Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 187 of 218
Found at i:55676541 original size:25 final size:24
Alignment explanation
Indices: 55676481--55676548 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 24
55676471 TTTTATTAAA
*
55676481 TTATATATTTTTATTAAATTAATT
1 TTATATATTATTATTAAATTAATT
*
55676505 TAATAATAATTATT-TTAAATTATATT
1 TTAT-AT-ATTATTATTAAATTA-ATT
55676531 TTATAGTATTATATATTA
1 TTATA-TATTAT-TATTA
55676549 TGATTTTAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
24 3 0.09
25 16 0.46
26 13 0.37
27 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (24 bp):
TTATATATTATTATTAAATTAATT
Found at i:55681923 original size:40 final size:40
Alignment explanation
Indices: 55681860--55681956 Score: 133
Period size: 40 Copynumber: 2.4 Consensus size: 40
55681850 TGGCGTTTGG
*
55681860 ACAATAAACGCCGCTAAAAATCGA-ATATTAGCGGCGCATCT
1 ACAA-AAACGCCGCTAAAAATCGAGA-ATTAGCGGCACATCT
* *
55681901 ACAAAAACGCCGCTAAAGATCGAGAATTAGCGGCACATTT
1 ACAAAAACGCCGCTAAAAATCGAGAATTAGCGGCACATCT
*
55681941 ACGAAAACGCCGCTAA
1 ACAAAAACGCCGCTAA
55681957 TAATAAGCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 46 0.90
41 5 0.10
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (40 bp):
ACAAAAACGCCGCTAAAAATCGAGAATTAGCGGCACATCT
Found at i:55682279 original size:113 final size:111
Alignment explanation
Indices: 55681967--55682280 Score: 373
Period size: 114 Copynumber: 2.8 Consensus size: 111
55681957 TAATAAGCAA
* * *
55681967 TAGCGGCGATTTATGAAAAGCGCCGCAAAAAACATAAGGCCAACGACGCCGTTTACTGAGTTTTT
1 TAGCGGCGATTTATAAAAAGCGCCGCAAAAAACCTAAGGCCAACGACGCCGTTTTCTGAGTTTTT
* * *
55682032 GGGCCTTTAGCGGCATTTTTAGAAAAACGCCGCTAATGCTCGGGGGACT
66 GGGCCTTTAGCGGCGTTTTT-GAAAAACACCGCTAATGCTC--GCGACT
* *
55682081 TAGCGGCGATTTATAAAAAGCGCCGCAAAAAACCTAATGCCAACGACGTCG-TTTCTGAGTTTTT
1 TAGCGGCGATTTATAAAAAGCGCCGCAAAAAACCTAAGGCCAACGACGCCGTTTTCTGAGTTTTT
** * *
55682145 GTCCCTGTT-GCGGCGCTTTTTGAAAAGCACCGCTAATGCTC-CTATCTT
66 GGGCCT-TTAGCGGCG-TTTTTGAAAAACACCGCTAATGCTCGCGA-C-T
* * * * **
55682193 TATCGGCGTTTTCTTAAAAGCGCCGCAAAAAAACCTAAGGCCAACGACGCCGTTTTCTTTGTTTT
1 TAGCGGCGATTTATAAAAAGCGCCGC-AAAAAACCTAAGGCCAACGACGCCGTTTTCTGAGTTTT
55682258 TGGGCCTTTAGCGGCGTTTTTGA
65 TGGGCCTTTAGCGGCGTTTTTGA
55682281 GGAAGTGCCT
Statistics
Matches: 171, Mismatches: 22, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
110 1 0.01
111 1 0.01
112 23 0.13
113 71 0.42
114 75 0.44
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28
Consensus pattern (111 bp):
TAGCGGCGATTTATAAAAAGCGCCGCAAAAAACCTAAGGCCAACGACGCCGTTTTCTGAGTTTTT
GGGCCTTTAGCGGCGTTTTTGAAAAACACCGCTAATGCTCGCGACT
Found at i:55683261 original size:14 final size:14
Alignment explanation
Indices: 55683210--55683274 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
55683200 ATTTTTGGTT
55683210 TTTGAG-TTTGGGG
1 TTTGAGTTTTGGGG
55683223 TTT-AGTTTTCGGGG
1 TTTGAGTTTT-GGGG
* * *
55683237 TTTGTGGTTTGTGG
1 TTTGAGTTTTGGGG
*
55683251 TTTGAGTTTTGGGTT
1 TTTGAGTTTTGGG-G
55683266 TTTGAGTTT
1 TTTGAGTTT
55683275 AGGGTTTAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
12 2 0.05
13 6 0.15
14 20 0.49
15 13 0.32
ACGTcount: A:0.06, C:0.02, G:0.37, T:0.55
Consensus pattern (14 bp):
TTTGAGTTTTGGGG
Found at i:55683271 original size:15 final size:15
Alignment explanation
Indices: 55683251--55683281 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55683241 TGGTTTGTGG
*
55683251 TTTGAGTTTTGGGTT
1 TTTGAGTTTAGGGTT
55683266 TTTGAGTTTAGGGTT
1 TTTGAGTTTAGGGTT
55683281 T
1 T
55683282 AATGTTTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.00, G:0.32, T:0.58
Consensus pattern (15 bp):
TTTGAGTTTAGGGTT
Found at i:55683274 original size:28 final size:27
Alignment explanation
Indices: 55683201--55683282 Score: 94
Period size: 28 Copynumber: 3.0 Consensus size: 27
55683191 ATGATTGGGA
*
55683201 TTTTTGGTTTTTGAGTTTGGGGTTTAG
1 TTTTGGGTTTTTGAGTTTGGGGTTTAG
* *
55683228 TTTTCGGGGTTTGTG-GTTTGTGGTTTGAG
1 TTTT--GGGTTTTTGAGTTTGGGGTTT-AG
*
55683257 TTTTGGGTTTTTGAGTTTAGGGTTTA
1 TTTTGGGTTTTTGAGTTTGGGGTTTA
55683283 ATGTTTGAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
27 13 0.29
28 19 0.42
29 13 0.29
ACGTcount: A:0.07, C:0.01, G:0.35, T:0.56
Consensus pattern (27 bp):
TTTTGGGTTTTTGAGTTTGGGGTTTAG
Found at i:55683289 original size:28 final size:27
Alignment explanation
Indices: 55683206--55683294 Score: 67
Period size: 28 Copynumber: 3.1 Consensus size: 27
55683196 TGGGATTTTT
*
55683206 GGTTTTTGAGTTTGGGGTTTAGT-TTTCGG
1 GGTTTTTGAGTTT-GGGTTTAATGTTT--G
* *
55683235 GGTTTGTG-GTTTGTGGTTTGA-GTTTTG
1 GGTTTTTGAGTTTG-GGTTTAATG-TTTG
55683262 GGTTTTTGAGTTTAGGGTTTAATGTTTG
1 GGTTTTTGAGTTT-GGGTTTAATGTTTG
55683290 AGGTT
1 -GGTT
55683295 AGGGGTTTGG
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
27 9 0.19
28 23 0.48
29 16 0.33
ACGTcount: A:0.09, C:0.01, G:0.37, T:0.53
Consensus pattern (27 bp):
GGTTTTTGAGTTTGGGTTTAATGTTTG
Found at i:55684353 original size:19 final size:19
Alignment explanation
Indices: 55684331--55684374 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
55684321 CTCTCATCTC
*
55684331 CCCCAAATCCCTAAAATTT
1 CCCCAAATCCCTAAAAGTT
* *
55684350 CCCCTAATCCCTAACAGTT
1 CCCCAAATCCCTAAAAGTT
55684369 CCCCAA
1 CCCCAA
55684375 CGTAGTCCAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.43, G:0.02, T:0.23
Consensus pattern (19 bp):
CCCCAAATCCCTAAAAGTT
Found at i:55686558 original size:18 final size:18
Alignment explanation
Indices: 55686500--55686559 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
55686490 TAAAAAATCG
55686500 AATTACATAACTTATACA
1 AATTACATAACTTATACA
** *
55686518 ATATTA-AGGTAAAATAT-CG
1 A-ATTACA--TAACTTATACA
55686537 AATTACATAACTTATACA
1 AATTACATAACTTATACA
55686555 AATTA
1 AATTA
55686560 AGATAAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 10
0.66 0.13 0.21
Matches are distributed among these distances:
17 6 0.19
18 12 0.39
19 7 0.23
20 6 0.19
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (18 bp):
AATTACATAACTTATACA
Found at i:55686567 original size:36 final size:37
Alignment explanation
Indices: 55686466--55686598 Score: 205
Period size: 37 Copynumber: 3.6 Consensus size: 37
55686456 TAACATAACA
* * *
55686466 TACATAACTTATATAATGTTAAGATAAAAAATCGAAT
1 TACATAACTTATACAATATTAAGATAAAATATCGAAT
*
55686503 TACATAACTTATACAATATTAAGGTAAAATATCGAAT
1 TACATAACTTATACAATATTAAGATAAAATATCGAAT
*
55686540 TACATAACTTATACAA-ATTAAGATAAAATTTCGAAT
1 TACATAACTTATACAATATTAAGATAAAATATCGAAT
*
55686576 TACATAACTTATATAATATTAAG
1 TACATAACTTATACAATATTAAG
55686599 GTTACTTTTA
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
36 33 0.38
37 55 0.62
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.34
Consensus pattern (37 bp):
TACATAACTTATACAATATTAAGATAAAATATCGAAT
Found at i:55686626 original size:57 final size:57
Alignment explanation
Indices: 55686543--55687052 Score: 551
Period size: 57 Copynumber: 9.1 Consensus size: 57
55686533 ATCGAATTAC
*
55686543 ATAACTTATACAA-ATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAG
1 ATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAG
* * * *
55686599 GTTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTAAG
1 ATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAG
** * *
55686656 ATTGCTTATATAATATTAAGATAAAATTTCTAATTACATAACTTATATAATATT-AC
1 ATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAG
* * *
55686712 ATAACTTATATAATGTTAAGATAAAATATCGAATTACATAACTTATACAATATTAAG
1 ATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAG
* * * * * * * ** *
55686769 ATAAAATT-T-TGA-ATT-ACAT-AACTTATACAATATTAAGATAAAATT-T-CGA-ATT-AC
1 AT-AACTTATATAATATTAAGATAAAATT-T-CGA-ATT-ACAT-AACTTATATAATATTAAG
* * *
55686823 ATAACTTATACAATATTAAGGTAAAATTCCGAATTACATAACTTATATAATATTAAG
1 ATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAG
* * *
55686880 ATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTAAG
1 ATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAG
** * *
55686937 ATTGCTTATATAATATTAAGAT-AAATTTCTAATTACATAACTTATATAATATT-AC
1 ATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAG
* * * *
55686992 ATAACTTATACAATGTTAAGATAAAATATCGAATTACATAACTTATACAATATTAAG
1 ATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAG
55687049 ATAA
1 ATAA
55687053 AATTTCGAAT
Statistics
Matches: 375, Mismatches: 60, Indels: 37
0.79 0.13 0.08
Matches are distributed among these distances:
53 11 0.03
54 12 0.03
55 31 0.08
56 131 0.35
57 178 0.47
58 12 0.03
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (57 bp):
ATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAG
Found at i:55686665 original size:20 final size:20
Alignment explanation
Indices: 55686640--55686677 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
55686630 AATTACATAA
55686640 CTTATATAATATTAAGATTG
1 CTTATATAATATTAAGATTG
55686660 CTTATATAATATTAAGAT
1 CTTATATAATATTAAGAT
55686678 AAAATTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (20 bp):
CTTATATAATATTAAGATTG
Found at i:55686757 original size:37 final size:37
Alignment explanation
Indices: 55686707--55686881 Score: 287
Period size: 37 Copynumber: 4.7 Consensus size: 37
55686697 CTTATATAAT
* * *
55686707 ATTACATAACTTATATAATGTTAAGATAAAATATCGA
1 ATTACATAACTTATACAATATTAAGATAAAATTTCGA
*
55686744 ATTACATAACTTATACAATATTAAGATAAAATTTTGA
1 ATTACATAACTTATACAATATTAAGATAAAATTTCGA
55686781 ATTACATAACTTATACAATATTAAGATAAAATTTCGA
1 ATTACATAACTTATACAATATTAAGATAAAATTTCGA
* *
55686818 ATTACATAACTTATACAATATTAAGGTAAAATTCCGA
1 ATTACATAACTTATACAATATTAAGATAAAATTTCGA
*
55686855 ATTACATAACTTATATAATATTAAGAT
1 ATTACATAACTTATACAATATTAAGAT
55686882 TACTTTTATA
Statistics
Matches: 129, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 129 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (37 bp):
ATTACATAACTTATACAATATTAAGATAAAATTTCGA
Found at i:55686891 original size:20 final size:20
Alignment explanation
Indices: 55686863--55686958 Score: 83
Period size: 20 Copynumber: 5.0 Consensus size: 20
55686853 GAATTACATA
55686863 ACTTATATAATATTAAGATT
1 ACTTATATAATATTAAGATT
* *
55686883 ACTTTTATAATATTAAGATCA
1 ACTTATATAATATTAAGAT-T
* ** * *
55686904 AATT-T-CGA-ATT-ACATA
1 ACTTATATAATATTAAGATT
55686920 ACTTATATAATATTAAGATT
1 ACTTATATAATATTAAGATT
*
55686940 GCTTATATAATATTAAGAT
1 ACTTATATAATATTAAGAT
55686959 AAATTTCTAA
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
16 4 0.07
17 4 0.07
18 4 0.07
19 4 0.07
20 40 0.68
21 3 0.05
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (20 bp):
ACTTATATAATATTAAGATT
Found at i:55686974 original size:280 final size:280
Alignment explanation
Indices: 55686466--55687199 Score: 1139
Period size: 280 Copynumber: 2.7 Consensus size: 280
55686456 TAACATAACA
* * ** *
55686466 TACATAACTTATATAATGTTAAGATAAAAAATCGAATTACATAACTTATACAATATTAAGGTAAA
1 TACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATACAATATTAAGATAAA
55686531 ATATCGAATTACATAACTTATACAA-ATTAAGATAAAATTTCGAATTACATAACTTATATAATAT
66 AT-TCGAATTACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAATAT
*
55686595 TAAGGTTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTAAGATTG
130 TAAGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTAAGATTG
*
55686660 CTTATATAATATTAAGATAAAATTTCTAATTACATAACTTATATAATATTACATAACTTATATAA
195 CTTATATAATATTAAGATAAAATTTCTAATTACATAACTTATATAATATTACATAACTTATACAA
55686725 TGTTAAGATAAAATATCGAAT
260 TGTTAAGATAAAATATCGAAT
*
55686746 TACATAACTTATACAATATTAAGATAAAATTTTGAATTACATAACTTATACAATATTAAGATAAA
1 TACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATACAATATTAAGATAAA
* *
55686811 ATTTCGAATTACATAACTTATACAATATTAAGGTAAAATTCCGAATTACATAACTTATATAATAT
66 A-TTCGAATTACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAATAT
55686876 TAAGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTAAGATTG
130 TAAGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTAAGATTG
55686941 CTTATATAATATTAAGAT-AAATTTCTAATTACATAACTTATATAATATTACATAACTTATACAA
195 CTTATATAATATTAAGATAAAATTTCTAATTACATAACTTATATAATATTACATAACTTATACAA
55687005 TGTTAAGATAAAATATCGAAT
260 TGTTAAGATAAAATATCGAAT
55687026 TACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAAC---T----TA-T---AT--A
1 TACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATACAATATTAAGATAAA
* *
55687078 A-T---ATTACATAACTTATATAATATTAAGATAAAATTTCTAATTACATAACTTATATAATATT
66 ATTCGAATTACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATT
* * * * * * *
55687139 -ACATAACTTATATAATGTTAAGATAAAATATCGAATTACATAACTTATACAATATTAAGAT
131 AAGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTAAGAT
55687200 AAAATTTCGA
Statistics
Matches: 430, Mismatches: 22, Indels: 23
0.91 0.05 0.05
Matches are distributed among these distances:
261 54 0.13
262 55 0.13
265 1 0.00
267 2 0.00
269 2 0.00
272 1 0.00
273 2 0.00
277 1 0.00
280 192 0.45
281 120 0.28
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (280 bp):
TACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATACAATATTAAGATAAA
ATTCGAATTACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATT
AAGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTAAGATTGC
TTATATAATATTAAGATAAAATTTCTAATTACATAACTTATATAATATTACATAACTTATACAAT
GTTAAGATAAAATATCGAAT
Found at i:55687037 original size:37 final size:37
Alignment explanation
Indices: 55686987--55687310 Score: 342
Period size: 37 Copynumber: 8.7 Consensus size: 37
55686977 CTTATATAAT
*
55686987 ATTACATAACTTATACAATGTTAAGATAAAATATCGA
1 ATTACATAACTTATACAATATTAAGATAAAATATCGA
*
55687024 ATTACATAACTTATACAATATTAAGATAAAATTTCGA
1 ATTACATAACTTATACAATATTAAGATAAAATATCGA
* * * *
55687061 ATTACATAACTTATATAATATT-ACATAACTTATAT-AA
1 ATTACATAACTTATACAATATTAAGATAA--AATATCGA
* * * * * *
55687098 TATTAAGATAAAATT-T-CTA-ATT-ACATAACTTATAT-AA
1 -ATT-ACAT-AACTTATACAATATTAAGATAA--AATATCGA
* *
55687135 TATTACATAACTTATATAATGTTAAGATAAAATATCGA
1 -ATTACATAACTTATACAATATTAAGATAAAATATCGA
*
55687173 ATTACATAACTTATACAATATTAAGATAAAATTTCGA
1 ATTACATAACTTATACAATATTAAGATAAAATATCGA
*
55687210 ATTACATAACTTATACAATATTAAGATAAAATTTCGA
1 ATTACATAACTTATACAATATTAAGATAAAATATCGA
55687247 ATTACATAACTTATACAATATTAA-AGTAAAAT-TCCGA
1 ATTACATAACTTATACAATATTAAGA-TAAAATAT-CGA
*
55687284 ATTACATAACTTATATAATATTAAGAT
1 ATTACATAACTTATACAATATTAAGAT
55687311 TACTTTTATA
Statistics
Matches: 251, Mismatches: 23, Indels: 26
0.84 0.08 0.09
Matches are distributed among these distances:
35 4 0.02
36 11 0.04
37 212 0.84
38 11 0.04
39 9 0.04
40 4 0.02
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.36
Consensus pattern (37 bp):
ATTACATAACTTATACAATATTAAGATAAAATATCGA
Found at i:55687064 original size:93 final size:92
Alignment explanation
Indices: 55686941--55687269 Score: 432
Period size: 93 Copynumber: 3.5 Consensus size: 92
55686931 ATTAAGATTG
* *
55686941 CTTATATAATATTAAGATAAATTTCTAATTACATAACTTATATAATATTACATAACTTATACAAT
1 CTTATACAATATTAAGATAAATTTCGAATTACATAACTTATATAATATTACATAACTTATACAAT
* *
55687006 GTTAAGATAAAATATCGAATTACATAA
66 ATTAAGATAAAATTTCGAATTACATAA
*
55687033 CTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTACATAACTTATATAA
1 CTTATACAATATTAAGAT-AAATTTCGAATTACATAACTTATATAATATTACATAACTTATACAA
*
55687098 TATTAAGATAAAATTTCTAATTACATAA
65 TATTAAGATAAAATTTCGAATTACATAA
* * * ** * * *
55687126 CTTATATAATATT-ACATAACTTATATAATGTTAAGATAA--AATATCGA-ATTACATAACTTAT
1 CTTATACAATATTAAGATAAATT-TCGAA--TT-ACATAACTTATAT-AATATTACATAACTTAT
55687187 ACAATATTAAGATAAAATTTCGAATTACATAA
61 ACAATATTAAGATAAAATTTCGAATTACATAA
*
55687219 CTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATACAATATTA
1 CTTATACAATATTAAGAT-AAATTTCGAATTACATAACTTATATAATATTA
55687270 AAGTAAAATT
Statistics
Matches: 201, Mismatches: 25, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
91 9 0.04
92 26 0.13
93 148 0.74
94 9 0.04
95 9 0.04
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (92 bp):
CTTATACAATATTAAGATAAATTTCGAATTACATAACTTATATAATATTACATAACTTATACAAT
ATTAAGATAAAATTTCGAATTACATAA
Found at i:55687070 original size:149 final size:150
Alignment explanation
Indices: 55686891--55687238 Score: 628
Period size: 149 Copynumber: 2.3 Consensus size: 150
55686881 TTACTTTTAT
* **
55686891 AATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTAAGATTGCTTATATAATATTAA
1 AATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATAACTTATATAATATTAA
55686956 GAT-AAATTTCTAATTACATAACTTATATAATATTACATAACTTATACAATGTTAAGATAAAATA
66 GATAAAATTTCTAATTACATAACTTATATAATATTACATAACTTATACAATGTTAAGATAAAATA
55687020 TCGAATTACATAACTTATAC
131 TCGAATTACATAACTTATAC
*
55687040 AATATTAAGATAAAATTTCGAATTACATAACTTATATAATATT-ACATAACTTATATAATATTAA
1 AATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATAACTTATATAATATTAA
*
55687104 GATAAAATTTCTAATTACATAACTTATATAATATTACATAACTTATATAATGTTAAGATAAAATA
66 GATAAAATTTCTAATTACATAACTTATATAATATTACATAACTTATACAATGTTAAGATAAAATA
55687169 TCGAATTACATAACTTATAC
131 TCGAATTACATAACTTATAC
*
55687189 AATATTAAGATAAAATTTCGAATTACATAACTTATACAATATTAAGATAA
1 AATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATAA
55687239 AATTTCGAAT
Statistics
Matches: 190, Mismatches: 7, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
148 21 0.11
149 164 0.86
150 5 0.03
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (150 bp):
AATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATAACTTATATAATATTAA
GATAAAATTTCTAATTACATAACTTATATAATATTACATAACTTATACAATGTTAAGATAAAATA
TCGAATTACATAACTTATAC
Found at i:55687084 original size:56 final size:56
Alignment explanation
Indices: 55687024--55687367 Score: 312
Period size: 56 Copynumber: 6.2 Consensus size: 56
55687014 AAAATATCGA
55687024 ATTACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAAT
1 ATTACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAAT
* *
55687080 ATTACATAACTTATATAATATTAAGATAAAATTTCTAATTACATAACTTATATAAT
1 ATTACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAAT
* * * *
55687136 ATTACATAACTTATATAATGTTAAGATAAAATATCGAATTACATAACTTATACAAT
1 ATTACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAAT
* * * * * * * * **
55687192 ATTAAGATAAAATT-T-CGA-ATT-ACAT-AACTTATACAATATTAAGATAAAATT-T-CGA-
1 ATT-ACAT-AACTTATACAATATTAAGATAAAATT-T-CGA-ATT-ACAT-AACTTATATAAT
*
55687247 ATTACATAACTTATACAATATTAA-AGTAAAATTCCGAATTACATAACTTATATAAT
1 ATTACATAACTTATACAATATTAAGA-TAAAATTTCGAATTACATAACTTATATAAT
* * * * * * *
55687303 ATTAAGATTACTTTTATAATATTAAGATCAAATTTCAAATTACATAACTTAAATAA-
1 ATT-ACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAAT
*
55687359 CTTACATAA
1 ATTACATAA
55687368 TACATAACCT
Statistics
Matches: 231, Mismatches: 39, Indels: 37
0.75 0.13 0.12
Matches are distributed among these distances:
53 11 0.05
54 12 0.05
55 17 0.07
56 126 0.55
57 52 0.23
58 13 0.06
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.37
Consensus pattern (56 bp):
ATTACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAAT
Found at i:55687320 original size:20 final size:20
Alignment explanation
Indices: 55687292--55687330 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
55687282 GAATTACATA
55687292 ACTTATATAATATTAAGATT
1 ACTTATATAATATTAAGATT
*
55687312 ACTTTTATAATATTAAGAT
1 ACTTATATAATATTAAGAT
55687331 CAAATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (20 bp):
ACTTATATAATATTAAGATT
Found at i:55687402 original size:34 final size:34
Alignment explanation
Indices: 55687343--55687607 Score: 255
Period size: 34 Copynumber: 7.7 Consensus size: 34
55687333 AATTTCAAAT
* *
55687343 TACATAACTTAAATAACTTACATAATACATAACC
1 TACATAACTTACATAACTTACATAATACATAGCC
* * * * *
55687377 TTCCTAACTTACATTATTTAGATAATACATAGCC
1 TACATAACTTACATAACTTACATAATACATAGCC
* *
55687411 TACATAACTTACATAACTTCCATAAATTAAATAGCC
1 TACATAACTTACATAACTTACAT-AA-TACATAGCC
* * *
55687447 TGCATAACTTAAATAACTTACATAATACATAACC
1 TACATAACTTACATAACTTACATAATACATAGCC
* * * * *
55687481 TTCCTAACTTACATTATTTAGATAATACATAGCC
1 TACATAACTTACATAACTTACATAATACATAGCC
* * *
55687515 TACATAACTTACATAACTTACATAAATTAAATAACT
1 TACATAACTTACATAACTTACAT-AA-TACATAGCC
* * * * *
55687551 TGCATAACTTACATAACTCACATAATACACAACT
1 TACATAACTTACATAACTTACATAATACATAGCC
55687585 TACATAACTTACATAA--TACATAA
1 TACATAACTTACATAACTTACATAA
55687608 CCTTCCTATC
Statistics
Matches: 187, Mismatches: 40, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
32 6 0.03
34 118 0.63
35 8 0.04
36 55 0.29
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.32
Consensus pattern (34 bp):
TACATAACTTACATAACTTACATAATACATAGCC
Found at i:55687423 original size:9 final size:9
Alignment explanation
Indices: 55687342--55687637 Score: 199
Period size: 9 Copynumber: 34.1 Consensus size: 9
55687332 AAATTTCAAA
55687342 TTACATAAC
1 TTACATAAC
*
55687351 TTAAATAAC
1 TTACATAAC
55687360 TTACATAA-
1 TTACATAAC
55687368 -TACATAACC
1 TTACATAA-C
*
55687377 TT-CCTAAC
1 TTACATAAC
* *
55687385 TTACATTAT
1 TTACATAAC
*
55687394 TTAGATAA-
1 TTACATAAC
*
55687402 -TACATAGC
1 TTACATAAC
*
55687410 CTACATAAC
1 TTACATAAC
55687419 TTACATAAC
1 TTACATAAC
* *
55687428 TTCCATAAA
1 TTACATAAC
* *
55687437 TTAAATAGC
1 TTACATAAC
* *
55687446 CTGCATAAC
1 TTACATAAC
*
55687455 TTAAATAAC
1 TTACATAAC
55687464 TTACATAA-
1 TTACATAAC
55687472 -TACATAACC
1 TTACATAA-C
*
55687481 TT-CCTAAC
1 TTACATAAC
* *
55687489 TTACATTAT
1 TTACATAAC
*
55687498 TTAGATAA-
1 TTACATAAC
*
55687506 -TACATAGC
1 TTACATAAC
*
55687514 CTACATAAC
1 TTACATAAC
55687523 TTACATAAC
1 TTACATAAC
*
55687532 TTACATAAA
1 TTACATAAC
*
55687541 TTAAATAAC
1 TTACATAAC
*
55687550 TTGCATAAC
1 TTACATAAC
55687559 TTACATAAC
1 TTACATAAC
*
55687568 TCACATAA-
1 TTACATAAC
*
55687576 -TACACAAC
1 TTACATAAC
55687584 TTACATAAC
1 TTACATAAC
55687593 TTACATAA-
1 TTACATAAC
55687601 -TACATAACC
1 TTACATAA-C
* *
55687610 TT-CCTATC
1 TTACATAAC
*
55687618 ATATCATAAC
1 TTA-CATAAC
55687628 TTACATAAC
1 TTACATAAC
55687637 T
1 T
55687638 CATTTATAGT
Statistics
Matches: 216, Mismatches: 52, Indels: 38
0.71 0.17 0.12
Matches are distributed among these distances:
7 36 0.17
8 8 0.04
9 163 0.75
10 9 0.04
ACGTcount: A:0.43, C:0.22, G:0.02, T:0.33
Consensus pattern (9 bp):
TTACATAAC
Found at i:55687464 original size:104 final size:104
Alignment explanation
Indices: 55687345--55687598 Score: 429
Period size: 104 Copynumber: 2.4 Consensus size: 104
55687335 TTTCAAATTA
55687345 CATAACTTAAATAACTTACATAATACATAACCTTCCTAACTTACATTATTTAGATAATACATAGC
1 CATAACTTAAATAACTTACATAATACATAACCTTCCTAACTTACATTATTTAGATAATACATAGC
* *
55687410 CTACATAACTTACATAACTTCCATAAATTAAATAGCCTG
66 CTACATAACTTACATAACTTACATAAATTAAATAACCTG
55687449 CATAACTTAAATAACTTACATAATACATAACCTTCCTAACTTACATTATTTAGATAATACATAGC
1 CATAACTTAAATAACTTACATAATACATAACCTTCCTAACTTACATTATTTAGATAATACATAGC
*
55687514 CTACATAACTTACATAACTTACATAAATTAAATAACTTG
66 CTACATAACTTACATAACTTACATAAATTAAATAACCTG
* * * *
55687553 CATAACTTACATAACTCACATAATACACAA-CTTACATAACTTACAT
1 CATAACTTAAATAACTTACATAATACATAACCTT-CCTAACTTACAT
55687599 AATACATAAC
Statistics
Matches: 142, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
103 3 0.02
104 139 0.98
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (104 bp):
CATAACTTAAATAACTTACATAATACATAACCTTCCTAACTTACATTATTTAGATAATACATAGC
CTACATAACTTACATAACTTACATAAATTAAATAACCTG
Found at i:55693111 original size:21 final size:21
Alignment explanation
Indices: 55693085--55693134 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
55693075 CTACAACTTA
* *
55693085 AAGCAGATGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
*
55693106 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
55693127 AAGCAGAG
1 AAGCAGAG
55693135 CAGAGCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.18, G:0.44, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:55693609 original size:42 final size:42
Alignment explanation
Indices: 55693448--55693606 Score: 214
Period size: 42 Copynumber: 3.8 Consensus size: 42
55693438 CGTTTTTGTA
* **
55693448 AAAAAACACCGCTAAAGACCATGTTCTTTAGCAACGCTTATT
1 AAAAAACACCGCTAAAGACCATGTTCTTTAGCGACGCTTAAG
*
55693490 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGACGCTT-AG
1 AAAAAACACCGCTAAAGACCATGTTCTTTAGCGACGCTTAAG
*
55693531 AAAAAA-ATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAG
1 AAAAAACA--CCGCTAAAGACCATGTTCTTTAGCGACGCTTAAG
* * *
55693574 AAAAAACACCGCTAAAGAACACGATCTTTAGCG
1 AAAAAACACCGCTAAAGACCATGTTCTTTAGCG
55693607 GCGTTTTTGT
Statistics
Matches: 104, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
41 6 0.06
42 89 0.86
43 8 0.08
44 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (42 bp):
AAAAAACACCGCTAAAGACCATGTTCTTTAGCGACGCTTAAG
Found at i:55696233 original size:18 final size:18
Alignment explanation
Indices: 55696210--55696269 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
55696200 ATGTAATTCT
55696210 AATGTAATTCTAATATAG
1 AATGTAATTCTAATATAG
* * **
55696228 AATGTAA-AC-AATTTTCT
1 AATGTAATTCTAA-TATAG
*
55696245 TATGTAATTCTAATATAG
1 AATGTAATTCTAATATAG
55696263 AATGTAA
1 AATGTAA
55696270 CTTGTTTTAA
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 2 0.07
17 9 0.31
18 16 0.55
19 2 0.07
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (18 bp):
AATGTAATTCTAATATAG
Found at i:55696533 original size:43 final size:43
Alignment explanation
Indices: 55696472--55696590 Score: 170
Period size: 43 Copynumber: 2.8 Consensus size: 43
55696462 TCATGTTTTT
* *
55696472 AGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGTTCTTGGTCTTC
1 AGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGTTCCTGGTCTTC
*
55696515 AGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAG-TCCTGGTCTTT
1 AGCGGCGTTTGTGGGAAAAGCGCCGCT-AAAGTTCCTGGTCTTC
*
55696558 AGCAGCGTTT-TCGGGAAAAGCGCCGCTAAAGTT
1 AGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAGTT
55696591 AGCGACGCGT
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
42 5 0.07
43 60 0.87
44 4 0.06
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.26
Consensus pattern (43 bp):
AGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGTTCCTGGTCTTC
Found at i:55706151 original size:18 final size:19
Alignment explanation
Indices: 55706118--55706162 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
55706108 TTAAAATTTT
55706118 ATTTTAATTTATTTAT-AC
1 ATTTTAATTTATTTATCAC
55706136 ATTTTAATTT-TATTATGCAC
1 ATTTTAATTTAT-TTAT-CAC
55706156 ATTTTAA
1 ATTTTAA
55706163 CTGTATATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.04
18 14 0.58
20 9 0.38
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTTAATTTATTTATCAC
Found at i:55709827 original size:40 final size:39
Alignment explanation
Indices: 55709761--55709849 Score: 115
Period size: 40 Copynumber: 2.3 Consensus size: 39
55709751 CCGTGTGGCC
* * *
55709761 CACATGGCCACACCTTCACCGTCACACGGCTGTGTCTCG
1 CACAAGGCCACACCTTCACAGTCACACAGCTGTGTCTCG
* * *
55709800 CACACGGCCTCACCTTCTACAGTCACACAGCTGTGTGTCG
1 CACAAGGCCACACCTTC-ACAGTCACACAGCTGTGTCTCG
55709840 CACAAGGCCA
1 CACAAGGCCA
55709850 GCCACACGCC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 15 0.36
40 27 0.64
ACGTcount: A:0.21, C:0.39, G:0.20, T:0.19
Consensus pattern (39 bp):
CACAAGGCCACACCTTCACAGTCACACAGCTGTGTCTCG
Found at i:55716123 original size:6 final size:6
Alignment explanation
Indices: 55716112--55716137 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
55716102 GTTTCCAAAG
55716112 TGGAAA TGGAAA TGGAAA TGGAAA TG
1 TGGAAA TGGAAA TGGAAA TGGAAA TG
55716138 ATCAATTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.35, T:0.19
Consensus pattern (6 bp):
TGGAAA
Found at i:55716334 original size:26 final size:26
Alignment explanation
Indices: 55716277--55716352 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
55716267 ACATATTTTC
*
55716277 TCAAAATTTTACCAGGGGTAAAATTA
1 TCAAAATTTTATCAGGGGTAAAATTA
* *
55716303 TCAAAAATTTATCAGGGGTAAAATTG
1 TCAAAATTTTATCAGGGGTAAAATTA
* **
55716329 TTAAAATTTTATTGGGGGTAAAAT
1 TCAAAATTTTATCAGGGGTAAAAT
55716353 AGGGATGAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (26 bp):
TCAAAATTTTATCAGGGGTAAAATTA
Found at i:55721330 original size:15 final size:15
Alignment explanation
Indices: 55721310--55721400 Score: 61
Period size: 14 Copynumber: 6.3 Consensus size: 15
55721300 ACTCGACCCC
55721310 TAAATCCCTAAACCT
1 TAAATCCCTAAACCT
55721325 TAAATCCCT-AACTCT
1 TAAATCCCTAAAC-CT
* *
55721340 T-AACCCCT-AACAT
1 TAAATCCCTAAACCT
*
55721353 CT-AACCCCTAAACCCT
1 -TAAATCCCTAAA-CCT
55721369 T-AA-CCTCTAAACCT
1 TAAATCC-CTAAACCT
*
55721383 TAAATCCC-AACCCT
1 TAAATCCCTAAACCT
55721397 TAAA
1 TAAA
55721401 CCATAATCCC
Statistics
Matches: 65, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
13 1 0.02
14 35 0.54
15 25 0.38
16 4 0.06
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAATCCCTAAACCT
Found at i:55721386 original size:22 final size:22
Alignment explanation
Indices: 55721341--55721386 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
55721331 CCTAACTCTT
*
55721341 AACCCCTAACATCTAACCCCTA
1 AACCCCTAACATCTAAACCCTA
* * *
55721363 AACCCTTAACCTCTAAACCTTA
1 AACCCCTAACATCTAAACCCTA
55721385 AA
1 AA
55721387 TCCCAACCCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.22
Consensus pattern (22 bp):
AACCCCTAACATCTAAACCCTA
Found at i:55721441 original size:15 final size:14
Alignment explanation
Indices: 55721397--55721443 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
55721387 TCCCAACCCT
*
55721397 TAAACCATAATCCC
1 TAAATCATAATCCC
*
55721411 TAATTCATAATCCC
1 TAAATCATAATCCC
*
55721425 TAAATCTATACTCCC
1 TAAATC-ATAATCCC
55721440 TAAA
1 TAAA
55721444 CCTTAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAATCATAATCCC
Found at i:55721658 original size:23 final size:22
Alignment explanation
Indices: 55721608--55721662 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
55721598 CCCTAACTCG
* * *
55721608 ACCCCTGAATCCCTAACTTTTA
1 ACCCCTAAACCCCTAACCTTTA
*
55721630 ATCCCTAAACCCCTAACCCTTTA
1 ACCCCTAAACCCCTAA-CCTTTA
55721653 ACCCCTAAAC
1 ACCCCTAAAC
55721663 TTTAAATCCC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.31, C:0.42, G:0.02, T:0.25
Consensus pattern (22 bp):
ACCCCTAAACCCCTAACCTTTA
Found at i:55721707 original size:15 final size:15
Alignment explanation
Indices: 55721683--55721713 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55721673 AACCCCTAAT
55721683 CCATAATCCCTAAAC
1 CCATAATCCCTAAAC
*
55721698 CCATACTCCCTAAAC
1 CCATAATCCCTAAAC
55721713 C
1 C
55721714 TTAAAGTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.45, G:0.00, T:0.19
Consensus pattern (15 bp):
CCATAATCCCTAAAC
Found at i:55722156 original size:114 final size:113
Alignment explanation
Indices: 55721968--55722289 Score: 493
Period size: 114 Copynumber: 2.8 Consensus size: 113
55721958 GCGCTTTTCC
*
55721968 AAAAACGCCACAAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGAC
1 AAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCG-C
* *
55722033 GCTTCCTCAAAAACGTCGCTAAAGCCCTGAGCATTAGCGACGCTTTCTT
65 GCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCTTTCTT
* * *
55722082 AAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCATCATTGGGCATAGGTTTTTTTGCAGC
1 AAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGC-GC
* *
55722147 GCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCGTTCGCGACGCTTTCTT
65 GCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCTTTCTT
* * *
55722196 AGAAACACCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG-TTTTTTGCGGC
1 AAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGC-GC
* *
55722260 GCTTTCCCAAAAACGCCGCTAAATCCCTGA
65 GCTTTCTCAAAAACGCCGCTAAAGCCCTGA
55722290 AAGCTTAGAA
Statistics
Matches: 190, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
113 38 0.20
114 151 0.79
115 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (113 bp):
AAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGCG
CTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCTTTCTT
Found at i:55722286 original size:72 final size:73
Alignment explanation
Indices: 55722183--55722355 Score: 240
Period size: 72 Copynumber: 2.4 Consensus size: 73
55722173 CTGAGCGTTC
** * * *
55722183 GCGACGCTTTCTTAGAAACACCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
1 GCGACGCTTTCCCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAG
55722248 G-TTTTTT
66 GTTTTTTT
* * * *
55722255 GCGGCGCTTTCCCAAAAACGCCGCTAAATCCCTGAAAGCTTAGAAAACTGCATCGTTGGGCTTAG
1 GCGACGCTTTCCCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAG
55722320 GTTTTTTT
66 GTTTTTTT
* *
55722328 GCGACGCTTTTCCAAAAACGCCACTAAA
1 GCGACGCTTTCCCAAAAACGCCGCTAAA
55722356 GCCCTGAGCA
Statistics
Matches: 88, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
72 57 0.65
73 31 0.35
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (73 bp):
GCGACGCTTTCCCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAG
GTTTTTTT
Found at i:55722302 original size:186 final size:186
Alignment explanation
Indices: 55722073--55722467 Score: 544
Period size: 186 Copynumber: 2.1 Consensus size: 186
55722063 GCATTAGCGA
** *
55722073 CGCTTTCTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCATCATTGGGCATAGGTTT
1 CGCTTTCCCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCATTGGGCATAGGTTT
* * * *
55722138 TTTTGC-AGCGC-TTTCTCAAAAACGCCGCTAAAGCCCTGAGCGTTCGCGACGCTTTCTTAGAAA
66 TTTTGCGA-CGCTTTTC-CAAAAACGCCACTAAAGCCCTGAGCATTCGCGACGCTTTCTCAAAAA
** *
55722201 CACCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTGCGG
129 CACCGCTAAATCCCCGAAAGCTCAGAAAACAACATCGTTGGGCTTAGGTTTTTTGCGG
* * * * *
55722259 CGCTTTCCCAAAAACGCCGCTAAATCCCTGAAAGCTTAGAAAACTGCATCGTTGGGCTTAGGTTT
1 CGCTTTCCCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCATTGGGCATAGGTTT
* * *
55722324 TTTTGCGACGCTTTTCCAAAAACGCCACTAAAGCCCTGAGCATTGGCGGCGCTTTCTCAAAAACG
66 TTTTGCGACGCTTTTCCAAAAACGCCACTAAAGCCCTGAGCATTCGCGACGCTTTCTCAAAAACA
* * * *
55722389 CCGCTAAATCCCCGAAAGCTCGGGAAACAACATCGTTGGGCTTAGTTTTTTTGTGG
131 CCGCTAAATCCCCGAAAGCTCAGAAAACAACATCGTTGGGCTTAGGTTTTTTGCGG
55722445 CGCTTTCTCC-AAAACGCCGCTAA
1 CGCTTTC-CCAAAAACGCCGCTAA
55722468 TGCTTATTTT
Statistics
Matches: 184, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
186 177 0.96
187 7 0.04
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (186 bp):
CGCTTTCCCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCATTGGGCATAGGTTT
TTTTGCGACGCTTTTCCAAAAACGCCACTAAAGCCCTGAGCATTCGCGACGCTTTCTCAAAAACA
CCGCTAAATCCCCGAAAGCTCAGAAAACAACATCGTTGGGCTTAGGTTTTTTGCGG
Found at i:55722391 original size:114 final size:113
Alignment explanation
Indices: 55722255--55722467 Score: 311
Period size: 114 Copynumber: 1.9 Consensus size: 113
55722245 TAGGTTTTTT
* * **
55722255 GCGGCGCTTTCCCAAAAACGCCGCTAAATCCCTGAAAGCTTAGAAAACTGCATCGTTGGGCTTAG
1 GCGGCGCTTTCCCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAACATCGTTGGGCTTA-
55722320 GTTTTTTTGCGACGCTTT-TCCAAAAACGCCACTAAAGCCCTGAGCATTG
65 GTTTTTTTGCGACGCTTTCTCC-AAAACGCCACTAAAGCCCTGAGCATTG
* * *
55722369 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCGGGAAACAACATCGTTGGGCTTAG
1 GCGGCGCTTTCCCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAACATCGTTGGGCTTAG
* * *
55722434 TTTTTTTGTGGCGCTTTCTCCAAAACGCCGCTAA
66 TTTTTTTGCGACGCTTTCTCCAAAACGCCACTAA
55722468 TGCTTATTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
113 28 0.32
114 60 0.68
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (113 bp):
GCGGCGCTTTCCCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAACATCGTTGGGCTTAG
TTTTTTTGCGACGCTTTCTCCAAAACGCCACTAAAGCCCTGAGCATTG
Found at i:55723489 original size:18 final size:18
Alignment explanation
Indices: 55723456--55723508 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
55723446 ATTCACCTAA
*
55723456 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
* *
55723475 ATCCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
*
55723493 ACCCAACCCAATCCAA
1 ACCCAACCCAACCCAA
55723509 TCATAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:55723496 original size:13 final size:13
Alignment explanation
Indices: 55723480--55723504 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55723470 CAAGTATCCA
55723480 ACCCAACCCAATT
1 ACCCAACCCAATT
55723493 ACCCAACCCAAT
1 ACCCAACCCAAT
55723505 CCAATCATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:55723642 original size:9 final size:9
Alignment explanation
Indices: 55723628--55723667 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
55723618 GTAGTGATTC
55723628 AATTCGGTT
1 AATTCGGTT
*
55723637 AATTCGGGT
1 AATTCGGTT
55723646 AATTCGGTT
1 AATTCGGTT
55723655 AATTCGGTT
1 AATTCGGTT
55723664 AATT
1 AATT
55723668 TTTAACCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:55727730 original size:19 final size:19
Alignment explanation
Indices: 55727706--55727743 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
55727696 AATGGTGAAG
*
55727706 AACAAATCAAATTTAGGGT
1 AACAAATCAAATTCAGGGT
55727725 AACAAATCAAATTCAGGGT
1 AACAAATCAAATTCAGGGT
55727744 TTGAGGATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (19 bp):
AACAAATCAAATTCAGGGT
Found at i:55731275 original size:34 final size:34
Alignment explanation
Indices: 55731236--55731303 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
55731226 CCATAATCAA
*
55731236 TGGTTCCCTTCATATATCTCAATATTCTCTTGGT
1 TGGTTCCCTTCACATATCTCAATATTCTCTTGGT
55731270 TGGTTCCCTTCACATATCTCAATATTCTCTTGGT
1 TGGTTCCCTTCACATATCTCAATATTCTCTTGGT
55731304 AGCCTCCCAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.18, C:0.25, G:0.12, T:0.46
Consensus pattern (34 bp):
TGGTTCCCTTCACATATCTCAATATTCTCTTGGT
Found at i:55734980 original size:14 final size:14
Alignment explanation
Indices: 55734961--55734992 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
55734951 TTGGTGCTTG
55734961 GAAACAATTACTTA
1 GAAACAATTACTTA
55734975 GAAACAATTACTTA
1 GAAACAATTACTTA
55734989 GAAA
1 GAAA
55734993 TAAGCTTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.25
Consensus pattern (14 bp):
GAAACAATTACTTA
Found at i:55738934 original size:65 final size:65
Alignment explanation
Indices: 55738830--55738960 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
55738820 CAAACCGACA
55738830 ATCTACAGAAAAAGGAAAAACACTGGGTAAGCATTTCAAATACTTAATAAGCCCATATAAAACTT
1 ATCTACAGAAAAAGGAAAAACACTGGGTAAGCATTTCAAATACTTAATAAGCCCATATAAAACTT
55738895 ATCTACAGAAAAAGGAAAAACACTGGGTAAGCATTTCAAATACTTAATAAGCCCATATAAAACTT
1 ATCTACAGAAAAAGGAAAAACACTGGGTAAGCATTTCAAATACTTAATAAGCCCATATAAAACTT
55738960 A
1 A
55738961 CTCAACTTAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (65 bp):
ATCTACAGAAAAAGGAAAAACACTGGGTAAGCATTTCAAATACTTAATAAGCCCATATAAAACTT
Found at i:55747616 original size:7 final size:7
Alignment explanation
Indices: 55747604--55747629 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
55747594 TAAATCTTGA
55747604 GTTTAGG
1 GTTTAGG
55747611 GTTTAGG
1 GTTTAGG
55747618 GTTTAGG
1 GTTTAGG
55747625 GTTTA
1 GTTTA
55747630 AGATCTTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:55749815 original size:29 final size:31
Alignment explanation
Indices: 55749747--55749835 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 31
55749737 ATTTTAAAAG
*
55749747 AATGTATATATATATATATTATAAAATATGA
1 AATGTATATATATATATATAATAAAATATGA
* * *
55749778 AA--AAAATATATAAATATAATAGAAATAT-A
1 AATGTATATATATATATATAATA-AAATATGA
*
55749807 AATGTATATACGTATATATGTATATAAAA
1 AATGTATATA--TATATATATA-ATAAAA
55749836 GCTAAAAAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
29 18 0.41
30 6 0.14
31 6 0.14
33 11 0.25
34 3 0.07
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.36
Consensus pattern (31 bp):
AATGTATATATATATATATAATAAAATATGA
Found at i:55749974 original size:3 final size:3
Alignment explanation
Indices: 55749945--55749990 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
55749935 ATATGTAAGT
* *
55749945 ATA ATT ATA ATA CTA TATA AT- ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55749990 A
1 A
55749991 CAAAACTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:55750012 original size:14 final size:14
Alignment explanation
Indices: 55749992--55750024 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
55749982 TAATAATAAC
55749992 AAAACTA-AAAAAA
1 AAAACTACAAAAAA
55750005 ATAAACTACAAAAAA
1 A-AAACTACAAAAAA
55750020 AAAAC
1 AAAAC
55750025 CTTAAAAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 10 0.56
15 7 0.39
ACGTcount: A:0.79, C:0.12, G:0.00, T:0.09
Consensus pattern (14 bp):
AAAACTACAAAAAA
Found at i:55750591 original size:12 final size:13
Alignment explanation
Indices: 55750574--55750602 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
55750564 ATTTTAAATT
55750574 AAAAAT-AAATAA
1 AAAAATAAAATAA
55750586 AAAAATAAAATAA
1 AAAAATAAAATAA
55750599 AAAA
1 AAAA
55750603 GAATGGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:55750599 original size:23 final size:25
Alignment explanation
Indices: 55750568--55750626 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 25
55750558 CTTTATATTT
*
55750568 TAAATTAAAAATA-AAT-AAAAAAA
1 TAAAATAAAAATAGAATGAAAAAAA
*
55750591 TAAAATAAAAA-AGAATGGAAAAAA
1 TAAAATAAAAATAGAATGAAAAAAA
*
55750615 TGAAA-AAAAATA
1 TAAAATAAAAATA
55750627 CGATTCACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 1 0.03
23 18 0.60
24 11 0.37
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (25 bp):
TAAAATAAAAATAGAATGAAAAAAA
Found at i:55758692 original size:57 final size:57
Alignment explanation
Indices: 55758585--55758717 Score: 151
Period size: 56 Copynumber: 2.3 Consensus size: 57
55758575 GGTTTAATAA
* * * * * **
55758585 TTTTTTTAATTTAAATTAGACTCTGAATTTAATAATTATTCCGTATTGAGA-TTAAAC
1 TTTTTTT-ATTCAAGTTAGACTCTAAACTTAACAATTATTCCACATTGAGACTTAAAC
*
55758642 TTTTTTTATTCAAGTTAGACTCTAAACTTAACAATTGTTCTCACATTGAGACTTAAAC
1 TTTTTTTATTCAAGTTAGACTCTAAACTTAACAATTATTC-CACATTGAGACTTAAAC
* *
55758700 TTTTTTTGTCCAAGTTAG
1 TTTTTTTATTCAAGTTAG
55758718 TCCTTGGAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
56 27 0.42
57 15 0.23
58 22 0.34
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.46
Consensus pattern (57 bp):
TTTTTTTATTCAAGTTAGACTCTAAACTTAACAATTATTCCACATTGAGACTTAAAC
Found at i:55759177 original size:19 final size:19
Alignment explanation
Indices: 55759153--55759190 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
55759143 TTATCAGTAT
55759153 TTATTTATAAATTTATTTA
1 TTATTTATAAATTTATTTA
* *
55759172 TTATTTATTATTTTATTTA
1 TTATTTATAAATTTATTTA
55759191 ATAATAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTTATAAATTTATTTA
Found at i:55761242 original size:11 final size:10
Alignment explanation
Indices: 55761226--55761287 Score: 54
Period size: 11 Copynumber: 5.9 Consensus size: 10
55761216 TTTTTTTATA
55761226 ATATAATAATT
1 ATATAA-AATT
55761237 ATATAAAATT
1 ATATAAAATT
*
55761247 TTA-AAAATT
1 ATATAAAATT
55761256 ATATCAAAATT
1 ATAT-AAAATT
* *
55761267 AATATATATATA
1 -ATATA-AAATT
55761279 ATATAAAAT
1 ATATAAAAT
55761288 GGTTGATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
9 8 0.19
10 9 0.21
11 18 0.43
12 7 0.17
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATAAAATT
Found at i:55767250 original size:21 final size:21
Alignment explanation
Indices: 55767224--55767264 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
55767214 ATCTGCTCAA
* *
55767224 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
55767245 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
55767265 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:55775986 original size:22 final size:22
Alignment explanation
Indices: 55775960--55776004 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
55775950 GAACTTCACA
55775960 ATTTTTCTTAATTTGGTACTTT
1 ATTTTTCTTAATTTGGTACTTT
*
55775982 ATTTTTTTTAATTTGGTACTTT
1 ATTTTTCTTAATTTGGTACTTT
55776004 A
1 A
55776005 ACTTGATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.07, G:0.09, T:0.64
Consensus pattern (22 bp):
ATTTTTCTTAATTTGGTACTTT
Found at i:55788668 original size:31 final size:31
Alignment explanation
Indices: 55788627--55788688 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
55788617 AGATAATTTT
*
55788627 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAATTTTATTAGGATTCAATTACTCTTG
55788658 AAAGAATTTTATTAGGATTCAATTACTCTTG
1 AAAGAATTTTATTAGGATTCAATTACTCTTG
55788689 TAATTTGCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.42
Consensus pattern (31 bp):
AAAGAATTTTATTAGGATTCAATTACTCTTG
Found at i:55789777 original size:18 final size:18
Alignment explanation
Indices: 55789754--55789789 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
55789744 CAATTAAACC
55789754 ATTTGATTGATATATTTA
1 ATTTGATTGATATATTTA
* *
55789772 ATTTGATTTATCTATTTA
1 ATTTGATTGATATATTTA
55789790 TAAATAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (18 bp):
ATTTGATTGATATATTTA
Found at i:55789846 original size:16 final size:16
Alignment explanation
Indices: 55789813--55789868 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 16
55789803 GCAATATATG
*
55789813 TATAAACAATTTA-AAA
1 TATAAA-AATTTATTAA
55789829 TATAAAAATTTATTAA
1 TATAAAAATTTATTAA
55789845 TATGTATATAAATTTATTAA
1 TA--TA-A-AAATTTATTAA
55789865 TATA
1 TATA
55789869 TGTAAAAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 6 0.18
16 10 0.29
18 4 0.12
19 1 0.03
20 13 0.38
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (16 bp):
TATAAAAATTTATTAA
Found at i:55789872 original size:22 final size:20
Alignment explanation
Indices: 55789829--55789867 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
55789819 CAATTTAAAA
55789829 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
55789849 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
55789868 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:55793677 original size:3 final size:3
Alignment explanation
Indices: 55793663--55793722 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
55793653 TTTGCATTGC
* * * * *
55793663 CAT CAC CAT CAT CAT CAT CAT TAT CAC CAT CAC CAT CTT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
*
55793711 CAT CAT CTT CAT
1 CAT CAT CAT CAT
55793723 GTGAGAACCC
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:55793692 original size:27 final size:27
Alignment explanation
Indices: 55793662--55793715 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
55793652 CTTTGCATTG
*
55793662 CCATCACCATCATCATCATCATTATCA
1 CCATCACCATCATCATCATCATCATCA
*
55793689 CCATCACCATCTTCATCATCATCATCA
1 CCATCACCATCATCATCATCATCATCA
55793716 TCTTCATGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.39, G:0.00, T:0.30
Consensus pattern (27 bp):
CCATCACCATCATCATCATCATCATCA
Found at i:55798010 original size:13 final size:13
Alignment explanation
Indices: 55797992--55798017 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55797982 AATATCTTTG
55797992 GTTTTTGTTGTTT
1 GTTTTTGTTGTTT
55798005 GTTTTTGTTGTTT
1 GTTTTTGTTGTTT
55798018 TTAATGCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (13 bp):
GTTTTTGTTGTTT
Found at i:55800883 original size:63 final size:63
Alignment explanation
Indices: 55800764--55800884 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
55800754 GCACTTCTTC
* ** *
55800764 CATGTCCTGCTTGTTGAATGCATTTGAAAGGGAGTGCACTTGGTCCTGTCTCTATAATGTTGT
1 CATGTCCTGCTTGTTGAATGCATTTGAAAGGGAGTGCACTTGGTACTGAATATATAATGTTGT
*
55800827 CATGTCCTGCTTGTTGAATGCATTTGAAAGGGAGTG-AC-TGGTTAGTGAAATATATAAT
1 CATGTCCTGCTTGTTGAATGCATTTGAAAGGGAGTGCACTTGG-TACTG-AATATATAAT
55800885 TTCAACCTCT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
61 3 0.06
62 5 0.10
63 43 0.84
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (63 bp):
CATGTCCTGCTTGTTGAATGCATTTGAAAGGGAGTGCACTTGGTACTGAATATATAATGTTGT
Found at i:55806494 original size:120 final size:120
Alignment explanation
Indices: 55806297--55806679 Score: 721
Period size: 120 Copynumber: 3.2 Consensus size: 120
55806287 TTTTCAAGTT
55806297 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
55806362 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
55806417 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
55806482 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
*
55806537 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* * * *
55806602 TAATATAAGAATATTAATTATTAAGAATTTTAATAAAATAAATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
55806657 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
55806680 TAAATATGAT
Statistics
Matches: 258, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 258 1.00
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
Found at i:55806664 original size:16 final size:16
Alignment explanation
Indices: 55806628--55806669 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
55806618 ATTATTAAGA
55806628 ATTTTAATAAAATAAAT
1 ATTTTAATAAAAT-AAT
55806645 ATTTTAATTAAAAT-AT
1 ATTTTAA-TAAAATAAT
55806661 A-TTTAATAA
1 ATTTTAATAA
55806670 TAATTATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.12
15 5 0.21
16 3 0.12
17 7 0.29
18 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTTAATAAAATAAT
Found at i:55806919 original size:16 final size:16
Alignment explanation
Indices: 55806898--55806965 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
55806888 GATTTGCTAT
55806898 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
55806914 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
55806930 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
55806946 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
55806962 TACA
1 TACA
55806966 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:55811590 original size:40 final size:40
Alignment explanation
Indices: 55811508--55811731 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
55811498 GCTACTCGTT
* *
55811508 CAAATGCCTTCGGGACAT-AGCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
55811547 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
55811587 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
55811627 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
55811666 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
55811707 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
55811732 CATCATTCGA
Statistics
Matches: 164, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.30
40 100 0.61
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:55811650 original size:79 final size:80
Alignment explanation
Indices: 55811508--55811731 Score: 269
Period size: 79 Copynumber: 2.8 Consensus size: 80
55811498 GCTACTCGTT
* * * *
55811508 CAAATGCCTTCGGGACAT-AGCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCG
*
55811571 GATTTAGTAACTCGCA
65 GAATTAGTAACTCGCA
55811587 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCGG
*
55811651 AATTAGTATCTCGCA
66 AATTAGTAACTCGCA
** * * * * *
55811666 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CAAAGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCACCAATGCCTTCGGGACTTAGCCC
55811729 GGA
64 GGA
55811732 CATCATTCGA
Statistics
Matches: 127, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
78 3 0.02
79 77 0.61
80 45 0.35
81 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCGG
AATTAGTAACTCGCA
Found at i:55811691 original size:119 final size:119
Alignment explanation
Indices: 55811510--55811731 Score: 290
Period size: 119 Copynumber: 1.9 Consensus size: 119
55811500 TACTCGTTCA
* *
55811510 AATGCCTTCGGGACATAGCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACATAGCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATA
*
55811575 TAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 TAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
55811629 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAG-CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
55811691 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
63 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
55811732 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
118 8 0.09
119 73 0.82
120 8 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAGCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATA
TAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:55812933 original size:56 final size:56
Alignment explanation
Indices: 55812866--55813041 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
55812856 TATTAGTTTA
55812866 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
55812922 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
55812978 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
55813034 TTGCCCAT
1 TTGCCCAT
55813042 CATCCCTTGT
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:55817636 original size:18 final size:17
Alignment explanation
Indices: 55817603--55817641 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
55817593 TTGTATAAAT
55817603 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
55817621 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
55817638 TGTG
1 TGTG
55817642 GAAGGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:55817772 original size:8 final size:8
Alignment explanation
Indices: 55817759--55817787 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
55817749 CACTAGAGAC
55817759 CAGTGTTA
1 CAGTGTTA
55817767 CAGTGTTA
1 CAGTGTTA
55817775 CAGTGTTA
1 CAGTGTTA
55817783 CAGTG
1 CAGTG
55817788 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:55817900 original size:23 final size:23
Alignment explanation
Indices: 55817873--55817950 Score: 129
Period size: 23 Copynumber: 3.3 Consensus size: 23
55817863 AGTGTTATTG
55817873 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
55817896 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
55817919 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
55817942 ATCATGTGG
1 ATCA-GTGG
55817951 CACTTATGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 46 0.92
24 4 0.08
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:55824956 original size:17 final size:17
Alignment explanation
Indices: 55824936--55824973 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
55824926 TTGTATAAAT
*
55824936 TGTGAATTTAT-TTGATA
1 TGTGAATTAATATTGA-A
55824953 TGTGAATTAATATTGAA
1 TGTGAATTAATATTGAA
55824970 TGTG
1 TGTG
55824974 GAAGGAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (17 bp):
TGTGAATTAATATTGAA
Found at i:55825239 original size:22 final size:23
Alignment explanation
Indices: 55825198--55825274 Score: 129
Period size: 23 Copynumber: 3.3 Consensus size: 23
55825188 AGTGTTATTG
55825198 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
55825221 TTCAGTGGTAGC-TCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
55825243 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
55825266 ATCATGTGG
1 ATCA-GTGG
55825275 CACTTATGTG
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
22 21 0.42
23 25 0.50
24 4 0.08
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:55832263 original size:17 final size:17
Alignment explanation
Indices: 55832243--55832280 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
55832233 TTGTATAAAT
*
55832243 TGTGAATTTAT-TTGATA
1 TGTGAATTAATATTGA-A
55832260 TGTGAATTAATATTGAA
1 TGTGAATTAATATTGAA
55832277 TGTG
1 TGTG
55832281 GAAGGAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (17 bp):
TGTGAATTAATATTGAA
Found at i:55832412 original size:8 final size:8
Alignment explanation
Indices: 55832399--55832427 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
55832389 CACTAGAGAC
55832399 CAGTGTTA
1 CAGTGTTA
55832407 CAGTGTTA
1 CAGTGTTA
55832415 CAGTGTTA
1 CAGTGTTA
55832423 CAGTG
1 CAGTG
55832428 AGTCCCGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:55832540 original size:23 final size:23
Alignment explanation
Indices: 55832513--55832585 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
55832503 AGTGTTATTG
55832513 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
55832536 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
55832559 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
55832582 ATCA
1 ATCA
55832586 ATGTGGCACT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:55834354 original size:16 final size:16
Alignment explanation
Indices: 55834335--55834368 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55834325 TAAGGTTATG
*
55834335 AGAATTTGGGGTTCTT
1 AGAATTTAGGGTTCTT
*
55834351 AGAATTTAGGGTTTTT
1 AGAATTTAGGGTTCTT
55834367 AG
1 AG
55834369 GTCCGAGCCT
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:0.24, C:0.03, G:0.29, T:0.44
Consensus pattern (16 bp):
AGAATTTAGGGTTCTT
Found at i:55835368 original size:2 final size:2
Alignment explanation
Indices: 55835361--55835387 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55835351 TTGTTAACTT
55835361 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
55835388 TATTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:55844640 original size:4 final size:4
Alignment explanation
Indices: 55844633--55844662 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
55844623 ATTTATATAT
*
55844633 ATAG ATAG ATAG ATAG ATAG ATAG AAAG AT
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
55844663 TTTAATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.23
Consensus pattern (4 bp):
ATAG
Found at i:55848158 original size:3 final size:3
Alignment explanation
Indices: 55848150--55848178 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
55848140 AATTGAGTCT
55848150 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
55848179 TGAAGTGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:55850176 original size:16 final size:15
Alignment explanation
Indices: 55850138--55850181 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
55850128 TATATAATTT
55850138 AATAA-TATTTTTAA
1 AATAATTATTTTTAA
*
55850152 TATAATTATTTTTAA
1 AATAATTATTTTTAA
*
55850167 AATATTTTATTTTTA
1 AATA-ATTATTTTTA
55850182 TATTTTCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 4 0.16
15 12 0.48
16 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATAATTATTTTTAA
Found at i:55852100 original size:5 final size:4
Alignment explanation
Indices: 55852080--55852125 Score: 67
Period size: 4 Copynumber: 11.5 Consensus size: 4
55852070 ATTAAAACTA
*
55852080 AAAT AAAT AAAT AAAT GAAAT AGA- AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
55852126 TAACAAGGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 2 0.05
4 32 0.84
5 4 0.11
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:55852106 original size:24 final size:23
Alignment explanation
Indices: 55852079--55852124 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
55852069 AATTAAAACT
55852079 AAAATAAATAAATAAATGAAATAG
1 AAAATAAATAAATAAAT-AAATAG
55852103 AAAATAAATAAATAAATAAATA
1 AAAATAAATAAATAAATAAATA
55852125 ATAACAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (23 bp):
AAAATAAATAAATAAATAAATAG
Found at i:55858308 original size:22 final size:22
Alignment explanation
Indices: 55858283--55858327 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
55858273 TTTAATAAAA
55858283 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
55858305 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
55858327 A
1 A
55858328 CACTCCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:55862902 original size:22 final size:22
Alignment explanation
Indices: 55862877--55862921 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
55862867 TTTAATAAAA
55862877 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
55862899 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
55862921 A
1 A
55862922 CAATTTCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:55866026 original size:9 final size:9
Alignment explanation
Indices: 55866012--55866048 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
55866002 TATAGTTTAA
55866012 TATTCGAAT
1 TATTCGAAT
55866021 TATTCGAAT
1 TATTCGAAT
55866030 TATTC-AAGT
1 TATTCGAA-T
55866039 TATTCGAAT
1 TATTCGAAT
55866048 T
1 T
55866049 CAAAAACTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:55876351 original size:2 final size:2
Alignment explanation
Indices: 55876344--55876376 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
55876334 GAAAGCAGTT
55876344 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
55876377 TTTTTTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:55885583 original size:26 final size:25
Alignment explanation
Indices: 55885552--55885600 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
55885542 TATATTATCT
*
55885552 TAAATATTTAATTAGATAATAAAAAA
1 TAAATATTTAATTAAATAA-AAAAAA
55885578 TAAATATTTAATTAAATAAAAAA
1 TAAATATTTAATTAAATAAAAAA
55885601 TAGATAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
TAAATATTTAATTAAATAAAAAAAA
Found at i:55889517 original size:25 final size:26
Alignment explanation
Indices: 55889466--55889517 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
55889456 AAACAGTAAC
* *
55889466 ACAATTAACAATAAAACAAGAGTAAT
1 ACAATTAACAACAAAACAAGAGCAAT
* *
55889492 ACAA-TAACAACAAAATAATAGCAAT
1 ACAATTAACAACAAAACAAGAGCAAT
55889517 A
1 A
55889518 TACTAGTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.63, C:0.13, G:0.06, T:0.17
Consensus pattern (26 bp):
ACAATTAACAACAAAACAAGAGCAAT
Found at i:55894165 original size:41 final size:42
Alignment explanation
Indices: 55894097--55894189 Score: 161
Period size: 41 Copynumber: 2.2 Consensus size: 42
55894087 AAAATTTATA
*
55894097 TTTAATATAATAAAAATATTTATTATATTTATGGTAGTGTTT
1 TTTAATATAATAAAAACATTTATTATATTTATGGTAGTGTTT
*
55894139 TTTGATATAAT-AAAACATTTATTATATTTATGGTAGTGTTT
1 TTTAATATAATAAAAACATTTATTATATTTATGGTAGTGTTT
55894180 TTTAATATAA
1 TTTAATATAA
55894190 ATATTTTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 38 0.79
42 10 0.21
ACGTcount: A:0.38, C:0.01, G:0.10, T:0.52
Consensus pattern (42 bp):
TTTAATATAATAAAAACATTTATTATATTTATGGTAGTGTTT
Found at i:55895257 original size:16 final size:16
Alignment explanation
Indices: 55895220--55895261 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
55895210 TTAATCATAT
*
55895220 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
55895236 TT-AAATATATTATAA
1 TTAAAATATATTATAA
55895251 TTAAAATATAT
1 TTAAAATATAT
55895262 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:55895268 original size:14 final size:15
Alignment explanation
Indices: 55895229--55895270 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
55895219 TTTAAACATA
*
55895229 ATTATTATTAAATAT
1 ATTATAATTAAATAT
55895244 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
55895258 A-TATAATTTAATA
1 ATTATAATTAAATA
55895271 AAATTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:55895388 original size:14 final size:15
Alignment explanation
Indices: 55895339--55895390 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
55895329 ATAAAATATA
55895339 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
55895354 TATTAAATATATTAT
1 AATTAAATATATTAT
55895369 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
55895382 AATTTAATA
1 AATTAAATA
55895391 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:55895508 original size:17 final size:15
Alignment explanation
Indices: 55895456--55895500 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
55895446 ACTATAAAAG
55895456 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
55895472 ATTATTAAATATATT
1 ATAATTAAATATATT
55895487 ATAATTAAATATAT
1 ATAATTAAATATAT
55895501 AATTTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 3 0.12
15 20 0.77
16 3 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:55895618 original size:16 final size:16
Alignment explanation
Indices: 55895575--55895620 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
55895565 ACTATAAAAG
*
55895575 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
55895591 ATTATT-AAATATATT
1 ATAATTAAAATATATT
55895606 ATAATTAAAATATAT
1 ATAATTAAAATATAT
55895621 AATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:55895627 original size:14 final size:15
Alignment explanation
Indices: 55895575--55895629 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
55895565 ACTATAAAAG
55895575 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
55895591 ATTATTAAATATATT
1 ATAATTAAATATATT
55895606 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
55895619 ATAATTTAATA
1 ATAATTAAATA
55895630 AAATTCTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 15 0.44
16 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:55895643 original size:239 final size:240
Alignment explanation
Indices: 55895218--55895754 Score: 986
Period size: 239 Copynumber: 2.2 Consensus size: 240
55895208 ATTTAATCAT
55895218 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATA
*
55895283 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATTAACAT
65 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTAACAT
55895348 AATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTC
130 AATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTC
55895413 TTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
195 TTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
*
55895459 ATTTAACATAATTATTATTAAATATATTATAATT-AAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
* *
55895523 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAACATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTAACATA
55895588 ATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCT
131 ATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCT
55895653 TATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
196 TATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* * * *
55895698 ATTTAAAATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
55895755 TAAAATAATT
Statistics
Matches: 287, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
239 232 0.81
240 51 0.18
241 4 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (240 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTAACATA
ATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCT
TATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:55895765 original size:120 final size:120
Alignment explanation
Indices: 55895218--55895754 Score: 986
Period size: 120 Copynumber: 4.5 Consensus size: 120
55895208 ATTTAATCAT
*
55895218 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
55895283 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
65 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
*
55895339 AATTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
55895404 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
55895459 ATTTAACATAATTATTATTAAATATATTATAATT-AAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
55895523 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
55895578 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
55895643 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* * * *
55895698 ATTTAAAATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
55895755 TAAAATAATT
Statistics
Matches: 406, Mismatches: 9, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
119 119 0.29
120 284 0.70
121 3 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:55902405 original size:20 final size:20
Alignment explanation
Indices: 55902363--55902408 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
55902353 AAAAATCATT
* *
55902363 AAAAATTGTAAAAGTTATAA
1 AAAAATTATAAAAGTTAGAA
*
55902383 AAAAATTATGAAAGTTAGCAA
1 AAAAATTATAAAAGTTAG-AA
55902404 AAAAA
1 AAAAA
55902409 CATTATTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.63, C:0.02, G:0.11, T:0.24
Consensus pattern (20 bp):
AAAAATTATAAAAGTTAGAA
Found at i:55903794 original size:30 final size:29
Alignment explanation
Indices: 55903756--55903820 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
55903746 TTTTTTTTGT
** *
55903756 TGTA-AAAATCGAATTAAATAAAAATTTCA
1 TGTATAAAATCGAACAAAAT-AAAAGTTCA
*
55903785 TGTATAAAATCGCACAAAATAAAAGTTCA
1 TGTATAAAATCGAACAAAATAAAAGTTCA
55903814 TGTATAA
1 TGTATAA
55903821 CATTGCGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.29
Consensus pattern (29 bp):
TGTATAAAATCGAACAAAATAAAAGTTCA
Found at i:55905217 original size:14 final size:15
Alignment explanation
Indices: 55905198--55905227 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
55905188 TAACAGGGTG
55905198 TATTATAA-TTTAAA
1 TATTATAATTTTAAA
55905212 TATTATAATTTTAAA
1 TATTATAATTTTAAA
55905227 T
1 T
55905228 TATCTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTATAATTTTAAA
Found at i:55909123 original size:9 final size:9
Alignment explanation
Indices: 55909109--55909254 Score: 57
Period size: 9 Copynumber: 15.2 Consensus size: 9
55909099 TTTTGGTACG
55909109 ATAATTTTT
1 ATAATTTTT
55909118 ATAATTTTT
1 ATAATTTTT
*
55909127 TTACGATTTTT
1 ATA--ATTTTT
*
55909138 ATATTTATTT
1 ATAATT-TTT
* *
55909148 ACATTTTTTT
1 ATA-ATTTTT
55909158 ATAATTTTCTT
1 ATAA-TTT-TT
*
55909169 ATGACTTTATT
1 AT-AATTT-TT
55909180 A-AATTTGTT
1 ATAATTT-TT
*
55909189 AT-ATTTCT
1 ATAATTTTT
55909197 AT-ATATTTT
1 ATAAT-TTTT
55909206 ATAATTTTT
1 ATAATTTTT
* *
55909215 TTACGATATTT
1 ATA--ATTTTT
55909226 ATAATTTTT
1 ATAATTTTT
*
55909235 CT-ATTTTT
1 ATAATTTTT
*
55909243 CCTAATTTTT
1 -ATAATTTTT
55909253 AT
1 AT
55909255 TATTAAAACT
Statistics
Matches: 105, Mismatches: 18, Indels: 28
0.70 0.12 0.19
Matches are distributed among these distances:
8 11 0.10
9 44 0.42
10 21 0.20
11 28 0.27
12 1 0.01
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (9 bp):
ATAATTTTT
Found at i:55909137 original size:20 final size:20
Alignment explanation
Indices: 55909112--55909234 Score: 72
Period size: 20 Copynumber: 5.8 Consensus size: 20
55909102 TGGTACGATA
55909112 ATTTTTATAATTTTTTTACG
1 ATTTTTATAATTTTTTTACG
*
55909132 ATTTTTAT-ATTTATTTAC-
1 ATTTTTATAATTTTTTTACG
* *
55909150 ATTTTTTTATAATTTTCTTATG
1 A--TTTTTATAATTTTTTTACG
* *
55909172 ACTTTATTA-AATTTGTTATATTTCTAT
1 A-TTT-TTATAA-TT-TT-T-TTAC--G
55909199 ATATTTTATAATTTTTTTACG
1 AT-TTTTATAATTTTTTTACG
*
55909220 ATATTTATAATTTTT
1 ATTTTTATAATTTTT
55909235 CTATTTTTCC
Statistics
Matches: 78, Mismatches: 12, Indels: 26
0.67 0.10 0.22
Matches are distributed among these distances:
18 1 0.01
19 9 0.12
20 27 0.35
21 14 0.18
22 6 0.08
23 5 0.06
24 1 0.01
25 4 0.05
26 6 0.08
27 5 0.06
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
ATTTTTATAATTTTTTTACG
Found at i:55909156 original size:19 final size:20
Alignment explanation
Indices: 55909112--55909155 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
55909102 TGGTACGATA
*
55909112 ATTTTTATAATTTTTTTACG
1 ATTTTTATAATTTATTTACG
55909132 ATTTTTAT-ATTTATTTAC-
1 ATTTTTATAATTTATTTACG
55909150 ATTTTT
1 ATTTTT
55909156 TTATAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.26
19 9 0.39
20 8 0.35
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (20 bp):
ATTTTTATAATTTATTTACG
Found at i:55909228 original size:29 final size:28
Alignment explanation
Indices: 55909114--55909233 Score: 84
Period size: 29 Copynumber: 4.1 Consensus size: 28
55909104 GTACGATAAT
55909114 TTTTATAATTTTTTTACGATTTT-TATA
1 TTTTATAATTTTTTTACGATTTTATATA
* ** *
55909141 TTTATTTACATTTTTTTATAATTTTCTTATGA
1 TTT-TATA-ATTTTTTTACGATTTT-ATAT-A
* * * *
55909173 CTTTATTAAATTTGTTA-TATTTCTATATA
1 TTTTA-TAATTTTTTTACGATTT-TATATA
55909202 TTTTATAATTTTTTTACGATATTTATA-A
1 TTTTATAATTTTTTTACGAT-TTTATATA
55909230 TTTT
1 TTTT
55909234 TCTATTTTTC
Statistics
Matches: 71, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
27 3 0.04
28 17 0.24
29 25 0.35
30 9 0.13
31 12 0.17
32 5 0.07
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (28 bp):
TTTTATAATTTTTTTACGATTTTATATA
Found at i:55909234 original size:29 final size:29
Alignment explanation
Indices: 55909109--55909242 Score: 68
Period size: 29 Copynumber: 4.6 Consensus size: 29
55909099 TTTTGGTACG
*
55909109 ATAATTTTTATAATTTTTTTACGATTTTT
1 ATAATTTTTATAATTTTTTTACGATATTT
** *
55909138 AT-ATTTATT-TACATTTTTTTATAATTTTCTT
1 ATAATTT-TTATA-ATTTTTTTACGA-TAT-TT
* *
55909169 ATGACTTTATTA-AA-TTTGTT---ATATTT
1 AT-AATTT-TTATAATTTTTTTACGATATTT
*
55909195 CTATATATTTTATAATTTTTTTACGATATTT
1 ATA-AT-TTTTATAATTTTTTTACGATATTT
*
55909226 ATAATTTTTCT-ATTTTT
1 ATAATTTTTATAATTTTT
55909243 CCTAATTTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 29
0.68 0.08 0.24
Matches are distributed among these distances:
25 1 0.01
26 7 0.09
27 6 0.07
28 18 0.22
29 19 0.23
30 5 0.06
31 17 0.21
32 1 0.01
33 7 0.09
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (29 bp):
ATAATTTTTATAATTTTTTTACGATATTT
Found at i:55910215 original size:37 final size:36
Alignment explanation
Indices: 55910164--55910244 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 36
55910154 TTTATGAGAC
* * * *
55910164 TTTTCTTTTGTTTAAGTTTGATAAATT-AAATTGATC
1 TTTTTTTTTATTTAAATTTGATAAATTGAAA-TGATA
55910200 TTTTATTTTTATTTAAATTTGATAAATTGAAATGATA
1 TTTT-TTTTTATTTAAATTTGATAAATTGAAATGATA
55910237 TTTTTTTT
1 TTTTTTTT
55910245 ACTTTATCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 8 0.21
37 28 0.72
38 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (36 bp):
TTTTTTTTTATTTAAATTTGATAAATTGAAATGATA
Found at i:55911149 original size:5 final size:5
Alignment explanation
Indices: 55911139--55911168 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
55911129 TTAAAAAGGA
55911139 AAATT AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT
55911169 TCATTTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:55915662 original size:67 final size:66
Alignment explanation
Indices: 55915546--55915675 Score: 224
Period size: 67 Copynumber: 2.0 Consensus size: 66
55915536 TTTCCATTTT
55915546 AGAGAGCACACTCCCGCGAACCTCATCCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTAC
1 AGAGAGCACACTCCCGCGAACCTCATCCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTAC
55915611 A
66 A
* **
55915612 AGAGAGCACACTCCCGCGAACCTTATTCCTTACAGTGGGATTACCAGTCCAGGCTAAATCCCCT
1 AGAGAGCACACTCCCGCGAACCTCA-TCCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCT
55915676 GTAATATAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
66 24 0.40
67 36 0.60
ACGTcount: A:0.28, C:0.35, G:0.18, T:0.19
Consensus pattern (66 bp):
AGAGAGCACACTCCCGCGAACCTCATCCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTAC
A
Found at i:55918569 original size:5 final size:5
Alignment explanation
Indices: 55918559--55918590 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
55918549 TTAAAAAGGA
55918559 AAATT AAATT AAATT AAATT AAATT AAATT AA
1 AAATT AAATT AAATT AAATT AAATT AAATT AA
55918591 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:55918602 original size:6 final size:6
Alignment explanation
Indices: 55918591--55918641 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
55918581 ATTAAATTAA
* * * *
55918591 TTTCAT TTTCAT TTTCAT TTTCAA TTTCAA TTTCAAT TTCCAT TTCCAT
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTC-AT TTTCAT TTTCAT
55918640 TT
1 TT
55918642 ATTTTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
6 37 0.90
7 4 0.10
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.59
Consensus pattern (6 bp):
TTTCAT
Found at i:55920313 original size:18 final size:19
Alignment explanation
Indices: 55920292--55920341 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
55920282 TTTATCCTTG
55920292 TTATTATTATTATT-TTAT
1 TTATTATTATTATTATTAT
* *
55920310 TTATTTTTCTT-TTATTAT
1 TTATTATTATTATTATTAT
*
55920328 TTA-TATTAGTATTA
1 TTATTATTATTATTA
55920342 GGGTAGTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (19 bp):
TTATTATTATTATTATTAT
Found at i:55927885 original size:25 final size:24
Alignment explanation
Indices: 55927824--55927887 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 24
55927814 TTTTGAGTTG
55927824 TTTATGTGTTTATA-TATAATTTT
1 TTTATGTGTTTATATTATAATTTT
* * *
55927847 TTGTTTGTG-CTATATTTTAAATTTT
1 TT-TATGTGTTTATATTAT-AATTTT
55927872 TTTATGTGTTTATATT
1 TTTATGTGTTTATATT
55927888 GTCACTCAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
23 6 0.19
24 12 0.38
25 14 0.44
ACGTcount: A:0.22, C:0.02, G:0.11, T:0.66
Consensus pattern (24 bp):
TTTATGTGTTTATATTATAATTTT
Found at i:55929395 original size:3 final size:3
Alignment explanation
Indices: 55929389--55929413 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
55929379 AATATGTTTA
55929389 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
55929414 GAAGAGCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:55936741 original size:32 final size:32
Alignment explanation
Indices: 55936700--55936765 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
55936690 AGAGATTCAA
55936700 TGGGATGCCAAGGAAATGGACAATAAACAATC
1 TGGGATGCCAAGGAAATGGACAATAAACAATC
55936732 TGGGATGCCAAGGAAATGGACAATAAACAATC
1 TGGGATGCCAAGGAAATGGACAATAAACAATC
55936764 TG
1 TG
55936766 AGCTACAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.42, C:0.15, G:0.26, T:0.17
Consensus pattern (32 bp):
TGGGATGCCAAGGAAATGGACAATAAACAATC
Done.