Multiple sequence alignment - TraesCS7B01G243200

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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 TraesCS7B01G243200 chr7B 100.000 5169 0 0 1 5169 451351292 451356460 0.000000e+00 9546.0
1 TraesCS7B01G243200 chr7B 100.000 29 0 0 5141 5169 648477881 648477909 3.000000e-03 54.7
2 TraesCS7B01G243200 chr7D 95.386 3901 123 22 647 4526 434146382 434150246 0.000000e+00 6154.0
3 TraesCS7B01G243200 chr7D 81.120 625 75 25 4566 5169 610651428 610650826 1.310000e-125 460.0
4 TraesCS7B01G243200 chr7D 93.088 217 15 0 1 217 434145529 434145745 8.350000e-83 318.0
5 TraesCS7B01G243200 chr7D 80.571 175 24 4 262 427 134106458 134106631 5.430000e-25 126.0
6 TraesCS7B01G243200 chr7D 90.141 71 5 2 5090 5159 610650956 610650887 1.980000e-14 91.6
7 TraesCS7B01G243200 chr7D 94.286 35 1 1 5135 5168 568063859 568063825 9.000000e-03 52.8
8 TraesCS7B01G243200 chr7A 95.972 2880 81 23 1475 4344 484594303 484597157 0.000000e+00 4643.0
9 TraesCS7B01G243200 chr7A 94.718 852 39 4 627 1477 484593401 484594247 0.000000e+00 1319.0
10 TraesCS7B01G243200 chr7A 88.703 239 24 1 1 239 484567482 484567717 6.550000e-74 289.0
11 TraesCS7B01G243200 chr7A 84.066 182 21 2 267 440 676361603 676361422 8.900000e-38 169.0
12 TraesCS7B01G243200 chr7A 81.143 175 25 4 259 425 608357710 608357884 3.250000e-27 134.0
13 TraesCS7B01G243200 chr4A 94.497 636 30 3 4539 5169 614548335 614547700 0.000000e+00 976.0
14 TraesCS7B01G243200 chr4A 83.673 196 15 7 259 440 319821510 319821318 8.900000e-38 169.0
15 TraesCS7B01G243200 chr4A 79.130 115 17 7 65 176 613692428 613692318 7.180000e-09 73.1
16 TraesCS7B01G243200 chr2B 93.985 532 20 6 4534 5064 170416110 170416630 0.000000e+00 795.0
17 TraesCS7B01G243200 chr2B 89.520 563 53 6 4537 5096 713969415 713968856 0.000000e+00 708.0
18 TraesCS7B01G243200 chr2B 87.011 562 66 6 4540 5096 93712675 93713234 1.220000e-175 627.0
19 TraesCS7B01G243200 chr2B 89.951 408 37 4 2529 2934 110854160 110854565 1.650000e-144 523.0
20 TraesCS7B01G243200 chr2B 76.832 764 153 17 1616 2362 110853234 110853990 4.820000e-110 409.0
21 TraesCS7B01G243200 chr2B 80.061 326 61 4 3393 3716 110855133 110855456 6.690000e-59 239.0
22 TraesCS7B01G243200 chr2B 82.584 178 19 7 262 427 787527034 787527211 4.170000e-31 147.0
23 TraesCS7B01G243200 chr2B 73.981 319 77 4 3405 3722 110796176 110795863 1.950000e-24 124.0
24 TraesCS7B01G243200 chr2B 92.593 81 4 2 5090 5169 713968888 713968809 1.180000e-21 115.0
25 TraesCS7B01G243200 chr3D 92.049 566 41 4 4535 5097 389640409 389639845 0.000000e+00 793.0
26 TraesCS7B01G243200 chr3D 89.558 565 54 5 4536 5097 157376886 157376324 0.000000e+00 712.0
27 TraesCS7B01G243200 chr5B 79.298 1082 190 29 3071 4132 127504531 127505598 0.000000e+00 726.0
28 TraesCS7B01G243200 chr5B 94.624 372 17 3 4536 4906 646351677 646351308 1.610000e-159 573.0
29 TraesCS7B01G243200 chr5B 96.567 233 8 0 4937 5169 646351313 646351081 2.260000e-103 387.0
30 TraesCS7B01G243200 chr5B 82.831 431 72 2 2513 2942 127503925 127504354 8.120000e-103 385.0
31 TraesCS7B01G243200 chr5B 75.701 535 112 13 1617 2142 127502955 127503480 8.590000e-63 252.0
32 TraesCS7B01G243200 chr5B 84.722 144 15 3 291 427 375380005 375380148 2.510000e-28 137.0
33 TraesCS7B01G243200 chr5A 79.278 1081 192 29 3071 4132 122956635 122957702 0.000000e+00 726.0
34 TraesCS7B01G243200 chr5A 82.558 430 73 2 2513 2941 122956029 122956457 1.360000e-100 377.0
35 TraesCS7B01G243200 chr5D 79.113 1082 192 30 3071 4132 115950527 115951594 0.000000e+00 715.0
36 TraesCS7B01G243200 chr5D 84.917 663 71 24 4524 5165 58234436 58233782 1.210000e-180 643.0
37 TraesCS7B01G243200 chr5D 82.651 415 69 3 2528 2941 115949937 115950349 1.060000e-96 364.0
38 TraesCS7B01G243200 chr5D 74.341 569 128 13 1617 2176 115948950 115949509 5.210000e-55 226.0
39 TraesCS7B01G243200 chr5D 84.896 192 13 5 251 427 462454608 462454798 4.110000e-41 180.0
40 TraesCS7B01G243200 chr5D 82.659 173 15 8 256 414 249258083 249257912 6.980000e-29 139.0
41 TraesCS7B01G243200 chr2A 80.217 920 137 38 2502 3397 72693412 72694310 0.000000e+00 649.0
42 TraesCS7B01G243200 chr2A 76.943 759 153 15 1616 2358 72692513 72693265 3.720000e-111 412.0
43 TraesCS7B01G243200 chr2A 82.036 167 20 4 271 427 27631860 27631694 3.250000e-27 134.0
44 TraesCS7B01G243200 chr6A 83.714 657 79 23 4535 5169 17039806 17039156 3.450000e-166 595.0
45 TraesCS7B01G243200 chr6A 97.468 79 2 0 349 427 37856836 37856758 9.030000e-28 135.0
46 TraesCS7B01G243200 chr3A 85.284 564 76 7 4537 5096 391496374 391496934 4.490000e-160 575.0
47 TraesCS7B01G243200 chr3A 83.060 183 14 6 259 427 550706640 550706819 3.220000e-32 150.0
48 TraesCS7B01G243200 chr2D 89.567 393 38 3 2541 2932 73323867 73323477 3.600000e-136 496.0
49 TraesCS7B01G243200 chr2D 76.842 760 152 17 1616 2358 73324861 73324109 1.730000e-109 407.0
50 TraesCS7B01G243200 chr2D 79.825 342 65 4 3393 3732 73322905 73322566 4.000000e-61 246.0
51 TraesCS7B01G243200 chr2D 73.977 342 84 5 3393 3731 73207277 73206938 3.250000e-27 134.0
52 TraesCS7B01G243200 chrUn 80.741 405 69 9 2499 2897 5436087 5435686 1.810000e-79 307.0
53 TraesCS7B01G243200 chr3B 83.607 183 14 7 261 427 107966103 107966285 1.930000e-34 158.0
54 TraesCS7B01G243200 chr1B 90.426 94 7 2 347 439 553893108 553893200 7.030000e-24 122.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G243200 chr7B 451351292 451356460 5168 False 9546.000000 9546 100.000000 1 5169 1 chr7B.!!$F1 5168
1 TraesCS7B01G243200 chr7D 434145529 434150246 4717 False 3236.000000 6154 94.237000 1 4526 2 chr7D.!!$F2 4525
2 TraesCS7B01G243200 chr7D 610650826 610651428 602 True 275.800000 460 85.630500 4566 5169 2 chr7D.!!$R2 603
3 TraesCS7B01G243200 chr7A 484593401 484597157 3756 False 2981.000000 4643 95.345000 627 4344 2 chr7A.!!$F3 3717
4 TraesCS7B01G243200 chr4A 614547700 614548335 635 True 976.000000 976 94.497000 4539 5169 1 chr4A.!!$R3 630
5 TraesCS7B01G243200 chr2B 170416110 170416630 520 False 795.000000 795 93.985000 4534 5064 1 chr2B.!!$F2 530
6 TraesCS7B01G243200 chr2B 93712675 93713234 559 False 627.000000 627 87.011000 4540 5096 1 chr2B.!!$F1 556
7 TraesCS7B01G243200 chr2B 713968809 713969415 606 True 411.500000 708 91.056500 4537 5169 2 chr2B.!!$R2 632
8 TraesCS7B01G243200 chr2B 110853234 110855456 2222 False 390.333333 523 82.281333 1616 3716 3 chr2B.!!$F4 2100
9 TraesCS7B01G243200 chr3D 389639845 389640409 564 True 793.000000 793 92.049000 4535 5097 1 chr3D.!!$R2 562
10 TraesCS7B01G243200 chr3D 157376324 157376886 562 True 712.000000 712 89.558000 4536 5097 1 chr3D.!!$R1 561
11 TraesCS7B01G243200 chr5B 646351081 646351677 596 True 480.000000 573 95.595500 4536 5169 2 chr5B.!!$R1 633
12 TraesCS7B01G243200 chr5B 127502955 127505598 2643 False 454.333333 726 79.276667 1617 4132 3 chr5B.!!$F2 2515
13 TraesCS7B01G243200 chr5A 122956029 122957702 1673 False 551.500000 726 80.918000 2513 4132 2 chr5A.!!$F1 1619
14 TraesCS7B01G243200 chr5D 58233782 58234436 654 True 643.000000 643 84.917000 4524 5165 1 chr5D.!!$R1 641
15 TraesCS7B01G243200 chr5D 115948950 115951594 2644 False 435.000000 715 78.701667 1617 4132 3 chr5D.!!$F2 2515
16 TraesCS7B01G243200 chr2A 72692513 72694310 1797 False 530.500000 649 78.580000 1616 3397 2 chr2A.!!$F1 1781
17 TraesCS7B01G243200 chr6A 17039156 17039806 650 True 595.000000 595 83.714000 4535 5169 1 chr6A.!!$R1 634
18 TraesCS7B01G243200 chr3A 391496374 391496934 560 False 575.000000 575 85.284000 4537 5096 1 chr3A.!!$F1 559
19 TraesCS7B01G243200 chr2D 73322566 73324861 2295 True 383.000000 496 82.078000 1616 3732 3 chr2D.!!$R2 2116

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
426 427 0.037734 TCGACTGAGACCTAGCCACA 59.962 55.000 0.0 0.0 0.00 4.17 F
746 1181 0.179100 CGCCACTCCACATCTCGATT 60.179 55.000 0.0 0.0 0.00 3.34 F
1911 2414 0.254178 ACTACCCGGTCGAGAAGCTA 59.746 55.000 0.0 0.0 0.00 3.32 F
2025 2528 1.078918 CAAGCACTCCATCGAGCCA 60.079 57.895 0.0 0.0 40.03 4.75 F
2376 2939 4.520492 GTCTCCATCAACACTGACCATTTT 59.480 41.667 0.0 0.0 33.30 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 2315 1.003839 GGCGGTGGAGATGAACACA 60.004 57.895 0.00 0.0 39.31 3.72 R
2376 2939 1.004504 GCGCGCCAAAATTCAAAAACA 60.005 42.857 23.24 0.0 0.00 2.83 R
2848 3555 2.263540 GTGCCGACGTACATGGGT 59.736 61.111 0.00 0.0 0.00 4.51 R
3037 3810 2.665185 GACTTGCCGAACCGCTGT 60.665 61.111 0.00 0.0 0.00 4.40 R
4171 5057 0.762418 ACCGATTTCCTGACCACACA 59.238 50.000 0.00 0.0 0.00 3.72 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
44 45 2.222213 TGCATCAGGTTGTTTAACGTCG 59.778 45.455 0.00 0.00 37.69 5.12
52 53 4.961431 GTTGTTTAACGTCGTCAACAAC 57.039 40.909 30.60 30.60 46.93 3.32
66 67 4.670621 CGTCAACAACATTGCTACAAAGAC 59.329 41.667 0.00 0.00 0.00 3.01
70 71 4.460263 ACAACATTGCTACAAAGACAGGA 58.540 39.130 0.00 0.00 0.00 3.86
72 73 3.679389 ACATTGCTACAAAGACAGGAGG 58.321 45.455 0.00 0.00 0.00 4.30
126 127 8.427902 AGCACTCATAGATCATCATTTACCTA 57.572 34.615 0.00 0.00 0.00 3.08
176 177 4.938226 GCTCAAACTATGAAGCCTACAACT 59.062 41.667 0.00 0.00 37.67 3.16
181 182 2.566833 ATGAAGCCTACAACTGCACA 57.433 45.000 0.00 0.00 0.00 4.57
212 213 6.554334 TTGGTTTGGTTCTTCTTTAGATCG 57.446 37.500 0.00 0.00 31.54 3.69
217 218 4.094476 TGGTTCTTCTTTAGATCGAGGGT 58.906 43.478 0.00 0.00 31.54 4.34
218 219 4.081642 TGGTTCTTCTTTAGATCGAGGGTG 60.082 45.833 0.00 0.00 31.54 4.61
219 220 4.081586 GGTTCTTCTTTAGATCGAGGGTGT 60.082 45.833 0.00 0.00 31.54 4.16
220 221 4.985538 TCTTCTTTAGATCGAGGGTGTC 57.014 45.455 0.00 0.00 0.00 3.67
221 222 4.341487 TCTTCTTTAGATCGAGGGTGTCA 58.659 43.478 0.00 0.00 0.00 3.58
222 223 4.158025 TCTTCTTTAGATCGAGGGTGTCAC 59.842 45.833 0.00 0.00 0.00 3.67
223 224 3.427573 TCTTTAGATCGAGGGTGTCACA 58.572 45.455 5.12 0.00 0.00 3.58
224 225 3.192844 TCTTTAGATCGAGGGTGTCACAC 59.807 47.826 0.00 0.00 0.00 3.82
225 226 2.509166 TAGATCGAGGGTGTCACACT 57.491 50.000 7.68 7.68 32.13 3.55
226 227 1.633774 AGATCGAGGGTGTCACACTT 58.366 50.000 9.64 0.00 27.47 3.16
227 228 1.273606 AGATCGAGGGTGTCACACTTG 59.726 52.381 15.53 15.53 34.23 3.16
228 229 0.321671 ATCGAGGGTGTCACACTTGG 59.678 55.000 20.38 11.00 33.73 3.61
229 230 1.961277 CGAGGGTGTCACACTTGGC 60.961 63.158 14.05 0.00 27.47 4.52
230 231 1.451936 GAGGGTGTCACACTTGGCT 59.548 57.895 9.64 0.00 27.47 4.75
231 232 0.179018 GAGGGTGTCACACTTGGCTT 60.179 55.000 9.64 0.00 27.47 4.35
232 233 0.179018 AGGGTGTCACACTTGGCTTC 60.179 55.000 8.12 0.00 34.40 3.86
236 237 0.396435 TGTCACACTTGGCTTCGGAT 59.604 50.000 0.00 0.00 0.00 4.18
242 243 1.147153 CTTGGCTTCGGATCCCCTC 59.853 63.158 6.06 0.00 0.00 4.30
252 253 1.059913 GGATCCCCTCGGTGATCATT 58.940 55.000 0.00 0.00 39.30 2.57
253 254 2.257207 GGATCCCCTCGGTGATCATTA 58.743 52.381 0.00 0.00 39.30 1.90
254 255 2.637872 GGATCCCCTCGGTGATCATTAA 59.362 50.000 0.00 0.00 39.30 1.40
255 256 3.264450 GGATCCCCTCGGTGATCATTAAT 59.736 47.826 0.00 0.00 39.30 1.40
256 257 4.508662 GATCCCCTCGGTGATCATTAATC 58.491 47.826 0.00 0.00 37.81 1.75
257 258 3.313791 TCCCCTCGGTGATCATTAATCA 58.686 45.455 0.00 0.00 42.21 2.57
258 259 3.714280 TCCCCTCGGTGATCATTAATCAA 59.286 43.478 0.00 0.00 45.88 2.57
259 260 4.350816 TCCCCTCGGTGATCATTAATCAAT 59.649 41.667 0.00 0.00 45.88 2.57
260 261 5.546110 TCCCCTCGGTGATCATTAATCAATA 59.454 40.000 0.00 0.00 45.88 1.90
261 262 5.643777 CCCCTCGGTGATCATTAATCAATAC 59.356 44.000 0.00 0.00 45.88 1.89
262 263 6.230472 CCCTCGGTGATCATTAATCAATACA 58.770 40.000 0.00 0.00 45.88 2.29
263 264 6.369890 CCCTCGGTGATCATTAATCAATACAG 59.630 42.308 0.00 0.00 45.88 2.74
264 265 6.931281 CCTCGGTGATCATTAATCAATACAGT 59.069 38.462 0.00 0.00 45.88 3.55
265 266 7.116948 CCTCGGTGATCATTAATCAATACAGTC 59.883 40.741 0.00 0.00 45.88 3.51
266 267 7.726216 TCGGTGATCATTAATCAATACAGTCT 58.274 34.615 0.00 0.00 45.88 3.24
267 268 8.204160 TCGGTGATCATTAATCAATACAGTCTT 58.796 33.333 0.00 0.00 45.88 3.01
268 269 8.278408 CGGTGATCATTAATCAATACAGTCTTG 58.722 37.037 0.00 0.00 45.88 3.02
269 270 8.072567 GGTGATCATTAATCAATACAGTCTTGC 58.927 37.037 0.00 0.00 45.88 4.01
270 271 8.834465 GTGATCATTAATCAATACAGTCTTGCT 58.166 33.333 0.00 0.00 45.88 3.91
274 275 9.890629 TCATTAATCAATACAGTCTTGCTAAGT 57.109 29.630 0.00 0.00 0.00 2.24
277 278 9.587772 TTAATCAATACAGTCTTGCTAAGTCTC 57.412 33.333 0.00 0.00 0.00 3.36
278 279 6.590234 TCAATACAGTCTTGCTAAGTCTCA 57.410 37.500 0.00 0.00 0.00 3.27
279 280 6.625362 TCAATACAGTCTTGCTAAGTCTCAG 58.375 40.000 0.00 0.00 0.00 3.35
280 281 6.209589 TCAATACAGTCTTGCTAAGTCTCAGT 59.790 38.462 0.00 0.00 0.00 3.41
281 282 4.513198 ACAGTCTTGCTAAGTCTCAGTC 57.487 45.455 0.00 0.00 0.00 3.51
282 283 3.057876 ACAGTCTTGCTAAGTCTCAGTCG 60.058 47.826 0.00 0.00 0.00 4.18
283 284 3.189495 CAGTCTTGCTAAGTCTCAGTCGA 59.811 47.826 0.00 0.00 0.00 4.20
284 285 3.189702 AGTCTTGCTAAGTCTCAGTCGAC 59.810 47.826 7.70 7.70 0.00 4.20
285 286 3.189702 GTCTTGCTAAGTCTCAGTCGACT 59.810 47.826 13.58 13.58 45.73 4.18
286 287 3.189495 TCTTGCTAAGTCTCAGTCGACTG 59.811 47.826 34.76 34.76 43.14 3.51
298 299 2.682952 GTCGACTGAGACTTCGTCAA 57.317 50.000 8.70 0.00 38.09 3.18
299 300 2.576406 GTCGACTGAGACTTCGTCAAG 58.424 52.381 8.70 0.00 38.09 3.02
300 301 2.031857 GTCGACTGAGACTTCGTCAAGT 60.032 50.000 8.70 0.19 46.21 3.16
309 310 2.775890 ACTTCGTCAAGTCCTAGTCGA 58.224 47.619 0.00 0.00 38.62 4.20
310 311 3.345414 ACTTCGTCAAGTCCTAGTCGAT 58.655 45.455 0.00 0.00 38.62 3.59
311 312 3.127203 ACTTCGTCAAGTCCTAGTCGATG 59.873 47.826 0.00 0.00 38.62 3.84
312 313 1.400846 TCGTCAAGTCCTAGTCGATGC 59.599 52.381 0.00 0.00 0.00 3.91
313 314 1.402259 CGTCAAGTCCTAGTCGATGCT 59.598 52.381 0.00 0.00 0.00 3.79
314 315 2.612672 CGTCAAGTCCTAGTCGATGCTA 59.387 50.000 0.00 0.00 0.00 3.49
315 316 3.251245 CGTCAAGTCCTAGTCGATGCTAT 59.749 47.826 0.00 0.00 0.00 2.97
316 317 4.451435 CGTCAAGTCCTAGTCGATGCTATA 59.549 45.833 0.00 0.00 0.00 1.31
317 318 5.122554 CGTCAAGTCCTAGTCGATGCTATAT 59.877 44.000 0.00 0.00 0.00 0.86
318 319 6.348622 CGTCAAGTCCTAGTCGATGCTATATT 60.349 42.308 0.00 0.00 0.00 1.28
319 320 7.024768 GTCAAGTCCTAGTCGATGCTATATTC 58.975 42.308 0.00 0.00 0.00 1.75
320 321 5.804692 AGTCCTAGTCGATGCTATATTCG 57.195 43.478 0.00 0.00 36.72 3.34
321 322 5.247084 AGTCCTAGTCGATGCTATATTCGT 58.753 41.667 0.00 0.00 36.74 3.85
322 323 6.404708 AGTCCTAGTCGATGCTATATTCGTA 58.595 40.000 0.00 0.00 36.74 3.43
323 324 6.877855 AGTCCTAGTCGATGCTATATTCGTAA 59.122 38.462 0.00 0.00 36.74 3.18
324 325 7.064847 AGTCCTAGTCGATGCTATATTCGTAAG 59.935 40.741 0.00 0.00 36.74 2.34
342 343 7.142306 TCGTAAGATCCTACATTAAGATCCG 57.858 40.000 2.51 0.00 45.01 4.18
343 344 6.713903 TCGTAAGATCCTACATTAAGATCCGT 59.286 38.462 2.51 0.00 45.01 4.69
344 345 6.802348 CGTAAGATCCTACATTAAGATCCGTG 59.198 42.308 2.51 0.00 37.69 4.94
345 346 5.140747 AGATCCTACATTAAGATCCGTGC 57.859 43.478 0.00 0.00 37.69 5.34
346 347 4.588951 AGATCCTACATTAAGATCCGTGCA 59.411 41.667 0.00 0.00 37.69 4.57
347 348 4.955811 TCCTACATTAAGATCCGTGCAT 57.044 40.909 0.00 0.00 0.00 3.96
348 349 5.290493 TCCTACATTAAGATCCGTGCATT 57.710 39.130 0.00 0.00 0.00 3.56
349 350 5.680619 TCCTACATTAAGATCCGTGCATTT 58.319 37.500 0.00 0.00 0.00 2.32
350 351 6.119536 TCCTACATTAAGATCCGTGCATTTT 58.880 36.000 0.00 0.00 0.00 1.82
351 352 6.601613 TCCTACATTAAGATCCGTGCATTTTT 59.398 34.615 0.00 0.00 0.00 1.94
376 377 9.467258 TTTTCTTTTTCTCTCTTGCATGTTATG 57.533 29.630 0.00 0.00 0.00 1.90
377 378 7.750229 TCTTTTTCTCTCTTGCATGTTATGT 57.250 32.000 0.00 0.00 0.00 2.29
378 379 7.810658 TCTTTTTCTCTCTTGCATGTTATGTC 58.189 34.615 0.00 0.00 0.00 3.06
379 380 7.445096 TCTTTTTCTCTCTTGCATGTTATGTCA 59.555 33.333 0.00 0.00 0.00 3.58
380 381 7.692460 TTTTCTCTCTTGCATGTTATGTCAT 57.308 32.000 0.00 0.00 0.00 3.06
381 382 7.692460 TTTCTCTCTTGCATGTTATGTCATT 57.308 32.000 0.00 0.00 0.00 2.57
382 383 7.692460 TTCTCTCTTGCATGTTATGTCATTT 57.308 32.000 0.00 0.00 0.00 2.32
383 384 7.080353 TCTCTCTTGCATGTTATGTCATTTG 57.920 36.000 0.00 0.00 0.00 2.32
384 385 6.880529 TCTCTCTTGCATGTTATGTCATTTGA 59.119 34.615 0.00 0.00 0.00 2.69
385 386 6.845302 TCTCTTGCATGTTATGTCATTTGAC 58.155 36.000 3.72 3.72 44.97 3.18
386 387 6.656270 TCTCTTGCATGTTATGTCATTTGACT 59.344 34.615 11.67 1.15 44.99 3.41
387 388 6.614160 TCTTGCATGTTATGTCATTTGACTG 58.386 36.000 11.67 2.37 44.99 3.51
388 389 6.430616 TCTTGCATGTTATGTCATTTGACTGA 59.569 34.615 11.67 0.00 44.99 3.41
389 390 6.185852 TGCATGTTATGTCATTTGACTGAG 57.814 37.500 11.67 0.00 44.99 3.35
390 391 5.939296 TGCATGTTATGTCATTTGACTGAGA 59.061 36.000 11.67 0.00 44.99 3.27
391 392 6.128200 TGCATGTTATGTCATTTGACTGAGAC 60.128 38.462 11.67 6.30 44.99 3.36
392 393 6.093219 GCATGTTATGTCATTTGACTGAGACT 59.907 38.462 11.67 0.00 44.99 3.24
393 394 7.361542 GCATGTTATGTCATTTGACTGAGACTT 60.362 37.037 11.67 0.00 44.99 3.01
394 395 7.658179 TGTTATGTCATTTGACTGAGACTTC 57.342 36.000 11.67 0.00 44.99 3.01
395 396 6.366061 TGTTATGTCATTTGACTGAGACTTCG 59.634 38.462 11.67 0.00 44.99 3.79
396 397 4.322080 TGTCATTTGACTGAGACTTCGT 57.678 40.909 11.67 0.00 44.99 3.85
397 398 4.693283 TGTCATTTGACTGAGACTTCGTT 58.307 39.130 11.67 0.00 44.99 3.85
398 399 5.838529 TGTCATTTGACTGAGACTTCGTTA 58.161 37.500 11.67 0.00 44.99 3.18
399 400 6.277605 TGTCATTTGACTGAGACTTCGTTAA 58.722 36.000 11.67 0.00 44.99 2.01
400 401 6.759356 TGTCATTTGACTGAGACTTCGTTAAA 59.241 34.615 11.67 0.00 44.99 1.52
401 402 7.441157 TGTCATTTGACTGAGACTTCGTTAAAT 59.559 33.333 11.67 3.52 44.99 1.40
402 403 7.952637 GTCATTTGACTGAGACTTCGTTAAATC 59.047 37.037 3.45 0.00 41.65 2.17
403 404 7.872993 TCATTTGACTGAGACTTCGTTAAATCT 59.127 33.333 0.00 0.00 31.07 2.40
404 405 7.639162 TTTGACTGAGACTTCGTTAAATCTC 57.361 36.000 0.00 0.00 38.46 2.75
405 406 6.327279 TGACTGAGACTTCGTTAAATCTCA 57.673 37.500 3.03 3.03 44.05 3.27
409 410 5.391449 TGAGACTTCGTTAAATCTCAGTCG 58.609 41.667 0.00 0.00 41.99 4.18
410 411 5.180680 TGAGACTTCGTTAAATCTCAGTCGA 59.819 40.000 0.00 0.00 41.99 4.20
411 412 5.392286 AGACTTCGTTAAATCTCAGTCGAC 58.608 41.667 7.70 7.70 36.56 4.20
412 413 5.181622 AGACTTCGTTAAATCTCAGTCGACT 59.818 40.000 13.58 13.58 36.56 4.18
413 414 5.154932 ACTTCGTTAAATCTCAGTCGACTG 58.845 41.667 34.76 34.76 45.08 3.51
423 424 0.736053 CAGTCGACTGAGACCTAGCC 59.264 60.000 36.73 0.00 46.59 3.93
424 425 0.328592 AGTCGACTGAGACCTAGCCA 59.671 55.000 19.30 0.00 41.83 4.75
425 426 0.452585 GTCGACTGAGACCTAGCCAC 59.547 60.000 8.70 0.00 35.22 5.01
426 427 0.037734 TCGACTGAGACCTAGCCACA 59.962 55.000 0.00 0.00 0.00 4.17
427 428 0.888619 CGACTGAGACCTAGCCACAA 59.111 55.000 0.00 0.00 0.00 3.33
428 429 1.478510 CGACTGAGACCTAGCCACAAT 59.521 52.381 0.00 0.00 0.00 2.71
429 430 2.480416 CGACTGAGACCTAGCCACAATC 60.480 54.545 0.00 0.00 0.00 2.67
484 486 6.937436 AAAATGAGTTACCGAATATCACCC 57.063 37.500 0.00 0.00 0.00 4.61
524 526 6.432403 AAAAAGAATATCACCCTTTTGCCA 57.568 33.333 0.00 0.00 39.29 4.92
525 527 6.625532 AAAAGAATATCACCCTTTTGCCAT 57.374 33.333 0.00 0.00 38.31 4.40
562 564 2.919602 TGGCAGTCCTATTTTCCTTCCT 59.080 45.455 0.00 0.00 0.00 3.36
565 567 4.158579 GGCAGTCCTATTTTCCTTCCTTTG 59.841 45.833 0.00 0.00 0.00 2.77
583 585 9.559958 CTTCCTTTGTGCACATAACTAATTTAG 57.440 33.333 22.39 5.06 0.00 1.85
638 737 7.524717 TCTTTGAAAACTAAAGGATTCCTGG 57.475 36.000 5.84 2.73 36.16 4.45
746 1181 0.179100 CGCCACTCCACATCTCGATT 60.179 55.000 0.00 0.00 0.00 3.34
791 1226 1.033746 AGCCATGCAAACATCTCCCG 61.034 55.000 0.00 0.00 32.87 5.14
868 1303 1.192146 AGCAACCTAGGAGGAACGCA 61.192 55.000 17.98 0.00 37.67 5.24
900 1335 2.992689 TCCGTGCCGAAGCTACCA 60.993 61.111 0.00 0.00 40.80 3.25
1198 1633 3.499737 GCGCCAAGATGGACCGTG 61.500 66.667 0.00 0.00 40.96 4.94
1203 1638 1.450312 CAAGATGGACCGTGGGCTC 60.450 63.158 0.00 0.00 0.00 4.70
1278 1713 0.320946 GGGAATTCGACCACAACCGA 60.321 55.000 0.00 0.00 0.00 4.69
1311 1746 2.497293 CAGGGCACGTACGGCATA 59.503 61.111 21.06 0.00 0.00 3.14
1471 1906 3.578282 CCCCTACAGGTTTGCAAAATTCT 59.422 43.478 14.67 9.12 0.00 2.40
1501 2000 5.908916 TCAATCAAAATGTTACGACACGA 57.091 34.783 0.00 0.00 38.91 4.35
1506 2005 4.329256 TCAAAATGTTACGACACGACACAA 59.671 37.500 0.00 0.00 38.91 3.33
1507 2006 5.006844 TCAAAATGTTACGACACGACACAAT 59.993 36.000 0.00 0.00 38.91 2.71
1509 2008 5.505165 AATGTTACGACACGACACAATAC 57.495 39.130 0.00 0.00 38.91 1.89
1510 2009 3.962423 TGTTACGACACGACACAATACA 58.038 40.909 0.00 0.00 0.00 2.29
1511 2010 3.730215 TGTTACGACACGACACAATACAC 59.270 43.478 0.00 0.00 0.00 2.90
1512 2011 2.495409 ACGACACGACACAATACACA 57.505 45.000 0.00 0.00 0.00 3.72
1513 2012 3.021269 ACGACACGACACAATACACAT 57.979 42.857 0.00 0.00 0.00 3.21
1514 2013 2.729360 ACGACACGACACAATACACATG 59.271 45.455 0.00 0.00 0.00 3.21
1515 2014 2.983803 CGACACGACACAATACACATGA 59.016 45.455 0.00 0.00 0.00 3.07
1516 2015 3.612423 CGACACGACACAATACACATGAT 59.388 43.478 0.00 0.00 0.00 2.45
1517 2016 4.259411 CGACACGACACAATACACATGATC 60.259 45.833 0.00 0.00 0.00 2.92
1518 2017 4.820897 ACACGACACAATACACATGATCT 58.179 39.130 0.00 0.00 0.00 2.75
1519 2018 5.237815 ACACGACACAATACACATGATCTT 58.762 37.500 0.00 0.00 0.00 2.40
1520 2019 5.348724 ACACGACACAATACACATGATCTTC 59.651 40.000 0.00 0.00 0.00 2.87
1549 2052 3.053291 GTGACGCGGGGATTTGCA 61.053 61.111 12.47 0.00 0.00 4.08
1552 2055 3.756413 GACGCGGGGATTTGCATGC 62.756 63.158 11.82 11.82 0.00 4.06
1600 2103 1.202639 TGGCGCTGTTTCTCTTCTTGA 60.203 47.619 7.64 0.00 0.00 3.02
1845 2348 1.682451 CCGCCGATCCCTACAAGGAA 61.682 60.000 0.00 0.00 40.04 3.36
1854 2357 2.047655 TACAAGGAACCGCCGCTG 60.048 61.111 0.00 0.00 43.43 5.18
1869 2372 2.111043 CTGGTGACGGCCAACACT 59.889 61.111 22.61 0.00 37.61 3.55
1890 2393 2.060383 CCTCTCCATCCTCGCCACA 61.060 63.158 0.00 0.00 0.00 4.17
1911 2414 0.254178 ACTACCCGGTCGAGAAGCTA 59.746 55.000 0.00 0.00 0.00 3.32
1926 2429 5.178623 CGAGAAGCTATTCGTCTACATCTCT 59.821 44.000 10.66 0.00 40.58 3.10
2025 2528 1.078918 CAAGCACTCCATCGAGCCA 60.079 57.895 0.00 0.00 40.03 4.75
2376 2939 4.520492 GTCTCCATCAACACTGACCATTTT 59.480 41.667 0.00 0.00 33.30 1.82
2422 3045 5.281693 CATGTGTGTTCATGTTACGATGT 57.718 39.130 0.00 0.00 39.93 3.06
2530 3237 4.760047 GTGGACGTGCGCATCCCT 62.760 66.667 23.78 3.36 33.69 4.20
4027 4913 1.509923 GCACTACTACCCGTTCGCT 59.490 57.895 0.00 0.00 0.00 4.93
4167 5053 1.753078 AGAGCGGCATCGAGGTGTA 60.753 57.895 1.45 0.00 39.00 2.90
4171 5057 1.515954 CGGCATCGAGGTGTAAGGT 59.484 57.895 0.00 0.00 39.00 3.50
4189 5080 1.156736 GTGTGTGGTCAGGAAATCGG 58.843 55.000 0.00 0.00 0.00 4.18
4194 5085 0.245539 TGGTCAGGAAATCGGTCGAC 59.754 55.000 7.13 7.13 0.00 4.20
4237 5129 1.094785 CGAAATGACCGGCCAAGAAT 58.905 50.000 0.00 0.00 0.00 2.40
4253 5152 0.875908 GAATCGCGCCATCAGCTACA 60.876 55.000 0.00 0.00 40.39 2.74
4268 5167 3.725740 CAGCTACAAAGTGCAGAAAAACG 59.274 43.478 0.00 0.00 0.00 3.60
4275 5174 2.017049 AGTGCAGAAAAACGACAGCTT 58.983 42.857 0.00 0.00 0.00 3.74
4276 5175 2.111756 GTGCAGAAAAACGACAGCTTG 58.888 47.619 0.00 0.00 0.00 4.01
4277 5176 1.065401 TGCAGAAAAACGACAGCTTGG 59.935 47.619 0.00 0.00 0.00 3.61
4278 5177 1.333619 GCAGAAAAACGACAGCTTGGA 59.666 47.619 0.00 0.00 0.00 3.53
4279 5178 2.603173 GCAGAAAAACGACAGCTTGGAG 60.603 50.000 0.00 0.00 0.00 3.86
4280 5179 2.872245 CAGAAAAACGACAGCTTGGAGA 59.128 45.455 0.00 0.00 0.00 3.71
4281 5180 3.312421 CAGAAAAACGACAGCTTGGAGAA 59.688 43.478 0.00 0.00 0.00 2.87
4290 5189 2.373169 ACAGCTTGGAGAATGGAGAACA 59.627 45.455 0.00 0.00 0.00 3.18
4321 5220 7.065283 GCATTGTTTGTCTTCTGTATTTTTGC 58.935 34.615 0.00 0.00 0.00 3.68
4348 5247 7.564793 TGTGGATGCACAAGATTAGTAGTAAT 58.435 34.615 18.56 2.31 31.35 1.89
4431 5337 1.545759 CGTACCTACGCACTGACATG 58.454 55.000 0.00 0.00 43.14 3.21
4438 5344 0.393402 ACGCACTGACATGATGGCAT 60.393 50.000 0.00 0.00 33.12 4.40
4439 5345 1.134431 ACGCACTGACATGATGGCATA 60.134 47.619 0.00 0.00 33.12 3.14
4440 5346 1.262417 CGCACTGACATGATGGCATAC 59.738 52.381 0.00 0.00 33.12 2.39
4449 5365 5.072193 TGACATGATGGCATACATACTCCTT 59.928 40.000 0.00 0.00 40.72 3.36
4450 5366 5.555017 ACATGATGGCATACATACTCCTTC 58.445 41.667 0.00 0.00 40.72 3.46
4518 5434 1.200716 CTGATTCGTTGCACATTGCCT 59.799 47.619 0.00 0.00 44.23 4.75
4531 5447 9.150348 GTTGCACATTGCCTTATATTACTTTTT 57.850 29.630 0.00 0.00 44.23 1.94
4694 5614 0.912487 TTTATGACAGGTCGGGCCCT 60.912 55.000 22.43 0.00 38.26 5.19
4745 5665 6.466730 CGTTTTGTTTGACTGTTACCTTACAC 59.533 38.462 0.00 0.00 0.00 2.90
4768 5689 1.475571 GGGACCCACGTGTAAGTTGTT 60.476 52.381 15.65 0.00 0.00 2.83
4872 5798 3.822192 CCACCATCCGTCTCGCGA 61.822 66.667 9.26 9.26 44.77 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 5.577835 TGTCTTTGTAGCAATGTTGTTGAC 58.422 37.500 0.00 0.00 0.00 3.18
52 53 3.012518 CCCTCCTGTCTTTGTAGCAATG 58.987 50.000 0.00 0.00 0.00 2.82
156 157 4.455533 TGCAGTTGTAGGCTTCATAGTTTG 59.544 41.667 0.00 0.00 0.00 2.93
170 171 3.138304 CAAGCTAGGTTGTGCAGTTGTA 58.862 45.455 23.52 0.00 0.00 2.41
197 198 5.074584 ACACCCTCGATCTAAAGAAGAAC 57.925 43.478 0.00 0.00 37.89 3.01
212 213 0.179018 AAGCCAAGTGTGACACCCTC 60.179 55.000 12.81 0.00 34.49 4.30
217 218 0.396435 ATCCGAAGCCAAGTGTGACA 59.604 50.000 0.00 0.00 0.00 3.58
218 219 1.079503 GATCCGAAGCCAAGTGTGAC 58.920 55.000 0.00 0.00 0.00 3.67
219 220 0.036388 GGATCCGAAGCCAAGTGTGA 60.036 55.000 0.00 0.00 0.00 3.58
220 221 1.026718 GGGATCCGAAGCCAAGTGTG 61.027 60.000 5.45 0.00 30.22 3.82
221 222 1.299976 GGGATCCGAAGCCAAGTGT 59.700 57.895 5.45 0.00 30.22 3.55
222 223 1.452108 GGGGATCCGAAGCCAAGTG 60.452 63.158 5.45 0.00 30.22 3.16
223 224 1.616628 AGGGGATCCGAAGCCAAGT 60.617 57.895 5.45 0.00 38.33 3.16
224 225 1.147153 GAGGGGATCCGAAGCCAAG 59.853 63.158 5.45 0.00 38.33 3.61
225 226 2.731571 CGAGGGGATCCGAAGCCAA 61.732 63.158 5.45 0.00 38.33 4.52
226 227 3.154473 CGAGGGGATCCGAAGCCA 61.154 66.667 5.45 0.00 38.33 4.75
227 228 3.930012 CCGAGGGGATCCGAAGCC 61.930 72.222 5.45 0.56 38.33 4.35
228 229 3.155167 ACCGAGGGGATCCGAAGC 61.155 66.667 5.45 0.00 38.33 3.86
229 230 1.115930 ATCACCGAGGGGATCCGAAG 61.116 60.000 5.45 0.00 38.33 3.79
230 231 1.075525 ATCACCGAGGGGATCCGAA 60.076 57.895 5.45 0.00 38.33 4.30
231 232 1.530891 GATCACCGAGGGGATCCGA 60.531 63.158 20.81 0.00 38.33 4.55
232 233 1.188219 ATGATCACCGAGGGGATCCG 61.188 60.000 26.40 0.00 39.30 4.18
236 237 3.313791 TGATTAATGATCACCGAGGGGA 58.686 45.455 0.00 0.00 39.83 4.81
242 243 7.953158 AGACTGTATTGATTAATGATCACCG 57.047 36.000 0.00 0.00 44.28 4.94
252 253 8.749354 TGAGACTTAGCAAGACTGTATTGATTA 58.251 33.333 18.49 5.69 33.75 1.75
253 254 7.615403 TGAGACTTAGCAAGACTGTATTGATT 58.385 34.615 18.49 8.28 33.75 2.57
254 255 7.093552 ACTGAGACTTAGCAAGACTGTATTGAT 60.094 37.037 18.49 14.70 33.75 2.57
255 256 6.209589 ACTGAGACTTAGCAAGACTGTATTGA 59.790 38.462 18.49 0.00 33.75 2.57
256 257 6.393990 ACTGAGACTTAGCAAGACTGTATTG 58.606 40.000 10.64 10.64 33.75 1.90
257 258 6.597832 ACTGAGACTTAGCAAGACTGTATT 57.402 37.500 5.85 0.00 33.75 1.89
258 259 5.163703 CGACTGAGACTTAGCAAGACTGTAT 60.164 44.000 5.85 0.00 33.75 2.29
259 260 4.154375 CGACTGAGACTTAGCAAGACTGTA 59.846 45.833 5.85 0.00 33.75 2.74
260 261 3.057876 CGACTGAGACTTAGCAAGACTGT 60.058 47.826 5.85 0.00 33.75 3.55
261 262 3.189495 TCGACTGAGACTTAGCAAGACTG 59.811 47.826 5.85 0.00 33.75 3.51
262 263 3.189702 GTCGACTGAGACTTAGCAAGACT 59.810 47.826 8.70 2.60 38.09 3.24
263 264 3.494232 GTCGACTGAGACTTAGCAAGAC 58.506 50.000 8.70 0.00 38.09 3.01
264 265 3.833545 GTCGACTGAGACTTAGCAAGA 57.166 47.619 8.70 0.00 38.09 3.02
276 277 1.880271 ACGAAGTCTCAGTCGACTGA 58.120 50.000 38.24 38.24 44.92 3.41
290 291 3.686128 CATCGACTAGGACTTGACGAAG 58.314 50.000 11.16 4.93 36.46 3.79
291 292 2.159421 GCATCGACTAGGACTTGACGAA 60.159 50.000 11.16 0.00 36.46 3.85
292 293 1.400846 GCATCGACTAGGACTTGACGA 59.599 52.381 9.91 9.91 37.05 4.20
293 294 1.402259 AGCATCGACTAGGACTTGACG 59.598 52.381 0.00 0.32 0.00 4.35
294 295 4.839668 ATAGCATCGACTAGGACTTGAC 57.160 45.455 0.00 0.00 0.00 3.18
295 296 6.128254 CGAATATAGCATCGACTAGGACTTGA 60.128 42.308 0.00 0.00 41.43 3.02
296 297 6.024664 CGAATATAGCATCGACTAGGACTTG 58.975 44.000 0.00 0.00 41.43 3.16
297 298 5.706369 ACGAATATAGCATCGACTAGGACTT 59.294 40.000 11.05 0.00 41.43 3.01
298 299 5.247084 ACGAATATAGCATCGACTAGGACT 58.753 41.667 11.05 0.00 41.43 3.85
299 300 5.548706 ACGAATATAGCATCGACTAGGAC 57.451 43.478 11.05 0.00 41.43 3.85
300 301 7.101700 TCTTACGAATATAGCATCGACTAGGA 58.898 38.462 11.05 0.56 41.43 2.94
301 302 7.304919 TCTTACGAATATAGCATCGACTAGG 57.695 40.000 11.05 0.00 41.43 3.02
302 303 8.065407 GGATCTTACGAATATAGCATCGACTAG 58.935 40.741 11.05 0.00 41.43 2.57
303 304 7.769507 AGGATCTTACGAATATAGCATCGACTA 59.230 37.037 11.05 0.00 41.43 2.59
304 305 6.600032 AGGATCTTACGAATATAGCATCGACT 59.400 38.462 11.05 0.00 41.43 4.18
305 306 6.787225 AGGATCTTACGAATATAGCATCGAC 58.213 40.000 11.05 0.00 41.43 4.20
306 307 7.551617 TGTAGGATCTTACGAATATAGCATCGA 59.448 37.037 10.11 0.00 41.43 3.59
307 308 7.694886 TGTAGGATCTTACGAATATAGCATCG 58.305 38.462 10.11 4.40 44.33 3.84
316 317 8.244802 CGGATCTTAATGTAGGATCTTACGAAT 58.755 37.037 10.11 2.24 40.14 3.34
317 318 7.230108 ACGGATCTTAATGTAGGATCTTACGAA 59.770 37.037 10.11 4.18 40.14 3.85
318 319 6.713903 ACGGATCTTAATGTAGGATCTTACGA 59.286 38.462 10.11 1.98 40.14 3.43
319 320 6.802348 CACGGATCTTAATGTAGGATCTTACG 59.198 42.308 10.11 5.60 40.14 3.18
320 321 6.586844 GCACGGATCTTAATGTAGGATCTTAC 59.413 42.308 8.01 8.01 40.14 2.34
321 322 6.266786 TGCACGGATCTTAATGTAGGATCTTA 59.733 38.462 7.17 0.00 40.14 2.10
322 323 5.070446 TGCACGGATCTTAATGTAGGATCTT 59.930 40.000 7.17 0.00 40.14 2.40
323 324 4.588951 TGCACGGATCTTAATGTAGGATCT 59.411 41.667 7.17 0.00 40.14 2.75
324 325 4.883083 TGCACGGATCTTAATGTAGGATC 58.117 43.478 0.00 0.07 39.70 3.36
325 326 4.955811 TGCACGGATCTTAATGTAGGAT 57.044 40.909 0.00 0.00 0.00 3.24
326 327 4.955811 ATGCACGGATCTTAATGTAGGA 57.044 40.909 0.00 0.00 0.00 2.94
327 328 6.377327 AAAATGCACGGATCTTAATGTAGG 57.623 37.500 0.00 0.00 0.00 3.18
350 351 9.467258 CATAACATGCAAGAGAGAAAAAGAAAA 57.533 29.630 0.00 0.00 0.00 2.29
351 352 8.632679 ACATAACATGCAAGAGAGAAAAAGAAA 58.367 29.630 0.00 0.00 0.00 2.52
352 353 8.169977 ACATAACATGCAAGAGAGAAAAAGAA 57.830 30.769 0.00 0.00 0.00 2.52
353 354 7.445096 TGACATAACATGCAAGAGAGAAAAAGA 59.555 33.333 0.00 0.00 0.00 2.52
354 355 7.587629 TGACATAACATGCAAGAGAGAAAAAG 58.412 34.615 0.00 0.00 0.00 2.27
355 356 7.509141 TGACATAACATGCAAGAGAGAAAAA 57.491 32.000 0.00 0.00 0.00 1.94
356 357 7.692460 ATGACATAACATGCAAGAGAGAAAA 57.308 32.000 0.00 0.00 0.00 2.29
357 358 7.692460 AATGACATAACATGCAAGAGAGAAA 57.308 32.000 0.00 0.00 0.00 2.52
358 359 7.391275 TCAAATGACATAACATGCAAGAGAGAA 59.609 33.333 0.00 0.00 0.00 2.87
359 360 6.880529 TCAAATGACATAACATGCAAGAGAGA 59.119 34.615 0.00 0.00 0.00 3.10
360 361 6.965500 GTCAAATGACATAACATGCAAGAGAG 59.035 38.462 8.63 0.00 44.18 3.20
361 362 6.845302 GTCAAATGACATAACATGCAAGAGA 58.155 36.000 8.63 0.00 44.18 3.10
370 371 7.950963 ACGAAGTCTCAGTCAAATGACATAACA 60.951 37.037 15.38 0.00 42.62 2.41
371 372 6.366332 ACGAAGTCTCAGTCAAATGACATAAC 59.634 38.462 15.38 7.93 42.62 1.89
372 373 6.455647 ACGAAGTCTCAGTCAAATGACATAA 58.544 36.000 15.38 0.33 42.62 1.90
373 374 6.025749 ACGAAGTCTCAGTCAAATGACATA 57.974 37.500 15.38 2.58 42.62 2.29
374 375 4.887748 ACGAAGTCTCAGTCAAATGACAT 58.112 39.130 15.38 0.00 42.62 3.06
375 376 4.322080 ACGAAGTCTCAGTCAAATGACA 57.678 40.909 15.38 0.00 42.62 3.58
376 377 6.764877 TTAACGAAGTCTCAGTCAAATGAC 57.235 37.500 5.40 5.40 45.00 3.06
377 378 7.872993 AGATTTAACGAAGTCTCAGTCAAATGA 59.127 33.333 0.00 0.00 45.00 2.57
378 379 8.023050 AGATTTAACGAAGTCTCAGTCAAATG 57.977 34.615 0.00 0.00 45.00 2.32
379 380 8.245701 GAGATTTAACGAAGTCTCAGTCAAAT 57.754 34.615 5.59 0.00 45.00 2.32
380 381 7.639162 GAGATTTAACGAAGTCTCAGTCAAA 57.361 36.000 5.59 0.00 45.00 2.69
387 388 5.508922 GTCGACTGAGATTTAACGAAGTCTC 59.491 44.000 8.70 0.00 45.00 3.36
388 389 5.181622 AGTCGACTGAGATTTAACGAAGTCT 59.818 40.000 19.30 0.00 45.00 3.24
389 390 5.284188 CAGTCGACTGAGATTTAACGAAGTC 59.716 44.000 36.73 0.00 44.12 3.01
390 391 5.154932 CAGTCGACTGAGATTTAACGAAGT 58.845 41.667 36.73 0.00 46.20 3.01
391 392 5.672653 CAGTCGACTGAGATTTAACGAAG 57.327 43.478 36.73 7.53 46.59 3.79
404 405 0.736053 GGCTAGGTCTCAGTCGACTG 59.264 60.000 34.76 34.76 45.08 3.51
405 406 0.328592 TGGCTAGGTCTCAGTCGACT 59.671 55.000 13.58 13.58 34.38 4.18
406 407 0.452585 GTGGCTAGGTCTCAGTCGAC 59.547 60.000 7.70 7.70 0.00 4.20
407 408 0.037734 TGTGGCTAGGTCTCAGTCGA 59.962 55.000 0.00 0.00 0.00 4.20
408 409 0.888619 TTGTGGCTAGGTCTCAGTCG 59.111 55.000 0.00 0.00 0.00 4.18
409 410 2.763448 AGATTGTGGCTAGGTCTCAGTC 59.237 50.000 0.00 0.00 0.00 3.51
410 411 2.826488 AGATTGTGGCTAGGTCTCAGT 58.174 47.619 0.00 0.00 0.00 3.41
411 412 5.069648 TGATTAGATTGTGGCTAGGTCTCAG 59.930 44.000 0.00 0.00 0.00 3.35
412 413 4.962362 TGATTAGATTGTGGCTAGGTCTCA 59.038 41.667 0.00 0.00 0.00 3.27
413 414 5.537300 TGATTAGATTGTGGCTAGGTCTC 57.463 43.478 0.00 0.00 0.00 3.36
414 415 5.957771 TTGATTAGATTGTGGCTAGGTCT 57.042 39.130 0.00 0.00 0.00 3.85
415 416 8.677148 TTTATTGATTAGATTGTGGCTAGGTC 57.323 34.615 0.00 0.00 0.00 3.85
416 417 8.903820 GTTTTATTGATTAGATTGTGGCTAGGT 58.096 33.333 0.00 0.00 0.00 3.08
417 418 8.352942 GGTTTTATTGATTAGATTGTGGCTAGG 58.647 37.037 0.00 0.00 0.00 3.02
418 419 9.125026 AGGTTTTATTGATTAGATTGTGGCTAG 57.875 33.333 0.00 0.00 0.00 3.42
420 421 7.961326 AGGTTTTATTGATTAGATTGTGGCT 57.039 32.000 0.00 0.00 0.00 4.75
421 422 8.903820 ACTAGGTTTTATTGATTAGATTGTGGC 58.096 33.333 0.00 0.00 0.00 5.01
427 428 9.553064 CAGCTCACTAGGTTTTATTGATTAGAT 57.447 33.333 0.00 0.00 0.00 1.98
428 429 8.540388 ACAGCTCACTAGGTTTTATTGATTAGA 58.460 33.333 0.00 0.00 0.00 2.10
429 430 8.607459 CACAGCTCACTAGGTTTTATTGATTAG 58.393 37.037 0.00 0.00 0.00 1.73
463 464 5.888982 AGGGTGATATTCGGTAACTCATT 57.111 39.130 0.00 0.00 0.00 2.57
501 503 6.432403 TGGCAAAAGGGTGATATTCTTTTT 57.568 33.333 0.00 0.00 38.27 1.94
502 504 6.625532 ATGGCAAAAGGGTGATATTCTTTT 57.374 33.333 0.00 0.00 40.16 2.27
503 505 6.625532 AATGGCAAAAGGGTGATATTCTTT 57.374 33.333 0.00 0.00 32.77 2.52
504 506 6.441604 AGAAATGGCAAAAGGGTGATATTCTT 59.558 34.615 0.00 0.00 0.00 2.52
505 507 5.960202 AGAAATGGCAAAAGGGTGATATTCT 59.040 36.000 0.00 0.00 0.00 2.40
506 508 6.225981 AGAAATGGCAAAAGGGTGATATTC 57.774 37.500 0.00 0.00 0.00 1.75
507 509 6.625532 AAGAAATGGCAAAAGGGTGATATT 57.374 33.333 0.00 0.00 0.00 1.28
508 510 6.625532 AAAGAAATGGCAAAAGGGTGATAT 57.374 33.333 0.00 0.00 0.00 1.63
509 511 6.432403 AAAAGAAATGGCAAAAGGGTGATA 57.568 33.333 0.00 0.00 0.00 2.15
510 512 4.980339 AAAGAAATGGCAAAAGGGTGAT 57.020 36.364 0.00 0.00 0.00 3.06
511 513 4.769345 AAAAGAAATGGCAAAAGGGTGA 57.231 36.364 0.00 0.00 0.00 4.02
539 541 2.403252 AGGAAAATAGGACTGCCACG 57.597 50.000 0.00 0.00 36.29 4.94
630 729 4.034975 CGCTCAGATTCTTTTCCAGGAATC 59.965 45.833 1.58 0.00 44.58 2.52
638 737 3.194062 AGCTAGCGCTCAGATTCTTTTC 58.806 45.455 16.34 0.00 45.15 2.29
678 1113 1.661112 GAGAAAGGCGCTGTCATACAC 59.339 52.381 7.64 0.00 0.00 2.90
723 1158 1.363744 GAGATGTGGAGTGGCGAAAG 58.636 55.000 0.00 0.00 0.00 2.62
725 1160 1.215382 CGAGATGTGGAGTGGCGAA 59.785 57.895 0.00 0.00 0.00 4.70
746 1181 2.515996 GAATTGTGCGGGAGGGACGA 62.516 60.000 0.00 0.00 40.35 4.20
791 1226 2.100879 AACTGAGTCCCACACGGAGC 62.101 60.000 0.00 0.00 43.19 4.70
831 1266 3.554696 TACGGCCGGTTTGGTGCAT 62.555 57.895 31.76 6.43 41.21 3.96
832 1267 4.251771 TACGGCCGGTTTGGTGCA 62.252 61.111 31.76 0.00 41.21 4.57
1101 1536 1.228124 TGGCAAGGGAAGGTTGTCG 60.228 57.895 0.00 0.00 31.87 4.35
1278 1713 1.599047 CTGGGTCTCGAACAGCCAT 59.401 57.895 13.81 0.00 40.62 4.40
1311 1746 4.078516 GGCCAGTACGCGTTCCCT 62.079 66.667 20.78 8.67 0.00 4.20
1512 2011 9.774742 GCGTCACTTTAAAATTTAGAAGATCAT 57.225 29.630 16.17 0.00 0.00 2.45
1513 2012 7.955324 CGCGTCACTTTAAAATTTAGAAGATCA 59.045 33.333 16.17 2.23 0.00 2.92
1514 2013 7.425595 CCGCGTCACTTTAAAATTTAGAAGATC 59.574 37.037 16.17 0.00 0.00 2.75
1515 2014 7.241376 CCGCGTCACTTTAAAATTTAGAAGAT 58.759 34.615 16.17 3.23 0.00 2.40
1516 2015 6.347888 CCCGCGTCACTTTAAAATTTAGAAGA 60.348 38.462 16.17 2.83 0.00 2.87
1517 2016 5.793457 CCCGCGTCACTTTAAAATTTAGAAG 59.207 40.000 4.92 10.36 0.00 2.85
1518 2017 5.335035 CCCCGCGTCACTTTAAAATTTAGAA 60.335 40.000 4.92 0.00 0.00 2.10
1519 2018 4.154556 CCCCGCGTCACTTTAAAATTTAGA 59.845 41.667 4.92 0.00 0.00 2.10
1520 2019 4.154556 TCCCCGCGTCACTTTAAAATTTAG 59.845 41.667 4.92 0.00 0.00 1.85
1600 2103 3.327754 GTTCGTCGCGCGCCATAT 61.328 61.111 27.95 0.00 41.07 1.78
1680 2183 1.692042 CTGGTCCAGGAGCCAGGAT 60.692 63.158 21.93 0.00 46.27 3.24
1812 2315 1.003839 GGCGGTGGAGATGAACACA 60.004 57.895 0.00 0.00 39.31 3.72
1854 2357 1.668151 GAGAGTGTTGGCCGTCACC 60.668 63.158 21.25 14.70 35.45 4.02
1857 2360 1.079750 GAGGAGAGTGTTGGCCGTC 60.080 63.158 0.00 0.00 0.00 4.79
1869 2372 1.152652 GGCGAGGATGGAGAGGAGA 60.153 63.158 0.00 0.00 0.00 3.71
1890 2393 1.031029 GCTTCTCGACCGGGTAGTCT 61.031 60.000 6.32 0.00 34.46 3.24
2376 2939 1.004504 GCGCGCCAAAATTCAAAAACA 60.005 42.857 23.24 0.00 0.00 2.83
2530 3237 1.466192 CGCGACAGGTACACGAACATA 60.466 52.381 0.00 0.00 0.00 2.29
2620 3327 3.637273 GGCCCGTTGGACAGGACT 61.637 66.667 0.00 0.00 40.65 3.85
2848 3555 2.263540 GTGCCGACGTACATGGGT 59.736 61.111 0.00 0.00 0.00 4.51
3037 3810 2.665185 GACTTGCCGAACCGCTGT 60.665 61.111 0.00 0.00 0.00 4.40
4167 5053 2.810400 CGATTTCCTGACCACACACCTT 60.810 50.000 0.00 0.00 0.00 3.50
4171 5057 0.762418 ACCGATTTCCTGACCACACA 59.238 50.000 0.00 0.00 0.00 3.72
4189 5080 2.767415 GATCGATCTCGGCGGTCGAC 62.767 65.000 25.83 7.13 45.72 4.20
4194 5085 1.226156 GATCGATCGATCTCGGCGG 60.226 63.158 38.45 6.62 45.42 6.13
4253 5152 2.423538 AGCTGTCGTTTTTCTGCACTTT 59.576 40.909 0.00 0.00 0.00 2.66
4268 5167 3.006247 GTTCTCCATTCTCCAAGCTGTC 58.994 50.000 0.00 0.00 0.00 3.51
4275 5174 1.361204 TGGCTGTTCTCCATTCTCCA 58.639 50.000 0.00 0.00 0.00 3.86
4276 5175 2.295885 CATGGCTGTTCTCCATTCTCC 58.704 52.381 0.00 0.00 42.11 3.71
4277 5176 1.674962 GCATGGCTGTTCTCCATTCTC 59.325 52.381 0.00 0.00 42.11 2.87
4278 5177 1.005097 TGCATGGCTGTTCTCCATTCT 59.995 47.619 0.00 0.00 42.11 2.40
4279 5178 1.466856 TGCATGGCTGTTCTCCATTC 58.533 50.000 0.00 0.00 42.11 2.67
4280 5179 2.154567 ATGCATGGCTGTTCTCCATT 57.845 45.000 0.00 0.00 42.11 3.16
4281 5180 1.754803 CAATGCATGGCTGTTCTCCAT 59.245 47.619 0.00 0.00 44.70 3.41
4290 5189 2.895404 AGAAGACAAACAATGCATGGCT 59.105 40.909 0.00 0.00 32.58 4.75
4375 5274 6.203723 GCTACAAAATTGACCTGCCTATCTAG 59.796 42.308 0.00 0.00 0.00 2.43
4376 5275 6.055588 GCTACAAAATTGACCTGCCTATCTA 58.944 40.000 0.00 0.00 0.00 1.98
4377 5276 4.884164 GCTACAAAATTGACCTGCCTATCT 59.116 41.667 0.00 0.00 0.00 1.98
4378 5277 4.884164 AGCTACAAAATTGACCTGCCTATC 59.116 41.667 0.00 0.00 0.00 2.08
4428 5334 4.628766 CGAAGGAGTATGTATGCCATCATG 59.371 45.833 0.00 0.00 34.86 3.07
4466 5382 5.722021 ACAATTAACCTTCCCATGTGAAC 57.278 39.130 0.00 0.00 0.00 3.18
4471 5387 7.461182 TTTCTGTACAATTAACCTTCCCATG 57.539 36.000 0.00 0.00 0.00 3.66
4475 5391 9.010029 TCAGAATTTCTGTACAATTAACCTTCC 57.990 33.333 22.44 0.00 44.58 3.46
4768 5689 9.320295 AGAGAAAAGAAGATAGAGGAAGAAGAA 57.680 33.333 0.00 0.00 0.00 2.52
4872 5798 0.179145 CGCCGTCGTCCTTGTCTTAT 60.179 55.000 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.