Multiple sequence alignment - TraesCS4A01G125300

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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 TraesCS4A01G125300 chr4A 100.000 3721 0 0 1 3721 161279237 161282957 0.000000e+00 6872
1 TraesCS4A01G125300 chr4D 93.047 2258 90 22 478 2717 314679289 314677081 0.000000e+00 3238
2 TraesCS4A01G125300 chr4D 91.487 928 76 2 2795 3721 80140429 80139504 0.000000e+00 1273
3 TraesCS4A01G125300 chr4D 93.855 179 5 3 1 174 314679464 314679287 7.920000e-67 265
4 TraesCS4A01G125300 chr4B 92.433 2141 82 30 683 2795 392659623 392657535 0.000000e+00 2983
5 TraesCS4A01G125300 chr4B 93.678 174 10 1 1 174 392659936 392659764 3.690000e-65 259
6 TraesCS4A01G125300 chr4B 93.919 148 8 1 478 625 392659766 392659620 4.840000e-54 222
7 TraesCS4A01G125300 chr6D 91.935 930 73 2 2793 3721 428663441 428662513 0.000000e+00 1301
8 TraesCS4A01G125300 chr6D 90.977 931 83 1 2792 3721 45622719 45623649 0.000000e+00 1253
9 TraesCS4A01G125300 chr2D 91.703 928 75 2 2795 3721 368975688 368974762 0.000000e+00 1286
10 TraesCS4A01G125300 chr2D 91.164 928 79 3 2795 3721 567015838 567014913 0.000000e+00 1256
11 TraesCS4A01G125300 chr2D 81.007 695 94 28 1124 1805 44470142 44469473 5.510000e-143 518
12 TraesCS4A01G125300 chr2D 80.113 709 108 24 1111 1805 44339765 44340454 7.180000e-137 497
13 TraesCS4A01G125300 chr2D 79.365 693 114 25 1124 1805 48028291 48027617 9.420000e-126 460
14 TraesCS4A01G125300 chr1D 91.300 931 78 2 2792 3721 232435569 232434641 0.000000e+00 1267
15 TraesCS4A01G125300 chr7D 91.300 931 76 3 2792 3721 206446110 206447036 0.000000e+00 1266
16 TraesCS4A01G125300 chr7A 91.164 928 81 1 2795 3721 82175038 82174111 0.000000e+00 1258
17 TraesCS4A01G125300 chr7A 92.787 305 22 0 174 478 435285064 435285368 3.410000e-120 442
18 TraesCS4A01G125300 chr7A 91.589 321 26 1 162 482 649492091 649491772 3.410000e-120 442
19 TraesCS4A01G125300 chr3A 90.851 940 79 6 2784 3721 119381692 119380758 0.000000e+00 1253
20 TraesCS4A01G125300 chr3A 93.160 307 21 0 174 480 579138478 579138784 5.670000e-123 451
21 TraesCS4A01G125300 chr3A 92.605 311 20 3 174 482 439405207 439405516 9.480000e-121 444
22 TraesCS4A01G125300 chr2B 80.288 695 100 27 1124 1805 71293664 71292994 1.200000e-134 490
23 TraesCS4A01G125300 chr2B 80.000 705 104 33 1124 1805 75990592 75991282 1.550000e-133 486
24 TraesCS4A01G125300 chr2B 79.969 654 96 26 1124 1766 71244283 71243654 2.040000e-122 449
25 TraesCS4A01G125300 chr2B 85.030 334 39 8 1479 1805 70837292 70837621 2.770000e-86 329
26 TraesCS4A01G125300 chr2A 80.635 661 94 29 1124 1762 51040893 51041541 7.230000e-132 481
27 TraesCS4A01G125300 chr2A 80.000 695 101 27 1124 1805 48347446 48346777 2.600000e-131 479
28 TraesCS4A01G125300 chr2A 80.275 654 89 27 1124 1766 48249983 48250607 1.220000e-124 457
29 TraesCS4A01G125300 chr2A 85.373 335 38 10 1478 1805 48246383 48246713 1.660000e-88 337
30 TraesCS4A01G125300 chr5A 93.770 305 17 2 175 478 537659905 537660208 1.220000e-124 457
31 TraesCS4A01G125300 chr5A 91.589 321 26 1 162 482 343130275 343129956 3.410000e-120 442
32 TraesCS4A01G125300 chr1B 93.421 304 20 0 174 477 619390674 619390371 5.670000e-123 451
33 TraesCS4A01G125300 chr1A 92.308 312 24 0 169 480 272073778 272074089 9.480000e-121 444
34 TraesCS4A01G125300 chr6A 92.233 309 24 0 174 482 131197119 131197427 4.410000e-119 438


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 TraesCS4A01G125300 chr4A 161279237 161282957 3720 False 6872.000000 6872 100.000000 1 3721 1 chr4A.!!$F1 3720
1 TraesCS4A01G125300 chr4D 314677081 314679464 2383 True 1751.500000 3238 93.451000 1 2717 2 chr4D.!!$R2 2716
2 TraesCS4A01G125300 chr4D 80139504 80140429 925 True 1273.000000 1273 91.487000 2795 3721 1 chr4D.!!$R1 926
3 TraesCS4A01G125300 chr4B 392657535 392659936 2401 True 1154.666667 2983 93.343333 1 2795 3 chr4B.!!$R1 2794
4 TraesCS4A01G125300 chr6D 428662513 428663441 928 True 1301.000000 1301 91.935000 2793 3721 1 chr6D.!!$R1 928
5 TraesCS4A01G125300 chr6D 45622719 45623649 930 False 1253.000000 1253 90.977000 2792 3721 1 chr6D.!!$F1 929
6 TraesCS4A01G125300 chr2D 368974762 368975688 926 True 1286.000000 1286 91.703000 2795 3721 1 chr2D.!!$R3 926
7 TraesCS4A01G125300 chr2D 567014913 567015838 925 True 1256.000000 1256 91.164000 2795 3721 1 chr2D.!!$R4 926
8 TraesCS4A01G125300 chr2D 44469473 44470142 669 True 518.000000 518 81.007000 1124 1805 1 chr2D.!!$R1 681
9 TraesCS4A01G125300 chr2D 44339765 44340454 689 False 497.000000 497 80.113000 1111 1805 1 chr2D.!!$F1 694
10 TraesCS4A01G125300 chr2D 48027617 48028291 674 True 460.000000 460 79.365000 1124 1805 1 chr2D.!!$R2 681
11 TraesCS4A01G125300 chr1D 232434641 232435569 928 True 1267.000000 1267 91.300000 2792 3721 1 chr1D.!!$R1 929
12 TraesCS4A01G125300 chr7D 206446110 206447036 926 False 1266.000000 1266 91.300000 2792 3721 1 chr7D.!!$F1 929
13 TraesCS4A01G125300 chr7A 82174111 82175038 927 True 1258.000000 1258 91.164000 2795 3721 1 chr7A.!!$R1 926
14 TraesCS4A01G125300 chr3A 119380758 119381692 934 True 1253.000000 1253 90.851000 2784 3721 1 chr3A.!!$R1 937
15 TraesCS4A01G125300 chr2B 71292994 71293664 670 True 490.000000 490 80.288000 1124 1805 1 chr2B.!!$R2 681
16 TraesCS4A01G125300 chr2B 75990592 75991282 690 False 486.000000 486 80.000000 1124 1805 1 chr2B.!!$F2 681
17 TraesCS4A01G125300 chr2B 71243654 71244283 629 True 449.000000 449 79.969000 1124 1766 1 chr2B.!!$R1 642
18 TraesCS4A01G125300 chr2A 51040893 51041541 648 False 481.000000 481 80.635000 1124 1762 1 chr2A.!!$F1 638
19 TraesCS4A01G125300 chr2A 48346777 48347446 669 True 479.000000 479 80.000000 1124 1805 1 chr2A.!!$R1 681
20 TraesCS4A01G125300 chr2A 48246383 48250607 4224 False 397.000000 457 82.824000 1124 1805 2 chr2A.!!$F2 681

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
989 1008 0.036294 TCTCGACGAGCCTCAAGAGA 60.036 55.0 20.11 6.67 33.02 3.10 F
1533 4085 0.037697 CCGACATCCAGGTGTTCGAA 60.038 55.0 0.00 0.00 31.16 3.71 F
2081 4638 0.879090 AATTTCGGTCGGTTTCTGGC 59.121 50.0 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 4546 0.035630 CCTTGACCTTCTCCAGCTGG 60.036 60.0 27.87 27.87 0.0 4.85 R
2534 5094 0.396811 CTTCACAAAGGGTCGAGGGT 59.603 55.0 0.00 0.00 0.0 4.34 R
3130 5699 0.813610 CTTGGTTGAGCACGTGTGGA 60.814 55.0 18.38 0.00 0.0 4.02 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
171 177 3.858638 AGGAATATCCCACCCAAGAAAGT 59.141 43.478 0.00 0.00 37.19 2.66
172 178 5.043762 AGGAATATCCCACCCAAGAAAGTA 58.956 41.667 0.00 0.00 37.19 2.24
174 180 5.828328 GGAATATCCCACCCAAGAAAGTAAG 59.172 44.000 0.00 0.00 0.00 2.34
175 181 3.739401 ATCCCACCCAAGAAAGTAAGG 57.261 47.619 0.00 0.00 0.00 2.69
177 183 1.545841 CCACCCAAGAAAGTAAGGGC 58.454 55.000 0.00 0.00 45.45 5.19
178 184 1.075536 CCACCCAAGAAAGTAAGGGCT 59.924 52.381 0.00 0.00 45.45 5.19
179 185 2.437413 CACCCAAGAAAGTAAGGGCTC 58.563 52.381 0.00 0.00 45.45 4.70
180 186 1.354705 ACCCAAGAAAGTAAGGGCTCC 59.645 52.381 0.00 0.00 45.45 4.70
181 187 1.636003 CCCAAGAAAGTAAGGGCTCCT 59.364 52.381 0.00 0.00 33.91 3.69
182 188 2.041755 CCCAAGAAAGTAAGGGCTCCTT 59.958 50.000 10.76 10.76 46.63 3.36
183 189 3.500471 CCCAAGAAAGTAAGGGCTCCTTT 60.500 47.826 11.15 0.00 41.69 3.11
184 190 3.507622 CCAAGAAAGTAAGGGCTCCTTTG 59.492 47.826 11.15 3.15 41.69 2.77
185 191 4.398319 CAAGAAAGTAAGGGCTCCTTTGA 58.602 43.478 11.15 0.00 41.69 2.69
186 192 4.936685 AGAAAGTAAGGGCTCCTTTGAT 57.063 40.909 11.15 0.00 41.69 2.57
187 193 5.262455 AGAAAGTAAGGGCTCCTTTGATT 57.738 39.130 11.15 5.15 41.69 2.57
189 195 4.657814 AAGTAAGGGCTCCTTTGATTCA 57.342 40.909 11.15 0.00 41.69 2.57
190 196 4.657814 AGTAAGGGCTCCTTTGATTCAA 57.342 40.909 11.15 0.00 41.69 2.69
204 210 7.766219 CTTTGATTCAAAGGAATTGCATAGG 57.234 36.000 25.14 2.45 44.75 2.57
205 211 7.479352 TTTGATTCAAAGGAATTGCATAGGA 57.521 32.000 7.74 0.00 43.69 2.94
207 213 7.664552 TGATTCAAAGGAATTGCATAGGATT 57.335 32.000 0.00 0.00 43.69 3.01
208 214 8.081517 TGATTCAAAGGAATTGCATAGGATTT 57.918 30.769 0.00 0.00 43.69 2.17
209 215 8.542080 TGATTCAAAGGAATTGCATAGGATTTT 58.458 29.630 0.00 0.00 43.69 1.82
210 216 9.387257 GATTCAAAGGAATTGCATAGGATTTTT 57.613 29.630 0.00 0.00 43.69 1.94
212 218 9.874205 TTCAAAGGAATTGCATAGGATTTTTAG 57.126 29.630 0.00 0.00 38.98 1.85
213 219 9.253832 TCAAAGGAATTGCATAGGATTTTTAGA 57.746 29.630 0.00 0.00 38.98 2.10
214 220 9.525409 CAAAGGAATTGCATAGGATTTTTAGAG 57.475 33.333 0.00 0.00 31.00 2.43
215 221 7.830099 AGGAATTGCATAGGATTTTTAGAGG 57.170 36.000 0.00 0.00 0.00 3.69
216 222 7.586349 AGGAATTGCATAGGATTTTTAGAGGA 58.414 34.615 0.00 0.00 0.00 3.71
217 223 8.230306 AGGAATTGCATAGGATTTTTAGAGGAT 58.770 33.333 0.00 0.00 0.00 3.24
218 224 8.864087 GGAATTGCATAGGATTTTTAGAGGATT 58.136 33.333 0.00 0.00 0.00 3.01
224 230 9.967346 GCATAGGATTTTTAGAGGATTTAAACC 57.033 33.333 0.00 0.00 0.00 3.27
237 243 9.615660 AGAGGATTTAAACCCTTAGGAATTTTT 57.384 29.630 1.57 0.00 36.73 1.94
238 244 9.871238 GAGGATTTAAACCCTTAGGAATTTTTC 57.129 33.333 1.57 0.00 36.73 2.29
252 258 6.721704 GGAATTTTTCCTATGATGCTCCTT 57.278 37.500 0.00 0.00 46.57 3.36
253 259 7.117285 GGAATTTTTCCTATGATGCTCCTTT 57.883 36.000 0.00 0.00 46.57 3.11
254 260 6.982724 GGAATTTTTCCTATGATGCTCCTTTG 59.017 38.462 0.00 0.00 46.57 2.77
255 261 7.147846 GGAATTTTTCCTATGATGCTCCTTTGA 60.148 37.037 0.00 0.00 46.57 2.69
256 262 7.909485 ATTTTTCCTATGATGCTCCTTTGAT 57.091 32.000 0.00 0.00 0.00 2.57
257 263 7.722949 TTTTTCCTATGATGCTCCTTTGATT 57.277 32.000 0.00 0.00 0.00 2.57
259 265 4.635223 TCCTATGATGCTCCTTTGATTCG 58.365 43.478 0.00 0.00 0.00 3.34
261 267 5.304357 TCCTATGATGCTCCTTTGATTCGTA 59.696 40.000 0.00 0.00 0.00 3.43
263 269 3.797039 TGATGCTCCTTTGATTCGTAGG 58.203 45.455 0.00 0.00 0.00 3.18
264 270 3.450817 TGATGCTCCTTTGATTCGTAGGA 59.549 43.478 6.45 6.45 36.65 2.94
265 271 4.101585 TGATGCTCCTTTGATTCGTAGGAT 59.898 41.667 6.94 0.00 37.44 3.24
266 272 4.487714 TGCTCCTTTGATTCGTAGGATT 57.512 40.909 6.94 0.00 37.44 3.01
267 273 4.191544 TGCTCCTTTGATTCGTAGGATTG 58.808 43.478 6.94 0.12 37.44 2.67
270 276 3.054728 TCCTTTGATTCGTAGGATTGGCA 60.055 43.478 3.21 0.00 33.23 4.92
271 277 3.885297 CCTTTGATTCGTAGGATTGGCAT 59.115 43.478 0.00 0.00 0.00 4.40
272 278 4.023707 CCTTTGATTCGTAGGATTGGCATC 60.024 45.833 0.00 0.00 0.00 3.91
284 290 5.859205 GGATTGGCATCCTTAGTGATTTT 57.141 39.130 8.23 0.00 45.41 1.82
285 291 6.225981 GGATTGGCATCCTTAGTGATTTTT 57.774 37.500 8.23 0.00 45.41 1.94
317 323 9.057089 GGATCTATTTGTACTACATTTTGGAGG 57.943 37.037 0.00 0.00 30.79 4.30
318 324 9.832445 GATCTATTTGTACTACATTTTGGAGGA 57.168 33.333 0.00 0.00 30.79 3.71
341 347 7.032377 GAAAATATCCATCCACTCAAACCTC 57.968 40.000 0.00 0.00 0.00 3.85
342 348 5.983333 AATATCCATCCACTCAAACCTCT 57.017 39.130 0.00 0.00 0.00 3.69
345 351 5.779241 ATCCATCCACTCAAACCTCTTTA 57.221 39.130 0.00 0.00 0.00 1.85
346 352 5.779241 TCCATCCACTCAAACCTCTTTAT 57.221 39.130 0.00 0.00 0.00 1.40
347 353 6.884472 TCCATCCACTCAAACCTCTTTATA 57.116 37.500 0.00 0.00 0.00 0.98
349 355 6.672218 TCCATCCACTCAAACCTCTTTATAGA 59.328 38.462 0.00 0.00 0.00 1.98
351 357 7.995488 CCATCCACTCAAACCTCTTTATAGAAT 59.005 37.037 0.00 0.00 0.00 2.40
352 358 9.401058 CATCCACTCAAACCTCTTTATAGAATT 57.599 33.333 0.00 0.00 0.00 2.17
353 359 9.620259 ATCCACTCAAACCTCTTTATAGAATTC 57.380 33.333 0.00 0.00 0.00 2.17
354 360 8.047310 TCCACTCAAACCTCTTTATAGAATTCC 58.953 37.037 0.65 0.00 0.00 3.01
356 362 9.454859 CACTCAAACCTCTTTATAGAATTCCTT 57.545 33.333 0.65 0.00 0.00 3.36
359 365 9.807921 TCAAACCTCTTTATAGAATTCCTTTGT 57.192 29.630 0.65 0.00 0.00 2.83
381 387 4.829064 TTTTTCTGCGCTATCAAACACT 57.171 36.364 9.73 0.00 0.00 3.55
384 390 3.319137 TCTGCGCTATCAAACACTCTT 57.681 42.857 9.73 0.00 0.00 2.85
385 391 3.664107 TCTGCGCTATCAAACACTCTTT 58.336 40.909 9.73 0.00 0.00 2.52
386 392 3.679980 TCTGCGCTATCAAACACTCTTTC 59.320 43.478 9.73 0.00 0.00 2.62
387 393 3.398406 TGCGCTATCAAACACTCTTTCA 58.602 40.909 9.73 0.00 0.00 2.69
388 394 3.812609 TGCGCTATCAAACACTCTTTCAA 59.187 39.130 9.73 0.00 0.00 2.69
389 395 4.274705 TGCGCTATCAAACACTCTTTCAAA 59.725 37.500 9.73 0.00 0.00 2.69
390 396 5.048782 TGCGCTATCAAACACTCTTTCAAAT 60.049 36.000 9.73 0.00 0.00 2.32
391 397 5.509622 GCGCTATCAAACACTCTTTCAAATC 59.490 40.000 0.00 0.00 0.00 2.17
392 398 6.602179 CGCTATCAAACACTCTTTCAAATCA 58.398 36.000 0.00 0.00 0.00 2.57
393 399 7.246311 CGCTATCAAACACTCTTTCAAATCAT 58.754 34.615 0.00 0.00 0.00 2.45
394 400 7.217636 CGCTATCAAACACTCTTTCAAATCATG 59.782 37.037 0.00 0.00 0.00 3.07
398 404 7.874940 TCAAACACTCTTTCAAATCATGTAGG 58.125 34.615 0.00 0.00 0.00 3.18
399 405 7.719193 TCAAACACTCTTTCAAATCATGTAGGA 59.281 33.333 0.00 0.00 0.00 2.94
402 408 6.094603 ACACTCTTTCAAATCATGTAGGATGC 59.905 38.462 0.00 0.00 0.00 3.91
403 409 6.318144 CACTCTTTCAAATCATGTAGGATGCT 59.682 38.462 0.00 0.00 0.00 3.79
404 410 7.496920 CACTCTTTCAAATCATGTAGGATGCTA 59.503 37.037 0.00 0.00 0.00 3.49
405 411 8.216423 ACTCTTTCAAATCATGTAGGATGCTAT 58.784 33.333 0.00 0.00 0.00 2.97
406 412 8.387190 TCTTTCAAATCATGTAGGATGCTATG 57.613 34.615 0.00 0.00 0.00 2.23
407 413 7.446319 TCTTTCAAATCATGTAGGATGCTATGG 59.554 37.037 0.00 0.00 0.00 2.74
408 414 5.563592 TCAAATCATGTAGGATGCTATGGG 58.436 41.667 0.00 0.00 0.00 4.00
409 415 5.310331 TCAAATCATGTAGGATGCTATGGGA 59.690 40.000 0.00 0.00 0.00 4.37
428 434 4.202461 TGGGACATACCATTCTATTCCTGC 60.202 45.833 0.00 0.00 41.20 4.85
429 435 4.202461 GGGACATACCATTCTATTCCTGCA 60.202 45.833 0.00 0.00 41.20 4.41
430 436 5.515534 GGGACATACCATTCTATTCCTGCAT 60.516 44.000 0.00 0.00 41.20 3.96
431 437 6.006449 GGACATACCATTCTATTCCTGCATT 58.994 40.000 0.00 0.00 38.79 3.56
432 438 6.491403 GGACATACCATTCTATTCCTGCATTT 59.509 38.462 0.00 0.00 38.79 2.32
433 439 7.014615 GGACATACCATTCTATTCCTGCATTTT 59.985 37.037 0.00 0.00 38.79 1.82
461 467 9.071276 TCTATTCCTTCATTTTGATAATCCTGC 57.929 33.333 0.00 0.00 0.00 4.85
462 468 5.756195 TCCTTCATTTTGATAATCCTGCG 57.244 39.130 0.00 0.00 0.00 5.18
463 469 5.436175 TCCTTCATTTTGATAATCCTGCGA 58.564 37.500 0.00 0.00 0.00 5.10
464 470 5.885352 TCCTTCATTTTGATAATCCTGCGAA 59.115 36.000 0.00 0.00 0.00 4.70
467 473 6.940831 TCATTTTGATAATCCTGCGAATCA 57.059 33.333 0.00 0.00 0.00 2.57
468 474 7.332213 TCATTTTGATAATCCTGCGAATCAA 57.668 32.000 0.00 0.00 36.75 2.57
469 475 7.770201 TCATTTTGATAATCCTGCGAATCAAA 58.230 30.769 5.48 5.48 43.15 2.69
471 477 7.389803 TTTTGATAATCCTGCGAATCAAAGA 57.610 32.000 8.73 0.86 44.59 2.52
472 478 6.609237 TTGATAATCCTGCGAATCAAAGAG 57.391 37.500 0.00 0.00 35.88 2.85
473 479 5.059161 TGATAATCCTGCGAATCAAAGAGG 58.941 41.667 0.00 0.00 0.00 3.69
474 480 1.673168 ATCCTGCGAATCAAAGAGGC 58.327 50.000 0.00 0.00 0.00 4.70
476 482 1.379642 CCTGCGAATCAAAGAGGCCC 61.380 60.000 0.00 0.00 0.00 5.80
493 499 7.512117 AGAGGCCCTAAACTCTAGTTAAAAT 57.488 36.000 0.00 0.00 42.00 1.82
653 659 2.853594 CCCGATTGACAATGCAATTTCG 59.146 45.455 5.14 1.76 38.53 3.46
767 773 2.047655 CCGCTACCGAAACTGCCA 60.048 61.111 0.00 0.00 36.29 4.92
891 909 0.462047 GGCGTTATCCAGTGGACCAG 60.462 60.000 15.86 7.68 32.98 4.00
924 942 4.989168 CGTTTCCTTATTTATAGCCTCGCT 59.011 41.667 0.00 0.00 43.41 4.93
966 985 2.371841 AGAAATCCCAAGCCAAAAACCC 59.628 45.455 0.00 0.00 0.00 4.11
973 992 1.341209 CAAGCCAAAAACCCCACTCTC 59.659 52.381 0.00 0.00 0.00 3.20
977 996 0.865769 CAAAAACCCCACTCTCGACG 59.134 55.000 0.00 0.00 0.00 5.12
978 997 0.754472 AAAAACCCCACTCTCGACGA 59.246 50.000 0.00 0.00 0.00 4.20
980 999 2.156051 AAACCCCACTCTCGACGAGC 62.156 60.000 20.11 0.00 43.85 5.03
981 1000 3.827898 CCCCACTCTCGACGAGCC 61.828 72.222 20.11 0.00 43.85 4.70
983 1002 2.766400 CCCACTCTCGACGAGCCTC 61.766 68.421 20.11 0.00 43.85 4.70
984 1003 2.041115 CCACTCTCGACGAGCCTCA 61.041 63.158 20.11 1.79 43.85 3.86
988 1007 0.376852 CTCTCGACGAGCCTCAAGAG 59.623 60.000 20.11 6.80 31.99 2.85
989 1008 0.036294 TCTCGACGAGCCTCAAGAGA 60.036 55.000 20.11 6.67 33.02 3.10
990 1009 1.021202 CTCGACGAGCCTCAAGAGAT 58.979 55.000 12.67 0.00 0.00 2.75
991 1010 1.002900 CTCGACGAGCCTCAAGAGATC 60.003 57.143 12.67 0.00 0.00 2.75
992 1011 0.735471 CGACGAGCCTCAAGAGATCA 59.265 55.000 0.00 0.00 0.00 2.92
993 1012 1.133216 CGACGAGCCTCAAGAGATCAA 59.867 52.381 0.00 0.00 0.00 2.57
996 1015 1.805871 CGAGCCTCAAGAGATCAAGCC 60.806 57.143 0.00 0.00 0.00 4.35
997 1016 0.545646 AGCCTCAAGAGATCAAGCCC 59.454 55.000 0.00 0.00 0.00 5.19
998 1017 0.813210 GCCTCAAGAGATCAAGCCCG 60.813 60.000 0.00 0.00 0.00 6.13
1046 1065 0.545548 AAAGCTTCCTCCCCGAGACT 60.546 55.000 0.00 0.00 0.00 3.24
1174 3652 1.198759 ACTACTGGATGGGCGTGGTT 61.199 55.000 0.00 0.00 0.00 3.67
1414 3907 1.812922 CCACCTGCATGTCTCGCTC 60.813 63.158 0.00 0.00 0.00 5.03
1435 3931 1.871039 ACGTTTGTCAGTGTGTATGGC 59.129 47.619 0.00 0.00 0.00 4.40
1458 3954 5.178061 CAGTAATGGTGTGCTGATCTGTTA 58.822 41.667 1.27 0.00 0.00 2.41
1463 3959 4.002982 TGGTGTGCTGATCTGTTATTGAC 58.997 43.478 1.27 0.00 0.00 3.18
1533 4085 0.037697 CCGACATCCAGGTGTTCGAA 60.038 55.000 0.00 0.00 31.16 3.71
1823 4378 4.440112 GCAGGTAAGCCGCTAATGATTTTT 60.440 41.667 0.00 0.00 40.50 1.94
1917 4473 6.070656 AGGATTTCCTGAACATGTTCTTCAA 58.929 36.000 32.57 21.60 46.55 2.69
1990 4546 3.644399 GAGGCACCCGGAGAACGTC 62.644 68.421 0.73 0.00 42.24 4.34
2040 4596 2.261671 CGCTGCGGTAAGTGGACT 59.738 61.111 15.40 0.00 0.00 3.85
2041 4597 2.094659 CGCTGCGGTAAGTGGACTG 61.095 63.158 15.40 0.00 0.00 3.51
2046 4603 1.079127 CGGTAAGTGGACTGCCCTG 60.079 63.158 0.00 0.00 35.38 4.45
2051 4608 3.626924 GTGGACTGCCCTGTCGGT 61.627 66.667 0.25 0.00 37.81 4.69
2066 4623 2.277084 GTCGGTCGCTGGTATGAATTT 58.723 47.619 0.00 0.00 0.00 1.82
2069 4626 1.597663 GGTCGCTGGTATGAATTTCGG 59.402 52.381 0.00 0.00 0.00 4.30
2080 4637 2.147958 TGAATTTCGGTCGGTTTCTGG 58.852 47.619 0.00 0.00 0.00 3.86
2081 4638 0.879090 AATTTCGGTCGGTTTCTGGC 59.121 50.000 0.00 0.00 0.00 4.85
2085 4642 0.899720 TCGGTCGGTTTCTGGCTATT 59.100 50.000 0.00 0.00 0.00 1.73
2108 4665 3.058639 GCTTGCATTCTTACGGATGGATC 60.059 47.826 0.00 0.00 0.00 3.36
2112 4669 3.318017 CATTCTTACGGATGGATCGGTC 58.682 50.000 3.34 0.00 40.28 4.79
2225 4782 1.200716 TGGGACATCTACAACGACGAC 59.799 52.381 0.00 0.00 0.00 4.34
2226 4783 1.531912 GGACATCTACAACGACGACG 58.468 55.000 5.58 5.58 45.75 5.12
2227 4784 1.129251 GGACATCTACAACGACGACGA 59.871 52.381 15.32 0.00 42.66 4.20
2464 5022 2.995258 GGTATTTTGCGTCTGTTCGGTA 59.005 45.455 0.00 0.00 0.00 4.02
2491 5051 7.965107 CCAAGTTAGCAGTATCATTTCAAGTTC 59.035 37.037 0.00 0.00 0.00 3.01
2534 5094 7.012610 TCGAAAGAGTCCACGTATGTGAATATA 59.987 37.037 16.87 0.00 41.51 0.86
2557 5118 2.353803 CCTCGACCCTTTGTGAAGTAGG 60.354 54.545 0.00 0.00 0.00 3.18
2561 5122 2.951229 CCCTTTGTGAAGTAGGGTGT 57.049 50.000 0.00 0.00 43.07 4.16
2667 5231 3.639538 TCACTTACGTTTGTCAGCTCTC 58.360 45.455 0.00 0.00 0.00 3.20
2691 5255 4.768130 TTCCTTGTCGTTCTGTCTCTAG 57.232 45.455 0.00 0.00 0.00 2.43
2744 5311 1.099295 ACATGCTGCGATGGGTGATG 61.099 55.000 13.79 4.49 0.00 3.07
2747 5314 3.104766 CTGCGATGGGTGATGCAC 58.895 61.111 0.00 0.00 33.12 4.57
2750 5317 3.576356 CGATGGGTGATGCACGGC 61.576 66.667 0.00 0.00 34.83 5.68
2769 5336 0.548510 CCAATCCTTCTCCCTGACCC 59.451 60.000 0.00 0.00 0.00 4.46
2781 5348 1.202770 CCCTGACCCTCTTCACGTTTT 60.203 52.381 0.00 0.00 0.00 2.43
2783 5350 2.290641 CCTGACCCTCTTCACGTTTTTG 59.709 50.000 0.00 0.00 0.00 2.44
2784 5351 3.202906 CTGACCCTCTTCACGTTTTTGA 58.797 45.455 0.00 0.00 0.00 2.69
2809 5376 1.078426 CTAAGGCCAACTCCACGGG 60.078 63.158 5.01 0.00 0.00 5.28
2834 5402 5.050227 ACGATTCAAATGGACGTTCGTTTTA 60.050 36.000 11.46 1.08 34.22 1.52
2866 5434 3.997681 TGTCCGTTTGAATAGCGATTTGA 59.002 39.130 0.00 0.00 0.00 2.69
2875 5444 2.736144 TAGCGATTTGAGGTCGTGTT 57.264 45.000 0.00 0.00 40.98 3.32
2883 5452 1.008079 GAGGTCGTGTTCGGACGTT 60.008 57.895 0.00 0.00 40.34 3.99
2896 5465 0.672401 GGACGTTTCTTGGGATGCGA 60.672 55.000 0.00 0.00 0.00 5.10
2905 5474 4.856801 GGGATGCGATGGCCGTGT 62.857 66.667 0.00 0.00 41.15 4.49
2907 5476 2.819595 GATGCGATGGCCGTGTGT 60.820 61.111 0.00 0.00 41.15 3.72
2911 5480 2.358125 CGATGGCCGTGTGTCCAA 60.358 61.111 0.00 0.00 35.75 3.53
2943 5512 3.513517 CATCCATTTGCCCCATCCTATT 58.486 45.455 0.00 0.00 0.00 1.73
2965 5534 2.681344 CGTCAGGGCCAAAAATACCTAC 59.319 50.000 6.18 0.00 0.00 3.18
2989 5558 7.889469 ACATTCTCATCAAAACTAGTTTGCAT 58.111 30.769 21.22 12.94 45.38 3.96
3109 5678 9.438291 GACTGAACATAAAATGAATCAATACGG 57.562 33.333 0.00 0.00 32.45 4.02
3155 5724 1.873591 ACGTGCTCAACCAAGTCATTC 59.126 47.619 0.00 0.00 0.00 2.67
3157 5726 3.244078 ACGTGCTCAACCAAGTCATTCTA 60.244 43.478 0.00 0.00 0.00 2.10
3184 5753 6.604396 AGATTCAAATGACTATGCCAATCACA 59.396 34.615 0.00 0.00 0.00 3.58
3194 5763 1.001860 TGCCAATCACACATCTCACGA 59.998 47.619 0.00 0.00 0.00 4.35
3195 5764 2.076100 GCCAATCACACATCTCACGAA 58.924 47.619 0.00 0.00 0.00 3.85
3214 5783 5.006552 CACGAAGGAATTGCACAAATTGTTT 59.993 36.000 0.00 0.00 38.64 2.83
3222 5791 8.341173 GGAATTGCACAAATTGTTTAAATGTGA 58.659 29.630 18.53 3.80 38.64 3.58
3223 5792 9.881529 GAATTGCACAAATTGTTTAAATGTGAT 57.118 25.926 18.53 5.55 38.64 3.06
3278 5847 5.893824 ACCTTGATAATCAAATCCTTGGTCC 59.106 40.000 0.00 0.00 35.73 4.46
3302 5871 2.025589 TACTCTCATCACGCTCGTCT 57.974 50.000 0.00 0.00 0.00 4.18
3341 5910 3.119602 GCATGATCACACAAGCAGTCATT 60.120 43.478 0.00 0.00 0.00 2.57
3343 5912 5.220989 GCATGATCACACAAGCAGTCATTAT 60.221 40.000 0.00 0.00 0.00 1.28
3346 5915 6.175471 TGATCACACAAGCAGTCATTATCTT 58.825 36.000 0.00 0.00 0.00 2.40
3357 5926 5.356470 GCAGTCATTATCTTCCAAAGCTTCT 59.644 40.000 0.00 0.00 0.00 2.85
3362 5931 7.483059 GTCATTATCTTCCAAAGCTTCTTTTCG 59.517 37.037 0.00 0.00 0.00 3.46
3391 5960 0.878961 AGTGCAGGGTTTCGAACGAC 60.879 55.000 0.00 0.00 0.00 4.34
3395 5964 0.249741 CAGGGTTTCGAACGACACCT 60.250 55.000 24.62 16.18 42.75 4.00
3414 5983 2.358957 CTCATCGGGATTGAAGCACAA 58.641 47.619 0.00 0.00 42.95 3.33
3420 5989 3.320541 TCGGGATTGAAGCACAACAAAAT 59.679 39.130 0.00 0.00 41.52 1.82
3438 6007 5.163457 ACAAAATCACGTTCCACATCCTTTT 60.163 36.000 0.00 0.00 0.00 2.27
3631 6200 1.270305 CCTTGCGAAGACTGGAGAACA 60.270 52.381 0.00 0.00 0.00 3.18
3706 6275 4.503817 CCATATCCAAAGATCCTGCGAAGA 60.504 45.833 0.00 0.00 33.67 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.883585 TGAATCATTCCTCTCCCATTTTCG 59.116 41.667 0.00 0.00 0.00 3.46
181 187 7.479352 TCCTATGCAATTCCTTTGAATCAAA 57.521 32.000 8.25 8.25 40.34 2.69
182 188 7.664552 ATCCTATGCAATTCCTTTGAATCAA 57.335 32.000 0.00 0.00 40.34 2.57
183 189 7.664552 AATCCTATGCAATTCCTTTGAATCA 57.335 32.000 0.00 0.00 40.34 2.57
184 190 8.953368 AAAATCCTATGCAATTCCTTTGAATC 57.047 30.769 0.00 0.00 40.34 2.52
186 192 9.874205 CTAAAAATCCTATGCAATTCCTTTGAA 57.126 29.630 0.00 0.00 37.53 2.69
187 193 9.253832 TCTAAAAATCCTATGCAATTCCTTTGA 57.746 29.630 0.00 0.00 37.53 2.69
189 195 8.699130 CCTCTAAAAATCCTATGCAATTCCTTT 58.301 33.333 0.00 0.00 0.00 3.11
190 196 8.061304 TCCTCTAAAAATCCTATGCAATTCCTT 58.939 33.333 0.00 0.00 0.00 3.36
211 217 9.615660 AAAAATTCCTAAGGGTTTAAATCCTCT 57.384 29.630 20.42 12.67 39.03 3.69
212 218 9.871238 GAAAAATTCCTAAGGGTTTAAATCCTC 57.129 33.333 20.42 0.13 39.03 3.71
213 219 8.822805 GGAAAAATTCCTAAGGGTTTAAATCCT 58.177 33.333 14.63 14.63 46.57 3.24
229 235 6.721704 AAGGAGCATCATAGGAAAAATTCC 57.278 37.500 0.75 0.75 44.11 3.01
230 236 7.775120 TCAAAGGAGCATCATAGGAAAAATTC 58.225 34.615 0.00 0.00 36.25 2.17
231 237 7.722949 TCAAAGGAGCATCATAGGAAAAATT 57.277 32.000 0.00 0.00 36.25 1.82
232 238 7.909485 ATCAAAGGAGCATCATAGGAAAAAT 57.091 32.000 0.00 0.00 36.25 1.82
233 239 7.415541 CGAATCAAAGGAGCATCATAGGAAAAA 60.416 37.037 0.00 0.00 36.25 1.94
234 240 6.038603 CGAATCAAAGGAGCATCATAGGAAAA 59.961 38.462 0.00 0.00 36.25 2.29
235 241 5.528690 CGAATCAAAGGAGCATCATAGGAAA 59.471 40.000 0.00 0.00 36.25 3.13
236 242 5.059161 CGAATCAAAGGAGCATCATAGGAA 58.941 41.667 0.00 0.00 36.25 3.36
237 243 4.101585 ACGAATCAAAGGAGCATCATAGGA 59.898 41.667 0.00 0.00 36.25 2.94
238 244 4.384056 ACGAATCAAAGGAGCATCATAGG 58.616 43.478 0.00 0.00 36.25 2.57
239 245 5.636965 CCTACGAATCAAAGGAGCATCATAG 59.363 44.000 0.00 0.00 36.25 2.23
240 246 5.304357 TCCTACGAATCAAAGGAGCATCATA 59.696 40.000 0.00 0.00 34.46 2.15
241 247 4.101585 TCCTACGAATCAAAGGAGCATCAT 59.898 41.667 0.00 0.00 34.46 2.45
243 249 4.060038 TCCTACGAATCAAAGGAGCATC 57.940 45.455 0.00 0.00 34.46 3.91
244 250 4.696479 ATCCTACGAATCAAAGGAGCAT 57.304 40.909 6.70 0.00 42.53 3.79
248 254 3.054728 TGCCAATCCTACGAATCAAAGGA 60.055 43.478 3.43 3.43 43.38 3.36
250 256 5.100751 GATGCCAATCCTACGAATCAAAG 57.899 43.478 0.00 0.00 0.00 2.77
290 296 9.838339 CTCCAAAATGTAGTACAAATAGATCCT 57.162 33.333 7.16 0.00 0.00 3.24
291 297 9.057089 CCTCCAAAATGTAGTACAAATAGATCC 57.943 37.037 7.16 0.00 0.00 3.36
300 306 9.403583 GGATATTTTCCTCCAAAATGTAGTACA 57.596 33.333 5.24 5.24 43.38 2.90
303 309 9.136323 GATGGATATTTTCCTCCAAAATGTAGT 57.864 33.333 3.12 0.00 44.41 2.73
305 311 8.064389 TGGATGGATATTTTCCTCCAAAATGTA 58.936 33.333 9.98 0.00 44.41 2.29
306 312 6.902416 TGGATGGATATTTTCCTCCAAAATGT 59.098 34.615 9.98 0.00 44.41 2.71
307 313 7.070322 AGTGGATGGATATTTTCCTCCAAAATG 59.930 37.037 12.47 0.00 45.50 2.32
308 314 7.134842 AGTGGATGGATATTTTCCTCCAAAAT 58.865 34.615 12.47 0.00 45.50 1.82
309 315 6.502138 AGTGGATGGATATTTTCCTCCAAAA 58.498 36.000 12.47 0.00 45.50 2.44
310 316 6.091076 AGTGGATGGATATTTTCCTCCAAA 57.909 37.500 12.47 0.00 45.50 3.28
311 317 5.193527 TGAGTGGATGGATATTTTCCTCCAA 59.806 40.000 12.47 1.18 45.50 3.53
312 318 4.726317 TGAGTGGATGGATATTTTCCTCCA 59.274 41.667 8.95 8.95 45.68 3.86
313 319 5.310409 TGAGTGGATGGATATTTTCCTCC 57.690 43.478 0.00 1.13 45.68 4.30
314 320 6.039829 GGTTTGAGTGGATGGATATTTTCCTC 59.960 42.308 0.00 0.00 45.68 3.71
315 321 5.893824 GGTTTGAGTGGATGGATATTTTCCT 59.106 40.000 0.00 0.00 45.68 3.36
317 323 6.830838 AGAGGTTTGAGTGGATGGATATTTTC 59.169 38.462 0.00 0.00 0.00 2.29
318 324 6.735556 AGAGGTTTGAGTGGATGGATATTTT 58.264 36.000 0.00 0.00 0.00 1.82
319 325 6.332976 AGAGGTTTGAGTGGATGGATATTT 57.667 37.500 0.00 0.00 0.00 1.40
321 327 5.983333 AAGAGGTTTGAGTGGATGGATAT 57.017 39.130 0.00 0.00 0.00 1.63
322 328 5.779241 AAAGAGGTTTGAGTGGATGGATA 57.221 39.130 0.00 0.00 0.00 2.59
324 330 5.779241 ATAAAGAGGTTTGAGTGGATGGA 57.221 39.130 0.00 0.00 0.00 3.41
325 331 6.889198 TCTATAAAGAGGTTTGAGTGGATGG 58.111 40.000 0.00 0.00 0.00 3.51
326 332 8.970859 ATTCTATAAAGAGGTTTGAGTGGATG 57.029 34.615 0.00 0.00 31.96 3.51
327 333 9.620259 GAATTCTATAAAGAGGTTTGAGTGGAT 57.380 33.333 0.00 0.00 31.96 3.41
329 335 8.049721 AGGAATTCTATAAAGAGGTTTGAGTGG 58.950 37.037 5.23 0.00 31.96 4.00
333 339 9.807921 ACAAAGGAATTCTATAAAGAGGTTTGA 57.192 29.630 5.23 0.00 31.96 2.69
360 366 4.515191 AGAGTGTTTGATAGCGCAGAAAAA 59.485 37.500 11.47 1.84 0.00 1.94
361 367 4.065088 AGAGTGTTTGATAGCGCAGAAAA 58.935 39.130 11.47 1.43 0.00 2.29
362 368 3.664107 AGAGTGTTTGATAGCGCAGAAA 58.336 40.909 11.47 0.00 0.00 2.52
364 370 3.319137 AAGAGTGTTTGATAGCGCAGA 57.681 42.857 11.47 0.00 0.00 4.26
365 371 3.433274 TGAAAGAGTGTTTGATAGCGCAG 59.567 43.478 11.47 0.00 0.00 5.18
366 372 3.398406 TGAAAGAGTGTTTGATAGCGCA 58.602 40.909 11.47 0.00 0.00 6.09
367 373 4.404507 TTGAAAGAGTGTTTGATAGCGC 57.595 40.909 0.00 0.00 0.00 5.92
368 374 6.602179 TGATTTGAAAGAGTGTTTGATAGCG 58.398 36.000 0.00 0.00 0.00 4.26
372 378 8.517878 CCTACATGATTTGAAAGAGTGTTTGAT 58.482 33.333 0.00 0.00 0.00 2.57
373 379 7.719193 TCCTACATGATTTGAAAGAGTGTTTGA 59.281 33.333 0.00 0.00 0.00 2.69
374 380 7.874940 TCCTACATGATTTGAAAGAGTGTTTG 58.125 34.615 0.00 0.00 0.00 2.93
375 381 8.517878 CATCCTACATGATTTGAAAGAGTGTTT 58.482 33.333 0.00 0.00 0.00 2.83
376 382 7.362401 GCATCCTACATGATTTGAAAGAGTGTT 60.362 37.037 0.00 0.00 0.00 3.32
380 386 6.939132 AGCATCCTACATGATTTGAAAGAG 57.061 37.500 0.00 0.00 0.00 2.85
381 387 7.446319 CCATAGCATCCTACATGATTTGAAAGA 59.554 37.037 0.00 0.00 0.00 2.52
384 390 6.005823 CCCATAGCATCCTACATGATTTGAA 58.994 40.000 0.00 0.00 0.00 2.69
385 391 5.310331 TCCCATAGCATCCTACATGATTTGA 59.690 40.000 0.00 0.00 0.00 2.69
386 392 5.413833 GTCCCATAGCATCCTACATGATTTG 59.586 44.000 0.00 0.00 0.00 2.32
387 393 5.073554 TGTCCCATAGCATCCTACATGATTT 59.926 40.000 0.00 0.00 0.00 2.17
388 394 4.598807 TGTCCCATAGCATCCTACATGATT 59.401 41.667 0.00 0.00 0.00 2.57
389 395 4.170449 TGTCCCATAGCATCCTACATGAT 58.830 43.478 0.00 0.00 0.00 2.45
390 396 3.586429 TGTCCCATAGCATCCTACATGA 58.414 45.455 0.00 0.00 0.00 3.07
391 397 4.564782 ATGTCCCATAGCATCCTACATG 57.435 45.455 0.00 0.00 0.00 3.21
392 398 4.471386 GGTATGTCCCATAGCATCCTACAT 59.529 45.833 8.20 0.00 0.00 2.29
393 399 3.838317 GGTATGTCCCATAGCATCCTACA 59.162 47.826 8.20 0.00 0.00 2.74
394 400 3.838317 TGGTATGTCCCATAGCATCCTAC 59.162 47.826 11.02 0.00 34.77 3.18
396 402 2.990195 TGGTATGTCCCATAGCATCCT 58.010 47.619 11.02 0.00 34.77 3.24
397 403 4.018960 AGAATGGTATGTCCCATAGCATCC 60.019 45.833 22.14 14.19 44.55 3.51
398 404 5.171339 AGAATGGTATGTCCCATAGCATC 57.829 43.478 22.14 16.83 44.55 3.91
399 405 6.898171 ATAGAATGGTATGTCCCATAGCAT 57.102 37.500 18.33 18.33 44.55 3.79
402 408 7.334090 CAGGAATAGAATGGTATGTCCCATAG 58.666 42.308 0.00 0.00 44.55 2.23
403 409 6.296432 GCAGGAATAGAATGGTATGTCCCATA 60.296 42.308 0.00 0.00 44.55 2.74
405 411 4.202461 GCAGGAATAGAATGGTATGTCCCA 60.202 45.833 0.00 0.00 39.27 4.37
406 412 4.202461 TGCAGGAATAGAATGGTATGTCCC 60.202 45.833 0.00 0.00 34.77 4.46
407 413 4.973168 TGCAGGAATAGAATGGTATGTCC 58.027 43.478 0.00 0.00 0.00 4.02
408 414 7.516198 AAATGCAGGAATAGAATGGTATGTC 57.484 36.000 0.00 0.00 0.00 3.06
409 415 7.902920 AAAATGCAGGAATAGAATGGTATGT 57.097 32.000 0.00 0.00 0.00 2.29
435 441 9.071276 GCAGGATTATCAAAATGAAGGAATAGA 57.929 33.333 0.00 0.00 0.00 1.98
436 442 8.019669 CGCAGGATTATCAAAATGAAGGAATAG 58.980 37.037 0.00 0.00 0.00 1.73
437 443 7.719193 TCGCAGGATTATCAAAATGAAGGAATA 59.281 33.333 0.00 0.00 0.00 1.75
438 444 6.547141 TCGCAGGATTATCAAAATGAAGGAAT 59.453 34.615 0.00 0.00 0.00 3.01
439 445 5.885352 TCGCAGGATTATCAAAATGAAGGAA 59.115 36.000 0.00 0.00 0.00 3.36
442 448 7.420002 TGATTCGCAGGATTATCAAAATGAAG 58.580 34.615 0.00 0.00 0.00 3.02
444 450 6.940831 TGATTCGCAGGATTATCAAAATGA 57.059 33.333 0.00 0.00 0.00 2.57
447 453 7.389803 TCTTTGATTCGCAGGATTATCAAAA 57.610 32.000 0.00 0.00 42.86 2.44
449 455 5.528690 CCTCTTTGATTCGCAGGATTATCAA 59.471 40.000 0.00 0.00 35.76 2.57
450 456 5.059161 CCTCTTTGATTCGCAGGATTATCA 58.941 41.667 0.00 0.00 0.00 2.15
451 457 4.083590 GCCTCTTTGATTCGCAGGATTATC 60.084 45.833 0.00 0.00 0.00 1.75
452 458 3.817647 GCCTCTTTGATTCGCAGGATTAT 59.182 43.478 0.00 0.00 0.00 1.28
453 459 3.206150 GCCTCTTTGATTCGCAGGATTA 58.794 45.455 0.00 0.00 0.00 1.75
454 460 2.019984 GCCTCTTTGATTCGCAGGATT 58.980 47.619 0.00 0.00 0.00 3.01
455 461 1.673168 GCCTCTTTGATTCGCAGGAT 58.327 50.000 0.00 0.00 0.00 3.24
456 462 0.392998 GGCCTCTTTGATTCGCAGGA 60.393 55.000 0.00 0.00 0.00 3.86
457 463 1.379642 GGGCCTCTTTGATTCGCAGG 61.380 60.000 0.84 0.00 0.00 4.85
459 465 0.908910 TAGGGCCTCTTTGATTCGCA 59.091 50.000 10.74 0.00 0.00 5.10
461 467 3.610911 AGTTTAGGGCCTCTTTGATTCG 58.389 45.455 10.74 0.00 0.00 3.34
462 468 4.849518 AGAGTTTAGGGCCTCTTTGATTC 58.150 43.478 10.74 0.00 34.40 2.52
463 469 4.936685 AGAGTTTAGGGCCTCTTTGATT 57.063 40.909 10.74 0.00 34.40 2.57
464 470 5.033522 ACTAGAGTTTAGGGCCTCTTTGAT 58.966 41.667 10.74 0.00 38.86 2.57
467 473 6.947376 TTAACTAGAGTTTAGGGCCTCTTT 57.053 37.500 10.74 0.00 38.86 2.52
468 474 6.947376 TTTAACTAGAGTTTAGGGCCTCTT 57.053 37.500 10.74 0.00 38.86 2.85
469 475 6.947376 TTTTAACTAGAGTTTAGGGCCTCT 57.053 37.500 10.74 0.00 40.94 3.69
471 477 6.216868 TCCATTTTAACTAGAGTTTAGGGCCT 59.783 38.462 12.58 12.58 39.31 5.19
472 478 6.420638 TCCATTTTAACTAGAGTTTAGGGCC 58.579 40.000 0.00 0.00 39.31 5.80
473 479 7.773690 TGATCCATTTTAACTAGAGTTTAGGGC 59.226 37.037 0.00 0.00 39.31 5.19
474 480 9.853177 ATGATCCATTTTAACTAGAGTTTAGGG 57.147 33.333 0.00 0.00 39.31 3.53
493 499 3.448301 GGTTGAAGGCAATTGATGATCCA 59.552 43.478 10.34 0.00 36.22 3.41
559 565 1.272781 CAACCGTCGCAGAATCTCTC 58.727 55.000 0.00 0.00 39.69 3.20
653 659 3.848726 CATTCACTGCCATGGTTAAACC 58.151 45.455 14.67 0.00 39.22 3.27
767 773 3.628280 GACGGAAGCTTCTCGCGGT 62.628 63.158 26.77 17.35 45.59 5.68
924 942 1.276989 GATGAGGTTTCACGGTGGGTA 59.723 52.381 8.50 0.00 35.83 3.69
973 992 0.735471 TGATCTCTTGAGGCTCGTCG 59.265 55.000 10.42 0.50 0.00 5.12
977 996 1.474855 GGGCTTGATCTCTTGAGGCTC 60.475 57.143 7.79 7.79 35.30 4.70
978 997 0.545646 GGGCTTGATCTCTTGAGGCT 59.454 55.000 0.00 0.00 35.30 4.58
980 999 0.826715 TCGGGCTTGATCTCTTGAGG 59.173 55.000 0.00 0.00 0.00 3.86
981 1000 2.275318 GTTCGGGCTTGATCTCTTGAG 58.725 52.381 0.00 0.00 0.00 3.02
983 1002 1.734465 GTGTTCGGGCTTGATCTCTTG 59.266 52.381 0.00 0.00 0.00 3.02
984 1003 1.347707 TGTGTTCGGGCTTGATCTCTT 59.652 47.619 0.00 0.00 0.00 2.85
988 1007 2.922335 GCTTTTGTGTTCGGGCTTGATC 60.922 50.000 0.00 0.00 0.00 2.92
989 1008 1.000274 GCTTTTGTGTTCGGGCTTGAT 60.000 47.619 0.00 0.00 0.00 2.57
990 1009 0.383949 GCTTTTGTGTTCGGGCTTGA 59.616 50.000 0.00 0.00 0.00 3.02
991 1010 0.385390 AGCTTTTGTGTTCGGGCTTG 59.615 50.000 0.00 0.00 0.00 4.01
992 1011 0.668535 GAGCTTTTGTGTTCGGGCTT 59.331 50.000 0.00 0.00 0.00 4.35
993 1012 0.465460 TGAGCTTTTGTGTTCGGGCT 60.465 50.000 0.00 0.00 0.00 5.19
996 1015 1.600413 GGCTTGAGCTTTTGTGTTCGG 60.600 52.381 2.66 0.00 41.70 4.30
997 1016 1.600413 GGGCTTGAGCTTTTGTGTTCG 60.600 52.381 2.66 0.00 41.70 3.95
998 1017 1.600413 CGGGCTTGAGCTTTTGTGTTC 60.600 52.381 2.66 0.00 41.70 3.18
1046 1065 2.242926 CTCGGGAGCCATCTTGATCTA 58.757 52.381 0.00 0.00 0.00 1.98
1150 3628 1.384643 GCCCATCCAGTAGTCCCCT 60.385 63.158 0.00 0.00 0.00 4.79
1414 3907 2.349438 GCCATACACACTGACAAACGTG 60.349 50.000 0.00 0.00 37.18 4.49
1435 3931 3.603532 ACAGATCAGCACACCATTACTG 58.396 45.455 0.00 0.00 0.00 2.74
1458 3954 3.130340 ACTGCGTTCAAAACCAAGTCAAT 59.870 39.130 0.00 0.00 0.00 2.57
1463 3959 3.060628 CACAAACTGCGTTCAAAACCAAG 59.939 43.478 0.00 0.00 0.00 3.61
1823 4378 3.617531 GCCAAATCTGGACTCTCGAGAAA 60.618 47.826 17.36 1.76 46.92 2.52
1826 4381 1.205655 TGCCAAATCTGGACTCTCGAG 59.794 52.381 5.93 5.93 46.92 4.04
1832 4387 4.876107 CGTTATTACTGCCAAATCTGGACT 59.124 41.667 0.00 0.00 46.92 3.85
1833 4388 4.035208 CCGTTATTACTGCCAAATCTGGAC 59.965 45.833 0.00 0.00 46.92 4.02
1843 4398 0.299597 CGAACGCCGTTATTACTGCC 59.700 55.000 0.79 0.00 31.54 4.85
1903 4459 3.817647 ACTGCTCCTTGAAGAACATGTTC 59.182 43.478 27.69 27.69 39.78 3.18
1917 4473 0.461961 GATCGGCTTGTACTGCTCCT 59.538 55.000 10.33 0.00 0.00 3.69
1990 4546 0.035630 CCTTGACCTTCTCCAGCTGG 60.036 60.000 27.87 27.87 0.00 4.85
2043 4599 1.226974 CATACCAGCGACCGACAGG 60.227 63.158 0.00 0.00 45.13 4.00
2046 4603 1.935933 AATTCATACCAGCGACCGAC 58.064 50.000 0.00 0.00 0.00 4.79
2051 4608 2.546778 GACCGAAATTCATACCAGCGA 58.453 47.619 0.00 0.00 0.00 4.93
2054 4611 2.901249 ACCGACCGAAATTCATACCAG 58.099 47.619 0.00 0.00 0.00 4.00
2066 4623 0.899720 AATAGCCAGAAACCGACCGA 59.100 50.000 0.00 0.00 0.00 4.69
2069 4626 1.739067 AGCAATAGCCAGAAACCGAC 58.261 50.000 0.00 0.00 43.56 4.79
2080 4637 3.312421 TCCGTAAGAATGCAAGCAATAGC 59.688 43.478 0.00 0.00 43.02 2.97
2081 4638 5.446709 CATCCGTAAGAATGCAAGCAATAG 58.553 41.667 0.00 0.00 43.02 1.73
2085 4642 2.016318 CCATCCGTAAGAATGCAAGCA 58.984 47.619 0.00 0.00 43.02 3.91
2108 4665 2.356913 TGCGACCATGTGTGACCG 60.357 61.111 0.00 0.00 0.00 4.79
2112 4669 1.078214 ATCCCTGCGACCATGTGTG 60.078 57.895 0.00 0.00 0.00 3.82
2226 4783 1.946745 CCCTTGAAATCGAGGCTCTC 58.053 55.000 13.50 3.68 44.60 3.20
2227 4784 0.107459 GCCCTTGAAATCGAGGCTCT 60.107 55.000 13.50 0.00 44.60 4.09
2400 4957 1.660560 CCGGCTTCCTGCTTTGATGG 61.661 60.000 0.00 0.00 42.39 3.51
2464 5022 6.942576 ACTTGAAATGATACTGCTAACTTGGT 59.057 34.615 0.00 0.00 0.00 3.67
2491 5051 6.341316 TCTTTCGATCAAACCTCCTATCTTG 58.659 40.000 0.00 0.00 0.00 3.02
2534 5094 0.396811 CTTCACAAAGGGTCGAGGGT 59.603 55.000 0.00 0.00 0.00 4.34
2535 5095 0.396811 ACTTCACAAAGGGTCGAGGG 59.603 55.000 0.00 0.00 36.78 4.30
2557 5118 2.230508 TCATACAGGACGAGACAACACC 59.769 50.000 0.00 0.00 0.00 4.16
2561 5122 5.462530 TTCTTTCATACAGGACGAGACAA 57.537 39.130 0.00 0.00 0.00 3.18
2667 5231 3.060602 GAGACAGAACGACAAGGAAAGG 58.939 50.000 0.00 0.00 0.00 3.11
2726 5293 1.652563 CATCACCCATCGCAGCATG 59.347 57.895 0.00 0.00 40.87 4.06
2738 5305 2.774799 GGATTGGCCGTGCATCACC 61.775 63.158 0.00 0.00 0.00 4.02
2744 5311 2.115291 GGAGAAGGATTGGCCGTGC 61.115 63.158 0.00 0.00 43.43 5.34
2747 5314 1.153086 CAGGGAGAAGGATTGGCCG 60.153 63.158 0.00 0.00 43.43 6.13
2750 5317 0.548510 GGGTCAGGGAGAAGGATTGG 59.451 60.000 0.00 0.00 0.00 3.16
2769 5336 9.322776 CTTAGAATCATTCAAAAACGTGAAGAG 57.677 33.333 0.00 0.00 40.72 2.85
2781 5348 4.949856 GGAGTTGGCCTTAGAATCATTCAA 59.050 41.667 3.32 0.00 0.00 2.69
2783 5350 4.336713 GTGGAGTTGGCCTTAGAATCATTC 59.663 45.833 3.32 0.00 0.00 2.67
2784 5351 4.273318 GTGGAGTTGGCCTTAGAATCATT 58.727 43.478 3.32 0.00 0.00 2.57
2809 5376 2.410730 ACGAACGTCCATTTGAATCGTC 59.589 45.455 0.66 0.00 35.43 4.20
2854 5422 3.247006 ACACGACCTCAAATCGCTATT 57.753 42.857 0.00 0.00 43.46 1.73
2866 5434 0.595825 GAAACGTCCGAACACGACCT 60.596 55.000 8.27 0.00 42.69 3.85
2875 5444 0.672401 GCATCCCAAGAAACGTCCGA 60.672 55.000 0.00 0.00 0.00 4.55
2883 5452 1.453745 GGCCATCGCATCCCAAGAA 60.454 57.895 0.00 0.00 36.38 2.52
2896 5465 2.513395 TGTTGGACACACGGCCAT 59.487 55.556 2.24 0.00 33.46 4.40
2943 5512 1.353022 AGGTATTTTTGGCCCTGACGA 59.647 47.619 0.00 0.00 0.00 4.20
2965 5534 7.811236 ACATGCAAACTAGTTTTGATGAGAATG 59.189 33.333 27.87 22.05 46.76 2.67
3125 5694 2.747446 GGTTGAGCACGTGTGGAATTAT 59.253 45.455 18.38 0.00 0.00 1.28
3130 5699 0.813610 CTTGGTTGAGCACGTGTGGA 60.814 55.000 18.38 0.00 0.00 4.02
3155 5724 9.674824 GATTGGCATAGTCATTTGAATCTTTAG 57.325 33.333 0.00 0.00 0.00 1.85
3157 5726 7.977853 GTGATTGGCATAGTCATTTGAATCTTT 59.022 33.333 0.00 0.00 0.00 2.52
3173 5742 2.011947 CGTGAGATGTGTGATTGGCAT 58.988 47.619 0.00 0.00 0.00 4.40
3184 5753 2.744202 GTGCAATTCCTTCGTGAGATGT 59.256 45.455 0.00 0.00 41.60 3.06
3194 5763 8.901793 ACATTTAAACAATTTGTGCAATTCCTT 58.098 25.926 2.13 0.00 32.24 3.36
3195 5764 8.344098 CACATTTAAACAATTTGTGCAATTCCT 58.656 29.630 2.13 0.00 32.24 3.36
3214 5783 3.509575 GCACCAAGACCCAATCACATTTA 59.490 43.478 0.00 0.00 0.00 1.40
3222 5791 1.077265 CCCTGCACCAAGACCCAAT 59.923 57.895 0.00 0.00 0.00 3.16
3223 5792 2.520458 CCCTGCACCAAGACCCAA 59.480 61.111 0.00 0.00 0.00 4.12
3224 5793 3.579302 CCCCTGCACCAAGACCCA 61.579 66.667 0.00 0.00 0.00 4.51
3302 5871 3.929610 TCATGCACAACATAATCGTCGAA 59.070 39.130 0.00 0.00 36.64 3.71
3341 5910 5.411669 GGACGAAAAGAAGCTTTGGAAGATA 59.588 40.000 0.00 0.00 0.00 1.98
3343 5912 3.564225 GGACGAAAAGAAGCTTTGGAAGA 59.436 43.478 0.00 0.00 0.00 2.87
3346 5915 2.227194 GGGACGAAAAGAAGCTTTGGA 58.773 47.619 0.00 0.00 0.00 3.53
3362 5931 1.377725 CCCTGCACTGTCATGGGAC 60.378 63.158 0.00 0.00 44.57 4.46
3391 5960 1.303309 GCTTCAATCCCGATGAGGTG 58.697 55.000 0.00 0.00 38.74 4.00
3395 5964 2.083774 GTTGTGCTTCAATCCCGATGA 58.916 47.619 0.00 0.00 38.38 2.92
3414 5983 3.486383 AGGATGTGGAACGTGATTTTGT 58.514 40.909 0.00 0.00 42.39 2.83
3420 5989 4.882427 TGTTAAAAAGGATGTGGAACGTGA 59.118 37.500 0.00 0.00 42.39 4.35
3438 6007 3.255642 GCCCAAATGCAAGAGAGTGTTAA 59.744 43.478 0.00 0.00 0.00 2.01
3631 6200 2.385013 TGATATCAACGTGCTGCAGT 57.615 45.000 16.64 0.23 0.00 4.40


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

AutoCloner maintained by Alex Coulton.