGGTACACTCCACCTCGTGTGGAGTATCGCTTGTCTGAATATCTTGATCTGT
66 GGAGTACACTCCACCTCGTGTGGAGTATCGCTCGTCTGAATATCTTGATCTGT
*
54949700 TTGTGGCTGGAGAATTAGACTTATTAACTGGGCAAATCCCCATCTGCTCAAACTCCACCTGTTTT
1 TTGTGGCTGGAGAATTAGACTTATTAACTGGGCAAATCCCCACCTGCTCAAACTCCACCTGTTTT
* *
54949765 GGAGTACACTCCACCT-GCTGTGGAGTATTGCTCGTCTGAATATCTTTATCTG
66 GGAGTACACTCCACCTCG-TGTGGAGTATCGCTCGTCTGAATATCTTGATCTG
54949817 CTACCTTTTT
Statistics
Matches: 111, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
117 1 0.01
118 110 0.99
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (118 bp):
TTGTGGCTGGAGAATTAGACTTATTAACTGGGCAAATCCCCACCTGCTCAAACTCCACCTGTTTT
GGAGTACACTCCACCTCGTGTGGAGTATCGCTCGTCTGAATATCTTGATCTGT
Found at i:54954556 original size:39 final size:40
Alignment explanation
Indices: 54954472--54954556 Score: 118
Period size: 39 Copynumber: 2.1 Consensus size: 40
54954462 ACTTAATTCA
* * *
54954472 CCAGCATTAAGCCTGCGGGACTTTAAACCCGGATACAATC
1 CCAGCATGAAGCCAGCGGGACTCTAAACCCGGATACAATC
*
54954512 CCAGCATGAAGCCAGCGGGTCTCT-AACCCGGATACAATC
1 CCAGCATGAAGCCAGCGGGACTCTAAACCCGGATACAATC
*
54954551 TCAGCA
1 CCAGCA
54954557 CAATTCATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 20 0.50
40 20 0.50
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.18
Consensus pattern (40 bp):
CCAGCATGAAGCCAGCGGGACTCTAAACCCGGATACAATC
Found at i:54954726 original size:47 final size:46
Alignment explanation
Indices: 54954627--54954782 Score: 199
Period size: 47 Copynumber: 3.3 Consensus size: 46
54954617 TGCACACTTT
* * *
54954627 TCACAATTGGTCATTCGGCCTTATCACA-TATTCACTTACACATAT-A
1 TCAC-ATTGGCCATTCGGCCTTATCACATTATACACTTTCACAT-TCA
** *
54954673 TCACATTAACCATTCGGCCTTATCACATGTATGCACTTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACAT-TATACACTTTCACATTCA
*
54954720 TCACATTGGCCATTCGGCCTTATCACATATACACACTTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACAT-TATACACTTTCACATTCA
54954767 TCACATTGGCCATTCG
1 TCACATTGGCCATTCG
54954783 ATCTTAAGCT
Statistics
Matches: 97, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
45 20 0.21
46 5 0.05
47 72 0.74
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (46 bp):
TCACATTGGCCATTCGGCCTTATCACATTATACACTTTCACATTCA
Found at i:54964009 original size:10 final size:10
Alignment explanation
Indices: 54963987--54964018 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
54963977 TAACAGTAGC
54963987 GCAAATGGACA
1 GCAAAT-GACA
54963998 GCAAATGACA
1 GCAAATGACA
54964008 GCAAATGACA
1 GCAAATGACA
54964018 G
1 G
54964019 TGATGAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.71
11 6 0.29
ACGTcount: A:0.47, C:0.19, G:0.25, T:0.09
Consensus pattern (10 bp):
GCAAATGACA
Found at i:54968628 original size:38 final size:38
Alignment explanation
Indices: 54968577--54968652 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
54968567 TCAAGCATAG
* *
54968577 CTGTCAAATATCTTGTAGCTATATACTTTCCTAAGAAT
1 CTGTCAAATATCTTGTAGATATATACTTTACTAAGAAT
*
54968615 CTGTCAAGTATCTTGTAGATATATACTTTACTAAGAAT
1 CTGTCAAATATCTTGTAGATATATACTTTACTAAGAAT
54968653 AGGTTACTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (38 bp):
CTGTCAAATATCTTGTAGATATATACTTTACTAAGAAT
Found at i:54968733 original size:22 final size:23
Alignment explanation
Indices: 54968708--54968755 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
54968698 TATTTTAGGA
* * *
54968708 TGTGATT-AGGGATTTGATTTGC
1 TGTGATTAAGGAATTTAATATGC
54968730 TGTGATTAAGGAATTTAATATGC
1 TGTGATTAAGGAATTTAATATGC
54968753 TGT
1 TGT
54968756 ACCAGTGCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.25, C:0.04, G:0.27, T:0.44
Consensus pattern (23 bp):
TGTGATTAAGGAATTTAATATGC
Found at i:54970687 original size:27 final size:27
Alignment explanation
Indices: 54970653--54970706 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
54970643 TTTTATTAAG
54970653 TTAGTGTGATACTAATTTATTTTTACT
1 TTAGTGTGATACTAATTTATTTTTACT
54970680 TTAGTGTGATACTAATTTATTTTTACT
1 TTAGTGTGATACTAATTTATTTTTACT
54970707 GTTTAAGGGG
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:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (27 bp):
TTAGTGTGATACTAATTTATTTTTACT
Found at i:54970704 original size:22 final size:24
Alignment explanation
Indices: 54970644--54970701 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 24
54970634 ATTAAATATT
* *
54970644 TTTATTAAGTTAGTGTGATACTAA
1 TTTATTTATTTAGTGTGATACTAA
54970668 TTTATTTTTACTTTAGTGTGATACTAA
1 TTTA--TTTA-TTTAGTGTGATACTAA
54970695 TTTATTT
1 TTTATTT
54970702 TTACTGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 4 0.14
25 3 0.10
26 3 0.10
27 19 0.66
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTATTTATTTAGTGTGATACTAA
Found at i:54978086 original size:10 final size:10
Alignment explanation
Indices: 54978063--54978095 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
54978053 TAAATAAAAT
54978063 TATTT-TTAA
1 TATTTATTAA
*
54978072 TATTTATTTA
1 TATTTATTAA
54978082 TATTTATTAA
1 TATTTATTAA
54978092 TATT
1 TATT
54978096 AAATATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 5 0.24
10 16 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TATTTATTAA
Found at i:54985742 original size:17 final size:17
Alignment explanation
Indices: 54985722--54985783 Score: 79
Period size: 17 Copynumber: 3.5 Consensus size: 17
54985712 CAATGATATG
54985722 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
* *
54985739 CAATTTTAGATATGATTG
1 CAATCTTAGATATGA-TA
54985757 CAATCTTAGATATGATATA
1 CAATCTTAGATATG--ATA
54985776 CAATCTTA
1 CAATCTTA
54985784 AAAGATATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 14 0.37
18 14 0.37
19 9 0.24
20 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:54990841 original size:92 final size:92
Alignment explanation
Indices: 54990683--54990862 Score: 333
Period size: 92 Copynumber: 2.0 Consensus size: 92
54990673 TTTTAGCATT
*
54990683 GATCTCCTGACAATGTGCTACATAGTACTGTCATTGACAACAAAGTATGTCATCCAAAGAATAAT
1 GATCTCCTGACAATGTGCTACATAGTACTGTCATTGACAACAAAGTATGTCATCCAAAGAACAAT
54990748 GATTTTTACCTTGGTACACATGCCGAG
66 GATTTTTACCTTGGTACACATGCCGAG
*
54990775 GATCTCCTGACAATGTGCTACATGGTACTGTCATTGACAACAAAGTATGTCATCCAAAGAACAAT
1 GATCTCCTGACAATGTGCTACATAGTACTGTCATTGACAACAAAGTATGTCATCCAAAGAACAAT
*
54990840 GATTTTTACCTTGGTACCCATGC
66 GATTTTTACCTTGGTACACATGC
54990863 TGGAATGATT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 85 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (92 bp):
GATCTCCTGACAATGTGCTACATAGTACTGTCATTGACAACAAAGTATGTCATCCAAAGAACAAT
GATTTTTACCTTGGTACACATGCCGAG
Found at i:54991657 original size:12 final size:11
Alignment explanation
Indices: 54991640--54991722 Score: 71
Period size: 11 Copynumber: 7.5 Consensus size: 11
54991630 CTTCTATTTC
*
54991640 AAAAAAATAAG
1 AAAAAAAAAAG
54991651 AAAAAAAATAAG
1 AAAAAAAA-AAG
*
54991663 AAAAGAAAAAG
1 AAAAAAAAAAG
*
54991674 AAAAGAAAAAG
1 AAAAAAAAAAG
*
54991685 -AGAAAAAAAG
1 AAAAAAAAAAG
54991695 AAAAAAGAGAAA-
1 AAAAAA-A-AAAG
* *
54991707 AGAGAAAAAAG
1 AAAAAAAAAAG
54991718 AAAAA
1 AAAAA
54991723 TGGAGAGGCC
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
10 11 0.19
11 29 0.50
12 15 0.26
13 3 0.05
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:54991670 original size:17 final size:16
Alignment explanation
Indices: 54991643--54991722 Score: 81
Period size: 17 Copynumber: 4.8 Consensus size: 16
54991633 CTATTTCAAA
*
54991643 AAAATAAGAAAAAAAAT
1 AAAA-AAGAAAAAAAAG
54991660 AAGAAAAGAAAAAGAAA-
1 AA-AAAAGAAAAA-AAAG
54991677 AGAAAAAGAGAAAAAAAG
1 A-AAAAAGA-AAAAAAAG
* *
54991695 AAAAAAGAGAAAAGAG
1 AAAAAAGAAAAAAAAG
54991711 AAAAAAGAAAAA
1 AAAAAAGAAAAA
54991723 TGGAGAGGCC
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
16 17 0.31
17 27 0.49
18 11 0.20
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAG
Found at i:54991688 original size:24 final size:24
Alignment explanation
Indices: 54991640--54991716 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 24
54991630 CTTCTATTTC
*
54991640 AAAAAAATAAGAAAA-AAAATA-AG
1 AAAAAAAGAAGAAAAGAAAA-AGAG
54991663 AAAAGAAA-AAGAAAAGAAAAAGAG
1 AAAA-AAAGAAGAAAAGAAAAAGAG
54991687 AAAAAAAGAA-AAAAGAGAAAAGAG
1 AAAAAAAGAAGAAAAGA-AAAAGAG
54991711 AAAAAA
1 AAAAAA
54991717 GAAAAATGGA
Statistics
Matches: 49, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
23 21 0.43
24 28 0.57
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (24 bp):
AAAAAAAGAAGAAAAGAAAAAGAG
Found at i:54991714 original size:23 final size:23
Alignment explanation
Indices: 54991642--54991722 Score: 89
Period size: 23 Copynumber: 3.6 Consensus size: 23
54991632 TCTATTTCAA
*
54991642 AAAAATAAGAAAAAA-AATAAGA-
1 AAAAA-AAGAAAAAAGAAAAAGAG
*
54991664 AAAGAAAA-AGAAAAGAAAAAGAG
1 AAA-AAAAGAAAAAAGAAAAAGAG
54991687 AAAAAAAGAAAAAAGAGAAAAGAG
1 AAAAAAAGAAAAAAGA-AAAAGAG
54991711 -AAAAAAGAAAAA
1 AAAAAAAGAAAAA
54991723 TGGAGAGGCC
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
21 5 0.10
22 15 0.29
23 24 0.47
24 7 0.14
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (23 bp):
AAAAAAAGAAAAAAGAAAAAGAG
Found at i:54992667 original size:43 final size:43
Alignment explanation
Indices: 54992620--54992762 Score: 132
Period size: 43 Copynumber: 3.3 Consensus size: 43
54992610 CGCCTTAACC
54992620 CCCTAAGCAGTAGGGTAACAGG-CTAAAATTATAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTC-AAAATTATAGATCTTATCT
* * ** * *
54992663 CCCTAAGTAGTAGTGG-AACAGATCAACAACGACTCG-CCTTAATC-
1 CCCTAAGCAGTAG-GGTAACAGGTCAA-AATTA-TAGATCTT-ATCT
* * *
54992707 CCCTAAGCAATAGGGTAACAGGTCAAAATTGTGGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTCAAAATTATAGATCTTATCT
54992750 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
54992763 TGGAGCAGAT
Statistics
Matches: 77, Mismatches: 15, Indels: 16
0.71 0.14 0.15
Matches are distributed among these distances:
42 5 0.06
43 38 0.49
44 29 0.38
45 5 0.06
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGTAACAGGTCAAAATTATAGATCTTATCT
Found at i:54992756 original size:87 final size:85
Alignment explanation
Indices: 54992609--54992817 Score: 291
Period size: 87 Copynumber: 2.5 Consensus size: 85
54992599 ACAAAATTCA
*
54992609 GCGCCTTAACCCCCTAAGCAGTAGGGTAACAGG-CTAAAATTATAGATCTTATCTCCCTAAGTAG
1 GCGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTCTAAAATTATAGATCTTATCTCCCTAAGCAG
54992673 TAGTGGAACAGATCAACAACGACT
66 TAGTGGAACAGATC--CAA-GA-T
* * * *
54992697 -CGCCTTAATCCCCTAAGCAATAGGGTAACAGGTC-AAAATTGTGGATCTTATCTCCCTAAGCAG
1 GCGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTCTAAAATTATAGATCTTATCTCCCTAAGCAG
* *
54992760 TAGTGGAGCAGATCGAAGAT
66 TAGTGGAACAGATCCAAGAT
54992780 GCGCCTTAACCCCCTAAGCAGTAGGGTAACAGGT-TAAA
1 GCGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTCTAAA
54992818 GTATAGTAGA
Statistics
Matches: 109, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
83 1 0.01
84 36 0.33
85 2 0.02
87 69 0.63
88 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (85 bp):
GCGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTCTAAAATTATAGATCTTATCTCCCTAAGCAG
TAGTGGAACAGATCCAAGAT
Found at i:54993300 original size:207 final size:207
Alignment explanation
Indices: 54992945--54994069 Score: 1793
Period size: 207 Copynumber: 5.4 Consensus size: 207
54992935 AGAGCAGATC
* *
54992945 GAAGACATAGCTGATTTGGCTTTCACGTGCTTATGATGAAGCAAATCTAAGATGATTTGGGATCT
1 GAAGACATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCT
*
54993010 TTGTATTGTCAAAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGC
66 CTGTATTGTCAAAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGC
*
54993075 AGATCTGGCCTTCAGATGTTTATCCTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTAC
131 AGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTAC
54993140 AAGGAACAAATT
196 AAGGAACAAATT
* * *
54993152 GAAGACATAGCTGATTTGGCTTTGACGTGCTTATGATGAAGCAAATCTAAGATGATTTGGGATCT
1 GAAGACATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCT
*
54993217 TTGTATTGTCAAAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGC
66 CTGTATTGTCAAAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGC
*
54993282 AGATCTGGCCTTCAGATGTTTATCCTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTAC
131 AGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTAC
54993347 AAGGAACAAATT
196 AAGGAACAAATT
* * * *
54993359 GAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGAATCT
1 GAAGACATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCT
* * *
54993424 CTGTATTGTTAGAGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGC
66 CTGTATTGTCAAAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGC
*
54993489 AGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGTTTAC
131 AGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTAC
54993554 AAGGAACAAATT
196 AAGGAACAAATT
54993566 GAAGACATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCT
1 GAAGACATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCT
* * * *
54993631 CTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTTGACGGAGTGCAGACACAAAGC
66 CTGTATTGTCAAAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGC
* * *
54993696 AGATCTGGCCTTCAGATGTTTATACTAAAACAAGATCCAAGATGGTTTGGCATCCTTGTCCTTAC
131 AGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTAC
*
54993761 AAGGAACAAATC
196 AAGGAACAAATT
* * * * *
54993773 GAAGGCATAGCTGATTTGGATTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCT
1 GAAGACATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCT
* * * *
54993838 CTGTATTGTCAGAGAACAAATCGAAGTTTGGCATCTCCATATTCGACGGAGGACAGACATATAGC
66 CTGTATTGTCAAAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGC
** * * * *
54993903 AGATCTAACCTTCAGATGATTAGACTGAAGC-AGATCCAAGATGGTTTGGTATCATTGTGCTTAC
131 AGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTAC
** *
54993967 AAGGAGTAAATC
196 AAGGAACAAATT
** * *
54993979 GAAGACATAGCTGATTTGGCTTTTGCGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCATCT
1 GAAGACATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCT
* * *
54994044 CTGTATTATCAAGGAACAAATTGAAG
66 CTGTATTGTCAAAGAACAAATCGAAG
54994070 AAGCAGATTT
Statistics
Matches: 859, Mismatches: 59, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
206 121 0.14
207 738 0.86
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (207 bp):
GAAGACATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCT
CTGTATTGTCAAAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGC
AGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTAC
AAGGAACAAATT
Found at i:54994495 original size:19 final size:19
Alignment explanation
Indices: 54994467--54994528 Score: 97
Period size: 19 Copynumber: 3.2 Consensus size: 19
54994457 AATCTTTAAG
*
54994467 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
54994486 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
54994505 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
54994526 GAT
1 GAT
54994529 CTTGTAATCT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 31 0.77
21 9 0.22
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:54996149 original size:31 final size:30
Alignment explanation
Indices: 54996088--54996154 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
54996078 CTAGTCTTAC
*
54996088 ATCAACATAAAAGCCTAATTTATAAGAAAAA
1 ATCAA-ATAAAAGCCTAAGTTATAAGAAAAA
54996119 ATCAAATAAAAGCCTAAGTTATAAGAAAAA
1 ATCAAATAAAAGCCTAAGTTATAAGAAAAA
54996149 ATCAAA
1 ATCAAA
54996155 CTTTCTGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 30 0.86
31 5 0.14
ACGTcount: A:0.60, C:0.12, G:0.07, T:0.21
Consensus pattern (30 bp):
ATCAAATAAAAGCCTAAGTTATAAGAAAAA
Found at i:55001023 original size:15 final size:15
Alignment explanation
Indices: 55001003--55001036 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
55000993 GAAGAGGAAG
55001003 AAGAATAAGCCATGA
1 AAGAATAAGCCATGA
55001018 AAGAATAAGCCATGA
1 AAGAATAAGCCATGA
55001033 AAGA
1 AAGA
55001037 GTAGTTAAGG
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:0.56, C:0.12, G:0.21, T:0.12
Consensus pattern (15 bp):
AAGAATAAGCCATGA
Found at i:55001915 original size:3 final size:3
Alignment explanation
Indices: 55001902--55001944 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
55001892 ATTTCAAAGA
55001902 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55001945 GGCCTCAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:55018038 original size:5 final size:5
Alignment explanation
Indices: 55018028--55018059 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
55018018 ATTTGTGTTC
55018028 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
55018060 TCACATTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:55018042 original size:9 final size:9
Alignment explanation
Indices: 55018028--55018058 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
55018018 ATTTGTGTTC
55018028 TTTATTTTA
1 TTTATTTTA
55018037 TTTATTTTA
1 TTTATTTTA
55018046 TTTTATTTTA
1 -TTTATTTTA
55018056 TTT
1 TTT
55018059 TTCACATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:55020391 original size:17 final size:17
Alignment explanation
Indices: 55020371--55020406 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55020361 TCCTCTCTGA
55020371 TCTTAATTCCTTCTTCT
1 TCTTAATTCCTTCTTCT
**
55020388 TCTTTTTTCCTTCTTCT
1 TCTTAATTCCTTCTTCT
55020405 TC
1 TC
55020407 ACCTACTATT
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:0.06, C:0.31, G:0.00, T:0.64
Consensus pattern (17 bp):
TCTTAATTCCTTCTTCT
Found at i:55023959 original size:38 final size:38
Alignment explanation
Indices: 55023916--55024025 Score: 157
Period size: 38 Copynumber: 2.9 Consensus size: 38
55023906 AGATTGGTAC
* * *
55023916 TAAATGGCCCCTATGCAATGTTGTTTTCTTCTTGAATT
1 TAAATGGCCCCTATCCAATGTTGTTTTCTTCCTGAACT
* *
55023954 TAAATGGCCCCTGTCCAATGTTGTTTACTTCCTGAACT
1 TAAATGGCCCCTATCCAATGTTGTTTTCTTCCTGAACT
* *
55023992 TAAGTGGCCCCTTTCCAATGTTGTTTTCTTCCTG
1 TAAATGGCCCCTATCCAATGTTGTTTTCTTCCTG
55024026 TATCAAATGG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.42
Consensus pattern (38 bp):
TAAATGGCCCCTATCCAATGTTGTTTTCTTCCTGAACT
Found at i:55025146 original size:46 final size:46
Alignment explanation
Indices: 55025079--55025291 Score: 365
Period size: 46 Copynumber: 4.6 Consensus size: 46
55025069 ATCTTTGACA
* * * * *
55025079 TCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATCTT
1 TCAACCATGGTCTTACACA-TTTCATATCAGGCTGCCATGGTATCTT
55025125 TCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTT
1 TCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTT
55025171 TCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTT
1 TCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTT
55025217 TCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTT
1 TCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTT
55025263 TCAACCATGGTCTTACACATTTCATATCA
1 TCAACCATGGTCTTACACATTTCATATCA
55025292 AAGAGCACAC
Statistics
Matches: 161, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
45 4 0.02
46 157 0.98
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.37
Consensus pattern (46 bp):
TCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTT
Found at i:55035103 original size:17 final size:17
Alignment explanation
Indices: 55035081--55035116 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55035071 CAATGATTTC
* *
55035081 TTATTTATTTATTATTA
1 TTATTTAATAATTATTA
55035098 TTATTTAATAATTATTA
1 TTATTTAATAATTATTA
55035115 TT
1 TT
55035117 TATAGTATTT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTAATAATTATTA
Found at i:55035111 original size:14 final size:14
Alignment explanation
Indices: 55035085--55035118 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
55035075 GATTTCTTAT
*
55035085 TTATTT-ATTATTA
1 TTATTTAATAATTA
55035098 TTATTTAATAATTA
1 TTATTTAATAATTA
55035112 TTATTTA
1 TTATTTA
55035119 TAGTATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTAATAATTA
Found at i:55052630 original size:18 final size:18
Alignment explanation
Indices: 55052607--55052703 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
55052597 CAATCCCAAC
*
55052607 TACCGTATACGTGAACAG
1 TACCGTATACGTGAATAG
*
55052625 TACCGTATACGTGAATAA
1 TACCGTATACGTGAATAG
* *
55052643 TGCCGTATACATGAATAG
1 TACCGTATACGTGAATAG
*
55052661 TACCGTATACGTAAATAG
1 TACCGTATACGTGAATAG
* *
55052679 TGCTGTATACGTGAATAG
1 TACCGTATACGTGAATAG
55052697 TACCGTA
1 TACCGTA
55052704 AACGATCGTA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (18 bp):
TACCGTATACGTGAATAG
Found at i:55052663 original size:36 final size:36
Alignment explanation
Indices: 55052609--55052703 Score: 145
Period size: 36 Copynumber: 2.6 Consensus size: 36
55052599 ATCCCAACTA
* *
55052609 CCGTATACGTGAACAGTACCGTATACGTGAATAATG
1 CCGTATACGTGAATAGTACCGTATACGTAAATAATG
* *
55052645 CCGTATACATGAATAGTACCGTATACGTAAATAGTG
1 CCGTATACGTGAATAGTACCGTATACGTAAATAATG
*
55052681 CTGTATACGTGAATAGTACCGTA
1 CCGTATACGTGAATAGTACCGTA
55052704 AACGATCGTA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (36 bp):
CCGTATACGTGAATAGTACCGTATACGTAAATAATG
Found at i:55056226 original size:33 final size:33
Alignment explanation
Indices: 55056179--55056249 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
55056169 CCCAATACAT
*
55056179 CAAATATAATTTTTTATTTGGATAGAGTCTAAG
1 CAAATATAAATTTTTATTTGGATAGAGTCTAAG
55056212 CAAATATAAATTTTTATTTGGATAGAGTCTAAG
1 CAAATATAAATTTTTATTTGGATAGAGTCTAAG
*
55056245 TAAAT
1 CAAAT
55056250 GATGCTCAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (33 bp):
CAAATATAAATTTTTATTTGGATAGAGTCTAAG
Found at i:55061163 original size:21 final size:21
Alignment explanation
Indices: 55061137--55061180 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
55061127 AGACGAGCAA
* *
55061137 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
55061158 TACTCCAAAACAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
55061179 TA
1 TA
55061181 ACAGCCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:55062635 original size:16 final size:16
Alignment explanation
Indices: 55062602--55062635 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55062592 GGAGATTGTT
* *
55062602 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
55062618 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
55062634 AA
1 AA
55062636 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:55075663 original size:31 final size:31
Alignment explanation
Indices: 55075625--55075687 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
55075615 CTTTGTTGAA
55075625 GTTGGTAAATTAAAAGGGTGGCATATAGAAG
1 GTTGGTAAATTAAAAGGGTGGCATATAGAAG
55075656 GTTGGTAAATTAAAAGGGTGGCATATAGAAG
1 GTTGGTAAATTAAAAGGGTGGCATATAGAAG
55075687 G
1 G
55075688 AGGCAAATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.03, G:0.33, T:0.25
Consensus pattern (31 bp):
GTTGGTAAATTAAAAGGGTGGCATATAGAAG
Found at i:55077247 original size:11 final size:11
Alignment explanation
Indices: 55077231--55077261 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
55077221 ATACCCATAC
55077231 CCCATACCTTG
1 CCCATACCTTG
*
55077242 CCCATACCTTT
1 CCCATACCTTG
55077253 CCCATACCT
1 CCCATACCT
55077262 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:55077833 original size:18 final size:18
Alignment explanation
Indices: 55077806--55077898 Score: 159
Period size: 18 Copynumber: 5.2 Consensus size: 18
55077796 TACGACCGTT
55077806 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
55077824 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
55077842 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
55077860 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
55077878 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
55077896 TAC
1 TAC
55077899 AGTAGTTGGG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:55077853 original size:36 final size:36
Alignment explanation
Indices: 55077806--55077898 Score: 177
Period size: 36 Copynumber: 2.6 Consensus size: 36
55077796 TACGACCGTT
55077806 TACGGTACTATTCACGTATACGGCACTATTCACGTA
1 TACGGTACTATTCACGTATACGGCACTATTCACGTA
55077842 TACGGTACTATTCACGTATACGGCACTATTCACGTA
1 TACGGTACTATTCACGTATACGGCACTATTCACGTA
*
55077878 TACGGTACTGTTCACGTATAC
1 TACGGTACTATTCACGTATAC
55077899 AGTAGTTGGG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACGGCACTATTCACGTA
Found at i:55082539 original size:18 final size:18
Alignment explanation
Indices: 55082512--55082604 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
55082502 TACGACCGTT
55082512 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
55082530 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
55082548 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
55082566 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
55082584 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
55082602 TAC
1 TAC
55082605 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:55086674 original size:11 final size:11
Alignment explanation
Indices: 55086658--55086688 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
55086648 ATACCCATAC
55086658 CCCATACCTTG
1 CCCATACCTTG
*
55086669 CCCATACCTTT
1 CCCATACCTTG
55086680 CCCATACCT
1 CCCATACCT
55086689 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:55089815 original size:39 final size:38
Alignment explanation
Indices: 55089647--55089815 Score: 194
Period size: 39 Copynumber: 4.3 Consensus size: 38
55089637 TATTTTATGT
* * * *
55089647 GGATGAAGATCAGTTTGATGAGATGAGCAAAGATGTATC
1 GGATGAAGATCA-ATTGATGAGACGAGCAATGATGCATC
* * *
55089686 GGGTGAAGGTCAGATTGATGAGACGAGCAATGATGAATC
1 GGATGAAGATCA-ATTGATGAGACGAGCAATGATGCATC
* * *
55089725 AGATGAAGATCAGATTGATGAGACGAGCAGTGAGGCATC
1 GGATGAAGATCA-ATTGATGAGACGAGCAATGATGCATC
* *
55089764 GGATGAAGATCAATTTGATAAGACGAGCAGTGATGCATC
1 GGATGAAGATCAA-TTGATGAGACGAGCAATGATGCATC
55089803 GGATGAAGATCAA
1 GGATGAAGATCAA
55089816 GAAAAGTTCA
Statistics
Matches: 114, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
38 1 0.01
39 113 0.99
ACGTcount: A:0.36, C:0.11, G:0.32, T:0.21
Consensus pattern (38 bp):
GGATGAAGATCAATTGATGAGACGAGCAATGATGCATC
Found at i:55093408 original size:142 final size:142
Alignment explanation
Indices: 55092912--55094317 Score: 1691
Period size: 142 Copynumber: 9.9 Consensus size: 142
55092902 AAAAATGTGA
* *
55092912 TTGTTGTCATTGATGATGTTAATGACCCAGATTAGATAGATTGTATGAGTGTTAAATATTTTAGT
1 TTGTTGTCATTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
* * * *
55092977 GATGGAAGTAGAATTATTTTGACAACTCAAAATAGATAAAGATGGGTTAACTA-GGTAAAGGACT
66 GATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAAC-AGGGTAAAGGACT
55093041 TTCTT-AGGTCTT
130 TTCTTCAGGTCTT
* * *
55093053 TTGTTGTCATTGATGATGTTAATGGCCCATATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
1 TTGTTGTCATTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
* * * *
55093118 GATGGAAGTAGAATCATTGTAACATCT-AGAGATAGACAAAGATGGGTTAACAAGG-AAAAGAGC
66 GATGGAAGTAGAATCATTGTAACATCTCA-AAATAGATAAAGATGGGTTAACAGGGTAAAGGA-C
55093181 TTTCTTCAGGTC--
129 TTTCTTCAGGTCTT
*
55093193 -TGTTGTCCTTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
1 TTGTTGTCATTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
* *
55093257 GATGGAAGTAGAACCATTATAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACTT
66 GATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACTT
*
55093322 TCTTCAAGTCTT
131 TCTTCAGGTCTT
* * * *
55093334 TTGTTGTCATTGATGATGTTAATGACCCAGATTAGATAGATTGTATGGGTATTTAATATTTTGGT
1 TTGTTGTCATTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
* * * * * *
55093399 GATGGAAGTAG-ATCCATTGTAACATCTCGAGATAGACAAAGATGGGTTAACAAGGAAAATGACT
66 GATGGAAGTAGAAT-CATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACT
*
55093463 TTCTTTAGGTC--
130 TTCTTCAGGTCTT
* * * *
55093474 -TGTTGTCCTTGATGATATTAATGACCCAAAATTCGATAGATTGTATGGGTATTAAATATTTTAG
1 TTGTTGTCATTGATGATATTAATGACCC-AGATTAGATAGATTGTATGGGTGTTAAATATTTTAG
55093538 TGATGGGTTGAAGAATCTTATTAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTA
65 TGA-----TG--G------A--AGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTA
* *
55093603 ATAAGGTAAAGGACTTTCTTCAGGTCTT
115 ACAGGGTAAAGGACTTTCTTCAGGTCTT
* * * *
55093631 TTGTTGTCATTGATGATGTTAATAACCGAGATTAGATAGATTGTATGGGTGTTAAATATTTTGGT
1 TTGTTGTCATTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
* * * * * * *
55093696 GATGGAAGTCGAATCATTGTAACATCTCGAGATAGACAAAGACGGGTTAACAGGGAAAAGGATTT
66 GATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACTT
55093761 TCTTCAGG-C--
131 TCTTCAGGTCTT
* * * * *
55093770 CTGTTGTCCTTAATGATATTAATGACCTAGATTAGATAGATTGTATGGGTGTTAAATATTCTT-C
1 TTGTTGTCATTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATT-TTAG
* * * * *
55093834 TGATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAATGTTTGGTTAATAGTGTAAACGG-C
65 TGATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAA-GGAC
55093898 TTTCTTCAGGTCTT
129 TTTCTTCAGGTCTT
*
55093912 TTGTTGTCATTGATGATATTAATGACTCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
1 TTGTTGTCATTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
* * * *
55093977 GATGGAAGTAGAGTCATTATAAAATCTCAAAATAGATAAAGATGGGTTAACAAGGTAAAGGACTT
66 GATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACTT
*
55094042 TCTTCTGGTCTT
131 TCTTCAGGTCTT
* *
55094054 TTGTTGTCATTGATGATGTTAATGACCCAGATT-GAATAGATTGTATGGGTGTTAAATATGTTAA
1 TTGTTGTCATTGATGATATTAATGACCCAGATTAG-ATAGATTGTATGGGTGTTAAATAT-TTTA
* * * * *
55094118 GTGATAGAAGTAGAATCATTGTAACATCTCTAGATAGACAAAGAT--G-----AGGGAAAAGGAC
64 GTGATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGAC
55094176 TTT-TTGCAGG-C--
129 TTTCTT-CAGGTCTT
* * * * * *
55094187 CTGTTGTCCTTAATAATATTAATGACTCTA-ATTAGATAGATTTTATGGGTGTTAAATATTTTAG
1 TTGTTGTCATTGATGATATTAATGAC-CCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAG
* *
55094251 AGATGGAAGTAGAATCATTGTAACTTCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACT
65 TGATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACT
55094316 TT
130 TT
55094318 GCTTAATCTT
Statistics
Matches: 1087, Mismatches: 129, Indels: 100
0.83 0.10 0.08
Matches are distributed among these distances:
132 42 0.04
133 47 0.04
134 4 0.00
135 3 0.00
136 16 0.01
139 272 0.25
140 53 0.05
141 122 0.11
142 360 0.33
143 41 0.04
144 1 0.00
145 2 0.00
147 1 0.00
150 1 0.00
152 2 0.00
153 1 0.00
155 59 0.05
156 2 0.00
157 35 0.03
158 23 0.02
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.35
Consensus pattern (142 bp):
TTGTTGTCATTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
GATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACTT
TCTTCAGGTCTT
Done.