Multiple sequence alignment - TraesCS4B01G224900

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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 TraesCS4B01G224900 chr4B 100.000 7929 0 0 1 7929 471330228 471338156 0.000000e+00 14643.0
1 TraesCS4B01G224900 chr4B 80.328 183 13 9 7238 7409 580986399 580986569 5.030000e-22 117.0
2 TraesCS4B01G224900 chr4B 78.392 199 20 8 7239 7426 377778387 377778573 3.030000e-19 108.0
3 TraesCS4B01G224900 chr4B 82.979 94 7 5 7341 7425 580771987 580771894 8.530000e-10 76.8
4 TraesCS4B01G224900 chr4B 95.455 44 2 0 5552 5595 642195606 642195649 3.970000e-08 71.3
5 TraesCS4B01G224900 chr4A 95.482 5954 144 42 1 5875 66140131 66146038 0.000000e+00 9389.0
6 TraesCS4B01G224900 chr4A 93.888 1129 47 10 6126 7245 66146295 66147410 0.000000e+00 1683.0
7 TraesCS4B01G224900 chr4A 93.525 417 11 9 7528 7929 66147618 66148033 2.450000e-169 606.0
8 TraesCS4B01G224900 chr4A 95.604 91 4 0 5922 6012 66146206 66146296 6.410000e-31 147.0
9 TraesCS4B01G224900 chr4A 88.889 81 8 1 7243 7322 513342813 513342733 1.820000e-16 99.0
10 TraesCS4B01G224900 chr4D 96.833 5526 101 29 1 5480 384262782 384268279 0.000000e+00 9167.0
11 TraesCS4B01G224900 chr4D 96.473 1134 29 3 6126 7259 384268762 384269884 0.000000e+00 1862.0
12 TraesCS4B01G224900 chr4D 96.289 485 11 5 5532 6014 384268282 384268761 0.000000e+00 789.0
13 TraesCS4B01G224900 chr4D 91.800 500 16 9 7449 7929 384270271 384270764 0.000000e+00 673.0
14 TraesCS4B01G224900 chr4D 94.444 126 7 0 6008 6133 428946498 428946373 2.260000e-45 195.0
15 TraesCS4B01G224900 chr4D 93.878 49 3 0 5552 5600 499394214 499394166 3.070000e-09 75.0
16 TraesCS4B01G224900 chr1A 98.225 169 2 1 7762 7929 490418640 490418472 2.160000e-75 294.0
17 TraesCS4B01G224900 chr1A 97.041 169 4 1 7762 7929 490760390 490760222 4.680000e-72 283.0
18 TraesCS4B01G224900 chr1A 97.006 167 5 0 7763 7929 62794165 62794331 1.680000e-71 281.0
19 TraesCS4B01G224900 chr1A 89.773 88 8 1 7238 7324 504525819 504525906 2.340000e-20 111.0
20 TraesCS4B01G224900 chr1A 88.235 85 9 1 7238 7321 504458107 504458191 5.060000e-17 100.0
21 TraesCS4B01G224900 chr1A 86.486 74 8 2 5471 5542 492806105 492806178 6.600000e-11 80.5
22 TraesCS4B01G224900 chr1D 98.765 162 2 0 7768 7929 384844721 384844882 1.010000e-73 289.0
23 TraesCS4B01G224900 chr1D 95.161 124 5 1 6009 6132 284915828 284915950 2.260000e-45 195.0
24 TraesCS4B01G224900 chr1D 87.931 58 5 2 5554 5610 344135258 344135202 5.140000e-07 67.6
25 TraesCS4B01G224900 chr6B 97.041 169 4 1 7762 7929 679983095 679983263 4.680000e-72 283.0
26 TraesCS4B01G224900 chr6B 95.935 123 5 0 6008 6130 343032970 343032848 4.850000e-47 200.0
27 TraesCS4B01G224900 chr6B 90.909 88 6 2 7238 7324 519784422 519784508 5.030000e-22 117.0
28 TraesCS4B01G224900 chr6B 78.626 131 12 4 7244 7371 569819559 569819442 1.100000e-08 73.1
29 TraesCS4B01G224900 chr5D 98.148 162 3 0 7768 7929 405334397 405334558 4.680000e-72 283.0
30 TraesCS4B01G224900 chr5D 95.238 126 6 0 6009 6134 473359765 473359890 4.850000e-47 200.0
31 TraesCS4B01G224900 chr5D 77.436 195 21 13 7244 7427 21975557 21975375 2.360000e-15 95.3
32 TraesCS4B01G224900 chr5D 91.667 48 3 1 7381 7427 205127368 205127415 1.850000e-06 65.8
33 TraesCS4B01G224900 chr2D 98.137 161 3 0 7769 7929 498767300 498767140 1.680000e-71 281.0
34 TraesCS4B01G224900 chr2D 95.968 124 5 0 6005 6128 572692612 572692735 1.350000e-47 202.0
35 TraesCS4B01G224900 chr2D 76.329 207 23 13 7241 7434 250618411 250618604 3.940000e-13 87.9
36 TraesCS4B01G224900 chr3B 94.531 128 6 1 6006 6133 61536208 61536334 6.280000e-46 196.0
37 TraesCS4B01G224900 chr3B 93.182 132 9 0 6005 6136 141125507 141125376 2.260000e-45 195.0
38 TraesCS4B01G224900 chr5B 95.161 124 5 1 6010 6133 451432988 451432866 2.260000e-45 195.0
39 TraesCS4B01G224900 chr5B 89.552 67 5 2 5480 5545 544610554 544610489 5.100000e-12 84.2
40 TraesCS4B01G224900 chr5B 89.394 66 4 3 5481 5545 34252105 34252168 6.600000e-11 80.5
41 TraesCS4B01G224900 chr5B 88.525 61 5 2 7381 7439 108525721 108525661 1.100000e-08 73.1
42 TraesCS4B01G224900 chr7B 94.444 126 6 1 6008 6133 411494571 411494447 8.120000e-45 193.0
43 TraesCS4B01G224900 chr7B 89.552 67 5 2 5480 5545 539218299 539218364 5.100000e-12 84.2
44 TraesCS4B01G224900 chr7A 90.588 85 7 1 7244 7327 53861917 53861833 2.340000e-20 111.0
45 TraesCS4B01G224900 chr7A 90.909 66 6 0 5480 5545 581374265 581374330 1.100000e-13 89.8
46 TraesCS4B01G224900 chr7A 89.394 66 7 0 5480 5545 581374329 581374264 5.100000e-12 84.2
47 TraesCS4B01G224900 chr7A 94.000 50 3 0 5549 5598 262465906 262465955 8.530000e-10 76.8
48 TraesCS4B01G224900 chr6D 92.405 79 5 1 7245 7322 376085152 376085230 2.340000e-20 111.0
49 TraesCS4B01G224900 chr6D 95.918 49 0 2 5480 5527 358980125 358980172 2.370000e-10 78.7
50 TraesCS4B01G224900 chr7D 83.761 117 17 1 5480 5596 261818668 261818554 8.410000e-20 110.0
51 TraesCS4B01G224900 chr2B 87.500 88 8 3 7239 7324 43189766 43189852 1.820000e-16 99.0
52 TraesCS4B01G224900 chr2B 97.727 44 1 0 5552 5595 206114770 206114727 8.530000e-10 76.8
53 TraesCS4B01G224900 chr3D 78.771 179 13 13 7264 7430 482502648 482502813 6.550000e-16 97.1
54 TraesCS4B01G224900 chr3D 76.000 200 22 16 7244 7431 43596042 43595857 6.600000e-11 80.5
55 TraesCS4B01G224900 chr3A 87.805 82 9 1 7244 7324 60834409 60834328 2.360000e-15 95.3
56 TraesCS4B01G224900 chr3A 87.805 82 9 1 7244 7324 60834888 60834807 2.360000e-15 95.3
57 TraesCS4B01G224900 chr3A 75.758 198 34 11 7238 7430 712848794 712848606 3.940000e-13 87.9
58 TraesCS4B01G224900 chr3A 75.758 198 34 11 7238 7430 712855900 712855712 3.940000e-13 87.9
59 TraesCS4B01G224900 chr2A 81.982 111 7 8 7332 7430 10728532 10728423 1.830000e-11 82.4
60 TraesCS4B01G224900 chr5A 95.918 49 2 0 5550 5598 11064126 11064174 6.600000e-11 80.5
61 TraesCS4B01G224900 chr5A 79.817 109 9 4 7264 7371 389163982 389164078 5.140000e-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 TraesCS4B01G224900 chr4B 471330228 471338156 7928 False 14643.00 14643 100.00000 1 7929 1 chr4B.!!$F2 7928
1 TraesCS4B01G224900 chr4A 66140131 66148033 7902 False 2956.25 9389 94.62475 1 7929 4 chr4A.!!$F1 7928
2 TraesCS4B01G224900 chr4D 384262782 384270764 7982 False 3122.75 9167 95.34875 1 7929 4 chr4D.!!$F1 7928

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
143 152 0.320160 GTACGGCCACGACTTCCTTT 60.320 55.000 2.24 0.00 44.60 3.11 F
183 192 0.390735 AATCGTTGGTACCACTCCGC 60.391 55.000 16.04 1.91 0.00 5.54 F
1115 1173 0.598065 GTGGATTGGTTGTGAGTGGC 59.402 55.000 0.00 0.00 0.00 5.01 F
1245 1304 1.064654 GTGCCGATTGGAGATTCTTGC 59.935 52.381 1.98 0.00 37.49 4.01 F
1823 1887 1.670811 ACTGTTGCCTTTGTCTTGTCG 59.329 47.619 0.00 0.00 0.00 4.35 F
3164 3258 1.859703 GCTGAGAATGATGCACTCTCG 59.140 52.381 10.61 7.76 38.77 4.04 F
4239 4333 1.110518 GTCCGAGGGATCTCCACTCC 61.111 65.000 0.00 0.00 36.70 3.85 F
5467 5562 0.026285 CGATCCGAATTGGTTGACGC 59.974 55.000 0.00 0.00 39.52 5.19 F
6026 6274 0.032813 AAATACTCCCTCCGTCCGGA 60.033 55.000 0.00 0.00 42.90 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1527 1590 1.065491 TGGCGCATGTATCCAAACTCT 60.065 47.619 10.83 0.00 0.00 3.24 R
2095 2179 4.955811 AGAATGACACCACTGACACTTA 57.044 40.909 0.00 0.00 0.00 2.24 R
2328 2413 1.006922 GCAAGGGCAGCAACTTGAC 60.007 57.895 25.19 15.76 45.22 3.18 R
3164 3258 0.103937 CCCGCTCTTGGAGTGATCTC 59.896 60.000 9.33 0.00 42.10 2.75 R
3626 3720 4.649692 ACTCATTCTCTTTCTGCATGTGT 58.350 39.130 0.00 0.00 0.00 3.72 R
4876 4970 1.031029 AAGTCGCTCGTAGTCCTCCC 61.031 60.000 0.00 0.00 0.00 4.30 R
6110 6358 0.033796 ACATACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30 R
6762 7013 0.179009 CCCATGACCCGCATTCATCT 60.179 55.000 0.00 0.00 34.15 2.90 R
7727 8236 1.531149 CTTGTTTACGGAGTGCCTGTG 59.469 52.381 0.00 0.00 45.73 3.66 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
81 82 1.901833 AGTGAATGAAATTGCCACCCC 59.098 47.619 0.00 0.00 36.07 4.95
143 152 0.320160 GTACGGCCACGACTTCCTTT 60.320 55.000 2.24 0.00 44.60 3.11
176 185 4.095334 GGTGGTATTTGAATCGTTGGTACC 59.905 45.833 4.43 4.43 0.00 3.34
183 192 0.390735 AATCGTTGGTACCACTCCGC 60.391 55.000 16.04 1.91 0.00 5.54
196 205 2.098607 CCACTCCGCGAGTACAAGATTA 59.901 50.000 8.23 0.00 41.37 1.75
197 206 3.364062 CACTCCGCGAGTACAAGATTAG 58.636 50.000 8.23 0.00 41.37 1.73
198 207 3.015327 ACTCCGCGAGTACAAGATTAGT 58.985 45.455 8.23 0.00 41.51 2.24
413 428 5.123820 GCGCCATCATCTTTATTATAGCCAA 59.876 40.000 0.00 0.00 0.00 4.52
471 487 3.518068 GGCGGCATGGTAGGTTGC 61.518 66.667 3.07 0.00 38.14 4.17
513 529 2.126424 GTCCGTCAGTCAGTCCGC 60.126 66.667 0.00 0.00 0.00 5.54
515 531 3.680786 CCGTCAGTCAGTCCGCCA 61.681 66.667 0.00 0.00 0.00 5.69
516 532 2.573869 CGTCAGTCAGTCCGCCAT 59.426 61.111 0.00 0.00 0.00 4.40
517 533 1.807165 CGTCAGTCAGTCCGCCATG 60.807 63.158 0.00 0.00 0.00 3.66
772 807 5.600069 AGATGAGCCATGACTATTGAGTACA 59.400 40.000 0.00 0.00 35.45 2.90
1115 1173 0.598065 GTGGATTGGTTGTGAGTGGC 59.402 55.000 0.00 0.00 0.00 5.01
1229 1288 5.364778 TGTATGTGTATGACCTTATGTGCC 58.635 41.667 0.00 0.00 0.00 5.01
1236 1295 1.557371 TGACCTTATGTGCCGATTGGA 59.443 47.619 1.98 0.00 37.49 3.53
1245 1304 1.064654 GTGCCGATTGGAGATTCTTGC 59.935 52.381 1.98 0.00 37.49 4.01
1300 1360 5.557136 CGCGCAGGAAAAAGATTACTGATAG 60.557 44.000 8.75 0.00 0.00 2.08
1336 1396 5.003804 AGTGACAATGGTGGAGTCAAATAC 58.996 41.667 0.00 0.00 43.16 1.89
1337 1397 5.003804 GTGACAATGGTGGAGTCAAATACT 58.996 41.667 0.00 0.00 43.16 2.12
1338 1398 5.473504 GTGACAATGGTGGAGTCAAATACTT 59.526 40.000 0.00 0.00 43.16 2.24
1339 1399 6.653320 GTGACAATGGTGGAGTCAAATACTTA 59.347 38.462 0.00 0.00 43.16 2.24
1351 1411 7.064728 GGAGTCAAATACTTACTTGCTTACTGG 59.935 40.741 0.00 0.00 39.07 4.00
1823 1887 1.670811 ACTGTTGCCTTTGTCTTGTCG 59.329 47.619 0.00 0.00 0.00 4.35
2492 2581 4.297510 CGAAATTTGTGCAGATTTCACCA 58.702 39.130 20.54 0.00 40.11 4.17
2571 2660 6.983906 AGGTGAAAACCTTGAATGAGAAAT 57.016 33.333 0.00 0.00 36.56 2.17
3164 3258 1.859703 GCTGAGAATGATGCACTCTCG 59.140 52.381 10.61 7.76 38.77 4.04
3626 3720 8.902806 CCTGATTATGCTTTTGATAACCTACAA 58.097 33.333 0.00 0.00 0.00 2.41
4001 4095 4.385358 AGAGAAAGTAGCTAAGAGCAGC 57.615 45.455 0.00 0.00 45.56 5.25
4076 4170 2.413453 GAGACTAGCTTGTTTGCCTTCG 59.587 50.000 1.43 0.00 0.00 3.79
4239 4333 1.110518 GTCCGAGGGATCTCCACTCC 61.111 65.000 0.00 0.00 36.70 3.85
4407 4501 9.918630 AAGTTTCTGAAAGTGAATCATTAATGG 57.081 29.630 15.36 0.00 33.76 3.16
4449 4543 4.209538 CATTGGGAGTAAGCATTCCATGA 58.790 43.478 0.00 0.00 35.09 3.07
4603 4697 7.600375 TGCACTAGTTGAGAAAGTTCTATCAAG 59.400 37.037 0.00 0.00 37.73 3.02
4952 5046 4.150274 GCGAGATGCAGTGAAATGATAGAG 59.850 45.833 0.00 0.00 45.45 2.43
5177 5271 2.808543 ACTCGGTGATGAAAGACAAAGC 59.191 45.455 0.00 0.00 0.00 3.51
5210 5304 7.187824 TGACTTAGCCAGATACAAAGATCTT 57.812 36.000 0.88 0.88 33.75 2.40
5455 5550 1.427809 TAGTACTCCCTCCGATCCGA 58.572 55.000 0.00 0.00 0.00 4.55
5456 5551 0.549950 AGTACTCCCTCCGATCCGAA 59.450 55.000 0.00 0.00 0.00 4.30
5457 5552 1.145325 AGTACTCCCTCCGATCCGAAT 59.855 52.381 0.00 0.00 0.00 3.34
5458 5553 1.962100 GTACTCCCTCCGATCCGAATT 59.038 52.381 0.00 0.00 0.00 2.17
5459 5554 0.753262 ACTCCCTCCGATCCGAATTG 59.247 55.000 0.00 0.00 0.00 2.32
5460 5555 0.034059 CTCCCTCCGATCCGAATTGG 59.966 60.000 0.00 0.00 37.74 3.16
5461 5556 0.689745 TCCCTCCGATCCGAATTGGT 60.690 55.000 0.00 0.00 37.65 3.67
5462 5557 0.180406 CCCTCCGATCCGAATTGGTT 59.820 55.000 0.00 0.00 37.65 3.67
5463 5558 1.299541 CCTCCGATCCGAATTGGTTG 58.700 55.000 0.00 0.00 37.65 3.77
5464 5559 1.134521 CCTCCGATCCGAATTGGTTGA 60.135 52.381 0.00 0.00 37.65 3.18
5465 5560 1.933853 CTCCGATCCGAATTGGTTGAC 59.066 52.381 0.00 0.00 37.65 3.18
5466 5561 0.650512 CCGATCCGAATTGGTTGACG 59.349 55.000 0.00 0.00 39.52 4.35
5467 5562 0.026285 CGATCCGAATTGGTTGACGC 59.974 55.000 0.00 0.00 39.52 5.19
5468 5563 1.083489 GATCCGAATTGGTTGACGCA 58.917 50.000 0.00 0.00 39.52 5.24
5469 5564 1.062587 GATCCGAATTGGTTGACGCAG 59.937 52.381 0.00 0.00 39.52 5.18
5470 5565 1.154225 CCGAATTGGTTGACGCAGC 60.154 57.895 0.00 0.00 0.00 5.25
5471 5566 1.154225 CGAATTGGTTGACGCAGCC 60.154 57.895 5.92 5.92 35.26 4.85
5472 5567 1.577328 CGAATTGGTTGACGCAGCCT 61.577 55.000 12.35 0.00 35.72 4.58
5473 5568 0.169009 GAATTGGTTGACGCAGCCTC 59.831 55.000 12.35 1.24 35.72 4.70
5474 5569 0.250901 AATTGGTTGACGCAGCCTCT 60.251 50.000 12.35 0.18 35.72 3.69
5475 5570 0.613260 ATTGGTTGACGCAGCCTCTA 59.387 50.000 12.35 1.66 35.72 2.43
5476 5571 0.613260 TTGGTTGACGCAGCCTCTAT 59.387 50.000 12.35 0.00 35.72 1.98
5477 5572 1.480789 TGGTTGACGCAGCCTCTATA 58.519 50.000 12.35 0.00 35.72 1.31
5478 5573 1.136305 TGGTTGACGCAGCCTCTATAC 59.864 52.381 12.35 0.00 35.72 1.47
5515 5610 6.108687 CAGCCTCTATACAATGTCAAACTGA 58.891 40.000 0.00 0.00 0.00 3.41
5530 5625 5.005779 GTCAAACTGACATTGTATAGAGGCG 59.994 44.000 1.92 0.00 46.22 5.52
5550 5645 4.378046 GGCGTCGACAATTAATTCAGTTGT 60.378 41.667 17.16 0.00 38.66 3.32
5565 5660 8.723942 AATTCAGTTGTCATTGTATAGAGGAC 57.276 34.615 0.00 0.00 0.00 3.85
5734 5832 8.491045 TGGATCCTTTTTCTTCTTTTGGTAAT 57.509 30.769 14.23 0.00 0.00 1.89
5779 5877 5.336150 TGGCAACAGAAATCAGTGAAAAA 57.664 34.783 0.00 0.00 46.17 1.94
5836 5934 4.572795 TCGTAATGTTTGTTTCACTGCTGA 59.427 37.500 0.00 0.00 0.00 4.26
5854 5952 3.863424 GCTGAAATTCTGCATGTTCATGG 59.137 43.478 17.95 0.00 40.47 3.66
5911 6159 7.439955 TGTTGTTGATGACGTAGAAATAGTGTT 59.560 33.333 0.00 0.00 0.00 3.32
5912 6160 7.346208 TGTTGATGACGTAGAAATAGTGTTG 57.654 36.000 0.00 0.00 0.00 3.33
5991 6239 7.491696 AGCAATAAACGATGTCCTACTAAGAAC 59.508 37.037 0.00 0.00 0.00 3.01
6014 6262 0.042100 GCGGCAAGCGCTAAATACTC 60.042 55.000 12.05 0.00 38.60 2.59
6015 6263 0.582005 CGGCAAGCGCTAAATACTCC 59.418 55.000 12.05 3.37 38.60 3.85
6016 6264 0.945099 GGCAAGCGCTAAATACTCCC 59.055 55.000 12.05 0.00 38.60 4.30
6017 6265 1.475213 GGCAAGCGCTAAATACTCCCT 60.475 52.381 12.05 0.00 38.60 4.20
6018 6266 1.867865 GCAAGCGCTAAATACTCCCTC 59.132 52.381 12.05 0.00 34.30 4.30
6019 6267 2.484889 CAAGCGCTAAATACTCCCTCC 58.515 52.381 12.05 0.00 0.00 4.30
6020 6268 0.674534 AGCGCTAAATACTCCCTCCG 59.325 55.000 8.99 0.00 0.00 4.63
6021 6269 0.388294 GCGCTAAATACTCCCTCCGT 59.612 55.000 0.00 0.00 0.00 4.69
6022 6270 1.602416 GCGCTAAATACTCCCTCCGTC 60.602 57.143 0.00 0.00 0.00 4.79
6023 6271 1.000496 CGCTAAATACTCCCTCCGTCC 60.000 57.143 0.00 0.00 0.00 4.79
6024 6272 1.000496 GCTAAATACTCCCTCCGTCCG 60.000 57.143 0.00 0.00 0.00 4.79
6025 6273 1.612463 CTAAATACTCCCTCCGTCCGG 59.388 57.143 0.00 0.00 0.00 5.14
6026 6274 0.032813 AAATACTCCCTCCGTCCGGA 60.033 55.000 0.00 0.00 42.90 5.14
6027 6275 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
6028 6276 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
6029 6277 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
6030 6278 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
6031 6279 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
6032 6280 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
6033 6281 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
6034 6282 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
6035 6283 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
6036 6284 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
6037 6285 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
6038 6286 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
6039 6287 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
6041 6289 3.241067 TCCGGAAATACTTGTCGGAAG 57.759 47.619 0.00 0.00 45.40 3.46
6042 6290 2.827322 TCCGGAAATACTTGTCGGAAGA 59.173 45.455 0.00 0.00 45.40 2.87
6043 6291 3.258872 TCCGGAAATACTTGTCGGAAGAA 59.741 43.478 0.00 0.00 45.40 2.52
6044 6292 4.081309 TCCGGAAATACTTGTCGGAAGAAT 60.081 41.667 0.00 0.00 45.40 2.40
6045 6293 4.034048 CCGGAAATACTTGTCGGAAGAATG 59.966 45.833 0.00 0.00 45.01 2.67
6046 6294 4.034048 CGGAAATACTTGTCGGAAGAATGG 59.966 45.833 2.55 0.00 45.01 3.16
6047 6295 5.183228 GGAAATACTTGTCGGAAGAATGGA 58.817 41.667 2.55 0.00 45.01 3.41
6048 6296 5.823045 GGAAATACTTGTCGGAAGAATGGAT 59.177 40.000 2.55 0.00 45.01 3.41
6049 6297 6.238484 GGAAATACTTGTCGGAAGAATGGATG 60.238 42.308 2.55 0.00 45.01 3.51
6050 6298 3.703001 ACTTGTCGGAAGAATGGATGT 57.297 42.857 2.55 0.00 45.01 3.06
6051 6299 4.819105 ACTTGTCGGAAGAATGGATGTA 57.181 40.909 2.55 0.00 45.01 2.29
6052 6300 5.359194 ACTTGTCGGAAGAATGGATGTAT 57.641 39.130 2.55 0.00 45.01 2.29
6053 6301 5.360591 ACTTGTCGGAAGAATGGATGTATC 58.639 41.667 2.55 0.00 45.01 2.24
6054 6302 5.129485 ACTTGTCGGAAGAATGGATGTATCT 59.871 40.000 2.55 0.00 45.01 1.98
6055 6303 6.323996 ACTTGTCGGAAGAATGGATGTATCTA 59.676 38.462 2.55 0.00 45.01 1.98
6056 6304 6.332735 TGTCGGAAGAATGGATGTATCTAG 57.667 41.667 0.00 0.00 45.01 2.43
6057 6305 6.068670 TGTCGGAAGAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 45.01 2.43
6058 6306 6.016192 TGTCGGAAGAATGGATGTATCTAGAC 60.016 42.308 0.00 0.00 45.01 2.59
6059 6307 5.181433 TCGGAAGAATGGATGTATCTAGACG 59.819 44.000 0.00 0.00 37.03 4.18
6060 6308 5.048643 CGGAAGAATGGATGTATCTAGACGT 60.049 44.000 0.00 0.00 0.00 4.34
6061 6309 6.148976 CGGAAGAATGGATGTATCTAGACGTA 59.851 42.308 0.00 0.00 0.00 3.57
6062 6310 7.148222 CGGAAGAATGGATGTATCTAGACGTAT 60.148 40.741 0.00 0.00 0.00 3.06
6063 6311 8.524487 GGAAGAATGGATGTATCTAGACGTATT 58.476 37.037 0.00 0.00 0.00 1.89
6064 6312 9.915629 GAAGAATGGATGTATCTAGACGTATTT 57.084 33.333 0.00 0.00 0.00 1.40
6074 6322 9.317936 TGTATCTAGACGTATTTTAGTTCTCGA 57.682 33.333 0.00 0.00 0.00 4.04
6092 6340 9.725019 AGTTCTCGATATATCCATTTTTATGCA 57.275 29.630 7.15 0.00 0.00 3.96
6101 6349 6.713762 ATCCATTTTTATGCATTTCTCCGA 57.286 33.333 3.54 0.00 0.00 4.55
6102 6350 5.890334 TCCATTTTTATGCATTTCTCCGAC 58.110 37.500 3.54 0.00 0.00 4.79
6103 6351 5.417266 TCCATTTTTATGCATTTCTCCGACA 59.583 36.000 3.54 0.00 0.00 4.35
6104 6352 6.071672 TCCATTTTTATGCATTTCTCCGACAA 60.072 34.615 3.54 0.00 0.00 3.18
6105 6353 6.254157 CCATTTTTATGCATTTCTCCGACAAG 59.746 38.462 3.54 0.00 0.00 3.16
6106 6354 5.957842 TTTTATGCATTTCTCCGACAAGT 57.042 34.783 3.54 0.00 0.00 3.16
6107 6355 7.441890 TTTTTATGCATTTCTCCGACAAGTA 57.558 32.000 3.54 0.00 0.00 2.24
6108 6356 7.624360 TTTTATGCATTTCTCCGACAAGTAT 57.376 32.000 3.54 0.00 0.00 2.12
6109 6357 7.624360 TTTATGCATTTCTCCGACAAGTATT 57.376 32.000 3.54 0.00 0.00 1.89
6110 6358 7.624360 TTATGCATTTCTCCGACAAGTATTT 57.376 32.000 3.54 0.00 0.00 1.40
6111 6359 5.957842 TGCATTTCTCCGACAAGTATTTT 57.042 34.783 0.00 0.00 0.00 1.82
6112 6360 5.938322 TGCATTTCTCCGACAAGTATTTTC 58.062 37.500 0.00 0.00 0.00 2.29
6113 6361 5.022021 GCATTTCTCCGACAAGTATTTTCG 58.978 41.667 0.00 0.00 0.00 3.46
6119 6367 2.598589 CGACAAGTATTTTCGGACGGA 58.401 47.619 0.00 0.00 0.00 4.69
6120 6368 2.597305 CGACAAGTATTTTCGGACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
6121 6369 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
6122 6370 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
6123 6371 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
6124 6372 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
6131 6379 0.102481 CGGACGGAGGGAGTATGTTG 59.898 60.000 0.00 0.00 0.00 3.33
6222 6470 7.142021 GGTCTTTTCTGGAAATTCAAGACTTC 58.858 38.462 17.07 4.47 35.95 3.01
6260 6508 8.973835 AACACACTTTTTCTTGTTTAAATCGA 57.026 26.923 0.00 0.00 0.00 3.59
6299 6547 1.212229 GGCTGCAGCAGAAAAGCTC 59.788 57.895 37.63 15.10 44.54 4.09
6475 6726 1.709115 ACCATCAGGCCAGCATGATAT 59.291 47.619 18.31 8.17 44.25 1.63
6554 6805 1.971149 TGACCCCTTCTGATGTGGAT 58.029 50.000 0.00 0.00 0.00 3.41
6608 6859 1.449601 CCCAAAGCATAGGTCGCGT 60.450 57.895 5.77 0.00 0.00 6.01
6659 6910 2.561373 CCCGAGAAACAAAGCCGC 59.439 61.111 0.00 0.00 0.00 6.53
6738 6989 2.880268 TCTGTGATGTTGGCTTGTTGAG 59.120 45.455 0.00 0.00 0.00 3.02
6792 7043 3.181458 GCGGGTCATGGGTTTCTATAGAA 60.181 47.826 11.24 11.24 0.00 2.10
6828 7079 6.194796 TCTGCTTGTGTATTATTTTGAGGC 57.805 37.500 0.00 0.00 0.00 4.70
6855 7106 2.260869 CGGTGGTTCAGTTGCTGGG 61.261 63.158 0.00 0.00 31.51 4.45
6909 7160 2.355197 CAGGTTGTGTGTGTGTGAGAA 58.645 47.619 0.00 0.00 0.00 2.87
7044 7302 4.869861 GCTGTTTGTTTGTGTTCCATTCTT 59.130 37.500 0.00 0.00 0.00 2.52
7174 7434 6.073058 TCGGTGTCAAAATCTGAAGAAAGATG 60.073 38.462 0.00 0.00 36.99 2.90
7176 7436 6.860023 GGTGTCAAAATCTGAAGAAAGATGTG 59.140 38.462 0.00 0.00 36.99 3.21
7187 7447 5.239306 TGAAGAAAGATGTGTGTTGTCCATC 59.761 40.000 0.00 0.00 36.16 3.51
7194 7454 3.351740 TGTGTGTTGTCCATCTTGTGTT 58.648 40.909 0.00 0.00 0.00 3.32
7229 7489 5.454966 TCATACTACATCCTTACTGCTGGA 58.545 41.667 0.00 0.00 36.72 3.86
7248 7508 3.391296 TGGAAAGACAGCTTAGACCTTGT 59.609 43.478 0.00 0.00 32.98 3.16
7259 7519 4.695455 GCTTAGACCTTGTACAATGCAAGA 59.305 41.667 9.13 0.00 44.29 3.02
7262 7522 7.227512 GCTTAGACCTTGTACAATGCAAGATAT 59.772 37.037 9.13 0.00 44.29 1.63
7264 7524 7.944729 AGACCTTGTACAATGCAAGATATTT 57.055 32.000 9.13 0.00 44.29 1.40
7267 7527 8.225603 ACCTTGTACAATGCAAGATATTTAGG 57.774 34.615 9.13 3.88 44.29 2.69
7268 7528 8.052748 ACCTTGTACAATGCAAGATATTTAGGA 58.947 33.333 9.13 0.00 44.29 2.94
7269 7529 8.562892 CCTTGTACAATGCAAGATATTTAGGAG 58.437 37.037 9.13 0.00 44.29 3.69
7270 7530 9.330063 CTTGTACAATGCAAGATATTTAGGAGA 57.670 33.333 9.13 0.00 44.29 3.71
7271 7531 8.893219 TGTACAATGCAAGATATTTAGGAGAG 57.107 34.615 0.00 0.00 0.00 3.20
7272 7532 7.933577 TGTACAATGCAAGATATTTAGGAGAGG 59.066 37.037 0.00 0.00 0.00 3.69
7273 7533 6.904626 ACAATGCAAGATATTTAGGAGAGGT 58.095 36.000 0.00 0.00 0.00 3.85
7274 7534 6.769822 ACAATGCAAGATATTTAGGAGAGGTG 59.230 38.462 0.00 0.00 0.00 4.00
7275 7535 5.957771 TGCAAGATATTTAGGAGAGGTGT 57.042 39.130 0.00 0.00 0.00 4.16
7276 7536 6.313519 TGCAAGATATTTAGGAGAGGTGTT 57.686 37.500 0.00 0.00 0.00 3.32
7277 7537 6.721318 TGCAAGATATTTAGGAGAGGTGTTT 58.279 36.000 0.00 0.00 0.00 2.83
7278 7538 6.599244 TGCAAGATATTTAGGAGAGGTGTTTG 59.401 38.462 0.00 0.00 0.00 2.93
7279 7539 6.038714 GCAAGATATTTAGGAGAGGTGTTTGG 59.961 42.308 0.00 0.00 0.00 3.28
7308 7653 9.471084 AAATAAATCAGGTTTTCTTAAACACCG 57.529 29.630 0.00 0.00 44.37 4.94
7320 7665 4.822896 TCTTAAACACCGGTGCTTATTTGT 59.177 37.500 34.26 11.55 0.00 2.83
7321 7666 5.996513 TCTTAAACACCGGTGCTTATTTGTA 59.003 36.000 34.26 15.46 0.00 2.41
7322 7667 4.492791 AAACACCGGTGCTTATTTGTAC 57.507 40.909 34.26 0.00 0.00 2.90
7323 7668 3.128852 ACACCGGTGCTTATTTGTACA 57.871 42.857 34.26 0.00 0.00 2.90
7324 7669 3.478509 ACACCGGTGCTTATTTGTACAA 58.521 40.909 34.26 3.59 0.00 2.41
7325 7670 3.500680 ACACCGGTGCTTATTTGTACAAG 59.499 43.478 34.26 5.11 0.00 3.16
7326 7671 3.749088 CACCGGTGCTTATTTGTACAAGA 59.251 43.478 24.02 0.90 0.00 3.02
7327 7672 4.394920 CACCGGTGCTTATTTGTACAAGAT 59.605 41.667 24.02 8.17 0.00 2.40
7328 7673 4.394920 ACCGGTGCTTATTTGTACAAGATG 59.605 41.667 6.12 5.02 0.00 2.90
7329 7674 4.394920 CCGGTGCTTATTTGTACAAGATGT 59.605 41.667 8.56 0.00 0.00 3.06
7330 7675 5.583061 CCGGTGCTTATTTGTACAAGATGTA 59.417 40.000 8.56 1.07 0.00 2.29
7331 7676 6.238103 CCGGTGCTTATTTGTACAAGATGTAG 60.238 42.308 8.56 4.97 32.84 2.74
7375 7728 4.207165 AGCATCTCTCCTCTAGAAGTGTC 58.793 47.826 0.00 0.00 32.46 3.67
7383 7736 8.164733 TCTCTCCTCTAGAAGTGTCTTAGAAAA 58.835 37.037 0.00 0.00 35.12 2.29
7411 7764 7.916552 TCGATTTATTTTTCTAAGCACCTAGC 58.083 34.615 0.00 0.00 46.19 3.42
7445 7799 6.660949 AGACCTATAGCAATTCAAAAACAGCT 59.339 34.615 0.00 0.00 33.75 4.24
7632 8133 3.769300 GGATTAAAAGGGGCACAATCACT 59.231 43.478 0.00 0.00 0.00 3.41
7718 8227 0.941542 ACATTCGACACCAAACACCG 59.058 50.000 0.00 0.00 0.00 4.94
7727 8236 2.568090 CAAACACCGCCAGGATGC 59.432 61.111 0.00 0.00 41.02 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 3.437741 GGGTAAAAATCGGTACTGTGTGG 59.562 47.826 0.64 0.00 0.00 4.17
176 185 2.279582 AATCTTGTACTCGCGGAGTG 57.720 50.000 17.67 4.97 43.30 3.51
277 291 7.126421 ACCAGATGTGACACTCCTATTAAATCT 59.874 37.037 7.20 0.64 0.00 2.40
285 299 6.428083 TTTTAACCAGATGTGACACTCCTA 57.572 37.500 7.20 0.00 0.00 2.94
413 428 0.472471 TCTTGAACGGAAGGTGGCTT 59.528 50.000 0.00 0.00 0.00 4.35
471 487 1.447643 GGTGGATGAGATGACCGGG 59.552 63.158 6.32 0.00 0.00 5.73
513 529 2.755469 CGGAGGGTTTGGCCATGG 60.755 66.667 6.09 7.63 39.65 3.66
515 531 3.301222 ATGCGGAGGGTTTGGCCAT 62.301 57.895 6.09 0.00 39.65 4.40
516 532 3.978193 ATGCGGAGGGTTTGGCCA 61.978 61.111 0.00 0.00 39.65 5.36
517 533 3.451894 CATGCGGAGGGTTTGGCC 61.452 66.667 0.00 0.00 0.00 5.36
772 807 2.353803 GGGCAAGTAAGAGTCGTGTCAT 60.354 50.000 0.00 0.00 0.00 3.06
878 925 2.335011 GTCCAAAGTTGCGGTGCC 59.665 61.111 0.00 0.00 0.00 5.01
879 926 2.051345 CGTCCAAAGTTGCGGTGC 60.051 61.111 0.00 0.00 0.00 5.01
881 928 2.406002 ATCCCGTCCAAAGTTGCGGT 62.406 55.000 8.61 0.00 42.36 5.68
883 930 1.794222 GATCCCGTCCAAAGTTGCG 59.206 57.895 0.00 0.00 0.00 4.85
884 931 1.644786 CCGATCCCGTCCAAAGTTGC 61.645 60.000 0.00 0.00 0.00 4.17
1229 1288 3.461061 TGCTAGCAAGAATCTCCAATCG 58.539 45.455 16.84 0.00 0.00 3.34
1236 1295 3.969287 TCACACTGCTAGCAAGAATCT 57.031 42.857 19.86 0.00 0.00 2.40
1245 1304 6.932356 AACATCCATAATTCACACTGCTAG 57.068 37.500 0.00 0.00 0.00 3.42
1300 1360 5.594317 ACCATTGTCACTATATGGAAAAGGC 59.406 40.000 8.05 0.00 41.05 4.35
1336 1396 6.575162 AACCAAATCCAGTAAGCAAGTAAG 57.425 37.500 0.00 0.00 0.00 2.34
1337 1397 6.737346 GCAAACCAAATCCAGTAAGCAAGTAA 60.737 38.462 0.00 0.00 0.00 2.24
1338 1398 5.278758 GCAAACCAAATCCAGTAAGCAAGTA 60.279 40.000 0.00 0.00 0.00 2.24
1339 1399 4.501400 GCAAACCAAATCCAGTAAGCAAGT 60.501 41.667 0.00 0.00 0.00 3.16
1351 1411 1.336755 ACGTGACCAGCAAACCAAATC 59.663 47.619 0.00 0.00 0.00 2.17
1527 1590 1.065491 TGGCGCATGTATCCAAACTCT 60.065 47.619 10.83 0.00 0.00 3.24
2095 2179 4.955811 AGAATGACACCACTGACACTTA 57.044 40.909 0.00 0.00 0.00 2.24
2235 2319 6.311935 TCGCAATGTATCTAGGTTACACAAAC 59.688 38.462 8.15 0.00 37.36 2.93
2241 2325 7.652105 TGATTCTTCGCAATGTATCTAGGTTAC 59.348 37.037 0.00 0.00 0.00 2.50
2328 2413 1.006922 GCAAGGGCAGCAACTTGAC 60.007 57.895 25.19 15.76 45.22 3.18
2373 2462 3.205338 CAACACAAGACACTCATGTGGA 58.795 45.455 11.20 0.00 46.72 4.02
2438 2527 5.416947 TCCTCCTGCGAAATAGAAGTTAAC 58.583 41.667 0.00 0.00 0.00 2.01
2452 2541 1.136305 TCGGAACTTTATCCTCCTGCG 59.864 52.381 0.00 0.00 37.34 5.18
2492 2581 8.743085 AATCAGTAAGATGTGCATATGTTTCT 57.257 30.769 11.04 8.65 36.96 2.52
2571 2660 4.276058 TCTCAGATTGTGATGCAGACAA 57.724 40.909 14.56 14.56 37.70 3.18
2732 2826 8.618240 TTATGGAAAATGAGGAAGGTCTAGTA 57.382 34.615 0.00 0.00 0.00 1.82
2810 2904 4.517285 TCATAAAAGGAGCACAGATCACC 58.483 43.478 0.00 0.00 0.00 4.02
2872 2966 4.878397 CAGCTTTCTCCCAACCTAACATAG 59.122 45.833 0.00 0.00 0.00 2.23
3164 3258 0.103937 CCCGCTCTTGGAGTGATCTC 59.896 60.000 9.33 0.00 42.10 2.75
3626 3720 4.649692 ACTCATTCTCTTTCTGCATGTGT 58.350 39.130 0.00 0.00 0.00 3.72
3836 3930 1.887854 TGTGCACCATCAAAGTGGATG 59.112 47.619 15.69 0.00 42.02 3.51
4001 4095 1.593787 ACTGGAGCCATCAGTCACG 59.406 57.895 0.00 0.00 41.10 4.35
4239 4333 5.426504 AGATAATCTGGACTGCAGTTTCAG 58.573 41.667 29.72 29.72 39.86 3.02
4407 4501 2.147150 GCTCAACCTCTTGTCTTGGTC 58.853 52.381 0.00 0.00 32.98 4.02
4449 4543 7.865706 AGACGGCATTTATAACTTCTTGATT 57.134 32.000 0.00 0.00 0.00 2.57
4876 4970 1.031029 AAGTCGCTCGTAGTCCTCCC 61.031 60.000 0.00 0.00 0.00 4.30
4952 5046 7.609056 TCTCACTAAACCTACACTTTGTATCC 58.391 38.462 0.00 0.00 31.66 2.59
5177 5271 2.702478 TCTGGCTAAGTCATCCTGATGG 59.298 50.000 7.26 0.00 39.24 3.51
5210 5304 8.260818 CAGTATTACCTTTCCATCTTCTCTTCA 58.739 37.037 0.00 0.00 0.00 3.02
5263 5357 3.681897 AGAAGAAACTAAGCAGATGCACG 59.318 43.478 7.68 0.00 45.16 5.34
5381 5475 7.279750 AGGAGCTCTAGCACTTATTAGTTAC 57.720 40.000 14.64 0.00 45.16 2.50
5382 5476 7.899648 AAGGAGCTCTAGCACTTATTAGTTA 57.100 36.000 14.64 0.00 45.16 2.24
5383 5477 6.800072 AAGGAGCTCTAGCACTTATTAGTT 57.200 37.500 14.64 0.00 45.16 2.24
5455 5550 0.250901 AGAGGCTGCGTCAACCAATT 60.251 50.000 22.55 0.00 0.00 2.32
5456 5551 0.613260 TAGAGGCTGCGTCAACCAAT 59.387 50.000 22.55 5.12 0.00 3.16
5457 5552 0.613260 ATAGAGGCTGCGTCAACCAA 59.387 50.000 22.55 4.83 0.00 3.67
5458 5553 1.136305 GTATAGAGGCTGCGTCAACCA 59.864 52.381 22.55 6.74 0.00 3.67
5459 5554 1.136305 TGTATAGAGGCTGCGTCAACC 59.864 52.381 22.55 9.11 0.00 3.77
5460 5555 2.579207 TGTATAGAGGCTGCGTCAAC 57.421 50.000 22.55 16.88 0.00 3.18
5461 5556 3.819564 ATTGTATAGAGGCTGCGTCAA 57.180 42.857 22.55 9.93 0.00 3.18
5462 5557 3.819564 AATTGTATAGAGGCTGCGTCA 57.180 42.857 22.55 10.28 0.00 4.35
5463 5558 6.423905 TCAATTAATTGTATAGAGGCTGCGTC 59.576 38.462 23.95 14.08 38.84 5.19
5464 5559 6.202954 GTCAATTAATTGTATAGAGGCTGCGT 59.797 38.462 23.95 0.00 38.84 5.24
5465 5560 6.593978 GTCAATTAATTGTATAGAGGCTGCG 58.406 40.000 23.95 0.00 38.84 5.18
5466 5561 6.593978 CGTCAATTAATTGTATAGAGGCTGC 58.406 40.000 23.95 0.00 38.84 5.25
5467 5562 6.202762 TGCGTCAATTAATTGTATAGAGGCTG 59.797 38.462 23.95 0.00 38.84 4.85
5468 5563 6.288294 TGCGTCAATTAATTGTATAGAGGCT 58.712 36.000 23.95 0.00 38.84 4.58
5469 5564 6.539649 TGCGTCAATTAATTGTATAGAGGC 57.460 37.500 23.95 20.42 38.84 4.70
5470 5565 6.347725 GGCTGCGTCAATTAATTGTATAGAGG 60.348 42.308 23.95 13.05 38.84 3.69
5471 5566 6.425114 AGGCTGCGTCAATTAATTGTATAGAG 59.575 38.462 23.95 16.01 38.84 2.43
5472 5567 6.288294 AGGCTGCGTCAATTAATTGTATAGA 58.712 36.000 23.95 5.40 38.84 1.98
5473 5568 6.425114 AGAGGCTGCGTCAATTAATTGTATAG 59.575 38.462 23.95 18.34 38.84 1.31
5474 5569 6.288294 AGAGGCTGCGTCAATTAATTGTATA 58.712 36.000 23.95 6.09 38.84 1.47
5475 5570 5.126067 AGAGGCTGCGTCAATTAATTGTAT 58.874 37.500 23.95 1.07 38.84 2.29
5476 5571 4.513442 AGAGGCTGCGTCAATTAATTGTA 58.487 39.130 23.95 11.02 38.84 2.41
5477 5572 3.347216 AGAGGCTGCGTCAATTAATTGT 58.653 40.909 23.95 5.84 38.84 2.71
5478 5573 5.679734 ATAGAGGCTGCGTCAATTAATTG 57.320 39.130 22.55 20.13 39.10 2.32
5515 5610 2.686405 TGTCGACGCCTCTATACAATGT 59.314 45.455 11.62 0.00 0.00 2.71
5527 5622 4.088648 CAACTGAATTAATTGTCGACGCC 58.911 43.478 11.62 0.00 0.00 5.68
5550 5645 2.946990 TGACGCGTCCTCTATACAATGA 59.053 45.455 34.34 9.87 0.00 2.57
5565 5660 2.409752 CCGATCCGAATTAATTGACGCG 60.410 50.000 3.53 3.53 0.00 6.01
5734 5832 7.327975 CCAGAATCCAACAGTATACTACAACA 58.672 38.462 4.74 0.00 0.00 3.33
5741 5839 4.941263 TGTTGCCAGAATCCAACAGTATAC 59.059 41.667 2.41 0.00 44.39 1.47
5814 5912 4.843147 TCAGCAGTGAAACAAACATTACG 58.157 39.130 0.00 0.00 41.43 3.18
5836 5934 3.618019 GCCACCATGAACATGCAGAATTT 60.618 43.478 9.03 0.00 37.49 1.82
5854 5952 7.096551 ACATAAGTAATTTGGAATTGTGCCAC 58.903 34.615 0.00 0.00 34.56 5.01
5911 6159 9.599866 CATTCAGAAATCACAAGGTATAGTACA 57.400 33.333 0.00 0.00 0.00 2.90
5912 6160 9.601217 ACATTCAGAAATCACAAGGTATAGTAC 57.399 33.333 0.00 0.00 0.00 2.73
5974 6222 4.113354 GCTTGGTTCTTAGTAGGACATCG 58.887 47.826 0.00 0.00 30.80 3.84
6014 6262 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
6015 6263 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
6016 6264 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
6017 6265 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
6018 6266 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
6019 6267 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
6020 6268 2.660189 TCCGACAAGTATTTCCGGAC 57.340 50.000 1.83 0.00 43.47 4.79
6021 6269 2.827322 TCTTCCGACAAGTATTTCCGGA 59.173 45.455 0.00 0.00 46.18 5.14
6022 6270 3.241067 TCTTCCGACAAGTATTTCCGG 57.759 47.619 0.00 0.00 41.36 5.14
6023 6271 4.034048 CCATTCTTCCGACAAGTATTTCCG 59.966 45.833 0.00 0.00 0.00 4.30
6024 6272 5.183228 TCCATTCTTCCGACAAGTATTTCC 58.817 41.667 0.00 0.00 0.00 3.13
6025 6273 6.316390 ACATCCATTCTTCCGACAAGTATTTC 59.684 38.462 0.00 0.00 0.00 2.17
6026 6274 6.180472 ACATCCATTCTTCCGACAAGTATTT 58.820 36.000 0.00 0.00 0.00 1.40
6027 6275 5.745227 ACATCCATTCTTCCGACAAGTATT 58.255 37.500 0.00 0.00 0.00 1.89
6028 6276 5.359194 ACATCCATTCTTCCGACAAGTAT 57.641 39.130 0.00 0.00 0.00 2.12
6029 6277 4.819105 ACATCCATTCTTCCGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
6030 6278 3.703001 ACATCCATTCTTCCGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
6031 6279 5.605534 AGATACATCCATTCTTCCGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
6032 6280 5.614324 AGATACATCCATTCTTCCGACAA 57.386 39.130 0.00 0.00 0.00 3.18
6033 6281 6.016192 GTCTAGATACATCCATTCTTCCGACA 60.016 42.308 0.00 0.00 0.00 4.35
6034 6282 6.383415 GTCTAGATACATCCATTCTTCCGAC 58.617 44.000 0.00 0.00 0.00 4.79
6035 6283 5.181433 CGTCTAGATACATCCATTCTTCCGA 59.819 44.000 0.00 0.00 0.00 4.55
6036 6284 5.048643 ACGTCTAGATACATCCATTCTTCCG 60.049 44.000 0.00 0.00 0.00 4.30
6037 6285 6.334102 ACGTCTAGATACATCCATTCTTCC 57.666 41.667 0.00 0.00 0.00 3.46
6038 6286 9.915629 AAATACGTCTAGATACATCCATTCTTC 57.084 33.333 0.00 0.00 0.00 2.87
6048 6296 9.317936 TCGAGAACTAAAATACGTCTAGATACA 57.682 33.333 0.00 0.00 0.00 2.29
6066 6314 9.725019 TGCATAAAAATGGATATATCGAGAACT 57.275 29.630 6.64 0.00 0.00 3.01
6075 6323 9.513906 TCGGAGAAATGCATAAAAATGGATATA 57.486 29.630 0.00 0.00 32.19 0.86
6076 6324 8.299570 GTCGGAGAAATGCATAAAAATGGATAT 58.700 33.333 0.00 0.00 39.69 1.63
6077 6325 7.284261 TGTCGGAGAAATGCATAAAAATGGATA 59.716 33.333 0.00 0.00 39.69 2.59
6078 6326 6.096705 TGTCGGAGAAATGCATAAAAATGGAT 59.903 34.615 0.00 0.00 39.69 3.41
6079 6327 5.417266 TGTCGGAGAAATGCATAAAAATGGA 59.583 36.000 0.00 0.00 39.69 3.41
6080 6328 5.649557 TGTCGGAGAAATGCATAAAAATGG 58.350 37.500 0.00 0.00 39.69 3.16
6081 6329 6.808212 ACTTGTCGGAGAAATGCATAAAAATG 59.192 34.615 0.00 0.00 39.69 2.32
6082 6330 6.924111 ACTTGTCGGAGAAATGCATAAAAAT 58.076 32.000 0.00 0.00 39.69 1.82
6083 6331 6.325919 ACTTGTCGGAGAAATGCATAAAAA 57.674 33.333 0.00 0.00 39.69 1.94
6084 6332 5.957842 ACTTGTCGGAGAAATGCATAAAA 57.042 34.783 0.00 0.00 39.69 1.52
6085 6333 7.624360 AATACTTGTCGGAGAAATGCATAAA 57.376 32.000 0.00 0.00 39.69 1.40
6086 6334 7.624360 AAATACTTGTCGGAGAAATGCATAA 57.376 32.000 0.00 0.00 39.69 1.90
6087 6335 7.465379 CGAAAATACTTGTCGGAGAAATGCATA 60.465 37.037 0.00 0.00 39.69 3.14
6088 6336 6.515272 AAAATACTTGTCGGAGAAATGCAT 57.485 33.333 0.00 0.00 39.69 3.96
6089 6337 5.390461 CGAAAATACTTGTCGGAGAAATGCA 60.390 40.000 0.00 0.00 39.69 3.96
6090 6338 5.022021 CGAAAATACTTGTCGGAGAAATGC 58.978 41.667 0.00 0.00 39.69 3.56
6099 6347 2.597305 CTCCGTCCGAAAATACTTGTCG 59.403 50.000 0.00 0.00 34.58 4.35
6100 6348 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
6101 6349 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
6102 6350 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
6103 6351 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
6104 6352 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
6105 6353 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
6106 6354 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
6107 6355 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
6108 6356 1.479323 CATACTCCCTCCGTCCGAAAA 59.521 52.381 0.00 0.00 0.00 2.29
6109 6357 1.108776 CATACTCCCTCCGTCCGAAA 58.891 55.000 0.00 0.00 0.00 3.46
6110 6358 0.033796 ACATACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30
6111 6359 0.033796 AACATACTCCCTCCGTCCGA 60.034 55.000 0.00 0.00 0.00 4.55
6112 6360 0.102481 CAACATACTCCCTCCGTCCG 59.898 60.000 0.00 0.00 0.00 4.79
6113 6361 1.192428 ACAACATACTCCCTCCGTCC 58.808 55.000 0.00 0.00 0.00 4.79
6114 6362 4.081807 AGTTTACAACATACTCCCTCCGTC 60.082 45.833 0.00 0.00 0.00 4.79
6115 6363 3.836562 AGTTTACAACATACTCCCTCCGT 59.163 43.478 0.00 0.00 0.00 4.69
6116 6364 4.081862 TGAGTTTACAACATACTCCCTCCG 60.082 45.833 0.00 0.00 37.97 4.63
6117 6365 5.416271 TGAGTTTACAACATACTCCCTCC 57.584 43.478 0.00 0.00 37.97 4.30
6118 6366 7.201530 CGAAATGAGTTTACAACATACTCCCTC 60.202 40.741 0.00 0.00 37.97 4.30
6119 6367 6.594159 CGAAATGAGTTTACAACATACTCCCT 59.406 38.462 0.00 0.00 37.97 4.20
6120 6368 6.183360 CCGAAATGAGTTTACAACATACTCCC 60.183 42.308 0.00 0.00 37.97 4.30
6121 6369 6.183360 CCCGAAATGAGTTTACAACATACTCC 60.183 42.308 0.00 0.00 37.97 3.85
6122 6370 6.592607 TCCCGAAATGAGTTTACAACATACTC 59.407 38.462 0.00 0.00 38.96 2.59
6123 6371 6.469410 TCCCGAAATGAGTTTACAACATACT 58.531 36.000 0.00 0.00 0.00 2.12
6124 6372 6.730960 TCCCGAAATGAGTTTACAACATAC 57.269 37.500 0.00 0.00 0.00 2.39
6131 6379 4.965119 AGCAATCCCGAAATGAGTTTAC 57.035 40.909 0.00 0.00 0.00 2.01
6222 6470 9.581099 AGAAAAAGTGTGTTATAAGTGTTTTGG 57.419 29.630 0.00 0.00 0.00 3.28
6260 6508 2.037772 CGCTATTTCTACCTCCTGCCAT 59.962 50.000 0.00 0.00 0.00 4.40
6299 6547 1.739562 GGTCTCTTGGCACTCTGCG 60.740 63.158 0.00 0.00 46.21 5.18
6311 6559 4.647564 ACCAAGAATCAACATGGTCTCT 57.352 40.909 0.00 0.00 42.36 3.10
6475 6726 4.033009 TGACTCCAGCATTTCCTGATCTA 58.967 43.478 0.00 0.00 34.77 1.98
6572 6823 0.317854 GGCGCTTGGAACTGTTTGTC 60.318 55.000 7.64 0.00 0.00 3.18
6608 6859 4.569943 CAAACGAGGAAGAAGATGAGGAA 58.430 43.478 0.00 0.00 0.00 3.36
6659 6910 0.989890 CGAAGAACCGACTAAAGCCG 59.010 55.000 0.00 0.00 0.00 5.52
6738 6989 2.217112 CGATCCATTCGCCGAAGAC 58.783 57.895 5.52 0.00 41.69 3.01
6762 7013 0.179009 CCCATGACCCGCATTCATCT 60.179 55.000 0.00 0.00 34.15 2.90
6792 7043 0.818296 AAGCAGATTCGCCGAGTAGT 59.182 50.000 0.00 0.00 0.00 2.73
6909 7160 5.073311 AGATAACGACAGCTAACACACAT 57.927 39.130 0.00 0.00 0.00 3.21
7044 7302 5.918576 CGACATACACAGACTACTTCACAAA 59.081 40.000 0.00 0.00 0.00 2.83
7151 7411 6.860023 CACATCTTTCTTCAGATTTTGACACC 59.140 38.462 0.00 0.00 34.94 4.16
7174 7434 4.370364 AAACACAAGATGGACAACACAC 57.630 40.909 0.00 0.00 0.00 3.82
7176 7436 5.248870 AGAAAACACAAGATGGACAACAC 57.751 39.130 0.00 0.00 0.00 3.32
7229 7489 5.546621 TGTACAAGGTCTAAGCTGTCTTT 57.453 39.130 0.00 0.00 33.85 2.52
7248 7508 7.933577 CACCTCTCCTAAATATCTTGCATTGTA 59.066 37.037 0.00 0.00 0.00 2.41
7259 7519 7.510675 TTCTCCAAACACCTCTCCTAAATAT 57.489 36.000 0.00 0.00 0.00 1.28
7262 7522 5.640158 TTTCTCCAAACACCTCTCCTAAA 57.360 39.130 0.00 0.00 0.00 1.85
7264 7524 6.945636 TTATTTCTCCAAACACCTCTCCTA 57.054 37.500 0.00 0.00 0.00 2.94
7265 7525 5.843019 TTATTTCTCCAAACACCTCTCCT 57.157 39.130 0.00 0.00 0.00 3.69
7267 7527 7.148171 CCTGATTTATTTCTCCAAACACCTCTC 60.148 40.741 0.00 0.00 0.00 3.20
7268 7528 6.660949 CCTGATTTATTTCTCCAAACACCTCT 59.339 38.462 0.00 0.00 0.00 3.69
7269 7529 6.434340 ACCTGATTTATTTCTCCAAACACCTC 59.566 38.462 0.00 0.00 0.00 3.85
7270 7530 6.314917 ACCTGATTTATTTCTCCAAACACCT 58.685 36.000 0.00 0.00 0.00 4.00
7271 7531 6.590234 ACCTGATTTATTTCTCCAAACACC 57.410 37.500 0.00 0.00 0.00 4.16
7272 7532 8.887036 AAAACCTGATTTATTTCTCCAAACAC 57.113 30.769 0.00 0.00 0.00 3.32
7273 7533 8.923270 AGAAAACCTGATTTATTTCTCCAAACA 58.077 29.630 0.00 0.00 37.52 2.83
7274 7534 9.764363 AAGAAAACCTGATTTATTTCTCCAAAC 57.236 29.630 0.00 0.00 40.28 2.93
7303 7648 3.128852 TGTACAAATAAGCACCGGTGT 57.871 42.857 33.92 19.11 0.00 4.16
7306 7651 4.394920 ACATCTTGTACAAATAAGCACCGG 59.605 41.667 10.03 0.00 0.00 5.28
7308 7653 7.611213 ACTACATCTTGTACAAATAAGCACC 57.389 36.000 10.03 0.00 0.00 5.01
7320 7665 7.498239 AGCGTCTATCTTGTACTACATCTTGTA 59.502 37.037 0.00 0.00 0.00 2.41
7321 7666 6.319152 AGCGTCTATCTTGTACTACATCTTGT 59.681 38.462 0.00 0.00 0.00 3.16
7322 7667 6.730175 AGCGTCTATCTTGTACTACATCTTG 58.270 40.000 0.00 0.00 0.00 3.02
7323 7668 6.945938 AGCGTCTATCTTGTACTACATCTT 57.054 37.500 0.00 0.00 0.00 2.40
7324 7669 6.945938 AAGCGTCTATCTTGTACTACATCT 57.054 37.500 0.00 0.00 0.00 2.90
7325 7670 9.680315 AATTAAGCGTCTATCTTGTACTACATC 57.320 33.333 0.00 0.00 0.00 3.06
7353 7698 4.079787 AGACACTTCTAGAGGAGAGATGCT 60.080 45.833 9.14 0.00 34.93 3.79
7358 7703 7.931578 TTTCTAAGACACTTCTAGAGGAGAG 57.068 40.000 9.14 0.00 34.93 3.20
7385 7738 8.560374 GCTAGGTGCTTAGAAAAATAAATCGAT 58.440 33.333 0.00 0.00 38.95 3.59
7386 7739 7.551262 TGCTAGGTGCTTAGAAAAATAAATCGA 59.449 33.333 0.00 0.00 43.37 3.59
7392 7745 7.938140 ACAATGCTAGGTGCTTAGAAAAATA 57.062 32.000 0.00 0.00 43.37 1.40
7401 7754 4.003648 GTCTTGTACAATGCTAGGTGCTT 58.996 43.478 9.13 0.00 43.37 3.91
7411 7764 8.437360 TGAATTGCTATAGGTCTTGTACAATG 57.563 34.615 9.13 3.87 0.00 2.82
7422 7776 6.840780 AGCTGTTTTTGAATTGCTATAGGT 57.159 33.333 1.04 0.00 0.00 3.08
7445 7799 3.254411 TGATGGCGCTTCAACATGTTTTA 59.746 39.130 8.77 0.00 0.00 1.52
7513 7994 1.975407 GCAGTGGCATGCCAGTTCT 60.975 57.895 38.91 29.20 46.84 3.01
7514 7995 2.270257 TGCAGTGGCATGCCAGTTC 61.270 57.895 38.91 34.46 46.84 3.01
7515 7996 2.203523 TGCAGTGGCATGCCAGTT 60.204 55.556 38.91 27.43 46.84 3.16
7545 8043 5.329035 TCTTTGGATAATTGCTTTGCTCC 57.671 39.130 0.00 0.00 0.00 4.70
7681 8183 5.049749 CGAATGTTGTGTTCCTGATGTAACA 60.050 40.000 0.00 0.00 33.35 2.41
7727 8236 1.531149 CTTGTTTACGGAGTGCCTGTG 59.469 52.381 0.00 0.00 45.73 3.66
7820 8333 2.358247 GTCACCGCCATGGACGTT 60.358 61.111 18.40 4.14 42.00 3.99


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

AutoCloner maintained by Alex Coulton.