Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 199 of 378
Found at i:58711129 original size:13 final size:13
Alignment explanation
Indices: 58711113--58711137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58711103 TTGTTTTTTC
58711113 TTTTTTTTTTTGT
1 TTTTTTTTTTTGT
58711126 TTTTTTTTTTTG
1 TTTTTTTTTTTG
58711138 GGGGGGGGGG
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTTTTTTTTTTGT
Found at i:58715090 original size:211 final size:205
Alignment explanation
Indices: 58714818--58715202 Score: 569
Period size: 211 Copynumber: 1.8 Consensus size: 205
58714808 ATAAATATTT
* * * *
58714818 TAAAATATATAAATATTATTTCATGTTGAAATGAACCTGGGCAACCATTTGTCTAGATTTATTCA
1 TAAAAAATATAAATATTATTTCATGTTGAAATGAACCTAGACAACCATTTATCTAGATTTATTCA
* *
58714883 AAGCA-TTTTTTAGTAGTTTTATAGGTGATTATTTTTTTTCATGAAATATTATTTTATATTATTA
66 AAGCATTTTTTTAGTAGTTTTATAGATGATTAATTTTTTTCATG-AA-A-TA---T-TATTATTA
58714947 TTTTAAAATTAAAAATATATAAAACCT-AAAAAATCATTAAAATATATATAATATACAATATTTT
124 TTTTAAAATTAAAAATATATAAAACCTAAAAAAATCATTAAAA-ATATATAATATACAATATTTT
58715011 AAAATACATAAATTTATA
188 AAAATACATAAATTTATA
* *
58715029 TAAAAAATATAAATATTATTTCATGTTGGAATGAACCTAGACAACTC-TTTATTTAGATTTATTC
1 TAAAAAATATAAATATTATTTCATGTTGAAATGAACCTAGACAAC-CATTTATCTAGATTTATTC
* *
58715093 CAAGCATTTTTTTATTAGTTTTATAGATGATTAATTTTTTTCATGAAATATTATTATTATTTTAA
65 AAAGCATTTTTTTAGTAGTTTTATAGATGATTAATTTTTTTCATGAAATATTATTATTATTTTAA
*
58715158 AATTAAAAATATATAAAATCTAAAAAAATCATTAAAAATATATAA
130 AATTAAAAATATATAAAACCTAAAAAAATCATTAAAAATATATAA
58715203 ATGTATCAAA
Statistics
Matches: 160, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
205 42 0.26
206 16 0.10
209 2 0.01
210 1 0.01
211 63 0.39
212 36 0.22
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (205 bp):
TAAAAAATATAAATATTATTTCATGTTGAAATGAACCTAGACAACCATTTATCTAGATTTATTCA
AAGCATTTTTTTAGTAGTTTTATAGATGATTAATTTTTTTCATGAAATATTATTATTATTTTAAA
ATTAAAAATATATAAAACCTAAAAAAATCATTAAAAATATATAATATACAATATTTTAAAATACA
TAAATTTATA
Found at i:58715241 original size:21 final size:21
Alignment explanation
Indices: 58715217--58715266 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 21
58715207 ATCAAAAACA
58715217 ATTATAAAATTTAATTTAAAT
1 ATTATAAAATTTAATTTAAAT
58715238 ATTAT--AA-TTAATTTAAAT
1 ATTATAAAATTTAATTTAAAT
*
58715256 ATATTTAAAAT
1 AT-TATAAAAT
58715267 ATATAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
18 13 0.54
19 4 0.17
21 7 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTATAAAATTTAATTTAAAT
Found at i:58716825 original size:22 final size:22
Alignment explanation
Indices: 58716800--58716857 Score: 53
Period size: 24 Copynumber: 2.5 Consensus size: 22
58716790 ACGGTGTGGT
58716800 TAAACCACTCAAACGGAGAAGA
1 TAAACCACTCAAACGGAGAAGA
** * **
58716822 TAAAAGCTGCTCAAACGGTGTGGA
1 T-AAA-CCACTCAAACGGAGAAGA
58716846 TAAACCACTCAA
1 TAAACCACTCAA
58716858 CGGTGCAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
22 7 0.26
23 6 0.22
24 14 0.52
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (22 bp):
TAAACCACTCAAACGGAGAAGA
Found at i:58719474 original size:19 final size:20
Alignment explanation
Indices: 58719436--58719474 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
58719426 CTAATTCTCC
* *
58719436 TTCTTTCTCTTTTTCTTTCT
1 TTCTTTCTCTGTTTCGTTCT
58719456 TTCTTT-TCTGTTTCGTTCT
1 TTCTTTCTCTGTTTCGTTCT
58719475 ATCTCTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.00, C:0.23, G:0.05, T:0.72
Consensus pattern (20 bp):
TTCTTTCTCTGTTTCGTTCT
Found at i:58720945 original size:19 final size:20
Alignment explanation
Indices: 58720904--58720945 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
58720894 ATAAGTTGTA
* *
58720904 AAATAAGTGATAAATGTGTG
1 AAATAAGTGAGAAATGTGGG
*
58720924 AAATAA-TGAGAATTGTGGG
1 AAATAAGTGAGAAATGTGGG
58720943 AAA
1 AAA
58720946 CTTTTAGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (20 bp):
AAATAAGTGAGAAATGTGGG
Found at i:58721573 original size:46 final size:46
Alignment explanation
Indices: 58721394--58721594 Score: 169
Period size: 46 Copynumber: 4.3 Consensus size: 46
58721384 ATTGTGTGCT
* ** *
58721394 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGATCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGATGAGAGCC
** * *
58721440 AGTGTAAGACCATGTCTGGGACATCGCATCGGC-ATTGAGACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-CAAGATGAGAGCC
* * * * *
58721488 AGTGTAAGACATATCTGGGACATACCTCAGCCT-CGAGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-GGCTACAAGATG-AGAGCC
* *
58721534 AGTGTAAGACATGTCTGGGGCATGCATCGGCTACAAGAT--GTGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGATGAGAGCC
*
58721578 AGTATAAGACCATGTCT
1 AGTGTAAGA-CATGTCT
58721595 AGGATATGGC
Statistics
Matches: 124, Mismatches: 22, Indels: 19
0.75 0.13 0.12
Matches are distributed among these distances:
44 11 0.09
45 10 0.08
46 49 0.40
47 31 0.25
48 23 0.19
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGATGAGAGCC
Found at i:58723071 original size:375 final size:375
Alignment explanation
Indices: 58722377--58723127 Score: 1432
Period size: 375 Copynumber: 2.0 Consensus size: 375
58722367 CAAGGGCTTG
58722377 GTAGATAGCCTTATATTGTCCACACAGGTAGACACACGGGCGTGTGTCTAGGCTGTGTGAGACAC
1 GTAGATAGCCTTATATTGTCCACACAGGTAGACACACGGGCGTGTGTCTAGGCTGTGTGAGACAC
58722442 ATGGCCAGCCCTATGGGCATGTTGTCCAGCCGTGTGTCCCCTGCACGTAAAAATTACAATTCAGT
66 ATGGCCAGCCCTATGGGCATGTTGTCCAGCCGTGTGTCCCCTGCACGTAAAAATTACAATTCAGT
58722507 ATGCATGGTAGTAAACACATGGGCAGAGACACGACCGTGTGTCTCAGCCGTGTGAAAGACACAAC
131 ATGCATGGTAGTAAACACATGGGCAGAGACACGACCGTGTGTCTCAGCCGTGTGAAAGACACAAC
58722572 CTTTGGCCACGAGCGTGTGCCTTGGCCATGTGCCCCTTATTGGATGCTGACGTCAGAAATAGAAT
196 CTTTGGCCACGAGCGTGTGCCTTGGCCATGTGCCCCTTATTGGATGCTGACGTCAGAAATAGAAT
* * *
58722637 GTCAAGGCTTTTAGACACGGGCTAGGACACGAGCGTGTCATGGCCGTGTAAGGGACACGGGCTAT
261 GTCAAGGCTTTTAGACACGGCCTAGGACACGAGCGTGTCACGGCCGTGTAAGAGACACGGGCTAT
58722702 AGACACGGGCGTGTGTCAAGCCTTGTGAAAACCCCTGTAGGTTCGAATTT
326 AGACACGGGCGTGTGTCAAGCCTTGTGAAAACCCCTGTAGGTTCGAATTT
58722752 GTAGATAGCCTTATATTGTCCACACAGGTAGACACACGGGCGTGTGTCTAGGCTGTGTGAGACAC
1 GTAGATAGCCTTATATTGTCCACACAGGTAGACACACGGGCGTGTGTCTAGGCTGTGTGAGACAC
*
58722817 ATGGCCAGCCCTATGGGCATGTTGTCCAGCTGTGTGTCCCCTGCACGTAAAAATTACAAGTT-AG
66 ATGGCCAGCCCTATGGGCATGTTGTCCAGCCGTGTGTCCCCTGCACGTAAAAATTACAA-TTCAG
*
58722881 TATGCATGGTAGTAAACACATGGGCAGAGACACGACCGTGTGTCTCAGCCGTGTGAAAGACATAA
130 TATGCATGGTAGTAAACACATGGGCAGAGACACGACCGTGTGTCTCAGCCGTGTGAAAGACACAA
58722946 CCTTTGGCCACGAGCGTGTGCCTTGGCCATGTGCCCCTTATTGGATGCTGACGTCAGAAATAGAA
195 CCTTTGGCCACGAGCGTGTGCCTTGGCCATGTGCCCCTTATTGGATGCTGACGTCAGAAATAGAA
*
58723011 TGTCAAGGCTTTTAGACACGGCCTAGGACACGGGCGTGTCACGGCCGTGTAAGAGACACGGGCTA
260 TGTCAAGGCTTTTAGACACGGCCTAGGACACGAGCGTGTCACGGCCGTGTAAGAGACACGGGCTA
58723076 TAGACACGGGCGTGTGTCAAGCCTTGTGAAAACCCCTGTAGGTTCGAATTT
325 TAGACACGGGCGTGTGTCAAGCCTTGTGAAAACCCCTGTAGGTTCGAATTT
58723127 G
1 G
58723128 GAATTAAATT
Statistics
Matches: 369, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
375 367 0.99
376 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.24
Consensus pattern (375 bp):
GTAGATAGCCTTATATTGTCCACACAGGTAGACACACGGGCGTGTGTCTAGGCTGTGTGAGACAC
ATGGCCAGCCCTATGGGCATGTTGTCCAGCCGTGTGTCCCCTGCACGTAAAAATTACAATTCAGT
ATGCATGGTAGTAAACACATGGGCAGAGACACGACCGTGTGTCTCAGCCGTGTGAAAGACACAAC
CTTTGGCCACGAGCGTGTGCCTTGGCCATGTGCCCCTTATTGGATGCTGACGTCAGAAATAGAAT
GTCAAGGCTTTTAGACACGGCCTAGGACACGAGCGTGTCACGGCCGTGTAAGAGACACGGGCTAT
AGACACGGGCGTGTGTCAAGCCTTGTGAAAACCCCTGTAGGTTCGAATTT
Found at i:58728304 original size:20 final size:20
Alignment explanation
Indices: 58728257--58728304 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
58728247 AGATAGGGGC
* * * *
58728257 ACATGCCTGTGTGGCTTGGG
1 ACATGCCCGTATGGCCTGGA
*
58728277 ACACGCCCGTATGGCCTGGA
1 ACATGCCCGTATGGCCTGGA
58728297 ACATGCCC
1 ACATGCCC
58728305 ATGTGCTACA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.21
Consensus pattern (20 bp):
ACATGCCCGTATGGCCTGGA
Found at i:58728565 original size:17 final size:21
Alignment explanation
Indices: 58728543--58728585 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
58728533 ACCTAAAAAT
58728543 TTTCAA-CC-AAACAA-T-TA
1 TTTCAAGCCAAAACAAGTATA
58728560 TTTCAAGCCAAAACAAGTATA
1 TTTCAAGCCAAAACAAGTATA
58728581 TTTCA
1 TTTCA
58728586 TTTTCCAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.27
18 2 0.09
19 6 0.27
20 1 0.05
21 7 0.32
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (21 bp):
TTTCAAGCCAAAACAAGTATA
Found at i:58729198 original size:53 final size:51
Alignment explanation
Indices: 58729082--58729268 Score: 190
Period size: 52 Copynumber: 3.7 Consensus size: 51
58729072 CACATCACAC
* * *
58729082 ACCGAAGCCATAGCCCTA-CCATGGTCTTATACGGATCAC--AT---ATCAT
1 ACCGATGCCATAGCCC-AGCTATGGTCTTATACGGAACACGAATCACATCAT
* * * *
58729128 ACCGATGCCATATCCCAGATATGGTCTTATACGGAATTAC-ATTATCACATCAC
1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAA-CACGA--ATCACATCAT
**
58729181 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAACACGAATCACATTGT
1 ACCGATGCCATAGCCCAGCTATGGTCTTATAC-GGAACACGAATCACATCAT
*
58729233 ACCGATGCCATAGCCCGGCTATGGTCTTATACGGAA
1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAA
58729269 GCATATATCA
Statistics
Matches: 117, Mismatches: 14, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
45 1 0.01
46 29 0.25
47 2 0.02
50 2 0.02
51 4 0.03
52 38 0.32
53 36 0.31
54 5 0.04
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (51 bp):
ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAACACGAATCACATCAT
Found at i:58729245 original size:52 final size:53
Alignment explanation
Indices: 58729123--58729282 Score: 193
Period size: 52 Copynumber: 3.1 Consensus size: 53
58729113 CGGATCACAT
* * *
58729123 ATCATACCGATGCCATATCCCAGATATGGTCTTATAC-GGAATTACATTATCAC
1 ATCATACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAATCACA-TATCAC
*
58729176 ATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAA-CACGA-ATCAC
1 ATCATACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAATCAC-ATATCAC
** * * *
58729228 ATTGTACCGATGCCATAGCCCGGCTATGGTCTTATAC-GGAAGCATATATCAC
1 ATCATACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAATCACATATCAC
58729280 ATC
1 ATC
58729283 TTTTCCGTCA
Statistics
Matches: 93, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
51 5 0.05
52 47 0.51
53 36 0.39
54 5 0.05
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (53 bp):
ATCATACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAATCACATATCAC
Found at i:58732230 original size:46 final size:44
Alignment explanation
Indices: 58732074--58732288 Score: 159
Period size: 46 Copynumber: 4.7 Consensus size: 44
58732064 GGGTTAATTG
* *
58732074 TGTGCTAGTGTAAGACATGTTTGGGACATGCATCGGCC-ACATTATGA
1 TGTGCCAGTGTAAGACATGTCTGGGACATGCATC-GCCTACA--A-GA
* * * * *
58732121 -GAGCCAGTGTAAGGCCATGTCTGGGACATGGCATCGGCATTGAGACGA
1 TGTGCCAGTGTAA-GACATGTCTGGGACAT-GCATC-GC-CT-ACAAGA
* * * * *
58732169 -GAGCTAGTGTAAGACATATCTGGGACATGCCTCAGCCT-CGAGA
1 TGTGCCAGTGTAAGACATGTCTGGGACATGCATC-GCCTACAAGA
*
58732212 TGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGA
1 TGT--GCCAGTGTAAGACATGTCTGGGACATGCATCGCCTACAAGA
*
58732258 TGTGTCAGTGTAAGACCATGTCTGGGACATG
1 TGTGCCAGTGTAAGA-CATGTCTGGGACATG
58732289 GGTTCGGTAC
Statistics
Matches: 135, Mismatches: 23, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
43 2 0.01
44 12 0.09
45 19 0.14
46 51 0.38
47 28 0.21
48 21 0.16
51 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (44 bp):
TGTGCCAGTGTAAGACATGTCTGGGACATGCATCGCCTACAAGA
Found at i:58733459 original size:159 final size:160
Alignment explanation
Indices: 58733239--58733553 Score: 461
Period size: 159 Copynumber: 2.0 Consensus size: 160
58733229 CCTACTTTTA
**
58733239 TTTTATGAGCATGATGATGAATGGAAAAGTTGTTGTTATATTTATTTTCATGCAACTTACTAAGC
1 TTTTATGAGCATGATGATGAATGGAAAAGTTGTTGTTATATTTATTTTCAAACAACTTACTAAGC
58733304 TTTATGCTTACCCCATTTCTTTCCATTTTCTTATAGTGCCACCTAATTAGCTCGTGGATCAACAA
66 TTTATGCTTACCCCATTTCTTTCCATTTTCTTATAGTGCCACCTAATTAGCTCGTGGATCAACAA
* * *
58733369 ACGTTGGAGGCATCGATCATACTATCTTGG
131 ACGTCGAAGGCATCGATCACACTATCTTGG
* *
58733399 TTTTATGAGCATGATGATGGATGGTAAAGTTG-TGTTATATTTATTTTCAAACAACTTACTAAGC
1 TTTTATGAGCATGATGATGAATGGAAAAGTTGTTGTTATATTTATTTTCAAACAACTTACTAAGC
*** ** ** * ***
58733463 TTTATGCTTACCTTGTTTCTTTTTATTTTCTTATAGTGCTGCCTAATTAGCTTGTGGATCAATGG
66 TTTATGCTTACCCCATTTCTTTCCATTTTCTTATAGTGCCACCTAATTAGCTCGTGGATCAACAA
58733528 ACGTCGAAGGCATCGATCACACTATC
131 ACGTCGAAGGCATCGATCACACTATC
58733554 ATTTGAAACA
Statistics
Matches: 137, Mismatches: 18, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
159 107 0.78
160 30 0.22
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (160 bp):
TTTTATGAGCATGATGATGAATGGAAAAGTTGTTGTTATATTTATTTTCAAACAACTTACTAAGC
TTTATGCTTACCCCATTTCTTTCCATTTTCTTATAGTGCCACCTAATTAGCTCGTGGATCAACAA
ACGTCGAAGGCATCGATCACACTATCTTGG
Found at i:58736975 original size:17 final size:19
Alignment explanation
Indices: 58736945--58736983 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
58736935 ATGTAGCCAA
58736945 CCCGTGTGGGCCCACA-AG
1 CCCGTGTGGGCCCACACAG
58736963 CCCGTGT-GGCCCACACAG
1 CCCGTGTGGGCCCACACAG
58736981 CCC
1 CCC
58736984 AAATTGACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.15, C:0.46, G:0.28, T:0.10
Consensus pattern (19 bp):
CCCGTGTGGGCCCACACAG
Found at i:58747700 original size:19 final size:18
Alignment explanation
Indices: 58747676--58747739 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 18
58747666 AATATTACAA
*
58747676 AAAAAATTAAAAATGATTT
1 AAAAAATTCAAAAT-ATTT
58747695 AAAAAAATTCAAAATAACTTT
1 -AAAAAATTCAAAAT-A-TTT
*
58747716 -TAAAATTCAAAATATTT
1 AAAAAATTCAAAATATTT
58747733 ATAAAAA
1 A-AAAAA
58747740 AAATTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
17 3 0.08
18 1 0.03
19 16 0.43
20 14 0.38
21 3 0.08
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAAAATTCAAAATATTT
Found at i:58747778 original size:28 final size:27
Alignment explanation
Indices: 58747727--58747784 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
58747717 AAAATTCAAA
* *
58747727 ATATTTATAAAAAAAATTTCAAAATTT
1 ATATTTATAAAAAAAATTTAAAAATAT
* *
58747754 ATATTTTTTAAAAAAATTCTAAAAATAT
1 ATATTTATAAAAAAAATT-TAAAAATAT
58747782 ATA
1 ATA
58747785 AGAAAAGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (27 bp):
ATATTTATAAAAAAAATTTAAAAATAT
Found at i:58748296 original size:2 final size:2
Alignment explanation
Indices: 58748289--58748326 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
58748279 TCCTTGTTAG
58748289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58748327 AGTTGTAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58748826 original size:30 final size:30
Alignment explanation
Indices: 58748790--58748848 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
58748780 CAACTTAACA
*
58748790 AGCAAATGCCTCTAAAATAATAACAAAATT
1 AGCAAATGCCTCTAAAATAATAAAAAAATT
* *
58748820 AGCAAATGTCTTTAAAATAATAAAAAAAT
1 AGCAAATGCCTCTAAAATAATAAAAAAAT
58748849 AAACAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.56, C:0.12, G:0.07, T:0.25
Consensus pattern (30 bp):
AGCAAATGCCTCTAAAATAATAAAAAAATT
Found at i:58748909 original size:22 final size:22
Alignment explanation
Indices: 58748884--58748926 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
58748874 TATCCAAACA
58748884 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
58748906 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
58748927 AGTAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:58751150 original size:43 final size:43
Alignment explanation
Indices: 58751091--58751277 Score: 288
Period size: 43 Copynumber: 4.3 Consensus size: 43
58751081 AGTTTTTCAG
58751091 AAAAAAGCGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTCTAC
1 AAAAAA-CGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTCTAC
*
58751135 AAAAAACGTCGCTAAAGACCAGGACCTTTAGCGGCGCTTCTAC
1 AAAAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTCTAC
* *
58751178 -AAAAACGCCGCTAAAAAACAGGACCTTTAGCGGCGCTTCTTA-
1 AAAAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTC-TAC
* * *
58751220 AAAAAACGCCGCTAAAGTCCAGGACCTTTAGCGACGCTTCTTC
1 AAAAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTCTAC
58751263 AAAAAACGCCGCTAA
1 AAAAAACGCCGCTAA
58751278 TTTGCCCAGT
Statistics
Matches: 131, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
42 37 0.28
43 88 0.67
44 6 0.05
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (43 bp):
AAAAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTCTAC
Found at i:58751236 original size:85 final size:86
Alignment explanation
Indices: 58751091--58751277 Score: 288
Period size: 85 Copynumber: 2.2 Consensus size: 86
58751081 AGTTTTTCAG
* * *
58751091 AAAAAAGCGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTCTACAAAAAACGTCGCTAAAGACCA
1 AAAAAA-CGCCGCTAAAAAACAGGACCTTTAGCGGCGCTTCTACAAAAAACGCCGCTAAAGACCA
*
58751156 GGACCTTTAGCGGCGCTTCTAC
65 GGACCTTTAGCGACGCTTCTAC
*
58751178 -AAAAACGCCGCTAAAAAACAGGACCTTTAGCGGCGCTTCTTA-AAAAAACGCCGCTAAAGTCCA
1 AAAAAACGCCGCTAAAAAACAGGACCTTTAGCGGCGCTTC-TACAAAAAACGCCGCTAAAGACCA
*
58751241 GGACCTTTAGCGACGCTTCTTC
65 GGACCTTTAGCGACGCTTCTAC
58751263 AAAAAACGCCGCTAA
1 AAAAAACGCCGCTAA
58751278 TTTGCCCAGT
Statistics
Matches: 92, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
85 71 0.77
86 21 0.23
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (86 bp):
AAAAAACGCCGCTAAAAAACAGGACCTTTAGCGGCGCTTCTACAAAAAACGCCGCTAAAGACCAG
GACCTTTAGCGACGCTTCTAC
Found at i:58751598 original size:21 final size:21
Alignment explanation
Indices: 58751574--58751616 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
58751564 GTTCTGCTCT
58751574 GCCTCCCTCGCTGCTGCCTCC
1 GCCTCCCTCGCTGCTGCCTCC
*
58751595 GCCTCCCTCGTTGCTGCCTCC
1 GCCTCCCTCGCTGCTGCCTCC
58751616 G
1 G
58751617 TTCTAAGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.53, G:0.21, T:0.26
Consensus pattern (21 bp):
GCCTCCCTCGCTGCTGCCTCC
Found at i:58757157 original size:9 final size:9
Alignment explanation
Indices: 58757143--58757270 Score: 112
Period size: 9 Copynumber: 13.6 Consensus size: 9
58757133 ATGTATTAGT
58757143 TAAGTTATG
1 TAAGTTATG
58757152 TAAGTTGTTATG
1 TAA---GTTATG
*
58757164 TACGTTATG
1 TAAGTTATG
*
58757173 TGAGTTATG
1 TAAGTTATG
*
58757182 TAAATTATG
1 TAAGTTATG
58757191 TAAGTTATG
1 TAAGTTATG
*
58757200 TGAGTTATG
1 TAAGTTATG
58757209 TAAGTTGTTATG
1 TAA---GTTATG
*
58757221 TAAATTATG
1 TAAGTTATG
*
58757230 TAAGTTATA
1 TAAGTTATG
* *
58757239 TGAGTTATT
1 TAAGTTATG
58757248 TAAGTTATG
1 TAAGTTATG
* *
58757257 TAATTTATT
1 TAAGTTATG
58757266 TAAGT
1 TAAGT
58757271 AATGATCAAT
Statistics
Matches: 95, Mismatches: 18, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
9 78 0.82
12 17 0.18
ACGTcount: A:0.31, C:0.01, G:0.20, T:0.48
Consensus pattern (9 bp):
TAAGTTATG
Found at i:58757270 original size:57 final size:57
Alignment explanation
Indices: 58757143--58757270 Score: 166
Period size: 57 Copynumber: 2.2 Consensus size: 57
58757133 ATGTATTAGT
** * *
58757143 TAAGTTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
* * * *
58757200 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATTTAAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
* *
58757257 TAATTTATTTAAGT
1 TAAGTTATGTAAGT
58757271 AATGATCAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.31, C:0.01, G:0.20, T:0.48
Consensus pattern (57 bp):
TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
Found at i:58757873 original size:241 final size:241
Alignment explanation
Indices: 58757450--58757936 Score: 902
Period size: 241 Copynumber: 2.0 Consensus size: 241
58757440 TTAAGGTTAT
*
58757450 ATAAATATTCAATAGTAAATGAGATCGATAGAAGTTTTTCCAAGTCTTTTTGAAGTTTTTAAGAT
1 ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTTCCAAGTCTTTTTGAAGTTTTTAAGAT
* *
58757515 TCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACTGCTCGATATAAGGCA
66 TCATCATACGTGGCGTTGTTACACCTAAGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
58757580 ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
131 ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
58757645 GGTCAGCTATTGTTGTAATTTTAATGAACAAGCAAGCTACATGGTA
196 GGTCAGCTATTGTTGTAATTTTAATGAACAAGCAAGCTACATGGTA
* * *
58757691 ATAAATATTCAATAGTAAATGAGCTCGATAGAACTTTTTTCAAGTCTTTTTGAATTTTTTAAGAT
1 ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTTCCAAGTCTTTTTGAAGTTTTTAAGAT
58757756 TCATCATACGTGGCGTTGTTACACCTAAGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
66 TCATCATACGTGGCGTTGTTACACCTAAGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
58757821 ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
131 ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
* *
58757886 GGTCAGTTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTA
196 GGTCAGCTATTGTTGTAATTTTAATGAACAAGCAAGCTACATGGTA
58757932 ATAAA
1 ATAAA
58757937 ATTAATTCAT
Statistics
Matches: 238, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
241 238 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34
Consensus pattern (241 bp):
ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTTCCAAGTCTTTTTGAAGTTTTTAAGAT
TCATCATACGTGGCGTTGTTACACCTAAGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
GGTCAGCTATTGTTGTAATTTTAATGAACAAGCAAGCTACATGGTA
Found at i:58763282 original size:41 final size:41
Alignment explanation
Indices: 58763225--58763439 Score: 258
Period size: 41 Copynumber: 5.3 Consensus size: 41
58763215 TTATATGACT
*
58763225 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTGGGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCGGGTC
*
58763266 TTTAGCGGCATTTTACCAAAAGCGCCGCTAATGCTCGGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCGGGTC
* *
58763307 TTTAGCAGCGTTATACCAAAAGCGCCGCTAATGCTCGGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCGGGTC
* * * * *
58763348 TTTAGCGCCGTTTTACCAAAAGCACTGCTAATGCTC-TGTT
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCGGGTC
* * * * * * *
58763388 TTTGGCGGTGTTTTA--AAAAACGCCACTATTGCTC-TGTT
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCGGGTC
58763426 TTTAGCGGCGTTTT
1 TTTAGCGGCGTTTT
58763440 TCGTAAGACG
Statistics
Matches: 152, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
38 30 0.20
40 14 0.09
41 108 0.71
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCGGGTC
Found at i:58764618 original size:85 final size:85
Alignment explanation
Indices: 58764462--58764623 Score: 211
Period size: 85 Copynumber: 1.9 Consensus size: 85
58764452 ACCACCACTG
* *
58764462 ATTTACAGTTACTGCTACTTGTTGTAGGTGCACAACATATTTGCAGATTAAACAAACTACTACTA
1 ATTTACAGTTACTGCCACTTGTTGTAGGTGCACAACATATTTGCAGATTAAAAAAACTACTACTA
* *
58764527 GGTTCATGATCGTACAATAT
66 GATTCATAATCGTACAATAT
* * * *
58764547 ATTTGCAGTTACTGCCACTTGTTGT-GAGTGTACAACGTATTTGCAGATTAAAAAAATTGAC-AC
1 ATTTACAGTTACTGCCACTTGTTGTAG-GTGCACAACATATTTGCAGATTAAAAAAACT-ACTAC
*
58764610 TTGATTCATAATCG
64 TAGATTCATAATCG
58764624 AACCACATAT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 1 0.02
85 63 0.95
86 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (85 bp):
ATTTACAGTTACTGCCACTTGTTGTAGGTGCACAACATATTTGCAGATTAAAAAAACTACTACTA
GATTCATAATCGTACAATAT
Found at i:58765777 original size:63 final size:63
Alignment explanation
Indices: 58765678--58765826 Score: 155
Period size: 63 Copynumber: 2.4 Consensus size: 63
58765668 GAGTCAAACG
* * *
58765678 GGTGAAACACACGAGCGTGTGTTTAGGTCGTGTAACTCAT-TGAG-TTTGTATTAGAGGCACATA
1 GGTGAAACACACGAGCGTGTGTCTAAGCCGTGTAACTC-TCTGAGCTTT-TATTAGAGGCACATA
* * *
58765741 GGTGAGACACACGGGTGTGTGTCTAAGCCGTGTAACTCTCTGAGCTTTTATTAGA-G-ACATA
1 GGTGAAACACACGAGCGTGTGTCTAAGCCGTGTAACTCTCTGAGCTTTTATTAGAGGCACATA
*
58765802 CGGGTGAGAA-ACATGAGCGTGTGTC
1 --GGTGA-AACACACGAGCGTGTGTC
58765827 CAAGATGTGT
Statistics
Matches: 71, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
61 5 0.07
62 2 0.03
63 60 0.85
64 4 0.06
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (63 bp):
GGTGAAACACACGAGCGTGTGTCTAAGCCGTGTAACTCTCTGAGCTTTTATTAGAGGCACATA
Found at i:58773360 original size:24 final size:24
Alignment explanation
Indices: 58773306--58773364 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 24
58773296 TAGATTTGTT
58773306 AAATCAAATT-TTTTAAATGTAAAA
1 AAAT-AAATTATTTTAAATGTAAAA
*
58773330 AATATAAATTATTTTAAAT-TATTAA
1 AA-ATAAATTATTTTAAATGTA-AAA
58773355 AAATAAATTA
1 AAATAAATTA
58773365 AGCTTTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 17 0.55
25 14 0.45
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
AAATAAATTATTTTAAATGTAAAA
Found at i:58773745 original size:21 final size:22
Alignment explanation
Indices: 58773695--58773749 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
58773685 TGAAAATGTC
*
58773695 AAATGTTATAAAATTTATTTTAA
1 AAATATTATAAAATTTA-TTTAA
*
58773718 AAA-ATTATAAGATTTA-TTAA
1 AAATATTATAAAATTTATTTAA
58773738 AAATATTA-AAAA
1 AAATATTATAAAA
58773750 CTTAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 10 0.36
21 4 0.14
22 11 0.39
23 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
AAATATTATAAAATTTATTTAA
Found at i:58776228 original size:15 final size:15
Alignment explanation
Indices: 58776208--58776236 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
58776198 TGTAAAGAAA
58776208 AATGAATATTGTAAC
1 AATGAATATTGTAAC
58776223 AATGAATATTGTAA
1 AATGAATATTGTAA
58776237 AAATCTTAGT
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:0.48, C:0.03, G:0.14, T:0.34
Consensus pattern (15 bp):
AATGAATATTGTAAC
Found at i:58783410 original size:15 final size:15
Alignment explanation
Indices: 58783381--58783429 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
58783371 ACGGAGAAGC
*
58783381 CCAAAATAAAGAAAT
1 CCAAGATAAAGAAAT
58783396 CCAAGATAAAGAAAT
1 CCAAGATAAAGAAAT
* *
58783411 CCACGATAAGGAAAT
1 CCAAGATAAAGAAAT
58783426 CCAA
1 CCAA
58783430 TTTACAGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.57, C:0.18, G:0.12, T:0.12
Consensus pattern (15 bp):
CCAAGATAAAGAAAT
Found at i:58789000 original size:2 final size:2
Alignment explanation
Indices: 58788993--58789020 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
58788983 ATAAAAATAC
58788993 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58789021 GCATATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58789407 original size:16 final size:16
Alignment explanation
Indices: 58789387--58789420 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
58789377 TTTATTTTTT
*
58789387 ATTTTT-TTAAGACCA
1 ATTTTTGTTTAGACCA
58789402 ATTTTTGTTTAGACCA
1 ATTTTTGTTTAGACCA
58789418 ATT
1 ATT
58789421 ACAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (16 bp):
ATTTTTGTTTAGACCA
Found at i:58790216 original size:29 final size:28
Alignment explanation
Indices: 58790170--58790269 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 28
58790160 TTCTGGGGCT
*
58790170 AAATGTAATTTTTAGAAAATTTAGGGTTA
1 AAATGTAA-TTTAAGAAAATTTAGGGTTA
*
58790199 AAATGTAATTTAAGGAAAGTTTAGGGTCT-
1 AAATGTAATTTAA-GAAAATTTAGGGT-TA
* * *
58790228 AAGTGAAATTTAAAGAAAAGTTTAGGTGTCA
1 AAATGTAATTT-AAGAAAA-TTTAGG-GTTA
*
58790259 AAATGCAATTT
1 AAATGTAATTT
58790270 TTTTATTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
28 4 0.07
29 33 0.58
30 9 0.16
31 11 0.19
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (28 bp):
AAATGTAATTTAAGAAAATTTAGGGTTA
Found at i:58790250 original size:30 final size:29
Alignment explanation
Indices: 58790183--58790269 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
58790173 TGTAATTTTT
*
58790183 AGAAAA-TTTAGGGTTAAAATGTAATTTA
1 AGAAAAGTTTAGGGTTAAAATGAAATTTA
* *
58790211 AGGAAAGTTTAGGGTCT-AAGTGAAATTTAA
1 AGAAAAGTTTAGGGT-TAAAATGAAATTT-A
* *
58790241 AGAAAAGTTTAGGTGTCAAAATGCAATTT
1 AGAAAAGTTTAGG-GTTAAAATGAAATTT
58790270 TTTTATTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
28 5 0.11
29 17 0.36
30 14 0.30
31 11 0.23
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.32
Consensus pattern (29 bp):
AGAAAAGTTTAGGGTTAAAATGAAATTTA
Found at i:58790861 original size:72 final size:73
Alignment explanation
Indices: 58790526--58791276 Score: 870
Period size: 72 Copynumber: 10.1 Consensus size: 73
58790516 AAAAGCCAAA
* * * ** * *
58790526 AAATTGAAAATACCTCAGCGTGTGACCTGAGGCTTAACTCACCTCTCGCAATACGAGTTGATTTT
1 AAATTGAAAATACCTCAACGTGT--CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TAT
*
58790591 TTTGACAACAG
63 TTTGAAAACAG
* * * ** *
58790602 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA---TAT
* * *
58790667 TTTAAAAGATAA
63 TTTGAAA-ACAG
* * * *
58790679 AAATTGAAAATACCTC-GCATGTCTTAAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA---TAT
58790743 TTTGAAAAACAG
63 TTTG-AAAACAG
* * *
58790755 AAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAGTATGAGTTGA-ATTTT
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTT
*
58790819 GAAAATAG
66 GAAAACAG
* * *
58790827 AAATTGAAATTACCTTAACGTGTCTTGAGGCTCAACTCATTTCTCGCACTATGAGTTGA-ATTTT
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTT
*
58790891 GAAAATAG
66 GAAAACAG
*
58790899 AAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTT
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTT
58790963 GAAAACAG
66 GAAAACAG
* * *
58790971 AAATTGAAAATAACTCAACGTGTCTTGAGGCTCAACTCATTTCTAGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTT
58791036 GAAAAACATAAATTGAATAG
66 G-AAAAC-----------AG
** *
58791056 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTT
58791121 GAAAAGCAG
66 GAAAA-CAG
*
58791130 AAATT-AAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTT
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTT
58791193 GAAAACAG
66 GAAAACAG
* *
58791201 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTTGCAATATGAGTTGA-ATTTT
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATA-TTT
58791265 TG-AAACAG
65 TGAAAACAG
58791273 AAAT
1 AAAT
58791277 AAAAGCATCA
Statistics
Matches: 609, Mismatches: 45, Indels: 46
0.87 0.06 0.07
Matches are distributed among these distances:
71 8 0.01
72 266 0.44
73 65 0.11
74 46 0.08
76 95 0.16
77 60 0.10
84 4 0.01
85 65 0.11
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (73 bp):
AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTT
GAAAACAG
Found at i:58791174 original size:230 final size:229
Alignment explanation
Indices: 58790822--58791269 Score: 754
Period size: 230 Copynumber: 2.0 Consensus size: 229
58790812 GAATTTTGAA
* * ** *
58790822 AATAGAAATTGAAATTACCTTAACGTGTCTTGAGGCTCAACTCATTTCTCGCACTATGAGTTGAA
1 AATAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAA
*
58790887 TTTTGAAAATAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCGCAATATG
66 TTTTGAAAACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCGCAATATG
58790952 AGTTGAATTTTGAAAACAGAAATTGAAAATAACTCAACGTGTCTTGAGGCTCAACTCATTTCTAG
131 AGTTGAATTTTGAAAACAGAAATTGAAAATAACTCAACGTGTCTTGAGGCTCAACTCATTTCTAG
*
58791017 CAATATGAGTTGATTTTTTGAAAAACATAAATTG
196 CAATATGAGTTGAATTTTTGAAAAACATAAATTG
58791051 AATAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AATAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
* **
58791116 TTTTTGAAAAGCAGAAATT-AAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATA
65 ATTTTGAAAA-CAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCGCAATA
* *
58791180 TGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCT
129 TGAGTTGAATTTTGAAAACAGAAATTGAAAATAACTCAACGTGTCTTGAGGCTCAACTCATTTCT
*
58791245 TGCAATATGAGTTGAATTTTTGAAA
194 AGCAATATGAGTTGAATTTTTGAAA
58791270 CAGAAATAAA
Statistics
Matches: 204, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
229 59 0.29
230 138 0.68
231 7 0.03
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (229 bp):
AATAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAA
TTTTGAAAACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCGCAATATG
AGTTGAATTTTGAAAACAGAAATTGAAAATAACTCAACGTGTCTTGAGGCTCAACTCATTTCTAG
CAATATGAGTTGAATTTTTGAAAAACATAAATTG
Found at i:58791196 original size:302 final size:294
Alignment explanation
Indices: 58790483--58791276 Score: 952
Period size: 302 Copynumber: 2.6 Consensus size: 294
58790473 CCCGAAGTTT
** * *
58790483 AACTCACCTCTCG-AATTATGAGTTGATTTTTAAAAAAGCCAAAAAATTGAAAATACCTCAGCGT
1 AACTCACCTCTCGCAA-TATGAGTTGATTTTTTGAAAAG-C-AGAAATTGAAAATACCTCA--AT
* * * ** * * *
58790547 GTGACCTGAGGCTTAACTCACCTCTCGCAATACGAGTTGATTTTTTTGACAACAGAAATTGAAAT
61 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAAT
* * ** * * *
58790612 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAAAGAT
124 TACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA----ATTTTGAAA-AC
* * * *
58790677 AAAAATTGAAAATACCTCGCATGTCTTAAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
184 AGAAATTGAAAATAACTCACATGTCTTAAGGCTCAACTCATTTCTAGCAATATGAGTTGATTTTT
** *
58790742 TTTTGAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTC
249 TCATGAAAAACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTC
** * * * * * *
58790788 AACTCATTTCTCGCAGTATGAGTTGA-ATTTTGAAAA-TAGAAATTGAAATTACCTTAACGTGTC
1 AACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGCAGAAATTGAAAATACCTCAATGTGTC
* * *
58790851 TTGAGGCTCAACTCATTTCTCGCACTATGAGTTGAATTTTGAAAATAGAAATTGAAAATACCTCA
66 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
*
58790916 ACATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAA
131 ACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAA
* *
58790981 TAACTCAACGTGTCTTGAGGCTCAACTCATTTCTAGCAATATGAGTTGATTTTTTGAAAAACAT-
196 TAACTC-ACATGTCTTAAGGCTCAACTCATTTCTAGCAATATGAGTTGATTTTTT------CATG
* *
58791045 AAATTGAATAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTC
254 AAA---AACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTC
58791089 AACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGCAGAAATT-AAAATACCTCAATGTGTC
1 AACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGCAGAAATTGAAAATACCTCAATGTGTC
58791153 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
66 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
*
58791218 ACGTGTCTTGAGGCTCAACTCATTTCTTGCAATATGAGTTGAATTTTTG-AAACAGAAAT
131 ACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA-TTTTGAAAACAGAAAT
58791277 AAAAGCATCA
Statistics
Matches: 420, Mismatches: 55, Indels: 31
0.83 0.11 0.06
Matches are distributed among these distances:
292 17 0.04
293 51 0.12
297 63 0.15
298 3 0.01
299 34 0.08
301 74 0.18
302 137 0.33
303 12 0.03
304 7 0.02
305 21 0.05
306 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (294 bp):
AACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGCAGAAATTGAAAATACCTCAATGTGTC
TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
ACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAA
TAACTCACATGTCTTAAGGCTCAACTCATTTCTAGCAATATGAGTTGATTTTTTCATGAAAAACA
GAAATTGAAAATACCTCAACATGTCTTGAGGCTC
Found at i:58798644 original size:24 final size:24
Alignment explanation
Indices: 58798617--58798666 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
58798607 ATGAAAGTTT
58798617 AATGCAAATG-ATGCAATGCAATGC
1 AATGCAAATGTATGCAATG-AATGC
*
58798641 AATGCAAATGTATGGAATGAATGC
1 AATGCAAATGTATGCAATGAATGC
58798665 AA
1 AA
58798667 AGAAAGGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (24 bp):
AATGCAAATGTATGCAATGAATGC
Found at i:58801069 original size:3 final size:3
Alignment explanation
Indices: 58801063--58801103 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
58801053 ATATATTTGG
58801063 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
58801104 TGTACATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:58801481 original size:13 final size:13
Alignment explanation
Indices: 58801463--58801487 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58801453 AATTTAAAAT
58801463 TTTTTTATTTTTA
1 TTTTTTATTTTTA
58801476 TTTTTTATTTTT
1 TTTTTTATTTTT
58801488 TTTAAGACCA
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:58801503 original size:17 final size:16
Alignment explanation
Indices: 58801482--58801516 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
58801472 TTTATTTTTT
58801482 ATTTTT-TTTAAGACCA
1 ATTTTTGTTT-AGACCA
58801498 ATTTTTGTTTAGACCA
1 ATTTTTGTTTAGACCA
58801514 ATT
1 ATT
58801517 ACAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (16 bp):
ATTTTTGTTTAGACCA
Found at i:58802048 original size:16 final size:16
Alignment explanation
Indices: 58802027--58802070 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
58802017 TTTTTTTGGT
58802027 TTTTTTTTGCTGGAAA
1 TTTTTTTTGCTGGAAA
* *
58802043 TTTTTTTTGTTGGAAT
1 TTTTTTTTGCTGGAAA
58802059 TTTTGTTTTGCT
1 TTTT-TTTTGCT
58802071 TTTTTTTCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.11, C:0.05, G:0.18, T:0.66
Consensus pattern (16 bp):
TTTTTTTTGCTGGAAA
Found at i:58802376 original size:30 final size:30
Alignment explanation
Indices: 58802295--58802379 Score: 102
Period size: 30 Copynumber: 2.9 Consensus size: 30
58802285 TAATTTTTAG
* *
58802295 AAAA-TTTA-GGGTTAAAATGTAATTTAAG
1 AAAAGTTTAGGGGTTAAAATGAAATTTAAA
* * *
58802323 GAAAGTTTAGGGGTTTAAGTGAAATTTAAA
1 AAAAGTTTAGGGGTTAAAATGAAATTTAAA
*
58802353 AAAAGTTTAGGGGTCAAAATGAAATTT
1 AAAAGTTTAGGGGTTAAAATGAAATTT
58802380 TTTTATTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
28 3 0.07
29 4 0.09
30 39 0.85
ACGTcount: A:0.44, C:0.01, G:0.22, T:0.33
Consensus pattern (30 bp):
AAAAGTTTAGGGGTTAAAATGAAATTTAAA
Found at i:58808930 original size:47 final size:47
Alignment explanation
Indices: 58808843--58809058 Score: 165
Period size: 47 Copynumber: 4.6 Consensus size: 47
58808833 TAAGGTGCCA
** * * *
58808843 ATGCCATGTCTTAGACACGGTCTTACACTGGCTCAT-ATCTCAAGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCATCTCAAGCCG
* * * *
58808890 ATGCCATATCTCAAACATGGTCTTACACTGACTATCATCTCGTAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTC-AAGCCG
** *
58808938 ATG-CATGTCCCAGACAT-GTCTTACACT-ACCCCTCGTCTCAATGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGA-CTATCATCTCAA-GCCG
* * * * ***
58808984 ATGCCATGTCCCAGACATTGTCTTACACTGGCTCTCATAATGTCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTATCAT-CTCAAGCCG
*
58809032 AT-ACATGTCCCAGACAT-GTCTTACACT
1 ATGCCATGTCCCAGACATGGTCTTACACT
58809059 AGCTCACACA
Statistics
Matches: 139, Mismatches: 22, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
45 2 0.01
46 36 0.26
47 72 0.52
48 28 0.20
49 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (47 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTCAAGCCG
Found at i:58809008 original size:94 final size:93
Alignment explanation
Indices: 58808880--58809059 Score: 245
Period size: 94 Copynumber: 1.9 Consensus size: 93
58808870 CTGGCTCATA
* * * *
58808880 TCTCAAGTCGATGCCATATCTCAAACATGGTCTTACACTGACTATCAT-CTCGTAGCCGATGCAT
1 TCTCAAGCCGATGCCATATCCCAAACATGGTCTTACACTGACTATCATAAT-GTAGCCGATACAT
58808944 GTCCCAGACATGTCTTACACTACCCCTCG
65 GTCCCAGACATGTCTTACACTACCCCTCG
* * * * * *
58808973 TCTCAATGCCGATGCCATGTCCCAGACATTGTCTTACACTGGCTCTCATAATGTCGCCGATACAT
1 TCTCAA-GCCGATGCCATATCCCAAACATGGTCTTACACTGACTATCATAATGTAGCCGATACAT
58809038 GTCCCAGACATGTCTTACACTA
65 GTCCCAGACATGTCTTACACTA
58809060 GCTCACACAC
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
93 6 0.08
94 68 0.91
95 1 0.01
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (93 bp):
TCTCAAGCCGATGCCATATCCCAAACATGGTCTTACACTGACTATCATAATGTAGCCGATACATG
TCCCAGACATGTCTTACACTACCCCTCG
Found at i:58812386 original size:29 final size:30
Alignment explanation
Indices: 58812344--58812402 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
58812334 ACTTAACAAG
58812344 CAAATGCCTCTAAAATAA-AAAAAAATTAA
1 CAAATGCCTCTAAAATAATAAAAAAATTAA
* * *
58812373 CAAATGTCTTTAAAATAATAATAAAATTAA
1 CAAATGCCTCTAAAATAATAAAAAAATTAA
58812403 TAATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAAAAAAATTAA
Found at i:58812405 original size:12 final size:12
Alignment explanation
Indices: 58812383--58812411 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
58812373 CAAATGTCTT
58812383 TAAAA-TAATAA
1 TAAAATTAATAA
58812394 TAAAATTAATAA
1 TAAAATTAATAA
58812406 TAAAAT
1 TAAAAT
58812412 AAGTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAATAA
Found at i:58812460 original size:22 final size:22
Alignment explanation
Indices: 58812435--58812477 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
58812425 TATCCAAACA
58812435 ATAACAACAAAATAGTAGCAAT
1 ATAACAACAAAATAGTAGCAAT
* **
58812457 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
58812478 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAT
Found at i:58812481 original size:11 final size:11
Alignment explanation
Indices: 58812442--58812482 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
58812432 ACAATAACAA
58812442 CAAAATAGTAG
1 CAAAATAGTAG
* *
58812453 CAATATAATAG
1 CAAAATAGTAG
*
58812464 TAAAATAGTAG
1 CAAAATAGTAG
58812475 CAAAATAG
1 CAAAATAG
58812483 GGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:58814000 original size:20 final size:19
Alignment explanation
Indices: 58813963--58814012 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
58813953 CTTTTACTGG
*
58813963 AAAAAAATAAAACTAATTTT
1 AAAAAAATAAAAC-AAATTT
**
58813983 AAAAAAATAAAGGAAATTT
1 AAAAAAATAAAACAAATTT
*
58814002 AAAAAGATAAA
1 AAAAAAATAAA
58814013 TGATTTTTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (19 bp):
AAAAAAATAAAACAAATTT
Found at i:58814729 original size:13 final size:13
Alignment explanation
Indices: 58814690--58814742 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
58814680 TTTAAACCAA
58814690 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
58814703 ACATATTC-ACAGC
1 AC-TTTTCAAAAGC
58814716 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
58814729 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
58814742 A
1 A
58814743 TTGCCAAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 4 0.12
13 26 0.76
14 4 0.12
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.28
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:58816536 original size:24 final size:24
Alignment explanation
Indices: 58816504--58816558 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
58816494 ACACCTTCAT
*
58816504 ATACATATACACATGAACACATAC
1 ATACATATACACATAAACACATAC
* * **
58816528 ATACTTATAGACATAAACACATTT
1 ATACATATACACATAAACACATAC
58816552 ATACATA
1 ATACATA
58816559 CCTTCCACAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (24 bp):
ATACATATACACATAAACACATAC
Found at i:58818487 original size:18 final size:18
Alignment explanation
Indices: 58818459--58818525 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 18
58818449 CTTTAACTAA
* * *
58818459 AAAAATTAAAATTAATTC
1 AAAAATAAAAATAAATCC
58818477 AAAAATAAAAAATAAATCC
1 AAAAAT-AAAAATAAATCC
*
58818496 AAAAGAT-AAAATAAATGAC
1 AAAA-ATAAAAATAAAT-CC
58818515 AAAAATGAAAA
1 AAAAAT-AAAA
58818526 CTTTATAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
18 17 0.43
19 18 0.45
20 5 0.12
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.19
Consensus pattern (18 bp):
AAAAATAAAAATAAATCC
Found at i:58818488 original size:19 final size:20
Alignment explanation
Indices: 58818466--58818506 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
58818456 TAAAAAAATT
* *
58818466 AAAATTAATTCAAAA-ATAA
1 AAAATAAATCCAAAAGATAA
58818485 AAAATAAATCCAAAAGATAA
1 AAAATAAATCCAAAAGATAA
58818505 AA
1 AA
58818507 TAAATGACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAATAAATCCAAAAGATAA
Found at i:58823748 original size:19 final size:20
Alignment explanation
Indices: 58823718--58823756 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
58823708 CAAATTAGGC
*
58823718 TTTTCTGATGCATTTAAGGA
1 TTTTCTGATGCACTTAAGGA
58823738 TTTTC-GATGCACTTAAGGA
1 TTTTCTGATGCACTTAAGGA
58823757 GCTTTTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.41
Consensus pattern (20 bp):
TTTTCTGATGCACTTAAGGA
Found at i:58827270 original size:48 final size:47
Alignment explanation
Indices: 58827210--58827486 Score: 293
Period size: 48 Copynumber: 5.8 Consensus size: 47
58827200 AACGGTGCAT
* * * * *
58827210 ATGCCATGTCCCAGACATGGTCTTATACGGGACCTCATATTGATGCCA
1 ATGCCATATCCCAGATATGGTCTTACACGGGATCTCAT-TTGATGCCG
* * * *
58827258 ATTCCATATCCCAGATATGGTCTTATATGGGATCTCATACTGATGCCG
1 ATGCCATATCCCAGATATGGTCTTACACGGGATCTCAT-TTGATGCCG
* * * * *
58827306 ATGCCATATCCTAGATATGGTTTTACACGAGATCTCATCTCGATGGCG
1 ATGCCATATCCCAGATATGGTCTTACACGGGATCTCAT-TTGATGCCG
* * * * *
58827354 ATGCCATATCGCAGATATAGTTTTACATGGGATCTCAGTTCGATGCCG
1 ATGCCATATCCCAGATATGGTCTTACACGGGATCTCA-TTTGATGCCG
* * **
58827402 ATGTCATATCCCATATATGGTCTTACACGGGATCTCATTTCGATGGTG
1 ATGCCATATCCCAGATATGGTCTTACACGGGATCTCATTT-GATGCCG
*
58827450 ATGCCATATCCCAGATATGGTCTTATACGGGATCTCA
1 ATGCCATATCCCAGATATGGTCTTACACGGGATCTCA
58827487 ATACTCACAT
Statistics
Matches: 192, Mismatches: 35, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
47 2 0.01
48 189 0.98
49 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (47 bp):
ATGCCATATCCCAGATATGGTCTTACACGGGATCTCATTTGATGCCG
Found at i:58827311 original size:96 final size:95
Alignment explanation
Indices: 58827210--58827491 Score: 332
Period size: 96 Copynumber: 2.9 Consensus size: 95
58827200 AACGGTGCAT
* * * * * * *
58827210 ATGCCATGTCCCAGACATGGTCTTATACGGGACCTCATATTGATGCCAATTCCATATCCCAGATA
1 ATGCCATATCCCAGATATGGTCTTACACGGGATCTCAT-TTGATGGCGATGCCATATCCCAGATA
58827275 TGGTCTTATATGGGATCTCATACTGATGCCG
65 TGGTCTTATATGGGATCTCATACTGATGCCG
* * * * *
58827306 ATGCCATATCCTAGATATGGTTTTACACGAGATCTCATCTCGATGGCGATGCCATATCGCAGATA
1 ATGCCATATCCCAGATATGGTCTTACACGGGATCTCAT-TTGATGGCGATGCCATATCCCAGATA
* * * *
58827371 TAGTTTTACATGGGATCTCAGTTC-GATGCCG
65 TGGTCTTATATGGGATCTCA-TACTGATGCCG
* * *
58827402 ATGTCATATCCCATATATGGTCTTACACGGGATCTCATTTCGATGGTGATGCCATATCCCAGATA
1 ATGCCATATCCCAGATATGGTCTTACACGGGATCTCATTT-GATGGCGATGCCATATCCCAGATA
*
58827467 TGGTCTTATACGGGATCTCAATACT
65 TGGTCTTATATGGGATCTC-ATACT
58827492 CACATGTCGT
Statistics
Matches: 152, Mismatches: 30, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
95 1 0.01
96 148 0.97
97 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (95 bp):
ATGCCATATCCCAGATATGGTCTTACACGGGATCTCATTTGATGGCGATGCCATATCCCAGATAT
GGTCTTATATGGGATCTCATACTGATGCCG
Found at i:58834893 original size:42 final size:41
Alignment explanation
Indices: 58834785--58834904 Score: 109
Period size: 43 Copynumber: 2.8 Consensus size: 41
58834775 GTCTGAGACA
*
58834785 TCGTGTAAGACCGTGTCTGGGACACAGGTC-TCGATTAGGATT
1 TCGTGTAAGACCATGTCTGGGACAC-GG-CATCGATTAGGATT
* * * *
58834827 TACGTATAAAACCATGTCTAGGACATCGGCATCGCATT-TGATT
1 T-CGTGTAAGACCATGTCTGGGACA-CGGCATCG-ATTAGGATT
* *
58834870 TCGTGTAAGACCCTGTCTGGGACAAAGGCATCGAT
1 TCGTGTAAGACCATGTCTGGGAC-ACGGCATCGAT
58834905 ATTGTACTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
41 2 0.03
42 27 0.43
43 30 0.48
44 4 0.06
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (41 bp):
TCGTGTAAGACCATGTCTGGGACACGGCATCGATTAGGATT
Found at i:58840655 original size:17 final size:17
Alignment explanation
Indices: 58840633--58840682 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
58840623 ACTTGTTAAA
58840633 GCCCGATAAATGA-AAGT
1 GCCCGATAAATGATAA-T
* *
58840650 GCCCGATCAATTATAAT
1 GCCCGATAAATGATAAT
*
58840667 GCCCGACAAATGATAA
1 GCCCGATAAATGATAA
58840683 ATGAACAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 25 0.93
18 2 0.07
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (17 bp):
GCCCGATAAATGATAAT
Found at i:58847977 original size:40 final size:39
Alignment explanation
Indices: 58847918--58848062 Score: 112
Period size: 40 Copynumber: 3.6 Consensus size: 39
58847908 AAATTGAATG
* * *
58847918 ATATCCGGGCTAAGCCCCGAGGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAGG-CAATTATGCTAGAAACT
* * ***
58847958 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCG-AGGCAATTATGCTAGAAACT
* * ** *
58847998 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCG-AGGCAATT-ATGCTAGAAACT
*
58848038 CTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCG-AGGCA
58848063 TTTGTGCACG
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
39 3 0.03
40 82 0.93
41 3 0.03
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAGGCAATTATGCTAGAAACT
Found at i:58848063 original size:40 final size:39
Alignment explanation
Indices: 58847957--58848085 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
58847947 TGCTGGAAAT
* * *
58847957 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
58847997 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
58848037 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
58848077 TATATCCGG
1 TATATCCGG
58848086 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:58852842 original size:46 final size:46
Alignment explanation
Indices: 58852537--58852849 Score: 218
Period size: 49 Copynumber: 6.6 Consensus size: 46
58852527 ATGCTGACGC
* * *
58852537 CATGTCCCAGACATGGTTTTACACTGGCTTTCATATAGTGAGGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTAGCTCTCATAT--TGAGGCCGATG
* * * ** * *
58852586 CCATGTCCTAGACAGGTCTTACACTGGCTCTCATCTACCGATGTCGATG
1 -CATGTCCCAGACATGTCTTACACTAGCTCTCA--TATTGAGGCCGATG
* * *
58852635 CCATGTCCCAGACAGGTCTTACACTAGCTTATCA-ATCTCGAGGTCGATG
1 -CATGTCCCAGACATGTCTTACACTAGC-TCTCATAT-T-GAGGCCGATG
* * ** * **
58852684 CATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAACGTTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATATTGAGGCCGATG
* * * * *
58852730 CATGTCCTAGACATATCTTACACTGGCT-TAAATATCTTGAGGCCAATG
1 CATGTCCCAGACATGTCTTACACTAGCTCT-CATA--TTGAGGCCGATG
* * * * *
58852778 -TTGTACCAGACATATCTTATACTAGCTCTCATATTGTGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATATTGAGGCCGATG
58852823 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
58852850 ACACACATCT
Statistics
Matches: 206, Mismatches: 46, Indels: 26
0.74 0.17 0.09
Matches are distributed among these distances:
45 11 0.05
46 55 0.27
47 29 0.14
48 34 0.17
49 59 0.29
50 16 0.08
51 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATATTGAGGCCGATG
Found at i:58853228 original size:30 final size:30
Alignment explanation
Indices: 58853187--58853243 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
58853177 CATAATTGGG
*
58853187 CAAAATGACCATTCTACCCCTAGACTTTCA
1 CAAAATAACCATTCTACCCCTAGACTTTCA
*
58853217 CAAAATAACCATTTTACCCCTAGACTT
1 CAAAATAACCATTCTACCCCTAGACTT
58853244 GAAAATCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.35, C:0.32, G:0.05, T:0.28
Consensus pattern (30 bp):
CAAAATAACCATTCTACCCCTAGACTTTCA
Found at i:58857305 original size:99 final size:99
Alignment explanation
Indices: 58857134--58857332 Score: 380
Period size: 99 Copynumber: 2.0 Consensus size: 99
58857124 CAATCCATGC
* *
58857134 CAAGAATTAGATCAAATTTATCAAACGGTAGTAGCATGAGGTTAGCTGAAAAACAATGACCTCTA
1 CAAGAATTAGATCAAATTCATCAAACAGTAGTAGCATGAGGTTAGCTGAAAAACAATGACCTCTA
58857199 ATCATCAAAAGACAACCTCTACACATTTTATCTA
66 ATCATCAAAAGACAACCTCTACACATTTTATCTA
58857233 CAAGAATTAGATCAAATTCATCAAACAGTAGTAGCATGAGGTTAGCTGAAAAACAATGACCTCTA
1 CAAGAATTAGATCAAATTCATCAAACAGTAGTAGCATGAGGTTAGCTGAAAAACAATGACCTCTA
58857298 ATCATCAAAAGACAACCTCTACACATTTTATCTA
66 ATCATCAAAAGACAACCTCTACACATTTTATCTA
58857332 C
1 C
58857333 TATCACATGC
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.26
Consensus pattern (99 bp):
CAAGAATTAGATCAAATTCATCAAACAGTAGTAGCATGAGGTTAGCTGAAAAACAATGACCTCTA
ATCATCAAAAGACAACCTCTACACATTTTATCTA
Found at i:58859369 original size:28 final size:28
Alignment explanation
Indices: 58859329--58859398 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
58859319 CTTGGCCTGA
*
58859329 CACACGCCCGTGTCCCCCACACAACCAT
1 CACATGCCCGTGTCCCCCACACAACCAT
** *
58859357 CACATGCCCGTGTCCCTTACACAGCCAT
1 CACATGCCCGTGTCCCCCACACAACCAT
58859385 CACATGCCCGTGTC
1 CACATGCCCGTGTC
58859399 TAAAAACCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.21, C:0.47, G:0.14, T:0.17
Consensus pattern (28 bp):
CACATGCCCGTGTCCCCCACACAACCAT
Found at i:58865499 original size:43 final size:41
Alignment explanation
Indices: 58865379--58865542 Score: 125
Period size: 43 Copynumber: 3.9 Consensus size: 41
58865369 AGCTCGTACA
* * * * * * *
58865379 ATGCCAACGTCCTAGGCGTGGTCTTTCATGTAATCAAATATCA
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAATCAAA-AT-G
* * *
58865422 ATGCC-ACTGTCCCAAACAGGGTCTTACACAAAATCAAACATG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGAAATCAAA-ATG
* *
58865464 ATGCCAATG-CCCTAGACATGGTCTTACACGTAAATCTCAAATG
1 ATGCCAACGTCCC-AGACATGGTCTTACACG-AAATC-AAAATG
**
58865507 ATGCCAACGTCCCAGATGTGGTCTTACACGAAATCA
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAATCA
58865543 CATATCGGAA
Statistics
Matches: 95, Mismatches: 20, Indels: 14
0.74 0.16 0.11
Matches are distributed among these distances:
41 3 0.03
42 27 0.28
43 60 0.63
44 5 0.05
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (41 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAAATCAAAATG
Found at i:58875212 original size:27 final size:27
Alignment explanation
Indices: 58875178--58875791 Score: 503
Period size: 27 Copynumber: 22.9 Consensus size: 27
58875168 TTGCCCTATA
*
58875178 AGGGTATTTCGATAATTTTATAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* **
58875205 AGGATATTTC-AGTAATTTTACAAATTA
1 AGGGTATTTCGA-TAATTTTACAAATCG
*
58875232 AGGGTATTTC-AGTAATTTTACAAATTG
1 AGGGTATTTCGA-TAATTTTACAAATCG
* *
58875259 GGGGTATTTC-AGTAATTTTACAAA-CTA
1 AGGGTATTTCGA-TAATTTTACAAATC-G
*
58875286 AGGGTATTTC-AGTAATTTTACAAATCA
1 AGGGTATTTCGA-TAATTTTACAAATCG
* *
58875313 AGGGTATTTC-AGTAATTTTATAAATTG
1 AGGGTATTTCGA-TAATTTTACAAATCG
* *
58875340 -GGGTTATTTC-AGCAA-TTTACAAACCG
1 AGGG-TATTTCGA-TAATTTTACAAATCG
*
58875366 GGGGTATTTC-AGTAATTTTACAAATCCG
1 AGGGTATTTCGA-TAATTTTACAAAT-CG
* * *
58875394 -GGGTCTTTCGGTAATTTTATAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
*
58875420 -GGGTATTTCGGTAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
*
58875446 -GAGGTATTTCGATAATTTTACAAAT-T
1 AG-GGTATTTCGATAATTTTACAAATCG
**
58875472 AGGGGTATTTTAATAATTTTACAAATCG
1 A-GGGTATTTCGATAATTTTACAAATCG
* *
58875500 -GGGATATTTTGATAATTTTACAAACCG
1 AGGG-TATTTCGATAATTTTACAAATCG
* * * * *
58875527 AGTGTATTTCAATTATTTTAAAAATTG
1 AGGGTATTTCGATAATTTTACAAATCG
* *
58875554 AGGGTATTTCGGTAATTTTACAAA-CT
1 AGGGTATTTCGATAATTTTACAAATCG
* * *
58875580 AGGGGTATTTTGGTAATTTTACAAACCG
1 A-GGGTATTTCGATAATTTTACAAATCG
* *
58875608 AAGGTATTTCAATAATTTTACAAA-CTG
1 AGGGTATTTCGATAATTTTACAAATC-G
* * *
58875635 AAGGTATTTCGGTAATTTTACAAA-CT
1 AGGGTATTTCGATAATTTTACAAATCG
* *
58875661 AGGGTATTTAGATAATTTTACAAATTG
1 AGGGTATTTCGATAATTTTACAAATCG
* *
58875688 AGGGTATTTCGGTAATTTTA-AAAACTG
1 AGGGTATTTCGATAATTTTACAAATC-G
* * * *
58875715 GGGGTATTTCGGTAATTTTACAAACCA
1 AGGGTATTTCGATAATTTTACAAATCG
*
58875742 AGGGTATTTCGGTAATTTTACAAA-CTG
1 AGGGTATTTCGATAATTTTACAAATC-G
* *
58875769 GGGGTATTTCGGTAATTTTACAA
1 AGGGTATTTCGATAATTTTACAA
58875792 TCCGGGGTCT
Statistics
Matches: 497, Mismatches: 69, Indels: 42
0.82 0.11 0.07
Matches are distributed among these distances:
26 79 0.16
27 406 0.82
28 12 0.02
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTACAAATCG
Found at i:58875294 original size:81 final size:81
Alignment explanation
Indices: 58875179--58875791 Score: 600
Period size: 81 Copynumber: 7.6 Consensus size: 81
58875169 TGCCCTATAA
* *
58875179 GGGTATTTC-GATAATTTTATAAA-TCGAGGATATTTCAGTAATTTTACAAATTAAGGGTATTTC
1 GGGTATTTCAG-TAATTTTACAAACT-GAGGGTATTTCAGTAATTTTACAAATTAAGGGTATTTC
* *
58875242 AGTAATTTTACAAATTGG
64 GGTAATTTTACAAACTGG
* * *
58875260 GGGTATTTCAGTAATTTTACAAACTAAGGGTATTTCAGTAATTTTACAAATCAAGGGTATTTCAG
1 GGGTATTTCAGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTACAAATTAAGGGTATTTCGG
* *
58875325 TAATTTTATAAATTGG
66 TAATTTTACAAACTGG
* * * * *** *
58875341 GGTTATTTCAGCAA-TTTACAAACCGGGGGTATTTCAGTAATTTTACAAATCCGGGGTCTTTCGG
1 GGGTATTTCAGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTACAAATTAAGGGTATTTCGG
* *
58875405 TAATTTTATAAA-TCG
66 TAATTTTACAAACTGG
* * * *
58875420 GGGTATTTCGGTAATTTTACAAATCGGA-GGTATTTC-GATAATTTTACAAATTAGGGGTATTTT
1 GGGTATTTCAGTAATTTTACAAA-CTGAGGGTATTTCAG-TAATTTTACAAATTAAGGGTATTTC
**
58875483 AATAATTTTACAAA-TCGG
64 GGTAATTTTACAAACT-GG
* * * * * * * *
58875501 GGATATTT-TGATAATTTTACAAACCGAGTGTATTTCAATTATTTTAAAAATTGAGGGTATTTCG
1 GGGTATTTCAG-TAATTTTACAAACTGAGGGTATTTCAGTAATTTTACAAATTAAGGGTATTTCG
*
58875565 GTAATTTTACAAACTAG
65 GTAATTTTACAAACTGG
** * * * *
58875582 GGGTATTTTGGTAATTTTACAAACCGAAGGTATTTCAATAATTTTACAAACTGAA-GGTATTTCG
1 GGGTATTTCAGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTACAAA-TTAAGGGTATTTCG
*
58875646 GTAATTTTACAAACT-A
65 GTAATTTTACAAACTGG
* * * * **
58875662 GGGTATTT-AGATAATTTTACAAATTGAGGGTATTTCGGTAATTTTAAAAACTGGGGGTATTTCG
1 GGGTATTTCAG-TAATTTTACAAACTGAGGGTATTTCAGTAATTTTACAAATTAAGGGTATTTCG
***
58875726 GTAATTTTACAAACCAA
65 GTAATTTTACAAACTGG
* * *
58875743 GGGTATTTCGGTAATTTTACAAACTGGGGGTATTTCGGTAATTTTACAA
1 GGGTATTTCAGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTACAA
58875792 TCCGGGGTCT
Statistics
Matches: 450, Mismatches: 66, Indels: 32
0.82 0.12 0.06
Matches are distributed among these distances:
79 15 0.03
80 172 0.38
81 256 0.57
82 7 0.02
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.39
Consensus pattern (81 bp):
GGGTATTTCAGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTACAAATTAAGGGTATTTCGG
TAATTTTACAAACTGG
Found at i:58876338 original size:22 final size:22
Alignment explanation
Indices: 58876310--58876351 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
58876300 AAACATAGCA
*
58876310 TACGGTCACACACTTGATCAAG
1 TACGGTCACACACCTGATCAAG
58876332 TACGGTCACACACCTGATCA
1 TACGGTCACACACCTGATCA
58876352 CGTAGACTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (22 bp):
TACGGTCACACACCTGATCAAG
Found at i:58880020 original size:48 final size:48
Alignment explanation
Indices: 58879951--58880059 Score: 191
Period size: 48 Copynumber: 2.3 Consensus size: 48
58879941 AAATAAATAT
*
58879951 ATATGTATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
*
58879999 ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAA
1 ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
*
58880047 ATATGTAGGAGAT
1 ATATGTATGAGAT
58880060 GTGTGTATAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (48 bp):
ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
Found at i:58880250 original size:37 final size:37
Alignment explanation
Indices: 58880200--58880302 Score: 188
Period size: 37 Copynumber: 2.8 Consensus size: 37
58880190 GGAAATATAT
58880200 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
58880237 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
58880274 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
58880303 GGACTATTCG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.24
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:58892643 original size:16 final size:16
Alignment explanation
Indices: 58892622--58892680 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
58892612 ATGTATCGGC
**
58892622 AAAAGCCGAAATTACG
1 AAAAGCCGAAATGCCG
*
58892638 AAAAGCCGAAAAGCCG
1 AAAAGCCGAAATGCCG
*
58892654 AAAAGTCGAAATGCCG
1 AAAAGCCGAAATGCCG
*
58892670 AAAAGCAGAAA
1 AAAAGCCGAAA
58892681 GTTTGGCTAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.53, C:0.19, G:0.22, T:0.07
Consensus pattern (16 bp):
AAAAGCCGAAATGCCG
Found at i:58892647 original size:8 final size:8
Alignment explanation
Indices: 58892622--58892680 Score: 64
Period size: 8 Copynumber: 7.4 Consensus size: 8
58892612 ATGTATCGGC
58892622 AAAAGCCG
1 AAAAGCCG
***
58892630 AAATTACG
1 AAAAGCCG
58892638 AAAAGCCG
1 AAAAGCCG
58892646 AAAAGCCG
1 AAAAGCCG
*
58892654 AAAAGTCG
1 AAAAGCCG
*
58892662 AAATGCCG
1 AAAAGCCG
*
58892670 AAAAGCAG
1 AAAAGCCG
58892678 AAA
1 AAA
58892681 GTTTGGCTAC
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
8 40 1.00
ACGTcount: A:0.53, C:0.19, G:0.22, T:0.07
Consensus pattern (8 bp):
AAAAGCCG
Found at i:58892649 original size:24 final size:23
Alignment explanation
Indices: 58892622--58892682 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
58892612 ATGTATCGGC
*
58892622 AAAAGCCGAAATTACGAAAAGCCG
1 AAAAGCCGAAAGT-CGAAAAGCCG
*
58892646 AAAAGCCGAAAAGTCGAAATGCCG
1 AAAAGCCG-AAAGTCGAAAAGCCG
*
58892670 AAAAGCAGAAAGT
1 AAAAGCCGAAAGT
58892683 TTGGCTACAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.15
24 24 0.73
25 4 0.12
ACGTcount: A:0.51, C:0.18, G:0.23, T:0.08
Consensus pattern (23 bp):
AAAAGCCGAAAGTCGAAAAGCCG
Found at i:58892939 original size:27 final size:29
Alignment explanation
Indices: 58892904--58892978 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 29
58892894 TGAACGTGAC
* *
58892904 TGGGCCTAACGGGCCATA-A-ATGTGATT
1 TGGGACTAACGGGCCATATACAGGTGATT
* *
58892931 TGGGTCTAATGGGCCATATACAGGTGATT
1 TGGGACTAACGGGCCATATACAGGTGATT
58892960 TGGGACTAACGGGCCATAT
1 TGGGACTAACGGGCCATAT
58892979 GAATATCATA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
27 16 0.39
28 1 0.02
29 24 0.59
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (29 bp):
TGGGACTAACGGGCCATATACAGGTGATT
Found at i:58899154 original size:16 final size:16
Alignment explanation
Indices: 58899133--58899164 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
58899123 GTAACACCCT
*
58899133 AAAAATCCCGAAATCC
1 AAAAATCCCAAAATCC
58899149 AAAAATCCCAAAATCC
1 AAAAATCCCAAAATCC
58899165 TGAATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.31, G:0.03, T:0.12
Consensus pattern (16 bp):
AAAAATCCCAAAATCC
Found at i:58906589 original size:15 final size:15
Alignment explanation
Indices: 58906569--58906606 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
58906559 CCTTTAGAAA
*
58906569 TTAAATTAAACTAAG
1 TTAAATAAAACTAAG
58906584 TTAAATAAAACTAA-
1 TTAAATAAAACTAAG
58906598 TATAAATAA
1 T-TAAATAA
58906607 GTAAAATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (15 bp):
TTAAATAAAACTAAG
Found at i:58907847 original size:24 final size:24
Alignment explanation
Indices: 58907801--58907872 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
58907791 ACTTTATCAT
** *
58907801 ATAACTGGAGGCCTAGCCTCTTTTA
1 ATAACTGG-GGCAAAGCCCCTTTTA
*
58907826 ATAACTGGGGCAAAGCCCCTTTTG
1 ATAACTGGGGCAAAGCCCCTTTTA
58907850 ATAAACTGGGGCAAAG-CCCTTTT
1 AT-AACTGGGGCAAAGCCCCTTTT
58907873 CGGTAAACTG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
24 21 0.50
25 21 0.50
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCAAAGCCCCTTTTA
Found at i:58907856 original size:25 final size:25
Alignment explanation
Indices: 58907815--58907887 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 25
58907805 CTGGAGGCCT
* *
58907815 AGCCTCTTTTAAT-AACTGGGGCAA
1 AGCCCCTTTTGATAAACTGGGGCAA
58907839 AGCCCCTTTTGATAAACTGGGGCAA
1 AGCCCCTTTTGATAAACTGGGGCAA
* *
58907864 AG-CCCTTTTCGGTAAACTGAGGCA
1 AGCCCCTTTT-GATAAACTGGGGCA
58907888 TAACCCTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
24 18 0.42
25 25 0.58
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.26
Consensus pattern (25 bp):
AGCCCCTTTTGATAAACTGGGGCAA
Found at i:58907894 original size:25 final size:24
Alignment explanation
Indices: 58907815--58907897 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 24
58907805 CTGGAGGCCT
* *
58907815 AGCCTCTTTTAAT-AACTGGGGCAA
1 AGCC-CTTTTGATAAACTGAGGCAA
*
58907839 AGCCCCTTTTGATAAACTGGGGCAA
1 AG-CCCTTTTGATAAACTGAGGCAA
*
58907864 AGCCCTTTTCGGTAAACTGAGGCATA
1 AGCCCTTTT-GATAAACTGAGGCA-A
58907890 A-CCCTTTT
1 AGCCCTTTT
58907898 AGCACTTCCT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
24 16 0.31
25 34 0.65
26 2 0.04
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (24 bp):
AGCCCTTTTGATAAACTGAGGCAA
Found at i:58908148 original size:27 final size:27
Alignment explanation
Indices: 58908118--58908312 Score: 146
Period size: 27 Copynumber: 7.3 Consensus size: 27
58908108 ACCCCAAAAG
* *
58908118 GGTATCTCAGAAATTCTACCTTACAGA
1 GGTATTTCAGAAATTCTACCCTACAGA
*
58908145 GGTATTTCA-ATAATTCTACCCTACAGG
1 GGTATTTCAGA-AATTCTACCCTACAGA
*
58908172 GGTATTTCAGTAATTCTACCCTACA-A
1 GGTATTTCAGAAATTCTACCCTACAGA
** * * * *
58908198 GGGT-TTTTGGTAATTCTACACTATAGG
1 -GGTATTTCAGAAATTCTACCCTACAGA
** * *
58908225 GGTATTTTGGTAATTCTACCCTATA-A
1 GGTATTTCAGAAATTCTACCCTACAGA
* * *
58908251 GGGTATTTCGGTAATTCTACCCTACAGG
1 -GGTATTTCAGAAATTCTACCCTACAGA
* * * *
58908279 GGTATTTCGGTAACTCTACCCTACAGG
1 GGTATTTCAGAAATTCTACCCTACAGA
58908306 GGTATTT
1 GGTATTT
58908313 TGATATTTTA
Statistics
Matches: 145, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
26 21 0.14
27 124 0.86
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (27 bp):
GGTATTTCAGAAATTCTACCCTACAGA
Found at i:58908284 original size:54 final size:54
Alignment explanation
Indices: 58908129--58908312 Score: 246
Period size: 54 Copynumber: 3.4 Consensus size: 54
58908119 GTATCTCAGA
* ** *
58908129 AATTCTACCTTAC-AGAGGTATTTCAATAATTCTACCCTACAGGGGTATTTCAGT
1 AATTCTACCCTACAAG-GGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGT
* * * *
58908183 AATTCTACCCTACAAGGGT-TTTTGGTAATTCTACACTATAGGGGTATTTTGGT
1 AATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGT
*
58908236 AATTCTACCCTATAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGT
1 AATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGT
* *
58908290 AACTCTACCCTACAGGGGTATTT
1 AATTCTACCCTACAAGGGTATTT
58908313 TGATATTTTA
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
53 45 0.40
54 65 0.58
55 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (54 bp):
AATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGT
Found at i:58908337 original size:107 final size:107
Alignment explanation
Indices: 58908129--58908346 Score: 273
Period size: 107 Copynumber: 2.0 Consensus size: 107
58908119 GTATCTCAGA
*
58908129 AATTCTACCTTACAGAGGTATTTCAATAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCT
1 AATTCTACCTTACAGAGGTATTTCAATAATTCTACCCTACAGGGGTATTTCAGTAACTCTACCCT
* * * *
58908194 ACAAGGGTTTTTGGTAATTCTACACTATAGGGGTATTTTGGT
66 ACAAGGGTTTTTGATAATTCTACACAATAGGAGTATTTTGAT
** *
58908236 AATTCTACCCTATA-AG-GGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAACTCTACC
1 AATTCTA-CCT-TACAGAGGTATTTCAATAATTCTACCCTACAGGGGTATTTCAGTAACTCTACC
* * *
58908299 CTACAGGGGTATTTTGAT-ATTTTACA-AATCGAGAGTATTTTGAT
64 CTACAAGGGT-TTTTGATAATTCTACACAATAG-GAGTATTTTGAT
58908343 AATT
1 AATT
58908347 TCACAAATCA
Statistics
Matches: 96, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
106 3 0.03
107 80 0.83
108 11 0.11
109 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (107 bp):
AATTCTACCTTACAGAGGTATTTCAATAATTCTACCCTACAGGGGTATTTCAGTAACTCTACCCT
ACAAGGGTTTTTGATAATTCTACACAATAGGAGTATTTTGAT
Found at i:58908340 original size:134 final size:134
Alignment explanation
Indices: 58908098--58908373 Score: 301
Period size: 134 Copynumber: 2.1 Consensus size: 134
58908088 TGGGGCGAAA
* * *
58908098 TGGTAATTTTACCCCAAAAGGGTATCTCAGAAATTCTACCTTACAGAGGTATTTCAATAATTCTA
1 TGGTAATTCTACCCCAAAAGGGTATCTCAGAAATTCTACCCTACAGAGGTATTTCAATAACTCTA
** * * *
58908163 CCCTACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTTTTTGGTAA-TTCTACACTAT-AGGG
66 CCCTACAGGGGTATTTCAGTAATTCTACAATACAAGAGTTTTTGATAATTTC-ACA-AATCAGGG
58908226 GTATTT
129 GTATTT
* * * * * * **
58908232 TGGTAATTCTACCCTATAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAACTCTA
1 TGGTAATTCTACCCCAAAAGGGTATCTCAGAAATTCTACCCTACAGAGGTATTTCAATAACTCTA
* * *
58908297 CCCTACAGGGGTATTT-TG-ATATTTTACAA-ATCGAGAGTATTTTGATAATTTCACAAATCAGG
66 CCCTACAGGGGTATTTCAGTA-ATTCTACAATA-CAAGAGT-TTTTGATAATTTCACAAATCAGG
58908359 GGTATTT
128 GGTATTT
58908366 TGGTAATT
1 TGGTAATT
58908374 TTACAAACCA
Statistics
Matches: 118, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
132 2 0.02
133 14 0.12
134 99 0.84
135 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.36
Consensus pattern (134 bp):
TGGTAATTCTACCCCAAAAGGGTATCTCAGAAATTCTACCCTACAGAGGTATTTCAATAACTCTA
CCCTACAGGGGTATTTCAGTAATTCTACAATACAAGAGTTTTTGATAATTTCACAAATCAGGGGT
ATTT
Found at i:58908346 original size:80 final size:80
Alignment explanation
Indices: 58908173--58908346 Score: 183
Period size: 80 Copynumber: 2.2 Consensus size: 80
58908163 CCCTACAGGG
* * * *
58908173 GTATTTC-AGTAATTCTACCCTACAAGGGTTTTTGGTAATTCTACACTATAGGGGTATTTTGGTA
1 GTATTTCGA-TAATTCTACCCTACAAGGGTTTTCGGTAACTCTACACTACAGGGGTATTTTGATA
** *
58908237 ATTCTACCCTATAAGG
65 ATTCTACCAAATAAGA
* * *
58908253 GTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAACTCTACCCTACAGGGGTATTTTGAT-
1 GTATTTCGATAATTCTACCCTACAAGGGT-TTTCGGTAACTCTACACTACAGGGGTATTTTGATA
* *
58908317 ATTTTA-CAAATCGAGA
65 ATTCTACCAAAT-AAGA
*
58908333 GTATTTTGATAATT
1 GTATTTCGATAATT
58908347 TCACAAATCA
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
79 3 0.04
80 45 0.58
81 29 0.38
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (80 bp):
GTATTTCGATAATTCTACCCTACAAGGGTTTTCGGTAACTCTACACTACAGGGGTATTTTGATAA
TTCTACCAAATAAGA
Found at i:58908362 original size:107 final size:107
Alignment explanation
Indices: 58908145--58908373 Score: 259
Period size: 107 Copynumber: 2.1 Consensus size: 107
58908135 ACCTTACAGA
** * *
58908145 GGTATTTCAATAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTTTTTGGTA
1 GGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAACTCTACCCTACAAGGGTTTTTGATA
* * * **
58908210 ATTCTACACTATAGGGGTATTTTGGTAATTCTACCCTATAAG
66 ATTCTACACAATAGGAGTATTTTGATAATTCTACCAAATAAG
* *
58908252 GGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAACTCTACCCTACAGGGGTATTTTGAT
1 GGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAACTCTACCCTACAAGGGT-TTTTGAT
* * *
58908317 -ATTTTACA-AATCGAGAGTATTTTGATAATT-T-CACAAATCAGG
65 AATTCTACACAATAG-GAGTATTTTGATAATTCTAC-CAAAT-AAG
*
58908359 GGTATTTTGGTAATT
1 GGTATTTCGGTAATT
58908374 TTACAAACCA
Statistics
Matches: 103, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
105 1 0.01
106 7 0.07
107 89 0.86
108 6 0.06
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (107 bp):
GGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAACTCTACCCTACAAGGGTTTTTGATA
ATTCTACACAATAGGAGTATTTTGATAATTCTACCAAATAAG
Found at i:58908419 original size:27 final size:27
Alignment explanation
Indices: 58908198--58908429 Score: 154
Period size: 27 Copynumber: 8.7 Consensus size: 27
58908188 TACCCTACAA
* *
58908198 GGGT-TTTTGGTAATTCTACACTAT-AG
1 GGGTATTTTGGTAATTTTACA-AATCAG
* ** *
58908224 GGGTATTTTGGTAATTCTACCCTAT-AA
1 GGGTATTTTGGTAATTTTA-CAAATCAG
* * **
58908251 GGGTATTTCGGTAATTCTAC-CCTACAG
1 GGGTATTTTGGTAATTTTACAAAT-CAG
* * * **
58908278 GGGTATTTCGGTAACTCTAC-CCTACAG
1 GGGTATTTTGGTAATTTTACAAAT-CAG
*
58908305 GGGTATTTTGAT-ATTTTACAAATC-G
1 GGGTATTTTGGTAATTTTACAAATCAG
* * *
58908330 AGAGTATTTTGATAATTTCACAAATCAG
1 -GGGTATTTTGGTAATTTTACAAATCAG
*
58908358 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAATCAG
** *
58908385 GGGTATTTTGGTAATTTTACTGATCAA
1 GGGTATTTTGGTAATTTTACAAATCAG
*
58908412 GGGCATTTTGGTAATTTT
1 GGGTATTTTGGTAATTTT
58908430 GTAAACTAAG
Statistics
Matches: 174, Mismatches: 24, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
25 2 0.01
26 22 0.13
27 148 0.85
28 2 0.01
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATCAG
Found at i:58908440 original size:27 final size:26
Alignment explanation
Indices: 58908358--58908461 Score: 91
Period size: 27 Copynumber: 3.9 Consensus size: 26
58908348 CACAAATCAG
** *
58908358 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTGTAAA-CAA
* * *
58908385 GGGTATTTTGGTAATTTTACTGATCAA
1 GGGTATTTTGGTAATTTT-GTAAACAA
*
58908412 GGGCATTTTGGTAATTTTGTAAACTAA
1 GGGTATTTTGGTAATTTTGTAAAC-AA
* **
58908439 GGATATTTCAGTAATTTTGTAAA
1 GGGTATTTTGGTAATTTTGTAAA
58908462 TCGAGGCTAA
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
26 3 0.05
27 58 0.94
28 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (26 bp):
GGGTATTTTGGTAATTTTGTAAACAA
Found at i:58908446 original size:54 final size:54
Alignment explanation
Indices: 58908309--58908456 Score: 129
Period size: 54 Copynumber: 2.8 Consensus size: 54
58908299 CTACAGGGGT
* * * * * * *
58908309 ATTTTGAT-ATTTTACAAATCGA-GAGTATTTTGATAATTTCACAAATCAGGGGT
1 ATTTTGGTAATTTTACAAACCAAGGA-TATTTTGGTAATTTTACAAATCAAGGGC
* * **
58908362 ATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACTGATCAAGGGC
1 ATTTTGGTAATTTTACAAACCAAGGATATTTTGGTAATTTTACAAATCAAGGGC
** * **
58908416 ATTTTGGTAATTTTGTAAACTAAGGATATTTCAGTAATTTT
1 ATTTTGGTAATTTTACAAACCAAGGATATTTTGGTAATTTT
58908457 GTAAATCGAG
Statistics
Matches: 75, Mismatches: 18, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
53 7 0.09
54 67 0.89
55 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (54 bp):
ATTTTGGTAATTTTACAAACCAAGGATATTTTGGTAATTTTACAAATCAAGGGC
Found at i:58909690 original size:17 final size:17
Alignment explanation
Indices: 58909668--58909704 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
58909658 ATCATTTAAC
58909668 AACAGTTTAACTAATCT
1 AACAGTTTAACTAATCT
58909685 AACAGTTTAACTAATCT
1 AACAGTTTAACTAATCT
58909702 AAC
1 AAC
58909705 CTTTTCAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.32
Consensus pattern (17 bp):
AACAGTTTAACTAATCT
Found at i:58914540 original size:40 final size:39
Alignment explanation
Indices: 58914496--58914702 Score: 200
Period size: 40 Copynumber: 5.2 Consensus size: 39
58914486 TCAGGACATT
* * *
58914496 GCCCGGTTATAGTGATTCGCACAATTGCCTTCGGGAATTA
1 GCCCGGTT-TAGTAACTCGCACAAATGCCTTCGGGAATTA
* * *
58914536 GCCCGGATTTAGTAACTCACACGAATGCCTTCGGGACTTA
1 GCCCGG-TTTAGTAACTCGCACAAATGCCTTCGGGAATTA
* * * *
58914576 ACCCGGTTTTGGTAACTCGCACAAATGCCTTCAGGACTTA
1 GCCCGG-TTTAGTAACTCGCACAAATGCCTTCGGGAATTA
* *
58914616 ACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGAATT-
1 GCCCGG-TTTAGTAACTCGCACAAATGCCTTCGGGAATTA
* * * *
58914655 GACCCGGATTTAGTCACTTAGCACAAAAGCCTTCGGGACTTA
1 G-CCCGG-TTTAGTAAC-TCGCACAAATGCCTTCGGGAATTA
58914697 GCCCGG
1 GCCCGG
58914703 ACACCATTCG
Statistics
Matches: 142, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
40 114 0.80
41 27 0.19
42 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (39 bp):
GCCCGGTTTAGTAACTCGCACAAATGCCTTCGGGAATTA
Found at i:58914596 original size:80 final size:81
Alignment explanation
Indices: 58914511--58914703 Score: 244
Period size: 80 Copynumber: 2.4 Consensus size: 81
58914501 GTTATAGTGA
* * * *
58914511 TTCGCACAATTGCCTTCGGGAATTAGCCCGGATTTAGTAACTCACACGAATGCCTTCGGGACTTA
1 TTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAATGCCTTCGGGAATTA
* *
58914576 ACCCGGTTTTGGTAAC
66 ACCCGGATTTAGTAAC
* * * * * *
58914592 -TCGCACAAATGCCTTCAGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGAATTG
1 TTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAATGCCTTCGGGAATTA
*
58914656 ACCCGGATTTAGTCAC
66 ACCCGGATTTAGTAAC
* *
58914672 TTAGCACAAAAGCCTTCGGGACTTAGCCCGGA
1 TTCGCACAAATGCCTTCGGGACTTAGCCCGGA
58914704 CACCATTCGA
Statistics
Matches: 93, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
80 67 0.72
81 26 0.28
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (81 bp):
TTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAATGCCTTCGGGAATTA
ACCCGGATTTAGTAAC
Found at i:58927959 original size:39 final size:39
Alignment explanation
Indices: 58927905--58928066 Score: 247
Period size: 39 Copynumber: 4.2 Consensus size: 39
58927895 TGTGTATGAA
58927905 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
*
58927944 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAA
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
*
58927983 TGTGCGAGA-TATGATATCCGGGCTAAGCCCGAAGGC-AT
1 TGTGCGA-ATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
58928021 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
58928061 TGTGCG
1 TGTGCG
58928067 GGTTATCATA
Statistics
Matches: 112, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
38 24 0.21
39 80 0.71
40 8 0.07
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (39 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:58928082 original size:40 final size:39
Alignment explanation
Indices: 58927905--58928097 Score: 244
Period size: 39 Copynumber: 4.9 Consensus size: 39
58927895 TGTGTATGAA
* *
58927905 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
58927944 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAA
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
*
58927983 TGTGCGAGATATGATATCCGGGCTAAGCCCGAAGGC-AT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
58928021 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAAT
* * * *
58928061 TGTGCGGGTTATCATAACCGGGCTATGTCCCGAAGGC
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGC
58928098 GTTTGAACGA
Statistics
Matches: 137, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
38 25 0.18
39 80 0.58
40 32 0.23
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:58938120 original size:31 final size:31
Alignment explanation
Indices: 58938061--58938120 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
58938051 ACCAAATGTT
* *
58938061 TAAAATATAAATTATATATTTAAAAATAACA
1 TAAAATATAAATTATAAAATTAAAAATAACA
*
58938092 TAAAATATATAATT-TAAAATTAATAATAA
1 TAAAATATA-AATTATAAAATTAAAAATAA
58938121 TAACACATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (31 bp):
TAAAATATAAATTATAAAATTAAAAATAACA
Found at i:58938159 original size:36 final size:33
Alignment explanation
Indices: 58938061--58938160 Score: 82
Period size: 38 Copynumber: 2.9 Consensus size: 33
58938051 ACCAAATGTT
* *
58938061 TAAAATATA-AA-TTATATATTTAAAAAT-AACA
1 TAAAATATATAATTTA-AAATTAAAAAATAAACA
58938092 TAAAATATATAATTTAAAATTAATAATAATAACACA
1 TAAAATATATAATTTAAAATTAA-AA-AATAA-ACA
*
58938128 TGAAATATATATGATATTAAAA-TAAAAAATAAA
1 T-AAA-ATATATAAT-TTAAAATTAAAAAATAAA
58938161 TTAAATTATA
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
31 9 0.16
32 7 0.12
33 5 0.09
34 3 0.05
35 2 0.04
36 9 0.16
37 5 0.09
38 11 0.19
39 6 0.11
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (33 bp):
TAAAATATATAATTTAAAATTAAAAAATAAACA
Found at i:58940955 original size:19 final size:19
Alignment explanation
Indices: 58940927--58940975 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
58940917 TCCTTTTTCT
* * *
58940927 TTTCTGGGTTCATTAAATA
1 TTTCTAGGTTCATCAAACA
*
58940946 TTTCTAGGTTCATCCAACA
1 TTTCTAGGTTCATCAAACA
58940965 TTTCTAGGTTC
1 TTTCTAGGTTC
58940976 CTTTGAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.45
Consensus pattern (19 bp):
TTTCTAGGTTCATCAAACA
Found at i:58941742 original size:19 final size:19
Alignment explanation
Indices: 58941718--58941766 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
58941708 GAGAATTAAA
58941718 AGAAAAGAAAAAAGAAAAG
1 AGAAAAGAAAAAAGAAAAG
** *
58941737 AGAAAAGAAAATGGAAACG
1 AGAAAAGAAAAAAGAAAAG
58941756 AGAAAGAGAAA
1 AGAAA-AGAAA
58941767 GGGAAAGGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.71, C:0.02, G:0.24, T:0.02
Consensus pattern (19 bp):
AGAAAAGAAAAAAGAAAAG
Found at i:58941753 original size:12 final size:12
Alignment explanation
Indices: 58941715--58941766 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
58941705 GAGGAGAATT
*
58941715 AAAAGAAAAGAA
1 AAAAGAAAAGAG
58941727 AAAAGAAAAGAG
1 AAAAGAAAAGAG
58941739 AAAAGAAAATG-G
1 AAAAGAAAA-GAG
*
58941751 AAACGAGAAAGAG
1 AAAAGA-AAAGAG
58941764 AAA
1 AAA
58941767 GGGAAAGGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 27 0.77
13 8 0.23
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02
Consensus pattern (12 bp):
AAAAGAAAAGAG
Found at i:58941771 original size:19 final size:19
Alignment explanation
Indices: 58941718--58941772 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
58941708 GAGAATTAAA
**
58941718 AGAAAAGAAAAAAGAAAAG
1 AGAAAAGAAAAGGGAAAAG
* *
58941737 AGAAAAGAAAATGGAAACG
1 AGAAAAGAAAAGGGAAAAG
58941756 AG-AAAGAGAAAGGGAAA
1 AGAAAAGA-AAAGGGAAA
58941773 GGGAAAGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 5 0.16
19 26 0.84
ACGTcount: A:0.69, C:0.02, G:0.27, T:0.02
Consensus pattern (19 bp):
AGAAAAGAAAAGGGAAAAG
Found at i:58943849 original size:58 final size:58
Alignment explanation
Indices: 58943779--58943895 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
58943769 CCCCATCCTC
*
58943779 TACCTCTAATATTGTATAAAAAAAAGAGTTAAACTTGATGTTGGACTTTACGCGTTTA
1 TACCTCTAATATTGTATAAAAAAAAGAGTAAAACTTGATGTTGGACTTTACGCGTTTA
58943837 TACCTCTAATATTGTATAAAAAAAAGAGTAAAACTTGATGTTGGACTTTACGCGTTTA
1 TACCTCTAATATTGTATAAAAAAAAGAGTAAAACTTGATGTTGGACTTTACGCGTTTA
58943895 T
1 T
58943896 TTATTAGTTG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (58 bp):
TACCTCTAATATTGTATAAAAAAAAGAGTAAAACTTGATGTTGGACTTTACGCGTTTA
Found at i:58944086 original size:60 final size:59
Alignment explanation
Indices: 58943989--58944120 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 59
58943979 TCTTTTTATT
* * *
58943989 TTTTATTTTTTAGTCACTCAACTATAAAAAAGTTACAAAATGGTCACCCAACTATTAGTAA
1 TTTTATTTTTTAATCACCCAACTATAAAAAAGATACAAAATGGTCACCCAACTATT--TAA
* * * * *
58944050 TTTTCTTTTTTAATCACCCAACTAT-GAAAAGATACAAAATTGTTACCTAACTATTTAA
1 TTTTATTTTTTAATCACCCAACTATAAAAAAGATACAAAATGGTCACCCAACTATTTAA
*
58944108 TTTTGTCTTTTTA
1 TTTTAT-TTTTTA
58944121 TGGTCATTGG
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
58 8 0.13
59 6 0.10
60 25 0.41
61 22 0.36
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.42
Consensus pattern (59 bp):
TTTTATTTTTTAATCACCCAACTATAAAAAAGATACAAAATGGTCACCCAACTATTTAA
Found at i:58946225 original size:30 final size:30
Alignment explanation
Indices: 58946187--58946283 Score: 149
Period size: 30 Copynumber: 3.2 Consensus size: 30
58946177 CTAGCCTTTC
*
58946187 CCACCACCAACTCCACTAGCCACACTTACT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
58946217 CTACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* * *
58946247 CCACCACCTACTCTACCAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
58946277 CCACCAC
1 CCACCAC
58946284 TACTTGTACC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.27, C:0.51, G:0.05, T:0.18
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:58946866 original size:25 final size:25
Alignment explanation
Indices: 58946838--58946905 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
58946828 CTATATTACG
58946838 TATATATATTATACTATTTTATGTA
1 TATATATATTATACTATTTTATGTA
* * *
58946863 TATATCT-TTAATACTATATTATTTA
1 TATATATATT-ATACTATTTTATGTA
58946888 TATATATA-TATA-TATTTT
1 TATATATATTATACTATTTT
58946906 TCTACATGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
23 5 0.14
24 5 0.14
25 26 0.72
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (25 bp):
TATATATATTATACTATTTTATGTA
Found at i:58946947 original size:22 final size:23
Alignment explanation
Indices: 58946919--58946980 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 23
58946909 ACATGTTATC
58946919 TTATGTATATATTTTA-A-TCATA
1 TTATGTATATATTTTACACT-ATA
*
58946941 TTATGTATGTATTTTTTACACTATA
1 TTATGTA--TATATTTTACACTATA
58946966 TTATGTATATATTTT
1 TTATGTATATATTTT
58946981 TTTATATCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 7 0.21
23 7 0.21
24 8 0.24
25 11 0.32
26 1 0.03
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.58
Consensus pattern (23 bp):
TTATGTATATATTTTACACTATA
Found at i:58946992 original size:25 final size:23
Alignment explanation
Indices: 58946919--58946992 Score: 71
Period size: 25 Copynumber: 3.1 Consensus size: 23
58946909 ACATGTTATC
58946919 TTATGTATATA--TTTTAATCATA
1 TTATGTATATATTTTTTAATC-TA
* *
58946941 TTATGTATGTATTTTTTACACTATA
1 TTATGTATATATTTTTTA-A-TCTA
58946966 TTATGTATATATTTTTTTATATCTA
1 TTATGTATATA-TTTTTTA-ATCTA
58946991 TT
1 TT
58946993 TTATACATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
22 10 0.24
24 5 0.12
25 18 0.43
26 9 0.21
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (23 bp):
TTATGTATATATTTTTTAATCTA
Found at i:58947071 original size:25 final size:24
Alignment explanation
Indices: 58947043--58947098 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
58947033 GTTATATTTT
*
58947043 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
58947068 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
58947091 CACTATTA
1 CACTATTA
58947099 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:58948640 original size:25 final size:25
Alignment explanation
Indices: 58948612--58948662 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
58948602 TTTAAGAAAG
58948612 ATTTCAAAATTTTAAAAATAAATTT
1 ATTTCAAAATTTTAAAAATAAATTT
58948637 ATTTCAAAATTTTAAAAATAAATTT
1 ATTTCAAAATTTTAAAAATAAATTT
58948662 A
1 A
58948663 CTTGTTTGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (25 bp):
ATTTCAAAATTTTAAAAATAAATTT
Found at i:58948885 original size:125 final size:125
Alignment explanation
Indices: 58948638--58948878 Score: 344
Period size: 125 Copynumber: 1.9 Consensus size: 125
58948628 AATAAATTTA
* * *
58948638 TTTCAAAATTTTAAAAATAAATTTACTTGTTTGGGTAAAAATATTGAAAAATTTTAGAACTTGTG
1 TTTCAAAATTCTAAAAATAAATTTACTTGTTTGGGTAAAAATATTGAAAAATTTCAAAACTTGTG
* * *
58948703 AGTAACTTTAAAAGGGGATTTCAACAGCTCAATTTTCTTTTCCAAATTCTAACTAAAGGT
66 AGTAACTTTAAAAGGAGATTTCAAAAGATCAATTTTCTTTTCCAAATTCTAACTAAAGGT
* *
58948763 TTTCAAAAATTCTAAAAATGAAA-TTACTT-TTTGGGTAAACATATTGGAAAATTTCAAAACTTG
1 TTTC-AAAATTCTAAAAAT-AAATTTACTTGTTTGGGTAAAAATATTGAAAAATTTCAAAACTTG
* *
58948826 TGAGTAA-TTTCAAAAGGAGATTTCAAAAGATGAATTTTCTTTTTCAAATTCTA
64 TGAGTAACTTT-AAAAGGAGATTTCAAAAGATCAATTTTCTTTTCCAAATTCTA
58948879 CTTAAAGAGG
Statistics
Matches: 103, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
124 3 0.03
125 78 0.76
126 19 0.18
127 3 0.03
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.38
Consensus pattern (125 bp):
TTTCAAAATTCTAAAAATAAATTTACTTGTTTGGGTAAAAATATTGAAAAATTTCAAAACTTGTG
AGTAACTTTAAAAGGAGATTTCAAAAGATCAATTTTCTTTTCCAAATTCTAACTAAAGGT
Found at i:58958102 original size:34 final size:34
Alignment explanation
Indices: 58958059--58958126 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
58958049 GAGTCCTAGT
58958059 TGAGACTAGTTTCGACTTGCCCTTTCCCATAATA
1 TGAGACTAGTTTCGACTTGCCCTTTCCCATAATA
58958093 TGAGACTAGTTTCGACTTGCCCTTTCCCATAATA
1 TGAGACTAGTTTCGACTTGCCCTTTCCCATAATA
58958127 ATAATTTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (34 bp):
TGAGACTAGTTTCGACTTGCCCTTTCCCATAATA
Found at i:58963405 original size:50 final size:49
Alignment explanation
Indices: 58963287--58963517 Score: 284
Period size: 50 Copynumber: 4.7 Consensus size: 49
58963277 CTAGTATGCA
* * *
58963287 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCTGGTACACG
** *
58963336 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCTGGTACACG
* * * ** *
58963386 TAGTAGCCTGCACTTAGTACTACACACATGATCAAAGTTATCGGGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCTGGTACACG
* *
58963437 TAGTAG-CTTCACTTAGTACTACACACGCGACCAATTATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCTGGTACACG
* *
58963485 TAGTAGCCTGCACTTAGTACTATACACATGACC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC
58963518 TCACAATAGA
Statistics
Matches: 151, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
48 16 0.11
49 56 0.37
50 65 0.43
51 14 0.09
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCTGGTACACG
Found at i:58963477 original size:99 final size:99
Alignment explanation
Indices: 58963287--58963516 Score: 302
Period size: 99 Copynumber: 2.3 Consensus size: 99
58963277 CTAGTATGCA
*** * *
58963287 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACATGACAAATTATCCGGTACACATAGTAGCCTGCACTTA
*
58963352 GTACTACACACGTGACCTAACCATCTGATACACG
66 GTACTACACACGCGACCTAACCATCTGATACACG
* ** *
58963386 TAGTAGCCTGCACTTAGTACTACACACATGATCAAAGTTATCGGGTATGCATAGTAG-CTTCACT
1 TAGTAGCCTGCACTTAGTACTACACACATGA-CAAA-TTATCCGGTACACATAGTAGCCTGCACT
** *
58963450 TAGTACTACACACGCGACC-AATTATCTGGTACACG
64 TAGTACTACACACGCGACCTAACCATCTGATACACG
*
58963485 TAGTAGCCTGCACTTAGTACTATACACATGAC
1 TAGTAGCCTGCACTTAGTACTACACACATGAC
58963517 CTCACAATAG
Statistics
Matches: 115, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
98 1 0.01
99 71 0.62
100 27 0.23
101 16 0.14
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACATGACAAATTATCCGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCTAACCATCTGATACACG
Found at i:58968249 original size:47 final size:48
Alignment explanation
Indices: 58968184--58968445 Score: 210
Period size: 47 Copynumber: 5.5 Consensus size: 48
58968174 TTTGTGTGCT
58968184 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
* *
58968230 AGTGTAAGACCATGTCTGGGACATGGCATCGG---CATTAAGACAAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATG---AGAGCC
* ** * *
58968278 AGTGTAAGA-CATGTCTGGGATAT-ATATCGGCCTCGA-GATGTA-AGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC-ATTATG-AGAGCC
* * * *
58968324 AGTGTAAGACCATGTATGGGACATGGCATCGGCCTCGATT-TCGATAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC-ATTAT-GAGAGCC
* * *
58968373 AGTGTAAGACCATGTATGGGACATGGCATC-G--AC-TTGATGGATAGGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATT-AT-GAGA-GCC
58968420 AGTGTAAGACCATGTCTGGGACATGG
1 AGTGTAAGACCATGTCTGGGACATGG
58968446 AATCAGTATT
Statistics
Matches: 179, Mismatches: 20, Indels: 33
0.77 0.09 0.14
Matches are distributed among these distances:
44 2 0.01
45 6 0.03
46 32 0.18
47 66 0.37
48 35 0.20
49 37 0.21
50 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
Found at i:58968344 original size:94 final size:94
Alignment explanation
Indices: 58968181--58968356 Score: 266
Period size: 94 Copynumber: 1.9 Consensus size: 94
58968171 TCATTTGTGT
* * *
58968181 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTC
1 GCTAGTGTAAGACATGTCTGGGACATACATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTA
58968246 TGGGACATGGCATCGGCATTAAGACAAGA
66 TGGGACATGGCATCGGCATTAAGACAAGA
* * *
58968275 GCTAGTGTAAGACATGTCTGGGATATATATCGGCCTCGA-GATGTA-AGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACATGTCTGGGACATACATCGGCCAC-ATGATG-AGAGCCAGTGTAAGACCATG
58968338 TATGGGACATGGCATCGGC
64 TATGGGACATGGCATCGGC
58968357 CTCGATTTCG
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
94 72 0.97
95 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (94 bp):
GCTAGTGTAAGACATGTCTGGGACATACATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTA
TGGGACATGGCATCGGCATTAAGACAAGA
Found at i:58972615 original size:33 final size:33
Alignment explanation
Indices: 58972578--58972642 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
58972568 AATTGTAGGC
58972578 TAATAATAAAGGGTGTGTAAAAAAATTCTAAAT
1 TAATAATAAAGGGTGTGTAAAAAAATTCTAAAT
58972611 TAATAATAAAGGGTGTGTAAAAAAATTCTAAA
1 TAATAATAAAGGGTGTGTAAAAAAATTCTAAA
58972643 CCGAAAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.52, C:0.03, G:0.15, T:0.29
Consensus pattern (33 bp):
TAATAATAAAGGGTGTGTAAAAAAATTCTAAAT
Found at i:58972968 original size:2 final size:2
Alignment explanation
Indices: 58972961--58972990 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
58972951 TTTTAATTAT
*
58972961 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58972991 AAAGAAACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:58973224 original size:71 final size:70
Alignment explanation
Indices: 58973098--58973241 Score: 236
Period size: 71 Copynumber: 2.0 Consensus size: 70
58973088 AAATTTTTTG
*
58973098 ATTTTTAATATTAATATTTTTTATAATAAATTTGAAATAAATTAAAATTAAAAGTAATACAATAT
1 ATTTTTAATATTAATATTTTTTATAATAAATTTGAAATAAATTAAAATTAAAAGTAATAAAATAT
58973163 ACTAA
66 ACTAA
* *
58973168 ATTTTTAATTTTTAAT-TTTTTTATAATGAATTTGAAATAAAATTAAAATTAAAAGTAATAAAAT
1 ATTTTTAA-TATTAATATTTTTTATAATAAATTTGAAAT-AAATTAAAATTAAAAGTAATAAAAT
58973232 ATACTAA
64 ATACTAA
58973239 ATT
1 ATT
58973242 GAAGAAAGAA
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
70 29 0.42
71 40 0.58
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.44
Consensus pattern (70 bp):
ATTTTTAATATTAATATTTTTTATAATAAATTTGAAATAAATTAAAATTAAAAGTAATAAAATAT
ACTAA
Done.