Multiple sequence alignment - TraesCS6D01G324200

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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 TraesCS6D01G324200 chr6D 100.000 5225 0 0 1 5225 430848575 430843351 0.000000e+00 9649
1 TraesCS6D01G324200 chr6D 85.803 1451 174 13 2952 4396 49182741 49184165 0.000000e+00 1509
2 TraesCS6D01G324200 chr6D 83.915 1604 203 29 2810 4396 50604941 50606506 0.000000e+00 1482
3 TraesCS6D01G324200 chr6D 84.774 1504 187 15 2986 4479 50179808 50181279 0.000000e+00 1471
4 TraesCS6D01G324200 chr6D 84.750 741 92 12 3734 4465 430751096 430750368 0.000000e+00 723
5 TraesCS6D01G324200 chr6D 89.706 272 27 1 354 625 430848126 430847856 3.870000e-91 346
6 TraesCS6D01G324200 chr6D 89.706 272 27 1 450 720 430848222 430847951 3.870000e-91 346
7 TraesCS6D01G324200 chr6D 90.960 177 15 1 353 529 430848031 430847856 2.430000e-58 237
8 TraesCS6D01G324200 chr6D 90.960 177 15 1 545 720 430848223 430848047 2.430000e-58 237
9 TraesCS6D01G324200 chr6D 75.046 549 108 21 949 1492 457269747 457269223 1.460000e-55 228
10 TraesCS6D01G324200 chr6D 93.590 78 4 1 356 433 430847932 430847856 1.190000e-21 115
11 TraesCS6D01G324200 chr6D 93.590 78 4 1 644 720 430848220 430848143 1.190000e-21 115
12 TraesCS6D01G324200 chr6B 93.593 4729 210 31 545 5225 649835013 649830330 0.000000e+00 6968
13 TraesCS6D01G324200 chr6B 81.232 2126 296 57 2307 4396 121960752 121958694 0.000000e+00 1620
14 TraesCS6D01G324200 chr6B 91.481 540 41 5 1 538 649835365 649834829 0.000000e+00 737
15 TraesCS6D01G324200 chr6B 83.502 297 31 12 2008 2295 122186827 122186540 1.440000e-65 261
16 TraesCS6D01G324200 chr6B 80.636 346 39 18 2728 3063 649833564 649833237 5.230000e-60 243
17 TraesCS6D01G324200 chr6B 81.940 299 38 12 2008 2295 121960288 121959995 6.760000e-59 239
18 TraesCS6D01G324200 chr6B 92.523 107 8 0 4995 5101 649815735 649815629 2.520000e-33 154
19 TraesCS6D01G324200 chr6B 80.383 209 34 5 1286 1492 695901267 695901064 9.060000e-33 152
20 TraesCS6D01G324200 chr6A 94.210 3713 170 26 643 4330 577725660 577721968 0.000000e+00 5624
21 TraesCS6D01G324200 chr6A 83.854 1505 202 16 2984 4479 64908445 64906973 0.000000e+00 1395
22 TraesCS6D01G324200 chr6A 82.843 1597 222 22 2816 4396 64679786 64678226 0.000000e+00 1384
23 TraesCS6D01G324200 chr6A 93.528 618 22 8 4613 5225 577721651 577721047 0.000000e+00 904
24 TraesCS6D01G324200 chr6A 75.040 1238 219 49 719 1914 64681004 64679815 4.700000e-135 492
25 TraesCS6D01G324200 chr6A 94.309 246 14 0 4370 4615 577721969 577721724 1.370000e-100 377
26 TraesCS6D01G324200 chr7B 81.869 2162 271 65 2354 4477 509737168 509735090 0.000000e+00 1709
27 TraesCS6D01G324200 chr7B 81.683 2080 265 69 2378 4418 517933862 517931860 0.000000e+00 1624
28 TraesCS6D01G324200 chr7B 83.612 299 34 11 2008 2294 509736763 509736468 3.100000e-67 267
29 TraesCS6D01G324200 chr7B 78.365 416 53 22 1545 1955 517933886 517933503 8.750000e-58 235
30 TraesCS6D01G324200 chr7B 74.905 526 117 11 972 1492 577200386 577200901 5.260000e-55 226
31 TraesCS6D01G324200 chr7B 77.427 412 65 15 1545 1955 509737168 509736784 2.450000e-53 220
32 TraesCS6D01G324200 chr7A 82.324 1799 241 47 2622 4396 591023873 591025618 0.000000e+00 1489
33 TraesCS6D01G324200 chr7A 84.628 592 72 7 3902 4484 551541816 551541235 5.870000e-159 571
34 TraesCS6D01G324200 chr7A 76.962 586 116 16 1082 1657 591023153 591023729 3.040000e-82 316
35 TraesCS6D01G324200 chr7A 81.928 332 41 11 1975 2299 551542797 551542478 4.010000e-66 263
36 TraesCS6D01G324200 chr7A 82.237 304 35 14 2002 2295 615785919 615786213 1.450000e-60 244
37 TraesCS6D01G324200 chrUn 82.782 1603 224 22 2810 4396 277361152 277362718 0.000000e+00 1384
38 TraesCS6D01G324200 chrUn 82.893 719 85 16 2816 3524 373933131 373932441 3.460000e-171 612
39 TraesCS6D01G324200 chrUn 75.186 1076 188 43 879 1914 373934196 373933160 8.040000e-118 435
40 TraesCS6D01G324200 chr2B 81.722 755 116 13 3734 4479 142296817 142297558 1.240000e-170 610
41 TraesCS6D01G324200 chr2B 80.072 276 36 9 4573 4840 142297685 142297949 2.480000e-43 187
42 TraesCS6D01G324200 chr2B 92.941 85 5 1 1581 1665 142295815 142295898 7.110000e-24 122
43 TraesCS6D01G324200 chr7D 83.446 296 32 11 2008 2295 535510840 535511126 5.190000e-65 259
44 TraesCS6D01G324200 chr7D 80.672 357 40 14 1545 1896 489311037 489310705 3.120000e-62 250


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 TraesCS6D01G324200 chr6D 430843351 430848575 5224 True 1577.857143 9649 92.644571 1 5225 7 chr6D.!!$R3 5224
1 TraesCS6D01G324200 chr6D 49182741 49184165 1424 False 1509.000000 1509 85.803000 2952 4396 1 chr6D.!!$F1 1444
2 TraesCS6D01G324200 chr6D 50604941 50606506 1565 False 1482.000000 1482 83.915000 2810 4396 1 chr6D.!!$F3 1586
3 TraesCS6D01G324200 chr6D 50179808 50181279 1471 False 1471.000000 1471 84.774000 2986 4479 1 chr6D.!!$F2 1493
4 TraesCS6D01G324200 chr6D 430750368 430751096 728 True 723.000000 723 84.750000 3734 4465 1 chr6D.!!$R1 731
5 TraesCS6D01G324200 chr6D 457269223 457269747 524 True 228.000000 228 75.046000 949 1492 1 chr6D.!!$R2 543
6 TraesCS6D01G324200 chr6B 649830330 649835365 5035 True 2649.333333 6968 88.570000 1 5225 3 chr6B.!!$R5 5224
7 TraesCS6D01G324200 chr6B 121958694 121960752 2058 True 929.500000 1620 81.586000 2008 4396 2 chr6B.!!$R4 2388
8 TraesCS6D01G324200 chr6A 577721047 577725660 4613 True 2301.666667 5624 94.015667 643 5225 3 chr6A.!!$R3 4582
9 TraesCS6D01G324200 chr6A 64906973 64908445 1472 True 1395.000000 1395 83.854000 2984 4479 1 chr6A.!!$R1 1495
10 TraesCS6D01G324200 chr6A 64678226 64681004 2778 True 938.000000 1384 78.941500 719 4396 2 chr6A.!!$R2 3677
11 TraesCS6D01G324200 chr7B 517931860 517933886 2026 True 929.500000 1624 80.024000 1545 4418 2 chr7B.!!$R2 2873
12 TraesCS6D01G324200 chr7B 509735090 509737168 2078 True 732.000000 1709 80.969333 1545 4477 3 chr7B.!!$R1 2932
13 TraesCS6D01G324200 chr7B 577200386 577200901 515 False 226.000000 226 74.905000 972 1492 1 chr7B.!!$F1 520
14 TraesCS6D01G324200 chr7A 591023153 591025618 2465 False 902.500000 1489 79.643000 1082 4396 2 chr7A.!!$F2 3314
15 TraesCS6D01G324200 chr7A 551541235 551542797 1562 True 417.000000 571 83.278000 1975 4484 2 chr7A.!!$R1 2509
16 TraesCS6D01G324200 chrUn 277361152 277362718 1566 False 1384.000000 1384 82.782000 2810 4396 1 chrUn.!!$F1 1586
17 TraesCS6D01G324200 chrUn 373932441 373934196 1755 True 523.500000 612 79.039500 879 3524 2 chrUn.!!$R1 2645
18 TraesCS6D01G324200 chr2B 142295815 142297949 2134 False 306.333333 610 84.911667 1581 4840 3 chr2B.!!$F1 3259

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
140 141 0.033920 CAATGGCGAGGATGATCCGA 59.966 55.0 5.71 0.0 42.75 4.55 F
547 550 0.249398 TCTTTAAGCTCCCCAGTCGC 59.751 55.0 0.00 0.0 0.00 5.19 F
579 582 0.681564 TCGGCCCTGAGAGAGAGTTC 60.682 60.0 0.00 0.0 0.00 3.01 F
2328 2401 0.036448 TTGGCCGTTCGATTGGGTAA 59.964 50.0 0.00 0.0 0.00 2.85 F
3524 4421 0.673333 CAGCCTGACAACGTGCCATA 60.673 55.0 0.00 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 1877 0.038166 AAATTCGCCCCTCTTCTGCA 59.962 50.0 0.00 0.0 0.00 4.41 R
1827 1884 0.392595 AACGGAGAAATTCGCCCCTC 60.393 55.0 10.12 0.0 32.26 4.30 R
2457 2530 0.895530 TTCAGGCTAACACGGGAGAG 59.104 55.0 0.00 0.0 0.00 3.20 R
3531 4428 0.099436 GGGCAGCAGAGTTAATTGCG 59.901 55.0 0.00 0.0 44.80 4.85 R
4939 5984 0.996583 TTTATCCCCGAGGGCTTTGT 59.003 50.0 1.76 0.0 43.94 2.83 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
48 49 2.750657 CCACATCTCCCAGGCCTCC 61.751 68.421 0.00 0.00 0.00 4.30
50 51 1.229951 ACATCTCCCAGGCCTCCAA 60.230 57.895 0.00 0.00 0.00 3.53
51 52 1.225704 CATCTCCCAGGCCTCCAAC 59.774 63.158 0.00 0.00 0.00 3.77
52 53 2.003548 ATCTCCCAGGCCTCCAACC 61.004 63.158 0.00 0.00 0.00 3.77
92 93 1.002366 GCGGTAGTAGAGTTCGACGA 58.998 55.000 0.00 0.00 0.00 4.20
97 98 2.125773 AGTAGAGTTCGACGACCCAT 57.874 50.000 0.00 0.00 0.00 4.00
104 105 0.963225 TTCGACGACCCATCAACAGA 59.037 50.000 0.00 0.00 0.00 3.41
122 123 1.458777 ACACCGAGACTTGGGGTCA 60.459 57.895 11.25 0.00 39.51 4.02
140 141 0.033920 CAATGGCGAGGATGATCCGA 59.966 55.000 5.71 0.00 42.75 4.55
142 143 0.979665 ATGGCGAGGATGATCCGAAT 59.020 50.000 5.71 0.00 42.75 3.34
157 158 1.901085 GAATGAGTCCGGAGTGGCT 59.099 57.895 18.77 3.78 37.80 4.75
160 161 2.997897 GAGTCCGGAGTGGCTGGT 60.998 66.667 18.77 0.00 44.00 4.00
174 175 3.023119 TGGCTGGTTTGCGATTGATAAT 58.977 40.909 0.00 0.00 0.00 1.28
175 176 3.181488 TGGCTGGTTTGCGATTGATAATG 60.181 43.478 0.00 0.00 0.00 1.90
195 197 1.273886 GGGGCGAAAAGTAATTTGCCA 59.726 47.619 16.05 0.00 42.28 4.92
216 218 4.088648 CAAAATCATCGCGAACCAGTAAC 58.911 43.478 15.24 0.00 0.00 2.50
217 219 1.556564 ATCATCGCGAACCAGTAACG 58.443 50.000 15.24 0.00 0.00 3.18
222 224 0.734942 CGCGAACCAGTAACGGATGT 60.735 55.000 0.00 0.00 0.00 3.06
226 228 3.432782 CGAACCAGTAACGGATGTACTC 58.567 50.000 0.00 0.00 0.00 2.59
227 229 3.432782 GAACCAGTAACGGATGTACTCG 58.567 50.000 0.00 0.00 0.00 4.18
256 258 4.513406 AGAAAACAAGACCACACCCTTA 57.487 40.909 0.00 0.00 0.00 2.69
261 263 6.644248 AAACAAGACCACACCCTTAATTAC 57.356 37.500 0.00 0.00 0.00 1.89
262 264 4.659115 ACAAGACCACACCCTTAATTACC 58.341 43.478 0.00 0.00 0.00 2.85
308 310 4.787286 TACCAACGCGGGCCATGG 62.787 66.667 12.47 7.63 40.22 3.66
325 327 1.298014 GGGCTAGCTGCTTCTGTGT 59.702 57.895 15.72 0.00 42.39 3.72
330 332 2.878580 CTAGCTGCTTCTGTGTGAGAG 58.121 52.381 7.79 0.00 30.18 3.20
337 339 1.483595 TTCTGTGTGAGAGGGGCCTG 61.484 60.000 0.84 0.00 30.18 4.85
391 394 1.970092 CCCCGAGAGAGAGTACGAAT 58.030 55.000 0.00 0.00 0.00 3.34
393 396 3.068560 CCCCGAGAGAGAGTACGAATAG 58.931 54.545 0.00 0.00 0.00 1.73
394 397 3.494749 CCCCGAGAGAGAGTACGAATAGT 60.495 52.174 0.00 0.00 0.00 2.12
406 409 9.528018 GAGAGTACGAATAGTAGTAGTACACTT 57.472 37.037 18.84 7.39 38.58 3.16
444 447 4.895961 AGTACAACACTCTTTAAGCTCCC 58.104 43.478 0.00 0.00 28.33 4.30
517 520 5.496133 GTACACTCGTACTACATGGATGT 57.504 43.478 0.00 0.00 43.97 3.06
518 521 6.609237 GTACACTCGTACTACATGGATGTA 57.391 41.667 0.00 0.00 43.97 2.29
531 534 6.360370 ACATGGATGTAGTACAACACTCTT 57.640 37.500 7.16 0.00 39.68 2.85
532 535 6.769512 ACATGGATGTAGTACAACACTCTTT 58.230 36.000 7.16 0.00 39.68 2.52
533 536 7.903145 ACATGGATGTAGTACAACACTCTTTA 58.097 34.615 7.16 0.00 39.68 1.85
534 537 8.372459 ACATGGATGTAGTACAACACTCTTTAA 58.628 33.333 7.16 0.00 39.68 1.52
535 538 8.873830 CATGGATGTAGTACAACACTCTTTAAG 58.126 37.037 7.16 0.00 38.80 1.85
536 539 6.872020 TGGATGTAGTACAACACTCTTTAAGC 59.128 38.462 7.16 0.00 38.80 3.09
537 540 7.097834 GGATGTAGTACAACACTCTTTAAGCT 58.902 38.462 7.16 0.00 38.80 3.74
538 541 7.275999 GGATGTAGTACAACACTCTTTAAGCTC 59.724 40.741 7.16 0.00 38.80 4.09
539 542 6.453092 TGTAGTACAACACTCTTTAAGCTCC 58.547 40.000 0.00 0.00 38.80 4.70
540 543 4.895961 AGTACAACACTCTTTAAGCTCCC 58.104 43.478 0.00 0.00 28.33 4.30
541 544 3.141767 ACAACACTCTTTAAGCTCCCC 57.858 47.619 0.00 0.00 0.00 4.81
542 545 2.441750 ACAACACTCTTTAAGCTCCCCA 59.558 45.455 0.00 0.00 0.00 4.96
543 546 3.077359 CAACACTCTTTAAGCTCCCCAG 58.923 50.000 0.00 0.00 0.00 4.45
544 547 2.339769 ACACTCTTTAAGCTCCCCAGT 58.660 47.619 0.00 0.00 0.00 4.00
545 548 2.303311 ACACTCTTTAAGCTCCCCAGTC 59.697 50.000 0.00 0.00 0.00 3.51
546 549 1.550976 ACTCTTTAAGCTCCCCAGTCG 59.449 52.381 0.00 0.00 0.00 4.18
547 550 0.249398 TCTTTAAGCTCCCCAGTCGC 59.751 55.000 0.00 0.00 0.00 5.19
548 551 0.744771 CTTTAAGCTCCCCAGTCGCC 60.745 60.000 0.00 0.00 0.00 5.54
549 552 1.198759 TTTAAGCTCCCCAGTCGCCT 61.199 55.000 0.00 0.00 0.00 5.52
550 553 1.614241 TTAAGCTCCCCAGTCGCCTC 61.614 60.000 0.00 0.00 0.00 4.70
556 559 2.365105 CCCAGTCGCCTCCCCTTA 60.365 66.667 0.00 0.00 0.00 2.69
557 560 2.435693 CCCAGTCGCCTCCCCTTAG 61.436 68.421 0.00 0.00 0.00 2.18
558 561 2.501610 CAGTCGCCTCCCCTTAGC 59.498 66.667 0.00 0.00 0.00 3.09
562 565 4.570663 CGCCTCCCCTTAGCGTCG 62.571 72.222 0.00 0.00 44.65 5.12
563 566 4.222847 GCCTCCCCTTAGCGTCGG 62.223 72.222 0.00 0.00 0.00 4.79
564 567 4.222847 CCTCCCCTTAGCGTCGGC 62.223 72.222 0.00 0.00 40.37 5.54
565 568 4.222847 CTCCCCTTAGCGTCGGCC 62.223 72.222 0.00 0.00 41.24 6.13
568 571 4.530857 CCCTTAGCGTCGGCCCTG 62.531 72.222 0.00 0.00 41.24 4.45
569 572 3.458163 CCTTAGCGTCGGCCCTGA 61.458 66.667 0.00 0.00 41.24 3.86
570 573 2.105128 CTTAGCGTCGGCCCTGAG 59.895 66.667 0.00 0.00 41.24 3.35
571 574 2.361992 TTAGCGTCGGCCCTGAGA 60.362 61.111 0.00 0.00 41.24 3.27
572 575 2.343163 CTTAGCGTCGGCCCTGAGAG 62.343 65.000 0.00 0.00 41.24 3.20
573 576 2.831894 TTAGCGTCGGCCCTGAGAGA 62.832 60.000 0.00 0.00 41.24 3.10
574 577 4.200283 GCGTCGGCCCTGAGAGAG 62.200 72.222 0.00 0.00 0.00 3.20
575 578 2.438614 CGTCGGCCCTGAGAGAGA 60.439 66.667 0.00 0.00 0.00 3.10
576 579 2.477176 CGTCGGCCCTGAGAGAGAG 61.477 68.421 0.00 0.00 0.00 3.20
577 580 1.379309 GTCGGCCCTGAGAGAGAGT 60.379 63.158 0.00 0.00 0.00 3.24
578 581 0.968393 GTCGGCCCTGAGAGAGAGTT 60.968 60.000 0.00 0.00 0.00 3.01
579 582 0.681564 TCGGCCCTGAGAGAGAGTTC 60.682 60.000 0.00 0.00 0.00 3.01
580 583 1.813192 GGCCCTGAGAGAGAGTTCG 59.187 63.158 0.00 0.00 0.00 3.95
581 584 0.681564 GGCCCTGAGAGAGAGTTCGA 60.682 60.000 0.00 0.00 0.00 3.71
582 585 1.178276 GCCCTGAGAGAGAGTTCGAA 58.822 55.000 0.00 0.00 0.00 3.71
583 586 1.135228 GCCCTGAGAGAGAGTTCGAAC 60.135 57.143 20.71 20.71 0.00 3.95
584 587 2.163509 CCCTGAGAGAGAGTTCGAACA 58.836 52.381 28.78 5.89 0.00 3.18
585 588 2.163412 CCCTGAGAGAGAGTTCGAACAG 59.837 54.545 28.78 14.78 0.00 3.16
586 589 2.817258 CCTGAGAGAGAGTTCGAACAGT 59.183 50.000 28.78 15.90 0.00 3.55
587 590 4.004314 CCTGAGAGAGAGTTCGAACAGTA 58.996 47.826 28.78 6.47 0.00 2.74
588 591 4.094294 CCTGAGAGAGAGTTCGAACAGTAG 59.906 50.000 28.78 14.26 0.00 2.57
589 592 4.643463 TGAGAGAGAGTTCGAACAGTAGT 58.357 43.478 28.78 8.91 0.00 2.73
590 593 5.791666 TGAGAGAGAGTTCGAACAGTAGTA 58.208 41.667 28.78 6.56 0.00 1.82
591 594 5.870433 TGAGAGAGAGTTCGAACAGTAGTAG 59.130 44.000 28.78 0.00 0.00 2.57
592 595 5.797051 AGAGAGAGTTCGAACAGTAGTAGT 58.203 41.667 28.78 6.59 0.00 2.73
593 596 6.934056 AGAGAGAGTTCGAACAGTAGTAGTA 58.066 40.000 28.78 0.00 0.00 1.82
594 597 6.813152 AGAGAGAGTTCGAACAGTAGTAGTAC 59.187 42.308 28.78 9.93 0.00 2.73
595 598 6.462500 AGAGAGTTCGAACAGTAGTAGTACA 58.538 40.000 28.78 0.00 0.00 2.90
596 599 6.368516 AGAGAGTTCGAACAGTAGTAGTACAC 59.631 42.308 28.78 0.00 0.00 2.90
597 600 6.229733 AGAGTTCGAACAGTAGTAGTACACT 58.770 40.000 28.78 3.61 41.62 3.55
598 601 6.368516 AGAGTTCGAACAGTAGTAGTACACTC 59.631 42.308 28.78 12.73 38.80 3.51
599 602 5.119898 AGTTCGAACAGTAGTAGTACACTCG 59.880 44.000 28.78 13.09 38.80 4.18
600 603 4.560128 TCGAACAGTAGTAGTACACTCGT 58.440 43.478 18.03 6.30 38.80 4.18
601 604 5.709966 TCGAACAGTAGTAGTACACTCGTA 58.290 41.667 18.03 8.63 38.80 3.43
632 635 5.407691 GGGTGTAGTACAACACTCTTTAAGC 59.592 44.000 19.74 0.00 45.63 3.09
633 636 6.740681 GGGTGTAGTACAACACTCTTTAAGCT 60.741 42.308 19.74 0.00 45.63 3.74
634 637 7.335861 GTGTAGTACAACACTCTTTAAGCTC 57.664 40.000 4.11 0.00 45.12 4.09
635 638 7.146648 GTGTAGTACAACACTCTTTAAGCTCT 58.853 38.462 4.11 0.00 45.12 4.09
636 639 7.326547 GTGTAGTACAACACTCTTTAAGCTCTC 59.673 40.741 4.11 0.00 45.12 3.20
637 640 5.785243 AGTACAACACTCTTTAAGCTCTCC 58.215 41.667 0.00 0.00 28.33 3.71
638 641 4.689612 ACAACACTCTTTAAGCTCTCCA 57.310 40.909 0.00 0.00 0.00 3.86
639 642 4.636249 ACAACACTCTTTAAGCTCTCCAG 58.364 43.478 0.00 0.00 0.00 3.86
640 643 9.821062 AGTACAACACTCTTTAAGCTCTCCAGC 62.821 44.444 0.00 0.00 38.48 4.85
648 651 3.791586 GCTCTCCAGCCACCTCCC 61.792 72.222 0.00 0.00 40.14 4.30
649 652 2.284921 CTCTCCAGCCACCTCCCA 60.285 66.667 0.00 0.00 0.00 4.37
654 657 1.997311 CCAGCCACCTCCCATCAGA 60.997 63.158 0.00 0.00 0.00 3.27
679 682 1.970092 CCCCGAGAGAGAGTACGAAT 58.030 55.000 0.00 0.00 0.00 3.34
690 693 9.612620 GAGAGAGAGTACGAATAGTAGTAGTAC 57.387 40.741 11.59 11.59 39.00 2.73
695 698 7.860373 AGAGTACGAATAGTAGTAGTACACTCG 59.140 40.741 18.84 17.56 39.00 4.18
741 754 1.079888 GAATGTTTGCTTGGCCCCG 60.080 57.895 0.00 0.00 0.00 5.73
777 793 2.884012 TCAAACGTGCATCCATCTGTTT 59.116 40.909 0.00 0.00 0.00 2.83
795 811 1.286305 TTATTCCTCCCCAGGGGCAC 61.286 60.000 21.90 0.00 43.94 5.01
825 841 2.593978 CACATCTCCCAGGGGCTG 59.406 66.667 5.33 3.43 34.68 4.85
880 896 4.680237 CGAACCTGCCTCGTGCCA 62.680 66.667 0.00 0.00 40.16 4.92
1011 1034 2.839098 CCAACCCACACCTGCTCT 59.161 61.111 0.00 0.00 0.00 4.09
1363 1391 4.344865 TTGCTGGGAAGGACGGCC 62.345 66.667 0.00 0.00 39.46 6.13
1392 1420 1.404391 GTCGTCGAGATCAAGCCCTTA 59.596 52.381 0.00 0.00 0.00 2.69
1393 1421 2.034812 GTCGTCGAGATCAAGCCCTTAT 59.965 50.000 0.00 0.00 0.00 1.73
1493 1539 1.725641 TTGCGATTGACTGCTGTAGG 58.274 50.000 0.00 0.00 0.00 3.18
1608 1662 7.451255 TGTTTAGAGATTTTGGATTGGATGTGT 59.549 33.333 0.00 0.00 0.00 3.72
1647 1701 3.500836 GGGTGAAGGGTTAGGCCTTTTTA 60.501 47.826 12.58 0.00 36.61 1.52
1783 1840 3.425359 CGTGAGCTTTGATGGTGATTCAC 60.425 47.826 8.34 8.34 0.00 3.18
1820 1877 8.950007 TTATAGTCAAAAGGGGTTGAAAATCT 57.050 30.769 0.00 0.00 39.18 2.40
1827 1884 3.160269 AGGGGTTGAAAATCTGCAGAAG 58.840 45.455 22.50 0.00 0.00 2.85
1832 1889 3.077484 TGAAAATCTGCAGAAGAGGGG 57.923 47.619 22.50 0.00 38.67 4.79
1940 2004 4.083565 AGACTAGGTTCAGTTCTCAGTCC 58.916 47.826 0.00 0.00 33.11 3.85
2006 2071 3.173151 TGGTACTTGCTGAATCCTGAGA 58.827 45.455 0.00 0.00 0.00 3.27
2322 2395 0.536460 AGTGGTTTGGCCGTTCGATT 60.536 50.000 0.00 0.00 41.21 3.34
2328 2401 0.036448 TTGGCCGTTCGATTGGGTAA 59.964 50.000 0.00 0.00 0.00 2.85
2335 2408 3.368116 CCGTTCGATTGGGTAAGAAGAGT 60.368 47.826 0.00 0.00 0.00 3.24
2340 2413 7.464178 CGTTCGATTGGGTAAGAAGAGTAATTG 60.464 40.741 0.00 0.00 0.00 2.32
2350 2423 7.886970 GGTAAGAAGAGTAATTGTTTAGGGGTT 59.113 37.037 0.00 0.00 0.00 4.11
2363 2436 1.231928 GGGGTTGGTGTTGGAAGGT 59.768 57.895 0.00 0.00 0.00 3.50
2373 2446 3.133901 GGTGTTGGAAGGTTGGATTTGTT 59.866 43.478 0.00 0.00 0.00 2.83
2431 2504 4.021632 TGGAATTGATTGGATGCGTTTTCA 60.022 37.500 0.00 0.00 0.00 2.69
2451 2524 6.588719 TTCATGAAGTGATTTGGGTTAAGG 57.411 37.500 3.38 0.00 36.54 2.69
2457 2530 4.341487 AGTGATTTGGGTTAAGGGCTTAC 58.659 43.478 0.00 0.00 0.00 2.34
2502 2575 1.378762 GGCTGGTAGGCTGTTTCCA 59.621 57.895 0.00 0.00 37.85 3.53
2516 2589 4.097286 GCTGTTTCCACACTGTTCCTTTTA 59.903 41.667 0.00 0.00 0.00 1.52
2544 2617 3.183574 GCGATTTTGGTTGTTTAGGTTGC 59.816 43.478 0.00 0.00 0.00 4.17
2546 2619 5.047188 CGATTTTGGTTGTTTAGGTTGCTT 58.953 37.500 0.00 0.00 0.00 3.91
2548 2621 6.866248 CGATTTTGGTTGTTTAGGTTGCTTAT 59.134 34.615 0.00 0.00 0.00 1.73
2555 2628 6.016610 GGTTGTTTAGGTTGCTTATCTTGTGA 60.017 38.462 0.00 0.00 0.00 3.58
2557 2630 7.377766 TGTTTAGGTTGCTTATCTTGTGATC 57.622 36.000 0.00 0.00 34.32 2.92
2609 2682 8.824159 ACTCATATGCTTACTGCTGTTTATAG 57.176 34.615 0.09 0.00 43.37 1.31
2689 2762 7.595819 TTCCTTGTTAGATGGTTGTTGATTT 57.404 32.000 0.00 0.00 0.00 2.17
2697 2770 1.336440 TGGTTGTTGATTTGCGTGAGG 59.664 47.619 0.00 0.00 0.00 3.86
2702 2775 2.884012 TGTTGATTTGCGTGAGGATTGT 59.116 40.909 0.00 0.00 0.00 2.71
2715 2788 5.119279 CGTGAGGATTGTTCTAGACTTGTTG 59.881 44.000 0.00 0.00 0.00 3.33
2783 2857 9.412460 ACTAAAAATATCCTTGATTCTGCATCA 57.588 29.630 0.00 0.00 40.43 3.07
2846 2920 4.061596 GCAAAGGTCTATAGCATGAGGTC 58.938 47.826 0.00 0.00 0.00 3.85
3472 4369 1.084289 AAATGCTTTCGTCTACCCGC 58.916 50.000 0.00 0.00 0.00 6.13
3524 4421 0.673333 CAGCCTGACAACGTGCCATA 60.673 55.000 0.00 0.00 0.00 2.74
3531 4428 1.400494 GACAACGTGCCATATGTTCCC 59.600 52.381 1.24 0.00 36.38 3.97
3729 4626 2.038033 GAGTAACACCTACAACCCAGCA 59.962 50.000 0.00 0.00 32.37 4.41
3844 4744 2.751806 GAGCCTTGGATGAGGTTTCTTG 59.248 50.000 0.00 0.00 39.11 3.02
3846 4746 2.893489 GCCTTGGATGAGGTTTCTTGTT 59.107 45.455 0.00 0.00 39.11 2.83
4045 4949 6.049955 TCGGTCTGAGGTTGATAATCTTTT 57.950 37.500 0.00 0.00 0.00 2.27
4205 5124 2.637872 CCCTTTCCCTAGTTGACTGTCA 59.362 50.000 6.36 6.36 0.00 3.58
4249 5171 5.607477 AGTCTGATGAACCGTTGTCTTTAA 58.393 37.500 0.00 0.00 0.00 1.52
4444 5371 9.087424 GTTAAATATGGATTTTCTTGGCTGTTC 57.913 33.333 0.00 0.00 36.62 3.18
4697 5741 6.359804 TCCATTTCAGTGCATTCTTATAGCT 58.640 36.000 0.00 0.00 0.00 3.32
4939 5984 5.939764 AGCACAGATTACACTGAGGATAA 57.060 39.130 0.00 0.00 40.63 1.75
5100 6146 7.522073 GCGCTTTCATTGAAATTCCTGGATATA 60.522 37.037 12.04 0.00 30.85 0.86
5101 6147 7.805071 CGCTTTCATTGAAATTCCTGGATATAC 59.195 37.037 12.04 0.00 30.85 1.47
5102 6148 8.854117 GCTTTCATTGAAATTCCTGGATATACT 58.146 33.333 12.04 0.00 30.85 2.12
5104 6150 9.699410 TTTCATTGAAATTCCTGGATATACTGT 57.301 29.630 7.74 0.00 0.00 3.55
5209 6258 2.291209 TCCTTGGATTTCTTGCTGCA 57.709 45.000 0.00 0.00 0.00 4.41
5218 6267 0.031585 TTCTTGCTGCAGCTGCTTTG 59.968 50.000 36.61 26.26 42.66 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.074648 TGGGAGATGTGGTATTTCAAACTTT 58.925 36.000 0.00 0.00 0.00 2.66
23 24 2.092429 GCCTGGGAGATGTGGTATTTCA 60.092 50.000 0.00 0.00 0.00 2.69
48 49 1.781555 GACGATGTCGCACAGGTTG 59.218 57.895 1.77 0.00 44.43 3.77
69 70 2.417933 GTCGAACTCTACTACCGCTTCA 59.582 50.000 0.00 0.00 0.00 3.02
73 74 1.002366 TCGTCGAACTCTACTACCGC 58.998 55.000 0.00 0.00 0.00 5.68
92 93 0.321671 CTCGGTGTCTGTTGATGGGT 59.678 55.000 0.00 0.00 0.00 4.51
97 98 1.068588 CCAAGTCTCGGTGTCTGTTGA 59.931 52.381 0.00 0.00 0.00 3.18
104 105 1.052124 TTGACCCCAAGTCTCGGTGT 61.052 55.000 0.00 0.00 46.46 4.16
122 123 0.758734 TTCGGATCATCCTCGCCATT 59.241 50.000 1.10 0.00 33.30 3.16
140 141 1.599047 CAGCCACTCCGGACTCATT 59.401 57.895 0.00 0.00 36.56 2.57
142 143 2.997315 CCAGCCACTCCGGACTCA 60.997 66.667 0.00 0.00 36.56 3.41
157 158 2.692557 CCCCATTATCAATCGCAAACCA 59.307 45.455 0.00 0.00 0.00 3.67
160 161 1.336440 CGCCCCATTATCAATCGCAAA 59.664 47.619 0.00 0.00 0.00 3.68
174 175 1.273886 GGCAAATTACTTTTCGCCCCA 59.726 47.619 0.00 0.00 36.40 4.96
175 176 1.273886 TGGCAAATTACTTTTCGCCCC 59.726 47.619 0.00 0.00 39.11 5.80
195 197 3.181524 CGTTACTGGTTCGCGATGATTTT 60.182 43.478 10.88 0.00 0.00 1.82
216 218 7.274904 TGTTTTCTTTTAGATCGAGTACATCCG 59.725 37.037 0.00 0.00 0.00 4.18
217 219 8.475331 TGTTTTCTTTTAGATCGAGTACATCC 57.525 34.615 0.00 0.00 0.00 3.51
222 224 8.145767 TGGTCTTGTTTTCTTTTAGATCGAGTA 58.854 33.333 0.00 0.00 0.00 2.59
226 228 6.851330 GTGTGGTCTTGTTTTCTTTTAGATCG 59.149 38.462 0.00 0.00 0.00 3.69
227 229 7.139392 GGTGTGGTCTTGTTTTCTTTTAGATC 58.861 38.462 0.00 0.00 0.00 2.75
381 384 9.311916 CAAGTGTACTACTACTATTCGTACTCT 57.688 37.037 0.00 0.00 39.18 3.24
513 516 7.275999 GGAGCTTAAAGAGTGTTGTACTACATC 59.724 40.741 13.21 11.20 40.53 3.06
514 517 7.097834 GGAGCTTAAAGAGTGTTGTACTACAT 58.902 38.462 13.21 3.24 40.53 2.29
515 518 6.453092 GGAGCTTAAAGAGTGTTGTACTACA 58.547 40.000 6.02 6.02 40.53 2.74
516 519 5.868258 GGGAGCTTAAAGAGTGTTGTACTAC 59.132 44.000 0.05 0.05 40.53 2.73
517 520 5.046807 GGGGAGCTTAAAGAGTGTTGTACTA 60.047 44.000 0.00 0.00 40.53 1.82
518 521 4.262938 GGGGAGCTTAAAGAGTGTTGTACT 60.263 45.833 0.00 0.00 44.02 2.73
519 522 4.001652 GGGGAGCTTAAAGAGTGTTGTAC 58.998 47.826 0.00 0.00 0.00 2.90
520 523 3.649023 TGGGGAGCTTAAAGAGTGTTGTA 59.351 43.478 0.00 0.00 0.00 2.41
521 524 2.441750 TGGGGAGCTTAAAGAGTGTTGT 59.558 45.455 0.00 0.00 0.00 3.32
522 525 3.077359 CTGGGGAGCTTAAAGAGTGTTG 58.923 50.000 0.00 0.00 0.00 3.33
523 526 2.711547 ACTGGGGAGCTTAAAGAGTGTT 59.288 45.455 0.00 0.00 0.00 3.32
524 527 2.303311 GACTGGGGAGCTTAAAGAGTGT 59.697 50.000 0.00 0.00 0.00 3.55
525 528 2.675317 CGACTGGGGAGCTTAAAGAGTG 60.675 54.545 0.00 0.00 0.00 3.51
526 529 1.550976 CGACTGGGGAGCTTAAAGAGT 59.449 52.381 0.00 0.00 0.00 3.24
527 530 1.740718 GCGACTGGGGAGCTTAAAGAG 60.741 57.143 0.00 0.00 0.00 2.85
528 531 0.249398 GCGACTGGGGAGCTTAAAGA 59.751 55.000 0.00 0.00 0.00 2.52
529 532 0.744771 GGCGACTGGGGAGCTTAAAG 60.745 60.000 0.00 0.00 0.00 1.85
530 533 1.198759 AGGCGACTGGGGAGCTTAAA 61.199 55.000 0.00 0.00 41.13 1.52
531 534 1.612442 AGGCGACTGGGGAGCTTAA 60.612 57.895 0.00 0.00 41.13 1.85
532 535 2.038975 AGGCGACTGGGGAGCTTA 59.961 61.111 0.00 0.00 41.13 3.09
533 536 3.394836 GAGGCGACTGGGGAGCTT 61.395 66.667 0.00 0.00 44.43 3.74
538 541 3.995809 TAAGGGGAGGCGACTGGGG 62.996 68.421 0.00 0.00 44.43 4.96
539 542 2.365105 TAAGGGGAGGCGACTGGG 60.365 66.667 0.00 0.00 44.43 4.45
540 543 3.095347 GCTAAGGGGAGGCGACTGG 62.095 68.421 0.00 0.00 44.43 4.00
541 544 2.501610 GCTAAGGGGAGGCGACTG 59.498 66.667 0.00 0.00 44.43 3.51
546 549 4.222847 CCGACGCTAAGGGGAGGC 62.223 72.222 0.00 0.00 0.00 4.70
547 550 4.222847 GCCGACGCTAAGGGGAGG 62.223 72.222 0.00 0.00 0.00 4.30
548 551 4.222847 GGCCGACGCTAAGGGGAG 62.223 72.222 0.00 0.00 34.44 4.30
551 554 4.530857 CAGGGCCGACGCTAAGGG 62.531 72.222 0.00 0.00 37.30 3.95
552 555 3.432051 CTCAGGGCCGACGCTAAGG 62.432 68.421 0.00 0.00 37.30 2.69
553 556 2.105128 CTCAGGGCCGACGCTAAG 59.895 66.667 0.00 0.00 37.30 2.18
554 557 2.361992 TCTCAGGGCCGACGCTAA 60.362 61.111 0.00 0.00 37.30 3.09
555 558 2.829003 CTCTCAGGGCCGACGCTA 60.829 66.667 0.00 0.00 37.30 4.26
556 559 4.742649 TCTCTCAGGGCCGACGCT 62.743 66.667 0.00 0.00 40.24 5.07
557 560 4.200283 CTCTCTCAGGGCCGACGC 62.200 72.222 0.00 0.00 0.00 5.19
558 561 2.438614 TCTCTCTCAGGGCCGACG 60.439 66.667 0.00 0.00 0.00 5.12
559 562 0.968393 AACTCTCTCTCAGGGCCGAC 60.968 60.000 0.00 0.00 0.00 4.79
560 563 0.681564 GAACTCTCTCTCAGGGCCGA 60.682 60.000 0.00 0.00 0.00 5.54
561 564 1.813192 GAACTCTCTCTCAGGGCCG 59.187 63.158 0.00 0.00 0.00 6.13
562 565 0.681564 TCGAACTCTCTCTCAGGGCC 60.682 60.000 0.00 0.00 0.00 5.80
563 566 1.135228 GTTCGAACTCTCTCTCAGGGC 60.135 57.143 20.97 0.00 0.00 5.19
564 567 2.163412 CTGTTCGAACTCTCTCTCAGGG 59.837 54.545 27.32 1.93 0.00 4.45
565 568 2.817258 ACTGTTCGAACTCTCTCTCAGG 59.183 50.000 27.32 8.29 0.00 3.86
566 569 4.693566 ACTACTGTTCGAACTCTCTCTCAG 59.306 45.833 27.32 16.35 0.00 3.35
567 570 4.643463 ACTACTGTTCGAACTCTCTCTCA 58.357 43.478 27.32 5.32 0.00 3.27
568 571 5.870978 ACTACTACTGTTCGAACTCTCTCTC 59.129 44.000 27.32 0.44 0.00 3.20
569 572 5.797051 ACTACTACTGTTCGAACTCTCTCT 58.203 41.667 27.32 9.44 0.00 3.10
570 573 6.589523 TGTACTACTACTGTTCGAACTCTCTC 59.410 42.308 27.32 1.97 0.00 3.20
571 574 6.368516 GTGTACTACTACTGTTCGAACTCTCT 59.631 42.308 27.32 10.55 0.00 3.10
572 575 6.368516 AGTGTACTACTACTGTTCGAACTCTC 59.631 42.308 27.32 3.12 38.04 3.20
573 576 6.229733 AGTGTACTACTACTGTTCGAACTCT 58.770 40.000 27.32 15.14 38.04 3.24
574 577 6.479095 AGTGTACTACTACTGTTCGAACTC 57.521 41.667 27.32 4.28 38.04 3.01
575 578 5.119898 CGAGTGTACTACTACTGTTCGAACT 59.880 44.000 27.32 12.18 40.53 3.01
576 579 5.107298 ACGAGTGTACTACTACTGTTCGAAC 60.107 44.000 21.42 21.42 40.53 3.95
577 580 4.991056 ACGAGTGTACTACTACTGTTCGAA 59.009 41.667 0.00 0.00 40.53 3.71
578 581 4.560128 ACGAGTGTACTACTACTGTTCGA 58.440 43.478 0.00 0.00 40.53 3.71
579 582 4.917887 ACGAGTGTACTACTACTGTTCG 57.082 45.455 0.00 0.00 40.53 3.95
591 594 4.635765 TACACCCATGTAGTACGAGTGTAC 59.364 45.833 15.18 0.00 44.21 2.90
592 595 3.689347 ACACCCATGTAGTACGAGTGTA 58.311 45.455 12.86 0.00 37.26 2.90
593 596 2.522185 ACACCCATGTAGTACGAGTGT 58.478 47.619 10.09 10.09 37.26 3.55
610 613 7.146648 AGAGCTTAAAGAGTGTTGTACTACAC 58.853 38.462 26.64 26.64 46.86 2.90
611 614 7.286215 AGAGCTTAAAGAGTGTTGTACTACA 57.714 36.000 6.02 6.02 40.53 2.74
612 615 6.807720 GGAGAGCTTAAAGAGTGTTGTACTAC 59.192 42.308 0.05 0.05 40.53 2.73
613 616 6.492429 TGGAGAGCTTAAAGAGTGTTGTACTA 59.508 38.462 0.00 0.00 40.53 1.82
614 617 5.304614 TGGAGAGCTTAAAGAGTGTTGTACT 59.695 40.000 0.00 0.00 44.02 2.73
615 618 5.539048 TGGAGAGCTTAAAGAGTGTTGTAC 58.461 41.667 0.00 0.00 0.00 2.90
616 619 5.784177 CTGGAGAGCTTAAAGAGTGTTGTA 58.216 41.667 0.00 0.00 0.00 2.41
617 620 4.636249 CTGGAGAGCTTAAAGAGTGTTGT 58.364 43.478 0.00 0.00 0.00 3.32
618 621 3.434984 GCTGGAGAGCTTAAAGAGTGTTG 59.565 47.826 0.00 0.00 42.52 3.33
619 622 3.558109 GGCTGGAGAGCTTAAAGAGTGTT 60.558 47.826 0.00 0.00 45.44 3.32
620 623 2.027653 GGCTGGAGAGCTTAAAGAGTGT 60.028 50.000 0.00 0.00 45.44 3.55
621 624 2.027745 TGGCTGGAGAGCTTAAAGAGTG 60.028 50.000 0.00 0.00 45.44 3.51
622 625 2.027653 GTGGCTGGAGAGCTTAAAGAGT 60.028 50.000 0.00 0.00 45.44 3.24
623 626 2.626840 GTGGCTGGAGAGCTTAAAGAG 58.373 52.381 0.00 0.00 45.44 2.85
624 627 1.279271 GGTGGCTGGAGAGCTTAAAGA 59.721 52.381 0.00 0.00 45.44 2.52
625 628 1.280421 AGGTGGCTGGAGAGCTTAAAG 59.720 52.381 0.00 0.00 45.44 1.85
626 629 1.279271 GAGGTGGCTGGAGAGCTTAAA 59.721 52.381 0.00 0.00 45.44 1.52
627 630 0.905357 GAGGTGGCTGGAGAGCTTAA 59.095 55.000 0.00 0.00 45.44 1.85
628 631 0.978146 GGAGGTGGCTGGAGAGCTTA 60.978 60.000 0.00 0.00 45.44 3.09
629 632 2.297129 GGAGGTGGCTGGAGAGCTT 61.297 63.158 0.00 0.00 45.44 3.74
630 633 2.686835 GGAGGTGGCTGGAGAGCT 60.687 66.667 0.00 0.00 45.44 4.09
631 634 3.791586 GGGAGGTGGCTGGAGAGC 61.792 72.222 0.00 0.00 45.40 4.09
632 635 1.692042 ATGGGAGGTGGCTGGAGAG 60.692 63.158 0.00 0.00 0.00 3.20
633 636 1.690633 GATGGGAGGTGGCTGGAGA 60.691 63.158 0.00 0.00 0.00 3.71
634 637 1.980784 CTGATGGGAGGTGGCTGGAG 61.981 65.000 0.00 0.00 0.00 3.86
635 638 1.997311 CTGATGGGAGGTGGCTGGA 60.997 63.158 0.00 0.00 0.00 3.86
636 639 1.980784 CTCTGATGGGAGGTGGCTGG 61.981 65.000 0.00 0.00 0.00 4.85
637 640 1.525923 CTCTGATGGGAGGTGGCTG 59.474 63.158 0.00 0.00 0.00 4.85
638 641 2.373707 GCTCTGATGGGAGGTGGCT 61.374 63.158 0.00 0.00 34.21 4.75
639 642 2.191641 GCTCTGATGGGAGGTGGC 59.808 66.667 0.00 0.00 34.21 5.01
640 643 2.914289 GGCTCTGATGGGAGGTGG 59.086 66.667 0.00 0.00 34.21 4.61
641 644 2.503061 CGGCTCTGATGGGAGGTG 59.497 66.667 0.00 0.00 34.21 4.00
642 645 2.765807 CCGGCTCTGATGGGAGGT 60.766 66.667 0.00 0.00 34.21 3.85
643 646 4.247380 GCCGGCTCTGATGGGAGG 62.247 72.222 22.15 0.00 34.21 4.30
644 647 4.247380 GGCCGGCTCTGATGGGAG 62.247 72.222 28.56 0.00 36.50 4.30
663 666 7.362662 ACTACTACTATTCGTACTCTCTCTCG 58.637 42.308 0.00 0.00 0.00 4.04
669 672 7.860373 CGAGTGTACTACTACTATTCGTACTCT 59.140 40.741 0.00 0.00 40.53 3.24
703 706 6.658816 ACATTCATTAGTTTGCACTACATCCA 59.341 34.615 0.00 0.00 35.05 3.41
705 708 8.853345 CAAACATTCATTAGTTTGCACTACATC 58.147 33.333 5.27 0.00 45.28 3.06
706 709 8.746922 CAAACATTCATTAGTTTGCACTACAT 57.253 30.769 5.27 0.00 45.28 2.29
717 720 3.055891 GGGCCAAGCAAACATTCATTAGT 60.056 43.478 4.39 0.00 0.00 2.24
741 754 5.004440 GCACGTTTGACTTTCTTTTTCCTTC 59.996 40.000 0.00 0.00 0.00 3.46
750 763 2.571212 TGGATGCACGTTTGACTTTCT 58.429 42.857 0.00 0.00 0.00 2.52
795 811 3.871594 GGGAGATGTGGTATTTCGAACAG 59.128 47.826 0.00 0.00 0.00 3.16
1011 1034 3.169908 GGCAGTTTTTAATGAAGGGGGA 58.830 45.455 0.00 0.00 0.00 4.81
1043 1067 2.582436 GAGGGTCGCCGGAATTGA 59.418 61.111 5.05 0.00 0.00 2.57
1370 1398 1.511305 GGCTTGATCTCGACGACCA 59.489 57.895 0.00 0.00 0.00 4.02
1392 1420 1.218316 GGACCTCTTGACGGCGAAT 59.782 57.895 16.62 0.00 0.00 3.34
1393 1421 2.654877 GGACCTCTTGACGGCGAA 59.345 61.111 16.62 0.00 0.00 4.70
1446 1475 4.509915 ACAATACGCGGATTAAAGAACG 57.490 40.909 17.86 4.92 0.00 3.95
1493 1539 4.878397 CCCAATCACACAATCTCCTAACTC 59.122 45.833 0.00 0.00 0.00 3.01
1647 1701 6.377146 ACCTAACAAACACAACAGAGAAATGT 59.623 34.615 0.00 0.00 33.96 2.71
1783 1840 8.184192 CCCTTTTGACTATAAACAGTAAGCATG 58.816 37.037 0.00 0.00 0.00 4.06
1820 1877 0.038166 AAATTCGCCCCTCTTCTGCA 59.962 50.000 0.00 0.00 0.00 4.41
1827 1884 0.392595 AACGGAGAAATTCGCCCCTC 60.393 55.000 10.12 0.00 32.26 4.30
1832 1889 2.331809 AGCAAAACGGAGAAATTCGC 57.668 45.000 0.00 0.00 0.00 4.70
1982 2047 5.604231 TCTCAGGATTCAGCAAGTACCATAT 59.396 40.000 0.00 0.00 0.00 1.78
2253 2326 7.168972 CAGACAAACTTCTCTCACAGAAAGTAG 59.831 40.741 0.00 0.00 40.83 2.57
2322 2395 7.399634 CCCTAAACAATTACTCTTCTTACCCA 58.600 38.462 0.00 0.00 0.00 4.51
2328 2401 6.183361 ACCAACCCCTAAACAATTACTCTTCT 60.183 38.462 0.00 0.00 0.00 2.85
2335 2408 4.589374 CCAACACCAACCCCTAAACAATTA 59.411 41.667 0.00 0.00 0.00 1.40
2340 2413 2.368311 TCCAACACCAACCCCTAAAC 57.632 50.000 0.00 0.00 0.00 2.01
2350 2423 2.697751 CAAATCCAACCTTCCAACACCA 59.302 45.455 0.00 0.00 0.00 4.17
2363 2436 4.657436 GTGTAACACCCAACAAATCCAA 57.343 40.909 0.00 0.00 36.32 3.53
2414 2487 4.218200 ACTTCATGAAAACGCATCCAATCA 59.782 37.500 9.88 0.00 0.00 2.57
2431 2504 3.769300 GCCCTTAACCCAAATCACTTCAT 59.231 43.478 0.00 0.00 0.00 2.57
2451 2524 1.471153 GCTAACACGGGAGAGTAAGCC 60.471 57.143 0.00 0.00 31.96 4.35
2457 2530 0.895530 TTCAGGCTAACACGGGAGAG 59.104 55.000 0.00 0.00 0.00 3.20
2502 2575 4.058817 CGCTTCTCTAAAAGGAACAGTGT 58.941 43.478 0.00 0.00 0.00 3.55
2516 2589 4.918810 AAACAACCAAAATCGCTTCTCT 57.081 36.364 0.00 0.00 0.00 3.10
2548 2621 8.481314 AGCTCATGAAAAGTATAGATCACAAGA 58.519 33.333 0.00 0.00 0.00 3.02
2555 2628 9.064706 CCATCAAAGCTCATGAAAAGTATAGAT 57.935 33.333 6.29 0.00 0.00 1.98
2557 2630 8.127327 CACCATCAAAGCTCATGAAAAGTATAG 58.873 37.037 6.29 0.00 0.00 1.31
2609 2682 4.612264 TCGGCCCTTTACCTTATATGAC 57.388 45.455 0.00 0.00 0.00 3.06
2620 2693 3.443145 TTGGAGAAATTCGGCCCTTTA 57.557 42.857 0.00 0.00 0.00 1.85
2624 2697 2.099405 TCAATTGGAGAAATTCGGCCC 58.901 47.619 5.42 1.47 36.28 5.80
2689 2762 2.826128 AGTCTAGAACAATCCTCACGCA 59.174 45.455 0.00 0.00 0.00 5.24
2887 2984 9.884465 CCCGCAAAACAAATAAAATGAAATAAA 57.116 25.926 0.00 0.00 0.00 1.40
2888 2985 9.057089 ACCCGCAAAACAAATAAAATGAAATAA 57.943 25.926 0.00 0.00 0.00 1.40
2889 2986 8.499162 CACCCGCAAAACAAATAAAATGAAATA 58.501 29.630 0.00 0.00 0.00 1.40
2890 2987 7.227512 TCACCCGCAAAACAAATAAAATGAAAT 59.772 29.630 0.00 0.00 0.00 2.17
2891 2988 6.538742 TCACCCGCAAAACAAATAAAATGAAA 59.461 30.769 0.00 0.00 0.00 2.69
2892 2989 6.018669 GTCACCCGCAAAACAAATAAAATGAA 60.019 34.615 0.00 0.00 0.00 2.57
2893 2990 5.463724 GTCACCCGCAAAACAAATAAAATGA 59.536 36.000 0.00 0.00 0.00 2.57
2894 2991 5.465056 AGTCACCCGCAAAACAAATAAAATG 59.535 36.000 0.00 0.00 0.00 2.32
2895 2992 5.465056 CAGTCACCCGCAAAACAAATAAAAT 59.535 36.000 0.00 0.00 0.00 1.82
2896 2993 4.806247 CAGTCACCCGCAAAACAAATAAAA 59.194 37.500 0.00 0.00 0.00 1.52
2910 3027 0.798776 GTGAAAGCATCAGTCACCCG 59.201 55.000 0.00 0.00 39.19 5.28
3472 4369 2.942710 CTTTGATGCAAAGTCAGCAGG 58.057 47.619 10.84 0.00 46.36 4.85
3524 4421 2.423538 GCAGAGTTAATTGCGGGAACAT 59.576 45.455 0.00 0.00 0.00 2.71
3531 4428 0.099436 GGGCAGCAGAGTTAATTGCG 59.901 55.000 0.00 0.00 44.80 4.85
3729 4626 0.392193 CAGCTCCTTCGGCAATCACT 60.392 55.000 0.00 0.00 0.00 3.41
3738 4635 1.760268 GCGCAGATTCAGCTCCTTCG 61.760 60.000 0.30 0.00 0.00 3.79
3844 4744 1.600957 CTCATCCACGCCATCATCAAC 59.399 52.381 0.00 0.00 0.00 3.18
3846 4746 0.533531 GCTCATCCACGCCATCATCA 60.534 55.000 0.00 0.00 0.00 3.07
4045 4949 6.148948 CGCAACAAAAAGTTCAGGATAATGA 58.851 36.000 0.00 0.00 38.74 2.57
4205 5124 6.655003 AGACTCATAAATGACAACGGTTCATT 59.345 34.615 2.89 2.89 35.83 2.57
4249 5171 6.189567 CGACGACATAAAAGTTGACAAAAGT 58.810 36.000 0.00 0.00 0.00 2.66
4490 5417 3.222173 TGCCAGAGCCTAAGTGAAAAA 57.778 42.857 0.00 0.00 38.69 1.94
4905 5950 5.874810 TGTAATCTGTGCTTCAGTGGAATAC 59.125 40.000 8.75 7.25 43.97 1.89
4939 5984 0.996583 TTTATCCCCGAGGGCTTTGT 59.003 50.000 1.76 0.00 43.94 2.83
4980 6025 1.603802 ACGATTAGAATGCAATGCCCG 59.396 47.619 1.53 0.00 0.00 6.13
5100 6146 6.547402 TCAGCTCAGGTCTATATCATACAGT 58.453 40.000 0.00 0.00 0.00 3.55
5101 6147 7.643569 ATCAGCTCAGGTCTATATCATACAG 57.356 40.000 0.00 0.00 0.00 2.74
5102 6148 9.533831 TTTATCAGCTCAGGTCTATATCATACA 57.466 33.333 0.00 0.00 0.00 2.29
5104 6150 9.760926 ACTTTATCAGCTCAGGTCTATATCATA 57.239 33.333 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.