Multiple sequence alignment - TraesCS5D01G373700

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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 TraesCS5D01G373700 chr5D 100.000 4434 0 0 1 4434 447144332 447139899 0.000000e+00 8189.0
1 TraesCS5D01G373700 chr5D 82.896 2555 337 51 984 3501 447194085 447191594 0.000000e+00 2206.0
2 TraesCS5D01G373700 chr5B 92.127 2934 181 24 891 3804 545574991 545577894 0.000000e+00 4093.0
3 TraesCS5D01G373700 chr5B 89.575 259 23 4 3829 4085 545578249 545578505 4.280000e-85 326.0
4 TraesCS5D01G373700 chr5B 91.892 111 9 0 1 111 545573124 545573234 5.940000e-34 156.0
5 TraesCS5D01G373700 chr5B 79.845 129 21 5 3763 3888 529963638 529963764 6.110000e-14 89.8
6 TraesCS5D01G373700 chr5B 85.714 84 11 1 685 768 545574664 545574746 2.200000e-13 87.9
7 TraesCS5D01G373700 chr5A 96.503 2202 72 4 2233 4433 565489549 565491746 0.000000e+00 3635.0
8 TraesCS5D01G373700 chr5A 94.884 1251 59 4 891 2140 565488252 565489498 0.000000e+00 1951.0
9 TraesCS5D01G373700 chr5A 81.697 2180 295 46 1339 3496 565416052 565418149 0.000000e+00 1720.0
10 TraesCS5D01G373700 chr5A 78.053 606 92 31 294 884 565487714 565488293 1.180000e-90 344.0
11 TraesCS5D01G373700 chr5A 91.250 160 10 1 1 156 565485549 565485708 9.660000e-52 215.0
12 TraesCS5D01G373700 chr5A 78.788 198 38 2 4229 4426 634082541 634082734 3.600000e-26 130.0
13 TraesCS5D01G373700 chr6D 85.332 1234 169 10 2222 3450 24376702 24375476 0.000000e+00 1266.0
14 TraesCS5D01G373700 chr6D 84.036 1234 190 6 2223 3454 24293706 24292478 0.000000e+00 1181.0
15 TraesCS5D01G373700 chr6D 77.107 1044 176 34 1085 2101 24377790 24376783 3.020000e-151 545.0
16 TraesCS5D01G373700 chr6D 82.386 176 27 4 1092 1265 24384058 24383885 2.760000e-32 150.0
17 TraesCS5D01G373700 chr6D 86.777 121 16 0 1369 1489 24383395 24383275 7.740000e-28 135.0
18 TraesCS5D01G373700 chr6B 85.212 1224 169 10 2222 3440 39368312 39369528 0.000000e+00 1247.0
19 TraesCS5D01G373700 chr6B 78.070 912 144 35 1086 1972 39367240 39368120 3.930000e-145 525.0
20 TraesCS5D01G373700 chr6A 84.967 1224 171 11 2222 3441 22954229 22955443 0.000000e+00 1229.0
21 TraesCS5D01G373700 chr6A 77.351 1042 171 39 1085 2098 22953141 22954145 1.390000e-154 556.0
22 TraesCS5D01G373700 chr6A 84.951 206 30 1 4229 4433 595073295 595073090 1.620000e-49 207.0
23 TraesCS5D01G373700 chrUn 82.072 1216 211 6 2244 3454 35133933 35135146 0.000000e+00 1031.0
24 TraesCS5D01G373700 chrUn 82.278 79 12 1 3837 3915 108877877 108877801 2.860000e-07 67.6
25 TraesCS5D01G373700 chr7D 86.058 208 29 0 4227 4434 41172823 41173030 1.600000e-54 224.0
26 TraesCS5D01G373700 chr7D 84.524 84 10 2 3830 3913 618771908 618771988 3.680000e-11 80.5
27 TraesCS5D01G373700 chr7B 84.058 207 27 5 4231 4434 468211097 468210894 1.260000e-45 195.0
28 TraesCS5D01G373700 chr4D 83.981 206 29 3 4231 4434 466387676 466387879 1.260000e-45 195.0
29 TraesCS5D01G373700 chr4D 89.583 48 4 1 3761 3808 43054528 43054482 4.790000e-05 60.2
30 TraesCS5D01G373700 chr1B 85.876 177 24 1 4249 4424 658390371 658390547 2.110000e-43 187.0
31 TraesCS5D01G373700 chr1B 84.507 71 9 2 3761 3830 302014724 302014655 7.960000e-08 69.4
32 TraesCS5D01G373700 chr1B 80.460 87 13 4 3790 3874 108837643 108837727 3.700000e-06 63.9
33 TraesCS5D01G373700 chr2A 82.162 185 29 1 4249 4433 162017364 162017184 5.940000e-34 156.0
34 TraesCS5D01G373700 chr3A 79.293 198 38 3 4228 4425 31588509 31588315 7.740000e-28 135.0
35 TraesCS5D01G373700 chr4B 79.518 166 22 11 3754 3914 658622862 658622704 1.690000e-19 108.0
36 TraesCS5D01G373700 chr4B 80.851 141 21 6 3754 3891 658592197 658592060 6.070000e-19 106.0
37 TraesCS5D01G373700 chr1A 79.851 134 18 8 3761 3888 31952956 31953086 6.110000e-14 89.8
38 TraesCS5D01G373700 chr3D 97.436 39 1 0 3762 3800 380483380 380483342 2.860000e-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 TraesCS5D01G373700 chr5D 447139899 447144332 4433 True 8189.000 8189 100.0000 1 4434 1 chr5D.!!$R1 4433
1 TraesCS5D01G373700 chr5D 447191594 447194085 2491 True 2206.000 2206 82.8960 984 3501 1 chr5D.!!$R2 2517
2 TraesCS5D01G373700 chr5B 545573124 545578505 5381 False 1165.725 4093 89.8270 1 4085 4 chr5B.!!$F2 4084
3 TraesCS5D01G373700 chr5A 565416052 565418149 2097 False 1720.000 1720 81.6970 1339 3496 1 chr5A.!!$F1 2157
4 TraesCS5D01G373700 chr5A 565485549 565491746 6197 False 1536.250 3635 90.1725 1 4433 4 chr5A.!!$F3 4432
5 TraesCS5D01G373700 chr6D 24292478 24293706 1228 True 1181.000 1181 84.0360 2223 3454 1 chr6D.!!$R1 1231
6 TraesCS5D01G373700 chr6D 24375476 24377790 2314 True 905.500 1266 81.2195 1085 3450 2 chr6D.!!$R2 2365
7 TraesCS5D01G373700 chr6B 39367240 39369528 2288 False 886.000 1247 81.6410 1086 3440 2 chr6B.!!$F1 2354
8 TraesCS5D01G373700 chr6A 22953141 22955443 2302 False 892.500 1229 81.1590 1085 3441 2 chr6A.!!$F1 2356
9 TraesCS5D01G373700 chrUn 35133933 35135146 1213 False 1031.000 1031 82.0720 2244 3454 1 chrUn.!!$F1 1210

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
78 79 0.248702 TTGCGCGTTTCAAACTTCCC 60.249 50.0 8.43 0.0 0.00 3.97 F
1648 4741 0.175760 GATGGACTCGTTGCTGGCTA 59.824 55.0 0.00 0.0 0.00 3.93 F
2172 5292 0.764271 TGTGAGATTGCACACCAGGA 59.236 50.0 0.00 0.0 43.35 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 5064 0.670546 CGTTGACGTCTTGGCATCCT 60.671 55.000 17.92 0.0 34.11 3.24 R
2594 5718 2.404215 CACCTCGTTGATGAACTCGTT 58.596 47.619 0.00 0.0 0.00 3.85 R
3947 7421 0.759346 CTCCCCTCATCCGGGTTTAG 59.241 60.000 0.00 0.0 43.06 1.85 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
36 37 3.509967 TCTTCGCTGACTGTTCCTATTGA 59.490 43.478 0.00 0.00 0.00 2.57
51 52 1.369625 ATTGACGCTCGATTTGGTCC 58.630 50.000 0.00 0.00 0.00 4.46
72 73 1.587613 GGCTGTTGCGCGTTTCAAA 60.588 52.632 8.43 0.00 40.82 2.69
78 79 0.248702 TTGCGCGTTTCAAACTTCCC 60.249 50.000 8.43 0.00 0.00 3.97
79 80 1.357334 GCGCGTTTCAAACTTCCCA 59.643 52.632 8.43 0.00 0.00 4.37
85 86 1.028905 TTTCAAACTTCCCACCGCTG 58.971 50.000 0.00 0.00 0.00 5.18
145 150 1.002624 GTGGAGGGATGAACGCCAA 60.003 57.895 0.00 0.00 0.00 4.52
165 1982 6.316390 CGCCAATTCTTTCTAACCTCATAAGT 59.684 38.462 0.00 0.00 0.00 2.24
192 2009 3.019564 GAGCCATAGAACACCATTTGCT 58.980 45.455 0.00 0.00 0.00 3.91
196 2013 3.131046 CCATAGAACACCATTTGCTTCCC 59.869 47.826 0.00 0.00 0.00 3.97
197 2014 2.683211 AGAACACCATTTGCTTCCCT 57.317 45.000 0.00 0.00 0.00 4.20
205 2022 2.028748 CCATTTGCTTCCCTCTTTGGTG 60.029 50.000 0.00 0.00 0.00 4.17
208 2026 0.843309 TGCTTCCCTCTTTGGTGTCA 59.157 50.000 0.00 0.00 0.00 3.58
213 2031 4.559502 GCTTCCCTCTTTGGTGTCAATTTC 60.560 45.833 0.00 0.00 32.28 2.17
216 2034 4.069304 CCCTCTTTGGTGTCAATTTCGTA 58.931 43.478 0.00 0.00 32.28 3.43
227 2045 6.369065 GGTGTCAATTTCGTAGAAGATGAACT 59.631 38.462 2.64 0.00 45.90 3.01
233 2051 7.820044 ATTTCGTAGAAGATGAACTGAAGAC 57.180 36.000 0.00 0.00 45.90 3.01
235 2053 6.184580 TCGTAGAAGATGAACTGAAGACTC 57.815 41.667 0.00 0.00 0.00 3.36
236 2054 5.941058 TCGTAGAAGATGAACTGAAGACTCT 59.059 40.000 0.00 0.00 0.00 3.24
299 2211 8.768957 TTAGCTTGCTATATCAATGAGATGAC 57.231 34.615 0.00 0.00 37.57 3.06
316 2228 5.855045 AGATGACTTGTAAACTTCTTCGGT 58.145 37.500 0.00 0.00 0.00 4.69
321 2233 4.743644 ACTTGTAAACTTCTTCGGTTCGAG 59.256 41.667 0.00 0.00 37.14 4.04
322 2234 4.311816 TGTAAACTTCTTCGGTTCGAGT 57.688 40.909 0.00 0.00 37.14 4.18
338 2250 1.303317 AGTGGACCGATTGGCAACC 60.303 57.895 0.00 0.00 39.70 3.77
352 2264 2.158986 TGGCAACCACCATGAAGTTTTG 60.159 45.455 0.00 0.00 33.75 2.44
353 2265 2.482864 GCAACCACCATGAAGTTTTGG 58.517 47.619 0.00 4.66 39.02 3.28
361 2273 5.879777 CCACCATGAAGTTTTGGTTTCTTTT 59.120 36.000 8.33 0.00 43.73 2.27
362 2274 6.037062 CCACCATGAAGTTTTGGTTTCTTTTC 59.963 38.462 8.33 0.00 43.73 2.29
367 2279 9.748708 CATGAAGTTTTGGTTTCTTTTCATCTA 57.251 29.630 0.00 0.00 33.04 1.98
369 2281 9.581099 TGAAGTTTTGGTTTCTTTTCATCTAAC 57.419 29.630 0.00 0.00 0.00 2.34
370 2282 8.942338 AAGTTTTGGTTTCTTTTCATCTAACC 57.058 30.769 0.00 0.00 38.92 2.85
373 2285 9.031360 GTTTTGGTTTCTTTTCATCTAACCTTC 57.969 33.333 0.00 0.00 39.16 3.46
374 2286 7.889873 TTGGTTTCTTTTCATCTAACCTTCA 57.110 32.000 0.00 0.00 39.16 3.02
376 2288 7.287061 TGGTTTCTTTTCATCTAACCTTCAGA 58.713 34.615 0.00 0.00 39.16 3.27
377 2289 7.445402 TGGTTTCTTTTCATCTAACCTTCAGAG 59.555 37.037 0.00 0.00 39.16 3.35
378 2290 7.301789 GTTTCTTTTCATCTAACCTTCAGAGC 58.698 38.462 0.00 0.00 0.00 4.09
379 2291 5.491982 TCTTTTCATCTAACCTTCAGAGCC 58.508 41.667 0.00 0.00 0.00 4.70
380 2292 5.249393 TCTTTTCATCTAACCTTCAGAGCCT 59.751 40.000 0.00 0.00 0.00 4.58
381 2293 5.505181 TTTCATCTAACCTTCAGAGCCTT 57.495 39.130 0.00 0.00 0.00 4.35
382 2294 4.744795 TCATCTAACCTTCAGAGCCTTC 57.255 45.455 0.00 0.00 0.00 3.46
384 2296 4.718774 TCATCTAACCTTCAGAGCCTTCAT 59.281 41.667 0.00 0.00 0.00 2.57
385 2297 5.899547 TCATCTAACCTTCAGAGCCTTCATA 59.100 40.000 0.00 0.00 0.00 2.15
387 2299 7.730332 TCATCTAACCTTCAGAGCCTTCATATA 59.270 37.037 0.00 0.00 0.00 0.86
388 2300 7.914427 TCTAACCTTCAGAGCCTTCATATAA 57.086 36.000 0.00 0.00 0.00 0.98
389 2301 7.727181 TCTAACCTTCAGAGCCTTCATATAAC 58.273 38.462 0.00 0.00 0.00 1.89
390 2302 6.567602 AACCTTCAGAGCCTTCATATAACT 57.432 37.500 0.00 0.00 0.00 2.24
391 2303 6.168270 ACCTTCAGAGCCTTCATATAACTC 57.832 41.667 0.00 0.00 0.00 3.01
392 2304 5.902431 ACCTTCAGAGCCTTCATATAACTCT 59.098 40.000 0.00 0.00 38.22 3.24
394 2306 6.705381 CCTTCAGAGCCTTCATATAACTCTTG 59.295 42.308 0.00 0.00 35.57 3.02
395 2307 6.166984 TCAGAGCCTTCATATAACTCTTGG 57.833 41.667 0.00 0.00 35.57 3.61
396 2308 5.899547 TCAGAGCCTTCATATAACTCTTGGA 59.100 40.000 0.00 0.00 35.57 3.53
397 2309 6.041409 TCAGAGCCTTCATATAACTCTTGGAG 59.959 42.308 0.00 0.00 35.57 3.86
398 2310 4.967036 AGCCTTCATATAACTCTTGGAGC 58.033 43.478 0.00 0.00 32.04 4.70
399 2311 4.068599 GCCTTCATATAACTCTTGGAGCC 58.931 47.826 0.00 0.00 32.04 4.70
400 2312 4.202409 GCCTTCATATAACTCTTGGAGCCT 60.202 45.833 0.00 0.00 32.04 4.58
402 2314 5.994668 CCTTCATATAACTCTTGGAGCCTTC 59.005 44.000 0.00 0.00 32.04 3.46
403 2315 6.408548 CCTTCATATAACTCTTGGAGCCTTCA 60.409 42.308 0.00 0.00 32.04 3.02
404 2316 6.753913 TCATATAACTCTTGGAGCCTTCAT 57.246 37.500 0.00 0.00 32.04 2.57
407 2319 9.547279 TCATATAACTCTTGGAGCCTTCATATA 57.453 33.333 0.00 0.00 32.04 0.86
410 2322 6.506538 AACTCTTGGAGCCTTCATATATGT 57.493 37.500 12.42 0.00 32.04 2.29
411 2323 6.506538 ACTCTTGGAGCCTTCATATATGTT 57.493 37.500 12.42 0.00 32.04 2.71
412 2324 6.529220 ACTCTTGGAGCCTTCATATATGTTC 58.471 40.000 12.42 4.57 32.04 3.18
413 2325 6.328672 ACTCTTGGAGCCTTCATATATGTTCT 59.671 38.462 12.42 5.74 32.04 3.01
414 2326 7.510685 ACTCTTGGAGCCTTCATATATGTTCTA 59.489 37.037 12.42 0.72 32.04 2.10
415 2327 7.671302 TCTTGGAGCCTTCATATATGTTCTAC 58.329 38.462 12.42 6.98 0.00 2.59
416 2328 7.510685 TCTTGGAGCCTTCATATATGTTCTACT 59.489 37.037 12.42 5.41 0.00 2.57
417 2329 8.721133 TTGGAGCCTTCATATATGTTCTACTA 57.279 34.615 12.42 1.88 0.00 1.82
459 2374 9.698617 CCTAATAAAATACAACGCTAGTGTTTC 57.301 33.333 18.89 0.00 30.55 2.78
462 2377 6.854496 AAAATACAACGCTAGTGTTTCTCA 57.146 33.333 18.89 5.26 30.55 3.27
464 2379 7.435068 AAATACAACGCTAGTGTTTCTCATT 57.565 32.000 18.89 12.13 0.00 2.57
466 2381 8.542497 AATACAACGCTAGTGTTTCTCATTAA 57.458 30.769 18.89 0.00 0.00 1.40
490 2405 1.344953 AACGGGAGCATCATAGGGCA 61.345 55.000 0.00 0.00 36.25 5.36
495 2410 2.101415 GGGAGCATCATAGGGCAAAAAC 59.899 50.000 0.00 0.00 36.25 2.43
517 2432 5.488341 ACGCTAAGGCAGAAATTCTTTAGA 58.512 37.500 13.99 0.00 38.60 2.10
521 2436 8.064814 CGCTAAGGCAGAAATTCTTTAGATAAC 58.935 37.037 13.99 0.43 38.60 1.89
577 3309 1.496857 TGGGGTTGTTGGTCATCTTGA 59.503 47.619 0.00 0.00 0.00 3.02
582 3314 3.550030 GGTTGTTGGTCATCTTGAAACCG 60.550 47.826 0.00 0.00 35.76 4.44
585 3317 4.452825 TGTTGGTCATCTTGAAACCGTAA 58.547 39.130 0.00 0.00 35.76 3.18
587 3319 5.533154 TGTTGGTCATCTTGAAACCGTAATT 59.467 36.000 0.00 0.00 35.76 1.40
589 3321 6.007936 TGGTCATCTTGAAACCGTAATTTG 57.992 37.500 0.00 0.00 35.76 2.32
591 3323 6.263392 TGGTCATCTTGAAACCGTAATTTGAA 59.737 34.615 0.00 0.00 35.76 2.69
592 3324 6.581166 GGTCATCTTGAAACCGTAATTTGAAC 59.419 38.462 0.00 0.00 0.00 3.18
595 3327 8.356657 TCATCTTGAAACCGTAATTTGAACATT 58.643 29.630 0.00 0.00 0.00 2.71
597 3329 7.708051 TCTTGAAACCGTAATTTGAACATTGA 58.292 30.769 0.00 0.00 0.00 2.57
599 3331 8.514136 TTGAAACCGTAATTTGAACATTGATC 57.486 30.769 0.00 0.00 0.00 2.92
600 3332 7.881142 TGAAACCGTAATTTGAACATTGATCT 58.119 30.769 0.00 0.00 0.00 2.75
601 3333 8.356657 TGAAACCGTAATTTGAACATTGATCTT 58.643 29.630 0.00 0.00 0.00 2.40
604 3336 7.461107 ACCGTAATTTGAACATTGATCTTACG 58.539 34.615 14.53 14.53 39.64 3.18
639 3371 8.702163 AGTTTGACCATTAACAAGAAAAGTTG 57.298 30.769 0.00 0.00 0.00 3.16
746 3640 6.155475 TGTTTTTGAATAGTCCAACTTGGG 57.845 37.500 8.01 0.00 38.32 4.12
755 3824 2.084546 GTCCAACTTGGGCATCTGTAC 58.915 52.381 7.59 0.00 42.98 2.90
763 3832 5.615289 ACTTGGGCATCTGTACTGATATTC 58.385 41.667 14.15 7.38 0.00 1.75
768 3837 5.872070 GGGCATCTGTACTGATATTCTTAGC 59.128 44.000 14.15 11.33 0.00 3.09
822 3891 6.986817 CGGTCCTTGTATGAGATATTTCTTGT 59.013 38.462 0.00 0.00 30.30 3.16
823 3892 7.495934 CGGTCCTTGTATGAGATATTTCTTGTT 59.504 37.037 0.00 0.00 30.30 2.83
840 3913 7.611213 TTCTTGTTAGTAGATAAAGCCAAGC 57.389 36.000 0.00 0.00 30.55 4.01
841 3914 6.947464 TCTTGTTAGTAGATAAAGCCAAGCT 58.053 36.000 0.00 0.00 42.56 3.74
849 3922 4.772678 AAGCCAAGCTTCCATCCC 57.227 55.556 0.00 0.00 46.77 3.85
850 3923 1.000866 AAGCCAAGCTTCCATCCCC 59.999 57.895 0.00 0.00 46.77 4.81
851 3924 1.513087 AAGCCAAGCTTCCATCCCCT 61.513 55.000 0.00 0.00 46.77 4.79
852 3925 1.755783 GCCAAGCTTCCATCCCCTG 60.756 63.158 0.00 0.00 0.00 4.45
853 3926 1.693640 CCAAGCTTCCATCCCCTGT 59.306 57.895 0.00 0.00 0.00 4.00
854 3927 0.918983 CCAAGCTTCCATCCCCTGTA 59.081 55.000 0.00 0.00 0.00 2.74
855 3928 1.408822 CCAAGCTTCCATCCCCTGTAC 60.409 57.143 0.00 0.00 0.00 2.90
856 3929 0.541863 AAGCTTCCATCCCCTGTACG 59.458 55.000 0.00 0.00 0.00 3.67
857 3930 1.146263 GCTTCCATCCCCTGTACGG 59.854 63.158 0.00 0.00 0.00 4.02
858 3931 1.335132 GCTTCCATCCCCTGTACGGA 61.335 60.000 2.31 0.00 33.16 4.69
859 3932 1.424638 CTTCCATCCCCTGTACGGAT 58.575 55.000 2.31 0.00 40.94 4.18
860 3933 2.605257 CTTCCATCCCCTGTACGGATA 58.395 52.381 2.31 0.00 38.08 2.59
861 3934 2.304221 TCCATCCCCTGTACGGATAG 57.696 55.000 2.31 0.00 38.08 2.08
862 3935 1.502039 TCCATCCCCTGTACGGATAGT 59.498 52.381 2.31 0.00 38.08 2.12
863 3936 2.718062 TCCATCCCCTGTACGGATAGTA 59.282 50.000 2.31 0.00 38.08 1.82
864 3937 3.140707 TCCATCCCCTGTACGGATAGTAA 59.859 47.826 2.31 0.00 38.08 2.24
865 3938 3.257624 CCATCCCCTGTACGGATAGTAAC 59.742 52.174 2.31 0.00 38.08 2.50
866 3939 2.575532 TCCCCTGTACGGATAGTAACG 58.424 52.381 2.31 0.00 37.02 3.18
867 3940 1.000938 CCCCTGTACGGATAGTAACGC 60.001 57.143 2.31 0.00 37.02 4.84
868 3941 1.677576 CCCTGTACGGATAGTAACGCA 59.322 52.381 2.31 0.00 37.02 5.24
869 3942 2.295349 CCCTGTACGGATAGTAACGCAT 59.705 50.000 2.31 0.00 37.02 4.73
870 3943 3.305964 CCTGTACGGATAGTAACGCATG 58.694 50.000 2.31 0.00 37.02 4.06
871 3944 2.724690 CTGTACGGATAGTAACGCATGC 59.275 50.000 7.91 7.91 37.02 4.06
872 3945 2.099427 TGTACGGATAGTAACGCATGCA 59.901 45.455 19.57 0.00 37.02 3.96
873 3946 1.567504 ACGGATAGTAACGCATGCAC 58.432 50.000 19.57 8.61 0.00 4.57
874 3947 0.859232 CGGATAGTAACGCATGCACC 59.141 55.000 19.57 1.48 0.00 5.01
875 3948 1.538204 CGGATAGTAACGCATGCACCT 60.538 52.381 19.57 9.37 0.00 4.00
876 3949 1.867233 GGATAGTAACGCATGCACCTG 59.133 52.381 19.57 3.36 0.00 4.00
877 3950 1.261619 GATAGTAACGCATGCACCTGC 59.738 52.381 19.57 2.04 42.50 4.85
889 3962 0.304705 GCACCTGCACGGATATTTCG 59.695 55.000 8.91 0.00 41.59 3.46
893 3966 1.472552 CCTGCACGGATATTTCGGTCA 60.473 52.381 4.80 0.00 33.54 4.02
913 3986 5.163982 GGTCAGTCAACGCTTGAATAGTAAC 60.164 44.000 2.65 0.61 42.15 2.50
924 3997 3.194861 TGAATAGTAACGCATGCACCTC 58.805 45.455 19.57 5.20 0.00 3.85
998 4073 2.916423 CGCGCACGCAGAAGATAG 59.084 61.111 16.04 0.00 42.06 2.08
1142 4217 0.462937 CCGTACCCATTCGGCATCAA 60.463 55.000 0.00 0.00 40.28 2.57
1260 4335 1.361204 TGGAGATCTCACTGGCCAAA 58.639 50.000 23.85 0.00 0.00 3.28
1395 4482 4.953868 CCGTTCGTGGTGTCGGCA 62.954 66.667 0.00 0.00 36.68 5.69
1599 4692 2.409870 CCGTCCCTACTACCGCGTT 61.410 63.158 4.92 0.00 0.00 4.84
1645 4738 0.460987 GGAGATGGACTCGTTGCTGG 60.461 60.000 0.00 0.00 45.76 4.85
1646 4739 1.078848 AGATGGACTCGTTGCTGGC 60.079 57.895 0.00 0.00 0.00 4.85
1648 4741 0.175760 GATGGACTCGTTGCTGGCTA 59.824 55.000 0.00 0.00 0.00 3.93
1906 5023 2.485122 GCTACGTGTGCCATTGCC 59.515 61.111 0.00 0.00 36.33 4.52
2172 5292 0.764271 TGTGAGATTGCACACCAGGA 59.236 50.000 0.00 0.00 43.35 3.86
2203 5323 4.412796 TGTTCCTCTGCTTCATATCAGG 57.587 45.455 0.00 0.00 0.00 3.86
2213 5333 5.769835 TGCTTCATATCAGGGAATTTTCCT 58.230 37.500 9.13 0.00 46.72 3.36
2235 5358 5.335426 CCTGAACCATGACACATTTTCTCTG 60.335 44.000 0.00 0.00 0.00 3.35
2236 5359 5.375773 TGAACCATGACACATTTTCTCTGA 58.624 37.500 0.00 0.00 0.00 3.27
2240 5363 5.771666 ACCATGACACATTTTCTCTGACATT 59.228 36.000 0.00 0.00 0.00 2.71
2404 5527 5.540337 CAGGGGACATCTACTAGAGCAATTA 59.460 44.000 0.00 0.00 0.00 1.40
2467 5590 2.596851 GGTGGAGCTGGAGAAGGCA 61.597 63.158 0.00 0.00 0.00 4.75
2509 5632 2.519780 GAGATCGGCGGAGGAGGT 60.520 66.667 7.21 0.00 0.00 3.85
3345 6469 7.147983 GGGTGTTATTGATGCACAAGGTTATAA 60.148 37.037 0.00 0.00 42.02 0.98
3367 6494 6.600882 AAAATGATTGAAGATGGAAGCACT 57.399 33.333 0.00 0.00 0.00 4.40
3527 6660 5.659440 AAATGGTGGCTTGTATTAACCAG 57.341 39.130 0.00 0.00 43.77 4.00
3589 6722 9.354673 ACATAAATCAAAGAACCGATGGATATT 57.645 29.630 0.00 0.00 0.00 1.28
3738 6875 2.739913 CCAAACAAAATGCCATGCTCAG 59.260 45.455 0.00 0.00 0.00 3.35
3743 6880 1.624336 AAATGCCATGCTCAGTGTGT 58.376 45.000 0.00 0.00 0.00 3.72
3744 6881 1.624336 AATGCCATGCTCAGTGTGTT 58.376 45.000 0.00 0.00 0.00 3.32
3947 7421 6.002653 ACCCAAAATATGAGGGAGACTAAC 57.997 41.667 12.89 0.00 45.80 2.34
3971 7445 1.152819 CCGGATGAGGGGAGTACGA 60.153 63.158 0.00 0.00 0.00 3.43
4033 7507 6.594744 AGGATGAATGTGCTACATGAATACA 58.405 36.000 0.00 0.00 37.97 2.29
4158 7633 8.983724 GTAGCAAATTCTATCAACACCTATCTC 58.016 37.037 0.00 0.00 0.00 2.75
4172 7647 7.437713 ACACCTATCTCACAATTATTGGAGA 57.562 36.000 20.15 20.15 39.53 3.71
4243 7718 2.582636 ACCAACTAAGGGCATCTCCAAT 59.417 45.455 0.00 0.00 36.21 3.16
4254 7729 2.497792 ATCTCCAATGCCAACCCGCA 62.498 55.000 0.00 0.00 44.35 5.69
4263 7738 1.452108 CCAACCCGCAGATTCCTCC 60.452 63.158 0.00 0.00 0.00 4.30
4277 7752 5.011125 CAGATTCCTCCGGTATATGTCTGTT 59.989 44.000 0.00 0.00 0.00 3.16
4309 7784 4.032960 GACATGGTCCATGGGCATAATA 57.967 45.455 30.96 0.00 45.16 0.98
4345 7820 7.333423 GCCATCCATCGCTAATTACAAAGTATA 59.667 37.037 0.00 0.00 0.00 1.47
4411 7886 8.548721 GGTGAGATATTTGTTATTTAGTGTCCG 58.451 37.037 0.00 0.00 0.00 4.79
4433 7908 3.023832 GTTGGGAGGAGAGAGAGAAGAG 58.976 54.545 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.744414 CCATGGACCAAATCGAGCGT 60.744 55.000 5.56 0.00 0.00 5.07
51 52 2.050168 AAACGCGCAACAGCCATG 60.050 55.556 5.73 0.00 0.00 3.66
78 79 3.365265 GTTTCAGGGGCAGCGGTG 61.365 66.667 10.98 10.98 0.00 4.94
79 80 4.660938 GGTTTCAGGGGCAGCGGT 62.661 66.667 0.00 0.00 0.00 5.68
85 86 0.603065 GTGTTGATGGTTTCAGGGGC 59.397 55.000 0.00 0.00 35.27 5.80
89 90 2.554032 GGTCTGGTGTTGATGGTTTCAG 59.446 50.000 0.00 0.00 35.27 3.02
145 150 9.003658 CACACAACTTATGAGGTTAGAAAGAAT 57.996 33.333 0.00 0.00 0.00 2.40
165 1982 2.105649 TGGTGTTCTATGGCTCACACAA 59.894 45.455 3.87 0.00 41.17 3.33
192 2009 3.568007 CGAAATTGACACCAAAGAGGGAA 59.432 43.478 0.00 0.00 43.89 3.97
196 2013 6.423905 TCTTCTACGAAATTGACACCAAAGAG 59.576 38.462 0.00 0.00 35.67 2.85
197 2014 6.285224 TCTTCTACGAAATTGACACCAAAGA 58.715 36.000 0.00 0.00 35.67 2.52
205 2022 7.582435 TCAGTTCATCTTCTACGAAATTGAC 57.418 36.000 0.00 0.00 0.00 3.18
208 2026 8.091449 AGTCTTCAGTTCATCTTCTACGAAATT 58.909 33.333 0.00 0.00 0.00 1.82
213 2031 6.189677 AGAGTCTTCAGTTCATCTTCTACG 57.810 41.667 0.00 0.00 0.00 3.51
216 2034 8.865090 TCTTAAAGAGTCTTCAGTTCATCTTCT 58.135 33.333 5.70 0.00 0.00 2.85
273 2091 9.212641 GTCATCTCATTGATATAGCAAGCTAAA 57.787 33.333 9.58 0.00 33.36 1.85
274 2092 8.591940 AGTCATCTCATTGATATAGCAAGCTAA 58.408 33.333 9.58 0.00 33.36 3.09
275 2093 8.131847 AGTCATCTCATTGATATAGCAAGCTA 57.868 34.615 9.58 4.00 33.36 3.32
286 2104 9.512588 AAGAAGTTTACAAGTCATCTCATTGAT 57.487 29.630 0.00 0.00 35.40 2.57
287 2105 8.908786 AAGAAGTTTACAAGTCATCTCATTGA 57.091 30.769 0.00 0.00 0.00 2.57
288 2106 7.954248 CGAAGAAGTTTACAAGTCATCTCATTG 59.046 37.037 0.00 0.00 0.00 2.82
289 2107 7.118390 CCGAAGAAGTTTACAAGTCATCTCATT 59.882 37.037 0.00 0.00 0.00 2.57
290 2108 6.591834 CCGAAGAAGTTTACAAGTCATCTCAT 59.408 38.462 0.00 0.00 0.00 2.90
291 2109 5.926542 CCGAAGAAGTTTACAAGTCATCTCA 59.073 40.000 0.00 0.00 0.00 3.27
299 2211 4.743644 ACTCGAACCGAAGAAGTTTACAAG 59.256 41.667 0.00 0.00 34.74 3.16
316 2228 1.079405 GCCAATCGGTCCACTCGAA 60.079 57.895 0.00 0.00 40.15 3.71
321 2233 1.602323 TGGTTGCCAATCGGTCCAC 60.602 57.895 0.00 0.00 33.28 4.02
322 2234 1.602323 GTGGTTGCCAATCGGTCCA 60.602 57.895 0.00 0.00 34.18 4.02
352 2264 7.574030 GCTCTGAAGGTTAGATGAAAAGAAACC 60.574 40.741 0.00 0.00 39.92 3.27
353 2265 7.301789 GCTCTGAAGGTTAGATGAAAAGAAAC 58.698 38.462 0.00 0.00 0.00 2.78
361 2273 4.096681 TGAAGGCTCTGAAGGTTAGATGA 58.903 43.478 0.00 0.00 0.00 2.92
362 2274 4.478206 TGAAGGCTCTGAAGGTTAGATG 57.522 45.455 0.00 0.00 0.00 2.90
367 2279 6.385467 AGAGTTATATGAAGGCTCTGAAGGTT 59.615 38.462 0.00 0.00 35.48 3.50
368 2280 5.902431 AGAGTTATATGAAGGCTCTGAAGGT 59.098 40.000 0.00 0.00 35.48 3.50
369 2281 6.418057 AGAGTTATATGAAGGCTCTGAAGG 57.582 41.667 0.00 0.00 35.48 3.46
370 2282 6.705381 CCAAGAGTTATATGAAGGCTCTGAAG 59.295 42.308 0.00 0.00 36.74 3.02
373 2285 6.166984 TCCAAGAGTTATATGAAGGCTCTG 57.833 41.667 0.00 0.00 36.74 3.35
374 2286 5.221621 GCTCCAAGAGTTATATGAAGGCTCT 60.222 44.000 0.00 0.00 38.06 4.09
376 2288 4.202409 GGCTCCAAGAGTTATATGAAGGCT 60.202 45.833 0.00 0.00 31.39 4.58
377 2289 4.068599 GGCTCCAAGAGTTATATGAAGGC 58.931 47.826 0.00 0.00 31.39 4.35
378 2290 5.559148 AGGCTCCAAGAGTTATATGAAGG 57.441 43.478 0.00 0.00 31.39 3.46
379 2291 6.586344 TGAAGGCTCCAAGAGTTATATGAAG 58.414 40.000 0.00 0.00 31.39 3.02
380 2292 6.560003 TGAAGGCTCCAAGAGTTATATGAA 57.440 37.500 0.00 0.00 31.39 2.57
381 2293 6.753913 ATGAAGGCTCCAAGAGTTATATGA 57.246 37.500 0.00 0.00 31.39 2.15
384 2296 9.326489 ACATATATGAAGGCTCCAAGAGTTATA 57.674 33.333 19.63 0.00 31.39 0.98
385 2297 8.212259 ACATATATGAAGGCTCCAAGAGTTAT 57.788 34.615 19.63 0.00 31.39 1.89
387 2299 6.506538 ACATATATGAAGGCTCCAAGAGTT 57.493 37.500 19.63 0.00 31.39 3.01
388 2300 6.328672 AGAACATATATGAAGGCTCCAAGAGT 59.671 38.462 19.63 0.00 31.39 3.24
389 2301 6.767456 AGAACATATATGAAGGCTCCAAGAG 58.233 40.000 19.63 0.00 0.00 2.85
390 2302 6.753913 AGAACATATATGAAGGCTCCAAGA 57.246 37.500 19.63 0.00 0.00 3.02
391 2303 7.675062 AGTAGAACATATATGAAGGCTCCAAG 58.325 38.462 19.63 0.00 0.00 3.61
392 2304 7.618019 AGTAGAACATATATGAAGGCTCCAA 57.382 36.000 19.63 0.00 0.00 3.53
436 2348 8.995220 TGAGAAACACTAGCGTTGTATTTTATT 58.005 29.630 0.00 0.00 0.00 1.40
438 2350 7.949903 TGAGAAACACTAGCGTTGTATTTTA 57.050 32.000 0.00 0.00 0.00 1.52
472 2387 1.344953 TTGCCCTATGATGCTCCCGT 61.345 55.000 0.00 0.00 0.00 5.28
474 2389 2.071778 TTTTGCCCTATGATGCTCCC 57.928 50.000 0.00 0.00 0.00 4.30
475 2390 2.223572 CGTTTTTGCCCTATGATGCTCC 60.224 50.000 0.00 0.00 0.00 4.70
483 2398 1.749063 GCCTTAGCGTTTTTGCCCTAT 59.251 47.619 0.00 0.00 34.65 2.57
490 2405 5.453567 AGAATTTCTGCCTTAGCGTTTTT 57.546 34.783 0.00 0.00 44.31 1.94
495 2410 6.610741 ATCTAAAGAATTTCTGCCTTAGCG 57.389 37.500 0.00 0.00 40.16 4.26
521 2436 8.163408 TGGGTAATAGATTGATGTCCCTTATTG 58.837 37.037 0.00 0.00 35.20 1.90
526 2441 5.227593 AGTGGGTAATAGATTGATGTCCCT 58.772 41.667 0.00 0.00 35.20 4.20
557 3289 1.496857 TCAAGATGACCAACAACCCCA 59.503 47.619 0.00 0.00 0.00 4.96
558 3290 2.286365 TCAAGATGACCAACAACCCC 57.714 50.000 0.00 0.00 0.00 4.95
577 3309 9.620660 GTAAGATCAATGTTCAAATTACGGTTT 57.379 29.630 0.00 0.00 0.00 3.27
587 3319 8.994170 TGATTTGTACGTAAGATCAATGTTCAA 58.006 29.630 11.95 2.33 43.62 2.69
589 3321 9.478019 CTTGATTTGTACGTAAGATCAATGTTC 57.522 33.333 20.52 10.09 36.48 3.18
591 3323 8.547967 ACTTGATTTGTACGTAAGATCAATGT 57.452 30.769 20.52 17.90 36.48 2.71
592 3324 9.825972 AAACTTGATTTGTACGTAAGATCAATG 57.174 29.630 20.52 17.52 36.48 2.82
595 3327 8.492748 GTCAAACTTGATTTGTACGTAAGATCA 58.507 33.333 0.00 4.84 46.70 2.92
597 3329 7.442969 TGGTCAAACTTGATTTGTACGTAAGAT 59.557 33.333 0.00 0.00 46.70 2.40
599 3331 6.950545 TGGTCAAACTTGATTTGTACGTAAG 58.049 36.000 0.00 0.00 46.70 2.34
600 3332 6.922247 TGGTCAAACTTGATTTGTACGTAA 57.078 33.333 0.00 0.00 46.70 3.18
601 3333 7.499321 AATGGTCAAACTTGATTTGTACGTA 57.501 32.000 0.00 0.00 46.70 3.57
604 3336 9.522804 TTGTTAATGGTCAAACTTGATTTGTAC 57.477 29.630 0.00 0.00 46.70 2.90
611 3343 8.527810 ACTTTTCTTGTTAATGGTCAAACTTGA 58.472 29.630 0.00 0.00 34.20 3.02
675 3565 8.519526 TCTCCAAAATTACAAGTGCGAATTTAT 58.480 29.630 0.00 0.00 32.88 1.40
683 3573 6.024552 TGGATTCTCCAAAATTACAAGTGC 57.975 37.500 0.00 0.00 45.00 4.40
718 3612 9.965824 CAAGTTGGACTATTCAAAAACATAAGT 57.034 29.630 0.00 0.00 0.00 2.24
722 3616 6.741240 GCCCAAGTTGGACTATTCAAAAACAT 60.741 38.462 24.06 0.00 40.96 2.71
725 3619 4.651503 TGCCCAAGTTGGACTATTCAAAAA 59.348 37.500 24.06 0.00 40.96 1.94
735 3629 2.084546 GTACAGATGCCCAAGTTGGAC 58.915 52.381 24.06 12.91 40.96 4.02
746 3640 7.869937 TCTTGCTAAGAATATCAGTACAGATGC 59.130 37.037 10.78 4.62 33.83 3.91
790 3859 3.007506 TCTCATACAAGGACCGAGCAAAA 59.992 43.478 0.00 0.00 0.00 2.44
792 3861 2.176045 TCTCATACAAGGACCGAGCAA 58.824 47.619 0.00 0.00 0.00 3.91
794 3863 4.792521 ATATCTCATACAAGGACCGAGC 57.207 45.455 0.00 0.00 0.00 5.03
797 3866 6.986817 ACAAGAAATATCTCATACAAGGACCG 59.013 38.462 0.00 0.00 33.77 4.79
798 3867 8.738645 AACAAGAAATATCTCATACAAGGACC 57.261 34.615 0.00 0.00 33.77 4.46
838 3911 1.338136 CCGTACAGGGGATGGAAGCT 61.338 60.000 0.00 0.00 35.97 3.74
839 3912 1.146263 CCGTACAGGGGATGGAAGC 59.854 63.158 0.00 0.00 35.97 3.86
840 3913 1.424638 ATCCGTACAGGGGATGGAAG 58.575 55.000 0.44 0.00 42.63 3.46
841 3914 2.090943 ACTATCCGTACAGGGGATGGAA 60.091 50.000 15.40 0.00 43.15 3.53
842 3915 1.502039 ACTATCCGTACAGGGGATGGA 59.498 52.381 15.40 2.84 43.15 3.41
843 3916 2.011122 ACTATCCGTACAGGGGATGG 57.989 55.000 10.17 9.67 43.96 3.51
844 3917 3.057736 CGTTACTATCCGTACAGGGGATG 60.058 52.174 10.17 4.46 43.96 3.51
845 3918 3.152341 CGTTACTATCCGTACAGGGGAT 58.848 50.000 6.12 6.12 45.94 3.85
846 3919 2.575532 CGTTACTATCCGTACAGGGGA 58.424 52.381 0.00 0.00 41.52 4.81
847 3920 1.000938 GCGTTACTATCCGTACAGGGG 60.001 57.143 0.00 0.00 41.52 4.79
848 3921 1.677576 TGCGTTACTATCCGTACAGGG 59.322 52.381 0.00 0.00 41.52 4.45
849 3922 3.305964 CATGCGTTACTATCCGTACAGG 58.694 50.000 0.00 0.00 42.97 4.00
850 3923 2.724690 GCATGCGTTACTATCCGTACAG 59.275 50.000 0.00 0.00 0.00 2.74
851 3924 2.099427 TGCATGCGTTACTATCCGTACA 59.901 45.455 14.09 0.00 0.00 2.90
852 3925 2.470257 GTGCATGCGTTACTATCCGTAC 59.530 50.000 14.09 0.00 0.00 3.67
853 3926 2.544277 GGTGCATGCGTTACTATCCGTA 60.544 50.000 14.09 0.00 0.00 4.02
854 3927 1.567504 GTGCATGCGTTACTATCCGT 58.432 50.000 14.09 0.00 0.00 4.69
855 3928 0.859232 GGTGCATGCGTTACTATCCG 59.141 55.000 14.09 0.00 0.00 4.18
856 3929 1.867233 CAGGTGCATGCGTTACTATCC 59.133 52.381 14.09 5.23 0.00 2.59
857 3930 1.261619 GCAGGTGCATGCGTTACTATC 59.738 52.381 14.09 0.00 41.59 2.08
858 3931 1.299541 GCAGGTGCATGCGTTACTAT 58.700 50.000 14.09 0.00 41.59 2.12
859 3932 2.762360 GCAGGTGCATGCGTTACTA 58.238 52.632 14.09 0.00 41.59 1.82
860 3933 3.578456 GCAGGTGCATGCGTTACT 58.422 55.556 14.09 5.31 41.59 2.24
870 3943 0.304705 CGAAATATCCGTGCAGGTGC 59.695 55.000 5.57 0.00 41.99 5.01
871 3944 0.937304 CCGAAATATCCGTGCAGGTG 59.063 55.000 5.57 0.00 41.99 4.00
872 3945 0.539986 ACCGAAATATCCGTGCAGGT 59.460 50.000 5.57 0.00 41.99 4.00
873 3946 1.217882 GACCGAAATATCCGTGCAGG 58.782 55.000 0.00 0.00 42.97 4.85
874 3947 1.860950 CTGACCGAAATATCCGTGCAG 59.139 52.381 0.00 0.00 0.00 4.41
875 3948 1.206132 ACTGACCGAAATATCCGTGCA 59.794 47.619 0.00 0.00 0.00 4.57
876 3949 1.859080 GACTGACCGAAATATCCGTGC 59.141 52.381 0.00 0.00 0.00 5.34
877 3950 3.159353 TGACTGACCGAAATATCCGTG 57.841 47.619 0.00 0.00 0.00 4.94
878 3951 3.518590 GTTGACTGACCGAAATATCCGT 58.481 45.455 0.00 0.00 0.00 4.69
879 3952 2.534349 CGTTGACTGACCGAAATATCCG 59.466 50.000 0.00 0.00 0.00 4.18
880 3953 2.284417 GCGTTGACTGACCGAAATATCC 59.716 50.000 0.00 0.00 0.00 2.59
881 3954 3.187700 AGCGTTGACTGACCGAAATATC 58.812 45.455 0.00 0.00 0.00 1.63
882 3955 3.247006 AGCGTTGACTGACCGAAATAT 57.753 42.857 0.00 0.00 0.00 1.28
883 3956 2.734606 CAAGCGTTGACTGACCGAAATA 59.265 45.455 0.00 0.00 0.00 1.40
884 3957 1.531149 CAAGCGTTGACTGACCGAAAT 59.469 47.619 0.00 0.00 0.00 2.17
885 3958 0.934496 CAAGCGTTGACTGACCGAAA 59.066 50.000 0.00 0.00 0.00 3.46
886 3959 0.103390 TCAAGCGTTGACTGACCGAA 59.897 50.000 0.00 0.00 34.08 4.30
887 3960 0.103390 TTCAAGCGTTGACTGACCGA 59.897 50.000 0.76 0.00 39.87 4.69
888 3961 1.148310 ATTCAAGCGTTGACTGACCG 58.852 50.000 0.76 0.00 39.87 4.79
889 3962 3.326747 ACTATTCAAGCGTTGACTGACC 58.673 45.455 0.76 0.00 39.87 4.02
893 3966 3.367025 GCGTTACTATTCAAGCGTTGACT 59.633 43.478 0.76 0.00 39.87 3.41
913 3986 4.758251 TCCGTGGAGGTGCATGCG 62.758 66.667 14.09 0.00 41.99 4.73
924 3997 5.891451 TCTGCTAAATATATCGATCCGTGG 58.109 41.667 0.00 0.00 0.00 4.94
998 4073 2.897350 CCGCCGGAAGCTTCATCC 60.897 66.667 27.02 10.83 40.39 3.51
1251 4326 1.603455 CACCGTGGATTTGGCCAGT 60.603 57.895 5.11 0.00 38.95 4.00
1395 4482 2.357034 ACGAACCTGTTGCGCGAT 60.357 55.556 12.10 0.00 0.00 4.58
1599 4692 2.721425 GGTCCATCCCCGTGAAATTA 57.279 50.000 0.00 0.00 0.00 1.40
1645 4738 4.143363 GCGCACCGAAACCGTAGC 62.143 66.667 0.30 0.00 0.00 3.58
1646 4739 3.834373 CGCGCACCGAAACCGTAG 61.834 66.667 8.75 0.00 40.02 3.51
1668 4761 3.379445 TCGAACCAGCCCGTCTCC 61.379 66.667 0.00 0.00 0.00 3.71
1735 4846 2.515398 CACCCACTCCAGCACCAA 59.485 61.111 0.00 0.00 0.00 3.67
1803 4920 3.978193 TCATTGGGGCAGCCCGTT 61.978 61.111 25.18 8.57 46.66 4.44
1906 5023 3.541713 GCCCTCGTAGCCCTCCTG 61.542 72.222 0.00 0.00 0.00 3.86
1947 5064 0.670546 CGTTGACGTCTTGGCATCCT 60.671 55.000 17.92 0.00 34.11 3.24
2140 5257 4.201657 CAATCTCACATGCTATGTTCCCA 58.798 43.478 0.00 0.00 42.70 4.37
2141 5258 3.004106 GCAATCTCACATGCTATGTTCCC 59.996 47.826 0.00 0.00 42.70 3.97
2142 5259 3.628942 TGCAATCTCACATGCTATGTTCC 59.371 43.478 0.00 0.00 42.70 3.62
2143 5260 4.095334 TGTGCAATCTCACATGCTATGTTC 59.905 41.667 0.00 0.00 42.70 3.18
2144 5261 4.011698 TGTGCAATCTCACATGCTATGTT 58.988 39.130 0.00 0.00 42.70 2.71
2145 5262 3.613030 TGTGCAATCTCACATGCTATGT 58.387 40.909 0.00 0.00 46.22 2.29
2172 5292 5.188555 TGAAGCAGAGGAACATTCTATGTCT 59.811 40.000 0.00 0.00 44.07 3.41
2213 5333 5.239306 GTCAGAGAAAATGTGTCATGGTTCA 59.761 40.000 0.00 0.00 0.00 3.18
2235 5358 9.543018 CGATACTTAAACCTGAAAAGAAATGTC 57.457 33.333 0.00 0.00 0.00 3.06
2236 5359 8.512138 CCGATACTTAAACCTGAAAAGAAATGT 58.488 33.333 0.00 0.00 0.00 2.71
2240 5363 5.998981 TGCCGATACTTAAACCTGAAAAGAA 59.001 36.000 0.00 0.00 0.00 2.52
2404 5527 0.463654 TGTCTGCCTTTTGCGACACT 60.464 50.000 7.42 0.00 43.48 3.55
2467 5590 2.752903 AGCTTTGTCGAAGTTGTTGGTT 59.247 40.909 1.73 0.00 37.69 3.67
2509 5632 2.445427 CCTTTGTACACCATGCCATGA 58.555 47.619 6.18 0.00 0.00 3.07
2594 5718 2.404215 CACCTCGTTGATGAACTCGTT 58.596 47.619 0.00 0.00 0.00 3.85
3345 6469 5.713389 TCAGTGCTTCCATCTTCAATCATTT 59.287 36.000 0.00 0.00 0.00 2.32
3367 6494 5.011125 GCTATATTGTCTGCTAACCTCCTCA 59.989 44.000 0.00 0.00 0.00 3.86
3504 6637 5.777732 TCTGGTTAATACAAGCCACCATTTT 59.222 36.000 0.00 0.00 36.91 1.82
3527 6660 8.723942 ATTCTTCCGCTTTGGTATATATGATC 57.276 34.615 0.00 0.00 39.52 2.92
3589 6722 9.196139 CCATGGTTTCCTTTGGTTTAGATATAA 57.804 33.333 2.57 0.00 0.00 0.98
3590 6723 8.561769 TCCATGGTTTCCTTTGGTTTAGATATA 58.438 33.333 12.58 0.00 32.17 0.86
3738 6875 4.976116 CCGAAATGGAGAAAAAGAACACAC 59.024 41.667 0.00 0.00 42.00 3.82
3744 6881 9.292195 ACTAATAAACCGAAATGGAGAAAAAGA 57.708 29.630 0.00 0.00 42.00 2.52
3947 7421 0.759346 CTCCCCTCATCCGGGTTTAG 59.241 60.000 0.00 0.00 43.06 1.85
3971 7445 3.310860 GATGCCCCTCGGTTGACGT 62.311 63.158 0.00 0.00 44.69 4.34
4023 7497 6.295236 CCCAACCTTGTCATTTGTATTCATGT 60.295 38.462 0.00 0.00 0.00 3.21
4033 7507 5.003096 AGAGAATCCCAACCTTGTCATTT 57.997 39.130 0.00 0.00 33.66 2.32
4152 7627 6.373774 GGGCATCTCCAATAATTGTGAGATAG 59.626 42.308 13.07 10.15 41.50 2.08
4158 7633 3.569491 AGGGGCATCTCCAATAATTGTG 58.431 45.455 0.00 0.00 36.21 3.33
4222 7697 1.668826 TGGAGATGCCCTTAGTTGGT 58.331 50.000 0.00 0.00 34.97 3.67
4243 7718 2.361104 GGAATCTGCGGGTTGGCA 60.361 61.111 0.00 0.00 41.45 4.92
4263 7738 6.073980 CCGGACATAAAAACAGACATATACCG 60.074 42.308 0.00 0.00 32.19 4.02
4309 7784 3.721172 ATGGATGGCTCCCTCCCGT 62.721 63.158 7.61 0.00 41.29 5.28
4345 7820 1.985895 ACCTTTTCTCCTTCCATCCGT 59.014 47.619 0.00 0.00 0.00 4.69
4389 7864 8.889717 CAACCGGACACTAAATAACAAATATCT 58.110 33.333 9.46 0.00 0.00 1.98
4411 7886 2.107366 CTTCTCTCTCTCCTCCCAACC 58.893 57.143 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.