Multiple sequence alignment - TraesCS3A01G283800

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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 TraesCS3A01G283800 chr3A 100.000 2609 0 0 1 2609 512306955 512309563 0.000000e+00 4819.0
1 TraesCS3A01G283800 chr3B 93.222 841 38 9 817 1654 511070921 511071745 0.000000e+00 1219.0
2 TraesCS3A01G283800 chr3B 88.265 392 32 8 2228 2609 511072181 511072568 8.510000e-125 457.0
3 TraesCS3A01G283800 chr3B 89.179 268 24 5 54 320 511070376 511070639 1.940000e-86 329.0
4 TraesCS3A01G283800 chr3B 92.126 127 10 0 1699 1825 795169745 795169619 2.060000e-41 180.0
5 TraesCS3A01G283800 chr3B 88.112 143 15 2 1685 1826 693601026 693600885 4.470000e-38 169.0
6 TraesCS3A01G283800 chr3B 83.505 194 10 7 1824 1995 511071780 511071973 7.470000e-36 161.0
7 TraesCS3A01G283800 chr3B 81.757 148 10 5 701 833 511070763 511070908 9.870000e-20 108.0
8 TraesCS3A01G283800 chr3B 95.833 48 1 1 2128 2175 511072104 511072150 2.780000e-10 76.8
9 TraesCS3A01G283800 chr3B 82.143 84 13 2 593 674 762954040 762953957 1.300000e-08 71.3
10 TraesCS3A01G283800 chr3D 87.968 989 50 30 702 1668 392054053 392054994 0.000000e+00 1103.0
11 TraesCS3A01G283800 chr3D 88.592 561 37 9 2067 2609 392055422 392055973 0.000000e+00 656.0
12 TraesCS3A01G283800 chr3D 90.943 265 15 2 54 318 392053383 392053638 5.340000e-92 348.0
13 TraesCS3A01G283800 chr3D 79.487 273 17 14 1821 2072 392055016 392055270 9.670000e-35 158.0
14 TraesCS3A01G283800 chr3D 94.643 56 2 1 1 55 392053309 392053364 4.630000e-13 86.1
15 TraesCS3A01G283800 chr6A 95.266 169 8 0 326 494 514037493 514037325 4.280000e-68 268.0
16 TraesCS3A01G283800 chr6A 94.220 173 7 2 326 498 182315006 182315175 7.160000e-66 261.0
17 TraesCS3A01G283800 chr6A 94.083 169 10 0 326 494 103297104 103296936 9.260000e-65 257.0
18 TraesCS3A01G283800 chr6A 92.126 127 10 0 1699 1825 26993705 26993579 2.060000e-41 180.0
19 TraesCS3A01G283800 chr6A 92.126 127 10 0 1699 1825 94235214 94235340 2.060000e-41 180.0
20 TraesCS3A01G283800 chr5A 94.675 169 9 0 326 494 85269596 85269764 1.990000e-66 263.0
21 TraesCS3A01G283800 chr5A 94.578 166 9 0 329 494 566178159 566177994 9.260000e-65 257.0
22 TraesCS3A01G283800 chr2A 94.675 169 9 0 326 494 625011848 625011680 1.990000e-66 263.0
23 TraesCS3A01G283800 chr2A 92.529 174 13 0 326 499 160602408 160602581 1.550000e-62 250.0
24 TraesCS3A01G283800 chr7A 93.642 173 11 0 326 498 7628274 7628102 2.580000e-65 259.0
25 TraesCS3A01G283800 chr1A 93.103 174 12 0 326 499 511704266 511704439 3.330000e-64 255.0
26 TraesCS3A01G283800 chr1A 96.000 50 2 0 1422 1471 535445735 535445784 5.980000e-12 82.4
27 TraesCS3A01G283800 chr1A 82.432 74 11 2 631 702 547323734 547323661 2.170000e-06 63.9
28 TraesCS3A01G283800 chr4A 91.852 135 11 0 1696 1830 16485468 16485602 3.430000e-44 189.0
29 TraesCS3A01G283800 chr2B 89.928 139 13 1 1694 1832 800544905 800545042 7.420000e-41 178.0
30 TraesCS3A01G283800 chr1B 91.473 129 11 0 1697 1825 169937787 169937659 7.420000e-41 178.0
31 TraesCS3A01G283800 chr1B 86.585 82 9 2 593 672 139374218 139374299 3.580000e-14 89.8
32 TraesCS3A01G283800 chr1B 98.000 50 1 0 1422 1471 596039017 596039066 1.290000e-13 87.9
33 TraesCS3A01G283800 chr1B 85.714 84 8 4 595 675 554234733 554234815 4.630000e-13 86.1
34 TraesCS3A01G283800 chr4B 89.781 137 10 4 1699 1832 450111806 450111941 3.450000e-39 172.0
35 TraesCS3A01G283800 chr7B 87.671 146 15 3 1681 1826 512744195 512744337 1.610000e-37 167.0
36 TraesCS3A01G283800 chr5B 86.555 119 11 4 595 710 44776094 44776210 2.730000e-25 126.0
37 TraesCS3A01G283800 chr5B 88.750 80 7 2 598 675 505145372 505145293 2.140000e-16 97.1
38 TraesCS3A01G283800 chr7D 85.047 107 14 2 598 702 518684845 518684951 9.870000e-20 108.0
39 TraesCS3A01G283800 chr1D 98.000 50 1 0 1422 1471 439305934 439305983 1.290000e-13 87.9
40 TraesCS3A01G283800 chr6B 83.133 83 8 4 597 675 30039183 30039103 1.300000e-08 71.3
41 TraesCS3A01G283800 chr6D 81.481 81 11 4 598 675 392887419 392887340 2.170000e-06 63.9


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 TraesCS3A01G283800 chr3A 512306955 512309563 2608 False 4819.00 4819 100.000000 1 2609 1 chr3A.!!$F1 2608
1 TraesCS3A01G283800 chr3B 511070376 511072568 2192 False 391.80 1219 88.626833 54 2609 6 chr3B.!!$F1 2555
2 TraesCS3A01G283800 chr3D 392053309 392055973 2664 False 470.22 1103 88.326600 1 2609 5 chr3D.!!$F1 2608

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
253 275 0.099436 CAAGCCTGGCGTAATCTTGC 59.901 55.0 13.96 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 1970 0.038744 TTTCGGACGGAGGGAGTAGT 59.961 55.0 0.0 0.0 0.0 2.73 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
59 81 1.144057 AATGATCGCACTCGGTCCC 59.856 57.895 0.00 0.00 44.84 4.46
64 86 3.770040 CGCACTCGGTCCCATGGA 61.770 66.667 15.22 0.00 0.00 3.41
102 124 1.393539 CACGCGTCCTCGAAATGATTT 59.606 47.619 9.86 0.00 39.71 2.17
221 243 2.158959 GTGACGCGGTCGAGGATTG 61.159 63.158 12.47 0.00 39.41 2.67
253 275 0.099436 CAAGCCTGGCGTAATCTTGC 59.901 55.000 13.96 0.00 0.00 4.01
296 318 3.601981 CTCGTGTATTCGGCGAGC 58.398 61.111 10.46 5.47 44.03 5.03
326 348 4.521062 GCTGCTGCGGTCGAGGAT 62.521 66.667 10.62 0.00 0.00 3.24
327 349 2.279120 CTGCTGCGGTCGAGGATC 60.279 66.667 0.00 0.00 0.00 3.36
328 350 2.755876 TGCTGCGGTCGAGGATCT 60.756 61.111 0.00 0.00 0.00 2.75
329 351 1.448119 CTGCTGCGGTCGAGGATCTA 61.448 60.000 0.00 0.00 0.00 1.98
330 352 0.823769 TGCTGCGGTCGAGGATCTAT 60.824 55.000 0.00 0.00 0.00 1.98
332 354 1.540267 GCTGCGGTCGAGGATCTATAA 59.460 52.381 0.00 0.00 0.00 0.98
333 355 2.164624 GCTGCGGTCGAGGATCTATAAT 59.835 50.000 0.00 0.00 0.00 1.28
334 356 3.763902 CTGCGGTCGAGGATCTATAATG 58.236 50.000 0.00 0.00 0.00 1.90
335 357 2.094700 TGCGGTCGAGGATCTATAATGC 60.095 50.000 0.00 0.00 0.00 3.56
336 358 2.164624 GCGGTCGAGGATCTATAATGCT 59.835 50.000 0.00 0.00 0.00 3.79
337 359 3.377485 GCGGTCGAGGATCTATAATGCTA 59.623 47.826 0.00 0.00 0.00 3.49
338 360 4.142447 GCGGTCGAGGATCTATAATGCTAA 60.142 45.833 0.00 0.00 0.00 3.09
340 362 6.565234 CGGTCGAGGATCTATAATGCTAAAT 58.435 40.000 0.00 0.00 0.00 1.40
341 363 7.036220 CGGTCGAGGATCTATAATGCTAAATT 58.964 38.462 0.00 0.00 0.00 1.82
342 364 7.545965 CGGTCGAGGATCTATAATGCTAAATTT 59.454 37.037 0.00 0.00 0.00 1.82
343 365 9.871238 GGTCGAGGATCTATAATGCTAAATTTA 57.129 33.333 0.00 0.00 0.00 1.40
388 410 5.981088 TGGCACATCTAATGTTGTTGATT 57.019 34.783 0.00 0.00 42.70 2.57
389 411 6.343716 TGGCACATCTAATGTTGTTGATTT 57.656 33.333 0.00 0.00 42.70 2.17
390 412 6.389091 TGGCACATCTAATGTTGTTGATTTC 58.611 36.000 0.00 0.00 42.70 2.17
391 413 6.015603 TGGCACATCTAATGTTGTTGATTTCA 60.016 34.615 0.00 0.00 42.70 2.69
392 414 6.308766 GGCACATCTAATGTTGTTGATTTCAC 59.691 38.462 0.00 0.00 42.70 3.18
393 415 6.862608 GCACATCTAATGTTGTTGATTTCACA 59.137 34.615 0.00 0.00 42.70 3.58
394 416 7.543172 GCACATCTAATGTTGTTGATTTCACAT 59.457 33.333 0.00 0.00 42.70 3.21
395 417 9.414295 CACATCTAATGTTGTTGATTTCACATT 57.586 29.630 0.00 0.00 42.70 2.71
396 418 9.630098 ACATCTAATGTTGTTGATTTCACATTC 57.370 29.630 0.00 0.00 41.63 2.67
397 419 9.850628 CATCTAATGTTGTTGATTTCACATTCT 57.149 29.630 0.00 0.00 0.00 2.40
447 469 6.928979 TTGATCAAAGTTTACGAGGTTTGA 57.071 33.333 5.45 0.00 41.74 2.69
448 470 6.295039 TGATCAAAGTTTACGAGGTTTGAC 57.705 37.500 0.00 0.00 40.67 3.18
449 471 6.053005 TGATCAAAGTTTACGAGGTTTGACT 58.947 36.000 0.00 0.00 40.67 3.41
450 472 6.540914 TGATCAAAGTTTACGAGGTTTGACTT 59.459 34.615 0.00 0.00 40.67 3.01
451 473 6.354039 TCAAAGTTTACGAGGTTTGACTTC 57.646 37.500 0.00 0.00 34.72 3.01
452 474 5.875910 TCAAAGTTTACGAGGTTTGACTTCA 59.124 36.000 0.00 0.00 34.72 3.02
453 475 5.986004 AAGTTTACGAGGTTTGACTTCAG 57.014 39.130 0.00 0.00 0.00 3.02
454 476 5.272283 AGTTTACGAGGTTTGACTTCAGA 57.728 39.130 0.00 0.00 0.00 3.27
455 477 5.048507 AGTTTACGAGGTTTGACTTCAGAC 58.951 41.667 0.00 0.00 0.00 3.51
456 478 4.659111 TTACGAGGTTTGACTTCAGACA 57.341 40.909 2.66 0.00 33.14 3.41
457 479 3.536956 ACGAGGTTTGACTTCAGACAA 57.463 42.857 2.66 0.00 33.14 3.18
458 480 3.869065 ACGAGGTTTGACTTCAGACAAA 58.131 40.909 2.66 1.04 37.36 2.83
459 481 4.451900 ACGAGGTTTGACTTCAGACAAAT 58.548 39.130 7.54 0.00 40.50 2.32
460 482 4.511826 ACGAGGTTTGACTTCAGACAAATC 59.488 41.667 7.54 7.19 40.50 2.17
462 484 5.237344 CGAGGTTTGACTTCAGACAAATCTT 59.763 40.000 15.60 3.91 45.82 2.40
463 485 6.423905 CGAGGTTTGACTTCAGACAAATCTTA 59.576 38.462 15.60 0.00 45.82 2.10
464 486 7.118390 CGAGGTTTGACTTCAGACAAATCTTAT 59.882 37.037 15.60 0.00 45.82 1.73
465 487 9.436957 GAGGTTTGACTTCAGACAAATCTTATA 57.563 33.333 15.60 0.00 45.82 0.98
466 488 9.965902 AGGTTTGACTTCAGACAAATCTTATAT 57.034 29.630 10.55 0.00 44.38 0.86
467 489 9.994432 GGTTTGACTTCAGACAAATCTTATATG 57.006 33.333 7.54 0.00 40.50 1.78
468 490 9.495754 GTTTGACTTCAGACAAATCTTATATGC 57.504 33.333 7.54 0.00 40.50 3.14
469 491 7.468922 TGACTTCAGACAAATCTTATATGCG 57.531 36.000 0.00 0.00 30.42 4.73
470 492 7.264947 TGACTTCAGACAAATCTTATATGCGA 58.735 34.615 0.00 0.00 30.42 5.10
471 493 7.763985 TGACTTCAGACAAATCTTATATGCGAA 59.236 33.333 0.00 0.00 30.42 4.70
472 494 7.910304 ACTTCAGACAAATCTTATATGCGAAC 58.090 34.615 0.00 0.00 30.42 3.95
473 495 7.766278 ACTTCAGACAAATCTTATATGCGAACT 59.234 33.333 0.00 0.00 30.42 3.01
474 496 9.249457 CTTCAGACAAATCTTATATGCGAACTA 57.751 33.333 0.00 0.00 30.42 2.24
475 497 9.594478 TTCAGACAAATCTTATATGCGAACTAA 57.406 29.630 0.00 0.00 30.42 2.24
476 498 9.594478 TCAGACAAATCTTATATGCGAACTAAA 57.406 29.630 0.00 0.00 30.42 1.85
483 505 7.781548 TCTTATATGCGAACTAAAAAGGACC 57.218 36.000 0.00 0.00 0.00 4.46
484 506 6.477688 TCTTATATGCGAACTAAAAAGGACCG 59.522 38.462 0.00 0.00 0.00 4.79
485 507 1.515081 TGCGAACTAAAAAGGACCGG 58.485 50.000 0.00 0.00 0.00 5.28
486 508 1.070445 TGCGAACTAAAAAGGACCGGA 59.930 47.619 9.46 0.00 0.00 5.14
487 509 1.730612 GCGAACTAAAAAGGACCGGAG 59.269 52.381 9.46 0.00 0.00 4.63
509 531 6.493802 GGAGGGAGTAACTTTCAAAGGATTTT 59.506 38.462 1.31 0.00 35.03 1.82
535 579 5.298989 ACCTTGTTTGTAGGTGTATGTGA 57.701 39.130 0.00 0.00 44.25 3.58
537 581 4.151689 CCTTGTTTGTAGGTGTATGTGACG 59.848 45.833 0.00 0.00 0.00 4.35
578 623 7.604164 ACCAATGATCGGATTCATGATTAGTAC 59.396 37.037 0.00 0.00 36.48 2.73
583 628 9.734984 TGATCGGATTCATGATTAGTACTACTA 57.265 33.333 0.91 0.00 0.00 1.82
585 630 9.742144 ATCGGATTCATGATTAGTACTACTAGT 57.258 33.333 0.91 0.00 31.47 2.57
608 653 8.474710 AGTACATTAATAAGTACTCCATCCGT 57.525 34.615 11.11 0.00 45.69 4.69
610 655 9.189723 GTACATTAATAAGTACTCCATCCGTTC 57.810 37.037 0.00 0.00 38.02 3.95
613 658 5.587388 AATAAGTACTCCATCCGTTCGAA 57.413 39.130 0.00 0.00 0.00 3.71
617 662 5.587388 AGTACTCCATCCGTTCGAAATTA 57.413 39.130 0.00 0.00 0.00 1.40
618 663 5.346522 AGTACTCCATCCGTTCGAAATTAC 58.653 41.667 0.00 0.00 0.00 1.89
619 664 4.467198 ACTCCATCCGTTCGAAATTACT 57.533 40.909 0.00 0.00 0.00 2.24
620 665 4.430908 ACTCCATCCGTTCGAAATTACTC 58.569 43.478 0.00 0.00 0.00 2.59
621 666 3.441163 TCCATCCGTTCGAAATTACTCG 58.559 45.455 0.00 0.00 40.25 4.18
622 667 2.538449 CCATCCGTTCGAAATTACTCGG 59.462 50.000 14.49 14.49 39.35 4.63
623 668 3.184541 CATCCGTTCGAAATTACTCGGT 58.815 45.455 18.49 7.05 39.35 4.69
624 669 3.302365 TCCGTTCGAAATTACTCGGTT 57.698 42.857 18.49 0.00 39.35 4.44
625 670 2.988493 TCCGTTCGAAATTACTCGGTTG 59.012 45.455 18.49 0.00 39.35 3.77
626 671 2.988493 CCGTTCGAAATTACTCGGTTGA 59.012 45.455 12.91 0.00 39.35 3.18
634 693 7.640852 TCGAAATTACTCGGTTGAAAAATGAA 58.359 30.769 0.00 0.00 39.35 2.57
637 696 9.191995 GAAATTACTCGGTTGAAAAATGAATGT 57.808 29.630 0.00 0.00 0.00 2.71
697 895 6.302535 TGATAAGTAATTCCAAACGGAGGA 57.697 37.500 0.00 0.00 32.88 3.71
706 904 2.827921 TCCAAACGGAGGAAGTAGTACC 59.172 50.000 0.00 0.00 30.71 3.34
707 905 2.564062 CCAAACGGAGGAAGTAGTACCA 59.436 50.000 0.00 0.00 0.00 3.25
734 940 5.010282 TGGAAGAAAGAAAATAGTGGGAGC 58.990 41.667 0.00 0.00 0.00 4.70
768 986 3.121160 CGCGCTTGTATATACGATTGCAA 60.121 43.478 19.16 0.00 0.00 4.08
772 990 6.418956 CGCTTGTATATACGATTGCAACTTT 58.581 36.000 0.00 0.00 0.00 2.66
775 993 9.710979 GCTTGTATATACGATTGCAACTTTTTA 57.289 29.630 0.00 0.00 0.00 1.52
1012 1265 3.707793 GTCACAGGATAGGACGCTAAAG 58.292 50.000 0.00 0.00 0.00 1.85
1045 1298 2.609427 TCATCGAGCTTCCAATCCAG 57.391 50.000 0.00 0.00 0.00 3.86
1049 1302 0.539051 CGAGCTTCCAATCCAGGTCT 59.461 55.000 0.00 0.00 35.72 3.85
1056 1309 2.619931 TCCAATCCAGGTCTTCACTCA 58.380 47.619 0.00 0.00 0.00 3.41
1062 1315 1.404717 CCAGGTCTTCACTCATCACCG 60.405 57.143 0.00 0.00 31.92 4.94
1097 1350 1.191647 CGAGTACAAAACCGCACAGAC 59.808 52.381 0.00 0.00 0.00 3.51
1303 1556 2.125229 CGACGACGAGGAGGAGGA 60.125 66.667 0.00 0.00 42.66 3.71
1304 1557 2.174969 CGACGACGAGGAGGAGGAG 61.175 68.421 0.00 0.00 42.66 3.69
1305 1558 1.820481 GACGACGAGGAGGAGGAGG 60.820 68.421 0.00 0.00 0.00 4.30
1468 1726 1.815421 CCGGCTTCATCGAAGGGTG 60.815 63.158 5.92 0.00 39.76 4.61
1469 1727 1.218047 CGGCTTCATCGAAGGGTGA 59.782 57.895 5.92 0.00 39.76 4.02
1470 1728 1.084370 CGGCTTCATCGAAGGGTGAC 61.084 60.000 5.92 0.00 39.76 3.67
1471 1729 1.084370 GGCTTCATCGAAGGGTGACG 61.084 60.000 5.92 0.00 39.76 4.35
1532 1790 2.022129 CAGTCACCACGCGTCTTCC 61.022 63.158 9.86 0.00 0.00 3.46
1598 1856 6.591834 CCGTGGTTGCCAATCAAATTAATTAA 59.408 34.615 0.01 0.00 36.26 1.40
1600 1858 8.663911 CGTGGTTGCCAATCAAATTAATTAATT 58.336 29.630 16.15 16.15 36.26 1.40
1625 1883 1.198867 TCCGTTGGTTGATGCAAATCG 59.801 47.619 0.00 0.00 0.00 3.34
1695 1969 9.436957 ACATTTTTCTGAATAATCTACGACTGT 57.563 29.630 3.53 0.00 0.00 3.55
1701 1975 9.610705 TTCTGAATAATCTACGACTGTACTACT 57.389 33.333 0.00 0.00 0.00 2.57
1702 1976 9.258826 TCTGAATAATCTACGACTGTACTACTC 57.741 37.037 0.00 0.00 0.00 2.59
1703 1977 8.375608 TGAATAATCTACGACTGTACTACTCC 57.624 38.462 0.00 0.00 0.00 3.85
1704 1978 7.443575 TGAATAATCTACGACTGTACTACTCCC 59.556 40.741 0.00 0.00 0.00 4.30
1705 1979 5.370875 AATCTACGACTGTACTACTCCCT 57.629 43.478 0.00 0.00 0.00 4.20
1706 1980 4.399004 TCTACGACTGTACTACTCCCTC 57.601 50.000 0.00 0.00 0.00 4.30
1707 1981 2.416680 ACGACTGTACTACTCCCTCC 57.583 55.000 0.00 0.00 0.00 4.30
1708 1982 1.297664 CGACTGTACTACTCCCTCCG 58.702 60.000 0.00 0.00 0.00 4.63
1709 1983 1.406614 CGACTGTACTACTCCCTCCGT 60.407 57.143 0.00 0.00 0.00 4.69
1710 1984 2.287769 GACTGTACTACTCCCTCCGTC 58.712 57.143 0.00 0.00 0.00 4.79
1711 1985 1.064832 ACTGTACTACTCCCTCCGTCC 60.065 57.143 0.00 0.00 0.00 4.79
1712 1986 0.107508 TGTACTACTCCCTCCGTCCG 60.108 60.000 0.00 0.00 0.00 4.79
1713 1987 0.179000 GTACTACTCCCTCCGTCCGA 59.821 60.000 0.00 0.00 0.00 4.55
1714 1988 0.911769 TACTACTCCCTCCGTCCGAA 59.088 55.000 0.00 0.00 0.00 4.30
1715 1989 0.038744 ACTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
1716 1990 1.180029 CTACTCCCTCCGTCCGAAAA 58.820 55.000 0.00 0.00 0.00 2.29
1717 1991 1.755380 CTACTCCCTCCGTCCGAAAAT 59.245 52.381 0.00 0.00 0.00 1.82
1718 1992 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
1719 1993 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
1720 1994 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
1721 1995 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
1722 1996 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1723 1997 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1724 1998 3.332034 CCTCCGTCCGAAAATACTTGTT 58.668 45.455 0.00 0.00 0.00 2.83
1725 1999 4.497300 CCTCCGTCCGAAAATACTTGTTA 58.503 43.478 0.00 0.00 0.00 2.41
1726 2000 5.114081 CCTCCGTCCGAAAATACTTGTTAT 58.886 41.667 0.00 0.00 0.00 1.89
1727 2001 5.233689 CCTCCGTCCGAAAATACTTGTTATC 59.766 44.000 0.00 0.00 0.00 1.75
1728 2002 5.722263 TCCGTCCGAAAATACTTGTTATCA 58.278 37.500 0.00 0.00 0.00 2.15
1729 2003 6.164876 TCCGTCCGAAAATACTTGTTATCAA 58.835 36.000 0.00 0.00 0.00 2.57
1730 2004 6.649973 TCCGTCCGAAAATACTTGTTATCAAA 59.350 34.615 0.00 0.00 32.87 2.69
1731 2005 7.172875 TCCGTCCGAAAATACTTGTTATCAAAA 59.827 33.333 0.00 0.00 32.87 2.44
1732 2006 7.966204 CCGTCCGAAAATACTTGTTATCAAAAT 59.034 33.333 0.00 0.00 32.87 1.82
1733 2007 8.785101 CGTCCGAAAATACTTGTTATCAAAATG 58.215 33.333 0.00 0.00 32.87 2.32
1734 2008 9.834628 GTCCGAAAATACTTGTTATCAAAATGA 57.165 29.630 0.00 0.00 32.87 2.57
1891 2165 2.032549 CGGAGAAGTTTCTGTTGCTGTG 60.033 50.000 0.00 0.00 37.73 3.66
1923 2220 2.223947 ACGGGCTTTTCAACATTTGACC 60.224 45.455 0.00 0.00 39.87 4.02
1930 2227 5.220643 GCTTTTCAACATTTGACCAAACAGG 60.221 40.000 0.00 0.00 39.87 4.00
1943 2240 1.474077 CAAACAGGGCAAGCCTGATAC 59.526 52.381 13.73 0.00 38.52 2.24
1946 2243 0.392998 CAGGGCAAGCCTGATACGTT 60.393 55.000 11.40 0.00 37.47 3.99
1953 2250 3.307242 GCAAGCCTGATACGTTGAAGTAG 59.693 47.826 0.00 0.00 0.00 2.57
1994 2291 5.860941 TTTAGCAGGTGGACAATTCAAAA 57.139 34.783 0.00 0.00 0.00 2.44
1995 2292 5.452078 TTAGCAGGTGGACAATTCAAAAG 57.548 39.130 0.00 0.00 0.00 2.27
1996 2293 2.629617 AGCAGGTGGACAATTCAAAAGG 59.370 45.455 0.00 0.00 0.00 3.11
1997 2294 2.365293 GCAGGTGGACAATTCAAAAGGT 59.635 45.455 0.00 0.00 0.00 3.50
1998 2295 3.552890 GCAGGTGGACAATTCAAAAGGTC 60.553 47.826 0.00 0.00 0.00 3.85
2003 2300 4.890158 GGACAATTCAAAAGGTCCCATT 57.110 40.909 0.00 0.00 43.14 3.16
2004 2301 4.820897 GGACAATTCAAAAGGTCCCATTC 58.179 43.478 0.00 0.00 43.14 2.67
2005 2302 4.283212 GGACAATTCAAAAGGTCCCATTCA 59.717 41.667 0.00 0.00 43.14 2.57
2006 2303 5.221621 GGACAATTCAAAAGGTCCCATTCAA 60.222 40.000 0.00 0.00 43.14 2.69
2007 2304 6.245890 ACAATTCAAAAGGTCCCATTCAAA 57.754 33.333 0.00 0.00 0.00 2.69
2017 2314 6.432403 AGGTCCCATTCAAAAATGCTAAAA 57.568 33.333 0.00 0.00 40.85 1.52
2045 2343 4.689612 TCAACTAGGCTTCACAGAAACT 57.310 40.909 0.00 0.00 0.00 2.66
2065 2363 3.641437 TGGCAACAGTTTATGCAGAAC 57.359 42.857 0.00 0.00 46.17 3.01
2067 2365 2.031157 GGCAACAGTTTATGCAGAACGT 60.031 45.455 0.00 1.00 44.32 3.99
2068 2366 3.187637 GGCAACAGTTTATGCAGAACGTA 59.812 43.478 0.00 0.00 44.32 3.57
2069 2367 4.394795 GCAACAGTTTATGCAGAACGTAG 58.605 43.478 0.00 0.00 42.12 3.51
2070 2368 4.394795 CAACAGTTTATGCAGAACGTAGC 58.605 43.478 0.00 0.00 32.38 3.58
2071 2369 3.659786 ACAGTTTATGCAGAACGTAGCA 58.340 40.909 11.82 11.82 45.92 3.49
2073 2371 3.000727 AGTTTATGCAGAACGTAGCACC 58.999 45.455 11.69 2.59 44.49 5.01
2122 2575 6.872585 AATCTTTATTCAATGGCCCTGAAA 57.127 33.333 18.38 5.28 36.43 2.69
2123 2576 6.872585 ATCTTTATTCAATGGCCCTGAAAA 57.127 33.333 18.38 10.23 36.43 2.29
2126 2579 6.669154 TCTTTATTCAATGGCCCTGAAAAGAT 59.331 34.615 18.38 7.37 36.43 2.40
2164 2617 6.426937 GGTTACTGCTCTGATACAAAGTGAAA 59.573 38.462 0.00 0.00 0.00 2.69
2198 2651 4.858850 TCTACAATGGATGCTGGATTTGT 58.141 39.130 3.73 3.73 0.00 2.83
2206 2659 3.698040 GGATGCTGGATTTGTCAATCTGT 59.302 43.478 0.00 0.00 39.17 3.41
2214 2667 5.647658 TGGATTTGTCAATCTGTGGTATGAC 59.352 40.000 0.00 0.00 41.90 3.06
2274 2737 3.553511 CGTAGGACAAAGAAGCTGCATAG 59.446 47.826 1.02 0.00 0.00 2.23
2277 2740 3.517100 AGGACAAAGAAGCTGCATAGAGA 59.483 43.478 1.02 0.00 0.00 3.10
2305 2768 6.773638 AGATTCTCTTTTGTTAAGGAGCTCA 58.226 36.000 17.19 0.00 37.39 4.26
2310 2773 5.072741 TCTTTTGTTAAGGAGCTCAGCAAT 58.927 37.500 17.19 0.00 0.00 3.56
2327 2795 5.305128 TCAGCAATCAAACTGGAAGGAAAAT 59.695 36.000 0.00 0.00 39.30 1.82
2330 2798 5.544650 CAATCAAACTGGAAGGAAAATGCT 58.455 37.500 0.00 0.00 39.30 3.79
2331 2799 4.853924 TCAAACTGGAAGGAAAATGCTC 57.146 40.909 0.00 0.00 39.30 4.26
2332 2800 3.253188 TCAAACTGGAAGGAAAATGCTCG 59.747 43.478 0.00 0.00 39.30 5.03
2354 2830 5.130477 TCGTTGGAATTTTAGGCCTCTATCT 59.870 40.000 9.68 0.00 0.00 1.98
2366 2842 2.555199 CCTCTATCTTGTGAAAGCCGG 58.445 52.381 0.00 0.00 0.00 6.13
2371 2847 2.631160 TCTTGTGAAAGCCGGAAGAA 57.369 45.000 5.05 0.00 0.00 2.52
2376 2852 2.098443 TGTGAAAGCCGGAAGAACAAAC 59.902 45.455 5.05 0.00 0.00 2.93
2382 2858 1.574428 CGGAAGAACAAACTGCGGG 59.426 57.895 0.00 0.00 0.00 6.13
2391 2867 0.523072 CAAACTGCGGGAATCACAGG 59.477 55.000 0.00 0.00 35.70 4.00
2535 3011 0.298707 CCATGTTCGCTTCGATCACG 59.701 55.000 2.63 0.00 38.18 4.35
2556 3032 5.470777 CACGTTTCCTTTCCATGTAGGTAAA 59.529 40.000 0.00 3.85 39.02 2.01
2608 3084 7.581213 AAACAGAGTGGTGTTTTAATCATGA 57.419 32.000 0.00 0.00 46.26 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.251297 TGCACTGCAGGCAAGGTAAT 60.251 50.000 22.49 0.00 38.54 1.89
7 8 2.908428 TGTGCACTGCAGGCAAGG 60.908 61.111 25.17 8.83 43.91 3.61
59 81 2.750237 TGCTGCTGCTGCTCCATG 60.750 61.111 27.67 3.48 40.48 3.66
78 100 1.282248 ATTTCGAGGACGCGTGTGTG 61.282 55.000 20.70 3.78 39.58 3.82
117 139 1.534729 GGAAGCAAACGGAATCCACT 58.465 50.000 0.00 0.00 0.00 4.00
118 140 0.526211 GGGAAGCAAACGGAATCCAC 59.474 55.000 0.00 0.00 31.63 4.02
141 163 1.804748 CGTGTAGCCTTTGGTCCTTTC 59.195 52.381 0.00 0.00 0.00 2.62
143 165 1.002087 CTCGTGTAGCCTTTGGTCCTT 59.998 52.381 0.00 0.00 0.00 3.36
221 243 3.505293 GCCAGGCTTGATCCAGATTAATC 59.495 47.826 3.29 7.41 0.00 1.75
253 275 5.640732 CGAGATCCCATTTTTAAAGTGTGG 58.359 41.667 8.03 8.03 0.00 4.17
257 279 3.181500 GCGCGAGATCCCATTTTTAAAGT 60.181 43.478 12.10 0.00 0.00 2.66
296 318 2.508887 GCAGCAGCTCTGACGAGG 60.509 66.667 14.86 0.00 45.72 4.63
314 336 2.094700 GCATTATAGATCCTCGACCGCA 60.095 50.000 0.00 0.00 0.00 5.69
315 337 2.164624 AGCATTATAGATCCTCGACCGC 59.835 50.000 0.00 0.00 0.00 5.68
316 338 5.562506 TTAGCATTATAGATCCTCGACCG 57.437 43.478 0.00 0.00 0.00 4.79
317 339 8.779354 AAATTTAGCATTATAGATCCTCGACC 57.221 34.615 0.00 0.00 0.00 4.79
346 368 9.995003 TGTGCCATGACTTTATTTTTCTTATTT 57.005 25.926 0.00 0.00 0.00 1.40
348 370 9.807649 GATGTGCCATGACTTTATTTTTCTTAT 57.192 29.630 0.00 0.00 0.00 1.73
349 371 9.023962 AGATGTGCCATGACTTTATTTTTCTTA 57.976 29.630 0.00 0.00 0.00 2.10
350 372 7.899973 AGATGTGCCATGACTTTATTTTTCTT 58.100 30.769 0.00 0.00 0.00 2.52
351 373 7.472334 AGATGTGCCATGACTTTATTTTTCT 57.528 32.000 0.00 0.00 0.00 2.52
352 374 9.807649 ATTAGATGTGCCATGACTTTATTTTTC 57.192 29.630 0.00 0.00 0.00 2.29
353 375 9.590451 CATTAGATGTGCCATGACTTTATTTTT 57.410 29.630 0.00 0.00 0.00 1.94
354 376 8.752187 ACATTAGATGTGCCATGACTTTATTTT 58.248 29.630 0.00 0.00 43.01 1.82
355 377 8.297470 ACATTAGATGTGCCATGACTTTATTT 57.703 30.769 0.00 0.00 43.01 1.40
356 378 7.886629 ACATTAGATGTGCCATGACTTTATT 57.113 32.000 0.00 0.00 43.01 1.40
357 379 7.340232 ACAACATTAGATGTGCCATGACTTTAT 59.660 33.333 0.00 0.00 44.07 1.40
358 380 6.658816 ACAACATTAGATGTGCCATGACTTTA 59.341 34.615 0.00 0.00 44.07 1.85
359 381 5.477984 ACAACATTAGATGTGCCATGACTTT 59.522 36.000 0.00 0.00 44.07 2.66
360 382 5.012239 ACAACATTAGATGTGCCATGACTT 58.988 37.500 0.00 0.00 44.07 3.01
361 383 4.592942 ACAACATTAGATGTGCCATGACT 58.407 39.130 0.00 0.00 44.07 3.41
362 384 4.970662 ACAACATTAGATGTGCCATGAC 57.029 40.909 0.00 0.00 44.07 3.06
363 385 5.008980 TCAACAACATTAGATGTGCCATGA 58.991 37.500 0.00 0.00 44.07 3.07
364 386 5.313520 TCAACAACATTAGATGTGCCATG 57.686 39.130 0.00 0.00 44.07 3.66
365 387 6.534475 AATCAACAACATTAGATGTGCCAT 57.466 33.333 0.00 0.00 44.07 4.40
366 388 5.981088 AATCAACAACATTAGATGTGCCA 57.019 34.783 0.00 0.00 44.07 4.92
367 389 6.308766 GTGAAATCAACAACATTAGATGTGCC 59.691 38.462 0.00 0.00 44.07 5.01
368 390 6.862608 TGTGAAATCAACAACATTAGATGTGC 59.137 34.615 0.00 0.00 44.07 4.57
369 391 8.975410 ATGTGAAATCAACAACATTAGATGTG 57.025 30.769 0.00 0.00 44.07 3.21
371 393 9.850628 AGAATGTGAAATCAACAACATTAGATG 57.149 29.630 0.23 0.00 0.00 2.90
423 445 6.851330 GTCAAACCTCGTAAACTTTGATCAAG 59.149 38.462 8.41 5.87 35.61 3.02
424 446 6.540914 AGTCAAACCTCGTAAACTTTGATCAA 59.459 34.615 3.38 3.38 35.61 2.57
425 447 6.053005 AGTCAAACCTCGTAAACTTTGATCA 58.947 36.000 0.00 0.00 35.61 2.92
426 448 6.541111 AGTCAAACCTCGTAAACTTTGATC 57.459 37.500 0.00 0.00 35.61 2.92
427 449 6.540914 TGAAGTCAAACCTCGTAAACTTTGAT 59.459 34.615 0.00 0.00 35.61 2.57
428 450 5.875910 TGAAGTCAAACCTCGTAAACTTTGA 59.124 36.000 0.00 0.00 31.68 2.69
429 451 6.036735 TCTGAAGTCAAACCTCGTAAACTTTG 59.963 38.462 0.00 0.00 0.00 2.77
430 452 6.036844 GTCTGAAGTCAAACCTCGTAAACTTT 59.963 38.462 0.00 0.00 0.00 2.66
431 453 5.522824 GTCTGAAGTCAAACCTCGTAAACTT 59.477 40.000 0.00 0.00 0.00 2.66
432 454 5.048507 GTCTGAAGTCAAACCTCGTAAACT 58.951 41.667 0.00 0.00 0.00 2.66
433 455 4.807304 TGTCTGAAGTCAAACCTCGTAAAC 59.193 41.667 0.00 0.00 0.00 2.01
434 456 5.013568 TGTCTGAAGTCAAACCTCGTAAA 57.986 39.130 0.00 0.00 0.00 2.01
435 457 4.659111 TGTCTGAAGTCAAACCTCGTAA 57.341 40.909 0.00 0.00 0.00 3.18
436 458 4.659111 TTGTCTGAAGTCAAACCTCGTA 57.341 40.909 0.00 0.00 0.00 3.43
437 459 3.536956 TTGTCTGAAGTCAAACCTCGT 57.463 42.857 0.00 0.00 0.00 4.18
438 460 4.752101 AGATTTGTCTGAAGTCAAACCTCG 59.248 41.667 5.13 0.00 36.30 4.63
439 461 6.625873 AAGATTTGTCTGAAGTCAAACCTC 57.374 37.500 5.13 1.70 36.30 3.85
440 462 9.965902 ATATAAGATTTGTCTGAAGTCAAACCT 57.034 29.630 5.13 0.00 36.30 3.50
441 463 9.994432 CATATAAGATTTGTCTGAAGTCAAACC 57.006 33.333 5.13 0.00 36.30 3.27
442 464 9.495754 GCATATAAGATTTGTCTGAAGTCAAAC 57.504 33.333 5.13 1.59 36.30 2.93
443 465 8.390354 CGCATATAAGATTTGTCTGAAGTCAAA 58.610 33.333 5.43 5.43 37.44 2.69
444 466 7.763985 TCGCATATAAGATTTGTCTGAAGTCAA 59.236 33.333 0.00 0.00 0.00 3.18
445 467 7.264947 TCGCATATAAGATTTGTCTGAAGTCA 58.735 34.615 0.00 0.00 0.00 3.41
446 468 7.700322 TCGCATATAAGATTTGTCTGAAGTC 57.300 36.000 0.00 0.00 0.00 3.01
447 469 7.766278 AGTTCGCATATAAGATTTGTCTGAAGT 59.234 33.333 0.00 0.00 0.00 3.01
448 470 8.136057 AGTTCGCATATAAGATTTGTCTGAAG 57.864 34.615 0.00 0.00 0.00 3.02
449 471 9.594478 TTAGTTCGCATATAAGATTTGTCTGAA 57.406 29.630 0.00 0.00 0.00 3.02
450 472 9.594478 TTTAGTTCGCATATAAGATTTGTCTGA 57.406 29.630 0.00 0.00 0.00 3.27
457 479 8.837389 GGTCCTTTTTAGTTCGCATATAAGATT 58.163 33.333 0.00 0.00 0.00 2.40
458 480 7.170998 CGGTCCTTTTTAGTTCGCATATAAGAT 59.829 37.037 0.00 0.00 0.00 2.40
459 481 6.477688 CGGTCCTTTTTAGTTCGCATATAAGA 59.522 38.462 0.00 0.00 0.00 2.10
460 482 6.292703 CCGGTCCTTTTTAGTTCGCATATAAG 60.293 42.308 0.00 0.00 0.00 1.73
461 483 5.524646 CCGGTCCTTTTTAGTTCGCATATAA 59.475 40.000 0.00 0.00 0.00 0.98
462 484 5.051816 CCGGTCCTTTTTAGTTCGCATATA 58.948 41.667 0.00 0.00 0.00 0.86
463 485 3.875134 CCGGTCCTTTTTAGTTCGCATAT 59.125 43.478 0.00 0.00 0.00 1.78
464 486 3.055963 TCCGGTCCTTTTTAGTTCGCATA 60.056 43.478 0.00 0.00 0.00 3.14
465 487 2.081462 CCGGTCCTTTTTAGTTCGCAT 58.919 47.619 0.00 0.00 0.00 4.73
466 488 1.070445 TCCGGTCCTTTTTAGTTCGCA 59.930 47.619 0.00 0.00 0.00 5.10
467 489 1.730612 CTCCGGTCCTTTTTAGTTCGC 59.269 52.381 0.00 0.00 0.00 4.70
468 490 2.344025 CCTCCGGTCCTTTTTAGTTCG 58.656 52.381 0.00 0.00 0.00 3.95
469 491 2.303890 TCCCTCCGGTCCTTTTTAGTTC 59.696 50.000 0.00 0.00 0.00 3.01
470 492 2.305052 CTCCCTCCGGTCCTTTTTAGTT 59.695 50.000 0.00 0.00 0.00 2.24
471 493 1.907255 CTCCCTCCGGTCCTTTTTAGT 59.093 52.381 0.00 0.00 0.00 2.24
472 494 1.907255 ACTCCCTCCGGTCCTTTTTAG 59.093 52.381 0.00 0.00 0.00 1.85
473 495 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
474 496 2.034436 TACTCCCTCCGGTCCTTTTT 57.966 50.000 0.00 0.00 0.00 1.94
475 497 1.627329 GTTACTCCCTCCGGTCCTTTT 59.373 52.381 0.00 0.00 0.00 2.27
476 498 1.203275 AGTTACTCCCTCCGGTCCTTT 60.203 52.381 0.00 0.00 0.00 3.11
477 499 0.412640 AGTTACTCCCTCCGGTCCTT 59.587 55.000 0.00 0.00 0.00 3.36
478 500 0.412640 AAGTTACTCCCTCCGGTCCT 59.587 55.000 0.00 0.00 0.00 3.85
479 501 1.206610 GAAAGTTACTCCCTCCGGTCC 59.793 57.143 0.00 0.00 0.00 4.46
480 502 1.897802 TGAAAGTTACTCCCTCCGGTC 59.102 52.381 0.00 0.00 0.00 4.79
481 503 2.019807 TGAAAGTTACTCCCTCCGGT 57.980 50.000 0.00 0.00 0.00 5.28
482 504 3.335579 CTTTGAAAGTTACTCCCTCCGG 58.664 50.000 0.00 0.00 0.00 5.14
483 505 3.007614 TCCTTTGAAAGTTACTCCCTCCG 59.992 47.826 4.02 0.00 0.00 4.63
484 506 4.635699 TCCTTTGAAAGTTACTCCCTCC 57.364 45.455 4.02 0.00 0.00 4.30
485 507 7.526142 AAAATCCTTTGAAAGTTACTCCCTC 57.474 36.000 4.02 0.00 0.00 4.30
486 508 7.450634 GGTAAAATCCTTTGAAAGTTACTCCCT 59.549 37.037 12.75 0.00 0.00 4.20
487 509 7.231925 TGGTAAAATCCTTTGAAAGTTACTCCC 59.768 37.037 12.75 3.32 0.00 4.30
488 510 8.080417 GTGGTAAAATCCTTTGAAAGTTACTCC 58.920 37.037 12.75 4.85 0.00 3.85
489 511 8.080417 GGTGGTAAAATCCTTTGAAAGTTACTC 58.920 37.037 12.75 8.44 0.00 2.59
490 512 7.783119 AGGTGGTAAAATCCTTTGAAAGTTACT 59.217 33.333 12.75 0.00 0.00 2.24
491 513 7.948357 AGGTGGTAAAATCCTTTGAAAGTTAC 58.052 34.615 4.02 6.01 0.00 2.50
535 579 3.923864 TGGCAGGTGACGAAGCGT 61.924 61.111 0.00 0.00 45.10 5.07
537 581 3.050275 GGTGGCAGGTGACGAAGC 61.050 66.667 0.00 0.00 0.00 3.86
584 629 9.189723 GAACGGATGGAGTACTTATTAATGTAC 57.810 37.037 0.00 7.64 39.26 2.90
585 630 8.077991 CGAACGGATGGAGTACTTATTAATGTA 58.922 37.037 0.00 0.00 0.00 2.29
588 633 7.281040 TCGAACGGATGGAGTACTTATTAAT 57.719 36.000 0.00 0.00 0.00 1.40
589 634 6.698008 TCGAACGGATGGAGTACTTATTAA 57.302 37.500 0.00 0.00 0.00 1.40
591 636 5.587388 TTCGAACGGATGGAGTACTTATT 57.413 39.130 0.00 0.00 0.00 1.40
592 637 5.587388 TTTCGAACGGATGGAGTACTTAT 57.413 39.130 0.00 0.00 0.00 1.73
596 641 5.346522 AGTAATTTCGAACGGATGGAGTAC 58.653 41.667 0.00 0.00 0.00 2.73
598 643 4.430908 GAGTAATTTCGAACGGATGGAGT 58.569 43.478 0.00 0.00 0.00 3.85
599 644 3.486108 CGAGTAATTTCGAACGGATGGAG 59.514 47.826 0.00 0.00 43.03 3.86
600 645 3.441163 CGAGTAATTTCGAACGGATGGA 58.559 45.455 0.00 0.00 43.03 3.41
601 646 2.538449 CCGAGTAATTTCGAACGGATGG 59.462 50.000 15.31 1.00 43.03 3.51
602 647 3.184541 ACCGAGTAATTTCGAACGGATG 58.815 45.455 24.13 3.90 43.03 3.51
603 648 3.515330 ACCGAGTAATTTCGAACGGAT 57.485 42.857 24.13 9.69 43.03 4.18
605 650 2.988493 TCAACCGAGTAATTTCGAACGG 59.012 45.455 17.91 17.91 43.03 4.44
606 651 4.634349 TTCAACCGAGTAATTTCGAACG 57.366 40.909 0.00 0.00 43.03 3.95
607 652 7.588488 TCATTTTTCAACCGAGTAATTTCGAAC 59.412 33.333 0.00 0.00 43.03 3.95
608 653 7.640852 TCATTTTTCAACCGAGTAATTTCGAA 58.359 30.769 0.00 0.00 43.03 3.71
610 655 7.845617 TTCATTTTTCAACCGAGTAATTTCG 57.154 32.000 0.00 0.00 40.18 3.46
670 840 9.116067 CCTCCGTTTGGAATTACTTATCATAAA 57.884 33.333 0.00 0.00 45.87 1.40
671 841 8.487848 TCCTCCGTTTGGAATTACTTATCATAA 58.512 33.333 0.00 0.00 45.87 1.90
676 846 6.718294 ACTTCCTCCGTTTGGAATTACTTAT 58.282 36.000 0.00 0.00 45.87 1.73
678 848 4.981812 ACTTCCTCCGTTTGGAATTACTT 58.018 39.130 0.00 0.00 45.87 2.24
679 849 4.635699 ACTTCCTCCGTTTGGAATTACT 57.364 40.909 0.00 0.00 45.87 2.24
680 850 5.485620 ACTACTTCCTCCGTTTGGAATTAC 58.514 41.667 0.00 0.00 45.87 1.89
681 851 5.750352 ACTACTTCCTCCGTTTGGAATTA 57.250 39.130 0.00 0.00 45.87 1.40
682 852 4.635699 ACTACTTCCTCCGTTTGGAATT 57.364 40.909 0.00 0.00 45.87 2.17
683 853 4.081254 GGTACTACTTCCTCCGTTTGGAAT 60.081 45.833 0.00 0.00 45.87 3.01
684 854 3.259123 GGTACTACTTCCTCCGTTTGGAA 59.741 47.826 0.00 0.00 45.87 3.53
685 855 2.827921 GGTACTACTTCCTCCGTTTGGA 59.172 50.000 0.00 0.00 43.88 3.53
686 856 2.564062 TGGTACTACTTCCTCCGTTTGG 59.436 50.000 0.00 0.00 0.00 3.28
687 857 3.947910 TGGTACTACTTCCTCCGTTTG 57.052 47.619 0.00 0.00 0.00 2.93
688 858 4.961438 TTTGGTACTACTTCCTCCGTTT 57.039 40.909 0.00 0.00 0.00 3.60
697 895 8.990163 TTCTTTCTTCCATTTTGGTACTACTT 57.010 30.769 0.00 0.00 39.03 2.24
706 904 8.367156 TCCCACTATTTTCTTTCTTCCATTTTG 58.633 33.333 0.00 0.00 0.00 2.44
707 905 8.491045 TCCCACTATTTTCTTTCTTCCATTTT 57.509 30.769 0.00 0.00 0.00 1.82
728 934 3.392228 AGCGATCAGTTGCTCCCA 58.608 55.556 0.00 0.00 41.34 4.37
894 1144 2.444706 TGGAGGATGAGGCCGGAG 60.445 66.667 5.05 0.00 0.00 4.63
1012 1265 4.332268 AGCTCGATGATCTTTCTTTTCTGC 59.668 41.667 0.00 0.00 0.00 4.26
1045 1298 0.608640 ACCGGTGATGAGTGAAGACC 59.391 55.000 6.12 0.00 0.00 3.85
1049 1302 0.107643 TTGCACCGGTGATGAGTGAA 59.892 50.000 38.30 14.05 33.21 3.18
1056 1309 2.762360 CACGTATTGCACCGGTGAT 58.238 52.632 38.30 24.64 0.00 3.06
1081 1334 2.546368 GACATGTCTGTGCGGTTTTGTA 59.454 45.455 18.83 0.00 35.14 2.41
1097 1350 1.139734 CTCCTCCACCGTCGACATG 59.860 63.158 17.16 12.80 0.00 3.21
1422 1675 3.716006 CACGGAGTTGCGCAGGTG 61.716 66.667 11.31 11.30 41.61 4.00
1504 1762 1.787155 CGTGGTGACTGACTTTTCTCG 59.213 52.381 0.00 0.00 0.00 4.04
1547 1805 3.191371 AGATGAGCCGAACAAAATTGACC 59.809 43.478 0.00 0.00 0.00 4.02
1598 1856 3.235157 CATCAACCAACGGATGCAAAT 57.765 42.857 0.00 0.00 35.03 2.32
1603 1861 2.721274 TTTGCATCAACCAACGGATG 57.279 45.000 0.00 0.00 42.92 3.51
1608 1866 1.349234 GCCGATTTGCATCAACCAAC 58.651 50.000 0.00 0.00 0.00 3.77
1625 1883 4.489306 AAATCCTAACTCACTACTGGCC 57.511 45.455 0.00 0.00 0.00 5.36
1675 1949 9.610705 AGTAGTACAGTCGTAGATTATTCAGAA 57.389 33.333 2.52 0.00 40.67 3.02
1677 1951 8.497554 GGAGTAGTACAGTCGTAGATTATTCAG 58.502 40.741 2.52 0.00 40.67 3.02
1678 1952 7.443575 GGGAGTAGTACAGTCGTAGATTATTCA 59.556 40.741 2.52 0.00 40.67 2.57
1679 1953 7.661027 AGGGAGTAGTACAGTCGTAGATTATTC 59.339 40.741 2.52 0.00 40.67 1.75
1681 1955 7.077050 AGGGAGTAGTACAGTCGTAGATTAT 57.923 40.000 2.52 0.00 40.67 1.28
1682 1956 6.463614 GGAGGGAGTAGTACAGTCGTAGATTA 60.464 46.154 2.52 0.00 40.67 1.75
1683 1957 5.367302 GAGGGAGTAGTACAGTCGTAGATT 58.633 45.833 2.52 0.00 40.67 2.40
1684 1958 4.202346 GGAGGGAGTAGTACAGTCGTAGAT 60.202 50.000 2.52 0.00 40.67 1.98
1685 1959 3.133721 GGAGGGAGTAGTACAGTCGTAGA 59.866 52.174 2.52 0.00 0.00 2.59
1686 1960 3.465871 GGAGGGAGTAGTACAGTCGTAG 58.534 54.545 2.52 0.00 0.00 3.51
1687 1961 2.159043 CGGAGGGAGTAGTACAGTCGTA 60.159 54.545 2.52 0.00 0.00 3.43
1688 1962 1.406614 CGGAGGGAGTAGTACAGTCGT 60.407 57.143 2.52 0.00 0.00 4.34
1689 1963 1.297664 CGGAGGGAGTAGTACAGTCG 58.702 60.000 2.52 0.00 0.00 4.18
1690 1964 2.287769 GACGGAGGGAGTAGTACAGTC 58.712 57.143 2.52 0.00 0.00 3.51
1691 1965 1.064832 GGACGGAGGGAGTAGTACAGT 60.065 57.143 2.52 0.00 0.00 3.55
1692 1966 1.677942 GGACGGAGGGAGTAGTACAG 58.322 60.000 2.52 0.00 0.00 2.74
1693 1967 0.107508 CGGACGGAGGGAGTAGTACA 60.108 60.000 2.52 0.00 0.00 2.90
1694 1968 0.179000 TCGGACGGAGGGAGTAGTAC 59.821 60.000 0.00 0.00 0.00 2.73
1695 1969 0.911769 TTCGGACGGAGGGAGTAGTA 59.088 55.000 0.00 0.00 0.00 1.82
1696 1970 0.038744 TTTCGGACGGAGGGAGTAGT 59.961 55.000 0.00 0.00 0.00 2.73
1697 1971 1.180029 TTTTCGGACGGAGGGAGTAG 58.820 55.000 0.00 0.00 0.00 2.57
1698 1972 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
1699 1973 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
1700 1974 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
1701 1975 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
1702 1976 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1703 1977 2.968675 ACAAGTATTTTCGGACGGAGG 58.031 47.619 0.00 0.00 0.00 4.30
1704 1978 5.808540 TGATAACAAGTATTTTCGGACGGAG 59.191 40.000 0.00 0.00 0.00 4.63
1705 1979 5.722263 TGATAACAAGTATTTTCGGACGGA 58.278 37.500 0.00 0.00 0.00 4.69
1706 1980 6.411630 TTGATAACAAGTATTTTCGGACGG 57.588 37.500 0.00 0.00 0.00 4.79
1707 1981 8.785101 CATTTTGATAACAAGTATTTTCGGACG 58.215 33.333 0.00 0.00 37.32 4.79
1708 1982 9.834628 TCATTTTGATAACAAGTATTTTCGGAC 57.165 29.630 0.00 0.00 37.32 4.79
1794 2068 8.802267 CCCTTTGTCTGGAAATACTTTTCATTA 58.198 33.333 1.38 0.00 42.55 1.90
1795 2069 7.508977 TCCCTTTGTCTGGAAATACTTTTCATT 59.491 33.333 1.38 0.00 42.55 2.57
1796 2070 7.010160 TCCCTTTGTCTGGAAATACTTTTCAT 58.990 34.615 1.38 0.00 42.55 2.57
1797 2071 6.369629 TCCCTTTGTCTGGAAATACTTTTCA 58.630 36.000 1.38 0.00 42.55 2.69
1798 2072 6.490381 ACTCCCTTTGTCTGGAAATACTTTTC 59.510 38.462 0.00 0.00 40.48 2.29
1799 2073 6.373759 ACTCCCTTTGTCTGGAAATACTTTT 58.626 36.000 0.00 0.00 0.00 2.27
1800 2074 5.953571 ACTCCCTTTGTCTGGAAATACTTT 58.046 37.500 0.00 0.00 0.00 2.66
1801 2075 5.584551 ACTCCCTTTGTCTGGAAATACTT 57.415 39.130 0.00 0.00 0.00 2.24
1802 2076 6.443849 TCATACTCCCTTTGTCTGGAAATACT 59.556 38.462 0.00 0.00 0.00 2.12
1803 2077 6.650120 TCATACTCCCTTTGTCTGGAAATAC 58.350 40.000 0.00 0.00 0.00 1.89
1804 2078 6.672218 TCTCATACTCCCTTTGTCTGGAAATA 59.328 38.462 0.00 0.00 0.00 1.40
1805 2079 5.488919 TCTCATACTCCCTTTGTCTGGAAAT 59.511 40.000 0.00 0.00 0.00 2.17
1806 2080 4.844085 TCTCATACTCCCTTTGTCTGGAAA 59.156 41.667 0.00 0.00 0.00 3.13
1807 2081 4.425772 TCTCATACTCCCTTTGTCTGGAA 58.574 43.478 0.00 0.00 0.00 3.53
1808 2082 4.061131 TCTCATACTCCCTTTGTCTGGA 57.939 45.455 0.00 0.00 0.00 3.86
1809 2083 5.130145 AGAATCTCATACTCCCTTTGTCTGG 59.870 44.000 0.00 0.00 0.00 3.86
1810 2084 6.232581 AGAATCTCATACTCCCTTTGTCTG 57.767 41.667 0.00 0.00 0.00 3.51
1811 2085 6.441924 TGAAGAATCTCATACTCCCTTTGTCT 59.558 38.462 0.00 0.00 0.00 3.41
1812 2086 6.644347 TGAAGAATCTCATACTCCCTTTGTC 58.356 40.000 0.00 0.00 0.00 3.18
1813 2087 6.441924 TCTGAAGAATCTCATACTCCCTTTGT 59.558 38.462 0.00 0.00 0.00 2.83
1814 2088 6.882656 TCTGAAGAATCTCATACTCCCTTTG 58.117 40.000 0.00 0.00 0.00 2.77
1815 2089 7.688918 ATCTGAAGAATCTCATACTCCCTTT 57.311 36.000 0.00 0.00 0.00 3.11
1816 2090 7.346698 TCAATCTGAAGAATCTCATACTCCCTT 59.653 37.037 0.00 0.00 0.00 3.95
1817 2091 6.843333 TCAATCTGAAGAATCTCATACTCCCT 59.157 38.462 0.00 0.00 0.00 4.20
1818 2092 7.060383 TCAATCTGAAGAATCTCATACTCCC 57.940 40.000 0.00 0.00 0.00 4.30
1819 2093 7.440856 GGTTCAATCTGAAGAATCTCATACTCC 59.559 40.741 0.29 0.00 37.00 3.85
1866 2140 2.807108 GCAACAGAAACTTCTCCGGACT 60.807 50.000 0.00 0.00 34.74 3.85
1912 2186 2.158986 TGCCCTGTTTGGTCAAATGTTG 60.159 45.455 0.00 0.00 32.36 3.33
1914 2188 1.786937 TGCCCTGTTTGGTCAAATGT 58.213 45.000 0.00 0.00 32.36 2.71
1930 2227 1.398390 CTTCAACGTATCAGGCTTGCC 59.602 52.381 2.97 2.97 0.00 4.52
1943 2240 2.941891 TTTTGCTCGCTACTTCAACG 57.058 45.000 0.00 0.00 0.00 4.10
1983 2280 5.467035 TGAATGGGACCTTTTGAATTGTC 57.533 39.130 0.00 0.00 0.00 3.18
1994 2291 6.432403 TTTTAGCATTTTTGAATGGGACCT 57.568 33.333 0.00 0.00 0.00 3.85
2017 2314 5.827797 TCTGTGAAGCCTAGTTGATGTTTTT 59.172 36.000 0.00 0.00 0.00 1.94
2045 2343 2.031245 CGTTCTGCATAAACTGTTGCCA 60.031 45.455 9.61 0.00 38.08 4.92
2057 2355 1.890876 TTTGGTGCTACGTTCTGCAT 58.109 45.000 12.35 0.00 41.45 3.96
2059 2357 2.766970 TTTTTGGTGCTACGTTCTGC 57.233 45.000 0.00 0.00 0.00 4.26
2116 2569 8.581253 ACCTTGGAAATAGTTATCTTTTCAGG 57.419 34.615 0.00 0.00 32.71 3.86
2122 2575 8.329502 AGCAGTAACCTTGGAAATAGTTATCTT 58.670 33.333 0.00 0.00 30.41 2.40
2123 2576 7.862675 AGCAGTAACCTTGGAAATAGTTATCT 58.137 34.615 0.00 0.00 30.41 1.98
2126 2579 7.038587 TCAGAGCAGTAACCTTGGAAATAGTTA 60.039 37.037 0.00 0.00 0.00 2.24
2175 2628 5.452255 ACAAATCCAGCATCCATTGTAGAT 58.548 37.500 0.00 0.00 29.89 1.98
2176 2629 4.858850 ACAAATCCAGCATCCATTGTAGA 58.141 39.130 0.00 0.00 29.89 2.59
2177 2630 4.641541 TGACAAATCCAGCATCCATTGTAG 59.358 41.667 0.00 0.00 31.68 2.74
2190 2643 5.647658 GTCATACCACAGATTGACAAATCCA 59.352 40.000 0.00 0.00 42.84 3.41
2194 2647 4.000325 CCGTCATACCACAGATTGACAAA 59.000 43.478 0.00 0.00 38.68 2.83
2196 2649 2.565391 ACCGTCATACCACAGATTGACA 59.435 45.455 0.00 0.00 38.68 3.58
2198 2651 3.973206 AACCGTCATACCACAGATTGA 57.027 42.857 0.00 0.00 0.00 2.57
2264 2727 6.177310 AGAATCTCATTCTCTATGCAGCTT 57.823 37.500 0.00 0.00 46.17 3.74
2295 2758 4.005650 CAGTTTGATTGCTGAGCTCCTTA 58.994 43.478 12.15 0.00 34.87 2.69
2305 2768 5.544650 CATTTTCCTTCCAGTTTGATTGCT 58.455 37.500 0.00 0.00 0.00 3.91
2310 2773 3.253188 CGAGCATTTTCCTTCCAGTTTGA 59.747 43.478 0.00 0.00 0.00 2.69
2327 2795 1.816224 GGCCTAAAATTCCAACGAGCA 59.184 47.619 0.00 0.00 0.00 4.26
2330 2798 3.713826 AGAGGCCTAAAATTCCAACGA 57.286 42.857 4.42 0.00 0.00 3.85
2331 2799 5.368989 AGATAGAGGCCTAAAATTCCAACG 58.631 41.667 4.42 0.00 0.00 4.10
2332 2800 6.603599 ACAAGATAGAGGCCTAAAATTCCAAC 59.396 38.462 4.42 0.00 0.00 3.77
2354 2830 2.045561 TGTTCTTCCGGCTTTCACAA 57.954 45.000 0.00 0.00 0.00 3.33
2366 2842 2.552315 TGATTCCCGCAGTTTGTTCTTC 59.448 45.455 0.00 0.00 0.00 2.87
2371 2847 1.238439 CTGTGATTCCCGCAGTTTGT 58.762 50.000 0.00 0.00 45.77 2.83
2382 2858 1.808133 GCGATGAGGTCCCTGTGATTC 60.808 57.143 0.00 0.00 0.00 2.52
2391 2867 0.250081 GGATCAAGGCGATGAGGTCC 60.250 60.000 0.00 2.22 33.17 4.46
2535 3011 7.556635 AGCTATTTACCTACATGGAAAGGAAAC 59.443 37.037 15.59 4.00 39.71 2.78
2556 3032 3.525609 TCCAGATCCCTCTCGATAGCTAT 59.474 47.826 5.76 5.76 0.00 2.97


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

AutoCloner maintained by Alex Coulton.