Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397275.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_34.0, 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: 2955990
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 53928 characters in sequence are not A, C, G, or T
File 1 of 8
Found at i:2094 original size:39 final size:39
Alignment explanation
Indices: 2051--2138 Score: 176
Period size: 39 Copynumber: 2.3 Consensus size: 39
2041 AACACTAATC
2051 ATTTGATGAGTTATAATATGGGTTTTCTTTGGAAAAATT
1 ATTTGATGAGTTATAATATGGGTTTTCTTTGGAAAAATT
2090 ATTTGATGAGTTATAATATGGGTTTTCTTTGGAAAAATT
1 ATTTGATGAGTTATAATATGGGTTTTCTTTGGAAAAATT
2129 ATTTGATGAG
1 ATTTGATGAG
2139 ATGTTGAAGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.45
Consensus pattern (39 bp):
ATTTGATGAGTTATAATATGGGTTTTCTTTGGAAAAATT
Found at i:3561 original size:247 final size:247
Alignment explanation
Indices: 2873--3745 Score: 1035
Period size: 247 Copynumber: 3.5 Consensus size: 247
2863 AACTTTTAAC
* * *
2873 TATAATTATTTTTATTTTTATTATTATTTATTTAAAATA-AAAATTTAAATATCGTTACATACTT
1 TATAATTATTTTTA---TTATTATT-TTTATTTAAAAAATAAAATTTATATATCGTTAAATACTT
* ** * *
2937 TTA-TCCCGATAATATAAATATAAATGCTTATTTCTCATTAAAATTAGACTTTTTTACTTAATTA
62 TTAGT-CCGAGAATATAAATATAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
* * * * * * *
3001 ACTTATTCTATTAACTCTAATACATTTACGTTAAAATTTAAAATTTGGTTATT-TCATCTTTATA
126 ACTTGTTATGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCT-ATCTTTATA
**
3065 AATTTTTACATCAATTGTTACAGTTTTATGTCAAGATTTATCTATGAC-AATTTTGAGC
190 AATTTTTACATCAATTGTTACAGTTTTATGTCAAGATTTATCTAT-ACTAATTTTGAAT
* * * *
3123 TATAATAATTTTTATTATTATTTTTATTTAAAAATTAAAATTTATATATCATTAAATACATTTAG
1 TATAATTATTTTTATTATTATTTTTATTTAAAAAATAAAATTTATATATCGTTAAATACTTTTAG
* * * * * * *
3188 T-CGAAGAAAATATATTTAAATATTTATTTTTTAATAAAATTAAAAATTTTTTTACTCAATTAAC
66 TCCG-AGAATATAAATATAAATATTTATTTTTCATTAAAATT--AGATTTTTTTACTTAATTAAC
** * * * * *
3252 TTGTTGCGTTAATTCTCACATATTTACGTTAAGATTTAAAATTTAATTATTCTACCTTTATAAGT
128 TTGTTATGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCTATCTTTATAAAT
* *
3317 TTTTA-AGTCAACTGTTACAGTTTTATGTCAAAATTTATCTATACTAATTTTGAAT
193 TTTTACA-TCAATTGTTACAGTTTTATGTCAAGATTTATCTATACTAATTTTGAAT
* *
3372 TATAATTATTTTTATTATT-TTTTTATTTAAAAAATAAAATTTATATATCGTTAAACACTTTTTG
1 TATAATTATTTTTATTATTATTTTTATTTAAAAAATAAAATTTATATATCGTTAAATACTTTTAG
* * * **
3436 TCCGAGAATATATATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTTACTTAATGGACTT
66 TCCGAGAATATAAATATAAATATTTATTTTTCATTAAAATTAGA-TTTTTTTACTTAATTAACTT
* *
3501 GTTATGTTAACTCTCACACGTTTACGTTAAGATTTAAAATTTAGTTATTCTATTTTTATAAATTT
130 GTTATGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCTATCTTTATAAATTT
* * *
3566 TTACATCAATTCTTACAGTTTTATGTTAAGACTTATCTATA-TCAATTTT-ATAT
195 TTACATCAATTGTTACAGTTTTATGTCAAGATTTATCTATACT-AATTTTGA-AT
* *
3619 TATAATTATTTTTATCCTTATTATTTTTATTTAAAAATTAAAATTTATATATCGTTACATACTTT
1 TATAATTATTTTTA---TTATTATTTTTATTTAAAAAATAAAATTTATATATCGTTAAATACTTT
* * * *
3684 TAGTTCGATAATATAAATATAAATATTTATTTTTCATTAAAATTAGACTTTTTTATTTAATT
63 TAGTCCGAGAATATAAATATAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATT
3746 CTTATAGTTT
Statistics
Matches: 531, Mismatches: 75, Indels: 34
0.83 0.12 0.05
Matches are distributed among these distances:
246 17 0.03
247 189 0.36
248 80 0.15
249 134 0.25
250 31 0.06
251 80 0.15
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (247 bp):
TATAATTATTTTTATTATTATTTTTATTTAAAAAATAAAATTTATATATCGTTAAATACTTTTAG
TCCGAGAATATAAATATAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTAACTTG
TTATGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCTATCTTTATAAATTTT
TACATCAATTGTTACAGTTTTATGTCAAGATTTATCTATACTAATTTTGAAT
Found at i:3868 original size:169 final size:169
Alignment explanation
Indices: 3610--3914 Score: 488
Period size: 169 Copynumber: 1.8 Consensus size: 169
3600 ATCTATATCA
* * *
3610 ATTTTATATTATAATTATTTTTATCCTTATTATTTTTATTTAAAAATTAAAATTTATATATCGTT
1 ATTTTAAACTATAATTATTTTAATCCTTATTATTTTTATTTAAAAATTAAAATTTATATATCGTT
* * * *
3675 ACATACTTTTAGTTCGATAATATAAATATAAATATTTATTTTTCATTAAAATTAGACTTTTTTAT
66 AAATACTTTTAGTTCGAAAATATAAATATAAATATTTATTTTTCACTAAAATTAGACTTTTTTAC
3740 TTAATTCTTATAGTTTTACTTTAAGCTTTTTTTATGTCC
131 TTAATTCTTATAGTTTTACTTTAAGCTTTTTTTATGTCC
*
3779 ATTTTAAACTATAATTATTTTAATTCTTATTATTCTTTATTTAAAAATTAAAATTTATATATCGT
1 ATTTTAAACTATAATTATTTTAATCCTTATTATT-TTTATTTAAAAATTAAAATTTATATATCGT
* *
3844 TAAATACTTTT-G-TCTGAAAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTT
65 TAAATACTTTTAGTTC-GAAAATATAAATATAAATATTTATTTTTCACTAAAATTAGACTTTTTT
3907 ACTTAATT
129 ACTTAATT
3915 GATTTGTTAA
Statistics
Matches: 124, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
168 2 0.02
169 82 0.66
170 40 0.32
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (169 bp):
ATTTTAAACTATAATTATTTTAATCCTTATTATTTTTATTTAAAAATTAAAATTTATATATCGTT
AAATACTTTTAGTTCGAAAATATAAATATAAATATTTATTTTTCACTAAAATTAGACTTTTTTAC
TTAATTCTTATAGTTTTACTTTAAGCTTTTTTTATGTCC
Found at i:3989 original size:169 final size:169
Alignment explanation
Indices: 3619--3989 Score: 373
Period size: 169 Copynumber: 2.2 Consensus size: 169
3609 AATTTTATAT
** * * *
3619 TATAATTATTTTTATCCTTATTATTTTTATTTAAAAATTAAAATTTATATATCGTTACATACTTT
1 TATAATTATTTCAATTCTTATAATTTTTATTTAAAAATTAAAATTTATATATCGTTAAATACTTT
* * * *
3684 TAGTTCGATAATATAAATATAAATATTTATTTTTCATTAAAATTAGACTTTTTTATTTAATTCTT
66 TAGTTCGAAAATATAAATATAAATATTTATTTTTCACTAAAATTAGACTTTTTTACTTAATTATT
* *** * * * *
3749 ATAGTTTTACTTTAAGCTTTTTTTATGTCCATTTTAAAC
131 ATAGTTTTACTCTAAGCTACATTTACGTCAAATTTAAAA
* *
3788 TATAATTATTTTAATTCTTATTATTCTTTATTTAAAAATTAAAATTTATATATCGTTAAATACTT
1 TATAATTATTTCAATTCTTATAATT-TTTATTTAAAAATTAAAATTTATATATCGTTAAATACTT
* *
3853 TT-G-TCTGAAAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTACTTAATTG
65 TTAGTTC-GAAAATATAAATATAAATATTTATTTTTCACTAAAATTAGACTTTTTTACTTAATT-
* *
3916 ATT-T-GTTAAGTTAACTCTCA-C-ACATTTACGTTAAGATTTAAAA
128 ATTATAGTT---TT-ACTCTAAGCTACATTTACGTCAA-ATTTAAAA
*
3959 T-TAGTTA-TTCAACTT-TTATAAATTTTTATTT
1 TATAATTATTTCAA-TTCTTAT-AATTTTTATTT
3990 TAGTTCTTAT
Statistics
Matches: 170, Mismatches: 22, Indels: 20
0.80 0.10 0.09
Matches are distributed among these distances:
168 5 0.03
169 91 0.54
170 59 0.35
171 10 0.06
172 5 0.03
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (169 bp):
TATAATTATTTCAATTCTTATAATTTTTATTTAAAAATTAAAATTTATATATCGTTAAATACTTT
TAGTTCGAAAATATAAATATAAATATTTATTTTTCACTAAAATTAGACTTTTTTACTTAATTATT
ATAGTTTTACTCTAAGCTACATTTACGTCAAATTTAAAA
Found at i:4031 original size:418 final size:422
Alignment explanation
Indices: 3383--4163 Score: 1248
Period size: 418 Copynumber: 1.9 Consensus size: 422
3373 ATAATTATTT
* *
3383 TTATTATTTTTTTATTTAAAAAATAAAATTTATATATCGTTAAACACTTTTTGTCCGAGAATATA
1 TTATTATTTCTTTATTTAAAAAATAAAATTTATATATCGTTAAACACTTTTTGTCCGAAAATATA
* *
3448 TATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTTACTTAATGGACTTGTTATGTTAACT
66 AATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTTACTTAATGGACTTGTTAAGTTAACT
* * *
3513 CTCACACGTTTACGTTAAGATTTAAAATTTAGTTATTCTATTTTTATAAATTTTTACATCAATTC
131 CTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCAACTTTTATAAATTTTTACATCAATTC
* * ** *
3578 TTACAGTTTTATGTTAAGACTTATCTATATCAATTTTATATTATAATTATTTTTATCCTTATTAT
196 TTACAGTTTTACGTTAAGACTTATCTATATCAATTTTAAACAATAATTATTTTCATCCTTATTAT
*
3643 TTTTATTTAAAAATTAAAATTTATATATCGTTACATACTTTTAG-TTCGATAATATAAATATAAA
261 TTTTATTTAAAAATTAAAATTTATATATCGTTACATACTTTTAGCCT-GATAATATAAATATAAA
*
3707 TATTTATTTTTCATTAAAATTAGACTTTTTTATTTAATTCTTATAGTTTTACTTTAAGCTTTTTT
325 TATTTATTTTTCATTAAAATTAGACTTTTTTACTTAATTCTTATAGTTTTACTTTAAGCTTTTTT
3772 TATGTCCATTTTAAACTATAATTATTTTAATTC
390 TATGTCCATTTTAAACTATAATTATTTTAATTC
* * *
3805 TTATTA-TTCTTTATTTAAAAATTAAAATTTATATATCGTTAAATAC-TTTTGTCTGAAAATATA
1 TTATTATTTCTTTATTTAAAAAATAAAATTTATATATCGTTAAACACTTTTTGTCCGAAAATATA
* *
3868 AATTTAAATATTTATTTTTCACTAAAATTAGA-TTTTTTTACTTAATTGATTTGTTAAGTTAACT
66 AATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTTACTTAATGGACTTGTTAAGTTAACT
** * *
3932 CTCACACATTTACGTTAAGATTTAAAA-TTAGTTATTCAACTTTTATAAATTTTTATTTTAGTTC
131 CTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCAACTTTTATAAATTTTTACATCAATTC
* * *
3996 TTATAGTTTTACGTTAAGATTTATCTATGTCAATTTTAAACAATAATTATTTTCATCCTTATTAT
196 TTACAGTTTTACGTTAAGACTTATCTATATCAATTTTAAACAATAATTATTTTCATCCTTATTAT
* *
4061 TTTTATTTAAAAATTAAAATTTGTATATTGTTACATACTTTTAGCCTGATAATATAAATATAAAT
261 TTTTATTTAAAAATTAAAATTTATATATCGTTACATACTTTTAGCCTGATAATATAAATATAAAT
* *
4126 GTTTATTTTTTATTAAAATTAGACTTTTTTACTTAATT
326 ATTTATTTTTCATTAAAATTAGACTTTTTTACTTAATT
4164 AACTTATTAT
Statistics
Matches: 328, Mismatches: 30, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
418 183 0.56
419 56 0.17
420 46 0.14
421 37 0.11
422 6 0.02
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (422 bp):
TTATTATTTCTTTATTTAAAAAATAAAATTTATATATCGTTAAACACTTTTTGTCCGAAAATATA
AATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTTACTTAATGGACTTGTTAAGTTAACT
CTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCAACTTTTATAAATTTTTACATCAATTC
TTACAGTTTTACGTTAAGACTTATCTATATCAATTTTAAACAATAATTATTTTCATCCTTATTAT
TTTTATTTAAAAATTAAAATTTATATATCGTTACATACTTTTAGCCTGATAATATAAATATAAAT
ATTTATTTTTCATTAAAATTAGACTTTTTTACTTAATTCTTATAGTTTTACTTTAAGCTTTTTTT
ATGTCCATTTTAAACTATAATTATTTTAATTC
Found at i:4310 original size:250 final size:250
Alignment explanation
Indices: 3742--5854 Score: 1557
Period size: 250 Copynumber: 8.5 Consensus size: 250
3732 TTTTTTATTT
* * * * * *
3742 AATTCTTATAGTTTTACTTTAAGCTTTTTTTATGTCCATTTTAAACTATAATTATTTTAATTCTT
1 AATTCTTATAGTTTTACGTTAAGATTTATTTATGTCAATTTTAAACTATAATTATTTTTATCCTT
* *
3807 ATTATTCTTTATTTAAAAATTAAAATTTATATATCGTTAAATACTTTT-GTCTGAAAATATAAAT
66 ATTATT-TTTATTTAAAAATTAAAATTTATATATCGTTAAATACTTTTAGCCTGAGAATATAAAT
* * *
3871 TTAAATATTTATTTTTCACTAAAATTAGATTTTTTTACTTAATTGATTTGTTAAGTTAACTCTCA
130 TTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTGACTTGTTATGTTAACTCTCA
* * * ** *
3936 CACATTTACGTTAAGATTTAAAA-TTAGTTATTCAACTTTTATAAATTTTTATTTT
195 CACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTC
* * * *
3991 AGTTCTTATAGTTTTACGTTAAGATTTATCTATGTCAATTTTAAACAATAATTATTTTCATCCTT
1 AATTCTTATAGTTTTACGTTAAGATTTATTTATGTCAATTTTAAACTATAATTATTTTTATCCTT
* * * * *
4056 ATTATTTTTATTTAAAAATTAAAATTTGTATATTGTTACATACTTTTAGCCTGATAATATAAATA
66 ATTATTTTTATTTAAAAATTAAAATTTATATATCGTTAAATACTTTTAGCCTGAGAATATAAATT
* * * * * **
4121 TAAATGTTTATTTTTTATTAAAATTAGACTTTTTTACTTAATTAACTTATTATGTTAACTCTTGC
131 TAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTGACTTGTTATGTTAACTCTCAC
* * * *
4186 ATATTTATGTTAAAATTTAAAATTTAATTATTCCACCTTTATAAGTTTTTACGTC
196 ACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTC
* *
4241 AATTCTTATAATTTTACGTTAAGATTTATTTATGTCAATTTCAAACTATAATTATTTTTATCCTT
1 AATTCTTATAGTTTTACGTTAAGATTTATTTATGTCAATTTTAAACTATAATTATTTTTATCCTT
** *
4306 ATTATTTTTATTTAAAAATTAAAATTTATATATCGTTAAATACTTTTATTCTAAGAATATAAATT
66 ATTATTTTTATTTAAAAATTAAAATTTATATATCGTTAAATACTTTTAGCCTGAGAATATAAATT
* * * * *
4371 TAAATATTTGTTGTTCAATAAAATTAAATTTTTTTACTTAATTGACTTGTTACGTTAACTCTCAC
131 TAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTGACTTGTTATGTTAACTCTCAC
* * *
4436 ACATTTATGTTAAGATTTAAAATTTAGTTATTCCAACTTTATAAGCTTTTACGTC
196 ACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTC
* * * * * * *
4491 AATTCTTACAGTTTTACGTCAAGGCTTT-TTTACGTCAATTTTGAATTATAATTAGTTTTATCCT
1 AATTCTTATAGTTTTACGTTAA-GATTTATTTATGTCAATTTTAAACTATAATTATTTTTATCCT
*
4555 TATTATCATTTATTTAAAAATTAAAATTGT-TATATCGTTAAATACTTTTAGTCC-GAGAATATA
65 TATTAT-TTTTATTTAAAAATTAAAATT-TATATATCGTTAAATACTTTTAG-CCTGAGAATATA
* * * *
4618 AATTTAAATATTTA-CTTTCATT-AAATATACATTATTTTTACTTAATTGATTTCTTATGTTAAC
127 AATTTAAATATTTATTTTTCATTAAAAT-TAGATT-TTTTTACTTAATTGACTTGTTATGTTAAC
*** ********** * *
4681 TCTCACATGCTTACGTTAAGATTTAAAATTTNNNNNNNNNNCCTTTACAAGCTTTTACGTC
190 TCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTC
* * * * * *
4742 AATTCTTATGGTTTTACGTCAAAACTTT-TTTATGTCAATTTTGAATTATAATTA--GTTAT-C-
1 AATTCTTATAGTTTTACGTTAAGA-TTTATTTATGTCAATTTTAAACTATAATTATTTTTATCCT
* * ** * * *
4802 ----A--TTTCTTTAAAAATTAAAATTTTTATATCGTTAAGCACTTTCAACTTGAGAATATAAAT
65 TATTATTTTTATTTAAAAATTAAAATTTATATATCGTTAAATACTTTTAGCCTGAGAATATAAAT
*********** **
4861 TTAAATATTTACTTTTT-NNNNNNNNNNCATTGTTTTTACTTAATTGACTTGTTACATTAACTCT
130 TTAAATATTTA-TTTTTCATTAAAATTAGATT-TTTTTACTTAATTGACTTGTTATGTTAACTCT
* ********** * * * *
4925 CACACACTTACGTTAAGATTTNNNNNNNNNNTATTTCACCTTTACAAGTTTTTACCTT
193 CACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTC
* * * * * * * * *
4983 AATTCTTACA-ATTTACGTTAAAACTTT-TTCATGTCAACTTTGAATTATAATTAGTTTTATCTT
1 AATTCTTATAGTTTTACGTTAAGA-TTTATTTATGTCAATTTTAAACTATAATTATTTTTATCCT
* * * *
5046 TATTATTCTTAATTTAAAAATTAAAAATTT-TATATCGTTAAACACTTTCAGACC-GATAATATA
65 TATTATT-TTTATTTAAAAATT-AAAATTTATATATCGTTAAATACTTTTAG-CCTGAGAATATA
* * * * * * *
5109 AATTTAAATATTTACTTTTGATTAAATTTACATTATTTTTACTTAGTTGACTTCTTACGTTAACT
127 AATTTAAATATTTATTTTTCATTAAAATTAGATT-TTTTTACTTAATTGACTTGTTATGTTAACT
* ** * * * * * *
5174 CTCATACGCTTAAGCTAAGATTTAAAATTTAATTATTCTACTTTTTTCAAGTTTTTACGTC
191 CTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTAT-AAGTTTTTACGTC
* * ** * * * * * *
5235 AATTCTTACAG-TTTACGTCAAGACTTT-TCCATGTCAACTTTGAATTATAATTAGTTTTAACTT
1 AATTCTTATAGTTTTACGTTAAGA-TTTATTTATGTCAATTTTAAACTATAATTATTTTTATCCT
* * * * * * * *
5298 TGTTATTCTTAATTTAAACATTAAAATTTTTATATCGTGAAACACTTTCAGCCTAAG-A-AT--A
65 TATTATT-TTTATTTAAAAATTAAAATTTATATATCGTTAAATACTTTTAGCCTGAGAATATAAA
* * * * * *
5359 --T-AA-ATTT-TTTTTGATTAAATTTACATTGCTTTTACTTAATTGACTTTTTATGTTAATTCT
129 TTTAAATATTTATTTTTCATTAAAATTAGATT-TTTTTACTTAATTGACTTGTTATGTTAACTCT
*** * * * * * **
5419 CACATGCTTACATTAAGATTTAAAATTTAATTATTTCACCTTTACAAGCTTTTACAAC
193 CACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTC
* * * * * * * * * * *
5477 AATTCTTACAATTTTATGTCAAGGCTTT-TTCACGCCAATTTTGAATTATAATTAGTTTTATCCT
1 AATTCTTATAGTTTTACGTTAA-GATTTATTTATGTCAATTTTAAACTATAATTATTTTTATCCT
* * * * *
5541 TATTATTCTTAATTTAAAAATTAAAATTTTTATATCATTAAACACTTTCAGTCC-GAGAATATAA
65 TATTATT-TTTATTTAAAAATTAAAATTTATATATCGTTAAATACTTTTAG-CCTGAGAATATAA
* ********** * * **
5605 ATTTAAATATTTACTTTTNNNNNNNNNNATATTGTTTTTACTTAATTGACTTCTTACATTAACTC
128 ATTTAAATATTTATTTTTCATTAAAATTAGATT-TTTTTACTTAATTGACTTGTTATGTTAACTC
*** * *********** *
5670 TCACATGCTTATGTTAAGATTTAAAATTTAGTTATNNNNNNNNNNCAAGCTTTTACGTC
192 TCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTC
* * * * * * *
5729 AATTCTTATAGTTTTACGTCAAGGCTTT-TTTACGTCAATTTTGAATTATAATTAGTTTTATCTT
1 AATTCTTATAGTTTTACGTTAA-GATTTATTTATGTCAATTTTAAACTATAATTATTTTTATCCT
* * * * * *
5793 TATTATTCTTAATTTAAAAATTAAAATTTTTATATCATTCAACACTTTCAG-CTCGAGAATAT
65 TATTATT-TTTATTTAAAAATTAAAATTTATATATCGTTAAATACTTTTAGCCT-GAGAATAT
5855 TAAGTAATTT
Statistics
Matches: 1537, Mismatches: 281, Indels: 89
0.81 0.15 0.05
Matches are distributed among these distances:
239 2 0.00
240 98 0.06
241 79 0.05
242 27 0.02
243 173 0.11
244 8 0.01
245 4 0.00
246 1 0.00
247 1 0.00
248 41 0.03
249 159 0.10
250 319 0.21
251 310 0.20
252 315 0.20
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.47
Consensus pattern (250 bp):
AATTCTTATAGTTTTACGTTAAGATTTATTTATGTCAATTTTAAACTATAATTATTTTTATCCTT
ATTATTTTTATTTAAAAATTAAAATTTATATATCGTTAAATACTTTTAGCCTGAGAATATAAATT
TAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTGACTTGTTATGTTAACTCTCAC
ACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTC
Found at i:4701 original size:251 final size:247
Alignment explanation
Indices: 3742--5854 Score: 1717
Period size: 252 Copynumber: 8.5 Consensus size: 247
3732 TTTTTTATTT
* * * * * *
3742 AATTCTTATAGTTTTACTTTAA-GCTTTTTTTATGTCCATTTTAAACTATAATTA-TTTTAATTC
1 AATTCTTATAGTTTTACGTCAAGGC-TTTTTTATGTCAATTTTGAATTATAATTAGTTTT-ATCC
* * * * *
3805 TTATTATTCTTTATTTAAAAATTAAAATTTATATATCGTTAAATACTTT-TGTCTGAAAATATAA
64 TTATTATTCTTAATTTAAAAATTAAAATTT-TATATCGTTAAACACTTTCAGTCCGAGAATATAA
* * * * * *
3869 ATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTACTTAATTGATTTGTTAAGTTAACTCT
128 ATTTAAATATTTA-CTTTCATTAAAA-TACATTTTTTTACTTAATTGACTTCTTACGTTAACTCT
* * * * ** ** *
3934 CACACATTTACGTTAAGATTTAAAA-TTAGTTATTCAACTTTTATAAATTTTTATTTT
191 CACACACTTACGTTAAGATTTAAAATTTAATTATTC-ACCTTTACAAGCTTTTACGTC
* * * * * **
3991 AGTTCTTATAGTTTTACGTTAA-GATTTATCTATGTCAATTTTAAACAATAATTA-TTTTCATCC
1 AATTCTTATAGTTTTACGTCAAGGCTTT-TTTATGTCAATTTTGAATTATAATTAGTTTT-ATCC
* * * * * *
4054 TTATTATT-TTTATTTAAAAATTAAAATTTGTATATTGTTACATACTTTTAG-CCTGATAATATA
64 TTATTATTCTTAATTTAAAAATTAAAATTT-TATATCGTTAAACACTTTCAGTCC-GAGAATATA
* * * * * * * * *
4117 AATATAAATGTTTATTTTTTATTAAAATTAGACTTTTTTACTTAATTAACTTATTATGTTAACTC
127 AATTTAAATATTTA-CTTTCATTAAAA-TACATTTTTTTACTTAATTGACTTCTTACGTTAACTC
** * * * * * *
4182 TTGCATATTTATGTTAAAATTTAAAATTTAATTATTCCACCTTTATAAGTTTTTACGTC
190 TCACACACTTACGTTAAGATTTAAAATTTAATTATT-CACCTTTACAAGCTTTTACGTC
* * * ** * *
4241 AATTCTTATAATTTTACGTTAA-GATTTATTTATGTCAATTTCAAACTATAATTATTTTTATCCT
1 AATTCTTATAGTTTTACGTCAAGGCTTT-TTTATGTCAATTTTGAATTATAATTAGTTTTATCCT
* * * * **
4305 TATTATT-TTTATTTAAAAATTAAAATTTATATATCGTTAAATACTTTTATTCTAAGAATATAAA
65 TATTATTCTTAATTTAAAAATTAAAATTT-TATATCGTTAAACACTTTCAGTCCGAGAATATAAA
** * * *
4369 TTTAAATATTTGTTGTTCAATAAAATTAAATTTTTTTACTTAATTGACTTGTTACGTTAACTCTC
129 TTTAAATATTTACT-TTCATTAAAA-TACATTTTTTTACTTAATTGACTTCTTACGTTAACTCTC
* * * * *
4434 ACACATTTATGTTAAGATTTAAAATTTAGTTATTCCAACTTTATAAGCTTTTACGTC
192 ACACACTTACGTTAAGATTTAAAATTTAATTATT-CACCTTTACAAGCTTTTACGTC
* *
4491 AATTCTTACAGTTTTACGTCAAGGCTTTTTTACGTCAATTTTGAATTATAATTAGTTTTATCCTT
1 AATTCTTATAGTTTTACGTCAAGGCTTTTTTATGTCAATTTTGAATTATAATTAGTTTTATCCTT
* * *
4556 ATTA-TCATTTATTTAAAAATTAAAATTGTTATATCGTTAAATACTTTTAGTCCGAGAATATAAA
66 ATTATTC-TTAATTTAAAAATTAAAATT-TTATATCGTTAAACACTTTCAGTCCGAGAATATAAA
* *
4620 TTTAAATATTTACTTTCATTAAATATACATTATTTTTACTTAATTGATTTCTTATGTTAACTCTC
129 TTTAAATATTTACTTTCATTAAA-ATACATT-TTTTTACTTAATTGACTTCTTACGTTAACTCTC
** *********
4685 ACATGCTTACGTTAAGATTTAAAATTTNNNNNNNNNNCCTTTACAAGCTTTTACGTC
192 ACACACTTACGTTAAGATTTAAAATTT-AATTATTCACCTTTACAAGCTTTTACGTC
* **
4742 AATTCTTATGGTTTTACGTCAAAACTTTTTTATGTCAATTTTGAATTATAATTAG--TTAT-C--
1 AATTCTTATAGTTTTACGTCAAGGCTTTTTTATGTCAATTTTGAATTATAATTAGTTTTATCCTT
* * *
4802 A-T-TTC----TTTAAAAATTAAAATTTTTATATCGTTAAGCACTTTCA-ACTTGAGAATATAAA
66 ATTATTCTTAATTTAAAAATTAAAA-TTTTATATCGTTAAACACTTTCAGTC-CGAGAATATAAA
****** * *
4860 TTTAAATATTTACTTT--TTNNNNNNNNNNCATTGTTTTTACTTAATTGACTTGTTACATTAACT
129 TTTAAATATTTACTTTCATT----AAAATACATT-TTTTTACTTAATTGACTTCTTACGTTAACT
********** * * *
4923 CTCACACACTTACGTTAAGATTTNNNNNNNNNNTATTTCACCTTTACAAGTTTTTACCTT
189 CTCACACACTTACGTTAAGATTTAAAATTTAATTA-TTCACCTTTACAAGCTTTTACGTC
* * * ** * * *
4983 AATTCTTACA-ATTTACGTTAAAACTTTTTCATGTCAACTTTGAATTATAATTAGTTTTATCTTT
1 AATTCTTATAGTTTTACGTCAAGGCTTTTTTATGTCAATTTTGAATTATAATTAGTTTTATCCTT
* *
5047 ATTATTCTTAATTTAAAAATTAAAAATTTTATATCGTTAAACACTTTCAGACCGATAATATAAAT
66 ATTATTCTTAATTTAAAAATT-AAAATTTTATATCGTTAAACACTTTCAGTCCGAGAATATAAAT
* * *
5112 TTAAATATTTACTTTTGATTAAATTTACATTATTTTTACTTAGTTGACTTCTTACGTTAACTCTC
130 TTAAATATTTAC-TTTCATTAAA-ATACATT-TTTTTACTTAATTGACTTCTTACGTTAACTCTC
* * * * * * *
5177 ATACGCTTAAGCTAAGATTTAAAATTTAATTATTCTACTTTTTTCAAGTTTTTACGTC
192 ACACACTTACGTTAAGATTTAAAATTTAATTATTC-AC-CTTTACAAGCTTTTACGTC
* * ** * * *
5235 AATTCTTACAG-TTTACGTCAAGACTTTTCCATGTCAACTTTGAATTATAATTAGTTTTAACTTT
1 AATTCTTATAGTTTTACGTCAAGGCTTTTTTATGTCAATTTTGAATTATAATTAGTTTTATCCTT
* * * *
5299 GTTATTCTTAATTTAAACATTAAAATTTTTATATCGTGAAACACTTTCAG-CCTAAGAATATAAA
66 ATTATTCTTAATTTAAAAATTAAAA-TTTTATATCGTTAAACACTTTCAGTCC-GAGAATATAAA
* * * * * *
5363 --T---T-TTT--TTTGATTAAATTTACATTGCTTTTACTTAATTGACTTTTTATGTTAATTCTC
129 TTTAAATATTTACTTTCATTAAA-ATACATT-TTTTTACTTAATTGACTTCTTACGTTAACTCTC
** * **
5420 ACATGCTTACATTAAGATTTAAAATTTAATTATTTCACCTTTACAAGCTTTTACAAC
192 ACACACTTACGTTAAGATTTAAAATTTAATTA-TTCACCTTTACAAGCTTTTACGTC
* * * * * *
5477 AATTCTTACAATTTTATGTCAAGGCTTTTTCACGCCAATTTTGAATTATAATTAGTTTTATCCTT
1 AATTCTTATAGTTTTACGTCAAGGCTTTTTTATGTCAATTTTGAATTATAATTAGTTTTATCCTT
*
5542 ATTATTCTTAATTTAAAAATTAAAATTTTTATATCATTAAACACTTTCAGTCCGAGAATATAAAT
66 ATTATTCTTAATTTAAAAATTAAAA-TTTTATATCGTTAAACACTTTCAGTCCGAGAATATAAAT
********* * *
5607 TTAAATATTTACTTTTNNNNNNNNNNATATTGTTTTTACTTAATTGACTTCTTACATTAACTCTC
130 TTAAATATTTAC-TTT-CATTAAAATACATT-TTTTTACTTAATTGACTTCTTACGTTAACTCTC
** * * *********
5672 ACATGCTTATGTTAAGATTTAAAATTTAGTTATNNNNNNNNNNCAAGCTTTTACGTC
192 ACACACTTACGTTAAGATTTAAAATTTAATTAT-TCACCTTTACAAGCTTTTACGTC
* *
5729 AATTCTTATAGTTTTACGTCAAGGCTTTTTTACGTCAATTTTGAATTATAATTAGTTTTATCTTT
1 AATTCTTATAGTTTTACGTCAAGGCTTTTTTATGTCAATTTTGAATTATAATTAGTTTTATCCTT
* *
5794 ATTATTCTTAATTTAAAAATTAAAATTTTTATATCATTCAACACTTTCAG-CTCGAGAATAT
66 ATTATTCTTAATTTAAAAATTAAAA-TTTTATATCGTTAAACACTTTCAGTC-CGAGAATAT
5855 TAAGTAATTT
Statistics
Matches: 1555, Mismatches: 249, Indels: 117
0.81 0.13 0.06
Matches are distributed among these distances:
238 2 0.00
239 1 0.00
240 102 0.07
241 78 0.05
242 28 0.02
243 176 0.11
244 5 0.00
245 5 0.00
246 5 0.00
247 4 0.00
248 43 0.03
249 155 0.10
250 307 0.20
251 313 0.20
252 329 0.21
254 2 0.00
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.47
Consensus pattern (247 bp):
AATTCTTATAGTTTTACGTCAAGGCTTTTTTATGTCAATTTTGAATTATAATTAGTTTTATCCTT
ATTATTCTTAATTTAAAAATTAAAATTTTATATCGTTAAACACTTTCAGTCCGAGAATATAAATT
TAAATATTTACTTTCATTAAAATACATTTTTTTACTTAATTGACTTCTTACGTTAACTCTCACAC
ACTTACGTTAAGATTTAAAATTTAATTATTCACCTTTACAAGCTTTTACGTC
Found at i:5854 original size:495 final size:497
Alignment explanation
Indices: 3742--5854 Score: 1872
Period size: 495 Copynumber: 4.3 Consensus size: 497
3732 TTTTTTATTT
* * * * *
3742 AATTCTTATAGTTTTACTTTAAG-CTTTTTTTATGTCCATTTTAAACTATAATTA-TTTTAAT-T
1 AATTCTTATAGTTTTACGTCAAGAC-TTTTTTATGTCAATTTTGAATTATAATTAGTTTT-ATCT
* * * * *
3804 CTTATTATTCTTTATTTAAAAATTAAAATTTATATATCGTTAAATACTTT-TG-TCTGAAAATAT
64 -TTATTATTCTTAATTTAAAAATTAAAATTTTTATATCGTTAAACACTTTCAGCTCT-AAGA-AT
* * * * *
3867 AAATTTAAATATTTATTTTTCACTAAAATTAGATT-TTTTTACTTAATTGATTTGTTAAGTTAAC
126 --A--T-AA-ATTTATTTTTGATTAAAATTACATTGTTTTTACTTAATTGACTTGTTACGTTAAC
* * * * ** ** * *
3931 TCTCACACATTTACGTTAAGATTTAAAA-TTAGTTA-TTCAACTTTTATAAATTTTTATTTTAGT
185 TCTCACACACTTACGTTAAGATTTAAAATTTAATTATTTC-ACCTTTACAAGCTTTTACATCAAT
* * * * * * * **
3994 TCTTATAGTTTTACGTTAA-GATTTATCTATGTCAATTTTAAACAATAATTA-TTTTCATCCTTA
249 TCTTACAATTTTACGTCAAGGCTTTTTC-ACGTCAATTTTGAATTATAATTAGTTTT-ATCCTTA
* * * * * * *
4057 TTATT-TTTATTTAAAAATTAAAATTTGTATATTGTTACATACTTTTAG-CCTGATAATATAAAT
312 TTATTCTTAATTTAAAAATTAAAATTTTTATATCGTTAAACACTTTCAGTCC-GAGAATATAAAT
* * * * * * * * *
4120 ATAAATGTTTATTTTTTATTAAA-ATTAGACT-TTTTTACTTAATTAACTTATTATGTTAACTCT
376 TTAAATATTTACTTTTCATTAAATA-TACATTATTTTTACTTAATTGACTTCTTACGTTAACTCT
** ** * * * * *
4183 TGCATATTTATGTTAAAATTTAAAATTTAATTAT-TCCACCTTTATAAGTTTTTACGTC
440 CACATGCTTAAGTTAAGATTTAAAATTTAATTATCTAC-CCTTTACAAGCTTTTACGTC
* * ** * * *
4241 AATTCTTATAATTTTACGTTAAGA-TTTATTTATGTCAATTTCAAACTATAATTATTTTTATCCT
1 AATTCTTATAGTTTTACGTCAAGACTTT-TTTATGTCAATTTTGAATTATAATTAGTTTTATCTT
* * * * *
4305 TATTATT-TTTATTTAAAAATTAAAATTTATATATCGTTAAATACTTTTA-TTCTAAGAATATAA
65 TATTATTCTTAATTTAAAAATTAAAATTTTTATATCGTTAAACACTTTCAGCTCTAAGAATATAA
* *
4368 ATTTAAATATTTGTTGTTCAATAAAATTAAATT-TTTTTACTTAATTGACTTGTTACGTTAACTC
130 A-TT---TATTT-TTG---ATTAAAATTACATTGTTTTTACTTAATTGACTTGTTACGTTAACTC
* * * * * * *
4432 TCACACATTTATGTTAAGATTTAAAATTTAGTTATTCCAACTTTATAAGCTTTTACGTCAATTCT
187 TCACACACTTACGTTAAGATTTAAAATTTAATTATTTCACCTTTACAAGCTTTTACATCAATTCT
* *
4497 TACAGTTTTACGTCAAGGCTTTTTTACGTCAATTTTGAATTATAATTAGTTTTATCCTTATTA-T
252 TACAATTTTACGTCAAGGCTTTTTCACGTCAATTTTGAATTATAATTAGTTTTATCCTTATTATT
* * * *
4561 CATTTATTTAAAAATTAAAATTGTTATATCGTTAAATACTTTTAGTCCGAGAATATAAATTTAAA
317 C-TTAATTTAAAAATTAAAATTTTTATATCGTTAAACACTTTCAGTCCGAGAATATAAATTTAAA
* *
4626 TATTTAC-TTTCATTAAATATACATTATTTTTACTTAATTGATTTCTTATGTTAACTCTCACATG
381 TATTTACTTTTCATTAAATATACATTATTTTTACTTAATTGACTTCTTACGTTAACTCTCACATG
* **********
4690 CTTACGTTAAGATTTAAAATTTNNNNNNNNNNCCTTTACAAGCTTTTACGTC
446 CTTAAGTTAAGATTTAAAATTTAATTATCTACCCTTTACAAGCTTTTACGTC
* *
4742 AATTCTTATGGTTTTACGTCAAAACTTTTTTATGTCAATTTTGAATTATAATTAG--TTATC---
1 AATTCTTATAGTTTTACGTCAAGACTTTTTTATGTCAATTTTGAATTATAATTAGTTTTATCTTT
* * *
4802 A-T-TTC----TTTAAAAATTAAAATTTTTATATCGTTAAGCACTTTCAACT-TGAGAATATAAA
66 ATTATTCTTAATTTAAAAATTAAAATTTTTATATCGTTAAACACTTTCAGCTCTAAGAATATAAA
** ******* *
4860 TTTAAATATTTACTTTTTNNNNNNNNNNCATTGTTTTTACTTAATTGACTTGTTACATTAACTCT
131 TTT--AT-TTT--TGATT---AAAATTACATTGTTTTTACTTAATTGACTTGTTACGTTAACTCT
********** * * *
4925 CACACACTTACGTTAAGATTTNNNNNNNNNNTATTTCACCTTTACAAGTTTTTACCTTAATTCTT
188 CACACACTTACGTTAAGATTTAAAATTTAATTATTTCACCTTTACAAGCTTTTACATCAATTCTT
* ** * * *
4990 ACAA-TTTACGTTAAAACTTTTTCATGTCAACTTTGAATTATAATTAGTTTTATCTTTATTATTC
253 ACAATTTTACGTCAAGGCTTTTTCACGTCAATTTTGAATTATAATTAGTTTTATCCTTATTATTC
* * *
5054 TTAATTTAAAAATTAAAAATTTTATATCGTTAAACACTTTCAGACCGATAATATAAATTTAAATA
318 TTAATTTAAAAATTAAAATTTTTATATCGTTAAACACTTTCAGTCCGAGAATATAAATTTAAATA
* * * * *
5119 TTTACTTTTGATTAAATTTACATTATTTTTACTTAGTTGACTTCTTACGTTAACTCTCATACGCT
383 TTTACTTTTCATTAAATATACATTATTTTTACTTAATTGACTTCTTACGTTAACTCTCACATGCT
* ** * *
5184 TAAGCTAAGATTTAAAATTTAATTATTCTACTTTTTTCAAGTTTTTACGTC
448 TAAGTTAAGATTTAAAATTTAATTA-TCTACCCTTTACAAGCTTTTACGTC
* ** * *
5235 AATTCTTACAG-TTTACGTCAAGACTTTTCCATGTCAACTTTGAATTATAATTAGTTTTAACTTT
1 AATTCTTATAGTTTTACGTCAAGACTTTTTTATGTCAATTTTGAATTATAATTAGTTTTATCTTT
* * *
5299 GTTATTCTTAATTTAAACATTAAAATTTTTATATCGTGAAACACTTTCAGC-CTAAGAATATAAA
66 ATTATTCTTAATTTAAAAATTAAAATTTTTATATCGTTAAACACTTTCAGCTCTAAGAATATAAA
* * * * * **
5363 TTT-TTTTTGATTAAATTTACATTGCTTTTACTTAATTGACTTTTTATGTTAATTCTCACATGCT
131 TTTATTTTTGATTAAAATTACATTGTTTTTACTTAATTGACTTGTTACGTTAACTCTCACACACT
* *
5427 TACATTAAGATTTAAAATTTAATTATTTCACCTTTACAAGCTTTTACAACAATTCTTACAATTTT
196 TACGTTAAGATTTAAAATTTAATTATTTCACCTTTACAAGCTTTTACATCAATTCTTACAATTTT
* *
5492 ATGTCAAGGCTTTTTCACGCCAATTTTGAATTATAATTAGTTTTATCCTTATTATTCTTAATTTA
261 ACGTCAAGGCTTTTTCACGTCAATTTTGAATTATAATTAGTTTTATCCTTATTATTCTTAATTTA
*
5557 AAAATTAAAATTTTTATATCATTAAACACTTTCAGTCCGAGAATATAAATTTAAATATTTACTTT
326 AAAATTAAAATTTTTATATCGTTAAACACTTTCAGTCCGAGAATATAAATTTAAATATTTACTTT
********** * * * *
5622 TNNNNNNNNNNATATTGTTTTTACTTAATTGACTTCTTACATTAACTCTCACATGCTTATGTTAA
391 TCATTAAATATACATTATTTTTACTTAATTGACTTCTTACGTTAACTCTCACATGCTTAAGTTAA
* **********
5687 GATTTAAAATTTAGTTATNNNNNNNNNNCAAGCTTTTACGTC
456 GATTTAAAATTTAATTATCTACCCTTTACAAGCTTTTACGTC
* *
5729 AATTCTTATAGTTTTACGTCAAGGCTTTTTTACGTCAATTTTGAATTATAATTAGTTTTATCTTT
1 AATTCTTATAGTTTTACGTCAAGACTTTTTTATGTCAATTTTGAATTATAATTAGTTTTATCTTT
* * *
5794 ATTATTCTTAATTTAAAAATTAAAATTTTTATATCATTCAACACTTTCAGCTC-GAGAATAT
66 ATTATTCTTAATTTAAAAATTAAAATTTTTATATCGTTAAACACTTTCAGCTCTAAGAATAT
5855 TAAGTAATTT
Statistics
Matches: 1317, Mismatches: 243, Indels: 112
0.79 0.15 0.07
Matches are distributed among these distances:
487 1 0.00
488 1 0.00
489 3 0.00
490 4 0.00
491 163 0.12
492 197 0.15
493 26 0.02
494 114 0.09
495 291 0.22
496 4 0.00
497 5 0.00
498 47 0.04
499 136 0.10
500 87 0.07
501 183 0.14
502 5 0.00
503 50 0.04
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.47
Consensus pattern (497 bp):
AATTCTTATAGTTTTACGTCAAGACTTTTTTATGTCAATTTTGAATTATAATTAGTTTTATCTTT
ATTATTCTTAATTTAAAAATTAAAATTTTTATATCGTTAAACACTTTCAGCTCTAAGAATATAAA
TTTATTTTTGATTAAAATTACATTGTTTTTACTTAATTGACTTGTTACGTTAACTCTCACACACT
TACGTTAAGATTTAAAATTTAATTATTTCACCTTTACAAGCTTTTACATCAATTCTTACAATTTT
ACGTCAAGGCTTTTTCACGTCAATTTTGAATTATAATTAGTTTTATCCTTATTATTCTTAATTTA
AAAATTAAAATTTTTATATCGTTAAACACTTTCAGTCCGAGAATATAAATTTAAATATTTACTTT
TCATTAAATATACATTATTTTTACTTAATTGACTTCTTACGTTAACTCTCACATGCTTAAGTTAA
GATTTAAAATTTAATTATCTACCCTTTACAAGCTTTTACGTC
Found at i:6427 original size:7 final size:7
Alignment explanation
Indices: 6415--6441 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
6405 ATTTATATCC
6415 TCCTCAA
1 TCCTCAA
6422 TCCTCAA
1 TCCTCAA
6429 TCCTCAA
1 TCCTCAA
6436 TCCTCA
1 TCCTCA
6442 TTCTCAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.44, G:0.00, T:0.30
Consensus pattern (7 bp):
TCCTCAA
Found at i:16297 original size:3 final size:3
Alignment explanation
Indices: 16289--16314 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16279 GGAGTGAGTT
16289 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
16315 GATCTTCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:16352 original size:13 final size:15
Alignment explanation
Indices: 16319--16350 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
16309 AGAAGAGATC
16319 TTCT-CAGAGCTTCT
1 TTCTCCAGAGCTTCT
16333 TTCTCCAGAGCTTCT
1 TTCTCCAGAGCTTCT
16348 TTC
1 TTC
16351 CATTGGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.12, C:0.31, G:0.12, T:0.44
Consensus pattern (15 bp):
TTCTCCAGAGCTTCT
Found at i:29939 original size:2 final size:2
Alignment explanation
Indices: 29932--29960 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29922 NNNNNNNNNN
29932 AT AT 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 AT AT A
29961 GTTTGGTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30965 original size:6 final size:6
Alignment explanation
Indices: 30954--30978 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
30944 ACAAATTGAG
30954 CCTCTC CCTCTC CCTCTC CCTCTC C
1 CCTCTC CCTCTC CCTCTC CCTCTC C
30979 ATCTTTCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CCTCTC
Found at i:32587 original size:2 final size:2
Alignment explanation
Indices: 32580--32606 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
32570 TTCATACATT
32580 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
32607 TCTCTTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36415 original size:22 final size:21
Alignment explanation
Indices: 36388--36430 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
36378 TGTTAATAGC
*
36388 TTTTTTCCTCTTTCCCCCTTTT
1 TTTTTTCCT-ATTCCCCCTTTT
36410 TTTTTTCCTATTCCCCCTTTT
1 TTTTTTCCTATTCCCCCTTTT
36431 CAATGTTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTTTCCTATTCCCCCTTTT
Found at i:49848 original size:21 final size:21
Alignment explanation
Indices: 49822--49861 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
49812 TTTGGTTTAA
49822 AAACTC-ACAACTCGAAACTCG
1 AAACTCGA-AACTCGAAACTCG
*
49843 AAACTCGAAACTTGAAACT
1 AAACTCGAAACTCGAAACT
49862 TCACTTCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.45, C:0.28, G:0.10, T:0.17
Consensus pattern (21 bp):
AAACTCGAAACTCGAAACTCG
Found at i:49862 original size:7 final size:7
Alignment explanation
Indices: 49830--49861 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
49820 AAAAACTCAC
49830 AACTCGA
1 AACTCGA
49837 AACTCGA
1 AACTCGA
49844 AACTCGA
1 AACTCGA
*
49851 AACTTGA
1 AACTCGA
49858 AACT
1 AACT
49862 TCACTTCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.19
Consensus pattern (7 bp):
AACTCGA
Found at i:57054 original size:14 final size:14
Alignment explanation
Indices: 57035--57061 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
57025 TCCAGTCAAT
57035 ACCAAAAACATTTC
1 ACCAAAAACATTTC
57049 ACCAAAAACATTT
1 ACCAAAAACATTT
57062 ACTTAGCCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (14 bp):
ACCAAAAACATTTC
Found at i:58327 original size:17 final size:17
Alignment explanation
Indices: 58305--58340 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
58295 GCCTTTGCTT
*
58305 TAGGCCTCACAATTTTA
1 TAGGCCCCACAATTTTA
*
58322 TAGGCCCCATAATTTTA
1 TAGGCCCCACAATTTTA
58339 TA
1 TA
58341 TAATACAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (17 bp):
TAGGCCCCACAATTTTA
Found at i:66354 original size:12 final size:12
Alignment explanation
Indices: 66339--66365 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
66329 TTATCTTTCC
66339 TAGCATCTATCG
1 TAGCATCTATCG
66351 TAGCATCTATCG
1 TAGCATCTATCG
66363 TAG
1 TAG
66366 AGGGCGCCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (12 bp):
TAGCATCTATCG
Found at i:68779 original size:56 final size:56
Alignment explanation
Indices: 68693--68803 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 56
68683 ACATATGTAT
68693 TCAATGTAGTACCTTGTGAGTAATCAATGTGGGCTCCAATCCCTTAAGCTCGATAA
1 TCAATGTAGTACCTTGTGAGTAATCAATGTGGGCTCCAATCCCTTAAGCTCGATAA
*
68749 TCAATGTAGTACCTTGTGAGTAATCAATGTGGGCTCTAATCCCTTAAGCTCGATA
1 TCAATGTAGTACCTTGTGAGTAATCAATGTGGGCTCCAATCCCTTAAGCTCGATA
68804 CGCTTGCATT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (56 bp):
TCAATGTAGTACCTTGTGAGTAATCAATGTGGGCTCCAATCCCTTAAGCTCGATAA
Found at i:72195 original size:38 final size:38
Alignment explanation
Indices: 72151--72225 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
72141 TTTGAAGAAT
* * *
72151 ATTAATATTTAAGTT-AGGATATTAAAAAACTTAAAAAC
1 ATTAATATTTAACTTCA-AATATTAAAAAAATTAAAAAC
72189 ATTAATATTTAACTTCAAATATTAAAAAAATTAAAAA
1 ATTAATATTTAACTTCAAATATTAAAAAAATTAAAAA
72226 ATACTTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 32 0.97
39 1 0.03
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (38 bp):
ATTAATATTTAACTTCAAATATTAAAAAAATTAAAAAC
Found at i:72236 original size:39 final size:38
Alignment explanation
Indices: 72169--72242 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
72159 TTAAGTTAGG
* *
72169 ATATTAAAAAACTTAAAAACATTAATATTTAACTTCAA
1 ATATTAAAAAAATTAAAAACATTAATATTGAACTTCAA
*
72207 ATATTAAAAAAATTAAAAA-ATACTTATATTGAACTT
1 ATATTAAAAAAATTAAAAACAT--TAATATTGAACTT
72243 AAAAATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 2 0.06
38 18 0.58
39 11 0.35
ACGTcount: A:0.55, C:0.08, G:0.01, T:0.35
Consensus pattern (38 bp):
ATATTAAAAAAATTAAAAACATTAATATTGAACTTCAA
Found at i:78359 original size:76 final size:76
Alignment explanation
Indices: 78203--79099 Score: 808
Period size: 76 Copynumber: 11.8 Consensus size: 76
78193 GACGCCATGC
* * * * *
78203 TTGTTAGATGTCGTTGACATCTTGTGGTGACAC-ATGAGTGGTTGCAGTATTATGGGGTGATAC-
1 TTGTTAGATGTCGTTGACATCTTATGGTGACACGCTGAGTAGTTGTAGTATTATGGGGTGACACG
*
78266 TAAACGCTCCAA
66 T-CACGCTCCAA
* * *
78278 TTGTTAGATGTCGTTGACATCTTATGGTGACACGCTGAGTAGTTGTAGTATCATGGGGTGAAAGG
1 TTGTTAGATGTCGTTGACATCTTATGGTGACACGCTGAGTAGTTGTAGTATTATGGGGTGACACG
*
78343 TCATGCTCCAA
66 TCACGCTCCAA
** * *
78354 TTGTTAGATGTCGTTGACATCTTATGGTGACACATTGAGTGGTTGTAGTATTAT-GGGTGACACA
1 TTGTTAGATGTCGTTGACATCTTATGGTGACACGCTGAGTAGTTGTAGTATTATGGGGTGACACG
*
78418 TCACACTCCAA
66 TCACGCTCCAA
* * * * * * * * * * *
78429 TTGTTTGATGTCATTGTCATCTTGTGGTTACATGCTGAGTTGTTGCAATATTATAGGGTGACACA
1 TTGTTAGATGTCGTTGACATCTTATGGTGACACGCTGAGTAGTTGTAGTATTATGGGGTGACACG
* *
78494 CCATGCTCCAA
66 TCACGCTCCAA
* ** * * * *
78505 TTGTTAGATGTCGTTGACATCTTGTAATGGCACGTTGCGTCA-TTGTAGTATTATGGGGTGGCAC
1 TTGTTAGATGTCGTTGACATCTTATGGTGACACGCTGAGT-AGTTGTAGTATTATGGGGTGACAC
* *
78569 -TCGACTCTCTAA
65 GTC-ACGCTCCAA
* * * *
78581 TTGTTAGATGTCGTTGACATCTTATGGTGACATGCTAAGTAATTGTAGTATTATGGGGTGACATG
1 TTGTTAGATGTCGTTGACATCTTATGGTGACACGCTGAGTAGTTGTAGTATTATGGGGTGACACG
**
78646 TCGTGC-CCTAA
66 TCACGCTCC-AA
** * * * ** * * * *
78657 TTGTTAGACATTGTTGAAATCTTGTGGTGACACATTGAGTCA-TTGTAGTGTTATAGGATGACAT
1 TTGTTAGATGTCGTTGACATCTTATGGTGACACGCTGAGT-AGTTGTAGTATTATGGGGTGACAC
* *
78721 GCCACACTCCAA
65 GTCACGCTCCAA
* * * * * * *
78733 TTGTTAGATGTCGTTGACATCTTGTGGTGACACGTTGACTGGTAGTAGTATTATAGGGTGACATG
1 TTGTTAGATGTCGTTGACATCTTATGGTGACACGCTGAGTAGTTGTAGTATTATGGGGTGACACG
* **
78798 CCACAATCCAA
66 TCACGCTCCAA
* * * * * *
78809 TTGTTAGATGTCGTTGACATCTTATGGTGACACTCTGAGTGGTTGTTGTGTTATTGGGTGGCACG
1 TTGTTAGATGTCGTTGACATCTTATGGTGACACGCTGAGTAGTTGTAGTATTATGGGGTGACAC-
78874 GT-ACGCTCCAA
65 GTCACGCTCCAA
* * * * *
78885 TTGTTAGATGTCGTTGACATCTTATGGTGACACGCTGAGTGGTTGTTGTGTTATTGGGTGGCACG
1 TTGTTAGATGTCGTTGACATCTTATGGTGACACGCTGAGTAGTTGTAGTATTATGGGGTGACAC-
78950 GT-ACGCTCCAA
65 GTCACGCTCCAA
** * * *
78961 TTGTTAGATGTTATTGACATCTTATGGTGACATGCTGAGTTGTTATAGTATTATGGAGG-GACAC
1 TTGTTAGATGTCGTTGACATCTTATGGTGACACGCTGAGTAGTTGTAGTATTATGG-GGTGACAC
* * *
79025 GTCATGTTTCAA
65 GTCACGCTCCAA
* * * * * **
79037 TTGTTAGATGTCATCGATATCTTGTGGTAACACTTTGAGTCA-TTGTAGTATTATGGGGTGACA
1 TTGTTAGATGTCGTTGACATCTTATGGTGACACGCTGAGT-AGTTGTAGTATTATGGGGTGACA
79100 TGCCACACTT
Statistics
Matches: 678, Mismatches: 128, Indels: 31
0.81 0.15 0.04
Matches are distributed among these distances:
75 98 0.14
76 571 0.84
77 9 0.01
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (76 bp):
TTGTTAGATGTCGTTGACATCTTATGGTGACACGCTGAGTAGTTGTAGTATTATGGGGTGACACG
TCACGCTCCAA
Found at i:80640 original size:81 final size:82
Alignment explanation
Indices: 80449--80666 Score: 210
Period size: 81 Copynumber: 2.7 Consensus size: 82
80439 AGAGTGTTTT
* * * * * *
80449 AAGGAACATAGT-TCCCTTCAGCCTGAACTGATGCAAGGTGCCTATCCCTTCCCACAACTGCCTT
1 AAGGAACATGGTCTCCTTTCAGCCTGAACTAATGCAAGGTCCCCATCCCTTCCCACAACTGCCTC
**
80513 GACTATCGTATCAACCA
66 GACTATCACATCAACCA
* * * *
80530 AAGGAACATGGTCTCCTTTAAG-TTGAACTAATGCAAGGTTCCCATCCCTTCCCATAACTGCCTC
1 AAGGAACATGGTCTCCTTTCAGCCTGAACTAATGCAAGGTCCCCATCCCTTCCCACAACTGCCTC
*** **
80594 GACTATCACATTGGCTT
66 GACTATCACATCAACCA
* * * *
80611 GAGGAACATGGTCT-CTTTCAGCCTCAACTAAGTG-AAGGTCCCCTTCCCTTCTCACA
1 AAGGAACATGGTCTCCTTTCAGCCTGAACTAA-TGCAAGGTCCCCATCCCTTCCCACA
80667 GATTCATCAA
Statistics
Matches: 110, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
80 6 0.05
81 95 0.86
82 9 0.08
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.27
Consensus pattern (82 bp):
AAGGAACATGGTCTCCTTTCAGCCTGAACTAATGCAAGGTCCCCATCCCTTCCCACAACTGCCTC
GACTATCACATCAACCA
Found at i:80782 original size:93 final size:93
Alignment explanation
Indices: 80612--80782 Score: 211
Period size: 93 Copynumber: 1.8 Consensus size: 93
80602 CATTGGCTTG
* * * * *
80612 AGGAACATGGTCTCTTTCAGCCTCAACTAAGTGAAGGTCCCCTTCCCTTCTCACAGATTCATCAA
1 AGGAACATGGTCTCCTTCAACCTCAACTAAGTGAAGGTCCCCTTCCCTTCCCACAAATGCATCAA
**
80677 CAACCGTGTTGACAATCGCATAAGTCAA
66 CAACCGCATTGACAATCGCATAAGTCAA
* * *
80705 AGGAACATGGTCTCCTTCAACCTCAATTGAGTGAAGGTCCTCC-TCTCC-TCCCGCAAATGCATC
1 AGGAACATGGTCTCCTTCAACCTCAACTAAGTGAAGGTCC-CCTTC-CCTTCCCACAAATGCATC
*
80768 AACAATCGCATTGAC
64 AACAACCGCATTGAC
80783 CTAAGAAACA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
93 61 0.94
94 4 0.06
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.25
Consensus pattern (93 bp):
AGGAACATGGTCTCCTTCAACCTCAACTAAGTGAAGGTCCCCTTCCCTTCCCACAAATGCATCAA
CAACCGCATTGACAATCGCATAAGTCAA
Found at i:80902 original size:81 final size:81
Alignment explanation
Indices: 80704--80905 Score: 219
Period size: 81 Copynumber: 2.5 Consensus size: 81
80694 GCATAAGTCA
*
80704 AAGGAACATGGTCTCCTTCAACCTCAATTGAGTGAAGGTCCTCCTCTCCTCCCGCAAATGCATCA
1 AAGGAACATGGTCTCCTTCAACCTCAATTGAGTGAAGGTCCTCCTCTCCTCCAGCAAATGCATCA
*
80769 ACAATCGCATTGACCT
66 ACAATCGCATCGACCT
* * * * * *
80785 AAGAAACACGGTCTCCTTAAACCTCAAGTGAGTGAAGGTCC-CC-CTCCTCTCTAGTAGATGCAT
1 AAGGAACATGGTCTCCTTCAACCTCAATTGAGTGAAGGTCCTCCTCTCCTC-C-AGCAAATGCAT
* * * *
80848 CGACAATTGCATCGGCTT
64 CAACAATCGCATCGACCT
* * * * *
80866 GAGGAACATGGTCTCTTTCAGCATCAATTGATTGAAGGTC
1 AAGGAACATGGTCTCCTTCAACCTCAATTGAGTGAAGGTC
80906 ACATCCCTTG
Statistics
Matches: 98, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
79 6 0.06
80 3 0.03
81 89 0.91
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (81 bp):
AAGGAACATGGTCTCCTTCAACCTCAATTGAGTGAAGGTCCTCCTCTCCTCCAGCAAATGCATCA
ACAATCGCATCGACCT
Found at i:83297 original size:31 final size:31
Alignment explanation
Indices: 83257--83390 Score: 131
Period size: 31 Copynumber: 4.5 Consensus size: 31
83247 AGAAAGAAAT
83257 AAATGTTGTTACACGCTATGCATACCAAGTC
1 AAATGTTGTTACACGCTATGCATACCAAGTC
* *
83288 AAATATTGTTACACACTATGCAT------TC
1 AAATGTTGTTACACGCTATGCATACCAAGTC
*
83313 CAATGTTGTTACACGCTATGCATACCAAG-C
1 AAATGTTGTTACACGCTATGCATACCAAGTC
* * * *
83343 AAAATATTTTTACATG-TGAAGCATACCAAGTC
1 -AAATGTTGTTACACGCT-ATGCATACCAAGTC
83375 AAATGTTGTTACACGC
1 AAATGTTGTTACACGC
83391 CAACATTGAG
Statistics
Matches: 80, Mismatches: 13, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
25 22 0.28
30 2 0.03
31 55 0.69
32 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (31 bp):
AAATGTTGTTACACGCTATGCATACCAAGTC
Found at i:83325 original size:25 final size:25
Alignment explanation
Indices: 83293--83340 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
83283 AAGTCAAATA
*
83293 TTGTTACACACTATGCATTCCAATG
1 TTGTTACACACTATGCATACCAATG
*
83318 TTGTTACACGCTATGCATACCAA
1 TTGTTACACACTATGCATACCAA
83341 GCAAAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (25 bp):
TTGTTACACACTATGCATACCAATG
Found at i:83460 original size:24 final size:24
Alignment explanation
Indices: 83433--83488 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
83423 TATTGTGTTG
83433 TGACACGTTAACCCTACCATGTCA
1 TGACACGTTAACCCTACCATGTCA
* *
83457 TGACATGTTAACCCTACCATGTCG
1 TGACACGTTAACCCTACCATGTCA
83481 TGACACGT
1 TGACACGT
83489 CGACTATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (24 bp):
TGACACGTTAACCCTACCATGTCA
Found at i:84166 original size:23 final size:23
Alignment explanation
Indices: 84140--84207 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
84130 TCATAGATTC
84140 TCACCATACCGTGTCACACATTT
1 TCACCATACCGTGTCACACATTT
* *
84163 TCACCATGCCGTCTCACACGA-TT
1 TCACCATACCGTGTCACAC-ATTT
*
84186 TCAACATACCGTGTCACACATT
1 TCACCATACCGTGTCACACATT
84208 CCCATCATGG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
22 1 0.03
23 36 0.95
24 1 0.03
ACGTcount: A:0.26, C:0.35, G:0.10, T:0.28
Consensus pattern (23 bp):
TCACCATACCGTGTCACACATTT
Found at i:84226 original size:46 final size:47
Alignment explanation
Indices: 84135--84226 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 47
84125 GTGTCTCATA
* ** * *
84135 GATTCTCACCATACCGTGTCACACATTTTCACCATGCCGTCTCACAC
1 GATTCTCAACATACCGTGTCACACATTCCCACCATGCAGTATCACAC
* *
84182 GATT-TCAACATACCGTGTCACACATTCCCATCATGGAGTATCACA
1 GATTCTCAACATACCGTGTCACACATTCCCACCATGCAGTATCACA
84227 AACTCTAAAC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
46 34 0.89
47 4 0.11
ACGTcount: A:0.27, C:0.34, G:0.12, T:0.27
Consensus pattern (47 bp):
GATTCTCAACATACCGTGTCACACATTCCCACCATGCAGTATCACAC
Found at i:84297 original size:23 final size:23
Alignment explanation
Indices: 84254--84330 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
84244 TGTCACAACA
* * * *
84254 GTGTCACAAATTCTTACCATGTT
1 GTGTCACAGATTCTCAACATGTC
*
84277 GTTTCACACGATT-TCAACATGTC
1 GTGTCACA-GATTCTCAACATGTC
* *
84300 GTGTCACAGATTCTCACCATGCC
1 GTGTCACAGATTCTCAACATGTC
84323 GTGTCACA
1 GTGTCACA
84331 ATCCCAACAT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
22 4 0.09
23 37 0.84
24 3 0.07
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (23 bp):
GTGTCACAGATTCTCAACATGTC
Found at i:84409 original size:125 final size:126
Alignment explanation
Indices: 84153--84432 Score: 282
Period size: 125 Copynumber: 2.2 Consensus size: 126
84143 CCATACCGTG
* *
84153 TCACACATTTTCACCATGCCGTCTCACACGATTTCAACATACCGTGTCACACATTCCCATCATGG
1 TCACACA-TTTCACCATGCCGTGTCACACGATTTCAACATACCGTGTCACACATTCCCAACATGG
** * * *** *
84218 AGTATCACAAACTCTAAACCCTATTGTGTCACAACAGTGTCACAAATTCTTACCATGTTGTT
65 AGTATCACAAACTCTAAACCCTACCGTGCCACAACAGTGTCACAAATGCTTACCATGCCATC
* * * *
84280 TCACACGATTTCAACATGTCGTGTCACA-GATTCTCACCATGCCGTGTCACA-A-TCCCAACATG
1 TCACAC-ATTTCACCATGCCGTGTCACACGATT-TCAACATACCGTGTCACACATTCCCAACATG
* * * * *
84342 GCA-TGTCATAAACTTTAAACTCTACCGTGCCACAATC-GTGTCACATATGCTTACCATGCCATC
64 G-AGTATCACAAACTCTAAACCCTACCGTGCCACAA-CAGTGTCACAAATGCTTACCATGCCATC
* *
84405 TCACATATTCTCACCATGGCGTGTCACA
1 TCACACATT-TCACCATGCCGTGTCACA
84433 TTTTCACACT
Statistics
Matches: 126, Mismatches: 22, Indels: 12
0.79 0.14 0.08
Matches are distributed among these distances:
124 3 0.02
125 76 0.60
126 7 0.06
127 39 0.31
128 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.12, T:0.29
Consensus pattern (126 bp):
TCACACATTTCACCATGCCGTGTCACACGATTTCAACATACCGTGTCACACATTCCCAACATGGA
GTATCACAAACTCTAAACCCTACCGTGCCACAACAGTGTCACAAATGCTTACCATGCCATC
Found at i:84431 original size:23 final size:23
Alignment explanation
Indices: 84378--84562 Score: 130
Period size: 23 Copynumber: 8.1 Consensus size: 23
84368 GTGCCACAAT
* * *
84378 CGTGTCACATATGCTTACCATGC
1 CGTGTCACATATTCTCACCATGG
* *
84401 CATCTCACATATTCTCACCATGG
1 CGTGTCACATATTCTCACCATGG
*
84424 CGTGTCACAT-TT-TCA-CACTAG
1 CGTGTCACATATTCTCACCA-TGG
* *
84445 TGTGTCACATATTCTCACCATGT
1 CGTGTCACATATTCTCACCATGG
* *
84468 CGTATCACATATTCTCA-CATTGC
1 CGTGTCACATATTCTCACCA-TGG
* *
84491 CGTATCACATATTC-CTTCCATGG
1 CGTGTCACATATTCTC-ACCATGG
* *
84514 CGTGTCACAGACTT-TCACCATGC
1 CGTGTCACATA-TTCTCACCATGG
* * * *
84537 CATTTCACACATTCCCACCATGG
1 CGTGTCACATATTCTCACCATGG
84560 CGT
1 CGT
84563 TTTACAAACT
Statistics
Matches: 126, Mismatches: 26, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
20 2 0.02
21 14 0.11
22 9 0.07
23 94 0.75
24 7 0.06
ACGTcount: A:0.23, C:0.32, G:0.13, T:0.32
Consensus pattern (23 bp):
CGTGTCACATATTCTCACCATGG
Found at i:90001 original size:16 final size:17
Alignment explanation
Indices: 89966--90004 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
89956 TGAAAATGAA
89966 TTTGTATGATATCTGAT
1 TTTGTATGATATCTGAT
89983 TTTGTATGATATCT-AT
1 TTTGTATGATATCTGAT
89999 TTTGTA
1 TTTGTA
90005 ACAAGTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.56
Consensus pattern (17 bp):
TTTGTATGATATCTGAT
Found at i:90310 original size:27 final size:27
Alignment explanation
Indices: 90239--90337 Score: 65
Period size: 27 Copynumber: 3.7 Consensus size: 27
90229 AATACCAACA
* *
90239 AAAGTGGATGGATAAATTTAATCACCG
1 AAAGTGGATGGATACATTAAATCACCG
* ** ** *
90266 AAAATGGATAAACGCATTAAATCACTG
1 AAAGTGGATGGATACATTAAATCACCG
* * * *
90293 AAAGTGGATGGATTCATTTAACCATC-
1 AAAGTGGATGGATACATTAAATCACCG
*
90319 AGAAGTAGATGGATACATT
1 A-AAGTGGATGGATACATT
90338 TAACCACCAG
Statistics
Matches: 52, Mismatches: 19, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
26 1 0.02
27 51 0.98
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.26
Consensus pattern (27 bp):
AAAGTGGATGGATACATTAAATCACCG
Found at i:90338 original size:27 final size:27
Alignment explanation
Indices: 90294--90351 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
90284 AAATCACTGA
* * *
90294 AAGTGGATGGATTCATTTAACCATCAG
1 AAGTAGATGGATACATTTAACCACCAG
90321 AAGTAGATGGATACATTTAACCACCAG
1 AAGTAGATGGATACATTTAACCACCAG
90348 AAGT
1 AAGT
90352 GAATGAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.26
Consensus pattern (27 bp):
AAGTAGATGGATACATTTAACCACCAG
Found at i:91026 original size:29 final size:29
Alignment explanation
Indices: 90984--91044 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
90974 CTTGTCATAG
*
90984 CCTATACAAGGTTGGCTCGTGACATCTTC
1 CCTATACAAGGTTGGCTCATGACATCTTC
91013 CCTATACAAGGTTGGCTCATGACATCTTC
1 CCTATACAAGGTTGGCTCATGACATCTTC
91042 CCT
1 CCT
91045 TACTCAATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.31
Consensus pattern (29 bp):
CCTATACAAGGTTGGCTCATGACATCTTC
Found at i:102162 original size:24 final size:22
Alignment explanation
Indices: 102106--102163 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
102096 ATGAAGATGC
102106 TTTAA-TATGTTCTTATTATAT
1 TTTAATTATGTTCTTATTATAT
* *
102127 TTAAATGATATGTTCTTATTATGTGT
1 TTTAAT--TATGTTCTTATTA--TAT
102153 TTTAATTATGT
1 TTTAATTATGT
102164 ATTTTTGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 4 0.14
24 18 0.62
26 7 0.24
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (22 bp):
TTTAATTATGTTCTTATTATAT
Found at i:109892 original size:14 final size:14
Alignment explanation
Indices: 109875--109921 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 14
109865 AAATTCAAAC
*
109875 AAAAAAA-TTTTTG
1 AAAAAAATTTTTTA
*
109888 AAAAAACTTTTTTA
1 AAAAAAATTTTTTA
*
109902 AAGAAATATTTTTTA
1 AA-AAAAATTTTTTA
109917 AAAAA
1 AAAAA
109922 CAAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
13 6 0.21
14 10 0.36
15 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38
Consensus pattern (14 bp):
AAAAAAATTTTTTA
Found at i:109942 original size:12 final size:12
Alignment explanation
Indices: 109914--109951 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
109904 GAAATATTTT
*
109914 TTAAAAAACAAAA
1 TTAAAAAA-AAAC
109927 TTAAAAAAAAAC
1 TTAAAAAAAAAC
109939 TTAAAAAAAAAC
1 TTAAAAAAAAAC
109951 T
1 T
109952 CTAGAGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (12 bp):
TTAAAAAAAAAC
Found at i:115073 original size:22 final size:22
Alignment explanation
Indices: 115028--115080 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
115018 GTAAATCAAT
* *
115028 TAGTTATTAGGCATTGCATTAC
1 TAGTTTTTAGGCATTGCATCAC
**
115050 TAGTTTTTAGGCATTGTGTCAC
1 TAGTTTTTAGGCATTGCATCAC
115072 TAGTTTTTA
1 TAGTTTTTA
115081 ACTATTACGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (22 bp):
TAGTTTTTAGGCATTGCATCAC
Found at i:115222 original size:23 final size:23
Alignment explanation
Indices: 115196--115291 Score: 115
Period size: 23 Copynumber: 4.2 Consensus size: 23
115186 ACAATGCCTA
*
115196 AGTCACACAATGCCTTACTAACT
1 AGTCACATAATGCCTTACTAACT
**
115219 AGTCACATAATGCCTTGTTAACT
1 AGTCACATAATGCCTTACTAACT
* *
115242 AGTCACGTAATGCCTTACTAACC
1 AGTCACATAATGCCTTACTAACT
*
115265 AGTCACGTAATG-CTTA-TCAACT
1 AGTCACATAATGCCTTACT-AACT
115287 AGTCA
1 AGTCA
115292 TGTAATGTCA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
21 1 0.02
22 12 0.19
23 51 0.80
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.29
Consensus pattern (23 bp):
AGTCACATAATGCCTTACTAACT
Found at i:115263 original size:46 final size:45
Alignment explanation
Indices: 115204--115298 Score: 136
Period size: 46 Copynumber: 2.1 Consensus size: 45
115194 TAAGTCACAC
* * *
115204 AATGCCTTACTAACTAGTCACATAATGCCTTGTTAACTAGTCACGT
1 AATGCCTTACTAACCAGTCACATAATG-CTTATCAACTAGTCACGT
* *
115250 AATGCCTTACTAACCAGTCACGTAATGCTTATCAACTAGTCATGT
1 AATGCCTTACTAACCAGTCACATAATGCTTATCAACTAGTCACGT
115295 AATG
1 AATG
115299 TCATATCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 19 0.43
46 25 0.57
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (45 bp):
AATGCCTTACTAACCAGTCACATAATGCTTATCAACTAGTCACGT
Found at i:115590 original size:61 final size:60
Alignment explanation
Indices: 115475--115598 Score: 176
Period size: 61 Copynumber: 2.0 Consensus size: 60
115465 CTTAACCAAT
* * * * *
115475 AATGCTCAAAATGCTCAAAGGTTTTTCTTTATTTATCAAAAACTACTCCCAAATGCTTAAA
1 AATGCTCAAAATGCTCAAAAGTTTTTCTTCATGTATCAAAAACCACTCCAAAATG-TTAAA
* *
115536 AATGCTCAAAATGCTCAAAAGTTTTTCTTCATGTATCAAAAACCATTCCAAAATGTTCAA
1 AATGCTCAAAATGCTCAAAAGTTTTTCTTCATGTATCAAAAACCACTCCAAAATGTTAAA
115596 AAT
1 AAT
115599 ACTTAAAGGT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
60 7 0.12
61 49 0.88
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (60 bp):
AATGCTCAAAATGCTCAAAAGTTTTTCTTCATGTATCAAAAACCACTCCAAAATGTTAAA
Found at i:115980 original size:2 final size:2
Alignment explanation
Indices: 115973--116005 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
115963 NNNNNNNNNN
*
115973 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
116006 GGGGTCTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:116208 original size:29 final size:29
Alignment explanation
Indices: 116150--116221 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
116140 TATTAAATTA
116150 TAAATAAA-TTTT-TATTTTTATTATAGT
1 TAAATAAATTTTTATATTTTTATTATAGT
*
116177 T-AATGAAATTTTTATATTTTTATTTTTA-T
1 TAAAT-AAATTTTTATATTTTTA-TTATAGT
*
116206 TAAATAAATTATTATA
1 TAAATAAATTTTTATA
116222 ATTAATTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
26 3 0.08
27 4 0.11
28 4 0.11
29 20 0.53
30 7 0.18
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (29 bp):
TAAATAAATTTTTATATTTTTATTATAGT
Found at i:116478 original size:29 final size:31
Alignment explanation
Indices: 116421--116497 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 31
116411 TAATTATTAA
* *
116421 ATAAAATTTTATTTAATTTAAAATAAAAAAT
1 ATAAAAATTTATTTAATATAAAATAAAAAAT
*
116452 ATAAAAATTTATTTAA-ATATAAT-AAAAAT
1 ATAAAAATTTATTTAATATAAAATAAAAAAT
*
116481 ATAAAGATTTATTTAAT
1 ATAAAAATTTATTTAAT
116498 TTTTAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 21 0.51
30 5 0.12
31 15 0.37
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (31 bp):
ATAAAAATTTATTTAATATAAAATAAAAAAT
Found at i:116523 original size:11 final size:12
Alignment explanation
Indices: 116494--116527 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
116484 AAGATTTATT
116494 TAATTTTTAAAA
1 TAATTTTTAAAA
116506 TAATTTTTAAAA
1 TAATTTTTAAAA
*
116518 T-TTTTTTAAA
1 TAATTTTTAAA
116528 TATTATGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TAATTTTTAAAA
Found at i:117147 original size:2 final size:2
Alignment explanation
Indices: 117112--117136 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
117102 CAAAGGAACC
117112 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
117137 TTCTTTATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:128603 original size:23 final size:23
Alignment explanation
Indices: 128567--128616 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
128557 AAAAATATGT
*
128567 TATTATTAAATTATAATTTAAAA
1 TATTAATAAATTATAATTTAAAA
* *
128590 TATTAATAATTTATCATTTAAAA
1 TATTAATAAATTATAATTTAAAA
128613 TATT
1 TATT
128617 GAGATGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTAATAAATTATAATTTAAAA
Found at i:137652 original size:41 final size:40
Alignment explanation
Indices: 137579--137656 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 40
137569 TTTTATTATC
* ** *
137579 AAAATAATAAAATATTTTTTATATTTTCAAATATATTTTAA
1 AAAATAATAAAATATTATTTATATCATAAAATA-ATTTTAA
137620 AAAATAAATAAAATATTATTTAT-TCATAAAATAATTT
1 AAAAT-AATAAAATATTATTTATATCATAAAATAATTT
137657 ATTAATCAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 4 0.12
41 12 0.38
42 16 0.50
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (40 bp):
AAAATAATAAAATATTATTTATATCATAAAATAATTTTAA
Found at i:137658 original size:16 final size:17
Alignment explanation
Indices: 137627--137659 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
137617 TAAAAAATAA
137627 ATAAAATATTATTTATTC
1 ATAAAATA-TATTTATTC
137645 ATAAAATA-ATTTATT
1 ATAAAATATATTTATT
137660 AATCAAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAAAATATATTTATTC
Found at i:149918 original size:15 final size:15
Alignment explanation
Indices: 149898--149930 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
149888 AATGATTGAC
149898 AAAAAGAGGGAGAGG
1 AAAAAGAGGGAGAGG
149913 AAAAAGAGGGAGAGG
1 AAAAAGAGGGAGAGG
149928 AAA
1 AAA
149931 GGGAGATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (15 bp):
AAAAAGAGGGAGAGG
Found at i:150545 original size:28 final size:29
Alignment explanation
Indices: 150495--150550 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
150485 CTCGATTAAT
*
150495 TTTTTAAACTGATTTAATGATTT-TTTTA
1 TTTTTAAACTGATTTAATAATTTATTTTA
* * *
150523 TTTTTAAATTTATTTAGTAATTTATTTT
1 TTTTTAAACTGATTTAATAATTTATTTT
150551 GAAAAATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (29 bp):
TTTTTAAACTGATTTAATAATTTATTTTA
Found at i:150612 original size:23 final size:24
Alignment explanation
Indices: 150584--150637 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
150574 TTTTATGGTT
150584 AATAAAACTTTA-TTTGAA-AATAA
1 AATAAAACTTTACTTT-AATAATAA
* *
150607 AATAAAATTTTACTTTAATATTAA
1 AATAAAACTTTACTTTAATAATAA
150631 AATAAAA
1 AATAAAA
150638 GAAATATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (24 bp):
AATAAAACTTTACTTTAATAATAA
Found at i:151005 original size:53 final size:53
Alignment explanation
Indices: 150924--151027 Score: 154
Period size: 53 Copynumber: 2.0 Consensus size: 53
150914 ACAAATATGT
* * * *
150924 ATTCAAATCATTTCATAGGCAGCTCATTATAATCAGTAATAAACCAATAAATC
1 ATTCAAATCATTTCATAGGCAACACATTATAACCAGCAATAAACCAATAAATC
* *
150977 ATTCAAATCATTTCATAGGCAACACATTATAGCCAGCAATAAACCTATAAA
1 ATTCAAATCATTTCATAGGCAACACATTATAACCAGCAATAAACCAATAAA
151028 CCATAAACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (53 bp):
ATTCAAATCATTTCATAGGCAACACATTATAACCAGCAATAAACCAATAAATC
Found at i:154267 original size:30 final size:29
Alignment explanation
Indices: 154225--154287 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
154215 TTTGTAAAGG
* *
154225 TTATGCTTAATTTTTGAAAAGTAGAGAGA
1 TTATGCTTAATTTTTAAAAAATAGAGAGA
*
154254 TTATGTTTCAATTTTTAAAAAATAGAGAGA
1 TTATGCTT-AATTTTTAAAAAATAGAGAGA
154284 TTAT
1 TTAT
154288 ACATGAGCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.40, C:0.03, G:0.16, T:0.41
Consensus pattern (29 bp):
TTATGCTTAATTTTTAAAAAATAGAGAGA
Found at i:155564 original size:16 final size:16
Alignment explanation
Indices: 155529--155585 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
155519 TGTAACTTGT
**
155529 TATATTAACTTATTTT
1 TATATTAACTTATTAA
*
155545 TATATTAAGTTATTAA
1 TATATTAACTTATTAA
155561 TATATTATACTCTATATAA
1 TATATTA-ACT-TAT-TAA
155580 TATATT
1 TATATT
155586 TATTAATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
16 20 0.59
17 2 0.06
18 3 0.09
19 9 0.26
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (16 bp):
TATATTAACTTATTAA
Found at i:155921 original size:21 final size:20
Alignment explanation
Indices: 155897--155939 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
155887 GCTTATATAT
155897 TATACAAGT-ATATATTAACTA
1 TATA-AAGTAATATATTAA-TA
*
155918 TATATAGTAATATATTAATA
1 TATAAAGTAATATATTAATA
155938 TA
1 TA
155940 CTATGCATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (20 bp):
TATAAAGTAATATATTAATA
Found at i:163787 original size:2 final size:2
Alignment explanation
Indices: 163782--163813 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
163772 GTGTGTGTGT
163782 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
163814 AAGCCAAGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:180272 original size:2 final size:2
Alignment explanation
Indices: 180265--180308 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
180255 AAATATGTGA
180265 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
180306 AT A
1 AT A
180309 ACCTGAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:197439 original size:160 final size:164
Alignment explanation
Indices: 197261--197588 Score: 441
Period size: 160 Copynumber: 2.0 Consensus size: 164
197251 ATTTAAAAAA
* * **
197261 AATTGATTATCGCATTATAACCCTAAATCAATTGTAAAAGTCACTTAAAAATGTAAAAATTATCT
1 AATTGATTATCACATTATAACCCTAAATCAATTGTAAAAATCACACAAAAATGTAAAAATTATCT
* * * * *
197326 TGAAGTCTCTT-TG-T-A-CAATTTTGGAAACTTAGTTTTAATGCTAAAAGAAGAATGGG-GAAG
66 TGAAATCTCTTAAGTTGATCAATTTTGCAAACTTAATTTTAATGCTAAAAGAAGAAGGGGTGAAG
* * *
197386 AAGATAATGAAGTTAGGATAAAAAAAAAAGAGAAC
131 AAGATAATCAAGTAACGAT-AAAAAAAAAGAGAAC
* *
197421 AATTGATTGTCACATTATAACCCTAAATTAATTGTAAAAATCACACAAAAATGTAAAAATTATCT
1 AATTGATTATCACATTATAACCCTAAATCAATTGTAAAAATCACACAAAAATGTAAAAATTATCT
* *
197486 TGAAATCTCTTGAAGTTGATCAATTTTGCAAGCTTAATTTTAATGCTAGAAGAAGAAGGGGTGAA
66 TGAAATCTCTT-AAGTTGATCAATTTTGCAAACTTAATTTTAATGCTAAAAGAAGAAGGGGTGAA
* *
197551 GAAGATAATCATGTAACGATAAAAAAGAAGAGAAC
130 GAAGATAATCAAGTAACGATAAAAAAAAAGAGAAC
197586 AAT
1 AAT
197589 CAAAGAACAT
Statistics
Matches: 144, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
160 69 0.48
162 1 0.01
163 1 0.01
164 1 0.01
165 53 0.37
166 19 0.13
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (164 bp):
AATTGATTATCACATTATAACCCTAAATCAATTGTAAAAATCACACAAAAATGTAAAAATTATCT
TGAAATCTCTTAAGTTGATCAATTTTGCAAACTTAATTTTAATGCTAAAAGAAGAAGGGGTGAAG
AAGATAATCAAGTAACGATAAAAAAAAAGAGAAC
Found at i:198639 original size:159 final size:161
Alignment explanation
Indices: 198410--198745 Score: 414
Period size: 159 Copynumber: 2.1 Consensus size: 161
198400 TTAATTATTT
* * * *
198410 GAAAA-AAAAATTGATTATCACATTATAACCTAAATAATTGTCAAAATCACTTAAAAATGTAAAA
1 GAAAAGAACAATTGATTATCACATTATAACCTAAATAATTGTAAAAATCACATAAAAATATAAAA
* * * * *
198474 CTTATCTTGAAGTTTC-T-TTGAACAATTTTGGAAACTTAGTTTTAATGCT-AGAAGAAGAATGG
66 CTTATCTTGAAATCTCTTATTGAACAATTTTGCAAACTTAATTTTAATGCTAAGAAGAAGAAGGG
***
198536 G-GAAGAAGATAATCAAGTTGGGATAAAAAA
131 GAGAAGAAGATAATCAAGTAAAGATAAAAAA
* *
198566 GAAGAGAGCAATTGATTATCAC-TTCATAACCCTAAATCAATTGTAAAAATCACATAAAAATATA
1 GAAAAGAACAATTGATTATCACATT-ATAA-CCTAAAT-AATTGTAAAAATCACATAAAAATATA
* *
198630 AAATTTATCTTGAAATCTCTTGAAGTTGAACAATTTTGCAAACTTAATTTTAATGTTAGAAGAAG
63 AAACTTATCTTGAAATCTCTT--A-TTGAACAATTTTGCAAACTTAATTTTAATGCT--AAGAAG
198695 AAGAAGGGGAGAAGAAGATAATCAAGTAAAGATAAAAAA
123 AAGAAGGGGAGAAGAAGATAATCAAGTAAAGATAAAAAA
198734 GAAAAGAACAAT
1 GAAAAGAACAAT
198746 CGAAGAACGT
Statistics
Matches: 149, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
156 6 0.04
157 18 0.12
158 7 0.05
159 39 0.26
160 1 0.01
164 29 0.19
167 13 0.09
168 36 0.24
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (161 bp):
GAAAAGAACAATTGATTATCACATTATAACCTAAATAATTGTAAAAATCACATAAAAATATAAAA
CTTATCTTGAAATCTCTTATTGAACAATTTTGCAAACTTAATTTTAATGCTAAGAAGAAGAAGGG
GAGAAGAAGATAATCAAGTAAAGATAAAAAA
Found at i:199815 original size:16 final size:17
Alignment explanation
Indices: 199784--199817 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
199774 AGGGGGATCC
*
199784 ATGAGAAAATTCAATTA
1 ATGAGAAAAGTCAATTA
199801 ATGAG-AAAGTCAATTA
1 ATGAGAAAAGTCAATTA
199817 A
1 A
199818 AAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (17 bp):
ATGAGAAAAGTCAATTA
Found at i:200036 original size:19 final size:19
Alignment explanation
Indices: 200013--200058 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
200003 ATTGTATTTG
*
200013 ATCATATCTAATGTATCTC
1 ATCATATCTAATGTACCTC
* *
200032 CTCATATTTAATGTACCTC
1 ATCATATCTAATGTACCTC
200051 ATCATATC
1 ATCATATC
200059 CAACATACAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.30, C:0.24, G:0.04, T:0.41
Consensus pattern (19 bp):
ATCATATCTAATGTACCTC
Found at i:202010 original size:20 final size:20
Alignment explanation
Indices: 201985--202026 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
201975 TTATTTTCTA
201985 TTAAGTTTCAAAAAAATTTG
1 TTAAGTTTCAAAAAAATTTG
* * *
202005 TTAAGTTTTAAAGATATTTG
1 TTAAGTTTCAAAAAAATTTG
202025 TT
1 TT
202027 TGAATGGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (20 bp):
TTAAGTTTCAAAAAAATTTG
Found at i:207036 original size:13 final size:14
Alignment explanation
Indices: 207018--207046 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
207008 AATTTAGAGT
207018 TTATATTAT-TTTA
1 TTATATTATCTTTA
207031 TTATATTATCTTTA
1 TTATATTATCTTTA
207045 TT
1 TT
207047 TTATATGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATATTATCTTTA
Found at i:225395 original size:32 final size:32
Alignment explanation
Indices: 225359--225437 Score: 131
Period size: 32 Copynumber: 2.5 Consensus size: 32
225349 ATTAACAATT
* *
225359 TAATTTGGCAGTAAAACTTTTTTGTCGTTAAA
1 TAATTTGGCATTAAAACTTTGTTGTCGTTAAA
*
225391 TAATTTGGCATTAAAACTTTGTTGTTGTTAAA
1 TAATTTGGCATTAAAACTTTGTTGTCGTTAAA
225423 TAATTTGGCATTAAA
1 TAATTTGGCATTAAA
225438 GCTTAAAACA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (32 bp):
TAATTTGGCATTAAAACTTTGTTGTCGTTAAA
Found at i:231284 original size:43 final size:42
Alignment explanation
Indices: 231223--231340 Score: 182
Period size: 43 Copynumber: 2.7 Consensus size: 42
231213 ATTTATAAAT
*
231223 CATGAAGGAAAACCTCTATCATATATAGTTATTATTGTACTAA
1 CATGAA-GAAAACCTCTATCACATATAGTTATTATTGTACTAA
*
231266 CATGAATGAAAACGTCTATCACATATAGTTATTATTGTACTAA
1 CATGAA-GAAAACCTCTATCACATATAGTTATTATTGTACTAA
*
231309 TATGAAGAAAAACCTCTATCACATATAGTTAT
1 CATGAAG-AAAACCTCTATCACATATAGTTAT
231341 ACGATTAAGT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (42 bp):
CATGAAGAAAACCTCTATCACATATAGTTATTATTGTACTAA
Found at i:234893 original size:35 final size:35
Alignment explanation
Indices: 234854--234944 Score: 166
Period size: 35 Copynumber: 2.6 Consensus size: 35
234844 TAAGTTGTCC
234854 GAGATATTTGTTTTTGGTTATTCAAGTTGTTGTTT
1 GAGATATTTGTTTTTGGTTATTCAAGTTGTTGTTT
*
234889 GAGATATTTGTTTTTGGTTATTTAAGTTGTTGTTT
1 GAGATATTTGTTTTTGGTTATTCAAGTTGTTGTTT
234924 GAGATATTTGTTTTT-GTTATT
1 GAGATATTTGTTTTTGGTTATT
234945 TAAATTTAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 6 0.11
35 49 0.89
ACGTcount: A:0.18, C:0.01, G:0.22, T:0.59
Consensus pattern (35 bp):
GAGATATTTGTTTTTGGTTATTCAAGTTGTTGTTT
Found at i:242478 original size:12 final size:12
Alignment explanation
Indices: 242461--242485 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
242451 AAAATTATTA
242461 AAATTTATTTTT
1 AAATTTATTTTT
242473 AAATTTATTTTT
1 AAATTTATTTTT
242485 A
1 A
242486 TAATAAGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AAATTTATTTTT
Found at i:243773 original size:312 final size:310
Alignment explanation
Indices: 243209--243799 Score: 950
Period size: 312 Copynumber: 1.9 Consensus size: 310
243199 GATTTAGTCA
* * *
243209 AAGACCTACATCCACTACCTTGATTATTTAACCAAGGATTTTTCAAACCAAATCACTATAAACGA
1 AAGACCTACATCCACCACCTTGATTATTCAACCAAAGATTTTTCAAACCAAATCACTATAAACGA
* *
243274 TGAAATTTTCAAACTTCCACCAAGCTTTTACAATGGCTTTTACAGGCTCAGCCACAACCTTTAAC
66 TGAAATTTTCAAACTTCCACCAAGCTTTTACAATGCCTTTTACAAGCTCAGCCACAACCTTTAAC
* * * *
243339 AATGATTTTTTATGGGATCAACTAAAACCCAAAACTAACTTTTTCTAGGCTGAGTTAGAACCCAT
131 AATGATTTTTTA-GGGATCAACCAAAACCAAAAACTAACTTTTCCTAGGCTGAGTTAGAACACAT
* * *
243404 ACACTCAATCCAGCTAAGCCAAGCTTTATCAATCCCCTTAAAGTGACTCACACACTCTAAGTAAT
195 ACACTCAATCAAGCTAAGCCAAGCTTGATCAATCCCCTTAAAGTAACTCACACACTCTAAGTAAT
* *
243469 CAAGGAGCATAGAAATAAAGATCACTAACCTGATCTAAATGGTACAAAGTG
260 CAAAGAGAATAGAAATAAAGATCACTAACCTGATCTAAATGGTACAAAGTG
* *
243520 AAGACCTACATCCACCACCTTGATTGTTCAGCCAAAGATTTTTCAAACCAAATCACTATAAACGA
1 AAGACCTACATCCACCACCTTGATTATTCAACCAAAGATTTTTCAAACCAAATCACTATAAACGA
*
243585 TGAAATTTTCAAGCTTCCACCAAGCTTTTACAATGCCTTTTTACAAGCTCAGCCACAACCTTTAA
66 TGAAATTTTCAAACTTCCACCAAGCTTTTACAATGCC-TTTTACAAGCTCAGCCACAACCTTTAA
*
243650 TAATGATTTTTCTCA-GGATCAACCAAAACCAAAAACTAACTTTTCCTAGGCTGAGTTAGAACAC
130 CAATGATTTTT-T-AGGGATCAACCAAAACCAAAAACTAACTTTTCCTAGGCTGAGTTAGAACAC
* * *
243714 ATACACTCAATCAAGCTAAGCCAAGCTTGATCAATCTCCTTAGAGTAACTCGCACACTCTAAGTA
193 ATACACTCAATCAAGCTAAGCCAAGCTTGATCAATCCCCTTAAAGTAACTCACACACTCTAAGTA
243779 ATCAAAGAGAATAGAAATAAA
258 ATCAAAGAGAATAGAAATAAA
243800 AAAGTACCTA
Statistics
Matches: 256, Mismatches: 21, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
311 95 0.37
312 159 0.62
313 1 0.00
314 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (310 bp):
AAGACCTACATCCACCACCTTGATTATTCAACCAAAGATTTTTCAAACCAAATCACTATAAACGA
TGAAATTTTCAAACTTCCACCAAGCTTTTACAATGCCTTTTACAAGCTCAGCCACAACCTTTAAC
AATGATTTTTTAGGGATCAACCAAAACCAAAAACTAACTTTTCCTAGGCTGAGTTAGAACACATA
CACTCAATCAAGCTAAGCCAAGCTTGATCAATCCCCTTAAAGTAACTCACACACTCTAAGTAATC
AAAGAGAATAGAAATAAAGATCACTAACCTGATCTAAATGGTACAAAGTG
Found at i:244241 original size:73 final size:73
Alignment explanation
Indices: 244092--244246 Score: 195
Period size: 73 Copynumber: 2.1 Consensus size: 73
244082 CAAACAGAAT
* * * *
244092 GCTCTTAGTCGACTAACATGCTTCTCAATCGATTAAGTCATTTCTGTCTTTTAATCCCAGCTTCT
1 GCTCTTAGTCGACTAAAATGCTTCTCAATCGATTAAGTCATTTCTATCTCTGAATCCCAGCTTCT
* *
244157 GGCAGTGA
66 AGCAGTAA
* * * * *
244165 GCTCTTAGTCGACTAATAATGCTTCTTAGTCGATTAAGTCGTTTCTATCTCTGAA-CCTAGTTTC
1 GCTCTTAGTCGACTAA-AATGCTTCTCAATCGATTAAGTCATTTCTATCTCTGAATCCCAGCTTC
244229 TAGCAGTAA
65 TAGCAGTAA
244238 GCTCTTAGT
1 GCTCTTAGT
244247 TGATTAGCAA
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
73 39 0.56
74 31 0.44
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (73 bp):
GCTCTTAGTCGACTAAAATGCTTCTCAATCGATTAAGTCATTTCTATCTCTGAATCCCAGCTTCT
AGCAGTAA
Found at i:244270 original size:73 final size:74
Alignment explanation
Indices: 244092--244280 Score: 177
Period size: 73 Copynumber: 2.6 Consensus size: 74
244082 CAAACAGAAT
* * * * * * *
244092 GCTCTTAGTCGACTAAC-ATGCTTCTCAATCGATTAAGTCATTTCTGTCTTTTAATCCCAGCTTC
1 GCTCTTAGTCGACTAACAATACCTCTTAGTCGATTAAGTCATTTCTATCTCTGAATCCCAGCTTC
* *
244156 TGGCAGTGA
66 TAGCAGTAA
* * * * * *
244165 GCTCTTAGTCGACTAATAATGCTTCTTAGTCGATTAAGTCGTTTCTATCTCTGAA-CCTAGTTTC
1 GCTCTTAGTCGACTAACAATACCTCTTAGTCGATTAAGTCATTTCTATCTCTGAATCCCAGCTTC
244229 TAGCAGTAA
66 TAGCAGTAA
* * * * *
244238 GCTCTTAGTTGATTAGCAATACCTCTTGGTCGACTAAGT-ATTT
1 GCTCTTAGTCGACTAACAATACCTCTTAGTCGATTAAGTCATTT
244281 TTTGTTTCAC
Statistics
Matches: 95, Mismatches: 20, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
72 3 0.03
73 61 0.64
74 31 0.33
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (74 bp):
GCTCTTAGTCGACTAACAATACCTCTTAGTCGATTAAGTCATTTCTATCTCTGAATCCCAGCTTC
TAGCAGTAA
Found at i:256415 original size:13 final size:12
Alignment explanation
Indices: 256390--256414 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
256380 ACGTGGCAGG
256390 TCAAAAAAATTT
1 TCAAAAAAATTT
256402 TCAAAAAAATTT
1 TCAAAAAAATTT
256414 T
1 T
256415 TTGCCACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (12 bp):
TCAAAAAAATTT
Found at i:264295 original size:30 final size:28
Alignment explanation
Indices: 264260--264329 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 28
264250 AATTTTTAAA
* *
264260 AAGTTTTTATTTTTATATTTATGATCAATT
1 AAGTTTTTATTTTTAT-TTTA-AATCAAAT
264290 AAGTTTTAATATTTTTATTTTAAATCAAAT
1 AAGTTTT--TATTTTTATTTTAAATCAAAT
*
264320 AAATTTTTAT
1 AAGTTTTTAT
264330 AATTAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 3 0.09
30 19 0.54
31 4 0.11
32 9 0.26
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (28 bp):
AAGTTTTTATTTTTATTTTAAATCAAAT
Found at i:264348 original size:11 final size:11
Alignment explanation
Indices: 264332--264360 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
264322 ATTTTTATAA
264332 TTAATTATTAT
1 TTAATTATTAT
264343 TTAATTATTAT
1 TTAATTATTAT
264354 TTAATTA
1 TTAATTA
264361 AAATATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTAATTATTAT
Found at i:264524 original size:30 final size:27
Alignment explanation
Indices: 264490--264567 Score: 75
Period size: 30 Copynumber: 2.7 Consensus size: 27
264480 AACTATTAAT
264490 TATAAAAATTTATTTAATTTAAAATAAATA
1 TATAAAAATTTATTTAATTT--AATAAA-A
* * *
264520 TATAAAAATTAAATTAAATGTAATAAAA
1 TATAAAAATT-TATTTAATTTAATAAAA
* *
264548 AATAAAAATGTATTTAATTT
1 TATAAAAATTTATTTAATTT
264568 TTTTAAAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
27 7 0.18
28 9 0.23
29 6 0.15
30 10 0.26
31 7 0.18
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.40
Consensus pattern (27 bp):
TATAAAAATTTATTTAATTTAATAAAA
Found at i:264531 original size:20 final size:21
Alignment explanation
Indices: 264508--264554 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
264498 TTTATTTAAT
264508 TTAAAATAAATAT-ATAAAAA
1 TTAAAATAAATATAATAAAAA
* *
264528 TTAAATTAAATGTAATAAAAA
1 TTAAAATAAATATAATAAAAA
*
264549 ATAAAA
1 TTAAAA
264555 ATGTATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
TTAAAATAAATATAATAAAAA
Found at i:271380 original size:15 final size:15
Alignment explanation
Indices: 271360--271388 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
271350 TTATTGGTTG
271360 CAGAAGGCAATTGCC
1 CAGAAGGCAATTGCC
271375 CAGAAGGCAATTGC
1 CAGAAGGCAATTGC
271389 TATATAAAAT
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:0.34, C:0.24, G:0.28, T:0.14
Consensus pattern (15 bp):
CAGAAGGCAATTGCC
Found at i:275997 original size:3 final size:3
Alignment explanation
Indices: 275983--276017 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
275973 ACAATGGTTT
*
275983 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
276018 CTCAATCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:282880 original size:38 final size:38
Alignment explanation
Indices: 282830--282913 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
282820 ATATATAAAA
* * * *
282830 AAATT-TTAAGTTAGACCATTTAATATTGTAAAAGGAG
1 AAATTATTAAGTTAGACCATTCAAGAGTGTAAAAAGAG
* *
282867 AAATTATTAAGTTAGACTATTCAGGAGTGTAAAAAGAG
1 AAATTATTAAGTTAGACCATTCAAGAGTGTAAAAAGAG
282905 AAATTATTA
1 AAATTATTA
282914 GACAGGACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
37 5 0.12
38 35 0.88
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (38 bp):
AAATTATTAAGTTAGACCATTCAAGAGTGTAAAAAGAG
Found at i:295988 original size:36 final size:36
Alignment explanation
Indices: 295941--296010 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
295931 AGCCGCTGGA
* *
295941 GGCGGAGGCGAAACTGAGGAGGAGGTGTTAGTAGTC
1 GGCGGAGGCGAAACTGAGGAGGAAGTATTAGTAGTC
*
295977 GGCGGAGGCGAAACTGCGGAGGAAGTATTAGTAG
1 GGCGGAGGCGAAACTGAGGAGGAAGTATTAGTAG
296011 ATGGCGCCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.27, C:0.11, G:0.46, T:0.16
Consensus pattern (36 bp):
GGCGGAGGCGAAACTGAGGAGGAAGTATTAGTAGTC
Found at i:296534 original size:2 final size:2
Alignment explanation
Indices: 296529--296577 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
296519 TTTTTTTTAA
296529 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
296571 AT AT AT A
1 AT AT AT A
296578 AAGACCAGAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:297176 original size:15 final size:15
Alignment explanation
Indices: 297156--297185 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
297146 CATGGCATTT
*
297156 GTCTGGTCTGGCCTG
1 GTCTGGCCTGGCCTG
297171 GTCTGGCCTGGCCTG
1 GTCTGGCCTGGCCTG
297186 TTCGAAGTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.30, G:0.40, T:0.30
Consensus pattern (15 bp):
GTCTGGCCTGGCCTG
Found at i:297621 original size:26 final size:28
Alignment explanation
Indices: 297592--297649 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
297582 TAAAAAAAGT
*
297592 TTTTAAATTAT-TTTAAT-AAATTTTTA
1 TTTTAAATTATATTAAATAAAATTTTTA
**
297618 TTTTTTATTATATTAAATAAAATTTTTA
1 TTTTAAATTATATTAAATAAAATTTTTA
297646 TTTT
1 TTTT
297650 TATTTTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
27 5 0.19
28 13 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTTAAATTATATTAAATAAAATTTTTA
Found at i:297631 original size:28 final size:27
Alignment explanation
Indices: 297600--297668 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
297590 GTTTTTAAAT
*
297600 TATTTTAATAAATTTTTATTTTTTATTA
1 TATTTAAATAAATTTTTA-TTTTTATTA
*
297628 TA-TTAAATAAAATTTTTATTTTTATTT
1 TATTTAAAT-AAATTTTTATTTTTATTA
297655 TAATTTAAATAAAT
1 T-ATTTAAATAAAT
297669 AAATTAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 14 0.39
28 16 0.44
29 6 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TATTTAAATAAATTTTTATTTTTATTA
Found at i:297650 original size:29 final size:28
Alignment explanation
Indices: 297601--297667 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
297591 TTTTTAAATT
*
297601 ATTTTAAT-AAATTTTTATTTT-TTATT-
1 ATTTAAATAAAATTTTTATTTTATT-TTA
297627 ATATTAAATAAAATTTTTATTTTTATTTTA
1 AT-TTAAATAAAATTTTTA-TTTTATTTTA
297657 ATTTAAATAAA
1 ATTTAAATAAA
297668 TAAATTAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
26 2 0.06
27 5 0.14
28 9 0.26
29 15 0.43
30 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTTAAATAAAATTTTTATTTTATTTTA
Found at i:299574 original size:22 final size:22
Alignment explanation
Indices: 299549--299594 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
299539 TTATTAGTTA
* *
299549 AAATATTATTTATATTG-ATAAT
1 AAATAATATTT-TAATGAATAAT
299571 AAATAATATTTTAATGAATAAT
1 AAATAATATTTTAATGAATAAT
299593 AA
1 AA
299595 TTTTTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
AAATAATATTTTAATGAATAAT
Found at i:299642 original size:14 final size:14
Alignment explanation
Indices: 299609--299643 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
299599 TTTATTTAAT
299609 TTAAAATAAAAATA
1 TTAAAATAAAAATA
*
299623 TATAAATTAAAAATA
1 T-TAAAATAAAAATA
299638 TTAAAA
1 TTAAAA
299644 AAATAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TTAAAATAAAAATA
Found at i:301545 original size:2 final size:2
Alignment explanation
Indices: 301540--301573 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
301530 ACTATATATA
301540 TG TG TG -G TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
301574 TTATCATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:321028 original size:15 final size:17
Alignment explanation
Indices: 320999--321031 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
320989 CTTGTTGAAG
320999 AAAAAGAAAATAAGAAT
1 AAAAAGAAAATAAGAAT
321016 AAAAA-AAAA-AAGAAT
1 AAAAAGAAAATAAGAAT
321031 A
1 A
321032 GCATTATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAAAGAAAATAAGAAT
Found at i:327466 original size:31 final size:31
Alignment explanation
Indices: 327400--327468 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
327390 ATATGAACCT
* *
327400 TTTTTTTGTTATATTTTCACTTGAACGAAAT
1 TTTTTTTATTATATTTTCACTTGAACGAAAG
* * *
327431 TTTTTTTATTGTATTTTCATTTGAA-TATAAG
1 TTTTTTTATTATATTTTCACTTGAACGA-AAG
327462 TTTTTTT
1 TTTTTTT
327469 TAATTGAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 1 0.03
31 31 0.97
ACGTcount: A:0.23, C:0.06, G:0.09, T:0.62
Consensus pattern (31 bp):
TTTTTTTATTATATTTTCACTTGAACGAAAG
Found at i:329804 original size:23 final size:23
Alignment explanation
Indices: 329759--329805 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
329749 TAATTTATTA
*
329759 AATAAAATTAAAGAATATTAAAT
1 AATAAAATTAAAGAAAATTAAAT
*
329782 AATAAATTTAAA-AAAATTGAAAT
1 AATAAAATTAAAGAAAATT-AAAT
329805 A
1 A
329806 TTTATATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (23 bp):
AATAAAATTAAAGAAAATTAAAT
Found at i:331644 original size:12 final size:12
Alignment explanation
Indices: 331627--331667 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
331617 TGTATCTTCT
331627 TTTTGGTGGTCG
1 TTTTGGTGGTCG
331639 TTTTGGTGGTCG
1 TTTTGGTGGTCG
331651 TTGTTGTGGTGGTCG
1 -T-TT-TGGTGGTCG
331666 TT
1 TT
331668 GTTGAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 12 0.46
13 2 0.08
14 3 0.12
15 9 0.35
ACGTcount: A:0.00, C:0.07, G:0.41, T:0.51
Consensus pattern (12 bp):
TTTTGGTGGTCG
Found at i:331660 original size:15 final size:15
Alignment explanation
Indices: 331630--331671 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
331620 ATCTTCTTTT
331630 TGGTGGTCG-T-TT-
1 TGGTGGTCGTTGTTG
331642 TGGTGGTCGTTGTTG
1 TGGTGGTCGTTGTTG
331657 TGGTGGTCGTTGTTG
1 TGGTGGTCGTTGTTG
331672 AGAATATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.33
13 1 0.04
14 2 0.07
15 15 0.56
ACGTcount: A:0.00, C:0.07, G:0.45, T:0.48
Consensus pattern (15 bp):
TGGTGGTCGTTGTTG
Found at i:338634 original size:2 final size:2
Alignment explanation
Indices: 338627--338655 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
338617 CTTACCAAAA
338627 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
338656 TCTTTGATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:340056 original size:18 final size:18
Alignment explanation
Indices: 340033--340068 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
340023 GGACCAACAC
*
340033 TGGAATGATTAGTTACTT
1 TGGAATCATTAGTTACTT
340051 TGGAATCATTAGTTACTT
1 TGGAATCATTAGTTACTT
340069 GTGCCTCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.08, G:0.19, T:0.44
Consensus pattern (18 bp):
TGGAATCATTAGTTACTT
Found at i:340630 original size:15 final size:15
Alignment explanation
Indices: 340610--340656 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
340600 CGATCCTCCT
340610 GAGGAAGAAGAGGAA
1 GAGGAAGAAGAGGAA
* *
340625 GAGGAAGAAAAGAAA
1 GAGGAAGAAGAGGAA
*
340640 GAGGAAGAAGAAGAA
1 GAGGAAGAAGAGGAA
340655 GA
1 GA
340657 CCCTGAAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (15 bp):
GAGGAAGAAGAGGAA
Found at i:343883 original size:14 final size:15
Alignment explanation
Indices: 343857--343885 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
343847 GTTCTTCAGT
343857 AAAGTCAAAACTTAA
1 AAAGTCAAAACTTAA
343872 AAAGTC-AAACTTAA
1 AAAGTCAAAACTTAA
343886 TCTATTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (15 bp):
AAAGTCAAAACTTAA
Found at i:343964 original size:21 final size:21
Alignment explanation
Indices: 343940--343982 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
343930 AGCTTACTGA
* *
343940 TTTAAAAGTATCAATATATTT
1 TTTAAAAATATCAATACATTT
343961 TTTAAAAATATCAATACATTT
1 TTTAAAAATATCAATACATTT
343982 T
1 T
343983 CAACAGAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (21 bp):
TTTAAAAATATCAATACATTT
Found at i:347173 original size:30 final size:28
Alignment explanation
Indices: 347138--347195 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
347128 TGTAAAGAAT
*
347138 TAAATTAGTTAATTTAAATTATTTTATAAA
1 TAAATTAGTTAA-TT-AATTAATTTATAAA
347168 TAAATTAGTTAATTAATTAATTTATAAA
1 TAAATTAGTTAATTAATTAATTTATAAA
347196 CTTTTAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 13 0.48
29 2 0.07
30 12 0.44
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (28 bp):
TAAATTAGTTAATTAATTAATTTATAAA
Found at i:348176 original size:135 final size:136
Alignment explanation
Indices: 347920--348164 Score: 377
Period size: 135 Copynumber: 1.8 Consensus size: 136
347910 TTAATATTTC
* * *
347920 AATTTATTATTAAATTATTGAATAATTTAATAATAAATTTGATATATAATTTTTAATTTTAATTA
1 AATTTATTATTAAATTATTAAATAATATAATAATAAATTAGATATATAATTTTTAATTTTAATTA
* * *
347985 TTTGAATCATTTTTCTCTATTTGTATTTTTCATGGCTTAATCTTTTAATTTCATTTTCATTAAAC
66 TTTAAATCATTGTTCTCTATTTGTATTTATCATGGCTTAATCTTTTAATTTCATTTTCATTAAAC
348050 AGCAAT
131 AGCAAT
* * *
348056 AATTTATTATTAAATTATTAAATAATAT-ATATTAAATTAGTTATATAATTTTTTATTTTAATTA
1 AATTTATTATTAAATTATTAAATAATATAATAATAAATTAGATATATAATTTTTAATTTTAATTA
* *
348120 TTTAAAT-ATTGTTCTCTATTTGTATTTATCATTGTTTAATCTTTT
66 TTTAAATCATTGTTCTCTATTTGTATTTATCATGGCTTAATCTTTT
348165 TGTTTTCATT
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
134 34 0.35
135 38 0.39
136 26 0.27
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (136 bp):
AATTTATTATTAAATTATTAAATAATATAATAATAAATTAGATATATAATTTTTAATTTTAATTA
TTTAAATCATTGTTCTCTATTTGTATTTATCATGGCTTAATCTTTTAATTTCATTTTCATTAAAC
AGCAAT
Found at i:352811 original size:18 final size:18
Alignment explanation
Indices: 352790--352827 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
352780 AAATAATCTG
*
352790 AATAATTTAAATTTTTTT
1 AATAATTTAAATGTTTTT
*
352808 AATAATTTATATGTTTTT
1 AATAATTTAAATGTTTTT
352826 AA
1 AA
352828 ATATTATGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
AATAATTTAAATGTTTTT
Found at i:355566 original size:15 final size:15
Alignment explanation
Indices: 355538--355568 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
355528 ATATGATTAC
355538 AAGTAATGTGATTGT
1 AAGTAATGTGATTGT
*
355553 AAGTAATTTGATTGT
1 AAGTAATGTGATTGT
355568 A
1 A
355569 GAAAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (15 bp):
AAGTAATGTGATTGT
Found at i:355820 original size:39 final size:37
Alignment explanation
Indices: 355773--355846 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 37
355763 CTTAAATATA
355773 TTTTATTTTTATTTTT-TATTATAATATTATATATTTTGT
1 TTTTATTTTTATTTTTATATTAT-ATATT-T-TATTTTGT
355812 TTTTATTTTTATTTTTATATTATATATTTTATTTT
1 TTTTATTTTTATTTTTATATTATATATTTTATTTT
355847 AATTTCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
37 6 0.18
38 1 0.03
39 21 0.62
40 6 0.18
ACGTcount: A:0.24, C:0.00, G:0.01, T:0.74
Consensus pattern (37 bp):
TTTTATTTTTATTTTTATATTATATATTTTATTTTGT
Found at i:359123 original size:14 final size:16
Alignment explanation
Indices: 359104--359142 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
359094 GATTAATAAG
359104 TATGTATA-G-ATATA
1 TATGTATATGTATATA
359118 TATGTATATGTATATA
1 TATGTATATGTATATA
*
359134 TATATATAT
1 TATGTATAT
359143 AAATGATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.36
15 1 0.05
16 13 0.59
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (16 bp):
TATGTATATGTATATA
Found at i:380447 original size:3 final size:3
Alignment explanation
Indices: 380439--380465 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
380429 ACGTTCACCA
380439 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
380466 TTTGCTCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:386877 original size:19 final size:19
Alignment explanation
Indices: 386841--386878 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
386831 CATGTAATAT
*
386841 TTTTTTTTATTTTAATCAA
1 TTTTTTTCATTTTAATCAA
386860 TTTTTTTCATGTTT-ATCAA
1 TTTTTTTCAT-TTTAATCAA
386879 AGATTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTTTTTCATTTTAATCAA
Found at i:392891 original size:14 final size:14
Alignment explanation
Indices: 392872--392905 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
392862 GCGGGTTTAG
392872 ATTATTAGGAATTA
1 ATTATTAGGAATTA
*
392886 ATTATTAGGATTTA
1 ATTATTAGGAATTA
392900 AGTTAT
1 A-TTAT
392906 CTTAGATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
ATTATTAGGAATTA
Found at i:395320 original size:24 final size:25
Alignment explanation
Indices: 395285--395331 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
395275 AACACAATTA
395285 TTCAATAATTATA-TCTAATAACCT
1 TTCAATAATTATATTCTAATAACCT
*
395309 TTCAA-AAGTTATATTTTAATAAC
1 TTCAATAA-TTATATTCTAATAAC
395332 GTAATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 10 0.50
25 8 0.40
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.43
Consensus pattern (25 bp):
TTCAATAATTATATTCTAATAACCT
Found at i:401537 original size:27 final size:28
Alignment explanation
Indices: 401507--401560 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
401497 ATATTACAAA
401507 CAAATAAAATACATCAAA-ATAAATAAG
1 CAAATAAAATACATCAAATATAAATAAG
* *
401534 CAAATACATTACATCAAATATAAATAA
1 CAAATAAAATACATCAAATATAAATAA
401561 AAATTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.63, C:0.13, G:0.02, T:0.22
Consensus pattern (28 bp):
CAAATAAAATACATCAAATATAAATAAG
Found at i:406378 original size:33 final size:34
Alignment explanation
Indices: 406332--406396 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
406322 TTGATGGGGA
* *
406332 GTTTCAACTTAATTTTGGA-CTTTTTGGATTGAT
1 GTTTCAACTTAATTTTGAACCTTCTTGGATTGAT
406365 GTTTCAAGC-TAATTTTGAACCTTCTTGGATTG
1 GTTTCAA-CTTAATTTTGAACCTTCTTGGATTG
406397 TTTTTGCATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (34 bp):
GTTTCAACTTAATTTTGAACCTTCTTGGATTGAT
Found at i:427601 original size:15 final size:15
Alignment explanation
Indices: 427581--427612 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
427571 TAATATTACA
*
427581 AAAATTATAACTTAT
1 AAAATTATAAATTAT
427596 AAAATTATAAATTAT
1 AAAATTATAAATTAT
427611 AA
1 AA
427613 TATATATACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATTATAAATTAT
Found at i:431947 original size:20 final size:20
Alignment explanation
Indices: 431922--431987 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
431912 AAAAATACAC
431922 AAATAATAAATATTAAATTT
1 AAATAATAAATATTAAATTT
* *
431942 AAATAATAAAAAATAAA--T
1 AAATAATAAATATTAAATTT
*
431960 ATAT-A-AAATATT-AATTT
1 AAATAATAAATATTAAATTT
431977 AAATAACTAAA
1 AAATAA-TAAA
431988 AATAAATATT
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
15 2 0.06
16 5 0.14
17 5 0.14
18 5 0.14
20 18 0.51
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAATAAATATTAAATTT
Found at i:431976 original size:35 final size:35
Alignment explanation
Indices: 431922--431996 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
431912 AAAAATACAC
431922 AAATA-ATAAATATTAAATTTAAATAA-TAAAAAAT
1 AAATATATAAATATTAAATTTAAATAACT-AAAAAT
431956 AAATATATAAAATATT-AATTTAAATAACTAAAAAT
1 AAATATAT-AAATATTAAATTTAAATAACTAAAAAT
431991 AAATAT
1 AAATAT
431997 TCAAACAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.13
35 25 0.66
36 8 0.21
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (35 bp):
AAATATATAAATATTAAATTTAAATAACTAAAAAT
Found at i:432243 original size:15 final size:15
Alignment explanation
Indices: 432231--432263 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
432221 TTTATATATT
432231 TAAAA-TATATATAC
1 TAAAAGTATATATAC
432245 TAAAAGTATATATAC
1 TAAAAGTATATATAC
432260 TAAA
1 TAAA
432264 GATAGAGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (15 bp):
TAAAAGTATATATAC
Found at i:436472 original size:17 final size:17
Alignment explanation
Indices: 436429--436475 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
436419 TCTATCCATT
*
436429 AAAAAAAA-AAAACAGG
1 AAAAAAAACAAAACAAG
* *
436445 AAAAATCAACAAAAGAAG
1 AAAAA-AAACAAAACAAG
436463 AAAAAAAACAAAA
1 AAAAAAAACAAAA
436476 TGCTCAACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 5 0.20
17 9 0.36
18 11 0.44
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.02
Consensus pattern (17 bp):
AAAAAAAACAAAACAAG
Done.