Multiple sequence alignment - TraesCS1D01G085000

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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 TraesCS1D01G085000 chr1D 100.000 3409 0 0 1 3409 69198842 69195434 0.000000e+00 6296.0
1 TraesCS1D01G085000 chr1D 82.108 721 105 14 2639 3350 69189436 69188731 2.260000e-166 595.0
2 TraesCS1D01G085000 chr1D 86.000 400 41 8 40 432 28185697 28186088 6.810000e-112 414.0
3 TraesCS1D01G085000 chr1D 90.667 75 6 1 616 689 246100054 246100128 7.790000e-17 99.0
4 TraesCS1D01G085000 chr1A 93.314 1705 74 17 710 2413 68460608 68458943 0.000000e+00 2481.0
5 TraesCS1D01G085000 chr1A 94.659 674 21 5 2704 3376 68457845 68457186 0.000000e+00 1031.0
6 TraesCS1D01G085000 chr1A 81.667 720 105 16 2639 3350 68418660 68417960 1.060000e-159 573.0
7 TraesCS1D01G085000 chr1A 98.438 64 1 0 2639 2702 68458799 68458736 2.780000e-21 113.0
8 TraesCS1D01G085000 chr1B 92.865 939 35 18 2474 3409 111050716 111049807 0.000000e+00 1334.0
9 TraesCS1D01G085000 chr1B 94.118 884 40 4 1536 2413 111051599 111050722 0.000000e+00 1334.0
10 TraesCS1D01G085000 chr1B 92.823 836 42 10 710 1543 111052512 111051693 0.000000e+00 1195.0
11 TraesCS1D01G085000 chr1B 92.541 429 29 3 1 428 623815408 623814982 2.250000e-171 612.0
12 TraesCS1D01G085000 chr1B 82.337 719 102 16 2639 3350 111033028 111032328 4.870000e-168 601.0
13 TraesCS1D01G085000 chr1B 84.944 445 47 12 1 432 150169386 150168949 1.880000e-117 433.0
14 TraesCS1D01G085000 chr1B 91.304 69 5 1 616 683 623814973 623814905 3.620000e-15 93.5
15 TraesCS1D01G085000 chr7A 92.045 440 27 5 1 435 184036197 184035761 2.250000e-171 612.0
16 TraesCS1D01G085000 chr7A 91.116 439 30 6 1 432 516479887 516480323 1.360000e-163 586.0
17 TraesCS1D01G085000 chr7A 90.112 445 28 9 1 435 712716748 712716310 6.390000e-157 564.0
18 TraesCS1D01G085000 chr7A 95.604 182 8 0 434 615 441112281 441112462 3.330000e-75 292.0
19 TraesCS1D01G085000 chr7A 73.735 415 90 17 2956 3355 669406338 669405928 9.860000e-31 145.0
20 TraesCS1D01G085000 chr7A 93.651 63 4 0 618 680 184035771 184035709 1.010000e-15 95.3
21 TraesCS1D01G085000 chr2A 89.498 438 33 6 1 432 7004123 7004553 2.990000e-150 542.0
22 TraesCS1D01G085000 chr2A 90.110 182 18 0 434 615 142693696 142693877 1.580000e-58 237.0
23 TraesCS1D01G085000 chr2A 77.014 422 74 18 1102 1516 713531214 713531619 1.590000e-53 220.0
24 TraesCS1D01G085000 chr2A 87.912 182 22 0 434 615 47836834 47837015 7.410000e-52 215.0
25 TraesCS1D01G085000 chr2A 72.948 536 115 20 1858 2372 713532062 713532588 3.520000e-35 159.0
26 TraesCS1D01G085000 chr6A 86.073 438 40 10 1 435 536221202 536220783 5.190000e-123 451.0
27 TraesCS1D01G085000 chr5B 85.294 442 48 7 1 435 230014934 230014503 1.120000e-119 440.0
28 TraesCS1D01G085000 chr7D 92.857 182 13 0 434 615 575189432 575189613 7.250000e-67 265.0
29 TraesCS1D01G085000 chr2D 76.722 421 77 16 1102 1516 575238884 575239289 7.410000e-52 215.0
30 TraesCS1D01G085000 chr2D 78.529 340 61 11 1102 1435 634407463 634407796 2.660000e-51 213.0
31 TraesCS1D01G085000 chr2D 87.027 185 20 1 435 615 43997576 43997760 4.460000e-49 206.0
32 TraesCS1D01G085000 chr2D 73.034 534 118 22 1858 2372 575239742 575240268 7.570000e-37 165.0
33 TraesCS1D01G085000 chr3B 80.586 273 47 6 2903 3172 66820866 66820597 4.460000e-49 206.0
34 TraesCS1D01G085000 chr2B 75.381 459 85 21 1102 1552 691417462 691417024 2.680000e-46 196.0
35 TraesCS1D01G085000 chr2B 79.508 244 46 4 2170 2409 691416306 691416063 1.630000e-38 171.0
36 TraesCS1D01G085000 chr2B 72.039 515 115 22 1858 2353 691271457 691271961 3.570000e-25 126.0
37 TraesCS1D01G085000 chr2B 89.333 75 7 1 616 689 701749504 701749430 3.620000e-15 93.5
38 TraesCS1D01G085000 chr5A 84.153 183 29 0 434 616 601987089 601986907 9.720000e-41 178.0
39 TraesCS1D01G085000 chr7B 73.913 414 91 15 2956 3355 640513844 640513434 2.120000e-32 150.0


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 TraesCS1D01G085000 chr1D 69195434 69198842 3408 True 6296.000000 6296 100.000000 1 3409 1 chr1D.!!$R2 3408
1 TraesCS1D01G085000 chr1D 69188731 69189436 705 True 595.000000 595 82.108000 2639 3350 1 chr1D.!!$R1 711
2 TraesCS1D01G085000 chr1A 68457186 68460608 3422 True 1208.333333 2481 95.470333 710 3376 3 chr1A.!!$R2 2666
3 TraesCS1D01G085000 chr1A 68417960 68418660 700 True 573.000000 573 81.667000 2639 3350 1 chr1A.!!$R1 711
4 TraesCS1D01G085000 chr1B 111049807 111052512 2705 True 1287.666667 1334 93.268667 710 3409 3 chr1B.!!$R3 2699
5 TraesCS1D01G085000 chr1B 111032328 111033028 700 True 601.000000 601 82.337000 2639 3350 1 chr1B.!!$R1 711
6 TraesCS1D01G085000 chr1B 623814905 623815408 503 True 352.750000 612 91.922500 1 683 2 chr1B.!!$R4 682

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
707 709 0.033366 ATGGTGCTTTGAAAACGGCC 59.967 50.000 0.00 0.0 0.00 6.13 F
708 710 1.040339 TGGTGCTTTGAAAACGGCCT 61.040 50.000 0.00 0.0 0.00 5.19 F
967 971 1.430632 GTGGTTGCATGCTGATCGG 59.569 57.895 20.33 0.0 0.00 4.18 F
1511 1520 1.519455 CCTCGACGTGGATTGCTCC 60.519 63.158 10.42 0.0 42.45 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1529 1538 1.602323 GATCACCACCAACGGCCAA 60.602 57.895 2.24 0.0 0.00 4.52 R
2356 2486 1.659622 TTCTATCTCCGCCGCGAACA 61.660 55.000 15.93 0.0 0.00 3.18 R
2400 2530 2.159627 CGACGCAGCTTATTTTTCAGGT 59.840 45.455 0.00 0.0 0.00 4.00 R
3168 4210 1.878734 GCTGATATGCTCCTTGCTTCC 59.121 52.381 0.00 0.0 43.37 3.46 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
24 25 1.569493 CAACAGAGGCCGTGTTTCG 59.431 57.895 20.39 9.54 35.93 3.46
29 30 1.332375 CAGAGGCCGTGTTTCGAAAAA 59.668 47.619 13.10 3.93 42.86 1.94
34 35 3.067601 AGGCCGTGTTTCGAAAAAGAAAT 59.932 39.130 13.10 0.00 41.46 2.17
41 42 6.291532 CGTGTTTCGAAAAAGAAATTGCATCA 60.292 34.615 13.10 0.00 41.46 3.07
71 72 2.505118 GAGCGACTGAGCGTCACC 60.505 66.667 0.00 0.00 42.98 4.02
149 150 8.791675 TCATGTTGTAGACATTTTTGCAAGATA 58.208 29.630 0.00 0.00 46.80 1.98
209 210 4.799564 TTTGCAACAGAGGTCTTGTTTT 57.200 36.364 0.00 0.00 0.00 2.43
265 267 2.202295 TTTTGCAACAAAGGTCTCGC 57.798 45.000 0.00 0.00 0.00 5.03
276 278 7.305474 CAACAAAGGTCTCGCTGTAAATTTAT 58.695 34.615 0.31 0.00 0.00 1.40
302 304 3.141398 TCTGAAACAGAGGTCATGTTGC 58.859 45.455 0.00 0.00 39.91 4.17
340 342 1.174712 GGCCTTGCTGCAGAAACTCA 61.175 55.000 20.43 1.69 0.00 3.41
342 344 1.135460 GCCTTGCTGCAGAAACTCATC 60.135 52.381 20.43 0.00 0.00 2.92
358 360 1.138859 TCATCGTAGTGGGCATTGAGG 59.861 52.381 0.00 0.00 0.00 3.86
362 364 0.811616 GTAGTGGGCATTGAGGAGCG 60.812 60.000 0.00 0.00 0.00 5.03
364 366 1.377202 GTGGGCATTGAGGAGCGAA 60.377 57.895 0.00 0.00 0.00 4.70
368 370 1.098050 GGCATTGAGGAGCGAACAAT 58.902 50.000 0.00 0.00 35.10 2.71
378 380 0.250467 AGCGAACAATGAGCAGTGGT 60.250 50.000 0.00 0.00 0.00 4.16
401 403 5.008712 GTCAGGTTGACCGAAAGAAAGAAAT 59.991 40.000 0.00 0.00 41.37 2.17
407 409 6.796705 TGACCGAAAGAAAGAAATAAGACC 57.203 37.500 0.00 0.00 0.00 3.85
408 410 5.407387 TGACCGAAAGAAAGAAATAAGACCG 59.593 40.000 0.00 0.00 0.00 4.79
409 411 4.153655 ACCGAAAGAAAGAAATAAGACCGC 59.846 41.667 0.00 0.00 0.00 5.68
410 412 4.392138 CCGAAAGAAAGAAATAAGACCGCT 59.608 41.667 0.00 0.00 0.00 5.52
411 413 5.446073 CCGAAAGAAAGAAATAAGACCGCTC 60.446 44.000 0.00 0.00 0.00 5.03
428 430 3.238497 CCCAGGGGACACGTGTCA 61.238 66.667 40.51 0.00 46.47 3.58
430 432 1.261938 CCCAGGGGACACGTGTCATA 61.262 60.000 40.51 0.00 46.47 2.15
431 433 0.108329 CCAGGGGACACGTGTCATAC 60.108 60.000 40.51 30.55 46.47 2.39
432 434 0.895530 CAGGGGACACGTGTCATACT 59.104 55.000 40.51 31.84 46.47 2.12
433 435 0.895530 AGGGGACACGTGTCATACTG 59.104 55.000 40.51 7.44 46.47 2.74
434 436 0.892755 GGGGACACGTGTCATACTGA 59.107 55.000 40.51 0.00 46.47 3.41
436 438 2.289195 GGGGACACGTGTCATACTGAAA 60.289 50.000 40.51 0.00 46.47 2.69
437 439 3.395639 GGGACACGTGTCATACTGAAAA 58.604 45.455 40.51 0.00 46.47 2.29
438 440 4.000988 GGGACACGTGTCATACTGAAAAT 58.999 43.478 40.51 8.57 46.47 1.82
439 441 4.142902 GGGACACGTGTCATACTGAAAATG 60.143 45.833 40.51 4.03 46.47 2.32
440 442 4.394795 GACACGTGTCATACTGAAAATGC 58.605 43.478 37.16 10.79 44.18 3.56
441 443 4.065088 ACACGTGTCATACTGAAAATGCT 58.935 39.130 17.22 0.00 0.00 3.79
442 444 4.152402 ACACGTGTCATACTGAAAATGCTC 59.848 41.667 17.22 0.00 0.00 4.26
443 445 3.684788 ACGTGTCATACTGAAAATGCTCC 59.315 43.478 0.00 0.00 0.00 4.70
444 446 3.684305 CGTGTCATACTGAAAATGCTCCA 59.316 43.478 0.00 0.00 0.00 3.86
445 447 4.436050 CGTGTCATACTGAAAATGCTCCAC 60.436 45.833 0.00 0.00 0.00 4.02
446 448 4.697352 GTGTCATACTGAAAATGCTCCACT 59.303 41.667 0.00 0.00 0.00 4.00
447 449 5.182001 GTGTCATACTGAAAATGCTCCACTT 59.818 40.000 0.00 0.00 0.00 3.16
448 450 6.371548 GTGTCATACTGAAAATGCTCCACTTA 59.628 38.462 0.00 0.00 0.00 2.24
449 451 6.371548 TGTCATACTGAAAATGCTCCACTTAC 59.628 38.462 0.00 0.00 0.00 2.34
450 452 5.580691 TCATACTGAAAATGCTCCACTTACG 59.419 40.000 0.00 0.00 0.00 3.18
451 453 3.074412 ACTGAAAATGCTCCACTTACGG 58.926 45.455 0.00 0.00 0.00 4.02
452 454 3.244422 ACTGAAAATGCTCCACTTACGGA 60.244 43.478 0.00 0.00 0.00 4.69
453 455 3.071479 TGAAAATGCTCCACTTACGGAC 58.929 45.455 0.00 0.00 0.00 4.79
454 456 3.244422 TGAAAATGCTCCACTTACGGACT 60.244 43.478 0.00 0.00 0.00 3.85
455 457 2.674796 AATGCTCCACTTACGGACTC 57.325 50.000 0.00 0.00 0.00 3.36
456 458 1.853963 ATGCTCCACTTACGGACTCT 58.146 50.000 0.00 0.00 0.00 3.24
457 459 2.502142 TGCTCCACTTACGGACTCTA 57.498 50.000 0.00 0.00 0.00 2.43
458 460 3.014304 TGCTCCACTTACGGACTCTAT 57.986 47.619 0.00 0.00 0.00 1.98
459 461 2.950309 TGCTCCACTTACGGACTCTATC 59.050 50.000 0.00 0.00 0.00 2.08
460 462 3.215975 GCTCCACTTACGGACTCTATCT 58.784 50.000 0.00 0.00 0.00 1.98
461 463 4.141551 TGCTCCACTTACGGACTCTATCTA 60.142 45.833 0.00 0.00 0.00 1.98
462 464 4.213906 GCTCCACTTACGGACTCTATCTAC 59.786 50.000 0.00 0.00 0.00 2.59
463 465 4.375272 TCCACTTACGGACTCTATCTACG 58.625 47.826 0.00 0.00 0.00 3.51
464 466 3.059051 CCACTTACGGACTCTATCTACGC 60.059 52.174 0.00 0.00 0.00 4.42
465 467 3.808726 CACTTACGGACTCTATCTACGCT 59.191 47.826 0.00 0.00 0.00 5.07
466 468 4.057432 ACTTACGGACTCTATCTACGCTC 58.943 47.826 0.00 0.00 0.00 5.03
467 469 2.616634 ACGGACTCTATCTACGCTCA 57.383 50.000 0.00 0.00 0.00 4.26
468 470 2.485903 ACGGACTCTATCTACGCTCAG 58.514 52.381 0.00 0.00 0.00 3.35
469 471 2.102757 ACGGACTCTATCTACGCTCAGA 59.897 50.000 0.00 0.00 0.00 3.27
470 472 2.734606 CGGACTCTATCTACGCTCAGAG 59.265 54.545 0.00 0.00 40.31 3.35
473 475 3.735591 ACTCTATCTACGCTCAGAGTCC 58.264 50.000 0.00 0.00 43.20 3.85
474 476 3.389983 ACTCTATCTACGCTCAGAGTCCT 59.610 47.826 0.00 0.00 43.20 3.85
475 477 4.589798 ACTCTATCTACGCTCAGAGTCCTA 59.410 45.833 0.00 0.00 43.20 2.94
476 478 4.885413 TCTATCTACGCTCAGAGTCCTAC 58.115 47.826 0.00 0.00 0.00 3.18
477 479 1.937278 TCTACGCTCAGAGTCCTACG 58.063 55.000 0.00 0.00 0.00 3.51
478 480 0.938713 CTACGCTCAGAGTCCTACGG 59.061 60.000 0.00 0.00 0.00 4.02
479 481 0.538584 TACGCTCAGAGTCCTACGGA 59.461 55.000 0.00 0.00 0.00 4.69
492 494 2.279918 ACGGACAGACGTGTTGCC 60.280 61.111 0.00 0.00 46.64 4.52
493 495 2.029073 CGGACAGACGTGTTGCCT 59.971 61.111 0.00 0.00 36.88 4.75
494 496 2.022129 CGGACAGACGTGTTGCCTC 61.022 63.158 0.00 0.00 36.88 4.70
495 497 1.668151 GGACAGACGTGTTGCCTCC 60.668 63.158 0.00 0.00 36.88 4.30
496 498 1.367840 GACAGACGTGTTGCCTCCT 59.632 57.895 0.00 0.00 36.88 3.69
497 499 0.601558 GACAGACGTGTTGCCTCCTA 59.398 55.000 0.00 0.00 36.88 2.94
498 500 1.000506 GACAGACGTGTTGCCTCCTAA 59.999 52.381 0.00 0.00 36.88 2.69
499 501 1.623811 ACAGACGTGTTGCCTCCTAAT 59.376 47.619 0.00 0.00 30.30 1.73
500 502 2.002586 CAGACGTGTTGCCTCCTAATG 58.997 52.381 0.00 0.00 0.00 1.90
501 503 0.727398 GACGTGTTGCCTCCTAATGC 59.273 55.000 0.00 0.00 0.00 3.56
502 504 0.036164 ACGTGTTGCCTCCTAATGCA 59.964 50.000 0.00 0.00 35.27 3.96
503 505 1.340017 ACGTGTTGCCTCCTAATGCAT 60.340 47.619 0.00 0.00 37.33 3.96
504 506 1.331756 CGTGTTGCCTCCTAATGCATC 59.668 52.381 0.00 0.00 37.33 3.91
505 507 1.678101 GTGTTGCCTCCTAATGCATCC 59.322 52.381 0.00 0.00 37.33 3.51
506 508 1.322442 GTTGCCTCCTAATGCATCCC 58.678 55.000 0.00 0.00 37.33 3.85
507 509 1.133668 GTTGCCTCCTAATGCATCCCT 60.134 52.381 0.00 0.00 37.33 4.20
508 510 0.767375 TGCCTCCTAATGCATCCCTC 59.233 55.000 0.00 0.00 31.31 4.30
509 511 0.767375 GCCTCCTAATGCATCCCTCA 59.233 55.000 0.00 0.00 0.00 3.86
510 512 1.544314 GCCTCCTAATGCATCCCTCAC 60.544 57.143 0.00 0.00 0.00 3.51
511 513 2.053244 CCTCCTAATGCATCCCTCACT 58.947 52.381 0.00 0.00 0.00 3.41
512 514 2.038295 CCTCCTAATGCATCCCTCACTC 59.962 54.545 0.00 0.00 0.00 3.51
513 515 2.038295 CTCCTAATGCATCCCTCACTCC 59.962 54.545 0.00 0.00 0.00 3.85
514 516 1.270518 CCTAATGCATCCCTCACTCCG 60.271 57.143 0.00 0.00 0.00 4.63
515 517 1.414181 CTAATGCATCCCTCACTCCGT 59.586 52.381 0.00 0.00 0.00 4.69
516 518 0.107508 AATGCATCCCTCACTCCGTG 60.108 55.000 0.00 0.00 34.45 4.94
517 519 0.977627 ATGCATCCCTCACTCCGTGA 60.978 55.000 0.00 0.00 40.50 4.35
518 520 0.977627 TGCATCCCTCACTCCGTGAT 60.978 55.000 0.00 0.00 41.94 3.06
519 521 0.179000 GCATCCCTCACTCCGTGATT 59.821 55.000 0.00 0.00 41.94 2.57
520 522 1.407437 GCATCCCTCACTCCGTGATTT 60.407 52.381 0.00 0.00 41.94 2.17
521 523 2.283298 CATCCCTCACTCCGTGATTTG 58.717 52.381 0.00 0.00 41.94 2.32
522 524 0.036388 TCCCTCACTCCGTGATTTGC 60.036 55.000 0.00 0.00 41.94 3.68
523 525 0.321564 CCCTCACTCCGTGATTTGCA 60.322 55.000 0.00 0.00 41.94 4.08
524 526 1.081892 CCTCACTCCGTGATTTGCAG 58.918 55.000 0.00 0.00 41.94 4.41
525 527 1.081892 CTCACTCCGTGATTTGCAGG 58.918 55.000 0.00 0.00 41.94 4.85
529 531 3.277133 CCGTGATTTGCAGGGTGG 58.723 61.111 0.00 0.00 45.36 4.61
530 532 2.342650 CCGTGATTTGCAGGGTGGG 61.343 63.158 0.00 0.00 45.36 4.61
531 533 2.342650 CGTGATTTGCAGGGTGGGG 61.343 63.158 0.00 0.00 0.00 4.96
532 534 2.283821 TGATTTGCAGGGTGGGGC 60.284 61.111 0.00 0.00 0.00 5.80
533 535 3.076916 GATTTGCAGGGTGGGGCC 61.077 66.667 0.00 0.00 0.00 5.80
534 536 3.604133 ATTTGCAGGGTGGGGCCT 61.604 61.111 0.84 0.00 37.43 5.19
535 537 3.607084 ATTTGCAGGGTGGGGCCTC 62.607 63.158 0.84 0.00 37.43 4.70
539 541 3.732849 CAGGGTGGGGCCTCCTTC 61.733 72.222 0.00 0.00 37.43 3.46
546 548 3.272847 GGGCCTCCTTCCCCCAAA 61.273 66.667 0.84 0.00 38.70 3.28
547 549 2.636617 GGGCCTCCTTCCCCCAAAT 61.637 63.158 0.84 0.00 38.70 2.32
548 550 1.392131 GGCCTCCTTCCCCCAAATT 59.608 57.895 0.00 0.00 0.00 1.82
549 551 0.634465 GGCCTCCTTCCCCCAAATTA 59.366 55.000 0.00 0.00 0.00 1.40
550 552 1.411644 GGCCTCCTTCCCCCAAATTAG 60.412 57.143 0.00 0.00 0.00 1.73
551 553 1.411644 GCCTCCTTCCCCCAAATTAGG 60.412 57.143 0.00 0.00 0.00 2.69
552 554 1.930204 CCTCCTTCCCCCAAATTAGGT 59.070 52.381 0.00 0.00 0.00 3.08
553 555 2.358195 CCTCCTTCCCCCAAATTAGGTG 60.358 54.545 0.00 0.00 0.00 4.00
554 556 2.580783 CTCCTTCCCCCAAATTAGGTGA 59.419 50.000 0.00 0.00 0.00 4.02
555 557 2.580783 TCCTTCCCCCAAATTAGGTGAG 59.419 50.000 0.00 0.00 0.00 3.51
556 558 2.358195 CCTTCCCCCAAATTAGGTGAGG 60.358 54.545 0.00 0.00 0.00 3.86
557 559 0.629058 TCCCCCAAATTAGGTGAGGC 59.371 55.000 0.00 0.00 0.00 4.70
558 560 0.397114 CCCCCAAATTAGGTGAGGCC 60.397 60.000 0.00 0.00 37.58 5.19
559 561 0.334676 CCCCAAATTAGGTGAGGCCA 59.665 55.000 5.01 0.00 40.61 5.36
560 562 1.474330 CCCAAATTAGGTGAGGCCAC 58.526 55.000 5.01 0.00 42.46 5.01
572 574 2.586792 GGCCACCTCTGCCTGTAG 59.413 66.667 0.00 0.00 45.70 2.74
573 575 2.586792 GCCACCTCTGCCTGTAGG 59.413 66.667 0.00 0.00 38.93 3.18
575 577 1.901085 CCACCTCTGCCTGTAGGTC 59.099 63.158 0.00 0.00 44.43 3.85
576 578 0.616111 CCACCTCTGCCTGTAGGTCT 60.616 60.000 0.00 0.00 44.43 3.85
577 579 1.270907 CACCTCTGCCTGTAGGTCTT 58.729 55.000 0.00 0.00 44.43 3.01
578 580 1.066573 CACCTCTGCCTGTAGGTCTTG 60.067 57.143 0.00 0.00 44.43 3.02
579 581 1.270907 CCTCTGCCTGTAGGTCTTGT 58.729 55.000 0.00 0.00 37.57 3.16
580 582 1.625818 CCTCTGCCTGTAGGTCTTGTT 59.374 52.381 0.00 0.00 37.57 2.83
581 583 2.039084 CCTCTGCCTGTAGGTCTTGTTT 59.961 50.000 0.00 0.00 37.57 2.83
582 584 3.330267 CTCTGCCTGTAGGTCTTGTTTC 58.670 50.000 0.00 0.00 37.57 2.78
583 585 2.069273 CTGCCTGTAGGTCTTGTTTCG 58.931 52.381 0.00 0.00 37.57 3.46
584 586 0.796927 GCCTGTAGGTCTTGTTTCGC 59.203 55.000 0.00 0.00 37.57 4.70
585 587 1.068474 CCTGTAGGTCTTGTTTCGCG 58.932 55.000 0.00 0.00 0.00 5.87
586 588 1.336517 CCTGTAGGTCTTGTTTCGCGA 60.337 52.381 3.71 3.71 0.00 5.87
587 589 2.400399 CTGTAGGTCTTGTTTCGCGAA 58.600 47.619 19.38 19.38 0.00 4.70
588 590 2.798283 CTGTAGGTCTTGTTTCGCGAAA 59.202 45.455 29.22 29.22 0.00 3.46
589 591 3.196463 TGTAGGTCTTGTTTCGCGAAAA 58.804 40.909 33.69 19.53 31.33 2.29
590 592 3.622163 TGTAGGTCTTGTTTCGCGAAAAA 59.378 39.130 33.69 27.23 31.33 1.94
607 609 1.799544 AAAACGCCCGTAACTGTAGG 58.200 50.000 0.00 0.00 0.00 3.18
608 610 0.968405 AAACGCCCGTAACTGTAGGA 59.032 50.000 0.00 0.00 0.00 2.94
609 611 1.188863 AACGCCCGTAACTGTAGGAT 58.811 50.000 0.00 0.00 0.00 3.24
610 612 1.188863 ACGCCCGTAACTGTAGGATT 58.811 50.000 0.00 0.00 0.00 3.01
611 613 1.134907 ACGCCCGTAACTGTAGGATTG 60.135 52.381 0.00 0.00 0.00 2.67
612 614 1.296727 GCCCGTAACTGTAGGATTGC 58.703 55.000 0.00 0.00 0.00 3.56
613 615 1.134491 GCCCGTAACTGTAGGATTGCT 60.134 52.381 0.00 0.00 0.00 3.91
614 616 2.822764 CCCGTAACTGTAGGATTGCTC 58.177 52.381 0.00 0.00 0.00 4.26
680 682 3.557264 CGGTAGAAGCCAAGAGTTTTCCT 60.557 47.826 0.00 0.00 0.00 3.36
681 683 4.322499 CGGTAGAAGCCAAGAGTTTTCCTA 60.322 45.833 0.00 0.00 0.00 2.94
682 684 5.627040 CGGTAGAAGCCAAGAGTTTTCCTAT 60.627 44.000 0.00 0.00 0.00 2.57
683 685 6.406624 CGGTAGAAGCCAAGAGTTTTCCTATA 60.407 42.308 0.00 0.00 0.00 1.31
684 686 6.987404 GGTAGAAGCCAAGAGTTTTCCTATAG 59.013 42.308 0.00 0.00 0.00 1.31
685 687 6.875972 AGAAGCCAAGAGTTTTCCTATAGA 57.124 37.500 0.00 0.00 0.00 1.98
686 688 7.259088 AGAAGCCAAGAGTTTTCCTATAGAA 57.741 36.000 0.00 0.00 0.00 2.10
687 689 7.690256 AGAAGCCAAGAGTTTTCCTATAGAAA 58.310 34.615 0.00 0.00 42.82 2.52
699 701 8.415950 TTTTCCTATAGAAAATGGTGCTTTGA 57.584 30.769 0.00 0.00 47.00 2.69
700 702 8.415950 TTTCCTATAGAAAATGGTGCTTTGAA 57.584 30.769 0.00 0.00 41.56 2.69
701 703 8.415950 TTCCTATAGAAAATGGTGCTTTGAAA 57.584 30.769 0.00 0.00 0.00 2.69
702 704 8.415950 TCCTATAGAAAATGGTGCTTTGAAAA 57.584 30.769 0.00 0.00 0.00 2.29
703 705 8.303876 TCCTATAGAAAATGGTGCTTTGAAAAC 58.696 33.333 0.00 0.00 0.00 2.43
704 706 7.273381 CCTATAGAAAATGGTGCTTTGAAAACG 59.727 37.037 0.00 0.00 0.00 3.60
705 707 4.119136 AGAAAATGGTGCTTTGAAAACGG 58.881 39.130 0.00 0.00 0.00 4.44
706 708 1.864565 AATGGTGCTTTGAAAACGGC 58.135 45.000 0.00 0.00 0.00 5.68
707 709 0.033366 ATGGTGCTTTGAAAACGGCC 59.967 50.000 0.00 0.00 0.00 6.13
708 710 1.040339 TGGTGCTTTGAAAACGGCCT 61.040 50.000 0.00 0.00 0.00 5.19
727 729 2.098117 CCTCATTGGCATTTTCCGAGAC 59.902 50.000 0.00 0.00 0.00 3.36
729 731 1.818060 CATTGGCATTTTCCGAGACCA 59.182 47.619 0.00 0.00 0.00 4.02
909 913 3.356529 ACCTAATTCCACTGCAGAAGG 57.643 47.619 23.35 21.04 0.00 3.46
967 971 1.430632 GTGGTTGCATGCTGATCGG 59.569 57.895 20.33 0.00 0.00 4.18
1046 1055 3.067180 CACCTCAAAAACACACAGAGCAT 59.933 43.478 0.00 0.00 0.00 3.79
1095 1104 2.430582 CACGCGGGGTGCAAATTG 60.431 61.111 12.47 0.00 46.97 2.32
1370 1379 2.743928 GGCAAGCTGGTCGTGGAG 60.744 66.667 0.00 0.00 0.00 3.86
1511 1520 1.519455 CCTCGACGTGGATTGCTCC 60.519 63.158 10.42 0.00 42.45 4.70
1512 1521 1.874019 CTCGACGTGGATTGCTCCG 60.874 63.158 0.00 0.00 45.37 4.63
1517 1526 4.778143 GTGGATTGCTCCGGCGGT 62.778 66.667 27.32 5.58 45.37 5.68
1552 1662 2.040544 CGTTGGTGGTGATCCAGGC 61.041 63.158 0.00 0.00 45.24 4.85
2273 2403 3.402681 CAGGTGCATCTCGGGGGT 61.403 66.667 0.00 0.00 0.00 4.95
2372 2502 2.411701 CTGTTCGCGGCGGAGATA 59.588 61.111 23.46 6.57 0.00 1.98
2384 2514 1.866063 GCGGAGATAGAAACCTCGCTG 60.866 57.143 0.00 0.00 0.00 5.18
2385 2515 1.676529 CGGAGATAGAAACCTCGCTGA 59.323 52.381 0.00 0.00 0.00 4.26
2397 2527 2.171448 ACCTCGCTGAAGGCTTGATTAT 59.829 45.455 3.46 0.00 40.34 1.28
2400 2530 4.371786 CTCGCTGAAGGCTTGATTATACA 58.628 43.478 3.46 0.00 39.13 2.29
2413 2543 9.736023 GGCTTGATTATACACCTGAAAAATAAG 57.264 33.333 0.00 0.00 0.00 1.73
2414 2544 9.237846 GCTTGATTATACACCTGAAAAATAAGC 57.762 33.333 0.00 0.00 0.00 3.09
2417 2547 8.405531 TGATTATACACCTGAAAAATAAGCTGC 58.594 33.333 0.00 0.00 0.00 5.25
2418 2548 3.559238 ACACCTGAAAAATAAGCTGCG 57.441 42.857 0.00 0.00 0.00 5.18
2419 2549 2.884639 ACACCTGAAAAATAAGCTGCGT 59.115 40.909 0.00 0.00 0.00 5.24
2420 2550 3.058224 ACACCTGAAAAATAAGCTGCGTC 60.058 43.478 0.00 0.00 0.00 5.19
2421 2551 2.159627 ACCTGAAAAATAAGCTGCGTCG 59.840 45.455 0.00 0.00 0.00 5.12
2422 2552 2.415168 CCTGAAAAATAAGCTGCGTCGA 59.585 45.455 0.00 0.00 0.00 4.20
2423 2553 3.408150 CTGAAAAATAAGCTGCGTCGAC 58.592 45.455 5.18 5.18 0.00 4.20
2424 2554 2.159894 TGAAAAATAAGCTGCGTCGACG 60.160 45.455 32.57 32.57 43.27 5.12
2425 2555 1.425412 AAAATAAGCTGCGTCGACGT 58.575 45.000 35.48 20.06 42.22 4.34
2426 2556 0.713883 AAATAAGCTGCGTCGACGTG 59.286 50.000 35.48 28.14 42.22 4.49
2427 2557 1.683790 AATAAGCTGCGTCGACGTGC 61.684 55.000 33.74 33.74 42.22 5.34
2431 2561 3.521220 CTGCGTCGACGTGCGTAC 61.521 66.667 35.48 20.00 42.22 3.67
2462 2592 8.343168 ACTCTCCTATTAATATGTCTTCTCCG 57.657 38.462 0.00 0.00 0.00 4.63
2463 2593 8.164733 ACTCTCCTATTAATATGTCTTCTCCGA 58.835 37.037 0.00 0.00 0.00 4.55
2464 2594 8.935614 TCTCCTATTAATATGTCTTCTCCGAA 57.064 34.615 0.00 0.00 0.00 4.30
2465 2595 9.363401 TCTCCTATTAATATGTCTTCTCCGAAA 57.637 33.333 0.00 0.00 0.00 3.46
2503 2633 4.684484 TCACAGATCTCATGCTGCTTAT 57.316 40.909 0.00 0.00 35.57 1.73
2504 2634 5.796424 TCACAGATCTCATGCTGCTTATA 57.204 39.130 0.00 0.00 35.57 0.98
2505 2635 6.356186 TCACAGATCTCATGCTGCTTATAT 57.644 37.500 0.00 0.00 35.57 0.86
2506 2636 6.396450 TCACAGATCTCATGCTGCTTATATC 58.604 40.000 0.00 0.00 35.57 1.63
2507 2637 6.210984 TCACAGATCTCATGCTGCTTATATCT 59.789 38.462 0.00 0.64 35.57 1.98
2508 2638 6.311690 CACAGATCTCATGCTGCTTATATCTG 59.688 42.308 20.41 20.41 42.92 2.90
2509 2639 6.210984 ACAGATCTCATGCTGCTTATATCTGA 59.789 38.462 24.90 9.14 40.86 3.27
2510 2640 7.093245 ACAGATCTCATGCTGCTTATATCTGAT 60.093 37.037 24.90 14.29 40.86 2.90
2511 2641 8.414778 CAGATCTCATGCTGCTTATATCTGATA 58.585 37.037 18.75 0.00 40.86 2.15
2512 2642 9.150028 AGATCTCATGCTGCTTATATCTGATAT 57.850 33.333 14.18 14.18 0.00 1.63
2535 2667 4.160329 TCTGAACTTCACCCACTCATACT 58.840 43.478 0.00 0.00 0.00 2.12
2544 2676 7.509318 ACTTCACCCACTCATACTGCTTATATA 59.491 37.037 0.00 0.00 0.00 0.86
2588 2720 7.949690 TGTGTACAACATACTACCAGATAGT 57.050 36.000 0.00 0.00 39.75 2.12
2600 2732 6.929625 ACTACCAGATAGTATAAGCATGCTG 58.070 40.000 23.48 6.33 42.69 4.41
2601 2733 5.815233 ACCAGATAGTATAAGCATGCTGT 57.185 39.130 23.48 15.79 0.00 4.40
2602 2734 6.918067 ACCAGATAGTATAAGCATGCTGTA 57.082 37.500 23.48 14.69 0.00 2.74
2603 2735 7.487822 ACCAGATAGTATAAGCATGCTGTAT 57.512 36.000 23.48 20.82 0.00 2.29
2604 2736 8.595362 ACCAGATAGTATAAGCATGCTGTATA 57.405 34.615 23.48 19.88 0.00 1.47
2605 2737 9.206690 ACCAGATAGTATAAGCATGCTGTATAT 57.793 33.333 23.48 17.43 0.00 0.86
2717 3757 7.280205 GGAAATATCCTGTAACTTACACACTGG 59.720 40.741 0.00 0.00 42.93 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.179067 TTCGAAACACGGCCTCTGTT 60.179 50.000 9.35 9.35 42.82 3.16
17 18 6.932051 TGATGCAATTTCTTTTTCGAAACAC 58.068 32.000 10.79 0.00 35.88 3.32
24 25 6.252228 GTCGGATCTGATGCAATTTCTTTTTC 59.748 38.462 7.68 0.00 0.00 2.29
29 30 3.877559 TGTCGGATCTGATGCAATTTCT 58.122 40.909 7.68 0.00 0.00 2.52
34 35 3.608796 TCAATTGTCGGATCTGATGCAA 58.391 40.909 7.68 8.68 0.00 4.08
41 42 1.478510 AGTCGCTCAATTGTCGGATCT 59.521 47.619 17.72 12.66 0.00 2.75
71 72 7.099266 TGACCTATGTTGCAATGATAAAAGG 57.901 36.000 0.59 5.96 0.00 3.11
163 164 6.463995 AAACTAAATTGCAACAAGACCTCA 57.536 33.333 0.00 0.00 0.00 3.86
302 304 3.550842 GGCCTCTGTTGCAGTAAAAACTG 60.551 47.826 0.00 1.14 40.51 3.16
319 321 0.892814 AGTTTCTGCAGCAAGGCCTC 60.893 55.000 5.23 0.00 0.00 4.70
340 342 1.414181 CTCCTCAATGCCCACTACGAT 59.586 52.381 0.00 0.00 0.00 3.73
342 344 0.811616 GCTCCTCAATGCCCACTACG 60.812 60.000 0.00 0.00 0.00 3.51
358 360 0.445436 CCACTGCTCATTGTTCGCTC 59.555 55.000 0.00 0.00 0.00 5.03
362 364 1.808945 CCTGACCACTGCTCATTGTTC 59.191 52.381 0.00 0.00 0.00 3.18
364 366 0.767375 ACCTGACCACTGCTCATTGT 59.233 50.000 0.00 0.00 0.00 2.71
368 370 0.106708 GTCAACCTGACCACTGCTCA 59.893 55.000 0.00 0.00 41.37 4.26
369 371 2.919971 GTCAACCTGACCACTGCTC 58.080 57.895 0.00 0.00 41.37 4.26
378 380 3.830744 TCTTTCTTTCGGTCAACCTGA 57.169 42.857 0.00 0.00 0.00 3.86
401 403 2.365105 CCCCTGGGAGCGGTCTTA 60.365 66.667 16.20 2.95 37.50 2.10
408 410 4.394712 CACGTGTCCCCTGGGAGC 62.395 72.222 16.20 6.94 46.16 4.70
409 411 2.923035 ACACGTGTCCCCTGGGAG 60.923 66.667 17.22 4.42 46.16 4.30
410 412 2.920912 GACACGTGTCCCCTGGGA 60.921 66.667 33.62 3.95 42.90 4.37
411 413 1.261938 TATGACACGTGTCCCCTGGG 61.262 60.000 38.12 5.50 44.15 4.45
428 430 4.876107 CCGTAAGTGGAGCATTTTCAGTAT 59.124 41.667 0.00 0.00 0.00 2.12
430 432 3.074412 CCGTAAGTGGAGCATTTTCAGT 58.926 45.455 0.00 0.00 0.00 3.41
431 433 3.125316 GTCCGTAAGTGGAGCATTTTCAG 59.875 47.826 0.00 0.00 39.14 3.02
432 434 3.071479 GTCCGTAAGTGGAGCATTTTCA 58.929 45.455 0.00 0.00 39.14 2.69
433 435 3.335579 AGTCCGTAAGTGGAGCATTTTC 58.664 45.455 0.00 0.00 39.14 2.29
434 436 3.008049 AGAGTCCGTAAGTGGAGCATTTT 59.992 43.478 0.00 0.00 39.14 1.82
436 438 2.180276 AGAGTCCGTAAGTGGAGCATT 58.820 47.619 0.00 0.00 39.14 3.56
437 439 1.853963 AGAGTCCGTAAGTGGAGCAT 58.146 50.000 0.00 0.00 39.14 3.79
438 440 2.502142 TAGAGTCCGTAAGTGGAGCA 57.498 50.000 0.00 0.00 39.14 4.26
439 441 3.215975 AGATAGAGTCCGTAAGTGGAGC 58.784 50.000 0.00 0.00 39.14 4.70
440 442 4.448395 CGTAGATAGAGTCCGTAAGTGGAG 59.552 50.000 0.00 0.00 39.14 3.86
441 443 4.375272 CGTAGATAGAGTCCGTAAGTGGA 58.625 47.826 0.00 0.00 35.04 4.02
442 444 3.059051 GCGTAGATAGAGTCCGTAAGTGG 60.059 52.174 0.00 0.00 0.00 4.00
443 445 3.808726 AGCGTAGATAGAGTCCGTAAGTG 59.191 47.826 0.00 0.00 0.00 3.16
444 446 4.057432 GAGCGTAGATAGAGTCCGTAAGT 58.943 47.826 0.00 0.00 0.00 2.24
445 447 4.056740 TGAGCGTAGATAGAGTCCGTAAG 58.943 47.826 0.00 0.00 0.00 2.34
446 448 4.056740 CTGAGCGTAGATAGAGTCCGTAA 58.943 47.826 0.00 0.00 0.00 3.18
447 449 3.320256 TCTGAGCGTAGATAGAGTCCGTA 59.680 47.826 0.00 0.00 0.00 4.02
448 450 2.102757 TCTGAGCGTAGATAGAGTCCGT 59.897 50.000 0.00 0.00 0.00 4.69
449 451 2.734606 CTCTGAGCGTAGATAGAGTCCG 59.265 54.545 0.00 0.00 33.65 4.79
450 452 3.735591 ACTCTGAGCGTAGATAGAGTCC 58.264 50.000 4.19 0.00 44.76 3.85
453 455 4.002906 AGGACTCTGAGCGTAGATAGAG 57.997 50.000 4.19 0.00 41.78 2.43
454 456 4.559099 CGTAGGACTCTGAGCGTAGATAGA 60.559 50.000 4.19 0.00 0.00 1.98
455 457 3.676172 CGTAGGACTCTGAGCGTAGATAG 59.324 52.174 4.19 0.00 0.00 2.08
456 458 3.651206 CGTAGGACTCTGAGCGTAGATA 58.349 50.000 4.19 0.00 0.00 1.98
457 459 2.485903 CGTAGGACTCTGAGCGTAGAT 58.514 52.381 4.19 0.00 0.00 1.98
458 460 1.937278 CGTAGGACTCTGAGCGTAGA 58.063 55.000 4.19 0.00 0.00 2.59
473 475 1.007336 GGCAACACGTCTGTCCGTAG 61.007 60.000 0.00 0.00 39.45 3.51
474 476 1.007038 GGCAACACGTCTGTCCGTA 60.007 57.895 0.00 0.00 39.45 4.02
475 477 2.279918 GGCAACACGTCTGTCCGT 60.280 61.111 0.00 0.00 42.87 4.69
476 478 2.022129 GAGGCAACACGTCTGTCCG 61.022 63.158 0.00 0.00 41.41 4.79
477 479 1.668151 GGAGGCAACACGTCTGTCC 60.668 63.158 0.00 0.00 41.41 4.02
478 480 0.601558 TAGGAGGCAACACGTCTGTC 59.398 55.000 0.00 0.00 41.41 3.51
479 481 1.045407 TTAGGAGGCAACACGTCTGT 58.955 50.000 0.00 0.00 41.41 3.41
480 482 2.002586 CATTAGGAGGCAACACGTCTG 58.997 52.381 0.00 0.00 41.41 3.51
481 483 1.676014 GCATTAGGAGGCAACACGTCT 60.676 52.381 0.00 0.00 41.41 4.18
482 484 0.727398 GCATTAGGAGGCAACACGTC 59.273 55.000 0.00 0.00 41.41 4.34
483 485 0.036164 TGCATTAGGAGGCAACACGT 59.964 50.000 0.00 0.00 40.00 4.49
484 486 1.331756 GATGCATTAGGAGGCAACACG 59.668 52.381 0.00 0.00 46.63 4.49
485 487 1.678101 GGATGCATTAGGAGGCAACAC 59.322 52.381 0.00 0.00 46.63 3.32
486 488 1.410083 GGGATGCATTAGGAGGCAACA 60.410 52.381 0.00 0.00 46.63 3.33
487 489 1.133668 AGGGATGCATTAGGAGGCAAC 60.134 52.381 0.00 0.00 46.63 4.17
488 490 1.143684 GAGGGATGCATTAGGAGGCAA 59.856 52.381 0.00 0.00 46.63 4.52
490 492 0.767375 TGAGGGATGCATTAGGAGGC 59.233 55.000 0.00 0.00 0.00 4.70
491 493 2.038295 GAGTGAGGGATGCATTAGGAGG 59.962 54.545 0.00 0.00 0.00 4.30
492 494 2.038295 GGAGTGAGGGATGCATTAGGAG 59.962 54.545 0.00 0.00 0.00 3.69
493 495 2.050144 GGAGTGAGGGATGCATTAGGA 58.950 52.381 0.00 0.00 0.00 2.94
494 496 1.270518 CGGAGTGAGGGATGCATTAGG 60.271 57.143 0.00 0.00 0.00 2.69
495 497 1.414181 ACGGAGTGAGGGATGCATTAG 59.586 52.381 0.00 0.00 42.51 1.73
496 498 1.496060 ACGGAGTGAGGGATGCATTA 58.504 50.000 0.00 0.00 42.51 1.90
497 499 2.300996 ACGGAGTGAGGGATGCATT 58.699 52.632 0.00 0.00 42.51 3.56
498 500 4.056805 ACGGAGTGAGGGATGCAT 57.943 55.556 0.00 0.00 42.51 3.96
510 512 1.308069 CCACCCTGCAAATCACGGAG 61.308 60.000 0.00 0.00 0.00 4.63
511 513 1.303236 CCACCCTGCAAATCACGGA 60.303 57.895 0.00 0.00 0.00 4.69
512 514 2.342650 CCCACCCTGCAAATCACGG 61.343 63.158 0.00 0.00 0.00 4.94
513 515 2.342650 CCCCACCCTGCAAATCACG 61.343 63.158 0.00 0.00 0.00 4.35
514 516 2.649129 GCCCCACCCTGCAAATCAC 61.649 63.158 0.00 0.00 0.00 3.06
515 517 2.283821 GCCCCACCCTGCAAATCA 60.284 61.111 0.00 0.00 0.00 2.57
516 518 3.076916 GGCCCCACCCTGCAAATC 61.077 66.667 0.00 0.00 0.00 2.17
517 519 3.604133 AGGCCCCACCCTGCAAAT 61.604 61.111 0.00 0.00 40.58 2.32
518 520 4.299796 GAGGCCCCACCCTGCAAA 62.300 66.667 0.00 0.00 40.58 3.68
522 524 3.732849 GAAGGAGGCCCCACCCTG 61.733 72.222 12.24 0.00 40.58 4.45
529 531 2.181523 AATTTGGGGGAAGGAGGCCC 62.182 60.000 0.00 0.00 45.25 5.80
530 532 0.634465 TAATTTGGGGGAAGGAGGCC 59.366 55.000 0.00 0.00 0.00 5.19
531 533 1.411644 CCTAATTTGGGGGAAGGAGGC 60.412 57.143 0.00 0.00 0.00 4.70
532 534 1.930204 ACCTAATTTGGGGGAAGGAGG 59.070 52.381 10.77 0.00 0.00 4.30
533 535 2.580783 TCACCTAATTTGGGGGAAGGAG 59.419 50.000 8.39 0.00 32.72 3.69
534 536 2.580783 CTCACCTAATTTGGGGGAAGGA 59.419 50.000 8.39 0.00 35.66 3.36
535 537 2.358195 CCTCACCTAATTTGGGGGAAGG 60.358 54.545 8.39 5.05 35.66 3.46
536 538 2.950418 GCCTCACCTAATTTGGGGGAAG 60.950 54.545 8.39 0.22 35.66 3.46
537 539 1.006639 GCCTCACCTAATTTGGGGGAA 59.993 52.381 8.39 0.00 35.66 3.97
538 540 0.629058 GCCTCACCTAATTTGGGGGA 59.371 55.000 8.39 3.48 34.81 4.81
539 541 0.397114 GGCCTCACCTAATTTGGGGG 60.397 60.000 8.39 8.92 34.81 5.40
540 542 0.334676 TGGCCTCACCTAATTTGGGG 59.665 55.000 10.77 6.35 40.22 4.96
541 543 1.474330 GTGGCCTCACCTAATTTGGG 58.526 55.000 10.77 0.00 40.22 4.12
556 558 2.245438 GACCTACAGGCAGAGGTGGC 62.245 65.000 9.43 0.00 46.36 5.01
557 559 0.616111 AGACCTACAGGCAGAGGTGG 60.616 60.000 9.43 0.00 46.36 4.61
558 560 1.066573 CAAGACCTACAGGCAGAGGTG 60.067 57.143 9.43 0.00 46.36 4.00
560 562 1.270907 ACAAGACCTACAGGCAGAGG 58.729 55.000 0.00 0.00 39.32 3.69
561 563 3.330267 GAAACAAGACCTACAGGCAGAG 58.670 50.000 0.00 0.00 39.32 3.35
562 564 2.288825 CGAAACAAGACCTACAGGCAGA 60.289 50.000 0.00 0.00 39.32 4.26
563 565 2.069273 CGAAACAAGACCTACAGGCAG 58.931 52.381 0.00 0.00 39.32 4.85
564 566 1.876416 GCGAAACAAGACCTACAGGCA 60.876 52.381 0.00 0.00 39.32 4.75
565 567 0.796927 GCGAAACAAGACCTACAGGC 59.203 55.000 0.00 0.00 39.32 4.85
566 568 1.068474 CGCGAAACAAGACCTACAGG 58.932 55.000 0.00 0.00 42.17 4.00
567 569 2.060326 TCGCGAAACAAGACCTACAG 57.940 50.000 6.20 0.00 0.00 2.74
568 570 2.512485 TTCGCGAAACAAGACCTACA 57.488 45.000 21.14 0.00 0.00 2.74
569 571 3.865224 TTTTCGCGAAACAAGACCTAC 57.135 42.857 32.32 0.00 0.00 3.18
587 589 2.145536 CCTACAGTTACGGGCGTTTTT 58.854 47.619 0.00 0.00 0.00 1.94
588 590 1.344114 TCCTACAGTTACGGGCGTTTT 59.656 47.619 0.00 0.00 0.00 2.43
589 591 0.968405 TCCTACAGTTACGGGCGTTT 59.032 50.000 0.00 0.00 0.00 3.60
590 592 1.188863 ATCCTACAGTTACGGGCGTT 58.811 50.000 0.00 0.00 0.00 4.84
591 593 1.134907 CAATCCTACAGTTACGGGCGT 60.135 52.381 0.00 0.00 0.00 5.68
592 594 1.567504 CAATCCTACAGTTACGGGCG 58.432 55.000 0.00 0.00 0.00 6.13
593 595 1.134491 AGCAATCCTACAGTTACGGGC 60.134 52.381 0.00 0.00 0.00 6.13
594 596 2.483188 GGAGCAATCCTACAGTTACGGG 60.483 54.545 0.00 0.00 0.00 5.28
595 597 2.798499 CGGAGCAATCCTACAGTTACGG 60.798 54.545 0.00 0.00 0.00 4.02
596 598 2.159282 ACGGAGCAATCCTACAGTTACG 60.159 50.000 0.00 0.00 0.00 3.18
597 599 3.187700 CACGGAGCAATCCTACAGTTAC 58.812 50.000 0.00 0.00 0.00 2.50
598 600 2.829720 ACACGGAGCAATCCTACAGTTA 59.170 45.455 0.00 0.00 0.00 2.24
599 601 1.623811 ACACGGAGCAATCCTACAGTT 59.376 47.619 0.00 0.00 0.00 3.16
600 602 1.204941 GACACGGAGCAATCCTACAGT 59.795 52.381 0.00 0.00 0.00 3.55
601 603 1.204704 TGACACGGAGCAATCCTACAG 59.795 52.381 0.00 0.00 0.00 2.74
602 604 1.262417 TGACACGGAGCAATCCTACA 58.738 50.000 0.00 0.00 0.00 2.74
603 605 2.604046 ATGACACGGAGCAATCCTAC 57.396 50.000 0.00 0.00 0.00 3.18
604 606 3.728076 GTATGACACGGAGCAATCCTA 57.272 47.619 0.00 0.00 0.00 2.94
605 607 2.604046 GTATGACACGGAGCAATCCT 57.396 50.000 0.00 0.00 0.00 3.24
637 639 1.431488 CGGATCCCACACAAGCATCG 61.431 60.000 6.06 0.00 0.00 3.84
639 641 1.750399 GCGGATCCCACACAAGCAT 60.750 57.895 6.06 0.00 0.00 3.79
646 648 3.151710 CTACCGGCGGATCCCACA 61.152 66.667 35.78 7.01 0.00 4.17
647 649 2.365095 CTTCTACCGGCGGATCCCAC 62.365 65.000 35.78 0.00 0.00 4.61
680 682 7.087639 CCGTTTTCAAAGCACCATTTTCTATA 58.912 34.615 0.00 0.00 0.00 1.31
681 683 5.925969 CCGTTTTCAAAGCACCATTTTCTAT 59.074 36.000 0.00 0.00 0.00 1.98
682 684 5.285651 CCGTTTTCAAAGCACCATTTTCTA 58.714 37.500 0.00 0.00 0.00 2.10
683 685 4.119136 CCGTTTTCAAAGCACCATTTTCT 58.881 39.130 0.00 0.00 0.00 2.52
684 686 3.303066 GCCGTTTTCAAAGCACCATTTTC 60.303 43.478 0.00 0.00 0.00 2.29
685 687 2.611751 GCCGTTTTCAAAGCACCATTTT 59.388 40.909 0.00 0.00 0.00 1.82
686 688 2.209273 GCCGTTTTCAAAGCACCATTT 58.791 42.857 0.00 0.00 0.00 2.32
687 689 1.540146 GGCCGTTTTCAAAGCACCATT 60.540 47.619 0.00 0.00 0.00 3.16
688 690 0.033366 GGCCGTTTTCAAAGCACCAT 59.967 50.000 0.00 0.00 0.00 3.55
689 691 1.040339 AGGCCGTTTTCAAAGCACCA 61.040 50.000 0.00 0.00 0.00 4.17
690 692 0.318699 GAGGCCGTTTTCAAAGCACC 60.319 55.000 0.00 0.00 0.00 5.01
691 693 0.383949 TGAGGCCGTTTTCAAAGCAC 59.616 50.000 0.00 0.00 0.00 4.40
692 694 1.327303 ATGAGGCCGTTTTCAAAGCA 58.673 45.000 0.00 0.00 0.00 3.91
693 695 2.061028 CAATGAGGCCGTTTTCAAAGC 58.939 47.619 0.00 0.00 0.00 3.51
694 696 2.676076 CCAATGAGGCCGTTTTCAAAG 58.324 47.619 0.00 0.00 0.00 2.77
695 697 2.810439 CCAATGAGGCCGTTTTCAAA 57.190 45.000 0.00 0.00 0.00 2.69
706 708 2.098117 GTCTCGGAAAATGCCAATGAGG 59.902 50.000 0.00 0.00 41.84 3.86
707 709 2.098117 GGTCTCGGAAAATGCCAATGAG 59.902 50.000 0.00 0.00 0.00 2.90
708 710 2.091541 GGTCTCGGAAAATGCCAATGA 58.908 47.619 0.00 0.00 0.00 2.57
727 729 7.712264 TGATTGTAAAGAAAAAGCATGTTGG 57.288 32.000 0.00 0.00 0.00 3.77
729 731 9.545105 TCAATGATTGTAAAGAAAAAGCATGTT 57.455 25.926 4.93 0.00 30.84 2.71
839 841 8.611257 TCTTACTAATGGAAATTGGAGAGGAAA 58.389 33.333 0.00 0.00 0.00 3.13
929 933 2.223340 ACGAGCACAAAAGTTTCTGCAG 60.223 45.455 7.63 7.63 34.99 4.41
967 971 4.094212 GTCGTCACTACTGTATTTCGACC 58.906 47.826 15.15 5.05 39.88 4.79
1089 1098 1.070038 GTGGGCGTCATTGCAATTTG 58.930 50.000 9.83 0.68 36.28 2.32
1090 1099 0.037419 GGTGGGCGTCATTGCAATTT 60.037 50.000 9.83 0.00 36.28 1.82
1091 1100 0.899717 AGGTGGGCGTCATTGCAATT 60.900 50.000 9.83 0.00 36.28 2.32
1092 1101 0.899717 AAGGTGGGCGTCATTGCAAT 60.900 50.000 5.99 5.99 36.28 3.56
1093 1102 1.523154 GAAGGTGGGCGTCATTGCAA 61.523 55.000 0.00 0.00 36.28 4.08
1094 1103 1.971167 GAAGGTGGGCGTCATTGCA 60.971 57.895 0.00 0.00 36.28 4.08
1095 1104 2.877691 GAAGGTGGGCGTCATTGC 59.122 61.111 0.00 0.00 0.00 3.56
1424 1433 4.219999 GCAGCCTCCTCGAGCTCC 62.220 72.222 6.99 0.00 37.18 4.70
1529 1538 1.602323 GATCACCACCAACGGCCAA 60.602 57.895 2.24 0.00 0.00 4.52
1619 1729 3.100671 GGACATGAACAGGTAGACTCCT 58.899 50.000 0.00 0.00 38.51 3.69
1855 1971 4.434938 CCTCGAACGTCGTCGCGA 62.435 66.667 18.25 18.25 41.35 5.87
1943 2073 2.590007 AAGCTCGCGATGATGCCC 60.590 61.111 10.36 0.00 0.00 5.36
2153 2283 4.409218 TTCGGCGAGTCGAACGGG 62.409 66.667 18.61 0.00 43.12 5.28
2356 2486 1.659622 TTCTATCTCCGCCGCGAACA 61.660 55.000 15.93 0.00 0.00 3.18
2366 2496 3.491792 CCTTCAGCGAGGTTTCTATCTCC 60.492 52.174 0.00 0.00 31.89 3.71
2372 2502 4.703703 GCCTTCAGCGAGGTTTCT 57.296 55.556 5.85 0.00 39.11 2.52
2384 2514 7.391148 TTTTCAGGTGTATAATCAAGCCTTC 57.609 36.000 0.00 0.00 0.00 3.46
2385 2515 7.775053 TTTTTCAGGTGTATAATCAAGCCTT 57.225 32.000 0.00 0.00 0.00 4.35
2397 2527 4.069304 ACGCAGCTTATTTTTCAGGTGTA 58.931 39.130 0.00 0.00 40.09 2.90
2400 2530 2.159627 CGACGCAGCTTATTTTTCAGGT 59.840 45.455 0.00 0.00 0.00 4.00
2414 2544 3.521220 GTACGCACGTCGACGCAG 61.521 66.667 35.92 28.36 44.43 5.18
2424 2554 2.275318 AGGAGAGTACTACGTACGCAC 58.725 52.381 16.72 8.42 43.05 5.34
2425 2555 2.680312 AGGAGAGTACTACGTACGCA 57.320 50.000 16.72 0.23 43.05 5.24
2426 2556 6.771188 TTAATAGGAGAGTACTACGTACGC 57.229 41.667 16.72 0.00 43.05 4.42
2436 2566 9.451002 CGGAGAAGACATATTAATAGGAGAGTA 57.549 37.037 13.77 0.00 0.00 2.59
2437 2567 8.164733 TCGGAGAAGACATATTAATAGGAGAGT 58.835 37.037 13.77 1.43 0.00 3.24
2438 2568 8.568676 TCGGAGAAGACATATTAATAGGAGAG 57.431 38.462 13.77 0.00 0.00 3.20
2439 2569 8.935614 TTCGGAGAAGACATATTAATAGGAGA 57.064 34.615 13.77 0.00 45.90 3.71
2448 2578 9.110502 GGTTTTCTATTTCGGAGAAGACATATT 57.889 33.333 7.95 0.00 45.90 1.28
2449 2579 8.265055 TGGTTTTCTATTTCGGAGAAGACATAT 58.735 33.333 7.95 0.00 45.90 1.78
2450 2580 7.617225 TGGTTTTCTATTTCGGAGAAGACATA 58.383 34.615 7.95 0.00 45.90 2.29
2451 2581 6.472887 TGGTTTTCTATTTCGGAGAAGACAT 58.527 36.000 7.95 0.00 45.90 3.06
2452 2582 5.860611 TGGTTTTCTATTTCGGAGAAGACA 58.139 37.500 7.95 0.00 45.90 3.41
2453 2583 5.932883 ACTGGTTTTCTATTTCGGAGAAGAC 59.067 40.000 0.00 0.00 45.90 3.01
2454 2584 6.110411 ACTGGTTTTCTATTTCGGAGAAGA 57.890 37.500 0.00 0.00 45.90 2.87
2455 2585 6.803154 AACTGGTTTTCTATTTCGGAGAAG 57.197 37.500 0.00 0.00 45.90 2.85
2456 2586 7.576861 AAAACTGGTTTTCTATTTCGGAGAA 57.423 32.000 5.72 0.00 39.17 2.87
2457 2587 7.576861 AAAAACTGGTTTTCTATTTCGGAGA 57.423 32.000 11.16 0.00 41.45 3.71
2495 2625 9.434420 AAGTTCAGAATATCAGATATAAGCAGC 57.566 33.333 3.17 0.00 0.00 5.25
2503 2633 7.345653 AGTGGGTGAAGTTCAGAATATCAGATA 59.654 37.037 5.62 0.00 0.00 1.98
2504 2634 6.157645 AGTGGGTGAAGTTCAGAATATCAGAT 59.842 38.462 5.62 0.00 0.00 2.90
2505 2635 5.485353 AGTGGGTGAAGTTCAGAATATCAGA 59.515 40.000 5.62 0.00 0.00 3.27
2506 2636 5.738909 AGTGGGTGAAGTTCAGAATATCAG 58.261 41.667 5.62 0.00 0.00 2.90
2507 2637 5.248248 TGAGTGGGTGAAGTTCAGAATATCA 59.752 40.000 5.62 5.93 0.00 2.15
2508 2638 5.734720 TGAGTGGGTGAAGTTCAGAATATC 58.265 41.667 5.62 3.37 0.00 1.63
2509 2639 5.762179 TGAGTGGGTGAAGTTCAGAATAT 57.238 39.130 5.62 0.00 0.00 1.28
2510 2640 5.762179 ATGAGTGGGTGAAGTTCAGAATA 57.238 39.130 5.62 0.00 0.00 1.75
2511 2641 4.647564 ATGAGTGGGTGAAGTTCAGAAT 57.352 40.909 5.62 0.00 0.00 2.40
2512 2642 4.593206 AGTATGAGTGGGTGAAGTTCAGAA 59.407 41.667 5.62 0.00 0.00 3.02
2535 2667 6.992123 CAGTGGGTGAAGTTCATATATAAGCA 59.008 38.462 9.18 0.00 0.00 3.91
2575 2707 7.670140 ACAGCATGCTTATACTATCTGGTAGTA 59.330 37.037 19.98 10.07 44.36 1.82
2578 2710 6.918067 ACAGCATGCTTATACTATCTGGTA 57.082 37.500 19.98 0.00 42.53 3.25
2610 2742 9.702494 CCATCAGAGCTTTAATTTTTCTTTCTT 57.298 29.630 0.00 0.00 0.00 2.52
2611 2743 8.864087 ACCATCAGAGCTTTAATTTTTCTTTCT 58.136 29.630 0.00 0.00 0.00 2.52
2612 2744 8.919661 CACCATCAGAGCTTTAATTTTTCTTTC 58.080 33.333 0.00 0.00 0.00 2.62
2613 2745 8.641541 TCACCATCAGAGCTTTAATTTTTCTTT 58.358 29.630 0.00 0.00 0.00 2.52
2614 2746 8.084684 GTCACCATCAGAGCTTTAATTTTTCTT 58.915 33.333 0.00 0.00 0.00 2.52
2615 2747 7.231317 TGTCACCATCAGAGCTTTAATTTTTCT 59.769 33.333 0.00 0.00 0.00 2.52
2616 2748 7.370383 TGTCACCATCAGAGCTTTAATTTTTC 58.630 34.615 0.00 0.00 0.00 2.29
2617 2749 7.288810 TGTCACCATCAGAGCTTTAATTTTT 57.711 32.000 0.00 0.00 0.00 1.94
2618 2750 6.899393 TGTCACCATCAGAGCTTTAATTTT 57.101 33.333 0.00 0.00 0.00 1.82
2619 2751 6.265196 TGTTGTCACCATCAGAGCTTTAATTT 59.735 34.615 0.00 0.00 0.00 1.82
2620 2752 5.769662 TGTTGTCACCATCAGAGCTTTAATT 59.230 36.000 0.00 0.00 0.00 1.40
2808 3849 3.854669 CGCAGGGCCTCCGAGAAT 61.855 66.667 12.64 0.00 38.33 2.40
2896 3938 4.568592 GGCCAGAAATATCTATGAAGGGGG 60.569 50.000 0.00 0.00 33.50 5.40
3168 4210 1.878734 GCTGATATGCTCCTTGCTTCC 59.121 52.381 0.00 0.00 43.37 3.46


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

AutoCloner maintained by Alex Coulton.