Multiple sequence alignment - TraesCS6B01G262900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G262900 chr6B 100.000 4300 0 0 1 4300 473089971 473085672 0.000000e+00 7941.0
1 TraesCS6B01G262900 chr6B 94.017 117 7 0 1 117 354580841 354580957 1.230000e-40 178.0
2 TraesCS6B01G262900 chr6D 93.562 3417 139 33 918 4300 306146123 306142754 0.000000e+00 5016.0
3 TraesCS6B01G262900 chr6D 80.934 792 106 22 118 865 306147035 306146245 6.200000e-163 584.0
4 TraesCS6B01G262900 chr6D 92.308 117 9 0 1 117 242066053 242065937 2.660000e-37 167.0
5 TraesCS6B01G262900 chr6A 92.852 2546 100 33 1697 4226 441521746 441519267 0.000000e+00 3618.0
6 TraesCS6B01G262900 chr6A 93.342 796 31 8 918 1692 441523393 441522599 0.000000e+00 1157.0
7 TraesCS6B01G262900 chr6A 79.434 778 113 23 118 865 441524243 441523483 1.380000e-139 507.0
8 TraesCS6B01G262900 chr7B 94.017 117 6 1 1 117 228287811 228287926 4.420000e-40 176.0
9 TraesCS6B01G262900 chr7B 91.339 127 10 1 1 126 208351085 208351211 5.720000e-39 172.0
10 TraesCS6B01G262900 chr7B 92.308 52 1 3 3452 3502 164155567 164155616 2.150000e-08 71.3
11 TraesCS6B01G262900 chr7B 94.444 36 2 0 4256 4291 523605263 523605228 6.010000e-04 56.5
12 TraesCS6B01G262900 chr3B 93.162 117 8 0 1 117 395131748 395131632 5.720000e-39 172.0
13 TraesCS6B01G262900 chr3B 89.091 55 5 1 3459 3512 578594682 578594628 2.780000e-07 67.6
14 TraesCS6B01G262900 chr3B 94.444 36 2 0 4256 4291 235878486 235878521 6.010000e-04 56.5
15 TraesCS6B01G262900 chr1D 93.162 117 8 0 1 117 184575557 184575673 5.720000e-39 172.0
16 TraesCS6B01G262900 chr1D 90.698 129 10 2 1 129 214627016 214626890 2.060000e-38 171.0
17 TraesCS6B01G262900 chr1D 87.931 58 5 2 3451 3508 10263558 10263503 2.780000e-07 67.6
18 TraesCS6B01G262900 chr4D 92.373 118 9 0 1 118 389192063 389192180 7.400000e-38 169.0
19 TraesCS6B01G262900 chr4D 95.745 47 0 2 3463 3508 14928718 14928763 1.660000e-09 75.0
20 TraesCS6B01G262900 chr1B 91.667 120 9 1 1 120 558743567 558743449 9.570000e-37 165.0
21 TraesCS6B01G262900 chr3A 92.000 50 4 0 3452 3501 53028046 53027997 2.150000e-08 71.3
22 TraesCS6B01G262900 chr3A 92.500 40 2 1 4253 4291 732049012 732048973 6.010000e-04 56.5
23 TraesCS6B01G262900 chr2A 88.525 61 3 4 3444 3503 615095337 615095280 2.150000e-08 71.3
24 TraesCS6B01G262900 chr4A 92.000 50 3 1 3452 3501 626981539 626981491 7.720000e-08 69.4
25 TraesCS6B01G262900 chr2D 95.238 42 2 0 4256 4297 23166612 23166653 2.780000e-07 67.6
26 TraesCS6B01G262900 chr2D 92.683 41 3 0 4257 4297 612956747 612956707 4.640000e-05 60.2
27 TraesCS6B01G262900 chr2D 94.444 36 2 0 4256 4291 584465882 584465917 6.010000e-04 56.5
28 TraesCS6B01G262900 chr5D 97.143 35 1 0 4257 4291 37635961 37635927 4.640000e-05 60.2
29 TraesCS6B01G262900 chr2B 97.059 34 1 0 4258 4291 259371602 259371569 1.670000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G262900 chr6B 473085672 473089971 4299 True 7941.000000 7941 100.000000 1 4300 1 chr6B.!!$R1 4299
1 TraesCS6B01G262900 chr6D 306142754 306147035 4281 True 2800.000000 5016 87.248000 118 4300 2 chr6D.!!$R2 4182
2 TraesCS6B01G262900 chr6A 441519267 441524243 4976 True 1760.666667 3618 88.542667 118 4226 3 chr6A.!!$R1 4108

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
248 250 0.029300 CCAGAACGTGGTGCACAAAG 59.971 55.0 20.43 12.93 42.17 2.77 F
426 429 0.040646 ACCATGGAGTCGAGGGTACA 59.959 55.0 21.47 0.00 0.00 2.90 F
670 704 0.104487 AGATGCTCCTCTGCGTGATG 59.896 55.0 0.00 0.00 35.36 3.07 F
671 705 0.179089 GATGCTCCTCTGCGTGATGT 60.179 55.0 0.00 0.00 35.36 3.06 F
672 706 0.461516 ATGCTCCTCTGCGTGATGTG 60.462 55.0 0.00 0.00 35.36 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2223 3235 0.042188 CACAAGTTTCAGTCCGTGCG 60.042 55.000 0.00 0.00 0.00 5.34 R
2306 3318 2.689983 CAAATCAGATAACTGGTGCCCC 59.310 50.000 0.00 0.00 43.60 5.80 R
2510 3522 2.540265 ACTGTCTCAACTTCTGGCAG 57.460 50.000 8.58 8.58 0.00 4.85 R
2750 3762 5.646793 CAGTTTCAATGACACCAGAGATGAT 59.353 40.000 0.00 0.00 0.00 2.45 R
3305 4317 4.465886 ACAGCTCTATCGGAGTTCATAGT 58.534 43.478 0.00 0.00 43.62 2.12 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.911788 ATTATTTGGATTTGTGTCTAGAGTCAT 57.088 29.630 0.00 0.00 0.00 3.06
31 32 7.621428 ATTTGGATTTGTGTCTAGAGTCATG 57.379 36.000 0.00 0.00 0.00 3.07
32 33 5.745312 TGGATTTGTGTCTAGAGTCATGT 57.255 39.130 0.00 0.00 0.00 3.21
33 34 6.114187 TGGATTTGTGTCTAGAGTCATGTT 57.886 37.500 0.00 0.00 0.00 2.71
34 35 7.239763 TGGATTTGTGTCTAGAGTCATGTTA 57.760 36.000 0.00 0.00 0.00 2.41
35 36 7.851228 TGGATTTGTGTCTAGAGTCATGTTAT 58.149 34.615 0.00 0.00 0.00 1.89
36 37 7.765819 TGGATTTGTGTCTAGAGTCATGTTATG 59.234 37.037 0.00 0.00 0.00 1.90
37 38 7.981789 GGATTTGTGTCTAGAGTCATGTTATGA 59.018 37.037 0.00 0.00 36.84 2.15
38 39 9.539825 GATTTGTGTCTAGAGTCATGTTATGAT 57.460 33.333 0.00 0.00 42.04 2.45
42 43 9.579932 TGTGTCTAGAGTCATGTTATGATATCT 57.420 33.333 3.98 11.63 42.04 1.98
46 47 8.951243 TCTAGAGTCATGTTATGATATCTTCCG 58.049 37.037 3.98 5.41 42.04 4.30
47 48 6.929625 AGAGTCATGTTATGATATCTTCCGG 58.070 40.000 3.98 0.00 42.04 5.14
48 49 6.495181 AGAGTCATGTTATGATATCTTCCGGT 59.505 38.462 0.00 0.00 42.04 5.28
49 50 6.459066 AGTCATGTTATGATATCTTCCGGTG 58.541 40.000 0.00 0.00 42.04 4.94
50 51 6.267699 AGTCATGTTATGATATCTTCCGGTGA 59.732 38.462 0.00 1.23 42.04 4.02
51 52 6.587990 GTCATGTTATGATATCTTCCGGTGAG 59.412 42.308 0.00 0.66 42.04 3.51
52 53 6.267699 TCATGTTATGATATCTTCCGGTGAGT 59.732 38.462 0.00 0.00 33.59 3.41
53 54 6.085555 TGTTATGATATCTTCCGGTGAGTC 57.914 41.667 0.00 5.12 0.00 3.36
54 55 5.010719 TGTTATGATATCTTCCGGTGAGTCC 59.989 44.000 0.00 0.00 0.00 3.85
55 56 2.317040 TGATATCTTCCGGTGAGTCCC 58.683 52.381 0.00 0.00 0.00 4.46
56 57 2.091278 TGATATCTTCCGGTGAGTCCCT 60.091 50.000 0.00 0.00 0.00 4.20
57 58 1.776662 TATCTTCCGGTGAGTCCCTG 58.223 55.000 0.00 0.00 0.00 4.45
58 59 0.041238 ATCTTCCGGTGAGTCCCTGA 59.959 55.000 0.00 0.00 0.00 3.86
59 60 0.041238 TCTTCCGGTGAGTCCCTGAT 59.959 55.000 0.00 0.00 0.00 2.90
60 61 0.461961 CTTCCGGTGAGTCCCTGATC 59.538 60.000 0.00 0.00 0.00 2.92
61 62 0.041238 TTCCGGTGAGTCCCTGATCT 59.959 55.000 0.00 0.00 0.00 2.75
62 63 0.041238 TCCGGTGAGTCCCTGATCTT 59.959 55.000 0.00 0.00 0.00 2.40
63 64 0.176680 CCGGTGAGTCCCTGATCTTG 59.823 60.000 0.00 0.00 0.00 3.02
64 65 1.186200 CGGTGAGTCCCTGATCTTGA 58.814 55.000 0.00 0.00 0.00 3.02
65 66 1.759445 CGGTGAGTCCCTGATCTTGAT 59.241 52.381 0.00 0.00 0.00 2.57
66 67 2.223923 CGGTGAGTCCCTGATCTTGATC 60.224 54.545 3.82 3.82 0.00 2.92
67 68 2.223923 GGTGAGTCCCTGATCTTGATCG 60.224 54.545 6.19 2.03 0.00 3.69
68 69 2.428890 GTGAGTCCCTGATCTTGATCGT 59.571 50.000 6.19 0.00 0.00 3.73
69 70 3.632604 GTGAGTCCCTGATCTTGATCGTA 59.367 47.826 6.19 0.00 0.00 3.43
70 71 3.632604 TGAGTCCCTGATCTTGATCGTAC 59.367 47.826 6.19 2.53 0.00 3.67
71 72 3.632333 AGTCCCTGATCTTGATCGTACA 58.368 45.455 6.19 0.00 0.00 2.90
72 73 3.381908 AGTCCCTGATCTTGATCGTACAC 59.618 47.826 6.19 1.73 0.00 2.90
73 74 3.381908 GTCCCTGATCTTGATCGTACACT 59.618 47.826 6.19 0.00 0.00 3.55
74 75 4.023980 TCCCTGATCTTGATCGTACACTT 58.976 43.478 6.19 0.00 0.00 3.16
75 76 4.466370 TCCCTGATCTTGATCGTACACTTT 59.534 41.667 6.19 0.00 0.00 2.66
76 77 5.046591 TCCCTGATCTTGATCGTACACTTTT 60.047 40.000 6.19 0.00 0.00 2.27
77 78 5.063944 CCCTGATCTTGATCGTACACTTTTG 59.936 44.000 6.19 0.00 0.00 2.44
78 79 5.446473 CCTGATCTTGATCGTACACTTTTGC 60.446 44.000 6.19 0.00 0.00 3.68
79 80 4.091365 TGATCTTGATCGTACACTTTTGCG 59.909 41.667 6.19 0.00 0.00 4.85
80 81 3.386486 TCTTGATCGTACACTTTTGCGT 58.614 40.909 0.00 0.00 0.00 5.24
81 82 3.183574 TCTTGATCGTACACTTTTGCGTG 59.816 43.478 0.00 0.00 40.67 5.34
83 84 3.640592 TGATCGTACACTTTTGCGTGTA 58.359 40.909 0.07 0.07 45.65 2.90
92 93 5.927030 ACACTTTTGCGTGTATGATTAGTG 58.073 37.500 0.00 0.00 45.65 2.74
93 94 5.468746 ACACTTTTGCGTGTATGATTAGTGT 59.531 36.000 0.00 0.00 45.65 3.55
94 95 6.647481 ACACTTTTGCGTGTATGATTAGTGTA 59.353 34.615 0.00 0.00 45.65 2.90
95 96 6.953743 CACTTTTGCGTGTATGATTAGTGTAC 59.046 38.462 0.00 0.00 0.00 2.90
96 97 5.689927 TTTGCGTGTATGATTAGTGTACG 57.310 39.130 0.00 0.00 0.00 3.67
97 98 4.619437 TGCGTGTATGATTAGTGTACGA 57.381 40.909 0.00 0.00 32.36 3.43
98 99 5.177725 TGCGTGTATGATTAGTGTACGAT 57.822 39.130 0.00 0.00 32.36 3.73
99 100 4.973663 TGCGTGTATGATTAGTGTACGATG 59.026 41.667 0.00 0.00 32.36 3.84
100 101 4.381863 GCGTGTATGATTAGTGTACGATGG 59.618 45.833 0.00 0.00 32.36 3.51
101 102 5.754778 CGTGTATGATTAGTGTACGATGGA 58.245 41.667 0.00 0.00 32.36 3.41
102 103 6.203647 CGTGTATGATTAGTGTACGATGGAA 58.796 40.000 0.00 0.00 32.36 3.53
103 104 6.861572 CGTGTATGATTAGTGTACGATGGAAT 59.138 38.462 0.00 0.00 32.36 3.01
104 105 7.060748 CGTGTATGATTAGTGTACGATGGAATC 59.939 40.741 0.00 0.00 40.89 2.52
113 114 2.280865 GATGGAATCGGGGGCGTC 60.281 66.667 0.00 0.00 31.13 5.19
114 115 3.087253 ATGGAATCGGGGGCGTCA 61.087 61.111 0.00 0.00 0.00 4.35
115 116 3.400599 ATGGAATCGGGGGCGTCAC 62.401 63.158 0.00 0.00 0.00 3.67
116 117 4.090588 GGAATCGGGGGCGTCACA 62.091 66.667 0.00 0.00 0.00 3.58
142 143 1.061131 GAGCATGTCCGTGTCAAATCG 59.939 52.381 0.00 0.00 0.00 3.34
161 162 2.680841 TCGTTGTCCACTTCTTTTGGTG 59.319 45.455 0.00 0.00 35.42 4.17
197 199 1.379527 GGCGAGGAAACCGATTTCAT 58.620 50.000 4.29 0.00 45.26 2.57
200 202 3.366985 GGCGAGGAAACCGATTTCATTTT 60.367 43.478 4.29 0.00 45.26 1.82
201 203 3.608073 GCGAGGAAACCGATTTCATTTTG 59.392 43.478 4.29 0.00 45.26 2.44
216 218 5.772825 TCATTTTGAAACCTTCTGGACAG 57.227 39.130 0.00 0.00 37.04 3.51
217 219 5.200483 TCATTTTGAAACCTTCTGGACAGT 58.800 37.500 0.00 0.00 37.04 3.55
220 222 1.843851 TGAAACCTTCTGGACAGTGGT 59.156 47.619 11.69 11.69 37.72 4.16
221 223 2.222027 GAAACCTTCTGGACAGTGGTG 58.778 52.381 15.94 1.73 36.83 4.17
248 250 0.029300 CCAGAACGTGGTGCACAAAG 59.971 55.000 20.43 12.93 42.17 2.77
249 251 0.592247 CAGAACGTGGTGCACAAAGC 60.592 55.000 20.43 0.95 45.96 3.51
259 261 3.863681 GCACAAAGCGTGGAATGAA 57.136 47.368 0.00 0.00 46.45 2.57
260 262 1.689959 GCACAAAGCGTGGAATGAAG 58.310 50.000 0.00 0.00 46.45 3.02
265 267 1.896220 AAGCGTGGAATGAAGAGCAA 58.104 45.000 0.00 0.00 0.00 3.91
267 269 0.874390 GCGTGGAATGAAGAGCAACA 59.126 50.000 0.00 0.00 0.00 3.33
283 285 2.929641 CAACAAATTGCCAACCCCTTT 58.070 42.857 0.00 0.00 0.00 3.11
285 287 4.064388 CAACAAATTGCCAACCCCTTTAG 58.936 43.478 0.00 0.00 0.00 1.85
362 365 3.550030 CCACTTCATTGGGAACGTCAAAC 60.550 47.826 0.00 0.00 32.35 2.93
391 394 9.948964 CAAATCATGGTAGATAATGAGGTGATA 57.051 33.333 0.00 0.00 36.31 2.15
426 429 0.040646 ACCATGGAGTCGAGGGTACA 59.959 55.000 21.47 0.00 0.00 2.90
478 490 2.030027 TGGTCTGACATCCCTTGAGT 57.970 50.000 10.38 0.00 0.00 3.41
479 491 2.338809 TGGTCTGACATCCCTTGAGTT 58.661 47.619 10.38 0.00 0.00 3.01
482 494 3.496870 GGTCTGACATCCCTTGAGTTGTT 60.497 47.826 10.38 0.00 0.00 2.83
509 521 4.005650 GTCAATTCTCACATGCCAAGAGA 58.994 43.478 0.00 0.00 36.68 3.10
521 533 1.371183 CAAGAGACCCAAGACGGCA 59.629 57.895 0.00 0.00 0.00 5.69
538 551 0.170339 GCAAGACCAATTACGGTGCC 59.830 55.000 0.00 0.00 40.22 5.01
541 554 2.032834 ACCAATTACGGTGCCGCA 59.967 55.556 10.87 0.00 44.19 5.69
551 564 0.519519 CGGTGCCGCAGATGTAAAAA 59.480 50.000 0.00 0.00 0.00 1.94
558 571 3.616317 GCCGCAGATGTAAAAACCCATTT 60.616 43.478 0.00 0.00 0.00 2.32
571 584 3.744940 ACCCATTTCATCAGATGTGGT 57.255 42.857 14.55 10.07 30.68 4.16
578 591 7.423199 CCATTTCATCAGATGTGGTTATTCTG 58.577 38.462 10.34 0.00 38.56 3.02
584 597 2.308570 AGATGTGGTTATTCTGCACCCA 59.691 45.455 0.00 0.00 31.24 4.51
618 634 4.164604 AGCCCGGGTGTGAATAGTAAAATA 59.835 41.667 24.63 0.00 0.00 1.40
619 635 4.514066 GCCCGGGTGTGAATAGTAAAATAG 59.486 45.833 24.63 0.00 0.00 1.73
620 636 5.685599 GCCCGGGTGTGAATAGTAAAATAGA 60.686 44.000 24.63 0.00 0.00 1.98
621 637 6.350906 CCCGGGTGTGAATAGTAAAATAGAA 58.649 40.000 14.18 0.00 0.00 2.10
622 638 6.824704 CCCGGGTGTGAATAGTAAAATAGAAA 59.175 38.462 14.18 0.00 0.00 2.52
623 639 7.337436 CCCGGGTGTGAATAGTAAAATAGAAAA 59.663 37.037 14.18 0.00 0.00 2.29
670 704 0.104487 AGATGCTCCTCTGCGTGATG 59.896 55.000 0.00 0.00 35.36 3.07
671 705 0.179089 GATGCTCCTCTGCGTGATGT 60.179 55.000 0.00 0.00 35.36 3.06
672 706 0.461516 ATGCTCCTCTGCGTGATGTG 60.462 55.000 0.00 0.00 35.36 3.21
681 723 2.799978 TCTGCGTGATGTGTGTACAAAG 59.200 45.455 0.00 0.00 40.84 2.77
688 730 5.646606 GTGATGTGTGTACAAAGTTTGGTT 58.353 37.500 19.45 2.40 40.84 3.67
695 737 7.823310 TGTGTGTACAAAGTTTGGTTAAGTCTA 59.177 33.333 19.45 0.00 32.88 2.59
698 740 9.269453 GTGTACAAAGTTTGGTTAAGTCTAGAT 57.731 33.333 19.45 0.00 34.12 1.98
699 741 9.485206 TGTACAAAGTTTGGTTAAGTCTAGATC 57.515 33.333 19.45 0.00 34.12 2.75
709 751 5.278120 GGTTAAGTCTAGATCTTCGAGGAGC 60.278 48.000 4.39 4.39 0.00 4.70
770 813 7.139896 ACTTTTGAAAACAAAATTCACACCC 57.860 32.000 8.24 0.00 36.57 4.61
772 815 4.720649 TGAAAACAAAATTCACACCCGA 57.279 36.364 0.00 0.00 32.10 5.14
773 816 5.269505 TGAAAACAAAATTCACACCCGAT 57.730 34.783 0.00 0.00 32.10 4.18
774 817 5.665459 TGAAAACAAAATTCACACCCGATT 58.335 33.333 0.00 0.00 32.10 3.34
775 818 6.109359 TGAAAACAAAATTCACACCCGATTT 58.891 32.000 0.00 0.00 32.10 2.17
777 820 7.764443 TGAAAACAAAATTCACACCCGATTTTA 59.236 29.630 0.00 0.00 32.10 1.52
780 826 6.394809 ACAAAATTCACACCCGATTTTATCC 58.605 36.000 0.00 0.00 0.00 2.59
782 828 6.850752 AAATTCACACCCGATTTTATCCTT 57.149 33.333 0.00 0.00 0.00 3.36
817 863 5.503662 TTCTCGAAAGTTTAAACAACCCC 57.496 39.130 20.06 4.12 0.00 4.95
869 915 5.662211 GCAACTTGCATCACAAAAGAATT 57.338 34.783 8.97 0.00 44.26 2.17
870 916 6.768029 GCAACTTGCATCACAAAAGAATTA 57.232 33.333 8.97 0.00 44.26 1.40
1281 1423 2.369983 TCTACCCCGGTGTTATCGAT 57.630 50.000 2.16 2.16 0.00 3.59
1283 1425 1.000506 CTACCCCGGTGTTATCGATGG 59.999 57.143 8.54 0.00 0.00 3.51
1380 1522 2.203056 CGGCCTGATCCATTCGCA 60.203 61.111 0.00 0.00 0.00 5.10
1620 1775 5.822519 AGCCACACAATATACATGTTCGATT 59.177 36.000 2.30 0.00 0.00 3.34
1744 2747 4.021368 AGGTTATATTACGCTGGCTACTGG 60.021 45.833 0.00 0.00 0.00 4.00
1762 2765 2.889512 TGGCTTAGACCAGAGAACTCA 58.110 47.619 4.64 0.00 33.75 3.41
1771 2774 4.764823 AGACCAGAGAACTCAACTCTAGTG 59.235 45.833 0.00 0.00 41.94 2.74
1837 2840 2.745821 TCAGATGCAGATGTTCAGTTGC 59.254 45.455 0.00 4.96 37.09 4.17
1874 2877 7.558161 TTATAGAACATGCTGATTTCTGTGG 57.442 36.000 5.92 0.00 31.93 4.17
1888 2891 2.556766 TCTGTGGTGTGGAATCCCATA 58.443 47.619 0.00 0.00 45.68 2.74
1916 2919 5.236695 ACTTCTTTTACAGCTCCGAGAAAAC 59.763 40.000 0.00 0.00 0.00 2.43
1917 2920 4.957296 TCTTTTACAGCTCCGAGAAAACT 58.043 39.130 0.00 0.00 0.00 2.66
1946 2949 8.289939 TGTTTGGTACTTTGTTGTGGTAATAA 57.710 30.769 0.00 0.00 0.00 1.40
1947 2950 8.915036 TGTTTGGTACTTTGTTGTGGTAATAAT 58.085 29.630 0.00 0.00 0.00 1.28
1969 2972 2.678471 CCCATCAGTTCAATTTGGGC 57.322 50.000 0.00 0.00 40.55 5.36
1989 2992 4.633565 GGGCAGTCTGACTAGAGAATTTTG 59.366 45.833 10.47 0.00 32.48 2.44
2057 3069 3.758755 AGCATTTCTCTGACACAGTGA 57.241 42.857 7.81 0.00 33.11 3.41
2058 3070 4.283363 AGCATTTCTCTGACACAGTGAT 57.717 40.909 7.81 0.00 34.64 3.06
2059 3071 5.411831 AGCATTTCTCTGACACAGTGATA 57.588 39.130 7.81 0.00 34.64 2.15
2060 3072 5.798132 AGCATTTCTCTGACACAGTGATAA 58.202 37.500 7.81 0.00 34.64 1.75
2061 3073 6.233434 AGCATTTCTCTGACACAGTGATAAA 58.767 36.000 7.81 0.00 34.64 1.40
2062 3074 6.883217 AGCATTTCTCTGACACAGTGATAAAT 59.117 34.615 7.81 1.45 34.64 1.40
2063 3075 8.043113 AGCATTTCTCTGACACAGTGATAAATA 58.957 33.333 7.81 0.00 34.64 1.40
2064 3076 8.834465 GCATTTCTCTGACACAGTGATAAATAT 58.166 33.333 7.81 0.00 34.64 1.28
2067 3079 9.725019 TTTCTCTGACACAGTGATAAATATTGT 57.275 29.630 7.81 0.00 34.64 2.71
2068 3080 9.725019 TTCTCTGACACAGTGATAAATATTGTT 57.275 29.630 7.81 0.00 34.64 2.83
2123 3135 3.430218 CAGCACTGTGAAGTTACTAGCAC 59.570 47.826 12.86 10.16 0.00 4.40
2195 3207 3.750371 TGGAACCGACATCTTTCATTGT 58.250 40.909 0.00 0.00 0.00 2.71
2208 3220 5.221880 TCTTTCATTGTCATTTTGGCTTCG 58.778 37.500 0.00 0.00 0.00 3.79
2223 3235 3.530398 TTCGGGCGCGCAGTTTTTC 62.530 57.895 34.42 13.43 0.00 2.29
2235 3247 1.329292 CAGTTTTTCGCACGGACTGAA 59.671 47.619 9.51 0.00 39.97 3.02
2295 3307 7.540474 TGTCACTTAGAGTTTATGGAGACTT 57.460 36.000 0.00 0.00 0.00 3.01
2296 3308 7.603651 TGTCACTTAGAGTTTATGGAGACTTC 58.396 38.462 0.00 0.00 0.00 3.01
2432 3444 4.339530 GGAATGGTCAAATTAGGAGAAGGC 59.660 45.833 0.00 0.00 0.00 4.35
2433 3445 4.870021 ATGGTCAAATTAGGAGAAGGCT 57.130 40.909 0.00 0.00 0.00 4.58
2510 3522 0.887387 TAAAGGTGGTTGCGTCAGGC 60.887 55.000 0.00 0.00 43.96 4.85
2750 3762 2.807967 CAAAATTGCTGAGGTCTCGTCA 59.192 45.455 0.00 0.00 0.00 4.35
2843 3855 0.898320 TCTGCTGCAACCTAGAGACC 59.102 55.000 3.02 0.00 0.00 3.85
3305 4317 5.783360 TGTTGATAGGTTCTTCTAGGGTCAA 59.217 40.000 0.00 0.00 0.00 3.18
3461 4476 5.483811 TCGAATTGCATGTACTACCTTCAA 58.516 37.500 0.00 0.00 0.00 2.69
3513 4528 4.100808 AGAGGGAGTACATCTCAATGCTTC 59.899 45.833 11.05 0.00 44.40 3.86
3533 4548 3.039743 TCCTGGGTATAATGGCGTTGTA 58.960 45.455 1.27 0.00 0.00 2.41
3537 4553 4.130857 TGGGTATAATGGCGTTGTATGTG 58.869 43.478 1.27 0.00 0.00 3.21
3541 4557 0.810648 AATGGCGTTGTATGTGGCTG 59.189 50.000 0.00 0.00 0.00 4.85
3543 4559 0.035534 TGGCGTTGTATGTGGCTGAT 60.036 50.000 0.00 0.00 0.00 2.90
3589 4605 6.552629 TGACTAGACTAAATGAACGTAGCTG 58.447 40.000 0.00 0.00 0.00 4.24
3614 4630 6.220726 AGCTGTTCAGTTACAACCAAAAAT 57.779 33.333 1.78 0.00 0.00 1.82
3755 4772 7.337942 GTCTCCTGGAATGAACAGTAAATCATT 59.662 37.037 0.00 0.94 46.15 2.57
4023 5042 1.878953 TTTTCCACCTGAGAGAACGC 58.121 50.000 0.00 0.00 0.00 4.84
4065 5087 3.421844 GCACCTTTGGAGTTTGGACTAT 58.578 45.455 0.00 0.00 35.88 2.12
4114 5137 9.533983 CAATATTACGATGATCATGTTACAAGC 57.466 33.333 14.30 0.00 0.00 4.01
4243 5266 5.356882 TGAATCGTTGTCAAAATCAGTCC 57.643 39.130 0.00 0.00 0.00 3.85
4254 5277 9.485206 TTGTCAAAATCAGTCCTAGTACTAAAC 57.515 33.333 3.76 5.62 0.00 2.01
4256 5279 8.923683 GTCAAAATCAGTCCTAGTACTAAACAC 58.076 37.037 14.37 7.37 0.00 3.32
4262 5285 7.108847 TCAGTCCTAGTACTAAACACTACTCC 58.891 42.308 14.37 0.00 0.00 3.85
4269 5292 3.504375 ACTAAACACTACTCCCTCCGTT 58.496 45.455 0.00 0.00 0.00 4.44
4284 5307 8.314751 ACTCCCTCCGTTTCATAATATAAGATG 58.685 37.037 0.00 0.00 0.00 2.90
4286 5309 7.236847 TCCCTCCGTTTCATAATATAAGATGGT 59.763 37.037 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.911788 ATGACTCTAGACACAAATCCAAATAAT 57.088 29.630 0.00 0.00 0.00 1.28
5 6 9.166173 CATGACTCTAGACACAAATCCAAATAA 57.834 33.333 0.00 0.00 0.00 1.40
6 7 8.321353 ACATGACTCTAGACACAAATCCAAATA 58.679 33.333 0.00 0.00 0.00 1.40
7 8 7.170965 ACATGACTCTAGACACAAATCCAAAT 58.829 34.615 0.00 0.00 0.00 2.32
8 9 6.533730 ACATGACTCTAGACACAAATCCAAA 58.466 36.000 0.00 0.00 0.00 3.28
9 10 6.114187 ACATGACTCTAGACACAAATCCAA 57.886 37.500 0.00 0.00 0.00 3.53
10 11 5.745312 ACATGACTCTAGACACAAATCCA 57.255 39.130 0.00 0.00 0.00 3.41
11 12 7.981789 TCATAACATGACTCTAGACACAAATCC 59.018 37.037 0.00 0.00 33.59 3.01
12 13 8.932945 TCATAACATGACTCTAGACACAAATC 57.067 34.615 0.00 0.00 33.59 2.17
16 17 9.579932 AGATATCATAACATGACTCTAGACACA 57.420 33.333 5.32 0.00 43.01 3.72
20 21 8.951243 CGGAAGATATCATAACATGACTCTAGA 58.049 37.037 5.32 0.00 43.01 2.43
21 22 8.187480 CCGGAAGATATCATAACATGACTCTAG 58.813 40.741 5.32 0.00 43.01 2.43
22 23 7.670140 ACCGGAAGATATCATAACATGACTCTA 59.330 37.037 9.46 0.00 43.01 2.43
23 24 6.495181 ACCGGAAGATATCATAACATGACTCT 59.505 38.462 9.46 0.00 43.01 3.24
24 25 6.587990 CACCGGAAGATATCATAACATGACTC 59.412 42.308 9.46 0.00 43.01 3.36
25 26 6.267699 TCACCGGAAGATATCATAACATGACT 59.732 38.462 9.46 0.00 43.01 3.41
26 27 6.455647 TCACCGGAAGATATCATAACATGAC 58.544 40.000 9.46 0.00 43.01 3.06
27 28 6.267699 ACTCACCGGAAGATATCATAACATGA 59.732 38.462 9.46 0.00 44.55 3.07
28 29 6.459066 ACTCACCGGAAGATATCATAACATG 58.541 40.000 9.46 0.00 0.00 3.21
29 30 6.295349 GGACTCACCGGAAGATATCATAACAT 60.295 42.308 9.46 0.00 0.00 2.71
30 31 5.010719 GGACTCACCGGAAGATATCATAACA 59.989 44.000 9.46 0.00 0.00 2.41
31 32 5.471257 GGACTCACCGGAAGATATCATAAC 58.529 45.833 9.46 0.00 0.00 1.89
32 33 4.527038 GGGACTCACCGGAAGATATCATAA 59.473 45.833 9.46 0.00 40.11 1.90
33 34 4.087182 GGGACTCACCGGAAGATATCATA 58.913 47.826 9.46 0.00 40.11 2.15
34 35 2.900546 GGGACTCACCGGAAGATATCAT 59.099 50.000 9.46 0.00 40.11 2.45
35 36 2.091278 AGGGACTCACCGGAAGATATCA 60.091 50.000 9.46 0.00 40.11 2.15
36 37 2.297597 CAGGGACTCACCGGAAGATATC 59.702 54.545 9.46 6.50 34.60 1.63
37 38 2.091278 TCAGGGACTCACCGGAAGATAT 60.091 50.000 9.46 0.00 34.60 1.63
38 39 1.286849 TCAGGGACTCACCGGAAGATA 59.713 52.381 9.46 0.00 34.60 1.98
39 40 0.041238 TCAGGGACTCACCGGAAGAT 59.959 55.000 9.46 0.00 34.60 2.40
40 41 0.041238 ATCAGGGACTCACCGGAAGA 59.959 55.000 9.46 4.56 38.22 2.87
41 42 0.461961 GATCAGGGACTCACCGGAAG 59.538 60.000 9.46 7.89 38.22 3.46
42 43 0.041238 AGATCAGGGACTCACCGGAA 59.959 55.000 9.46 0.00 38.22 4.30
43 44 0.041238 AAGATCAGGGACTCACCGGA 59.959 55.000 9.46 0.00 39.05 5.14
44 45 0.176680 CAAGATCAGGGACTCACCGG 59.823 60.000 0.00 0.00 34.60 5.28
45 46 1.186200 TCAAGATCAGGGACTCACCG 58.814 55.000 0.00 0.00 34.60 4.94
46 47 2.223923 CGATCAAGATCAGGGACTCACC 60.224 54.545 10.39 0.00 34.60 4.02
47 48 2.428890 ACGATCAAGATCAGGGACTCAC 59.571 50.000 10.39 0.00 34.60 3.51
48 49 2.739943 ACGATCAAGATCAGGGACTCA 58.260 47.619 10.39 0.00 34.60 3.41
49 50 3.632604 TGTACGATCAAGATCAGGGACTC 59.367 47.826 10.39 0.00 34.60 3.36
50 51 3.381908 GTGTACGATCAAGATCAGGGACT 59.618 47.826 10.39 0.00 43.88 3.85
51 52 3.381908 AGTGTACGATCAAGATCAGGGAC 59.618 47.826 10.39 2.84 37.69 4.46
52 53 3.632333 AGTGTACGATCAAGATCAGGGA 58.368 45.455 10.39 0.00 37.69 4.20
53 54 4.392921 AAGTGTACGATCAAGATCAGGG 57.607 45.455 10.39 0.00 37.69 4.45
54 55 5.446473 GCAAAAGTGTACGATCAAGATCAGG 60.446 44.000 10.39 0.00 37.69 3.86
55 56 5.554636 GCAAAAGTGTACGATCAAGATCAG 58.445 41.667 10.39 5.82 37.69 2.90
56 57 4.091365 CGCAAAAGTGTACGATCAAGATCA 59.909 41.667 10.39 0.00 37.69 2.92
57 58 4.091509 ACGCAAAAGTGTACGATCAAGATC 59.908 41.667 0.00 0.00 34.56 2.75
58 59 3.994392 ACGCAAAAGTGTACGATCAAGAT 59.006 39.130 0.00 0.00 0.00 2.40
59 60 3.183574 CACGCAAAAGTGTACGATCAAGA 59.816 43.478 0.00 0.00 37.35 3.02
60 61 3.469629 CACGCAAAAGTGTACGATCAAG 58.530 45.455 0.00 0.00 37.35 3.02
61 62 3.513462 CACGCAAAAGTGTACGATCAA 57.487 42.857 0.00 0.00 37.35 2.57
70 71 5.927030 ACACTAATCATACACGCAAAAGTG 58.073 37.500 0.00 0.00 46.83 3.16
71 72 6.183360 CGTACACTAATCATACACGCAAAAGT 60.183 38.462 0.00 0.00 0.00 2.66
72 73 6.034150 TCGTACACTAATCATACACGCAAAAG 59.966 38.462 0.00 0.00 0.00 2.27
73 74 5.862860 TCGTACACTAATCATACACGCAAAA 59.137 36.000 0.00 0.00 0.00 2.44
74 75 5.400703 TCGTACACTAATCATACACGCAAA 58.599 37.500 0.00 0.00 0.00 3.68
75 76 4.984205 TCGTACACTAATCATACACGCAA 58.016 39.130 0.00 0.00 0.00 4.85
76 77 4.619437 TCGTACACTAATCATACACGCA 57.381 40.909 0.00 0.00 0.00 5.24
77 78 4.381863 CCATCGTACACTAATCATACACGC 59.618 45.833 0.00 0.00 0.00 5.34
78 79 5.754778 TCCATCGTACACTAATCATACACG 58.245 41.667 0.00 0.00 0.00 4.49
79 80 8.228921 GATTCCATCGTACACTAATCATACAC 57.771 38.462 0.00 0.00 0.00 2.90
96 97 2.280865 GACGCCCCCGATTCCATC 60.281 66.667 0.00 0.00 38.29 3.51
97 98 3.087253 TGACGCCCCCGATTCCAT 61.087 61.111 0.00 0.00 38.29 3.41
98 99 4.090588 GTGACGCCCCCGATTCCA 62.091 66.667 0.00 0.00 38.29 3.53
99 100 4.090588 TGTGACGCCCCCGATTCC 62.091 66.667 0.00 0.00 38.29 3.01
100 101 2.511600 CTGTGACGCCCCCGATTC 60.512 66.667 0.00 0.00 38.29 2.52
101 102 3.319198 ACTGTGACGCCCCCGATT 61.319 61.111 0.00 0.00 38.29 3.34
102 103 4.082523 CACTGTGACGCCCCCGAT 62.083 66.667 0.32 0.00 38.29 4.18
104 105 4.619227 AACACTGTGACGCCCCCG 62.619 66.667 15.86 0.00 41.14 5.73
105 106 2.978010 CAACACTGTGACGCCCCC 60.978 66.667 15.86 0.00 0.00 5.40
106 107 1.961277 CTCAACACTGTGACGCCCC 60.961 63.158 15.86 0.00 0.00 5.80
107 108 2.607892 GCTCAACACTGTGACGCCC 61.608 63.158 15.86 0.00 0.00 6.13
108 109 1.230635 ATGCTCAACACTGTGACGCC 61.231 55.000 15.86 0.00 0.00 5.68
109 110 0.110509 CATGCTCAACACTGTGACGC 60.111 55.000 15.86 10.87 0.00 5.19
110 111 1.193203 GACATGCTCAACACTGTGACG 59.807 52.381 15.86 4.86 0.00 4.35
111 112 1.532868 GGACATGCTCAACACTGTGAC 59.467 52.381 15.86 0.00 0.00 3.67
112 113 1.873486 CGGACATGCTCAACACTGTGA 60.873 52.381 15.86 0.00 0.00 3.58
113 114 0.514255 CGGACATGCTCAACACTGTG 59.486 55.000 6.19 6.19 0.00 3.66
114 115 0.106708 ACGGACATGCTCAACACTGT 59.893 50.000 0.00 0.00 0.00 3.55
115 116 0.514255 CACGGACATGCTCAACACTG 59.486 55.000 0.00 0.00 0.00 3.66
116 117 0.106708 ACACGGACATGCTCAACACT 59.893 50.000 0.00 0.00 0.00 3.55
142 143 2.427095 AGCACCAAAAGAAGTGGACAAC 59.573 45.455 0.00 0.00 39.62 3.32
161 162 3.818787 CGCATGCAGGGGTCAAGC 61.819 66.667 19.57 0.00 0.00 4.01
180 182 5.041951 TCAAAATGAAATCGGTTTCCTCG 57.958 39.130 18.18 3.22 42.44 4.63
197 199 3.699038 CCACTGTCCAGAAGGTTTCAAAA 59.301 43.478 0.40 0.00 35.89 2.44
200 202 1.843851 ACCACTGTCCAGAAGGTTTCA 59.156 47.619 0.40 0.00 37.17 2.69
201 203 2.222027 CACCACTGTCCAGAAGGTTTC 58.778 52.381 11.57 0.00 37.93 2.78
211 213 1.003233 GAAGCCTCCACCACTGTCC 60.003 63.158 0.00 0.00 0.00 4.02
221 223 1.376037 CCACGTTCTGGAAGCCTCC 60.376 63.158 0.00 0.00 43.95 4.30
235 237 2.352229 CACGCTTTGTGCACCACG 60.352 61.111 15.69 14.63 42.70 4.94
244 246 1.536766 TGCTCTTCATTCCACGCTTTG 59.463 47.619 0.00 0.00 0.00 2.77
245 247 1.896220 TGCTCTTCATTCCACGCTTT 58.104 45.000 0.00 0.00 0.00 3.51
248 250 0.874390 TGTTGCTCTTCATTCCACGC 59.126 50.000 0.00 0.00 0.00 5.34
249 251 3.624326 TTTGTTGCTCTTCATTCCACG 57.376 42.857 0.00 0.00 0.00 4.94
259 261 1.070601 GGGTTGGCAATTTGTTGCTCT 59.929 47.619 1.92 0.00 46.56 4.09
260 262 1.511850 GGGTTGGCAATTTGTTGCTC 58.488 50.000 1.92 4.41 46.56 4.26
265 267 2.637382 CCTAAAGGGGTTGGCAATTTGT 59.363 45.455 1.92 0.00 0.00 2.83
267 269 1.628340 GCCTAAAGGGGTTGGCAATTT 59.372 47.619 1.92 2.29 44.34 1.82
283 285 1.763968 ACTCACATGCTAGACGCCTA 58.236 50.000 0.00 0.00 38.05 3.93
285 287 2.579207 TAACTCACATGCTAGACGCC 57.421 50.000 0.00 0.00 38.05 5.68
296 298 2.289547 GAGCGGTGCTTTTTAACTCACA 59.710 45.455 0.00 0.00 39.88 3.58
297 299 2.661979 CGAGCGGTGCTTTTTAACTCAC 60.662 50.000 0.00 0.00 39.88 3.51
309 311 3.554692 CCAATCGTCGAGCGGTGC 61.555 66.667 0.00 0.00 41.72 5.01
391 394 1.338107 TGGTGATGTCCAGACGAAGT 58.662 50.000 0.00 0.00 36.33 3.01
478 490 5.921976 GCATGTGAGAATTGACAATGAACAA 59.078 36.000 0.34 0.00 0.00 2.83
479 491 5.463286 GCATGTGAGAATTGACAATGAACA 58.537 37.500 0.34 4.94 0.00 3.18
482 494 4.080687 TGGCATGTGAGAATTGACAATGA 58.919 39.130 0.34 0.00 0.00 2.57
509 521 1.990160 TTGGTCTTGCCGTCTTGGGT 61.990 55.000 0.00 0.00 41.21 4.51
521 533 1.303091 GCGGCACCGTAATTGGTCTT 61.303 55.000 11.27 0.00 41.38 3.01
538 551 4.804108 TGAAATGGGTTTTTACATCTGCG 58.196 39.130 0.00 0.00 0.00 5.18
541 554 8.472413 CATCTGATGAAATGGGTTTTTACATCT 58.528 33.333 12.27 0.00 35.30 2.90
551 564 3.744940 ACCACATCTGATGAAATGGGT 57.255 42.857 23.59 17.14 36.27 4.51
558 571 4.877823 GTGCAGAATAACCACATCTGATGA 59.122 41.667 23.59 1.52 42.48 2.92
571 584 0.991146 TGAGCCTGGGTGCAGAATAA 59.009 50.000 1.59 0.00 0.00 1.40
578 591 1.153208 CTCATCTGAGCCTGGGTGC 60.153 63.158 1.59 0.00 35.13 5.01
635 651 3.391965 GCATCTTGCACCAACAAAATCA 58.608 40.909 0.00 0.00 44.26 2.57
670 704 7.080353 AGACTTAACCAAACTTTGTACACAC 57.920 36.000 0.00 0.00 0.00 3.82
671 705 8.259411 TCTAGACTTAACCAAACTTTGTACACA 58.741 33.333 0.00 0.00 0.00 3.72
672 706 8.652810 TCTAGACTTAACCAAACTTTGTACAC 57.347 34.615 0.00 0.00 0.00 2.90
681 723 6.752815 CCTCGAAGATCTAGACTTAACCAAAC 59.247 42.308 0.00 0.00 33.89 2.93
688 730 5.298989 AGCTCCTCGAAGATCTAGACTTA 57.701 43.478 0.00 0.00 33.89 2.24
760 803 6.850752 AAAGGATAAAATCGGGTGTGAATT 57.149 33.333 0.00 0.00 0.00 2.17
764 807 5.778862 ACAAAAAGGATAAAATCGGGTGTG 58.221 37.500 0.00 0.00 0.00 3.82
765 808 5.536916 TGACAAAAAGGATAAAATCGGGTGT 59.463 36.000 0.00 0.00 0.00 4.16
766 809 5.861787 GTGACAAAAAGGATAAAATCGGGTG 59.138 40.000 0.00 0.00 0.00 4.61
767 810 5.335348 CGTGACAAAAAGGATAAAATCGGGT 60.335 40.000 0.00 0.00 0.00 5.28
768 811 5.092781 CGTGACAAAAAGGATAAAATCGGG 58.907 41.667 0.00 0.00 0.00 5.14
770 813 5.508224 GCTCGTGACAAAAAGGATAAAATCG 59.492 40.000 0.00 0.00 0.00 3.34
772 815 6.575162 AGCTCGTGACAAAAAGGATAAAAT 57.425 33.333 0.00 0.00 0.00 1.82
773 816 6.262273 AGAAGCTCGTGACAAAAAGGATAAAA 59.738 34.615 0.00 0.00 0.00 1.52
774 817 5.763204 AGAAGCTCGTGACAAAAAGGATAAA 59.237 36.000 0.00 0.00 0.00 1.40
775 818 5.305585 AGAAGCTCGTGACAAAAAGGATAA 58.694 37.500 0.00 0.00 0.00 1.75
777 820 3.744660 AGAAGCTCGTGACAAAAAGGAT 58.255 40.909 0.00 0.00 0.00 3.24
830 876 3.322828 AGTTGCTCAAATGCCTGATGTTT 59.677 39.130 0.00 0.00 0.00 2.83
833 879 3.250744 CAAGTTGCTCAAATGCCTGATG 58.749 45.455 0.00 0.00 0.00 3.07
838 884 1.997606 GATGCAAGTTGCTCAAATGCC 59.002 47.619 27.17 5.29 45.31 4.40
839 885 2.410730 GTGATGCAAGTTGCTCAAATGC 59.589 45.455 27.17 12.58 45.31 3.56
887 933 9.667107 CCCTGTGAACAGTAGATTATTAGAAAA 57.333 33.333 9.49 0.00 42.27 2.29
888 934 8.822805 ACCCTGTGAACAGTAGATTATTAGAAA 58.177 33.333 9.49 0.00 42.27 2.52
889 935 8.258007 CACCCTGTGAACAGTAGATTATTAGAA 58.742 37.037 9.49 0.00 42.27 2.10
890 936 7.399191 ACACCCTGTGAACAGTAGATTATTAGA 59.601 37.037 9.49 0.00 42.27 2.10
891 937 7.556844 ACACCCTGTGAACAGTAGATTATTAG 58.443 38.462 9.49 0.00 42.27 1.73
892 938 7.490657 ACACCCTGTGAACAGTAGATTATTA 57.509 36.000 9.49 0.00 42.27 0.98
893 939 6.374417 ACACCCTGTGAACAGTAGATTATT 57.626 37.500 9.49 0.00 42.27 1.40
894 940 6.173339 CAACACCCTGTGAACAGTAGATTAT 58.827 40.000 9.49 0.00 42.27 1.28
895 941 5.071250 ACAACACCCTGTGAACAGTAGATTA 59.929 40.000 9.49 0.00 42.27 1.75
896 942 4.141482 ACAACACCCTGTGAACAGTAGATT 60.141 41.667 9.49 0.00 42.27 2.40
897 943 3.391296 ACAACACCCTGTGAACAGTAGAT 59.609 43.478 9.49 0.00 42.27 1.98
901 947 2.420967 GGTACAACACCCTGTGAACAGT 60.421 50.000 9.49 0.00 42.07 3.55
952 1085 7.414098 CGGTGAAGGGATTATTAGTTTTCAGTG 60.414 40.741 0.00 0.00 0.00 3.66
985 1118 0.997196 GACATTGCCGGAGTTACGAC 59.003 55.000 5.05 0.00 35.47 4.34
987 1120 0.999406 CAGACATTGCCGGAGTTACG 59.001 55.000 5.05 0.00 0.00 3.18
998 1131 0.371301 CGACGGTGATGCAGACATTG 59.629 55.000 0.00 0.00 36.35 2.82
1260 1402 2.455557 TCGATAACACCGGGGTAGAAA 58.544 47.619 11.42 0.00 0.00 2.52
1281 1423 0.460109 CAATGACGTCCAGATCGCCA 60.460 55.000 14.12 0.00 0.00 5.69
1283 1425 1.083806 TGCAATGACGTCCAGATCGC 61.084 55.000 14.12 7.73 0.00 4.58
1380 1522 3.613563 CGAATTAACGCACACAAACAGT 58.386 40.909 0.00 0.00 0.00 3.55
1395 1537 4.439305 AGCTTTCTGCATTTGCGAATTA 57.561 36.364 0.00 0.00 45.94 1.40
1441 1586 7.703058 AAGAAACCCAATAAATCACGAATCT 57.297 32.000 0.00 0.00 0.00 2.40
1541 1695 4.840772 CACGTGTTTCTGATTGAACGATTC 59.159 41.667 7.58 0.00 33.88 2.52
1555 1709 9.015577 TCATTAAATTTCTTGTTCACGTGTTTC 57.984 29.630 16.51 7.83 0.00 2.78
1620 1775 3.054655 GCTGTCTGGGTTATTTGGTAGGA 60.055 47.826 0.00 0.00 0.00 2.94
1692 1847 2.270352 ACGACCTTCCAGAAATTGCA 57.730 45.000 0.00 0.00 0.00 4.08
1693 1848 3.643159 AAACGACCTTCCAGAAATTGC 57.357 42.857 0.00 0.00 0.00 3.56
1717 2720 2.750948 CCAGCGTAATATAACCTGCGT 58.249 47.619 0.00 0.00 0.00 5.24
1744 2747 4.219725 AGAGTTGAGTTCTCTGGTCTAAGC 59.780 45.833 1.53 0.00 40.26 3.09
1762 2765 6.042208 GGGCTACAAATATCTCCACTAGAGTT 59.958 42.308 0.00 0.00 43.71 3.01
1771 2774 4.439253 AACCAGGGCTACAAATATCTCC 57.561 45.455 0.00 0.00 0.00 3.71
1837 2840 6.974622 GCATGTTCTATAAACACAATTGAGGG 59.025 38.462 13.59 3.76 32.37 4.30
1888 2891 5.185249 TCTCGGAGCTGTAAAAGAAGTACAT 59.815 40.000 0.00 0.00 31.27 2.29
1916 2919 5.804979 CCACAACAAAGTACCAAACAGAAAG 59.195 40.000 0.00 0.00 0.00 2.62
1917 2920 5.244178 ACCACAACAAAGTACCAAACAGAAA 59.756 36.000 0.00 0.00 0.00 2.52
1946 2949 5.937975 CCCAAATTGAACTGATGGGTTAT 57.062 39.130 0.00 0.00 44.67 1.89
1969 2972 7.151308 ACACTCAAAATTCTCTAGTCAGACTG 58.849 38.462 13.84 3.68 0.00 3.51
2123 3135 4.323868 CCGAAAACTCGTAACTTCTAGCAG 59.676 45.833 0.00 0.00 0.00 4.24
2195 3207 2.988688 GCGCCCGAAGCCAAAATGA 61.989 57.895 0.00 0.00 38.78 2.57
2223 3235 0.042188 CACAAGTTTCAGTCCGTGCG 60.042 55.000 0.00 0.00 0.00 5.34
2273 3285 7.776618 TGAAGTCTCCATAAACTCTAAGTGA 57.223 36.000 0.00 0.00 0.00 3.41
2286 3298 5.430089 GCCCCCTATTATATGAAGTCTCCAT 59.570 44.000 0.00 0.00 0.00 3.41
2295 3307 3.881871 ACTGGTGCCCCCTATTATATGA 58.118 45.455 0.00 0.00 0.00 2.15
2296 3308 4.657814 AACTGGTGCCCCCTATTATATG 57.342 45.455 0.00 0.00 0.00 1.78
2306 3318 2.689983 CAAATCAGATAACTGGTGCCCC 59.310 50.000 0.00 0.00 43.60 5.80
2510 3522 2.540265 ACTGTCTCAACTTCTGGCAG 57.460 50.000 8.58 8.58 0.00 4.85
2750 3762 5.646793 CAGTTTCAATGACACCAGAGATGAT 59.353 40.000 0.00 0.00 0.00 2.45
3305 4317 4.465886 ACAGCTCTATCGGAGTTCATAGT 58.534 43.478 0.00 0.00 43.62 2.12
3429 4444 4.264543 ACATGCAATTCGATCGAAGAAC 57.735 40.909 31.66 23.03 43.58 3.01
3513 4528 2.341846 ACAACGCCATTATACCCAGG 57.658 50.000 0.00 0.00 0.00 4.45
3533 4548 5.472148 CACATTTACAACAATCAGCCACAT 58.528 37.500 0.00 0.00 0.00 3.21
3537 4553 3.253230 GCCACATTTACAACAATCAGCC 58.747 45.455 0.00 0.00 0.00 4.85
3541 4557 6.595772 TTTTGTGCCACATTTACAACAATC 57.404 33.333 0.00 0.00 34.38 2.67
3543 4559 6.036517 GTCATTTTGTGCCACATTTACAACAA 59.963 34.615 0.00 0.00 34.38 2.83
3589 4605 4.893424 TTGGTTGTAACTGAACAGCTTC 57.107 40.909 1.46 0.00 31.87 3.86
3600 4616 6.610741 TTTGGATGCATTTTTGGTTGTAAC 57.389 33.333 0.00 0.00 0.00 2.50
3651 4668 8.573035 TCACCTATTTTGTAGTGCTTTTTAAGG 58.427 33.333 0.00 0.00 0.00 2.69
3720 4737 6.213397 TGTTCATTCCAGGAGACATTTCTCTA 59.787 38.462 8.72 0.00 46.80 2.43
3843 4861 0.886563 GCATTGAAGCTGCCAAGAGT 59.113 50.000 0.00 0.00 33.44 3.24
4082 5105 7.787084 ACATGATCATCGTAATATTGTGAACG 58.213 34.615 4.86 0.00 36.71 3.95
4096 5119 3.551485 TGTCGCTTGTAACATGATCATCG 59.449 43.478 4.86 4.04 0.00 3.84
4114 5137 3.611517 CTTGAAGTTTGAGCAAGTGTCG 58.388 45.455 0.00 0.00 35.49 4.35
4231 5254 8.867097 AGTGTTTAGTACTAGGACTGATTTTGA 58.133 33.333 18.50 0.00 0.00 2.69
4243 5266 5.526846 CGGAGGGAGTAGTGTTTAGTACTAG 59.473 48.000 2.23 0.00 41.89 2.57
4254 5277 4.730949 TTATGAAACGGAGGGAGTAGTG 57.269 45.455 0.00 0.00 0.00 2.74
4256 5279 9.021807 TCTTATATTATGAAACGGAGGGAGTAG 57.978 37.037 0.00 0.00 0.00 2.57
4262 5285 8.848474 AACCATCTTATATTATGAAACGGAGG 57.152 34.615 0.00 0.00 0.00 4.30


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.