Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008639.1 Hibiscus syriacus cultivar Beakdansim tig00111614_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: 1076872
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:566758 original size:21 final size:21
Alignment explanation
Indices: 566733--566777 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
566723 GAAATATTAA
* *
566733 AAAAATATTGATGTTTTAGAT
1 AAAAATAATAATGTTTTAGAT
566754 AAAAATAATAATGTTTTAGAT
1 AAAAATAATAATGTTTTAGAT
566775 AAA
1 AAA
566778 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (21 bp):
AAAAATAATAATGTTTTAGAT
Found at i:574989 original size:74 final size:74
Alignment explanation
Indices: 574868--575220 Score: 607
Period size: 74 Copynumber: 4.7 Consensus size: 74
574858 TAGTTTTTTT
574868 CTATTTTATCGGTGCTAATAAGGCCCTGGTCTTTCAATTACGGCTTGATTTGCTGACTATAAGGA
1 CTATTTTATCGGTGCTAATAAGGCCCTGGTCTTTCAATTACGGCTTGATTTGCTGACTATAAGGA
574933 TTTTCCCCC
66 TTTTCCCCC
574942 CTATTTTATCGGTGCTAATAAGGCCCTGGTCTTTCAATTACGGCTTGATTTGCTGACTATAAGGA
1 CTATTTTATCGGTGCTAATAAGGCCCTGGTCTTTCAATTACGGCTTGATTTGCTGACTATAAGGA
575007 TTTTCCCCC
66 TTTTCCCCC
575016 CTATTTTATCGGTGCTAATAAGGCCCTGGTCTTTCAATTACGGCTTGATTTGCTGACTATAAGGA
1 CTATTTTATCGGTGCTAATAAGGCCCTGGTCTTTCAATTACGGCTTGATTTGCTGACTATAAGGA
575081 TTTTCCCCC
66 TTTTCCCCC
* *
575090 CTATTTTATCGGTGCTAATAAGGCCATGGTCTTTCAATTACGGCTTGATTTGCCGACTATAAGGA
1 CTATTTTATCGGTGCTAATAAGGCCCTGGTCTTTCAATTACGGCTTGATTTGCTGACTATAAGGA
* ***
575155 TTTTTTTCTTT
66 --TTTTCCCCC
* * *
575166 CTATTTTATAGGTGCTAATAAGGCTCTGGTCTTTCAATTGCGGCTTGATTTGCTG
1 CTATTTTATCGGTGCTAATAAGGCCCTGGTCTTTCAATTACGGCTTGATTTGCTG
575221 TGATGGAGTA
Statistics
Matches: 266, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
74 211 0.79
76 55 0.21
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.40
Consensus pattern (74 bp):
CTATTTTATCGGTGCTAATAAGGCCCTGGTCTTTCAATTACGGCTTGATTTGCTGACTATAAGGA
TTTTCCCCC
Found at i:576442 original size:23 final size:23
Alignment explanation
Indices: 576415--576459 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
576405 CTTATGAAAA
576415 GTCAAAAATTTCAGCTTACAATG
1 GTCAAAAATTTCAGCTTACAATG
*
576438 GTCAAAATTTTCAGCTTACAAT
1 GTCAAAAATTTCAGCTTACAAT
576460 AGTCCAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (23 bp):
GTCAAAAATTTCAGCTTACAATG
Found at i:577157 original size:18 final size:17
Alignment explanation
Indices: 577122--577177 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
577112 ATAATAAATT
577122 TTATATTTTGATTTAAA
1 TTATATTTTGATTTAAA
577139 TTATATTTGGTGA-TTAAA
1 TTATATTT--TGATTTAAA
*
577157 TTAAATTTT-A-TTATAA
1 TTATATTTTGATTTA-AA
577173 TTATA
1 TTATA
577178 GTGGTTAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
15 4 0.12
16 7 0.21
17 8 0.24
18 12 0.35
19 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (17 bp):
TTATATTTTGATTTAAA
Found at i:578119 original size:8 final size:8
Alignment explanation
Indices: 578108--578132 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
578098 ATTAAAAATT
578108 AAAAAGAA
1 AAAAAGAA
578116 AAAAAGAA
1 AAAAAGAA
578124 AAAAAGAA
1 AAAAAGAA
578132 A
1 A
578133 CGGTGAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:579141 original size:70 final size:70
Alignment explanation
Indices: 579016--579151 Score: 166
Period size: 70 Copynumber: 1.9 Consensus size: 70
579006 ATGAACACTT
* *
579016 AACGAACATATTCATGAACACGTTCGTTAACATATAAACAAATAAGTTTGTGAACATTAAACGAA
1 AACGAACATATTCATGAACACGTTCGTTAACATATAAACAAACAAGTTTGCGAACATTAAACGAA
579081 CGATA
66 CGATA
* ** * * * * *
579086 AACGAACATGTTCATGAACGTGTTCGTTTACGTATAAACGAACATGTTCT-CGAACATTAAATGA
1 AACGAACATATTCATGAACACGTTCGTTAACATATAAACAAACAAGTT-TGCGAACATTAAACGA
579150 AC
65 AC
579152 ATATTCGTGA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
70 54 0.98
71 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (70 bp):
AACGAACATATTCATGAACACGTTCGTTAACATATAAACAAACAAGTTTGCGAACATTAAACGAA
CGATA
Found at i:579151 original size:23 final size:23
Alignment explanation
Indices: 579119--579175 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
579109 TCGTTTACGT
* *
579119 ATAAACGAACATGTTC-TCGAACA
1 ATAAATGAACATATTCGT-GAACA
*
579142 TTAAATGAACATATTCGTGAACA
1 ATAAATGAACATATTCGTGAACA
*
579165 ATAAATAAACA
1 ATAAATGAACA
579176 AACACGAACA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.25
Consensus pattern (23 bp):
ATAAATGAACATATTCGTGAACA
Found at i:581924 original size:154 final size:146
Alignment explanation
Indices: 581712--582014 Score: 446
Period size: 154 Copynumber: 2.0 Consensus size: 146
581702 GAGATTTAAT
* * *
581712 GCAACTATAGAAATGTTCAGCACACAACCTAACTGGAAAATATAGACAAAACGTGTATGCACTCT
1 GCAACTATAGAAATGTTCAGCACACAACCGAACTGAAAAATATAGACAAAACGTGTATGCACTCA
* *
581777 GCAAGTGTAAAACATCAAAAACACCAAGGTGACAAATAACAGAACCTAAACTTTTGAAGAAAACA
66 GAAAGTGTAAAACAT---------CAAGGTGACAAATAACAAAACCTAAACTTTTGAAGAAAACA
* *
581842 AGGATTTAAACCAATATATG-TTAG
122 AGGAGTTAAACAAATATATGATTAG
*
581866 GCAACTCTAGAAATGTTCAGCACACAACCGAACTGAAAAATATAGACAAAACGTGTATGCACTCA
1 GCAACTATAGAAATGTTCAGCACACAACCGAACTGAAAAATATAGACAAAACGTGTATGCACTCA
581931 GAAAGTGTAAAACATCAAGGTGACAAATAACAAAACCTAAACTTTTGAAGAAAACAAGGAGTTAA
66 GAAAGTGTAAAACATCAAGGTGACAAATAACAAAACCTAAACTTTTGAAGAAAACAAGGAGTTAA
581996 ACAAATATATGATTAG
131 ACAAATATATGATTAG
582012 GCA
1 GCA
582015 TACCTTCTAG
Statistics
Matches: 140, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
145 58 0.41
146 7 0.05
154 75 0.54
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.20
Consensus pattern (146 bp):
GCAACTATAGAAATGTTCAGCACACAACCGAACTGAAAAATATAGACAAAACGTGTATGCACTCA
GAAAGTGTAAAACATCAAGGTGACAAATAACAAAACCTAAACTTTTGAAGAAAACAAGGAGTTAA
ACAAATATATGATTAG
Found at i:583467 original size:21 final size:21
Alignment explanation
Indices: 583441--583498 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
583431 TAAACCCCAA
583441 ATTCTAAAATACTTCAATTAC
1 ATTCTAAAATACTTCAATTAC
583462 ATTCT-AAAT-C-TC-A--A-
1 ATTCTAAAATACTTCAATTAC
583476 ATTCTAAAATACTTCAATTAC
1 ATTCTAAAATACTTCAATTAC
583497 AT
1 AT
583499 GCCGAACCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 14
0.68 0.00 0.32
Matches are distributed among these distances:
14 5 0.17
15 5 0.17
16 1 0.03
17 3 0.10
18 3 0.10
19 1 0.03
20 5 0.17
21 7 0.23
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTCTAAAATACTTCAATTAC
Found at i:583477 original size:35 final size:35
Alignment explanation
Indices: 583419--583498 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
583409 AACACAATCA
583419 TCAATTACATTATAAACCCCAAATTCTAAAATACT
1 TCAATTACATTATAAACCCCAAATTCTAAAATACT
* * *
583454 TCAATTACATTCTAAATCTCAAATTCTAAAATACT
1 TCAATTACATTATAAACCCCAAATTCTAAAATACT
583489 TCAATTACAT
1 TCAATTACAT
583499 GCCGAACCCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (35 bp):
TCAATTACATTATAAACCCCAAATTCTAAAATACT
Found at i:583963 original size:147 final size:148
Alignment explanation
Indices: 583671--584105 Score: 712
Period size: 148 Copynumber: 3.0 Consensus size: 148
583661 ACTCAATTCA
* * * * *
583671 GTTTACAAAATATTTGACTCAAAAATTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAAT
1 GTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTTGAAT
* * *
583736 TAAATTGAATTTTTGA-TTTCTATTTAAATTTAATTATAAATATTTATCATATTATAATATTATT
66 TGAATTGAATTTTTGAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATATTATT
*
583800 TTATTCTAATTCAGTT-C
131 TGATTCTAATTCAGTTCC
*
583817 GTTTATAAAATAGTTGACTCGAAATTTTTTTGATTTGAGTTTATAAAATTTAAATCAAGTTGAAT
1 GTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTTGAAT
*
583882 TGAATTGAATTTTTGAGTTTCTATTTAAATGTAATTATAAATATTTATAATACTATAATATTATT
66 TGAATTGAATTTTTGAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATATTATT
583947 TGATTCTAATTCAGTTCC
131 TGATTCTAATTCAGTTCC
583965 GTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTTGAAT
1 GTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTTGAAT
* * * * *
584030 TGAACTGAATTTTAGAGTTTATGTTTAAATTTAATTATAAATATTTTTAATACTATAATATTATT
66 TGAATTGAATTTTTGAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATATTATT
584095 TGATTCTAATT
131 TGATTCTAATT
584106 TAAATAGTTT
Statistics
Matches: 269, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
146 74 0.28
147 60 0.22
148 135 0.50
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (148 bp):
GTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTTGAAT
TGAATTGAATTTTTGAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATATTATT
TGATTCTAATTCAGTTCC
Found at i:584646 original size:35 final size:35
Alignment explanation
Indices: 584607--584686 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
584597 GGGGTTGGGC
** *
584607 ATGTAATTGAAGTGTTTTGGAATTTAATGTTTAGA
1 ATGTAATTGAAGCATTTTAGAATTTAATGTTTAGA
* **
584642 ATGTAATTAAAGCATTTTAGAATTTGTTGTTTAGA
1 ATGTAATTGAAGCATTTTAGAATTTAATGTTTAGA
*
584677 ATATAATTGA
1 ATGTAATTGA
584687 TGACTGTGTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.35, C:0.01, G:0.19, T:0.45
Consensus pattern (35 bp):
ATGTAATTGAAGCATTTTAGAATTTAATGTTTAGA
Found at i:585740 original size:23 final size:23
Alignment explanation
Indices: 585714--585761 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
585704 ATCAAGTACA
585714 ATAA-CAAATTAGGTAGCGCTTAT
1 ATAATCAAA-TAGGTAGCGCTTAT
**
585737 ATAATGTAATAGGTAGCGCTTAT
1 ATAATCAAATAGGTAGCGCTTAT
585760 AT
1 AT
585762 TGACCCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAATCAAATAGGTAGCGCTTAT
Found at i:585969 original size:24 final size:24
Alignment explanation
Indices: 585923--585969 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
585913 TGGAAAAAAT
* * *
585923 TATCGACACATATTTAAAGAGTGG
1 TATCGACACAAATTAAAAAAGTGG
585947 TATCGACACAAATTAAAAAAGTG
1 TATCGACACAAATTAAAAAAGTG
585970 TCGATACTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.26
Consensus pattern (24 bp):
TATCGACACAAATTAAAAAAGTGG
Found at i:589735 original size:201 final size:202
Alignment explanation
Indices: 589234--590040 Score: 882
Period size: 201 Copynumber: 4.0 Consensus size: 202
589224 ACACTAAATT
*
589234 AGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGATAAATTTAAACCGGTTACATTAT
1 AGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGATAAATTTAAACCGGTTACATTGT
* * * *
589299 AAAGTGACCTATTACATTATAATTACGAGTTTCGATGTTTTCAGGATCAACACTTTTTCTAAATG
66 AAAGTGACCTATTACATTATAATTACGAGTTTCGATGTTTTTAGGATCGACACTTGTTATAAATG
* ** *
589364 TATCGACAC-TTTTTCGTGAACTT-GTTTCGAAAATTTATTATGGACATA-AAGTGTCGACACAA
131 TATCGACACTTTTTTCGTGAACTTGGTTTCGGAAATACATTATGGACA-ACAAGTATCGACACAA
*
589426 ATGTATAA
195 ATGAATAA
* * * * * *
589434 AGTATCGATACATTATGTATACCT-TTTT-T-TTAATAACCGGTATATTTAGACCGGTTACATTG
1 AGTGTCGATACATTATGTAGACCTATTTTCTCATAA-AACCGATAAATTTAAACCGGTTACATTG
* * * * * *
589496 TTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTATAAAT
65 TAAAGTGACCTATTACATTATAATTACGAGTTTCGATGTTTTTAGGATCGACACTTGTTATAAAT
* * * * *
589561 GTATCGACATTTTTTTCGTGCACTTGGTTT-GGAAATACATTCTAGACAACATGTATCGACACAA
130 GTATCGACACTTTTTTCGTGAACTTGGTTTCGGAAATACATTATGGACAACAAGTATCGACACAA
589625 ATGAATAA
195 ATGAATAA
* * * *
589633 AGTGTCGATACA-TATTGTAGACCTATTTTCTCATAAAATCGGTAAATTAAAATCGGTTACATTG
1 AGTGTCGATACATTA-TGTAGACCTATTTTCTCATAAAACCGATAAATTTAAACCGGTTACATTG
* *
589697 TAAAGTGACCTATTACATTATAGTTACGAGTTTCGATGTTTTTAGGATCGACACTTGATATAAAT
65 TAAAGTGACCTATTACATTATAATTACGAGTTTCGATGTTTTTAGGATCGACACTTGTTATAAAT
* * * *
589762 GTATCGATACTTATTT-GTGAACTTGTTTTGGTTAGAAAATACATTATGGAC-ACAAAGTATCGA
130 GTATCGACACTTTTTTCGTGAACTTGGTTTCG---G-AAATACATTATGGACAAC-AAGTATCGA
*
589825 CACAAATGTATAA
190 CACAAATGAATAA
* * * * * * * *
589838 AGTGTCGATACTTTATGTATACATCTTTTCTCAT-AAACTGATATATTTAGACCGATTACATTGT
1 AGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGATAAATTTAAACCGGTTACATTGT
* ** * * * * * * * *
589902 TATTTTACCTATTACATTATAATTATGGGTCTCGATATTTTTTGGGATCGATACTTTTTATAAAT
66 AAAGTGACCTATTACATTATAATTACGAGTTTCGAT-GTTTTTAGGATCGACACTTGTTATAAAT
* * * * * *
589967 GTATCGACACTTTGTTCGTGCACTTGGTTT-GGAAATACATTCTGGACTACATGTATCGACACGA
130 GTATCGACACTTTTTTCGTGAACTTGGTTTCGGAAATACATTATGGACAACAAGTATCGACACAA
590031 ATGAATAA
195 ATGAATAA
590039 AG
1 AG
590041 CAAATTCATT
Statistics
Matches: 503, Mismatches: 86, Indels: 35
0.81 0.14 0.06
Matches are distributed among these distances:
197 3 0.01
198 92 0.18
199 68 0.14
200 41 0.08
201 130 0.26
202 6 0.01
204 53 0.11
205 97 0.19
206 13 0.03
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (202 bp):
AGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGATAAATTTAAACCGGTTACATTGT
AAAGTGACCTATTACATTATAATTACGAGTTTCGATGTTTTTAGGATCGACACTTGTTATAAATG
TATCGACACTTTTTTCGTGAACTTGGTTTCGGAAATACATTATGGACAACAAGTATCGACACAAA
TGAATAA
Found at i:590871 original size:23 final size:23
Alignment explanation
Indices: 590840--590886 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
590830 ACTCAAGCAA
*
590840 CTATATTATCATCT-TCATTTATT
1 CTATATTATCA-CTATCATTGATT
*
590863 CTATTTTATCACTATCATTGATT
1 CTATATTATCACTATCATTGATT
590886 C
1 C
590887 CTTTCATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.26, C:0.19, G:0.02, T:0.53
Consensus pattern (23 bp):
CTATATTATCACTATCATTGATT
Found at i:591128 original size:23 final size:23
Alignment explanation
Indices: 591074--591132 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
591064 CACCACAGCT
* *
591074 CATATAATTGCACCGAAGTGCCA
1 CATAGAATTGCACCGAAGTACCA
* * *
591097 CATATAATTGCACCGGAGTACCG
1 CATAGAATTGCACCGAAGTACCA
*
591120 CGTAGAATTGCAC
1 CATAGAATTGCAC
591133 TGTAGTGCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (23 bp):
CATAGAATTGCACCGAAGTACCA
Found at i:591329 original size:103 final size:103
Alignment explanation
Indices: 591158--591375 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
591148 TAATGTCCAT
* * *
591158 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAATATGTGTCTCACCA
*
591223 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
*
591261 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAATATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAATATGTGTCTCACCA
* *
591326 GACTTCACACATGTTCCAAATAATACATATATATCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
591364 AAGGACCACATA
1 AAGGACCACATA
591376 GACCCTCGAC
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAATATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATATCCCG
Found at i:592206 original size:19 final size:19
Alignment explanation
Indices: 592182--592237 Score: 89
Period size: 19 Copynumber: 3.0 Consensus size: 19
592172 TATTACTGGG
592182 ATGCATCGATGCACTACTT
1 ATGCATCGATGCACTACTT
592201 ATGCATCGATGCACTAC-T
1 ATGCATCGATGCACTACTT
592219 -TGCATTCGATGCACTACTT
1 ATGCA-TCGATGCACTACTT
592238 GCATTCGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.11
18 13 0.37
19 18 0.51
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (19 bp):
ATGCATCGATGCACTACTT
Found at i:592229 original size:18 final size:17
Alignment explanation
Indices: 592183--592247 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 17
592173 ATTACTGGGA
592183 TGCATCGATGCACTACTT
1 TGCATCGATGCACTAC-T
592201 ATGCATCGATGCACTACT
1 -TGCATCGATGCACTACT
592219 TGCATTCGATGCACTACT
1 TGCA-TCGATGCACTACT
592237 TGCATTCGATG
1 TGCA-TCGATG
592248 TATTTAAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.09
18 25 0.56
19 16 0.36
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.32
Consensus pattern (17 bp):
TGCATCGATGCACTACT
Found at i:594937 original size:182 final size:180
Alignment explanation
Indices: 594627--595275 Score: 809
Period size: 182 Copynumber: 3.6 Consensus size: 180
594617 ATTAAAGTAC
* * ** * * * * * *
594627 CGACACTTTCAACATAACTGGTAGCACTTTACCGGGTTTGTCATTTCGATATCGGTTTTGTCATA
1 CGACACTTTCAATATATCCAGTAGCTCTTTACCGGTTTTATCATTTCAAGACCGGTTTTGTCATA
* * *
594692 TTTTTACCTATTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACATTTTTTAGGCGCT
66 TTTTTACCTATTATATTGCTATGGATCGATACATTTT-ATAAAGTATCGACACTTTATAGGCGCT
* *
594757 ATAACTTATTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
130 ATAACTTCTTCTCTTTTAAATT-CAAAAGTGTCGATACTTATATTAATTTAT
* * * * *
594809 CGACACTTTCAATATATCCGGTAGCTTTTTACCAGTTTTATGATTTCAAGACCTGTTTTGTCATA
1 CGACACTTTCAATATATCCAGTAGCTCTTTACCGGTTTTATCATTTCAAGACCGGTTTTGTCATA
* *
594874 TTCTTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTATAGGCGCT
66 TTTTTACCTATTATATTGCTATGGATCGATACATTT-TATAAAGTATCGACACTTTATAGGCGCT
**
594939 ATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAACGTAT
130 ATAACTTCTTCTCTTTTAAATTC-AAAAGTGTCGATACTTATATTAATTTAT
**
594991 CGACACTTTCAATATA-CTCAGTAGCTCTTTACCGGTTTTATCATTTCGTGACCGGTTTTGTCAT
1 CGACACTTTCAATATATC-CAGTAGCTCTTTACCGGTTTTATCATTTCAAGACCGGTTTTGTCAT
* * * *
595055 ACTTATACCTATTATATTGTTTTGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGC
65 ATTTTTACCTATTATATTGCTATGGATCGATACA-TTTTATAAAGTATCGACACTTTATAGGCGC
* *
595120 TATTACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTAT-TTAAATCTAAT
129 TATAACTTCTTCTCTTTTAAATT-CAAAAGTGTCGATACTTATATT-AAT-TTAT
* * ** * * *
595174 CGATACTTTCGATATATCCAGTAGCGGTTTACCGGTTTTATCATAATGAA-ACCGGTTTTATCAT
1 CGACACTTTCAATATATCCAGTAGCTCTTTACCGGTTTTATCAT-TTCAAGACCGGTTTTGTCAT
* * *
595238 ATTTTTACCTGTTATATTGCTATAGAGCGATACATTTT
65 ATTTTTACCTATTATATTGCTATGGATCGATACATTTT
595276 TCATTTGTAT
Statistics
Matches: 403, Mismatches: 55, Indels: 18
0.85 0.12 0.04
Matches are distributed among these distances:
181 4 0.01
182 312 0.77
183 85 0.21
184 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.42
Consensus pattern (180 bp):
CGACACTTTCAATATATCCAGTAGCTCTTTACCGGTTTTATCATTTCAAGACCGGTTTTGTCATA
TTTTTACCTATTATATTGCTATGGATCGATACATTTTATAAAGTATCGACACTTTATAGGCGCTA
TAACTTCTTCTCTTTTAAATTCAAAAGTGTCGATACTTATATTAATTTAT
Found at i:597363 original size:161 final size:162
Alignment explanation
Indices: 597101--597423 Score: 639
Period size: 161 Copynumber: 2.0 Consensus size: 162
597091 ATTTATCATG
597101 TCAATATCATTTTATAGATTAATATTCGATATATTGACAATCTATAATTATATGTATTATTAATG
1 TCAATATCATTTTATAGATTAATATTCGATATATTGACAATCTATAATTATATGTATTATTAATG
597166 AATCGAATAATGGAACATTATCATTAAATTTAAATTCTTTTAAATACAAATCACACATCATCTAC
66 AATCGAATAATGGAACATTATCATTAAATTTAAATTCTTTTAAATACAAATCACACATCATCTAC
597231 -TCACTACGATTATATGTTGATATTATATATA
131 TTCACTACGATTATATGTTGATATTATATATA
597262 TCAATATCATTTTATAGATTAATATTCGATATATTGACAATCTATAATTATATGTATTATTAATG
1 TCAATATCATTTTATAGATTAATATTCGATATATTGACAATCTATAATTATATGTATTATTAATG
597327 AATCGAATAATGGAACATTATCATTAAATTTAAATTCTTTTAAATACAAATCACACATCATCTAC
66 AATCGAATAATGGAACATTATCATTAAATTTAAATTCTTTTAAATACAAATCACACATCATCTAC
597392 TTCACTACGATTATATGTTGATATTATATATA
131 TTCACTACGATTATATGTTGATATTATATATA
597424 ACTAACGCGT
Statistics
Matches: 161, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
161 130 0.81
162 31 0.19
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (162 bp):
TCAATATCATTTTATAGATTAATATTCGATATATTGACAATCTATAATTATATGTATTATTAATG
AATCGAATAATGGAACATTATCATTAAATTTAAATTCTTTTAAATACAAATCACACATCATCTAC
TTCACTACGATTATATGTTGATATTATATATA
Found at i:600454 original size:24 final size:24
Alignment explanation
Indices: 600427--600498 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
600417 AAACGGAGTT
*
600427 ATCAGAAATCAAAACAGAATTCAG
1 ATCAAAAATCAAAACAGAATTCAG
* * * * *
600451 ATCATATATCAGAATAGAATCCAG
1 ATCAAAAATCAAAACAGAATTCAG
* *
600475 ATCAAAAATCATAACAAAATTCAG
1 ATCAAAAATCAAAACAGAATTCAG
600499 GTAATGTATC
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.21
Consensus pattern (24 bp):
ATCAAAAATCAAAACAGAATTCAG
Found at i:604779 original size:18 final size:19
Alignment explanation
Indices: 604744--604780 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
604734 TTAAATTGTA
604744 GACTAACAGTATATGATGG
1 GACTAACAGTATATGATGG
*
604763 GACTAGCAGTA-ATGATGG
1 GACTAACAGTATATGATGG
604781 CATATTGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.35, C:0.11, G:0.30, T:0.24
Consensus pattern (19 bp):
GACTAACAGTATATGATGG
Found at i:606000 original size:15 final size:15
Alignment explanation
Indices: 605958--606000 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
605948 CTATCGTCTT
* *
605958 CTTCTCCTCAGCGGG
1 CTTCTTCTCAGCTGG
605973 CTTCTTCTCAGCTGG
1 CTTCTTCTCAGCTGG
605988 CTTCTTCTCAGCT
1 CTTCTTCTCAGCT
606001 TTTGGTGCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.07, C:0.37, G:0.19, T:0.37
Consensus pattern (15 bp):
CTTCTTCTCAGCTGG
Found at i:608803 original size:3 final size:3
Alignment explanation
Indices: 608795--608833 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
608785 AATTATTTTT
608795 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
608834 AATTAGTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:609428 original size:113 final size:112
Alignment explanation
Indices: 609061--609472 Score: 628
Period size: 112 Copynumber: 3.7 Consensus size: 112
609051 TAGAGTCATT
* ** * *
609061 CAAAAGGTTGAATAAGCTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * * *
609126 TTATGAACTCTCTCTGAAAAGTTGATCTATCGAGTGATGAATTCGAG
66 TTATGAACTTTCTCTGGAAAGCTGATCCATCAAGTGATGGATTTGAG
*
609173 CGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 C-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
609237 ATTATGAACTTTTTCTGGAGAGCTGATCCATCAAATGATGGATTTGAG
65 ATTATGAACTTTCTCTGGAAAGCTGATCCATCAAGTGATGGATTTGAG
*
609285 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
609350 TTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGG-AAAGCTGATCCATCAAGTGATGGATTTGAG
*
609398 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
609463 TTATGAACTT
66 TTATGAACTT
609473 CTTCTTCATT
Statistics
Matches: 277, Mismatches: 20, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
111 4 0.01
112 167 0.60
113 106 0.38
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (112 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAGCTGATCCATCAAGTGATGGATTTGAG
Found at i:609458 original size:225 final size:224
Alignment explanation
Indices: 609061--609477 Score: 656
Period size: 225 Copynumber: 1.9 Consensus size: 224
609051 TAGAGTCATT
* * * *
609061 CAAAAGGTTGAATAAGCTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * *
609126 TTATGAACTCTCTCTGAAAAGTTGATCTATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAGTT
66 TTATGAACTCTCTCTGAAAAGCTAATCCATCAAGTGATGAATTCGAGCGAAAAGTTGAACAAATT
*
609191 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTGGA
609256 GAGCTGATCCATCAAATGATGGATTTGAG
196 GAGCTGATCCATCAAATGATGGATTTGAG
* *
609285 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
609350 TTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGAGC-AAAAGGTTGAACAAA
66 TTATGAACTCTCTCT-GAAAAGCTAATCCATCAAGTGATGAATTCGAGCGAAAA-GTTGAACAAA
*
609414 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCT
129 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCT
609478 TCATTCTTCA
Statistics
Matches: 174, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
224 77 0.44
225 97 0.56
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (224 bp):
CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTCTCTGAAAAGCTAATCCATCAAGTGATGAATTCGAGCGAAAAGTTGAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTGGA
GAGCTGATCCATCAAATGATGGATTTGAG
Found at i:609469 original size:40 final size:40
Alignment explanation
Indices: 609414--609515 Score: 177
Period size: 40 Copynumber: 2.5 Consensus size: 40
609404 GTTGAACAAA
*
609414 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAG
*
609454 TTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAG
609494 TTCTTCTCATTATGAACTTTCT
1 TTCTTCTCATTATGAA-TTTCT
609516 CTGGCAAAGC
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
40 54 0.93
41 4 0.07
ACGTcount: A:0.19, C:0.23, G:0.09, T:0.50
Consensus pattern (40 bp):
TTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAG
Found at i:609485 original size:153 final size:153
Alignment explanation
Indices: 609301--609625 Score: 623
Period size: 153 Copynumber: 2.1 Consensus size: 153
609291 GTTGAACAAA
* *
609301 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
609366 GCAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
66 GCAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
609431 TTCTTCTTCCTTCTTCAGATGAG
131 TTCTTCTTCCTTCTTCAGATGAG
609454 TTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
609519 GCAAAGCTAATCTATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
66 GCAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
609584 TTCTTCTTCCTTCTTCAGATGAG
131 TTCTTCTTCCTTCTTCAGATGAG
609607 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAACTT
609626 TCTCTGACAA
Statistics
Matches: 169, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
153 169 1.00
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (153 bp):
TTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GCAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
TTCTTCTTCCTTCTTCAGATGAG
Found at i:609571 original size:113 final size:113
Alignment explanation
Indices: 609454--609736 Score: 530
Period size: 113 Copynumber: 2.5 Consensus size: 113
609444 TTCAGATGAG
* *
609454 TTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
609519 GCAAAGCTAATCTATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
66 ACAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
609567 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
609632 ACAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
66 ACAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
609680 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
609737 ACTAACGGAC
Statistics
Matches: 166, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 166 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (113 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
ACAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
Found at i:609660 original size:266 final size:265
Alignment explanation
Indices: 609187--609736 Score: 1028
Period size: 266 Copynumber: 2.1 Consensus size: 265
609177 AAGTTGAACA
* *
609187 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
609252 TGGAGAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
66 TGGAAAGCTAATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
*
609317 TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATC
131 TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGACAAAGCTAATCCATC
609382 AAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTC
196 AAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTC
609447 AGATG
261 AGATG
609452 AGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
609517 TGGCAAAGCTAATCTATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
66 TGG-AAAGCTAATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
609582 ATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGACAAAGCTAATCCAT
130 ATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGACAAAGCTAATCCAT
609647 CAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTT
195 CAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTT
609712 CAGATG
260 CAGATG
609718 AGTTCTTCTCATTATGAAC
1 AGTTCTTCTCATTATGAAC
609737 ACTAACGGAC
Statistics
Matches: 277, Mismatches: 7, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
265 66 0.24
266 211 0.76
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (265 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAGCTAATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGACAAAGCTAATCCATC
AAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTC
AGATG
Found at i:610730 original size:93 final size:88
Alignment explanation
Indices: 610461--610905 Score: 581
Period size: 83 Copynumber: 5.0 Consensus size: 88
610451 GATTATGCAG
* * *
610461 TTCATCTTTTAATTTCAATGATTGGTTCTGGGTTTTATATCAAACCAAATCAGATAACTCAAAGA
1 TTCATC-TTTAAATTCAATGATTGGTT-TGGG--TTATACCAAACCAGATCAGATAACTCAAAGA
* *
610526 ACACTTCCAGAAGATGCTATGGGCATA
62 ACACTTCCAGAAGATGCTATGAGCACA
* * * *
610553 TTCTTCTTCCAAATTCAATGACTGGTTCTGTGGTTCATACCAAACTAGATCAGATAACTCAAAGA
1 TTCATCTT-TAAATTCAATGATTGGTT-TG-GGTT-ATACCAAACCAGATCAGATAACTCAAAGA
610618 ACACTTCCAGAAGATGCTATGAGCACA
62 ACACTTCCAGAAGATGCTATGAGCACA
*
610645 TTCATCTTCTAAATTTAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTT-TAAATTCAATGATTGG--TTT-GGGTT-ATACCAAACCAGATCAGATAACTCAAAG
610710 AACACTTCCAGAAGATGCTATGAGCACA
61 AACACTTCCAGAAGATGCTATGAGCACA
610738 TTCATCTTTCAAATTCAATGATTGG--T---TT-TACCAAACCAGATCAGATAACTCAAAGAACA
1 TTCATCTTT-AAATTCAATGATTGGTTTGGGTTATACCAAACCAGATCAGATAACTCAAAGAACA
610797 CTTCCAGAAGATGCTATGAGCACA
65 CTTCCAGAAGATGCTATGAGCACA
610821 TTCATCTTTCAAATTCAATGATTGG--T---TT-TACCAAACCAGATCAGATAACTCAAAGAACA
1 TTCATCTTT-AAATTCAATGATTGGTTTGGGTTATACCAAACCAGATCAGATAACTCAAAGAACA
610880 CTTCCAGAAGATGCTATGAGCACA
65 CTTCCAGAAGATGCTATGAGCACA
610904 TT
1 TT
610906 GCATTTGTTC
Statistics
Matches: 331, Mismatches: 15, Indels: 23
0.90 0.04 0.06
Matches are distributed among these distances:
83 140 0.42
85 2 0.01
89 1 0.00
91 4 0.01
92 96 0.29
93 85 0.26
94 3 0.01
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.30
Consensus pattern (88 bp):
TTCATCTTTAAATTCAATGATTGGTTTGGGTTATACCAAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATGAGCACA
Found at i:611950 original size:16 final size:16
Alignment explanation
Indices: 611914--611951 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
611904 TGAATTTTCG
611914 AAAATAAATTGAATCT
1 AAAATAAATTGAATCT
*
611930 CAAATAAATTGAA-CTT
1 AAAATAAATTGAATC-T
611946 AAAATA
1 AAAATA
611952 GATAGAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (16 bp):
AAAATAAATTGAATCT
Found at i:612292 original size:16 final size:16
Alignment explanation
Indices: 612271--612327 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
612261 CTTGACCCTA
612271 TTTTTTCTTTTTTTCT
1 TTTTTTCTTTTTTTCT
612287 TTTTTT-TTTCTTTTCT
1 TTTTTTCTTT-TTTTCT
*
612303 TTTTTCTCTCTTTTT-T
1 TTTTT-TCTTTTTTTCT
*
612319 TTTCTTCTT
1 TTTTTTCTT
612328 CTTCAAGCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
15 6 0.17
16 22 0.63
17 5 0.14
18 2 0.06
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTCTTTTTTTCT
Found at i:612294 original size:11 final size:11
Alignment explanation
Indices: 612278--612320 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 11
612268 CTATTTTTTC
612278 TTTTTTTCTTT
1 TTTTTTTCTTT
612289 TTTTTTTCTTT
1 TTTTTTTCTTT
612300 TCTTTTTTCTCTCT
1 T-TTTTTTCT-T-T
612314 TTTTTTT
1 TTTTTTT
612321 TCTTCTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 12 0.41
12 8 0.28
13 7 0.24
14 2 0.07
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:612295 original size:12 final size:13
Alignment explanation
Indices: 612273--612330 Score: 68
Period size: 13 Copynumber: 4.5 Consensus size: 13
612263 TGACCCTATT
612273 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
612286 -TTT-TTTTTTTC
1 TTTTCTTTTTTTC
612297 TTTTCTTTTTTCTC
1 TTTTCTTTTTT-TC
*
612311 TCTT-TTTTTTTC
1 TTTTCTTTTTTTC
612323 TTCTTCTT
1 TT-TTCTT
612331 CAAGCATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 8 0.21
12 9 0.24
13 14 0.37
14 7 0.18
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:612300 original size:24 final size:26
Alignment explanation
Indices: 612273--612330 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
612263 TGACCCTATT
612273 TTTTCTTTTTT-TCT-TTTTTTTTTC
1 TTTTCTTTTTTCTCTCTTTTTTTTTC
612297 TTTTCTTTTTTCTCTCTTTTTTTTTC
1 TTTTCTTTTTTCTCTCTTTTTTTTTC
612323 TTCTTCTT
1 TT-TTCTT
612331 CAAGCATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 11 0.35
25 3 0.10
26 12 0.39
27 5 0.16
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (26 bp):
TTTTCTTTTTTCTCTCTTTTTTTTTC
Found at i:616839 original size:15 final size:15
Alignment explanation
Indices: 616816--616847 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
616806 TGAAATGAAT
616816 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
616831 AATGCATGTATGCAA
1 AATGAATGTATGCAA
616846 AA
1 AA
616848 ATGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:620181 original size:30 final size:32
Alignment explanation
Indices: 620128--620186 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 32
620118 TGCAAATAAA
*
620128 ATGAAATATTAATAAGAAAATATATAAATACT
1 ATGAAATATTAATAAGAAAATATAAAAATACT
* *
620160 ATGAAA-A-TAATAAGTATATATAAAAAT
1 ATGAAATATTAATAAGAAAATATAAAAAT
620187 TTTTTGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.71
31 1 0.04
32 6 0.25
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.31
Consensus pattern (32 bp):
ATGAAATATTAATAAGAAAATATAAAAATACT
Found at i:622325 original size:3 final size:3
Alignment explanation
Indices: 622317--622376 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
622307 AATTATTTTT
* *
622317 TAA TAA TAA TAA TTA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
622365 TAA TAA TAA TAA
1 TAA TAA TAA TAA
622377 AATTAGTAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:624146 original size:2 final size:2
Alignment explanation
Indices: 624139--624163 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
624129 GCAATTAACT
624139 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
624164 GGATGGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:624538 original size:126 final size:126
Alignment explanation
Indices: 624229--624515 Score: 511
Period size: 126 Copynumber: 2.3 Consensus size: 126
624219 CCTAATATTT
*
624229 TCAAATCCATCAACCGCCCACTACCCATGATGGGTAAAATTTTTCAAATTCACACCCGTCCAAGC
1 TCAAACCCATCAACCGCCCACTACCCATGATGGGTAAAATTTTTCAAATTCACACCCGTCCAAGC
*
624294 TGGTACATTCTCAAATTTAATAGGTATTTAGTGGGCGGGTGGATGTGGGGCGGGTAAGGTC
66 GGGTACATTCTCAAATTTAATAGGTATTTAGTGGGCGGGTGGATGTGGGGCGGGTAAGGTC
*
624355 TCAAACCCATCAACCGCCCACCACCCATGATGGGTAAAATTTTTCAAATTCACACCCGTCCAAGC
1 TCAAACCCATCAACCGCCCACTACCCATGATGGGTAAAATTTTTCAAATTCACACCCGTCCAAGC
*
624420 GGGTACATTCTCAAATTTAATGGGTATTTAGTGGGCGGGTGGATGTGGGGCGGGTAAGGTC
66 GGGTACATTCTCAAATTTAATAGGTATTTAGTGGGCGGGTGGATGTGGGGCGGGTAAGGTC
* * *
624481 TCAAACCCATCACCCGCCCACTACCCGTGACGGGT
1 TCAAACCCATCAACCGCCCACTACCCATGATGGGT
624516 GCCACTTTCT
Statistics
Matches: 153, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
126 153 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (126 bp):
TCAAACCCATCAACCGCCCACTACCCATGATGGGTAAAATTTTTCAAATTCACACCCGTCCAAGC
GGGTACATTCTCAAATTTAATAGGTATTTAGTGGGCGGGTGGATGTGGGGCGGGTAAGGTC
Found at i:624882 original size:22 final size:22
Alignment explanation
Indices: 624857--624899 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
624847 AATTTTGATA
*
624857 AATTTAATGATCAATTTATAAT
1 AATTCAATGATCAATTTATAAT
* *
624879 AATTCAATGATTATTTTATAA
1 AATTCAATGATCAATTTATAA
624900 CCGTTTATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (22 bp):
AATTCAATGATCAATTTATAAT
Found at i:624920 original size:32 final size:32
Alignment explanation
Indices: 624871--624931 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
624861 TAATGATCAA
624871 TTTATAATAATTCAATGATTATTTTATAACCG
1 TTTATAATAATTCAATGATTATTTTATAACCG
*
624903 TTTATTAA-AATTTAATGATTATTTTATAA
1 TTTA-TAATAATTCAATGATTATTTTATAA
624932 TTTTTTGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 24 0.89
33 3 0.11
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (32 bp):
TTTATAATAATTCAATGATTATTTTATAACCG
Found at i:630933 original size:23 final size:23
Alignment explanation
Indices: 630907--630952 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
630897 CACCACAGCT
* *
630907 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTACACCGAAGTGCCA
*
630930 CGTAGAATTACACCGTAGTGCCA
1 CGTAGAATTACACCGAAGTGCCA
630953 TATAATAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
CGTAGAATTACACCGAAGTGCCA
Found at i:631169 original size:149 final size:149
Alignment explanation
Indices: 630930--631234 Score: 574
Period size: 149 Copynumber: 2.0 Consensus size: 149
630920 CGAAGTGCCA
630930 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
630995 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAAAATATA
66 AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAAAATATA
631060 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
*
631079 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
631144 AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACATAATATA
66 AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAAAATATA
631209 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
*
631228 CATAGAA
1 CGTAGAA
631235 CCCTCGACTC
Statistics
Matches: 152, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.28
Consensus pattern (149 bp):
CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAAAATATA
TATATATCCCGAAGGACCG
Found at i:636134 original size:23 final size:23
Alignment explanation
Indices: 636108--636153 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
636098 CACCACAGCT
*
636108 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
636131 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
636154 TATAATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:636370 original size:149 final size:149
Alignment explanation
Indices: 636131--636435 Score: 601
Period size: 149 Copynumber: 2.0 Consensus size: 149
636121 CGAAGTGCCA
636131 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
636196 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
636261 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
636280 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
636345 AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
636410 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
636429 CGTAGAA
1 CGTAGAA
636436 CCCTCGACTC
Statistics
Matches: 155, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 155 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCG
Found at i:638579 original size:29 final size:29
Alignment explanation
Indices: 638513--638580 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
638503 ACCGTTGACC
* *
638513 GGTGCTATTTTAGTAATTAATTCGAAATA
1 GGTGATATTTTAGTAATTAATTCGAAAAA
*
638542 GGT-ACTATTTTAGTAATTAATT-TAAAAA
1 GGTGA-TATTTTAGTAATTAATTCGAAAAA
638570 GGGTGATATTT
1 -GGTGATATTT
638581 CTGTAAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 4 0.12
29 28 0.85
30 1 0.03
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.43
Consensus pattern (29 bp):
GGTGATATTTTAGTAATTAATTCGAAAAA
Found at i:639916 original size:17 final size:19
Alignment explanation
Indices: 639891--639929 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
639881 ATATCTGTAT
639891 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
639909 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
639928 TA
1 TA
639930 AGTTGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:640789 original size:23 final size:23
Alignment explanation
Indices: 640763--640810 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
640753 TAAAGAACCG
*
640763 AAATAAACTT-AAATATACCATTA
1 AAATAAACTTCAAACA-ACCATTA
*
640786 AAATAAAGTTCAAACAACCATTA
1 AAATAAACTTCAAACAACCATTA
640809 AA
1 AA
640811 TCAACCACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.25
Consensus pattern (23 bp):
AAATAAACTTCAAACAACCATTA
Found at i:646342 original size:23 final size:23
Alignment explanation
Indices: 646316--646363 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
646306 TAAAGAACCG
*
646316 AAATAAACTT-AAATATACCATTA
1 AAATAAACTTCAAACA-ACCATTA
*
646339 AAATAAAGTTCAAACAACCATTA
1 AAATAAACTTCAAACAACCATTA
646362 AA
1 AA
646364 TCAACCACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.25
Consensus pattern (23 bp):
AAATAAACTTCAAACAACCATTA
Found at i:652945 original size:29 final size:29
Alignment explanation
Indices: 652872--652939 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
652862 ACCGTTTACC
*
652872 GGTGATATTTTAGTAATTAATTCGAAATA
1 GGTGATATTTTAGTAATTAATTCGAAAAA
*
652901 GGT-ACTATTTTAGTAATTAATT-TAAAAA
1 GGTGA-TATTTTAGTAATTAATTCGAAAAA
652929 GGGTGATATTT
1 -GGTGATATTT
652940 CTGTAAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 5 0.15
29 28 0.82
30 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.43
Consensus pattern (29 bp):
GGTGATATTTTAGTAATTAATTCGAAAAA
Found at i:654242 original size:17 final size:19
Alignment explanation
Indices: 654217--654255 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
654207 ATATCTGCAT
654217 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
654235 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
654254 TA
1 TA
654256 AGTTGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:657492 original size:21 final size:20
Alignment explanation
Indices: 657406--657563 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
657396 AAATGACCAA
**
657406 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
657425 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
657445 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
657465 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
657486 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
657507 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
657527 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
657548 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
657564 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:657592 original size:20 final size:20
Alignment explanation
Indices: 657530--657723 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
657520 CGATTTTCCA
* ** *
657530 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
657550 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
657570 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
657590 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
* **
657610 AAATCGCAACGCATATGGGT
1 AAATCGCAACGCGTATCCGT
*
657630 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
657650 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
657670 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
657690 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
657711 AAATCGCAACGCG
1 AAATCGCAACGCG
657724 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:657614 original size:60 final size:59
Alignment explanation
Indices: 657530--657723 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 59
657520 CGATTTTCCA
* ** * *
657530 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGC-AATACATAAATCGCAACGCGTATCCGT
* *** *
657590 AAATCGCAACGTGTATCCGTAAATCGCAACGCATATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCA-ATACATAAATCGCAACGCGTATCCGT
* *
657650 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACG-CAATACAT-AAATCGCAACGCGTATCCGT
657711 AAATCGCAACGCG
1 AAATCGCAACGCG
657724 ATATTTAAAG
Statistics
Matches: 113, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
59 1 0.01
60 80 0.71
61 32 0.28
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (59 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCAATACATAAATCGCAACGCGTATCCGT
Found at i:658144 original size:33 final size:33
Alignment explanation
Indices: 658105--658175 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
658095 TTCACTTAGA
*
658105 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
658138 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
658171 TTTCA
1 TTTCA
658176 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.25, G:0.15, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:658281 original size:21 final size:20
Alignment explanation
Indices: 658255--658358 Score: 87
Period size: 21 Copynumber: 5.5 Consensus size: 20
658245 TGCAGAAGAG
658255 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
658276 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
658296 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
658317 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
658331 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
658350 TCGCAACGA
1 TCGCAACGA
658359 CAGAATCGCA
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 10 0.15
20 16 0.25
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.11
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:658299 original size:20 final size:21
Alignment explanation
Indices: 658253--658331 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
658243 TTTGCAGAAG
*
658253 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
658275 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
658294 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
658316 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
658332 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:658312 original size:41 final size:41
Alignment explanation
Indices: 658254--658331 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
658244 TTGCAGAAGA
* *
658254 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAATGACT
658295 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAAT
658332 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.27, T:0.12
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAATGACT
Found at i:658347 original size:33 final size:33
Alignment explanation
Indices: 658307--658376 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
658297 CGCAACGAGA
*
658307 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGACAGAATCGCAACGC
*
658340 GAAATGAAAATCGCAACGACAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGACAGAATCGCAACGC
658373 GAAA
1 GAAA
658377 CCAAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.47, C:0.21, G:0.24, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGACAGAATCGCAACGC
Found at i:658383 original size:33 final size:33
Alignment explanation
Indices: 658313--658387 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
658303 GAGAGAAATG
* * **
658313 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGACAGAATCGCAACGCGAAACC
658346 AAAATCGCAACGACAGAATCGCAACGCGAAACC
1 AAAATCGCAACGACAGAATCGCAACGCGAAACC
658379 AAAATCGCA
1 AAAATCGCA
658388 TTGCGATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.47, C:0.25, G:0.21, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGACAGAATCGCAACGCGAAACC
Found at i:658386 original size:19 final size:18
Alignment explanation
Indices: 658329--658387 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
658319 GCAACGAGAG
*
658329 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-CAA
*
658348 AATCGCAA--CG--ACAG
1 AATCGCAACGCGAAACAA
658362 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-CAA
658381 AATCGCA
1 AATCGCA
658388 TTGCGATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 9 0.28
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.53
ACGTcount: A:0.46, C:0.27, G:0.19, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAACAA
Found at i:658405 original size:19 final size:19
Alignment explanation
Indices: 658383--658480 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
658373 GAAACCAAAA
*
658383 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
658402 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
658416 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
658435 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
658449 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
658468 TCGCGTTGCGATT
1 TCGCGTTGCGATT
658481 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:658424 original size:14 final size:14
Alignment explanation
Indices: 658405--658494 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
658395 TTTCATTTCG
658405 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
658419 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
658438 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
658452 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
658469 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
658485 CGTTGCGATT
1 CGTTGCGATT
658495 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:658430 original size:33 final size:33
Alignment explanation
Indices: 658388--658502 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
658378 CAAAATCGCA
658388 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
658421 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
658454 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
658487 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
658503 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:660353 original size:93 final size:93
Alignment explanation
Indices: 660194--660574 Score: 726
Period size: 93 Copynumber: 4.1 Consensus size: 93
660184 TAGATTGCTT
* *
660194 AGTAAATTTATTCGGTTACTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
660259 TTTGTTTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
660287 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
660352 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
660380 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
660445 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
660473 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
660538 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
660566 AGTAAATTT
1 AGTAAATTT
660575 ATCCATTCAA
Statistics
Matches: 283, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 283 1.00
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:660658 original size:19 final size:19
Alignment explanation
Indices: 660618--660746 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
660608 TAGTTTACTT
* *
660618 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
660638 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
660657 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
660676 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
660690 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* *
660709 TCGCAA--CG--A-TAAGA
1 TCGCAACGCGAAACCAAAA
660723 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
660742 TCGCA
1 TCGCA
660747 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 18 0.20
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:660697 original size:33 final size:32
Alignment explanation
Indices: 660654--660746 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
660644 CGCGAAACCA
**
660654 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
660686 AGAATCGCAACGCGAAACCAAAATCGCAACGAT
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
660719 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
660747 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:660744 original size:52 final size:52
Alignment explanation
Indices: 660618--660746 Score: 138
Period size: 52 Copynumber: 2.5 Consensus size: 52
660608 TAGTTTACTT
** *
660618 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAA
* * * *
660670 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGATAAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAA-A
*
660723 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
660747 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.69
53 2 0.03
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAA
Found at i:660764 original size:19 final size:19
Alignment explanation
Indices: 660742--660860 Score: 132
Period size: 19 Copynumber: 6.8 Consensus size: 19
660732 GAAACCAAAA
660742 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
660761 TCGCGTTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
660777 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
660794 TCGCATTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
660810 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
**
660827 TCGCATTGCGATTTTGGTT
1 TCGCATTGCGATTTTCATT
*
660846 TCGCGTTGCGATTTT
1 TCGCATTGCGATTTT
660861 AAGTTTCGTG
Statistics
Matches: 86, Mismatches: 4, Indels: 20
0.78 0.04 0.18
Matches are distributed among these distances:
14 12 0.14
16 16 0.19
17 16 0.19
19 42 0.49
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:660783 original size:14 final size:14
Alignment explanation
Indices: 660764--660820 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
660754 TTTCATTTCG
660764 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
660778 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
660795 CGCATTGCGATTCTTT
1 CG--TTGCGATTCTTT
660811 CGTTGCGATT
1 CGTTGCGATT
660821 TTCATTTCGC
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 16 0.42
16 8 0.21
17 8 0.21
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:660789 original size:33 final size:33
Alignment explanation
Indices: 660747--660839 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
660737 CAAAATCGCA
*
660747 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
660780 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
660813 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
660840 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.12, C:0.20, G:0.19, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
Found at i:660868 original size:20 final size:19
Alignment explanation
Indices: 660811--660876 Score: 80
Period size: 19 Copynumber: 3.4 Consensus size: 19
660801 GCGATTCTTT
660811 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
* *
660830 CATTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
660849 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-AGTTTCG
*
660869 TGTTGCGA
1 CGTTGCGA
660877 AAGTAAACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
19 27 0.68
20 13 0.32
ACGTcount: A:0.12, C:0.17, G:0.26, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:662822 original size:14 final size:14
Alignment explanation
Indices: 662803--662838 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
662793 ATTGTTTAAT
662803 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
662817 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
662831 TGATTTGT
1 TGATTTGT
662839 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:662969 original size:19 final size:19
Alignment explanation
Indices: 662945--663042 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
662935 AAAATTGACT
662945 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
662964 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
662983 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
662997 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
663016 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
663036 ATCGCAA
1 ATCGCAA
663043 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:663074 original size:53 final size:53
Alignment explanation
Indices: 662945--663061 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
662935 AAAATTGACT
662945 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
662997 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
663050 ATCGCAATGCGA
1 ATCGCAATGCGA
663062 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:665396 original size:12 final size:12
Alignment explanation
Indices: 665379--665403 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
665369 TCTTCGGGGA
665379 CTTTTTCTTCTT
1 CTTTTTCTTCTT
665391 CTTTTTCTTCTT
1 CTTTTTCTTCTT
665403 C
1 C
665404 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:665611 original size:24 final size:24
Alignment explanation
Indices: 665577--665623 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
665567 CTGAAACATC
665577 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
665601 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
665624 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:666334 original size:20 final size:20
Alignment explanation
Indices: 666306--666555 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
666296 AAATTTCAGT
* *
666306 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
666326 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
666346 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
666366 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
666386 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
666406 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
666426 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
666446 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
666466 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
666486 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
666506 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
666526 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
666546 GTTGCGATTT
1 GTTGCGATTT
666556 TGGAAAATCG
Statistics
Matches: 200, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 199 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:666572 original size:21 final size:21
Alignment explanation
Indices: 666542--666624 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
666532 ATTTTCATAT
*
666542 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
666563 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
666584 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
666605 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
666625 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:666615 original size:42 final size:43
Alignment explanation
Indices: 666522--666620 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
666512 ATTTATGTGT
* *
666522 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
666563 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
666605 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
666621 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:671502 original size:21 final size:21
Alignment explanation
Indices: 671476--671540 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
671466 AGAATCAATC
671476 AAATATTTCAGTGATTGAATA
1 AAATATTTCAGTGATTGAATA
* *
671497 AAATA-TT-A-T--TTCAATC
1 AAATATTTCAGTGATTGAATA
671513 AAATATTTCAGTGATTGAATA
1 AAATATTTCAGTGATTGAATA
671534 AAATATT
1 AAATATT
671541 ATTTTTTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
16 10 0.29
17 2 0.06
18 2 0.06
19 2 0.06
20 2 0.06
21 17 0.49
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (21 bp):
AAATATTTCAGTGATTGAATA
Found at i:671511 original size:37 final size:37
Alignment explanation
Indices: 671470--671544 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
671460 GTTAGCAGAA
671470 TCAATCAAATATTTCAGTGATTGAATAAAATATTATT
1 TCAATCAAATATTTCAGTGATTGAATAAAATATTATT
671507 TCAATCAAATATTTCAGTGATTGAATAAAATATTATT
1 TCAATCAAATATTTCAGTGATTGAATAAAATATTATT
671544 T
1 T
671545 TTTTCATAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (37 bp):
TCAATCAAATATTTCAGTGATTGAATAAAATATTATT
Found at i:680424 original size:21 final size:21
Alignment explanation
Indices: 680400--680445 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
680390 CTTCAAATCC
*
680400 TAAAAT-ATAAACTCTAAATTA
1 TAAAATCATAAACACT-AATTA
*
680421 T-AAATCATAAACACTAATTC
1 TAAAATCATAAACACTAATTA
680441 TAAAA
1 TAAAA
680446 GGGACAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAATCATAAACACTAATTA
Found at i:690515 original size:51 final size:51
Alignment explanation
Indices: 690432--690573 Score: 230
Period size: 51 Copynumber: 2.8 Consensus size: 51
690422 ATAAACACTT
* *
690432 TAAAATCATCCACCTCACACATGTCTACTCAGCCCATAAGTTCAATATCAC
1 TAAACTCATCCACCTCACACGTGTCTACTCAGCCCATAAGTTCAATATCAC
* *
690483 TAAACTCATCCACCTCACACGTGTCTATTCAGCCCATAAGTTTAATATCAC
1 TAAACTCATCCACCTCACACGTGTCTACTCAGCCCATAAGTTCAATATCAC
* *
690534 TAAACTCATCCATCTCACACGGGTCTACTCAGCCCATAAG
1 TAAACTCATCCACCTCACACGTGTCTACTCAGCCCATAAG
690574 ACACTGAGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 84 1.00
ACGTcount: A:0.32, C:0.33, G:0.08, T:0.26
Consensus pattern (51 bp):
TAAACTCATCCACCTCACACGTGTCTACTCAGCCCATAAGTTCAATATCAC
Found at i:693472 original size:23 final size:23
Alignment explanation
Indices: 693442--693499 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
693432 GTTCATATTC
693442 GAACTCGAGTTCAAATTTAAGTT
1 GAACTCGAGTTCAAATTTAAGTT
693465 GAACTCGAGTTCAAATTTAAGTT
1 GAACTCGAGTTCAAATTTAAGTT
693488 GAACTCGAGTTC
1 GAACTCGAGTTC
693500 GACCCTAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (23 bp):
GAACTCGAGTTCAAATTTAAGTT
Found at i:694171 original size:30 final size:30
Alignment explanation
Indices: 694113--694177 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
694103 AAAATCGAAT
* * *
694113 TAAACGGGGATGAGGAAAAATCGTTTATGC
1 TAAACGGGGACGAGGAAAAACCGCTTATGC
* * *
694143 TAAACGGGGACGGGGGAAAACCGCTTATGT
1 TAAACGGGGACGAGGAAAAACCGCTTATGC
694173 TAAAC
1 TAAAC
694178 AAGAACGGGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.31, T:0.20
Consensus pattern (30 bp):
TAAACGGGGACGAGGAAAAACCGCTTATGC
Found at i:699534 original size:21 final size:21
Alignment explanation
Indices: 699510--699566 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
699500 AGATTAACTA
699510 ATATCCATACCAAAGGCTTGG
1 ATATCCATACCAAAGGCTTGG
* *
699531 ATATCCATACCGAGGGCTTGG
1 ATATCCATACCAAAGGCTTGG
*
699552 -TATCAATACCCAAAG
1 ATATCCATA-CCAAAG
699567 TGGTTGAGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 7 0.23
21 23 0.77
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (21 bp):
ATATCCATACCAAAGGCTTGG
Found at i:702589 original size:117 final size:117
Alignment explanation
Indices: 702291--702574 Score: 523
Period size: 117 Copynumber: 2.4 Consensus size: 117
702281 TGTATATTTT
*
702291 CCAGAACCATACACCCACCTGCACACTAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
1 CCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
702356 CGGTAATAACTTTCCCATCCAATCACTCCGATCACCAAAATGTGTAGGTTCC
66 CGGTAATAACTTTCCCATCCAATCACTCCGATCACCAAAATGTGTAGGTTCC
* * *
702408 CCAGAACCATACACACACATGCACACCAGTAAGGACTTACCCTAAGCACAAAGCCGAGGAGCCTG
1 CCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
*
702473 CGGTAATAACTTTCCCATCCCATCACTCCGATCACCAAAATGTGTAGGTTCC
66 CGGTAATAACTTTCCCATCCAATCACTCCGATCACCAAAATGTGTAGGTTCC
702525 CCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACA
1 CCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACA
702575 CAACAAAGGA
Statistics
Matches: 159, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
117 159 1.00
ACGTcount: A:0.32, C:0.35, G:0.16, T:0.17
Consensus pattern (117 bp):
CCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
CGGTAATAACTTTCCCATCCAATCACTCCGATCACCAAAATGTGTAGGTTCC
Found at i:703562 original size:29 final size:29
Alignment explanation
Indices: 703529--703592 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
703519 TTTTCTTAGG
703529 AAAATAGCACCA-ATTTAAAATTAATTACC
1 AAAATAGCACCATATTTAAAA-TAATTACC
* * * *
703558 AAAATAGCATCATTTTTAACATAATTACT
1 AAAATAGCACCATATTTAAAATAATTACC
703587 AAAATA
1 AAAATA
703593 TCACTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 24 0.80
30 6 0.20
ACGTcount: A:0.52, C:0.14, G:0.03, T:0.31
Consensus pattern (29 bp):
AAAATAGCACCATATTTAAAATAATTACC
Found at i:703671 original size:29 final size:29
Alignment explanation
Indices: 703632--703711 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 29
703622 TTTTTTTAAA
* * *
703632 AAAAAAATTACAAAAATAGCACCTTTTTC
1 AAAATAATTACCAAAATAGCACCATTTTC
* *
703661 AAAATATTTACCAGAATAGCACCATTTTC
1 AAAATAATTACCAAAATAGCACCATTTTC
* *
703690 CAAATAATTACCGAAATAGCAC
1 AAAATAATTACCAAAATAGCAC
703712 TCAGTGAACG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.47, C:0.20, G:0.06, T:0.26
Consensus pattern (29 bp):
AAAATAATTACCAAAATAGCACCATTTTC
Found at i:715246 original size:17 final size:17
Alignment explanation
Indices: 715224--715269 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
715214 CTTGGAGTAG
715224 CACTTTGTGTACTATGA
1 CACTTTGTGTACTATGA
715241 CACTTTGTGTACTATGA
1 CACTTTGTGTACTATGA
715258 CACTTTGTGTAC
1 CACTTTGTGTAC
715270 AAGGATGGTA
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:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (17 bp):
CACTTTGTGTACTATGA
Found at i:716834 original size:14 final size:12
Alignment explanation
Indices: 716765--716863 Score: 59
Period size: 10 Copynumber: 8.3 Consensus size: 12
716755 ATCATAATAT
716765 ATTTATATTATAA
1 ATTTATATTAT-A
*
716778 ATATAATAATT-TA
1 AT-TTAT-ATTATA
716791 ATTTATA-TA-A
1 ATTTATATTATA
* *
716801 AATT-TAGTA-A
1 ATTTATATTATA
716811 ATTATATATTATA
1 ATT-TATATTATA
*
716824 ATTTTTATATTTTA
1 A--TTTATATTATA
716838 ATTTATA-TA-A
1 ATTTATATTATA
716848 ATTTATATTATA
1 ATTTATATTATA
716860 ATTT
1 ATTT
716864 TGATAAAATT
Statistics
Matches: 68, Mismatches: 7, Indels: 23
0.69 0.07 0.23
Matches are distributed among these distances:
9 2 0.03
10 18 0.26
11 5 0.07
12 18 0.26
13 7 0.10
14 13 0.19
15 5 0.07
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (12 bp):
ATTTATATTATA
Found at i:726102 original size:20 final size:19
Alignment explanation
Indices: 726077--726136 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
726067 TTTTGGTACA
*
726077 GAGGGAATCGATATCCCCAT
1 GAGGGAACCGAT-TCCCCAT
*
726097 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATT-CCCC-AT
726118 GAAGGGGAACCGATTCCCC
1 G-A-GGGAACCGATTCCCC
726137 CTGGGGTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.44
21 2 0.06
22 5 0.15
23 11 0.32
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.18
Consensus pattern (19 bp):
GAGGGAACCGATTCCCCAT
Found at i:730579 original size:20 final size:20
Alignment explanation
Indices: 730556--730594 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
730546 TTTGAAACTT
730556 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
*
730576 AAATTCGCAATACGAAAAT
1 AAATTCGCAACACGAAAAT
730595 CGCAACGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:730636 original size:20 final size:20
Alignment explanation
Indices: 730601--730663 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
730591 AAATCGCAAC
*
730601 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
730620 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
730640 ACGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
730660 GCGA
1 GCGA
730664 ATTTAAGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 8 0.20
20 32 0.80
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.46
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:730674 original size:20 final size:20
Alignment explanation
Indices: 730604--730674 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
730594 TCGCAACGCG
*
730604 ATTTTAGTTTCGCGTTGCGA
1 ATTTCAGTTTCGCGTTGCGA
* * *
730624 TTTTCATTTTCGCGTTACGA
1 ATTTCAGTTTCGCGTTGCGA
* *
730644 TTTTCATTTTCGCGTTGCGA
1 ATTTCAGTTTCGCGTTGCGA
*
730664 ATTTAAGTTTC
1 ATTTCAGTTTC
730675 AGAAACTACT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.15, C:0.17, G:0.18, T:0.49
Consensus pattern (20 bp):
ATTTCAGTTTCGCGTTGCGA
Found at i:731987 original size:41 final size:41
Alignment explanation
Indices: 731930--732023 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
731920 TGGGAAGATT
731930 TACTACCATATAAGATGATGAATGATATAAGTTAACACAAA
1 TACTACCATATAAGATGATGAATGATATAAGTTAACACAAA
731971 TACTACCATATAAGATGATGAATGATATAAGTTAACACAAA
1 TACTACCATATAAGATGATGAATGATATAAGTTAACACAAA
732012 TACTACCATATA
1 TACTACCATATA
732024 TAAACAAATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.28
Consensus pattern (41 bp):
TACTACCATATAAGATGATGAATGATATAAGTTAACACAAA
Found at i:732830 original size:21 final size:21
Alignment explanation
Indices: 732802--732920 Score: 175
Period size: 21 Copynumber: 5.7 Consensus size: 21
732792 GATTCACCTG
732802 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
732823 TTATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
732844 CCATCGTTCAAGAGGCCTCTC
1 TCATCGTTCAAGAGGCCCCTC
*
732865 TCATCGTTTAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
732886 TCATCGTTCAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
732907 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
732921 CCCGATTCAC
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 87 1.00
ACGTcount: A:0.20, C:0.35, G:0.19, T:0.25
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:732881 original size:63 final size:63
Alignment explanation
Indices: 732802--732920 Score: 202
Period size: 63 Copynumber: 1.9 Consensus size: 63
732792 GATTCACCTG
* *
732802 TCATCGTTCAAGAGGCCCCTCTTATCGTTCAAGAGGCCCCTCCCATCGTTCAAGAGGCCTCTC
1 TCATCGTTCAAGAGGCCCCTCTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCTCTC
* *
732865 TCATCGTTTAAGAGGCCCCTCTCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGGCCCCTCTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAG
732921 CCCGATTCAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.20, C:0.35, G:0.19, T:0.25
Consensus pattern (63 bp):
TCATCGTTCAAGAGGCCCCTCTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCTCTC
Found at i:734610 original size:18 final size:18
Alignment explanation
Indices: 734587--734622 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
734577 AAGCCGGTTG
*
734587 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
734605 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
734623 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:736923 original size:24 final size:24
Alignment explanation
Indices: 736896--736942 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
736886 CAAAATCTGA
*
736896 GTATTGGCCAAGATCAAAGTTTGG
1 GTATTGACCAAGATCAAAGTTTGG
*
736920 GTATTGACCAAGATCAAATTTTG
1 GTATTGACCAAGATCAAAGTTTG
736943 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTTGG
Found at i:736951 original size:24 final size:24
Alignment explanation
Indices: 736903--736951 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
736893 TGAGTATTGG
** *
736903 CCAAGATCAAAGTTTGGGTATTGA
1 CCAAGATCAAAGTTTGAATACTGA
*
736927 CCAAGATCAAATTTTGAATACTGA
1 CCAAGATCAAAGTTTGAATACTGA
736951 C
1 C
736952 TAGTACTCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
CCAAGATCAAAGTTTGAATACTGA
Found at i:738012 original size:20 final size:20
Alignment explanation
Indices: 737969--738012 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
737959 AATCTTGTTG
* * *
737969 CGAAAAGGAAACTTGTGTTG
1 CGAAAAAGAAACTTGCGTTA
*
737989 CGAAAAAGAAATTTGCGTTA
1 CGAAAAAGAAACTTGCGTTA
738009 CGAA
1 CGAA
738013 TTCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.23
Consensus pattern (20 bp):
CGAAAAAGAAACTTGCGTTA
Found at i:738029 original size:40 final size:40
Alignment explanation
Indices: 737985--738112 Score: 127
Period size: 40 Copynumber: 3.2 Consensus size: 40
737975 GGAAACTTGT
*
737985 GTTGCGAAAAAGAAATTTGCGTTACGAATTCAGAAATCGA
1 GTTGCGAAAAAGAAATTTGCGTTGCGAATTCAGAAATCGA
** * * * *
738025 GTTGCG-AATTGAAATTCCGTGTTGCGAATTTAGAAATCGC
1 GTTGCGAAAAAGAAATT-TGCGTTGCGAATTCAGAAATCGA
* *
738065 GTTGCGAGAAAGAAATTTTCGTTGCG-ATTGCAGAAA-CTGA
1 GTTGCGAAAAAGAAATTTGCGTTGCGAATT-CAGAAATC-GA
738105 GTTGCGAA
1 GTTGCGAA
738113 TTTGGAAACT
Statistics
Matches: 68, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
39 12 0.18
40 49 0.72
41 7 0.10
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (40 bp):
GTTGCGAAAAAGAAATTTGCGTTGCGAATTCAGAAATCGA
Found at i:738034 original size:20 final size:19
Alignment explanation
Indices: 738009--738071 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
737999 ATTTGCGTTA
738009 CGAATTCAGAAATCGAGTTG
1 CGAATT-AGAAATCGAGTTG
*
738029 CGAATT-GAAATTCCGTGTTG
1 CGAATTAGAAA-T-CGAGTTG
*
738049 CGAATTTAGAAATCGCGTTG
1 CGAA-TTAGAAATCGAGTTG
738069 CGA
1 CGA
738072 GAAAGAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 4 0.11
19 1 0.03
20 25 0.68
21 3 0.08
22 4 0.11
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (19 bp):
CGAATTAGAAATCGAGTTG
Found at i:738129 original size:80 final size:79
Alignment explanation
Indices: 737985--738152 Score: 189
Period size: 80 Copynumber: 2.1 Consensus size: 79
737975 GGAAACTTGT
*
737985 GTTGCGAAAAAGAAATTTGCGTTACGAATTCAGAAATCGAGTTGCGAATTGAAATTCCGTGTTGC
1 GTTGCGAAAAAGAAATTTGCGTTACGAATTCAGAAATCGAGTTGCGAATTGAAA-TCCGAGTTGC
*
738050 GAATTTAGAAATCGC
65 GAAATTAGAAATCGC
* * * *
738065 GTTGCGAGAAAGAAATTTTCGTTGCG-ATTGCAGAAA-CTGAGTTGCGAATTTGGAAA-CTGAGT
1 GTTGCGAAAAAGAAATTTGCGTTACGAATT-CAGAAATC-GAGTTGCGAA-TT-GAAATCCGAGT
* **
738127 TGCGAAATTGGAGTTCGC
62 TGCGAAATTAGAAATCGC
738145 GTTGCGAA
1 GTTGCGAA
738153 TTTTTTGTTC
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
79 4 0.05
80 64 0.86
81 2 0.03
82 4 0.05
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (79 bp):
GTTGCGAAAAAGAAATTTGCGTTACGAATTCAGAAATCGAGTTGCGAATTGAAATCCGAGTTGCG
AAATTAGAAATCGC
Found at i:738132 original size:20 final size:20
Alignment explanation
Indices: 738097--738138 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
738087 TGCGATTGCA
*
738097 GAAACTGAGTTGCGAATTTG
1 GAAACTGAGTTGCGAAATTG
738117 GAAACTGAGTTGCGAAATTG
1 GAAACTGAGTTGCGAAATTG
738137 GA
1 GA
738139 GTTCGCGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.26
Consensus pattern (20 bp):
GAAACTGAGTTGCGAAATTG
Found at i:738985 original size:45 final size:43
Alignment explanation
Indices: 738891--738989 Score: 123
Period size: 45 Copynumber: 2.3 Consensus size: 43
738881 TCATTCCCCT
*
738891 AATTAAATAAATAATATACAAATTAAAATATAAACTAATACTA
1 AATTAAATAAATAATATAAAAATTAAAATATAAACTAATACTA
*
738934 AA-TAAATAAATAA-ATAAAATATTCACAATAATAAAACTAATAC-A
1 AATTAAATAAATAATATAAAA-ATT-AAAAT-AT-AAACTAATACTA
738978 AATTAAATAAAT
1 AATTAAATAAAT
738990 TGTTACTGTA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
41 5 0.10
42 14 0.29
43 6 0.12
44 5 0.10
45 19 0.39
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (43 bp):
AATTAAATAAATAATATAAAAATTAAAATATAAACTAATACTA
Found at i:741824 original size:23 final size:23
Alignment explanation
Indices: 741794--741842 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
741784 AATCCGTAGG
*
741794 ATGCCATTCCATC-CTGGTAAGTT
1 ATGCCATTCCA-CACTGGTAAGCT
741817 ATGCCATTCCACACTGGTAAGCT
1 ATGCCATTCCACACTGGTAAGCT
741840 ATG
1 ATG
741843 TAATGTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (23 bp):
ATGCCATTCCACACTGGTAAGCT
Found at i:741865 original size:36 final size:36
Alignment explanation
Indices: 741818--741897 Score: 160
Period size: 36 Copynumber: 2.2 Consensus size: 36
741808 TGGTAAGTTA
741818 TGCCATTCCACACTGGTAAGCTATGTAATGTGTTTC
1 TGCCATTCCACACTGGTAAGCTATGTAATGTGTTTC
741854 TGCCATTCCACACTGGTAAGCTATGTAATGTGTTTC
1 TGCCATTCCACACTGGTAAGCTATGTAATGTGTTTC
741890 TGCCATTC
1 TGCCATTC
741898 TGTTCCTGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (36 bp):
TGCCATTCCACACTGGTAAGCTATGTAATGTGTTTC
Found at i:743802 original size:137 final size:136
Alignment explanation
Indices: 743619--743926 Score: 358
Period size: 137 Copynumber: 2.2 Consensus size: 136
743609 AAATGTAGGT
* * * * * *
743619 TCTAATATTAAACCCTAACAAATTTTAAAAATTTATTGAATCGAATAGTTAATTTGG-AGCACCA
1 TCTAATATTAAA-CCTAACAAATTTTAGAATTTTATTGAATCGAATAATTAAATCGGAAAC-CCA
*
743683 AGCTAAGGTA-A-AGATCATTTTAGAAATTCTCCTAA-TTT-AGGGACAAAAGTGAAATTAAAAC
64 AGC-AAGG-ACAGAGATCA-TTTAAAAATTCTCCTAAGTTTAAGGG-CAAAAGTGAAATTAAAAC
** *
743744 TAA-AGTGGATGC
125 TAAGA-TAAAGGC
*
743756 TCTAATATTGAAACCTAACAAATTTTAGAATTTTATTGAATTGAATAATTAAATCGGAAACCCAA
1 TCTAATATT-AAACCTAACAAATTTTAGAATTTTATTGAATCGAATAATTAAATCGGAAACCCAA
* *
743821 GCAATGACAGAGATCATTTAAAAATTCTCCTAAGTTTAAGGGCTAAAGTGAAATTAAAACTAAGA
65 GCAAGGACAGAGATCATTTAAAAATTCTCCTAAGTTTAAGGGCAAAAGTGAAATTAAAACTAAGA
743886 TAAAGGC
130 TAAAGGC
* *
743893 TATAATATTAAAACTTAACAAATTTTAGAATTTT
1 TCTAATATT-AAACCTAACAAATTTTAGAATTTT
743927 TATTCTAATA
Statistics
Matches: 148, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
135 1 0.01
136 20 0.14
137 117 0.79
138 10 0.07
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (136 bp):
TCTAATATTAAACCTAACAAATTTTAGAATTTTATTGAATCGAATAATTAAATCGGAAACCCAAG
CAAGGACAGAGATCATTTAAAAATTCTCCTAAGTTTAAGGGCAAAAGTGAAATTAAAACTAAGAT
AAAGGC
Found at i:744626 original size:104 final size:103
Alignment explanation
Indices: 744466--744667 Score: 266
Period size: 104 Copynumber: 2.0 Consensus size: 103
744456 TTCATTTTAG
* * * * * *
744466 AATTTTACCCGGACTATAAATAATACGGATCATACCGAGGACGAGTCACCGTGAGGT-AGTATGA
1 AATTTTACCCGAACCATAAATAACACGGATCATACCGAGGACGAGTCACAGTGAGGTCA-AAGGA
744530 TAGATTTGTAACAAATTAAAAAGTTACTGGTTAGAGTTAA
65 TAGATTTGTAACAAATT-AAAAGTTACTGGTTAGAGTTAA
*
744570 AATTTTACTCGAACCATAAATAACACGGATCATACACG-GGACG-GTTCACAGTGAGGTCAAAGG
1 AATTTTACCCGAACCATAAATAACACGGATCATAC-CGAGGACGAG-TCACAGTGAGGTCAAAGG
* *
744633 ATCGATTTGTAACAAATTAAAAGTTAGTGGTTAGA
64 ATAGATTTGTAACAAATTAAAAGTTACTGGTTAGA
744668 ATCGAAATAA
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
103 17 0.20
104 66 0.77
105 3 0.03
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (103 bp):
AATTTTACCCGAACCATAAATAACACGGATCATACCGAGGACGAGTCACAGTGAGGTCAAAGGAT
AGATTTGTAACAAATTAAAAGTTACTGGTTAGAGTTAA
Found at i:749927 original size:15 final size:15
Alignment explanation
Indices: 749904--749936 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
749894 CGTAGGACTC
749904 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
749919 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
749934 CTA
1 CTA
749937 TTATACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:750532 original size:64 final size:64
Alignment explanation
Indices: 750424--750600 Score: 214
Period size: 64 Copynumber: 2.8 Consensus size: 64
750414 TAATGAAGGT
* * ** ** * * **
750424 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT-GTCACTATTAATGGG
* *
750488 ATGCATCGATGCACTCCTTATGCATCGATGCACCG-ATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGAATTGCATTCGATGTGTCACTATTAATGGG
750552 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
750601 CTTTATTTTA
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
63 3 0.03
64 94 0.97
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTGTCACTATTAATGGG
Found at i:750621 original size:64 final size:63
Alignment explanation
Indices: 750487--750648 Score: 202
Period size: 64 Copynumber: 2.5 Consensus size: 63
750477 TTATTGCTGG
* * *
750487 GATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTTTCACTATTAAAGA
* *
750551 GATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCGATGT-TTCACTATTAAAGA
** *
750614 GAGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCAC
750649 ATTCAAACAA
Statistics
Matches: 87, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
63 4 0.05
64 80 0.92
65 3 0.03
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (63 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTTTCACTATTAAAGA
Found at i:768952 original size:15 final size:15
Alignment explanation
Indices: 768929--768976 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
768919 CGTAGGACTC
768929 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
768944 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
* *
768959 CTATATCCCGAAGAA
1 CTACATCCCGAAGGA
768974 CTA
1 CTA
768977 TTATACCCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Done.