Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008163.1 Hibiscus syriacus cultivar Beakdansim tig00110737_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 266294
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:195974 original size:23 final size:20
Alignment explanation
Indices: 195917--196005 Score: 65
Period size: 23 Copynumber: 4.2 Consensus size: 20
195907 TTTTTTCTTC
195917 TTTT-TCTTTA-TTTCTTTA
1 TTTTATCTTTATTTTCTTTA
*
195935 TTTTTTATATTTATTTTACTTACTA
1 --TTTTATCTTTATTTT-CTT--TA
*
195960 TTTTATCTTTGTTTTCTTTA
1 TTTTATCTTTATTTTCTTTA
* *
195980 TCTTATCTTTTATTTTATTTTA
1 TTTTATC-TTTATTTT-CTTTA
196002 TTTT
1 TTTT
196006 TTTCTTCATT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
20 12 0.22
21 12 0.22
22 13 0.24
23 16 0.29
25 2 0.04
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.74
Consensus pattern (20 bp):
TTTTATCTTTATTTTCTTTA
Found at i:195980 original size:32 final size:31
Alignment explanation
Indices: 195931--196005 Score: 73
Period size: 32 Copynumber: 2.4 Consensus size: 31
195921 TCTTTATTTC
* * *
195931 TTTATTTT-TTATATTTATTTTA-CTTACTAT
1 TTTATTTTATTTTCTTTATCTTATCTT-CTAT
* *
195961 TTTATCTTTGTTTTCTTTATCTTATCTTTTAT
1 TTTAT-TTTATTTTCTTTATCTTATCTTCTAT
195993 TTTATTTTATTTT
1 TTTATTTTATTTT
196006 TTTCTTCATT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
30 5 0.14
31 10 0.27
32 19 0.51
33 3 0.08
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.73
Consensus pattern (31 bp):
TTTATTTTATTTTCTTTATCTTATCTTCTAT
Found at i:195991 original size:50 final size:52
Alignment explanation
Indices: 195883--196001 Score: 138
Period size: 53 Copynumber: 2.3 Consensus size: 52
195873 GCTAACACTT
* * *
195883 TTTTATTATTATTTTATTTATATATTTTTTCTTCTTTTTCTTTATTTCTTTATT
1 TTTTATT-TTATTTTACTTATATATTTTATCTTCTTTTTCTTTA-TTCTTTATC
*
195937 TTTTATATTTATTTTACTTA-CTATTTTATCTT-TGTTTTCTTTA-TC-TTATC
1 TTTTAT-TTTATTTTACTTATATATTTTATCTTCT-TTTTCTTTATTCTTTATC
195987 TTTTATTTTATTTTA
1 TTTTATTTTATTTTA
196002 TTTTTTTCTT
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
49 9 0.15
50 10 0.17
51 2 0.03
52 1 0.02
53 19 0.32
54 17 0.29
55 1 0.02
ACGTcount: A:0.18, C:0.08, G:0.01, T:0.73
Consensus pattern (52 bp):
TTTTATTTTATTTTACTTATATATTTTATCTTCTTTTTCTTTATTCTTTATC
Found at i:196005 original size:54 final size:53
Alignment explanation
Indices: 195883--196005 Score: 135
Period size: 54 Copynumber: 2.3 Consensus size: 53
195873 GCTAACACTT
* * *
195883 TTTTATTATTATTTTATTTATATATTTTTTCTTCTTTTTCTTTATTTCTTTATT
1 TTTTATT-TTATTTTACTTATATATTTTATCTTCTTTTTCTTTATTTCTTTATA
*
195937 TTTTATATTTATTTTACTTA-CTATTTTATCTT-TGTTTTCTTTATCTTATCTTT-TA
1 TTTTAT-TTTATTTTACTTATATATTTTATCTTCT-TTTTCTTTA--TT-TCTTTATA
195992 TTTTATTTTATTTT
1 TTTTATTTTATTTT
196006 TTTCTTCATT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
52 1 0.02
53 19 0.32
54 25 0.42
55 10 0.17
56 5 0.08
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.74
Consensus pattern (53 bp):
TTTTATTTTATTTTACTTATATATTTTATCTTCTTTTTCTTTATTTCTTTATA
Found at i:196007 original size:17 final size:17
Alignment explanation
Indices: 195881--196007 Score: 66
Period size: 18 Copynumber: 7.4 Consensus size: 17
195871 GTGCTAACAC
195881 TTTTTTATTATTATTTTA
1 TTTTTTATT-TTATTTTA
* *
195899 TTTATATATTTT-TTCTTC
1 TTT-TTTATTTTATT-TTA
195917 TTTTTCT-TTATT-TCTTTA
1 TTTTT-TATT-TTAT-TTTA
195935 TTTTTTATATTTATTTTA
1 TTTTTTAT-TTTATTTTA
* ** *
195953 CTTACTATTTTATCTT-
1 TTTTTTATTTTATTTTA
* * *
195969 TGTTTT-CTTTATCTTA
1 TTTTTTATTTTATTTTA
*
195985 TCTTTTATTTTATTTTA
1 TTTTTTATTTTATTTTA
196002 TTTTTT
1 TTTTTT
196008 TCTTCATTTT
Statistics
Matches: 82, Mismatches: 17, Indels: 21
0.68 0.14 0.17
Matches are distributed among these distances:
15 8 0.10
16 7 0.09
17 26 0.32
18 33 0.40
19 8 0.10
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.75
Consensus pattern (17 bp):
TTTTTTATTTTATTTTA
Found at i:196038 original size:22 final size:20
Alignment explanation
Indices: 195987--196038 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 20
195977 TTATCTTATC
* *
195987 TTTTATTTTATTTTATTTTT
1 TTTTATTTTAATTAATTTTT
196007 TTCTTCATTTTAATTAATTAATTT
1 TT-TT-ATTTTAATTAATT--TTT
196031 TTTTATTT
1 TTTTATTT
196039 CTTACCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 2 0.08
21 2 0.08
22 15 0.58
23 2 0.08
24 5 0.19
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTATTTTAATTAATTTTT
Found at i:196342 original size:22 final size:21
Alignment explanation
Indices: 196249--196373 Score: 85
Period size: 21 Copynumber: 5.9 Consensus size: 21
196239 TTTTTTCTTC
196249 TTTTTCTTTATTTT-TTATATT
1 TTTTTCTTTATTTTATT-TATT
* * *
196270 TTTATATTTATTTTACTTACTAT
1 TTTTTCTTTATTTTATTTA-T-T
* * *
196293 TTTATCTTTGTTTTCTTTA-T
1 TTTTTCTTTATTTTATTTATT
* * *
196313 CTTATCTTTTATTTTATTTGTT
1 TTTTTC-TTTATTTTATTTATT
*
196335 TTTTTCTTCATTTTAATTTATT
1 TTTTTCTTTATTTT-ATTTATT
*
196357 TTTTTATTTA-TTTATTT
1 TTTTTCTTTATTTTATTT
196374 CTTACCTTTT
Statistics
Matches: 81, Mismatches: 17, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
20 10 0.12
21 34 0.42
22 21 0.26
23 16 0.20
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTTCTTTATTTTATTTATT
Found at i:196373 original size:26 final size:26
Alignment explanation
Indices: 196319--196373 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
196309 TTATCTTATC
* *
196319 TTTTATTTTATTTGTTTTTTTCTTCA
1 TTTTAATTTATTTGTTTTTTTATTCA
*
196345 TTTTAATTTATTT-TTTTATTTATTTA
1 TTTTAATTTATTTGTTTT-TTTATTCA
196371 TTT
1 TTT
196374 CTTACCTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (26 bp):
TTTTAATTTATTTGTTTTTTTATTCA
Found at i:197317 original size:31 final size:31
Alignment explanation
Indices: 197282--197342 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
197272 AAAACATAAG
*
197282 ATATGATCACTTTCGTTTTTATTTAGTTAAT
1 ATATGATCACTTTCGTTTTTATTTAATTAAT
*
197313 ATATGGTCACTTTCGTTTTTATTTAATTAA
1 ATATGATCACTTTCGTTTTTATTTAATTAA
197343 GATGGGGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (31 bp):
ATATGATCACTTTCGTTTTTATTTAATTAAT
Found at i:197352 original size:31 final size:31
Alignment explanation
Indices: 197278--197353 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
197268 TTAAAAAACA
* * *
197278 TAAGATATGATCACTTTCGTTTTTATTTAGT
1 TAAGATAGGGTCACTTTCGTTTTTATTTAAT
* *
197309 TAATATATGGTCACTTTCGTTTTTATTTAAT
1 TAAGATAGGGTCACTTTCGTTTTTATTTAAT
*
197340 TAAGATGGGGTCAC
1 TAAGATAGGGTCAC
197354 CCTGAGTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (31 bp):
TAAGATAGGGTCACTTTCGTTTTTATTTAAT
Found at i:198356 original size:31 final size:31
Alignment explanation
Indices: 198321--198384 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
198311 GTCCACATCA
*
198321 TAATTAAATAAAAATGAATA-TGACCATATCT
1 TAATTAAATAAAAACGAA-AGTGACCATATCT
*
198352 TAATTAAATAAAAACGAAAGTGACTATATCT
1 TAATTAAATAAAAACGAAAGTGACCATATCT
198383 TA
1 TA
198385 TGTTTTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.52, C:0.09, G:0.08, T:0.31
Consensus pattern (31 bp):
TAATTAAATAAAAACGAAAGTGACCATATCT
Found at i:201772 original size:29 final size:29
Alignment explanation
Indices: 201738--201797 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
201728 CCATATTTTG
201738 TAAACTCGGATTATCATTATGTTTTATCT
1 TAAACTCGGATTATCATTATGTTTTATCT
*
201767 TAAACTTGGATTATCATTATGTTTTATCT
1 TAAACTCGGATTATCATTATGTTTTATCT
201796 TA
1 TA
201798 CTTATTTTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (29 bp):
TAAACTCGGATTATCATTATGTTTTATCT
Found at i:208067 original size:20 final size:20
Alignment explanation
Indices: 208050--208124 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
208040 TTTACTAAGT
*
208050 AGTCAGTATCGATACT-AAT
1 AGTCAGTATCGATACTCAAG
*
208069 AGGTGAGTATCGATACTCAAG
1 A-GTCAGTATCGATACTCAAG
* *
208090 -GTTCATTATCGATACTGAAG
1 AG-TCAGTATCGATACTCAAG
*
208110 GGTCAGTATCGATAC
1 AGTCAGTATCGATAC
208125 CCATGGACAG
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
19 2 0.04
20 41 0.89
21 3 0.07
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (20 bp):
AGTCAGTATCGATACTCAAG
Found at i:210377 original size:21 final size:20
Alignment explanation
Indices: 210349--210388 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
210339 ACTCGACATT
210349 ACTCAAAATTTAT-AAAGTCG
1 ACTCAAAATTT-TCAAAGTCG
210369 ACTCGAAAATTTTCAAAGTC
1 ACTC-AAAATTTTCAAAGTC
210389 AACTTTGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.30
Consensus pattern (20 bp):
ACTCAAAATTTTCAAAGTCG
Found at i:212637 original size:179 final size:181
Alignment explanation
Indices: 211964--212800 Score: 1030
Period size: 181 Copynumber: 4.6 Consensus size: 181
211954 GATACAAATA
* * * * * * * * *
211964 AAAAATGTATCGATCTATAGCAATATAACATGTTAAAATATAACAAAATCGGTTTC-ATTATGAC
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGATCTCGA-AATGAC
* * * * * * *
212028 AAAACCGGTAAAGTGGTACCGGATATGTTGAAAGTATCGATTAGATTGAA-ATAAGTATAAATAC
65 AAAACCGGTAAA-AGCTACCGGATATGTTGAAAGTGTCGA-TA-CTTTAATATAAGTATAGACAC
* * * *
212092 TTTTAGAATTTAAAAGAG--G-AGTAATAGTGTCTATAAAGTGTCGATACTTTAAA
127 TTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTT-AT
* *
212145 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTAGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGATCTCGAAATGACA
* * * * *
212210 AAATCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTATATTA-AATTATCGACACTT
66 AAACCGGTAAA-AGCTACCGGATATGTTGAAAGTGTCGATACTT-TAATATAAGTATAGACACTT
* * *
212274 TTGGAATTTAAAAGAGAAGTAGTAATAACGCCTATAAAGTATCGATACTTTAT
129 TTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
*
212327 -AAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAACCGATCTCGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGATCTCGAAATGACA
** * * *
212391 AAACCATTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACGCTTT
66 AAACCGGTAAA-AGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATAGACACTTT
* *
212456 TGGAATTTAAAAGAGAAGCATTTATAGCGCCTATAAAGTGTCGATACTTTAT
130 TGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
*
212508 AAAAATGTATCGATTCATAAC-A-ATAACAGGTAAAAATATGACAAAACC-ATCTCGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGATCTCGAAATGACA
* * *
212570 AAACGGGTAAAATGCTACCGGATATGTTGAAAGTGCCAATACTTTAATATAAGTATAGACACTTT
66 AAACCGGTAAAA-GCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATAGACACTTT
* *
212635 TGGAATTTAAAAGAGAAGCAGTAATA-CTGCCTATAAAGTGCCAATACTTTAT
130 TGGAATTTAAAAGAGAAGCAGTAATAGC-GCCTATAAAGTGTCGATACTTTAT
* * * * *
212687 AGAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCAAAATTACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGATCTCGAAATGACA
* * *
212752 AAGCCGGTTAAACGCTGCCGGATATGTTGAAAGTGTCGATACTTTAATA
66 AAACCGG-TAAAAGCTACCGGATATGTTGAAAGTGTCGATACTTTAATA
212801 AGTATGCGTA
Statistics
Matches: 575, Mismatches: 67, Indels: 27
0.86 0.10 0.04
Matches are distributed among these distances:
178 2 0.00
179 136 0.24
180 58 0.10
181 277 0.48
182 71 0.12
183 31 0.05
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (181 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGATCTCGAAATGACA
AAACCGGTAAAAGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATAGACACTTTT
GGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
Found at i:212723 original size:361 final size:360
Alignment explanation
Indices: 211965--212800 Score: 1071
Period size: 361 Copynumber: 2.3 Consensus size: 360
211955 ATACAAATAA
* * * * * * *
211965 AAAATGTATCGATCTATAGCAATATAACATGTTAAAATATAACAAAATCGGTTTCATTATGACAA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCA-AATGACAA
* * * * * * *
212030 AACCGGTAAAGTGGTACCGGATATGTTGAAAGTATCGATTAGATTGAA-ATAAGTATAAATACTT
65 AACCGTTAAAGAGCTACCGGATATGTTGAAAGTGTCGA-TA-CTTTAATATAAGTATAAACACTT
* *
212094 TTAGAATTTAAAAGAGGAGTAATAGTGTCTATAAAGTGTCGATACTTTAAAAAAAATGTATCGAT
128 TTAGAATTTAAAAGAGGAGTAATAGCGCCTATAAAGTGTCGATACTTTAAAAAAAATGTATCGAT
*
212159 CCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTAGAAATGACAAAATCGGTAAAGAG
193 CCATAACAATATAACAGGTAAAAATATGACAAAACCGATCTAGAAATGACAAAATCGGTAAAGAG
* * * * *
212224 CTACCAGATATGTTGAAAGTGTCGATACTTATATTAAATTATCGACACTTTTGGAATTTAAAAGA
258 CTACCAGATATGTTGAAAGTGCCAATACTTATAATAAAGTATAGACACTTTTGGAATTTAAAAGA
* * *
212289 GAAGTAGTAATAACGCCTATAAAGTATCGATACTTTAT
323 GAAGCAGTAATAACGCCTATAAAGTACCAATACTTTAT
* * *
212327 AAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAACCGATCTCGAAATGACAA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTC-AAATGACAA
* * ** *
212392 AACCATTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACGCTTTT
65 AACCGTTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATAAACACTTTT
* * * *
212457 GGAATTTAAAAGAGAAGCATTTATAGCGCCTATAAAGTGTCGATACTTT-ATAAAAATGTATCGA
130 AGAATTTAAAAGAG--G-AGTAATAGCGCCTATAAAGTGTCGATACTTTAAAAAAAATGTATCGA
* *
212521 TTCATAAC-A-ATAACAGGTAAAAATATGACAAAACC-ATCTCGAAATGACAAAA-CGGGTAAA-
192 TCCATAACAATATAACAGGTAAAAATATGACAAAACCGATCTAGAAATGACAAAATC-GGTAAAG
*
212581 ATGCTACCGGATATGTTGAAAGTGCCAATACTT-TAATATAAGTATAGACACTTTTGGAATTTAA
256 A-GCTACCAGATATGTTGAAAGTGCCAATACTTATAATA-AAGTATAGACACTTTTGGAATTTAA
*
212645 AAGAGAAGCAGTAAT-ACTGCCTATAAAGTGCCAATACTTTAT
319 AAGAGAAGCAGTAATAAC-GCCTATAAAGTACCAATACTTTAT
*
212687 AGAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCAAAATTACA
1 A-AAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTC-AAATGACA
* * *
212752 AAGCCGGTTAAA-CGCTGCCGGATATGTTGAAAGTGTCGATACTTTAATA
64 AAACC-GTTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAATA
212801 AGTATGCGTA
Statistics
Matches: 412, Mismatches: 51, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
359 8 0.02
360 112 0.27
361 151 0.37
362 91 0.22
363 23 0.06
364 27 0.07
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.28
Consensus pattern (360 bp):
AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCAAATGACAAA
ACCGTTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATAAACACTTTTA
GAATTTAAAAGAGGAGTAATAGCGCCTATAAAGTGTCGATACTTTAAAAAAAATGTATCGATCCA
TAACAATATAACAGGTAAAAATATGACAAAACCGATCTAGAAATGACAAAATCGGTAAAGAGCTA
CCAGATATGTTGAAAGTGCCAATACTTATAATAAAGTATAGACACTTTTGGAATTTAAAAGAGAA
GCAGTAATAACGCCTATAAAGTACCAATACTTTAT
Found at i:218000 original size:199 final size:199
Alignment explanation
Indices: 217630--218309 Score: 1012
Period size: 199 Copynumber: 3.4 Consensus size: 199
217620 GTAAACAAAT
*
217630 GTGTCGATACATTTATTAAA--AGTATTGATCCCAAAAACATCGAAACCGATAATTATAATATAA
1 GTGTCGATACATTTA--AAATTA-TATCGATCCCAAAAACATCGAAACCGATAATTATAATATAA
* * *
217693 TAGGTAAATTTACAATGTAACCAGTAGAAATATACCGGTTTTATGAGAAAATATGTCTACATAAT
63 TAGGTAAATTTACAATGTAACCGGTAGAAATATATCGGTTTTATGAGAAAATAGGTCTACATAAT
* * *
217758 GTATCGACACTTTATAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGACAAACTAGGTGCAC
128 GTATCAACACTTTTTAAATTTGTGTCGATACTTTTTTTCCAGAATGAATGACAAACTAGGTGCAC
217823 GCATAAA
193 GCATAAA
* *
217830 GTGTCAATACATTTAAAATTATATCGATCCCAAAAACATCGAAACCGATAATTACAATATAATAG
1 GTGTCGATACATTTAAAATTATATCGATCCCAAAAACATCGAAACCGATAATTATAATATAATAG
* * * *
217895 GTAAATTTAAAATGTAACCGGTAGAAATATATCGATTTTATGAGAGAATAGGTCAACATAATGTA
66 GTAAATTTACAATGTAACCGGTAGAAATATATCGGTTTTATGAGAAAATAGGTCTACATAATGTA
*
217960 TCAACACTTTTTAAATTTGTGTCGATACTTTTTTTCCAGAATGAATGACATACTAGGTGCACGCA
131 TCAACACTTTTTAAATTTGTGTCGATACTTTTTTTCCAGAATGAATGACAAACTAGGTGCACGCA
218025 TAAA
196 TAAA
* *
218029 GTGTCGATACATTTATTAAA--AGTATCGATCCCAAAAATATCGAAACCGATAATTATAATGTAA
1 GTGTCGATACATTTA--AAATTA-TATCGATCCCAAAAACATCGAAACCGATAATTATAATATAA
* * *
218092 TAGGTAAATTTACAATGTAATCGGTATAAATATATTGGTTTTATGAGAAAATAGGTCTACATAAT
63 TAGGTAAATTTACAATGTAACCGGTAGAAATATATCGGTTTTATGAGAAAATAGGTCTACATAAT
* * *
218157 GTATCAACAC-TTTTAAATTTGTGTCGATA-TTTTTTGTCCAGAATGAATGCCCAACGAGGTGCA
128 GTATCAACACTTTTTAAATTTGTGTCGATACTTTTTT-TCCAGAATGAATGACAAACTAGGTGCA
218220 CGCATAAA
192 CGCATAAA
* * *
218228 GTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAT
1 GTGTCGATACATTTAAAATTATATCGATCCCAAAAACATCGAAACCGATAATTATAATATAATAG
* *
218293 GTAACTTTGCAATGTAA
66 GTAAATTTACAATGTAA
218310 TTGTTTATGT
Statistics
Matches: 438, Mismatches: 34, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
197 3 0.01
198 66 0.15
199 245 0.56
200 121 0.28
201 3 0.01
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (199 bp):
GTGTCGATACATTTAAAATTATATCGATCCCAAAAACATCGAAACCGATAATTATAATATAATAG
GTAAATTTACAATGTAACCGGTAGAAATATATCGGTTTTATGAGAAAATAGGTCTACATAATGTA
TCAACACTTTTTAAATTTGTGTCGATACTTTTTTTCCAGAATGAATGACAAACTAGGTGCACGCA
TAAA
Found at i:218470 original size:23 final size:23
Alignment explanation
Indices: 218444--218494 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
218434 TCAATAATTA
**
218444 ACCTATTTTATTATATAAGC-GCT
1 ACCTATTACATTATATAAGCAG-T
218467 ACCTATTACATTATATAAGCAGT
1 ACCTATTACATTATATAAGCAGT
218490 ACCTA
1 ACCTA
218495 ATATGTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCAGT
Found at i:221748 original size:23 final size:24
Alignment explanation
Indices: 221711--221767 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
221701 CTGGTTTTTT
*
221711 AAAAAATCGATTTTTAATCCGGTA
1 AAAAAACCGATTTTTAATCCGGTA
221735 AAAAAACCGATTTTTAATCCGGTA
1 AAAAAACCGATTTTTAATCCGGTA
221759 AAAAAACCG
1 AAAAAACCG
221768 GTCGTCCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (24 bp):
AAAAAACCGATTTTTAATCCGGTA
Found at i:224490 original size:27 final size:27
Alignment explanation
Indices: 224449--224500 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
224439 TGTGCGTCTT
* *
224449 TTTTTAAATTTAATAATATTTTTATGC
1 TTTTTAAATTTAATAAAAATTTTATGC
224476 TTTTT-AATTTCAATAAAAATTTTAT
1 TTTTTAAATTT-AATAAAAATTTTAT
224501 AAATATCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTTTAAATTTAATAAAAATTTTATGC
Found at i:235523 original size:4 final size:4
Alignment explanation
Indices: 235514--235648 Score: 162
Period size: 4 Copynumber: 33.8 Consensus size: 4
235504 GATCGAGAAA
*
235514 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC AAAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * * * **
235562 ACAC GCGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGT ACAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
235610 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACA
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACA
235649 TACATACATG
Statistics
Matches: 123, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 123 1.00
ACGTcount: A:0.44, C:0.48, G:0.07, T:0.01
Consensus pattern (4 bp):
ACAC
Found at i:236182 original size:36 final size:36
Alignment explanation
Indices: 236153--236256 Score: 111
Period size: 36 Copynumber: 2.9 Consensus size: 36
236143 TTGAGATCGC
*
236153 TTTCTC-AAAAACAACTTTTGTCTCGCTTGAGATAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGATAA
* * * * *
236188 TTTTTCTAAAAACAAATTTTGTCTTGCTGGAAACAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGATAA
* * * *
236224 TTTCTCTCAAAACAAATTTCGACTTGCTTGAGA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGA
236257 CATTTTTCTC
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
35 5 0.09
36 51 0.91
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.38
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGATAA
Found at i:236477 original size:28 final size:28
Alignment explanation
Indices: 236446--236507 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
236436 TCTTGAGACA
* *
236446 GTTTCTCTTGAAACAAGTCTTTGAGTTT
1 GTTTCTCTTCAAACAAATCTTTGAGTTT
* *
236474 GTTTCTTTTCAAACAAATTTTTGAGTTT
1 GTTTCTCTTCAAACAAATCTTTGAGTTT
236502 GTTTCT
1 GTTTCT
236508 ACTAACAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.52
Consensus pattern (28 bp):
GTTTCTCTTCAAACAAATCTTTGAGTTT
Found at i:236739 original size:63 final size:64
Alignment explanation
Indices: 236611--236731 Score: 174
Period size: 64 Copynumber: 1.9 Consensus size: 64
236601 CTATAAGAAC
**
236611 AAAAATCTTTGAGTCTGTTTCTCTGAAAACAATTTTTTTGTCACTTGAGACAATTTCTGTGGAA
1 AAAAATCTTTGAGTCTGTTTCTCTGAAAACAATAATTTTGTCACTTGAGACAATTTCTGTGGAA
* * *
236675 AAAAATCTTTGAGTTTGTTTCTTTTG-AAACAA-AATTTTGTCTCTTGAGACAATTTCT
1 AAAAATCTTTGAGTCTGTTTC-TCTGAAAACAATAATTTTGTCACTTGAGACAATTTCT
236732 TTTGAAAATG
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
63 22 0.43
64 26 0.51
65 3 0.06
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (64 bp):
AAAAATCTTTGAGTCTGTTTCTCTGAAAACAATAATTTTGTCACTTGAGACAATTTCTGTGGAA
Found at i:236853 original size:32 final size:31
Alignment explanation
Indices: 236816--236930 Score: 99
Period size: 31 Copynumber: 3.7 Consensus size: 31
236806 CATAAAATCA
*
236816 TTGAGTCTATTTCTCTTGAAATAAAACCATCT
1 TTGAGTCTATTTCTCTTGAAA-AAAATCATCT
* ** *
236848 TTGAG--TAGTTTCTTTTGAAACACCATTATCT
1 TTGAGTCTA-TTTCTCTTGAAA-AAAATCATCT
* * *
236879 TTGAGTCTGTTTCTTTTGAAAAAAATCACCT
1 TTGAGTCTATTTCTCTTGAAAAAAATCATCT
* *
236910 TTGAGTCGATTTCCCTTGAAA
1 TTGAGTCTATTTCTCTTGAAA
236931 CCTTTATACT
Statistics
Matches: 65, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
30 2 0.03
31 45 0.69
32 17 0.26
33 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (31 bp):
TTGAGTCTATTTCTCTTGAAAAAAATCATCT
Found at i:236866 original size:31 final size:31
Alignment explanation
Indices: 236785--236916 Score: 101
Period size: 31 Copynumber: 4.2 Consensus size: 31
236775 TTTGTCTCCC
* * *
236785 TTGAGGCAGTTTCTTTGGAAACATAAA--ATCA
1 TTGAGTCAGTTTCTTTTGAAA-A-AAATCATCT
* *
236816 TTGAGTCTA-TTTCTCTTGAAATAAAACCATCT
1 TTGAGTC-AGTTTCTTTTGAAA-AAAATCATCT
** *
236848 TTGAGT-AGTTTCTTTTGAAACACCATTATCT
1 TTGAGTCAGTTTCTTTTGAAA-AAAATCATCT
* *
236879 TTGAGTCTGTTTCTTTTGAAAAAAATCACCT
1 TTGAGTCAGTTTCTTTTGAAAAAAATCATCT
236910 TTGAGTC
1 TTGAGTC
236917 GATTTCCCTT
Statistics
Matches: 80, Mismatches: 16, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
30 4 0.05
31 53 0.66
32 23 0.29
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (31 bp):
TTGAGTCAGTTTCTTTTGAAAAAAATCATCT
Found at i:236868 original size:62 final size:62
Alignment explanation
Indices: 236792--236915 Score: 151
Period size: 62 Copynumber: 2.0 Consensus size: 62
236782 CCCTTGAGGC
* *
236792 AGTTTCTTTGGAAACA-TAAAATCATTGAGTCTATTTCTCTTGAAATAAAACCATCTTTGAGT
1 AGTTTCTTTGGAAACACCAAAATCATTGAGTCTATTTCTCTTGAAA-AAAACCACCTTTGAGT
* ** * * * *
236854 AGTTTCTTTTGAAACACCATTATCTTTGAGTCTGTTTCTTTTGAAAAAAATCACCTTTGAGT
1 AGTTTCTTTGGAAACACCAAAATCATTGAGTCTATTTCTCTTGAAAAAAACCACCTTTGAGT
236916 CGATTTCCCT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
62 29 0.56
63 23 0.44
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (62 bp):
AGTTTCTTTGGAAACACCAAAATCATTGAGTCTATTTCTCTTGAAAAAAACCACCTTTGAGT
Found at i:237399 original size:135 final size:132
Alignment explanation
Indices: 236941--237453 Score: 437
Period size: 135 Copynumber: 3.9 Consensus size: 132
236931 CCTTTATACT
* * * *
236941 TAAAGATGGCCAAGAACTCTTCATCACGTATGAG-CAGTGTCATCCCCCGACCAGATTTCCCCAG
1 TAAAGATGACCAAGAACTCTTCATCACGTATGAGCCA-TGTCAT-CCCCGACTAGATCTCCCCAT
* * * **
237005 CAGAGT-GGAATCGTGTCAACCTCAGATAACCAG--TCGTCCCCA-GTAGAGTGGAACCGTGTTA
64 CA-TGTAGGAATCGTGTCAACCTTAGATAACCAGACTCTTCATCACGT--A-T-GAACCGTGTTA
*
237066 TCACCCTTCC
124 TCA-CATTCC
* *
237076 TAAAGATGACCAA-AACTCTTTATCACGTATGAGCCATGTCATCACCAGACCT-GATCTCCCCAT
1 TAAAGATGACCAAGAACTCTTCATCACGTATGAGCCATGTCATC-CCCGA-CTAGATCTCCCCAT
* * * * * * * *
237139 CACGTAGGAGTTGTTTCAA-CTTAGATAATCAGCCGTCCTCATCACGTAGGAACCGTGTTATCAC
64 CATGTAGGAATCGTGTCAACCTTAGATAACCAGAC-TCTTCATCACGTATGAACCGTGTTATCAC
237203 ATT--
128 ATTCC
* * * * *
237206 T--AGATGGCC-AGAACTCTTCATCACGTATGAGCCATGTCATCACCCGACTAAATTTCCTCATT
1 TAAAGATGACCAAGAACTCTTCATCACGTATGAGCCATGTCATC-CCCGACTAGATCTCCCCATC
* * *
237268 ATGTAGGAATCGTGTCAATCCTT-GATAATCAGAACTCTTCATCACGTATGAGCCGAGTTATCAC
65 ATGTAGGAATCGTGTCAA-CCTTAGATAACCAG-ACTCTTCATCACGTATGAACCGTGTTATCAC
237332 TATTCC
128 -ATTCC
*
237338 TAAAGATGACCAAGAACTCTTCATCACGTATGAG-CAGTGTCATCCCCTGACTAGATCTCCTCAT
1 TAAAGATGACCAAGAACTCTTCATCACGTATGAGCCA-TGTCATCCCC-GACTAGATCTCCCCAT
* * * * *
237402 TATGTAGGAGTCTTGTC-ACCTTTAGACAACCCGAACTCTTCATCACGTATGA
64 CATGTAGGAATCGTGTCAACC-TTAGATAACCAG-ACTCTTCATCACGTATGA
237454 GCAGTGTCGT
Statistics
Matches: 314, Mismatches: 41, Indels: 46
0.78 0.10 0.11
Matches are distributed among these distances:
127 3 0.01
128 63 0.20
129 34 0.11
130 8 0.03
132 4 0.01
133 30 0.10
134 65 0.21
135 99 0.32
136 6 0.02
137 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.27
Consensus pattern (132 bp):
TAAAGATGACCAAGAACTCTTCATCACGTATGAGCCATGTCATCCCCGACTAGATCTCCCCATCA
TGTAGGAATCGTGTCAACCTTAGATAACCAGACTCTTCATCACGTATGAACCGTGTTATCACATT
CC
Found at i:237622 original size:3 final size:3
Alignment explanation
Indices: 237614--237677 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
237604 CTGGGTCGAA
* * * * *
237614 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAC TAC AAC TAT TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
*
237663 TAAT TAT TTT TAT TA
1 T-AT TAT TAT TAT TA
237678 CATTTTACAG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 47 0.87
4 7 0.13
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:239249 original size:2 final size:2
Alignment explanation
Indices: 239242--239298 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
239232 TCTGCTTTAA
239242 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
239284 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
239299 AGTATGCACA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:240784 original size:14 final size:14
Alignment explanation
Indices: 240765--240796 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
240755 TGGCTAGTTG
240765 GCAACTACTTGTAA
1 GCAACTACTTGTAA
*
240779 GCAACTAGTTGTAA
1 GCAACTACTTGTAA
240793 GCAA
1 GCAA
240797 TTTAGAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (14 bp):
GCAACTACTTGTAA
Found at i:240966 original size:20 final size:20
Alignment explanation
Indices: 240943--240994 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
240933 AACGCGATCC
240943 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
240963 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
240983 CCAAAATCGCAA
1 CCAGAATCGCAA
240995 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:241011 original size:21 final size:20
Alignment explanation
Indices: 240984--241082 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
240974 AATCAGTTTC
240984 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
241005 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
241026 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
241046 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
241067 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
241083 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:241111 original size:20 final size:20
Alignment explanation
Indices: 241049--241242 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
241039 CGATTTTCCA
* ** *
241049 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
241069 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
241089 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
241109 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
241129 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
241149 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
241169 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
241189 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
241209 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
241230 AAATCGCAACGCG
1 AAATCGCAACGCG
241243 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:241133 original size:60 final size:60
Alignment explanation
Indices: 241049--241242 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
241039 CGATTTTCCA
* ** * *
241049 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
241109 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
241169 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
241230 AAATCGCAACGCG
1 AAATCGCAACGCG
241243 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:241662 original size:33 final size:33
Alignment explanation
Indices: 241623--241693 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
241613 TTCACTTAGA
*
241623 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
241656 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
241689 TTTCA
1 TTTCA
241694 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:241833 original size:14 final size:14
Alignment explanation
Indices: 241814--241868 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
241804 AGAATGACTG
241814 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
241828 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
241847 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
241861 TCGCAACG
1 TCGCAACG
241869 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:241881 original size:33 final size:33
Alignment explanation
Indices: 241814--241884 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
241804 AGAATGACTG
***
241814 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
241847 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
241880 TCGCA
1 TCGCA
241885 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:241902 original size:19 final size:19
Alignment explanation
Indices: 241880--241977 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
241870 GAAACCAAAA
*
241880 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
241899 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
241913 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
241932 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
241946 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
241965 TCGCGTTGCGATT
1 TCGCGTTGCGATT
241978 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:241921 original size:14 final size:14
Alignment explanation
Indices: 241902--241991 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
241892 TTTCATTTCG
241902 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
241916 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
241935 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
241949 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
241966 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
241982 CGTTGCGATT
1 CGTTGCGATT
241992 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:241927 original size:33 final size:33
Alignment explanation
Indices: 241885--241999 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
241875 CAAAATCGCA
241885 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
241918 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
241951 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
241984 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
242000 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:244008 original size:185 final size:185
Alignment explanation
Indices: 243697--244077 Score: 737
Period size: 185 Copynumber: 2.1 Consensus size: 185
243687 TAGATTGCTT
243697 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATCTTTAACACTGTGAAATAGTAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATCTTTAACACTGTGAAATAGTAT
243762 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
243827 TGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
243881 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTA-TCTTTAACACTGTGAAATAGTA
243946 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
244011 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
244067 AGTAAATTTAT
1 AGTAAATTTAT
244078 CCATTCAAGT
Statistics
Matches: 193, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 41 0.21
185 112 0.58
186 40 0.21
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (185 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATCTTTAACACTGTGAAATAGTAT
TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:244010 original size:93 final size:93
Alignment explanation
Indices: 243697--244075 Score: 735
Period size: 93 Copynumber: 4.1 Consensus size: 93
243687 TAGATTGCTT
*
243697 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTA-TCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
243761 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
243789 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
243853 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
243881 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
243946 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
243974 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
244039 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
244067 AGTAAATTT
1 AGTAAATTT
244076 ATCCATTCAA
Statistics
Matches: 284, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
92 133 0.47
93 151 0.53
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:244179 original size:33 final size:32
Alignment explanation
Indices: 244136--244228 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
244126 ACGAAACTTA
**
244136 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
244168 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
244201 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
244229 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:244228 original size:19 final size:19
Alignment explanation
Indices: 244119--244228 Score: 87
Period size: 19 Copynumber: 6.3 Consensus size: 19
244109 TAGTTTACTT
* *
244119 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
**
244139 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
244158 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
244172 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
244191 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
244205 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
244224 TCGCA
1 TCGCA
244229 TTGCGATTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.26
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 29 0.40
20 12 0.17
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:244246 original size:19 final size:19
Alignment explanation
Indices: 244224--244358 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
244214 GAAACCAAAA
*
244224 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
244243 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
244259 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
244276 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
244292 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
244309 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
244328 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
244348 TCGTGTTGCGA
1 TCGCGTTGCGA
244359 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:244265 original size:14 final size:14
Alignment explanation
Indices: 244246--244302 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
244236 TTTCATTTCG
244246 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
244260 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
244277 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
244293 CGTTGCGATT
1 CGTTGCGATT
244303 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:244271 original size:33 final size:33
Alignment explanation
Indices: 244229--244321 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
244219 CAAAATCGCA
*
244229 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
244262 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
244295 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
244322 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:246206 original size:38 final size:38
Alignment explanation
Indices: 246163--246235 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
246153 AATTGATTGT
*
246163 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
246201 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
246236 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:246222 original size:19 final size:19
Alignment explanation
Indices: 246158--246222 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
246148 AGTTTAATTG
*
246158 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
246177 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
246195 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
246215 ATTGATTT
1 ATTGATTT
246223 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:246236 original size:14 final size:14
Alignment explanation
Indices: 246217--246252 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
246207 ATTGTTTAAT
246217 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
246231 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
246245 TGATTTGT
1 TGATTTGT
246253 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:246375 original size:19 final size:19
Alignment explanation
Indices: 246359--246460 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
246349 AAAAATGACT
246359 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
246378 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
246397 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
246411 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
246430 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
246450 ATCGCAATGCG
1 ATCGCAATGCG
246461 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:246513 original size:19 final size:19
Alignment explanation
Indices: 246489--246814 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
246479 GATTATCTCG
246489 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
246508 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
246527 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
246541 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
246560 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
246579 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
246598 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
246617 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
246636 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
246650 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
246669 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
246688 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
246702 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
246721 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
246740 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
246754 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
246774 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
246788 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
246807 TTGCGATT
1 TTGCGATT
246815 GTATTTTCCG
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
16 31 0.12
17 28 0.10
18 3 0.01
19 160 0.59
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:246529 original size:52 final size:52
Alignment explanation
Indices: 246467--246786 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
246457 TGCGTTTATA
*
246467 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
246519 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
246571 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
246628 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
246680 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
246732 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
246785 AT
1 AT
246787 GTTGGGATTT
Statistics
Matches: 257, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
52 182 0.71
53 17 0.07
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:246564 original size:71 final size:72
Alignment explanation
Indices: 246489--246814 Score: 389
Period size: 71 Copynumber: 4.6 Consensus size: 72
246479 GATTATCTCG
246489 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
246553 TTTCGCA
66 TTTCGCA
* *
246560 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG-ATTGCGATT
246625 TTCATTTCGCA
62 TTCATTTCGCA
*
246636 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG-ATTGCGATT
*
246694 TTC-TCTCG--
62 TTCATTTCGCA
*
246702 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
246766 TTTCCGCA
66 TTT-CGCA
* *
246774 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
246815 GTATTTTCCG
Statistics
Matches: 227, Mismatches: 11, Indels: 38
0.82 0.04 0.14
Matches are distributed among these distances:
66 12 0.05
67 25 0.11
68 14 0.06
69 13 0.06
70 3 0.01
71 109 0.48
72 12 0.05
73 6 0.03
74 8 0.04
76 25 0.11
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (72 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
TTTCGCA
Found at i:246732 original size:161 final size:157
Alignment explanation
Indices: 246467--246786 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
246457 TGCGTTTATA
246467 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
246532 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
246597 ATTGCGATTTTAATTT-CGCATTGCGATTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
*
246628 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
246693 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
246758 GATTTTCATTTCCGCATTGCGATTTTC
131 GATTTTAATTTCCGCATTGCGATTTTC
246785 AT
1 AT
246787 GTTGGGATTT
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 14 0.09
157 17 0.11
158 4 0.03
159 3 0.02
161 116 0.75
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (157 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTAATTTCCGCATTGCGATTTTC
Found at i:246758 original size:33 final size:33
Alignment explanation
Indices: 246508--246814 Score: 280
Period size: 33 Copynumber: 8.8 Consensus size: 33
246498 TCATTTCGCA
*
246508 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
246541 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
246577 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
246615 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
246650 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
246686 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
246721 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
246754 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
246788 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
246815 GTATTTTCCG
Statistics
Matches: 235, Mismatches: 20, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 87 0.37
34 29 0.12
35 13 0.06
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:249342 original size:24 final size:24
Alignment explanation
Indices: 249308--249354 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
249298 CTGAAACATC
249308 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
249332 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
249355 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:250048 original size:20 final size:20
Alignment explanation
Indices: 250020--250385 Score: 456
Period size: 20 Copynumber: 18.4 Consensus size: 20
250010 AAATTTCAGT
* * * *
250020 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
250040 GTTGCGATTTACGGAT---C
1 GTTGCGATTTACGGATACGC
* * *
250057 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
250077 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
250097 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
250117 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
250137 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
250157 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
250177 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
250197 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
250217 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
250237 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
250257 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
250277 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
250297 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
250317 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
250337 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
250357 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
250377 GTTGCGATT
1 GTTGCGATT
250386 ATGGAAAATC
Statistics
Matches: 307, Mismatches: 30, Indels: 18
0.86 0.08 0.05
Matches are distributed among these distances:
17 16 0.05
19 4 0.01
20 283 0.92
21 4 0.01
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:257744 original size:2 final size:2
Alignment explanation
Indices: 257737--257761 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
257727 GATCCTGCCC
257737 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
257762 AAGTTTGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.