Multiple sequence alignment - TraesCS3A01G277200

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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 TraesCS3A01G277200 chr3A 100.000 2609 0 0 1 2609 507272094 507274702 0.000000e+00 4819.0
1 TraesCS3A01G277200 chr3A 86.598 582 37 13 1247 1803 507286980 507287545 2.870000e-169 604.0
2 TraesCS3A01G277200 chr3A 87.190 242 28 1 982 1220 507286676 507286917 3.310000e-69 272.0
3 TraesCS3A01G277200 chr3A 90.566 159 5 6 805 954 507286442 507286599 4.400000e-48 202.0
4 TraesCS3A01G277200 chr3D 89.929 1271 79 22 958 2204 384655153 384656398 0.000000e+00 1592.0
5 TraesCS3A01G277200 chr3D 84.205 880 72 26 982 1803 384659571 384660441 0.000000e+00 793.0
6 TraesCS3A01G277200 chr3D 83.937 442 32 15 526 951 384654692 384655110 1.130000e-103 387.0
7 TraesCS3A01G277200 chr3D 88.506 174 10 3 229 400 384654492 384654657 4.400000e-48 202.0
8 TraesCS3A01G277200 chr3D 90.604 149 6 4 1697 1839 21769528 21769382 9.530000e-45 191.0
9 TraesCS3A01G277200 chr3D 91.071 112 4 2 1 112 384652246 384652351 2.090000e-31 147.0
10 TraesCS3A01G277200 chr3B 87.699 878 63 23 958 1798 500307662 500308531 0.000000e+00 981.0
11 TraesCS3A01G277200 chr3B 87.699 878 63 23 958 1798 500316209 500317078 0.000000e+00 981.0
12 TraesCS3A01G277200 chr3B 81.538 1105 88 50 806 1803 500539564 500540659 0.000000e+00 804.0
13 TraesCS3A01G277200 chr3B 87.327 505 55 4 1850 2353 500318655 500319151 1.050000e-158 569.0
14 TraesCS3A01G277200 chr3B 86.175 434 25 13 526 951 500307213 500307619 1.110000e-118 436.0
15 TraesCS3A01G277200 chr3B 86.175 434 25 13 526 951 500315760 500316166 1.110000e-118 436.0
16 TraesCS3A01G277200 chr3B 84.778 427 29 13 1 400 500306761 500307178 1.880000e-106 396.0
17 TraesCS3A01G277200 chr3B 86.786 280 29 6 2337 2609 500321618 500321896 3.260000e-79 305.0
18 TraesCS3A01G277200 chr6A 96.581 117 3 1 424 539 64543067 64543183 2.650000e-45 193.0
19 TraesCS3A01G277200 chr2A 95.000 120 5 1 417 535 650256585 650256704 1.230000e-43 187.0
20 TraesCS3A01G277200 chr2A 92.126 127 5 4 417 538 399386387 399386513 9.600000e-40 174.0
21 TraesCS3A01G277200 chr5D 96.429 112 3 1 425 535 70640484 70640595 1.590000e-42 183.0
22 TraesCS3A01G277200 chr5D 92.000 125 6 4 417 538 395046379 395046256 3.450000e-39 172.0
23 TraesCS3A01G277200 chr5D 92.857 42 0 2 921 959 233309162 233309121 1.010000e-04 58.4
24 TraesCS3A01G277200 chr5B 95.575 113 4 1 425 536 622393445 622393557 2.060000e-41 180.0
25 TraesCS3A01G277200 chr5B 91.270 126 10 1 423 547 81252620 81252495 1.240000e-38 171.0
26 TraesCS3A01G277200 chr2B 92.126 127 6 4 415 539 783405506 783405630 2.670000e-40 176.0
27 TraesCS3A01G277200 chr2B 94.595 37 2 0 919 955 240930970 240930934 1.010000e-04 58.4
28 TraesCS3A01G277200 chr2D 92.000 125 8 2 417 540 43918937 43919060 9.600000e-40 174.0
29 TraesCS3A01G277200 chr7D 92.105 114 6 2 1735 1847 544155083 544154972 9.670000e-35 158.0
30 TraesCS3A01G277200 chr7D 97.143 35 1 0 927 961 77829041 77829007 2.800000e-05 60.2
31 TraesCS3A01G277200 chr7A 92.105 114 6 2 1735 1847 675749409 675749298 9.670000e-35 158.0
32 TraesCS3A01G277200 chr1B 92.105 114 6 2 1735 1847 659104271 659104160 9.670000e-35 158.0
33 TraesCS3A01G277200 chr4A 90.351 114 8 2 1735 1847 504676475 504676364 2.090000e-31 147.0
34 TraesCS3A01G277200 chr4A 97.143 35 0 1 924 958 721448007 721448040 1.010000e-04 58.4
35 TraesCS3A01G277200 chr6D 100.000 33 0 0 926 958 21222977 21222945 7.800000e-06 62.1


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 TraesCS3A01G277200 chr3A 507272094 507274702 2608 False 4819.000000 4819 100.000000 1 2609 1 chr3A.!!$F1 2608
1 TraesCS3A01G277200 chr3A 507286442 507287545 1103 False 359.333333 604 88.118000 805 1803 3 chr3A.!!$F2 998
2 TraesCS3A01G277200 chr3D 384652246 384660441 8195 False 624.200000 1592 87.529600 1 2204 5 chr3D.!!$F1 2203
3 TraesCS3A01G277200 chr3B 500539564 500540659 1095 False 804.000000 804 81.538000 806 1803 1 chr3B.!!$F1 997
4 TraesCS3A01G277200 chr3B 500306761 500308531 1770 False 604.333333 981 86.217333 1 1798 3 chr3B.!!$F2 1797
5 TraesCS3A01G277200 chr3B 500315760 500321896 6136 False 572.750000 981 86.996750 526 2609 4 chr3B.!!$F3 2083

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
955 3024 0.168568 GCAAGAGCAAGAGCAAGAGC 59.831 55.0 0.0 0.0 45.49 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2396 11504 0.250295 CTCAACGACCAGCTTTGGGA 60.25 55.0 0.0 0.0 28.01 4.37 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
55 56 1.134907 GGCGTCTCCGTATCTCCAAAA 60.135 52.381 0.00 0.00 36.15 2.44
56 57 2.483188 GGCGTCTCCGTATCTCCAAAAT 60.483 50.000 0.00 0.00 36.15 1.82
57 58 3.243636 GGCGTCTCCGTATCTCCAAAATA 60.244 47.826 0.00 0.00 36.15 1.40
58 59 3.734735 GCGTCTCCGTATCTCCAAAATAC 59.265 47.826 0.00 0.00 36.15 1.89
59 60 4.499357 GCGTCTCCGTATCTCCAAAATACT 60.499 45.833 0.00 0.00 36.15 2.12
60 61 5.213675 CGTCTCCGTATCTCCAAAATACTC 58.786 45.833 0.00 0.00 0.00 2.59
61 62 5.008811 CGTCTCCGTATCTCCAAAATACTCT 59.991 44.000 0.00 0.00 0.00 3.24
62 63 6.204301 CGTCTCCGTATCTCCAAAATACTCTA 59.796 42.308 0.00 0.00 0.00 2.43
63 64 7.361894 GTCTCCGTATCTCCAAAATACTCTAC 58.638 42.308 0.00 0.00 0.00 2.59
64 65 7.013083 GTCTCCGTATCTCCAAAATACTCTACA 59.987 40.741 0.00 0.00 0.00 2.74
65 66 7.013083 TCTCCGTATCTCCAAAATACTCTACAC 59.987 40.741 0.00 0.00 0.00 2.90
66 67 6.832384 TCCGTATCTCCAAAATACTCTACACT 59.168 38.462 0.00 0.00 0.00 3.55
67 68 6.918569 CCGTATCTCCAAAATACTCTACACTG 59.081 42.308 0.00 0.00 0.00 3.66
68 69 6.918569 CGTATCTCCAAAATACTCTACACTGG 59.081 42.308 0.00 0.00 0.00 4.00
117 1978 7.114811 GGCATCAGTGTTTGTTTGTAATAACTG 59.885 37.037 0.00 0.00 0.00 3.16
142 2003 4.335874 CCGATCGATTATAGAGGTTCCGAT 59.664 45.833 18.66 0.00 37.88 4.18
146 2007 3.921021 CGATTATAGAGGTTCCGATGCAC 59.079 47.826 0.00 0.00 0.00 4.57
150 2030 0.892755 AGAGGTTCCGATGCACGTAA 59.107 50.000 0.00 0.00 40.78 3.18
159 2039 3.369756 TCCGATGCACGTAAGATTTTGAC 59.630 43.478 0.00 0.00 40.78 3.18
165 2045 4.151798 GCACGTAAGATTTTGACAAGAGC 58.848 43.478 0.00 0.00 43.62 4.09
213 2093 3.921021 GCGATGAATTATCACCTCCTACG 59.079 47.826 0.00 0.00 38.69 3.51
221 2101 0.697079 TCACCTCCTACGGTCTGTCT 59.303 55.000 0.00 0.00 34.29 3.41
231 2257 6.520272 TCCTACGGTCTGTCTAATAGTAGTC 58.480 44.000 0.00 0.00 0.00 2.59
233 2259 3.559242 ACGGTCTGTCTAATAGTAGTCGC 59.441 47.826 0.00 0.00 0.00 5.19
273 2309 1.444553 CGACGAGTCAGCTCCCAAC 60.445 63.158 4.02 0.00 38.49 3.77
281 2317 0.251742 TCAGCTCCCAACCCCAATTG 60.252 55.000 0.00 0.00 0.00 2.32
336 2372 1.497722 GCTCCGCTCCGTTCAAAAG 59.502 57.895 0.00 0.00 0.00 2.27
374 2410 0.750546 TGCAAGGCAGCATCATCTCC 60.751 55.000 0.22 0.00 40.11 3.71
380 2416 0.319727 GCAGCATCATCTCCTCTCCG 60.320 60.000 0.00 0.00 0.00 4.63
416 2465 1.971695 CTCGCAAACCAACTCCCCC 60.972 63.158 0.00 0.00 0.00 5.40
426 2475 2.042569 ACCAACTCCCCCAAAAGGATAC 59.957 50.000 0.00 0.00 38.24 2.24
441 2490 3.889520 GGATACTCCCTCGTTCACTTT 57.110 47.619 0.00 0.00 0.00 2.66
442 2491 4.203654 GGATACTCCCTCGTTCACTTTT 57.796 45.455 0.00 0.00 0.00 2.27
443 2492 3.933332 GGATACTCCCTCGTTCACTTTTG 59.067 47.826 0.00 0.00 0.00 2.44
444 2493 4.562963 GGATACTCCCTCGTTCACTTTTGT 60.563 45.833 0.00 0.00 0.00 2.83
445 2494 5.337009 GGATACTCCCTCGTTCACTTTTGTA 60.337 44.000 0.00 0.00 0.00 2.41
446 2495 4.411256 ACTCCCTCGTTCACTTTTGTAA 57.589 40.909 0.00 0.00 0.00 2.41
447 2496 4.377897 ACTCCCTCGTTCACTTTTGTAAG 58.622 43.478 0.00 0.00 37.40 2.34
448 2497 4.141779 ACTCCCTCGTTCACTTTTGTAAGT 60.142 41.667 0.00 0.00 45.40 2.24
449 2498 4.374399 TCCCTCGTTCACTTTTGTAAGTC 58.626 43.478 0.00 0.00 42.67 3.01
450 2499 3.183775 CCCTCGTTCACTTTTGTAAGTCG 59.816 47.826 0.00 0.00 42.67 4.18
451 2500 3.800506 CCTCGTTCACTTTTGTAAGTCGT 59.199 43.478 0.00 0.00 42.67 4.34
452 2501 4.269363 CCTCGTTCACTTTTGTAAGTCGTT 59.731 41.667 0.00 0.00 42.67 3.85
453 2502 5.220529 CCTCGTTCACTTTTGTAAGTCGTTT 60.221 40.000 0.00 0.00 42.67 3.60
454 2503 5.788467 TCGTTCACTTTTGTAAGTCGTTTC 58.212 37.500 0.00 0.00 42.67 2.78
455 2504 5.348179 TCGTTCACTTTTGTAAGTCGTTTCA 59.652 36.000 0.00 0.00 42.67 2.69
456 2505 5.671140 CGTTCACTTTTGTAAGTCGTTTCAG 59.329 40.000 0.00 0.00 42.67 3.02
457 2506 6.454583 CGTTCACTTTTGTAAGTCGTTTCAGA 60.455 38.462 0.00 0.00 42.67 3.27
458 2507 6.340537 TCACTTTTGTAAGTCGTTTCAGAC 57.659 37.500 0.00 0.00 42.67 3.51
459 2508 5.870433 TCACTTTTGTAAGTCGTTTCAGACA 59.130 36.000 0.00 0.00 42.67 3.41
460 2509 6.369340 TCACTTTTGTAAGTCGTTTCAGACAA 59.631 34.615 0.00 0.00 42.67 3.18
461 2510 6.464834 CACTTTTGTAAGTCGTTTCAGACAAC 59.535 38.462 0.00 0.00 42.67 3.32
462 2511 6.370718 ACTTTTGTAAGTCGTTTCAGACAACT 59.629 34.615 0.00 0.00 40.60 3.16
463 2512 6.730960 TTTGTAAGTCGTTTCAGACAACTT 57.269 33.333 0.00 0.00 43.24 2.66
464 2513 7.830940 TTTGTAAGTCGTTTCAGACAACTTA 57.169 32.000 0.00 0.00 43.24 2.24
465 2514 7.830940 TTGTAAGTCGTTTCAGACAACTTAA 57.169 32.000 0.00 0.00 43.24 1.85
466 2515 7.459394 TGTAAGTCGTTTCAGACAACTTAAG 57.541 36.000 0.00 0.00 43.24 1.85
467 2516 7.259882 TGTAAGTCGTTTCAGACAACTTAAGA 58.740 34.615 10.09 0.00 43.24 2.10
468 2517 7.924412 TGTAAGTCGTTTCAGACAACTTAAGAT 59.076 33.333 10.09 0.00 43.24 2.40
469 2518 9.403110 GTAAGTCGTTTCAGACAACTTAAGATA 57.597 33.333 10.09 0.00 43.24 1.98
470 2519 8.522178 AAGTCGTTTCAGACAACTTAAGATAG 57.478 34.615 10.09 0.82 43.24 2.08
471 2520 7.091443 AGTCGTTTCAGACAACTTAAGATAGG 58.909 38.462 10.09 0.00 43.24 2.57
472 2521 5.867716 TCGTTTCAGACAACTTAAGATAGGC 59.132 40.000 10.09 0.23 0.00 3.93
473 2522 5.869888 CGTTTCAGACAACTTAAGATAGGCT 59.130 40.000 10.09 2.78 0.00 4.58
474 2523 6.183360 CGTTTCAGACAACTTAAGATAGGCTG 60.183 42.308 10.09 14.88 0.00 4.85
475 2524 6.360370 TTCAGACAACTTAAGATAGGCTGT 57.640 37.500 20.59 10.22 0.00 4.40
476 2525 6.360370 TCAGACAACTTAAGATAGGCTGTT 57.640 37.500 20.59 0.00 0.00 3.16
477 2526 6.769512 TCAGACAACTTAAGATAGGCTGTTT 58.230 36.000 20.59 5.26 0.00 2.83
478 2527 7.224297 TCAGACAACTTAAGATAGGCTGTTTT 58.776 34.615 20.59 0.00 0.00 2.43
479 2528 7.173218 TCAGACAACTTAAGATAGGCTGTTTTG 59.827 37.037 20.59 9.98 0.00 2.44
480 2529 6.013842 ACAACTTAAGATAGGCTGTTTTGC 57.986 37.500 10.09 0.00 0.00 3.68
481 2530 5.534654 ACAACTTAAGATAGGCTGTTTTGCA 59.465 36.000 10.09 0.00 34.04 4.08
482 2531 5.629079 ACTTAAGATAGGCTGTTTTGCAC 57.371 39.130 10.09 0.00 34.04 4.57
483 2532 5.070001 ACTTAAGATAGGCTGTTTTGCACA 58.930 37.500 10.09 0.00 34.04 4.57
484 2533 5.711976 ACTTAAGATAGGCTGTTTTGCACAT 59.288 36.000 10.09 0.00 33.76 3.21
485 2534 6.209391 ACTTAAGATAGGCTGTTTTGCACATT 59.791 34.615 10.09 0.00 33.76 2.71
486 2535 4.445452 AGATAGGCTGTTTTGCACATTG 57.555 40.909 0.00 0.00 33.76 2.82
487 2536 3.828451 AGATAGGCTGTTTTGCACATTGT 59.172 39.130 0.00 0.00 33.76 2.71
488 2537 2.514205 AGGCTGTTTTGCACATTGTC 57.486 45.000 0.00 0.00 33.76 3.18
489 2538 2.034124 AGGCTGTTTTGCACATTGTCT 58.966 42.857 0.00 0.00 33.76 3.41
490 2539 2.129607 GGCTGTTTTGCACATTGTCTG 58.870 47.619 0.00 0.00 33.76 3.51
491 2540 2.223782 GGCTGTTTTGCACATTGTCTGA 60.224 45.455 0.00 0.00 33.76 3.27
492 2541 3.446799 GCTGTTTTGCACATTGTCTGAA 58.553 40.909 0.00 0.00 33.76 3.02
493 2542 3.864583 GCTGTTTTGCACATTGTCTGAAA 59.135 39.130 0.00 0.00 33.76 2.69
494 2543 4.508861 GCTGTTTTGCACATTGTCTGAAAT 59.491 37.500 0.00 0.00 33.76 2.17
495 2544 5.557514 GCTGTTTTGCACATTGTCTGAAATG 60.558 40.000 0.00 9.50 42.21 2.32
497 2546 5.519566 TGTTTTGCACATTGTCTGAAATGTC 59.480 36.000 12.25 9.51 45.47 3.06
498 2547 5.518848 TTTGCACATTGTCTGAAATGTCT 57.481 34.783 12.25 0.00 45.47 3.41
499 2548 5.518848 TTGCACATTGTCTGAAATGTCTT 57.481 34.783 12.25 0.00 45.47 3.01
500 2549 5.112220 TGCACATTGTCTGAAATGTCTTC 57.888 39.130 12.25 7.82 45.47 2.87
501 2550 4.579753 TGCACATTGTCTGAAATGTCTTCA 59.420 37.500 12.25 9.40 45.47 3.02
502 2551 5.067544 TGCACATTGTCTGAAATGTCTTCAA 59.932 36.000 12.25 0.00 45.47 2.69
503 2552 5.628193 GCACATTGTCTGAAATGTCTTCAAG 59.372 40.000 12.25 5.42 45.47 3.02
504 2553 6.147581 CACATTGTCTGAAATGTCTTCAAGG 58.852 40.000 12.25 0.00 45.47 3.61
505 2554 5.829924 ACATTGTCTGAAATGTCTTCAAGGT 59.170 36.000 10.41 0.00 45.47 3.50
506 2555 6.016777 ACATTGTCTGAAATGTCTTCAAGGTC 60.017 38.462 10.41 0.00 45.47 3.85
507 2556 5.296151 TGTCTGAAATGTCTTCAAGGTCT 57.704 39.130 0.00 0.00 0.00 3.85
508 2557 5.684704 TGTCTGAAATGTCTTCAAGGTCTT 58.315 37.500 0.00 0.00 0.00 3.01
509 2558 6.826668 TGTCTGAAATGTCTTCAAGGTCTTA 58.173 36.000 0.00 0.00 0.00 2.10
510 2559 7.453393 TGTCTGAAATGTCTTCAAGGTCTTAT 58.547 34.615 0.00 0.00 0.00 1.73
511 2560 8.593679 TGTCTGAAATGTCTTCAAGGTCTTATA 58.406 33.333 0.00 0.00 0.00 0.98
512 2561 9.436957 GTCTGAAATGTCTTCAAGGTCTTATAA 57.563 33.333 0.00 0.00 0.00 0.98
525 2574 9.231297 TCAAGGTCTTATAAAAATGAACAGAGG 57.769 33.333 0.00 0.00 0.00 3.69
526 2575 8.462016 CAAGGTCTTATAAAAATGAACAGAGGG 58.538 37.037 0.00 0.00 0.00 4.30
527 2576 7.928873 AGGTCTTATAAAAATGAACAGAGGGA 58.071 34.615 0.00 0.00 0.00 4.20
528 2577 8.049721 AGGTCTTATAAAAATGAACAGAGGGAG 58.950 37.037 0.00 0.00 0.00 4.30
529 2578 7.829706 GGTCTTATAAAAATGAACAGAGGGAGT 59.170 37.037 0.00 0.00 0.00 3.85
530 2579 9.886132 GTCTTATAAAAATGAACAGAGGGAGTA 57.114 33.333 0.00 0.00 0.00 2.59
540 2589 9.712305 AATGAACAGAGGGAGTAATAATAATCG 57.288 33.333 0.00 0.00 0.00 3.34
575 2627 3.650139 TCAGCGAACAAACTAAGGAGAC 58.350 45.455 0.00 0.00 0.00 3.36
576 2628 2.408704 CAGCGAACAAACTAAGGAGACG 59.591 50.000 0.00 0.00 0.00 4.18
577 2629 1.725164 GCGAACAAACTAAGGAGACGG 59.275 52.381 0.00 0.00 0.00 4.79
578 2630 2.608752 GCGAACAAACTAAGGAGACGGA 60.609 50.000 0.00 0.00 0.00 4.69
593 2645 1.813786 GACGGAGGAGATAAGATCGGG 59.186 57.143 0.00 0.00 0.00 5.14
618 2670 4.962836 GGCACCACCAGCAGCAGT 62.963 66.667 0.00 0.00 38.86 4.40
619 2671 3.667282 GCACCACCAGCAGCAGTG 61.667 66.667 8.32 8.32 0.00 3.66
664 2716 2.282462 GGTGGGAGTGGCCAACAG 60.282 66.667 7.24 0.00 43.00 3.16
669 2721 0.890996 GGGAGTGGCCAACAGACTTG 60.891 60.000 7.24 0.00 38.95 3.16
672 2724 1.604278 GAGTGGCCAACAGACTTGAAC 59.396 52.381 7.24 0.00 0.00 3.18
673 2725 0.307760 GTGGCCAACAGACTTGAACG 59.692 55.000 7.24 0.00 0.00 3.95
675 2727 1.282875 GCCAACAGACTTGAACGCC 59.717 57.895 0.00 0.00 0.00 5.68
707 2759 5.743636 TCATTTCTGAAAGGGAAATTGGG 57.256 39.130 14.01 0.00 40.18 4.12
708 2760 4.531732 TCATTTCTGAAAGGGAAATTGGGG 59.468 41.667 14.01 0.00 40.18 4.96
709 2761 2.621556 TCTGAAAGGGAAATTGGGGG 57.378 50.000 0.00 0.00 0.00 5.40
710 2762 2.077803 TCTGAAAGGGAAATTGGGGGA 58.922 47.619 0.00 0.00 0.00 4.81
711 2763 2.452823 TCTGAAAGGGAAATTGGGGGAA 59.547 45.455 0.00 0.00 0.00 3.97
712 2764 3.116551 TCTGAAAGGGAAATTGGGGGAAA 60.117 43.478 0.00 0.00 0.00 3.13
713 2765 3.247162 TGAAAGGGAAATTGGGGGAAAG 58.753 45.455 0.00 0.00 0.00 2.62
714 2766 2.342406 AAGGGAAATTGGGGGAAAGG 57.658 50.000 0.00 0.00 0.00 3.11
715 2767 0.252696 AGGGAAATTGGGGGAAAGGC 60.253 55.000 0.00 0.00 0.00 4.35
716 2768 1.613317 GGGAAATTGGGGGAAAGGCG 61.613 60.000 0.00 0.00 0.00 5.52
717 2769 0.902984 GGAAATTGGGGGAAAGGCGT 60.903 55.000 0.00 0.00 0.00 5.68
718 2770 0.246360 GAAATTGGGGGAAAGGCGTG 59.754 55.000 0.00 0.00 0.00 5.34
719 2771 1.191489 AAATTGGGGGAAAGGCGTGG 61.191 55.000 0.00 0.00 0.00 4.94
746 2798 0.918983 TCATGGGGTCCAAGTCATCC 59.081 55.000 0.00 0.00 36.95 3.51
778 2830 3.483574 CGAACCTAACTTGCGCAATGTAG 60.484 47.826 25.26 24.18 0.00 2.74
788 2840 2.461110 GCAATGTAGACACGCCGGG 61.461 63.158 2.18 0.00 0.00 5.73
869 2930 4.929707 GCCCAGCGTTATCCCCCG 62.930 72.222 0.00 0.00 0.00 5.73
870 2931 3.476419 CCCAGCGTTATCCCCCGT 61.476 66.667 0.00 0.00 0.00 5.28
872 2933 2.279252 CAGCGTTATCCCCCGTCG 60.279 66.667 0.00 0.00 0.00 5.12
873 2934 2.757099 AGCGTTATCCCCCGTCGT 60.757 61.111 0.00 0.00 0.00 4.34
874 2935 2.279054 GCGTTATCCCCCGTCGTC 60.279 66.667 0.00 0.00 0.00 4.20
875 2936 2.779033 GCGTTATCCCCCGTCGTCT 61.779 63.158 0.00 0.00 0.00 4.18
876 2937 1.358046 CGTTATCCCCCGTCGTCTC 59.642 63.158 0.00 0.00 0.00 3.36
942 3010 0.669932 ACAGCGAGCAAGAGCAAGAG 60.670 55.000 0.00 0.00 45.49 2.85
954 3023 1.733360 GAGCAAGAGCAAGAGCAAGAG 59.267 52.381 0.00 0.00 45.49 2.85
955 3024 0.168568 GCAAGAGCAAGAGCAAGAGC 59.831 55.000 0.00 0.00 45.49 4.09
1050 3173 2.741092 GTGCACCAGGAGGACGAA 59.259 61.111 5.22 0.00 38.69 3.85
1220 3349 2.903135 AGCTCTCTGCCAAGTAAGTCTT 59.097 45.455 0.00 0.00 44.23 3.01
1222 3351 3.682377 GCTCTCTGCCAAGTAAGTCTTTC 59.318 47.826 0.00 0.00 33.63 2.62
1228 3357 4.787551 TGCCAAGTAAGTCTTTCAGGAAA 58.212 39.130 0.00 0.00 33.63 3.13
1229 3358 4.578928 TGCCAAGTAAGTCTTTCAGGAAAC 59.421 41.667 0.00 0.00 33.63 2.78
1230 3359 4.578928 GCCAAGTAAGTCTTTCAGGAAACA 59.421 41.667 0.00 0.00 33.63 2.83
1235 3368 6.890268 AAGTAAGTCTTTCAGGAAACACCTTT 59.110 34.615 0.00 0.00 39.08 3.11
1250 3383 9.342308 GGAAACACCTTTCTTCATATATCATCA 57.658 33.333 0.00 0.00 36.71 3.07
1272 3436 0.825010 ACAGCAGCAAAAGGGAGGTG 60.825 55.000 0.00 0.00 36.39 4.00
1416 3582 3.055094 GCCCCTACAAGAAGATCAAGTCA 60.055 47.826 0.00 0.00 0.00 3.41
1443 3609 3.181475 GGAGCAACATCAATCTAGACGGA 60.181 47.826 0.00 0.00 0.00 4.69
1451 3617 4.720649 TCAATCTAGACGGAAACCAGAG 57.279 45.455 0.00 0.00 0.00 3.35
1454 3620 3.715638 TCTAGACGGAAACCAGAGAGA 57.284 47.619 0.00 0.00 0.00 3.10
1465 3631 0.830648 CCAGAGAGATTGCCCCGTAA 59.169 55.000 0.00 0.00 0.00 3.18
1584 3753 3.470888 CCTCCGGCGATCCCTGTT 61.471 66.667 9.30 0.00 0.00 3.16
1602 3771 1.837538 TTAACAAGAGCGCGTGCCAC 61.838 55.000 19.02 12.46 44.31 5.01
1633 3805 1.941999 GCAGCTGCCTGGAAATGTCC 61.942 60.000 28.76 0.00 39.54 4.02
1672 3847 3.426292 GCGCCTCTTATTTGTTCCTTGAC 60.426 47.826 0.00 0.00 0.00 3.18
1919 5644 2.694065 GCATAAGCCGTGCTCATCA 58.306 52.632 0.00 0.00 38.25 3.07
1952 5678 1.244816 GGTGTCCAGCAAACCTAACC 58.755 55.000 0.00 0.00 0.00 2.85
1979 5705 1.567357 TGTGGAGATGTCCCAATCGA 58.433 50.000 6.41 0.00 43.15 3.59
1982 5708 1.134401 TGGAGATGTCCCAATCGAAGC 60.134 52.381 6.41 0.00 43.15 3.86
2022 5749 1.318576 CACAAGGTTGGGTCTTGACC 58.681 55.000 11.13 11.13 42.94 4.02
2052 5779 2.429250 TCCAAGTGAATCGCCGATTCTA 59.571 45.455 32.47 19.99 45.92 2.10
2055 5782 2.810650 AGTGAATCGCCGATTCTACAC 58.189 47.619 32.47 24.79 45.92 2.90
2072 5799 1.880027 ACACGTGAATTTCCTTGAGCC 59.120 47.619 25.01 0.00 0.00 4.70
2080 5807 1.789576 TTTCCTTGAGCCCACCCTCC 61.790 60.000 0.00 0.00 0.00 4.30
2111 5838 6.349611 GGGGTCATGGAATAATTTGATGATCG 60.350 42.308 0.00 0.00 0.00 3.69
2129 5856 6.465439 TGATCGTTCTCCTATTGAAGCTTA 57.535 37.500 0.00 0.00 0.00 3.09
2154 5881 2.125912 CTTGTCTCTCGCCCGGTG 60.126 66.667 0.00 0.00 0.00 4.94
2158 5885 1.065928 GTCTCTCGCCCGGTGTATG 59.934 63.158 0.00 0.00 0.00 2.39
2211 5938 1.964373 CGGGCTGTGGTTTTAGCGT 60.964 57.895 0.00 0.00 40.78 5.07
2221 5948 0.992802 GTTTTAGCGTGAGGAGCTCG 59.007 55.000 7.83 0.00 44.79 5.03
2246 5973 6.016276 GGTGTAGAAAGCCTCTTTTTGATTGA 60.016 38.462 0.00 0.00 35.41 2.57
2251 5978 5.397142 AAGCCTCTTTTTGATTGATGGTC 57.603 39.130 0.00 0.00 0.00 4.02
2258 5985 2.577606 TTGATTGATGGTCGTTGGGT 57.422 45.000 0.00 0.00 0.00 4.51
2265 5992 3.340034 TGATGGTCGTTGGGTCATAAAC 58.660 45.455 0.00 0.00 0.00 2.01
2291 6018 4.041567 TGGTTAGCCAGAAACTCTCATTCA 59.958 41.667 0.00 0.00 40.46 2.57
2297 6024 4.077822 CCAGAAACTCTCATTCAAAGCCT 58.922 43.478 0.00 0.00 0.00 4.58
2312 6039 5.569355 TCAAAGCCTGAATCATCACCTTAA 58.431 37.500 0.00 0.00 0.00 1.85
2331 6058 3.413105 AAGAGATAGGCAGAACTCCCT 57.587 47.619 0.00 0.00 35.22 4.20
2344 6071 3.515502 AGAACTCCCTGATCACGAAATCA 59.484 43.478 0.00 0.00 34.55 2.57
2353 6080 1.173043 TCACGAAATCAATGCACCCC 58.827 50.000 0.00 0.00 0.00 4.95
2354 6081 0.887247 CACGAAATCAATGCACCCCA 59.113 50.000 0.00 0.00 0.00 4.96
2356 6083 1.967066 ACGAAATCAATGCACCCCAAA 59.033 42.857 0.00 0.00 0.00 3.28
2357 6084 2.288763 ACGAAATCAATGCACCCCAAAC 60.289 45.455 0.00 0.00 0.00 2.93
2358 6085 2.029110 CGAAATCAATGCACCCCAAACT 60.029 45.455 0.00 0.00 0.00 2.66
2359 6086 3.554752 CGAAATCAATGCACCCCAAACTT 60.555 43.478 0.00 0.00 0.00 2.66
2360 6087 3.405823 AATCAATGCACCCCAAACTTG 57.594 42.857 0.00 0.00 0.00 3.16
2361 6088 1.786937 TCAATGCACCCCAAACTTGT 58.213 45.000 0.00 0.00 0.00 3.16
2363 6090 2.158986 TCAATGCACCCCAAACTTGTTG 60.159 45.455 0.00 0.00 0.00 3.33
2364 6091 1.494960 ATGCACCCCAAACTTGTTGT 58.505 45.000 0.00 0.00 0.00 3.32
2365 6092 0.820871 TGCACCCCAAACTTGTTGTC 59.179 50.000 0.00 0.00 0.00 3.18
2376 11484 5.243730 CCAAACTTGTTGTCATCCCATAACT 59.756 40.000 0.00 0.00 0.00 2.24
2383 11491 6.177610 TGTTGTCATCCCATAACTAAAGGAC 58.822 40.000 0.00 0.00 0.00 3.85
2396 11504 2.120718 AGGACGCCTCCTCTGGTT 59.879 61.111 0.00 0.00 44.59 3.67
2405 11513 0.695347 CTCCTCTGGTTCCCAAAGCT 59.305 55.000 0.00 0.00 33.95 3.74
2408 11516 0.111253 CTCTGGTTCCCAAAGCTGGT 59.889 55.000 0.00 0.00 41.72 4.00
2434 11542 3.944650 TGAGCGAAATTTTGCAGCCTATA 59.055 39.130 28.02 7.03 40.10 1.31
2441 11549 2.889170 TTTGCAGCCTATAACCACCA 57.111 45.000 0.00 0.00 0.00 4.17
2452 11560 5.450550 GCCTATAACCACCAAAGAAAGATGC 60.451 44.000 0.00 0.00 0.00 3.91
2458 11566 2.293122 CACCAAAGAAAGATGCGGTGAA 59.707 45.455 0.00 0.00 45.41 3.18
2466 11574 4.701651 AGAAAGATGCGGTGAATTGATCAA 59.298 37.500 11.26 11.26 40.50 2.57
2486 11594 4.286549 TCAATGTTGGCCAATTTGGATTCT 59.713 37.500 29.24 7.16 40.96 2.40
2488 11596 6.013898 TCAATGTTGGCCAATTTGGATTCTTA 60.014 34.615 29.24 15.03 40.96 2.10
2490 11598 5.792741 TGTTGGCCAATTTGGATTCTTAAG 58.207 37.500 23.66 0.00 40.96 1.85
2496 11604 5.640732 CCAATTTGGATTCTTAAGGACACG 58.359 41.667 10.03 0.00 40.96 4.49
2498 11606 2.004583 TGGATTCTTAAGGACACGCG 57.995 50.000 3.53 3.53 0.00 6.01
2505 11613 3.961182 TCTTAAGGACACGCGATATGAC 58.039 45.455 15.93 0.19 0.00 3.06
2528 11636 1.198713 GGGAAGCAGAGATGGTCTCA 58.801 55.000 9.42 0.00 45.73 3.27
2561 11669 2.569404 ACGCTCTTTCATCTTCCCTCTT 59.431 45.455 0.00 0.00 0.00 2.85
2562 11670 3.769844 ACGCTCTTTCATCTTCCCTCTTA 59.230 43.478 0.00 0.00 0.00 2.10
2568 11676 7.473228 GCTCTTTCATCTTCCCTCTTAGATCAT 60.473 40.741 0.00 0.00 0.00 2.45
2570 11678 8.209584 TCTTTCATCTTCCCTCTTAGATCATTG 58.790 37.037 0.00 0.00 0.00 2.82
2573 11688 4.302067 TCTTCCCTCTTAGATCATTGCCT 58.698 43.478 0.00 0.00 0.00 4.75
2581 11696 1.210538 AGATCATTGCCTGCTCCTGA 58.789 50.000 0.00 0.00 0.00 3.86
2587 11702 0.251354 TTGCCTGCTCCTGATGTCTC 59.749 55.000 0.00 0.00 0.00 3.36
2589 11704 0.251354 GCCTGCTCCTGATGTCTCAA 59.749 55.000 0.00 0.00 0.00 3.02
2605 11720 5.253330 TGTCTCAAGATATTGGACCCAAAC 58.747 41.667 14.86 1.50 39.55 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.616953 AGTAAAATTTGCACGAGGTTTGG 58.383 39.130 0.00 0.00 0.00 3.28
60 61 1.742761 CCCATTCTGCACCAGTGTAG 58.257 55.000 9.35 9.35 43.36 2.74
61 62 0.322456 GCCCATTCTGCACCAGTGTA 60.322 55.000 0.00 0.00 32.61 2.90
62 63 1.604593 GCCCATTCTGCACCAGTGT 60.605 57.895 0.00 0.00 32.61 3.55
63 64 1.303888 AGCCCATTCTGCACCAGTG 60.304 57.895 0.00 0.00 32.61 3.66
64 65 1.303888 CAGCCCATTCTGCACCAGT 60.304 57.895 0.00 0.00 32.61 4.00
65 66 2.050350 CCAGCCCATTCTGCACCAG 61.050 63.158 0.00 0.00 32.87 4.00
66 67 2.036098 CCAGCCCATTCTGCACCA 59.964 61.111 0.00 0.00 32.87 4.17
67 68 2.757099 CCCAGCCCATTCTGCACC 60.757 66.667 0.00 0.00 32.87 5.01
68 69 2.036256 ACCCAGCCCATTCTGCAC 59.964 61.111 0.00 0.00 32.87 4.57
117 1978 3.429135 GGAACCTCTATAATCGATCGGCC 60.429 52.174 16.41 0.00 0.00 6.13
142 2003 4.319477 GCTCTTGTCAAAATCTTACGTGCA 60.319 41.667 0.00 0.00 0.00 4.57
146 2007 5.551760 ATGGCTCTTGTCAAAATCTTACG 57.448 39.130 0.00 0.00 0.00 3.18
150 2030 4.834496 TCCAAATGGCTCTTGTCAAAATCT 59.166 37.500 0.00 0.00 34.44 2.40
159 2039 0.529378 GTGGCTCCAAATGGCTCTTG 59.471 55.000 0.00 0.00 34.44 3.02
188 2068 4.384056 AGGAGGTGATAATTCATCGCTTG 58.616 43.478 0.00 0.00 42.73 4.01
213 2093 4.334759 TGTGCGACTACTATTAGACAGACC 59.665 45.833 0.00 0.00 0.00 3.85
221 2101 6.017605 GCTAACCTACTGTGCGACTACTATTA 60.018 42.308 0.00 0.00 0.00 0.98
231 2257 0.460284 CCCTGCTAACCTACTGTGCG 60.460 60.000 0.00 0.00 0.00 5.34
233 2259 0.107654 GGCCCTGCTAACCTACTGTG 60.108 60.000 0.00 0.00 0.00 3.66
273 2309 1.552799 GGTTGCCCTTCCAATTGGGG 61.553 60.000 24.29 17.93 43.53 4.96
336 2372 2.544685 CAAGTCACCATGTCGATCTCC 58.455 52.381 0.00 0.00 0.00 3.71
374 2410 3.895025 CCATGTTGTGGCGGAGAG 58.105 61.111 0.00 0.00 42.12 3.20
426 2475 4.377897 ACTTACAAAAGTGAACGAGGGAG 58.622 43.478 0.00 0.00 44.40 4.30
427 2476 4.374399 GACTTACAAAAGTGAACGAGGGA 58.626 43.478 0.00 0.00 46.09 4.20
428 2477 3.183775 CGACTTACAAAAGTGAACGAGGG 59.816 47.826 0.00 0.00 46.09 4.30
429 2478 3.800506 ACGACTTACAAAAGTGAACGAGG 59.199 43.478 0.00 0.00 46.09 4.63
430 2479 5.385396 AACGACTTACAAAAGTGAACGAG 57.615 39.130 0.00 0.00 46.09 4.18
431 2480 5.348179 TGAAACGACTTACAAAAGTGAACGA 59.652 36.000 0.00 0.00 46.09 3.85
432 2481 5.552807 TGAAACGACTTACAAAAGTGAACG 58.447 37.500 0.00 0.00 46.09 3.95
433 2482 6.681599 GTCTGAAACGACTTACAAAAGTGAAC 59.318 38.462 0.00 0.00 46.09 3.18
434 2483 6.369340 TGTCTGAAACGACTTACAAAAGTGAA 59.631 34.615 0.00 0.00 46.09 3.18
435 2484 5.870433 TGTCTGAAACGACTTACAAAAGTGA 59.130 36.000 0.00 0.00 46.09 3.41
436 2485 6.102006 TGTCTGAAACGACTTACAAAAGTG 57.898 37.500 0.00 0.00 46.09 3.16
447 2496 6.183360 GCCTATCTTAAGTTGTCTGAAACGAC 60.183 42.308 1.63 0.00 41.93 4.34
448 2497 5.867716 GCCTATCTTAAGTTGTCTGAAACGA 59.132 40.000 1.63 0.00 35.13 3.85
449 2498 5.869888 AGCCTATCTTAAGTTGTCTGAAACG 59.130 40.000 1.63 0.00 35.13 3.60
450 2499 6.651225 ACAGCCTATCTTAAGTTGTCTGAAAC 59.349 38.462 15.65 0.00 0.00 2.78
451 2500 6.769512 ACAGCCTATCTTAAGTTGTCTGAAA 58.230 36.000 15.65 0.00 0.00 2.69
452 2501 6.360370 ACAGCCTATCTTAAGTTGTCTGAA 57.640 37.500 15.65 0.00 0.00 3.02
453 2502 6.360370 AACAGCCTATCTTAAGTTGTCTGA 57.640 37.500 15.65 0.00 0.00 3.27
454 2503 7.301054 CAAAACAGCCTATCTTAAGTTGTCTG 58.699 38.462 1.63 7.47 0.00 3.51
455 2504 6.072452 GCAAAACAGCCTATCTTAAGTTGTCT 60.072 38.462 1.63 0.00 0.00 3.41
456 2505 6.086871 GCAAAACAGCCTATCTTAAGTTGTC 58.913 40.000 1.63 0.00 0.00 3.18
457 2506 5.534654 TGCAAAACAGCCTATCTTAAGTTGT 59.465 36.000 1.63 0.00 0.00 3.32
458 2507 5.858581 GTGCAAAACAGCCTATCTTAAGTTG 59.141 40.000 1.63 0.00 0.00 3.16
459 2508 5.534654 TGTGCAAAACAGCCTATCTTAAGTT 59.465 36.000 1.63 0.00 33.78 2.66
460 2509 5.070001 TGTGCAAAACAGCCTATCTTAAGT 58.930 37.500 1.63 0.00 33.78 2.24
461 2510 5.627499 TGTGCAAAACAGCCTATCTTAAG 57.373 39.130 0.00 0.00 33.78 1.85
462 2511 6.015519 ACAATGTGCAAAACAGCCTATCTTAA 60.016 34.615 0.00 0.00 43.64 1.85
463 2512 5.476599 ACAATGTGCAAAACAGCCTATCTTA 59.523 36.000 0.00 0.00 43.64 2.10
464 2513 4.281688 ACAATGTGCAAAACAGCCTATCTT 59.718 37.500 0.00 0.00 43.64 2.40
465 2514 3.828451 ACAATGTGCAAAACAGCCTATCT 59.172 39.130 0.00 0.00 43.64 1.98
466 2515 4.082571 AGACAATGTGCAAAACAGCCTATC 60.083 41.667 0.00 0.00 43.64 2.08
467 2516 3.828451 AGACAATGTGCAAAACAGCCTAT 59.172 39.130 0.00 0.00 43.64 2.57
468 2517 3.004629 CAGACAATGTGCAAAACAGCCTA 59.995 43.478 0.00 0.00 43.64 3.93
469 2518 2.034124 AGACAATGTGCAAAACAGCCT 58.966 42.857 0.00 0.00 43.64 4.58
470 2519 2.129607 CAGACAATGTGCAAAACAGCC 58.870 47.619 0.00 0.00 43.64 4.85
471 2520 3.082698 TCAGACAATGTGCAAAACAGC 57.917 42.857 0.00 0.00 43.64 4.40
472 2521 5.521010 ACATTTCAGACAATGTGCAAAACAG 59.479 36.000 0.00 0.00 44.19 3.16
473 2522 5.417811 ACATTTCAGACAATGTGCAAAACA 58.582 33.333 0.00 0.00 44.19 2.83
474 2523 5.750067 AGACATTTCAGACAATGTGCAAAAC 59.250 36.000 12.82 2.36 45.55 2.43
475 2524 5.904941 AGACATTTCAGACAATGTGCAAAA 58.095 33.333 12.82 0.00 45.55 2.44
476 2525 5.518848 AGACATTTCAGACAATGTGCAAA 57.481 34.783 12.82 0.00 45.55 3.68
477 2526 5.067544 TGAAGACATTTCAGACAATGTGCAA 59.932 36.000 12.82 0.00 45.55 4.08
478 2527 4.579753 TGAAGACATTTCAGACAATGTGCA 59.420 37.500 12.82 0.00 45.55 4.57
479 2528 5.112220 TGAAGACATTTCAGACAATGTGC 57.888 39.130 12.82 7.29 45.55 4.57
480 2529 6.147581 CCTTGAAGACATTTCAGACAATGTG 58.852 40.000 12.82 2.31 45.55 3.21
482 2531 6.206243 AGACCTTGAAGACATTTCAGACAATG 59.794 38.462 0.00 0.00 39.67 2.82
483 2532 6.302269 AGACCTTGAAGACATTTCAGACAAT 58.698 36.000 0.00 0.00 0.00 2.71
484 2533 5.684704 AGACCTTGAAGACATTTCAGACAA 58.315 37.500 0.00 0.00 0.00 3.18
485 2534 5.296151 AGACCTTGAAGACATTTCAGACA 57.704 39.130 0.00 0.00 0.00 3.41
486 2535 7.913674 ATAAGACCTTGAAGACATTTCAGAC 57.086 36.000 0.00 0.00 0.00 3.51
499 2548 9.231297 CCTCTGTTCATTTTTATAAGACCTTGA 57.769 33.333 0.00 0.00 0.00 3.02
500 2549 8.462016 CCCTCTGTTCATTTTTATAAGACCTTG 58.538 37.037 0.00 0.00 0.00 3.61
501 2550 8.390921 TCCCTCTGTTCATTTTTATAAGACCTT 58.609 33.333 0.00 0.00 0.00 3.50
502 2551 7.928873 TCCCTCTGTTCATTTTTATAAGACCT 58.071 34.615 0.00 0.00 0.00 3.85
503 2552 7.829706 ACTCCCTCTGTTCATTTTTATAAGACC 59.170 37.037 0.00 0.00 0.00 3.85
504 2553 8.794335 ACTCCCTCTGTTCATTTTTATAAGAC 57.206 34.615 0.00 0.00 0.00 3.01
514 2563 9.712305 CGATTATTATTACTCCCTCTGTTCATT 57.288 33.333 0.00 0.00 0.00 2.57
515 2564 8.871125 ACGATTATTATTACTCCCTCTGTTCAT 58.129 33.333 0.00 0.00 0.00 2.57
516 2565 8.246430 ACGATTATTATTACTCCCTCTGTTCA 57.754 34.615 0.00 0.00 0.00 3.18
540 2589 9.859692 GTTTGTTCGCTGATAGGTTTATTATAC 57.140 33.333 0.00 0.00 0.00 1.47
554 2606 3.650139 GTCTCCTTAGTTTGTTCGCTGA 58.350 45.455 0.00 0.00 0.00 4.26
575 2627 1.813786 GACCCGATCTTATCTCCTCCG 59.186 57.143 0.00 0.00 0.00 4.63
576 2628 1.813786 CGACCCGATCTTATCTCCTCC 59.186 57.143 0.00 0.00 0.00 4.30
577 2629 1.813786 CCGACCCGATCTTATCTCCTC 59.186 57.143 0.00 0.00 0.00 3.71
578 2630 1.548128 CCCGACCCGATCTTATCTCCT 60.548 57.143 0.00 0.00 0.00 3.69
608 2660 1.654954 GGATTCTGCACTGCTGCTGG 61.655 60.000 11.29 1.84 44.57 4.85
610 2662 1.744368 CGGATTCTGCACTGCTGCT 60.744 57.895 1.98 0.00 44.57 4.24
615 2667 0.169672 CTTTGGCGGATTCTGCACTG 59.830 55.000 18.80 2.78 0.00 3.66
616 2668 1.589716 GCTTTGGCGGATTCTGCACT 61.590 55.000 18.80 0.00 0.00 4.40
617 2669 1.153958 GCTTTGGCGGATTCTGCAC 60.154 57.895 18.80 9.01 0.00 4.57
618 2670 3.277133 GCTTTGGCGGATTCTGCA 58.723 55.556 18.80 2.99 0.00 4.41
664 2716 0.878961 AACGGAGTGGCGTTCAAGTC 60.879 55.000 0.00 0.00 45.00 3.01
669 2721 0.872388 ATGAAAACGGAGTGGCGTTC 59.128 50.000 0.00 0.00 45.00 3.95
672 2724 1.535462 AGAAATGAAAACGGAGTGGCG 59.465 47.619 0.00 0.00 45.00 5.69
673 2725 2.552315 TCAGAAATGAAAACGGAGTGGC 59.448 45.455 0.00 0.00 45.00 5.01
675 2727 5.215160 CCTTTCAGAAATGAAAACGGAGTG 58.785 41.667 5.08 0.00 45.00 3.51
686 2738 4.323715 CCCCCAATTTCCCTTTCAGAAATG 60.324 45.833 0.00 0.00 41.84 2.32
697 2749 1.613317 CGCCTTTCCCCCAATTTCCC 61.613 60.000 0.00 0.00 0.00 3.97
746 2798 0.788391 GTTAGGTTCGCTTGGACACG 59.212 55.000 0.00 0.00 0.00 4.49
778 2830 3.351416 GTTGGTTCCCGGCGTGTC 61.351 66.667 6.01 0.00 0.00 3.67
788 2840 3.915437 ATTTGACATCACCGTTGGTTC 57.085 42.857 0.00 0.00 31.02 3.62
792 2844 1.978097 CGCAATTTGACATCACCGTTG 59.022 47.619 0.00 0.00 0.00 4.10
868 2929 4.205996 CGGGTATATATAGACGAGACGACG 59.794 50.000 9.33 0.00 39.31 5.12
869 2930 4.026145 GCGGGTATATATAGACGAGACGAC 60.026 50.000 16.15 0.00 0.00 4.34
870 2931 4.115516 GCGGGTATATATAGACGAGACGA 58.884 47.826 16.15 0.00 0.00 4.20
872 2933 3.563390 GGGCGGGTATATATAGACGAGAC 59.437 52.174 16.15 0.61 0.00 3.36
873 2934 3.457380 AGGGCGGGTATATATAGACGAGA 59.543 47.826 16.15 0.00 0.00 4.04
874 2935 3.814283 GAGGGCGGGTATATATAGACGAG 59.186 52.174 16.15 0.00 0.00 4.18
875 2936 3.434167 GGAGGGCGGGTATATATAGACGA 60.434 52.174 16.15 0.00 0.00 4.20
876 2937 2.883386 GGAGGGCGGGTATATATAGACG 59.117 54.545 10.23 10.23 0.00 4.18
942 3010 1.242665 AAGGCTGCTCTTGCTCTTGC 61.243 55.000 0.00 0.00 40.48 4.01
954 3023 1.743252 CCTCACGGAGAAAGGCTGC 60.743 63.158 0.00 0.00 0.00 5.25
955 3024 0.390472 GACCTCACGGAGAAAGGCTG 60.390 60.000 0.00 0.00 36.49 4.85
1044 3167 0.879765 TCTCGAACAGGTCTTCGTCC 59.120 55.000 1.63 0.00 42.97 4.79
1071 3194 1.388065 CGGAGTCGCAGGAGAAGGAT 61.388 60.000 0.00 0.00 0.00 3.24
1110 3236 3.236003 AAACTGGTCCTCGCCGTCC 62.236 63.158 0.00 0.00 0.00 4.79
1191 3320 4.205287 GCAGAGAGCTCAGCCTTG 57.795 61.111 17.77 7.46 41.15 3.61
1228 3357 7.443575 GTGCTGATGATATATGAAGAAAGGTGT 59.556 37.037 0.00 0.00 0.00 4.16
1229 3358 7.443272 TGTGCTGATGATATATGAAGAAAGGTG 59.557 37.037 0.00 0.00 0.00 4.00
1230 3359 7.512130 TGTGCTGATGATATATGAAGAAAGGT 58.488 34.615 0.00 0.00 0.00 3.50
1235 3368 6.105397 TGCTGTGCTGATGATATATGAAGA 57.895 37.500 0.00 0.00 0.00 2.87
1243 3376 2.406596 TTGCTGCTGTGCTGATGATA 57.593 45.000 0.00 0.00 0.00 2.15
1244 3377 1.541379 TTTGCTGCTGTGCTGATGAT 58.459 45.000 0.00 0.00 0.00 2.45
1246 3379 1.668919 CCTTTTGCTGCTGTGCTGATG 60.669 52.381 0.00 0.00 0.00 3.07
1247 3380 0.601558 CCTTTTGCTGCTGTGCTGAT 59.398 50.000 0.00 0.00 0.00 2.90
1248 3381 1.457823 CCCTTTTGCTGCTGTGCTGA 61.458 55.000 0.00 0.00 0.00 4.26
1249 3382 1.006571 CCCTTTTGCTGCTGTGCTG 60.007 57.895 0.00 0.00 0.00 4.41
1250 3383 1.152694 TCCCTTTTGCTGCTGTGCT 60.153 52.632 0.00 0.00 0.00 4.40
1251 3384 1.288127 CTCCCTTTTGCTGCTGTGC 59.712 57.895 0.00 0.00 0.00 4.57
1272 3436 2.028930 AGAAGAACATCACGGTCAGGAC 60.029 50.000 0.00 0.00 0.00 3.85
1432 3598 4.601084 TCTCTCTGGTTTCCGTCTAGATT 58.399 43.478 0.00 0.00 0.00 2.40
1443 3609 0.035056 CGGGGCAATCTCTCTGGTTT 60.035 55.000 0.00 0.00 0.00 3.27
1451 3617 0.252197 ACCAGTTACGGGGCAATCTC 59.748 55.000 6.48 0.00 0.00 2.75
1454 3620 0.696501 AGAACCAGTTACGGGGCAAT 59.303 50.000 6.48 0.00 0.00 3.56
1465 3631 3.632145 CCTTTGCTGTTGTTAGAACCAGT 59.368 43.478 0.00 0.00 0.00 4.00
1512 3681 0.175531 TCATCAGATTCGCGCAGGAA 59.824 50.000 8.75 3.83 0.00 3.36
1584 3753 2.029815 TGGCACGCGCTCTTGTTA 59.970 55.556 5.73 0.00 38.60 2.41
1602 3771 3.465403 AGCTGCGAGCCCTACTGG 61.465 66.667 4.77 0.00 43.77 4.00
1622 3791 1.382522 CCATGGACGGACATTTCCAG 58.617 55.000 5.56 0.00 45.20 3.86
1623 3792 0.679640 GCCATGGACGGACATTTCCA 60.680 55.000 18.40 0.00 46.06 3.53
1624 3793 0.394352 AGCCATGGACGGACATTTCC 60.394 55.000 18.40 0.00 38.77 3.13
1625 3794 0.734889 CAGCCATGGACGGACATTTC 59.265 55.000 18.40 0.00 0.00 2.17
1672 3847 0.451783 CCCGCCAAGAAAAATCCTCG 59.548 55.000 0.00 0.00 0.00 4.63
1813 4013 4.572389 TCTCGGAGAATTTTGCTAATCAGC 59.428 41.667 4.96 0.00 42.57 4.26
1832 5545 4.764679 AGATCTCAGAATTCGGATCTCG 57.235 45.455 23.24 9.68 40.25 4.04
1919 5644 0.608640 GACACCGATGACTTGGACCT 59.391 55.000 0.00 0.00 0.00 3.85
1952 5678 1.741706 GGACATCTCCACATTGCACAG 59.258 52.381 0.00 0.00 36.42 3.66
1979 5705 4.615588 AACTAGACTCTTTCTGCAGCTT 57.384 40.909 9.47 0.00 35.55 3.74
1982 5708 4.060900 TGCAAACTAGACTCTTTCTGCAG 58.939 43.478 7.63 7.63 35.55 4.41
2022 5749 3.179830 CGATTCACTTGGAGTAACGAGG 58.820 50.000 0.00 0.00 0.00 4.63
2052 5779 1.880027 GGCTCAAGGAAATTCACGTGT 59.120 47.619 16.51 0.00 0.00 4.49
2055 5782 1.200020 GTGGGCTCAAGGAAATTCACG 59.800 52.381 0.00 0.00 0.00 4.35
2088 5815 7.206981 ACGATCATCAAATTATTCCATGACC 57.793 36.000 0.00 0.00 0.00 4.02
2101 5828 6.258727 GCTTCAATAGGAGAACGATCATCAAA 59.741 38.462 0.00 0.00 0.00 2.69
2121 5848 7.542477 CGAGAGACAAGAATAAGTTAAGCTTCA 59.458 37.037 0.00 0.00 38.57 3.02
2129 5856 3.676324 CGGGCGAGAGACAAGAATAAGTT 60.676 47.826 0.00 0.00 45.40 2.66
2200 5927 0.685097 AGCTCCTCACGCTAAAACCA 59.315 50.000 0.00 0.00 35.63 3.67
2211 5938 1.819288 CTTTCTACACCGAGCTCCTCA 59.181 52.381 8.47 0.00 0.00 3.86
2221 5948 5.966742 ATCAAAAAGAGGCTTTCTACACC 57.033 39.130 0.00 0.00 34.14 4.16
2246 5973 2.718563 GGTTTATGACCCAACGACCAT 58.281 47.619 0.00 0.00 43.06 3.55
2251 5978 0.800012 CCACGGTTTATGACCCAACG 59.200 55.000 0.00 0.00 46.35 4.10
2258 5985 2.568062 TCTGGCTAACCACGGTTTATGA 59.432 45.455 6.80 0.00 42.67 2.15
2265 5992 1.002087 AGAGTTTCTGGCTAACCACGG 59.998 52.381 0.00 0.00 42.67 4.94
2266 5993 2.288825 TGAGAGTTTCTGGCTAACCACG 60.289 50.000 0.00 0.00 42.67 4.94
2269 5996 4.579869 TGAATGAGAGTTTCTGGCTAACC 58.420 43.478 0.00 0.00 0.00 2.85
2270 5997 6.560253 TTTGAATGAGAGTTTCTGGCTAAC 57.440 37.500 0.00 0.00 0.00 2.34
2291 6018 5.819991 TCTTAAGGTGATGATTCAGGCTTT 58.180 37.500 1.85 0.00 30.85 3.51
2297 6024 6.327365 TGCCTATCTCTTAAGGTGATGATTCA 59.673 38.462 16.70 0.00 35.16 2.57
2303 6030 5.902431 AGTTCTGCCTATCTCTTAAGGTGAT 59.098 40.000 1.85 9.40 35.16 3.06
2312 6039 2.246067 TCAGGGAGTTCTGCCTATCTCT 59.754 50.000 12.27 0.00 34.91 3.10
2331 6058 2.423185 GGGTGCATTGATTTCGTGATCA 59.577 45.455 0.00 0.00 34.37 2.92
2344 6071 1.836802 ACAACAAGTTTGGGGTGCATT 59.163 42.857 0.00 0.00 0.00 3.56
2353 6080 6.331369 AGTTATGGGATGACAACAAGTTTG 57.669 37.500 0.00 0.00 0.00 2.93
2354 6081 8.472007 TTTAGTTATGGGATGACAACAAGTTT 57.528 30.769 0.00 0.00 0.00 2.66
2356 6083 6.659242 CCTTTAGTTATGGGATGACAACAAGT 59.341 38.462 0.00 0.00 0.00 3.16
2357 6084 6.884295 TCCTTTAGTTATGGGATGACAACAAG 59.116 38.462 0.00 0.00 0.00 3.16
2358 6085 6.657541 GTCCTTTAGTTATGGGATGACAACAA 59.342 38.462 0.00 0.00 0.00 2.83
2359 6086 6.177610 GTCCTTTAGTTATGGGATGACAACA 58.822 40.000 0.00 0.00 0.00 3.33
2360 6087 5.293569 CGTCCTTTAGTTATGGGATGACAAC 59.706 44.000 0.00 0.00 37.11 3.32
2361 6088 5.424757 CGTCCTTTAGTTATGGGATGACAA 58.575 41.667 0.00 0.00 37.11 3.18
2363 6090 3.808174 GCGTCCTTTAGTTATGGGATGAC 59.192 47.826 0.00 0.00 37.11 3.06
2364 6091 3.181458 GGCGTCCTTTAGTTATGGGATGA 60.181 47.826 0.00 0.00 37.11 2.92
2365 6092 3.139077 GGCGTCCTTTAGTTATGGGATG 58.861 50.000 0.00 0.00 37.77 3.51
2396 11504 0.250295 CTCAACGACCAGCTTTGGGA 60.250 55.000 0.00 0.00 28.01 4.37
2434 11542 1.613437 CCGCATCTTTCTTTGGTGGTT 59.387 47.619 0.00 0.00 0.00 3.67
2441 11549 5.183713 TGATCAATTCACCGCATCTTTCTTT 59.816 36.000 0.00 0.00 0.00 2.52
2452 11560 3.181397 GCCAACATTGATCAATTCACCG 58.819 45.455 18.41 9.41 32.84 4.94
2458 11566 4.944930 CCAAATTGGCCAACATTGATCAAT 59.055 37.500 32.42 15.36 34.56 2.57
2466 11574 4.914177 AAGAATCCAAATTGGCCAACAT 57.086 36.364 23.27 10.41 37.47 2.71
2486 11594 3.129813 AGTGTCATATCGCGTGTCCTTAA 59.870 43.478 5.77 0.00 0.00 1.85
2488 11596 1.476891 AGTGTCATATCGCGTGTCCTT 59.523 47.619 5.77 0.00 0.00 3.36
2490 11598 1.200483 CAGTGTCATATCGCGTGTCC 58.800 55.000 5.77 0.00 0.00 4.02
2496 11604 1.221414 GCTTCCCAGTGTCATATCGC 58.779 55.000 0.00 0.00 0.00 4.58
2498 11606 3.386078 TCTCTGCTTCCCAGTGTCATATC 59.614 47.826 0.00 0.00 42.38 1.63
2505 11613 0.617413 ACCATCTCTGCTTCCCAGTG 59.383 55.000 0.00 0.00 42.38 3.66
2528 11636 2.046892 GAGCGTGCCACTGTCCAT 60.047 61.111 0.00 0.00 0.00 3.41
2561 11669 2.401568 TCAGGAGCAGGCAATGATCTA 58.598 47.619 6.40 0.00 44.04 1.98
2562 11670 1.210538 TCAGGAGCAGGCAATGATCT 58.789 50.000 6.40 0.00 44.04 2.75
2568 11676 0.251354 GAGACATCAGGAGCAGGCAA 59.749 55.000 0.00 0.00 0.00 4.52
2570 11678 0.251354 TTGAGACATCAGGAGCAGGC 59.749 55.000 0.00 0.00 36.61 4.85
2573 11688 5.454329 CCAATATCTTGAGACATCAGGAGCA 60.454 44.000 0.00 0.00 43.91 4.26
2581 11696 5.715439 TTGGGTCCAATATCTTGAGACAT 57.285 39.130 0.00 0.00 35.75 3.06
2587 11702 2.099098 GGCGTTTGGGTCCAATATCTTG 59.901 50.000 3.00 0.00 35.70 3.02
2589 11704 2.052782 GGCGTTTGGGTCCAATATCT 57.947 50.000 3.00 0.00 35.70 1.98


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

AutoCloner maintained by Alex Coulton.