Multiple sequence alignment - TraesCS5B01G092300

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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 TraesCS5B01G092300 chr5B 100.000 5561 0 0 1 5561 121204582 121210142 0.000000e+00 10270.0
1 TraesCS5B01G092300 chr5B 94.828 58 3 0 5501 5558 121245522 121245579 2.130000e-14 91.6
2 TraesCS5B01G092300 chr5B 93.023 43 3 0 5519 5561 455364216 455364174 4.650000e-06 63.9
3 TraesCS5B01G092300 chr5D 96.636 4429 127 17 293 4701 112048850 112053276 0.000000e+00 7334.0
4 TraesCS5B01G092300 chr5D 97.590 498 8 4 4808 5302 112053277 112053773 0.000000e+00 850.0
5 TraesCS5B01G092300 chr5D 92.405 158 12 0 9 166 112048632 112048789 5.610000e-55 226.0
6 TraesCS5B01G092300 chr5D 93.525 139 7 1 5299 5437 112055266 112055402 7.300000e-49 206.0
7 TraesCS5B01G092300 chr5D 89.565 115 12 0 5444 5558 112103889 112104003 4.490000e-31 147.0
8 TraesCS5B01G092300 chr5D 94.937 79 3 1 5483 5561 112055402 112055479 7.570000e-24 122.0
9 TraesCS5B01G092300 chr5A 94.042 4683 204 34 8 4668 115024779 115029408 0.000000e+00 7033.0
10 TraesCS5B01G092300 chr5A 87.824 501 32 12 4805 5305 115029514 115029985 1.350000e-155 560.0
11 TraesCS5B01G092300 chr5A 100.000 29 0 0 4673 4701 115029487 115029515 3.000000e-03 54.7
12 TraesCS5B01G092300 chr1B 96.667 120 4 0 4693 4812 113565117 113565236 3.400000e-47 200.0
13 TraesCS5B01G092300 chr7B 99.091 110 1 0 4700 4809 730205114 730205223 1.220000e-46 198.0
14 TraesCS5B01G092300 chr6A 99.083 109 1 0 4700 4808 70933927 70934035 4.390000e-46 196.0
15 TraesCS5B01G092300 chr6D 98.198 111 2 0 4696 4806 128989263 128989373 1.580000e-45 195.0
16 TraesCS5B01G092300 chr6D 95.868 121 3 2 4688 4806 397359802 397359922 1.580000e-45 195.0
17 TraesCS5B01G092300 chr4D 98.198 111 2 0 4696 4806 29093365 29093475 1.580000e-45 195.0
18 TraesCS5B01G092300 chr4D 98.198 111 2 0 4696 4806 333227601 333227491 1.580000e-45 195.0
19 TraesCS5B01G092300 chr7A 93.846 130 5 3 4680 4806 442029986 442030115 5.690000e-45 193.0
20 TraesCS5B01G092300 chr3B 97.297 111 2 1 4696 4805 205478067 205478177 2.650000e-43 187.0
21 TraesCS5B01G092300 chr4B 95.556 45 2 0 5516 5560 28296265 28296309 7.730000e-09 73.1
22 TraesCS5B01G092300 chr1D 100.000 38 0 0 5521 5558 338832300 338832337 2.780000e-08 71.3
23 TraesCS5B01G092300 chr2A 95.455 44 1 1 5518 5561 55972305 55972347 1.000000e-07 69.4
24 TraesCS5B01G092300 chr2A 95.455 44 1 1 5518 5561 56106684 56106726 1.000000e-07 69.4
25 TraesCS5B01G092300 chr2D 90.566 53 2 3 5508 5558 176520014 176519963 3.600000e-07 67.6


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 TraesCS5B01G092300 chr5B 121204582 121210142 5560 False 10270.000000 10270 100.000000 1 5561 1 chr5B.!!$F1 5560
1 TraesCS5B01G092300 chr5D 112048632 112055479 6847 False 1747.600000 7334 95.018600 9 5561 5 chr5D.!!$F2 5552
2 TraesCS5B01G092300 chr5A 115024779 115029985 5206 False 2549.233333 7033 93.955333 8 5305 3 chr5A.!!$F1 5297

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
199 200 0.464373 ACAAGACAGTGCCACACAGG 60.464 55.000 0.00 0.0 36.74 4.00 F
920 964 1.152368 AATATGGGCCAGGCTCTGC 59.848 57.895 14.13 0.0 0.00 4.26 F
1696 1748 0.468226 AGTTCCACTCGGTGCTTCAA 59.532 50.000 0.00 0.0 31.34 2.69 F
3147 3200 2.058798 CAGCAAGAAAGAGTAACGCGA 58.941 47.619 15.93 0.0 0.00 5.87 F
3310 3370 1.078848 GAAGGTCTGTCTGGCGCAT 60.079 57.895 10.83 0.0 0.00 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1492 1544 0.251634 GCCTTGTGAGGGAGAAGAGG 59.748 60.000 0.00 0.00 43.75 3.69 R
1845 1897 1.207329 GTATCCGAACCAGTTCCTGCT 59.793 52.381 4.99 0.00 36.27 4.24 R
3208 3261 3.320673 AGTACAGAAGCTTGCTACCAC 57.679 47.619 2.10 0.55 0.00 4.16 R
4202 4262 0.251698 TGCCCCATGTCATGCTCAAA 60.252 50.000 7.35 0.00 0.00 2.69 R
5158 5300 0.107268 TCTCCATCATGGCGTGGATG 59.893 55.000 6.90 9.08 43.20 3.51 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
29 30 3.824815 TGCCAAGCATGAGGGAGA 58.175 55.556 0.00 0.00 31.71 3.71
83 84 8.833493 CATTGCAGATTGTATCAGTAGAATTCA 58.167 33.333 8.44 0.00 0.00 2.57
105 106 5.953548 TCAATCATTGTGAGTGAATCCCATT 59.046 36.000 7.54 0.00 46.66 3.16
130 131 4.401519 AGCCCAAGAAACATCATCATGAAG 59.598 41.667 0.00 0.00 33.72 3.02
150 151 3.838317 AAGCTACACTTGTGGATCTACCA 59.162 43.478 6.77 0.00 41.23 3.25
166 167 8.439971 TGGATCTACCAATGCTCACTATTAATT 58.560 33.333 0.00 0.00 46.75 1.40
167 168 8.940952 GGATCTACCAATGCTCACTATTAATTC 58.059 37.037 0.00 0.00 38.79 2.17
168 169 9.494271 GATCTACCAATGCTCACTATTAATTCA 57.506 33.333 0.00 0.00 0.00 2.57
169 170 9.851686 ATCTACCAATGCTCACTATTAATTCAA 57.148 29.630 0.00 0.00 0.00 2.69
170 171 9.109393 TCTACCAATGCTCACTATTAATTCAAC 57.891 33.333 0.00 0.00 0.00 3.18
171 172 7.701539 ACCAATGCTCACTATTAATTCAACA 57.298 32.000 0.00 0.00 0.00 3.33
172 173 8.121305 ACCAATGCTCACTATTAATTCAACAA 57.879 30.769 0.00 0.00 0.00 2.83
173 174 8.584157 ACCAATGCTCACTATTAATTCAACAAA 58.416 29.630 0.00 0.00 0.00 2.83
174 175 9.421806 CCAATGCTCACTATTAATTCAACAAAA 57.578 29.630 0.00 0.00 0.00 2.44
191 192 8.795786 TCAACAAAAATAATACAAGACAGTGC 57.204 30.769 0.00 0.00 0.00 4.40
192 193 7.865385 TCAACAAAAATAATACAAGACAGTGCC 59.135 33.333 0.00 0.00 0.00 5.01
193 194 7.283625 ACAAAAATAATACAAGACAGTGCCA 57.716 32.000 0.00 0.00 0.00 4.92
194 195 7.145323 ACAAAAATAATACAAGACAGTGCCAC 58.855 34.615 0.00 0.00 0.00 5.01
195 196 6.892658 AAAATAATACAAGACAGTGCCACA 57.107 33.333 0.00 0.00 0.00 4.17
196 197 5.880054 AATAATACAAGACAGTGCCACAC 57.120 39.130 0.00 0.00 34.10 3.82
197 198 2.928801 ATACAAGACAGTGCCACACA 57.071 45.000 0.00 0.00 36.74 3.72
198 199 2.238942 TACAAGACAGTGCCACACAG 57.761 50.000 0.00 0.00 36.74 3.66
199 200 0.464373 ACAAGACAGTGCCACACAGG 60.464 55.000 0.00 0.00 36.74 4.00
210 211 2.486472 CCACACAGGCTCTCAGAAAT 57.514 50.000 0.00 0.00 0.00 2.17
211 212 3.616956 CCACACAGGCTCTCAGAAATA 57.383 47.619 0.00 0.00 0.00 1.40
212 213 3.942829 CCACACAGGCTCTCAGAAATAA 58.057 45.455 0.00 0.00 0.00 1.40
213 214 3.686726 CCACACAGGCTCTCAGAAATAAC 59.313 47.826 0.00 0.00 0.00 1.89
242 243 4.186926 TGCAATCTGAAGACTATGAGCAC 58.813 43.478 0.00 0.00 0.00 4.40
252 253 7.432059 TGAAGACTATGAGCACAGAATGATAG 58.568 38.462 0.00 0.00 39.69 2.08
255 256 5.295950 ACTATGAGCACAGAATGATAGCAC 58.704 41.667 0.00 0.00 39.69 4.40
325 350 4.095946 TCCAATAATCTGCCTGCCTTTTT 58.904 39.130 0.00 0.00 0.00 1.94
339 364 2.557056 GCCTTTTTGGTCCAAGGTCTAC 59.443 50.000 4.09 0.00 41.63 2.59
348 373 4.100498 TGGTCCAAGGTCTACCGAATAATC 59.900 45.833 0.00 0.00 42.08 1.75
377 402 3.500448 TCACCAAACTAGCAACCATGA 57.500 42.857 0.00 0.00 0.00 3.07
386 411 5.505173 ACTAGCAACCATGACATATTTGC 57.495 39.130 18.94 18.94 42.35 3.68
397 422 7.229306 ACCATGACATATTTGCTATTCGTCAAT 59.771 33.333 0.00 0.00 35.72 2.57
398 423 7.536281 CCATGACATATTTGCTATTCGTCAATG 59.464 37.037 0.00 0.00 35.72 2.82
399 424 6.429624 TGACATATTTGCTATTCGTCAATGC 58.570 36.000 0.00 0.00 0.00 3.56
400 425 6.260714 TGACATATTTGCTATTCGTCAATGCT 59.739 34.615 0.00 0.00 0.00 3.79
401 426 6.662616 ACATATTTGCTATTCGTCAATGCTC 58.337 36.000 0.00 0.00 0.00 4.26
413 443 2.941720 GTCAATGCTCAGGGAGTTCATC 59.058 50.000 0.00 0.00 31.39 2.92
428 458 5.406780 GGAGTTCATCATCCATAAGCTAACG 59.593 44.000 0.00 0.00 35.54 3.18
444 474 4.079710 GCTAACGTCAAAATTCTACGCAC 58.920 43.478 6.99 0.00 40.18 5.34
445 475 4.376615 GCTAACGTCAAAATTCTACGCACA 60.377 41.667 6.99 0.00 40.18 4.57
453 484 4.503741 AAATTCTACGCACACAAATGCT 57.496 36.364 0.00 0.00 43.80 3.79
496 527 2.870372 GCCCGCAGCACAACTAAG 59.130 61.111 0.00 0.00 42.97 2.18
497 528 1.671054 GCCCGCAGCACAACTAAGA 60.671 57.895 0.00 0.00 42.97 2.10
595 627 4.075793 TCCACCCTCTCCTCCCCG 62.076 72.222 0.00 0.00 0.00 5.73
726 758 2.119655 GTAGGAAGAGAGGCCGCGA 61.120 63.158 8.23 0.00 0.00 5.87
800 837 3.053896 CTCGCGGGGGTTTTGGTC 61.054 66.667 6.13 0.00 0.00 4.02
915 959 1.891150 CTCAATCAATATGGGCCAGGC 59.109 52.381 13.78 1.26 0.00 4.85
920 964 1.152368 AATATGGGCCAGGCTCTGC 59.848 57.895 14.13 0.00 0.00 4.26
957 1001 2.687566 TTCTTCCTCCTCCGGCCC 60.688 66.667 0.00 0.00 0.00 5.80
1042 1094 1.730487 CCGACATCGACTCAGGAGG 59.270 63.158 2.09 0.00 43.02 4.30
1295 1347 2.934570 GCATGGCTTGTGGTGGGTG 61.935 63.158 2.12 0.00 0.00 4.61
1432 1484 2.997315 TCCTGCGAGGACCCTGTG 60.997 66.667 0.00 0.00 40.06 3.66
1436 1488 3.311110 GCGAGGACCCTGTGGACA 61.311 66.667 0.00 0.00 34.81 4.02
1467 1519 2.260434 GGAGTGCGGCTTCACGTA 59.740 61.111 0.00 0.00 41.61 3.57
1492 1544 2.087009 CGTTCGGCTCGTCAAGGTC 61.087 63.158 0.00 0.00 0.00 3.85
1500 1552 1.135228 GCTCGTCAAGGTCCTCTTCTC 60.135 57.143 0.00 0.00 32.41 2.87
1530 1582 6.825721 ACAAGGCAAATGTTTTCACCATTTAA 59.174 30.769 0.00 0.00 39.77 1.52
1556 1608 2.031069 TCGTGTAGCACTGTGAAGTCTC 60.031 50.000 12.86 0.00 31.34 3.36
1557 1609 2.287608 CGTGTAGCACTGTGAAGTCTCA 60.288 50.000 12.86 0.00 31.34 3.27
1575 1627 6.634805 AGTCTCATCGATTACATTGTGTCTT 58.365 36.000 0.00 0.00 0.00 3.01
1576 1628 7.099764 AGTCTCATCGATTACATTGTGTCTTT 58.900 34.615 0.00 0.00 0.00 2.52
1589 1641 3.351740 TGTGTCTTTTGCTGTTCTTGGA 58.648 40.909 0.00 0.00 0.00 3.53
1696 1748 0.468226 AGTTCCACTCGGTGCTTCAA 59.532 50.000 0.00 0.00 31.34 2.69
1732 1784 2.774439 TTCTCAAACCGAAAGCTTGC 57.226 45.000 0.00 0.00 0.00 4.01
1774 1826 4.701171 GTGACCTACACTCTGCTTAGTAGT 59.299 45.833 0.00 0.00 45.13 2.73
1797 1849 3.935203 GAGATCATTCTCTTGCCGTGAAA 59.065 43.478 0.00 0.00 44.29 2.69
1798 1850 3.686726 AGATCATTCTCTTGCCGTGAAAC 59.313 43.478 0.00 0.00 0.00 2.78
1838 1890 4.708726 GCTTGATGCTAAGTTGGATTGT 57.291 40.909 0.00 0.00 38.95 2.71
1843 1895 6.899393 TGATGCTAAGTTGGATTGTTCTTT 57.101 33.333 0.00 0.00 0.00 2.52
1845 1897 8.402798 TGATGCTAAGTTGGATTGTTCTTTTA 57.597 30.769 0.00 0.00 0.00 1.52
1905 1957 4.984161 CAGAATGATGTGGTTGTTTTGGAC 59.016 41.667 0.00 0.00 39.69 4.02
1989 2041 4.662468 TCCTGAGATCAGACAATACAGC 57.338 45.455 11.44 0.00 46.59 4.40
2024 2076 5.476254 TGTGGATAGATGAGCATACTGAGAG 59.524 44.000 0.00 0.00 0.00 3.20
2599 2652 2.162921 CTCGGTGTCGTTGCAGCAAG 62.163 60.000 8.49 3.14 36.75 4.01
2625 2678 4.516698 CAGAATGTTGGTCTTAGTGTGCTT 59.483 41.667 0.00 0.00 0.00 3.91
2802 2855 8.777865 TGTGAACTATGTCTAAAGAATGGAAG 57.222 34.615 0.00 0.00 0.00 3.46
3147 3200 2.058798 CAGCAAGAAAGAGTAACGCGA 58.941 47.619 15.93 0.00 0.00 5.87
3208 3261 3.164268 TGGGGTCAAAATGAACTCCATG 58.836 45.455 0.00 0.00 32.27 3.66
3238 3298 6.647067 AGCAAGCTTCTGTACTAACTTAACTG 59.353 38.462 0.00 0.00 0.00 3.16
3310 3370 1.078848 GAAGGTCTGTCTGGCGCAT 60.079 57.895 10.83 0.00 0.00 4.73
3442 3502 6.497785 TCTTTTTCAACCAACTCGTTTGTA 57.502 33.333 0.08 0.00 32.71 2.41
3607 3667 1.388547 TTCTCTGCTTGCACGGTTTT 58.611 45.000 0.00 0.00 0.00 2.43
3836 3896 2.821378 CACACCATGCAAGATTGGAAGA 59.179 45.455 11.04 0.00 36.79 2.87
3883 3943 6.176183 CCTTCAGTATCAGGAACAAACAGAT 58.824 40.000 0.00 0.00 30.81 2.90
3886 3946 5.248248 TCAGTATCAGGAACAAACAGATGGA 59.752 40.000 0.00 0.00 0.00 3.41
3892 3952 5.832595 TCAGGAACAAACAGATGGATTCAAA 59.167 36.000 0.00 0.00 0.00 2.69
3893 3953 5.922544 CAGGAACAAACAGATGGATTCAAAC 59.077 40.000 0.00 0.00 0.00 2.93
3947 4007 1.523154 GGACGGCAACTTTGATGGCA 61.523 55.000 0.00 0.00 43.00 4.92
4110 4170 2.592308 GCTCCCCTCGCTCCATTT 59.408 61.111 0.00 0.00 0.00 2.32
4163 4223 1.973281 GCAAGCAGGGCAAGCACTA 60.973 57.895 0.00 0.00 32.47 2.74
4454 4514 7.946381 TGTGGATGGTGCAAAATAGTTATTA 57.054 32.000 0.00 0.00 0.00 0.98
4483 4548 7.274367 CGCGTACTGTATAAAATCATGTCTTC 58.726 38.462 0.00 0.00 0.00 2.87
4597 4663 5.602145 TGTTTGACCTTCAGGGAAAAATGAT 59.398 36.000 0.00 0.00 40.27 2.45
4647 4713 8.141268 ACATGTATTTGGTTTAGGACAAACTTG 58.859 33.333 0.00 0.00 39.15 3.16
4705 4847 9.582648 ACATGGTATAAAATTGGTATTACTCCC 57.417 33.333 0.00 0.00 0.00 4.30
4706 4848 9.807921 CATGGTATAAAATTGGTATTACTCCCT 57.192 33.333 0.00 0.00 0.00 4.20
4708 4850 8.442374 TGGTATAAAATTGGTATTACTCCCTCC 58.558 37.037 0.00 0.00 0.00 4.30
4709 4851 7.605309 GGTATAAAATTGGTATTACTCCCTCCG 59.395 40.741 0.00 0.00 0.00 4.63
4710 4852 5.446260 AAAATTGGTATTACTCCCTCCGT 57.554 39.130 0.00 0.00 0.00 4.69
4711 4853 5.446260 AAATTGGTATTACTCCCTCCGTT 57.554 39.130 0.00 0.00 0.00 4.44
4712 4854 4.684484 ATTGGTATTACTCCCTCCGTTC 57.316 45.455 0.00 0.00 0.00 3.95
4713 4855 2.026641 TGGTATTACTCCCTCCGTTCG 58.973 52.381 0.00 0.00 0.00 3.95
4714 4856 1.339291 GGTATTACTCCCTCCGTTCGG 59.661 57.143 4.74 4.74 0.00 4.30
4715 4857 2.301346 GTATTACTCCCTCCGTTCGGA 58.699 52.381 13.34 13.34 0.00 4.55
4716 4858 1.856629 ATTACTCCCTCCGTTCGGAA 58.143 50.000 14.79 0.04 33.41 4.30
4717 4859 1.856629 TTACTCCCTCCGTTCGGAAT 58.143 50.000 14.79 2.09 33.41 3.01
4718 4860 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
4719 4861 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
4720 4862 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
4721 4863 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
4722 4864 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
4723 4865 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
4724 4866 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
4725 4867 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
4726 4868 3.581755 CTCCGTTCGGAATTACTTGTCA 58.418 45.455 14.79 0.00 33.41 3.58
4727 4869 3.319755 TCCGTTCGGAATTACTTGTCAC 58.680 45.455 11.66 0.00 0.00 3.67
4728 4870 3.061322 CCGTTCGGAATTACTTGTCACA 58.939 45.455 5.19 0.00 0.00 3.58
4729 4871 3.495377 CCGTTCGGAATTACTTGTCACAA 59.505 43.478 5.19 0.00 0.00 3.33
4730 4872 4.024725 CCGTTCGGAATTACTTGTCACAAA 60.025 41.667 5.19 0.00 0.00 2.83
4731 4873 5.503498 CGTTCGGAATTACTTGTCACAAAA 58.497 37.500 0.00 0.00 0.00 2.44
4732 4874 5.966503 CGTTCGGAATTACTTGTCACAAAAA 59.033 36.000 0.00 0.00 0.00 1.94
4733 4875 6.635239 CGTTCGGAATTACTTGTCACAAAAAT 59.365 34.615 0.00 0.00 0.00 1.82
4734 4876 7.357206 CGTTCGGAATTACTTGTCACAAAAATG 60.357 37.037 0.00 0.00 0.00 2.32
4735 4877 6.442952 TCGGAATTACTTGTCACAAAAATGG 58.557 36.000 0.00 0.00 0.00 3.16
4736 4878 6.263392 TCGGAATTACTTGTCACAAAAATGGA 59.737 34.615 0.00 0.00 0.00 3.41
4737 4879 7.040062 TCGGAATTACTTGTCACAAAAATGGAT 60.040 33.333 0.00 0.00 0.00 3.41
4738 4880 7.062138 CGGAATTACTTGTCACAAAAATGGATG 59.938 37.037 0.00 0.00 0.00 3.51
4739 4881 7.148590 GGAATTACTTGTCACAAAAATGGATGC 60.149 37.037 0.00 0.00 0.00 3.91
4740 4882 4.669206 ACTTGTCACAAAAATGGATGCA 57.331 36.364 0.00 0.00 0.00 3.96
4741 4883 5.217978 ACTTGTCACAAAAATGGATGCAT 57.782 34.783 0.00 0.00 0.00 3.96
4742 4884 5.232463 ACTTGTCACAAAAATGGATGCATC 58.768 37.500 18.81 18.81 0.00 3.91
4743 4885 5.011329 ACTTGTCACAAAAATGGATGCATCT 59.989 36.000 25.28 4.53 0.00 2.90
4744 4886 6.209192 ACTTGTCACAAAAATGGATGCATCTA 59.791 34.615 25.28 20.79 0.00 1.98
4745 4887 5.953183 TGTCACAAAAATGGATGCATCTAC 58.047 37.500 25.28 11.04 0.00 2.59
4746 4888 5.476254 TGTCACAAAAATGGATGCATCTACA 59.524 36.000 25.28 16.33 0.00 2.74
4747 4889 6.015603 TGTCACAAAAATGGATGCATCTACAA 60.016 34.615 25.28 10.04 0.00 2.41
4748 4890 6.308766 GTCACAAAAATGGATGCATCTACAAC 59.691 38.462 25.28 9.59 0.00 3.32
4749 4891 6.209192 TCACAAAAATGGATGCATCTACAACT 59.791 34.615 25.28 2.21 0.00 3.16
4750 4892 7.392953 TCACAAAAATGGATGCATCTACAACTA 59.607 33.333 25.28 0.00 0.00 2.24
4751 4893 8.028354 CACAAAAATGGATGCATCTACAACTAA 58.972 33.333 25.28 3.09 0.00 2.24
4752 4894 8.584157 ACAAAAATGGATGCATCTACAACTAAA 58.416 29.630 25.28 2.12 0.00 1.85
4753 4895 9.421806 CAAAAATGGATGCATCTACAACTAAAA 57.578 29.630 25.28 0.70 0.00 1.52
4757 4899 8.978874 ATGGATGCATCTACAACTAAAATACA 57.021 30.769 25.28 10.32 0.00 2.29
4758 4900 8.978874 TGGATGCATCTACAACTAAAATACAT 57.021 30.769 25.28 0.00 0.00 2.29
4759 4901 9.056005 TGGATGCATCTACAACTAAAATACATC 57.944 33.333 25.28 3.59 0.00 3.06
4760 4902 9.277783 GGATGCATCTACAACTAAAATACATCT 57.722 33.333 25.28 0.00 31.89 2.90
4781 4923 9.553064 ACATCTAGATACATTCATTTCTTGGAC 57.447 33.333 4.54 0.00 0.00 4.02
4782 4924 8.706936 CATCTAGATACATTCATTTCTTGGACG 58.293 37.037 4.54 0.00 0.00 4.79
4783 4925 8.007405 TCTAGATACATTCATTTCTTGGACGA 57.993 34.615 0.00 0.00 0.00 4.20
4784 4926 8.138074 TCTAGATACATTCATTTCTTGGACGAG 58.862 37.037 0.00 0.00 0.00 4.18
4785 4927 6.644347 AGATACATTCATTTCTTGGACGAGT 58.356 36.000 0.00 0.00 0.00 4.18
4786 4928 7.782049 AGATACATTCATTTCTTGGACGAGTA 58.218 34.615 0.00 0.00 0.00 2.59
4787 4929 8.258007 AGATACATTCATTTCTTGGACGAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
4788 4930 8.964476 ATACATTCATTTCTTGGACGAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
4789 4931 7.687941 ACATTCATTTCTTGGACGAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
4790 4932 7.752695 ACATTCATTTCTTGGACGAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
4791 4933 6.737254 TTCATTTCTTGGACGAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
4792 4934 4.868171 TCATTTCTTGGACGAGTAATTCCG 59.132 41.667 0.00 0.00 0.00 4.30
4793 4935 4.524316 TTTCTTGGACGAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
4794 4936 4.524316 TTCTTGGACGAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
4795 4937 3.841643 TCTTGGACGAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
4796 4938 2.267188 TGGACGAGTAATTCCGAACG 57.733 50.000 0.00 0.00 0.00 3.95
4797 4939 1.135315 TGGACGAGTAATTCCGAACGG 60.135 52.381 6.94 6.94 0.00 4.44
4798 4940 1.133025 GGACGAGTAATTCCGAACGGA 59.867 52.381 12.04 12.04 43.52 4.69
4799 4941 2.448219 GACGAGTAATTCCGAACGGAG 58.552 52.381 15.34 5.60 46.06 4.63
4800 4942 1.133790 ACGAGTAATTCCGAACGGAGG 59.866 52.381 15.34 4.28 46.06 4.30
4801 4943 1.535437 CGAGTAATTCCGAACGGAGGG 60.535 57.143 15.34 0.00 46.06 4.30
4802 4944 1.753073 GAGTAATTCCGAACGGAGGGA 59.247 52.381 15.34 2.49 46.06 4.20
4803 4945 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
4804 4946 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
4805 4947 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
4898 5040 0.402504 TATTTGTCTTGGTGGCCGGT 59.597 50.000 1.90 0.00 0.00 5.28
4903 5045 4.335647 CTTGGTGGCCGGTCAGCT 62.336 66.667 35.39 0.00 36.25 4.24
4966 5108 6.038985 TGATAGTTCAGAATGCTCTTTCTCG 58.961 40.000 0.00 0.00 33.69 4.04
4980 5122 3.319405 TCTTTCTCGATAGCCATCTCACC 59.681 47.826 0.00 0.00 0.00 4.02
5158 5300 5.701290 ACAAACTAGACTAGTGATTGCCAAC 59.299 40.000 20.03 0.00 39.39 3.77
5199 5341 7.923878 GGAGATAGAATGGTGAGACTTTAGTTC 59.076 40.741 0.00 0.00 0.00 3.01
5233 5375 5.724328 TGCCTCAAACACAAAACACATAAA 58.276 33.333 0.00 0.00 0.00 1.40
5305 6946 5.663106 TCTCTCACTTCCCTGTGCTAAATAT 59.337 40.000 0.00 0.00 37.81 1.28
5335 6976 1.450312 GCGAGGTGGACCATGGAAG 60.450 63.158 21.47 1.18 38.89 3.46
5344 6985 0.541764 GACCATGGAAGTTTGGGCCA 60.542 55.000 21.47 0.00 34.73 5.36
5364 7005 3.181503 CCATGGCTTTCTGATTTCGTCTG 60.182 47.826 0.00 0.00 0.00 3.51
5365 7006 1.806542 TGGCTTTCTGATTTCGTCTGC 59.193 47.619 0.00 0.00 0.00 4.26
5395 7036 9.426837 CACATGTTATGTTTCCAATTTTCATCT 57.573 29.630 0.00 0.00 42.70 2.90
5404 7045 9.263538 TGTTTCCAATTTTCATCTCATTTTCTG 57.736 29.630 0.00 0.00 0.00 3.02
5405 7046 9.480053 GTTTCCAATTTTCATCTCATTTTCTGA 57.520 29.630 0.00 0.00 0.00 3.27
5425 7066 9.829507 TTTCTGAAAAACAAATTCCATATGTGT 57.170 25.926 0.00 0.00 0.00 3.72
5445 7086 4.622701 GTTGTGATCCAACCAGATAAGC 57.377 45.455 13.20 0.00 46.39 3.09
5446 7087 3.998913 TGTGATCCAACCAGATAAGCA 57.001 42.857 0.00 0.00 0.00 3.91
5447 7088 4.299586 TGTGATCCAACCAGATAAGCAA 57.700 40.909 0.00 0.00 0.00 3.91
5448 7089 4.661222 TGTGATCCAACCAGATAAGCAAA 58.339 39.130 0.00 0.00 0.00 3.68
5449 7090 4.458989 TGTGATCCAACCAGATAAGCAAAC 59.541 41.667 0.00 0.00 0.00 2.93
5450 7091 4.702131 GTGATCCAACCAGATAAGCAAACT 59.298 41.667 0.00 0.00 0.00 2.66
5451 7092 5.880332 GTGATCCAACCAGATAAGCAAACTA 59.120 40.000 0.00 0.00 0.00 2.24
5452 7093 6.037610 GTGATCCAACCAGATAAGCAAACTAG 59.962 42.308 0.00 0.00 0.00 2.57
5453 7094 4.843728 TCCAACCAGATAAGCAAACTAGG 58.156 43.478 0.00 0.00 0.00 3.02
5454 7095 4.288626 TCCAACCAGATAAGCAAACTAGGT 59.711 41.667 0.00 0.00 0.00 3.08
5455 7096 4.636206 CCAACCAGATAAGCAAACTAGGTC 59.364 45.833 0.00 0.00 0.00 3.85
5456 7097 5.491982 CAACCAGATAAGCAAACTAGGTCT 58.508 41.667 0.00 0.00 0.00 3.85
5457 7098 6.351881 CCAACCAGATAAGCAAACTAGGTCTA 60.352 42.308 0.00 0.00 0.00 2.59
5458 7099 6.869206 ACCAGATAAGCAAACTAGGTCTAA 57.131 37.500 0.00 0.00 0.00 2.10
5459 7100 7.439108 ACCAGATAAGCAAACTAGGTCTAAT 57.561 36.000 0.00 0.00 0.00 1.73
5460 7101 8.548880 ACCAGATAAGCAAACTAGGTCTAATA 57.451 34.615 0.00 0.00 0.00 0.98
5461 7102 8.989131 ACCAGATAAGCAAACTAGGTCTAATAA 58.011 33.333 0.00 0.00 0.00 1.40
5466 7107 7.787725 AAGCAAACTAGGTCTAATAATTCGG 57.212 36.000 0.00 0.00 0.00 4.30
5467 7108 6.885922 AGCAAACTAGGTCTAATAATTCGGT 58.114 36.000 0.00 0.00 0.00 4.69
5468 7109 7.336396 AGCAAACTAGGTCTAATAATTCGGTT 58.664 34.615 0.00 0.00 0.00 4.44
5469 7110 7.280205 AGCAAACTAGGTCTAATAATTCGGTTG 59.720 37.037 0.00 0.00 0.00 3.77
5470 7111 7.065443 GCAAACTAGGTCTAATAATTCGGTTGT 59.935 37.037 0.00 0.00 0.00 3.32
5471 7112 8.388103 CAAACTAGGTCTAATAATTCGGTTGTG 58.612 37.037 0.00 0.00 0.00 3.33
5472 7113 6.579865 ACTAGGTCTAATAATTCGGTTGTGG 58.420 40.000 0.00 0.00 0.00 4.17
5473 7114 5.431179 AGGTCTAATAATTCGGTTGTGGT 57.569 39.130 0.00 0.00 0.00 4.16
5474 7115 5.812286 AGGTCTAATAATTCGGTTGTGGTT 58.188 37.500 0.00 0.00 0.00 3.67
5475 7116 6.243148 AGGTCTAATAATTCGGTTGTGGTTT 58.757 36.000 0.00 0.00 0.00 3.27
5476 7117 7.396418 AGGTCTAATAATTCGGTTGTGGTTTA 58.604 34.615 0.00 0.00 0.00 2.01
5477 7118 8.050930 AGGTCTAATAATTCGGTTGTGGTTTAT 58.949 33.333 0.00 0.00 0.00 1.40
5478 7119 8.126700 GGTCTAATAATTCGGTTGTGGTTTATG 58.873 37.037 0.00 0.00 0.00 1.90
5479 7120 8.671028 GTCTAATAATTCGGTTGTGGTTTATGT 58.329 33.333 0.00 0.00 0.00 2.29
5480 7121 8.670135 TCTAATAATTCGGTTGTGGTTTATGTG 58.330 33.333 0.00 0.00 0.00 3.21
5481 7122 6.827586 ATAATTCGGTTGTGGTTTATGTGT 57.172 33.333 0.00 0.00 0.00 3.72
5482 7123 4.759516 ATTCGGTTGTGGTTTATGTGTC 57.240 40.909 0.00 0.00 0.00 3.67
5497 7138 9.244799 GGTTTATGTGTCTTACCTTTCTTTTTG 57.755 33.333 0.00 0.00 0.00 2.44
5532 7173 7.554959 TCTAGTGACAAAAATCTACTCCCTT 57.445 36.000 0.00 0.00 0.00 3.95
5536 7177 5.120363 GTGACAAAAATCTACTCCCTTCGTC 59.880 44.000 0.00 0.00 0.00 4.20
5547 7188 4.035112 ACTCCCTTCGTCCCATAATGTAA 58.965 43.478 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.961019 GCTTGGCATTTGGTCTGTCA 59.039 50.000 0.00 0.00 0.00 3.58
1 2 0.961019 TGCTTGGCATTTGGTCTGTC 59.039 50.000 0.00 0.00 31.71 3.51
2 3 3.130264 TGCTTGGCATTTGGTCTGT 57.870 47.368 0.00 0.00 31.71 3.41
22 23 3.636153 AAATGCTGGTAACTCTCCCTC 57.364 47.619 0.00 0.00 37.61 4.30
28 29 8.458843 TCTATTTTGCTAAAATGCTGGTAACTC 58.541 33.333 13.65 0.00 41.01 3.01
29 30 8.348285 TCTATTTTGCTAAAATGCTGGTAACT 57.652 30.769 13.65 0.00 41.01 2.24
83 84 5.953548 TGAATGGGATTCACTCACAATGATT 59.046 36.000 0.00 0.00 41.71 2.57
92 93 1.064463 TGGGCTGAATGGGATTCACTC 60.064 52.381 0.00 0.00 43.84 3.51
105 106 3.438216 TGATGATGTTTCTTGGGCTGA 57.562 42.857 0.00 0.00 0.00 4.26
130 131 3.887621 TGGTAGATCCACAAGTGTAGC 57.112 47.619 0.00 0.00 41.93 3.58
166 167 7.865385 GGCACTGTCTTGTATTATTTTTGTTGA 59.135 33.333 0.00 0.00 0.00 3.18
167 168 7.651304 TGGCACTGTCTTGTATTATTTTTGTTG 59.349 33.333 0.00 0.00 0.00 3.33
168 169 7.651704 GTGGCACTGTCTTGTATTATTTTTGTT 59.348 33.333 11.13 0.00 0.00 2.83
169 170 7.145323 GTGGCACTGTCTTGTATTATTTTTGT 58.855 34.615 11.13 0.00 0.00 2.83
170 171 7.114811 GTGTGGCACTGTCTTGTATTATTTTTG 59.885 37.037 19.83 0.00 0.00 2.44
171 172 7.145323 GTGTGGCACTGTCTTGTATTATTTTT 58.855 34.615 19.83 0.00 0.00 1.94
172 173 6.264292 TGTGTGGCACTGTCTTGTATTATTTT 59.736 34.615 19.83 0.00 35.11 1.82
173 174 5.767665 TGTGTGGCACTGTCTTGTATTATTT 59.232 36.000 19.83 0.00 35.11 1.40
174 175 5.312895 TGTGTGGCACTGTCTTGTATTATT 58.687 37.500 19.83 0.00 35.11 1.40
175 176 4.905429 TGTGTGGCACTGTCTTGTATTAT 58.095 39.130 19.83 0.00 35.11 1.28
176 177 4.314961 CTGTGTGGCACTGTCTTGTATTA 58.685 43.478 19.83 0.00 35.11 0.98
177 178 3.141398 CTGTGTGGCACTGTCTTGTATT 58.859 45.455 19.83 0.00 35.11 1.89
178 179 2.550855 CCTGTGTGGCACTGTCTTGTAT 60.551 50.000 19.83 0.00 35.11 2.29
179 180 1.202639 CCTGTGTGGCACTGTCTTGTA 60.203 52.381 19.83 0.00 35.11 2.41
180 181 0.464373 CCTGTGTGGCACTGTCTTGT 60.464 55.000 19.83 0.00 35.11 3.16
181 182 2.324215 CCTGTGTGGCACTGTCTTG 58.676 57.895 19.83 3.28 35.11 3.02
182 183 4.885426 CCTGTGTGGCACTGTCTT 57.115 55.556 19.83 0.00 35.11 3.01
191 192 2.486472 ATTTCTGAGAGCCTGTGTGG 57.514 50.000 0.00 0.00 39.35 4.17
192 193 4.318332 TGTTATTTCTGAGAGCCTGTGTG 58.682 43.478 0.00 0.00 0.00 3.82
193 194 4.623932 TGTTATTTCTGAGAGCCTGTGT 57.376 40.909 0.00 0.00 0.00 3.72
194 195 5.947228 TTTGTTATTTCTGAGAGCCTGTG 57.053 39.130 0.00 0.00 0.00 3.66
195 196 7.335422 CAGTATTTGTTATTTCTGAGAGCCTGT 59.665 37.037 0.00 0.00 0.00 4.00
196 197 7.678218 GCAGTATTTGTTATTTCTGAGAGCCTG 60.678 40.741 0.00 0.00 0.00 4.85
197 198 6.317391 GCAGTATTTGTTATTTCTGAGAGCCT 59.683 38.462 0.00 0.00 0.00 4.58
198 199 6.094048 TGCAGTATTTGTTATTTCTGAGAGCC 59.906 38.462 0.00 0.00 0.00 4.70
199 200 7.076842 TGCAGTATTTGTTATTTCTGAGAGC 57.923 36.000 0.00 0.00 0.00 4.09
200 201 9.713740 GATTGCAGTATTTGTTATTTCTGAGAG 57.286 33.333 0.00 0.00 0.00 3.20
201 202 9.453572 AGATTGCAGTATTTGTTATTTCTGAGA 57.546 29.630 0.00 0.00 0.00 3.27
202 203 9.499585 CAGATTGCAGTATTTGTTATTTCTGAG 57.500 33.333 0.00 0.00 0.00 3.35
203 204 9.230122 TCAGATTGCAGTATTTGTTATTTCTGA 57.770 29.630 0.00 0.00 0.00 3.27
204 205 9.844790 TTCAGATTGCAGTATTTGTTATTTCTG 57.155 29.630 0.00 0.00 0.00 3.02
207 208 9.846248 GTCTTCAGATTGCAGTATTTGTTATTT 57.154 29.630 0.00 0.00 0.00 1.40
208 209 9.236006 AGTCTTCAGATTGCAGTATTTGTTATT 57.764 29.630 0.00 0.00 0.00 1.40
209 210 8.798859 AGTCTTCAGATTGCAGTATTTGTTAT 57.201 30.769 0.00 0.00 0.00 1.89
210 211 9.890629 ATAGTCTTCAGATTGCAGTATTTGTTA 57.109 29.630 0.00 0.00 0.00 2.41
211 212 8.671921 CATAGTCTTCAGATTGCAGTATTTGTT 58.328 33.333 0.00 0.00 0.00 2.83
212 213 8.043113 TCATAGTCTTCAGATTGCAGTATTTGT 58.957 33.333 0.00 0.00 0.00 2.83
213 214 8.429493 TCATAGTCTTCAGATTGCAGTATTTG 57.571 34.615 0.00 0.00 0.00 2.32
231 232 5.404968 GTGCTATCATTCTGTGCTCATAGTC 59.595 44.000 0.00 0.00 0.00 2.59
252 253 4.811024 TCCGTATCTGAATTCTGAATGTGC 59.189 41.667 17.62 5.94 0.00 4.57
255 256 6.259608 AGCTTTCCGTATCTGAATTCTGAATG 59.740 38.462 17.62 12.12 0.00 2.67
325 350 1.946984 ATTCGGTAGACCTTGGACCA 58.053 50.000 0.00 0.00 32.39 4.02
339 364 4.058817 GGTGAAGTAGGCAGATTATTCGG 58.941 47.826 0.00 0.00 0.00 4.30
348 373 3.003480 GCTAGTTTGGTGAAGTAGGCAG 58.997 50.000 0.00 0.00 40.28 4.85
377 402 6.260714 TGAGCATTGACGAATAGCAAATATGT 59.739 34.615 0.00 0.00 0.00 2.29
386 411 3.181471 ACTCCCTGAGCATTGACGAATAG 60.181 47.826 0.00 0.00 32.04 1.73
397 422 1.487976 GGATGATGAACTCCCTGAGCA 59.512 52.381 0.00 0.00 32.04 4.26
398 423 1.487976 TGGATGATGAACTCCCTGAGC 59.512 52.381 0.00 0.00 32.04 4.26
399 424 5.549347 CTTATGGATGATGAACTCCCTGAG 58.451 45.833 0.00 0.00 35.52 3.35
400 425 4.202398 GCTTATGGATGATGAACTCCCTGA 60.202 45.833 0.00 0.00 0.00 3.86
401 426 4.070716 GCTTATGGATGATGAACTCCCTG 58.929 47.826 0.00 0.00 0.00 4.45
413 443 7.697691 AGAATTTTGACGTTAGCTTATGGATG 58.302 34.615 0.00 0.00 0.00 3.51
428 458 5.387342 GCATTTGTGTGCGTAGAATTTTGAC 60.387 40.000 0.00 0.00 35.10 3.18
453 484 7.966753 CAGTTACACTAATTCTGTAGAGCGTTA 59.033 37.037 0.00 0.00 0.00 3.18
492 523 1.461127 GAAAGGTGCGTGTGCTCTTAG 59.539 52.381 0.00 0.00 43.34 2.18
494 525 0.179045 AGAAAGGTGCGTGTGCTCTT 60.179 50.000 0.00 0.00 43.34 2.85
496 527 0.880278 TCAGAAAGGTGCGTGTGCTC 60.880 55.000 0.00 0.00 43.34 4.26
497 528 0.882042 CTCAGAAAGGTGCGTGTGCT 60.882 55.000 0.00 0.00 43.34 4.40
706 738 1.737201 GCGGCCTCTCTTCCTACTC 59.263 63.158 0.00 0.00 0.00 2.59
709 741 2.119655 GTCGCGGCCTCTCTTCCTA 61.120 63.158 6.13 0.00 0.00 2.94
734 766 3.785859 GCTCATGGAGGCCACCGA 61.786 66.667 15.06 5.70 35.80 4.69
874 911 1.666553 CGCGGCCTCTACACACAAA 60.667 57.895 0.00 0.00 0.00 2.83
915 959 4.767255 AGGCCGGCTTTCGCAGAG 62.767 66.667 28.56 0.00 38.43 3.35
957 1001 2.046285 CAAAACCCTAGGCGGCTGG 61.046 63.158 23.55 19.59 0.00 4.85
1029 1081 0.323816 TGTGCTCCTCCTGAGTCGAT 60.324 55.000 0.00 0.00 43.48 3.59
1042 1094 0.676151 CCTTCCTCCTGCTTGTGCTC 60.676 60.000 0.00 0.00 40.48 4.26
1047 1099 1.077858 GCCTCCTTCCTCCTGCTTG 60.078 63.158 0.00 0.00 0.00 4.01
1226 1278 2.835389 GGGGGAGAACTAGAAAGAGGT 58.165 52.381 0.00 0.00 0.00 3.85
1271 1323 2.568090 CACAAGCCATGCGGGAAC 59.432 61.111 0.00 0.00 40.01 3.62
1278 1330 2.934570 GCACCCACCACAAGCCATG 61.935 63.158 0.00 0.00 0.00 3.66
1282 1334 1.391157 TTCAAGCACCCACCACAAGC 61.391 55.000 0.00 0.00 0.00 4.01
1285 1337 1.411977 CAAATTCAAGCACCCACCACA 59.588 47.619 0.00 0.00 0.00 4.17
1295 1347 2.460757 ATGTGGCCACAAATTCAAGC 57.539 45.000 40.48 9.32 45.41 4.01
1432 1484 2.266055 CTGGCGACCCTCTTGTCC 59.734 66.667 0.00 0.00 31.35 4.02
1436 1488 2.685380 CTCCCTGGCGACCCTCTT 60.685 66.667 0.00 0.00 0.00 2.85
1467 1519 3.441290 CGAGCCGAACGGAGAGGT 61.441 66.667 17.63 0.00 37.50 3.85
1468 1520 3.398353 GACGAGCCGAACGGAGAGG 62.398 68.421 17.63 5.15 37.50 3.69
1492 1544 0.251634 GCCTTGTGAGGGAGAAGAGG 59.748 60.000 0.00 0.00 43.75 3.69
1500 1552 3.181467 TGAAAACATTTGCCTTGTGAGGG 60.181 43.478 0.00 0.00 43.75 4.30
1546 1598 6.311200 CACAATGTAATCGATGAGACTTCACA 59.689 38.462 0.00 0.00 35.83 3.58
1556 1608 6.249893 CAGCAAAAGACACAATGTAATCGATG 59.750 38.462 0.00 0.00 0.00 3.84
1557 1609 6.072508 ACAGCAAAAGACACAATGTAATCGAT 60.073 34.615 0.00 0.00 0.00 3.59
1575 1627 2.433604 TGCCAATTCCAAGAACAGCAAA 59.566 40.909 0.00 0.00 0.00 3.68
1576 1628 2.036217 CTGCCAATTCCAAGAACAGCAA 59.964 45.455 0.00 0.00 0.00 3.91
1589 1641 1.839424 GTAACCAGCTCCTGCCAATT 58.161 50.000 0.00 0.00 40.80 2.32
1696 1748 1.499007 AGAATCAACCCACCCACACTT 59.501 47.619 0.00 0.00 0.00 3.16
1724 1776 2.426024 CAGCCAGATGTATGCAAGCTTT 59.574 45.455 0.00 0.00 0.00 3.51
1732 1784 4.034858 GTCACATTGACAGCCAGATGTATG 59.965 45.833 1.34 0.00 46.22 2.39
1797 1849 6.712095 TCAAGCTCTTGATTAAACATCTGTGT 59.288 34.615 8.14 0.00 43.90 3.72
1798 1850 7.137490 TCAAGCTCTTGATTAAACATCTGTG 57.863 36.000 8.14 0.00 43.90 3.66
1838 1890 3.813166 CGAACCAGTTCCTGCTAAAAGAA 59.187 43.478 4.99 0.00 36.27 2.52
1843 1895 1.344065 TCCGAACCAGTTCCTGCTAA 58.656 50.000 4.99 0.00 36.27 3.09
1845 1897 1.207329 GTATCCGAACCAGTTCCTGCT 59.793 52.381 4.99 0.00 36.27 4.24
1905 1957 2.791560 CGTCTCATACAGATTCCTTGCG 59.208 50.000 0.00 0.00 32.08 4.85
1989 2041 2.905075 TCTATCCACAATGGCAAGTCG 58.095 47.619 0.00 0.00 37.47 4.18
2024 2076 6.854496 TCATAATTGATTTACCACGTAGCC 57.146 37.500 0.00 0.00 0.00 3.93
2599 2652 3.815401 ACACTAAGACCAACATTCTGCAC 59.185 43.478 0.00 0.00 0.00 4.57
2625 2678 5.127194 GTCATCTTAGGTACCTGACATGTGA 59.873 44.000 25.33 16.38 36.94 3.58
2802 2855 6.968131 TTACAGATATTTCACAGCACTGTC 57.032 37.500 0.00 0.00 42.83 3.51
3000 3053 6.665680 CCTACATAGCATATGGACTTCTAGGT 59.334 42.308 4.56 7.24 0.00 3.08
3147 3200 7.436118 TCCCTACAAAATTAGCGAATATACGT 58.564 34.615 0.00 0.00 35.59 3.57
3208 3261 3.320673 AGTACAGAAGCTTGCTACCAC 57.679 47.619 2.10 0.55 0.00 4.16
3442 3502 8.455903 TCTCAGACAAAAATGAATTGAAGACT 57.544 30.769 0.00 0.00 0.00 3.24
3490 3550 4.890088 ACTAACTCGGAAGCAATACACAA 58.110 39.130 0.00 0.00 0.00 3.33
3491 3551 4.530710 ACTAACTCGGAAGCAATACACA 57.469 40.909 0.00 0.00 0.00 3.72
3607 3667 6.479001 CCTTAAAGTTTGAAGAGTTCTGACGA 59.521 38.462 0.00 0.00 0.00 4.20
3700 3760 6.007076 TGGTTGGTATACAAATGAAAGCTCA 58.993 36.000 5.01 0.00 41.58 4.26
3883 3943 7.506599 AGGTATGCATATGATTGTTTGAATCCA 59.493 33.333 10.16 0.00 0.00 3.41
3886 3946 8.916062 TCAAGGTATGCATATGATTGTTTGAAT 58.084 29.630 10.16 0.00 0.00 2.57
3892 3952 7.886629 ACTTTCAAGGTATGCATATGATTGT 57.113 32.000 10.16 8.54 0.00 2.71
3947 4007 0.912486 CCCTGGGAGAAACCGAGAAT 59.088 55.000 7.01 0.00 45.50 2.40
4110 4170 4.735132 CTTCACCGCCGCCGAAGA 62.735 66.667 7.69 0.00 38.75 2.87
4163 4223 2.224113 CCTCAAACATGCCAGCAAGTTT 60.224 45.455 17.52 17.52 44.99 2.66
4202 4262 0.251698 TGCCCCATGTCATGCTCAAA 60.252 50.000 7.35 0.00 0.00 2.69
4293 4353 3.756082 AAGCACATCCCCTATTTTCCA 57.244 42.857 0.00 0.00 0.00 3.53
4454 4514 5.204409 TGATTTTATACAGTACGCGGGAT 57.796 39.130 12.47 0.00 0.00 3.85
4483 4548 2.684881 AGCAGAATAACAGGCAAATCCG 59.315 45.455 0.00 0.00 40.77 4.18
4597 4663 9.126151 TGTTACATTTTGTTCAAAGTCTCCATA 57.874 29.630 0.00 0.00 0.00 2.74
4647 4713 5.904362 ATTAGCAGAGAAATTGTTGGTCC 57.096 39.130 0.00 0.00 0.00 4.46
4701 4843 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
4702 4844 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
4703 4845 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
4704 4846 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
4705 4847 3.367025 GTGACAAGTAATTCCGAACGGAG 59.633 47.826 15.34 5.60 46.06 4.63
4706 4848 3.243805 TGTGACAAGTAATTCCGAACGGA 60.244 43.478 12.04 12.04 43.52 4.69
4707 4849 3.061322 TGTGACAAGTAATTCCGAACGG 58.939 45.455 6.94 6.94 0.00 4.44
4708 4850 4.718858 TTGTGACAAGTAATTCCGAACG 57.281 40.909 0.00 0.00 0.00 3.95
4709 4851 7.096230 CCATTTTTGTGACAAGTAATTCCGAAC 60.096 37.037 0.00 0.00 0.00 3.95
4710 4852 6.920758 CCATTTTTGTGACAAGTAATTCCGAA 59.079 34.615 0.00 0.00 0.00 4.30
4711 4853 6.263392 TCCATTTTTGTGACAAGTAATTCCGA 59.737 34.615 0.00 0.00 0.00 4.55
4712 4854 6.442952 TCCATTTTTGTGACAAGTAATTCCG 58.557 36.000 0.00 0.00 0.00 4.30
4713 4855 7.148590 GCATCCATTTTTGTGACAAGTAATTCC 60.149 37.037 0.00 0.00 0.00 3.01
4714 4856 7.384660 TGCATCCATTTTTGTGACAAGTAATTC 59.615 33.333 0.00 0.00 0.00 2.17
4715 4857 7.215789 TGCATCCATTTTTGTGACAAGTAATT 58.784 30.769 0.00 0.00 0.00 1.40
4716 4858 6.757237 TGCATCCATTTTTGTGACAAGTAAT 58.243 32.000 0.00 0.32 0.00 1.89
4717 4859 6.154203 TGCATCCATTTTTGTGACAAGTAA 57.846 33.333 0.00 0.00 0.00 2.24
4718 4860 5.781210 TGCATCCATTTTTGTGACAAGTA 57.219 34.783 0.00 0.00 0.00 2.24
4719 4861 4.669206 TGCATCCATTTTTGTGACAAGT 57.331 36.364 0.00 0.00 0.00 3.16
4720 4862 5.475719 AGATGCATCCATTTTTGTGACAAG 58.524 37.500 23.06 0.00 0.00 3.16
4721 4863 5.471556 AGATGCATCCATTTTTGTGACAA 57.528 34.783 23.06 0.00 0.00 3.18
4722 4864 5.476254 TGTAGATGCATCCATTTTTGTGACA 59.524 36.000 23.06 8.75 0.00 3.58
4723 4865 5.953183 TGTAGATGCATCCATTTTTGTGAC 58.047 37.500 23.06 6.53 0.00 3.67
4724 4866 6.209192 AGTTGTAGATGCATCCATTTTTGTGA 59.791 34.615 23.06 0.00 0.00 3.58
4725 4867 6.392354 AGTTGTAGATGCATCCATTTTTGTG 58.608 36.000 23.06 0.00 0.00 3.33
4726 4868 6.594788 AGTTGTAGATGCATCCATTTTTGT 57.405 33.333 23.06 4.58 0.00 2.83
4727 4869 8.984891 TTTAGTTGTAGATGCATCCATTTTTG 57.015 30.769 23.06 0.00 0.00 2.44
4731 4873 9.407380 TGTATTTTAGTTGTAGATGCATCCATT 57.593 29.630 23.06 7.62 0.00 3.16
4732 4874 8.978874 TGTATTTTAGTTGTAGATGCATCCAT 57.021 30.769 23.06 8.39 0.00 3.41
4733 4875 8.978874 ATGTATTTTAGTTGTAGATGCATCCA 57.021 30.769 23.06 12.10 0.00 3.41
4734 4876 9.277783 AGATGTATTTTAGTTGTAGATGCATCC 57.722 33.333 23.06 9.46 39.26 3.51
4755 4897 9.553064 GTCCAAGAAATGAATGTATCTAGATGT 57.447 33.333 15.79 0.00 0.00 3.06
4756 4898 8.706936 CGTCCAAGAAATGAATGTATCTAGATG 58.293 37.037 15.79 0.00 0.00 2.90
4757 4899 8.642432 TCGTCCAAGAAATGAATGTATCTAGAT 58.358 33.333 10.73 10.73 0.00 1.98
4758 4900 8.007405 TCGTCCAAGAAATGAATGTATCTAGA 57.993 34.615 0.00 0.00 0.00 2.43
4759 4901 7.923344 ACTCGTCCAAGAAATGAATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
4760 4902 7.782049 ACTCGTCCAAGAAATGAATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
4761 4903 6.644347 ACTCGTCCAAGAAATGAATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
4762 4904 6.910536 ACTCGTCCAAGAAATGAATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
4763 4905 8.964476 ATTACTCGTCCAAGAAATGAATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
4764 4906 8.786826 AATTACTCGTCCAAGAAATGAATGTA 57.213 30.769 0.00 0.00 0.00 2.29
4765 4907 7.148239 GGAATTACTCGTCCAAGAAATGAATGT 60.148 37.037 0.00 0.00 33.79 2.71
4766 4908 7.189512 GGAATTACTCGTCCAAGAAATGAATG 58.810 38.462 0.00 0.00 33.79 2.67
4767 4909 6.037172 CGGAATTACTCGTCCAAGAAATGAAT 59.963 38.462 0.00 0.00 33.10 2.57
4768 4910 5.350365 CGGAATTACTCGTCCAAGAAATGAA 59.650 40.000 0.00 0.00 33.10 2.57
4769 4911 4.868171 CGGAATTACTCGTCCAAGAAATGA 59.132 41.667 0.00 0.00 33.10 2.57
4770 4912 4.868171 TCGGAATTACTCGTCCAAGAAATG 59.132 41.667 0.00 0.00 33.10 2.32
4771 4913 5.080969 TCGGAATTACTCGTCCAAGAAAT 57.919 39.130 0.00 0.00 33.10 2.17
4772 4914 4.524316 TCGGAATTACTCGTCCAAGAAA 57.476 40.909 0.00 0.00 33.10 2.52
4773 4915 4.240096 GTTCGGAATTACTCGTCCAAGAA 58.760 43.478 0.00 0.00 33.10 2.52
4774 4916 3.671433 CGTTCGGAATTACTCGTCCAAGA 60.671 47.826 0.00 0.00 33.10 3.02
4775 4917 2.597305 CGTTCGGAATTACTCGTCCAAG 59.403 50.000 0.00 0.00 33.10 3.61
4776 4918 2.598589 CGTTCGGAATTACTCGTCCAA 58.401 47.619 0.00 0.00 33.10 3.53
4777 4919 1.135315 CCGTTCGGAATTACTCGTCCA 60.135 52.381 5.19 0.00 33.10 4.02
4778 4920 1.133025 TCCGTTCGGAATTACTCGTCC 59.867 52.381 11.66 0.00 0.00 4.79
4779 4921 2.448219 CTCCGTTCGGAATTACTCGTC 58.552 52.381 14.79 0.00 33.41 4.20
4780 4922 1.133790 CCTCCGTTCGGAATTACTCGT 59.866 52.381 14.79 0.00 33.41 4.18
4781 4923 1.535437 CCCTCCGTTCGGAATTACTCG 60.535 57.143 14.79 1.97 33.41 4.18
4782 4924 1.753073 TCCCTCCGTTCGGAATTACTC 59.247 52.381 14.79 0.00 33.41 2.59
4783 4925 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
4784 4926 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
4785 4927 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
4786 4928 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
4787 4929 1.064166 TCTACTCCCTCCGTTCGGAAT 60.064 52.381 14.79 2.09 33.41 3.01
4788 4930 0.329261 TCTACTCCCTCCGTTCGGAA 59.671 55.000 14.79 0.04 33.41 4.30
4789 4931 0.549950 ATCTACTCCCTCCGTTCGGA 59.450 55.000 13.34 13.34 0.00 4.55
4790 4932 1.400737 AATCTACTCCCTCCGTTCGG 58.599 55.000 4.74 4.74 0.00 4.30
4791 4933 3.521947 AAAATCTACTCCCTCCGTTCG 57.478 47.619 0.00 0.00 0.00 3.95
4792 4934 7.046033 TGAATAAAAATCTACTCCCTCCGTTC 58.954 38.462 0.00 0.00 0.00 3.95
4793 4935 6.954232 TGAATAAAAATCTACTCCCTCCGTT 58.046 36.000 0.00 0.00 0.00 4.44
4794 4936 6.555463 TGAATAAAAATCTACTCCCTCCGT 57.445 37.500 0.00 0.00 0.00 4.69
4795 4937 7.859325 TTTGAATAAAAATCTACTCCCTCCG 57.141 36.000 0.00 0.00 0.00 4.63
4796 4938 9.244292 ACTTTTGAATAAAAATCTACTCCCTCC 57.756 33.333 0.00 0.00 37.14 4.30
4898 5040 5.068987 ACCTAAAAACAAATCTTGCAGCTGA 59.931 36.000 20.43 0.00 0.00 4.26
4903 5045 8.637986 ACTAATCACCTAAAAACAAATCTTGCA 58.362 29.630 0.00 0.00 0.00 4.08
4980 5122 5.914635 CACATAGTACAAACCTGCACAAAAG 59.085 40.000 0.00 0.00 0.00 2.27
5158 5300 0.107268 TCTCCATCATGGCGTGGATG 59.893 55.000 6.90 9.08 43.20 3.51
5199 5341 3.127548 GTGTTTGAGGCAGTGATGTATGG 59.872 47.826 0.00 0.00 0.00 2.74
5266 5411 4.017407 AGTGAGAGAAGACATGTACCCCTA 60.017 45.833 0.00 0.00 0.00 3.53
5335 6976 0.037046 CAGAAAGCCATGGCCCAAAC 60.037 55.000 33.14 18.96 43.17 2.93
5344 6985 2.421424 GCAGACGAAATCAGAAAGCCAT 59.579 45.455 0.00 0.00 0.00 4.40
5364 7005 4.235939 TGGAAACATAACATGTGTGTGC 57.764 40.909 15.47 11.41 44.07 4.57
5365 7006 7.712264 AAATTGGAAACATAACATGTGTGTG 57.288 32.000 15.47 9.98 44.07 3.82
5404 7045 9.039870 TCACAACACATATGGAATTTGTTTTTC 57.960 29.630 7.80 0.00 36.32 2.29
5405 7046 8.954950 TCACAACACATATGGAATTTGTTTTT 57.045 26.923 7.80 0.00 36.32 1.94
5425 7066 4.299586 TGCTTATCTGGTTGGATCACAA 57.700 40.909 0.00 0.00 36.54 3.33
5440 7081 9.490379 CCGAATTATTAGACCTAGTTTGCTTAT 57.510 33.333 0.00 0.00 0.00 1.73
5441 7082 8.480501 ACCGAATTATTAGACCTAGTTTGCTTA 58.519 33.333 0.00 0.00 0.00 3.09
5442 7083 7.336396 ACCGAATTATTAGACCTAGTTTGCTT 58.664 34.615 0.00 0.00 0.00 3.91
5443 7084 6.885922 ACCGAATTATTAGACCTAGTTTGCT 58.114 36.000 0.00 0.00 0.00 3.91
5444 7085 7.065443 ACAACCGAATTATTAGACCTAGTTTGC 59.935 37.037 0.00 0.00 0.00 3.68
5445 7086 8.388103 CACAACCGAATTATTAGACCTAGTTTG 58.612 37.037 0.00 0.00 0.00 2.93
5446 7087 7.551617 CCACAACCGAATTATTAGACCTAGTTT 59.448 37.037 0.00 0.00 0.00 2.66
5447 7088 7.046033 CCACAACCGAATTATTAGACCTAGTT 58.954 38.462 0.00 0.00 0.00 2.24
5448 7089 6.155737 ACCACAACCGAATTATTAGACCTAGT 59.844 38.462 0.00 0.00 0.00 2.57
5449 7090 6.579865 ACCACAACCGAATTATTAGACCTAG 58.420 40.000 0.00 0.00 0.00 3.02
5450 7091 6.549433 ACCACAACCGAATTATTAGACCTA 57.451 37.500 0.00 0.00 0.00 3.08
5451 7092 5.431179 ACCACAACCGAATTATTAGACCT 57.569 39.130 0.00 0.00 0.00 3.85
5452 7093 6.505044 AAACCACAACCGAATTATTAGACC 57.495 37.500 0.00 0.00 0.00 3.85
5453 7094 8.671028 ACATAAACCACAACCGAATTATTAGAC 58.329 33.333 0.00 0.00 0.00 2.59
5454 7095 8.670135 CACATAAACCACAACCGAATTATTAGA 58.330 33.333 0.00 0.00 0.00 2.10
5455 7096 8.455682 ACACATAAACCACAACCGAATTATTAG 58.544 33.333 0.00 0.00 0.00 1.73
5456 7097 8.338072 ACACATAAACCACAACCGAATTATTA 57.662 30.769 0.00 0.00 0.00 0.98
5457 7098 7.175990 AGACACATAAACCACAACCGAATTATT 59.824 33.333 0.00 0.00 0.00 1.40
5458 7099 6.657541 AGACACATAAACCACAACCGAATTAT 59.342 34.615 0.00 0.00 0.00 1.28
5459 7100 5.998981 AGACACATAAACCACAACCGAATTA 59.001 36.000 0.00 0.00 0.00 1.40
5460 7101 4.825085 AGACACATAAACCACAACCGAATT 59.175 37.500 0.00 0.00 0.00 2.17
5461 7102 4.394729 AGACACATAAACCACAACCGAAT 58.605 39.130 0.00 0.00 0.00 3.34
5462 7103 3.811083 AGACACATAAACCACAACCGAA 58.189 40.909 0.00 0.00 0.00 4.30
5463 7104 3.478857 AGACACATAAACCACAACCGA 57.521 42.857 0.00 0.00 0.00 4.69
5464 7105 4.083696 GGTAAGACACATAAACCACAACCG 60.084 45.833 0.00 0.00 0.00 4.44
5465 7106 5.067954 AGGTAAGACACATAAACCACAACC 58.932 41.667 0.00 0.00 32.43 3.77
5466 7107 6.628919 AAGGTAAGACACATAAACCACAAC 57.371 37.500 0.00 0.00 32.43 3.32
5467 7108 7.057894 AGAAAGGTAAGACACATAAACCACAA 58.942 34.615 0.00 0.00 32.43 3.33
5468 7109 6.597562 AGAAAGGTAAGACACATAAACCACA 58.402 36.000 0.00 0.00 32.43 4.17
5469 7110 7.506328 AAGAAAGGTAAGACACATAAACCAC 57.494 36.000 0.00 0.00 32.43 4.16
5470 7111 8.528044 AAAAGAAAGGTAAGACACATAAACCA 57.472 30.769 0.00 0.00 32.43 3.67
5471 7112 9.244799 CAAAAAGAAAGGTAAGACACATAAACC 57.755 33.333 0.00 0.00 0.00 3.27
5472 7113 9.797556 ACAAAAAGAAAGGTAAGACACATAAAC 57.202 29.630 0.00 0.00 0.00 2.01
5473 7114 9.796120 CACAAAAAGAAAGGTAAGACACATAAA 57.204 29.630 0.00 0.00 0.00 1.40
5474 7115 9.179909 TCACAAAAAGAAAGGTAAGACACATAA 57.820 29.630 0.00 0.00 0.00 1.90
5475 7116 8.740123 TCACAAAAAGAAAGGTAAGACACATA 57.260 30.769 0.00 0.00 0.00 2.29
5476 7117 7.556275 TCTCACAAAAAGAAAGGTAAGACACAT 59.444 33.333 0.00 0.00 0.00 3.21
5477 7118 6.882140 TCTCACAAAAAGAAAGGTAAGACACA 59.118 34.615 0.00 0.00 0.00 3.72
5478 7119 7.065923 ACTCTCACAAAAAGAAAGGTAAGACAC 59.934 37.037 0.00 0.00 0.00 3.67
5479 7120 7.065803 CACTCTCACAAAAAGAAAGGTAAGACA 59.934 37.037 0.00 0.00 0.00 3.41
5480 7121 7.410485 CACTCTCACAAAAAGAAAGGTAAGAC 58.590 38.462 0.00 0.00 0.00 3.01
5481 7122 6.542370 CCACTCTCACAAAAAGAAAGGTAAGA 59.458 38.462 0.00 0.00 0.00 2.10
5482 7123 6.318900 ACCACTCTCACAAAAAGAAAGGTAAG 59.681 38.462 0.00 0.00 31.71 2.34
5497 7138 4.585955 TTGTCACTAGAACCACTCTCAC 57.414 45.455 0.00 0.00 35.41 3.51


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

AutoCloner maintained by Alex Coulton.