Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008964.1 Hibiscus syriacus cultivar Beakdansim tig00112305_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: 2156694
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 8 of 11
Found at i:1347740 original size:21 final size:19
Alignment explanation
Indices: 1347706--1347744 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
1347696 CATTCCAACT
1347706 TTTTTACTATTTTCTTTAA
1 TTTTTACTATTTTCTTTAA
1347725 TTTTTACTTATATTTCTTTA
1 TTTTTAC-TAT-TTTCTTTA
1347745 TTCCCTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
21 8 0.44
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTACTATTTTCTTTAA
Found at i:1349124 original size:18 final size:18
Alignment explanation
Indices: 1349101--1349142 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1349091 AAAAGCTCCT
*
1349101 CTAAAAATGTTGTCGGCG
1 CTAAAAATGTTGCCGGCG
1349119 CTAAAAATGTTGCCGGCG
1 CTAAAAATGTTGCCGGCG
1349137 C-AAAAA
1 CTAAAAA
1349143 AACACCGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (18 bp):
CTAAAAATGTTGCCGGCG
Found at i:1349442 original size:43 final size:44
Alignment explanation
Indices: 1349395--1349489 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 44
1349385 AATATTTCGT
* * *
1349395 GGCGTTTGTT-GTAAAAAACACCGTAATATATTTTATATATAGC
1 GGCGTTTGTTAGTAAAAAACACCGCAATAGATTTGATATATAGC
* * *
1349438 GGCGTTT-TTAGTTACAAACGCCGCAATAGATTTGATATATAGC
1 GGCGTTTGTTAGTAAAAAACACCGCAATAGATTTGATATATAGC
*
1349481 GGCATTTGT
1 GGCGTTTGT
1349490 GGTAGAAATG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
42 2 0.05
43 40 0.93
44 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.36
Consensus pattern (44 bp):
GGCGTTTGTTAGTAAAAAACACCGCAATAGATTTGATATATAGC
Found at i:1358496 original size:80 final size:80
Alignment explanation
Indices: 1358363--1358517 Score: 274
Period size: 80 Copynumber: 1.9 Consensus size: 80
1358353 AATGAAAGAC
* *
1358363 TAATTGCCTAGTTGTGCATTTAACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATA
1 TAATTGCCTAGCTGTGCATTTAACAGAAAGGTGTAAATCATGCCAGTTAGATGAAAGGTTAAATA
1358428 CCTTATAGTACAGAA
66 CCTTATAGTACAGAA
*
1358443 TAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTAAATCATGCCAGTTAGATGAAAGGTTAAATA
1 TAATTGCCTAGCTGTGCATTTAACAGAAAGGTGTAAATCATGCCAGTTAGATGAAAGGTTAAATA
*
1358508 CCTTTTAGTA
66 CCTTATAGTA
1358518 AAAGATTAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 71 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.31
Consensus pattern (80 bp):
TAATTGCCTAGCTGTGCATTTAACAGAAAGGTGTAAATCATGCCAGTTAGATGAAAGGTTAAATA
CCTTATAGTACAGAA
Found at i:1358587 original size:46 final size:46
Alignment explanation
Indices: 1358528--1359944 Score: 1900
Period size: 46 Copynumber: 30.9 Consensus size: 46
1358518 AAAGATTAAT
* * *
1358528 TGCATTATAGGTATGAAAGGATGCCATAAATAAAAATGCATAACGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* * *
1358574 TGAATTATCGGTATGAAAGGATGCCATAAACGAAAATGCATAACGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* *
1358620 TGCATTATCGGTATGAAAGGATGTCATAAATGAAAATGCATAACGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* * * *
1358666 TGCATTATAGGCATGAAAGGATGTCATAAATGAAAATTCATAATGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* *
1358712 TGCATTATCGGAATGAAAGGATGCCATAAGTGAAAA-GCATAACGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* * *
1358757 TGGATTATAC-ACATGAAAGGATGCCATAAATGAAAATGCGTAACGG
1 TGCATTAT-CGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* *
1358803 TGCAGTATCGGCATGAAAAGAATGCCATAAATGAAAATGCATAACGG
1 TGCATTATCGGCATG-AAAGGATGCCATAAATGAAAATGCATAACGG
* * *
1358850 TGCATTATCGACATGAAAGGATGACATAAATAAAAATGCATAACGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* ** *
1358896 TGCATTATCGACATGAAAGGATGCCCCAAATGAAAATGCATAACGA
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
** *
1358942 TGCATTATCGATATGAAAGGATGTCATAAATGAAAATGCATAACGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* *
1358988 TGCATTATCAGCATGAAAGGATGCCATAAATAAAAATGCATAACGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
*
1359034 TGCATTATAGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
1359080 TGCATTATCGGCATG--AGGATGCCATAAATGAAAATGCATAACGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* *
1359124 TGCATTATCGGCATGAAAGGATGTCATAAATGAAAATACATAACGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* * * * *
1359170 TACATTATAGGCATGAAAGGATACCATAAATAAAAACGCATAACGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
*
1359216 TGCATTATCGGCCTGAAAGGATGCCATAAATGAAAATGCATAACGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* * * *
1359262 TACATTATCGGCATGAAAAGATGCCATAAATGAAAATGCATAGCGA
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* * * * * *
1359308 TGTATTATCAGAATGAATGGATGCCATAAATGAAAATGTATAACTG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* * *
1359354 TGAATTATCGACATGAAAAGGATGTCATAAATGAAAATGCATAACGG
1 TGCATTATCGGCATG-AAAGGATGCCATAAATGAAAATGCATAACGG
* *
1359401 AT-CATTATCAGCATGAAAGGATGCCATAAATAAAAATGCATAACGG
1 -TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* * * * * *
1359447 TTCATTATCGGCATGAAATGATTCCATAAACGAAAATACATAAAGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
*
1359493 TGCATTATCGGCATAAAAGGATGCCATAAATGAAAATGCATAACGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* * * *
1359539 TGCATTATCGGCATGAATGGATGTCATAAATGAAAATGTATAATGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* * *
1359585 TACATTATGGGCATGAAAGGATGCCATAAATG-AAA---ATAACAG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* * * * *
1359627 TGCATTATCGGCATGAAAGAATGCCATTAATGAAATTGCACAATGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
*
1359673 TGCATTATCGGCATGAAAGGATGACATAAATGAAAATGCATAACGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
*
1359719 TGCATTATCAGCATGAAAGGATGCCATAAATG-AAATGCATAACGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* * *
1359764 TGTATTATCGGTATGAAAGGATGCCATAAATGAAAATGCATAATGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* *
1359810 TGCATTATAGGCATGAAAAGATGCCATAAATGAAAATGCATAACGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* * * * *
1359856 TGCATTATCAGTATGAAAGGATGTCATATATGAAAATGCGTAACGG
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
** * ** *
1359902 TGCATTATCGAAATGAAAGCATGCCACCAATGAAAATACATAA
1 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAA
1359945 TGGTATATTA
Statistics
Matches: 1196, Mismatches: 161, Indels: 28
0.86 0.12 0.02
Matches are distributed among these distances:
42 33 0.03
43 2 0.00
44 44 0.04
45 84 0.07
46 953 0.80
47 79 0.07
48 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.23
Consensus pattern (46 bp):
TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
Found at i:1364527 original size:44 final size:44
Alignment explanation
Indices: 1364414--1364800 Score: 456
Period size: 44 Copynumber: 8.9 Consensus size: 44
1364404 TTGCTCTAAA
* * * *
1364414 ATAAATGAAAATGCATAACGGTGCATTATTGGCAAAAAGATGCT
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
** * *
1364458 AT-AA--AAAATGTGTAATGGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* ** * * * **
1364499 ATAAATAAAAATGCATAACTCTGAATTATTAGTAGAAAGGTAAC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
1364543 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* * * *
1364587 ACAAATGAAAATGCATAACGATGCATTATTTGCATAAATGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* * * *
1364631 ATAAATGAAAATGCATAATGGTGCATTATTGGCAAAAAGGTGCA
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* * * *
1364675 ATAAATGAAAATGCATAACGGTACATTACTGGCAGAAAGGTGTC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* * *
1364719 ATAAATGGAAATGCATAACGGTGCATTATTGGTAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* *
1364763 ATAAATGAAAATGCATTACGATACATTATTGGCAGAAA
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAA
1364801 TGTATCACTC
Statistics
Matches: 289, Mismatches: 51, Indels: 6
0.84 0.15 0.02
Matches are distributed among these distances:
41 33 0.11
42 2 0.01
43 2 0.01
44 252 0.87
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
Found at i:1365232 original size:219 final size:221
Alignment explanation
Indices: 1364851--1365292 Score: 870
Period size: 219 Copynumber: 2.0 Consensus size: 221
1364841 CTAAGACAAG
1364851 TAATTCTGTGCAAGTATACACAATCTAATCAAGTAATAAAAGGTAAGTGAGTTATCGTCTACTCA
1 TAATTCTGTGCAAGTATACACAATCTAATCAAGTAATAAAAGGTAAGTGAGTTATCGTCTACTCA
1364916 GGGATTGGTCAGTTCTTTTTAAGTTTAACCACAACCAGAACTAGTTGTGACAAGCTAATTCCTGA
66 GGGATTGGTCAGTTCTTTTTAAGTTTAACCACAACCAGAACTAGTTGTGACAAGCTAATTCCTGA
1364981 AGTCTTGTCAAACTAGAAAACTATTAGTGATAAAGCAAGAAAATATTATAAAGTATGATTGTAGA
131 AGTCTTGTCAAACTAGAAAACTATTAGTGATAAAGCAAGAAAATATTATAAAGTATGATTGTAGA
1365046 AAAGTTTGGTTGAGGCTAAATAAACT
196 AAAGTTTGGTTGAGGCTAAATAAACT
1365072 TAATTCTGTGCAAGTATACACAATCTAA-CAAGT-ATAAAAGGTAAGTGAGTTATCGTCTACTCA
1 TAATTCTGTGCAAGTATACACAATCTAATCAAGTAATAAAAGGTAAGTGAGTTATCGTCTACTCA
1365135 GGGATTGGTCAGTTCTTTTTAAGTTTAACCACAACCAGAACTAGTTGTGACAAGCTAATTCCTGA
66 GGGATTGGTCAGTTCTTTTTAAGTTTAACCACAACCAGAACTAGTTGTGACAAGCTAATTCCTGA
1365200 AGTCTTGTCAAACTAGAAAACTATTAGTGATAAAGCAAGAAAATATTATAAAGTATGATTGTAGA
131 AGTCTTGTCAAACTAGAAAACTATTAGTGATAAAGCAAGAAAATATTATAAAGTATGATTGTAGA
1365265 AAAGTTTGGTTGAGGCTAAATAAACT
196 AAAGTTTGGTTGAGGCTAAATAAACT
1365291 TA
1 TA
1365293 TCGAATTAAA
Statistics
Matches: 221, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
219 188 0.85
220 5 0.02
221 28 0.13
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (221 bp):
TAATTCTGTGCAAGTATACACAATCTAATCAAGTAATAAAAGGTAAGTGAGTTATCGTCTACTCA
GGGATTGGTCAGTTCTTTTTAAGTTTAACCACAACCAGAACTAGTTGTGACAAGCTAATTCCTGA
AGTCTTGTCAAACTAGAAAACTATTAGTGATAAAGCAAGAAAATATTATAAAGTATGATTGTAGA
AAAGTTTGGTTGAGGCTAAATAAACT
Found at i:1371156 original size:49 final size:50
Alignment explanation
Indices: 1371084--1371190 Score: 171
Period size: 50 Copynumber: 2.2 Consensus size: 50
1371074 CTGGTGGAAC
* *
1371084 AACAATTAGGGCTGATGAAAGTTT-TTTTTCAAATCTATAAAAACATTTA
1 AACAATCAGGGCTGATGAAAGTTTGTTCTTCAAATCTATAAAAACATTTA
* *
1371133 AACAATCAGGGTTGATGAAAGTTTGTTCTTCAAATCTATAAAAGCATTTA
1 AACAATCAGGGCTGATGAAAGTTTGTTCTTCAAATCTATAAAAACATTTA
1371183 AACAATCA
1 AACAATCA
1371191 TCATTAAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
49 22 0.42
50 31 0.58
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (50 bp):
AACAATCAGGGCTGATGAAAGTTTGTTCTTCAAATCTATAAAAACATTTA
Found at i:1380662 original size:44 final size:44
Alignment explanation
Indices: 1380614--1380963 Score: 420
Period size: 44 Copynumber: 8.0 Consensus size: 44
1380604 CTCCTCTAAA
* * *
1380614 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTACA
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * *
1380658 ATAAATGAAAATGCATAATGGTGCATTATTGGCATAAAGGTTCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * *
1380702 ATAAATAAAAATGCATAATGGTGCATTATTGACAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * * * * *
1380746 ATAAATAAAAATACACAAAGGTGTATTATT-GCAAGAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGC-AGAAAGGTGCC
* *
1380790 ATAAATGGAAATGCATAACGGTG--TTATTGGCAGAAAGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
1380832 ATAAATGAAAATGCATAACGGTGCATTATTGGCA-AAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * * ** * **
1380875 ATAAATGGAAATGGATAATGGTGCATTATTGTTAAAAAGGTGTT
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* *
1380919 ATAAATGAAAATGTATAACGGTACATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
1380963 A
1 A
1380964 CTCAAGGTAT
Statistics
Matches: 261, Mismatches: 40, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
42 36 0.14
43 40 0.15
44 185 0.71
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
Found at i:1385429 original size:2 final size:2
Alignment explanation
Indices: 1385383--1385420 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1385373 ATTATTCATA
1385383 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
1385421 TCGTATATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1385680 original size:15 final size:16
Alignment explanation
Indices: 1385662--1385691 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1385652 ATAACTAGTA
1385662 ATAATATAA-TATATT
1 ATAATATAATTATATT
1385677 ATAATATAATTATAT
1 ATAATATAATTATAT
1385692 AAACCCAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATATAATTATATT
Found at i:1388407 original size:81 final size:81
Alignment explanation
Indices: 1388309--1388495 Score: 320
Period size: 81 Copynumber: 2.3 Consensus size: 81
1388299 TGTTTTGATA
* *
1388309 TAAAAGATTAATGGCCTAGATATGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1388374 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
1388390 TAAAAGAATAATGGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCGGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1388455 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
1388471 TAAAAGATTAATGGCCTAGCTATGC
1 TAAAAGATTAATGGCCTAGCTATGC
1388496 TATAATGCCC
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 98 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:1389913 original size:60 final size:60
Alignment explanation
Indices: 1389820--1390294 Score: 715
Period size: 60 Copynumber: 8.0 Consensus size: 60
1389810 ATTACCAAAT
*
1389820 GGCACTAAGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
1 GGCACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * * * *
1389880 GGCACTAAGTGTGCTAAAAATATTAAGATATTCATCCTAAGTGTATGAATTT-CGTATTA
1 GGCACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
1389939 GGCACTATGTGTGCTAAAAATGTTAA-AATATTCATACTAAGTGTATGAATTTCCGTATTG
1 GGCACTATGTGTGCTAAAAATGTTAAGAA-ATTCATACTAAGTGTATGAATTTCCGTATTG
* *
1389999 GGCACTATGTGTCCTAAAAATGTTAAGAAAATCATACTAAGTGTATGAATTTCCGTATTG
1 GGCACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
1390059 GGCACTATGTGTGCTAAAAATGTTAAGGAATTCATACTAAGTGTATGAATTTCCATATTG
1 GGCACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * *
1390119 GGCACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTGTTA
1 GGCACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* **
1390179 GGCACTATGTGTGCT-AAAATGTTAAGAAAGTCATACTAAGTGTATGAATTTTTGTATTG
1 GGCACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * * * * *
1390238 GGCACTTTATGTG-TAAACATGTTAATAAATTCATACTAGGTGTATGAATTTTCGTAT
1 GGCACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
1390295 ATGAAATATA
Statistics
Matches: 380, Mismatches: 31, Indels: 9
0.90 0.07 0.02
Matches are distributed among these distances:
58 2 0.01
59 140 0.37
60 236 0.62
61 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (60 bp):
GGCACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
Found at i:1390039 original size:119 final size:119
Alignment explanation
Indices: 1389820--1390294 Score: 722
Period size: 119 Copynumber: 4.0 Consensus size: 119
1389810 ATTACCAAAT
*
1389820 GGCACTAAGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCAC
1 GGCACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCAC
* * * *
1389885 TAAGTGTGCTAAAAATATTAAGATATTCATCCTAAGTGTATGAATTTCGTATTA
66 TATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCGTATTA
1389939 GGCACTATGTGTGCTAAAAATGTTAA-AATATTCATACTAAGTGTATGAATTTCCGTATTGGGCA
1 GGCACTATGTGTGCTAAAAATGTTAAGAA-ATTCATACTAAGTGTATGAATTTCCGTATTGGGCA
* * *
1390003 CTATGTGTCCTAAAAATGTTAAGAAAATCATACTAAGTGTATGAATTTCCGTATTG
65 CTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTT-CGTATTA
* *
1390059 GGCACTATGTGTGCTAAAAATGTTAAGGAATTCATACTAAGTGTATGAATTTCCATATTGGGCAC
1 GGCACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCAC
*
1390124 TATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTGTTA
66 TATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTC-GTATTA
* **
1390179 GGCACTATGTGTGCT-AAAATGTTAAGAAAGTCATACTAAGTGTATGAATTTTTGTATTGGGCAC
1 GGCACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCAC
* * * * *
1390243 TTTATGTG-TAAACATGTTAATAAATTCATACTAGGTGTATGAATTTTCGTAT
66 TATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAA-TTTCGTAT
1390295 ATGAAATATA
Statistics
Matches: 326, Mismatches: 25, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
118 37 0.11
119 157 0.48
120 131 0.40
121 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (119 bp):
GGCACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCAC
TATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCGTATTA
Found at i:1390200 original size:179 final size:178
Alignment explanation
Indices: 1389820--1390288 Score: 701
Period size: 179 Copynumber: 2.6 Consensus size: 178
1389810 ATTACCAAAT
* *
1389820 GGCACTAAGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCAC
1 GGCACTATGTGTGCTAAAAATGTTAAGAAAATCATACTAAGTGTATGAATTTCCGTATTGGGCAC
* * * *
1389885 TAAGTGTGCTAAAAATATTAAGATATTCATCCTAAGTGTATGAATTTCGTATTAGGCACTATGTG
66 TATGTGTGCTAAAAATGTTAAGA-ATTCATACTAAGTGTATGAATTTCATATTAGGCACTATGTG
*
1389950 TGCTAAAAATGTTAAAATATTCATACTAAGTGTATGAATTTCCGTATTG
130 TGCTAAAAATGTTAAAATATTCATACTAAGTGTATGAATTTCCGTATTA
*
1389999 GGCACTATGTGTCCTAAAAATGTTAAGAAAATCATACTAAGTGTATGAATTTCCGTATTGGGCAC
1 GGCACTATGTGTGCTAAAAATGTTAAGAAAATCATACTAAGTGTATGAATTTCCGTATTGGGCAC
*
1390064 TATGTGTGCTAAAAATGTTAAGGAATTCATACTAAGTGTATGAATTTCCATATTGGGCACTATGT
66 TATGTGTGCTAAAAATGTTAA-GAATTCATACTAAGTGTATGAATTT-CATATTAGGCACTATGT
* *
1390129 GTGCTAAAAATGTTAAGAA-ATTCATACTAAGTGTATGAATTTCTGTGTTA
129 GTGCTAAAAATGTTAA-AATATTCATACTAAGTGTATGAATTTCCGTATTA
* **
1390179 GGCACTATGTGTGCT-AAAATGTTAAGAAAGTCATACTAAGTGTATGAATTTTTGTATTGGGCAC
1 GGCACTATGTGTGCTAAAAATGTTAAGAAAATCATACTAAGTGTATGAATTTCCGTATTGGGCAC
* * * * *
1390243 TTTATGTG-TAAACATGTTAATAAATTCATACTAGGTGTATGAATTT
66 TATGTGTGCTAAAAATGTTAA-GAATTCATACTAAGTGTATGAATTT
1390289 TCGTATATGA
Statistics
Matches: 266, Mismatches: 21, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
178 34 0.13
179 155 0.58
180 75 0.28
181 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (178 bp):
GGCACTATGTGTGCTAAAAATGTTAAGAAAATCATACTAAGTGTATGAATTTCCGTATTGGGCAC
TATGTGTGCTAAAAATGTTAAGAATTCATACTAAGTGTATGAATTTCATATTAGGCACTATGTGT
GCTAAAAATGTTAAAATATTCATACTAAGTGTATGAATTTCCGTATTA
Found at i:1395500 original size:90 final size:89
Alignment explanation
Indices: 1395390--1395557 Score: 300
Period size: 90 Copynumber: 1.9 Consensus size: 89
1395380 CTGAAGATTT
* *
1395390 AATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAGGG
1 AATTCCAATTAATTAAATATAGAATTAATTAATTTGAAATAATAAAAT-CCTAATATGATTAGGG
1395455 TAACTTGGATATAAGAGGATTATTA
65 TAACTTGGATATAAGAGGATTATTA
1395480 AATTCCAATTAATTAAATATAGAATTAATTAATTTGAAATAATAAAATCCTAATATGATTAGGGT
1 AATTCCAATTAATTAAATATAGAATTAATTAATTTGAAATAATAAAATCCTAATATGATTAGGGT
*
1395545 AACTTGGCTATAA
66 AACTTGGATATAA
1395558 AAGGGTGTGT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 29 0.39
90 46 0.61
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (89 bp):
AATTCCAATTAATTAAATATAGAATTAATTAATTTGAAATAATAAAATCCTAATATGATTAGGGT
AACTTGGATATAAGAGGATTATTA
Found at i:1398070 original size:20 final size:20
Alignment explanation
Indices: 1398000--1398095 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
1397990 ATGCAAAAAC
1398000 GGTATCGATACCATAGG--AG
1 GGTATCGATACCAT-GGTAAG
* * * *
1398019 GATATCGGTACCATAGTATG
1 GGTATCGATACCATGGTAAG
1398039 GTAGTATCGATACCATGGTAAG
1 G--GTATCGATACCATGGTAAG
* * *
1398061 GGTGTCGATACAATAGTAAG
1 GGTATCGATACCATGGTAAG
1398081 GGTATCGATACCATG
1 GGTATCGATACCATG
1398096 TAACATCAAA
Statistics
Matches: 59, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
18 1 0.02
19 12 0.20
20 30 0.51
22 16 0.27
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (20 bp):
GGTATCGATACCATGGTAAG
Found at i:1398566 original size:60 final size:60
Alignment explanation
Indices: 1398494--1398966 Score: 702
Period size: 60 Copynumber: 7.9 Consensus size: 60
1398484 ACCAAATTGT
*
1398494 ACTAAGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGC
1 ACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGC
* * * * *
1398554 ACTAAGTGTGCTAAAAATATTAAGATATTCATCCTAAGTGTATGAAATTT-CGTATTAGGC
1 ACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATG-AATTTCCGTATTGGGC
*
1398614 ACTATGTGTGCTAAATATGTTAA-AATATTCATACTAAGTGTATGAATTTCCGTATTGGGC
1 ACTATGTGTGCTAAAAATGTTAAGAA-ATTCATACTAAGTGTATGAATTTCCGTATTGGGC
*
1398674 ACTATGTGTCCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGC
1 ACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGC
* *
1398734 ACTATGTGTGCTAAAAATGTTAAGGAATTCATACTAAGTGTATGAATTTCCATATTGGGC
1 ACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGC
* * *
1398794 ACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTGTTAGGC
1 ACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGC
* **
1398854 ACTATGTGTGCT-AAAATGTTAAGAAAGTCATACTAAGTGTATGAATTTTTGTATTGGGC
1 ACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGC
* * * * * *
1398913 ACTTTATGTG-TAAACATGTTAATAAATTCATACTAGGTGTATGAATTTTCGTAT
1 ACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
1398967 ATGAAATATA
Statistics
Matches: 377, Mismatches: 31, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
58 1 0.00
59 94 0.25
60 275 0.73
61 7 0.02
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.37
Consensus pattern (60 bp):
ACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGC
Found at i:1399677 original size:81 final size:81
Alignment explanation
Indices: 1399542--1399836 Score: 421
Period size: 81 Copynumber: 3.6 Consensus size: 81
1399532 AAGTATTACA
* *
1399542 TGTGCATGTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAA
1 TGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAA
1399607 AGATTAATGGCCTAGT
66 AGATTAATGGCCTAGT
*
1399623 TGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAA
1 TGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAA
1399688 AGATTAATGGCCTAGT
66 AGATTAATGGCCTAGT
* * * * * *
1399704 TGTGCATTTGGA-AGAAAGGTGTCAACTATTCTAGTTAGATGAAAGGTTACATGCCTTTGTGTAA
1 TGTGCATTT-GACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAA
* ** *
1399768 AAGACTAAAAGCCTATT
65 AAGATTAATGGCCTAGT
* * * *
1399785 TTTACATTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAAT
1 TGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAT
1399837 GCTTTCGAAG
Statistics
Matches: 190, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
80 1 0.01
81 187 0.98
82 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (81 bp):
TGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAA
AGATTAATGGCCTAGT
Found at i:1401749 original size:2 final size:2
Alignment explanation
Indices: 1401742--1401771 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1401732 TGTCAGAAAG
1401742 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
1401772 CTTTTATTGC
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:1404622 original size:81 final size:81
Alignment explanation
Indices: 1404516--1405233 Score: 954
Period size: 81 Copynumber: 8.9 Consensus size: 81
1404506 TGTTCTAAAA
** * *
1404516 TAAAAGAACAATGGCCTAGCTGTGCATTTAACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
1404581 GATAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * * * *
1404597 GAAAATATTAATGGCCTAGCTGTGCATTTTAAATAAAGGTGTCGATTATGCTAGTTAGATGAAAT
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1404662 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
1404678 TAAAAGATTAATGGCCTAGCTATGCATTTGACAAAAAGGTATCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1404743 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
1404759 TAAAAGATTAATGGCCTAGTTGTGCATATGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1404824 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* ** * *
1404840 TAAAAGATTAATGGTCTAGCTACGCATTTGACAGAAATGTGTCAATTATGACAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
1404905 GTTAAATACATTTGAG
66 GTTAAATACCTTTGAG
* * * * * *
1404921 TAAAAGATTAATAGTCTAGCTATGCATATGACATAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1404986 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
1405002 TAAAAGATTAATGGCCTAGTTGTGCATTTGACATAAATGTGTCAATTATGCCAGTTATATGAAAT
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
1405067 TTTAAATATCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
1405083 TAAAAGAGTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAA
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
1405148 GTTAAATGCCTTTGAG
66 GTTAAATACCTTTGAG
* *** * * * *
1405164 TAAAAGACTAAAAACCTAGTTGTGCATTAGGCAGAAAGGTGTCAATCATGCCAGTTAGA--AAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1405227 GTTAAAT
66 GTTAAAT
1405234 GCTTTAGAAA
Statistics
Matches: 570, Mismatches: 67, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
79 10 0.02
81 560 0.98
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:1406425 original size:9 final size:9
Alignment explanation
Indices: 1406413--1406463 Score: 57
Period size: 9 Copynumber: 5.3 Consensus size: 9
1406403 ATTTATTTTC
1406413 TTTTTCTCT
1 TTTTTCTCT
*
1406422 TTTTTTTCT
1 TTTTTCTCT
1406431 TTTTTCTTCAT
1 TTTTTC-TC-T
*
1406442 TTTTTCCCT
1 TTTTTCTCT
1406451 TTTTTCCTCT
1 TTTTT-CTCT
1406461 TTT
1 TTT
1406464 CTTTTTTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 19 0.54
10 9 0.26
11 7 0.20
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTCTCT
Found at i:1406475 original size:6 final size:7
Alignment explanation
Indices: 1406408--1406480 Score: 60
Period size: 7 Copynumber: 10.0 Consensus size: 7
1406398 CTTTTATTTA
1406408 TTTTCTT
1 TTTTCTT
1406415 TTTCTCTT
1 TTT-TCTT
1406423 TTTT-TT
1 TTTTCTT
*
1406429 CTTT-TT
1 TTTTCTT
*
1406435 TCTTCATT
1 TTTTC-TT
1406443 TTTTCCCTT
1 TTTT--CTT
*
1406452 TTTTCCTC
1 TTTT-CTT
1406460 TTTTCTT
1 TTTTCTT
1406467 TTTTCTT
1 TTTTCTT
1406474 TTTTCTT
1 TTTTCTT
1406481 CAGGAAAAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
6 9 0.16
7 20 0.36
8 19 0.35
9 6 0.11
10 1 0.02
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTCTT
Found at i:1408021 original size:20 final size:21
Alignment explanation
Indices: 1407996--1408042 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1407986 CAACTCTCCA
1407996 AATTCAACTG-AAAAATATAT
1 AATTCAACTGAAAAAATATAT
1408016 AATTCAACTGAAAAAATATAT
1 AATTCAACTGAAAAAATATAT
1408037 AATTCA
1 AATTCA
1408043 TCATTTACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (21 bp):
AATTCAACTGAAAAAATATAT
Found at i:1418220 original size:56 final size:56
Alignment explanation
Indices: 1418144--1418267 Score: 205
Period size: 56 Copynumber: 2.2 Consensus size: 56
1418134 GGTACTTTCT
* *
1418144 CAAAAACTAAGAAATTCATAATGAGTTTGTGAATTTTCGTATGGGCACTTTGTGTG
1 CAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTG
* *
1418200 CAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTT
1 CAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTG
1418256 CAAAAA-TAAGAA
1 CAAAAACTAAGAA
1418268 GTAAGAAGTT
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
55 6 0.10
56 57 0.90
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (56 bp):
CAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTG
Found at i:1425972 original size:19 final size:21
Alignment explanation
Indices: 1425948--1426017 Score: 67
Period size: 19 Copynumber: 3.5 Consensus size: 21
1425938 TGTAGAAATG
*
1425948 GTATCGATACCGTA-ATAG-A
1 GTATCGATACCATAGATAGTA
*
1425967 GTATCGGTACCATAGTATAGTA
1 GTATCGATACCATAG-ATAGTA
* *
1425989 GTATCGATACCAT-GGTAG-G
1 GTATCGATACCATAGATAGTA
1426008 GTATCGATAC
1 GTATCGATAC
1426018 TATTGAGCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 22 0.51
20 3 0.07
21 5 0.12
22 13 0.30
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (21 bp):
GTATCGATACCATAGATAGTA
Found at i:1426408 original size:56 final size:56
Alignment explanation
Indices: 1426341--1426750 Score: 578
Period size: 56 Copynumber: 7.3 Consensus size: 56
1426331 TGGCATTATA
* * *
1426341 TGTGCGCAAAAACTAAGAAATTCATAATGAATTTATG-ATATTCCGTATGGACATTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAAT-TTCCGTATGGACACTT
* * *
1426397 TGTGTGCAAAAACTAAGAAAATCATAATGCGTTTATGAATTTCTGTATGTGA-ACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG-GACACTT
* * *
1426453 TGTGTGCAAAAACTAAGAAATTTATAATGAGTTTATGAATTTCTGTATGGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGACACTT
* *
1426509 TGTGTGCAAAAACTAAGAAATTCATATTGAGTTTATGAATTTCCGTATGGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGACACTT
* *
1426565 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGACACTT
* * * **
1426621 TTTGTGCAAAAACTAAAAAATTCATAATGAGTTTATAAATTTTTGTATAGG-CACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTAT-GGACACTT
*
1426677 TGTGTGCAAAAACTAAGAAATTTATAATGAGTTTATGAATTTCCGTATGGGA-ACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTAT-GGACACTT
1426733 TGTGTGC-AAAACTAAGAA
1 TGTGTGCAAAAACTAAGAA
1426751 GTAAGAAGTT
Statistics
Matches: 323, Mismatches: 26, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
55 12 0.04
56 305 0.94
57 6 0.02
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (56 bp):
TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGACACTT
Found at i:1427106 original size:34 final size:30
Alignment explanation
Indices: 1427068--1427136 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
1427058 TTGATATAAC
1427068 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
1427102 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
1427131 AATTTA
1 AATTTA
1427137 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:1427147 original size:29 final size:30
Alignment explanation
Indices: 1427077--1427136 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1427067 CAATTTAAGG
1427077 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1427108 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1427137 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1427242 original size:21 final size:21
Alignment explanation
Indices: 1427216--1427273 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
1427206 AGGGTGTCAA
*
1427216 AGTGCATCTATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
1427237 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
*
1427258 AGTGCATCCCTGCATC
1 AGTGCATCCATGCATC
1427274 TGCACTAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.26
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:1427244 original size:13 final size:13
Alignment explanation
Indices: 1427226--1427271 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
1427216 AGTGCATCTA
1427226 TGCATCCCTGCAG
1 TGCATCCCTGCAG
1427239 TGCAT--C--CA-
1 TGCATCCCTGCAG
1427247 TGCATCCCTGCAG
1 TGCATCCCTGCAG
1427260 TGCATCCCTGCA
1 TGCATCCCTGCA
1427272 TCTGCACTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
8 5 0.18
9 2 0.07
10 1 0.04
11 1 0.04
12 2 0.07
13 17 0.61
ACGTcount: A:0.17, C:0.39, G:0.20, T:0.24
Consensus pattern (13 bp):
TGCATCCCTGCAG
Found at i:1427377 original size:20 final size:21
Alignment explanation
Indices: 1427336--1427389 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
1427326 ATGCAATTAG
*
1427336 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATACTTGCCA
1427357 TGCATCGATGCATAC-TGCCA
1 TGCATCGATGCATACTTGCCA
*
1427377 TGCATCCATGCAT
1 TGCATCGATGCAT
1427390 CAAGGCTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (21 bp):
TGCATCGATGCATACTTGCCA
Found at i:1428708 original size:19 final size:20
Alignment explanation
Indices: 1428684--1428731 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1428674 AATGATTTTC
*
1428684 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1428703 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1428723 TTTTGAAAA
1 TTTTGAAAA
1428732 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1430031 original size:34 final size:30
Alignment explanation
Indices: 1429993--1430061 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
1429983 TTGATATAAC
1429993 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
1430027 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
1430056 AATTTA
1 AATTTA
1430062 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:1430072 original size:29 final size:30
Alignment explanation
Indices: 1430002--1430061 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1429992 CAATTTAAGG
1430002 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1430033 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1430062 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1430167 original size:21 final size:21
Alignment explanation
Indices: 1430141--1430198 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
1430131 AGGGTGTCAA
* *
1430141 AGTGCATCTATGCATCCCTGC
1 AGTGCATCCATACATCCCTGC
*
1430162 AGTGCACCCATACATCCCTGC
1 AGTGCATCCATACATCCCTGC
1430183 AGTGCATCCATACATC
1 AGTGCATCCATACATC
1430199 TGCACTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.36, G:0.16, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATACATCCCTGC
Found at i:1430302 original size:20 final size:21
Alignment explanation
Indices: 1430261--1430307 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1430251 ATGCAATTAG
*
1430261 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATACTTGCCA
1430282 TGCATCGATGCATAC-TGCCA
1 TGCATCGATGCATACTTGCCA
1430302 TGCATC
1 TGCATC
1430308 AAGGCTGCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.21, C:0.32, G:0.19, T:0.28
Consensus pattern (21 bp):
TGCATCGATGCATACTTGCCA
Found at i:1430711 original size:34 final size:32
Alignment explanation
Indices: 1430672--1430741 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1430662 TTTTGTAAAG
* *
1430672 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1430706 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1430738 GGGA
1 GGGA
1430742 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1435185 original size:17 final size:17
Alignment explanation
Indices: 1435163--1435208 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
1435153 TTTTCTCTCC
1435163 TCAAATTTTAGGTGTGG
1 TCAAATTTTAGGTGTGG
1435180 TCAAATTTTAGGTGTGG
1 TCAAATTTTAGGTGTGG
1435197 TCAAATTTTAGG
1 TCAAATTTTAGG
1435209 GTTTCACTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (17 bp):
TCAAATTTTAGGTGTGG
Found at i:1437287 original size:17 final size:18
Alignment explanation
Indices: 1437255--1437292 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1437245 CATAATATAT
*
1437255 ATATATATATACACATAC
1 ATATATATATAAACATAC
1437273 ATATA-ATATAAACATAC
1 ATATATATATAAACATAC
1437290 ATA
1 ATA
1437293 CGTATATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (18 bp):
ATATATATATAAACATAC
Found at i:1437424 original size:5 final size:5
Alignment explanation
Indices: 1437414--1437468 Score: 67
Period size: 5 Copynumber: 10.6 Consensus size: 5
1437404 TATGTAAGTC
*
1437414 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ACTAAC AT-AT ATATAT ATATAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT ATA-AT ATA-AT
1437466 ATA
1 ATA
1437469 CAAACGTATG
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
4 3 0.07
5 27 0.60
6 15 0.33
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:1439403 original size:2 final size:2
Alignment explanation
Indices: 1439392--1439423 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1439382 CATGCATACC
1439392 TA TA TA -A 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
1439424 CGAAGTAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1442653 original size:4 final size:4
Alignment explanation
Indices: 1442646--1442683 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
1442636 ATAAAGCAAA
* *
1442646 AAAG AAAG AAA- AATG AAAG AAAG AGAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1442684 AAGTCAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
3 2 0.07
4 27 0.93
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:1442664 original size:23 final size:22
Alignment explanation
Indices: 1442634--1442679 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
1442624 AAATTAAATT
1442634 AAATAAAGCAAA-AAAGAAAGAA
1 AAATAAAG-AAAGAAAGAAAGAA
*
1442656 AAATGAAAGAAAGAGAGAAAGAA
1 AAAT-AAAGAAAGAAAGAAAGAA
1442679 A
1 A
1442680 GAAAAAGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.74, C:0.02, G:0.20, T:0.04
Consensus pattern (22 bp):
AAATAAAGAAAGAAAGAAAGAA
Found at i:1442709 original size:12 final size:11
Alignment explanation
Indices: 1442694--1442754 Score: 52
Period size: 12 Copynumber: 5.4 Consensus size: 11
1442684 AAGTCAAAGG
1442694 AAAAGAATAAAT
1 AAAAG-ATAAAT
*
1442706 AAAA-AGAAAT
1 AAAAGATAAAT
* *
1442716 CAAAGATAAAG
1 AAAAGATAAAT
*
1442727 ATAAAGATAAAG
1 A-AAAGATAAAT
1442739 ATAAAGATAAAT
1 A-AAAGATAAAT
1442751 AAAA
1 AAAA
1442755 TAAGATAAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
10 8 0.20
11 7 0.17
12 26 0.63
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (11 bp):
AAAAGATAAAT
Found at i:1442728 original size:6 final size:6
Alignment explanation
Indices: 1442717--1442773 Score: 72
Period size: 6 Copynumber: 10.5 Consensus size: 6
1442707 AAAAGAAATC
1442717 AAAGAT AAAGAT AAAGAT AAAGAT AAAGAT -AA-AT AAA-AT -AAGAT
1 AAAGAT AAAGAT AAAGAT AAAGAT AAAGAT AAAGAT AAAGAT AAAGAT
1442761 -AAGAT -AAGAT AAA
1 AAAGAT AAAGAT AAA
1442774 AAATAATTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.08
5 18 0.38
6 26 0.54
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (6 bp):
AAAGAT
Found at i:1444044 original size:15 final size:15
Alignment explanation
Indices: 1444020--1444090 Score: 74
Period size: 15 Copynumber: 4.9 Consensus size: 15
1444010 ACCTGAGAAA
*
1444020 AAAATGAATTAAATT
1 AAAATAAATTAAATT
1444035 AAAATAAATTAAATT
1 AAAATAAATTAAATT
* *
1444050 AAATTAAATGAAA--
1 AAAATAAATTAAATT
* *
1444063 AAAATAAAATAAAAT
1 AAAATAAATTAAATT
*
1444078 AAAATAAAATAAA
1 AAAATAAATTAAA
1444091 AATAATATAC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
13 10 0.21
15 38 0.79
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (15 bp):
AAAATAAATTAAATT
Found at i:1444071 original size:5 final size:5
Alignment explanation
Indices: 1444029--1444091 Score: 67
Period size: 5 Copynumber: 13.0 Consensus size: 5
1444019 AAAAATGAAT
* * * * *
1444029 TAAAT TAAAA T-AAA TTAAA TTAAA TTAAA TGAAA -AAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1444077 TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA
1444092 ATAATATACT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
4 7 0.13
5 46 0.87
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (5 bp):
TAAAA
Found at i:1444104 original size:29 final size:29
Alignment explanation
Indices: 1444035--1444097 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
1444025 GAATTAAATT
* * *
1444035 AAAAT-AAATTAAATTAAATTAAATGAAA
1 AAAATAAAATAAAATAAAATAAAATGAAA
1444063 AAAATAAAATAAAATAAAATAAAAT-AAA
1 AAAATAAAATAAAATAAAATAAAATGAAA
1444091 AATAATA
1 AA-AATA
1444098 TACTAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 10 0.33
29 20 0.67
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (29 bp):
AAAATAAAATAAAATAAAATAAAATGAAA
Found at i:1444294 original size:77 final size:76
Alignment explanation
Indices: 1444211--1444392 Score: 244
Period size: 77 Copynumber: 2.4 Consensus size: 76
1444201 AATTATTTTT
*
1444211 TATATTATATAGTTTTTTCAAAAAGGTTTTTTT-AACTATATATTATATAATTTTTAAAAAAATG
1 TATATTATATAGTTTTTTCAAAAAGGTTTTTTTAAACTATATATTATATAAGTTTT--AAAAATG
* *
1444275 TTTTTTAAAACTA
64 ATTTTAAAAACTA
* *
1444288 TGTATTATATAGTTTTTTCAAAAAGGTTTTTTTAAAACTATATATTATATAAGTTTTCAAAATGA
1 TATATTATATAGTTTTTTCAAAAAGGTTTTTTT-AAACTATATATTATATAAGTTTTAAAAATGA
1444353 TTTTAAAAACTA
65 TTTTAAAAACTA
* * *
1444365 TACATTATATA--ATTTTCAAAAATGTTTT
1 TATATTATATAGTTTTTTCAAAAAGGTTTT
1444393 AAAACTATAA
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
75 15 0.16
77 58 0.62
79 21 0.22
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (76 bp):
TATATTATATAGTTTTTTCAAAAAGGTTTTTTTAAACTATATATTATATAAGTTTTAAAAATGAT
TTTAAAAACTA
Found at i:1444387 original size:37 final size:38
Alignment explanation
Indices: 1444211--1444421 Score: 204
Period size: 37 Copynumber: 5.6 Consensus size: 38
1444201 AATTATTTTT
* *
1444211 TATATTATAT-AGTTTTTTCAAAAAGGTTTTTT-TAACTA
1 TATATTATATAAG--TTTTCAAAAATGTTTTTTAAAACTA
* *
1444249 TATATTATATAATTTTTAAAAAAATGTTTTTTAAAACTA
1 TATATTATATAAGTTTT-CAAAAATGTTTTTTAAAACTA
* *
1444288 TGTATTATAT-AGTTTTTTCAAAAAGGTTTTTTTAAAACTA
1 TATATTATATAAG--TTTTCAAAAATG-TTTTTTAAAACTA
* *
1444328 TATATTATATAAGTTTTC-AAAATGATTTTAAAAACTA
1 TATATTATATAAGTTTTCAAAAATGTTTTTTAAAACTA
*
1444365 TACATTATATAA-TTTTCAAAAATG--TTTTAAAACTA
1 TATATTATATAAGTTTTCAAAAATGTTTTTTAAAACTA
* *
1444400 TAAAATATA-AATGTTTTCAAAA
1 TATATTATATAA-GTTTTCAAAA
1444422 CTATATATTA
Statistics
Matches: 147, Mismatches: 16, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
34 2 0.01
35 17 0.12
36 14 0.10
37 32 0.22
38 28 0.19
39 26 0.18
40 26 0.18
41 2 0.01
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (38 bp):
TATATTATATAAGTTTTCAAAAATGTTTTTTAAAACTA
Found at i:1444417 original size:36 final size:37
Alignment explanation
Indices: 1444225--1444421 Score: 152
Period size: 39 Copynumber: 5.2 Consensus size: 37
1444215 TTATATAGTT
* * ** * *
1444225 TTTTCAAAAAGGTTTTTTTAACTATATATTATATAAT
1 TTTTCAAAAATGATTTTAAAACTATAAATTATATAAG
* * **
1444262 TTTTAAAAAAATGTTTTTTAAAACTATGTATTATAT-AG
1 TTTT-CAAAAATG-ATTTTAAAACTATAAATTATATAAG
** *
1444300 TTTTTTCAAAAAGGTTTTTTTAAAACTATATATTATATAAG
1 --TTTTCAAAAA--TGATTTTAAAACTATAAATTATATAAG
*
1444341 TTTTC-AAAATGATTTTAAAAACTATACATTATATAA-
1 TTTTCAAAAATGATTTT-AAAACTATAAATTATATAAG
*
1444377 TTTTCAAAAATG-TTTTAAAACTATAAAATATA-AATG
1 TTTTCAAAAATGATTTTAAAACTATAAATTATATAA-G
1444413 TTTTCAAAA
1 TTTTCAAAA
1444422 CTATATATTA
Statistics
Matches: 135, Mismatches: 14, Indels: 23
0.78 0.08 0.13
Matches are distributed among these distances:
34 2 0.01
35 14 0.10
36 23 0.17
37 28 0.21
38 11 0.08
39 29 0.21
40 25 0.19
41 3 0.02
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (37 bp):
TTTTCAAAAATGATTTTAAAACTATAAATTATATAAG
Found at i:1444432 original size:60 final size:63
Alignment explanation
Indices: 1444347--1444489 Score: 177
Period size: 60 Copynumber: 2.3 Consensus size: 63
1444337 TAAGTTTTCA
* *
1444347 AAATGATTTTAAAAACTATACATTATATA-ATTTTCAAAAATGTTTT-AAAACTATA-A-AATAT
1 AAATG-TTTTCAAAACTATACATTATATATATATT-AAAAATGTTTTCAAAACTATATATAATAT
* *
1444408 AAATGTTTTCAAAACTATATATTATATATATATTAAAAATGTTTTCAAAATTATATATAATAT
1 AAATGTTTTCAAAACTATACATTATATATATATTAAAAATGTTTTCAAAACTATATATAATAT
* *
1444471 ATATATTTTCGAAAACTAT
1 AAATGTTTTC-AAAACTAT
1444490 TTTATGAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
60 32 0.45
61 17 0.24
62 1 0.01
63 13 0.18
64 8 0.11
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (63 bp):
AAATGTTTTCAAAACTATACATTATATATATATTAAAAATGTTTTCAAAACTATATATAATAT
Found at i:1444448 original size:36 final size:36
Alignment explanation
Indices: 1444408--1444477 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
1444398 TATAAAATAT
*
1444408 AAATGTTTTCAAAACTATATATTATATATATATTAA
1 AAATGTTTTCAAAACTATATATAATATATATATTAA
*
1444444 AAATGTTTTCAAAATTATATATAATATATATATT
1 AAATGTTTTCAAAACTATATATAATATATATATT
1444478 TTCGAAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (36 bp):
AAATGTTTTCAAAACTATATATAATATATATATTAA
Found at i:1445330 original size:84 final size:84
Alignment explanation
Indices: 1445219--1445895 Score: 775
Period size: 84 Copynumber: 8.0 Consensus size: 84
1445209 AGATAGCTCT
* * * * *
1445219 TTCTCGACTTAAGCTATGCTGCAAATGATGTGCTTTGGAGCTGAGTGTAGTCAAACTCGAAGGTC
1 TTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
1445284 TTTGGTTGGCAGATAACCC
66 TTTGGTTGGCAGATAACCC
* * * *
1445303 TTCTGGACTTAAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC
1 TTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
*
1445368 TTTTGGTT-ACAGATAACCC
66 -TTTGGTTGGCAGATAACCC
* * * * * * * * * *
1445387 TTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGATGAGTGTAATCGAACTCAAAGAT
1 TTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
*
1445452 CTTTGGTTGGCAGATAGCCC
65 CTTTGGTTGGCAGATAACCC
* * * * * * * * *
1445472 TTCTTGACTTAAGCTATGTTGCAAATCATATACCTTTGAGCTGAGCGTAGTTGAACTCTAAGGTC
1 TTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
*
1445537 TTT-GTTGGCAGATAACTC
66 TTTGGTTGGCAGATAACCC
* * * * * * * * *
1445555 TTCTAGCCTTGAGTTATGCTGCAAATGATGTACTTTCGAAGCTAAGTGTAATCGAACTCAAAGGT
1 TTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GGAGCTGAGCGTAGTCGAACTCGAAGGT
*
1445620 CTTTGGTTGGCAGATAGCCC
65 CTTTGGTTGGCAGATAACCC
* * * *
1445640 TTCTCGACTTAAGTTATGCTGCAAATGATGGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
1 TTCTAGACTTAAGTTATGCTGCAAATGAT-GTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
1445705 CTTTGGTTGGCAGATAACCC
65 CTTTGGTTGGCAGATAACCC
* * *
1445725 TTCTCGACTTAAGTTATGTTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
1 TTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
* **
1445790 TTTGGGTGGCAGATGGCCC
66 TTTGGTTGGCAGATAACCC
* * * *
1445809 TTCTAGCCTTGAGCTATGCTGAAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
1 TTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
* * *
1445874 -TTGGTCGACAGACAACCC
66 TTTGGTTGGCAGATAACCC
1445892 TTCT
1 TTCT
1445896 CGCCTTGAGT
Statistics
Matches: 498, Mismatches: 89, Indels: 13
0.83 0.15 0.02
Matches are distributed among these distances:
83 57 0.11
84 262 0.53
85 174 0.35
86 5 0.01
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (84 bp):
TTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
TTTGGTTGGCAGATAACCC
Found at i:1445537 original size:253 final size:251
Alignment explanation
Indices: 1445204--1445908 Score: 894
Period size: 253 Copynumber: 2.8 Consensus size: 251
1445194 TCGAGGGTTT
* * * * * *
1445204 TTGGAAGATAGCTCTTTCTCGACTTAAGCTATGCTGCAAATGATGTGCTTTGGAGCTGAGTGTAG
1 TTGGCAGATAGC-CCTTCTCGACTTAAGCTATGTTGCAAATGATATCCTTT-GAGCTGAGCGTAG
* * * * * *
1445269 TCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTGGACTTAAGTTATGCTGTAAATGATAT
64 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGAAAATGATGT
* *
1445334 GCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGA
129 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTACAGATAACCCTTCTCGCCTTGA
*
1445399 GTTATGCTGTAAATGAT-GTGCCCTCGAAGATGAGTGTAATCGAACTCAAAGATCTTTGG
193 GTTATGCTGCAAATGATGGTGCCCTCG-AGATGAGTGTAATCGAACTCAAAGATCTTTGG
* *
1445458 TTGGCAGATAGCCCTTCTTGACTTAAGCTATGTTGCAAATCATATACCTTTGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATAT-CCTTTGAGCTGAGCGTAGT
* * * * *
1445523 TGAACTCTAAGGTCTTT-GTTGGCAGATAACTCTTCTAGCCTTGAGTTATGCTGCAAATGATGTA
65 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGAAAATGATGTG
* * * * * * * * * *
1445587 CTTTCGAAGCTAAGTGTAATCGAACTCAAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAA
130 CCTT-GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTT-ACAGATAACCCTTCTCGCCTTGA
* * * * *
1445652 GTTATGCTGCAAATGATGGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGG
193 GTTATGCTGCAAATGATGGTGCCCTCGAGATGAGTGTAATCGAACTCAAAGATCTTTGG
* * *
1445711 TTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATAT-CCTTTGAGCTGAGCGTAGT
* ** *
1445776 CGAACTCGAAGGTCTTTGGGTGGCAGATGGCCCTTCTAGCCTTGAGCTATGCTGAAAATGATGTG
65 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGAAAATGATGTG
* *
1445841 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTGGTCGACAGACAACCCTTCTCGCCTTGAG
130 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT-TACAGATAACCCTTCTCGCCTTGAG
1445905 TTAT
194 TTAT
1445909 ATTGCCGATA
Statistics
Matches: 382, Mismatches: 63, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
252 78 0.20
253 239 0.63
254 65 0.17
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (251 bp):
TTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATATCCTTTGAGCTGAGCGTAGTC
GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGAAAATGATGTGC
CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTACAGATAACCCTTCTCGCCTTGAGTT
ATGCTGCAAATGATGGTGCCCTCGAGATGAGTGTAATCGAACTCAAAGATCTTTGG
Found at i:1445781 original size:337 final size:336
Alignment explanation
Indices: 1445233--1445908 Score: 888
Period size: 337 Copynumber: 2.0 Consensus size: 336
1445223 CGACTTAAGC
* * * * *
1445233 TATGCTGCAAATGATGTGCTTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGAT
1 TATGCTGCAAATGATGTACTTTGAAGCTAAGTGTAATCAAACTCAAAGGTCTTTGGTTGGCAGAT
* * *
1445298 AACCCTTCTGGACTTAAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGA
66 AACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAATCAAACTCGA
* * * *
1445363 AGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAG
131 AGGTCTTTTGGTTACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAG
* * * *
1445428 ATGAGTGTAATCGAACTCAAAGATCTTTGGTTGGCAGATAGCCCTTCTTGACTTAAGCTATGTTG
196 ATGAGCGTAATCGAACTCAAAGATCTTTGGGTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTG
* * * * * * * * *
1445493 CAAATCATATACCTTTGAGCTGAGCGTAGTTGAACTCTAAGGTCTTTGTTGGCAGATAACTCTTC
261 AAAATCATATACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTCGACAGACAACCCTTC
1445558 TAGCCTTGAGT
326 TAGCCTTGAGT
*
1445569 TATGCTGCAAATGATGTACTTTCGAAGCTAAGTGTAATCGAACTCAAAGGTCTTTGGTTGGCAGA
1 TATGCTGCAAATGATGTACTTT-GAAGCTAAGTGTAATCAAACTCAAAGGTCTTTGGTTGGCAGA
* * * * *
1445634 TAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGGTGCCTTTGAGCTGAGTGTAATCGAACTC
65 TAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT-ATGCCTTGGAGCTGAGCGTAATCAAACTC
* * * *
1445699 GAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATATG-CCTTG
129 GAAGGTCTTTTGGTT-ACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCG
* * * * * * * *
1445762 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGGTGGCAGATGGCCCTTCTAGCCTTGAGCTATG
193 AAGATGAGCGTAATCGAACTCAAAGATCTTTGGGTGGCAGATAGCCCTTCTAGACTTAAGCTATG
* * *
1445827 CTGAAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTCGACAGACAACCC
258 CTGAAAATCATATACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTCGACAGACAACCC
*
1445892 TTCTCGCCTTGAGT
323 TTCTAGCCTTGAGT
1445906 TAT
1 TAT
1445909 ATTGCCGATA
Statistics
Matches: 290, Mismatches: 47, Indels: 5
0.85 0.14 0.01
Matches are distributed among these distances:
336 21 0.07
337 202 0.70
338 67 0.23
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (336 bp):
TATGCTGCAAATGATGTACTTTGAAGCTAAGTGTAATCAAACTCAAAGGTCTTTGGTTGGCAGAT
AACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAATCAAACTCGA
AGGTCTTTTGGTTACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAG
ATGAGCGTAATCGAACTCAAAGATCTTTGGGTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTG
AAAATCATATACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTCGACAGACAACCCTTC
TAGCCTTGAGT
Found at i:1447131 original size:83 final size:89
Alignment explanation
Indices: 1447029--1447247 Score: 263
Period size: 95 Copynumber: 2.5 Consensus size: 89
1447019 GGCTAGCTGA
1447029 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTC-A-A-TAT-GTA-AA-CA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAATATTATAGTATAATCA
* *
1447088 CCTTTATCAGGTTAGCTAAATATT
66 CATTTATCAGGCTAGCTAAATATT
* *
1447112 ATCCACAAAGGCGGGGCGTTTAACCAATTGC-CTTAGAGGGACAGCTCAAGCTTTATTGTATAGT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTC-TAGAGGGACAGCTCAA----TA-T-TATAGT
* * *
1447176 ATAATTACATTTATTAGGCTAGCTGAATATT
59 ATAATCACATTTATCAGGCTAGCTAAATATT
1447207 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGA
1447248 TAACTCAAGC
Statistics
Matches: 113, Mismatches: 9, Indels: 16
0.82 0.07 0.12
Matches are distributed among these distances:
82 1 0.01
83 43 0.38
84 1 0.01
89 1 0.01
92 3 0.03
93 3 0.03
94 2 0.02
95 58 0.51
96 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (89 bp):
ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAATATTATAGTATAATCA
CATTTATCAGGCTAGCTAAATATT
Found at i:1447255 original size:95 final size:95
Alignment explanation
Indices: 1447090--1447266 Score: 275
Period size: 95 Copynumber: 1.9 Consensus size: 95
1447080 TGTAAACACC
*
1447090 TTTATCAGGTTAGCTAAATATTATCCACAAAGGCGGGGCGTTTAACCAATTGCCTTAGAGGGACA
1 TTTATCAGGCTAGCTAAATATTATCCACAAAGGCGGGGCGTTTAACCAATTGCCTTAGAGGGACA
*
1447155 GCTCAAGCTTTATTGTATAGTATAATTACA
66 ACTCAAGCTTTATTGTATAGTATAATTACA
* * * * *
1447185 TTTATTAGGCTAGCTGAATATTATCCATAAAGTCGGGGCGTTTAACCAATTG-CTCTAGAGGGAT
1 TTTATCAGGCTAGCTAAATATTATCCACAAAGGCGGGGCGTTTAACCAATTGCCT-TAGAGGGAC
1447249 AACTCAAGCTTTATTGTA
65 AACTCAAGCTTTATTGTA
1447267 CATATATAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
94 2 0.03
95 72 0.97
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (95 bp):
TTTATCAGGCTAGCTAAATATTATCCACAAAGGCGGGGCGTTTAACCAATTGCCTTAGAGGGACA
ACTCAAGCTTTATTGTATAGTATAATTACA
Found at i:1450904 original size:13 final size:13
Alignment explanation
Indices: 1450888--1450917 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1450878 CTTAATTACG
1450888 AAAATTAAAAATT
1 AAAATTAAAAATT
*
1450901 AAAATTAAAATTT
1 AAAATTAAAAATT
1450914 AAAA
1 AAAA
1450918 ATCCGATTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:1451026 original size:16 final size:15
Alignment explanation
Indices: 1451003--1451032 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1450993 ATGAATTAAT
1451003 AAATAAATAAATAAG
1 AAATAAATAAATAAG
1451018 AAATAAAATAAATAA
1 AAAT-AAATAAATAA
1451033 ATGTTAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (15 bp):
AAATAAATAAATAAG
Found at i:1451117 original size:24 final size:23
Alignment explanation
Indices: 1451080--1451139 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 23
1451070 ATATATATTA
* * *
1451080 AAAAATAATAAAAATTAAATAAAG
1 AAAAA-AATGAAAATGAAAGAAAG
1451104 CAAAAAAATGAAAATGAAAGAAAG
1 -AAAAAAATGAAAATGAAAGAAAG
*
1451128 AAAGAAA-GAAAA
1 AAAAAAATGAAAA
1451140 AGTCAAGGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 5 0.16
23 6 0.19
24 15 0.48
25 5 0.16
ACGTcount: A:0.75, C:0.02, G:0.12, T:0.12
Consensus pattern (23 bp):
AAAAAAATGAAAATGAAAGAAAG
Found at i:1451237 original size:13 final size:14
Alignment explanation
Indices: 1451210--1451238 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1451200 GATAAAGATA
1451210 AAGATAAATAAAAT
1 AAGATAAATAAAAT
1451224 AAGATAAA-AAAAT
1 AAGATAAATAAAAT
1451237 AA
1 AA
1451239 TTAAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (14 bp):
AAGATAAATAAAAT
Found at i:1452489 original size:5 final size:5
Alignment explanation
Indices: 1452448--1452477 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1452438 AGAAAAAAAA
1452448 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT
1452478 GAATAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:1452489 original size:23 final size:22
Alignment explanation
Indices: 1452440--1452508 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 22
1452430 TGGACTTGAG
*
1452440 AAAAAAAATAAAT-TAAAT--T
1 AAAATAAATAAATATAAATAAT
*
1452459 AAATTAAATTAAAT-TAAATGAAT
1 AAAATAAA-TAAATATAAAT-AAT
1452482 AAAATAAATAAATAATAAATAAT
1 AAAATAAATAAAT-ATAAATAAT
1452505 AAAA
1 AAAA
1452509 ATAATATACT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
19 6 0.15
20 10 0.24
22 5 0.12
23 15 0.37
24 5 0.12
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (22 bp):
AAAATAAATAAATATAAATAAT
Found at i:1452682 original size:40 final size:38
Alignment explanation
Indices: 1452638--1452773 Score: 109
Period size: 37 Copynumber: 3.6 Consensus size: 38
1452628 AACTGTTTTT
* *
1452638 TATATTATATAGTTTTTTCAAAAAGGTTTTTTTAAAACTA
1 TATATTATATAGTTTTTTC-AAAAGG-ATTTTAAAAACTA
*
1452678 TATATTATATAAG--TTTTCAAAATGATTTTAAAAACTA
1 TATATTATAT-AGTTTTTTCAAAAGGATTTTAAAAACTA
* *** * *
1452715 TATATTATATAATTTTCAAAAAATG-TTTTAAAAATTA
1 TATATTATATAGTTTTTTCAAAAGGATTTTAAAAACTA
* * *
1452752 TATAATATA-AATGTTTTCAAAA
1 TATATTATATAGTTTTTTCAAAA
1452774 CTATATATTA
Statistics
Matches: 80, Mismatches: 13, Indels: 10
0.78 0.13 0.10
Matches are distributed among these distances:
36 10 0.12
37 40 0.50
38 13 0.16
39 5 0.06
40 10 0.12
41 2 0.03
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (38 bp):
TATATTATATAGTTTTTTCAAAAGGATTTTAAAAACTA
Found at i:1452718 original size:37 final size:36
Alignment explanation
Indices: 1452666--1452773 Score: 139
Period size: 37 Copynumber: 2.9 Consensus size: 36
1452656 CAAAAAGGTT
*
1452666 TTTTTAAAACTATATATTATATAAGTTTTCAAAATG
1 TTTTAAAAACTATATATTATATAAGTTTTCAAAATG
1452702 ATTTTAAAAACTATATATTATATAA-TTTTCAAAAAATG
1 -TTTTAAAAACTATATATTATATAAGTTTTC--AAAATG
* *
1452740 TTTTAAAAATTATATAATATA-AATGTTTTCAAAA
1 TTTTAAAAACTATATATTATATAA-GTTTTCAAAA
1452774 CTATATATTA
Statistics
Matches: 64, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
36 11 0.17
37 42 0.66
38 11 0.17
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (36 bp):
TTTTAAAAACTATATATTATATAAGTTTTCAAAATG
Found at i:1452731 original size:36 final size:35
Alignment explanation
Indices: 1452666--1452823 Score: 147
Period size: 36 Copynumber: 4.7 Consensus size: 35
1452656 CAAAAAGGTT
*
1452666 TTTTTAAAACTATATATTATATAAGTTTTCAAAATG
1 TTTTAAAAACTATATATTATATAA-TTTTCAAAATG
1452702 ATTTTAAAAACTATATATTATATAATTTTCAAAAAATG
1 -TTTTAAAAACTATATATTATATAATTTTC--AAAATG
1452740 TTTTAAAAA-T-TATA-TA-AT-A---T--AAATG
1 TTTTAAAAACTATATATTATATAATTTTCAAAATG
* *
1452765 TTTTCAAAACTATATATTATATATATTTTAAAAATG
1 TTTTAAAAACTATATATTATATA-ATTTTCAAAATG
* * *
1452801 TTTTCAAAATTATATATAATATA
1 TTTTAAAAACTATATATTATATA
1452824 TATATTTTTG
Statistics
Matches: 104, Mismatches: 4, Indels: 27
0.77 0.03 0.20
Matches are distributed among these distances:
25 13 0.12
26 1 0.01
27 4 0.04
28 2 0.02
29 3 0.03
31 1 0.01
32 1 0.01
33 2 0.02
34 3 0.03
35 4 0.04
36 32 0.31
37 32 0.31
38 6 0.06
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (35 bp):
TTTTAAAAACTATATATTATATAATTTTCAAAATG
Found at i:1452763 original size:25 final size:25
Alignment explanation
Indices: 1452735--1452799 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
1452725 AATTTTCAAA
1452735 AAATGTTTTAAAAATTATATAATAT
1 AAATGTTTTAAAAATTATATAATAT
* * *
1452760 AAATGTTTTCAAAACTATATATTAT
1 AAATGTTTTAAAAATTATATAATAT
* *
1452785 ATATATTTTAAAAAT
1 AAATGTTTTAAAAAT
1452800 GTTTTCAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (25 bp):
AAATGTTTTAAAAATTATATAATAT
Found at i:1452783 original size:62 final size:62
Alignment explanation
Indices: 1452697--1452816 Score: 190
Period size: 61 Copynumber: 1.9 Consensus size: 62
1452687 TAAGTTTTCA
1452697 AAATGATTTTAAAAACTATATATTATATA-ATTTTCAAAAAATGTTTTAAAAATTATATAATAT
1 AAATGATTTTAAAAACTATATATTATATATATTTT--AAAAATGTTTTAAAAATTATATAATAT
* *
1452760 AAATG-TTTTCAAAACTATATATTATATATATTTTAAAAATGTTTTCAAAATTATATA
1 AAATGATTTTAAAAACTATATATTATATATATTTTAAAAATGTTTTAAAAATTATATA
1452817 TAATATATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
61 22 0.41
62 22 0.41
63 10 0.19
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.44
Consensus pattern (62 bp):
AAATGATTTTAAAAACTATATATTATATATATTTTAAAAATGTTTTAAAAATTATATAATAT
Found at i:1452843 original size:40 final size:36
Alignment explanation
Indices: 1452760--1452863 Score: 136
Period size: 36 Copynumber: 2.7 Consensus size: 36
1452750 TATATAATAT
*
1452760 AAATGTTTTCAAAACTATATATTATATATATTTTAA
1 AAATGTTTTCAAAATTATATATTATATATATTTTAA
1452796 AAATGTTTTCAAAATTATATATAATATATATATTTTTGAA
1 AAATGTTTTCAAAATTATATAT--TATATATA-TTTT-AA
*
1452836 AACTGTTTTCTGAAAATTATATATTATA
1 AAATGTTTTC--AAAATTATATATTATA
1452864 CTTTGTCAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
36 21 0.35
38 8 0.13
39 4 0.07
40 15 0.25
42 12 0.20
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (36 bp):
AAATGTTTTCAAAATTATATATTATATATATTTTAA
Found at i:1453375 original size:13 final size:13
Alignment explanation
Indices: 1453348--1453390 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1453338 AAGTGTTGTA
*
1453348 TAAAAGAAT-TTT
1 TAAAAGTATATTT
1453360 TAAAAGTATATTT
1 TAAAAGTATATTT
* *
1453373 TAAAAGTACAGTT
1 TAAAAGTATATTT
1453386 TAAAA
1 TAAAA
1453391 TTTAACTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 8 0.30
13 19 0.70
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.37
Consensus pattern (13 bp):
TAAAAGTATATTT
Found at i:1453526 original size:21 final size:20
Alignment explanation
Indices: 1453475--1453527 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
1453465 TTATTAATCT
1453475 TTAATATATAAAAATATCAAA
1 TTAA-ATATAAAAATATCAAA
1453496 TTAAATTATAAAAATAT-AAA
1 TTAAA-TATAAAAATATCAAA
1453516 TGATAAATATAA
1 T--TAAATATAA
1453528 TTATAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.17
21 20 0.69
22 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
TTAAATATAAAAATATCAAA
Found at i:1453572 original size:48 final size:51
Alignment explanation
Indices: 1453482--1453578 Score: 128
Period size: 51 Copynumber: 2.0 Consensus size: 51
1453472 TCTTTAATAT
* * *
1453482 ATAAAAATATCAAATTAAATTATAAAAATATAAATGATAAATATAATTATA
1 ATAAAAATATCAAATGAAACTATAAAAATATAAATCATAAATATAATTATA
* *
1453533 ATAAAAATATGAAATGAAACTA-AAAAATATAGA-CA-AAATATAATTA
1 ATAAAAATATCAAATGAAACTATAAAAATATAAATCATAAATATAATTA
1453579 GTATATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
48 11 0.27
49 1 0.02
50 10 0.24
51 19 0.46
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (51 bp):
ATAAAAATATCAAATGAAACTATAAAAATATAAATCATAAATATAATTATA
Found at i:1457720 original size:200 final size:201
Alignment explanation
Indices: 1457346--1458027 Score: 941
Period size: 200 Copynumber: 3.4 Consensus size: 201
1457336 TTTAAGTATA
* * * **
1457346 CCGGTAACATTGCAAATTTACTTATTACATTATAATTATCGGTTTCGAAATTTTTGGGATCGATA
1 CCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATA
* * * * * * *
1457411 C-AATTTTAAATGTATCGACATTTTATGCATGTACCTCGTTGGGCATTCATTCTGGA-AAAAAGT
66 CTTATTATAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATTCTGGACAAAAAGT
* * * * * *
1457474 ATCGACACAAACTT-AAAAAGTGTCGATACATTATGTAGAACTATTTTCTTATAAAACTGGTATA
131 ATCGACAC-AAGTTCCACAAGTGTCGATACATTATGTAGACCTATTTTCTTATAAAACCGGTAAA
1457538 TTTCTAT
195 TTTCTAT
* *
1457545 CCGG-TACATTGTAAATTTACCTATTACATTGTAATTATCGATTTCGATGTTTTTGGGATCGATA
1 CCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATA
*
1457609 CTTATAATAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATTCTGGACAAAAAGT
66 CTTATTATAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATTCTGGACAAAAAGT
1457674 ATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACCTATTTT-TTCATAAAACCGGTAAA
131 ATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACCTATTTTCTT-ATAAAACCGGTAAA
1457738 TTTCTA-
195 TTTCTAT
* * *
1457744 CCGGTTACATGGTAAATTTACATATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATA
1 CCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATA
* * * * *
1457809 CTTTTTATAAATGTATCGACACTTTATGTGTGCA-CCCTTTTCGGCTTTCATTCTGGACAATAAG
66 CTTATTATAAATGTATCGACACTTTATGCGTGCACCCCGTTT-GGCATTCATTCTGGACAAAAAG
* * *
1457873 TATCGACACAAGTTCCACAAGAGTCGATACATTATGTAGACCTATTTTCTCATAAAACCAGTAAA
130 TATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACCTATTTTCTTATAAAACCGGTAAA
*
1457938 TTTATAT
195 TTTCTAT
*
1457945 -CGGTTACATTGTAAATTTGCCTATTACATTATAATTAT-GTGTTTCGATGTTTTTGGGATCGAT
1 CCGGTTACATTGTAAATTTACCTATTACATTATAATTATCG-GTTTCGATGTTTTTGGGATCGAT
* *
1458008 ACTTTTTATAAATATATCGA
65 ACTTATTATAAATGTATCGA
1458028 TACATATTTA
Statistics
Matches: 434, Mismatches: 40, Indels: 17
0.88 0.08 0.03
Matches are distributed among these distances:
198 54 0.12
199 68 0.16
200 311 0.72
201 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (201 bp):
CCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATA
CTTATTATAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATTCTGGACAAAAAGT
ATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACCTATTTTCTTATAAAACCGGTAAAT
TTCTAT
Found at i:1465758 original size:19 final size:19
Alignment explanation
Indices: 1465734--1465781 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
1465724 TTACATTGAC
1465734 ATACAAAATTATAAATCAT
1 ATACAAAATTATAAATCAT
* *
1465753 ATACAAAATTATGAATCGT
1 ATACAAAATTATAAATCAT
1465772 ATACAAAATT
1 ATACAAAATT
1465782 TCCTCTCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCAT
Found at i:1466388 original size:22 final size:23
Alignment explanation
Indices: 1466360--1466415 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
1466350 AACCTGCATT
*
1466360 TATAATAAAAT-TTATCATTTTA
1 TATAATAAAATACTATCATTTTA
*
1466382 TATAATAACTATACTATCATTTTA
1 TATAATAA-AATACTATCATTTTA
*
1466406 TATAAAAAAA
1 TATAATAAAA
1466416 CAAAAATGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 8 0.29
23 3 0.11
24 17 0.61
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAATAAAATACTATCATTTTA
Found at i:1468430 original size:20 final size:21
Alignment explanation
Indices: 1468402--1468440 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1468392 GTAGCTCTTT
*
1468402 ACCGATTTTTTCAT-TTTTAG
1 ACCGATTTTATCATATTTTAG
*
1468422 ACCGGTTTTATCATATTTT
1 ACCGATTTTATCATATTTT
1468441 TACTTGTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.21, C:0.15, G:0.10, T:0.54
Consensus pattern (21 bp):
ACCGATTTTATCATATTTTAG
Found at i:1468587 original size:182 final size:182
Alignment explanation
Indices: 1468280--1468837 Score: 834
Period size: 182 Copynumber: 3.1 Consensus size: 182
1468270 AACCCAAGTG
* * *
1468280 TCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCGATTACTGCTTCTTTTTTAAATTCCA
1 TCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTTCA
*
1468345 AAAGTGTCGATACTTATAATAAAGTATCGACACTTTTAACATAT-TCGGTAGCTCTTTACCGATT
66 AAAGTGTCGATACTTATAATAAAGTATCGACACTTTTAACATATCT-GGTAGCTCTTTACCGGTT
*
1468409 TTTTCATTTTTAGACCGGTTTTATCATATTTTTACTTGTTATATTGTTATGGA
130 TTGTCATTTTTAGACCGGTTTTATCATATTTTTACTTGTTATATTGTTATGGA
1468462 TCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTTCA
1 TCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTTCA
*
1468527 AAAGTGTCGATACTTATAATAAAGTATCGACACTTTTAACATATCTGGTGGCTCTTTACCGGTTT
66 AAAGTGTCGATACTTATAATAAAGTATCGACACTTTTAACATATCTGGTAGCTCTTTACCGGTTT
* * * *
1468592 TGTCAGTTTTAGATCGGTTTTATCGTATTTTTACATG-TATATTGTTATGGA
131 TGTCATTTTTAGACCGGTTTTATCATATTTTTACTTGTTATATTGTTATGGA
* * *** * *
1468643 TCGATACATTTTTTTAAAGTATCAACACTTTATAAATGCTATTACTGTTTGTCTTTTAAATTTCA
1 TCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTTCA
* * * *
1468708 AAAGTGTTGATACTTATAATAAAGTATCGACACTTTCAACATATCTAGTAG-TGCTTAACCGGTT
66 AAAGTGTCGATACTTATAATAAAGTATCGACACTTTTAACATATCTGGTAGCT-CTTTACCGGTT
* * * * *
1468772 TGGTCATTTTGAGACCGGTTATGTCATATTTTTACTTGTTATATTGCTATGGA
130 TTGTCATTTTTAGACCGGTTTTATCATATTTTTACTTGTTATATTGTTATGGA
*
1468825 TCAATACATTTTT
1 TCGATACATTTTT
1468838 TATTTGTATC
Statistics
Matches: 341, Mismatches: 32, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
180 1 0.00
181 159 0.47
182 180 0.53
183 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (182 bp):
TCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTTCA
AAAGTGTCGATACTTATAATAAAGTATCGACACTTTTAACATATCTGGTAGCTCTTTACCGGTTT
TGTCATTTTTAGACCGGTTTTATCATATTTTTACTTGTTATATTGTTATGGA
Found at i:1472568 original size:156 final size:158
Alignment explanation
Indices: 1472279--1472592 Score: 589
Period size: 156 Copynumber: 2.0 Consensus size: 158
1472269 CTAGTATACT
*
1472279 TGACTTTCATGAGTGTTTTCTTCACTTAATTATCTTTTGGTGGTTTCGACATCTGGAGGAAAATA
1 TGACTTTCATGAGCGTTTTCTTCACTTAATTATCTTTTGGTGGTTTCGACATCTGGAGGAAAATA
1472344 CTCCTCTTTCCGAAGTATCGATATTTAGTGGATACACTGTTTTCAAAACAATAAAAAATTAATCT
66 CTCCTCTTTCCGAAGTATCGATATTTAGTGGATACACTGTTTTCAAAACAATAAAAAATTAATCT
1472409 TGCTCAAAACA-TTTCGGTGAGCTAGTG
131 TGCTCAAAACATTTTCGGTGAGCTAGTG
1472436 TGAC-TTCATGAGCGTTTTCTTCAC-TAATTATCTTTTGGTGGTTTCGACCATCTGGAGGAAAAT
1 TGACTTTCATGAGCGTTTTCTTCACTTAATTATCTTTTGGTGGTTTCGA-CATCTGGAGGAAAAT
1472499 ACTCCTCTTTCCGAAGTATCGATATTTAGTGGATACACTGTTTTCAAAACAATAAAAAATTAATC
65 ACTCCTCTTTCCGAAGTATCGATATTTAGTGGATACACTGTTTTCAAAACAATAAAAAATTAATC
1472564 TTGCTCAAAACATTTTCGGTGAGCTAGTG
130 TTGCTCAAAACATTTTCGGTGAGCTAGTG
1472593 GACACTGTAA
Statistics
Matches: 154, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
155 23 0.15
156 111 0.72
157 20 0.13
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (158 bp):
TGACTTTCATGAGCGTTTTCTTCACTTAATTATCTTTTGGTGGTTTCGACATCTGGAGGAAAATA
CTCCTCTTTCCGAAGTATCGATATTTAGTGGATACACTGTTTTCAAAACAATAAAAAATTAATCT
TGCTCAAAACATTTTCGGTGAGCTAGTG
Found at i:1477050 original size:18 final size:18
Alignment explanation
Indices: 1477023--1477084 Score: 108
Period size: 18 Copynumber: 3.5 Consensus size: 18
1477013 TAGAATGCAA
1477023 AAAT-GGTACTGATACCC
1 AAATGGGTACTGATACCC
1477040 AAATGGGTACTGATACCC
1 AAATGGGTACTGATACCC
*
1477058 AAATGGGTACCGATACCC
1 AAATGGGTACTGATACCC
1477076 AAATGGGTA
1 AAATGGGTA
1477085 TCGACGATAC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
17 4 0.09
18 39 0.91
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (18 bp):
AAATGGGTACTGATACCC
Found at i:1477980 original size:20 final size:20
Alignment explanation
Indices: 1477938--1477987 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1477928 AAATATAGTT
*
1477938 GTATCGATACTGCTATAACA
1 GTATCGATACTGCTATAAAA
*
1477958 GTATCGATACTGTTA-AAGAA
1 GTATCGATACTGCTATAA-AA
*
1477978 GTATCAATAC
1 GTATCGATAC
1477988 ATATATTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACTGCTATAAAA
Found at i:1478186 original size:95 final size:95
Alignment explanation
Indices: 1478023--1478227 Score: 297
Period size: 95 Copynumber: 2.2 Consensus size: 95
1478013 AATGAAGAAA
* *
1478023 TATCGATACTGCTGATACAGTACCGATACTGTCAAAAATGAATGCTAAAATGGTAGCGATACCAT
1 TATCGATACTGCTGAGACAGTACCGATACTGTCAAAAATGAATGCTAAAACGGTAGCGATACCAT
*
1478088 ATATGATATTGATACTACTCATAGTAGTAG
66 ATATGATATTGATACTACTCAGAGTAGTAG
* * *
1478118 TATCGATACTGCTGAGACAGTACTGATACTGTCAAAACA-GAATGCTAGAACGGTATCGATACCA
1 TATCGATACTGCTGAGACAGTACCGATACTGTCAAAA-ATGAATGCTAAAACGGTAGCGATACCA
* * *
1478182 TATATGATATTGATACTATTTAGATTAGTAG
65 TATATGATATTGATACTACTCAGAGTAGTAG
*
1478213 TACCGATACT-CTGAG
1 TATCGATACTGCTGAG
1478228 TAATGGTACC
Statistics
Matches: 99, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
94 5 0.05
95 93 0.94
96 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (95 bp):
TATCGATACTGCTGAGACAGTACCGATACTGTCAAAAATGAATGCTAAAACGGTAGCGATACCAT
ATATGATATTGATACTACTCAGAGTAGTAG
Found at i:1481984 original size:32 final size:31
Alignment explanation
Indices: 1481948--1482022 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 31
1481938 TCGGGCCGGG
1481948 TATATATATATTTAAATTAAATATATAA-ATAT
1 TATATATATATTTAAATTAAAT-TA-AATATAT
* * * *
1481980 TATATATTTTTTTAATTTAAATTAAATTTAT
1 TATATATATATTTAAATTAAATTAAATATAT
1482011 TAATATATATAT
1 T-ATATATATAT
1482023 ATAATAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 2 0.06
31 6 0.17
32 27 0.77
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TATATATATATTTAAATTAAATTAAATATAT
Found at i:1482859 original size:19 final size:19
Alignment explanation
Indices: 1482835--1482889 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 19
1482825 TTCTAAAAAA
1482835 TAAAATTCATAATTTTTTT
1 TAAAATTCATAATTTTTTT
1482854 TAAAATAT-ATGAATTTCTTTT
1 TAAAAT-TCAT-AATTT-TTTT
1482875 TAAAATTC-TAATTTT
1 TAAAATTCATAATTTT
1482890 GTAAAAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
18 1 0.03
19 13 0.41
20 8 0.25
21 10 0.31
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (19 bp):
TAAAATTCATAATTTTTTT
Found at i:1483478 original size:13 final size:13
Alignment explanation
Indices: 1483445--1483492 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
1483435 TCTATGACCG
*
1483445 CATTTATAACACA
1 CATTTATGACACA
1483458 CATTTATGACACA
1 CATTTATGACACA
* * *
1483471 CATTTATGGCGCG
1 CATTTATGACACA
1483484 CATTTATGA
1 CATTTATGA
1483493 TGTTCATTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (13 bp):
CATTTATGACACA
Found at i:1488849 original size:16 final size:16
Alignment explanation
Indices: 1488828--1488871 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
1488818 ACAGAGATTC
*
1488828 TGAATCATTCAGTATT
1 TGAATCATTCAATATT
1488844 TGAATCATTCAATATT
1 TGAATCATTCAATATT
1488860 TGAATCATTCAA
1 TGAATCATTCAA
1488872 CTTAATCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (16 bp):
TGAATCATTCAATATT
Found at i:1492384 original size:13 final size:13
Alignment explanation
Indices: 1492366--1492390 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1492356 GACCTTGGTA
1492366 ATTTAAAAAAATT
1 ATTTAAAAAAATT
1492379 ATTTAAAAAAAT
1 ATTTAAAAAAAT
1492391 CATAAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATTTAAAAAAATT
Found at i:1493290 original size:59 final size:60
Alignment explanation
Indices: 1493163--1493295 Score: 164
Period size: 60 Copynumber: 2.2 Consensus size: 60
1493153 AAAGTAAGGT
*
1493163 AAAGTATAC-AAATAGTCTCTCAATTATAAGATACTATTTTGTTGAGTCCATCGACTATTA
1 AAAGT-TACAAAATAGTCTCTCAATTATAAGATACTACTTTGTTGAGTCCATCGACTATTA
* * * ** *
1493223 GAAGTTACAAAATAGTCTCTCGATTATAGGATGTTACTTTGTTGAGTCTC-TC-ATTATTA
1 AAAGTTACAAAATAGTCTCTCAATTATAAGATACTACTTTGTTGAGTC-CATCGACTATTA
1493282 AAAGTTACAAAATA
1 AAAGTTACAAAATA
1493296 ATCACCATGC
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
59 22 0.35
60 40 0.63
61 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (60 bp):
AAAGTTACAAAATAGTCTCTCAATTATAAGATACTACTTTGTTGAGTCCATCGACTATTA
Found at i:1494060 original size:60 final size:61
Alignment explanation
Indices: 1493955--1494118 Score: 160
Period size: 60 Copynumber: 2.7 Consensus size: 61
1493945 ATTATGATAC
* * * * ** *
1493955 TCATTCTAAGTTAGTCCCTAAAC-TTTT-AAGTATTCCAA-TCTCATCCTTAAAATATGA-TT
1 TCATTCTAAATTAATCCCTAAACTTTTTGAA-CATTTCAATTC-CATCCCCAAAATATGACCT
* * *
1494014 GTCATTCTAAATTAA-CCCTCAAGC-TTTTGAACATTTTAATTCCATCCCCAAACTATGACCT
1 -TCATTCTAAATTAATCCCT-AAACTTTTTGAACATTTCAATTCCATCCCCAAAATATGACCT
1494075 TCATTCTAAATTAATCCCTAAACTTTTTGAACATTTCAATTCCA
1 TCATTCTAAATTAATCCCTAAACTTTTTGAACATTTCAATTCCA
1494119 CCCTAAACTA
Statistics
Matches: 86, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
59 4 0.05
60 54 0.63
61 28 0.33
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.38
Consensus pattern (61 bp):
TCATTCTAAATTAATCCCTAAACTTTTTGAACATTTCAATTCCATCCCCAAAATATGACCT
Found at i:1494127 original size:60 final size:60
Alignment explanation
Indices: 1494015--1494129 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
1494005 AATATGATTG
* *
1494015 TCATTCTAAATTAACCCTCAAGCTTTTGAACATTTTAATTCCATCCCCAAACTATGACCT
1 TCATTCTAAATTAACCCTCAAACTTTTGAACATTTCAATTCCATCCCCAAACTATGACCT
*
1494075 TCATTCTAAATTAATCCCT-AAACTTTTTGAACATTTCAATTCCA-CCCTAAACTAT
1 TCATTCTAAATTAA-CCCTCAAAC-TTTTGAACATTTCAATTCCATCCCCAAACTAT
1494130 ACGTATAAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
60 27 0.54
61 23 0.46
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (60 bp):
TCATTCTAAATTAACCCTCAAACTTTTGAACATTTCAATTCCATCCCCAAACTATGACCT
Found at i:1494362 original size:60 final size:60
Alignment explanation
Indices: 1494250--1494434 Score: 176
Period size: 60 Copynumber: 3.1 Consensus size: 60
1494240 TATTTGGATG
* * **
1494250 AATTTGGGGGTAAAATTGAAAGATTCAAAAGTTTGGGGACCAAATTAAAATGATG-GTCAT
1 AATTTGGGGGTGAAATTGAAATATTCAAAAGTTTAAGGACCAAATTAAAATGA-GAGTCAT
* * * * ** *
1494310 AGTTTGGGGGTGAAAGTGGAATATTCAAAAGTTTAAGGACTAGCTTACAATGAGAGTCAT
1 AATTTGGGGGTGAAATTGAAATATTCAAAAGTTTAAGGACCAAATTAAAATGAGAGTCAT
* * * * * **
1494370 AATTTAGGGATGAAATTAAAATATTCAAAAAG-TTCAGGACCAATTTAAAATGAGTTTCAT
1 AATTTGGGGGTGAAATTGAAATATTC-AAAAGTTTAAGGACCAAATTAAAATGAGAGTCAT
1494430 AATTT
1 AATTT
1494435 AAGGACATAT
Statistics
Matches: 99, Mismatches: 24, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
59 1 0.01
60 93 0.94
61 5 0.05
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (60 bp):
AATTTGGGGGTGAAATTGAAATATTCAAAAGTTTAAGGACCAAATTAAAATGAGAGTCAT
Found at i:1495438 original size:30 final size:30
Alignment explanation
Indices: 1495380--1495439 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1495370 GCGGCTTTCA
* *
1495380 ACAAACGCCGCAACAGGTGTTAATATTTAG
1 ACAAACGCCGCAACAAGTGTTAACATTTAG
* * *
1495410 ACAAACGCCGCAATAAGTTTTGACATTTAG
1 ACAAACGCCGCAACAAGTGTTAACATTTAG
1495440 CGACATTTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (30 bp):
ACAAACGCCGCAACAAGTGTTAACATTTAG
Found at i:1495470 original size:40 final size:40
Alignment explanation
Indices: 1495410--1495507 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 40
1495400 TAATATTTAG
*
1495410 ACAAACGCCGCAATAAGTTTTGACATTTAGCGACATTTGT
1 ACAAACGCCGCAATAAGTTTTGACATTAAGCGACATTTGT
* * *
1495450 ACAAACGTCGCAATAGGTTTTGACATTAAGCGACGTTTGTCTT
1 ACAAACGCCGCAATAAGTTTTGACATTAAGCGACATTTG---T
*
1495493 ACAAACGCTGCAATA
1 ACAAACGCCGCAATA
1495508 GGATTTGGTA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
40 35 0.71
43 14 0.29
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (40 bp):
ACAAACGCCGCAATAAGTTTTGACATTAAGCGACATTTGT
Found at i:1495607 original size:44 final size:43
Alignment explanation
Indices: 1495559--1495661 Score: 125
Period size: 44 Copynumber: 2.4 Consensus size: 43
1495549 TAAAGATCTG
* * * * * *
1495559 GTATATAGCGGCGTTTTTAGGATACAAACGTCGGTGATGGTCTA
1 GTATATAGCGGCGTTTTGAGAACACAAACGTCGCTAAAGGT-TA
* *
1495603 GTATATAGCGGCGTTTTGAGAACACAGACGTCGCTAAAGGTTG
1 GTATATAGCGGCGTTTTGAGAACACAAACGTCGCTAAAGGTTA
1495646 GTATATAGCGGCGTTT
1 GTATATAGCGGCGTTT
1495662 GTAACAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 17 0.33
44 34 0.67
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (43 bp):
GTATATAGCGGCGTTTTGAGAACACAAACGTCGCTAAAGGTTA
Found at i:1496444 original size:22 final size:22
Alignment explanation
Indices: 1496419--1496462 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1496409 AATAATTAAT
1496419 TAAA-ATAAA-AAATGTCATGGTA
1 TAAATATAAATAAA-GTCA-GGTA
1496441 TAAATATAAATAAAGTCAGGTA
1 TAAATATAAATAAAGTCAGGTA
1496463 AATTTAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.40
23 9 0.45
24 3 0.15
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.27
Consensus pattern (22 bp):
TAAATATAAATAAAGTCAGGTA
Found at i:1504489 original size:22 final size:22
Alignment explanation
Indices: 1504464--1504505 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1504454 TTCAGAAGCT
1504464 ATTATTTTCCTATTCGAAAGAA
1 ATTATTTTCCTATTCGAAAGAA
*
1504486 ATTATTTTTCTATTCGAAAG
1 ATTATTTTCCTATTCGAAAG
1504506 CAAAAAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
ATTATTTTCCTATTCGAAAGAA
Found at i:1505180 original size:41 final size:41
Alignment explanation
Indices: 1505042--1505184 Score: 112
Period size: 41 Copynumber: 3.4 Consensus size: 41
1505032 AGTGTTTTTG
* * *
1505042 TAAACAAACGCTGCTAAATTACCACTCTATTGTGGCGTTTGTT
1 TAAA-AAACGCCGCTAAATTACC-CTCTATTGCGGCGTTTATT
* * * **
1505085 GAAAAAAACGCCACTATAA--ACATCTCTATTGCGGCGTTTGAGC
1 -TAAAAAACGCCGCTA-AATTAC-CCTCTATTGCGGCGTTT-ATT
* * *
1505128 T-ATAAATGCCGCTAAATTACCCTCTATTACGGCGTTTATT
1 TAAAAAACGCCGCTAAATTACCCTCTATTGCGGCGTTTATT
1505168 TAAAAAACGCCGCTAAA
1 TAAAAAACGCCGCTAAA
1505185 GTATCATTTT
Statistics
Matches: 75, Mismatches: 18, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
40 4 0.05
41 38 0.51
42 19 0.25
43 9 0.12
44 5 0.07
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (41 bp):
TAAAAAACGCCGCTAAATTACCCTCTATTGCGGCGTTTATT
Found at i:1505789 original size:23 final size:23
Alignment explanation
Indices: 1505715--1505792 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
1505705 TAAACGACGC
* *
1505715 TAAACGAACATGTTCGTGAACAC
1 TAAACAAACATGTTCGTGAACAA
* * * * *
1505738 TAAATAAATATATTCATTAACATA
1 TAAACAAACATGTTCGTGAACA-A
1505762 TAAACAAACATGTTCGTGAACAA
1 TAAACAAACATGTTCGTGAACAA
1505785 TAAACAAA
1 TAAACAAA
1505793 TGAACACAAA
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
23 25 0.60
24 17 0.40
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (23 bp):
TAAACAAACATGTTCGTGAACAA
Found at i:1508763 original size:34 final size:34
Alignment explanation
Indices: 1508725--1508791 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
1508715 ACTGTAAACC
*
1508725 TCAAATATTAAATTATAAA-CTATAAACTCTAAAT
1 TCAAACATTAAATTATAAATCT-TAAACTCTAAAT
* * *
1508759 TCAAACCTTAAATTCTAAATCTTAAACTTTAAA
1 TCAAACATTAAATTATAAATCTTAAACTCTAAA
1508792 CATAAACCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (34 bp):
TCAAACATTAAATTATAAATCTTAAACTCTAAAT
Found at i:1508770 original size:20 final size:21
Alignment explanation
Indices: 1508747--1508792 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1508737 TTATAAACTA
1508747 TAAACTCTAAAT-TCAAACCT
1 TAAACTCTAAATCTCAAACCT
* * *
1508767 TAAATTCTAAATCTTAAACTT
1 TAAACTCTAAATCTCAAACCT
1508788 TAAAC
1 TAAAC
1508793 ATAAACCCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAACTCTAAATCTCAAACCT
Found at i:1510000 original size:20 final size:21
Alignment explanation
Indices: 1509975--1510014 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1509965 CCGATTCACC
1509975 TCGGTT-TTCCTGGTT-TTTAG
1 TCGGTTCTTCC-GGTTCTTTAG
1509995 TCGGTTCTTCCGGTTCTTTA
1 TCGGTTCTTCCGGTTCTTTA
1510015 CCAGTTCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.05, C:0.20, G:0.23, T:0.53
Consensus pattern (21 bp):
TCGGTTCTTCCGGTTCTTTAG
Found at i:1511343 original size:23 final size:23
Alignment explanation
Indices: 1511286--1511344 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
1511276 ATAGACGAAG
* * *
1511286 ACGTTCACAAACATTAAACGAAC
1 ACGTTCGCGAACATTAAAAGAAC
* *
1511309 ACGTTTGTGAACATTAAAAGAAC
1 ACGTTCGCGAACATTAAAAGAAC
*
1511332 ATGTTCGCGAACA
1 ACGTTCGCGAACA
1511345 ATAATTAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.22
Consensus pattern (23 bp):
ACGTTCGCGAACATTAAAAGAAC
Found at i:1514687 original size:64 final size:64
Alignment explanation
Indices: 1514586--1514716 Score: 262
Period size: 64 Copynumber: 2.0 Consensus size: 64
1514576 TGTTATTACT
1514586 TTTAGAATTATTATAGTGCTCGCTGTTGCTTGCAAACTTGATGTGGTTTTCCAAAAAATGGATA
1 TTTAGAATTATTATAGTGCTCGCTGTTGCTTGCAAACTTGATGTGGTTTTCCAAAAAATGGATA
1514650 TTTAGAATTATTATAGTGCTCGCTGTTGCTTGCAAACTTGATGTGGTTTTCCAAAAAATGGATA
1 TTTAGAATTATTATAGTGCTCGCTGTTGCTTGCAAACTTGATGTGGTTTTCCAAAAAATGGATA
1514714 TTT
1 TTT
1514717 TGATTTTGAC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.40
Consensus pattern (64 bp):
TTTAGAATTATTATAGTGCTCGCTGTTGCTTGCAAACTTGATGTGGTTTTCCAAAAAATGGATA
Found at i:1518996 original size:58 final size:59
Alignment explanation
Indices: 1518900--1519068 Score: 171
Period size: 58 Copynumber: 2.8 Consensus size: 59
1518890 TATGATTACT
* * *
1518900 ATTTTAAATTGATCTTTAAACTTTTGAATATTTTAATTTCATCCCCAAATTA-G-CACTC
1 ATTTTAAATTG-TCTTTAAACTTATGAATATTTCAATTTCATCCCCAAACTATGACACTC
* * * *
1518958 ATTTTAAATTAGTCTTTAAACTTATGAATATTCCAATTTCTTCCTCAAACTATGACTCTC
1 ATTTTAAATT-GTCTTTAAACTTATGAATATTTCAATTTCATCCCCAAACTATGACACTC
* ** * * * *
1519018 ATTCTAAATTTGTCTCCAAACTTCTAAATCTTTCAATTTCATCTCCAAACT
1 ATTTTAAA-TTGTCTTTAAACTTATGAATATTTCAATTTCATCCCCAAACT
1519069 CATCCAAATA
Statistics
Matches: 90, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
58 44 0.49
59 2 0.02
60 42 0.47
61 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.43
Consensus pattern (59 bp):
ATTTTAAATTGTCTTTAAACTTATGAATATTTCAATTTCATCCCCAAACTATGACACTC
Found at i:1519067 original size:60 final size:57
Alignment explanation
Indices: 1518934--1519068 Score: 126
Period size: 60 Copynumber: 2.3 Consensus size: 57
1518924 TGAATATTTT
* * ** *
1518934 AATTTCATCCCCAAATTAGCACTCATTTTAAATTAGTCTTTAAACTTATGAATATTCC
1 AATTTCAT-CCCAAACTAGCACTCATTCTAAATTAGTCTCCAAACTTATAAATATTCC
* * * * * *
1518992 AATTTCTTCCTCAAACTATGACTCTCATTCTAAATTTGTCTCCAAACTTCTAAATCTTTC
1 AATTTCATCC-CAAACTA-G-CACTCATTCTAAATTAGTCTCCAAACTTATAAATATTCC
1519052 AATTTCATCTCCAAACT
1 AATTTCATC-CCAAACT
1519069 CATCCAAATA
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
57 2 0.03
58 13 0.21
59 1 0.02
60 44 0.72
61 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (57 bp):
AATTTCATCCCAAACTAGCACTCATTCTAAATTAGTCTCCAAACTTATAAATATTCC
Found at i:1519106 original size:85 final size:85
Alignment explanation
Indices: 1519011--1519180 Score: 340
Period size: 85 Copynumber: 2.0 Consensus size: 85
1519001 CTCAAACTAT
1519011 GACTCTCATTCTAAATTTGTCTCCAAACTTCTAAATCTTTCAATTTCATCTCCAAACTCATCCAA
1 GACTCTCATTCTAAATTTGTCTCCAAACTTCTAAATCTTTCAATTTCATCTCCAAACTCATCCAA
1519076 ATATGTTATTAATTTTAACC
66 ATATGTTATTAATTTTAACC
1519096 GACTCTCATTCTAAATTTGTCTCCAAACTTCTAAATCTTTCAATTTCATCTCCAAACTCATCCAA
1 GACTCTCATTCTAAATTTGTCTCCAAACTTCTAAATCTTTCAATTTCATCTCCAAACTCATCCAA
1519161 ATATGTTATTAATTTTAACC
66 ATATGTTATTAATTTTAACC
1519181 ATAGTTTAAC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.40
Consensus pattern (85 bp):
GACTCTCATTCTAAATTTGTCTCCAAACTTCTAAATCTTTCAATTTCATCTCCAAACTCATCCAA
ATATGTTATTAATTTTAACC
Found at i:1519375 original size:60 final size:60
Alignment explanation
Indices: 1519298--1519441 Score: 152
Period size: 60 Copynumber: 2.4 Consensus size: 60
1519288 AAATGTTGAA
** * ** *
1519298 AAAAATTTGGGGACTAATTTAAAA-TA-AATGATATAGTTTGGGGATGAAAA-TAAAATATTC
1 AAAAATTTAAGGACTAATTTAAAATTATAAT--TATAATTTAAGGAT-AAAATTAAAACATTC
*
1519358 AAAAATTTAAGGACTAATTTAAAATTATAATTATAATTTAAGGATAAAATTAAAACATTT
1 AAAAATTTAAGGACTAATTTAAAATTATAATTATAATTTAAGGATAAAATTAAAACATTC
*
1519418 AAAAGTTTAAGGA-TCAATTTAAAA
1 AAAAATTTAAGGACT-AATTTAAAA
1519442 AGATCATAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
59 5 0.07
60 62 0.86
61 2 0.03
62 3 0.04
ACGTcount: A:0.51, C:0.03, G:0.12, T:0.33
Consensus pattern (60 bp):
AAAAATTTAAGGACTAATTTAAAATTATAATTATAATTTAAGGATAAAATTAAAACATTC
Found at i:1524570 original size:32 final size:33
Alignment explanation
Indices: 1524526--1524595 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
1524516 ACCTTACAAC
* *
1524526 TCCCTAG-TTTTTACGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTAACGGGATAAACTAGAACCTT
*
1524558 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTA-ACGGGATAAACTAGAACCTT
1524592 TCCC
1 TCCC
1524596 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 4 0.12
34 22 0.67
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (33 bp):
TCCCTAGCTTTTAACGGGATAAACTAGAACCTT
Found at i:1524835 original size:20 final size:22
Alignment explanation
Indices: 1524810--1524849 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1524800 TGTTGTATAT
1524810 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1524830 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1524850 TCTACTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1525081 original size:20 final size:19
Alignment explanation
Indices: 1525056--1525132 Score: 100
Period size: 20 Copynumber: 3.8 Consensus size: 19
1525046 CTGTGTTTGA
1525056 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCA-G
*
1525076 GTGCATCGATGCACTAGTGCAG
1 GTGCATGGATGCAC---TGCAG
1525098 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCA-G
1525118 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1525133 TTGACACCCT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
19 4 0.08
20 29 0.57
22 14 0.27
23 4 0.08
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.23
Consensus pattern (19 bp):
GTGCATGGATGCACTGCAG
Found at i:1525269 original size:30 final size:29
Alignment explanation
Indices: 1525212--1525270 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
1525202 AAACTTTGAA
* *
1525212 TAAATTCAATTAAGTTCAAAAATATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
*
1525241 TAAATTCAATTCAAGTCCAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACATTTTG
1525271 CCTTAGATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:1526919 original size:53 final size:54
Alignment explanation
Indices: 1526838--1526946 Score: 202
Period size: 53 Copynumber: 2.0 Consensus size: 54
1526828 CTTCATAGAT
1526838 TTCATGACCAAATGAACAAAACAGCATGTGCATGGCCTTGGCATTAAGTTGAGC
1 TTCATGACCAAATGAACAAAACAGCATGTGCATGGCCTTGGCATTAAGTTGAGC
*
1526892 TTCATGACC-AATGCACAAAACAGCATGTGCATGGCCTTGGCATTAAGTTGAGC
1 TTCATGACCAAATGAACAAAACAGCATGTGCATGGCCTTGGCATTAAGTTGAGC
1526945 TT
1 TT
1526947 TCTTCCGTTC
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 45 0.83
54 9 0.17
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (54 bp):
TTCATGACCAAATGAACAAAACAGCATGTGCATGGCCTTGGCATTAAGTTGAGC
Found at i:1527788 original size:20 final size:22
Alignment explanation
Indices: 1527763--1527802 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1527753 TGTTGTATAT
1527763 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1527783 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1527803 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1528034 original size:22 final size:23
Alignment explanation
Indices: 1528003--1528045 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1527993 ATGGATACAC
1528003 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
1528026 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
1528046 GCAGGGGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:1528056 original size:21 final size:21
Alignment explanation
Indices: 1527989--1528087 Score: 123
Period size: 21 Copynumber: 4.7 Consensus size: 21
1527979 CGGTGTTTGA
* *
1527989 GTGCATGGATACACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
*
1528009 GTGCATCGATGCACT--AGTGCAG
1 GTGCATGGATGCACTGCAG-G--G
1528031 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
1528052 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
1528073 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1528088 TTGACACCCT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
18 1 0.01
20 13 0.19
21 37 0.54
22 15 0.22
23 1 0.01
24 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.22
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:1528201 original size:30 final size:31
Alignment explanation
Indices: 1528167--1528225 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1528157 AAACTTTGAA
1528167 TAAATTCAATT-AAGTCCAAAAACATTTTTG
1 TAAATTCAATTCAAGTCCAAAAACATTTTTG
*
1528197 TAAATTCAATTCAAGTCCAAAACCATTTT
1 TAAATTCAATTCAAGTCCAAAAACATTTT
1528226 GCCTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACATTTTTG
Found at i:1530362 original size:39 final size:39
Alignment explanation
Indices: 1530319--1530398 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
1530309 TAATTAAAAA
1530319 ATAAAATCATATCCAAATTCATCTATATCCTTTTTTATT
1 ATAAAATCATATCCAAATTCATCTATATCCTTTTTTATT
*
1530358 ATAAAATCATATCCTAATTCATCTATATCCTTTTTTATT
1 ATAAAATCATATCCAAATTCATCTATATCCTTTTTTATT
1530397 AT
1 AT
1530399 TTAAATCTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.47
Consensus pattern (39 bp):
ATAAAATCATATCCAAATTCATCTATATCCTTTTTTATT
Found at i:1538139 original size:20 final size:19
Alignment explanation
Indices: 1538114--1538168 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
1538104 TGGAAAGCAT
1538114 ATTTTAGGTTGCAACCAAAA
1 ATTTTAGGTTGCAACC-AAA
* * * * *
1538134 ATTTTAAGCTGGAAACTAA
1 ATTTTAGGTTGCAACCAAA
1538153 ATTTTAGGTTGCAACC
1 ATTTTAGGTTGCAACC
1538169 TAGATTCTAT
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (19 bp):
ATTTTAGGTTGCAACCAAA
Found at i:1543410 original size:80 final size:81
Alignment explanation
Indices: 1543110--1543521 Score: 451
Period size: 80 Copynumber: 5.1 Consensus size: 81
1543100 TATAATTCCT
* * * * * * * * * * * *
1543110 TTATTCTTTTACCCAAAGGTATTTAGCTTTTAATCTAACTTGCATATTTTACACTTTTATGTCAA
1 TTATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTGACTCCTTTCTGCCAA
* * *
1543175 ATGCACAACTAGTCTA
66 ATGCACAATTAGGCCA
* *
1543191 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGA-TACCTTTTTGCCA
1 TTATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTGACT-CCTTTCTGCCA
*
1543255 AATGCACAGTTAGGCCA
65 AATGCACAATTAGGCCA
* * *
1543272 TT-TATCTTTTACT--ACGGTCTTTAACTGTTCATCTAACTGGCATAATTGACACATTTCTGCCA
1 TTAT-TCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTGACTCCTTTCTGCCA
* *
1543334 AATTCACAACTAGGCCA
65 AATGCACAATTAGGCCA
* * *
1543351 TTGTTCTTTTACTCAACGGTATTT-ACCGTTAATCTAACTGGCATAATTGACTCCTTTCTGCCAA
1 TTATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTGACTCCTTTCTGCCAA
1543415 ATGCACAATTAGGCCA
66 ATGCACAATTAGGCCA
* * * * *
1543431 -TATTCTTTTACTCAATGGTATTTAACTATTCATATAACTGGCATAATTGACAT-TTTTTTGCCA
1 TTATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTGAC-TCCTTTCTGCCA
*
1543494 AATGCACAGTTAGGCCA
65 AATGCACAATTAGGCCA
*
1543511 TTAATCTTTTA
1 TTATTCTTTTA
1543522 TTTTTTTTAA
Statistics
Matches: 280, Mismatches: 42, Indels: 18
0.82 0.12 0.05
Matches are distributed among these distances:
79 89 0.32
80 99 0.35
81 92 0.33
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (81 bp):
TTATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTGACTCCTTTCTGCCAA
ATGCACAATTAGGCCA
Done.