Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000074.1 Hibiscus syriacus cultivar Beakdansim tig00000136_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: 1055225
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:499674 original size:15 final size:16
Alignment explanation
Indices: 499654--499686 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
499644 AAAGGAATTT
*
499654 ATATATACA-AAATAA
1 ATATATAAAGAAATAA
499669 ATATATAAAGAAATAA
1 ATATATAAAGAAATAA
499685 AT
1 AT
499687 TTGAGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (16 bp):
ATATATAAAGAAATAA
Found at i:499770 original size:21 final size:20
Alignment explanation
Indices: 499734--499773 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
499724 ATATCGAATT
*
499734 AAAAATAAAAGGAAATAATA
1 AAAAATAAAAGAAAATAATA
499754 AAAAATAAAAGAAAAATAAT
1 AAAAATAAAAG-AAAATAAT
499774 TAATTTAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (20 bp):
AAAAATAAAAGAAAATAATA
Found at i:499950 original size:17 final size:19
Alignment explanation
Indices: 499918--499955 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
499908 ACCAAATTAA
499918 AAAGAAAAATAATGG-TAG
1 AAAGAAAAATAATGGTTAG
*
499936 AAAGTAAAA-AATGGTTAG
1 AAAGAAAAATAATGGTTAG
499954 AA
1 AA
499956 TAAAGAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.61, C:0.00, G:0.21, T:0.18
Consensus pattern (19 bp):
AAAGAAAAATAATGGTTAG
Found at i:499994 original size:18 final size:18
Alignment explanation
Indices: 499957--499995 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
499947 TGGTTAGAAT
* **
499957 AAAGAAACTCAAATTTAA
1 AAAGAAAATCAAATAAAA
499975 AAAGAAAATCAAATAAAA
1 AAAGAAAATCAAATAAAA
499993 AAA
1 AAA
499996 CATTAGAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAGAAAATCAAATAAAA
Found at i:501147 original size:85 final size:85
Alignment explanation
Indices: 501055--501551 Score: 352
Period size: 85 Copynumber: 5.9 Consensus size: 85
501045 CCAAGCCGTC
* * * * * *
501055 ATCAATAGTTGATTTGCTACTTTCTCTAAAGTATACCAAATCGAAGAATGATATTGCTCCTTTCT
1 ATCAATGGTTGATATGCTCCTTTCTCTAAAGGATGCCAAATCGAAGAATGATCTTGCTCCTTTCT
501120 CTAAAGGACGTCAAGTTGTA
66 CTAAAGGACGTCAAGTTGTA
* * * * * *
501140 ATCAATAGTTGATATGGT-CTTATCTATGAAGGATGTCAAATCCCAA-AATGATCTTGCT-CTAT
1 ATCAATGGTTGATATGCTCCTT-TCTCTAAAGGATGCCAAAT-CGAAGAATGATCTTGCTCCT-T
*
501202 TCTCTTAAGGAC-TCCAAGTTGTA
63 TCTCTAAAGGACGT-CAAGTTGTA
* * * * *
501225 ATCAATGGTT-ATCTGC-CCGTTTCTTTAAAGGACGCCAGATTGAAGAATGATCTTGCTCCTTTC
1 ATCAATGGTTGATATGCTCC-TTTCTCTAAAGGATGCCAAATCGAAGAATGATCTTGCTCCTTTC
* * * * *
501288 TATGAAA-GATGCCAACTCGTA
65 TCT-AAAGGACGTCAAGTTGTA
* ** * * * * *
501309 ATCAATGGTAGATATGCTTTTTTCTCTAATGGGTTCCAAATC-AGAGAACGATCTTGCTCCATTC
1 ATCAATGGTTGATATGCTCCTTTCTCTAAAGGATGCCAAATCGA-AGAATGATCTTGCTCCTTTC
* * *
501373 TCTAAAGGACATCAGGTAGTA
65 TCTAAAGGACGTCAAGTTGTA
* * * * ** **
501394 ATCAATGGTTGA-ACTGCTCCTTTGTCTAAAAGATGCAAAAT-TAGAGAACAATCTTGCTATTTT
1 ATCAATGGTTGATA-TGCTCCTTTCTCTAAAGGATGCCAAATCGA-AGAATGATCTTGCTCCTTT
* * * *
501457 CTCTCAATGACGCCATGTTGTA
64 CTCTAAAGGACGTCAAGTTGTA
* * * * *
501479 ATCAATGGTTGATCTGCTCCTTTCTCTGAATGATG-CATAATCTG-GGAACGATCTTGCTCCTTT
1 ATCAATGGTTGATATGCTCCTTTCTCTAAAGGATGCCA-AATC-GAAGAATGATCTTGCTCCTTT
501542 CTCTAAAGGA
64 CTCTAAAGGA
501552 TAGCAAGTCA
Statistics
Matches: 315, Mismatches: 77, Indels: 40
0.73 0.18 0.09
Matches are distributed among these distances:
83 2 0.01
84 66 0.21
85 244 0.77
86 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (85 bp):
ATCAATGGTTGATATGCTCCTTTCTCTAAAGGATGCCAAATCGAAGAATGATCTTGCTCCTTTCT
CTAAAGGACGTCAAGTTGTA
Found at i:501566 original size:40 final size:40
Alignment explanation
Indices: 501489--501573 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
501479 ATCAATGGTT
* * *
501489 GATC-TGCTCCTTTCTCTGAATGATGCATAATCTGGGAAC
1 GATCTTGCTCCTTTCTCTAAAGGATGCATAATCAGGGAAC
*
501528 GATCTTGCTCCTTTCTCTAAAGGATAGCA-AGTCAGGGAAC
1 GATCTTGCTCCTTTCTCTAAAGGAT-GCATAATCAGGGAAC
*
501568 AATCTT
1 GATCTT
501574 TCTTTTTTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 4 0.10
40 32 0.82
41 3 0.08
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (40 bp):
GATCTTGCTCCTTTCTCTAAAGGATGCATAATCAGGGAAC
Found at i:503147 original size:44 final size:44
Alignment explanation
Indices: 503084--503168 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
503074 TACCAAAACA
*
503084 CATTCCCAATTCTGATTTTAGGCTTGAATGCCTTTAAATTAAAT
1 CATTCCCAATTCTGATTTTAGGCTCGAATGCCTTTAAATTAAAT
* *
503128 CATTCCCAATTTTGATTTTAGTCTCGAATGCCTTTAAATTA
1 CATTCCCAATTCTGATTTTAGGCTCGAATGCCTTTAAATTA
503169 CATTTCATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (44 bp):
CATTCCCAATTCTGATTTTAGGCTCGAATGCCTTTAAATTAAAT
Found at i:503294 original size:21 final size:21
Alignment explanation
Indices: 503265--503306 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
503255 AGTTACTCAT
503265 TAGTATCATGATCTGAATGCA
1 TAGTATCATGATCTGAATGCA
*
503286 TAGTGTCATGATCTGAATGCA
1 TAGTATCATGATCTGAATGCA
503307 ATCATATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Consensus pattern (21 bp):
TAGTATCATGATCTGAATGCA
Found at i:506646 original size:2 final size:2
Alignment explanation
Indices: 506639--506674 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
506629 AAAATATGAG
*
506639 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
506675 TAAAACATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:507105 original size:2 final size:2
Alignment explanation
Indices: 507098--507143 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
507088 TAACTTTGTA
*
507098 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
507140 AT AT
1 AT AT
507144 TACTTAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:508409 original size:16 final size:16
Alignment explanation
Indices: 508388--508418 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
508378 CCTGCATATA
508388 AATTAATAATAATAAT
1 AATTAATAATAATAAT
508404 AATTAATAATAATAA
1 AATTAATAATAATAA
508419 AATATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATTAATAATAATAAT
Found at i:508412 original size:13 final size:13
Alignment explanation
Indices: 508394--508418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
508384 TATAAATTAA
508394 TAATAATAATAAT
1 TAATAATAATAAT
508407 TAATAATAATAA
1 TAATAATAATAA
508419 AATATTAAAA
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):
TAATAATAATAAT
Found at i:510517 original size:15 final size:15
Alignment explanation
Indices: 510499--510531 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
510489 GACAAGGAAT
510499 AAAATAAAAAT-TTGG
1 AAAAT-AAAATCTTGG
510514 AAAATAAAATCTTGG
1 AAAATAAAATCTTGG
510529 AAA
1 AAA
510532 CAAATGTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.61, C:0.03, G:0.12, T:0.24
Consensus pattern (15 bp):
AAAATAAAATCTTGG
Found at i:510748 original size:18 final size:18
Alignment explanation
Indices: 510725--510759 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
510715 GACTCGTAAA
510725 GAAAATCAAA-TTAAAAAG
1 GAAAAT-AAAGTTAAAAAG
510743 GAAAATAAAGTTAAAAA
1 GAAAATAAAGTTAAAAA
510760 AAGAGAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.69, C:0.03, G:0.11, T:0.17
Consensus pattern (18 bp):
GAAAATAAAGTTAAAAAG
Found at i:514118 original size:24 final size:25
Alignment explanation
Indices: 514086--514138 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
514076 ATTTGATTAC
*
514086 TTGAGTTAA-TGACAATTAATTATTG
1 TTGAGTTAAGT-ACAATTAATCATTG
514111 TTGA-TTAAGTACAATTAATCATTG
1 TTGAGTTAAGTACAATTAATCATTG
514135 TTGA
1 TTGA
514139 CATATAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (25 bp):
TTGAGTTAAGTACAATTAATCATTG
Found at i:516620 original size:23 final size:21
Alignment explanation
Indices: 516594--516652 Score: 55
Period size: 25 Copynumber: 2.6 Consensus size: 21
516584 TAGTTTTATA
*
516594 AAGTTCTTATTTTCTTTATTTT
1 AAGTT-TTATTTTATTTATTTT
*
516616 CAAGTTTTTGTTTTTTATTTATTTT
1 -AAG--TTT-TATTTTATTTATTTT
516641 AAGTTTTATTTT
1 AAGTTTTATTTT
516653 TAAACATGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 5 0.17
22 3 0.10
23 3 0.10
24 4 0.13
25 15 0.50
ACGTcount: A:0.19, C:0.05, G:0.07, T:0.69
Consensus pattern (21 bp):
AAGTTTTATTTTATTTATTTT
Found at i:526258 original size:3 final size:3
Alignment explanation
Indices: 526250--526303 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
526240 GTATTTTTTG
526250 TAA TAA TAA TAA TAA TAA TAA T-A 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
526297 TATA TAA
1 TA-A TAA
526304 ACTCAGACGA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:527084 original size:262 final size:262
Alignment explanation
Indices: 526588--527206 Score: 940
Period size: 262 Copynumber: 2.4 Consensus size: 262
526578 AGGTTTTACG
* * * *
526588 GATGGCCCTAAGGACTTAA-CATC-TGACTCAAAAGACTGACAGAAGACCCGAAGGATTTACAAA
1 GATGACCCTAAGGATTTAAGCATCATG-CTCGAAAGACTGACAGATGACCCGAAGGATTTACAAA
* *
526651 TTTGTGGGAAATAATTCATTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAGAATTTC
65 TTTGTGGGAAATAATTTATTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTC
* * *
526716 ATTTTCTAGAACATTAAATGATAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAGATCATAT
130 ATTTCCTAGAACATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAATCATAT
* * * **
526781 GTAAACATCCTACCTAAAGGTCTGACGGATGTCTTTAAGGACTTATCATCTTGT-TCAAAAGACT
195 GTAAACATCCTACCCAAAGGTCTAACGGATGGCCCTAAGGACTTATCATCTT-TCTCAAAAGACT
526845 GGCA
259 GGCA
* *
526849 GATGACCCTAAGGATTTAAGCATCATGCTCGAAAGACTAACAGATGACCTGAAGGATTTACAAAT
1 GATGACCCTAAGGATTTAAGCATCATGCTCGAAAGACTGACAGATGACCCGAAGGATTTACAAAT
* *
526914 TTGTGAGAAATAATTTATTGGGTATGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCA
66 TTGTGGGAAATAATTTATTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCA
* * *
526979 TTTCCTTGAACATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCTAAAATCATATT
131 TTTCCTAGAACATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAATCATATG
* *
527044 TAAACATCCTACCCAAAGGTCTAATGGATGGCCCTAAGGACTTATCATCTTTCTCAAAAGACTTG
196 TAAACATCCTACCCAAAGGTCTAACGGATGGCCCTAAGGACTTATCATCTTTCTCAAAAGACTGG
527109 CA
261 CA
* * *
527111 GAT-ACCATAAGGATTTAAGCAACATGCTCGAAAGACTGACAGATAACCCGAAGGATTTACAAAT
1 GATGACCCTAAGGATTTAAGCATCATGCTCGAAAGACTGACAGATGACCCGAAGGATTTACAAAT
* *
527175 TTGTGGGAAATAATTTACTAGGTAAGAAACTT
66 TTGTGGGAAATAATTTATTGGGTAAGAAACTT
527207 CTTACTTTTA
Statistics
Matches: 323, Mismatches: 32, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
261 102 0.32
262 219 0.68
263 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (262 bp):
GATGACCCTAAGGATTTAAGCATCATGCTCGAAAGACTGACAGATGACCCGAAGGATTTACAAAT
TTGTGGGAAATAATTTATTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCA
TTTCCTAGAACATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAATCATATG
TAAACATCCTACCCAAAGGTCTAACGGATGGCCCTAAGGACTTATCATCTTTCTCAAAAGACTGG
CA
Found at i:530847 original size:3 final size:3
Alignment explanation
Indices: 530839--530878 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
530829 TTGTATTTTT
*
530839 ATA ATA ATA ATA GTA AT- ATA ATA ATA ATA ATA ATA TATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A
530879 ACTCGGATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:530860 original size:17 final size:17
Alignment explanation
Indices: 530838--530875 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
530828 TTTGTATTTT
*
530838 TATAATAATAATAGTAA
1 TATAATAATAATAATAA
530855 TATAATAATAATAATAA
1 TATAATAATAATAATAA
530872 TATA
1 TATA
530876 TAAACTCGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
TATAATAATAATAATAA
Found at i:541800 original size:10 final size:10
Alignment explanation
Indices: 541785--541821 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
541775 AGTGTCACTC
*
541785 GAAAAATAAA
1 GAAAAATATA
541795 GAAAAATATA
1 GAAAAATATA
*
541805 GAAAATTATA
1 GAAAAATATA
541815 GAAAAAT
1 GAAAAAT
541822 GTTTTAAGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (10 bp):
GAAAAATATA
Found at i:542828 original size:24 final size:24
Alignment explanation
Indices: 542793--542848 Score: 96
Period size: 24 Copynumber: 2.3 Consensus size: 24
542783 TAGTAGTCCA
542793 ATTGTGAA-GAACTACATGAACATG
1 ATTGT-AACGAACTACATGAACATG
542817 ATTGTAACGAACTACATGAACATG
1 ATTGTAACGAACTACATGAACATG
542841 ATTGTAAC
1 ATTGTAAC
542849 CCCCTAGACC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 2 0.06
24 29 0.94
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (24 bp):
ATTGTAACGAACTACATGAACATG
Found at i:543722 original size:36 final size:35
Alignment explanation
Indices: 543654--543725 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
543644 CCTTAGGTCC
** *
543654 ATAAGGAATTACCAGTTGATCATTGTTCAACCTGT
1 ATAAGGAATTACCAGTTGATCAGAGCTCAACCTGT
* *
543689 ATAAGGAATTACTAGCTTGATCAGAGCTGAACCTGT
1 ATAAGGAATTACCAG-TTGATCAGAGCTCAACCTGT
543725 A
1 A
543726 GAGACTTCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
35 14 0.45
36 17 0.55
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (35 bp):
ATAAGGAATTACCAGTTGATCAGAGCTCAACCTGT
Found at i:544628 original size:20 final size:20
Alignment explanation
Indices: 544592--544629 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
544582 CTATTTTGGA
*
544592 TGACTCAGGTCGGTTCAAGT
1 TGACTCAGGTCGATTCAAGT
544612 TGACTCAGAG-CGATTCAA
1 TGACTCAG-GTCGATTCAA
544630 ACCAGTTCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (20 bp):
TGACTCAGGTCGATTCAAGT
Found at i:547111 original size:113 final size:113
Alignment explanation
Indices: 546913--547139 Score: 409
Period size: 113 Copynumber: 2.0 Consensus size: 113
546903 GAGCTACACC
* *
546913 AGTAGGACCTTCAAAGGTCCTAACTTCATTAACAATAAGAGCTATTCCTATATAGAAGAGAGGAA
1 AGTAGGACCTTCAAAGGTCCTAACTCCATTAACAATAAGAGCTACTCCTATATAGAAGAGAGGAA
*
546978 AAGGGGAGACTCTATAAGAAGAAAAAGAAATGCTCTTAGTAGGTTTAG
66 AAGGGAAGACTCTATAAGAAGAAAAAGAAATGCTCTTAGTAGGTTTAG
* *
547026 AGTAGGACCTTCAAAGGTCCTAACTCCGTTAACAATAAGAGCTACTCCTATCTAGAAGAGAGGAA
1 AGTAGGACCTTCAAAGGTCCTAACTCCATTAACAATAAGAGCTACTCCTATATAGAAGAGAGGAA
547091 AAGGGAAGACTCTATAAGAAGAAAAAGAAATGCTCTTAGTAGGTTTAG
66 AAGGGAAGACTCTATAAGAAGAAAAAGAAATGCTCTTAGTAGGTTTAG
547139 A
1 A
547140 ACTTTTGATC
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 109 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.23
Consensus pattern (113 bp):
AGTAGGACCTTCAAAGGTCCTAACTCCATTAACAATAAGAGCTACTCCTATATAGAAGAGAGGAA
AAGGGAAGACTCTATAAGAAGAAAAAGAAATGCTCTTAGTAGGTTTAG
Found at i:548711 original size:21 final size:21
Alignment explanation
Indices: 548685--548724 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
548675 AGATTATAAA
*
548685 TAAAAAAAATTACGCATATTG
1 TAAAAAAAATTACACATATTG
548706 TAAAAAAAATTACACATAT
1 TAAAAAAAATTACACATAT
548725 AACATTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (21 bp):
TAAAAAAAATTACACATATTG
Found at i:550602 original size:54 final size:53
Alignment explanation
Indices: 550457--550602 Score: 195
Period size: 54 Copynumber: 2.7 Consensus size: 53
550447 AAGGCTATTT
* * *
550457 ATTAATATCCGAAA-AAATTAAAAATAATCAATTAATACCAATGTGAACTGCTA
1 ATTAATATCC-AAATAAAATCAAAATAATCAATTAATATCAATGTGAACTGCTA
* * * *
550510 ATTAGTATCCAAATAAAGTCAGAAATTATCAATTAATATCAATGTGAACTGCTG
1 ATTAATATCCAAATAAAATCA-AAATAATCAATTAATATCAATGTGAACTGCTA
550564 ATTAATATCCAAATAAAATCGAAAATAATCAATTAATAT
1 ATTAATATCCAAATAAAATC-AAAATAATCAATTAATAT
550603 TTGAATTAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
52 3 0.04
53 14 0.17
54 63 0.78
55 1 0.01
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.30
Consensus pattern (53 bp):
ATTAATATCCAAATAAAATCAAAATAATCAATTAATATCAATGTGAACTGCTA
Found at i:553068 original size:18 final size:17
Alignment explanation
Indices: 553030--553069 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
553020 ATAAAATAAA
553030 TAATAAAAAAGAAACAT
1 TAATAAAAAAGAAACAT
* *
553047 TAATAAAATAATAAATAT
1 TAATAAAA-AAGAAACAT
553065 TAATA
1 TAATA
553070 GTAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (17 bp):
TAATAAAAAAGAAACAT
Found at i:553145 original size:18 final size:18
Alignment explanation
Indices: 553110--553148 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
553100 GTTGTTTCTA
* *
553110 AAATAAAAGATACGAATT
1 AAATAAAAGAAAAGAATT
*
553128 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
553146 AAA
1 AAA
553149 CAAACAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:553791 original size:64 final size:63
Alignment explanation
Indices: 553720--553841 Score: 201
Period size: 64 Copynumber: 1.9 Consensus size: 63
553710 TAAAACATCT
553720 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAAAATAATATAATATTC
1 TAAATCCTAATTAAAACAC-TAAAACCTATTTAAACTAAAATACCTAAAAAA-AATATAATATTC
* *
553784 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAATAAATATAA
1 TAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAAAAAATATAA
553842 AATATAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
63 12 0.22
64 43 0.78
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (63 bp):
TAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAAAAAATATAATATTC
Found at i:553811 original size:19 final size:19
Alignment explanation
Indices: 553755--553893 Score: 70
Period size: 19 Copynumber: 7.2 Consensus size: 19
553745 CTATTTAAAC
**
553755 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
553775 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
553795 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
*
553814 TAAACTA--AAATACCTAA-
1 TAAAATACTAAA-ACCTAAT
* ** *
553831 AATAAATA-TAAAATATAAA
1 TA-AAATACTAAAACCTAAT
* *
553850 AAAAATATCCTAAAACTTAAT
1 TAAAATA--CTAAAACCTAAT
*
553871 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
553890 TAAA
1 TAAA
553894 CTAAAATACA
Statistics
Matches: 90, Mismatches: 21, Indels: 16
0.71 0.17 0.13
Matches are distributed among these distances:
17 4 0.04
18 18 0.20
19 40 0.44
20 9 0.10
21 19 0.21
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:553864 original size:32 final size:32
Alignment explanation
Indices: 553820--553883 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
553810 TATTTAAACT
553820 AAAATACCTAAAA-TAAATATAAAATA-TAAAA
1 AAAATACCTAAAACTAAAT-TAAAATACTAAAA
*
553851 AAAATATCCTAAAACTTAATTAAAATACTAAAA
1 AAAATA-CCTAAAACTAAATTAAAATACTAAAA
553884 CCTATTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 6 0.21
32 14 0.48
33 9 0.31
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (32 bp):
AAAATACCTAAAACTAAATTAAAATACTAAAA
Found at i:555565 original size:5 final size:5
Alignment explanation
Indices: 555555--555620 Score: 55
Period size: 5 Copynumber: 13.0 Consensus size: 5
555545 TTCAGAGAAA
** *
555555 AAAAT AAAAT AAAATT AAAAAT AAAAT -AAAT GGAAT GAAAT -AAAT AAAAT
1 AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
*
555605 GAAAAT AAAAT GAAAT
1 -AAAAT AAAAT AAAAT
555621 GGGTTGCCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
4 8 0.15
5 34 0.64
6 7 0.13
7 4 0.08
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:555597 original size:14 final size:15
Alignment explanation
Indices: 555551--555613 Score: 57
Period size: 14 Copynumber: 4.6 Consensus size: 15
555541 TCTGTTCAGA
555551 GAAAA-AAATAAAAT
1 GAAAATAAATAAAAT
*
555565 -AAAAT-TA-AAAAT
1 GAAAATAAATAAAAT
**
555577 -AAAATAAATGGAAT
1 GAAAATAAATAAAAT
555591 G-AAATAAATAAAAT
1 GAAAATAAATAAAAT
555605 GAAAATAAA
1 GAAAATAAA
555614 ATGAAATGGG
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
12 10 0.26
13 6 0.16
14 15 0.39
15 7 0.18
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (15 bp):
GAAAATAAATAAAAT
Found at i:555616 original size:11 final size:10
Alignment explanation
Indices: 555555--555620 Score: 55
Period size: 9 Copynumber: 6.5 Consensus size: 10
555545 TTCAGAGAAA
555555 AAAATAAAAT
1 AAAATAAAAT
555565 AAAATTAAAAAT
1 AAAA-T-AAAAT
555577 AAAAT-AAAT
1 AAAATAAAAT
** *
555586 GGAATGAAAT
1 AAAATAAAAT
555596 -AAATAAAAT
1 AAAATAAAAT
555605 GAAAATAAAAT
1 -AAAATAAAAT
*
555616 GAAAT
1 AAAAT
555621 GGGTTGCCTC
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
9 14 0.30
10 12 0.26
11 11 0.24
12 9 0.20
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:557916 original size:13 final size:13
Alignment explanation
Indices: 557882--557914 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
557872 TGGTTGGGCC
*
557882 TGGGGTTTGTATT
1 TGGGCTTTGTATT
557895 TGGGCTTTG-ATT
1 TGGGCTTTGTATT
557907 TGGGCTTT
1 TGGGCTTT
557915 TGTAGTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.06, C:0.06, G:0.36, T:0.52
Consensus pattern (13 bp):
TGGGCTTTGTATT
Found at i:557950 original size:3 final size:3
Alignment explanation
Indices: 557924--558015 Score: 130
Period size: 3 Copynumber: 30.0 Consensus size: 3
557914 TTGTAGTATT
* *
557924 TAA TAAA TAA TATA TAA TAT TAA TAA TAA TAT TAA TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
557971 TAA TAA TAA TAA TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
558016 ATTTAAATTT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
3 73 0.92
4 6 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:558200 original size:45 final size:45
Alignment explanation
Indices: 558149--558251 Score: 197
Period size: 45 Copynumber: 2.3 Consensus size: 45
558139 GATGGAAATG
*
558149 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
558194 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
558239 TTTGAAAACATCA
1 TTTGAAAACATCA
558252 AAAAGCTCCC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (45 bp):
TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
Found at i:558319 original size:76 final size:76
Alignment explanation
Indices: 558185--558555 Score: 647
Period size: 76 Copynumber: 4.9 Consensus size: 76
558175 TTACAGATGA
* * * *
558185 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
558248 ATCAAAAAGCT
66 ATCAAAAAGCT
**
558259 CCCGAAGGCTTTTTGGAAACATCATGCTTTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
558324 ATCAAAAAGCT
66 ATCAAAAAGCT
558335 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
558400 ATCAAAAAGCT
66 ATCAAAAAGCT
*
558411 CCCGAAGCCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
558476 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
558487 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
558552 ATCA
66 ATCA
558556 TGCACTGATG
Statistics
Matches: 283, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
74 8 0.03
76 275 0.97
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
ATCAAAAAGCT
Found at i:558554 original size:197 final size:197
Alignment explanation
Indices: 558345--558752 Score: 737
Period size: 197 Copynumber: 2.1 Consensus size: 197
558335 CCCGAAGGCT
* *
558345 TTTTGGAAACATCATGCACTG-TAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAG
1 TTTTGAAAACATCATGCACTGAT-GGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAG
558409 CTCCCGAAGCCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAA
65 CTCCCGAAGCCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAA
*
558474 ACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTA
130 ACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACATACAGATGACCCTA
558539 AGG
195 AGG
*
558542 TTTTGAAAACATCATGCACTGATGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGATGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
* *
558607 TCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTTAAAA
66 TCCCGAAGCCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAA
558672 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACATACAGATGACCCTAA
131 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACATACAGATGACCCTAA
558737 GG
196 GG
*
558739 CTTTGAAAACATCA
1 TTTTGAAAACATCA
558753 AAAAGCTCCC
Statistics
Matches: 203, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
197 202 1.00
198 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (197 bp):
TTTTGAAAACATCATGCACTGATGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
TCCCGAAGCCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAA
CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACATACAGATGACCCTAA
GG
Found at i:558561 original size:45 final size:45
Alignment explanation
Indices: 558487--558600 Score: 176
Period size: 45 Copynumber: 2.5 Consensus size: 45
558477 TCAAAAAGCT
*
558487 CCCGAAGGCTTTTTGGAAACATCATGCACTGCA-GGACTTACAGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTG-ATGGACTTACAGATGA
*
558534 CCCTAAGGTTTTGAAAACATCATGCACTGATGGACTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGATGGACTTACAGATGA
558579 CCCGAAGGTTTTGAAAACATCA
1 CCCGAAGGTTTTGAAAACATCA
558601 AAAAGCTCCC
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
44 1 0.02
45 55 0.87
47 7 0.11
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGATGGACTTACAGATGA
Found at i:558577 original size:121 final size:122
Alignment explanation
Indices: 558421--558676 Score: 446
Period size: 121 Copynumber: 2.1 Consensus size: 122
558411 CCCGAAGCCT
* *
558421 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
558486 TCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-
66 TCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGC
*
558542 TTTTGAAAACATCATGCACTG-ATGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAG
1 TTTTGAAAACATCATGCACTGTA-GGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAG
*
558606 CTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGC
65 CTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGC
558664 TTTT-AAAACATCA
1 TTTTGAAAACATCA
558677 AAAAGCTCCC
Statistics
Matches: 129, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
120 1 0.01
121 124 0.96
122 4 0.03
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (122 bp):
TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
TCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGC
Found at i:558641 original size:273 final size:273
Alignment explanation
Indices: 558269--558828 Score: 1005
Period size: 273 Copynumber: 2.1 Consensus size: 273
558259 CCCGAAGGCT
* ** *
558269 TTTTGGAAACATCATGCTTTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
558334 TCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAA
66 TCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAA
* *
558399 CATCAAAAAGCTCCCGAAGCCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAA
131 CATCAAAAAGCTCCCGAAGCCTTTTTGGAAACATCATGCACTGCAGGACATACAGATGACCCTAA
558464 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
196 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
558529 GATGACCCTAAGG
261 GATGACCCTAAGG
*
558542 TTTTGAAAACATCATGCACTG-ATGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAG
1 TTTTGAAAACATCATGCACTGTA-GGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAG
*
558606 CTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTTAAA
65 CTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAA
*
558671 ACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACATACAGATGACCCTA
130 ACATCAAAAAGCTCCCGAAGCCTTTTTGGAAACATCATGCACTGCAGGACATACAGATGACCCTA
558736 AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTAC
195 AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTAC
558801 AGATGACCCTAAGG
260 AGATGACCCTAAGG
* *
558815 CTTTAAAAACATCA
1 TTTTGAAAACATCA
558829 AAAAGCTCCC
Statistics
Matches: 275, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
272 1 0.00
273 274 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (273 bp):
TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
TCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAA
CATCAAAAAGCTCCCGAAGCCTTTTTGGAAACATCATGCACTGCAGGACATACAGATGACCCTAA
GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
GATGACCCTAAGG
Found at i:558672 original size:76 final size:76
Alignment explanation
Indices: 558542--558881 Score: 594
Period size: 76 Copynumber: 4.5 Consensus size: 76
558532 GACCCTAAGG
* *
558542 TTTTGAAAACATCATGCACTG-ATGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAA
1 TTTTGGAAACATCATGCACTGCA-GGACTTACAGATGACCCTAAGGCTTTT-AAAACATCAAAAA
558605 GCTCCCGAAGGCT
64 GCTCCCGAAGGCT
*
558618 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTTAAAACATCAAAAAGC
1 TTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTTAAAACATCAAAAAGC
558683 TCCCGAAGGCT
66 TCCCGAAGGCT
* *
558694 TTTTGGAAACATCATGCACTGCAGGACATACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTTAAAACATCAAAAAGC
558759 TCCCGAAGGCT
66 TCCCGAAGGCT
*
558770 TTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGC
1 TTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTTAAAACATCAAAAAGC
558835 TCCCGAAGGCT
66 TCCCGAAGGCT
558846 TTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTTTGGAAACATCATGCACTGCAGGACTTACAGATG
558882 TAGGAAATAG
Statistics
Matches: 255, Mismatches: 7, Indels: 4
0.96 0.03 0.02
Matches are distributed among these distances:
76 250 0.98
77 5 0.02
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
TTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTTAAAACATCAAAAAGC
TCCCGAAGGCT
Found at i:558798 original size:349 final size:349
Alignment explanation
Indices: 558149--558881 Score: 1349
Period size: 349 Copynumber: 2.1 Consensus size: 349
558139 GATGGAAATG
* * *
558149 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTG
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTG
558214 AAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
66 AAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
**
558279 ATCATGCTTTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
131 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
* *
558344 TTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAG
196 TTTTTGGAAACATCATGCACTGCAGGACATACAGATGACCCTAAGGCTTTGAAAACATCAAAAAG
* *
558409 CTCCCGAAGCCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAA
261 CTCCCGAAGCCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAA
558474 ACATCAAAAAGCTCCCGAAGGCTT
326 ACATCAAAAAGCTCCCGAAGGCTT
*
558498 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCATGCACTG
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTG
*
558563 ATGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
66 AAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
*
558628 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTTAAAACATCAAAAAGCTCCCGAAGGC
131 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
558693 TTTTTGGAAACATCATGCACTGCAGGACATACAGATGACCCTAAGGCTTTGAAAACATCAAAAAG
196 TTTTTGGAAACATCATGCACTGCAGGACATACAGATGACCCTAAGGCTTTGAAAACATCAAAAAG
*
558758 CTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAA
261 CTCCCGAAGCCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAA
558823 ACATCAAAAAGCTCCCGAAGGCTT
326 ACATCAAAAAGCTCCCGAAGGCTT
558847 TTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATG
558882 TAGGAAATAG
Statistics
Matches: 371, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
349 371 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (349 bp):
TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTG
AAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
TTTTTGGAAACATCATGCACTGCAGGACATACAGATGACCCTAAGGCTTTGAAAACATCAAAAAG
CTCCCGAAGCCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAA
ACATCAAAAAGCTCCCGAAGGCTT
Found at i:559131 original size:184 final size:185
Alignment explanation
Indices: 558822--559191 Score: 661
Period size: 184 Copynumber: 2.0 Consensus size: 185
558812 AGGCTTTAAA
558822 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTAGGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTAGGA
558887 AATAGTTTAATAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCA-TTTTAG
66 AATAGTTTAATAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
*
558951 AAAATATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
131 AAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
* * *
559006 AACATCAAAAATCTCCCGAAGGCTTTTTGGAAATATCATGCACTGCAGGACTTACAGATGTGGGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTAGGA
*
559071 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
66 AATAGTTTAATAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
** *
559136 AAAAGATTGAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCGAAATAAC
131 AAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
559191 A
1 A
559192 TGTCGATTAG
Statistics
Matches: 177, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
184 119 0.67
185 58 0.33
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (185 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTAGGA
AATAGTTTAATAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
AAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
Found at i:559769 original size:22 final size:22
Alignment explanation
Indices: 559741--559795 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
559731 CATAAAGCTT
*
559741 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAACCTA
*
559763 TCATCTTTAAAAAGAGAACCTA
1 TCATCTTTGAAAAGAGAACCTA
559785 TCATCTTTGAA
1 TCATCTTTGAA
559796 GATTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAACCTA
Found at i:562420 original size:114 final size:114
Alignment explanation
Indices: 562208--562427 Score: 343
Period size: 114 Copynumber: 1.9 Consensus size: 114
562198 GATCATGTAG
* * * *
562208 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
*
562273 ACACTTCCAGAATATGCTATTGGGCCTCTTTATTTCTACTATAAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGCCTCTTTATTTCTACTATAAGCAAA
* *
562322 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
* *
562387 ACACTTCCAGAAGATGCTATTAGGTCT-TCTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGGCCTCT-TTATTTCTACTA
562428 CGAGAATGTG
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
113 1 0.01
114 95 0.99
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGCCTCTTTATTTCTACTATAAGCAAA
Found at i:564597 original size:19 final size:19
Alignment explanation
Indices: 564573--564615 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
564563 CTTGGTTCAA
564573 TTTTTTTTC-TTTTTTCCT
1 TTTTTTTTCATTTTTTCCT
564591 TTTTTTTTCATTTTTTCCT
1 TTTTTTTTCATTTTTTCCT
564610 TTTTTT
1 TTTTTT
564616 CCAAGCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTTTCATTTTTTCCT
Found at i:567454 original size:8 final size:8
Alignment explanation
Indices: 567413--567454 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
567403 TTTTAATGTG
567413 AAAATGCA
1 AAAATGCA
567421 ATAAATGCA
1 A-AAATGCA
*
567430 TAAATGCA
1 AAAATGCA
567438 AAAAT--A
1 AAAATGCA
567444 AAAATGCA
1 AAAATGCA
567452 AAA
1 AAA
567455 TGTAATACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 6 0.21
8 16 0.55
9 7 0.24
ACGTcount: A:0.64, C:0.10, G:0.10, T:0.17
Consensus pattern (8 bp):
AAAATGCA
Found at i:569887 original size:28 final size:28
Alignment explanation
Indices: 569856--569928 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 28
569846 ACTTGCAAAA
* *
569856 AAAATGAAATAATATATATAAATACTAT
1 AAAATGAAATAATATATATAAAAAATAT
*
569884 AAAA--ATAATAAGTATATATAAAAAATTT
1 AAAATGA-AATAA-TATATATAAAAAATAT
*
569912 GAAATGAAATAAT-TATA
1 AAAATGAAATAATATATA
569929 AATTAAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
26 1 0.03
27 9 0.24
28 21 0.57
29 5 0.14
30 1 0.03
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (28 bp):
AAAATGAAATAATATATATAAAAAATAT
Found at i:571877 original size:3 final size:3
Alignment explanation
Indices: 571835--571923 Score: 74
Period size: 3 Copynumber: 29.0 Consensus size: 3
571825 TTGTAATATT
* *
571835 TAA TAAA TAA TAA -ATA TTA TAT TAA TAA -AA TAA TTAA TAA TAA TAA
1 TAA T-AA TAA TAA TA-A TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
** **
571881 TAA TAA TAA TAA TAAA TAA TTT TAA TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
571924 ATTTAAATTT
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
2 3 0.04
3 56 0.82
4 9 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:571906 original size:34 final size:35
Alignment explanation
Indices: 571828--571923 Score: 101
Period size: 34 Copynumber: 2.8 Consensus size: 35
571818 TTGGGCTTTG
* *
571828 TAATATTTAATAAATAATAA-ATATTATATTAATAAAA
1 TAAT-TTTAAT-AATAATAATA-ATAATAATAATAAAA
571865 TAA--TTAATAATAATAATAATAATAATAAT-AAA
1 TAATTTTAATAATAATAATAATAATAATAATAAAA
**
571897 TAATTTTAATTTTAATAATAATAATAA
1 TAATTTTAATAATAATAATAATAATAA
571924 ATTTAAATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
32 6 0.12
33 17 0.33
34 26 0.50
37 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
TAATTTTAATAATAATAATAATAATAATAATAAAA
Found at i:571926 original size:25 final size:25
Alignment explanation
Indices: 571828--571929 Score: 97
Period size: 28 Copynumber: 4.1 Consensus size: 25
571818 TTGGGCTTTG
571828 TAATATT--TAATAAATAATAAATAT
1 TAATATTAATAAT-AATAATAAATAT
* *
571852 T-ATATTAATAA-AATAATTAATAA
1 TAATATTAATAATAATAATAAATAT
*
571875 TAATAATAATAATAATAATAAATAATTT
1 TAATATTAATAATAATAATAAAT-A--T
*
571903 TAATTTTAATAATAATAATAAAT-T
1 TAATATTAATAATAATAATAAATAT
571927 TAA
1 TAA
571930 ATTTAAAATG
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
23 16 0.25
24 14 0.22
25 12 0.19
26 1 0.02
28 21 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
TAATATTAATAATAATAATAAATAT
Found at i:571932 original size:25 final size:25
Alignment explanation
Indices: 571884--571933 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
571874 ATAATAATAA
*
571884 TAATAATAATAAATAATTTTAATTT
1 TAATAATAATAAATAATTTAAATTT
571909 TAATAATAAT-AATAAATTTAAATTT
1 TAATAATAATAAAT-AATTTAAATTT
571934 AAAATGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TAATAATAATAAATAATTTAAATTT
Found at i:574548 original size:18 final size:18
Alignment explanation
Indices: 574527--574569 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
574517 GTTGTTTTTA
* *
574527 AAATAAAATATAAGAATT
1 AAATAAAAGAAAAGAATT
*
574545 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
574563 AAATAAA
1 AAATAAA
574570 CAAATTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:575239 original size:64 final size:69
Alignment explanation
Indices: 575160--575336 Score: 233
Period size: 69 Copynumber: 2.6 Consensus size: 69
575150 CTAAACATCT
* *
575160 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCT--AA-AAA-ATAATA-TAA
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATTAA
575219 TATTCC
65 TA-TCC
575225 -AAATCCTAATTAAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATTAA
1 TAAATCCTAATT-AAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATTAA
575289 TATCC
65 TATCC
* * *
575294 TAAAACTTAATTAAAATAATAAAACCTATTTAAACTAAAATAC
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
575337 AAAGATAAAA
Statistics
Matches: 99, Mismatches: 5, Indels: 12
0.85 0.04 0.10
Matches are distributed among these distances:
64 16 0.16
65 26 0.26
67 2 0.02
68 3 0.03
69 38 0.38
70 14 0.14
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (69 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATTAAT
ATCC
Found at i:575264 original size:24 final size:24
Alignment explanation
Indices: 575237--575336 Score: 75
Period size: 24 Copynumber: 4.3 Consensus size: 24
575227 ATCCTAATTA
575237 AAAATACTAAAACCTATTTAAACT
1 AAAATACTAAAACCTATTTAAACT
** * *
575261 AAAATACCTAAAACAAATATAAAATT
1 AAAATA-CTAAAACCTAT-TTAAACT
* * *
575287 AATATCCTAAAA-C---TT-AATT
1 AAAATACTAAAACCTATTTAAACT
*
575306 AAAATAATAAAACCTATTTAAACT
1 AAAATACTAAAACCTATTTAAACT
575330 AAAATAC
1 AAAATAC
575337 AAAGATAAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 14
0.67 0.16 0.17
Matches are distributed among these distances:
19 13 0.23
20 2 0.04
23 2 0.04
24 15 0.27
25 15 0.27
26 9 0.16
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAATACTAAAACCTATTTAAACT
Found at i:575283 original size:25 final size:24
Alignment explanation
Indices: 575237--575283 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
575227 ATCCTAATTA
** *
575237 AAAATACTAAAACCTATTTAAACT
1 AAAATACTAAAACAAATATAAACT
575261 AAAATACCTAAAACAAATATAAA
1 AAAATA-CTAAAACAAATATAAA
575284 ATTAATATCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 6 0.32
25 13 0.68
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (24 bp):
AAAATACTAAAACAAATATAAACT
Found at i:575308 original size:25 final size:23
Alignment explanation
Indices: 575263--575314 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
575253 TTTAAACTAA
575263 AATACCTAAAACAAATATAAAATT
1 AATACCTAAAACAAATATAAAA-T
*
575287 AATATCCTAAAACTTAAT-TAAAAT
1 AATA-CCTAAAAC-AAATATAAAAT
575311 AATA
1 AATA
575315 AAACCTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 9 0.36
25 13 0.52
26 3 0.12
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.29
Consensus pattern (23 bp):
AATACCTAAAACAAATATAAAAT
Found at i:583019 original size:25 final size:25
Alignment explanation
Indices: 582989--583038 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
582979 AACATTTACA
*
582989 CTCCAATCGATCACTCTCGAACTTG
1 CTCCAATCGATCACACTCGAACTTG
583014 CTCCAATCGATCACACTCGAACTTG
1 CTCCAATCGATCACACTCGAACTTG
583039 AATCCAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.36, G:0.12, T:0.26
Consensus pattern (25 bp):
CTCCAATCGATCACACTCGAACTTG
Found at i:584805 original size:38 final size:39
Alignment explanation
Indices: 584743--584816 Score: 123
Period size: 38 Copynumber: 1.9 Consensus size: 39
584733 TAGTGCACAA
*
584743 TTATGCATTTTCATTTATGGCATCCTTTTATGCCAACCG
1 TTATGCATTTTCATTTATGACATCCTTTTATGCCAACCG
*
584782 TTATGCA-TTTCATTTGTGACATCCTTTTATGCCAA
1 TTATGCATTTTCATTTATGACATCCTTTTATGCCAA
584817 TAATGCACCG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
38 26 0.79
39 7 0.21
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.45
Consensus pattern (39 bp):
TTATGCATTTTCATTTATGACATCCTTTTATGCCAACCG
Found at i:584824 original size:84 final size:83
Alignment explanation
Indices: 584705--584859 Score: 184
Period size: 84 Copynumber: 1.9 Consensus size: 83
584695 TATACTTTAT
** * * * **
584705 TTTCATTTATAACATCCTTTCATGCTTATAGTGCACAATTATGCATTTTCATTTATGGCATCCTT
1 TTTCATTTATAACATCCTTTCATGCCAATAATGCACAATTACGCATTTT-AGTTATGAAATCCTT
*
584770 TTATGCCAACCGTTATGCA
65 TCATGCCAACCGTTATGCA
* * * **
584789 TTTCATTTGTGACATCCTTTTATGCCAATAATGCACCGTTACGCATTTTAGTTATGAAATCCTTT
1 TTTCATTTATAACATCCTTTCATGCCAATAATGCACAATTACGCATTTTAGTTATGAAATCCTTT
584854 CATGCC
66 CATGCC
584860 GATAATGCAC
Statistics
Matches: 58, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
83 18 0.31
84 40 0.69
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.42
Consensus pattern (83 bp):
TTTCATTTATAACATCCTTTCATGCCAATAATGCACAATTACGCATTTTAGTTATGAAATCCTTT
CATGCCAACCGTTATGCA
Found at i:584955 original size:135 final size:136
Alignment explanation
Indices: 584778--585108 Score: 456
Period size: 135 Copynumber: 2.4 Consensus size: 136
584768 TTTTATGCCA
* * * *
584778 ACCGTTATGCATTTCATTTGTGACATCCTTTTATGCCAATAATGCACCGTTACGCATTTTA-GT-
1 ACCGTTATGCA-TTCATTTGTGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTACGTA
*
584841 TATGAAATCCTTTCATGCCGATAATGCACCGTTATGCATTACATATATGGCATCCTTTCATGCCT
65 TATGAAATCCTTTCATGCCGATAATGCACCGTTATGCATTACATATATGGCATCCTTTCAAGCCT
*
584906 -ATATTAC
130 AAAATT-C
*
584913 ACCGTTATGCATATCATTTGTGGCATCCTTTCATGCCTATAATGCACTGTTATGCA--TTACGTA
1 ACCGTTATGCAT-TCATTTGTGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTACGTA
** * *
584976 TATGTCATCCTTTCATGCCTATAATGCACGGTTATGCATTACATATATGGCATCCTTTCAAGCCT
65 TATGAAATCCTTTCATGCCGATAATGCACCGTTATGCATTACATATATGGCATCCTTTCAAGCCT
585041 AAAATTC
130 AAAATTC
* * * *
585048 ACCATTATACATTACATATATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTA
1 ACCGTTATGCATT-CATTTGTGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTA
585109 TATATTCATC
Statistics
Matches: 173, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
133 3 0.02
134 4 0.02
135 159 0.92
136 4 0.02
137 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (136 bp):
ACCGTTATGCATTCATTTGTGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTACGTAT
ATGAAATCCTTTCATGCCGATAATGCACCGTTATGCATTACATATATGGCATCCTTTCAAGCCTA
AAATTC
Found at i:585136 original size:45 final size:45
Alignment explanation
Indices: 584778--585105 Score: 399
Period size: 45 Copynumber: 7.3 Consensus size: 45
584768 TTTTATGCCA
* * * * * *
584778 ACCGTTATGCATTTCATTTGTGACATCCTTTTATGCCAATAATGC
1 ACCGTTATGCATTACATATATGGCATCCTTTCATGCCTATAATGC
* ** ** *
584823 ACCGTTACGCATTTTAGT-TATGAAATCCTTTCATGCCGATAATGC
1 ACCGTTATGCATTACA-TATATGGCATCCTTTCATGCCTATAATGC
* *
584868 ACCGTTATGCATTACATATATGGCATCCTTTCATGCCTATATTAC
1 ACCGTTATGCATTACATATATGGCATCCTTTCATGCCTATAATGC
* *
584913 ACCGTTATGCA-TATCATTTGTGGCATCCTTTCATGCCTATAATGC
1 ACCGTTATGCATTA-CATATATGGCATCCTTTCATGCCTATAATGC
* * *
584958 ACTGTTATGCATTACGTATATGTCATCCTTTCATGCCTATAATGC
1 ACCGTTATGCATTACATATATGGCATCCTTTCATGCCTATAATGC
* * * *
585003 ACGGTTATGCATTACATATATGGCATCCTTTCAAGCCTAAAATTC
1 ACCGTTATGCATTACATATATGGCATCCTTTCATGCCTATAATGC
* *
585048 ACCATTATACATTACATATATGGCATCCTTTCATGCCTATAATGC
1 ACCGTTATGCATTACATATATGGCATCCTTTCATGCCTATAATGC
585093 ACCGTTATGCATT
1 ACCGTTATGCATT
585106 TTATATATTC
Statistics
Matches: 242, Mismatches: 37, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
44 3 0.01
45 236 0.98
46 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (45 bp):
ACCGTTATGCATTACATATATGGCATCCTTTCATGCCTATAATGC
Found at i:585728 original size:21 final size:21
Alignment explanation
Indices: 585699--585758 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
585689 TATCGATACC
*
585699 TACAGCAGTATCGATACTAAT
1 TACATCAGTATCGATACTAAT
585720 TACATCAGTATCGATACTAAT
1 TACATCAGTATCGATACTAAT
*
585741 TACATCACTATCGATACT
1 TACATCAGTATCGATACT
585759 TTTCAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.32
Consensus pattern (21 bp):
TACATCAGTATCGATACTAAT
Found at i:592119 original size:45 final size:45
Alignment explanation
Indices: 591780--592102 Score: 369
Period size: 45 Copynumber: 7.1 Consensus size: 45
591770 TATACTTTAT
* * * *
591780 TTTCGTTTATAGCATCATTTCATGCTTATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
* * * * *
591825 TTTTTATTTATGGCATTCTTTTCATGCCAATAATTCACCGTTATGTA
1 -TTTCATTTATGGCA-TCCTTTCATGCCTATAATGCACCGTTATGCA
* * * * *
591872 TTTTATTTATGACATCCTTTCATGCCGATAATACACCGTTATACA
1 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
* * * *
591917 TTTCATTTATGTCATCCTTTCATGTCGATAATGCACCGTTATACA
1 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
* * *
591962 TTAT-ATATAGGGCATCCTTTCATGCTTATAATGCACCGTTATGCA
1 TT-TCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
* *
592007 TCTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGTA
1 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
* * * *
592052 TTACATATATGACATCCTTTCATGCCTATAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
592097 TTTCAT
1 TTTCAT
592103 ATATTCATCT
Statistics
Matches: 237, Mismatches: 37, Indels: 7
0.84 0.13 0.02
Matches are distributed among these distances:
44 1 0.00
45 185 0.78
46 25 0.11
47 26 0.11
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.41
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
Found at i:592119 original size:90 final size:90
Alignment explanation
Indices: 591792--592102 Score: 406
Period size: 90 Copynumber: 3.4 Consensus size: 90
591782 TCGTTTATAG
* * * *
591792 CATCATTTCATGCTTATAATGCACCGTTATGCATTTTTATTTATGGCATTCTTTTCATGCCAATA
1 CATCCTTTCATGCCTATAATGCACCGTTATGCA-TTTCATTTATGGCA-TCCTTTCATGCCAATA
* * *
591857 ATTCACCGTTATGTATTTTATTTATGA
64 ATGCACCGTTATGTATTATATATATGA
* * * * * *
591884 CATCCTTTCATGCCGATAATACACCGTTATACATTTCATTTATGTCATCCTTTCATGTCGATAAT
1 CATCCTTTCATGCCTATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCAATAAT
** * *
591949 GCACCGTTATACATTATATATAGGG
66 GCACCGTTATGTATTATATATATGA
* * *
591974 CATCCTTTCATGCTTATAATGCACCGTTATGCATCTCATTTATGGCATCCTTTCATGCCTATAAT
1 CATCCTTTCATGCCTATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCAATAAT
*
592039 GCACCGTTATGTATTACATATATGA
66 GCACCGTTATGTATTATATATATGA
*
592064 CATCCTTTCATGCCTATAATGCACCATTATGCATTTCAT
1 CATCCTTTCATGCCTATAATGCACCGTTATGCATTTCAT
592103 ATATTCATCT
Statistics
Matches: 186, Mismatches: 33, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
90 146 0.78
91 12 0.06
92 28 0.15
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (90 bp):
CATCCTTTCATGCCTATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCAATAAT
GCACCGTTATGTATTATATATATGA
Found at i:592638 original size:97 final size:95
Alignment explanation
Indices: 592489--592691 Score: 271
Period size: 97 Copynumber: 2.1 Consensus size: 95
592479 CCCTACCATG
* * * * *
592489 GTATCGATACTTTTATACTATGTTACCAATACTCCCTTTCAGTATTGCTACCATTTATACATTCT
1 GTATCGATACTTTTATACTATGGTACCAATAATCCCTTTCAGTATCGATACCATATATACATTCT
*
592554 GTAATCCATGGTATCGATACCTTCCTCTTA
66 GGAATCCATGGTATCGATACCTTCCTCTTA
* * *
592584 GTATCGATACTTCTATATATTATGGTACCGATAATCCCTTTCAGTATCGATACCATATCTACATT
1 GTATCGATACTT-T-TATACTATGGTACCAATAATCCCTTTCAGTATCGATACCATATATACATT
* * *
592649 TTGGAATCCCTGGTATCGATACCTTTCTCTTA
64 CTGGAATCCATGGTATCGATACCTTCCTCTTA
*
592681 ATATCGATACT
1 GTATCGATACT
592692 AATTGCATCA
Statistics
Matches: 93, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 12 0.13
96 1 0.01
97 80 0.86
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (95 bp):
GTATCGATACTTTTATACTATGGTACCAATAATCCCTTTCAGTATCGATACCATATATACATTCT
GGAATCCATGGTATCGATACCTTCCTCTTA
Found at i:595235 original size:138 final size:138
Alignment explanation
Indices: 594982--595238 Score: 322
Period size: 138 Copynumber: 1.9 Consensus size: 138
594972 TGTATATAGT
* * * *
594982 AGTTATCGATCGATTTTGTGTAATGTAAAACGATGCATTTTTGTATCAGTACCATATGTACTTTC
1 AGTTATCGATCGATTTTATGTAATGCAAAACGATACATTTTTGTATCAGTACCATATGTACATTC
* *
595047 GACACTAGATGTGCAACTATGGTATTCATAAGGAGTTTGTGAATTACCATTTCGATATACAATTA
66 GACACTAGATGTGCAACCATGGAATTCATAAGGAGTTTGTGAATTACCATTTCGATATACAATTA
595112 TGTATAAA
131 TGTATAAA
* * * *
595120 AGTTATCGATCGATTTTATTTAATGCATAACTG-TAC-TTTTTCGTATCAGTACTATGTGTACAT
1 AGTTATCGATCGATTTTATGTAATGCAAAAC-GATACATTTTT-GTATCAGTACCATATGTACAT
* * ** * *
595183 TCGACACTATG-TGTGTATCCATGGAATTTGTAATGAGTTTGTGAATTTCCATTTCG
64 TCGACACTA-GATGTGCAACCATGGAATTCATAAGGAGTTTGTGAATTACCATTTCG
595239 GCACATCGGT
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
137 5 0.05
138 93 0.93
139 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.40
Consensus pattern (138 bp):
AGTTATCGATCGATTTTATGTAATGCAAAACGATACATTTTTGTATCAGTACCATATGTACATTC
GACACTAGATGTGCAACCATGGAATTCATAAGGAGTTTGTGAATTACCATTTCGATATACAATTA
TGTATAAA
Found at i:600611 original size:3 final size:3
Alignment explanation
Indices: 600603--600652 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
600593 GTCAACCCTT
* *
600603 TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
600651 TT
1 TT
600653 TCACGTGGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:601592 original size:54 final size:54
Alignment explanation
Indices: 601534--601845 Score: 396
Period size: 54 Copynumber: 5.8 Consensus size: 54
601524 CCAAATAGGA
* * *
601534 ACTAAGTGTGCAATTCACGAAATTCATCATATATTAATGAATAACCATTTCAGC
1 ACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAATCATTTCAGC
* * *
601588 ACTAAGTGTGCAATTCACTAAATTCATCATATGTTGATGAATAATCGTTTCAAC
1 ACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAATCATTTCAGC
**
601642 ACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAATCATTTTGGC
1 ACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAATCATTTCAGC
* **
601696 ACTAAGTGTGTAATTCAC-ACAATTCATCATATGTTGATGAATAATTGTTTC-GAC
1 ACTAAGTGTGCAATTCACGA-AATTCATCATATGTTGATGAATAATCATTTCAG-C
* * *
601750 ACTAAGTGTGCAATTCAC-AGAATTCATCATATGTTGATGAATAATTATTTCGGT
1 ACTAAGTGTGCAATTCACGA-AATTCATCATATGTTGATGAATAATCATTTCAGC
* ** * * *
601804 ACTATGTGTGCAAACCATGAAATTCATAATATGTTTATGAAT
1 ACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAAT
601846 GATCGTATGG
Statistics
Matches: 229, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
53 2 0.01
54 225 0.98
55 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (54 bp):
ACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAATCATTTCAGC
Found at i:601723 original size:108 final size:108
Alignment explanation
Indices: 601534--601851 Score: 444
Period size: 108 Copynumber: 2.9 Consensus size: 108
601524 CCAAATAGGA
* * * *
601534 ACTAAGTGTGCAATTCACGAAATTCATCATATATTAATGAATAACCATTTCAGCACTAAGTGTGC
1 ACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAATCATTTCGGCACTAAGTGTGC
601599 AATTCACTAAATTCATCATATGTTGATGAATAATCGTTTCAAC
66 AATTCACTAAATTCATCATATGTTGATGAATAATCGTTTCAAC
* *
601642 ACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAATCATTTTGGCACTAAGTGTGT
1 ACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAATCATTTCGGCACTAAGTGTGC
* *
601707 AATTCAC-ACAATTCATCATATGTTGATGAATAATTGTTTCGAC
66 AATTCACTA-AATTCATCATATGTTGATGAATAATCGTTTCAAC
* * *
601750 ACTAAGTGTGCAATTCAC-AGAATTCATCATATGTTGATGAATAATTATTTCGGTACTATGTGTG
1 ACTAAGTGTGCAATTCACGA-AATTCATCATATGTTGATGAATAATCATTTCGGCACTAAGTGTG
** * * *
601814 CAAACCA-TGAAATTCATAATATGTTTATGAATGATCGT
65 CAATTCACT-AAATTCATCATATGTTGATGAATAATCGT
601852 ATGGGAACCA
Statistics
Matches: 187, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
107 2 0.01
108 184 0.98
109 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (108 bp):
ACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAATCATTTCGGCACTAAGTGTGC
AATTCACTAAATTCATCATATGTTGATGAATAATCGTTTCAAC
Found at i:608065 original size:22 final size:23
Alignment explanation
Indices: 608037--608082 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
608027 ACCAAAATAA
*
608037 AGTATCGGTACCATAGTAT-AGT
1 AGTATCGATACCATAGTATGAGT
*
608059 AGTATCGATACCATGGTATGAGT
1 AGTATCGATACCATAGTATGAGT
608082 A
1 A
608083 TCAATACTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (23 bp):
AGTATCGATACCATAGTATGAGT
Found at i:608084 original size:20 final size:22
Alignment explanation
Indices: 608037--608089 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
608027 ACCAAAATAA
*
608037 AGTATCGGTACCATAGTATAGT
1 AGTATCGATACCATAGTATAGT
*
608059 AGTATCGATACCATGGTAT-G-
1 AGTATCGATACCATAGTATAGT
*
608079 AGTATCAATAC
1 AGTATCGATAC
608090 TAATGAGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 10 0.36
21 1 0.04
22 17 0.61
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (22 bp):
AGTATCGATACCATAGTATAGT
Found at i:608503 original size:54 final size:54
Alignment explanation
Indices: 608417--608684 Score: 338
Period size: 54 Copynumber: 5.0 Consensus size: 54
608407 ACCAAATAGG
* * * * * * * *
608417 CACTAAGTGTGCAAATCATGAAATTCAACATATGTTGATGAATAATCGTTTTGG
1 CACTAAGTATGCAATTCACGAAATTCATCATATGTTGATGAATAACCATTTCGA
* * *
608471 CAATAAGTATGGAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGA
1 CACTAAGTATGCAATTCACGAAATTCATCATATGTTGATGAATAACCATTTCGA
* * *
608525 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCATTTTGG
1 CACTAAGTATGCAATTCACGAAATTCATCATATGTTGATGAATAACCATTTCGA
* * * *
608579 TACTCAGTATGCAATTCACGGAATTCATCATATGCTGATGAATAACCATTTCGA
1 CACTAAGTATGCAATTCACGAAATTCATCATATGTTGATGAATAACCATTTCGA
* * * *
608633 CACTAAGTGTACAATTCACGAATTTCATCATATGTTGATGAATAACTATTTC
1 CACTAAGTATGCAATTCACGAAATTCATCATATGTTGATGAATAACCATTTC
608685 ACCAGATGAA
Statistics
Matches: 184, Mismatches: 30, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 184 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (54 bp):
CACTAAGTATGCAATTCACGAAATTCATCATATGTTGATGAATAACCATTTCGA
Found at i:608606 original size:108 final size:108
Alignment explanation
Indices: 608417--608683 Score: 399
Period size: 108 Copynumber: 2.5 Consensus size: 108
608407 ACCAAATAGG
* * * * *
608417 CACTAAGTGTGCAAATCATGAAATTCAACATATGTTGATGAATAATCGTTTTGGCAATAAGTATG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCATTTTGGCAATAAGTATG
* * *
608482 GAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGA
66 CAATTCACGAAATTCATCATATGCTGATGAATAACCATTTCGA
* * *
608525 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCATTTTGGTACTCAGTATG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCATTTTGGCAATAAGTATG
*
608590 CAATTCACGGAATTCATCATATGCTGATGAATAACCATTTCGA
66 CAATTCACGAAATTCATCATATGCTGATGAATAACCATTTCGA
* * *
608633 CACTAAGTGTACAATTCACGAATTTCATCATATGTTGATGAATAACTATTT
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCATTT
608684 CACCAGATGA
Statistics
Matches: 144, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 144 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (108 bp):
CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCATTTTGGCAATAAGTATG
CAATTCACGAAATTCATCATATGCTGATGAATAACCATTTCGA
Found at i:608692 original size:20 final size:20
Alignment explanation
Indices: 608669--608708 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
608659 ATCATATGTT
608669 GATGAATAACTATTTCACCA
1 GATGAATAACTATTTCACCA
608689 GATGAATAACTATTTCACCA
1 GATGAATAACTATTTCACCA
608709 CTATGTGTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (20 bp):
GATGAATAACTATTTCACCA
Found at i:611266 original size:3 final size:3
Alignment explanation
Indices: 611258--611285 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
611248 GAATAGGGTT
611258 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
611286 ATTTTGGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:611569 original size:43 final size:43
Alignment explanation
Indices: 611520--611828 Score: 372
Period size: 43 Copynumber: 7.2 Consensus size: 43
611510 TGTAAAATAA
** * *
611520 AAACGCCTTAAAAAGTCAAGATCTATAGCGGCGTTTTT-GACAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATAC
* * *
611563 AAACGCCGCAAACGGTCGGATCTATAGCTGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* *
611606 AAACGCCGCAAAAGGTCGAGATATATAGCGGTGTTTTTGGA-AC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATAC
* * * * **
611649 AAAAGTCGCAAAAGGTCAGATCTATAGCGCCATTTTTTAATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* * * *
611692 AAACACCGTAAAAGGTCAGATCTATAGCGGCATTTTT-GAAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
*
611734 AAACGCCGCAAAAGGTCAGATCTATAGCAGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* *
611777 AAACGCCACAAAAGGTCAGATCTATAGCAGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
*
611820 AAACACCGC
1 AAACGCCGC
611829 TAATTACCAT
Statistics
Matches: 227, Mismatches: 35, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
42 71 0.31
43 137 0.60
44 19 0.08
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
Found at i:614489 original size:24 final size:24
Alignment explanation
Indices: 614443--614489 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
614433 TACAAGTGCC
* *
614443 TTACATCAAGTGGCATCAGAAGCA
1 TTACATCAAGCGGAATCAGAAGCA
614467 TTACATCAAGCGGTAATCA-AAGC
1 TTACATCAAGCGG-AATCAGAAGC
614490 TTTGGTGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (24 bp):
TTACATCAAGCGGAATCAGAAGCA
Found at i:619947 original size:13 final size:13
Alignment explanation
Indices: 619929--619961 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
619919 GGAACAAAGC
619929 GAAATCAGTAATA
1 GAAATCAGTAATA
619942 GAAATCAGTAATA
1 GAAATCAGTAATA
619955 GAAATCA
1 GAAATCA
619962 ATAGAAATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.55, C:0.09, G:0.15, T:0.21
Consensus pattern (13 bp):
GAAATCAGTAATA
Found at i:620779 original size:33 final size:33
Alignment explanation
Indices: 620735--620801 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
620725 AACGGTGACA
*
620735 GCAGCTTCAAGACTACTTGACGACAAGAATACG
1 GCAGCTGCAAGACTACTTGACGACAAGAATACG
** * *
620768 GCAGCTGCAAGACTTTTTGATGGCAAGAATACG
1 GCAGCTGCAAGACTACTTGACGACAAGAATACG
620801 G
1 G
620802 TAGTGTCGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (33 bp):
GCAGCTGCAAGACTACTTGACGACAAGAATACG
Found at i:621260 original size:82 final size:81
Alignment explanation
Indices: 621073--621310 Score: 286
Period size: 81 Copynumber: 2.9 Consensus size: 81
621063 TATTGCAGCG
* * **
621073 TTTTATACATAAACGCCACTAAAGTACGCATTTTAAGCAGCGTTTTTATGAAAACGC-CGCTATA
1 TTTT-TACATAAACGCCACTAAAGTACGCATTTTTAGCAGCGTTTTCACAAAAAC-CACGCTATA
621137 TATTAGGATATTACGGCA
64 TATTAGGATATTACGGCA
621155 TTTTTACATAAACGCCACTAAAGTACGCATTTTTAGCAGCGTTTTCA-AAAAACCATCGCTATAT
1 TTTTTACATAAACGCCACTAAAGTACGCATTTTTAGCAGCGTTTTCACAAAAACCA-CGCTATAT
* *
621219 ATTCGGATATTGCGGCAA
65 ATTAGGATATTACGGC-A
* * * * *
621237 TTTTTACATAAACGCCACTAAAGTATG-AGTTTTTAGCGGTGTTTGCACAAAAA-CACCACTATA
1 TTTTTACATAAACGCCACTAAAGTACGCA-TTTTTAGCAGCGTTTTCACAAAAACCA-CGCTATA
*
621300 TATTTGGATAT
64 TATTAGGATAT
621311 CGCGACGTTT
Statistics
Matches: 139, Mismatches: 12, Indels: 10
0.86 0.07 0.06
Matches are distributed among these distances:
79 1 0.01
80 5 0.04
81 64 0.46
82 64 0.46
83 5 0.04
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (81 bp):
TTTTTACATAAACGCCACTAAAGTACGCATTTTTAGCAGCGTTTTCACAAAAACCACGCTATATA
TTAGGATATTACGGCA
Found at i:622469 original size:2 final size:2
Alignment explanation
Indices: 622462--622493 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
622452 TATGTATTTA
622462 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
622494 TGAATATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:625083 original size:21 final size:21
Alignment explanation
Indices: 625042--625081 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
625032 ATATCTATTA
625042 AATATGCATATATATGTTTTG
1 AATATGCATATATATGTTTTG
625063 AATAT-CATATGATA-GTTTT
1 AATATGCATAT-ATATGTTTT
625082 TGCTTAAGAT
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:0.35, C:0.05, G:0.12, T:0.47
Consensus pattern (21 bp):
AATATGCATATATATGTTTTG
Found at i:631293 original size:30 final size:30
Alignment explanation
Indices: 631257--631317 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
631247 TCTCACATTA
631257 ACCAATCATGGAAGTTGTGTTATTTGATGT
1 ACCAATCATGGAAGTTGTGTTATTTGATGT
631287 ACCAATCATGGAAGTTGTGTTATTTGATGT
1 ACCAATCATGGAAGTTGTGTTATTTGATGT
631317 A
1 A
631318 TAGGGTCTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (30 bp):
ACCAATCATGGAAGTTGTGTTATTTGATGT
Found at i:636202 original size:21 final size:22
Alignment explanation
Indices: 636170--636214 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
636160 TAAATATTAC
636170 AAAGGTAGTACTGATACTCATT
1 AAAGGTAGTACTGATACTCATT
636192 AAAGG-AGTACTGATACTCATT
1 AAAGGTAGTACTGATACTCATT
636213 AA
1 AA
636215 TCCCCAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (22 bp):
AAAGGTAGTACTGATACTCATT
Found at i:645209 original size:21 final size:21
Alignment explanation
Indices: 645183--645222 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
645173 AAGACTTTAT
645183 TTTCAAAATTAAAAAATGATA
1 TTTCAAAATTAAAAAATGATA
645204 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
645223 AAATAGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATA
Found at i:649069 original size:22 final size:22
Alignment explanation
Indices: 649040--649112 Score: 85
Period size: 23 Copynumber: 3.3 Consensus size: 22
649030 ATGAGGTATC
649040 GATACCCCCTTGAATGGGTACT
1 GATACCCCCTTGAATGGGTACT
* *
649062 GATTCCCCCTTTGAGTGGGTACT
1 GATACCCCC-TTGAATGGGTACT
* * *
649085 GATACCCCCTAGGA-GGGTACC
1 GATACCCCCTTGAATGGGTACT
649106 GATACCC
1 GATACCC
649113 TCCACGGGGT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
21 13 0.30
22 10 0.23
23 20 0.47
ACGTcount: A:0.21, C:0.30, G:0.25, T:0.25
Consensus pattern (22 bp):
GATACCCCCTTGAATGGGTACT
Found at i:653388 original size:43 final size:44
Alignment explanation
Indices: 653266--653390 Score: 153
Period size: 47 Copynumber: 2.8 Consensus size: 44
653256 TATAAAATCT
* *
653266 CTTACCATTTATCCCATAAGCTCTTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAT-TCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
653311 CTTACGATTTAAATTCCATAAGCTCGTAAACTTATTTTACCAATATA
1 CTTACCATTT--ATT-CATAAGCTCGTAAGCTTATTTTACCAAAATA
*
653358 CTTACCA-TTATTCATAAGTTCGTAAGCTTATTT
1 CTTACCATTTATTCATAAGCTCGTAAGCTTATTT
653391 GCATACTTAC
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
43 19 0.28
44 3 0.04
45 9 0.13
46 2 0.03
47 36 0.52
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (44 bp):
CTTACCATTTATTCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:661976 original size:18 final size:18
Alignment explanation
Indices: 661953--661987 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
661943 ATGATGTTGA
661953 GGCATCATCTGCTACTGC
1 GGCATCATCTGCTACTGC
*
661971 GGCATCATTTGCTACTG
1 GGCATCATCTGCTACTG
661988 ATTGTACTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.29, G:0.23, T:0.31
Consensus pattern (18 bp):
GGCATCATCTGCTACTGC
Found at i:662757 original size:34 final size:32
Alignment explanation
Indices: 662718--662787 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
662708 TTTTGTAAAG
*
662718 GGGAAACGTTCTAGCTTAGCACGTGTAAAAGCTA
1 GGGAAACGTTCTAGCTTAGCACG-G-AAAAACTA
* * *
662752 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAACGTTCTAGCTTAGCACGGAAAAACTA
662784 GGGA
1 GGGA
662788 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (32 bp):
GGGAAACGTTCTAGCTTAGCACGGAAAAACTA
Found at i:674287 original size:19 final size:19
Alignment explanation
Indices: 674263--674308 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
674253 AGAACTTAGT
674263 GAATAAATTAGAGGAATAA
1 GAATAAATTAGAGGAATAA
674282 GAATAAATTAGAGGAATAA
1 GAATAAATTAGAGGAATAA
674301 GAATAAAT
1 GAATAAAT
674309 ATTGAATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.20, T:0.22
Consensus pattern (19 bp):
GAATAAATTAGAGGAATAA
Found at i:674485 original size:33 final size:34
Alignment explanation
Indices: 674426--674524 Score: 107
Period size: 33 Copynumber: 3.0 Consensus size: 34
674416 ATATATACTT
* * *
674426 ATAAATAAAA-ACACTCC-ATTCTGGGTGTATTG
1 ATAAATAAAAGTCACTCCAATGCTGGGTGCATTG
*
674458 CTAAATAAAAGTCACTCCAATGC-GGGTGCATTG
1 ATAAATAAAAGTCACTCCAATGCTGGGTGCATTG
* * *
674491 AGAAATAAATGTCACTCCAACG-TGGGTGCATTG
1 ATAAATAAAAGTCACTCCAATGCTGGGTGCATTG
674524 A
1 A
674525 ACAGAGACAA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
32 9 0.16
33 44 0.79
34 3 0.05
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26
Consensus pattern (34 bp):
ATAAATAAAAGTCACTCCAATGCTGGGTGCATTG
Found at i:679208 original size:90 final size:89
Alignment explanation
Indices: 679086--679262 Score: 273
Period size: 90 Copynumber: 2.0 Consensus size: 89
679076 TAATCCCGAA
* * *
679086 TATTTAATTTCAAATAATTAAATATATATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAAATAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGAT
679151 TAGGGTAACTTGGATATAAAAGGAT
65 TAGGGTAACTTGGATATAAAAGGAT
* * *
679176 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGGAATAATAAAACCCTATTATGATT
1 TATTAAATTCCAAATAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
* *
679241 TGGGTAACTTGGCTATAAAAGG
66 AGGGTAACTTGGATATAAAAGG
679263 GTGTGTTAGG
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
89 32 0.41
90 47 0.59
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (89 bp):
TATTAAATTCCAAATAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
AGGGTAACTTGGATATAAAAGGAT
Found at i:685903 original size:23 final size:23
Alignment explanation
Indices: 685860--685903 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
685850 AAAACTAATT
* *
685860 AACCTAAAACTATTAATAAATAA
1 AACCTAAAACTAGTAAAAAATAA
685883 AACCT-AAACTAAGTAAAAAAT
1 AACCTAAAACT-AGTAAAAAAT
685904 CTAACCTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.61, C:0.14, G:0.02, T:0.23
Consensus pattern (23 bp):
AACCTAAAACTAGTAAAAAATAA
Found at i:685975 original size:28 final size:28
Alignment explanation
Indices: 685935--685988 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
685925 CCTACCCAAC
* *
685935 CTCACGCTTCACTCTTCAGTTTCCCTAT
1 CTCACGCCTCACTCTTCACTTTCCCTAT
685963 CTCACGCCTCACTCTTCACTTTCCCT
1 CTCACGCCTCACTCTTCACTTTCCCT
685989 CACCCATGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.13, C:0.44, G:0.06, T:0.37
Consensus pattern (28 bp):
CTCACGCCTCACTCTTCACTTTCCCTAT
Found at i:688125 original size:12 final size:12
Alignment explanation
Indices: 688108--688132 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
688098 ATATTGCTAA
688108 AGTTACTGTAGC
1 AGTTACTGTAGC
688120 AGTTACTGTAGC
1 AGTTACTGTAGC
688132 A
1 A
688133 ATTATCGTAG
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:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (12 bp):
AGTTACTGTAGC
Found at i:688234 original size:7 final size:7
Alignment explanation
Indices: 688222--688246 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
688212 CCGATTCCCC
688222 CACTGTT
1 CACTGTT
688229 CACTGTT
1 CACTGTT
688236 CACTGTT
1 CACTGTT
688243 CACT
1 CACT
688247 ATTACCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.32, G:0.12, T:0.40
Consensus pattern (7 bp):
CACTGTT
Found at i:689383 original size:55 final size:54
Alignment explanation
Indices: 689323--689756 Score: 309
Period size: 55 Copynumber: 8.0 Consensus size: 54
689313 AGACTTGGAA
*
689323 AATCTTCTAATGACGGGTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAAC
1 AATCTTCTAA-AACGGGTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAAC
* * * * * * *
689378 CATCTTC-AGTAAATGTGTCTACCCCCTATTCGTTTAGGGAGTATAAGACTCGAAC
1 AATCTTCTA--AAACGGGTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAAC
* * * * *
689433 AATCTT-TAGCAACTGTGTATGCTCCCTATTCGTTTAGGGAGTATAAGACTCGAAC
1 AATCTTCTA-AAAC-GGGTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAAC
* * * * * *
689488 AATCTT-TAATAAATGGGTCCGCTACCTATTCGTTAATGGAGTAT-AGAACTCGAAC
1 AATCTTCT-A-AAACGGGTCTGCTCCCTATTCCTTCAGGGAGTATAAG-ACTCGAAC
* *
689543 AATCTTCATAAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAC
1 AATCTTC-TAAAACGGGTCTGCTCCCTATTCCTTCAGGGAGTATAAG-ACTCGAAC
* * * * *
689598 AATCATCATAAAATGGGT-TCGCTCTCC-ATTCCTTAAGAGAGTAT-AGAAATCGAAC
1 AATCTTC-TAAAACGGGTCT-GCTC-CCTATTCCTTCAGGGAGTATAAG-ACTCGAAC
* * * * *
689653 AATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTTG---
1 AATCTTCTA-AAACGGGTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAAC
* * * *
689705 -ATCTTCAACAAACGTGT-TCGCTCCCTATTCCTTCAGAGAGTATAAGAATCGA
1 AATCTTCTA-AAACGGGTCT-GCTCCCTATTCCTTCAGGGAGTATAAGACTCGA
689757 TCTTCAAAAA
Statistics
Matches: 313, Mismatches: 50, Indels: 35
0.79 0.13 0.09
Matches are distributed among these distances:
51 45 0.14
54 9 0.03
55 251 0.80
56 7 0.02
57 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (54 bp):
AATCTTCTAAAACGGGTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAAC
Found at i:689730 original size:51 final size:51
Alignment explanation
Indices: 689544--689813 Score: 231
Period size: 51 Copynumber: 5.1 Consensus size: 51
689534 AACTCGAACA
* * * *
689544 ATCTTCATA-AAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCG
1 ATCTTCA-ACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG
* * * * * * *
689595 AACAATCATCATA-AAATGGGTTCGCTCTCC-ATTCCTTAAGAGAGTATAGAAATCG
1 ----ATCTTCA-ACAAACGTGTCCGCTC-CCTATTCCTTCAGAGAGTATAGGACTCG
* *
689650 AACAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTTG
1 ----ATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG
* * *
689705 ATCTTCAACAAACGTGTTCGCTCCCTATTCCTTCAGAGAGTATAAGAATCG
1 ATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG
* * * * *
689756 ATCTTCAAAAAACGTGTCCACTCCCTATTTCTTCAAAGAGTGTAGGACTCG
1 ATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG
689807 ATCTTCA
1 ATCTTCA
689814 TAAAATGAGT
Statistics
Matches: 185, Mismatches: 27, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
51 96 0.52
54 3 0.02
55 85 0.46
56 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Consensus pattern (51 bp):
ATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG
Found at i:689796 original size:102 final size:103
Alignment explanation
Indices: 689543--689813 Score: 271
Period size: 102 Copynumber: 2.6 Consensus size: 103
689533 GAACTCGAAC
* ** * * * *
689543 AATCTTCATAAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCATCATA
1 AATCTTCAAAAAACGGGTCCACTCCCTATTCCTTCAAAGAGTATAGGACTCG----ATCTTCA-A
* *
689608 -AAATGGGTTCGCTCTCCATTCCTTAAGAGAGTATAGAAATCG
61 CAAACGTGTTCGCTCTCCATTCCTTAAGAGAGTATAGAAATCG
* * * *
689650 AACAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTTGATCTTCAACA
1 ---AATCTTCAAAAAACGGGTCCACTCCCTATTCCTTCAAAGAGTATAGGACTCGATCTTCAACA
*
689715 AACGTGTTCGCTC-CCTATTCCTTCAGAGAGTATA-AGAATCG
63 AACGTGTTCGCTCTCC-ATTCCTTAAGAGAGTATAGA-AATCG
* * *
689756 -ATCTTCAAAAAACGTGTCCACTCCCTATTTCTTCAAAGAGTGTAGGACTCGATCTTCA
1 AATCTTCAAAAAACGGGTCCACTCCCTATTCCTTCAAAGAGTATAGGACTCGATCTTCA
689814 TAAAATGAGT
Statistics
Matches: 141, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
102 51 0.36
105 4 0.03
106 40 0.28
110 46 0.33
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (103 bp):
AATCTTCAAAAAACGGGTCCACTCCCTATTCCTTCAAAGAGTATAGGACTCGATCTTCAACAAAC
GTGTTCGCTCTCCATTCCTTAAGAGAGTATAGAAATCG
Found at i:689978 original size:37 final size:37
Alignment explanation
Indices: 689827--689974 Score: 226
Period size: 37 Copynumber: 4.0 Consensus size: 37
689817 AATGAGTTTT
*
689827 CTTCACTACTCTTTCGTGAAGGCTTATAGA-TGATTTG
1 CTTCACTACTCTTTCGTGAAGGCTTA-AGATTGAATTG
* * *
689864 CTTCACTACTCTTCCATGAACGCTTAAGATTGAATTG
1 CTTCACTACTCTTTCGTGAAGGCTTAAGATTGAATTG
689901 CTTCACTACTCTTTCGTGAAGGCTTAAGATTGAATTG
1 CTTCACTACTCTTTCGTGAAGGCTTAAGATTGAATTG
* *
689938 TTTCACTGCTCTTTCGTGAAGGCTTAAGATTGAATTG
1 CTTCACTACTCTTTCGTGAAGGCTTAAGATTGAATTG
689975 TTTCGAAGGT
Statistics
Matches: 101, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
36 3 0.03
37 98 0.97
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.39
Consensus pattern (37 bp):
CTTCACTACTCTTTCGTGAAGGCTTAAGATTGAATTG
Found at i:691226 original size:8 final size:8
Alignment explanation
Indices: 691203--691307 Score: 91
Period size: 7 Copynumber: 13.6 Consensus size: 8
691193 CCCCCTTTTA
691203 TTTTC-TT
1 TTTTCATT
691210 TTTTC-TT
1 TTTTCATT
691217 TTTTCATTT
1 TTTTCA-TT
691226 TTTTCA-T
1 TTTTCATT
691233 TTTTCATTTT
1 TTTTCA--TT
691243 TTTTCATT
1 TTTTCATT
691251 TTTTCATT
1 TTTTCATT
*
691259 TTTTC--C
1 TTTTCATT
*
691265 TTTTCCTT
1 TTTTCATT
691273 TTTT-ATT
1 TTTTCATT
691280 TTTT-ATT
1 TTTTCATT
691287 TTTTC-TCT
1 TTTTCAT-T
*
691295 TTTTCCTT
1 TTTTCATT
691303 TTTTC
1 TTTTC
691308 CCTTTTCCAT
Statistics
Matches: 85, Mismatches: 3, Indels: 19
0.79 0.03 0.18
Matches are distributed among these distances:
6 5 0.06
7 33 0.39
8 31 0.36
9 9 0.11
10 7 0.08
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTCATT
Found at i:691227 original size:9 final size:9
Alignment explanation
Indices: 691215--691262 Score: 66
Period size: 9 Copynumber: 5.6 Consensus size: 9
691205 TTCTTTTTTC
691215 TTTTTTCAT
1 TTTTTTCAT
691224 TTTTTTCA-
1 TTTTTTCAT
691232 -TTTTTCATT
1 TTTTTTCA-T
691241 TTTTTTCA-
1 TTTTTTCAT
691249 TTTTTTCAT
1 TTTTTTCAT
691258 TTTTT
1 TTTTT
691263 CCTTTTCCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 7 0.20
8 8 0.23
9 13 0.37
10 7 0.20
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:691308 original size:8 final size:8
Alignment explanation
Indices: 691203--691313 Score: 65
Period size: 8 Copynumber: 14.2 Consensus size: 8
691193 CCCCCTTTTA
691203 TTTT-CTT
1 TTTTCCTT
691210 TTTT-CTT
1 TTTTCCTT
*
691217 TTTTCATT
1 TTTTCCTT
* *
691225 TTTTTCAT
1 TTTTCCTT
*
691233 TTTTCATTTT
1 TTTTC--CTT
*
691243 TTTTCATT
1 TTTTCCTT
*
691251 TTTTCATT
1 TTTTCCTT
691259 TTTTCC--
1 TTTTCCTT
691265 TTTTCCTT
1 TTTTCCTT
*
691273 TTTT-ATT
1 TTTTCCTT
*
691280 TTTT-ATT
1 TTTTCCTT
691287 TTTT-CTCT
1 TTTTCCT-T
691295 TTTTCCTT
1 TTTTCCTT
691303 TTTTCCCTT
1 TTTT-CCTT
691312 TT
1 TT
691314 CCATAATTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
6 6 0.07
7 25 0.29
8 40 0.47
9 8 0.09
10 6 0.07
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTCCTT
Found at i:691313 original size:15 final size:14
Alignment explanation
Indices: 691251--691315 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
691241 TTTTTTCATT
*
691251 TTTTCATTTTTTCC
1 TTTTCCTTTTTTCC
**
691265 TTTTCCTTTTTTAT
1 TTTTCCTTTTTTCC
**
691279 TTTTTATTTTTTCTC
1 TTTTCCTTTTTTC-C
691294 TTTTTCCTTTTTTCCC
1 -TTTTCCTTTTTT-CC
691310 TTTTCC
1 TTTTCC
691316 ATAATTTTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
14 21 0.54
15 6 0.15
16 11 0.28
17 1 0.03
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTCCTTTTTTCC
Found at i:691326 original size:44 final size:44
Alignment explanation
Indices: 691241--691339 Score: 121
Period size: 44 Copynumber: 2.2 Consensus size: 44
691231 ATTTTTCATT
* **
691241 TTTTTTCATTTTTTCATTTTTTCCTTTTCCTTTTTTATTTTTTA
1 TTTTTTCATTTTTTCATTTTTTCCTTTTCCATAATTATTTTTTA
* *
691285 TTTTTTC-TCTTTTTCCTTTTTTCCCTTTTCCATAATT-TTTTTTC
1 TTTTTTCAT-TTTTTCATTTTTT-CCTTTTCCATAATTATTTTTTA
691329 TTTTTTCATTT
1 TTTTTTCATTT
691340 CTTTTTCAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.02
44 34 0.72
45 12 0.26
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (44 bp):
TTTTTTCATTTTTTCATTTTTTCCTTTTCCATAATTATTTTTTA
Found at i:696709 original size:17 final size:17
Alignment explanation
Indices: 696687--696729 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
696677 AAACGAACTG
*
696687 GACAGGAACCCAACCCC
1 GACAGGAACCAAACCCC
*
696704 GACAGGAACTAAACCCC
1 GACAGGAACCAAACCCC
*
696721 GACATGAAC
1 GACAGGAAC
696730 GGCATAAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.40, C:0.37, G:0.19, T:0.05
Consensus pattern (17 bp):
GACAGGAACCAAACCCC
Found at i:698253 original size:22 final size:22
Alignment explanation
Indices: 698222--698296 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 22
698212 AATCTTTCAT
*
698222 AAAATTTTTAATTATAATATTA
1 AAAATATTTAATTATAATATTA
* *
698244 AAAATATTT-ATT-TAATTTTT
1 AAAATATTTAATTATAATATTA
*
698264 AAAATCATATTAATTA-ATTATTTA
1 AAAAT-AT-TTAATTATAATA-TTA
698288 AATAATATT
1 AA-AATATT
698297 ATTTTTAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
20 11 0.27
21 5 0.12
22 10 0.24
23 6 0.15
24 6 0.15
25 3 0.07
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
AAAATATTTAATTATAATATTA
Found at i:698297 original size:22 final size:21
Alignment explanation
Indices: 698241--698297 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
698231 AATTATAATA
*
698241 TTAAA-AATATTTATTTAATTT
1 TTAAATAATA-TTAATTAATTT
*
698262 TTAAAATCATATTAATTAATTAT
1 TT-AAATAATATTAATTAATT-T
698285 TTAAATAATATTA
1 TTAAATAATATTA
698298 TTTTTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 2 0.07
22 22 0.73
23 6 0.20
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAAATAATATTAATTAATTT
Found at i:698862 original size:22 final size:22
Alignment explanation
Indices: 698839--698879 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
698829 ATTAAATATA
698839 AAAATAAT-AAAAATAAAAAGT
1 AAAATAATAAAAAATAAAAAGT
* *
698860 AAATTACTAAAAAATAAAAA
1 AAAATAATAAAAAATAAAAA
698880 ATATATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (22 bp):
AAAATAATAAAAAATAAAAAGT
Found at i:702630 original size:42 final size:42
Alignment explanation
Indices: 702519--702630 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
702509 CCGAAGGTCA
* **
702519 TATTGATGGCTCGAAGGACTTATCAT-ATTTTTCGATAGACT
1 TATTGATGGCCCGAAGGACTTATCATCATTGCTCGATAGACT
* * * *
702560 TATAGATGACCCGAAGGATTTAAGCATCA-TGCTCG-TAAGACT
1 TATTGATGGCCCGAAGGACTT-ATCATCATTGCTCGAT-AGACT
702602 TATTGATGGCCCGAAGGACTTACTCATCA
1 TATTGATGGCCCGAAGGACTTA-TCATCA
702631 AGAAACCCTT
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
41 19 0.34
42 36 0.64
43 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (42 bp):
TATTGATGGCCCGAAGGACTTATCATCATTGCTCGATAGACT
Found at i:703069 original size:295 final size:293
Alignment explanation
Indices: 702494--703252 Score: 1037
Period size: 295 Copynumber: 2.6 Consensus size: 293
702484 GAAGGAAATG
* * * * * * * *
702494 TTGAAAACACCCTTCCCGAAGGTCATATTGATGGCTCGAAGGACTTATCATATTTTTCGATAGAC
1 TTGAAAACATCCTTCCCGAAGGTCTTATGGATGGCCCAAAGGACTTATCAT-CTTCTCGAAAGAC
* * *
702559 TTATAGATGACCCGAAGGATTTAAGCATCATGCTCGTAAGACTTATTGATGGCCCGAAGGACTTA
65 TTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTA
* *
702624 CTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAAAATCTTTTATTTTCAGTTGTCATCA
130 CTCATCAAGAAACCCTTGAAAAACAAGCTTAGTTTCTTAAAATCTTTCATTTTCAGTTGTCATCA
* * * *
702689 AGGAATCCCTAAAAGTTAGGCTTAGCTTCCTTTAAAAATTCTTTGGAGATAATCATCAAGAAACC
195 AGGAACCCCTAAAAGTTAGGCTTAGCTTCCTTTAAAAAATCTTTAGAGAGAATCATCAAGAAACC
*
702754 CCTGAAAAATCATTCTTAGTTTTTTTAAAACTCAT
260 CCTGAAAAATCATTCTTAG-TTTTTAAAAACTCAT
*
702789 TTGAAAATATCCTTCCCGAAGGTCTTATGGATGGCCCAAAGGACTTATCATCTATCTCGAAAGAC
1 TTGAAAACATCCTTCCCGAAGGTCTTATGGATGGCCCAAAGGACTTATCATCT-TCTCGAAAGAC
* * * * * *
702854 TTATAGATGACCTGAACGATTTAAGCATCATGTTCGAAAGACTTAGTGATGGCCCAAATGACTAA
65 TTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTA
*
702919 CTCATCAAGAAACCCTTGAAAAACAAGCTTATTTTCTTTAAAATCTTTCATTTTCAGTTGTCATC
130 CTCATCAAGAAACCCTTGAAAAACAAGCTTAGTTTC-TTAAAATCTTTCATTTTCAGTTGTCATC
*
702984 AAGGAACCCCTAAAAAG-TATGCTTAGCTTCCTTTAAAAAATCTTTAGAGAGAATCATCAAGAAA
194 AAGGAACCCCT-AAAAGTTAGGCTTAGCTTCCTTTAAAAAATCTTTAGAGAGAATCATCAAGAAA
703048 CCCCT-AAAAAT-ATTACTTAGTTTTTAAAAACTCAT
258 CCCCTGAAAAATCATT-CTTAGTTTTTAAAAACTCAT
* *
703083 TTGAAAACATCCTACCCGAAGGTCTTATGAATGG-CCAGAAGGACTTATCATCTTGCTCGAAAGA
1 TTGAAAACATCCTTCCCGAAGGTCTTATGGATGGCCCA-AAGGACTTATCATCTT-CTCGAAAGA
* ** * **
703147 CTTACAGATGACCCGAAGGATTTAAAATATCATGCTCAAAAGACTTACTGAT-AACCAGAAGGAC
64 CTTATAGATGACCCGAAGGATTT-AAGCATCATGCTCGAAAGACTTACTGATGGCCCA-AAGGAC
*
703211 TTACTGATCAAGAAACCCTT-AAAAATCAAG-TTCAGTTTCTTA
127 TTACTCATCAAGAAACCCTTGAAAAA-CAAGCTT-AGTTTCTTA
703253 GTTGTCATCA
Statistics
Matches: 411, Mismatches: 43, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
293 4 0.01
294 106 0.26
295 211 0.51
296 85 0.21
297 5 0.01
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (293 bp):
TTGAAAACATCCTTCCCGAAGGTCTTATGGATGGCCCAAAGGACTTATCATCTTCTCGAAAGACT
TATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTAC
TCATCAAGAAACCCTTGAAAAACAAGCTTAGTTTCTTAAAATCTTTCATTTTCAGTTGTCATCAA
GGAACCCCTAAAAGTTAGGCTTAGCTTCCTTTAAAAAATCTTTAGAGAGAATCATCAAGAAACCC
CTGAAAAATCATTCTTAGTTTTTAAAAACTCAT
Found at i:705463 original size:24 final size:26
Alignment explanation
Indices: 705417--705473 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
705407 TTTTCCTTCA
* *
705417 TTTTTCTTTCTTTTATATCTCTATT-
1 TTTTTCTTTCTTTGATATATCTATTC
*
705442 TTTTTCTTT-TTTGCTATATCTATTC
1 TTTTTCTTTCTTTGATATATCTATTC
705467 TTTTTCT
1 TTTTTCT
705474 CTTCGTGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 12 0.43
25 16 0.57
ACGTcount: A:0.11, C:0.16, G:0.02, T:0.72
Consensus pattern (26 bp):
TTTTTCTTTCTTTGATATATCTATTC
Found at i:708012 original size:148 final size:148
Alignment explanation
Indices: 707742--708035 Score: 500
Period size: 148 Copynumber: 2.0 Consensus size: 148
707732 AGTCATCTAA
*
707742 CCCAACACTTCTTATTGAGAAACTAATGCTTGACTTCTTATCCTCTGTTGTAGCGTGGCCATCTG
1 CCCAACACTTCTTATTGAGAAACTAATGCTTGACTTCTCATCCTCTGTTGTAGCGTGGCCATCTG
*
707807 ATCTCACATTTGATCCTGTAACTCTCACTAGGACTACTCTATTGCTTTTAACGTCTTATTCATCG
66 ATCTCACATTTGATCCTGTAACTCTCACTAGGACTACTCTATTGCTTTTAACCTCTTATTCATCG
*
707872 AGAGTGGAGGATAAATGT
131 AGAGTGGAGGAGAAATGT
* *
707890 CCCAACGCTTCTTCTTGAGAAACTAATGCTTGACTTCTCATCCTCTGTTGTAGCGTGGCCATCTG
1 CCCAACACTTCTTATTGAGAAACTAATGCTTGACTTCTCATCCTCTGTTGTAGCGTGGCCATCTG
* * *
707955 ATCTCACATTTGATCTTGTAACTCTC-CTTGGGACTGCTCTATTGCTTTTAACCTCTTATTCATC
66 ATCTCACATTTGATCCTGTAACTCTCAC-TAGGACTACTCTATTGCTTTTAACCTCTTATTCATC
708019 GAGAGTGGAGGAGAAAT
130 GAGAGTGGAGGAGAAAT
708036 CTAGATGGGT
Statistics
Matches: 137, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
147 1 0.01
148 136 0.99
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.36
Consensus pattern (148 bp):
CCCAACACTTCTTATTGAGAAACTAATGCTTGACTTCTCATCCTCTGTTGTAGCGTGGCCATCTG
ATCTCACATTTGATCCTGTAACTCTCACTAGGACTACTCTATTGCTTTTAACCTCTTATTCATCG
AGAGTGGAGGAGAAATGT
Found at i:713085 original size:19 final size:19
Alignment explanation
Indices: 713042--713087 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
713032 GTTTTCATTA
*
713042 AAAATAACATAATTAAATC
1 AAAATAACATAATTAAAAC
713061 AGAAATAACA-AATTTAAAAC
1 A-AAATAACATAA-TTAAAAC
713081 AAAATAA
1 AAAATAA
713088 TTTTTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAATAACATAATTAAAAC
Found at i:731529 original size:13 final size:13
Alignment explanation
Indices: 731511--731535 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
731501 TCGAATATAA
731511 AATCTTAAAATTC
1 AATCTTAAAATTC
731524 AATCTTAAAATT
1 AATCTTAAAATT
731536 TATTTACACT
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:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
AATCTTAAAATTC
Found at i:740749 original size:18 final size:18
Alignment explanation
Indices: 740726--740763 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
740716 ATGCTTTCTC
*
740726 TCTTGTTTATCAATGAAT
1 TCTTGTTGATCAATGAAT
*
740744 TCTTGTTGATCAATGGAT
1 TCTTGTTGATCAATGAAT
740762 TC
1 TC
740764 AGAACTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (18 bp):
TCTTGTTGATCAATGAAT
Done.