Multiple sequence alignment - TraesCS6D01G140500

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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 TraesCS6D01G140500 chr6D 100.000 4947 0 0 1 4947 110152618 110157564 0.000000e+00 9136.0
1 TraesCS6D01G140500 chr6D 82.573 241 28 4 465 705 109590077 109589851 3.020000e-47 200.0
2 TraesCS6D01G140500 chr6D 91.045 67 4 2 4879 4944 147877711 147877646 6.820000e-14 89.8
3 TraesCS6D01G140500 chr6A 96.648 3640 77 21 753 4366 134544314 134547934 0.000000e+00 6004.0
4 TraesCS6D01G140500 chr6A 92.929 198 13 1 4750 4947 134548009 134548205 2.250000e-73 287.0
5 TraesCS6D01G140500 chr6A 88.060 67 7 1 4879 4944 199815526 199815592 1.480000e-10 78.7
6 TraesCS6D01G140500 chr6B 94.088 3569 154 20 775 4311 198914639 198918182 0.000000e+00 5369.0
7 TraesCS6D01G140500 chr6B 92.436 661 35 11 1 648 198912820 198913478 0.000000e+00 929.0
8 TraesCS6D01G140500 chr6B 94.444 90 5 0 4370 4459 654053510 654053421 6.680000e-29 139.0
9 TraesCS6D01G140500 chr1B 82.700 711 109 9 3 703 447549954 447549248 1.960000e-173 619.0
10 TraesCS6D01G140500 chr1B 79.084 502 69 24 214 704 34257730 34257254 3.720000e-81 313.0
11 TraesCS6D01G140500 chr1B 88.128 219 16 6 4522 4733 250417539 250417324 8.220000e-63 252.0
12 TraesCS6D01G140500 chr4D 83.710 620 86 12 1 611 425098168 425098781 5.560000e-159 571.0
13 TraesCS6D01G140500 chr4D 88.837 215 16 4 4522 4728 98888365 98888151 1.770000e-64 257.0
14 TraesCS6D01G140500 chr4D 87.615 218 19 4 4528 4738 298773296 298773080 3.820000e-61 246.0
15 TraesCS6D01G140500 chr4D 82.727 110 11 7 4839 4944 43651268 43651163 1.900000e-14 91.6
16 TraesCS6D01G140500 chr7D 81.402 699 110 16 17 704 600060005 600059316 2.010000e-153 553.0
17 TraesCS6D01G140500 chr7D 80.892 157 13 7 4620 4759 575918740 575918896 1.880000e-19 108.0
18 TraesCS6D01G140500 chr5D 88.075 478 41 9 1 465 542031416 542030942 2.010000e-153 553.0
19 TraesCS6D01G140500 chr5D 85.477 241 26 4 4522 4753 191705375 191705615 4.950000e-60 243.0
20 TraesCS6D01G140500 chr3D 81.047 707 109 14 2 703 577391554 577392240 1.570000e-149 540.0
21 TraesCS6D01G140500 chr3D 80.959 688 112 15 2 679 550435081 550434403 1.220000e-145 527.0
22 TraesCS6D01G140500 chr3D 88.182 110 8 4 4347 4455 81200902 81201007 5.200000e-25 126.0
23 TraesCS6D01G140500 chr1D 80.532 714 107 23 2 708 10922710 10922022 2.040000e-143 520.0
24 TraesCS6D01G140500 chr1D 88.546 227 15 4 4522 4741 156126714 156126492 1.060000e-66 265.0
25 TraesCS6D01G140500 chr1D 91.860 86 5 2 4860 4944 344593813 344593897 8.700000e-23 119.0
26 TraesCS6D01G140500 chr7B 79.184 711 118 20 2 704 516868474 516867786 2.700000e-127 466.0
27 TraesCS6D01G140500 chr7B 96.471 85 3 0 4374 4458 405051401 405051317 1.860000e-29 141.0
28 TraesCS6D01G140500 chr1A 89.041 219 13 5 4522 4733 171462477 171462691 1.370000e-65 261.0
29 TraesCS6D01G140500 chr1A 81.452 248 26 12 4532 4760 557965967 557966213 8.460000e-43 185.0
30 TraesCS6D01G140500 chr1A 89.381 113 12 0 4354 4466 12556281 12556169 5.160000e-30 143.0
31 TraesCS6D01G140500 chr1A 90.196 102 8 1 4370 4469 30338592 30338693 1.120000e-26 132.0
32 TraesCS6D01G140500 chr3A 88.372 215 19 5 4524 4733 83218616 83218829 2.290000e-63 254.0
33 TraesCS6D01G140500 chr3A 94.595 37 2 0 4726 4762 693444501 693444537 1.920000e-04 58.4
34 TraesCS6D01G140500 chr4B 87.558 217 17 5 4522 4728 140706893 140706677 4.950000e-60 243.0
35 TraesCS6D01G140500 chr4B 94.505 91 4 1 4370 4459 192792831 192792741 6.680000e-29 139.0
36 TraesCS6D01G140500 chr4B 78.182 110 22 2 4836 4944 464159009 464159117 8.890000e-08 69.4
37 TraesCS6D01G140500 chr4B 92.857 42 3 0 4719 4760 628306823 628306864 1.490000e-05 62.1
38 TraesCS6D01G140500 chr3B 86.758 219 21 4 4528 4738 154190568 154190350 2.300000e-58 237.0
39 TraesCS6D01G140500 chrUn 81.061 264 41 7 391 649 43398230 43398489 8.400000e-48 202.0
40 TraesCS6D01G140500 chr4A 81.148 244 26 11 4537 4760 593338332 593338575 1.420000e-40 178.0
41 TraesCS6D01G140500 chr4A 96.512 86 3 0 4370 4455 603447671 603447586 5.160000e-30 143.0
42 TraesCS6D01G140500 chr4A 79.545 132 11 7 4645 4760 472195725 472195594 4.110000e-11 80.5
43 TraesCS6D01G140500 chr2A 79.920 249 28 11 4532 4759 600526373 600526620 3.960000e-36 163.0
44 TraesCS6D01G140500 chr2A 93.137 102 3 4 4364 4463 73546208 73546109 3.990000e-31 147.0
45 TraesCS6D01G140500 chr2A 96.552 87 3 0 4370 4456 473417588 473417502 1.440000e-30 145.0
46 TraesCS6D01G140500 chr2A 80.255 157 12 11 4628 4766 203459641 203459486 3.150000e-17 100.0
47 TraesCS6D01G140500 chr5A 85.981 107 12 3 4839 4944 609244650 609244546 1.460000e-20 111.0


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 TraesCS6D01G140500 chr6D 110152618 110157564 4946 False 9136.0 9136 100.0000 1 4947 1 chr6D.!!$F1 4946
1 TraesCS6D01G140500 chr6A 134544314 134548205 3891 False 3145.5 6004 94.7885 753 4947 2 chr6A.!!$F2 4194
2 TraesCS6D01G140500 chr6B 198912820 198918182 5362 False 3149.0 5369 93.2620 1 4311 2 chr6B.!!$F1 4310
3 TraesCS6D01G140500 chr1B 447549248 447549954 706 True 619.0 619 82.7000 3 703 1 chr1B.!!$R3 700
4 TraesCS6D01G140500 chr4D 425098168 425098781 613 False 571.0 571 83.7100 1 611 1 chr4D.!!$F1 610
5 TraesCS6D01G140500 chr7D 600059316 600060005 689 True 553.0 553 81.4020 17 704 1 chr7D.!!$R1 687
6 TraesCS6D01G140500 chr3D 577391554 577392240 686 False 540.0 540 81.0470 2 703 1 chr3D.!!$F2 701
7 TraesCS6D01G140500 chr3D 550434403 550435081 678 True 527.0 527 80.9590 2 679 1 chr3D.!!$R1 677
8 TraesCS6D01G140500 chr1D 10922022 10922710 688 True 520.0 520 80.5320 2 708 1 chr1D.!!$R1 706
9 TraesCS6D01G140500 chr7B 516867786 516868474 688 True 466.0 466 79.1840 2 704 1 chr7B.!!$R2 702

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
790 814 0.036952 CTTGGATCTGACGTGGTGCT 60.037 55.000 0.0 0.0 0.00 4.40 F
1133 2233 1.379044 CCTCCAAAGCCGCCAGATT 60.379 57.895 0.0 0.0 0.00 2.40 F
2962 4068 0.880278 TTGTGGCTTCTGCTCGTCAC 60.880 55.000 0.0 0.0 39.59 3.67 F
3763 4890 0.179234 TGAAGAACAGCCACCACGAA 59.821 50.000 0.0 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 3251 0.741927 CAGACGCATCCATCTGTGCA 60.742 55.000 0.00 0.00 41.32 4.57 R
2439 3545 2.084610 ACGTCACATCCACATGAGTG 57.915 50.000 0.00 0.29 45.47 3.51 R
3904 5031 0.178861 AGGAGGTGACCTTCATGGGT 60.179 55.000 13.44 0.00 43.07 4.51 R
4733 5872 1.284785 TGGCCTCCTTTGGTTCATAGG 59.715 52.381 3.32 0.00 34.61 2.57 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
32 33 7.932491 TGTACACTTTAACACCTAATTGCACTA 59.068 33.333 0.00 0.00 0.00 2.74
37 38 7.822822 ACTTTAACACCTAATTGCACTACTAGG 59.177 37.037 7.66 7.66 37.52 3.02
182 183 0.674581 CGTGCACTCCATGGTCACAT 60.675 55.000 16.19 0.00 37.99 3.21
324 326 0.602106 AGACGACGAGGACGAGTCAA 60.602 55.000 0.00 0.00 44.89 3.18
420 438 2.358247 GCGCGAGAGGGGAACAAA 60.358 61.111 12.10 0.00 45.27 2.83
426 444 0.974383 GAGAGGGGAACAAACGGAGA 59.026 55.000 0.00 0.00 0.00 3.71
539 561 2.589442 GCCACGTGGTTCCGACAA 60.589 61.111 33.92 0.00 37.57 3.18
540 562 2.181521 GCCACGTGGTTCCGACAAA 61.182 57.895 33.92 0.00 37.57 2.83
565 587 3.531538 GGTCGATATGTCAGCTTTCCAA 58.468 45.455 0.00 0.00 0.00 3.53
632 654 8.522830 CACTTACCACATAAATGATGGTCTTTT 58.477 33.333 15.76 0.00 40.30 2.27
651 673 7.357303 GTCTTTTGTTACTTTCGGCAAAGATA 58.643 34.615 13.77 3.55 41.60 1.98
652 674 7.858879 GTCTTTTGTTACTTTCGGCAAAGATAA 59.141 33.333 13.77 7.73 41.60 1.75
654 676 9.834628 CTTTTGTTACTTTCGGCAAAGATAATA 57.165 29.630 13.77 6.71 41.60 0.98
668 690 7.338449 GGCAAAGATAATAGTTTTGGAGTACCA 59.662 37.037 0.00 0.00 45.34 3.25
680 702 6.489127 TTTGGAGTACCATAATCACAAACG 57.511 37.500 0.00 0.00 46.34 3.60
685 707 6.982141 GGAGTACCATAATCACAAACGTGATA 59.018 38.462 8.41 0.00 43.00 2.15
719 742 2.489938 ACTCCCTCAAGCGCATTTTA 57.510 45.000 11.47 0.00 0.00 1.52
727 750 1.641123 AAGCGCATTTTACCGGTCGG 61.641 55.000 12.40 7.97 42.03 4.79
731 754 1.988834 GCATTTTACCGGTCGGCCAG 61.989 60.000 12.40 0.00 39.32 4.85
755 778 3.056536 TGCGGGATCTATGCTCTCATTAC 60.057 47.826 0.00 0.00 34.22 1.89
790 814 0.036952 CTTGGATCTGACGTGGTGCT 60.037 55.000 0.00 0.00 0.00 4.40
939 2033 5.186603 GCTCCTCTCCCAAATTTCAAATTCT 59.813 40.000 0.00 0.00 0.00 2.40
1132 2232 2.273449 CCTCCAAAGCCGCCAGAT 59.727 61.111 0.00 0.00 0.00 2.90
1133 2233 1.379044 CCTCCAAAGCCGCCAGATT 60.379 57.895 0.00 0.00 0.00 2.40
2960 4066 0.944386 TTTTGTGGCTTCTGCTCGTC 59.056 50.000 0.00 0.00 39.59 4.20
2962 4068 0.880278 TTGTGGCTTCTGCTCGTCAC 60.880 55.000 0.00 0.00 39.59 3.67
2963 4069 1.005630 GTGGCTTCTGCTCGTCACT 60.006 57.895 0.00 0.00 39.59 3.41
3150 4257 7.405292 TCTTGAGTCATATCACCTCCATTTTT 58.595 34.615 0.00 0.00 0.00 1.94
3152 4259 5.887598 TGAGTCATATCACCTCCATTTTTGG 59.112 40.000 0.00 0.00 0.00 3.28
3404 4530 3.026694 GGTTAGGAAATCTGGCTGCATT 58.973 45.455 0.50 0.00 0.00 3.56
3470 4596 6.095860 TGAGCTTCATTATCTTTGTTGATGGG 59.904 38.462 0.00 0.00 0.00 4.00
3494 4620 3.138884 TGGTTGACTCTGCTGCATTTA 57.861 42.857 1.31 0.00 0.00 1.40
3574 4700 2.766263 TCACAATAGCCTGAACGATCCT 59.234 45.455 0.00 0.00 0.00 3.24
3579 4705 4.762289 ATAGCCTGAACGATCCTCTTTT 57.238 40.909 0.00 0.00 0.00 2.27
3619 4746 1.677576 CCTGCACTGAACAATGTGTGT 59.322 47.619 4.62 0.00 44.64 3.72
3620 4747 2.542205 CCTGCACTGAACAATGTGTGTG 60.542 50.000 4.62 6.72 40.60 3.82
3662 4789 6.150641 TCAAGCACTCAATCTAGTAACTACGT 59.849 38.462 0.00 0.00 0.00 3.57
3763 4890 0.179234 TGAAGAACAGCCACCACGAA 59.821 50.000 0.00 0.00 0.00 3.85
3775 4902 3.009723 CCACCACGAATGCTACAAGAAT 58.990 45.455 0.00 0.00 0.00 2.40
4154 5286 7.558161 TGATTTGTACTGGCTAGATTGATTG 57.442 36.000 3.17 0.00 0.00 2.67
4318 5457 7.485810 CAATCTCCACAAAATCATAGATTGCA 58.514 34.615 9.23 0.00 41.70 4.08
4328 5467 5.686159 ATCATAGATTGCAGCTGCTTTAC 57.314 39.130 36.61 24.08 42.66 2.01
4344 5483 6.233905 TGCTTTACAGTATCTAAGCATGGA 57.766 37.500 12.35 0.00 45.63 3.41
4349 5488 8.856153 TTTACAGTATCTAAGCATGGACAAAA 57.144 30.769 0.00 0.00 0.00 2.44
4362 5501 7.163441 AGCATGGACAAAATTTGCTCTTTAAT 58.837 30.769 5.52 0.00 39.32 1.40
4374 5513 9.946165 AATTTGCTCTTTAATTAATACTACGCC 57.054 29.630 0.00 0.00 0.00 5.68
4375 5514 7.486802 TTGCTCTTTAATTAATACTACGCCC 57.513 36.000 0.00 0.00 0.00 6.13
4376 5515 6.823497 TGCTCTTTAATTAATACTACGCCCT 58.177 36.000 0.00 0.00 0.00 5.19
4377 5516 6.927381 TGCTCTTTAATTAATACTACGCCCTC 59.073 38.462 0.00 0.00 0.00 4.30
4378 5517 7.153315 GCTCTTTAATTAATACTACGCCCTCT 58.847 38.462 0.00 0.00 0.00 3.69
4379 5518 7.116519 GCTCTTTAATTAATACTACGCCCTCTG 59.883 40.741 0.00 0.00 0.00 3.35
4380 5519 8.015185 TCTTTAATTAATACTACGCCCTCTGT 57.985 34.615 0.00 0.00 0.00 3.41
4381 5520 9.135189 TCTTTAATTAATACTACGCCCTCTGTA 57.865 33.333 0.00 0.00 0.00 2.74
4382 5521 9.754382 CTTTAATTAATACTACGCCCTCTGTAA 57.246 33.333 0.00 0.00 0.00 2.41
4384 5523 9.533253 TTAATTAATACTACGCCCTCTGTAAAC 57.467 33.333 0.00 0.00 0.00 2.01
4385 5524 6.528537 TTAATACTACGCCCTCTGTAAACA 57.471 37.500 0.00 0.00 0.00 2.83
4386 5525 5.410355 AATACTACGCCCTCTGTAAACAA 57.590 39.130 0.00 0.00 0.00 2.83
4387 5526 3.756933 ACTACGCCCTCTGTAAACAAA 57.243 42.857 0.00 0.00 0.00 2.83
4388 5527 4.281898 ACTACGCCCTCTGTAAACAAAT 57.718 40.909 0.00 0.00 0.00 2.32
4389 5528 5.410355 ACTACGCCCTCTGTAAACAAATA 57.590 39.130 0.00 0.00 0.00 1.40
4390 5529 5.985911 ACTACGCCCTCTGTAAACAAATAT 58.014 37.500 0.00 0.00 0.00 1.28
4391 5530 7.116075 ACTACGCCCTCTGTAAACAAATATA 57.884 36.000 0.00 0.00 0.00 0.86
4392 5531 7.558604 ACTACGCCCTCTGTAAACAAATATAA 58.441 34.615 0.00 0.00 0.00 0.98
4393 5532 6.920569 ACGCCCTCTGTAAACAAATATAAG 57.079 37.500 0.00 0.00 0.00 1.73
4394 5533 6.646267 ACGCCCTCTGTAAACAAATATAAGA 58.354 36.000 0.00 0.00 0.00 2.10
4395 5534 6.761714 ACGCCCTCTGTAAACAAATATAAGAG 59.238 38.462 0.00 0.00 0.00 2.85
4396 5535 6.761714 CGCCCTCTGTAAACAAATATAAGAGT 59.238 38.462 0.00 0.00 0.00 3.24
4397 5536 7.254455 CGCCCTCTGTAAACAAATATAAGAGTG 60.254 40.741 0.00 0.00 0.00 3.51
4398 5537 7.553044 GCCCTCTGTAAACAAATATAAGAGTGT 59.447 37.037 0.00 0.00 0.00 3.55
4399 5538 9.449719 CCCTCTGTAAACAAATATAAGAGTGTT 57.550 33.333 0.00 0.00 35.77 3.32
4449 5588 8.361592 ACGTTCTTATATTTCTTTACGGATGG 57.638 34.615 0.00 0.00 32.54 3.51
4450 5589 8.199449 ACGTTCTTATATTTCTTTACGGATGGA 58.801 33.333 0.00 0.00 32.54 3.41
4451 5590 8.700644 CGTTCTTATATTTCTTTACGGATGGAG 58.299 37.037 0.00 0.00 0.00 3.86
4463 5602 6.548441 TTACGGATGGAGTACTTGTTTTTG 57.452 37.500 0.00 0.00 0.00 2.44
4520 5659 3.753787 AAGGCCTCCTTTGGTTCAG 57.246 52.632 5.23 0.00 41.69 3.02
4521 5660 1.149101 AAGGCCTCCTTTGGTTCAGA 58.851 50.000 5.23 0.00 41.69 3.27
4522 5661 0.695347 AGGCCTCCTTTGGTTCAGAG 59.305 55.000 0.00 0.00 0.00 3.35
4523 5662 4.221299 AAGGCCTCCTTTGGTTCAGAGG 62.221 54.545 5.23 0.43 41.69 3.69
4524 5663 0.322906 GCCTCCTTTGGTTCAGAGGG 60.323 60.000 7.01 0.00 45.08 4.30
4525 5664 1.362224 CCTCCTTTGGTTCAGAGGGA 58.638 55.000 4.92 0.00 41.90 4.20
4526 5665 1.918957 CCTCCTTTGGTTCAGAGGGAT 59.081 52.381 4.92 0.00 41.90 3.85
4527 5666 2.310052 CCTCCTTTGGTTCAGAGGGATT 59.690 50.000 4.92 0.00 41.90 3.01
4528 5667 3.245407 CCTCCTTTGGTTCAGAGGGATTT 60.245 47.826 4.92 0.00 41.90 2.17
4529 5668 4.411013 CTCCTTTGGTTCAGAGGGATTTT 58.589 43.478 4.92 0.00 36.53 1.82
4530 5669 4.151883 TCCTTTGGTTCAGAGGGATTTTG 58.848 43.478 4.92 0.00 36.53 2.44
4531 5670 3.897505 CCTTTGGTTCAGAGGGATTTTGT 59.102 43.478 0.00 0.00 32.83 2.83
4532 5671 5.076873 CCTTTGGTTCAGAGGGATTTTGTA 58.923 41.667 0.00 0.00 32.83 2.41
4533 5672 5.183904 CCTTTGGTTCAGAGGGATTTTGTAG 59.816 44.000 0.00 0.00 32.83 2.74
4534 5673 5.576563 TTGGTTCAGAGGGATTTTGTAGA 57.423 39.130 0.00 0.00 0.00 2.59
4535 5674 5.576563 TGGTTCAGAGGGATTTTGTAGAA 57.423 39.130 0.00 0.00 0.00 2.10
4536 5675 5.947663 TGGTTCAGAGGGATTTTGTAGAAA 58.052 37.500 0.00 0.00 0.00 2.52
4537 5676 6.369629 TGGTTCAGAGGGATTTTGTAGAAAA 58.630 36.000 0.00 0.00 35.52 2.29
4538 5677 6.836527 TGGTTCAGAGGGATTTTGTAGAAAAA 59.163 34.615 1.47 0.00 34.72 1.94
4557 5696 4.356405 AAAATTCCTTTGGAGCCCTTTG 57.644 40.909 0.00 0.00 31.21 2.77
4558 5697 1.942776 ATTCCTTTGGAGCCCTTTGG 58.057 50.000 0.00 0.00 31.21 3.28
4559 5698 0.560688 TTCCTTTGGAGCCCTTTGGT 59.439 50.000 0.00 0.00 31.21 3.67
4560 5699 0.560688 TCCTTTGGAGCCCTTTGGTT 59.439 50.000 0.00 0.00 0.00 3.67
4561 5700 1.062505 TCCTTTGGAGCCCTTTGGTTT 60.063 47.619 0.00 0.00 0.00 3.27
4562 5701 1.070601 CCTTTGGAGCCCTTTGGTTTG 59.929 52.381 0.00 0.00 0.00 2.93
4563 5702 1.762370 CTTTGGAGCCCTTTGGTTTGT 59.238 47.619 0.00 0.00 0.00 2.83
4564 5703 2.757894 TTGGAGCCCTTTGGTTTGTA 57.242 45.000 0.00 0.00 0.00 2.41
4565 5704 2.286365 TGGAGCCCTTTGGTTTGTAG 57.714 50.000 0.00 0.00 0.00 2.74
4566 5705 1.777878 TGGAGCCCTTTGGTTTGTAGA 59.222 47.619 0.00 0.00 0.00 2.59
4567 5706 2.378547 TGGAGCCCTTTGGTTTGTAGAT 59.621 45.455 0.00 0.00 0.00 1.98
4568 5707 2.755103 GGAGCCCTTTGGTTTGTAGATG 59.245 50.000 0.00 0.00 0.00 2.90
4569 5708 2.755103 GAGCCCTTTGGTTTGTAGATGG 59.245 50.000 0.00 0.00 0.00 3.51
4570 5709 2.378547 AGCCCTTTGGTTTGTAGATGGA 59.621 45.455 0.00 0.00 0.00 3.41
4571 5710 3.011708 AGCCCTTTGGTTTGTAGATGGAT 59.988 43.478 0.00 0.00 0.00 3.41
4572 5711 3.769300 GCCCTTTGGTTTGTAGATGGATT 59.231 43.478 0.00 0.00 0.00 3.01
4573 5712 4.142160 GCCCTTTGGTTTGTAGATGGATTC 60.142 45.833 0.00 0.00 0.00 2.52
4574 5713 4.402474 CCCTTTGGTTTGTAGATGGATTCC 59.598 45.833 0.00 0.00 0.00 3.01
4575 5714 5.264395 CCTTTGGTTTGTAGATGGATTCCT 58.736 41.667 3.95 0.00 0.00 3.36
4576 5715 6.423182 CCTTTGGTTTGTAGATGGATTCCTA 58.577 40.000 3.95 0.00 0.00 2.94
4577 5716 7.062957 CCTTTGGTTTGTAGATGGATTCCTAT 58.937 38.462 3.95 0.00 0.00 2.57
4578 5717 7.561356 CCTTTGGTTTGTAGATGGATTCCTATT 59.439 37.037 3.95 0.00 0.00 1.73
4579 5718 8.519799 TTTGGTTTGTAGATGGATTCCTATTC 57.480 34.615 3.95 0.00 0.00 1.75
4580 5719 6.601332 TGGTTTGTAGATGGATTCCTATTCC 58.399 40.000 3.95 0.00 0.00 3.01
4581 5720 6.389869 TGGTTTGTAGATGGATTCCTATTCCT 59.610 38.462 3.95 0.00 34.17 3.36
4582 5721 7.570982 TGGTTTGTAGATGGATTCCTATTCCTA 59.429 37.037 3.95 0.00 34.17 2.94
4583 5722 8.606830 GGTTTGTAGATGGATTCCTATTCCTAT 58.393 37.037 3.95 0.00 34.17 2.57
4584 5723 9.442047 GTTTGTAGATGGATTCCTATTCCTATG 57.558 37.037 3.95 0.00 34.17 2.23
4585 5724 8.742125 TTGTAGATGGATTCCTATTCCTATGT 57.258 34.615 3.95 0.00 34.17 2.29
4586 5725 9.837681 TTGTAGATGGATTCCTATTCCTATGTA 57.162 33.333 3.95 0.00 34.17 2.29
4587 5726 9.480861 TGTAGATGGATTCCTATTCCTATGTAG 57.519 37.037 3.95 0.00 34.17 2.74
4588 5727 7.986553 AGATGGATTCCTATTCCTATGTAGG 57.013 40.000 3.95 0.00 45.02 3.18
4604 5743 9.225682 TCCTATGTAGGATAGAAACCAATTCTT 57.774 33.333 4.66 0.00 45.40 2.52
4605 5744 9.495572 CCTATGTAGGATAGAAACCAATTCTTC 57.504 37.037 0.00 0.00 45.00 2.87
4607 5746 8.738645 ATGTAGGATAGAAACCAATTCTTCAC 57.261 34.615 0.00 0.00 46.39 3.18
4608 5747 7.685481 TGTAGGATAGAAACCAATTCTTCACA 58.315 34.615 0.00 0.00 46.39 3.58
4609 5748 8.328758 TGTAGGATAGAAACCAATTCTTCACAT 58.671 33.333 0.00 0.00 46.39 3.21
4610 5749 9.178758 GTAGGATAGAAACCAATTCTTCACATT 57.821 33.333 0.00 0.00 46.39 2.71
4611 5750 8.655935 AGGATAGAAACCAATTCTTCACATTT 57.344 30.769 0.00 0.00 46.39 2.32
4612 5751 8.743714 AGGATAGAAACCAATTCTTCACATTTC 58.256 33.333 0.00 0.00 46.39 2.17
4613 5752 8.522830 GGATAGAAACCAATTCTTCACATTTCA 58.477 33.333 0.00 0.00 46.39 2.69
4614 5753 9.912634 GATAGAAACCAATTCTTCACATTTCAA 57.087 29.630 0.00 0.00 46.39 2.69
4616 5755 8.652810 AGAAACCAATTCTTCACATTTCAAAG 57.347 30.769 0.00 0.00 46.39 2.77
4617 5756 7.712205 AGAAACCAATTCTTCACATTTCAAAGG 59.288 33.333 0.00 0.00 46.39 3.11
4618 5757 5.857268 ACCAATTCTTCACATTTCAAAGGG 58.143 37.500 0.00 0.00 0.00 3.95
4619 5758 5.602145 ACCAATTCTTCACATTTCAAAGGGA 59.398 36.000 0.00 0.00 0.00 4.20
4620 5759 6.099557 ACCAATTCTTCACATTTCAAAGGGAA 59.900 34.615 0.00 0.00 0.00 3.97
4680 5819 9.902684 ATTCTATGAATCAAGTGACATCTCTTT 57.097 29.630 0.00 0.00 0.00 2.52
4681 5820 8.939201 TCTATGAATCAAGTGACATCTCTTTC 57.061 34.615 0.00 0.00 0.00 2.62
4682 5821 8.756927 TCTATGAATCAAGTGACATCTCTTTCT 58.243 33.333 0.00 0.00 0.00 2.52
4683 5822 7.846644 ATGAATCAAGTGACATCTCTTTCTC 57.153 36.000 0.00 0.00 0.00 2.87
4684 5823 7.002250 TGAATCAAGTGACATCTCTTTCTCT 57.998 36.000 0.00 0.00 0.00 3.10
4685 5824 8.127150 TGAATCAAGTGACATCTCTTTCTCTA 57.873 34.615 0.00 0.00 0.00 2.43
4686 5825 8.756927 TGAATCAAGTGACATCTCTTTCTCTAT 58.243 33.333 0.00 0.00 0.00 1.98
4689 5828 8.231692 TCAAGTGACATCTCTTTCTCTATAGG 57.768 38.462 0.00 0.00 0.00 2.57
4690 5829 8.055790 TCAAGTGACATCTCTTTCTCTATAGGA 58.944 37.037 0.00 0.00 0.00 2.94
4691 5830 8.690884 CAAGTGACATCTCTTTCTCTATAGGAA 58.309 37.037 0.00 0.00 0.00 3.36
4692 5831 9.432982 AAGTGACATCTCTTTCTCTATAGGAAT 57.567 33.333 0.00 0.00 0.00 3.01
4693 5832 9.432982 AGTGACATCTCTTTCTCTATAGGAATT 57.567 33.333 0.00 0.00 0.00 2.17
4694 5833 9.474920 GTGACATCTCTTTCTCTATAGGAATTG 57.525 37.037 0.00 0.60 0.00 2.32
4695 5834 9.426534 TGACATCTCTTTCTCTATAGGAATTGA 57.573 33.333 0.00 4.25 0.00 2.57
4696 5835 9.691362 GACATCTCTTTCTCTATAGGAATTGAC 57.309 37.037 0.00 0.00 0.00 3.18
4697 5836 9.206690 ACATCTCTTTCTCTATAGGAATTGACA 57.793 33.333 0.00 0.00 0.00 3.58
4700 5839 9.206690 TCTCTTTCTCTATAGGAATTGACATGT 57.793 33.333 0.00 0.00 0.00 3.21
4701 5840 9.474920 CTCTTTCTCTATAGGAATTGACATGTC 57.525 37.037 19.27 19.27 0.00 3.06
4702 5841 8.981659 TCTTTCTCTATAGGAATTGACATGTCA 58.018 33.333 24.56 24.56 37.91 3.58
4703 5842 9.775854 CTTTCTCTATAGGAATTGACATGTCAT 57.224 33.333 28.32 15.41 39.64 3.06
4704 5843 9.770097 TTTCTCTATAGGAATTGACATGTCATC 57.230 33.333 28.32 22.35 39.64 2.92
4705 5844 8.718158 TCTCTATAGGAATTGACATGTCATCT 57.282 34.615 28.32 22.36 39.64 2.90
4706 5845 8.801299 TCTCTATAGGAATTGACATGTCATCTC 58.199 37.037 28.32 24.17 39.64 2.75
4707 5846 8.482852 TCTATAGGAATTGACATGTCATCTCA 57.517 34.615 28.32 14.57 39.64 3.27
4708 5847 8.363390 TCTATAGGAATTGACATGTCATCTCAC 58.637 37.037 28.32 18.59 39.64 3.51
4709 5848 5.432680 AGGAATTGACATGTCATCTCACT 57.567 39.130 28.32 20.08 39.64 3.41
4710 5849 5.813383 AGGAATTGACATGTCATCTCACTT 58.187 37.500 28.32 14.57 39.64 3.16
4711 5850 5.879223 AGGAATTGACATGTCATCTCACTTC 59.121 40.000 28.32 20.38 39.64 3.01
4712 5851 5.065731 GGAATTGACATGTCATCTCACTTCC 59.934 44.000 28.32 24.01 39.64 3.46
4713 5852 4.897509 TTGACATGTCATCTCACTTCCT 57.102 40.909 28.32 0.00 39.64 3.36
4714 5853 6.550938 ATTGACATGTCATCTCACTTCCTA 57.449 37.500 28.32 9.95 39.64 2.94
4715 5854 6.550938 TTGACATGTCATCTCACTTCCTAT 57.449 37.500 28.32 0.00 39.64 2.57
4716 5855 7.660030 TTGACATGTCATCTCACTTCCTATA 57.340 36.000 28.32 6.20 39.64 1.31
4717 5856 7.282332 TGACATGTCATCTCACTTCCTATAG 57.718 40.000 24.56 0.00 34.14 1.31
4718 5857 6.836007 TGACATGTCATCTCACTTCCTATAGT 59.164 38.462 24.56 0.00 34.14 2.12
4719 5858 7.343057 TGACATGTCATCTCACTTCCTATAGTT 59.657 37.037 24.56 0.00 34.14 2.24
4720 5859 8.083828 ACATGTCATCTCACTTCCTATAGTTT 57.916 34.615 0.00 0.00 0.00 2.66
4721 5860 8.543774 ACATGTCATCTCACTTCCTATAGTTTT 58.456 33.333 0.00 0.00 0.00 2.43
4722 5861 9.039870 CATGTCATCTCACTTCCTATAGTTTTC 57.960 37.037 0.00 0.00 0.00 2.29
4723 5862 7.556844 TGTCATCTCACTTCCTATAGTTTTCC 58.443 38.462 0.00 0.00 0.00 3.13
4724 5863 7.400339 TGTCATCTCACTTCCTATAGTTTTCCT 59.600 37.037 0.00 0.00 0.00 3.36
4725 5864 8.915036 GTCATCTCACTTCCTATAGTTTTCCTA 58.085 37.037 0.00 0.00 0.00 2.94
4726 5865 9.661954 TCATCTCACTTCCTATAGTTTTCCTAT 57.338 33.333 0.00 0.00 39.71 2.57
4743 5882 9.847224 GTTTTCCTATTTCTATCCTATGAACCA 57.153 33.333 0.00 0.00 0.00 3.67
4747 5886 8.660435 TCCTATTTCTATCCTATGAACCAAAGG 58.340 37.037 0.00 0.00 0.00 3.11
4748 5887 8.660435 CCTATTTCTATCCTATGAACCAAAGGA 58.340 37.037 0.00 0.00 43.38 3.36
4749 5888 9.717942 CTATTTCTATCCTATGAACCAAAGGAG 57.282 37.037 0.00 0.00 42.53 3.69
4763 5902 4.089361 CCAAAGGAGGCCAAAAAGTCTAT 58.911 43.478 5.01 0.00 0.00 1.98
4768 5907 7.453141 AAGGAGGCCAAAAAGTCTATATACT 57.547 36.000 5.01 0.00 0.00 2.12
4783 5922 9.191479 AGTCTATATACTAATATCTGTGGTGGC 57.809 37.037 0.00 0.00 30.72 5.01
4802 5941 2.346803 GCGACATACTGACATGTGGTT 58.653 47.619 1.15 0.00 39.25 3.67
4807 5946 6.534059 CGACATACTGACATGTGGTTTTTAG 58.466 40.000 1.15 0.00 39.25 1.85
4837 5976 3.462021 GAAGACTGATTCCGAATCCTGG 58.538 50.000 16.82 10.25 37.09 4.45
4844 5983 5.110814 TGATTCCGAATCCTGGTTTGTAT 57.889 39.130 16.82 0.00 37.09 2.29
4895 6034 5.698089 GGAAATTTTCCTTCAGAGCCTTTTG 59.302 40.000 19.01 0.00 46.57 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 1.417592 CACGTTGTGAGCATCGAGC 59.582 57.895 5.28 0.00 46.19 5.03
182 183 6.719370 ACTCATTTTCCTTATGTTTAGCCACA 59.281 34.615 0.00 0.00 0.00 4.17
324 326 3.909732 TGGTTTCTTGGTCTGATGGTTT 58.090 40.909 0.00 0.00 0.00 3.27
402 420 3.171828 TTTGTTCCCCTCTCGCGCA 62.172 57.895 8.75 0.00 0.00 6.09
420 438 1.587054 CAACCGCTCTCTTCTCCGT 59.413 57.895 0.00 0.00 0.00 4.69
426 444 2.859165 TTTCATCCAACCGCTCTCTT 57.141 45.000 0.00 0.00 0.00 2.85
539 561 2.050144 AGCTGACATATCGACCCCATT 58.950 47.619 0.00 0.00 0.00 3.16
540 562 1.722034 AGCTGACATATCGACCCCAT 58.278 50.000 0.00 0.00 0.00 4.00
565 587 0.606604 AGTTGTGACCCGCGACTAAT 59.393 50.000 8.23 0.00 36.90 1.73
611 633 6.916360 ACAAAAGACCATCATTTATGTGGT 57.084 33.333 13.29 13.29 41.52 4.16
620 642 5.335661 GCCGAAAGTAACAAAAGACCATCAT 60.336 40.000 0.00 0.00 0.00 2.45
623 645 3.886505 TGCCGAAAGTAACAAAAGACCAT 59.113 39.130 0.00 0.00 0.00 3.55
632 654 8.556213 AACTATTATCTTTGCCGAAAGTAACA 57.444 30.769 0.00 0.00 39.79 2.41
680 702 8.957466 AGGGAGTAAATTGCTTAAAACTATCAC 58.043 33.333 0.00 0.00 0.00 3.06
685 707 7.523873 GCTTGAGGGAGTAAATTGCTTAAAACT 60.524 37.037 0.00 0.00 0.00 2.66
691 713 2.749621 CGCTTGAGGGAGTAAATTGCTT 59.250 45.455 0.00 0.00 0.00 3.91
727 750 1.510480 GCATAGATCCCGCAACTGGC 61.510 60.000 0.00 0.00 39.90 4.85
731 754 1.069204 TGAGAGCATAGATCCCGCAAC 59.931 52.381 1.94 0.00 0.00 4.17
755 778 3.976169 TCCAAGCTTTGTCCGAATTTTG 58.024 40.909 0.00 0.00 0.00 2.44
790 814 6.128117 GCCTTTTTCGAATTGGTCAGTATACA 60.128 38.462 5.50 0.00 0.00 2.29
939 2033 2.252012 AATGGGAGGGGAGCGTAGGA 62.252 60.000 0.00 0.00 0.00 2.94
2145 3251 0.741927 CAGACGCATCCATCTGTGCA 60.742 55.000 0.00 0.00 41.32 4.57
2439 3545 2.084610 ACGTCACATCCACATGAGTG 57.915 50.000 0.00 0.29 45.47 3.51
2960 4066 9.981114 AACATAAAGGTAGAAATCCAAAAAGTG 57.019 29.630 0.00 0.00 0.00 3.16
3150 4257 2.899900 CTGGTCCTATATGCTAGTGCCA 59.100 50.000 0.00 0.00 38.71 4.92
3152 4259 2.300152 TGCTGGTCCTATATGCTAGTGC 59.700 50.000 0.00 0.00 40.20 4.40
3404 4530 2.613133 GCAGCCAATGAAGCAACAAAAA 59.387 40.909 0.00 0.00 0.00 1.94
3461 4587 4.042809 AGAGTCAACCATTACCCATCAACA 59.957 41.667 0.00 0.00 0.00 3.33
3470 4596 2.426522 TGCAGCAGAGTCAACCATTAC 58.573 47.619 0.00 0.00 0.00 1.89
3574 4700 7.254863 GGCAGAAAATTTTCTCAATGCAAAAGA 60.255 33.333 29.07 0.00 45.23 2.52
3579 4705 4.992319 CAGGCAGAAAATTTTCTCAATGCA 59.008 37.500 29.07 0.00 45.23 3.96
3619 4746 6.483307 GTGCTTGATACCAGATAGTAAATGCA 59.517 38.462 0.00 0.00 0.00 3.96
3620 4747 6.708054 AGTGCTTGATACCAGATAGTAAATGC 59.292 38.462 0.00 0.00 0.00 3.56
3662 4789 2.484770 GCTTGCCATTATCCGTGACCTA 60.485 50.000 0.00 0.00 0.00 3.08
3676 4803 2.547640 GATGCCTCTCCTGCTTGCCA 62.548 60.000 0.00 0.00 0.00 4.92
3763 4890 2.441001 CCCCTCCTGATTCTTGTAGCAT 59.559 50.000 0.00 0.00 0.00 3.79
3775 4902 0.178891 AACTCTTGAGCCCCTCCTGA 60.179 55.000 0.00 0.00 0.00 3.86
3889 5016 3.712881 GGTGTCGCGACAACCAGC 61.713 66.667 40.37 27.85 42.99 4.85
3895 5022 1.374125 CTTCATGGGTGTCGCGACA 60.374 57.895 36.40 36.40 39.32 4.35
3904 5031 0.178861 AGGAGGTGACCTTCATGGGT 60.179 55.000 13.44 0.00 43.07 4.51
3988 5118 0.946221 GACAGCACGGAGACCAACAG 60.946 60.000 0.00 0.00 0.00 3.16
4072 5202 9.632638 ACATAATCATAAATCCTGTAACAAGCT 57.367 29.630 0.00 0.00 0.00 3.74
4154 5286 5.479716 TTCCTTCGTTCAAAGAAGTTCAC 57.520 39.130 11.54 0.00 42.48 3.18
4318 5457 5.344743 TGCTTAGATACTGTAAAGCAGCT 57.655 39.130 17.13 0.00 46.83 4.24
4328 5467 7.221452 GCAAATTTTGTCCATGCTTAGATACTG 59.779 37.037 10.65 0.00 34.29 2.74
4349 5488 8.565416 GGGCGTAGTATTAATTAAAGAGCAAAT 58.435 33.333 1.21 0.00 0.00 2.32
4362 5501 6.528537 TGTTTACAGAGGGCGTAGTATTAA 57.471 37.500 0.00 0.00 0.00 1.40
4366 5505 4.870123 TTTGTTTACAGAGGGCGTAGTA 57.130 40.909 0.00 0.00 0.00 1.82
4368 5507 7.924412 TCTTATATTTGTTTACAGAGGGCGTAG 59.076 37.037 0.00 0.00 0.00 3.51
4369 5508 7.784037 TCTTATATTTGTTTACAGAGGGCGTA 58.216 34.615 0.00 0.00 0.00 4.42
4370 5509 6.646267 TCTTATATTTGTTTACAGAGGGCGT 58.354 36.000 0.00 0.00 0.00 5.68
4372 5511 7.553044 ACACTCTTATATTTGTTTACAGAGGGC 59.447 37.037 0.00 0.00 0.00 5.19
4373 5512 9.449719 AACACTCTTATATTTGTTTACAGAGGG 57.550 33.333 0.00 0.00 0.00 4.30
4423 5562 8.823818 CCATCCGTAAAGAAATATAAGAACGTT 58.176 33.333 0.00 0.00 0.00 3.99
4424 5563 8.199449 TCCATCCGTAAAGAAATATAAGAACGT 58.801 33.333 0.00 0.00 0.00 3.99
4425 5564 8.583810 TCCATCCGTAAAGAAATATAAGAACG 57.416 34.615 0.00 0.00 0.00 3.95
4426 5565 9.543783 ACTCCATCCGTAAAGAAATATAAGAAC 57.456 33.333 0.00 0.00 0.00 3.01
4431 5570 9.976511 CAAGTACTCCATCCGTAAAGAAATATA 57.023 33.333 0.00 0.00 0.00 0.86
4432 5571 8.483758 ACAAGTACTCCATCCGTAAAGAAATAT 58.516 33.333 0.00 0.00 0.00 1.28
4433 5572 7.844009 ACAAGTACTCCATCCGTAAAGAAATA 58.156 34.615 0.00 0.00 0.00 1.40
4434 5573 6.708285 ACAAGTACTCCATCCGTAAAGAAAT 58.292 36.000 0.00 0.00 0.00 2.17
4435 5574 6.105397 ACAAGTACTCCATCCGTAAAGAAA 57.895 37.500 0.00 0.00 0.00 2.52
4436 5575 5.733620 ACAAGTACTCCATCCGTAAAGAA 57.266 39.130 0.00 0.00 0.00 2.52
4437 5576 5.733620 AACAAGTACTCCATCCGTAAAGA 57.266 39.130 0.00 0.00 0.00 2.52
4438 5577 6.796705 AAAACAAGTACTCCATCCGTAAAG 57.203 37.500 0.00 0.00 0.00 1.85
4439 5578 6.766944 TCAAAAACAAGTACTCCATCCGTAAA 59.233 34.615 0.00 0.00 0.00 2.01
4440 5579 6.289834 TCAAAAACAAGTACTCCATCCGTAA 58.710 36.000 0.00 0.00 0.00 3.18
4441 5580 5.856156 TCAAAAACAAGTACTCCATCCGTA 58.144 37.500 0.00 0.00 0.00 4.02
4442 5581 4.710324 TCAAAAACAAGTACTCCATCCGT 58.290 39.130 0.00 0.00 0.00 4.69
4443 5582 5.238650 AGTTCAAAAACAAGTACTCCATCCG 59.761 40.000 0.00 0.00 37.88 4.18
4444 5583 6.635030 AGTTCAAAAACAAGTACTCCATCC 57.365 37.500 0.00 0.00 37.88 3.51
4445 5584 9.447040 GTTAAGTTCAAAAACAAGTACTCCATC 57.553 33.333 0.00 0.00 37.88 3.51
4446 5585 8.962679 TGTTAAGTTCAAAAACAAGTACTCCAT 58.037 29.630 0.00 0.00 37.88 3.41
4447 5586 8.338072 TGTTAAGTTCAAAAACAAGTACTCCA 57.662 30.769 0.00 0.00 37.88 3.86
4448 5587 9.628746 TTTGTTAAGTTCAAAAACAAGTACTCC 57.371 29.630 0.00 0.00 42.28 3.85
4535 5674 4.446167 CCAAAGGGCTCCAAAGGAATTTTT 60.446 41.667 0.00 0.00 0.00 1.94
4536 5675 3.072915 CCAAAGGGCTCCAAAGGAATTTT 59.927 43.478 0.00 0.00 0.00 1.82
4537 5676 2.639347 CCAAAGGGCTCCAAAGGAATTT 59.361 45.455 0.00 0.00 0.00 1.82
4538 5677 2.259917 CCAAAGGGCTCCAAAGGAATT 58.740 47.619 0.00 0.00 0.00 2.17
4539 5678 1.149923 ACCAAAGGGCTCCAAAGGAAT 59.850 47.619 0.00 0.00 37.90 3.01
4540 5679 0.560688 ACCAAAGGGCTCCAAAGGAA 59.439 50.000 0.00 0.00 37.90 3.36
4541 5680 0.560688 AACCAAAGGGCTCCAAAGGA 59.439 50.000 0.00 0.00 37.90 3.36
4542 5681 1.070601 CAAACCAAAGGGCTCCAAAGG 59.929 52.381 0.00 0.00 37.90 3.11
4543 5682 1.762370 ACAAACCAAAGGGCTCCAAAG 59.238 47.619 0.00 0.00 37.90 2.77
4544 5683 1.872773 ACAAACCAAAGGGCTCCAAA 58.127 45.000 0.00 0.00 37.90 3.28
4545 5684 2.175931 TCTACAAACCAAAGGGCTCCAA 59.824 45.455 0.00 0.00 37.90 3.53
4546 5685 1.777878 TCTACAAACCAAAGGGCTCCA 59.222 47.619 0.00 0.00 37.90 3.86
4547 5686 2.579410 TCTACAAACCAAAGGGCTCC 57.421 50.000 0.00 0.00 37.90 4.70
4548 5687 2.755103 CCATCTACAAACCAAAGGGCTC 59.245 50.000 0.00 0.00 37.90 4.70
4549 5688 2.378547 TCCATCTACAAACCAAAGGGCT 59.621 45.455 0.00 0.00 37.90 5.19
4550 5689 2.802719 TCCATCTACAAACCAAAGGGC 58.197 47.619 0.00 0.00 37.90 5.19
4551 5690 4.402474 GGAATCCATCTACAAACCAAAGGG 59.598 45.833 0.00 0.00 41.29 3.95
4552 5691 5.264395 AGGAATCCATCTACAAACCAAAGG 58.736 41.667 0.61 0.00 0.00 3.11
4553 5692 8.525290 AATAGGAATCCATCTACAAACCAAAG 57.475 34.615 0.61 0.00 0.00 2.77
4554 5693 7.559897 GGAATAGGAATCCATCTACAAACCAAA 59.440 37.037 0.61 0.00 36.92 3.28
4555 5694 7.060421 GGAATAGGAATCCATCTACAAACCAA 58.940 38.462 0.61 0.00 36.92 3.67
4556 5695 6.389869 AGGAATAGGAATCCATCTACAAACCA 59.610 38.462 0.61 0.00 39.55 3.67
4557 5696 6.842676 AGGAATAGGAATCCATCTACAAACC 58.157 40.000 0.61 0.00 39.55 3.27
4558 5697 9.442047 CATAGGAATAGGAATCCATCTACAAAC 57.558 37.037 0.61 0.00 39.55 2.93
4559 5698 9.170890 ACATAGGAATAGGAATCCATCTACAAA 57.829 33.333 0.61 0.00 39.55 2.83
4560 5699 8.742125 ACATAGGAATAGGAATCCATCTACAA 57.258 34.615 0.61 0.00 39.55 2.41
4561 5700 9.480861 CTACATAGGAATAGGAATCCATCTACA 57.519 37.037 0.61 0.00 39.55 2.74
4562 5701 8.919145 CCTACATAGGAATAGGAATCCATCTAC 58.081 40.741 0.61 0.00 46.63 2.59
4564 5703 7.986553 CCTACATAGGAATAGGAATCCATCT 57.013 40.000 0.61 0.00 46.63 2.90
4577 5716 9.225682 AGAATTGGTTTCTATCCTACATAGGAA 57.774 33.333 11.67 1.62 44.77 3.36
4578 5717 8.798975 AGAATTGGTTTCTATCCTACATAGGA 57.201 34.615 10.09 10.09 45.14 2.94
4579 5718 9.495572 GAAGAATTGGTTTCTATCCTACATAGG 57.504 37.037 0.00 0.00 44.09 2.57
4581 5720 9.832445 GTGAAGAATTGGTTTCTATCCTACATA 57.168 33.333 0.00 0.00 44.09 2.29
4582 5721 8.328758 TGTGAAGAATTGGTTTCTATCCTACAT 58.671 33.333 0.00 0.00 44.09 2.29
4583 5722 7.685481 TGTGAAGAATTGGTTTCTATCCTACA 58.315 34.615 0.00 0.00 44.09 2.74
4584 5723 8.738645 ATGTGAAGAATTGGTTTCTATCCTAC 57.261 34.615 0.00 0.00 44.09 3.18
4585 5724 9.753674 AAATGTGAAGAATTGGTTTCTATCCTA 57.246 29.630 0.00 0.00 44.09 2.94
4586 5725 8.655935 AAATGTGAAGAATTGGTTTCTATCCT 57.344 30.769 0.00 0.00 44.09 3.24
4587 5726 8.522830 TGAAATGTGAAGAATTGGTTTCTATCC 58.477 33.333 0.00 0.00 44.09 2.59
4588 5727 9.912634 TTGAAATGTGAAGAATTGGTTTCTATC 57.087 29.630 0.00 0.00 44.09 2.08
4590 5729 9.748708 CTTTGAAATGTGAAGAATTGGTTTCTA 57.251 29.630 0.00 0.00 44.09 2.10
4591 5730 7.712205 CCTTTGAAATGTGAAGAATTGGTTTCT 59.288 33.333 0.00 0.00 46.92 2.52
4592 5731 7.041848 CCCTTTGAAATGTGAAGAATTGGTTTC 60.042 37.037 0.00 0.00 34.31 2.78
4593 5732 6.767423 CCCTTTGAAATGTGAAGAATTGGTTT 59.233 34.615 0.00 0.00 0.00 3.27
4594 5733 6.099557 TCCCTTTGAAATGTGAAGAATTGGTT 59.900 34.615 0.00 0.00 0.00 3.67
4595 5734 5.602145 TCCCTTTGAAATGTGAAGAATTGGT 59.398 36.000 0.00 0.00 0.00 3.67
4596 5735 6.100404 TCCCTTTGAAATGTGAAGAATTGG 57.900 37.500 0.00 0.00 0.00 3.16
4597 5736 8.436046 TTTTCCCTTTGAAATGTGAAGAATTG 57.564 30.769 0.00 0.00 42.38 2.32
4654 5793 9.902684 AAAGAGATGTCACTTGATTCATAGAAT 57.097 29.630 0.00 0.00 0.00 2.40
4655 5794 9.376075 GAAAGAGATGTCACTTGATTCATAGAA 57.624 33.333 0.00 0.00 0.00 2.10
4656 5795 8.756927 AGAAAGAGATGTCACTTGATTCATAGA 58.243 33.333 0.00 0.00 0.00 1.98
4657 5796 8.945481 AGAAAGAGATGTCACTTGATTCATAG 57.055 34.615 0.00 0.00 0.00 2.23
4658 5797 8.756927 AGAGAAAGAGATGTCACTTGATTCATA 58.243 33.333 0.00 0.00 0.00 2.15
4659 5798 7.622713 AGAGAAAGAGATGTCACTTGATTCAT 58.377 34.615 0.00 0.00 0.00 2.57
4660 5799 7.002250 AGAGAAAGAGATGTCACTTGATTCA 57.998 36.000 0.00 0.00 0.00 2.57
4663 5802 8.859090 CCTATAGAGAAAGAGATGTCACTTGAT 58.141 37.037 0.00 0.00 0.00 2.57
4664 5803 8.055790 TCCTATAGAGAAAGAGATGTCACTTGA 58.944 37.037 0.00 0.00 0.00 3.02
4665 5804 8.231692 TCCTATAGAGAAAGAGATGTCACTTG 57.768 38.462 0.00 0.00 0.00 3.16
4666 5805 8.830915 TTCCTATAGAGAAAGAGATGTCACTT 57.169 34.615 0.00 0.00 0.00 3.16
4667 5806 9.432982 AATTCCTATAGAGAAAGAGATGTCACT 57.567 33.333 0.00 0.00 0.00 3.41
4668 5807 9.474920 CAATTCCTATAGAGAAAGAGATGTCAC 57.525 37.037 0.00 0.00 0.00 3.67
4669 5808 9.426534 TCAATTCCTATAGAGAAAGAGATGTCA 57.573 33.333 0.00 0.00 0.00 3.58
4670 5809 9.691362 GTCAATTCCTATAGAGAAAGAGATGTC 57.309 37.037 0.00 0.00 0.00 3.06
4671 5810 9.206690 TGTCAATTCCTATAGAGAAAGAGATGT 57.793 33.333 0.00 0.00 0.00 3.06
4674 5813 9.206690 ACATGTCAATTCCTATAGAGAAAGAGA 57.793 33.333 0.00 5.52 0.00 3.10
4675 5814 9.474920 GACATGTCAATTCCTATAGAGAAAGAG 57.525 37.037 21.07 0.00 0.00 2.85
4676 5815 8.981659 TGACATGTCAATTCCTATAGAGAAAGA 58.018 33.333 26.02 0.00 36.53 2.52
4677 5816 9.775854 ATGACATGTCAATTCCTATAGAGAAAG 57.224 33.333 31.00 1.90 43.58 2.62
4678 5817 9.770097 GATGACATGTCAATTCCTATAGAGAAA 57.230 33.333 31.00 2.84 43.58 2.52
4679 5818 9.152327 AGATGACATGTCAATTCCTATAGAGAA 57.848 33.333 31.00 3.24 43.58 2.87
4680 5819 8.718158 AGATGACATGTCAATTCCTATAGAGA 57.282 34.615 31.00 3.92 43.58 3.10
4681 5820 8.583296 TGAGATGACATGTCAATTCCTATAGAG 58.417 37.037 31.00 0.00 43.58 2.43
4682 5821 8.363390 GTGAGATGACATGTCAATTCCTATAGA 58.637 37.037 31.00 12.01 43.58 1.98
4683 5822 8.366401 AGTGAGATGACATGTCAATTCCTATAG 58.634 37.037 31.00 0.00 43.58 1.31
4684 5823 8.255111 AGTGAGATGACATGTCAATTCCTATA 57.745 34.615 31.00 12.94 43.58 1.31
4685 5824 7.134362 AGTGAGATGACATGTCAATTCCTAT 57.866 36.000 31.00 13.87 43.58 2.57
4686 5825 6.550938 AGTGAGATGACATGTCAATTCCTA 57.449 37.500 31.00 14.14 43.58 2.94
4687 5826 5.432680 AGTGAGATGACATGTCAATTCCT 57.567 39.130 31.00 23.10 43.58 3.36
4688 5827 6.116680 GAAGTGAGATGACATGTCAATTCC 57.883 41.667 30.56 21.22 45.82 3.01
4690 5829 5.813383 AGGAAGTGAGATGACATGTCAATT 58.187 37.500 31.00 23.30 42.37 2.32
4691 5830 5.432680 AGGAAGTGAGATGACATGTCAAT 57.567 39.130 31.00 22.34 43.58 2.57
4692 5831 4.897509 AGGAAGTGAGATGACATGTCAA 57.102 40.909 31.00 13.12 43.58 3.18
4693 5832 6.836007 ACTATAGGAAGTGAGATGACATGTCA 59.164 38.462 29.67 29.67 44.59 3.58
4694 5833 7.283625 ACTATAGGAAGTGAGATGACATGTC 57.716 40.000 19.27 19.27 0.00 3.06
4695 5834 7.667575 AACTATAGGAAGTGAGATGACATGT 57.332 36.000 0.00 0.00 0.00 3.21
4696 5835 8.954950 AAAACTATAGGAAGTGAGATGACATG 57.045 34.615 4.43 0.00 0.00 3.21
4697 5836 8.207545 GGAAAACTATAGGAAGTGAGATGACAT 58.792 37.037 4.43 0.00 0.00 3.06
4698 5837 7.400339 AGGAAAACTATAGGAAGTGAGATGACA 59.600 37.037 4.43 0.00 0.00 3.58
4699 5838 7.787028 AGGAAAACTATAGGAAGTGAGATGAC 58.213 38.462 4.43 0.00 0.00 3.06
4700 5839 7.979786 AGGAAAACTATAGGAAGTGAGATGA 57.020 36.000 4.43 0.00 0.00 2.92
4717 5856 9.847224 TGGTTCATAGGATAGAAATAGGAAAAC 57.153 33.333 0.00 0.00 0.00 2.43
4721 5860 8.660435 CCTTTGGTTCATAGGATAGAAATAGGA 58.340 37.037 0.00 0.00 35.14 2.94
4722 5861 8.660435 TCCTTTGGTTCATAGGATAGAAATAGG 58.340 37.037 3.54 0.00 36.84 2.57
4723 5862 9.717942 CTCCTTTGGTTCATAGGATAGAAATAG 57.282 37.037 7.38 0.00 39.94 1.73
4724 5863 8.660435 CCTCCTTTGGTTCATAGGATAGAAATA 58.340 37.037 7.38 0.00 39.94 1.40
4725 5864 7.521669 CCTCCTTTGGTTCATAGGATAGAAAT 58.478 38.462 7.38 0.00 39.94 2.17
4726 5865 6.634955 GCCTCCTTTGGTTCATAGGATAGAAA 60.635 42.308 7.38 0.00 39.94 2.52
4727 5866 5.163195 GCCTCCTTTGGTTCATAGGATAGAA 60.163 44.000 7.38 0.00 39.94 2.10
4728 5867 4.348168 GCCTCCTTTGGTTCATAGGATAGA 59.652 45.833 7.38 0.00 39.94 1.98
4729 5868 4.505742 GGCCTCCTTTGGTTCATAGGATAG 60.506 50.000 0.00 4.66 39.94 2.08
4730 5869 3.394606 GGCCTCCTTTGGTTCATAGGATA 59.605 47.826 0.00 0.00 39.94 2.59
4731 5870 2.175715 GGCCTCCTTTGGTTCATAGGAT 59.824 50.000 0.00 0.00 39.94 3.24
4732 5871 1.564348 GGCCTCCTTTGGTTCATAGGA 59.436 52.381 0.00 6.86 38.81 2.94
4733 5872 1.284785 TGGCCTCCTTTGGTTCATAGG 59.715 52.381 3.32 0.00 34.61 2.57
4734 5873 2.806945 TGGCCTCCTTTGGTTCATAG 57.193 50.000 3.32 0.00 0.00 2.23
4735 5874 3.534357 TTTGGCCTCCTTTGGTTCATA 57.466 42.857 3.32 0.00 0.00 2.15
4736 5875 2.397044 TTTGGCCTCCTTTGGTTCAT 57.603 45.000 3.32 0.00 0.00 2.57
4737 5876 2.166907 TTTTGGCCTCCTTTGGTTCA 57.833 45.000 3.32 0.00 0.00 3.18
4738 5877 2.434336 ACTTTTTGGCCTCCTTTGGTTC 59.566 45.455 3.32 0.00 0.00 3.62
4739 5878 2.434336 GACTTTTTGGCCTCCTTTGGTT 59.566 45.455 3.32 0.00 0.00 3.67
4740 5879 2.039418 GACTTTTTGGCCTCCTTTGGT 58.961 47.619 3.32 0.00 0.00 3.67
4741 5880 2.319844 AGACTTTTTGGCCTCCTTTGG 58.680 47.619 3.32 0.00 0.00 3.28
4742 5881 7.775561 AGTATATAGACTTTTTGGCCTCCTTTG 59.224 37.037 3.32 0.00 0.00 2.77
4743 5882 7.873195 AGTATATAGACTTTTTGGCCTCCTTT 58.127 34.615 3.32 0.00 0.00 3.11
4744 5883 7.453141 AGTATATAGACTTTTTGGCCTCCTT 57.547 36.000 3.32 0.00 0.00 3.36
4745 5884 8.562949 TTAGTATATAGACTTTTTGGCCTCCT 57.437 34.615 5.15 0.00 0.00 3.69
4763 5902 5.771165 TGTCGCCACCACAGATATTAGTATA 59.229 40.000 0.00 0.00 0.00 1.47
4768 5907 4.587262 AGTATGTCGCCACCACAGATATTA 59.413 41.667 0.00 0.00 0.00 0.98
4783 5922 5.356882 AAAAACCACATGTCAGTATGTCG 57.643 39.130 0.00 0.00 39.17 4.35
4807 5946 6.737254 TCGGAATCAGTCTTCCATAAAAAC 57.263 37.500 3.95 0.00 44.18 2.43
4828 5967 6.683974 AGAATTCATACAAACCAGGATTCG 57.316 37.500 8.44 0.00 0.00 3.34
4831 5970 9.170890 TCCTATAGAATTCATACAAACCAGGAT 57.829 33.333 8.44 0.00 0.00 3.24
4832 5971 8.561536 TCCTATAGAATTCATACAAACCAGGA 57.438 34.615 8.44 4.29 0.00 3.86
4833 5972 9.224267 CATCCTATAGAATTCATACAAACCAGG 57.776 37.037 8.44 2.25 0.00 4.45


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

AutoCloner maintained by Alex Coulton.