Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold54
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: 3629595
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8670 characters in sequence are not A, C, G, or T
File 2 of 20
Found at i:171680 original size:2 final size:2
Alignment explanation
Indices: 171673--171705 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
171663 TGCAATAGTG
171673 TA TA TA 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 TA TA TA T
171706 TTCTTCAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:176674 original size:18 final size:19
Alignment explanation
Indices: 176643--176684 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
176633 AGAAAAAAAT
* *
176643 TATTTTTATGTCATATTTA
1 TATTTTTATATCATAATTA
176662 TATTTTT-TATCATAATTA
1 TATTTTTATATCATAATTA
176680 TATTT
1 TATTT
176685 AATATATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (19 bp):
TATTTTTATATCATAATTA
Found at i:178653 original size:13 final size:14
Alignment explanation
Indices: 178629--178660 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
178619 CAAATATGTT
178629 TATAATATAAATTA
1 TATAATATAAATTA
178643 TATAA-ATAAATTA
1 TATAATATAAATTA
178656 T-TAAT
1 TATAAT
178661 TTTAACATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 9 0.53
14 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TATAATATAAATTA
Found at i:181464 original size:21 final size:20
Alignment explanation
Indices: 181417--181464 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
181407 ATCACTTTGC
* *
181417 AAAAT-AACTAAATTTAATT
1 AAAATAAACTAAATATAAGT
*
181436 AGAATAAACTAAATAATAAGT
1 AAAATAAACTAAAT-ATAAGT
181457 AAAATAAA
1 AAAATAAA
181465 ATTACAATCC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 4 0.17
20 8 0.35
21 11 0.48
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (20 bp):
AAAATAAACTAAATATAAGT
Found at i:184186 original size:27 final size:29
Alignment explanation
Indices: 184151--184209 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 29
184141 TGTATAAAAT
* *
184151 ATATTTAATTTAT-TATTTTAAAT-ATTA
1 ATATGTAATATATATATTTTAAATAATTA
*
184178 ATATGTAATATATCATATTTTATATAATTA
1 ATATGTAATATAT-ATATTTTAAATAATTA
184208 AT
1 AT
184210 TATTAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 11 0.42
29 9 0.35
30 6 0.23
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (29 bp):
ATATGTAATATATATATTTTAAATAATTA
Found at i:186935 original size:2 final size:2
Alignment explanation
Indices: 186928--186953 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
186918 TTTAAGACAG
186928 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
186954 TGGTAATGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:188022 original size:2 final size:2
Alignment explanation
Indices: 188017--188047 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
188007 CTCTCTCTCT
188017 CA CA CA CA -A CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
188048 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:188052 original size:2 final size:2
Alignment explanation
Indices: 188047--188095 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
188037 ACACACACAC
188047 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
188089 AT AT AT A
1 AT AT AT A
188096 CACACACACA
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:191835 original size:72 final size:72
Alignment explanation
Indices: 191718--191865 Score: 203
Period size: 72 Copynumber: 2.1 Consensus size: 72
191708 ATTGCTTCTA
*
191718 TTTGTCAACATTAGATGTTAGCAATAACAAACTCGTTGGTGGGATACCAAATTGGATGGAGAATA
1 TTTGTCAACATTAGATGTTAGCAATAACAAACTCGTTGGTGGGATACCAAAGTGGATGGAGAATA
191783 TGTCAAG
66 TGTCAAG
* * *
191790 TTTGTCAACATTGGAT-TTAAGCAATAACAAACT-TTCTGG-GCGGATACCAAAGTGGATGGGGA
1 TTTGTCAACATTAGATGTT-AGCAATAACAAACTCGT-TGGTG-GGATACCAAAGTGGATGGAGA
*
191852 ATTTGTCAAG
63 ATATGTCAAG
191862 TTTG
1 TTTG
191866 GAAGAAATTG
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
71 4 0.06
72 64 0.94
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.30
Consensus pattern (72 bp):
TTTGTCAACATTAGATGTTAGCAATAACAAACTCGTTGGTGGGATACCAAAGTGGATGGAGAATA
TGTCAAG
Found at i:195228 original size:2 final size:2
Alignment explanation
Indices: 195221--195257 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
195211 TACAATCGGA
195221 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
195258 AGGGATGTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:195564 original size:60 final size:60
Alignment explanation
Indices: 195495--195613 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 60
195485 AAATTTTGCC
* *
195495 AGCTTAACACTAGAAAATAATAACATAGTCCA-TGGGAATTTTAAGTTATTTTTTATTTAA
1 AGCTTAACACTAGAAAAGAATAACATAGT-CAGTGGGAATTTTAAGTTATTATTTATTTAA
* * * *
195555 AGCTTAACACTAGAAAAGAATGACCTTGTTAGTGGGAATTTTAAGTTATTATTTATTTA
1 AGCTTAACACTAGAAAAGAATAACATAGTCAGTGGGAATTTTAAGTTATTATTTATTTA
195614 CTTTCAAGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 1 0.02
60 51 0.98
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (60 bp):
AGCTTAACACTAGAAAAGAATAACATAGTCAGTGGGAATTTTAAGTTATTATTTATTTAA
Found at i:196760 original size:2 final size:2
Alignment explanation
Indices: 196753--196783 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
196743 CAATCGGAAA
196753 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
196784 AGGGATGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:197088 original size:60 final size:60
Alignment explanation
Indices: 197015--197140 Score: 182
Period size: 60 Copynumber: 2.1 Consensus size: 60
197005 TTAAGATAAT
* * *
197015 TTTACCAGCTTAACACTAGAAAATAATAACCTAGTCCA-TGGGAATTTTAAGTTATTTTTTA
1 TTTA-CAGCTTAACACTAGAAAAGAATAACCTAGT-CAGTGGGAATTTTAAGCTATTATTTA
* *
197076 TTTACAGCTTAACACTAGAAAAGAATGACCTTGTCAGTGGGAATTTTAAGCTATTATTTA
1 TTTACAGCTTAACACTAGAAAAGAATAACCTAGTCAGTGGGAATTTTAAGCTATTATTTA
197136 TTTAC
1 TTTAC
197141 TTTCAAGCAA
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
59 2 0.03
60 53 0.90
61 4 0.07
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.37
Consensus pattern (60 bp):
TTTACAGCTTAACACTAGAAAAGAATAACCTAGTCAGTGGGAATTTTAAGCTATTATTTA
Found at i:199321 original size:22 final size:22
Alignment explanation
Indices: 199287--199346 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
199277 GAGTACAACA
* *
199287 TAAATCAGGAAACTAATCTCAC
1 TAAATTAGGAAACTAATCCCAC
*
199309 TGAATTAGGAAACTAATCCCAC
1 TAAATTAGGAAACTAATCCCAC
199331 TAAATTAGGAAACTAA
1 TAAATTAGGAAACTAA
199347 CTCTAACAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (22 bp):
TAAATTAGGAAACTAATCCCAC
Found at i:214436 original size:2 final size:2
Alignment explanation
Indices: 214429--214469 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
214419 CAATGATGTG
214429 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
214470 TCATCTATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:214718 original size:23 final size:23
Alignment explanation
Indices: 214682--214728 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
214672 TTAAAATTAG
214682 TAAAATTTTCAATACTTTAATAA
1 TAAAATTTTCAATACTTTAATAA
* *
214705 TAAATATTTT-AATATTTTCATAA
1 TAAA-ATTTTCAATACTTTAATAA
214728 T
1 T
214729 TATATCATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAAATTTTCAATACTTTAATAA
Found at i:215133 original size:30 final size:30
Alignment explanation
Indices: 215097--215157 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
215087 ATGTTAATAA
215097 TTTATA-TTATATAAATTTTATGATATATTT
1 TTTATATTTATAT-AATTTTATGATATATTT
*
215127 TTTATATTTATATTATTTTATGATATATTT
1 TTTATATTTATATAATTTTATGATATATTT
215157 T
1 T
215158 AATTATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 23 0.79
31 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (30 bp):
TTTATATTTATATAATTTTATGATATATTT
Found at i:215153 original size:15 final size:15
Alignment explanation
Indices: 215111--215155 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
215101 TATTATATAA
215111 ATTTTATGATATATT
1 ATTTTATGATATATT
215126 -TTTTAT-ATTTATATT
1 ATTTTATGA--TATATT
215141 ATTTTATGATATATT
1 ATTTTATGATATATT
215156 TTAATTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 1 0.04
14 6 0.23
15 12 0.46
16 6 0.23
17 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (15 bp):
ATTTTATGATATATT
Found at i:215608 original size:24 final size:24
Alignment explanation
Indices: 215563--215610 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
215553 TTTATATGAT
*
215563 ATAAATTACTTATATAAATAAAAA
1 ATAAATTAATTATATAAATAAAAA
*
215587 ATAAATTATATTAT-TAACTAAAAA
1 ATAAATTA-ATTATATAAATAAAAA
215611 CAAATTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAAATTAATTATATAAATAAAAA
Found at i:216088 original size:6 final size:6
Alignment explanation
Indices: 216077--216102 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
216067 ACCCTAACTG
216077 GACCCA GACCCA GACCCA GACCCA GA
1 GACCCA GACCCA GACCCA GACCCA GA
216103 ATCCACTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.46, G:0.19, T:0.00
Consensus pattern (6 bp):
GACCCA
Found at i:216128 original size:2 final size:2
Alignment explanation
Indices: 216121--216166 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
216111 TGTGCTCAGG
*
216121 TC TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
216163 TC TC
1 TC TC
216167 GCTTCGCTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:218114 original size:15 final size:15
Alignment explanation
Indices: 218096--218144 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
218086 CGGCGAAGAC
*
218096 GATGACGATGATGGG
1 GATGACGATGATGAG
* * *
218111 GATGAAGATGAAGAT
1 GATGACGATGATGAG
*
218126 GATGACGATGATGAT
1 GATGACGATGATGAG
218141 GATG
1 GATG
218145 GGGAAGAAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.35, C:0.04, G:0.39, T:0.22
Consensus pattern (15 bp):
GATGACGATGATGAG
Found at i:218154 original size:30 final size:30
Alignment explanation
Indices: 218090--218154 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
218080 AGAGGACGGC
* *
218090 GAAGACGATGACGATGATGGGGATGAAGAT
1 GAAGACGATGACGATGATGAGGATGAAGAA
* * **
218120 GAAGATGATGACGATGATGATGATGGGGAA
1 GAAGACGATGACGATGATGAGGATGAAGAA
218150 GAAGA
1 GAAGA
218155 AGAAGAGGAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.05, G:0.40, T:0.17
Consensus pattern (30 bp):
GAAGACGATGACGATGATGAGGATGAAGAA
Found at i:219367 original size:16 final size:15
Alignment explanation
Indices: 219342--219380 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
219332 TCAGTTTAGT
219342 ATAAATTATTATTTA
1 ATAAATTATTATTTA
*
219357 ATAATATTATTTTTTA
1 ATAA-ATTATTATTTA
*
219373 AAAAATTA
1 ATAAATTA
219381 ATTACAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATAAATTATTATTTA
Found at i:219817 original size:13 final size:13
Alignment explanation
Indices: 219798--219830 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
219788 ATATTTCATT
219798 CTTTAATTTG-TG
1 CTTTAATTTGTTG
219810 CTTATAATTTGTTG
1 CTT-TAATTTGTTG
219824 CTTTAAT
1 CTTTAAT
219831 AGCTTGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 11 0.58
14 5 0.26
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.58
Consensus pattern (13 bp):
CTTTAATTTGTTG
Found at i:225121 original size:21 final size:22
Alignment explanation
Indices: 225095--225147 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
225085 AAAAGTATCT
*
225095 TTGGATGAAATG-ATGCATTGG
1 TTGGATGAAAAGAATGCATTGG
**
225116 TTGGAT-AAAAGAATGCATTTT
1 TTGGATGAAAAGAATGCATTGG
225137 TTGGATGAAAA
1 TTGGATGAAAA
225148 AATACAACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 19 0.70
22 4 0.15
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (22 bp):
TTGGATGAAAAGAATGCATTGG
Found at i:228522 original size:21 final size:21
Alignment explanation
Indices: 228479--228522 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
228469 CATCCATTGG
* * **
228479 TTGGATGAAAGAATGTATTTT
1 TTGGATGAAAAAATGCAACTT
228500 TTGGATGAAAAAATGCAACTT
1 TTGGATGAAAAAATGCAACTT
228521 TT
1 TT
228523 AATAACCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (21 bp):
TTGGATGAAAAAATGCAACTT
Found at i:237978 original size:2 final size:2
Alignment explanation
Indices: 237960--238009 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
237950 AGATGCATAC
* *
237960 AT AT AC AT AT CT 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
238002 AT AT AT AT
1 AT AT AT AT
238010 CATGGATGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:243183 original size:20 final size:20
Alignment explanation
Indices: 243145--243183 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
243135 AATATTTTTA
** *
243145 AAAAAAAGTTAAGACAAAAT
1 AAAAAAAGAAAAGAAAAAAT
243165 AAAAAAAGAAAAGAAAAAA
1 AAAAAAAGAAAAGAAAAAA
243184 AAGGTGATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.03, G:0.10, T:0.08
Consensus pattern (20 bp):
AAAAAAAGAAAAGAAAAAAT
Found at i:243340 original size:22 final size:21
Alignment explanation
Indices: 243289--243340 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
243279 ACGTGAGTGG
243289 GAGAGAAAAAAGAAAGAAAAA
1 GAGAGAAAAAAGAAAGAAAAA
* * *
243310 AATAGGAAACAAGAAAAGAAAAA
1 GAGA-GAAAAAAG-AAAGAAAAA
243333 GAGAGAAA
1 GAGAGAAA
243341 TTTCATTGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 2 0.08
22 11 0.46
23 11 0.46
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02
Consensus pattern (21 bp):
GAGAGAAAAAAGAAAGAAAAA
Found at i:244648 original size:26 final size:28
Alignment explanation
Indices: 244619--244678 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
244609 ATATTGAATC
244619 TTAAAATTT-T-TATAATTTTTCTTATG
1 TTAAAATTTATCTATAATTTTTCTTATG
* *
244645 TTAAAATTTAGTCTTTAATTTTTCTTTTG
1 TTAAAATTTA-TCTATAATTTTTCTTATG
244674 TTAAA
1 TTAAA
244679 CACATGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 9 0.31
28 1 0.03
29 19 0.66
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (28 bp):
TTAAAATTTATCTATAATTTTTCTTATG
Found at i:245457 original size:19 final size:19
Alignment explanation
Indices: 245422--245459 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
245412 TATTAATAAA
*
245422 AATAATATTATATATTTTT
1 AATAATATTATAAATTTTT
245441 AATAATAATT-TAAATTTTT
1 AATAAT-ATTATAAATTTTT
245460 CTAACTCAGT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATAATATTATAAATTTTT
Found at i:246638 original size:21 final size:20
Alignment explanation
Indices: 246614--246669 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
246604 GTTGATATTC
* *
246614 ATATATTTAATTTTTTTAAAA
1 ATATATTT-ATATTTGTAAAA
*
246635 ATATATATATATTTGTAAAA
1 ATATATTTATATTTGTAAAA
*
246655 TTATATTTTATATTT
1 ATATA-TTTATATTT
246670 ATATTAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
ATATATTTATATTTGTAAAA
Found at i:247259 original size:2 final size:2
Alignment explanation
Indices: 247254--247300 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
247244 TGTGTGTGTC
247254 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
247296 TA TA T
1 TA TA T
247301 TGCATACTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:250941 original size:29 final size:30
Alignment explanation
Indices: 250879--250942 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
250869 ATAAAGCATA
* * *
250879 TTTTTAAATAAATTATTAAAATAATATTCG
1 TTTTGAAATAAATCATGAAAATAATATTCG
*
250909 -TTTGAAATAAATCATGAAAATATTATT-G
1 TTTTGAAATAAATCATGAAAATAATATTCG
250937 TTTTGA
1 TTTTGA
250943 TATTAAAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (30 bp):
TTTTGAAATAAATCATGAAAATAATATTCG
Found at i:251350 original size:2 final size:2
Alignment explanation
Indices: 251334--251369 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
251324 GGCATGTTAC
* *
251334 AT AT AT AA AT GT 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
251370 GTATGTATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:253153 original size:16 final size:15
Alignment explanation
Indices: 253132--253183 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
253122 ATATTATATT
253132 TTTTATTTTTTAAAAA
1 TTTTATTTTTT-AAAA
*
253148 TTTTATTTTTT-AAT
1 TTTTATTTTTTAAAA
253162 TTTATATTTTTTATAAA
1 TTT-TATTTTTTA-AAA
253179 TTTTA
1 TTTTA
253184 AAATATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 5 0.16
15 8 0.26
16 13 0.42
17 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTATTTTTTAAAA
Found at i:255467 original size:250 final size:251
Alignment explanation
Indices: 255022--255493 Score: 716
Period size: 250 Copynumber: 1.9 Consensus size: 251
255012 GCAACTTACG
* * *
255022 GTTAAATTCTTCTTATCGTAATTTACTATACAAATTAAAATATGATACGTTATAAAAAAAATAAT
1 GTTAAATTCTTCTTACCGTAATTTACTATACAAATTAAAACATGATACATTATAAAAAAAATAAT
*
255087 ACGAACATAATATGACTATAAAAATACGTTAAAATCTATATTATATAAATCATAATACATAAAAC
66 AC-AACATAATATGACTATAAAAATACGTTAAAATCTATATTATATAAATCATAACACATAAAAC
* *
255152 ATACAAATACAATATAAATATTAAAACATTATTTTTTAAATGAAACTTACATTCACTTGTCATTG
130 ATACAAATACAATATAAATATTAAAACATTATTTTTTAAACGAAACTTACATTCACTTATCATTG
255217 AA-CTAAAGGCTGAAACAATACTTATTTTTTAATACGATCTAATGAAAGTAATTTATA
195 AATC-AAAGGCTGAAACAATACTTATTTTTTAATACGATCTAATGAAAGTAATTTATA
* * *
255274 GTTAAATTCTTTTTACCGTAATTTATTATACAAATTAAAACATGATACATTATAAAAATAAT-AT
1 GTTAAATTCTTCTTACCGTAATTTACTATACAAATTAAAACATGATACATTATAAAAAAAATAAT
* * * * *
255338 A-AATATAATATGATTATAAAAATACGTTAAAATTTATATTATATAAATTATAACATATGAAAAC
66 ACAACATAATATGACTATAAAAATACGTTAAAATCTATATTATATAAATCATAACACAT-AAAAC
* * * *
255402 ATACAAATATAATATAAATATTAAAATATTATTTTTTAAACGAAACTTACTTTTACTTATCATTG
130 ATACAAATACAATATAAATATTAAAACATTATTTTTTAAACGAAACTTACATTCACTTATCATTG
**
255467 AATCAAAGGCTGAAACTCTACTTATTT
195 AATCAAAGGCTGAAACAATACTTATTT
255494 GAGTTGTACA
Statistics
Matches: 198, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
249 51 0.26
250 87 0.44
251 4 0.02
252 56 0.28
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (251 bp):
GTTAAATTCTTCTTACCGTAATTTACTATACAAATTAAAACATGATACATTATAAAAAAAATAAT
ACAACATAATATGACTATAAAAATACGTTAAAATCTATATTATATAAATCATAACACATAAAACA
TACAAATACAATATAAATATTAAAACATTATTTTTTAAACGAAACTTACATTCACTTATCATTGA
ATCAAAGGCTGAAACAATACTTATTTTTTAATACGATCTAATGAAAGTAATTTATA
Found at i:262127 original size:23 final size:23
Alignment explanation
Indices: 262097--262144 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
262087 ATAAATATGT
*
262097 TTGATTTAATATT-CATAAATAAA
1 TTGATTTAAT-TTAAATAAATAAA
262120 TTGATTTAATTTAAATAAATAAA
1 TTGATTTAATTTAAATAAATAAA
262143 TT
1 TT
262145 CGAATAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (23 bp):
TTGATTTAATTTAAATAAATAAA
Found at i:262222 original size:11 final size:12
Alignment explanation
Indices: 262206--262256 Score: 63
Period size: 11 Copynumber: 4.5 Consensus size: 12
262196 TAACAAACAC
262206 AAATATA-AAAT
1 AAATATATAAAT
*
262217 AAATATATTAA-
1 AAATATATAAAT
*
262228 AAATAAATAAAT
1 AAATATATAAAT
262240 AAA-ATATAAAT
1 AAATATATAAAT
262251 AAATAT
1 AAATAT
262257 TTATTTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
11 26 0.79
12 7 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATATATAAAT
Found at i:262232 original size:15 final size:14
Alignment explanation
Indices: 262206--262255 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
262196 TAACAAACAC
262206 AAATATAAAATAAAT
1 AAATA-AAAATAAAT
*
262221 ATATTAAAAATAAAT
1 A-AATAAAAATAAAT
262236 AAATAAAATATAAAT
1 AAATAAAA-ATAAAT
262251 AAATA
1 AAATA
262256 TTTATTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 6 0.19
15 22 0.71
16 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:262237 original size:19 final size:19
Alignment explanation
Indices: 262213--262255 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
262203 CACAAATATA
* *
262213 AAATAAATATATTAAAAAT
1 AAATAAATAAAATAAAAAT
*
262232 AAATAAATAAAATATAAAT
1 AAATAAATAAAATAAAAAT
262251 AAATA
1 AAATA
262256 TTTATTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATAAATAAAATAAAAAT
Found at i:262501 original size:17 final size:18
Alignment explanation
Indices: 262473--262523 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
262463 TTTAATATTT
*
262473 TATTTATATATTTTTTACA
1 TATTTAT-TATTTTTTAAA
262492 T-TTTATTA-TTTTTAAA
1 TATTTATTATTTTTTAAA
*
262508 TATTTTTTATTTTTTA
1 TATTTATTATTTTTTA
262524 TTTTGTACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 8 0.29
17 8 0.29
18 11 0.39
19 1 0.04
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TATTTATTATTTTTTAAA
Found at i:262505 original size:16 final size:17
Alignment explanation
Indices: 262473--262521 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
262463 TTTAATATTT
*
262473 TATTTATATATTTTTTACA
1 TATTTAT-TA-TTTTTAAA
262492 T-TTTATTATTTTTAAA
1 TATTTATTATTTTTAAA
*
262508 TATTTTTTATTTTT
1 TATTTATTATTTTT
262522 TATTTTGTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 8 0.30
17 13 0.48
18 5 0.19
19 1 0.04
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTATTATTTTTAAA
Found at i:262510 original size:27 final size:24
Alignment explanation
Indices: 262475--262527 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 24
262465 TAATATTTTA
*
262475 TTTATATATTTTTTACATTTTATTATT
1 TTTAAATATTTTTT--ATTTT-TTATT
262502 TTTAAATATTTTTTATTTTTTATT
1 TTTAAATATTTTTTATTTTTTATT
262526 TT
1 TT
262528 GTACCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 7 0.28
25 5 0.20
27 13 0.52
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTAAATATTTTTTATTTTTTATT
Found at i:262565 original size:29 final size:29
Alignment explanation
Indices: 262497--262590 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
262487 TTACATTTTA
* * *
262497 TTATTTTTAAATATT-TTTTATTTTTTATT
1 TTATATTTAAAT-TTATTTTAATTTTTAAT
* **
262526 TTGTACCTAAATTTATTTTAATTTTTAAT
1 TTATATTTAAATTTATTTTAATTTTTAAT
**
262555 TTATATTTAAATAAATTTTAAATTTTTAAT
1 TTATATTTAAATTTATTTT-AATTTTTAAT
*
262585 CTATAT
1 TTATAT
262591 CGAAATAATC
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
28 2 0.04
29 34 0.67
30 15 0.29
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (29 bp):
TTATATTTAAATTTATTTTAATTTTTAAT
Found at i:262597 original size:30 final size:29
Alignment explanation
Indices: 262540--262598 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
262530 ACCTAAATTT
* **
262540 ATTTTAATTTTTAATTTATATTTAAATAA
1 ATTTTAATTTTTAATCTATATCGAAATAA
262569 ATTTTAAATTTTTAATCTATATCGAAATAA
1 ATTTT-AATTTTTAATCTATATCGAAATAA
262599 TCTCTTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (29 bp):
ATTTTAATTTTTAATCTATATCGAAATAA
Found at i:263379 original size:19 final size:19
Alignment explanation
Indices: 263339--263382 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
263329 CAGGCATTAG
* *
263339 TTTTTATTGTTTTATGAGT
1 TTTTTATTATTTTATGAAT
263358 TTTTTATTATTTTAT-ATAT
1 TTTTTATTATTTTATGA-AT
263377 TTTTTA
1 TTTTTA
263383 AAAAAATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (19 bp):
TTTTTATTATTTTATGAAT
Found at i:263789 original size:2 final size:2
Alignment explanation
Indices: 263776--263813 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
263766 AAAGAGTTTT
*
263776 TA TA TT TA TA TA TA TA TA TA TA TA TA TA T- TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
263814 GATAAGATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:264813 original size:10 final size:10
Alignment explanation
Indices: 264788--264832 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
264778 TCTATGTATC
*
264788 TATATATATA
1 TATATTTATA
264798 -ATATTTATA
1 TATATTTATA
*
264807 TATATTTTTA
1 TATATTTATA
*
264817 TATATTTACA
1 TATATTTATA
264827 TATATT
1 TATATT
264833 AGAATGGAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (10 bp):
TATATTTATA
Found at i:264818 original size:25 final size:25
Alignment explanation
Indices: 264772--264821 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
264762 CACTTCCCTA
* *
264772 AATATTTCTATGTATCTATATATAT
1 AATATTTATATATATCTATATATAT
* *
264797 AATATTTATATATATTTTTATATAT
1 AATATTTATATATATCTATATATAT
264822 TTACATATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (25 bp):
AATATTTATATATATCTATATATAT
Found at i:265402 original size:2 final size:2
Alignment explanation
Indices: 265395--265423 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
265385 CTAAAAGTTA
265395 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
265424 GATCTTTGAA
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:267955 original size:14 final size:13
Alignment explanation
Indices: 267928--267978 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
267918 TATCATACAA
267928 GATAAAAGTT-AATT
1 GATAAAA-TTCAA-T
267942 GATAAAATTCAAT
1 GATAAAATTCAAT
*
267955 --TAAAATTTAAT
1 GATAAAATTCAAT
267966 GATAAAATTCAAT
1 GATAAAATTCAAT
267979 AAAACAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
11 10 0.31
13 13 0.41
14 9 0.28
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (13 bp):
GATAAAATTCAAT
Found at i:267973 original size:24 final size:24
Alignment explanation
Indices: 267929--267982 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
267919 ATCATACAAG
267929 ATAAAAGTTAATTGATAAAATTCA
1 ATAAAAGTTAATTGATAAAATTCA
*
267953 ATTAAAATTTAA-TGATAAAATTCA
1 A-TAAAAGTTAATTGATAAAATTCA
267977 ATAAAA
1 ATAAAA
267983 CAAAAGTAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 5 0.18
24 14 0.50
25 9 0.32
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (24 bp):
ATAAAAGTTAATTGATAAAATTCA
Found at i:271648 original size:14 final size:14
Alignment explanation
Indices: 271613--271650 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
271603 ATATATTTAA
271613 ATTTTAATATTTTT
1 ATTTTAATATTTTT
*
271627 ATTATAAT-TTTTT
1 ATTTTAATATTTTT
271640 ATTTTTAATAT
1 A-TTTTAATAT
271651 AGATATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 6 0.30
14 13 0.65
15 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTAATATTTTT
Found at i:271729 original size:29 final size:31
Alignment explanation
Indices: 271695--271755 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
271685 TGAATAAAGC
271695 ATTTTAATTTTTATATTATTAA-ATT-TAAT
1 ATTTTAATTTTTATATTATTAATATTATAAT
* *
271724 ATTTTAGTTTTTATATTTTTAATATTATAAT
1 ATTTTAATTTTTATATTATTAATATTATAAT
271755 A
1 A
271756 AATAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 20 0.71
30 3 0.11
31 5 0.18
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (31 bp):
ATTTTAATTTTTATATTATTAATATTATAAT
Found at i:271739 original size:14 final size:14
Alignment explanation
Indices: 271695--271742 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
271685 TGAATAAAGC
271695 ATTTTAATTTTTAT
1 ATTTTAATTTTTAT
* *
271709 ATTATTAAATTTAAT
1 ATT-TTAATTTTTAT
*
271724 ATTTTAGTTTTTAT
1 ATTTTAATTTTTAT
271738 ATTTT
1 ATTTT
271743 TAATATTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
ATTTTAATTTTTAT
Found at i:271743 original size:15 final size:15
Alignment explanation
Indices: 271696--271746 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
271686 GAATAAAGCA
271696 TTTTAATTTTTATAT
1 TTTTAATTTTTATAT
* * *
271711 TATTAAATTTAATA-
1 TTTTAATTTTTATAT
*
271725 TTTTAGTTTTTATAT
1 TTTTAATTTTTATAT
271740 TTTTAAT
1 TTTTAAT
271747 ATTATAATAA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTTAATTTTTATAT
Found at i:271830 original size:23 final size:24
Alignment explanation
Indices: 271804--271850 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
271794 CTGATAAAAT
* *
271804 AATAATTTTAAATTT-TATACAAA
1 AATAAATTTAAATTTAAATACAAA
271827 AATAAATTTAAATTTAAATACAAA
1 AATAAATTTAAATTTAAATACAAA
271851 TTTGAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
AATAAATTTAAATTTAAATACAAA
Found at i:271881 original size:20 final size:21
Alignment explanation
Indices: 271843--271881 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
271833 TTTAAATTTA
* *
271843 AATACAAATTTGAATTTTTTT
1 AATACAAATTTAAACTTTTTT
271864 AATA-AAATTTAAACTTTT
1 AATACAAATTTAAACTTTT
271882 ACGATACGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (21 bp):
AATACAAATTTAAACTTTTTT
Found at i:274178 original size:3 final size:3
Alignment explanation
Indices: 274170--274212 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
274160 CCTAATCCTG
274170 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
274213 GCTCGACCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:279759 original size:67 final size:68
Alignment explanation
Indices: 279651--279778 Score: 195
Period size: 67 Copynumber: 1.9 Consensus size: 68
279641 AAAAGGTCGT
* *
279651 GGGTTCGACTCCCACTGTGGTCGATGCTTTCTGCTCTCTTTT-GGTTTCTTTCATTAATTACGGT
1 GGGTTCGACTCCCACTGTGGTCGATACTTTCTGCTCTCTTTTGGGTTTCCTTCATTAATTACGGT
279715 TGA
66 TGA
* * * *
279718 GGGTTCGACTCTCAGTGTGGTCGATATTTTCTGTTCTCTTTTGGGTTTCCTTCATTAATTA
1 GGGTTCGACTCCCACTGTGGTCGATACTTTCTGCTCTCTTTTGGGTTTCCTTCATTAATTA
279779 AGGCCCATGC
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
67 37 0.69
68 17 0.31
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.45
Consensus pattern (68 bp):
GGGTTCGACTCCCACTGTGGTCGATACTTTCTGCTCTCTTTTGGGTTTCCTTCATTAATTACGGT
TGA
Found at i:279964 original size:13 final size:13
Alignment explanation
Indices: 279927--279969 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
279917 TTTATATTAT
279927 ATATATTAAATATAA
1 ATAT-TTAAA-ATAA
*
279942 ATATTGAAAATAA
1 ATATTTAAAATAA
*
279955 ATATTTAAAAAAA
1 ATATTTAAAATAA
279968 AT
1 AT
279970 TAGAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 17 0.68
14 4 0.16
15 4 0.16
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:282031 original size:2 final size:2
Alignment explanation
Indices: 282024--282050 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
282014 GCAAACTTTA
282024 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 A
282051 GATGGATAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:285676 original size:6 final size:6
Alignment explanation
Indices: 285665--285691 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
285655 ATATTTAATA
285665 AAATTT AAATTT AAATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAA
285692 AATATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
AAATTT
Found at i:285771 original size:23 final size:21
Alignment explanation
Indices: 285743--285787 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
285733 CGTATTTATT
285743 TTTAAAA-TATAATATTTAATAAA
1 TTTAAAAGT-TAA-ATTTAA-AAA
285766 TTTAAAAGTTAAATTTAAAAA
1 TTTAAAAGTTAAATTTAAAAA
285787 T
1 T
285788 ATGTAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.19
22 6 0.29
23 10 0.48
24 1 0.05
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTAAAAGTTAAATTTAAAAA
Found at i:286563 original size:15 final size:15
Alignment explanation
Indices: 286543--286573 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
286533 CATAAAAAAT
*
286543 TTAAATATATTTTTA
1 TTAAATATATATTTA
286558 TTAAATATATATTTA
1 TTAAATATATATTTA
286573 T
1 T
286574 ATTTAGTATT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAAATATATATTTA
Found at i:286567 original size:17 final size:17
Alignment explanation
Indices: 286547--286591 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
286537 AAAAATTTAA
286547 ATATATTTTTATTAAAT
1 ATATATTTTTATTAAAT
* * *
286564 ATATATTTATATTTAGT
1 ATATATTTTTATTAAAT
*
286581 ATTTATTTTTA
1 ATATATTTTTA
286592 AATTCAAGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
ATATATTTTTATTAAAT
Found at i:287453 original size:16 final size:15
Alignment explanation
Indices: 287428--287463 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
287418 TTATATAATA
*
287428 TATATTATTTTATATT
1 TATATCATTTTAT-TT
287444 TATATCATTTTATTT
1 TATATCATTTTATTT
287459 TATAT
1 TATAT
287464 AATATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TATATCATTTTATTT
Found at i:287630 original size:27 final size:27
Alignment explanation
Indices: 287549--287631 Score: 89
Period size: 28 Copynumber: 3.0 Consensus size: 27
287539 TTATGTTATC
* *
287549 TTTTTAAAATTTATTAAAAAAATTATA
1 TTTTTAAAAATTATTAAAAAAATAATA
* *
287576 TTATTAAAGATTAAATT-AAAAAATAATA
1 TTTTTAAAAATT--ATTAAAAAAATAATA
287604 TTTTTAAAAATT-TTAAAAAATATAATA
1 TTTTTAAAAATTATTAAAAAA-ATAATA
287631 T
1 T
287632 AAATTAATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
25 2 0.04
26 5 0.11
27 16 0.35
28 20 0.43
29 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (27 bp):
TTTTTAAAAATTATTAAAAAAATAATA
Found at i:287639 original size:10 final size:10
Alignment explanation
Indices: 287621--287697 Score: 52
Period size: 10 Copynumber: 7.4 Consensus size: 10
287611 AAATTTTAAA
287621 AAATATAATAT
1 AAAT-TAATAT
287632 AAATTAATCA-
1 AAATTAAT-AT
* *
287642 AAATAAATTT
1 AAATTAATAT
*
287652 AAATTATTATT
1 AAATTAATA-T
287663 AAATTTAA-AT
1 AAA-TTAATAT
287673 AAATATAA-AT
1 AAAT-TAATAT
287683 AATATTAATAT
1 AA-ATTAATAT
287694 AAAT
1 AAAT
287698 ACTTAGATTG
Statistics
Matches: 53, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
9 1 0.02
10 33 0.62
11 16 0.30
12 3 0.06
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (10 bp):
AAATTAATAT
Found at i:292246 original size:15 final size:16
Alignment explanation
Indices: 292221--292255 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
292211 TATATTTAAT
292221 TTTTAAAAAAATTATA
1 TTTTAAAAAAATTATA
292237 TTTT-AAAAAATTATA
1 TTTTAAAAAAATTATA
292252 TTTT
1 TTTT
292256 TTATAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTTAAAAAAATTATA
Found at i:292256 original size:16 final size:16
Alignment explanation
Indices: 292219--292270 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
292209 AATATATTTA
292219 ATTTTTAAAAAAATTAT
1 ATTTTT-AAAAAATTAT
292236 A-TTTTAAAAAATTAT
1 ATTTTTAAAAAATTAT
* * *
292251 ATTTTTTATAATTTAT
1 ATTTTTAAAAAATTAT
292267 ATTT
1 ATTT
292271 AAATATGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 11 0.35
16 19 0.61
17 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTTAAAAAATTAT
Found at i:292257 original size:17 final size:17
Alignment explanation
Indices: 292219--292258 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
292209 AATATATTTA
*
292219 ATTTTTAAAAAAATTAT
1 ATTTTTTAAAAAATTAT
292236 A--TTTTAAAAAATTAT
1 ATTTTTTAAAAAATTAT
292251 ATTTTTTA
1 ATTTTTTA
292259 TAATTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 14 0.70
17 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTTTAAAAAATTAT
Found at i:292321 original size:24 final size:24
Alignment explanation
Indices: 292261--292313 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
292251 ATTTTTTATA
*
292261 ATTTATATTTAAATATGTAATAAAT
1 ATTTA-ATTTAAATATGTAAAAAAT
*
292286 ATTTAATATAAATAT-TAAAAAAT
1 ATTTAATTTAAATATGTAAAAAAT
292309 -TTTAA
1 ATTTAA
292314 AATTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 5 0.19
23 7 0.27
24 9 0.35
25 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
ATTTAATTTAAATATGTAAAAAAT
Found at i:296137 original size:21 final size:19
Alignment explanation
Indices: 296113--296160 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
296103 ATTATTTTAA
296113 AAATTAATATTTTATAAATTT
1 AAATTAA-ATTTTA-AAATTT
*
296134 AAATTTAAATTTTAATATTT
1 AAA-TTAAATTTTAAAATTT
296154 ATAATTA
1 A-AATTA
296161 TTTATTCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 9 0.38
21 11 0.46
22 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AAATTAAATTTTAAAATTT
Found at i:296317 original size:18 final size:18
Alignment explanation
Indices: 296294--296335 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
296284 GACTAAAACT
296294 AATATT-ATTATTTAAAAA
1 AATATTAATT-TTTAAAAA
*
296312 AATATTAATTTTTTAAAA
1 AATATTAATTTTTAAAAA
296330 AATATT
1 AATATT
296336 TATATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATATTAATTTTTAAAAA
Found at i:296345 original size:18 final size:18
Alignment explanation
Indices: 296294--296345 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
296284 GACTAAAACT
*
296294 AATATTATTAT-TTAAAAA
1 AATATTAATATATT-AAAA
* *
296312 AATATTAATTTTTTAAAA
1 AATATTAATATATTAAAA
*
296330 AATATTTATATATTAA
1 AATATTAATATATTAA
296346 TATTTATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 26 0.93
19 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATATTAATATATTAAAA
Found at i:296364 original size:12 final size:14
Alignment explanation
Indices: 296330--296379 Score: 70
Period size: 13 Copynumber: 3.8 Consensus size: 14
296320 TTTTTTAAAA
296330 AATATTTATATATT
1 AATATTTATATATT
296344 AATATTTAT-TATT
1 AATATTTATATATT
*
296357 AA-ATTTATATA-A
1 AATATTTATATATT
296369 AATATTTATAT
1 AATATTTATAT
296380 TATAAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
12 8 0.24
13 16 0.48
14 9 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATATTTATATATT
Found at i:296628 original size:2 final size:2
Alignment explanation
Indices: 296621--296654 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
296611 AAGGTTCAAG
296621 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
296655 AAACCATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:296872 original size:16 final size:16
Alignment explanation
Indices: 296851--296884 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
296841 TCTTCCAATA
296851 TGATGAGTACTGTATT
1 TGATGAGTACTGTATT
296867 TGATGAGTACTGTATT
1 TGATGAGTACTGTATT
296883 TG
1 TG
296885 GCAAGATCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44
Consensus pattern (16 bp):
TGATGAGTACTGTATT
Found at i:297009 original size:15 final size:16
Alignment explanation
Indices: 296991--297029 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
296981 ATTTAATTTA
296991 ATAAAATAAAATA-TT
1 ATAAAATAAAATACTT
*
297006 ATAAATTAAAATACTT
1 ATAAAATAAAATACTT
297022 -TAAAATAA
1 ATAAAATAA
297030 TTTTTTACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 19 0.90
16 2 0.10
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAAAATAAAATACTT
Found at i:297267 original size:14 final size:14
Alignment explanation
Indices: 297248--297274 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
297238 GAAGATTATT
297248 TAATATATTTAATA
1 TAATATATTTAATA
297262 TAATATATTTAAT
1 TAATATATTTAAT
297275 TTTATTAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATATATTTAATA
Found at i:300541 original size:19 final size:19
Alignment explanation
Indices: 300519--300559 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
300509 ATTTATTATA
300519 ATATTAAAATATTAT-TTTT
1 ATATTAAAAT-TTATATTTT
*
300538 ATATTAATATTTATATTTT
1 ATATTAAAATTTATATTTT
300557 ATA
1 ATA
300560 ATTACATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATTAAAATTTATATTTT
Found at i:302407 original size:3 final size:3
Alignment explanation
Indices: 302401--302433 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
302391 AAAATAATAT
302401 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
302434 CCAAATTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:303985 original size:19 final size:17
Alignment explanation
Indices: 303954--303988 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
303944 ATTTATAATT
303954 ATTTTTAAAATTTATTG
1 ATTTTTAAAATTTATTG
303971 ATTTATTAAATATTTATT
1 ATTT-TTAAA-ATTTATT
303989 TTAGTGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 5 0.31
19 7 0.44
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
ATTTTTAAAATTTATTG
Found at i:304404 original size:19 final size:20
Alignment explanation
Indices: 304380--304419 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
304370 CAATCATTAA
304380 TATTAAAATTAAT-AAATTT
1 TATTAAAATTAATCAAATTT
*
304399 TATTAAAATTTATCAAATTT
1 TATTAAAATTAATCAAATTT
304419 T
1 T
304420 CATTGATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTAAAATTAATCAAATTT
Found at i:304855 original size:23 final size:22
Alignment explanation
Indices: 304830--304910 Score: 69
Period size: 23 Copynumber: 3.7 Consensus size: 22
304820 TAAATAAAAT
304830 ATTTTATTAATATTTATATTTT-
1 ATTTTATTAA-ATTTATATTTTA
* * *
304852 -TATTATTAAA-TAATAATTTA
1 ATTTTATTAAATTTATATTTTA
* *
304872 ATTTAATTAAAAATTATATTTTA
1 ATTTTATT-AAATTTATATTTTA
*
304895 AATTTATTAAATTTAT
1 ATTTTATTAAATTTAT
304911 TAAATTAAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
19 7 0.16
20 1 0.02
21 13 0.29
22 10 0.22
23 14 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTATTAAATTTATATTTTA
Found at i:304906 original size:9 final size:9
Alignment explanation
Indices: 304892--304916 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
304882 AAATTATATT
304892 TTAAATTTA
1 TTAAATTTA
304901 TTAAATTTA
1 TTAAATTTA
304910 TTAAATT
1 TTAAATT
304917 AAATAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTAAATTTA
Found at i:306635 original size:3 final size:3
Alignment explanation
Indices: 306627--306666 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
306617 TTCATTTTCT
306627 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
306667 TTCTTAGTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:307189 original size:11 final size:10
Alignment explanation
Indices: 307156--307228 Score: 53
Period size: 11 Copynumber: 7.3 Consensus size: 10
307146 ATATAGTAAA
*
307156 TTTTAATTA-
1 TTTTAAATAT
307165 TTTTAAA-A-
1 TTTTAAATAT
307173 TTTTAAATAT
1 TTTTAAATAT
*
307183 TTATTAAAAAT
1 TT-TTAAATAT
*
307194 TGTTTAAAAAGT
1 T-TTTAAATA-T
*
307206 TTTTAAATAA
1 TTTTAAATAT
*
307216 TTTAAAATAT
1 TTTTAAATAT
307226 TTT
1 TTT
307229 ATATTTAGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
8 8 0.15
9 7 0.13
10 13 0.25
11 22 0.42
12 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (10 bp):
TTTTAAATAT
Found at i:309862 original size:14 final size:14
Alignment explanation
Indices: 309843--309869 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
309833 AGATTCGGGG
309843 CCATTAGAATCAAT
1 CCATTAGAATCAAT
309857 CCATTAGAATCAA
1 CCATTAGAATCAA
309870 GAACAAGCTG
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:0.44, C:0.22, G:0.07, T:0.26
Consensus pattern (14 bp):
CCATTAGAATCAAT
Found at i:316935 original size:21 final size:22
Alignment explanation
Indices: 316911--316971 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 22
316901 TATATGTTAT
316911 ATAATTTATAAAATATAA-ATG
1 ATAATTTATAAAATATAATATG
*
316932 ATAA-TTATAAAAAATAATATG
1 ATAATTTATAAAATATAATATG
*
316953 ATATTATTATTAAAATATA
1 ATAAT-TTA-TAAAATATA
316972 TAAGTTGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 12 0.36
21 10 0.30
23 3 0.09
24 8 0.24
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (22 bp):
ATAATTTATAAAATATAATATG
Found at i:316967 original size:23 final size:21
Alignment explanation
Indices: 316911--316971 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 21
316901 TATATGTTAT
316911 ATAATT-TATAAAATATAAATG
1 ATAATTAT-TAAAATATAAATG
*
316932 ATAATTA-TAAAAAATAATATG
1 ATAATTATTAAAATATAA-ATG
316953 ATATTATTATTAAAATATA
1 ATA--ATTATTAAAATATA
316972 TAAGTTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
20 9 0.27
21 12 0.36
23 4 0.12
24 8 0.24
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (21 bp):
ATAATTATTAAAATATAAATG
Found at i:317016 original size:15 final size:16
Alignment explanation
Indices: 316986--317016 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
316976 TTGTTTGAGC
316986 ATAAATTTTAATAAAA
1 ATAAATTTTAATAAAA
317002 ATAAATTTT-ATAAAA
1 ATAAATTTTAATAAAA
317017 TTATTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAAATTTTAATAAAA
Found at i:317067 original size:10 final size:10
Alignment explanation
Indices: 317052--317079 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
317042 TACTCATTTA
317052 AAATAAATAT
1 AAATAAATAT
317062 AAATAAATAT
1 AAATAAATAT
317072 AAATAAAT
1 AAATAAAT
317080 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAATAAATAT
Found at i:317374 original size:14 final size:14
Alignment explanation
Indices: 317357--317391 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
317347 ATTTTTATTT
317357 AAAT-TTAATTATAA
1 AAATATTAA-TATAA
317371 AAATATTAATATAA
1 AAATATTAATATAA
317385 AAATATT
1 AAATATT
317392 TTTAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATATTAATATAA
Found at i:317388 original size:28 final size:29
Alignment explanation
Indices: 317330--317388 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 29
317320 TATAATTATT
** **
317330 ATTTAATAATTAAAAATATTTTTATTTAA
1 ATTTAATAATTAAAAATATTAATATAAAA
*
317359 ATTTAATTA-TAAAAATATTAATATAAAA
1 ATTTAATAATTAAAAATATTAATATAAAA
317387 AT
1 AT
317389 ATTTTTAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
ATTTAATAATTAAAAATATTAATATAAAA
Found at i:318011 original size:3 final size:3
Alignment explanation
Indices: 317997--318027 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
317987 GTGGTCATCT
317997 TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
318028 TTTTGGTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:318093 original size:21 final size:21
Alignment explanation
Indices: 318055--318117 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 21
318045 GGAGAGGAGG
*
318055 AGAGGG-GA-GAAAGCGAAAA
1 AGAGGGAGAGGAAAGAGAAAA
318074 AGAGGGAGAGGAAAGAG-AAA
1 AGAGGGAGAGGAAAGAGAAAA
** * *
318094 AGACAGAGAGGAAGGAAAAAA
1 AGAGGGAGAGGAAAGAGAAAA
318115 AGA
1 AGA
318118 CGGAAAAAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 6 0.17
20 18 0.50
21 12 0.33
ACGTcount: A:0.57, C:0.03, G:0.40, T:0.00
Consensus pattern (21 bp):
AGAGGGAGAGGAAAGAGAAAA
Found at i:318304 original size:8 final size:8
Alignment explanation
Indices: 318282--318313 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
318272 AAATTTTATG
318282 TATATTTT
1 TATATTTT
318290 ATATATTTT
1 -TATATTTT
318299 TATATTTT
1 TATATTTT
318307 TATATTT
1 TATATTT
318314 GTATTATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TATATTTT
Found at i:318363 original size:85 final size:85
Alignment explanation
Indices: 318218--318382 Score: 285
Period size: 85 Copynumber: 1.9 Consensus size: 85
318208 ATTTCTGCAT
* *
318218 TTTTTTTATTTATGTTATAGTATTAATATTATTTTTTATCATAAATTTATGTATAAATTTTATGT
1 TTTTTATATTTATATTATAGTATTAATATTATTTTTTATCATAAATTTATGTATAAATTTTATGT
318283 ATATTTTATATATTTTTATA
66 ATATTTTATATATTTTTATA
* * *
318303 TTTTTATATTTGTATTATAGTGTTAATATTATTTTTTATCATAAATTTATGTATAGATTTTATGT
1 TTTTTATATTTATATTATAGTATTAATATTATTTTTTATCATAAATTTATGTATAAATTTTATGT
318368 ATATTTTATATATTT
66 ATATTTTATATATTT
318383 ACATAATTAT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 75 1.00
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.62
Consensus pattern (85 bp):
TTTTTATATTTATATTATAGTATTAATATTATTTTTTATCATAAATTTATGTATAAATTTTATGT
ATATTTTATATATTTTTATA
Found at i:318641 original size:22 final size:21
Alignment explanation
Indices: 318603--318644 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
318593 ATTAATTATT
318603 TAAATATTAAATAAATTTAAA
1 TAAATATTAAATAAATTTAAA
318624 TAAATTATTACAAT-AATTTAA
1 TAAA-TATTA-AATAAATTTAA
318645 TTTTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 12 0.63
23 3 0.16
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAAATAAATTTAAA
Found at i:319045 original size:15 final size:14
Alignment explanation
Indices: 319015--319092 Score: 56
Period size: 15 Copynumber: 5.6 Consensus size: 14
319005 ATTTTAATTT
319015 TTATAATTAAAATA
1 TTATAATTAAAATA
*
319029 TTATAATATATAATA
1 TTATAAT-TAAAATA
*
319044 TTGAT-ATTAATATTA
1 TT-ATAATTAA-AATA
*
319059 TTACAATTTAAAATA
1 TTATAA-TTAAAATA
*
319074 --A-AAATAAAATA
1 TTATAATTAAAATA
319085 TTATAATT
1 TTATAATT
319093 TAATAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
11 7 0.14
12 2 0.04
13 2 0.04
14 13 0.27
15 19 0.39
16 6 0.12
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (14 bp):
TTATAATTAAAATA
Found at i:323537 original size:23 final size:22
Alignment explanation
Indices: 323511--323560 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
323501 TTTATTATTT
*
323511 AATTT-TTAAATATTTTATTAAAA
1 AATTTATT-AATATATT-TTAAAA
323534 AATTTAATTAATATATTTTAAAA
1 AATTT-ATTAATATATTTTAAAA
323557 AATT
1 AATT
323561 AAATAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 15 0.62
24 7 0.29
25 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTTATTAATATATTTTAAAA
Found at i:323569 original size:23 final size:24
Alignment explanation
Indices: 323517--323571 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
323507 ATTTAATTTT
* *
323517 TAAATATTTTATTAAAAAATTTAA
1 TAAATATATTATTAAAAAATTAAA
*
323541 TTAATATATT-TTAAAAAATTAAA
1 TAAATATATTATTAAAAAATTAAA
323564 TAAATATA
1 TAAATATA
323572 AAATATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAATATATTATTAAAAAATTAAA
Found at i:323672 original size:16 final size:16
Alignment explanation
Indices: 323651--323685 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
323641 ATGTAAGATC
323651 TAAGCTAGAAATCTAT
1 TAAGCTAGAAATCTAT
323667 TAAGCTAGAAATCTAT
1 TAAGCTAGAAATCTAT
323683 TAA
1 TAA
323686 TAATCTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (16 bp):
TAAGCTAGAAATCTAT
Found at i:324473 original size:14 final size:14
Alignment explanation
Indices: 324391--324476 Score: 55
Period size: 14 Copynumber: 5.5 Consensus size: 14
324381 ATTTTTTGAC
*
324391 ATTTTTTTAAAGTT
1 ATTTTTTTAAAATT
*
324405 ATTTCTTTAAAATTT
1 ATTTTTTTAAAA-TT
*
324420 ATTTTTTTATTTTTAATTT
1 ATTTTTTTA-----AAATT
*
324439 ATTATTTTTAAATAATA
1 ATT-TTTTT-AA-AATT
324456 ATTTTTTTAAAATT
1 ATTTTTTTAAAATT
324470 ATTTTTT
1 ATTTTTT
324477 AACCCGCACA
Statistics
Matches: 56, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
14 20 0.36
15 12 0.21
16 6 0.11
17 5 0.09
19 5 0.09
20 7 0.12
21 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (14 bp):
ATTTTTTTAAAATT
Found at i:327000 original size:29 final size:26
Alignment explanation
Indices: 326964--327021 Score: 89
Period size: 29 Copynumber: 2.1 Consensus size: 26
326954 TTTAAATAAG
326964 TGTACATATATATACTTATATATATAACT
1 TGTACATATATATA--TATA-ATATAACT
326993 TGTACATATATATATATAATATAACT
1 TGTACATATATATATATAATATAACT
327019 TGT
1 TGT
327022 GTGCATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 11 0.38
27 4 0.14
29 14 0.48
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (26 bp):
TGTACATATATATATATAATATAACT
Found at i:334048 original size:28 final size:27
Alignment explanation
Indices: 334003--334055 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
333993 TAATATTTTA
334003 ATATTATAATTTAAATATATTAAAATAT
1 ATATTATAATTTAAATAT-TTAAAATAT
*
334031 ATATTATAATGTT-TATATTTAAAAT
1 ATATTATAAT-TTAAATATTTAAAAT
334056 TTTAAAGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 7 0.30
28 14 0.61
29 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATAATTTAAATATTTAAAATAT
Found at i:335810 original size:23 final size:23
Alignment explanation
Indices: 335784--335837 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
335774 GTAATTTTTT
*
335784 AATATAAATCAATCTTAAAT-TAA
1 AATAAAAATCAAT-TTAAATATAA
**
335807 AATAAAAATTTATTTAAATATAA
1 AATAAAAATCAATTTAAATATAA
335830 AATAAAAA
1 AATAAAAA
335838 ATATTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
AATAAAAATCAATTTAAATATAA
Found at i:335842 original size:22 final size:22
Alignment explanation
Indices: 335798--335843 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
335788 TAAATCAATC
*
335798 TTAAATTAAAATAAAAATTTAT
1 TTAAATTAAAATAAAAATATAT
335820 TTAAATATAAAATAAAAA-ATAT
1 TTAAAT-TAAAATAAAAATATAT
335842 TT
1 TT
335844 TTTTAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAAATTAAAATAAAAATATAT
Found at i:335859 original size:22 final size:23
Alignment explanation
Indices: 335798--335863 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 23
335788 TAAATCAATC
335798 TTAAAT-TAAAATAAAAAT-TTAT
1 TTAAATAT-AAATAAAAATATTAT
*
335820 TTAAATATAAAATAAAAAATATTTT
1 TTAAATAT-AAAT-AAAAATATTAT
*
335845 TTTAATAT-AATAAAAATAT
1 TTAAATATAAATAAAAATAT
335864 AAAAATTTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 14 0.36
23 9 0.23
24 6 0.15
25 10 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TTAAATATAAATAAAAATATTAT
Found at i:335872 original size:24 final size:22
Alignment explanation
Indices: 335845--335888 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
335835 AAAATATTTT
335845 TTTAATATAATAAAAATATAAAAA
1 TTTAATAT-A-AAAAATATAAAAA
*
335869 TTTACTATAAAAAATATAAA
1 TTTAATATAAAAAATATAAA
335889 TAGTTTGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 1 0.05
24 7 0.37
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
TTTAATATAAAAAATATAAAAA
Found at i:336678 original size:13 final size:13
Alignment explanation
Indices: 336640--336679 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
336630 TTAATGAATG
*
336640 TATCGATACATTG
1 TATCGATACATTA
336653 TATCGATACATTA
1 TATCGATACATTA
*
336666 TATCAATACATTA
1 TATCGATACATTA
336679 T
1 T
336680 CATTGTATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:339866 original size:21 final size:18
Alignment explanation
Indices: 339837--339886 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 18
339827 AAAATATATA
339837 TTATTTAAATTATTATTTAT
1 TTATTTAAATTA-TATTT-T
* *
339857 CTTATGTAAAATATATTTT
1 -TTATTTAAATTATATTTT
339876 TTATTTAAATT
1 TTATTTAAATT
339887 TAATTATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 9 0.36
19 1 0.04
20 5 0.20
21 10 0.40
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTATTTAAATTATATTTT
Found at i:343059 original size:18 final size:18
Alignment explanation
Indices: 343027--343061 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
343017 TTAGTGTAAA
**
343027 AAAATATTATTAAAAATT
1 AAAATATTAAAAAAAATT
343045 AAAATATTAAAAAAAAT
1 AAAATATTAAAAAAAAT
343062 ATGCTTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATATTAAAAAAAATT
Found at i:343405 original size:2 final size:2
Alignment explanation
Indices: 343398--343438 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
343388 AAAATCTTCA
343398 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
343439 AATCAAATGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:345773 original size:15 final size:15
Alignment explanation
Indices: 345749--345778 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
345739 TATCATATTG
345749 TTATTATTTTATTTT
1 TTATTATTTTATTTT
*
345764 TTATTTTTTTATTTT
1 TTATTATTTTATTTT
345779 CATAATTTTT
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:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTATTATTTTATTTT
Found at i:346868 original size:23 final size:22
Alignment explanation
Indices: 346824--346870 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
346814 ATTTAACGAT
* *
346824 AAAATAAAAATATAATATATTA
1 AAAATAAAAAAATAATAAATTA
*
346846 AAAATAAAAAAAATTATAAATTA
1 AAAAT-AAAAAAATAATAAATTA
346869 AA
1 AA
346871 TTGAATGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATAAAAAAATAATAAATTA
Done.