Multiple sequence alignment - TraesCS2D01G424900

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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 TraesCS2D01G424900 chr2D 100.000 2210 0 0 1 2210 537457948 537455739 0.000000e+00 4082
1 TraesCS2D01G424900 chr2D 94.674 582 18 6 1642 2210 16240428 16241009 0.000000e+00 891
2 TraesCS2D01G424900 chr2D 94.320 581 21 2 1642 2210 373613470 373612890 0.000000e+00 880
3 TraesCS2D01G424900 chr2D 79.882 338 55 10 880 1211 537448524 537448194 3.670000e-58 235
4 TraesCS2D01G424900 chr4B 94.983 578 18 3 1644 2210 622314543 622315120 0.000000e+00 896
5 TraesCS2D01G424900 chr4B 87.615 218 27 0 994 1211 621985443 621985660 1.010000e-63 254
6 TraesCS2D01G424900 chr4B 79.899 199 38 2 1001 1198 558753852 558753655 6.360000e-31 145
7 TraesCS2D01G424900 chr2A 94.521 584 21 5 1638 2210 759093906 759093323 0.000000e+00 891
8 TraesCS2D01G424900 chr2A 89.199 574 31 9 899 1454 679985898 679985338 0.000000e+00 688
9 TraesCS2D01G424900 chr2A 93.169 366 14 5 1644 1998 759091491 759091126 5.400000e-146 527
10 TraesCS2D01G424900 chr2A 80.687 466 39 22 437 875 679986423 679985982 4.580000e-82 315
11 TraesCS2D01G424900 chr2A 84.694 294 27 11 2 295 679991899 679991624 6.010000e-71 278
12 TraesCS2D01G424900 chr2A 81.602 337 41 12 880 1211 679982554 679982234 2.180000e-65 259
13 TraesCS2D01G424900 chr2A 90.909 110 8 2 298 407 70936101 70936208 1.770000e-31 147
14 TraesCS2D01G424900 chr3D 94.810 578 17 5 1645 2210 606920567 606921143 0.000000e+00 889
15 TraesCS2D01G424900 chr3D 86.514 393 14 10 1645 1998 251296149 251296541 1.590000e-106 396
16 TraesCS2D01G424900 chr1B 94.801 577 19 4 1645 2210 76735765 76735189 0.000000e+00 889
17 TraesCS2D01G424900 chr1B 93.651 567 34 2 1645 2210 133164030 133164595 0.000000e+00 846
18 TraesCS2D01G424900 chr6D 94.885 567 28 1 1645 2210 403401894 403402460 0.000000e+00 885
19 TraesCS2D01G424900 chr6B 94.483 580 21 4 1642 2210 78309258 78309837 0.000000e+00 883
20 TraesCS2D01G424900 chr6B 94.310 580 22 2 1642 2210 78264800 78265379 0.000000e+00 878
21 TraesCS2D01G424900 chr2B 90.815 577 42 4 1645 2210 423814455 423813879 0.000000e+00 761
22 TraesCS2D01G424900 chr2B 84.507 497 35 19 405 878 640102505 640102028 9.300000e-124 453
23 TraesCS2D01G424900 chr2B 91.667 336 8 7 875 1210 640101953 640101638 4.330000e-122 448
24 TraesCS2D01G424900 chr2B 81.065 338 41 14 880 1211 640086031 640085711 4.710000e-62 248
25 TraesCS2D01G424900 chr2B 82.707 266 23 13 58 310 640102750 640102495 4.780000e-52 215
26 TraesCS2D01G424900 chr7B 90.984 366 22 5 1644 1998 651070920 651070555 1.190000e-132 483
27 TraesCS2D01G424900 chr4D 88.679 212 24 0 1000 1211 487045738 487045949 2.180000e-65 259
28 TraesCS2D01G424900 chr5A 87.963 216 25 1 1000 1214 667942001 667942216 1.010000e-63 254
29 TraesCS2D01G424900 chr5A 88.889 126 11 2 283 407 554560547 554560670 3.800000e-33 152
30 TraesCS2D01G424900 chr5A 88.889 126 9 4 293 415 573562624 573562501 1.370000e-32 150
31 TraesCS2D01G424900 chr5A 88.430 121 11 3 288 407 422874728 422874846 2.290000e-30 143
32 TraesCS2D01G424900 chr1A 87.050 139 10 6 275 410 115437304 115437171 1.370000e-32 150
33 TraesCS2D01G424900 chr1D 90.909 110 8 1 298 407 41754355 41754462 1.770000e-31 147
34 TraesCS2D01G424900 chr3A 88.983 118 11 2 298 415 91478229 91478344 6.360000e-31 145
35 TraesCS2D01G424900 chr3A 88.983 118 10 3 296 412 51447866 51447981 2.290000e-30 143
36 TraesCS2D01G424900 chr7A 88.333 120 12 1 295 414 638698965 638699082 2.290000e-30 143


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 TraesCS2D01G424900 chr2D 537455739 537457948 2209 True 4082.000000 4082 100.000000 1 2210 1 chr2D.!!$R3 2209
1 TraesCS2D01G424900 chr2D 16240428 16241009 581 False 891.000000 891 94.674000 1642 2210 1 chr2D.!!$F1 568
2 TraesCS2D01G424900 chr2D 373612890 373613470 580 True 880.000000 880 94.320000 1642 2210 1 chr2D.!!$R1 568
3 TraesCS2D01G424900 chr4B 622314543 622315120 577 False 896.000000 896 94.983000 1644 2210 1 chr4B.!!$F2 566
4 TraesCS2D01G424900 chr2A 759091126 759093906 2780 True 709.000000 891 93.845000 1638 2210 2 chr2A.!!$R3 572
5 TraesCS2D01G424900 chr2A 679982234 679986423 4189 True 420.666667 688 83.829333 437 1454 3 chr2A.!!$R2 1017
6 TraesCS2D01G424900 chr3D 606920567 606921143 576 False 889.000000 889 94.810000 1645 2210 1 chr3D.!!$F2 565
7 TraesCS2D01G424900 chr1B 76735189 76735765 576 True 889.000000 889 94.801000 1645 2210 1 chr1B.!!$R1 565
8 TraesCS2D01G424900 chr1B 133164030 133164595 565 False 846.000000 846 93.651000 1645 2210 1 chr1B.!!$F1 565
9 TraesCS2D01G424900 chr6D 403401894 403402460 566 False 885.000000 885 94.885000 1645 2210 1 chr6D.!!$F1 565
10 TraesCS2D01G424900 chr6B 78309258 78309837 579 False 883.000000 883 94.483000 1642 2210 1 chr6B.!!$F2 568
11 TraesCS2D01G424900 chr6B 78264800 78265379 579 False 878.000000 878 94.310000 1642 2210 1 chr6B.!!$F1 568
12 TraesCS2D01G424900 chr2B 423813879 423814455 576 True 761.000000 761 90.815000 1645 2210 1 chr2B.!!$R1 565
13 TraesCS2D01G424900 chr2B 640101638 640102750 1112 True 372.000000 453 86.293667 58 1210 3 chr2B.!!$R3 1152

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
954 1145 0.107508 CTGGTCGGTCCTCCTACGTA 60.108 60.0 0.0 0.0 37.07 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 2422 0.963355 CCCCACGTTGTAACCCATGG 60.963 60.0 4.14 4.14 0.0 3.66 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.873732 GTGATCTCCACTGCTTTAATTGAC 58.126 41.667 0.00 0.00 42.44 3.18
24 25 5.412594 GTGATCTCCACTGCTTTAATTGACA 59.587 40.000 0.00 0.00 42.44 3.58
25 26 6.003326 TGATCTCCACTGCTTTAATTGACAA 58.997 36.000 0.00 0.00 0.00 3.18
26 27 5.689383 TCTCCACTGCTTTAATTGACAAC 57.311 39.130 0.00 0.00 0.00 3.32
27 28 4.213270 TCTCCACTGCTTTAATTGACAACG 59.787 41.667 0.00 0.00 0.00 4.10
28 29 2.979813 CCACTGCTTTAATTGACAACGC 59.020 45.455 0.00 0.00 0.00 4.84
29 30 2.979813 CACTGCTTTAATTGACAACGCC 59.020 45.455 0.00 0.00 0.00 5.68
30 31 2.030274 ACTGCTTTAATTGACAACGCCC 60.030 45.455 0.00 0.00 0.00 6.13
31 32 1.957177 TGCTTTAATTGACAACGCCCA 59.043 42.857 0.00 0.00 0.00 5.36
32 33 2.030363 TGCTTTAATTGACAACGCCCAG 60.030 45.455 0.00 0.00 0.00 4.45
33 34 2.595386 CTTTAATTGACAACGCCCAGC 58.405 47.619 0.00 0.00 0.00 4.85
34 35 0.885196 TTAATTGACAACGCCCAGCC 59.115 50.000 0.00 0.00 0.00 4.85
35 36 1.302383 TAATTGACAACGCCCAGCCG 61.302 55.000 0.00 0.00 0.00 5.52
36 37 3.842925 ATTGACAACGCCCAGCCGT 62.843 57.895 0.00 0.00 44.41 5.68
42 43 4.572571 ACGCCCAGCCGTTTGGAA 62.573 61.111 4.13 0.00 40.87 3.53
43 44 4.038080 CGCCCAGCCGTTTGGAAC 62.038 66.667 4.13 0.00 40.87 3.62
44 45 2.909965 GCCCAGCCGTTTGGAACA 60.910 61.111 4.13 0.00 40.87 3.18
45 46 2.275380 GCCCAGCCGTTTGGAACAT 61.275 57.895 4.13 0.00 40.87 2.71
46 47 1.586028 CCCAGCCGTTTGGAACATG 59.414 57.895 4.13 0.00 40.87 3.21
47 48 0.893270 CCCAGCCGTTTGGAACATGA 60.893 55.000 0.00 0.00 40.87 3.07
48 49 0.523072 CCAGCCGTTTGGAACATGAG 59.477 55.000 0.00 0.00 40.87 2.90
49 50 0.109597 CAGCCGTTTGGAACATGAGC 60.110 55.000 0.00 0.00 39.30 4.26
50 51 1.212751 GCCGTTTGGAACATGAGCC 59.787 57.895 0.00 0.00 39.30 4.70
51 52 1.501741 CCGTTTGGAACATGAGCCG 59.498 57.895 0.00 0.00 39.30 5.52
52 53 1.234615 CCGTTTGGAACATGAGCCGT 61.235 55.000 0.00 0.00 39.30 5.68
53 54 0.110238 CGTTTGGAACATGAGCCGTG 60.110 55.000 0.00 0.00 39.30 4.94
54 55 0.387239 GTTTGGAACATGAGCCGTGC 60.387 55.000 0.00 0.00 39.30 5.34
55 56 0.537143 TTTGGAACATGAGCCGTGCT 60.537 50.000 0.00 0.00 39.65 4.40
56 57 1.236616 TTGGAACATGAGCCGTGCTG 61.237 55.000 0.00 0.00 37.27 4.41
60 61 3.857854 CATGAGCCGTGCTGCGAC 61.858 66.667 2.98 0.00 44.77 5.19
120 121 4.503714 ACTTTCTCTGAAACTGAACCCA 57.496 40.909 0.00 0.00 0.00 4.51
128 129 4.061596 CTGAAACTGAACCCAACTCTCTC 58.938 47.826 0.00 0.00 0.00 3.20
129 130 3.711704 TGAAACTGAACCCAACTCTCTCT 59.288 43.478 0.00 0.00 0.00 3.10
131 132 5.365605 TGAAACTGAACCCAACTCTCTCTAA 59.634 40.000 0.00 0.00 0.00 2.10
132 133 5.476091 AACTGAACCCAACTCTCTCTAAG 57.524 43.478 0.00 0.00 0.00 2.18
133 134 4.484912 ACTGAACCCAACTCTCTCTAAGT 58.515 43.478 0.00 0.00 0.00 2.24
140 141 4.282195 CCCAACTCTCTCTAAGTCACAACT 59.718 45.833 0.00 0.00 37.32 3.16
142 143 5.242838 CCAACTCTCTCTAAGTCACAACTCT 59.757 44.000 0.00 0.00 33.48 3.24
143 144 5.957842 ACTCTCTCTAAGTCACAACTCTG 57.042 43.478 0.00 0.00 33.48 3.35
144 145 5.381757 ACTCTCTCTAAGTCACAACTCTGT 58.618 41.667 0.00 0.00 33.48 3.41
163 164 2.891580 TGTTGTACCCACTCTCTCTGAC 59.108 50.000 0.00 0.00 0.00 3.51
164 165 2.217510 TGTACCCACTCTCTCTGACC 57.782 55.000 0.00 0.00 0.00 4.02
174 185 1.105457 CTCTCTGACCCTCTCTGCAG 58.895 60.000 7.63 7.63 0.00 4.41
176 187 1.203112 TCTCTGACCCTCTCTGCAGTT 60.203 52.381 14.67 0.00 0.00 3.16
187 198 3.850098 CTGCAGTTTGGCGACCCCT 62.850 63.158 5.25 0.00 36.28 4.79
201 212 2.267961 CCCTCCTTACCCACACGC 59.732 66.667 0.00 0.00 0.00 5.34
204 215 1.258445 CCTCCTTACCCACACGCTCT 61.258 60.000 0.00 0.00 0.00 4.09
205 216 0.108615 CTCCTTACCCACACGCTCTG 60.109 60.000 0.00 0.00 0.00 3.35
206 217 0.541063 TCCTTACCCACACGCTCTGA 60.541 55.000 0.00 0.00 0.00 3.27
207 218 0.537188 CCTTACCCACACGCTCTGAT 59.463 55.000 0.00 0.00 0.00 2.90
208 219 1.066143 CCTTACCCACACGCTCTGATT 60.066 52.381 0.00 0.00 0.00 2.57
209 220 2.002586 CTTACCCACACGCTCTGATTG 58.997 52.381 0.00 0.00 0.00 2.67
210 221 0.249120 TACCCACACGCTCTGATTGG 59.751 55.000 0.00 0.00 0.00 3.16
211 222 1.003355 CCCACACGCTCTGATTGGT 60.003 57.895 0.00 0.00 0.00 3.67
212 223 1.021390 CCCACACGCTCTGATTGGTC 61.021 60.000 0.00 0.00 0.00 4.02
213 224 1.354337 CCACACGCTCTGATTGGTCG 61.354 60.000 0.00 0.00 0.00 4.79
214 225 0.388520 CACACGCTCTGATTGGTCGA 60.389 55.000 0.00 0.00 0.00 4.20
215 226 0.388649 ACACGCTCTGATTGGTCGAC 60.389 55.000 7.13 7.13 0.00 4.20
216 227 1.078759 CACGCTCTGATTGGTCGACC 61.079 60.000 28.17 28.17 0.00 4.79
222 233 2.181021 GATTGGTCGACCGACGCT 59.819 61.111 27.04 11.61 45.41 5.07
239 250 1.383523 GCTGAGCACCTCCCAATAAC 58.616 55.000 0.00 0.00 0.00 1.89
246 257 3.322254 AGCACCTCCCAATAACTATCTCG 59.678 47.826 0.00 0.00 0.00 4.04
247 258 3.555168 GCACCTCCCAATAACTATCTCGG 60.555 52.174 0.00 0.00 0.00 4.63
253 264 4.058817 CCCAATAACTATCTCGGTGCTTC 58.941 47.826 0.00 0.00 0.00 3.86
279 290 0.476771 AGGGGAGGCGTGAAGAAAAA 59.523 50.000 0.00 0.00 0.00 1.94
280 291 1.075536 AGGGGAGGCGTGAAGAAAAAT 59.924 47.619 0.00 0.00 0.00 1.82
308 319 9.699410 TCACATGAAAAATTATATTCCCTCTGT 57.301 29.630 0.00 0.00 0.00 3.41
313 324 9.753674 TGAAAAATTATATTCCCTCTGTTCACT 57.246 29.630 0.00 0.00 0.00 3.41
346 357 7.719871 AGTAGTTTAGGACAGCTAAGATTGA 57.280 36.000 0.00 0.00 0.00 2.57
347 358 8.135382 AGTAGTTTAGGACAGCTAAGATTGAA 57.865 34.615 0.00 0.00 0.00 2.69
348 359 8.035984 AGTAGTTTAGGACAGCTAAGATTGAAC 58.964 37.037 0.00 0.00 0.00 3.18
349 360 7.010339 AGTTTAGGACAGCTAAGATTGAACT 57.990 36.000 0.00 0.00 0.00 3.01
350 361 6.876257 AGTTTAGGACAGCTAAGATTGAACTG 59.124 38.462 0.00 0.00 0.00 3.16
351 362 4.899352 AGGACAGCTAAGATTGAACTGT 57.101 40.909 0.00 0.00 43.93 3.55
352 363 5.234466 AGGACAGCTAAGATTGAACTGTT 57.766 39.130 0.00 0.00 41.45 3.16
353 364 5.625150 AGGACAGCTAAGATTGAACTGTTT 58.375 37.500 0.00 0.00 41.45 2.83
354 365 6.064717 AGGACAGCTAAGATTGAACTGTTTT 58.935 36.000 0.00 0.00 41.45 2.43
355 366 7.224297 AGGACAGCTAAGATTGAACTGTTTTA 58.776 34.615 0.00 0.00 41.45 1.52
356 367 7.389053 AGGACAGCTAAGATTGAACTGTTTTAG 59.611 37.037 0.00 0.00 41.45 1.85
357 368 7.387948 GGACAGCTAAGATTGAACTGTTTTAGA 59.612 37.037 11.27 0.00 41.45 2.10
358 369 8.854614 ACAGCTAAGATTGAACTGTTTTAGAT 57.145 30.769 11.27 4.23 38.38 1.98
359 370 8.725148 ACAGCTAAGATTGAACTGTTTTAGATG 58.275 33.333 18.34 18.34 38.38 2.90
360 371 7.695618 CAGCTAAGATTGAACTGTTTTAGATGC 59.304 37.037 11.78 4.27 30.85 3.91
361 372 7.609532 AGCTAAGATTGAACTGTTTTAGATGCT 59.390 33.333 11.27 5.53 0.00 3.79
362 373 8.883731 GCTAAGATTGAACTGTTTTAGATGCTA 58.116 33.333 11.27 0.00 0.00 3.49
365 376 8.798859 AGATTGAACTGTTTTAGATGCTATGT 57.201 30.769 0.00 0.00 0.00 2.29
366 377 9.236006 AGATTGAACTGTTTTAGATGCTATGTT 57.764 29.630 0.00 0.00 0.00 2.71
381 392 9.686683 AGATGCTATGTTAAATGTCTAAAAGGT 57.313 29.630 0.00 0.00 0.00 3.50
382 393 9.937175 GATGCTATGTTAAATGTCTAAAAGGTC 57.063 33.333 0.00 0.00 0.00 3.85
383 394 9.686683 ATGCTATGTTAAATGTCTAAAAGGTCT 57.313 29.630 0.00 0.00 0.00 3.85
384 395 9.515226 TGCTATGTTAAATGTCTAAAAGGTCTT 57.485 29.630 0.00 0.00 0.00 3.01
394 405 8.974060 ATGTCTAAAAGGTCTTACAAAAGTGA 57.026 30.769 0.00 0.00 34.13 3.41
395 406 8.795842 TGTCTAAAAGGTCTTACAAAAGTGAA 57.204 30.769 0.00 0.00 34.13 3.18
396 407 8.671028 TGTCTAAAAGGTCTTACAAAAGTGAAC 58.329 33.333 0.00 0.00 34.13 3.18
397 408 7.849515 GTCTAAAAGGTCTTACAAAAGTGAACG 59.150 37.037 0.00 0.00 34.13 3.95
398 409 5.494632 AAAGGTCTTACAAAAGTGAACGG 57.505 39.130 0.00 0.00 34.13 4.44
399 410 4.411256 AGGTCTTACAAAAGTGAACGGA 57.589 40.909 0.00 0.00 34.13 4.69
400 411 4.377897 AGGTCTTACAAAAGTGAACGGAG 58.622 43.478 0.00 0.00 34.13 4.63
401 412 3.497262 GGTCTTACAAAAGTGAACGGAGG 59.503 47.826 0.00 0.00 34.13 4.30
402 413 3.497262 GTCTTACAAAAGTGAACGGAGGG 59.503 47.826 0.00 0.00 34.13 4.30
403 414 3.388676 TCTTACAAAAGTGAACGGAGGGA 59.611 43.478 0.00 0.00 34.13 4.20
410 421 2.606378 AGTGAACGGAGGGAGTACTTT 58.394 47.619 0.00 0.00 0.00 2.66
419 430 6.301486 ACGGAGGGAGTACTTTTGTTTAATT 58.699 36.000 0.00 0.00 0.00 1.40
422 433 7.605309 CGGAGGGAGTACTTTTGTTTAATTACT 59.395 37.037 0.00 0.00 0.00 2.24
423 434 8.727910 GGAGGGAGTACTTTTGTTTAATTACTG 58.272 37.037 0.00 0.00 0.00 2.74
455 466 8.833231 TTTCACTAAGAAAACTGATCCTGTAG 57.167 34.615 0.00 0.00 43.00 2.74
460 471 5.669164 AGAAAACTGATCCTGTAGAGACC 57.331 43.478 0.00 0.00 0.00 3.85
474 485 2.669569 GACCAGTGGTGCGCATGT 60.670 61.111 22.50 4.25 35.25 3.21
477 488 2.042259 CCAGTGGTGCGCATGTCAT 61.042 57.895 15.91 0.00 0.00 3.06
478 489 1.426621 CAGTGGTGCGCATGTCATC 59.573 57.895 15.91 0.00 0.00 2.92
479 490 1.003476 AGTGGTGCGCATGTCATCA 60.003 52.632 15.91 2.82 0.00 3.07
480 491 0.606130 AGTGGTGCGCATGTCATCAA 60.606 50.000 15.91 0.00 0.00 2.57
481 492 0.179181 GTGGTGCGCATGTCATCAAG 60.179 55.000 15.91 0.00 0.00 3.02
482 493 0.321475 TGGTGCGCATGTCATCAAGA 60.321 50.000 15.91 0.00 0.00 3.02
497 508 4.152223 TCATCAAGACTTAACGTGCATGTG 59.848 41.667 13.39 2.57 0.00 3.21
535 546 2.090524 GCAAAGGCGTGAATGCAGC 61.091 57.895 0.00 0.00 38.63 5.25
536 547 1.286570 CAAAGGCGTGAATGCAGCA 59.713 52.632 0.00 0.00 36.28 4.41
537 548 0.731514 CAAAGGCGTGAATGCAGCAG 60.732 55.000 0.00 0.00 36.28 4.24
578 589 3.463048 AATGCATTCCCTTCCTTCACT 57.537 42.857 5.99 0.00 0.00 3.41
582 593 1.555075 CATTCCCTTCCTTCACTCGGA 59.445 52.381 0.00 0.00 0.00 4.55
586 597 2.642807 TCCCTTCCTTCACTCGGAATTT 59.357 45.455 0.00 0.00 39.64 1.82
587 598 3.841845 TCCCTTCCTTCACTCGGAATTTA 59.158 43.478 0.00 0.00 39.64 1.40
671 699 4.164981 AGTATATCAAAGGCCATACCGGA 58.835 43.478 9.46 0.00 46.52 5.14
698 733 7.040409 ACAGCTTTGTTGGGAAGTTAAGATAAG 60.040 37.037 0.00 0.00 0.00 1.73
707 742 9.939802 TTGGGAAGTTAAGATAAGAAACTACTC 57.060 33.333 0.00 0.00 33.24 2.59
728 764 2.880890 CCTAAGTATCCATTGCTGCACC 59.119 50.000 0.00 0.00 0.00 5.01
746 782 3.941483 GCACCACAAGTAGCAACATATCT 59.059 43.478 0.00 0.00 0.00 1.98
769 805 6.258947 TCTGAGTACAGATTAGTCACGATCAG 59.741 42.308 0.00 0.00 46.55 2.90
771 807 4.884744 AGTACAGATTAGTCACGATCAGCT 59.115 41.667 0.00 0.00 0.00 4.24
772 808 4.727507 ACAGATTAGTCACGATCAGCTT 57.272 40.909 0.00 0.00 0.00 3.74
773 809 5.078411 ACAGATTAGTCACGATCAGCTTT 57.922 39.130 0.00 0.00 0.00 3.51
774 810 6.208988 ACAGATTAGTCACGATCAGCTTTA 57.791 37.500 0.00 0.00 0.00 1.85
776 812 7.941919 ACAGATTAGTCACGATCAGCTTTATA 58.058 34.615 0.00 0.00 0.00 0.98
777 813 8.580720 ACAGATTAGTCACGATCAGCTTTATAT 58.419 33.333 0.00 0.00 0.00 0.86
824 869 4.887615 TGGGACAAACATGCGTGA 57.112 50.000 14.17 0.00 31.92 4.35
849 894 2.002586 GCAGCACATGTGTACCAGTAG 58.997 52.381 26.01 9.07 0.00 2.57
878 1003 4.697352 CACTCACATTAGAGAAAACCCCAG 59.303 45.833 0.00 0.00 38.98 4.45
904 1089 2.091098 TATATACACGGCCACACCCT 57.909 50.000 2.24 0.00 33.26 4.34
938 1129 1.897225 CTCCTGCCACTCTCCACTGG 61.897 65.000 0.00 0.00 0.00 4.00
941 1132 2.262915 GCCACTCTCCACTGGTCG 59.737 66.667 0.00 0.00 0.00 4.79
942 1133 2.973899 CCACTCTCCACTGGTCGG 59.026 66.667 0.00 0.00 0.00 4.79
943 1134 1.908793 CCACTCTCCACTGGTCGGT 60.909 63.158 0.00 0.00 0.00 4.69
945 1136 1.606889 ACTCTCCACTGGTCGGTCC 60.607 63.158 0.00 0.00 0.00 4.46
946 1137 1.304547 CTCTCCACTGGTCGGTCCT 60.305 63.158 0.00 0.00 37.07 3.85
947 1138 1.304217 TCTCCACTGGTCGGTCCTC 60.304 63.158 0.00 0.00 37.07 3.71
948 1139 2.283676 TCCACTGGTCGGTCCTCC 60.284 66.667 0.00 0.00 37.07 4.30
949 1140 2.283966 CCACTGGTCGGTCCTCCT 60.284 66.667 2.42 0.00 37.07 3.69
950 1141 1.000019 CCACTGGTCGGTCCTCCTA 60.000 63.158 2.42 0.00 37.07 2.94
951 1142 1.321074 CCACTGGTCGGTCCTCCTAC 61.321 65.000 2.42 0.00 37.07 3.18
952 1143 1.378250 ACTGGTCGGTCCTCCTACG 60.378 63.158 2.42 0.00 37.07 3.51
953 1144 1.378250 CTGGTCGGTCCTCCTACGT 60.378 63.158 0.00 0.00 37.07 3.57
954 1145 0.107508 CTGGTCGGTCCTCCTACGTA 60.108 60.000 0.00 0.00 37.07 3.57
963 1154 3.244044 GGTCCTCCTACGTAGTACGATCT 60.244 52.174 28.47 9.50 46.05 2.75
966 1157 3.989167 CCTCCTACGTAGTACGATCTCAG 59.011 52.174 28.47 15.52 46.05 3.35
967 1158 4.261952 CCTCCTACGTAGTACGATCTCAGA 60.262 50.000 28.47 13.93 46.05 3.27
968 1159 4.615949 TCCTACGTAGTACGATCTCAGAC 58.384 47.826 28.47 0.00 46.05 3.51
969 1160 4.340666 TCCTACGTAGTACGATCTCAGACT 59.659 45.833 28.47 5.84 46.05 3.24
970 1161 4.681025 CCTACGTAGTACGATCTCAGACTC 59.319 50.000 28.47 0.00 46.05 3.36
971 1162 3.114809 ACGTAGTACGATCTCAGACTCG 58.885 50.000 28.47 5.32 46.05 4.18
1077 1268 2.581354 CTGCTCTTCCAGGTCCCG 59.419 66.667 0.00 0.00 0.00 5.14
1165 1356 1.609072 TCATCTACTTCGCCCTCATCG 59.391 52.381 0.00 0.00 0.00 3.84
1211 1402 1.542328 CCACGTCATCCTTGGTTGACA 60.542 52.381 22.85 0.00 41.85 3.58
1212 1403 1.800586 CACGTCATCCTTGGTTGACAG 59.199 52.381 22.85 18.49 41.85 3.51
1235 1430 3.723348 GCAGACGCCGGAAACCAC 61.723 66.667 5.05 0.00 0.00 4.16
1238 1433 2.280592 GACGCCGGAAACCACAGT 60.281 61.111 5.05 0.00 0.00 3.55
1241 1436 1.008995 CGCCGGAAACCACAGTTTG 60.009 57.895 5.05 0.00 46.25 2.93
1324 1531 5.533903 TCTTAACACGAACTAGAGGAACAGT 59.466 40.000 0.00 0.00 0.00 3.55
1336 1543 3.819877 GAACAGTCGTGGCCCGGTT 62.820 63.158 12.77 9.33 37.11 4.44
1364 1571 2.626840 TGTTTGGCCTTTTCTTGTTGC 58.373 42.857 3.32 0.00 0.00 4.17
1365 1572 2.027745 TGTTTGGCCTTTTCTTGTTGCA 60.028 40.909 3.32 0.00 0.00 4.08
1366 1573 2.600470 TTGGCCTTTTCTTGTTGCAG 57.400 45.000 3.32 0.00 0.00 4.41
1367 1574 0.752054 TGGCCTTTTCTTGTTGCAGG 59.248 50.000 3.32 0.00 0.00 4.85
1410 1619 1.534595 GCATCCTTGCTTGTAATGGCG 60.535 52.381 0.00 0.00 45.77 5.69
1411 1620 1.745087 CATCCTTGCTTGTAATGGCGT 59.255 47.619 0.00 0.00 0.00 5.68
1412 1621 2.772077 TCCTTGCTTGTAATGGCGTA 57.228 45.000 0.00 0.00 0.00 4.42
1432 1641 6.797033 GGCGTAGTAATTGATATTGCAACATC 59.203 38.462 10.85 10.85 0.00 3.06
1433 1642 7.351981 GCGTAGTAATTGATATTGCAACATCA 58.648 34.615 16.29 16.29 0.00 3.07
1441 1650 7.583860 TTGATATTGCAACATCATTTGTGTG 57.416 32.000 20.45 0.00 38.99 3.82
1447 1656 4.142204 TGCAACATCATTTGTGTGACTTGT 60.142 37.500 0.00 0.00 38.99 3.16
1448 1657 4.207635 GCAACATCATTTGTGTGACTTGTG 59.792 41.667 0.00 0.00 38.99 3.33
1449 1658 3.968649 ACATCATTTGTGTGACTTGTGC 58.031 40.909 0.00 0.00 37.11 4.57
1450 1659 3.243501 ACATCATTTGTGTGACTTGTGCC 60.244 43.478 0.00 0.00 37.11 5.01
1451 1660 1.680735 TCATTTGTGTGACTTGTGCCC 59.319 47.619 0.00 0.00 0.00 5.36
1452 1661 1.408340 CATTTGTGTGACTTGTGCCCA 59.592 47.619 0.00 0.00 0.00 5.36
1453 1662 1.550327 TTTGTGTGACTTGTGCCCAA 58.450 45.000 0.00 0.00 0.00 4.12
1454 1663 1.774110 TTGTGTGACTTGTGCCCAAT 58.226 45.000 0.00 0.00 0.00 3.16
1455 1664 1.774110 TGTGTGACTTGTGCCCAATT 58.226 45.000 0.00 0.00 0.00 2.32
1456 1665 2.106566 TGTGTGACTTGTGCCCAATTT 58.893 42.857 0.00 0.00 0.00 1.82
1457 1666 2.499289 TGTGTGACTTGTGCCCAATTTT 59.501 40.909 0.00 0.00 0.00 1.82
1458 1667 3.055530 TGTGTGACTTGTGCCCAATTTTT 60.056 39.130 0.00 0.00 0.00 1.94
1479 1688 3.505835 TTTTTGCGAGGGGTGACTT 57.494 47.368 0.00 0.00 0.00 3.01
1480 1689 1.028905 TTTTTGCGAGGGGTGACTTG 58.971 50.000 0.00 0.00 0.00 3.16
1488 1697 1.282157 GAGGGGTGACTTGTGCCTAAT 59.718 52.381 0.00 0.00 0.00 1.73
1499 1708 8.673711 GTGACTTGTGCCTAATTGATATTACAA 58.326 33.333 0.00 0.00 0.00 2.41
1521 1730 2.124151 GCAATCCGGAGCACCCAT 60.124 61.111 11.34 0.00 34.14 4.00
1523 1732 1.322538 GCAATCCGGAGCACCCATTT 61.323 55.000 11.34 0.00 34.14 2.32
1528 1737 0.609131 CCGGAGCACCCATTTTCTGT 60.609 55.000 0.00 0.00 34.14 3.41
1531 1740 2.355756 CGGAGCACCCATTTTCTGTATG 59.644 50.000 0.00 0.00 34.14 2.39
1539 1748 3.956199 CCCATTTTCTGTATGTGCCATCT 59.044 43.478 0.00 0.00 0.00 2.90
1541 1750 4.641541 CCATTTTCTGTATGTGCCATCTGA 59.358 41.667 0.00 0.00 0.00 3.27
1546 1755 1.908619 TGTATGTGCCATCTGACACCT 59.091 47.619 0.00 0.00 35.90 4.00
1566 1775 4.960469 ACCTAGTCCAGTTCGATATTTCCA 59.040 41.667 0.00 0.00 0.00 3.53
1568 1777 5.986135 CCTAGTCCAGTTCGATATTTCCAAG 59.014 44.000 0.00 0.00 0.00 3.61
1569 1778 4.192317 AGTCCAGTTCGATATTTCCAAGC 58.808 43.478 0.00 0.00 0.00 4.01
1614 1823 6.875726 GTGATACTGTATGTCATGCCATGTAT 59.124 38.462 4.79 0.00 30.22 2.29
1633 1842 7.390440 CCATGTATTTCAAACCTTGTAGACTCA 59.610 37.037 0.00 0.00 0.00 3.41
1743 2316 1.030488 CGAACTCGCCTACTCCCTGA 61.030 60.000 0.00 0.00 0.00 3.86
1848 2422 0.386226 GCCTGTCGCTATCTAGTCGC 60.386 60.000 0.00 0.00 0.00 5.19
2091 3432 3.639538 TGTGTTGTCTTCTTCGTAGCTC 58.360 45.455 0.00 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.412594 TGTCAATTAAAGCAGTGGAGATCAC 59.587 40.000 0.00 0.00 46.39 3.06
1 2 5.559770 TGTCAATTAAAGCAGTGGAGATCA 58.440 37.500 0.00 0.00 0.00 2.92
2 3 6.317857 GTTGTCAATTAAAGCAGTGGAGATC 58.682 40.000 0.00 0.00 0.00 2.75
3 4 5.106555 CGTTGTCAATTAAAGCAGTGGAGAT 60.107 40.000 0.00 0.00 0.00 2.75
5 6 4.466828 CGTTGTCAATTAAAGCAGTGGAG 58.533 43.478 0.00 0.00 0.00 3.86
6 7 3.304391 GCGTTGTCAATTAAAGCAGTGGA 60.304 43.478 0.00 0.00 33.62 4.02
7 8 2.979813 GCGTTGTCAATTAAAGCAGTGG 59.020 45.455 0.00 0.00 33.62 4.00
8 9 2.979813 GGCGTTGTCAATTAAAGCAGTG 59.020 45.455 0.00 0.00 34.82 3.66
9 10 2.030274 GGGCGTTGTCAATTAAAGCAGT 60.030 45.455 0.00 0.00 34.82 4.40
10 11 2.030363 TGGGCGTTGTCAATTAAAGCAG 60.030 45.455 0.00 0.00 34.82 4.24
11 12 1.957177 TGGGCGTTGTCAATTAAAGCA 59.043 42.857 0.00 0.00 34.82 3.91
12 13 2.595386 CTGGGCGTTGTCAATTAAAGC 58.405 47.619 0.00 0.00 32.83 3.51
13 14 2.595386 GCTGGGCGTTGTCAATTAAAG 58.405 47.619 0.00 0.00 0.00 1.85
14 15 1.271102 GGCTGGGCGTTGTCAATTAAA 59.729 47.619 0.00 0.00 0.00 1.52
15 16 0.885196 GGCTGGGCGTTGTCAATTAA 59.115 50.000 0.00 0.00 0.00 1.40
16 17 1.302383 CGGCTGGGCGTTGTCAATTA 61.302 55.000 8.37 0.00 0.00 1.40
17 18 2.625823 CGGCTGGGCGTTGTCAATT 61.626 57.895 8.37 0.00 0.00 2.32
18 19 3.055719 CGGCTGGGCGTTGTCAAT 61.056 61.111 8.37 0.00 0.00 2.57
19 20 4.555709 ACGGCTGGGCGTTGTCAA 62.556 61.111 16.05 0.00 0.00 3.18
20 21 4.555709 AACGGCTGGGCGTTGTCA 62.556 61.111 28.48 0.00 0.00 3.58
21 22 3.284449 AAACGGCTGGGCGTTGTC 61.284 61.111 29.38 0.00 0.00 3.18
22 23 3.591835 CAAACGGCTGGGCGTTGT 61.592 61.111 29.38 18.63 0.00 3.32
23 24 4.341502 CCAAACGGCTGGGCGTTG 62.342 66.667 29.38 22.52 32.32 4.10
24 25 4.572571 TCCAAACGGCTGGGCGTT 62.573 61.111 24.93 24.93 37.06 4.84
25 26 4.572571 TTCCAAACGGCTGGGCGT 62.573 61.111 16.05 16.05 37.06 5.68
26 27 4.038080 GTTCCAAACGGCTGGGCG 62.038 66.667 14.67 14.67 37.06 6.13
27 28 2.275380 ATGTTCCAAACGGCTGGGC 61.275 57.895 0.00 0.79 37.06 5.36
28 29 0.893270 TCATGTTCCAAACGGCTGGG 60.893 55.000 0.00 0.00 37.06 4.45
29 30 0.523072 CTCATGTTCCAAACGGCTGG 59.477 55.000 0.00 0.00 37.87 4.85
30 31 0.109597 GCTCATGTTCCAAACGGCTG 60.110 55.000 0.00 0.00 0.00 4.85
31 32 1.244019 GGCTCATGTTCCAAACGGCT 61.244 55.000 0.00 0.00 0.00 5.52
32 33 1.212751 GGCTCATGTTCCAAACGGC 59.787 57.895 0.00 0.00 0.00 5.68
33 34 1.234615 ACGGCTCATGTTCCAAACGG 61.235 55.000 0.00 0.00 0.00 4.44
34 35 0.110238 CACGGCTCATGTTCCAAACG 60.110 55.000 0.00 0.00 0.00 3.60
35 36 0.387239 GCACGGCTCATGTTCCAAAC 60.387 55.000 0.00 0.00 0.00 2.93
36 37 0.537143 AGCACGGCTCATGTTCCAAA 60.537 50.000 0.00 0.00 30.62 3.28
37 38 1.073025 AGCACGGCTCATGTTCCAA 59.927 52.632 0.00 0.00 30.62 3.53
38 39 1.672030 CAGCACGGCTCATGTTCCA 60.672 57.895 0.00 0.00 36.40 3.53
39 40 3.044059 GCAGCACGGCTCATGTTCC 62.044 63.158 0.00 0.00 36.40 3.62
40 41 2.482374 GCAGCACGGCTCATGTTC 59.518 61.111 0.00 0.00 36.40 3.18
41 42 3.425713 CGCAGCACGGCTCATGTT 61.426 61.111 0.00 0.00 36.40 2.71
42 43 4.377708 TCGCAGCACGGCTCATGT 62.378 61.111 0.00 0.00 43.89 3.21
43 44 3.857854 GTCGCAGCACGGCTCATG 61.858 66.667 0.00 0.00 45.03 3.07
50 51 4.680237 TGGAAGGGTCGCAGCACG 62.680 66.667 0.00 0.00 45.62 5.34
51 52 1.452145 TTTTGGAAGGGTCGCAGCAC 61.452 55.000 0.00 0.00 0.00 4.40
52 53 0.753479 TTTTTGGAAGGGTCGCAGCA 60.753 50.000 0.00 0.00 0.00 4.41
53 54 2.037871 TTTTTGGAAGGGTCGCAGC 58.962 52.632 0.00 0.00 0.00 5.25
88 89 6.709846 AGTTTCAGAGAAAGTTGGATTCAGAG 59.290 38.462 0.00 0.00 0.00 3.35
120 121 5.830991 ACAGAGTTGTGACTTAGAGAGAGTT 59.169 40.000 0.00 0.00 35.88 3.01
128 129 4.989168 GGGTACAACAGAGTTGTGACTTAG 59.011 45.833 21.89 0.00 37.67 2.18
129 130 4.406326 TGGGTACAACAGAGTTGTGACTTA 59.594 41.667 21.89 2.63 37.67 2.24
131 132 2.769663 TGGGTACAACAGAGTTGTGACT 59.230 45.455 21.89 1.66 37.67 3.41
132 133 2.870411 GTGGGTACAACAGAGTTGTGAC 59.130 50.000 21.89 14.90 37.67 3.67
133 134 2.769663 AGTGGGTACAACAGAGTTGTGA 59.230 45.455 21.89 6.86 37.67 3.58
140 141 3.157881 CAGAGAGAGTGGGTACAACAGA 58.842 50.000 0.00 0.00 0.00 3.41
142 143 2.891580 GTCAGAGAGAGTGGGTACAACA 59.108 50.000 0.00 0.00 0.00 3.33
143 144 2.231721 GGTCAGAGAGAGTGGGTACAAC 59.768 54.545 0.00 0.00 0.00 3.32
144 145 2.526432 GGTCAGAGAGAGTGGGTACAA 58.474 52.381 0.00 0.00 0.00 2.41
163 164 2.037136 CGCCAAACTGCAGAGAGGG 61.037 63.158 23.35 16.37 0.00 4.30
164 165 1.004560 TCGCCAAACTGCAGAGAGG 60.005 57.895 23.35 18.48 0.00 3.69
174 185 0.675837 GTAAGGAGGGGTCGCCAAAC 60.676 60.000 8.89 0.00 35.12 2.93
176 187 2.295602 GGTAAGGAGGGGTCGCCAA 61.296 63.158 8.89 0.00 35.12 4.52
187 198 0.541063 TCAGAGCGTGTGGGTAAGGA 60.541 55.000 0.00 0.00 0.00 3.36
201 212 0.523546 CGTCGGTCGACCAATCAGAG 60.524 60.000 32.80 15.53 41.76 3.35
204 215 2.126228 GCGTCGGTCGACCAATCA 60.126 61.111 32.80 11.67 41.76 2.57
205 216 2.158959 CAGCGTCGGTCGACCAATC 61.159 63.158 32.80 20.20 41.76 2.67
206 217 2.126071 CAGCGTCGGTCGACCAAT 60.126 61.111 32.80 11.42 41.76 3.16
207 218 3.263503 CTCAGCGTCGGTCGACCAA 62.264 63.158 32.80 14.43 41.76 3.67
208 219 3.733960 CTCAGCGTCGGTCGACCA 61.734 66.667 32.80 17.85 41.76 4.02
210 221 4.400109 TGCTCAGCGTCGGTCGAC 62.400 66.667 7.13 7.13 42.86 4.20
211 222 4.400109 GTGCTCAGCGTCGGTCGA 62.400 66.667 0.00 0.00 42.86 4.20
213 224 3.973267 GAGGTGCTCAGCGTCGGTC 62.973 68.421 0.00 0.00 0.00 4.79
214 225 4.057428 GAGGTGCTCAGCGTCGGT 62.057 66.667 0.00 0.00 0.00 4.69
215 226 4.803426 GGAGGTGCTCAGCGTCGG 62.803 72.222 0.00 0.00 31.08 4.79
216 227 4.803426 GGGAGGTGCTCAGCGTCG 62.803 72.222 0.00 0.00 31.08 5.12
222 233 4.298626 AGATAGTTATTGGGAGGTGCTCA 58.701 43.478 0.00 0.00 31.08 4.26
246 257 2.361230 CCCTTTCCCGGAAGCACC 60.361 66.667 0.73 0.00 0.00 5.01
247 258 2.361230 CCCCTTTCCCGGAAGCAC 60.361 66.667 0.73 0.00 0.00 4.40
320 331 9.251440 TCAATCTTAGCTGTCCTAAACTACTTA 57.749 33.333 0.00 0.00 35.68 2.24
321 332 8.135382 TCAATCTTAGCTGTCCTAAACTACTT 57.865 34.615 0.00 0.00 35.68 2.24
322 333 7.719871 TCAATCTTAGCTGTCCTAAACTACT 57.280 36.000 0.00 0.00 35.68 2.57
323 334 8.035984 AGTTCAATCTTAGCTGTCCTAAACTAC 58.964 37.037 0.00 0.00 35.68 2.73
324 335 8.035394 CAGTTCAATCTTAGCTGTCCTAAACTA 58.965 37.037 0.00 0.00 35.68 2.24
325 336 6.876257 CAGTTCAATCTTAGCTGTCCTAAACT 59.124 38.462 0.00 0.00 35.68 2.66
326 337 6.651225 ACAGTTCAATCTTAGCTGTCCTAAAC 59.349 38.462 0.00 0.00 35.78 2.01
327 338 6.769512 ACAGTTCAATCTTAGCTGTCCTAAA 58.230 36.000 0.00 0.00 35.78 1.85
328 339 6.360370 ACAGTTCAATCTTAGCTGTCCTAA 57.640 37.500 0.00 0.00 35.78 2.69
329 340 6.360370 AACAGTTCAATCTTAGCTGTCCTA 57.640 37.500 0.00 0.00 39.19 2.94
330 341 4.899352 ACAGTTCAATCTTAGCTGTCCT 57.101 40.909 0.00 0.00 35.78 3.85
331 342 5.948992 AAACAGTTCAATCTTAGCTGTCC 57.051 39.130 0.00 0.00 39.19 4.02
332 343 8.311650 TCTAAAACAGTTCAATCTTAGCTGTC 57.688 34.615 0.00 0.00 39.19 3.51
333 344 8.725148 CATCTAAAACAGTTCAATCTTAGCTGT 58.275 33.333 0.00 0.00 41.51 4.40
334 345 7.695618 GCATCTAAAACAGTTCAATCTTAGCTG 59.304 37.037 0.00 0.00 0.00 4.24
335 346 7.609532 AGCATCTAAAACAGTTCAATCTTAGCT 59.390 33.333 0.00 0.00 0.00 3.32
336 347 7.756558 AGCATCTAAAACAGTTCAATCTTAGC 58.243 34.615 0.00 0.00 0.00 3.09
339 350 9.236006 ACATAGCATCTAAAACAGTTCAATCTT 57.764 29.630 0.00 0.00 0.00 2.40
340 351 8.798859 ACATAGCATCTAAAACAGTTCAATCT 57.201 30.769 0.00 0.00 0.00 2.40
355 366 9.686683 ACCTTTTAGACATTTAACATAGCATCT 57.313 29.630 0.00 0.00 0.00 2.90
356 367 9.937175 GACCTTTTAGACATTTAACATAGCATC 57.063 33.333 0.00 0.00 0.00 3.91
357 368 9.686683 AGACCTTTTAGACATTTAACATAGCAT 57.313 29.630 0.00 0.00 0.00 3.79
358 369 9.515226 AAGACCTTTTAGACATTTAACATAGCA 57.485 29.630 0.00 0.00 0.00 3.49
368 379 9.403583 TCACTTTTGTAAGACCTTTTAGACATT 57.596 29.630 0.00 0.00 35.30 2.71
369 380 8.974060 TCACTTTTGTAAGACCTTTTAGACAT 57.026 30.769 0.00 0.00 35.30 3.06
370 381 8.671028 GTTCACTTTTGTAAGACCTTTTAGACA 58.329 33.333 0.00 0.00 35.30 3.41
371 382 7.849515 CGTTCACTTTTGTAAGACCTTTTAGAC 59.150 37.037 0.00 0.00 35.30 2.59
372 383 7.011669 CCGTTCACTTTTGTAAGACCTTTTAGA 59.988 37.037 0.00 0.00 35.30 2.10
373 384 7.011669 TCCGTTCACTTTTGTAAGACCTTTTAG 59.988 37.037 0.00 0.00 35.30 1.85
374 385 6.822676 TCCGTTCACTTTTGTAAGACCTTTTA 59.177 34.615 0.00 0.00 35.30 1.52
375 386 5.648960 TCCGTTCACTTTTGTAAGACCTTTT 59.351 36.000 0.00 0.00 35.30 2.27
376 387 5.187687 TCCGTTCACTTTTGTAAGACCTTT 58.812 37.500 0.00 0.00 35.30 3.11
377 388 4.773013 TCCGTTCACTTTTGTAAGACCTT 58.227 39.130 0.00 0.00 35.30 3.50
378 389 4.377897 CTCCGTTCACTTTTGTAAGACCT 58.622 43.478 0.00 0.00 35.30 3.85
379 390 3.497262 CCTCCGTTCACTTTTGTAAGACC 59.503 47.826 0.00 0.00 35.30 3.85
380 391 3.497262 CCCTCCGTTCACTTTTGTAAGAC 59.503 47.826 0.00 0.00 35.30 3.01
381 392 3.388676 TCCCTCCGTTCACTTTTGTAAGA 59.611 43.478 0.00 0.00 35.30 2.10
382 393 3.735591 TCCCTCCGTTCACTTTTGTAAG 58.264 45.455 0.00 0.00 37.40 2.34
383 394 3.135167 ACTCCCTCCGTTCACTTTTGTAA 59.865 43.478 0.00 0.00 0.00 2.41
384 395 2.701951 ACTCCCTCCGTTCACTTTTGTA 59.298 45.455 0.00 0.00 0.00 2.41
385 396 1.489230 ACTCCCTCCGTTCACTTTTGT 59.511 47.619 0.00 0.00 0.00 2.83
386 397 2.256117 ACTCCCTCCGTTCACTTTTG 57.744 50.000 0.00 0.00 0.00 2.44
387 398 2.970640 AGTACTCCCTCCGTTCACTTTT 59.029 45.455 0.00 0.00 0.00 2.27
388 399 2.606378 AGTACTCCCTCCGTTCACTTT 58.394 47.619 0.00 0.00 0.00 2.66
389 400 2.305858 AGTACTCCCTCCGTTCACTT 57.694 50.000 0.00 0.00 0.00 3.16
390 401 2.305858 AAGTACTCCCTCCGTTCACT 57.694 50.000 0.00 0.00 0.00 3.41
391 402 3.064931 CAAAAGTACTCCCTCCGTTCAC 58.935 50.000 0.00 0.00 0.00 3.18
392 403 2.701951 ACAAAAGTACTCCCTCCGTTCA 59.298 45.455 0.00 0.00 0.00 3.18
393 404 3.397849 ACAAAAGTACTCCCTCCGTTC 57.602 47.619 0.00 0.00 0.00 3.95
394 405 3.851458 AACAAAAGTACTCCCTCCGTT 57.149 42.857 0.00 0.00 0.00 4.44
395 406 3.851458 AAACAAAAGTACTCCCTCCGT 57.149 42.857 0.00 0.00 0.00 4.69
396 407 6.812879 AATTAAACAAAAGTACTCCCTCCG 57.187 37.500 0.00 0.00 0.00 4.63
397 408 8.727910 CAGTAATTAAACAAAAGTACTCCCTCC 58.272 37.037 0.00 0.00 37.97 4.30
398 409 9.281371 ACAGTAATTAAACAAAAGTACTCCCTC 57.719 33.333 0.00 0.00 37.97 4.30
428 439 8.697507 ACAGGATCAGTTTTCTTAGTGAAATT 57.302 30.769 0.00 0.00 43.34 1.82
429 440 9.442047 CTACAGGATCAGTTTTCTTAGTGAAAT 57.558 33.333 0.00 0.00 43.34 2.17
432 443 7.670140 TCTCTACAGGATCAGTTTTCTTAGTGA 59.330 37.037 0.00 0.00 32.36 3.41
433 444 7.757624 GTCTCTACAGGATCAGTTTTCTTAGTG 59.242 40.741 0.00 0.00 0.00 2.74
450 461 0.109086 CGCACCACTGGTCTCTACAG 60.109 60.000 0.00 0.00 41.64 2.74
455 466 2.046892 ATGCGCACCACTGGTCTC 60.047 61.111 14.90 0.00 31.02 3.36
460 471 1.300266 TGATGACATGCGCACCACTG 61.300 55.000 14.90 10.25 0.00 3.66
474 485 4.152223 CACATGCACGTTAAGTCTTGATGA 59.848 41.667 3.71 0.00 0.00 2.92
477 488 2.223144 GCACATGCACGTTAAGTCTTGA 59.777 45.455 0.00 0.00 41.59 3.02
478 489 2.574322 GCACATGCACGTTAAGTCTTG 58.426 47.619 0.00 0.00 41.59 3.02
479 490 2.969443 GCACATGCACGTTAAGTCTT 57.031 45.000 0.00 0.00 41.59 3.01
497 508 2.665185 ACTCGGCCTCACGTTTGC 60.665 61.111 0.00 0.00 34.94 3.68
535 546 4.182693 TCGTAACTGTGAACCCATACTG 57.817 45.455 0.00 0.00 0.00 2.74
536 547 4.877378 TTCGTAACTGTGAACCCATACT 57.123 40.909 0.00 0.00 0.00 2.12
537 548 5.927954 TTTTCGTAACTGTGAACCCATAC 57.072 39.130 0.00 0.00 0.00 2.39
578 589 8.600625 CGTCTCTTTTTGATGTATAAATTCCGA 58.399 33.333 0.00 0.00 0.00 4.55
586 597 7.546667 GGTTGTACCGTCTCTTTTTGATGTATA 59.453 37.037 0.00 0.00 0.00 1.47
587 598 6.370718 GGTTGTACCGTCTCTTTTTGATGTAT 59.629 38.462 0.00 0.00 0.00 2.29
698 733 7.439655 CAGCAATGGATACTTAGGAGTAGTTTC 59.560 40.741 0.00 0.00 41.45 2.78
707 742 2.880890 GGTGCAGCAATGGATACTTAGG 59.119 50.000 11.86 0.00 37.61 2.69
728 764 7.035612 TGTACTCAGATATGTTGCTACTTGTG 58.964 38.462 0.00 0.00 0.00 3.33
746 782 5.220873 GCTGATCGTGACTAATCTGTACTCA 60.221 44.000 0.00 0.00 0.00 3.41
778 814 9.938280 TTTAGCTACTTGTTGTTCATGTAGTAT 57.062 29.630 16.40 11.09 46.94 2.12
779 815 9.199982 GTTTAGCTACTTGTTGTTCATGTAGTA 57.800 33.333 16.40 9.08 46.94 1.82
780 816 7.931948 AGTTTAGCTACTTGTTGTTCATGTAGT 59.068 33.333 16.40 9.70 46.94 2.73
810 846 0.110056 CCAGCTCACGCATGTTTGTC 60.110 55.000 0.00 0.00 39.10 3.18
824 869 0.957395 GTACACATGTGCTGCCAGCT 60.957 55.000 25.68 6.16 42.97 4.24
849 894 6.292919 GGTTTTCTCTAATGTGAGTGTGACAC 60.293 42.308 7.83 7.83 38.55 3.67
904 1089 2.276116 GGAGTGTGAGGCCACGAGA 61.276 63.158 5.01 0.00 46.06 4.04
938 1129 2.205911 GTACTACGTAGGAGGACCGAC 58.794 57.143 25.63 0.50 41.83 4.79
941 1132 2.604046 TCGTACTACGTAGGAGGACC 57.396 55.000 23.08 4.74 43.14 4.46
942 1133 3.987220 GAGATCGTACTACGTAGGAGGAC 59.013 52.174 27.77 21.05 43.14 3.85
943 1134 3.638627 TGAGATCGTACTACGTAGGAGGA 59.361 47.826 27.48 27.48 43.14 3.71
945 1136 4.681025 GTCTGAGATCGTACTACGTAGGAG 59.319 50.000 25.63 15.84 43.14 3.69
946 1137 4.340666 AGTCTGAGATCGTACTACGTAGGA 59.659 45.833 25.63 16.07 43.14 2.94
947 1138 4.619973 AGTCTGAGATCGTACTACGTAGG 58.380 47.826 25.63 9.09 43.14 3.18
948 1139 4.379498 CGAGTCTGAGATCGTACTACGTAG 59.621 50.000 20.97 20.97 43.14 3.51
949 1140 4.286101 CGAGTCTGAGATCGTACTACGTA 58.714 47.826 8.42 0.00 43.14 3.57
950 1141 3.114809 CGAGTCTGAGATCGTACTACGT 58.885 50.000 8.42 0.00 43.14 3.57
951 1142 2.472115 CCGAGTCTGAGATCGTACTACG 59.528 54.545 1.93 1.93 44.19 3.51
952 1143 3.715495 TCCGAGTCTGAGATCGTACTAC 58.285 50.000 10.27 0.00 37.23 2.73
953 1144 3.799574 GCTCCGAGTCTGAGATCGTACTA 60.800 52.174 15.09 0.00 37.23 1.82
954 1145 2.828877 CTCCGAGTCTGAGATCGTACT 58.171 52.381 5.69 0.00 37.23 2.73
963 1154 0.315251 CACACTTGCTCCGAGTCTGA 59.685 55.000 0.00 0.00 0.00 3.27
966 1157 3.555428 GCACACTTGCTCCGAGTC 58.445 61.111 0.00 0.00 46.17 3.36
991 1182 2.060980 AGTCCGCCATGTCTCCTCC 61.061 63.158 0.00 0.00 0.00 4.30
1077 1268 0.895559 CCAGGAACCTGTTCTTGCCC 60.896 60.000 17.92 0.00 42.93 5.36
1165 1356 2.514824 GGCGAGGGTGAAGATGGC 60.515 66.667 0.00 0.00 0.00 4.40
1233 1428 9.169468 GTAGTGTACATGAAAATTCAAACTGTG 57.831 33.333 0.00 2.78 41.13 3.66
1294 1489 6.433404 TCCTCTAGTTCGTGTTAAGAGACATT 59.567 38.462 0.00 0.00 36.60 2.71
1336 1543 6.041523 ACAAGAAAAGGCCAAACAAAGCTATA 59.958 34.615 5.01 0.00 0.00 1.31
1364 1571 2.824936 TGCATTTGACAACATACCCCTG 59.175 45.455 0.00 0.00 0.00 4.45
1365 1572 3.168035 TGCATTTGACAACATACCCCT 57.832 42.857 0.00 0.00 0.00 4.79
1366 1573 3.509575 TCTTGCATTTGACAACATACCCC 59.490 43.478 0.00 0.00 0.00 4.95
1367 1574 4.782019 TCTTGCATTTGACAACATACCC 57.218 40.909 0.00 0.00 0.00 3.69
1432 1641 1.408340 TGGGCACAAGTCACACAAATG 59.592 47.619 0.00 0.00 0.00 2.32
1433 1642 1.774110 TGGGCACAAGTCACACAAAT 58.226 45.000 0.00 0.00 0.00 2.32
1461 1670 1.028905 CAAGTCACCCCTCGCAAAAA 58.971 50.000 0.00 0.00 0.00 1.94
1462 1671 0.106918 ACAAGTCACCCCTCGCAAAA 60.107 50.000 0.00 0.00 0.00 2.44
1463 1672 0.817634 CACAAGTCACCCCTCGCAAA 60.818 55.000 0.00 0.00 0.00 3.68
1464 1673 1.227823 CACAAGTCACCCCTCGCAA 60.228 57.895 0.00 0.00 0.00 4.85
1465 1674 2.425592 CACAAGTCACCCCTCGCA 59.574 61.111 0.00 0.00 0.00 5.10
1466 1675 3.050275 GCACAAGTCACCCCTCGC 61.050 66.667 0.00 0.00 0.00 5.03
1467 1676 1.541310 TAGGCACAAGTCACCCCTCG 61.541 60.000 0.00 0.00 0.00 4.63
1468 1677 0.690762 TTAGGCACAAGTCACCCCTC 59.309 55.000 0.00 0.00 0.00 4.30
1469 1678 1.372501 ATTAGGCACAAGTCACCCCT 58.627 50.000 0.00 0.00 0.00 4.79
1470 1679 1.818674 CAATTAGGCACAAGTCACCCC 59.181 52.381 0.00 0.00 0.00 4.95
1471 1680 2.790433 TCAATTAGGCACAAGTCACCC 58.210 47.619 0.00 0.00 0.00 4.61
1472 1681 6.699575 AATATCAATTAGGCACAAGTCACC 57.300 37.500 0.00 0.00 0.00 4.02
1473 1682 8.208718 TGTAATATCAATTAGGCACAAGTCAC 57.791 34.615 0.00 0.00 0.00 3.67
1474 1683 8.800370 TTGTAATATCAATTAGGCACAAGTCA 57.200 30.769 0.00 0.00 0.00 3.41
1475 1684 9.669353 CATTGTAATATCAATTAGGCACAAGTC 57.331 33.333 0.00 0.00 36.10 3.01
1476 1685 9.189156 ACATTGTAATATCAATTAGGCACAAGT 57.811 29.630 0.00 0.00 36.10 3.16
1478 1687 9.800433 CAACATTGTAATATCAATTAGGCACAA 57.200 29.630 0.00 0.00 36.10 3.33
1479 1688 7.920151 GCAACATTGTAATATCAATTAGGCACA 59.080 33.333 0.00 0.00 36.10 4.57
1480 1689 7.920151 TGCAACATTGTAATATCAATTAGGCAC 59.080 33.333 0.00 0.00 36.10 5.01
1488 1697 6.319911 TCCGGATTGCAACATTGTAATATCAA 59.680 34.615 0.00 0.00 42.30 2.57
1499 1708 1.315257 GGTGCTCCGGATTGCAACAT 61.315 55.000 24.58 0.00 45.32 2.71
1541 1750 5.163437 GGAAATATCGAACTGGACTAGGTGT 60.163 44.000 0.00 0.00 0.00 4.16
1546 1755 5.105106 TGCTTGGAAATATCGAACTGGACTA 60.105 40.000 0.00 0.00 0.00 2.59
1552 1761 9.921637 TTTATTTTTGCTTGGAAATATCGAACT 57.078 25.926 0.00 0.00 30.36 3.01
1580 1789 9.755804 CATGACATACAGTATCACACTAGATTT 57.244 33.333 0.00 0.00 34.98 2.17
1586 1795 4.162131 TGGCATGACATACAGTATCACACT 59.838 41.667 0.00 0.00 38.32 3.55
1592 1801 7.938490 TGAAATACATGGCATGACATACAGTAT 59.062 33.333 32.74 14.72 0.00 2.12
1595 1804 6.622833 TGAAATACATGGCATGACATACAG 57.377 37.500 32.74 4.59 0.00 2.74
1602 1811 5.245751 ACAAGGTTTGAAATACATGGCATGA 59.754 36.000 32.74 16.92 0.00 3.07
1603 1812 5.481105 ACAAGGTTTGAAATACATGGCATG 58.519 37.500 25.31 25.31 0.00 4.06
1614 1823 7.639113 AACAATGAGTCTACAAGGTTTGAAA 57.361 32.000 0.00 0.00 0.00 2.69
1659 1871 1.389609 ATGGATCGACCGCGTACCTT 61.390 55.000 4.92 0.00 42.61 3.50
1743 2316 2.186903 CGCCCGTAGTCATTGCCT 59.813 61.111 0.00 0.00 0.00 4.75
1848 2422 0.963355 CCCCACGTTGTAACCCATGG 60.963 60.000 4.14 4.14 0.00 3.66


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

AutoCloner maintained by Alex Coulton.