Multiple sequence alignment - TraesCS4B01G346400

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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 TraesCS4B01G346400 chr4B 100.000 3642 0 0 1 3642 640028367 640024726 0.000000e+00 6726.0
1 TraesCS4B01G346400 chr4B 96.923 65 2 0 2674 2738 178808892 178808956 3.840000e-20 110.0
2 TraesCS4B01G346400 chr4D 94.505 2002 73 14 677 2677 498063577 498061612 0.000000e+00 3053.0
3 TraesCS4B01G346400 chr4D 92.737 537 19 8 2738 3254 498061463 498060927 0.000000e+00 758.0
4 TraesCS4B01G346400 chr4D 93.820 356 15 4 1 353 498064149 498063798 2.490000e-146 529.0
5 TraesCS4B01G346400 chr4D 91.977 349 26 1 3294 3642 498060935 498060589 4.230000e-134 488.0
6 TraesCS4B01G346400 chr4D 92.179 179 12 2 510 688 347324613 347324789 6.040000e-63 252.0
7 TraesCS4B01G346400 chr5A 94.214 2005 76 16 675 2677 678584221 678582255 0.000000e+00 3024.0
8 TraesCS4B01G346400 chr5A 88.367 447 38 9 3198 3642 678581448 678581014 3.220000e-145 525.0
9 TraesCS4B01G346400 chr5A 93.884 327 15 4 1 326 678585546 678585224 4.230000e-134 488.0
10 TraesCS4B01G346400 chr5A 82.955 440 33 8 2750 3163 678582122 678581699 3.460000e-95 359.0
11 TraesCS4B01G346400 chr2A 76.984 504 99 14 1052 1551 575685951 575686441 4.630000e-69 272.0
12 TraesCS4B01G346400 chr2A 74.952 523 93 29 1052 1551 578117839 578118346 4.770000e-49 206.0
13 TraesCS4B01G346400 chr2B 81.707 328 56 4 1226 1551 483463701 483464026 1.670000e-68 270.0
14 TraesCS4B01G346400 chr2B 74.525 526 90 33 1052 1551 484591421 484591928 4.800000e-44 189.0
15 TraesCS4B01G346400 chr2B 93.056 72 5 0 2674 2745 167893822 167893751 4.970000e-19 106.0
16 TraesCS4B01G346400 chr3A 93.605 172 11 0 513 684 50219521 50219692 1.300000e-64 257.0
17 TraesCS4B01G346400 chr3A 92.179 179 14 0 510 688 336959309 336959131 1.680000e-63 254.0
18 TraesCS4B01G346400 chr7D 92.697 178 12 1 513 690 449505573 449505397 4.670000e-64 255.0
19 TraesCS4B01G346400 chr7D 88.136 59 7 0 1086 1144 309913850 309913792 1.810000e-08 71.3
20 TraesCS4B01G346400 chr1D 92.655 177 11 2 512 688 238940215 238940389 1.680000e-63 254.0
21 TraesCS4B01G346400 chr6D 91.005 189 14 3 507 693 128888365 128888178 6.040000e-63 252.0
22 TraesCS4B01G346400 chr6D 92.179 179 13 1 510 688 371444275 371444452 6.040000e-63 252.0
23 TraesCS4B01G346400 chr6D 92.179 179 13 1 510 688 465287295 465287118 6.040000e-63 252.0
24 TraesCS4B01G346400 chr6D 90.476 189 16 2 510 698 308662856 308663042 7.810000e-62 248.0
25 TraesCS4B01G346400 chr7B 96.923 65 2 0 2674 2738 237517984 237518048 3.840000e-20 110.0
26 TraesCS4B01G346400 chr7B 88.136 59 7 0 1086 1144 304523878 304523936 1.810000e-08 71.3
27 TraesCS4B01G346400 chr6B 93.846 65 4 0 2674 2738 492305198 492305134 8.320000e-17 99.0
28 TraesCS4B01G346400 chr5B 90.000 60 6 0 1088 1147 764811 764752 1.080000e-10 78.7
29 TraesCS4B01G346400 chr5D 88.136 59 7 0 1086 1144 1887253 1887195 1.810000e-08 71.3


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 TraesCS4B01G346400 chr4B 640024726 640028367 3641 True 6726 6726 100.00000 1 3642 1 chr4B.!!$R1 3641
1 TraesCS4B01G346400 chr4D 498060589 498064149 3560 True 1207 3053 93.25975 1 3642 4 chr4D.!!$R1 3641
2 TraesCS4B01G346400 chr5A 678581014 678585546 4532 True 1099 3024 89.85500 1 3642 4 chr5A.!!$R1 3641
3 TraesCS4B01G346400 chr2A 578117839 578118346 507 False 206 206 74.95200 1052 1551 1 chr2A.!!$F2 499

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
336 618 0.976641 TGCAGTAAGGACACTCCCAG 59.023 55.0 0.0 0.0 37.19 4.45 F
1275 2189 0.110486 TTGCAGACCTTCTTCCCCAC 59.890 55.0 0.0 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 2397 0.745486 TGAGCATGGCGAGGTTCATG 60.745 55.0 0.00 0.00 42.47 3.07 R
2686 3600 0.029681 ATCTATGCTGGGTCCCACCT 60.030 55.0 6.47 0.17 38.64 4.00 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
62 63 7.253618 CGTGGTTGTGACAAGAGTTTTAAATTG 60.254 37.037 0.00 0.00 0.00 2.32
157 159 4.123497 ACAATACGACTTCTATGCAGCA 57.877 40.909 0.00 0.00 0.00 4.41
234 238 5.006358 CGTGCTTAGTATCACATTTACACCC 59.994 44.000 0.00 0.00 33.03 4.61
255 259 7.183293 ACACCCAAGTATAGGTTGGTTAGTTAT 59.817 37.037 11.30 0.00 42.69 1.89
261 265 7.799081 AGTATAGGTTGGTTAGTTATTCACCC 58.201 38.462 0.00 0.00 0.00 4.61
282 286 2.170187 CAATCTTGAGTCAGCTAGCCCT 59.830 50.000 12.13 4.86 0.00 5.19
283 287 1.189752 TCTTGAGTCAGCTAGCCCTG 58.810 55.000 12.13 4.11 0.00 4.45
329 611 2.038952 AGCTTGTCATGCAGTAAGGACA 59.961 45.455 12.76 0.00 38.41 4.02
336 618 0.976641 TGCAGTAAGGACACTCCCAG 59.023 55.000 0.00 0.00 37.19 4.45
353 635 1.406614 CCAGTGCTCCATCTTGGACTC 60.407 57.143 0.00 0.00 42.67 3.36
354 636 1.277273 CAGTGCTCCATCTTGGACTCA 59.723 52.381 0.00 0.00 42.67 3.41
357 639 3.776969 AGTGCTCCATCTTGGACTCATAA 59.223 43.478 0.00 0.00 42.67 1.90
358 640 4.125703 GTGCTCCATCTTGGACTCATAAG 58.874 47.826 0.00 0.00 42.67 1.73
359 641 4.033009 TGCTCCATCTTGGACTCATAAGA 58.967 43.478 0.00 0.00 42.67 2.10
360 642 4.471025 TGCTCCATCTTGGACTCATAAGAA 59.529 41.667 0.00 0.00 42.67 2.52
361 643 5.131642 TGCTCCATCTTGGACTCATAAGAAT 59.868 40.000 0.00 0.00 42.67 2.40
364 646 7.067981 GCTCCATCTTGGACTCATAAGAATTTT 59.932 37.037 0.00 0.00 42.67 1.82
366 648 8.960591 TCCATCTTGGACTCATAAGAATTTTTC 58.039 33.333 0.00 0.00 42.67 2.29
368 650 9.784680 CATCTTGGACTCATAAGAATTTTTCTG 57.215 33.333 0.00 0.00 40.59 3.02
369 651 8.924511 TCTTGGACTCATAAGAATTTTTCTGT 57.075 30.769 0.00 0.00 40.59 3.41
371 653 9.403110 CTTGGACTCATAAGAATTTTTCTGTTG 57.597 33.333 0.00 0.00 40.59 3.33
373 655 9.130661 TGGACTCATAAGAATTTTTCTGTTGAA 57.869 29.630 0.00 0.00 40.59 2.69
382 664 9.546428 AAGAATTTTTCTGTTGAATAGTTTGGG 57.454 29.630 0.00 0.00 40.59 4.12
383 665 8.704668 AGAATTTTTCTGTTGAATAGTTTGGGT 58.295 29.630 0.00 0.00 38.91 4.51
384 666 9.325198 GAATTTTTCTGTTGAATAGTTTGGGTT 57.675 29.630 0.00 0.00 31.56 4.11
385 667 8.661352 ATTTTTCTGTTGAATAGTTTGGGTTG 57.339 30.769 0.00 0.00 31.56 3.77
386 668 4.846779 TCTGTTGAATAGTTTGGGTTGC 57.153 40.909 0.00 0.00 0.00 4.17
387 669 4.469657 TCTGTTGAATAGTTTGGGTTGCT 58.530 39.130 0.00 0.00 0.00 3.91
388 670 4.892934 TCTGTTGAATAGTTTGGGTTGCTT 59.107 37.500 0.00 0.00 0.00 3.91
390 672 6.016610 TCTGTTGAATAGTTTGGGTTGCTTAC 60.017 38.462 0.00 0.00 0.00 2.34
391 673 5.010213 TGTTGAATAGTTTGGGTTGCTTACC 59.990 40.000 0.43 0.43 46.99 2.85
405 687 7.347508 GGTTGCTTACCACGTATATTATCTG 57.652 40.000 4.00 0.00 46.92 2.90
406 688 6.367969 GGTTGCTTACCACGTATATTATCTGG 59.632 42.308 4.00 0.00 46.92 3.86
407 689 6.659745 TGCTTACCACGTATATTATCTGGT 57.340 37.500 0.00 0.00 38.75 4.00
415 753 8.746530 ACCACGTATATTATCTGGTACCTATTG 58.253 37.037 14.36 1.07 33.29 1.90
491 1381 5.636965 CACGAAGGGAGCAATAATATCTCAG 59.363 44.000 0.00 0.00 0.00 3.35
512 1402 7.935755 TCTCAGAAATTTTCTCTCACAACAGAT 59.064 33.333 8.71 0.00 38.11 2.90
513 1403 9.212641 CTCAGAAATTTTCTCTCACAACAGATA 57.787 33.333 8.71 0.00 38.11 1.98
514 1404 8.993121 TCAGAAATTTTCTCTCACAACAGATAC 58.007 33.333 8.71 0.00 38.11 2.24
515 1405 8.997323 CAGAAATTTTCTCTCACAACAGATACT 58.003 33.333 8.71 0.00 38.11 2.12
516 1406 9.213799 AGAAATTTTCTCTCACAACAGATACTC 57.786 33.333 5.82 0.00 34.07 2.59
517 1407 7.913674 AATTTTCTCTCACAACAGATACTCC 57.086 36.000 0.00 0.00 0.00 3.85
518 1408 5.407407 TTTCTCTCACAACAGATACTCCC 57.593 43.478 0.00 0.00 0.00 4.30
519 1409 4.323569 TCTCTCACAACAGATACTCCCT 57.676 45.455 0.00 0.00 0.00 4.20
520 1410 4.274147 TCTCTCACAACAGATACTCCCTC 58.726 47.826 0.00 0.00 0.00 4.30
521 1411 3.366396 TCTCACAACAGATACTCCCTCC 58.634 50.000 0.00 0.00 0.00 4.30
522 1412 3.099905 CTCACAACAGATACTCCCTCCA 58.900 50.000 0.00 0.00 0.00 3.86
523 1413 3.708631 CTCACAACAGATACTCCCTCCAT 59.291 47.826 0.00 0.00 0.00 3.41
524 1414 4.104086 TCACAACAGATACTCCCTCCATT 58.896 43.478 0.00 0.00 0.00 3.16
525 1415 4.536090 TCACAACAGATACTCCCTCCATTT 59.464 41.667 0.00 0.00 0.00 2.32
526 1416 5.014123 TCACAACAGATACTCCCTCCATTTT 59.986 40.000 0.00 0.00 0.00 1.82
527 1417 5.711976 CACAACAGATACTCCCTCCATTTTT 59.288 40.000 0.00 0.00 0.00 1.94
528 1418 6.884295 CACAACAGATACTCCCTCCATTTTTA 59.116 38.462 0.00 0.00 0.00 1.52
529 1419 7.393234 CACAACAGATACTCCCTCCATTTTTAA 59.607 37.037 0.00 0.00 0.00 1.52
530 1420 7.947890 ACAACAGATACTCCCTCCATTTTTAAA 59.052 33.333 0.00 0.00 0.00 1.52
531 1421 8.971073 CAACAGATACTCCCTCCATTTTTAAAT 58.029 33.333 0.00 0.00 0.00 1.40
539 1429 9.547279 ACTCCCTCCATTTTTAAATATTTGTCT 57.453 29.630 11.05 0.00 0.00 3.41
578 1468 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
579 1469 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
580 1470 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
581 1471 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
582 1472 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
583 1473 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
584 1474 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
585 1475 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
586 1476 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
587 1477 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
589 1479 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
618 1508 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
619 1509 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
620 1510 5.412594 GTGTAGATTCACTCATTTTGCTCCA 59.587 40.000 0.00 0.00 35.68 3.86
621 1511 6.094603 GTGTAGATTCACTCATTTTGCTCCAT 59.905 38.462 0.00 0.00 35.68 3.41
622 1512 7.280876 GTGTAGATTCACTCATTTTGCTCCATA 59.719 37.037 0.00 0.00 35.68 2.74
623 1513 7.994911 TGTAGATTCACTCATTTTGCTCCATAT 59.005 33.333 0.00 0.00 0.00 1.78
624 1514 7.273320 AGATTCACTCATTTTGCTCCATATG 57.727 36.000 0.00 0.00 0.00 1.78
625 1515 6.832384 AGATTCACTCATTTTGCTCCATATGT 59.168 34.615 1.24 0.00 0.00 2.29
626 1516 7.994911 AGATTCACTCATTTTGCTCCATATGTA 59.005 33.333 1.24 0.00 0.00 2.29
627 1517 7.558161 TTCACTCATTTTGCTCCATATGTAG 57.442 36.000 1.24 0.00 0.00 2.74
628 1518 6.057533 TCACTCATTTTGCTCCATATGTAGG 58.942 40.000 1.24 0.00 0.00 3.18
629 1519 4.823989 ACTCATTTTGCTCCATATGTAGGC 59.176 41.667 1.24 3.68 0.00 3.93
630 1520 4.790937 TCATTTTGCTCCATATGTAGGCA 58.209 39.130 1.24 6.22 0.00 4.75
631 1521 4.580167 TCATTTTGCTCCATATGTAGGCAC 59.420 41.667 12.03 0.00 32.47 5.01
632 1522 3.931907 TTTGCTCCATATGTAGGCACT 57.068 42.857 12.03 0.00 46.37 4.40
633 1523 3.931907 TTGCTCCATATGTAGGCACTT 57.068 42.857 12.03 0.00 41.75 3.16
634 1524 3.198409 TGCTCCATATGTAGGCACTTG 57.802 47.619 1.24 0.00 41.75 3.16
635 1525 2.505407 TGCTCCATATGTAGGCACTTGT 59.495 45.455 1.24 0.00 41.75 3.16
636 1526 3.054434 TGCTCCATATGTAGGCACTTGTT 60.054 43.478 1.24 0.00 41.75 2.83
637 1527 3.313526 GCTCCATATGTAGGCACTTGTTG 59.686 47.826 1.24 0.00 41.75 3.33
638 1528 4.769688 CTCCATATGTAGGCACTTGTTGA 58.230 43.478 1.24 0.00 41.75 3.18
639 1529 5.172687 TCCATATGTAGGCACTTGTTGAA 57.827 39.130 1.24 0.00 41.75 2.69
640 1530 5.565509 TCCATATGTAGGCACTTGTTGAAA 58.434 37.500 1.24 0.00 41.75 2.69
641 1531 6.186957 TCCATATGTAGGCACTTGTTGAAAT 58.813 36.000 1.24 0.00 41.75 2.17
642 1532 6.663093 TCCATATGTAGGCACTTGTTGAAATT 59.337 34.615 1.24 0.00 41.75 1.82
643 1533 7.178274 TCCATATGTAGGCACTTGTTGAAATTT 59.822 33.333 1.24 0.00 41.75 1.82
644 1534 7.489113 CCATATGTAGGCACTTGTTGAAATTTC 59.511 37.037 11.41 11.41 41.75 2.17
645 1535 6.655078 ATGTAGGCACTTGTTGAAATTTCT 57.345 33.333 18.64 0.00 41.75 2.52
646 1536 7.759489 ATGTAGGCACTTGTTGAAATTTCTA 57.241 32.000 18.64 8.95 41.75 2.10
647 1537 7.202016 TGTAGGCACTTGTTGAAATTTCTAG 57.798 36.000 18.64 12.38 41.75 2.43
648 1538 5.712152 AGGCACTTGTTGAAATTTCTAGG 57.288 39.130 18.64 8.51 27.25 3.02
649 1539 5.385198 AGGCACTTGTTGAAATTTCTAGGA 58.615 37.500 18.64 2.87 27.25 2.94
650 1540 5.833131 AGGCACTTGTTGAAATTTCTAGGAA 59.167 36.000 18.64 2.39 27.25 3.36
651 1541 6.015940 AGGCACTTGTTGAAATTTCTAGGAAG 60.016 38.462 18.64 16.16 27.25 3.46
652 1542 6.016276 GGCACTTGTTGAAATTTCTAGGAAGA 60.016 38.462 18.64 1.18 0.00 2.87
653 1543 6.858478 GCACTTGTTGAAATTTCTAGGAAGAC 59.142 38.462 18.64 9.95 0.00 3.01
654 1544 7.468631 GCACTTGTTGAAATTTCTAGGAAGACA 60.469 37.037 18.64 9.10 0.00 3.41
655 1545 8.405531 CACTTGTTGAAATTTCTAGGAAGACAA 58.594 33.333 18.64 14.42 0.00 3.18
656 1546 8.966868 ACTTGTTGAAATTTCTAGGAAGACAAA 58.033 29.630 18.64 0.00 0.00 2.83
657 1547 9.971922 CTTGTTGAAATTTCTAGGAAGACAAAT 57.028 29.630 18.64 0.00 0.00 2.32
672 1562 9.413734 AGGAAGACAAATATTTAGAAATGGAGG 57.586 33.333 0.00 0.00 0.00 4.30
673 1563 8.633561 GGAAGACAAATATTTAGAAATGGAGGG 58.366 37.037 0.00 0.00 0.00 4.30
674 1564 9.408648 GAAGACAAATATTTAGAAATGGAGGGA 57.591 33.333 0.00 0.00 0.00 4.20
675 1565 8.986929 AGACAAATATTTAGAAATGGAGGGAG 57.013 34.615 0.00 0.00 0.00 4.30
719 1612 9.650539 TTTAAATGCAACACAAATATAGTGCAT 57.349 25.926 3.22 3.22 42.57 3.96
721 1614 7.528481 AATGCAACACAAATATAGTGCATTG 57.472 32.000 17.98 10.75 45.92 2.82
722 1615 6.264841 TGCAACACAAATATAGTGCATTGA 57.735 33.333 2.61 0.00 40.59 2.57
723 1616 6.324042 TGCAACACAAATATAGTGCATTGAG 58.676 36.000 2.61 0.00 40.59 3.02
724 1617 6.150809 TGCAACACAAATATAGTGCATTGAGA 59.849 34.615 2.61 0.00 40.59 3.27
725 1618 7.148035 TGCAACACAAATATAGTGCATTGAGAT 60.148 33.333 2.61 0.00 40.59 2.75
746 1639 8.267183 TGAGATTTGAGAGTGCCATATCTAAAA 58.733 33.333 0.00 0.00 34.19 1.52
762 1655 6.839124 ATCTAAAACATGAATGCCAACTCA 57.161 33.333 0.00 0.00 0.00 3.41
833 1726 9.832445 AAGTTGACCAATCTATAAATACACGAT 57.168 29.630 0.00 0.00 0.00 3.73
895 1788 3.710926 CTGCCAGTCAGCTCTCCT 58.289 61.111 0.00 0.00 35.78 3.69
904 1797 3.003275 CAGTCAGCTCTCCTTCTCGATAC 59.997 52.174 0.00 0.00 0.00 2.24
918 1811 1.822990 TCGATACCTTGACCAGTGACC 59.177 52.381 0.00 0.00 0.00 4.02
933 1828 2.303022 AGTGACCACAATACTCCACTGG 59.697 50.000 2.78 0.00 34.08 4.00
934 1829 2.038557 GTGACCACAATACTCCACTGGT 59.961 50.000 0.00 0.00 37.96 4.00
948 1843 2.159366 CCACTGGTAGTAGCACGAGAAG 60.159 54.545 0.00 0.00 0.00 2.85
966 1861 3.365265 CCTTTGCAGGGCGTCCAC 61.365 66.667 9.71 0.00 36.36 4.02
967 1862 2.281761 CTTTGCAGGGCGTCCACT 60.282 61.111 9.71 0.00 34.83 4.00
968 1863 2.281484 TTTGCAGGGCGTCCACTC 60.281 61.111 9.71 0.00 34.83 3.51
969 1864 3.842925 TTTGCAGGGCGTCCACTCC 62.843 63.158 9.71 0.00 34.83 3.85
972 1867 3.625897 CAGGGCGTCCACTCCACA 61.626 66.667 9.71 0.00 34.83 4.17
973 1868 3.626924 AGGGCGTCCACTCCACAC 61.627 66.667 9.71 0.00 34.83 3.82
993 1897 0.986019 ACACACACAACAGGGGAGGA 60.986 55.000 0.00 0.00 0.00 3.71
1164 2069 2.027192 TCAGATTCACCCACAGCTTACC 60.027 50.000 0.00 0.00 0.00 2.85
1166 2071 2.084546 GATTCACCCACAGCTTACCAC 58.915 52.381 0.00 0.00 0.00 4.16
1212 2117 6.374613 TCTCGTTTCTGATCTCTTGCTAACTA 59.625 38.462 0.00 0.00 0.00 2.24
1214 2119 8.221965 TCGTTTCTGATCTCTTGCTAACTATA 57.778 34.615 0.00 0.00 0.00 1.31
1215 2120 8.851145 TCGTTTCTGATCTCTTGCTAACTATAT 58.149 33.333 0.00 0.00 0.00 0.86
1221 2126 9.755804 CTGATCTCTTGCTAACTATATTGTGAA 57.244 33.333 0.00 0.00 0.00 3.18
1275 2189 0.110486 TTGCAGACCTTCTTCCCCAC 59.890 55.000 0.00 0.00 0.00 4.61
1282 2196 1.672356 CTTCTTCCCCACGGTGCTG 60.672 63.158 1.68 0.00 0.00 4.41
1286 2200 4.631740 TCCCCACGGTGCTGAGGA 62.632 66.667 1.68 3.15 0.00 3.71
1673 2587 3.672447 TCAACTACGGCACCGCGA 61.672 61.111 8.23 0.00 44.19 5.87
1984 2898 2.743928 CCGTTCTGCCACCAGCTC 60.744 66.667 0.00 0.00 44.23 4.09
2174 3088 3.272334 GCGCGGTGATCATGGTCC 61.272 66.667 8.83 0.00 0.00 4.46
2176 3090 1.592669 CGCGGTGATCATGGTCCTC 60.593 63.158 2.86 0.00 0.00 3.71
2210 3124 2.814604 CGTGGATCATGGGAGCGA 59.185 61.111 0.00 0.00 0.00 4.93
2377 3291 2.179517 CAGTCGGTGAGCGTCTCC 59.820 66.667 3.30 1.40 0.00 3.71
2428 3342 3.378399 GACCTTCCTCGCCCTGCTC 62.378 68.421 0.00 0.00 0.00 4.26
2455 3369 2.027897 AAGTACGCCACGTTCGCA 59.972 55.556 6.86 0.00 41.54 5.10
2473 3387 2.496291 ATACTACGCGGCCTGGGTC 61.496 63.158 12.47 0.00 43.62 4.46
2506 3420 1.673329 GCCTTCGTCTTGGTCTTCCTC 60.673 57.143 0.00 0.00 34.23 3.71
2554 3468 3.083997 ATGGGCTCCGTCTGGGAC 61.084 66.667 0.00 0.00 40.94 4.46
2646 3560 2.283617 CGTCTGCATCAACATGAGCTAC 59.716 50.000 0.00 0.00 30.57 3.58
2677 3591 2.159128 TGTCCGTTCAACGACAACCTTA 60.159 45.455 12.68 0.00 46.05 2.69
2678 3592 2.473984 GTCCGTTCAACGACAACCTTAG 59.526 50.000 12.68 0.00 46.05 2.18
2679 3593 2.361757 TCCGTTCAACGACAACCTTAGA 59.638 45.455 12.68 0.00 46.05 2.10
2681 3595 2.729882 CGTTCAACGACAACCTTAGAGG 59.270 50.000 3.01 0.00 46.05 3.69
2682 3596 2.450609 TCAACGACAACCTTAGAGGC 57.549 50.000 0.00 0.00 39.63 4.70
2683 3597 1.968493 TCAACGACAACCTTAGAGGCT 59.032 47.619 0.00 0.00 39.63 4.58
2684 3598 2.069273 CAACGACAACCTTAGAGGCTG 58.931 52.381 0.00 0.00 39.63 4.85
2685 3599 1.629043 ACGACAACCTTAGAGGCTGA 58.371 50.000 4.50 0.00 39.63 4.26
2686 3600 1.968493 ACGACAACCTTAGAGGCTGAA 59.032 47.619 4.50 0.00 39.63 3.02
2687 3601 2.028930 ACGACAACCTTAGAGGCTGAAG 60.029 50.000 4.50 0.00 39.63 3.02
2688 3602 2.675317 CGACAACCTTAGAGGCTGAAGG 60.675 54.545 18.86 18.86 46.56 3.46
2693 3607 1.573108 CTTAGAGGCTGAAGGTGGGA 58.427 55.000 0.00 0.00 0.00 4.37
2694 3608 1.208293 CTTAGAGGCTGAAGGTGGGAC 59.792 57.143 0.00 0.00 0.00 4.46
2695 3609 0.617820 TAGAGGCTGAAGGTGGGACC 60.618 60.000 0.00 0.00 38.99 4.46
2696 3610 2.936032 AGGCTGAAGGTGGGACCC 60.936 66.667 2.45 2.45 39.75 4.46
2697 3611 3.256960 GGCTGAAGGTGGGACCCA 61.257 66.667 9.95 9.95 39.75 4.51
2698 3612 2.352805 GCTGAAGGTGGGACCCAG 59.647 66.667 15.52 1.48 39.75 4.45
2706 3620 3.713902 GTGGGACCCAGCATAGATG 57.286 57.895 15.52 0.00 32.34 2.90
2717 3631 1.454976 CATAGATGCAGCCCAGCCT 59.545 57.895 0.00 0.00 0.00 4.58
2718 3632 0.605860 CATAGATGCAGCCCAGCCTC 60.606 60.000 0.00 0.00 0.00 4.70
2720 3634 0.105504 TAGATGCAGCCCAGCCTCTA 60.106 55.000 0.00 4.92 39.64 2.43
2724 3638 0.690744 TGCAGCCCAGCCTCTATACA 60.691 55.000 0.00 0.00 0.00 2.29
2726 3640 1.418334 CAGCCCAGCCTCTATACACT 58.582 55.000 0.00 0.00 0.00 3.55
2728 3735 0.250081 GCCCAGCCTCTATACACTGC 60.250 60.000 0.00 0.00 0.00 4.40
2735 3742 2.869636 GCCTCTATACACTGCTGATGCC 60.870 54.545 0.00 0.00 38.71 4.40
2736 3743 2.289320 CCTCTATACACTGCTGATGCCC 60.289 54.545 0.00 0.00 38.71 5.36
2741 3748 1.206878 ACACTGCTGATGCCCTCATA 58.793 50.000 0.00 0.00 38.71 2.15
2838 3846 9.719355 ATGTATACATGTTCTTGTGTAGTGAAA 57.281 29.630 17.60 0.00 34.60 2.69
2839 3847 9.719355 TGTATACATGTTCTTGTGTAGTGAAAT 57.281 29.630 2.30 0.00 34.60 2.17
2842 3850 7.807977 ACATGTTCTTGTGTAGTGAAATCTT 57.192 32.000 0.00 0.00 0.00 2.40
2843 3851 8.225603 ACATGTTCTTGTGTAGTGAAATCTTT 57.774 30.769 0.00 0.00 0.00 2.52
2844 3852 8.345565 ACATGTTCTTGTGTAGTGAAATCTTTC 58.654 33.333 0.00 0.00 37.69 2.62
2845 3853 8.562892 CATGTTCTTGTGTAGTGAAATCTTTCT 58.437 33.333 4.46 0.00 38.02 2.52
2846 3854 9.778741 ATGTTCTTGTGTAGTGAAATCTTTCTA 57.221 29.630 4.46 0.00 38.02 2.10
2918 3941 5.119588 GTCAACCAATCGTAATTGACTCGAA 59.880 40.000 8.36 0.00 44.83 3.71
2929 3952 8.172484 TCGTAATTGACTCGAACCAAAAATATG 58.828 33.333 3.67 4.33 0.00 1.78
2932 3965 5.545658 TGACTCGAACCAAAAATATGAGC 57.454 39.130 0.00 0.00 0.00 4.26
3051 4100 7.817478 CCCATTAGAAGGTTTTTAATGTTCCAC 59.183 37.037 9.71 0.00 34.51 4.02
3084 4133 3.367992 TTGTGATGTTCCATTGTGTGC 57.632 42.857 0.00 0.00 0.00 4.57
3104 4153 5.595133 TGTGCCATCATTATTGTGATCACAT 59.405 36.000 28.32 19.48 37.90 3.21
3192 4481 5.415701 TCCTGATACAACTTGGAGCAAATTC 59.584 40.000 0.00 0.00 0.00 2.17
3256 4545 2.158445 GCAGTATGACTCTAGAGGGGGA 60.158 54.545 23.50 4.86 39.69 4.81
3280 4573 3.363787 GGCATTCCCTCTGTTTGGT 57.636 52.632 0.00 0.00 0.00 3.67
3281 4574 1.177401 GGCATTCCCTCTGTTTGGTC 58.823 55.000 0.00 0.00 0.00 4.02
3282 4575 1.272147 GGCATTCCCTCTGTTTGGTCT 60.272 52.381 0.00 0.00 0.00 3.85
3283 4576 2.026262 GGCATTCCCTCTGTTTGGTCTA 60.026 50.000 0.00 0.00 0.00 2.59
3284 4577 3.010420 GCATTCCCTCTGTTTGGTCTAC 58.990 50.000 0.00 0.00 0.00 2.59
3285 4578 3.307762 GCATTCCCTCTGTTTGGTCTACT 60.308 47.826 0.00 0.00 0.00 2.57
3286 4579 4.807643 GCATTCCCTCTGTTTGGTCTACTT 60.808 45.833 0.00 0.00 0.00 2.24
3287 4580 5.316987 CATTCCCTCTGTTTGGTCTACTTT 58.683 41.667 0.00 0.00 0.00 2.66
3288 4581 6.472887 CATTCCCTCTGTTTGGTCTACTTTA 58.527 40.000 0.00 0.00 0.00 1.85
3289 4582 5.740290 TCCCTCTGTTTGGTCTACTTTAG 57.260 43.478 0.00 0.00 0.00 1.85
3313 4606 0.472471 TCGCAGGGTCCAAGTCTTTT 59.528 50.000 0.00 0.00 0.00 2.27
3329 4622 6.120507 AGTCTTTTTGTGGCTTCTATCTCT 57.879 37.500 0.00 0.00 0.00 3.10
3332 4625 7.604545 AGTCTTTTTGTGGCTTCTATCTCTTAC 59.395 37.037 0.00 0.00 0.00 2.34
3349 4643 7.642082 TCTCTTACCAAACCTATGACTAGAC 57.358 40.000 0.00 0.00 0.00 2.59
3351 4645 7.672660 TCTCTTACCAAACCTATGACTAGACAA 59.327 37.037 0.00 0.00 0.00 3.18
3453 4747 7.096312 GCTCTTTGATTGTGCAGTTTCTAAAAG 60.096 37.037 0.00 0.00 0.00 2.27
3544 4838 0.466555 TTGGCCCGCTAACAACAACT 60.467 50.000 0.00 0.00 0.00 3.16
3548 4842 0.441145 CCCGCTAACAACAACTACGC 59.559 55.000 0.00 0.00 0.00 4.42
3566 4860 2.745281 ACGCGTGCCTAATTTTACATGT 59.255 40.909 12.93 2.69 0.00 3.21
3579 4873 9.229784 CTAATTTTACATGTGCTTGCATCTTAG 57.770 33.333 9.11 0.52 0.00 2.18
3587 4881 2.289565 GCTTGCATCTTAGGGTGTACC 58.710 52.381 0.00 0.00 40.67 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 5.776519 TGGCGCAAATACAAAATCATTTC 57.223 34.783 10.83 0.00 0.00 2.17
183 185 8.553085 TTCCTATCACTATCCTTGAATCTTCA 57.447 34.615 0.00 0.00 34.92 3.02
184 186 9.651913 GATTCCTATCACTATCCTTGAATCTTC 57.348 37.037 0.00 0.00 35.91 2.87
234 238 9.106070 GGTGAATAACTAACCAACCTATACTTG 57.894 37.037 0.00 0.00 33.94 3.16
255 259 2.373169 AGCTGACTCAAGATTGGGTGAA 59.627 45.455 2.08 0.00 43.16 3.18
261 265 2.170187 AGGGCTAGCTGACTCAAGATTG 59.830 50.000 15.72 0.00 0.00 2.67
329 611 0.617413 CAAGATGGAGCACTGGGAGT 59.383 55.000 0.00 0.00 0.00 3.85
344 626 8.924511 ACAGAAAAATTCTTATGAGTCCAAGA 57.075 30.769 0.00 1.20 38.11 3.02
357 639 8.704668 ACCCAAACTATTCAACAGAAAAATTCT 58.295 29.630 0.00 0.00 41.70 2.40
358 640 8.887036 ACCCAAACTATTCAACAGAAAAATTC 57.113 30.769 0.00 0.00 0.00 2.17
359 641 9.108284 CAACCCAAACTATTCAACAGAAAAATT 57.892 29.630 0.00 0.00 0.00 1.82
360 642 7.226523 GCAACCCAAACTATTCAACAGAAAAAT 59.773 33.333 0.00 0.00 0.00 1.82
361 643 6.536941 GCAACCCAAACTATTCAACAGAAAAA 59.463 34.615 0.00 0.00 0.00 1.94
364 646 4.892934 AGCAACCCAAACTATTCAACAGAA 59.107 37.500 0.00 0.00 0.00 3.02
366 648 4.853924 AGCAACCCAAACTATTCAACAG 57.146 40.909 0.00 0.00 0.00 3.16
368 650 5.466819 GGTAAGCAACCCAAACTATTCAAC 58.533 41.667 0.00 0.00 43.16 3.18
369 651 5.715434 GGTAAGCAACCCAAACTATTCAA 57.285 39.130 0.00 0.00 43.16 2.69
382 664 6.927381 ACCAGATAATATACGTGGTAAGCAAC 59.073 38.462 0.00 0.00 39.80 4.17
383 665 7.058023 ACCAGATAATATACGTGGTAAGCAA 57.942 36.000 0.00 0.00 39.80 3.91
384 666 6.659745 ACCAGATAATATACGTGGTAAGCA 57.340 37.500 0.00 0.00 39.80 3.91
385 667 7.031975 GGTACCAGATAATATACGTGGTAAGC 58.968 42.308 7.15 1.64 43.65 3.09
386 668 8.345724 AGGTACCAGATAATATACGTGGTAAG 57.654 38.462 15.94 0.00 43.65 2.34
387 669 9.979897 ATAGGTACCAGATAATATACGTGGTAA 57.020 33.333 15.94 0.00 43.65 2.85
388 670 9.979897 AATAGGTACCAGATAATATACGTGGTA 57.020 33.333 15.94 0.00 41.76 3.25
390 672 8.963725 TCAATAGGTACCAGATAATATACGTGG 58.036 37.037 15.94 0.00 0.00 4.94
468 1358 5.540337 TCTGAGATATTATTGCTCCCTTCGT 59.460 40.000 0.00 0.00 0.00 3.85
469 1359 6.030548 TCTGAGATATTATTGCTCCCTTCG 57.969 41.667 0.00 0.00 0.00 3.79
491 1381 8.447053 GGAGTATCTGTTGTGAGAGAAAATTTC 58.553 37.037 0.00 0.00 33.73 2.17
513 1403 9.547279 AGACAAATATTTAAAAATGGAGGGAGT 57.453 29.630 0.00 0.00 0.00 3.85
545 1435 9.614792 GTATGTGGTAGTCCATTTAAAATCTCT 57.385 33.333 0.00 0.00 46.20 3.10
546 1436 8.548721 CGTATGTGGTAGTCCATTTAAAATCTC 58.451 37.037 0.00 0.00 46.20 2.75
547 1437 7.497909 CCGTATGTGGTAGTCCATTTAAAATCT 59.502 37.037 0.00 0.00 46.20 2.40
548 1438 7.496591 TCCGTATGTGGTAGTCCATTTAAAATC 59.503 37.037 0.00 0.00 46.20 2.17
549 1439 7.340256 TCCGTATGTGGTAGTCCATTTAAAAT 58.660 34.615 0.00 0.00 46.20 1.82
550 1440 6.709281 TCCGTATGTGGTAGTCCATTTAAAA 58.291 36.000 0.00 0.00 46.20 1.52
551 1441 6.297080 TCCGTATGTGGTAGTCCATTTAAA 57.703 37.500 0.00 0.00 46.20 1.52
552 1442 5.936187 TCCGTATGTGGTAGTCCATTTAA 57.064 39.130 0.00 0.00 46.20 1.52
553 1443 5.364446 ACATCCGTATGTGGTAGTCCATTTA 59.636 40.000 0.00 0.00 44.79 1.40
554 1444 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
555 1445 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
556 1446 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
557 1447 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
558 1448 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
559 1449 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
560 1450 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
561 1451 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
563 1453 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
596 1486 5.412594 TGGAGCAAAATGAGTGAATCTACAC 59.587 40.000 0.00 0.00 40.60 2.90
597 1487 5.559770 TGGAGCAAAATGAGTGAATCTACA 58.440 37.500 0.00 0.00 0.00 2.74
598 1488 6.690194 ATGGAGCAAAATGAGTGAATCTAC 57.310 37.500 0.00 0.00 0.00 2.59
599 1489 7.994911 ACATATGGAGCAAAATGAGTGAATCTA 59.005 33.333 7.80 0.00 0.00 1.98
600 1490 6.832384 ACATATGGAGCAAAATGAGTGAATCT 59.168 34.615 7.80 0.00 0.00 2.40
601 1491 7.035840 ACATATGGAGCAAAATGAGTGAATC 57.964 36.000 7.80 0.00 0.00 2.52
602 1492 7.230108 CCTACATATGGAGCAAAATGAGTGAAT 59.770 37.037 9.70 0.00 0.00 2.57
603 1493 6.543465 CCTACATATGGAGCAAAATGAGTGAA 59.457 38.462 9.70 0.00 0.00 3.18
604 1494 6.057533 CCTACATATGGAGCAAAATGAGTGA 58.942 40.000 9.70 0.00 0.00 3.41
605 1495 5.278169 GCCTACATATGGAGCAAAATGAGTG 60.278 44.000 9.70 0.00 0.00 3.51
606 1496 4.823989 GCCTACATATGGAGCAAAATGAGT 59.176 41.667 9.70 0.00 0.00 3.41
607 1497 4.823442 TGCCTACATATGGAGCAAAATGAG 59.177 41.667 9.70 0.00 0.00 2.90
608 1498 4.580167 GTGCCTACATATGGAGCAAAATGA 59.420 41.667 9.70 0.00 34.79 2.57
609 1499 4.581824 AGTGCCTACATATGGAGCAAAATG 59.418 41.667 9.70 0.00 34.79 2.32
610 1500 4.796606 AGTGCCTACATATGGAGCAAAAT 58.203 39.130 9.70 1.54 34.79 1.82
611 1501 4.235079 AGTGCCTACATATGGAGCAAAA 57.765 40.909 9.70 0.00 34.79 2.44
612 1502 3.931907 AGTGCCTACATATGGAGCAAA 57.068 42.857 9.70 0.00 34.79 3.68
613 1503 3.054434 ACAAGTGCCTACATATGGAGCAA 60.054 43.478 9.70 0.00 34.79 3.91
614 1504 2.505407 ACAAGTGCCTACATATGGAGCA 59.495 45.455 9.70 10.59 0.00 4.26
615 1505 3.199880 ACAAGTGCCTACATATGGAGC 57.800 47.619 9.70 8.06 0.00 4.70
616 1506 4.769688 TCAACAAGTGCCTACATATGGAG 58.230 43.478 8.10 8.10 0.00 3.86
617 1507 4.835284 TCAACAAGTGCCTACATATGGA 57.165 40.909 7.80 0.00 0.00 3.41
618 1508 5.895636 TTTCAACAAGTGCCTACATATGG 57.104 39.130 7.80 0.00 0.00 2.74
619 1509 8.246180 AGAAATTTCAACAAGTGCCTACATATG 58.754 33.333 19.99 0.00 0.00 1.78
620 1510 8.353423 AGAAATTTCAACAAGTGCCTACATAT 57.647 30.769 19.99 0.00 0.00 1.78
621 1511 7.759489 AGAAATTTCAACAAGTGCCTACATA 57.241 32.000 19.99 0.00 0.00 2.29
622 1512 6.655078 AGAAATTTCAACAAGTGCCTACAT 57.345 33.333 19.99 0.00 0.00 2.29
623 1513 6.206634 CCTAGAAATTTCAACAAGTGCCTACA 59.793 38.462 19.99 0.00 0.00 2.74
624 1514 6.430000 TCCTAGAAATTTCAACAAGTGCCTAC 59.570 38.462 19.99 0.00 0.00 3.18
625 1515 6.539173 TCCTAGAAATTTCAACAAGTGCCTA 58.461 36.000 19.99 0.00 0.00 3.93
626 1516 5.385198 TCCTAGAAATTTCAACAAGTGCCT 58.615 37.500 19.99 0.00 0.00 4.75
627 1517 5.705609 TCCTAGAAATTTCAACAAGTGCC 57.294 39.130 19.99 0.00 0.00 5.01
628 1518 6.858478 GTCTTCCTAGAAATTTCAACAAGTGC 59.142 38.462 19.99 9.49 30.65 4.40
629 1519 7.930217 TGTCTTCCTAGAAATTTCAACAAGTG 58.070 34.615 19.99 5.11 30.65 3.16
630 1520 8.519799 TTGTCTTCCTAGAAATTTCAACAAGT 57.480 30.769 19.99 0.99 30.65 3.16
631 1521 9.971922 ATTTGTCTTCCTAGAAATTTCAACAAG 57.028 29.630 19.99 14.44 30.65 3.16
646 1536 9.413734 CCTCCATTTCTAAATATTTGTCTTCCT 57.586 33.333 11.05 0.00 0.00 3.36
647 1537 8.633561 CCCTCCATTTCTAAATATTTGTCTTCC 58.366 37.037 11.05 0.00 0.00 3.46
648 1538 9.408648 TCCCTCCATTTCTAAATATTTGTCTTC 57.591 33.333 11.05 0.00 0.00 2.87
649 1539 9.413734 CTCCCTCCATTTCTAAATATTTGTCTT 57.586 33.333 11.05 0.00 0.00 3.01
650 1540 8.560903 ACTCCCTCCATTTCTAAATATTTGTCT 58.439 33.333 11.05 0.00 0.00 3.41
651 1541 8.753497 ACTCCCTCCATTTCTAAATATTTGTC 57.247 34.615 11.05 0.00 0.00 3.18
691 1584 9.739786 GCACTATATTTGTGTTGCATTTAAAAC 57.260 29.630 9.34 0.00 37.70 2.43
719 1612 6.244552 AGATATGGCACTCTCAAATCTCAA 57.755 37.500 0.00 0.00 0.00 3.02
720 1613 5.883685 AGATATGGCACTCTCAAATCTCA 57.116 39.130 0.00 0.00 0.00 3.27
721 1614 8.555361 GTTTTAGATATGGCACTCTCAAATCTC 58.445 37.037 4.80 0.00 0.00 2.75
722 1615 8.049117 TGTTTTAGATATGGCACTCTCAAATCT 58.951 33.333 4.80 1.51 0.00 2.40
723 1616 8.213518 TGTTTTAGATATGGCACTCTCAAATC 57.786 34.615 4.80 4.12 0.00 2.17
724 1617 8.627403 CATGTTTTAGATATGGCACTCTCAAAT 58.373 33.333 4.80 0.00 0.00 2.32
725 1618 7.828717 TCATGTTTTAGATATGGCACTCTCAAA 59.171 33.333 4.80 4.83 0.00 2.69
830 1723 3.282157 CAAGGGCCGGCATCATCG 61.282 66.667 30.85 7.13 0.00 3.84
833 1726 3.008517 TCTCAAGGGCCGGCATCA 61.009 61.111 30.85 5.65 0.00 3.07
855 1748 2.582978 GTACCGAGGAAGGGTGCC 59.417 66.667 0.00 0.00 38.50 5.01
895 1788 3.192844 GTCACTGGTCAAGGTATCGAGAA 59.807 47.826 0.00 0.00 0.00 2.87
904 1797 2.276732 ATTGTGGTCACTGGTCAAGG 57.723 50.000 2.66 0.00 0.00 3.61
918 1811 4.159693 TGCTACTACCAGTGGAGTATTGTG 59.840 45.833 18.40 8.37 0.00 3.33
933 1828 2.924290 CAAAGGCTTCTCGTGCTACTAC 59.076 50.000 0.00 0.00 0.00 2.73
934 1829 2.674177 GCAAAGGCTTCTCGTGCTACTA 60.674 50.000 13.06 0.00 36.96 1.82
965 1860 1.271108 TGTTGTGTGTGTGTGTGGAGT 60.271 47.619 0.00 0.00 0.00 3.85
966 1861 1.398041 CTGTTGTGTGTGTGTGTGGAG 59.602 52.381 0.00 0.00 0.00 3.86
967 1862 1.447945 CTGTTGTGTGTGTGTGTGGA 58.552 50.000 0.00 0.00 0.00 4.02
968 1863 0.451383 CCTGTTGTGTGTGTGTGTGG 59.549 55.000 0.00 0.00 0.00 4.17
969 1864 0.451383 CCCTGTTGTGTGTGTGTGTG 59.549 55.000 0.00 0.00 0.00 3.82
970 1865 0.679640 CCCCTGTTGTGTGTGTGTGT 60.680 55.000 0.00 0.00 0.00 3.72
971 1866 0.393673 TCCCCTGTTGTGTGTGTGTG 60.394 55.000 0.00 0.00 0.00 3.82
972 1867 0.107214 CTCCCCTGTTGTGTGTGTGT 60.107 55.000 0.00 0.00 0.00 3.72
973 1868 0.819259 CCTCCCCTGTTGTGTGTGTG 60.819 60.000 0.00 0.00 0.00 3.82
993 1897 2.510691 CCTACGGCCATCGCGTTT 60.511 61.111 5.77 0.00 43.89 3.60
1164 2069 3.112075 ACACCGCGCAAGATCGTG 61.112 61.111 8.75 4.06 43.02 4.35
1166 2071 4.505217 GCACACCGCGCAAGATCG 62.505 66.667 8.75 0.00 43.02 3.69
1212 2117 4.432712 GCCGCCTGAATTTTTCACAATAT 58.567 39.130 0.00 0.00 35.46 1.28
1214 2119 2.687370 GCCGCCTGAATTTTTCACAAT 58.313 42.857 0.00 0.00 35.46 2.71
1215 2120 1.601663 CGCCGCCTGAATTTTTCACAA 60.602 47.619 0.00 0.00 35.46 3.33
1221 2126 1.635663 CGAGACGCCGCCTGAATTTT 61.636 55.000 0.00 0.00 0.00 1.82
1275 2189 2.503061 CCATCCTCCTCAGCACCG 59.497 66.667 0.00 0.00 0.00 4.94
1282 2196 4.593864 GCGTCCGCCATCCTCCTC 62.594 72.222 0.00 0.00 34.56 3.71
1286 2200 4.514577 CTTCGCGTCCGCCATCCT 62.515 66.667 5.77 0.00 37.98 3.24
1393 2307 4.849329 GACCTAGTGACGCGGCCG 62.849 72.222 24.05 24.05 41.14 6.13
1483 2397 0.745486 TGAGCATGGCGAGGTTCATG 60.745 55.000 0.00 0.00 42.47 3.07
1954 2868 4.224274 AACGGCACCACGACGGAA 62.224 61.111 0.00 0.00 38.63 4.30
2174 3088 2.811317 GTTCGCGACCTGGCAGAG 60.811 66.667 17.94 8.80 0.00 3.35
2386 3300 3.965539 CTGCAGGAAGGTGAGCCCG 62.966 68.421 5.57 0.00 38.74 6.13
2428 3342 3.188786 GCGTACTTGAGGCGGCAG 61.189 66.667 13.08 1.84 0.00 4.85
2434 3348 1.342082 CGAACGTGGCGTACTTGAGG 61.342 60.000 0.00 0.00 39.99 3.86
2455 3369 2.443390 ACCCAGGCCGCGTAGTAT 60.443 61.111 4.92 0.00 0.00 2.12
2554 3468 1.079127 CTTCCAGTACCAGTGGCGG 60.079 63.158 9.78 5.08 38.59 6.13
2615 3529 1.137675 TGATGCAGACGGAGATGAAGG 59.862 52.381 0.00 0.00 0.00 3.46
2646 3560 0.646381 TGAACGGACAAACGAACACG 59.354 50.000 0.00 0.00 37.61 4.49
2677 3591 1.920835 GGTCCCACCTTCAGCCTCT 60.921 63.158 0.00 0.00 34.73 3.69
2678 3592 2.671682 GGTCCCACCTTCAGCCTC 59.328 66.667 0.00 0.00 34.73 4.70
2679 3593 2.936032 GGGTCCCACCTTCAGCCT 60.936 66.667 1.78 0.00 38.64 4.58
2681 3595 2.352805 CTGGGTCCCACCTTCAGC 59.647 66.667 6.47 0.00 38.64 4.26
2682 3596 1.856539 ATGCTGGGTCCCACCTTCAG 61.857 60.000 6.47 0.00 38.64 3.02
2683 3597 0.548926 TATGCTGGGTCCCACCTTCA 60.549 55.000 6.47 3.19 38.64 3.02
2684 3598 0.181350 CTATGCTGGGTCCCACCTTC 59.819 60.000 6.47 0.00 38.64 3.46
2685 3599 0.253160 TCTATGCTGGGTCCCACCTT 60.253 55.000 6.47 1.27 38.64 3.50
2686 3600 0.029681 ATCTATGCTGGGTCCCACCT 60.030 55.000 6.47 0.17 38.64 4.00
2687 3601 0.109342 CATCTATGCTGGGTCCCACC 59.891 60.000 6.47 0.17 37.60 4.61
2688 3602 3.713902 CATCTATGCTGGGTCCCAC 57.286 57.895 6.47 4.99 0.00 4.61
2699 3613 0.605860 GAGGCTGGGCTGCATCTATG 60.606 60.000 0.50 0.00 40.16 2.23
2701 3615 3.234349 GAGGCTGGGCTGCATCTA 58.766 61.111 0.50 0.00 40.16 1.98
2703 3617 0.979665 TATAGAGGCTGGGCTGCATC 59.020 55.000 0.50 8.98 43.14 3.91
2705 3619 0.690744 TGTATAGAGGCTGGGCTGCA 60.691 55.000 0.50 0.00 34.04 4.41
2706 3620 0.250081 GTGTATAGAGGCTGGGCTGC 60.250 60.000 0.33 0.00 0.00 5.25
2708 3622 1.418334 CAGTGTATAGAGGCTGGGCT 58.582 55.000 0.00 0.00 0.00 5.19
2709 3623 0.250081 GCAGTGTATAGAGGCTGGGC 60.250 60.000 0.00 0.00 0.00 5.36
2710 3624 1.069823 CAGCAGTGTATAGAGGCTGGG 59.930 57.143 13.02 0.00 46.10 4.45
2711 3625 2.522836 CAGCAGTGTATAGAGGCTGG 57.477 55.000 13.02 0.00 46.10 4.85
2713 3627 2.036992 GCATCAGCAGTGTATAGAGGCT 59.963 50.000 0.00 0.00 41.58 4.58
2714 3628 2.411904 GCATCAGCAGTGTATAGAGGC 58.588 52.381 0.00 0.00 41.58 4.70
2715 3629 2.289320 GGGCATCAGCAGTGTATAGAGG 60.289 54.545 0.00 0.00 44.61 3.69
2717 3631 2.630098 GAGGGCATCAGCAGTGTATAGA 59.370 50.000 0.00 0.00 44.61 1.98
2718 3632 2.366590 TGAGGGCATCAGCAGTGTATAG 59.633 50.000 0.00 0.00 44.61 1.31
2720 3634 1.206878 TGAGGGCATCAGCAGTGTAT 58.793 50.000 0.00 0.00 44.61 2.29
2724 3638 1.798626 TCTATGAGGGCATCAGCAGT 58.201 50.000 8.21 0.00 42.53 4.40
2726 3640 1.271217 GCATCTATGAGGGCATCAGCA 60.271 52.381 8.21 0.00 42.53 4.41
2728 3735 4.548451 TTAGCATCTATGAGGGCATCAG 57.452 45.455 8.21 0.00 42.53 2.90
2731 3738 5.013913 AGACATTTAGCATCTATGAGGGCAT 59.986 40.000 0.00 0.00 38.54 4.40
2735 3742 7.222872 AGGAAAGACATTTAGCATCTATGAGG 58.777 38.462 0.00 0.00 0.00 3.86
2736 3743 8.674263 AAGGAAAGACATTTAGCATCTATGAG 57.326 34.615 0.00 0.00 0.00 2.90
2741 3748 8.414629 AAGAAAAGGAAAGACATTTAGCATCT 57.585 30.769 0.00 0.00 32.10 2.90
2833 3841 7.059945 CAGCACGTTTCATTAGAAAGATTTCAC 59.940 37.037 7.97 0.00 43.95 3.18
2834 3842 7.041440 TCAGCACGTTTCATTAGAAAGATTTCA 60.041 33.333 7.97 0.00 43.95 2.69
2835 3843 7.298122 TCAGCACGTTTCATTAGAAAGATTTC 58.702 34.615 0.00 0.00 43.95 2.17
2836 3844 7.202016 TCAGCACGTTTCATTAGAAAGATTT 57.798 32.000 0.00 0.00 43.95 2.17
2837 3845 6.801539 TCAGCACGTTTCATTAGAAAGATT 57.198 33.333 0.00 0.00 43.95 2.40
2838 3846 6.595326 TGATCAGCACGTTTCATTAGAAAGAT 59.405 34.615 0.00 0.00 43.95 2.40
2839 3847 5.931724 TGATCAGCACGTTTCATTAGAAAGA 59.068 36.000 0.00 0.00 43.95 2.52
2840 3848 6.017933 GTGATCAGCACGTTTCATTAGAAAG 58.982 40.000 0.00 0.00 39.89 2.62
2841 3849 5.927030 GTGATCAGCACGTTTCATTAGAAA 58.073 37.500 0.00 0.00 38.35 2.52
2842 3850 5.530519 GTGATCAGCACGTTTCATTAGAA 57.469 39.130 0.00 0.00 37.83 2.10
2932 3965 9.582431 AAAACAATCATTTCAGCTCATTATGAG 57.418 29.630 17.16 17.16 46.90 2.90
3051 4100 7.757526 TGGAACATCACAATAAACCTTTATCG 58.242 34.615 0.00 0.00 32.46 2.92
3154 4203 7.515514 AGTTGTATCAGGATTCTATCAGGGAAT 59.484 37.037 0.00 0.00 36.29 3.01
3164 4453 4.225942 TGCTCCAAGTTGTATCAGGATTCT 59.774 41.667 1.45 0.00 0.00 2.40
3192 4481 9.896263 GTTATTACTAAAAGAGATAGACCGGAG 57.104 37.037 9.46 0.00 0.00 4.63
3269 4562 5.932883 GGAACTAAAGTAGACCAAACAGAGG 59.067 44.000 0.00 0.00 0.00 3.69
3279 4572 3.429135 CCCTGCGAGGAACTAAAGTAGAC 60.429 52.174 4.00 0.00 41.55 2.59
3280 4573 2.758979 CCCTGCGAGGAACTAAAGTAGA 59.241 50.000 4.00 0.00 41.55 2.59
3281 4574 2.496470 ACCCTGCGAGGAACTAAAGTAG 59.504 50.000 0.00 0.00 41.55 2.57
3282 4575 2.494870 GACCCTGCGAGGAACTAAAGTA 59.505 50.000 0.00 0.00 41.55 2.24
3283 4576 1.275573 GACCCTGCGAGGAACTAAAGT 59.724 52.381 0.00 0.00 41.55 2.66
3284 4577 1.405661 GGACCCTGCGAGGAACTAAAG 60.406 57.143 0.00 0.00 41.55 1.85
3285 4578 0.611714 GGACCCTGCGAGGAACTAAA 59.388 55.000 0.00 0.00 41.55 1.85
3286 4579 0.543410 TGGACCCTGCGAGGAACTAA 60.543 55.000 0.00 0.00 41.55 2.24
3287 4580 0.543410 TTGGACCCTGCGAGGAACTA 60.543 55.000 0.00 0.00 41.55 2.24
3289 4582 1.376037 CTTGGACCCTGCGAGGAAC 60.376 63.158 0.00 0.00 37.67 3.62
3313 4606 5.755409 TTGGTAAGAGATAGAAGCCACAA 57.245 39.130 0.00 0.00 0.00 3.33
3329 4622 9.802039 ATTTTTGTCTAGTCATAGGTTTGGTAA 57.198 29.630 0.00 0.00 0.00 2.85
3332 4625 9.410556 CAAATTTTTGTCTAGTCATAGGTTTGG 57.589 33.333 0.00 0.00 33.59 3.28
3381 4675 5.182950 TCATTGCAAAGTACACAATCCGAAT 59.817 36.000 1.71 0.00 31.82 3.34
3384 4678 4.406069 CTCATTGCAAAGTACACAATCCG 58.594 43.478 1.71 0.00 31.82 4.18
3415 4709 5.106791 ACAATCAAAGAGCAGATGAGAAACG 60.107 40.000 0.00 0.00 0.00 3.60
3531 4825 3.538346 CGCGTAGTTGTTGTTAGCG 57.462 52.632 0.00 0.00 40.14 4.26
3544 4838 3.933955 ACATGTAAAATTAGGCACGCGTA 59.066 39.130 13.44 0.00 0.00 4.42
3548 4842 4.355543 AGCACATGTAAAATTAGGCACG 57.644 40.909 0.00 0.00 0.00 5.34
3566 4860 2.355716 GGTACACCCTAAGATGCAAGCA 60.356 50.000 0.00 0.00 0.00 3.91
3579 4873 4.628963 TTCTAGTTTTCCAGGTACACCC 57.371 45.455 0.00 0.00 36.42 4.61
3587 4881 5.437289 TGTGTGCATTTCTAGTTTTCCAG 57.563 39.130 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.