Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008213.1 Hibiscus syriacus cultivar Beakdansim tig00110839_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2348840
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1300081 original size:200 final size:200
Alignment explanation
Indices: 1299318--1302284 Score: 4821
Period size: 200 Copynumber: 14.8 Consensus size: 200
1299308 CCTTTTCAAG
* * * *
1299318 TATACCGACTTTTGAGAAAACATATGTACAAAAAGTATCGACAAAAATAAAAAAAGTGTTGATAC
1 TATACCGATTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGATAC
* *
1299383 ATCTTGTCCAGATTGTATTTTAAAAACCAACTGCACAACAAATTGTCGATACGTTTATAACAAGT
66 ATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAGT
* * *
1299448 GTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATATGTAAAATATTAATGTAACCGAT
131 GTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGGT
1299513 CTAAA
196 CTAAA
* *
1299518 TATACCGATTTTTGAGAAAACATGTGTATAAAAAGTATCGACACAAATAAAAAAAAATGTCGATA
1 TATACCGATTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAAT-AAAAAAAGTGTCGATA
*
1299583 CATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCAATACGTTTATAACAAG
65 CATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAG
* *
1299648 TGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGCAAATTATTAATGTAACAGG
130 TGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGG
*
1299713 TTTAAA
195 TCTAAA
*
1299719 TATACCGATTTTTGAGAAAACATGTGTAAAAAAAGTATCGACACAAATAAAAAAAAGTGTCGATA
1 TATACCGATTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAAT-AAAAAAAGTGTCGATA
*
1299784 CATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTTGATACGTTTATAACAAG
65 CATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAG
* * * *
1299849 TGTCAATCCCGAAATCATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAATCAG
130 TGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGG
1299914 TCTAAA
195 TCTAAA
* * *
1299920 TATACCGGTTTTTGAGAAAACATGTGTACAAAAAATATTGACACAAATAAAAAAAGTGTCGATAC
1 TATACCGATTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGATAC
* * * * *
1299985 ATCTTGTCCAGAATGTATTTTAAAAACCAAGTGCAAAATAAAGTGTTGATACATTTATAACAAGT
66 ATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAGT
* * *
1300050 GTCGATTCCGAAAACATCGAAAAATATAATTATAAAGTAATAGGTAAATTATTAATGTAACCGGT
131 GTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGGT
1300115 CTAAA
196 CTAAA
* *
1300120 TATACCGATTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAATTGTCGATAC
1 TATACCGATTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGATAC
1300185 ATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAGT
66 ATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAGT
* * * *
1300250 GTCGATCCCGAAAACATCAAAAAACATAAATATAATGTAATAGGTAAATTATTAATGTAGCCGGA
131 GTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGGT
1300315 CTAAA
196 CTAAA
* * *
1300320 TATACC-AGTTTTTGAGAAAACAGGTATACAAAAAGTATCGACACAAATAAAAAAAGTGTTGATA
1 TATACCGA-TTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGATA
* * * * *
1300384 CATCTTGTCCAGATTATTTTTTAAAAACCAAGTGCACAACAAATTGTCAATACATTTATAACAAG
65 CATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAG
1300449 TGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGG
130 TGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGG
1300514 TCTAAA
195 TCTAAA
* * * * *
1300520 TATAACGATTTTTGAGAAAACAGGTGTATAAAAAGTATCGACACAAATAAAAAAAATGTTGATAC
1 TATACCGATTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGATAC
1300585 ATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAGT
66 ATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAGT
* *
1300650 GTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGCAAATTATTAATGTAACCAGT
131 GTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGGT
*
1300715 TTAAA
196 CTAAA
*
1300720 TATACCGATTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCAATAC
1 TATACCGATTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGATAC
* * * *
1300785 ATCTTGTCCAGTTTGTATTTTAAAAACCAAGAGCACAACAAAGTGTCAATACGTTTATAATAAGT
66 ATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAGT
* *
1300850 GTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATATAACCAGT
131 GTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGGT
1300915 CTAAA
196 CTAAA
* * *
1300920 TATACCGGTTTTTGAGAAAACAGGTGTACAAAAAATATCGACACAAATAAAAAAAAGTGTCGATA
1 TATACCGATTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAAT-AAAAAAAGTGTCGATA
* * *
1300985 CATCTTGTCCAGATAGTATTTTAAAAACCATGTGCCCAACAAAGTGTCGATACGTTTATAACAAG
65 CATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAG
* *
1301050 TGGCGATCCCGAAAACATCGAAAAATATAATTATAATGTAATAGGTAAATTATTAATGTAACCGG
130 TGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGG
*
1301115 TTTAAA
195 TCTAAA
* * *
1301121 TATATCGATTTTTGAGAAAACATGTGTATAAAAAGTATCGACACAAATAAAAAAAGTGTTGATAC
1 TATACCGATTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGATAC
* *
1301186 ATCTTGTACAAATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTAT---AAGT
66 ATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAGT
* *
1301248 GTCGATCCCGAAAACATCGAAAAACATAATTATATTGAAATAGG-ACAATTATTAATGTAACCGG
131 GTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTA-AATTATTAATGTAACCGG
1301312 TCTAAA
195 TCTAAA
* * * *
1301318 TATACCGGTTTTTGAGAAAACAGGTGTACAAAAAATATCGTCACAAATAAAAAAAGTGTCGATAC
1 TATACCGATTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGATAC
1301383 ATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAGT
66 ATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAGT
*
1301448 GTCGATCCCGAGAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGGT
131 GTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGGT
1301513 CTAAA
196 CTAAA
* * * *
1301518 TATACCGGTTTTTGAGAAAACAGGTGTACAAAAAATATCGACACAAATAAAAGAAGTGTCGATAC
1 TATACCGATTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGATAC
* *
1301583 ATCTTGTCTAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCAATACGTTTATAACAAGT
66 ATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAGT
* * *
1301648 TTCGATCCCGAAAAAATCGAAAAACATAATTATAATATAATAGGTAAATTATTAATGTAACCGGT
131 GTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGGT
*
1301713 TTAAA
196 CTAAA
* * * *
1301718 TATACCGATTTTTTAGAAAACATTTGTATAAAAAGTATCGACACAAATAAAAAAAGTGTTGATAC
1 TATACCGATTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGATAC
* * *
1301783 ATCTTGTCCTGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGACACGTTTAGAACAAGT
66 ATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAGT
1301848 GTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGG-ACAATTATTAATGTAACCGG
131 GTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTA-AATTATTAATGTAACCGG
1301912 TCTAAA
195 TCTAAA
* *
1301918 TATACCGATTTTTGAGAAAACATGTGTACAAAAAGTATCGTCACAAATAAAAAAAATGTCGATAC
1 TATACCGATTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGATAC
* *
1301983 ATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTTGATACGCTTATAACAAGT
66 ATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAGT
* * * * *
1302048 GTCAATCCCGAAAATATCAAAAAACATAATTATAATGTAATAGGTAAATTAGTAATATAACCGGT
131 GTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGGT
1302113 CTAAA
196 CTAAA
*
1302118 TATACCGATTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAAGTGTCGATA
1 TATACCGATTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAAT-AAAAAAAGTGTCGATA
* *
1302183 CATCTTGTCCAGAATGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTATAACAAG
65 CATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAG
*
1302248 TGTCGATCCCAAAAACATCGAAAAACATAATTATAAT
130 TGTCGATCCCGAAAACATCGAAAAACATAATTATAAT
1302285 CAACAACAAC
Statistics
Matches: 2563, Mismatches: 192, Indels: 23
0.92 0.07 0.01
Matches are distributed among these distances:
196 1 0.00
197 181 0.07
199 2 0.00
200 1710 0.67
201 669 0.26
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (200 bp):
TATACCGATTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGATAC
ATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTATAACAAGT
GTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGGT
CTAAA
Found at i:1302536 original size:264 final size:264
Alignment explanation
Indices: 1302066--1302548 Score: 835
Period size: 264 Copynumber: 1.8 Consensus size: 264
1302056 CGAAAATATC
*
1302066 AAAAAACATAATTATAATGTAATAGGTAAATTAGTAATATAACCGGTCTAAATATACCGATTTTT
1 AAAAAACATAATTATAATATAATAGGTAAATTAGTAATATAACCGGTCTAAATATACCGATTTTT
*
1302131 GAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAAGTGTCGATACATCTTGTCCAGA
66 GAGAAAACAGGAGTACAAAAAGTATCGACACAAATAAAAAAAAGTGTCGATACATCTTGTCCAGA
* *
1302196 ATGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAA
131 ATCTATTTTAAAAACCAAATGCACAACAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAA
1302261 AACATCGAAAAACATAATTATAATCAACAACAACAAAACTAAATTCCCATGTGTAATAGAATAAG
196 AACATCGAAAAACATAATTATAATCAACAACAACAAAACTAAATTCCCATGTGTAATAGAATAAG
1302326 GGGT
261 GGGT
* * * *
1302330 AAAAAACATAATTATAATATAATAGGTAAATTATTAATGTAATCGGTCTAAATATACCGTTTTTT
1 AAAAAACATAATTATAATATAATAGGTAAATTAGTAATATAACCGGTCTAAATATACCG-ATTTT
1302395 TGAGAAAACAGGAGTACAAAAAGTATCGACACAAAT-AAAAAAAG-GATCGATACATCTTGTCCA
65 TGAGAAAACAGGAGTACAAAAAGTATCGACACAAATAAAAAAAAGTG-TCGATACATCTTGTCCA
* * *
1302458 GATTCTATTTTAAAAACCAAATGCACAACAAAGTGTCGATACATTTATAACAAGTGTTGATCCCG
129 GAATCTATTTTAAAAACCAAATGCACAACAAAGTGTCGATACATTTATAACAAGTGTCGATCCCA
1302523 AAAACATCGAAAAACATAATTATAAT
194 AAAACATCGAAAAACATAATTATAAT
1302549 GTAATAGGTA
Statistics
Matches: 206, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
263 1 0.00
264 166 0.81
265 39 0.19
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.26
Consensus pattern (264 bp):
AAAAAACATAATTATAATATAATAGGTAAATTAGTAATATAACCGGTCTAAATATACCGATTTTT
GAGAAAACAGGAGTACAAAAAGTATCGACACAAATAAAAAAAAGTGTCGATACATCTTGTCCAGA
ATCTATTTTAAAAACCAAATGCACAACAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAA
AACATCGAAAAACATAATTATAATCAACAACAACAAAACTAAATTCCCATGTGTAATAGAATAAG
GGGT
Found at i:1302676 original size:201 final size:199
Alignment explanation
Indices: 1302331--1303124 Score: 1076
Period size: 200 Copynumber: 4.1 Consensus size: 199
1302321 ATAAGGGGTA
* *
1302331 AAAAACATAATTATAATATAATAGGTAAATTATTAATGTAATCGGTCTAAATATACCGTTTTTTT
1 AAAAACATAATTATAATATAATAGGTAAATTATTAATGTAACCGGTCTAAATATACCG-ATTTTT
* *
1302396 GAGAAAACAGGAGTACAAAAAGTATCGACACAAATAAAAAAAGGATCGATACATCTTGTCCAGAT
65 GAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTATCGATACATCTTGTCCAGAT
* * *
1302461 TCTATTTTAAAAACCAAATGCACAACAAAGTGTCGATACATTTATAACAAGTGTTGATCCCGAAA
130 TGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTATAACAATTG-TGATCCCGAAA
1302526 ACATCG
194 ACATCG
* * *
1302532 AAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACCGGTCTAAATATATCGATTTTTT
1 AAAAACATAATTATAATATAATAGGTAAATTATTAATGTAACCGGTCTAAATATACCGATTTTTG
* * * * *
1302597 AGAAAACAAGTGTACAAAAAGTATCGAAACAAATAAAAAAAAATATCGATACATCTTGTACAAAT
66 AGAAAACAGGTGTACAAAAAGTATCGACACAAAT-AAAAAAAGTATCGATACATCTTGTCCAGAT
1302662 TGTATTTTAAAAACCAAGTGCACAACAAA--GT-G---------T--C------GATCCCGAAAA
130 TGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTATAACAATTGTGATCCCGAAAA
1302707 CATCG
195 CATCG
* * *
1302712 AAAAACATAATGATAATGTAATAGGTAAATTATTAATGTAACCGGTCTAACTATACCGATTTTTG
1 AAAAACATAATTATAATATAATAGGTAAATTATTAATGTAACCGGTCTAAATATACCGATTTTTG
* *
1302777 AGAAAACAGGTGTACAAAAAGAATCGACACAAATAAAAAAAGTGTCGATACATCTTGTCCAGATT
66 AGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTATCGATACATCTTGTCCAGATT
* *
1302842 GTATTTTAAAAACCAAGTGCACAACAAATTGTCGATACGTTTATAACAATTGTGGATCCCGAAAA
131 GTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTATAACAATTGT-GATCCCGAAAA
*
1302907 CATTG
195 CATCG
* *
1302912 AAAAATATAATTATAATATAATAGGTAAATTATTAATGTAACCGGTCTAAATATACCTATTTTTG
1 AAAAACATAATTATAATATAATAGGTAAATTATTAATGTAACCGGTCTAAATATACCGATTTTTG
** * * *
1302977 AGAAAACAGGTGT-TTAAAAGTATCGACAC-AA-AAAAAAAGTGTCGTTACATCTTGTTCAGATT
66 AGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTATCGATACATCTTGTCCAGATT
* * * *
1303039 GTATTTTAAAAACCAAGTGCACAACAAAATTTCGATACATTTATAACAATTGTCGATCTCAAAAA
131 GTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTATAACAATTGT-GATCCCGAAAA
1303104 CATCG
195 CATCG
1303109 AAAAACATAATTATAA
1 AAAAACATAATTATAA
1303125 CCAAATATCT
Statistics
Matches: 527, Mismatches: 44, Indels: 48
0.85 0.07 0.08
Matches are distributed among these distances:
179 55 0.10
180 108 0.20
181 2 0.00
182 1 0.00
187 1 0.00
189 1 0.00
191 1 0.00
193 1 0.00
197 107 0.20
198 3 0.01
199 15 0.03
200 124 0.24
201 108 0.20
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (199 bp):
AAAAACATAATTATAATATAATAGGTAAATTATTAATGTAACCGGTCTAAATATACCGATTTTTG
AGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTATCGATACATCTTGTCCAGATT
GTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTATAACAATTGTGATCCCGAAAAC
ATCG
Found at i:1303084 original size:197 final size:200
Alignment explanation
Indices: 1302692--1303124 Score: 694
Period size: 197 Copynumber: 2.2 Consensus size: 200
1302682 CACAACAAAG
* *
1302692 TGTCGATCCCGAAAACATCGAAAAACATAATGATAATGTAATAGGTAAATTATTAATGTAACCGG
1 TGTCGATCCCGAAAACATCGAAAAACATAATTATAATATAATAGGTAAATTATTAATGTAACCGG
*
1302757 TCTAACTATACCGATTTTTGAGAAAACAGGTGTACAAAAAGAATCGACACAAATAAAAAAAGTGT
66 TCTAAATATACCGATTTTTGAGAAAACAGGTGTACAAAAAGAATCGACACAAATAAAAAAAGTGT
*
1302822 CGATACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAATTGTCGATACGTTTATA
131 CGATACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAATTGTCGATACATTTATA
1302887 ACAAT
196 ACAAT
* * *
1302892 TGTGGATCCCGAAAACATTGAAAAATATAATTATAATATAATAGGTAAATTATTAATGTAACCGG
1 TGTCGATCCCGAAAACATCGAAAAACATAATTATAATATAATAGGTAAATTATTAATGTAACCGG
* ** *
1302957 TCTAAATATACCTATTTTTGAGAAAACAGGTGT-TTAAAAGTATCGACAC-AA-AAAAAAAGTGT
66 TCTAAATATACCGATTTTTGAGAAAACAGGTGTACAAAAAGAATCGACACAAATAAAAAAAGTGT
* *
1303019 CGTTACATCTTGTTCAGATTGTATTTTAAAAACCAAGTGCACAACAAAATT-TCGATACATTTAT
131 CGATACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAAC-AAATTGTCGATACATTTAT
1303083 AACAAT
195 AACAAT
* *
1303089 TGTCGATCTCAAAAACATCGAAAAACATAATTATAA
1 TGTCGATCCCGAAAACATCGAAAAACATAATTATAA
1303125 CCAAATATCT
Statistics
Matches: 214, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
197 103 0.48
198 7 0.03
199 13 0.06
200 91 0.43
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (200 bp):
TGTCGATCCCGAAAACATCGAAAAACATAATTATAATATAATAGGTAAATTATTAATGTAACCGG
TCTAAATATACCGATTTTTGAGAAAACAGGTGTACAAAAAGAATCGACACAAATAAAAAAAGTGT
CGATACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAATTGTCGATACATTTATA
ACAAT
Found at i:1306109 original size:23 final size:23
Alignment explanation
Indices: 1306053--1306109 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1306043 TTTATGAGAA
*
1306053 AATATGTCAATATAAACGCTATCT
1 AATATGT-TATATAAACGCTATCT
* ** *
1306077 ATTACATTATATAAGCGCTATCT
1 AATATGTTATATAAACGCTATCT
1306100 AATATGTTAT
1 AATATGTTAT
1306110 TGTACTTGAT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (23 bp):
AATATGTTATATAAACGCTATCT
Found at i:1306180 original size:64 final size:64
Alignment explanation
Indices: 1306082--1306228 Score: 233
Period size: 64 Copynumber: 2.3 Consensus size: 64
1306072 TATCTATTAC
* * *
1306082 ATTATATAAGCGCTATCTAATATGTTATTGTACTTGATAATATTT-TCGGTTAAATGCCTATTTT
1 ATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTTCT-GGTTAAATACCTATTTT
* *
1306146 ATTATATAAACGCTACCTAATATTTTATTTTACTTGATAATATTTCTGGTTAAATACCTATTTT
1 ATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTTCTGGTTAAATACCTATTTT
1306210 ATTATATAAACGCTACCTA
1 ATTATATAAACGCTACCTA
1306229 TTGCATTATA
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
64 76 0.99
65 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.46
Consensus pattern (64 bp):
ATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTTCTGGTTAAATACCTATTTT
Found at i:1306226 original size:23 final size:23
Alignment explanation
Indices: 1306200--1306251 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
1306190 TCTGGTTAAA
**
1306200 TACCTATTTTATTATATAAACGC
1 TACCTATTGCATTATATAAACGC
* *
1306223 TACCTATTGCATTATATAAGCGT
1 TACCTATTGCATTATATAAACGC
1306246 TACCTA
1 TACCTA
1306252 ATATGTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (23 bp):
TACCTATTGCATTATATAAACGC
Found at i:1306330 original size:16 final size:16
Alignment explanation
Indices: 1306311--1306355 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
1306301 CGGTCTAAAT
*
1306311 TTTAACCGGTCACTTC
1 TTTAACCAGTCACTTC
1306327 TTTAACCAGTCACTTC
1 TTTAACCAGTCACTTC
*
1306343 TTTAACTAGTCAC
1 TTTAACCAGTCAC
1306356 ACCGTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.24, C:0.29, G:0.09, T:0.38
Consensus pattern (16 bp):
TTTAACCAGTCACTTC
Found at i:1312796 original size:17 final size:17
Alignment explanation
Indices: 1312776--1312813 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1312766 GAAAGTCAAC
*
1312776 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCCGGTCG
1312793 GGTCAACGGTCCGGTCG
1 GGTCAACGGTCCGGTCG
1312810 GGTC
1 GGTC
1312814 GGGTCAGACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.26, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCCGGTCG
Found at i:1312810 original size:22 final size:23
Alignment explanation
Indices: 1312770--1312819 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
1312760 GTCAAAGAAA
1312770 GTCAACGGTCAACGGTCGGGTCGG
1 GTCAACGGTC-ACGGTCGGGTCGG
1312794 GTCAACGGTC-CGGTCGGGTCGG
1 GTCAACGGTCACGGTCGGGTCGG
1312816 GTCA
1 GTCA
1312820 GACCGGTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 16 0.62
24 10 0.38
ACGTcount: A:0.14, C:0.26, G:0.42, T:0.18
Consensus pattern (23 bp):
GTCAACGGTCACGGTCGGGTCGG
Found at i:1323187 original size:303 final size:303
Alignment explanation
Indices: 1322640--1323247 Score: 1216
Period size: 303 Copynumber: 2.0 Consensus size: 303
1322630 TTGCAGTTGG
1322640 ATACATTTTGACTTCTCCAAGACAAGTTGGGATAATTTTGGAAACCTAGGTGTTGGTATTTTCAA
1 ATACATTTTGACTTCTCCAAGACAAGTTGGGATAATTTTGGAAACCTAGGTGTTGGTATTTTCAA
1322705 TCCTATTGTAATTCCTCACAAAGTACATAGCCTATGGGTTTTATGGACATTCCTCAAAATTATGA
66 TCCTATTGTAATTCCTCACAAAGTACATAGCCTATGGGTTTTATGGACATTCCTCAAAATTATGA
1322770 TCATTACCACAATAAACACAAGAAACAATAGATGTAGATTTTACCTTATACACACCTCCAGACTT
131 TCATTACCACAATAAACACAAGAAACAATAGATGTAGATTTTACCTTATACACACCTCCAGACTT
1322835 TTGCATTCTCTTCATCATTTCAGTCAATATTGTAACCTGTGTGGTCAGTGTGTTTAAAGCATCAT
196 TTGCATTCTCTTCATCATTTCAGTCAATATTGTAACCTGTGTGGTCAGTGTGTTTAAAGCATCAT
1322900 TGTCTACTATTACAGCAATGTGTATACCTGACATAATTCTTGT
261 TGTCTACTATTACAGCAATGTGTATACCTGACATAATTCTTGT
1322943 ATACATTTTGACTTCTCCAAGACAAGTTGGGATAATTTTGGAAACCTAGGTGTTGGTATTTTCAA
1 ATACATTTTGACTTCTCCAAGACAAGTTGGGATAATTTTGGAAACCTAGGTGTTGGTATTTTCAA
1323008 TCCTATTGTAATTCCTCACAAAGTACATAGCCTATGGGTTTTATGGACATTCCTCAAAATTATGA
66 TCCTATTGTAATTCCTCACAAAGTACATAGCCTATGGGTTTTATGGACATTCCTCAAAATTATGA
1323073 TCATTACCACAATAAACACAAGAAACAATAGATGTAGATTTTACCTTATACACACCTCCAGACTT
131 TCATTACCACAATAAACACAAGAAACAATAGATGTAGATTTTACCTTATACACACCTCCAGACTT
1323138 TTGCATTCTCTTCATCATTTCAGTCAATATTGTAACCTGTGTGGTCAGTGTGTTTAAAGCATCAT
196 TTGCATTCTCTTCATCATTTCAGTCAATATTGTAACCTGTGTGGTCAGTGTGTTTAAAGCATCAT
1323203 TGTCTACTATTACAGCAATGTGTATACCTGACATAATTCTTGT
261 TGTCTACTATTACAGCAATGTGTATACCTGACATAATTCTTGT
1323246 AT
1 AT
1323248 TAGGGTATTG
Statistics
Matches: 305, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
303 305 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (303 bp):
ATACATTTTGACTTCTCCAAGACAAGTTGGGATAATTTTGGAAACCTAGGTGTTGGTATTTTCAA
TCCTATTGTAATTCCTCACAAAGTACATAGCCTATGGGTTTTATGGACATTCCTCAAAATTATGA
TCATTACCACAATAAACACAAGAAACAATAGATGTAGATTTTACCTTATACACACCTCCAGACTT
TTGCATTCTCTTCATCATTTCAGTCAATATTGTAACCTGTGTGGTCAGTGTGTTTAAAGCATCAT
TGTCTACTATTACAGCAATGTGTATACCTGACATAATTCTTGT
Found at i:1338462 original size:337 final size:336
Alignment explanation
Indices: 1337841--1338519 Score: 1151
Period size: 337 Copynumber: 2.0 Consensus size: 336
1337831 TGAAGAAGTC
* *
1337841 ATCAAATTTGACATATACAAGGATATGAAATACTCGGATAATGTGGTGAGCTTGAATTTTGTTGA
1 ATCAAATTTGACATATACAAGGATATGAAATACTCGGATAATGTAGTGAGCTTGAATTTTATTGA
* * *
1337906 TATTCTCGATCCATTAGCTGACAAATTTTTGGAAAATAATTTTGTATTTGATTTTTATAGGGAGT
66 TATTCTCAATCCATTAGATGACAAATTTTTGGAAAATAATTTTGTATTTGATTTTTATAGAGAGT
1337971 TGGAGAAAGAGGAATTTGATGATAGGGAGTTTGAAGAAATTTCTTCGATAATTTCTTATTATATT
131 TGGAGAAAGAGGAATTTGATGATAGGGAGTTTGAAGAAATTTCTTCGATAATTTCTTATTATATT
* **
1338036 TCTAATTTTTGTTTAATGTTGTTTAAGTTTAAAACTCTTCCATCAATTTTGCAGGCACCTAAGTT
196 TCTAATGTTTGTTTAATGCCGTTTAAGTTTAAAACTCTTCCATCAATTTTGCAGGCACCTAAGTT
* * *
1338101 GGAGTTGAAGTAATTGCCGACGCATTTTAAGTACACATTTCTGGGCGAAAATGATATTTTGCCAA
261 GGAGTTGAAGCAATTGCCGACGCATCTTAAGTACACATTTCTGGGCGAAAATGATACTTTGCCAA
1338166 TCATAATTTCA
326 TCATAATTTCA
* *
1338177 ATCATAATTTGACATATACAAGGCTATGAAATACTCGTATAATGTAGTGAGCTTGAATTTTATTG
1 ATCA-AATTTGACATATACAAGGATATGAAATACTCGGATAATGTAGTGAGCTTGAATTTTATTG
* *
1338242 ATATTGTCAATCCATTAGATGACAAATTTTTGGAAAATAATTTTGTATTTGATTTTTGTAGAGAG
65 ATATTCTCAATCCATTAGATGACAAATTTTTGGAAAATAATTTTGTATTTGATTTTTATAGAGAG
*
1338307 TTGGAGAAAGAGGAATTTGATGATAGGGAGTTTGAAGAAATTTCTTCGATAATTTCTTATTCTAT
130 TTGGAGAAAGAGGAATTTGATGATAGGGAGTTTGAAGAAATTTCTTCGATAATTTCTTATTATAT
* *
1338372 TTCTAATGTTTGTTTAATGCCGTTTAAGTTTAAAACTCTTCCATCAATTTTGTAGGCACCTATGT
195 TTCTAATGTTTGTTTAATGCCGTTTAAGTTTAAAACTCTTCCATCAATTTTGCAGGCACCTAAGT
* **
1338437 TGGAGTTGAAGCAATTGCTGACGCATCTTAAGTACATGTTTCTGGGCGAAAATGATACTTTGCCA
260 TGGAGTTGAAGCAATTGCCGACGCATCTTAAGTACACATTTCTGGGCGAAAATGATACTTTGCCA
1338502 ATCATAATTTCA
325 ATCATAATTTCA
*
1338514 AGCAAA
1 ATCAAA
1338520 CTATCAAAGG
Statistics
Matches: 320, Mismatches: 22, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
336 6 0.02
337 314 0.98
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.39
Consensus pattern (336 bp):
ATCAAATTTGACATATACAAGGATATGAAATACTCGGATAATGTAGTGAGCTTGAATTTTATTGA
TATTCTCAATCCATTAGATGACAAATTTTTGGAAAATAATTTTGTATTTGATTTTTATAGAGAGT
TGGAGAAAGAGGAATTTGATGATAGGGAGTTTGAAGAAATTTCTTCGATAATTTCTTATTATATT
TCTAATGTTTGTTTAATGCCGTTTAAGTTTAAAACTCTTCCATCAATTTTGCAGGCACCTAAGTT
GGAGTTGAAGCAATTGCCGACGCATCTTAAGTACACATTTCTGGGCGAAAATGATACTTTGCCAA
TCATAATTTCA
Found at i:1341561 original size:28 final size:28
Alignment explanation
Indices: 1341521--1341619 Score: 198
Period size: 28 Copynumber: 3.5 Consensus size: 28
1341511 TTGTTTCATT
1341521 AAGTTTGGGTACGGCTCACGTTAGTGGG
1 AAGTTTGGGTACGGCTCACGTTAGTGGG
1341549 AAGTTTGGGTACGGCTCACGTTAGTGGG
1 AAGTTTGGGTACGGCTCACGTTAGTGGG
1341577 AAGTTTGGGTACGGCTCACGTTAGTGGG
1 AAGTTTGGGTACGGCTCACGTTAGTGGG
1341605 AAGTTTGGGTACGGC
1 AAGTTTGGGTACGGC
1341620 CCCACCAAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 71 1.00
ACGTcount: A:0.18, C:0.14, G:0.39, T:0.28
Consensus pattern (28 bp):
AAGTTTGGGTACGGCTCACGTTAGTGGG
Found at i:1341956 original size:16 final size:16
Alignment explanation
Indices: 1341935--1341982 Score: 96
Period size: 16 Copynumber: 3.0 Consensus size: 16
1341925 ATCAATAATG
1341935 GTCAGAACCCAAAATC
1 GTCAGAACCCAAAATC
1341951 GTCAGAACCCAAAATC
1 GTCAGAACCCAAAATC
1341967 GTCAGAACCCAAAATC
1 GTCAGAACCCAAAATC
1341983 AAGGTAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.44, C:0.31, G:0.12, T:0.12
Consensus pattern (16 bp):
GTCAGAACCCAAAATC
Found at i:1343597 original size:176 final size:176
Alignment explanation
Indices: 1343303--1343656 Score: 708
Period size: 176 Copynumber: 2.0 Consensus size: 176
1343293 ATTCGATCCA
1343303 ATAGCCTTTTAATCCTTGGTCCTTACATTACAAATTTAGTGTCTCATGTTGCTAATTTTGATATT
1 ATAGCCTTTTAATCCTTGGTCCTTACATTACAAATTTAGTGTCTCATGTTGCTAATTTTGATATT
1343368 ATGGACTTTACTTGCACGTTCTATATGGATGGATTAGATGAATGTTGCTTGGATCTAATGGGCTT
66 ATGGACTTTACTTGCACGTTCTATATGGATGGATTAGATGAATGTTGCTTGGATCTAATGGGCTT
1343433 GCTTGCAGGAACGGCCATTGCACCGTATTTTGTTCCACTGGGAGTG
131 GCTTGCAGGAACGGCCATTGCACCGTATTTTGTTCCACTGGGAGTG
1343479 ATAGCCTTTTAATCCTTGGTCCTTACATTACAAATTTAGTGTCTCATGTTGCTAATTTTGATATT
1 ATAGCCTTTTAATCCTTGGTCCTTACATTACAAATTTAGTGTCTCATGTTGCTAATTTTGATATT
1343544 ATGGACTTTACTTGCACGTTCTATATGGATGGATTAGATGAATGTTGCTTGGATCTAATGGGCTT
66 ATGGACTTTACTTGCACGTTCTATATGGATGGATTAGATGAATGTTGCTTGGATCTAATGGGCTT
1343609 GCTTGCAGGAACGGCCATTGCACCGTATTTTGTTCCACTGGGAGTG
131 GCTTGCAGGAACGGCCATTGCACCGTATTTTGTTCCACTGGGAGTG
1343655 AT
1 AT
1343657 GATGCCACAT
Statistics
Matches: 178, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
176 178 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (176 bp):
ATAGCCTTTTAATCCTTGGTCCTTACATTACAAATTTAGTGTCTCATGTTGCTAATTTTGATATT
ATGGACTTTACTTGCACGTTCTATATGGATGGATTAGATGAATGTTGCTTGGATCTAATGGGCTT
GCTTGCAGGAACGGCCATTGCACCGTATTTTGTTCCACTGGGAGTG
Found at i:1360898 original size:24 final size:24
Alignment explanation
Indices: 1360871--1360916 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1360861 GCATGACATG
1360871 GTACATAGATGTTTTATACATCGT
1 GTACATAGATGTTTTATACATCGT
1360895 GTACATAGATGTTTTATACATC
1 GTACATAGATGTTTTATACATC
1360917 ATCTGGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCGT
Found at i:1372014 original size:3 final size:3
Alignment explanation
Indices: 1372006--1372076 Score: 65
Period size: 3 Copynumber: 23.7 Consensus size: 3
1371996 TAACTTCTAT
* *
1372006 TTC TTC TTC ATT- TT- TTC TTT TTC TTTC TTC TTC TTC TTC TTC TTT
1 TTC TTC TTC -TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC
* * *
1372051 TTA TTT TTC TTT TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
1372077 TTTTTTTTCT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
2 4 0.07
3 48 0.84
4 5 0.09
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.75
Consensus pattern (3 bp):
TTC
Found at i:1372026 original size:6 final size:6
Alignment explanation
Indices: 1372017--1372101 Score: 84
Period size: 6 Copynumber: 13.8 Consensus size: 6
1372007 TCTTCTTCAT
* * *
1372017 TTTTTC TTTTTC TTTCTTC TTCTTC TTCTTC TTTTTA TTTTTC TTTTTC
1 TTTTTC TTTTTC TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
*
1372066 TTCTTCTTC TTTTT- TTTTTC TTTTT- ATTTTC TTTTT
1 -T-TT-TTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1372102 ATGTGGGGTT
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
5 9 0.13
6 44 0.66
7 8 0.12
8 3 0.04
9 3 0.04
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:1372036 original size:33 final size:32
Alignment explanation
Indices: 1372006--1372090 Score: 120
Period size: 31 Copynumber: 2.7 Consensus size: 32
1371996 TAACTTCTAT
1372006 TTCTTCTTCATTTTTTCTTTTTCTTTCTTCTTC
1 TTCTTCTTC-TTTTTTCTTTTTCTTTCTTCTTC
*
1372039 TTCTTCTTC-TTTTTATTTTTCTTT-TTCTTC
1 TTCTTCTTCTTTTTTCTTTTTCTTTCTTCTTC
*
1372069 TTCTTCTTTTTTTTTTCTTTTT
1 TTCTTC-TTCTTTTTTCTTTTT
1372091 ATTTTCTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
30 12 0.26
31 16 0.34
32 10 0.21
33 9 0.19
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (32 bp):
TTCTTCTTCTTTTTTCTTTTTCTTTCTTCTTC
Found at i:1372059 original size:27 final size:26
Alignment explanation
Indices: 1372005--1372087 Score: 109
Period size: 27 Copynumber: 3.2 Consensus size: 26
1371995 ATAACTTCTA
*
1372005 TTTCTTCTTCATT-TT-TTC-TTTTTC
1 TTTCTTCTTC-TTCTTCTTCTTTTTTT
1372029 TTTCTTCTTCTTCTTCTTCTTTTTATT
1 TTTCTTCTTCTTCTTCTTCTTTTT-TT
*
1372056 TTTCTTTTTCTTCTTCTTCTTTTTTT
1 TTTCTTCTTCTTCTTCTTCTTTTTTT
1372082 TTTCTT
1 TTTCTT
1372088 TTTATTTTCT
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
23 2 0.04
24 12 0.23
25 3 0.06
26 12 0.23
27 24 0.45
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTCTTCTTCTTCTTCTTCTTTTTTT
Found at i:1372102 original size:11 final size:11
Alignment explanation
Indices: 1372072--1372103 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1372062 TTTCTTCTTC
*
1372072 TTCTTTTTTTT
1 TTCTTTTTATT
1372083 TTCTTTTTATT
1 TTCTTTTTATT
1372094 TTCTTTTTAT
1 TTCTTTTTAT
1372104 GTGGGGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.84
Consensus pattern (11 bp):
TTCTTTTTATT
Found at i:1381052 original size:13 final size:13
Alignment explanation
Indices: 1381028--1381117 Score: 108
Period size: 13 Copynumber: 6.9 Consensus size: 13
1381018 TAAATATCAG
*
1381028 ATGACGCGCATTT
1 ATGACGCACATTT
*
1381041 ATGACACACATTT
1 ATGACGCACATTT
*
1381054 ATGACGCTCATTT
1 ATGACGCACATTT
*
1381067 ATGACGCGCATTT
1 ATGACGCACATTT
*
1381080 ATGACGCATATTT
1 ATGACGCACATTT
* *
1381093 GTGATGCACATTT
1 ATGACGCACATTT
*
1381106 ATGACGCTCATT
1 ATGACGCACATT
1381118 GCACGTCATT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 64 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (13 bp):
ATGACGCACATTT
Found at i:1381057 original size:26 final size:26
Alignment explanation
Indices: 1381028--1381117 Score: 119
Period size: 26 Copynumber: 3.5 Consensus size: 26
1381018 TAAATATCAG
* *
1381028 ATGACGCGCATTTATGACACACATTT
1 ATGACGCTCATTTATGACGCACATTT
*
1381054 ATGACGCTCATTTATGACGCGCATTT
1 ATGACGCTCATTTATGACGCACATTT
* *
1381080 ATGACGCAT-ATTTGTGATGCACATTT
1 ATGACGC-TCATTTATGACGCACATTT
1381106 ATGACGCTCATT
1 ATGACGCTCATT
1381118 GCACGTCATT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
25 1 0.02
26 54 0.96
27 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (26 bp):
ATGACGCTCATTTATGACGCACATTT
Found at i:1381082 original size:39 final size:39
Alignment explanation
Indices: 1381028--1381117 Score: 126
Period size: 39 Copynumber: 2.3 Consensus size: 39
1381018 TAAATATCAG
*
1381028 ATGACGCGCATTTATGACACACATTTATGACGCTCATTT
1 ATGACGCGCATTTATGACACACATTTATGACGCACATTT
* * * *
1381067 ATGACGCGCATTTATGACGCATATTTGTGATGCACATTT
1 ATGACGCGCATTTATGACACACATTTATGACGCACATTT
*
1381106 ATGACGCTCATT
1 ATGACGCGCATT
1381118 GCACGTCATT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (39 bp):
ATGACGCGCATTTATGACACACATTTATGACGCACATTT
Found at i:1385231 original size:24 final size:24
Alignment explanation
Indices: 1385199--1385264 Score: 114
Period size: 24 Copynumber: 2.8 Consensus size: 24
1385189 AGATAGGAAT
*
1385199 GTTACCCTCCAAAGAGGAGCCCAA
1 GTTAACCTCCAAAGAGGAGCCCAA
1385223 GTTAACCTCCAAAGAGGAGCCCAA
1 GTTAACCTCCAAAGAGGAGCCCAA
*
1385247 GTTAACCTCCAAGGAGGA
1 GTTAACCTCCAAAGAGGA
1385265 AATCATTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.35, C:0.29, G:0.23, T:0.14
Consensus pattern (24 bp):
GTTAACCTCCAAAGAGGAGCCCAA
Found at i:1385365 original size:29 final size:29
Alignment explanation
Indices: 1385317--1385496 Score: 166
Period size: 29 Copynumber: 6.2 Consensus size: 29
1385307 TAGAAGATAT
* * * *
1385317 CATGCATAATCAAGAAGAGGATACAATCC
1 CATGCAGAATCAGGACGAGGATATAATCC
*
1385346 CATGCAGAATCAGGACGAGGATATAACCC
1 CATGCAGAATCAGGACGAGGATATAATCC
* * * *
1385375 CATACAGAATTAGGGCGTGGATATAATCC
1 CATGCAGAATCAGGACGAGGATATAATCC
* * *
1385404 CATGCAAAATTAGGATGAGGATATAATCC
1 CATGCAGAATCAGGACGAGGATATAATCC
* * * *
1385433 TAGGTAGAATCAGGAC-AGGGATATGATCC
1 CATGCAGAATCAGGACGA-GGATATAATCC
*
1385462 CATGCAGAATCAGGA-TAGGGATATAATCC
1 CATGCAGAATCAGGACGA-GGATATAATCC
*
1385491 AATGCA
1 CATGCA
1385497 TAATAAGGTC
Statistics
Matches: 122, Mismatches: 27, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
28 1 0.01
29 121 0.99
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (29 bp):
CATGCAGAATCAGGACGAGGATATAATCC
Found at i:1386052 original size:6 final size:6
Alignment explanation
Indices: 1386030--1386076 Score: 67
Period size: 6 Copynumber: 7.5 Consensus size: 6
1386020 GGTCTTCAAA
*
1386030 AAAGTC AATACGTC AAAGTC AAAGTC AAAGTC AAAGTC AACGTC AAA
1 AAAGTC AA-A-GTC AAAGTC AAAGTC AAAGTC AAAGTC AAAGTC AAA
1386077 AAAACAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 30 0.81
7 2 0.05
8 5 0.14
ACGTcount: A:0.49, C:0.19, G:0.15, T:0.17
Consensus pattern (6 bp):
AAAGTC
Found at i:1398183 original size:14 final size:13
Alignment explanation
Indices: 1398147--1398183 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
1398137 AAATTTTATC
1398147 AAATTAAATTAAA
1 AAATTAAATTAAA
1398160 AAATTAAAATTAAA
1 AAATT-AAATTAAA
1398174 AAATGTAAAT
1 AAAT-TAAAT
1398184 ACTATTGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.23
14 16 0.73
15 1 0.05
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
AAATTAAATTAAA
Found at i:1398517 original size:2 final size:2
Alignment explanation
Indices: 1398510--1398562 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1398500 TTATTTGATT
*
1398510 TA TA TA TA TA TA TA TA TA TG 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
1398552 TA TA TA TA TA T
1 TA TA TA TA TA T
1398563 TAACGTATCA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1400597 original size:16 final size:16
Alignment explanation
Indices: 1400576--1400624 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
1400566 ACCCGACCTA
*
1400576 TTTTCAACCTGACTTG
1 TTTTCAACCTGACATG
1400592 TTTTCAACCTGACATG
1 TTTTCAACCTGACATG
*
1400608 TTTTTAACCTGACATG
1 TTTTCAACCTGACATG
1400624 T
1 T
1400625 AAATGATCCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.43
Consensus pattern (16 bp):
TTTTCAACCTGACATG
Found at i:1400822 original size:13 final size:13
Alignment explanation
Indices: 1400806--1400832 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1400796 TACCTATTAT
1400806 ATAAAATTATTTA
1 ATAAAATTATTTA
1400819 ATAAAATTATTTA
1 ATAAAATTATTTA
1400832 A
1 A
1400833 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:1401402 original size:19 final size:20
Alignment explanation
Indices: 1401366--1401410 Score: 83
Period size: 19 Copynumber: 2.3 Consensus size: 20
1401356 AATTTTTATA
1401366 TTCCCTCTAAATTTCCCAAT
1 TTCCCTCTAAATTTCCCAAT
1401386 TTCCCTCTAAA-TTCCCAAT
1 TTCCCTCTAAATTTCCCAAT
1401405 TTCCCT
1 TTCCCT
1401411 ATATTCTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.22, C:0.38, G:0.00, T:0.40
Consensus pattern (20 bp):
TTCCCTCTAAATTTCCCAAT
Found at i:1401526 original size:2 final size:2
Alignment explanation
Indices: 1401519--1401548 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1401509 ACTTTGAATA
1401519 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
1401549 TAATTAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1401991 original size:2 final size:2
Alignment explanation
Indices: 1401984--1402010 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1401974 TATGTTTAAT
1401984 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
1402011 TATTCAAAGT
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:1402179 original size:20 final size:19
Alignment explanation
Indices: 1402120--1402182 Score: 99
Period size: 19 Copynumber: 3.2 Consensus size: 19
1402110 TGAGAATATA
1402120 GGAAATTTGGGAATTTAGAG
1 GGAAA-TTGGGAATTTAGAG
*
1402140 CGAAATTGGGAATTTAGAG
1 GGAAATTGGGAATTTAGAG
1402159 GGAAATTGGGAAATTTAGAG
1 GGAAATTGGG-AATTTAGAG
1402179 GGAA
1 GGAA
1402183 TAGAGAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.38, C:0.02, G:0.35, T:0.25
Consensus pattern (19 bp):
GGAAATTGGGAATTTAGAG
Found at i:1402192 original size:19 final size:20
Alignment explanation
Indices: 1402131--1402193 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 20
1402121 GAAATTTGGG
* * *
1402131 AATTTAGAGCGAAATTG-GG
1 AATTTAGAGGGAAATAGAGA
* *
1402150 AATTTAGAGGGAAATTGGGA
1 AATTTAGAGGGAAATAGAGA
1402170 AATTTAGAGGG-AATAGAGA
1 AATTTAGAGGGAAATAGAGA
1402189 AATTT
1 AATTT
1402194 GGGAAGTTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 27 0.69
20 12 0.31
ACGTcount: A:0.41, C:0.02, G:0.30, T:0.27
Consensus pattern (20 bp):
AATTTAGAGGGAAATAGAGA
Found at i:1402426 original size:7 final size:7
Alignment explanation
Indices: 1402416--1402551 Score: 112
Period size: 7 Copynumber: 19.4 Consensus size: 7
1402406 ATATACACCT
1402416 TAAACCC
1 TAAACCC
1402423 TAAACCC
1 TAAACCC
**
1402430 TAAACTT
1 TAAACCC
**
1402437 TAAACAA
1 TAAACCC
1402444 TAAACCC
1 TAAACCC
*
1402451 TAACCCC
1 TAAACCC
*
1402458 TAACCCC
1 TAAACCC
1402465 T-AACCAC
1 TAAACC-C
**
1402472 TAAACTT
1 TAAACCC
*
1402479 TAAATCC
1 TAAACCC
**
1402486 TAAACAA
1 TAAACCC
1402493 TAAACCC
1 TAAACCC
1402500 TAAACCC
1 TAAACCC
* *
1402507 TAAATCA
1 TAAACCC
*
1402514 TAAACTC
1 TAAACCC
1402521 TAAACCC
1 TAAACCC
*
1402528 TAAACAC
1 TAAACCC
*
1402535 TAAACCA
1 TAAACCC
1402542 TAAACCC
1 TAAACCC
1402549 TAA
1 TAA
1402552 TGTATGTATA
Statistics
Matches: 99, Mismatches: 28, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
6 3 0.03
7 93 0.94
8 3 0.03
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:1402490 original size:42 final size:42
Alignment explanation
Indices: 1402416--1402551 Score: 152
Period size: 42 Copynumber: 3.2 Consensus size: 42
1402406 ATATACACCT
* * *
1402416 TAAACCCTAAACC-CTAAACTTTAAACAATAAACCCTAACCCC
1 TAAACCCTAAACCACTAAACTTTAAAC-CTAAACACTAAACCC
* *
1402458 TAACCCCT-AACCACTAAACTTTAAATCCTAAACAATAAACCC
1 TAAACCCTAAACCACTAAACTTTAAA-CCTAAACACTAAACCC
* * *
1402500 TAAACCCTAAATCA-TAAACTCTAAACCCTAAACACTAAACCA
1 TAAACCCTAAACCACTAAACTTTAAA-CCTAAACACTAAACCC
1402542 TAAACCCTAA
1 TAAACCCTAA
1402552 TGTATGTATA
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
41 4 0.05
42 71 0.89
43 5 0.06
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (42 bp):
TAAACCCTAAACCACTAAACTTTAAACCTAAACACTAAACCC
Found at i:1402592 original size:20 final size:20
Alignment explanation
Indices: 1402541--1402592 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
1402531 ACACTAAACC
* *
1402541 ATAAACCCTA-AT-GTATGT
1 ATAAACCATATATAGTATAT
*
1402559 ATAAACCATGTATAGTATAT
1 ATAAACCATATATAGTATAT
*
1402579 ATAAACTATATATA
1 ATAAACCATATATA
1402593 TACCTATATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 8 0.30
19 2 0.07
20 17 0.63
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.35
Consensus pattern (20 bp):
ATAAACCATATATAGTATAT
Found at i:1402601 original size:12 final size:12
Alignment explanation
Indices: 1402574--1402606 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1402564 CCATGTATAG
1402574 TATATATA-AAC
1 TATATATATAAC
*
1402585 TATATATATACC
1 TATATATATAAC
1402597 TATATATATA
1 TATATATATA
1402607 TAAACTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATATAAC
Found at i:1402811 original size:79 final size:79
Alignment explanation
Indices: 1402724--1402873 Score: 192
Period size: 79 Copynumber: 1.9 Consensus size: 79
1402714 TACATATATC
* * *
1402724 TACTATATTAATATAAATTATAACATATAAACTATGTAGTTTATATAGTTTATACATATATAATT
1 TACTATATTAATATAAATAATAACATATAAACTATATACTTTATATAGTTTATACATATATAATT
1402789 TATATATATGTATA
66 TATATATATGTATA
* *** *** * *
1402803 TACTATATTCATATAAATAATATTTTATAGTTTATATACTTTTTATAGTTTATACATATATAGTT
1 TACTATATTAATATAAATAATAACATATAAACTATATACTTTATATAGTTTATACATATATAATT
1402868 TATATA
66 TATATA
1402874 CATAGTTTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
79 59 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (79 bp):
TACTATATTAATATAAATAATAACATATAAACTATATACTTTATATAGTTTATACATATATAATT
TATATATATGTATA
Found at i:1402878 original size:13 final size:13
Alignment explanation
Indices: 1402846--1403078 Score: 102
Period size: 13 Copynumber: 17.3 Consensus size: 13
1402836 ATATACTTTT
1402846 TATAGTTTATACATA
1 TATAGTTTAT--ATA
1402861 TATAGTTTATATA
1 TATAGTTTATATA
*
1402874 CATAGTTTATATA
1 TATAGTTTATATA
* *
1402887 TATAGTTCACATAAA
1 TATAGTT--TATATA
* *
1402902 CATAATTTATATA
1 TATAGTTTATATA
1402915 TATAGCTTATAATAATTA
1 TATAG-TT-T-AT-A-TA
1402933 TATAGTTTATA-A
1 TATAGTTTATATA
* * *
1402945 TATAAATATTGTTTA
1 TAT-AGT-TTATATA
*
1402960 TA-ATTTTATATA
1 TATAGTTTATATA
**
1402972 CGTAGTTTATATA
1 TATAGTTTATATA
* *
1402985 TATAGTTCACATAGA
1 TATAGTT--TATATA
*
1403000 TATAATTTATATA
1 TATAGTTTATATA
1403013 TATAGTTTATA-A
1 TATAGTTTATATA
1403025 TA-A--TTATATA
1 TATAGTTTATATA
* *** *
1403035 GTTTAAAATATAAA
1 -TATAGTTTATATA
1403049 TATAGTTTATATA
1 TATAGTTTATATA
*
1403062 TA-ATTTTATATTA
1 TATAGTTTATA-TA
1403075 TATA
1 TATA
1403079 TATATTATAT
Statistics
Matches: 162, Mismatches: 36, Indels: 41
0.68 0.15 0.17
Matches are distributed among these distances:
9 5 0.03
10 1 0.01
11 2 0.01
12 20 0.12
13 74 0.46
14 12 0.07
15 35 0.22
16 3 0.02
17 3 0.02
18 7 0.04
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:1402904 original size:28 final size:26
Alignment explanation
Indices: 1402847--1402919 Score: 83
Period size: 28 Copynumber: 2.7 Consensus size: 26
1402837 TATACTTTTT
* *
1402847 ATAGTTTATACATATATAGTTTATATAC
1 ATAGTTTAT--ATATATAGTTCATAAAC
1402875 ATAGTTTATATATATAGTTCACATAAAC
1 ATAGTTTATATATATAGTT--CATAAAC
*
1402903 ATAATTTATATATATAG
1 ATAGTTTATATATATAG
1402920 CTTATAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
26 10 0.25
28 30 0.75
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (26 bp):
ATAGTTTATATATATAGTTCATAAAC
Found at i:1402926 original size:26 final size:25
Alignment explanation
Indices: 1402858--1402926 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 25
1402848 TAGTTTATAC
* *
1402858 ATATATAGTTTATATACATAGTTTAT
1 ATATATAG-TTATAAACATAATTTAT
1402884 ATATATAGTTCACATAAACATAATTTAT
1 ATATATAGTT---ATAAACATAATTTAT
1402912 ATATATAGCTTATAA
1 ATATATAG-TTATAA
1402927 TAATTATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
25 2 0.05
26 12 0.32
28 21 0.57
29 2 0.05
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.43
Consensus pattern (25 bp):
ATATATAGTTATAAACATAATTTAT
Found at i:1402953 original size:18 final size:18
Alignment explanation
Indices: 1402909--1403063 Score: 111
Period size: 18 Copynumber: 8.2 Consensus size: 18
1402899 AAACATAATT
*
1402909 TATATATATAGCTTATAA
1 TATATATATAGTTTATAA
1402927 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
* *
1402945 TATAAATATTGTTTATAA
1 TATATATATAGTTTATAA
*
1402963 TTTTATATACGTAGTTTATATA
1 -TATATATA--TAGTTTATA-A
* *
1402985 TATAGTTCACATAG-ATATAA
1 TATA--T-ATATAGTTTATAA
1403005 TTTATATATATAGTTTATAA
1 --TATATATATAGTTTATAA
*
1403025 TA-ATTATATAGTTTAAAA
1 TATA-TATATAGTTTATAA
*
1403043 TATAAATATAGTTTAT-A
1 TATATATATAGTTTATAA
1403060 TATA
1 TATA
1403064 ATTTTATATT
Statistics
Matches: 109, Mismatches: 14, Indels: 29
0.72 0.09 0.19
Matches are distributed among these distances:
17 7 0.06
18 56 0.51
19 13 0.12
20 7 0.06
21 15 0.14
22 8 0.07
23 1 0.01
24 2 0.02
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (18 bp):
TATATATATAGTTTATAA
Found at i:1402994 original size:98 final size:98
Alignment explanation
Indices: 1402866--1403059 Score: 334
Period size: 98 Copynumber: 2.0 Consensus size: 98
1402856 ACATATATAG
1402866 TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAAT
1 TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAAT
* *
1402931 TATATAGTTTATAATATAAATATTGTTTATAAT
66 TATATAGTTTAAAATATAAATATAGTTTATAAT
* * * *
1402964 TTTATATACGTAGTTTATATATATAGTTCACATAGATATAATTTATATATATAGTTTATAATAAT
1 TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAAT
1403029 TATATAGTTTAAAATATAAATATAGTTTATA
66 TATATAGTTTAAAATATAAATATAGTTTATA
1403060 TATAATTTTA
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (98 bp):
TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAAT
TATATAGTTTAAAATATAAATATAGTTTATAAT
Found at i:1405212 original size:39 final size:39
Alignment explanation
Indices: 1405158--1405232 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
1405148 AAGCTAAAGT
* *
1405158 CTCTAGGATTTTTCGGTATCTTCAGGCCAACCAGGAAGA
1 CTCTAAGATTTTTCGGCATCTTCAGGCCAACCAGGAAGA
1405197 CTCTAAGATTTTTCGGCATCTTCAGGCCAACCAGGA
1 CTCTAAGATTTTTCGGCATCTTCAGGCCAACCAGGA
1405233 GGATTTCTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (39 bp):
CTCTAAGATTTTTCGGCATCTTCAGGCCAACCAGGAAGA
Found at i:1406110 original size:25 final size:25
Alignment explanation
Indices: 1406081--1406136 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
1406071 ACTTGTGGTA
*
1406081 GAAAAATAATATTTATTATAATGAC
1 GAAAAATAATATTAATTATAATGAC
*
1406106 GAAAAATAATATTAATTATCATGAC
1 GAAAAATAATATTAATTATAATGAC
*
1406131 AAAAAA
1 GAAAAA
1406137 ATGACACCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (25 bp):
GAAAAATAATATTAATTATAATGAC
Found at i:1406200 original size:38 final size:38
Alignment explanation
Indices: 1406149--1406262 Score: 219
Period size: 38 Copynumber: 3.0 Consensus size: 38
1406139 GACACCAGTA
1406149 ATTAATTATCCATTAATAACCCGAGTAGGTTAGTGGTT
1 ATTAATTATCCATTAATAACCCGAGTAGGTTAGTGGTT
*
1406187 ATTAATTATCCATTAATAACCCGAGTAGGTTGGTGGTT
1 ATTAATTATCCATTAATAACCCGAGTAGGTTAGTGGTT
1406225 ATTAATTATCCATTAATAACCCGAGTAGGTTAGTGGTT
1 ATTAATTATCCATTAATAACCCGAGTAGGTTAGTGGTT
1406263 GGTGGTTGAA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 74 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (38 bp):
ATTAATTATCCATTAATAACCCGAGTAGGTTAGTGGTT
Found at i:1406516 original size:38 final size:38
Alignment explanation
Indices: 1406438--1406524 Score: 122
Period size: 38 Copynumber: 2.3 Consensus size: 38
1406428 ATAGATTGGT
**
1406438 GGTTGGTGGTTAATAATTATCCATTAATAACTTGGATA
1 GGTTGGTGGTTAATAATTATCCATTAATAACCAGGATA
* *
1406476 GGTTGGTGGTTATTAATTATCCATTAATATCCCAGG-TA
1 GGTTGGTGGTTAATAATTATCCATTAATA-ACCAGGATA
1406514 GGTTGGTGGTT
1 GGTTGGTGGTT
1406525 GCACGAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 41 0.93
39 3 0.07
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.40
Consensus pattern (38 bp):
GGTTGGTGGTTAATAATTATCCATTAATAACCAGGATA
Found at i:1410353 original size:27 final size:27
Alignment explanation
Indices: 1410316--1410478 Score: 110
Period size: 27 Copynumber: 5.7 Consensus size: 27
1410306 CATATGATGG
* *
1410316 ATAATACCAATATTTGAATGAATGTGA
1 ATAATATCAATAGTTGAATGAATGTGA
* *
1410343 ATAATATCAATAGTTGAATTAATGCGA
1 ATAATATCAATAGTTGAATGAATGTGA
* * * *
1410370 TTAATAACAATAATTGAATTAATATGATGA
1 ATAATATCAATAGTTGAA-TGA-ATG-TGA
* * * * *
1410400 ATATTTGTTGACGATATATTTTAATGAATATGA
1 ATA-AT-AT--C-A-ATAGTTGAATGAATGTGA
* *
1410433 TTAATATCAATAGTTGAATGAACGTGA
1 ATAATATCAATAGTTGAATGAATGTGA
1410460 ATAATATCAATAGTTGAAT
1 ATAATATCAATAGTTGAAT
1410479 TAATATGATG
Statistics
Matches: 102, Mismatches: 25, Indels: 18
0.70 0.17 0.12
Matches are distributed among these distances:
27 70 0.69
28 3 0.03
29 4 0.04
30 4 0.04
31 2 0.02
32 1 0.01
33 5 0.05
34 3 0.03
35 3 0.03
36 7 0.07
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.37
Consensus pattern (27 bp):
ATAATATCAATAGTTGAATGAATGTGA
Found at i:1410465 original size:90 final size:90
Alignment explanation
Indices: 1410325--1410488 Score: 247
Period size: 90 Copynumber: 1.8 Consensus size: 90
1410315 GATAATACCA
* * * *
1410325 ATATTTGAATGAATGTGAATAATATCAATAGTTGAATTAATGCGATTAATAACAATAATTGAATT
1 ATATTTGAATGAATATGAATAATATCAATAGTTGAATGAACGCGAATAATAACAATAATTGAATT
1410390 AATATGATGAATATTTGTTGACGAT
66 AATATGATGAATATTTGTTGACGAT
* * * * *
1410415 ATATTTTAATGAATATGATTAATATCAATAGTTGAATGAACGTGAATAATATCAATAGTTGAATT
1 ATATTTGAATGAATATGAATAATATCAATAGTTGAATGAACGCGAATAATAACAATAATTGAATT
1410480 AATATGATG
66 AATATGATG
1410489 GATGTTAATA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 65 1.00
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (90 bp):
ATATTTGAATGAATATGAATAATATCAATAGTTGAATGAACGCGAATAATAACAATAATTGAATT
AATATGATGAATATTTGTTGACGAT
Found at i:1418125 original size:22 final size:21
Alignment explanation
Indices: 1418088--1418170 Score: 94
Period size: 21 Copynumber: 3.9 Consensus size: 21
1418078 TTGGTGCAGA
* *
1418088 GGGAATCGATACCCCCATTGAAG
1 GGGAACCGATTCCCCC--TGAAG
*
1418111 GGGAACCGATTCCCCCTGTAG
1 GGGAACCGATTCCCCCTGAAG
*
1418132 GGGAACCGATTCCCCCTGTAG
1 GGGAACCGATTCCCCCTGAAG
* *
1418153 GGGAATCGATACCCCCTG
1 GGGAACCGATTCCCCCTG
1418171 GAGGTTCTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
21 41 0.75
23 14 0.25
ACGTcount: A:0.23, C:0.31, G:0.28, T:0.18
Consensus pattern (21 bp):
GGGAACCGATTCCCCCTGAAG
Found at i:1418135 original size:21 final size:21
Alignment explanation
Indices: 1418109--1418170 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
1418099 CCCCCATTGA
1418109 AGGGGAACCGATTCCCCCTGT
1 AGGGGAACCGATTCCCCCTGT
1418130 AGGGGAACCGATTCCCCCTGT
1 AGGGGAACCGATTCCCCCTGT
* *
1418151 AGGGGAATCGATACCCCCTG
1 AGGGGAACCGATTCCCCCTG
1418171 GAGGTTCTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.21, C:0.32, G:0.29, T:0.18
Consensus pattern (21 bp):
AGGGGAACCGATTCCCCCTGT
Found at i:1422527 original size:24 final size:24
Alignment explanation
Indices: 1422499--1422546 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1422489 TTACAACTGG
*
1422499 AAATCTTCAAGAAAAAATATCAAC
1 AAATCTTCAAGAAAAAAGATCAAC
*
1422523 AAATCTTCAAGAAACAAGATCAAC
1 AAATCTTCAAGAAAAAAGATCAAC
1422547 CCATCCAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.56, C:0.19, G:0.06, T:0.19
Consensus pattern (24 bp):
AAATCTTCAAGAAAAAAGATCAAC
Found at i:1429131 original size:12 final size:12
Alignment explanation
Indices: 1429114--1429145 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1429104 CCCCAGAACC
1429114 GTACACCCACCT
1 GTACACCCACCT
1429126 GTACACCCACCT
1 GTACACCCACCT
1429138 GTACACCC
1 GTACACCC
1429146 GGTAAGGGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.25, C:0.50, G:0.09, T:0.16
Consensus pattern (12 bp):
GTACACCCACCT
Found at i:1430007 original size:14 final size:14
Alignment explanation
Indices: 1429988--1430027 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1429978 TTTGTCGAAC
1429988 TCAACGGTCAAAGA
1 TCAACGGTCAAAGA
*
1430002 TCAACGGTCAACGA
1 TCAACGGTCAAAGA
*
1430016 TCAGCGGTCAAA
1 TCAACGGTCAAA
1430028 CTGGGTCAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.15
Consensus pattern (14 bp):
TCAACGGTCAAAGA
Found at i:1433490 original size:45 final size:46
Alignment explanation
Indices: 1433405--1433492 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
1433395 AAATAGCATG
* * *
1433405 AGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTA
1 AGTGCAACGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
1433451 AGTGCAACGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCAACGATGCATGGTCATGTGCATCGATGCATAAAATGCA
1433493 TTCGATGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 22 0.56
46 17 0.44
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (46 bp):
AGTGCAACGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
Found at i:1433520 original size:45 final size:45
Alignment explanation
Indices: 1433471--1433574 Score: 208
Period size: 45 Copynumber: 2.3 Consensus size: 45
1433461 TGCATGGTAT
1433471 GTGCATCGATGCATAAAATGCATTCGATGTTCAATTAATTCCATG
1 GTGCATCGATGCATAAAATGCATTCGATGTTCAATTAATTCCATG
1433516 GTGCATCGATGCATAAAATGCATTCGATGTTCAATTAATTCCATG
1 GTGCATCGATGCATAAAATGCATTCGATGTTCAATTAATTCCATG
1433561 GTGCATCGATGCAT
1 GTGCATCGATGCAT
1433575 GGATTGGTGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (45 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTCAATTAATTCCATG
Found at i:1436290 original size:146 final size:146
Alignment explanation
Indices: 1436126--1436417 Score: 584
Period size: 146 Copynumber: 2.0 Consensus size: 146
1436116 GAAAGGAGAT
1436126 TTTTAGAGAGAGAGAGATGAACGGTGGGTGTATGTTTAGTTTTAGGGTTTTGAAAATAAAGAAAA
1 TTTTAGAGAGAGAGAGATGAACGGTGGGTGTATGTTTAGTTTTAGGGTTTTGAAAATAAAGAAAA
1436191 AAGAGGCATATAAACCCACAAACCCGACGGATGCATCGATGCATGACCCTGTGCATCGATGCACA
66 AAGAGGCATATAAACCCACAAACCCGACGGATGCATCGATGCATGACCCTGTGCATCGATGCACA
1436256 TTCAAGGCGTGCATCG
131 TTCAAGGCGTGCATCG
1436272 TTTTAGAGAGAGAGAGATGAACGGTGGGTGTATGTTTAGTTTTAGGGTTTTGAAAATAAAGAAAA
1 TTTTAGAGAGAGAGAGATGAACGGTGGGTGTATGTTTAGTTTTAGGGTTTTGAAAATAAAGAAAA
1436337 AAGAGGCATATAAACCCACAAACCCGACGGATGCATCGATGCATGACCCTGTGCATCGATGCACA
66 AAGAGGCATATAAACCCACAAACCCGACGGATGCATCGATGCATGACCCTGTGCATCGATGCACA
1436402 TTCAAGGCGTGCATCG
131 TTCAAGGCGTGCATCG
1436418 ATGCATCAAC
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
146 146 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (146 bp):
TTTTAGAGAGAGAGAGATGAACGGTGGGTGTATGTTTAGTTTTAGGGTTTTGAAAATAAAGAAAA
AAGAGGCATATAAACCCACAAACCCGACGGATGCATCGATGCATGACCCTGTGCATCGATGCACA
TTCAAGGCGTGCATCG
Found at i:1451340 original size:35 final size:35
Alignment explanation
Indices: 1451301--1451369 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
1451291 TCTTAGATCC
**
1451301 ATAAGGAATTATTAGTTTGATCG-GTCTGAACCTAT
1 ATAAGGAATTACCAGTTTGATCGAG-CTGAACCTAT
1451336 ATAAGGAATTACCAGTTTGATCGAGCTGAACCTA
1 ATAAGGAATTACCAGTTTGATCGAGCTGAACCTA
1451370 CAGACACTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 30 0.97
36 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.32
Consensus pattern (35 bp):
ATAAGGAATTACCAGTTTGATCGAGCTGAACCTAT
Found at i:1456985 original size:17 final size:17
Alignment explanation
Indices: 1456965--1456998 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1456955 CCTACATGCC
1456965 CCCTAATTACACATGTG
1 CCCTAATTACACATGTG
1456982 CCCTAATTACACATGTG
1 CCCTAATTACACATGTG
1456999 TTGTACTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (17 bp):
CCCTAATTACACATGTG
Found at i:1460734 original size:20 final size:21
Alignment explanation
Indices: 1460709--1460748 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
1460699 GTTGTGGTCG
1460709 TTTCTAGCCA-TTGGGGATGA
1 TTTCTAGCCATTTGGGGATGA
1460729 TTTCTAGCCATTTGGGGATG
1 TTTCTAGCCATTTGGGGATG
1460749 TTTTATCTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.38
Consensus pattern (21 bp):
TTTCTAGCCATTTGGGGATGA
Found at i:1465898 original size:2 final size:2
Alignment explanation
Indices: 1465891--1465924 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1465881 TTAGTTATTA
1465891 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
1465925 TAAATGTGTG
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):
AT
Found at i:1476415 original size:29 final size:29
Alignment explanation
Indices: 1476376--1476535 Score: 202
Period size: 29 Copynumber: 5.6 Consensus size: 29
1476366 CACGTTTAAA
*
1476376 AATTACAAAAATATCACCTTTTTAAAAAT
1 AATTACCAAAATATCACCTTTTTAAAAAT
*
1476405 AATTACCAAAATATCA-ATGTTTTAAAAAT
1 AATTACCAAAATATCACCT-TTTTAAAAAT
*
1476434 AATTACCAGAATATCA-CTGTTTT-AAAAT
1 AATTACCAAAATATCACCT-TTTTAAAAAT
*
1476462 AATTACCAAAATATCACCGTTTTAAAAAT
1 AATTACCAAAATATCACCTTTTTAAAAAT
* * *
1476491 AATTACCAGAATATCACCGTTTTAAAAAC
1 AATTACCAAAATATCACCTTTTTAAAAAT
1476520 AATT-CTCAAAATATCA
1 AATTAC-CAAAATATCA
1476536 TCGGGCCGGG
Statistics
Matches: 118, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
28 26 0.22
29 92 0.78
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.33
Consensus pattern (29 bp):
AATTACCAAAATATCACCTTTTTAAAAAT
Found at i:1476484 original size:57 final size:58
Alignment explanation
Indices: 1476376--1476535 Score: 227
Period size: 57 Copynumber: 2.8 Consensus size: 58
1476366 CACGTTTAAA
* * *
1476376 AATTACAAAAATATCACCT-TTTTAAAAATAATTACCAAAATATCAATGTTTTAAAAAT
1 AATTACCAGAATATCA-CTGTTTTAAAAATAATTACCAAAATATCAACGTTTTAAAAAT
*
1476434 AATTACCAGAATATCACTGTTTT-AAAATAATTACCAAAATATCACCGTTTTAAAAAT
1 AATTACCAGAATATCACTGTTTTAAAAATAATTACCAAAATATCAACGTTTTAAAAAT
* *
1476491 AATTACCAGAATATCACCGTTTTAAAAACAATT-CTCAAAATATCA
1 AATTACCAGAATATCACTGTTTTAAAAATAATTAC-CAAAATATCA
1476536 TCGGGCCGGG
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
57 57 0.61
58 36 0.39
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.33
Consensus pattern (58 bp):
AATTACCAGAATATCACTGTTTTAAAAATAATTACCAAAATATCAACGTTTTAAAAAT
Found at i:1476533 original size:86 final size:86
Alignment explanation
Indices: 1476376--1476535 Score: 241
Period size: 86 Copynumber: 1.9 Consensus size: 86
1476366 CACGTTTAAA
* * *
1476376 AATTACAAAAATATCACCTTTTTAAAAATAATTACCAAAATATCAATGTTTTAAAAATAATTACC
1 AATTACAAAAATATCACCGTTTTAAAAATAATTACCAAAATATCAACGTTTTAAAAACAATTACC
*
1476441 AGAATATCACTGTTTTAAAAT
66 AAAATATCACTGTTTTAAAAT
* * *
1476462 AATTACCAAAATATCACCGTTTTAAAAATAATTACCAGAATATCACCGTTTTAAAAACAATT-CT
1 AATTACAAAAATATCACCGTTTTAAAAATAATTACCAAAATATCAACGTTTTAAAAACAATTAC-
1476526 CAAAATATCA
65 CAAAATATCA
1476536 TCGGGCCGGG
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
85 1 0.02
86 65 0.98
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.33
Consensus pattern (86 bp):
AATTACAAAAATATCACCGTTTTAAAAATAATTACCAAAATATCAACGTTTTAAAAACAATTACC
AAAATATCACTGTTTTAAAAT
Found at i:1482806 original size:29 final size:29
Alignment explanation
Indices: 1482766--1482956 Score: 260
Period size: 29 Copynumber: 6.7 Consensus size: 29
1482756 TACATTCAAA
* * *
1482766 AATTACAAAAATATCACCTTTTTAGAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
* *
1482795 AATTACCTAAATATCACTGTTTTAAAAA-
1 AATTACCAAAATATCACCGTTTTAAAAAT
*** **
1482823 AA-TACTGGAATATCATTGTTTTAAAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
1482851 AATTACCAAAATATCACCGTTTTAAAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
1482880 AATTACCAAAATATCACCGTTTTAAAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
*
1482909 AATTATCAAAATATCACCGTTTTAAAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
*
1482938 AATTCCCAAAATATCACCG
1 AATTACCAAAATATCACCG
1482957 GCCGGGTCGG
Statistics
Matches: 143, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
27 21 0.15
28 4 0.03
29 118 0.83
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.33
Consensus pattern (29 bp):
AATTACCAAAATATCACCGTTTTAAAAAT
Found at i:1484087 original size:29 final size:29
Alignment explanation
Indices: 1484048--1484239 Score: 253
Period size: 29 Copynumber: 6.7 Consensus size: 29
1484038 TACATTCGAA
* * *
1484048 AATTACAAAAATATCTCCTTTTTAAAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
* *
1484077 AATTATCAAAATATCACTGTTTTAAAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
** *
1484106 AATTACCGGAATATCACAGTTTTAAAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
* *
1484135 AATTACTAAAATATCACCGTTTAAAAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
1484164 AATTACCAAAATATCACC-TATTT-AAAAT
1 AATTACCAAAATATCACCGT-TTTAAAAAT
*
1484192 AATTACCAAAATATCAGCGTTTTAAAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
*
1484221 AATTCCCAAAATATCACCG
1 AATTACCAAAATATCACCG
1484240 GGCCGGGTCG
Statistics
Matches: 141, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
28 26 0.18
29 115 0.82
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (29 bp):
AATTACCAAAATATCACCGTTTTAAAAAT
Found at i:1485336 original size:29 final size:29
Alignment explanation
Indices: 1485297--1485486 Score: 249
Period size: 29 Copynumber: 6.6 Consensus size: 29
1485287 TATATTCGAA
*
1485297 AATTACAAAAATATCACCTTTTTAAAAAT
1 AATTACCAAAATATCACCTTTTTAAAAAT
* *
1485326 AATTATCAAAATATCA-ATGTTTTAAAAAT
1 AATTACCAAAATATCACCT-TTTTAAAAAT
**
1485355 AATTACCGGAATATCA-CTGTTTTAAAAAT
1 AATTACCAAAATATCACCT-TTTTAAAAAT
* *
1485384 AATTACCAAAATATCACCGTTTAAAAAAT
1 AATTACCAAAATATCACCTTTTTAAAAAT
* *
1485413 AATTACCAAAATATCACCGTTTTAATAAT
1 AATTACCAAAATATCACCTTTTTAAAAAT
*
1485442 AATTACCAAAATATCACCATTTTAAAAAT
1 AATTACCAAAATATCACCTTTTTAAAAAT
*
1485471 AATTCCCAAAATATCA
1 AATTACCAAAATATCA
1485487 GCGGGTAAGG
Statistics
Matches: 143, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
28 1 0.01
29 141 0.99
30 1 0.01
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (29 bp):
AATTACCAAAATATCACCTTTTTAAAAAT
Found at i:1489529 original size:21 final size:22
Alignment explanation
Indices: 1489505--1489547 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1489495 CTCATGACAG
*
1489505 GAGTATCGATAC-TCCATTAAT
1 GAGTATCAATACTTCCATTAAT
*
1489526 GAGTATCAATACTTCCTTTAAT
1 GAGTATCAATACTTCCATTAAT
1489548 ATATTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (22 bp):
GAGTATCAATACTTCCATTAAT
Found at i:1491875 original size:12 final size:11
Alignment explanation
Indices: 1491860--1491919 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 11
1491850 ACCTAAAACA
1491860 AAATGAAAAAAT
1 AAAT-AAAAAAT
1491872 AAATAAATAAAT
1 AAATAAA-AAAT
**
1491884 AAATAAAATGT
1 AAATAAAAAAT
1491895 AAATAAAAACCAT
1 AAATAAAAA--AT
1491908 ATAATAAAAAAT
1 A-AATAAAAAAT
1491920 GTGTTCTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 13 0.32
12 17 0.43
13 2 0.05
14 8 0.20
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:1491991 original size:37 final size:37
Alignment explanation
Indices: 1491950--1492291 Score: 372
Period size: 38 Copynumber: 9.1 Consensus size: 37
1491940 AAAAAAACTA
* *
1491950 TATATAAATTTTCGAAAATGTTTTTC-AAACTATATAT
1 TATATATATTTTCAAAAATG-TTTTCAAAACTATATAT
* *
1491987 TATATATATTTTAAAAAAAGTTTT--AAACTATGA-AT
1 TATATATATTTTCAAAAATGTTTTCAAAACTAT-ATAT
**
1492022 TATATATATTTTCGAAAAATG-TTTCAAATTTATATAT
1 TATATATATTTTC-AAAAATGTTTTCAAAACTATATAT
* *
1492059 TATATATATTTTTTCAAAAA-ATATTCAAAACTATATAT
1 TATATATA--TTTTCAAAAATGTTTTCAAAACTATATAT
*
1492097 TATATATATTTTCAAAAATGTTTTCAAAAGTATATAT
1 TATATATATTTTCAAAAATGTTTTCAAAACTATATAT
*
1492134 TATATATATTTTCAAAACAATGTTCTCAAAACTATATAT
1 TATATATATTTTC-AAA-AATGTTTTCAAAACTATATAT
*
1492173 TATATATATTTTCAAAAAATGTTTTCAGAACTATATAT
1 TATATATATTTTC-AAAAATGTTTTCAAAACTATATAT
* ** *
1492211 TATATATATTTTAAAAAAAAATTCTCAAAACTATATAT
1 TATATATATTTT-CAAAAATGTTTTCAAAACTATATAT
* * *
1492249 TATATATATTTTTGAAAAAAATGCTTTCAACACTATATAT
1 TATATATA-TTTT--CAAAAATGTTTTCAAAACTATATAT
1492289 TAT
1 TAT
1492292 GTACACTATA
Statistics
Matches: 262, Mismatches: 29, Indels: 25
0.83 0.09 0.08
Matches are distributed among these distances:
35 24 0.09
36 22 0.08
37 59 0.23
38 88 0.34
39 45 0.17
40 24 0.09
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (37 bp):
TATATATATTTTCAAAAATGTTTTCAAAACTATATAT
Found at i:1504306 original size:2 final size:2
Alignment explanation
Indices: 1504299--1504349 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1504289 AATAATTCTA
1504299 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
1504341 AT AT AT AT A
1 AT AT AT AT A
1504350 ACGAAAATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1505478 original size:18 final size:18
Alignment explanation
Indices: 1505444--1505489 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1505434 TTGGACATAA
*
1505444 AAAAAGAAA-AAAGAAAT
1 AAAAATAAATAAAGAAAT
*
1505461 AAAAATAAATAAATAAAT
1 AAAAATAAATAAAGAAAT
1505479 AAAATATAAAT
1 AAAA-ATAAAT
1505490 GTAAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.32
18 11 0.44
19 6 0.24
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.17
Consensus pattern (18 bp):
AAAAATAAATAAAGAAAT
Found at i:1505572 original size:39 final size:38
Alignment explanation
Indices: 1505529--1505603 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 38
1505519 GTTATAAAAA
1505529 AAATTTAAAACTATATATAGTTTTTC-AAAAATGTTTTTG
1 AAATTTAAAACTATATATA--TTTTCAAAAAATGTTTTTG
* * *
1505568 AAATTTTATATTATATATATTTTCAAAAAATGTTTT
1 AAATTTAAAACTATATATATTTTCAAAAAATGTTTT
1505604 AAAACTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 5 0.16
38 11 0.34
39 16 0.50
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.49
Consensus pattern (38 bp):
AAATTTAAAACTATATATATTTTCAAAAAATGTTTTTG
Found at i:1505592 original size:37 final size:35
Alignment explanation
Indices: 1505540--1505630 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 35
1505530 AATTTAAAAC
* * *
1505540 TATATATAGT-TTTTCAAAAATGTTTTTGAAATTTTA
1 TATATATA-TATTTTCAAAAATG-TTTTAAAACTATA
1505576 TATTATATATATTTTCAAAAAATGTTTTAAAACTATA
1 TA-TATATATATTTTC-AAAAATGTTTTAAAACTATA
1505613 TAT-TATATATTTTCAAAA
1 TATATATATATTTTCAAAA
1505631 TTATATATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
34 4 0.08
35 11 0.22
36 4 0.08
37 23 0.47
38 7 0.14
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (35 bp):
TATATATATATTTTCAAAAATGTTTTAAAACTATA
Found at i:1505620 original size:35 final size:36
Alignment explanation
Indices: 1505532--1505630 Score: 109
Period size: 35 Copynumber: 2.8 Consensus size: 36
1505522 ATAAAAAAAA
*
1505532 TTTAAAACTATATA-TA-GT-TTTTC-AAAAATGTT
1 TTTAAAACTATATATTATATATTTTCAAAAAATGTT
* * *
1505564 TTTGAAATTTTATATTATATATATTTTCAAAAAATG-T
1 TTTAAAACTATATA-T-TATATATTTTCAAAAAATGTT
1505601 TTTAAAACTATATATTATATATTTTCAAAA
1 TTTAAAACTATATATTATATATTTTCAAAA
1505631 TTATATATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
32 11 0.20
35 17 0.31
36 2 0.04
37 17 0.31
38 7 0.13
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.48
Consensus pattern (36 bp):
TTTAAAACTATATATTATATATTTTCAAAAAATGTT
Found at i:1505650 original size:25 final size:22
Alignment explanation
Indices: 1505600--1505645 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
1505590 TCAAAAAATG
1505600 TTTTAAAACTATATATTATATA
1 TTTTAAAACTATATATTATATA
*
1505622 TTTTCAAAATTATATATTATATA
1 TTTT-AAAACTATATATTATATA
1505645 T
1 T
1505646 ATTTTTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTAAAACTATATATTATATA
Found at i:1519794 original size:3 final size:3
Alignment explanation
Indices: 1519786--1519811 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1519776 GAATAGGGTT
1519786 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
1519812 ATGCATGATG
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:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:1524246 original size:22 final size:20
Alignment explanation
Indices: 1524209--1524248 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
1524199 GGAATCCAAC
*
1524209 AATTTAGGTTTGTAGATGTT
1 AATTTAGGTTTCTAGATGTT
1524229 AATTTGAGCGTTTCTAGATG
1 AATTT-AG-GTTTCTAGATG
1524249 AGTTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.45
Consensus pattern (20 bp):
AATTTAGGTTTCTAGATGTT
Found at i:1524946 original size:81 final size:81
Alignment explanation
Indices: 1524861--1525270 Score: 560
Period size: 81 Copynumber: 5.1 Consensus size: 81
1524851 GCCTTTATTA
* * * * *
1524861 TTTTACCCAATGGCATTTAGCCTTTCATCTAACTGACATAATTGACACATTTCTATCAAATGCAC
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACATTTCTGTCAAATGCAC
1524926 AGCTAGGCCATTAATC
66 AGCTAGGCCATTAATC
1524942 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGA-ATAATTGACACATTTCTGTCAAATGCA
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACT-GACATAATTGACACATTTCTGTCAAATGCA
* *
1525006 AAGCTAGGACATTAATC
65 CAGCTAGGCCATTAATC
* * * *
1525023 ATTTACTCAAAGGTATTTAACCTTTCATCTGACTAGA-ATAATTGAAACCTTTCTGTCAAATGCA
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACT-GACATAATTGACACATTTCTGTCAAATGCA
* *
1525087 CGGCTAAGCCATTAATC
65 CAGCTAGGCCATTAATC
* * *
1525104 TATTACTCAATGGTATTTAACCTTTCATCTAACT-AGCATAATTGACACTTTTCTGTCAAATGCA
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGA-CATAATTGACACATTTCTGTCAAATGCA
1525168 CAAG-TAGGCCATTAATC
65 C-AGCTAGGCCATTAATC
* * *
1525185 TTTTACTCAAAGGTATTTAACCTTTCATCTAAAT-AGCATAATTAACACATTTCTGTCAAATACA
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGA-CATAATTGACACATTTCTGTCAAATGCA
*
1525249 CAGCTAGACCATTAATC
65 CAGCTAGGCCATTAATC
1525266 TTTTA
1 TTTTA
1525271 TTTAGAACAG
Statistics
Matches: 294, Mismatches: 30, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
79 1 0.00
80 2 0.01
81 288 0.98
82 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.35
Consensus pattern (81 bp):
TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACATTTCTGTCAAATGCAC
AGCTAGGCCATTAATC
Found at i:1529110 original size:82 final size:82
Alignment explanation
Indices: 1528860--1529154 Score: 459
Period size: 82 Copynumber: 3.6 Consensus size: 82
1528850 TCTAACTCTT
* * * *
1528860 ATTAATGGAACCTTTCTGCCAAAATGCACAGTTAGACA-TTAGTCTTTTATCCTAAAGGCATTTA
1 ATTATTGGCACCTTTCTACC-AAATGCACAGTTAGGCATTTAGTCTTTTATCCTAAAGGCATTTA
1528924 ACCTTTCTTCTAACTTGC
65 ACCTTTCTTCTAACTTGC
* * * * *
1528942 ATTATTGGTATCTTTCTACCAAATGCACAGTTAGGCAATT-GTCTTTTATTCTAAAGGCATATAA
1 ATTATTGGCACCTTTCTACCAAATGCACAGTTAGGCATTTAGTCTTTTATCCTAAAGGCATTTAA
1529006 CCTTTCTTCTAACTTGC
66 CCTTTCTTCTAACTTGC
* *
1529023 ATTATTGCCACCTTTCTGCCAAATGCACAGTTAGGCATTTAGTCTTTTATCCTAAAGGCATTTAA
1 ATTATTGGCACCTTTCTACCAAATGCACAGTTAGGCATTTAGTCTTTTATCCTAAAGGCATTTAA
1529088 CCTTTCTTCTAACTTGC
66 CCTTTCTTCTAACTTGC
*
1529105 ATTATTGGCACCTTTCTACCAAATGCAAAGTTAGGCATTTAGTCTTTTAT
1 ATTATTGGCACCTTTCTACCAAATGCACAGTTAGGCATTTAGTCTTTTAT
1529155 TTTAGAACAA
Statistics
Matches: 194, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
81 90 0.46
82 104 0.54
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (82 bp):
ATTATTGGCACCTTTCTACCAAATGCACAGTTAGGCATTTAGTCTTTTATCCTAAAGGCATTTAA
CCTTTCTTCTAACTTGC
Found at i:1529451 original size:54 final size:54
Alignment explanation
Indices: 1529291--1529849 Score: 563
Period size: 54 Copynumber: 10.4 Consensus size: 54
1529281 TTTATTAAGA
* * * * * *
1529291 TGCACACCTAGTGCCTATACGATCGTTCAT-ACACATATGATGAATTCCGTGAGT
1 TGCACACATAGTGCTTGTACGGTTGTTCATCA-ACTTATGATGAATTCCGTGAGT
* *** * * *
1529345 TGCAGACATAGTGCCTTGTATATTTGTTAATCAACATATGATAAATTCCGTGAGT
1 TGCACACATAGTG-CTTGTACGGTTGTTCATCAACTTATGATGAATTCCGTGAGT
* * * * *
1529400 TTCACACATAATGCTTGTACGGTTGTTAATTAACTTATGATGAATTTCGTGAGT
1 TGCACACATAGTGCTTGTACGGTTGTTCATCAACTTATGATGAATTCCGTGAGT
* * * * * * *
1529454 TGCACACATA-TATCCTATACAGTTGTTCATCAGCTTATGATGAATT-TGTGGGT
1 TGCACACATAGT-GCTTGTACGGTTGTTCATCAACTTATGATGAATTCCGTGAGT
* * * * * *
1529507 TGCACACATAGTGCATGTATGGTTGTTTATCAACTTATGATTAATTTCATGAGT
1 TGCACACATAGTGCTTGTACGGTTGTTCATCAACTTATGATGAATTCCGTGAGT
* **
1529561 TGCACACATAGTGCCTGTATAGTTGTTCATCAACTTATGATGAATTCCGTGAGT
1 TGCACACATAGTGCTTGTACGGTTGTTCATCAACTTATGATGAATTCCGTGAGT
* * *
1529615 TGCACACATAGTG-TCTGTACGGTTATTCATAAACTTATGATGAATTCCGTGGGT
1 TGCACACATAGTGCT-TGTACGGTTGTTCATCAACTTATGATGAATTCCGTGAGT
* *** * *
1529669 TACATGTATAGTGCTTGTACGATTGTTCATCAACTTATGATGAATTCCATGAGT
1 TGCACACATAGTGCTTGTACGGTTGTTCATCAACTTATGATGAATTCCGTGAGT
* *
1529723 TGCACACATAGTG-TCTGTACGGTTGTTCATCAA-TATATGATGAATTACGTGGGT
1 TGCACACATAGTGCT-TGTACGGTTGTTCATCAACT-TATGATGAATTCCGTGAGT
* * * * *
1529777 TGCACACATACTGCATATACGGTTGTTCATCAACTTATTATGAATTACGTGAGT
1 TGCACACATAGTGCTTGTACGGTTGTTCATCAACTTATGATGAATTCCGTGAGT
*
1529831 TGCACACATAGTGCCTGTA
1 TGCACACATAGTGCTTGTA
1529850 GTACAGATAG
Statistics
Matches: 416, Mismatches: 78, Indels: 22
0.81 0.15 0.04
Matches are distributed among these distances:
53 44 0.11
54 328 0.79
55 43 0.10
56 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (54 bp):
TGCACACATAGTGCTTGTACGGTTGTTCATCAACTTATGATGAATTCCGTGAGT
Found at i:1530306 original size:19 final size:20
Alignment explanation
Indices: 1530263--1530311 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1530253 GTAATCAATG
* *
1530263 GTATCGATACCTCCTCTATA
1 GTATCGATACCCCCTCTACA
1530283 GTATCGATACCCCCTCT-CA
1 GTATCGATACCCCCTCTACA
1530302 GTATCGATAC
1 GTATCGATAC
1530312 GAATTGCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.24, C:0.33, G:0.12, T:0.31
Consensus pattern (20 bp):
GTATCGATACCCCCTCTACA
Found at i:1534688 original size:82 final size:81
Alignment explanation
Indices: 1534549--1534853 Score: 425
Period size: 82 Copynumber: 3.7 Consensus size: 81
1534539 TGTTCTTTAC
* * * * *
1534549 CTAACTTGTATTAGTGGAACCTTTCTGCCAAAATGCACCGTTAGGCATTAGTCTTTTATCCTAAA
1 CTAACTTGCATTATTGGAACCTTTCTGCC-AAATGCACAGTTAGGCATTTGTTTTTTATCCTAAA
1534614 GGCATTTAACCTTTCTT
65 GGCATTTAACCTTTCTT
* *
1534631 CTAACTTGCATTATTGGAATCTTTCTGCCAAATACACAGTTAGGCATTTGTATTTTTATCCTAAA
1 CTAACTTGCATTATTGGAACCTTTCTGCCAAATGCACAGTTAGGCATTTGT-TTTTTATCCTAAA
*
1534696 GGAATTTAACCTTTCTT
65 GGCATTTAACCTTTCTT
* *
1534713 CTAACTTGCATTATTGGCACCTTTCTGCCAAATTCACAGTTAAGG-ATTTAGTTTTTTATCCTAA
1 CTAACTTGCATTATTGGAACCTTTCTGCCAAATGCACAGTT-AGGCATTT-GTTTTTTATCCTAA
1534777 AGGCATTTAACCTTTCTT
64 AGGCATTTAACCTTTCTT
* * *
1534795 CTAACTTGCATTATTGGCACTTTTCTGCCAAATGCGA-AGTTAGGCATTTAGTCTTTTAT
1 CTAACTTGCATTATTGGAACCTTTCTGCCAAATGC-ACAGTTAGGCATTT-GTTTTTTAT
1534854 TTTAGAATAG
Statistics
Matches: 203, Mismatches: 15, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
81 22 0.11
82 175 0.86
83 6 0.03
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (81 bp):
CTAACTTGCATTATTGGAACCTTTCTGCCAAATGCACAGTTAGGCATTTGTTTTTTATCCTAAAG
GCATTTAACCTTTCTT
Found at i:1535071 original size:54 final size:54
Alignment explanation
Indices: 1534989--1535925 Score: 1125
Period size: 54 Copynumber: 17.4 Consensus size: 54
1534979 TTTATTAAGA
* * * * ** *
1534989 TGCACACGTAGTGCTTATACGGTCGTTCATCAACACATGATGAATTTTGTGAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATTTCGTGAGT
* ** * *
1535043 TGCACACATAGTGCATGTACAATTGTTCATCAACATATGATGAATTTCATGAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATTTCGTGAGT
* * * * * *
1535097 TGCACAGACAATGCCTATACGGTTGTTCATCAACTTATGGTGAATTAT-GTGGGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATT-TCGTGAGT
* * * * *
1535151 TGCACACATAGTGCCTGTACAGTTTTTCATCAACTTATGATGAATTCCATGGGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATTTCGTGAGT
* * *
1535205 TGCACACATAGTGCTTGTACGGTTGTTCATTAACTTATGATGAATTTCATGAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATTTCGTGAGT
* * *
1535259 TAG-ACACATAGTGTCTGTACGGTTGTTCATCAATTTATGATGAATTCCGTGAGT
1 T-GCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATTTCGTGAGT
* * *
1535313 TGCACACATAGTGCATGTACGGTTGTTCATCAACTTATGATGAA-TTCTTTGGGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATTTC-GTGAGT
* * *
1535367 TGCACACATAGTGCATGTACGGTTGTTCATCAACTTATGATAAATTTCGTAAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATTTCGTGAGT
* * * * *
1535421 TGCACACATAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCCCTGGGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATTTCGTGAGT
* * * *
1535475 TACACACATAGTGCATGAATGGTTGTTCATCAACTTATGATGAA-TTCAGTGAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATTTC-GTGAGT
* *
1535529 TGCACACTTAGTGTCTGTACGGTTGTTCATCAACTTATGATGAATTTCGTGAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATTTCGTGAGT
* * * *
1535583 TGCACAAATAGTTCCTGTACTGTTGTTCATCAACTGATGATGAA-TTCTGTGAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATTTC-GTGAGT
* * *
1535637 TGCACACATAGTGCTTGTATGGTTGTTCATCAACTTATGATGAATTTCGTGGGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATTTCGTGAGT
* * * * *
1535691 TACACACATAGTTCCTATACGGTTGTTCATCAATTTATGATGAA-TTCTTTGAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATTTC-GTGAGT
* * * * *
1535745 TACACACATAGTACCTGTACGATTGTTCATCAACATATGATGAA-TTCTGTGGGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATTTC-GTGAGT
* * * *
1535799 TGCACATATAGTGCCTATACGGTTGTTTATCAACTTATGATGAA-TTCTGTTAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATTTC-GTGAGT
* *
1535853 TGCACACATAGTGCCTGTATGGTTGTTCATCAACTTATGATGAATTACGTGAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATTTCGTGAGT
1535907 TGCACACATAGTGCCTGTA
1 TGCACACATAGTGCCTGTA
1535926 GTACACGTAG
Statistics
Matches: 754, Mismatches: 117, Indels: 24
0.84 0.13 0.03
Matches are distributed among these distances:
53 11 0.01
54 730 0.97
55 13 0.02
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (54 bp):
TGCACACATAGTGCCTGTACGGTTGTTCATCAACTTATGATGAATTTCGTGAGT
Found at i:1540550 original size:81 final size:81
Alignment explanation
Indices: 1540456--1540937 Score: 617
Period size: 81 Copynumber: 6.1 Consensus size: 81
1540446 AAGCCTTTAT
* * * ** * *
1540456 TCTTTTACCCAAAGGCATTTAGCCTTTCATCTAACAAGCCTAATTGACACCTTTTTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1540521 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* *
1540537 ACTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
1540602 ATAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * * *
1540618 -----TA-T-----TTATTTAACCTTTTATCTAACTGTCGTAATTGACACCTTTCTCTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1540672 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * * *
1540688 TTTTTTACTCAAAGGTATTTAACATTTCATCTAATTGGCATAATTAACACCTTTCTGTCAAATAC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
1540753 ACAGCTAAGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
1540769 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAACTGACAGCTTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
1540834 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * * *
1540850 TCTTTTACTCAAAGGTAATTAACCTTTCATCTAACTGTCATAATTGAGATCTTTATGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1540915 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
1540931 TCTTTTA
1 TCTTTTA
1540938 TTTAGAACAG
Statistics
Matches: 346, Mismatches: 44, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
70 60 0.17
75 3 0.01
76 3 0.01
81 280 0.81
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
ACAGCTAGGCCATTAA
Found at i:1540844 original size:232 final size:237
Alignment explanation
Indices: 1540456--1540937 Score: 632
Period size: 232 Copynumber: 2.0 Consensus size: 237
1540446 AAGCCTTTAT
* * * * * *
1540456 TCTTTTACCCAAAGGCATTTAGCCTTTCATCTAACAAGCCTAATTGACACCTTTTTGTCAAATGC
1 TCTTTTACCCAAAGGCATTTAACATTTCATCTAACAAGCATAATTAACACCTTTCTGTCAAATAC
* *
1540521 ACAGCTAGGCCATTAAACTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA
66 ACAGCTAAGCCATTAAACTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAACTGACA
* * * *
1540586 CCTTTATGTCAAATGCATAGCTAGGCCATTAA-TATT-T-A-T-TTAACCTTTTATCTAACTGTC
131 CCTTTATATCAAATGCACAACTAGGCCATTAACTATTATAAGTATTAACCTTTCATCTAACTGTC
* *
1540646 GTAATTGACACCTTTCTCTCAAATGCACAGCTAGGCCATTAA
196 ATAATTGACACCTTTATCTCAAATGCACAGCTAGGCCATTAA
* * * ***
1540688 TTTTTTACTCAAAGGTATTTAACATTTCATCTAATTGGCATAATTAACACCTTTCTGTCAAATAC
1 TCTTTTACCCAAAGGCATTTAACATTTCATCTAACAAGCATAATTAACACCTTTCTGTCAAATAC
*
1540753 ACAGCTAAGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAACTGACA
66 ACAGCTAAGCCATTAAACTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAACTGACA
* * *
1540818 GCTTTCTATCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTAATTAACCTTTCATCTA
131 CCTTTATATCAAATGCACAACTAGGCCATTAA-CTATTA-T--AA-GT-ATTAACCTTTCATCTA
* * *
1540883 ACTGTCATAATTGAGATCTTTATGTCAAATGCACAGCTAGGCCATTAA
190 ACTGTCATAATTGACACCTTTATCTCAAATGCACAGCTAGGCCATTAA
1540931 TCTTTTA
1 TCTTTTA
1540938 TTTAGAACAG
Statistics
Matches: 211, Mismatches: 28, Indels: 11
0.84 0.11 0.04
Matches are distributed among these distances:
232 142 0.67
234 3 0.01
236 1 0.00
239 1 0.00
241 1 0.00
243 63 0.30
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (237 bp):
TCTTTTACCCAAAGGCATTTAACATTTCATCTAACAAGCATAATTAACACCTTTCTGTCAAATAC
ACAGCTAAGCCATTAAACTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAACTGACA
CCTTTATATCAAATGCACAACTAGGCCATTAACTATTATAAGTATTAACCTTTCATCTAACTGTC
ATAATTGACACCTTTATCTCAAATGCACAGCTAGGCCATTAA
Found at i:1544659 original size:10 final size:9
Alignment explanation
Indices: 1544638--1544680 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
1544628 AACACTCAAA
1544638 GAAAAT-AT
1 GAAAATAAT
1544646 GAAAAATAAT
1 G-AAAATAAT
1544656 GAAAATAATT
1 GAAAATAA-T
1544666 GAAAATAAT
1 GAAAATAAT
*
1544675 AAAAAT
1 GAAAAT
1544681 GTACGTGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
8 1 0.03
9 18 0.58
10 12 0.39
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.23
Consensus pattern (9 bp):
GAAAATAAT
Found at i:1559909 original size:137 final size:136
Alignment explanation
Indices: 1559629--1559895 Score: 340
Period size: 137 Copynumber: 1.9 Consensus size: 136
1559619 ACTGAAGTGC
* * * * *
1559629 CAAAATAGAAATTCACAAACTCATTATGAATTCCATGGATACACACATAATGCCGAAAGTACCTA
1 CAAAATGGTAATTCACAAACTCATTATAAATACCATGGATACACACATAATGCCGAAAGTACATA
* *
1559694 TAGTACTGATACGAAATGCACCATTATGCATTAAACAAAATCGATCGATAACTTTTATACAAAAT
66 TAGTACTGATACGAAATGCACCATTATACATTAAACAAAATCGATCGATAACTTGTATAC-AAAT
1559759 TGTATAT
130 TGTATAT
* * *
1559766 CAAAATGGTAATTCACAAACTCATTATAAATACCAT-GATTGCACATC-TAGTGCTGAAAGTACA
1 CAAAATGGTAATTCACAAACTCATTATAAATACCATGGA-TACACA-CATAATGCCGAAAGTACA
* * * *
1559829 TGTAGTACTGATACGAAAATGTACCATTATACATTACATAAAATCGATCGATAACCATTGTATAC
64 TATAGTACTGATACG-AAATGCACCATTATACATTAAACAAAATCGATCGATAA-C-TTGTATAC
1559894 AA
126 AA
1559896 TTTATGTCGA
Statistics
Matches: 111, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
136 2 0.02
137 64 0.58
138 35 0.32
139 3 0.03
140 7 0.06
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (136 bp):
CAAAATGGTAATTCACAAACTCATTATAAATACCATGGATACACACATAATGCCGAAAGTACATA
TAGTACTGATACGAAATGCACCATTATACATTAAACAAAATCGATCGATAACTTGTATACAAATT
GTATAT
Found at i:1560606 original size:21 final size:21
Alignment explanation
Indices: 1560579--1560637 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
1560569 CGATACCTCC
1560579 ACATCAGTATCGATACTACTT
1 ACATCAGTATCGATACTACTT
*
1560600 GCATCAGTATCGATACTACTT
1 ACATCAGTATCGATACTACTT
1560621 ACATCAGTATCGATACT
1 ACATCAGTATCGATACT
1560638 GATCATCGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (21 bp):
ACATCAGTATCGATACTACTT
Found at i:1566395 original size:13 final size:13
Alignment explanation
Indices: 1566395--1566473 Score: 89
Period size: 13 Copynumber: 6.3 Consensus size: 13
1566385 CCGTTGACCC
1566395 GACCCGACCCGTT
1 GACCCGACCCGTT
1566408 GACCCGACCCGTT
1 GACCCGACCCGTT
1566421 GACCCGA-CC--T
1 GACCCGACCCGTT
1566431 GACCCGTTGACCC---
1 GACCC---GACCCGTT
1566444 GACCCGACCCGTT
1 GACCCGACCCGTT
1566457 GACCCGACCCGTT
1 GACCCGACCCGTT
1566470 GACC
1 GACC
1566474 GTTGACCGGA
Statistics
Matches: 59, Mismatches: 0, Indels: 14
0.81 0.00 0.19
Matches are distributed among these distances:
10 11 0.19
12 2 0.03
13 44 0.75
14 2 0.03
ACGTcount: A:0.16, C:0.47, G:0.23, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1566396 original size:18 final size:18
Alignment explanation
Indices: 1566373--1566467 Score: 146
Period size: 18 Copynumber: 5.6 Consensus size: 18
1566363 ACCGGTCACA
1566373 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1566391 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
1566408 ----GACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
1566422 ACCCGACCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
1566440 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1566458 ACCCGACCCG
1 ACCCGACCCG
1566468 TTGACCGTTG
Statistics
Matches: 70, Mismatches: 2, Indels: 10
0.85 0.02 0.12
Matches are distributed among these distances:
13 13 0.19
18 57 0.81
ACGTcount: A:0.17, C:0.49, G:0.22, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1566415 original size:31 final size:31
Alignment explanation
Indices: 1566377--1566473 Score: 137
Period size: 31 Copynumber: 3.1 Consensus size: 31
1566367 GTCACAACCC
1566377 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
1566408 GACCCGACCCGTTGACCCGACCTGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
1566439 GACCCGACCC---GACCCGTTGACCCGACCCGTT
1 GACCCGACCCGTTGACCC---GACCCGACCCGTT
1566470 GACC
1 GACC
1566474 GTTGACCGGA
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
28 5 0.08
31 56 0.92
ACGTcount: A:0.16, C:0.47, G:0.23, T:0.13
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:1569053 original size:24 final size:25
Alignment explanation
Indices: 1568929--1569046 Score: 147
Period size: 24 Copynumber: 4.9 Consensus size: 25
1568919 TTTTTGATTT
1568929 GATTTCTGATCTGATACTTGACATG
1 GATTTCTGATCTGATACTTGACATG
*
1568954 GA-TTCTGATCTAATA-TCTGACATG
1 GATTTCTGATCTGATACT-TGACATG
*
1568978 GA-TTCTGATCTGATACTTGACTTG
1 GATTTCTGATCTGATACTTGACATG
* *
1569002 GATTT-TGATCTGTTACTTGACCT-
1 GATTTCTGATCTGATACTTGACATG
*
1569025 GATTTCTGATATGATACTTGAC
1 GATTTCTGATCTGATACTTGAC
1569047 CTGATTTATG
Statistics
Matches: 82, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
23 6 0.07
24 71 0.87
25 5 0.06
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.42
Consensus pattern (25 bp):
GATTTCTGATCTGATACTTGACATG
Found at i:1569069 original size:24 final size:24
Alignment explanation
Indices: 1568983--1569056 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
1568973 ACATGGATTC
* *
1568983 TGATCTGATACTTGACTTGGATTT-
1 TGATATGATACTTGACCT-GATTTA
* * *
1569007 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
1569031 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
1569055 TG
1 TG
1569057 TTTTGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 5 0.11
24 39 0.89
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.45
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:1571239 original size:13 final size:13
Alignment explanation
Indices: 1571239--1571317 Score: 80
Period size: 13 Copynumber: 6.3 Consensus size: 13
1571229 CCGTTGACCC
1571239 GACCCGACCCGTT
1 GACCCGACCCGTT
1571252 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1571265 GACCC-AACC--T
1 GACCCGACCCGTT
1571275 GACCCGTTGACCC---
1 GACCC---GACCCGTT
1571288 GACCCGACCCGTT
1 GACCCGACCCGTT
1571301 GACCCGACCCGTT
1 GACCCGACCCGTT
1571314 GACC
1 GACC
1571318 GTTGACCGGA
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
10 11 0.19
12 3 0.05
13 40 0.70
14 3 0.05
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1571240 original size:18 final size:18
Alignment explanation
Indices: 1571217--1571311 Score: 137
Period size: 18 Copynumber: 5.6 Consensus size: 18
1571207 ACCGGTCACA
1571217 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1571235 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
1571252 ----GACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
1571266 ACCCAACCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
1571284 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1571302 ACCCGACCCG
1 ACCCGACCCG
1571312 TTGACCGTTG
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
13 13 0.19
18 55 0.81
ACGTcount: A:0.18, C:0.49, G:0.21, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1571259 original size:31 final size:31
Alignment explanation
Indices: 1571221--1571317 Score: 128
Period size: 31 Copynumber: 3.1 Consensus size: 31
1571211 GTCACAACCC
1571221 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* *
1571252 GACCCGACCCGTTGACCCAACCTGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
1571283 GACCCGACCC---GACCCGTTGACCCGACCCGTT
1 GACCCGACCCGTTGACCC---GACCCGACCCGTT
1571314 GACC
1 GACC
1571318 GTTGACCGGA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
28 5 0.08
31 54 0.92
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.13
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:1571279 original size:49 final size:49
Alignment explanation
Indices: 1571217--1571317 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
1571207 ACCGGTCACA
*
1571217 ACCCGACCCGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCAACCCGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
*
1571266 ACCCAACCTGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCAACCCGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
1571315 ACC
1 ACC
1571318 GTTGACCGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.18, C:0.49, G:0.21, T:0.13
Consensus pattern (49 bp):
ACCCAACCCGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
Found at i:1573811 original size:48 final size:48
Alignment explanation
Indices: 1573759--1573890 Score: 151
Period size: 48 Copynumber: 2.8 Consensus size: 48
1573749 AATATTTTAC
*
1573759 CTGATTTTTGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTTGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * * *
1573807 CTGATATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTTGA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* ** *
1573855 CTG-TTACTTGACCTGATTTCTGATATGATACTTGAC
1 CTGATT-TTTGAATTGATTTCTGATCTGATACTTGAC
1573891 CTGATTTATG
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
47 3 0.04
48 63 0.91
49 3 0.04
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (48 bp):
CTGATTTTTGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:1573897 original size:24 final size:24
Alignment explanation
Indices: 1573776--1573890 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
1573766 TTGATTTGAT
1573776 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
1573800 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
1573824 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
1573848 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
1573871 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
1573891 CTGATTTATG
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:1573913 original size:24 final size:24
Alignment explanation
Indices: 1573827--1573900 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
1573817 ACATGGATTC
* * *
1573827 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
1573851 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
1573875 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
1573899 TG
1 TG
1573901 TTTTGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:1574026 original size:35 final size:35
Alignment explanation
Indices: 1573980--1574073 Score: 170
Period size: 35 Copynumber: 2.7 Consensus size: 35
1573970 ACCTGGAGGC
*
1573980 TCCTCAGCTGTGTGCTCAGGGCCTTATTTACCGGT
1 TCCTCGGCTGTGTGCTCAGGGCCTTATTTACCGGT
*
1574015 TCCTCGGCTGTGTGCTCAGGGCCTTATTTACCTGT
1 TCCTCGGCTGTGTGCTCAGGGCCTTATTTACCGGT
1574050 TCCTCGGCTGTGTGCTCAGGGCCT
1 TCCTCGGCTGTGTGCTCAGGGCCT
1574074 ACTGGACTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 57 1.00
ACGTcount: A:0.09, C:0.30, G:0.28, T:0.34
Consensus pattern (35 bp):
TCCTCGGCTGTGTGCTCAGGGCCTTATTTACCGGT
Found at i:1574146 original size:2 final size:2
Alignment explanation
Indices: 1574139--1574171 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1574129 TGGATGGGGG
1574139 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
1574172 CTGGGGAACC
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:1574216 original size:71 final size:71
Alignment explanation
Indices: 1574100--1574242 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
1574090 GGTGTATGGT
1574100 TCTGGGGAACCTACACAACTTGGACTTGTTGGATGGGGGTATATATATATATATATATATATATA
1 TCTGGGGAACCTACACAACTTGGACTTGTTGGATGGGGGTATATATATATATATATATATATATA
1574165 TATATA
66 TATATA
1574171 TCTGGGGAACCTACACAACTTGGACTTGTTGGATGGGGGTATATATATATATATATATATATATA
1 TCTGGGGAACCTACACAACTTGGACTTGTTGGATGGGGGTATATATATATATATATATATATATA
1574236 TATATA
66 TATATA
1574242 T
1 T
1574243 ATATATATAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.37
Consensus pattern (71 bp):
TCTGGGGAACCTACACAACTTGGACTTGTTGGATGGGGGTATATATATATATATATATATATATA
TATATA
Found at i:1574217 original size:2 final size:2
Alignment explanation
Indices: 1574210--1574256 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1574200 TGGATGGGGG
1574210 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
1574252 TA TA T
1 TA TA T
1574257 GTTTTTTTTT
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:1575453 original size:27 final size:28
Alignment explanation
Indices: 1575401--1575482 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 28
1575391 CTTTCAGTGG
* *
1575401 TTACAAAAATCTTAAAGTCATA-ACATT-
1 TTACAAAAATCATAAA-TCAAATACATTC
1575428 TTACAAAAATCATAAATCAAATACATTC
1 TTACAAAAATCATAAATCAAATACATTC
** * *
1575456 CAAAAAAAATTCATAAGTCAAATACAT
1 TTACAAAAA-TCATAAATCAAATACAT
1575483 GTCATCTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 4 0.09
27 20 0.43
28 6 0.13
29 16 0.35
ACGTcount: A:0.54, C:0.16, G:0.02, T:0.28
Consensus pattern (28 bp):
TTACAAAAATCATAAATCAAATACATTC
Found at i:1576160 original size:137 final size:137
Alignment explanation
Indices: 1575880--1576140 Score: 319
Period size: 137 Copynumber: 1.9 Consensus size: 137
1575870 ACCGAAGTGC
* * * * *
1575880 CGAAATGGAAATTCACAAACTCATTATGAATTCCATGGATACACATATAGTGCCGAAAGTACATA
1 CGAAATGGAAATTCACAAACTCATTATAAATACCATGGATACACATATAGTACCGAAAGGACACA
* ** *
1575945 TAGTACTGATACGAAATGCACCATTATGCATAAAACAAAATCGATCGGTAACTTTTATACATAAT
66 TAGTACTGATACGAAATGCACCATTATGCATAAAACAAAATCGATCGATAACCATTATACACAAT
1576010 TGTCTAT
131 TGTCTAT
* * * * *
1576017 CGAAATGGTAATTCACAAACTCATTATAAATACCAT-GATTGCACATCTAGTATCGAACGGACAC
1 CGAAATGGAAATTCACAAACTCATTATAAATACCATGGA-TACACATATAGTACCGAAAGGACAC
* * * *
1576081 GTAGTACTGATACGAAAATGCACCATTATGCATTACAA-AAAATTGATTGATAACCATTAT
65 ATAGTACTGATACG-AAATGCACCATTATGCA-TAAAACAAAATCGATCGATAACCATTAT
1576141 TTACAATTCA
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
136 2 0.02
137 64 0.62
138 34 0.33
139 4 0.04
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (137 bp):
CGAAATGGAAATTCACAAACTCATTATAAATACCATGGATACACATATAGTACCGAAAGGACACA
TAGTACTGATACGAAATGCACCATTATGCATAAAACAAAATCGATCGATAACCATTATACACAAT
TGTCTAT
Found at i:1578242 original size:17 final size:19
Alignment explanation
Indices: 1578210--1578247 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
1578200 GATACATGGT
*
1578210 TTTTTTATATATTTTTTTA
1 TTTTTTATATATTTTTGTA
1578229 TTTTTTAT-TA-TTTTGTA
1 TTTTTTATATATTTTTGTA
1578246 TT
1 TT
1578248 AACTTTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 2 0.11
19 8 0.44
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (19 bp):
TTTTTTATATATTTTTGTA
Found at i:1578319 original size:39 final size:39
Alignment explanation
Indices: 1578257--1578375 Score: 127
Period size: 39 Copynumber: 3.1 Consensus size: 39
1578247 TAACTTTTGT
* *
1578257 ATTCA-AAATTCTCAAATTATTTCATTCTAACATTCTAA
1 ATTCATAATTTCTCAAATTATTTCATTATAACATTCTAA
* * *
1578295 ATTCATAATTTCTGAAATTTTTTCATTATAACATTTTAA
1 ATTCATAATTTCTCAAATTATTTCATTATAACATTCTAA
* * *
1578334 ATTCTTAATTTCTTACATTATTTCACATTA-AA-ATTCTAA
1 ATTCATAATTTCTCAAATTATTT--CATTATAACATTCTAA
1578373 ATT
1 ATT
1578376 ATTTTTTTAA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
38 5 0.07
39 56 0.82
40 2 0.03
41 5 0.07
ACGTcount: A:0.37, C:0.14, G:0.01, T:0.48
Consensus pattern (39 bp):
ATTCATAATTTCTCAAATTATTTCATTATAACATTCTAA
Found at i:1578455 original size:18 final size:19
Alignment explanation
Indices: 1578432--1578486 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 19
1578422 TATATTTTTT
1578432 ATTTTATTTTTTAAAT-AA
1 ATTTTATTTTTTAAATGAA
*
1578450 ATTTTATTTTTTAATTATGTA
1 ATTTTATTTTTTAA--ATGAA
1578471 ATTTTAATTTTTTAAA
1 ATTTT-ATTTTTTAAA
1578487 AATTATGTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 14 0.44
20 3 0.09
21 6 0.19
22 9 0.28
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTATTTTTTAAATGAA
Found at i:1584100 original size:9 final size:9
Alignment explanation
Indices: 1584081--1584126 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
1584071 GTTAAAAGAG
*
1584081 AAAAAAGAT
1 AAAAAAAAT
1584090 AAAAAAAAT
1 AAAAAAAAT
1584099 AAAAAAAAT
1 AAAAAAAAT
*
1584108 AAATAATAAT
1 AAA-AAAAAT
1584118 AATAAAAAA
1 AA-AAAAAA
1584127 ACACCTGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 20 0.62
10 11 0.34
11 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:1585383 original size:21 final size:21
Alignment explanation
Indices: 1585354--1585439 Score: 82
Period size: 24 Copynumber: 3.8 Consensus size: 21
1585344 CTTGGACCGA
1585354 ATAAAATAAAATTAATAAAAC
1 ATAAAATAAAATTAATAAAAC
* *
1585375 ATAATATAAAATATATAATAAAAA
1 ATAAAAT-AAA-AT-TAATAAAAC
*
1585399 ATAAAAAATTAAAATTAATATAAC
1 AT--AAAA-TAAAATTAATAAAAC
*
1585423 ATAAAATAATATTAATA
1 ATAAAATAAAATTAATA
1585440 TAATATATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
21 16 0.30
22 7 0.13
23 2 0.04
24 19 0.36
25 2 0.04
26 6 0.11
27 1 0.02
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
ATAAAATAAAATTAATAAAAC
Found at i:1585539 original size:42 final size:38
Alignment explanation
Indices: 1585437--1585610 Score: 176
Period size: 42 Copynumber: 4.4 Consensus size: 38
1585427 AATAATATTA
*
1585437 ATATAATATATAATATGTTTTCAAAAAAATCATTTTCAAAACT
1 ATATAATATAT-ATA--TTTTC--AAAAATCGTTTTCAAAACT
* * *
1585480 ATAT-A-ATATATATTTTCAAAATTTGTTTTTCAAAATT
1 ATATAATATATATATTTTCAAAAATCG-TTTTCAAAACT
1585517 ATATAATATATACATATATTTCAAAAAATCGTTTTCAAAACT
1 ATATAATATAT--ATAT-TTTC-AAAAATCGTTTTCAAAACT
*
1585559 ATATAATATATATATTTTCAAAAA-C-TTTTAAAAACT
1 ATATAATATATATATTTTCAAAAATCGTTTTCAAAACT
1585595 ATATATATATATATAT
1 ATATA-ATATATATAT
1585611 ATATATATAT
Statistics
Matches: 115, Mismatches: 8, Indels: 22
0.79 0.06 0.15
Matches are distributed among these distances:
36 20 0.17
37 25 0.22
38 11 0.10
39 8 0.07
40 7 0.06
41 8 0.07
42 26 0.23
43 10 0.09
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (38 bp):
ATATAATATATATATTTTCAAAAATCGTTTTCAAAACT
Found at i:1585571 original size:36 final size:35
Alignment explanation
Indices: 1585469--1585610 Score: 115
Period size: 37 Copynumber: 3.7 Consensus size: 35
1585459 AAAAAAATCA
* **
1585469 TTTTCAAAACTATATAATATATAT-TTTCAAAATTTGT
1 TTTTAAAAACTATATAATATATATATTTCAAAA---AC
* *
1585506 TTTTCAAAATTATATAATATATACATATATTTCAAAAAATC
1 TTTTAAAAACTATAT-A-ATAT--ATATATTTC-AAAAA-C
*
1585547 GTTTTCAAAACTATATAATATATATATTTTCAAAAAC
1 -TTTTAAAAACTATATAATATATATA-TTTCAAAAAC
1585584 TTTTAAAAACTATATATATATATATAT
1 TTTTAAAAACTATATA-ATATATATAT
1585611 ATATATATAT
Statistics
Matches: 90, Mismatches: 5, Indels: 21
0.78 0.04 0.18
Matches are distributed among these distances:
36 16 0.18
37 24 0.27
38 11 0.12
39 8 0.09
40 4 0.04
41 5 0.06
42 18 0.20
43 4 0.04
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.44
Consensus pattern (35 bp):
TTTTAAAAACTATATAATATATATATTTCAAAAAC
Found at i:1585601 original size:2 final size:2
Alignment explanation
Indices: 1585594--1585624 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1585584 TTTTAAAAAC
1585594 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 T
1585625 TCAAAAACCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1585605 original size:79 final size:77
Alignment explanation
Indices: 1585437--1585614 Score: 216
Period size: 79 Copynumber: 2.2 Consensus size: 77
1585427 AATAATATTA
*
1585437 ATATAATATATAATATGTTTTCAAAAAAATCATTTTCAAAACTATATAATATATATTTTCAAAAT
1 ATATAATATATAATAT-ATTTCAAAAAAATCATTTTCAAAACTATATAATATATATTTTCAAAA-
** * *
1585502 TTGTTTTTCAAAATT
64 -TACTTTTAAAAACT
*
1585517 ATATAATATATACATATATTTC-AAAAAATCGTTTTCAAAACTATATAATATATATATTTTCAAA
1 ATATAATATATA-ATATATTTCAAAAAAATCATTTTCAAAACTATAT-A-ATATATATTTTCAAA
1585581 A-ACTTTTAAAAACT
63 ATACTTTTAAAAACT
1585595 ATATATATATATATATATAT
1 ATATA-ATATATA-ATATAT
1585615 ATATATATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
78 14 0.16
79 36 0.41
80 17 0.20
81 20 0.23
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (77 bp):
ATATAATATATAATATATTTCAAAAAAATCATTTTCAAAACTATATAATATATATTTTCAAAATA
CTTTTAAAAACT
Found at i:1585659 original size:88 final size:88
Alignment explanation
Indices: 1585514--1585697 Score: 209
Period size: 88 Copynumber: 2.1 Consensus size: 88
1585504 GTTTTTCAAA
*
1585514 ATTATATAATATATACATATATTTCAAAAAATCGTTTTCAAAACTATATAATATATATATTTTCA
1 ATTATATAATATATACATATATTTCAAAAAATCGTTTTAAAAACTATATAATATATATATTTTCA
1585579 AAAA-C-TTT-TAAAAACTATAT
66 AAAACCGTTTCTAAAAACTATAT
* * * *
1585599 ATATATATATATATATATATATATATTCAAAAACCAT-TTTTTAAATAAGTATAT-AT-TATATG
1 AT-TATATA-ATATATACATATAT-TTCAAAAA--ATCGTTTTAAA-AACTATATAATATATATA
*
1585661 TTTTCAAAAACCGTTTTCTAAAAATTATAT
60 TTTTCAAAAACCG-TTTCTAAAAACTATAT
1585691 ATTATAT
1 ATTATAT
1585698 TTTTCAAAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 14
0.81 0.06 0.14
Matches are distributed among these distances:
85 2 0.02
86 6 0.07
87 13 0.16
88 23 0.28
89 9 0.11
90 9 0.11
91 8 0.10
92 13 0.16
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.43
Consensus pattern (88 bp):
ATTATATAATATATACATATATTTCAAAAAATCGTTTTAAAAACTATATAATATATATATTTTCA
AAAACCGTTTCTAAAAACTATAT
Done.