Multiple sequence alignment - TraesCS2A01G494500

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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 TraesCS2A01G494500 chr2A 100.000 2399 0 0 1 2399 726386309 726388707 0.000000e+00 4431.0
1 TraesCS2A01G494500 chr2A 91.871 529 33 2 881 1399 726322159 726322687 0.000000e+00 730.0
2 TraesCS2A01G494500 chr2D 92.590 1228 56 10 565 1773 591703770 591704981 0.000000e+00 1731.0
3 TraesCS2A01G494500 chr2D 90.541 592 32 5 808 1399 591602936 591603503 0.000000e+00 761.0
4 TraesCS2A01G494500 chr2D 90.619 533 35 5 881 1399 591575159 591575690 0.000000e+00 693.0
5 TraesCS2A01G494500 chr2D 87.473 455 42 7 1937 2391 591706272 591706711 5.920000e-141 510.0
6 TraesCS2A01G494500 chr2D 86.480 429 31 13 1 407 591597231 591597654 1.690000e-121 446.0
7 TraesCS2A01G494500 chr2D 81.593 364 58 5 1073 1432 592031325 592031683 2.330000e-75 292.0
8 TraesCS2A01G494500 chr2D 91.429 175 13 1 396 568 161907026 161906852 3.080000e-59 239.0
9 TraesCS2A01G494500 chr2D 90.110 182 14 3 403 581 24312360 24312180 1.430000e-57 233.0
10 TraesCS2A01G494500 chr2D 98.148 108 2 0 658 765 591597785 591597892 3.150000e-44 189.0
11 TraesCS2A01G494500 chr2D 88.991 109 4 6 565 669 591597651 591597755 6.960000e-26 128.0
12 TraesCS2A01G494500 chr2B 91.272 1226 69 11 565 1773 717344853 717346057 0.000000e+00 1637.0
13 TraesCS2A01G494500 chr2B 88.194 1008 98 14 565 1562 717327608 717328604 0.000000e+00 1182.0
14 TraesCS2A01G494500 chr2B 85.076 918 94 20 688 1562 717131283 717132200 0.000000e+00 896.0
15 TraesCS2A01G494500 chr2B 89.414 529 46 2 881 1399 717237220 717237748 0.000000e+00 658.0
16 TraesCS2A01G494500 chr2B 91.146 192 13 4 1868 2059 717348771 717348958 8.510000e-65 257.0
17 TraesCS2A01G494500 chr2B 81.413 269 37 7 150 407 717327345 717327611 8.690000e-50 207.0
18 TraesCS2A01G494500 chr2B 86.905 84 11 0 2165 2248 792483153 792483236 7.060000e-16 95.3
19 TraesCS2A01G494500 chr5B 92.857 168 10 1 405 570 427931367 427931200 2.380000e-60 243.0
20 TraesCS2A01G494500 chr5B 85.398 226 26 2 2065 2290 679577730 679577512 6.670000e-56 228.0
21 TraesCS2A01G494500 chr5B 85.308 211 25 4 2063 2269 368502689 368502481 1.870000e-51 213.0
22 TraesCS2A01G494500 chr5B 90.000 50 5 0 1796 1845 19697112 19697063 5.540000e-07 65.8
23 TraesCS2A01G494500 chr5B 90.000 50 5 0 1796 1845 95226562 95226513 5.540000e-07 65.8
24 TraesCS2A01G494500 chr5B 93.182 44 3 0 1796 1839 639263031 639263074 5.540000e-07 65.8
25 TraesCS2A01G494500 chr4D 92.262 168 11 1 405 570 39853857 39854024 1.110000e-58 237.0
26 TraesCS2A01G494500 chr4D 91.379 174 12 2 401 572 238640333 238640161 3.990000e-58 235.0
27 TraesCS2A01G494500 chr3B 92.262 168 11 1 406 571 571752525 571752692 1.110000e-58 237.0
28 TraesCS2A01G494500 chr1B 90.960 177 14 1 394 568 614556882 614556706 1.110000e-58 237.0
29 TraesCS2A01G494500 chr1B 79.435 248 36 10 2061 2304 62716481 62716245 6.860000e-36 161.0
30 TraesCS2A01G494500 chr1B 93.182 44 3 0 1796 1839 169530000 169530043 5.540000e-07 65.8
31 TraesCS2A01G494500 chr1B 93.182 44 3 0 1796 1839 633302405 633302448 5.540000e-07 65.8
32 TraesCS2A01G494500 chr1B 94.595 37 2 0 2354 2390 489541741 489541705 9.260000e-05 58.4
33 TraesCS2A01G494500 chr7B 90.110 182 15 2 406 585 588861846 588861666 1.430000e-57 233.0
34 TraesCS2A01G494500 chr7B 82.353 255 35 6 2055 2307 623945867 623946113 1.870000e-51 213.0
35 TraesCS2A01G494500 chr7B 83.417 199 23 3 2060 2257 468693376 468693565 2.450000e-40 176.0
36 TraesCS2A01G494500 chr3A 91.716 169 12 1 406 572 70479209 70479041 1.430000e-57 233.0
37 TraesCS2A01G494500 chr3A 83.684 190 24 4 2062 2251 20296722 20296904 3.170000e-39 172.0
38 TraesCS2A01G494500 chr3A 95.455 44 2 0 1796 1839 602421570 602421613 1.190000e-08 71.3
39 TraesCS2A01G494500 chr3D 82.353 221 26 8 2059 2278 542802396 542802188 1.890000e-41 180.0
40 TraesCS2A01G494500 chr3D 80.263 228 34 7 2061 2286 429780537 429780755 6.860000e-36 161.0
41 TraesCS2A01G494500 chr5D 79.600 250 36 8 2061 2308 458155552 458155316 5.310000e-37 165.0
42 TraesCS2A01G494500 chr4B 78.279 244 42 6 2068 2309 656142581 656142815 1.920000e-31 147.0
43 TraesCS2A01G494500 chr6D 90.741 108 6 4 2057 2163 248510453 248510557 8.940000e-30 141.0
44 TraesCS2A01G494500 chr6B 92.500 80 6 0 1796 1875 41440317 41440238 5.420000e-22 115.0
45 TraesCS2A01G494500 chr6B 79.429 175 22 6 2063 2236 578292464 578292303 7.010000e-21 111.0
46 TraesCS2A01G494500 chr6B 93.182 44 3 0 1796 1839 201322433 201322476 5.540000e-07 65.8
47 TraesCS2A01G494500 chr5A 86.364 66 6 3 2165 2229 569542960 569542897 4.280000e-08 69.4
48 TraesCS2A01G494500 chr4A 90.000 50 5 0 1796 1845 22219623 22219574 5.540000e-07 65.8


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 TraesCS2A01G494500 chr2A 726386309 726388707 2398 False 4431.000000 4431 100.000000 1 2399 1 chr2A.!!$F2 2398
1 TraesCS2A01G494500 chr2A 726322159 726322687 528 False 730.000000 730 91.871000 881 1399 1 chr2A.!!$F1 518
2 TraesCS2A01G494500 chr2D 591703770 591706711 2941 False 1120.500000 1731 90.031500 565 2391 2 chr2D.!!$F5 1826
3 TraesCS2A01G494500 chr2D 591602936 591603503 567 False 761.000000 761 90.541000 808 1399 1 chr2D.!!$F2 591
4 TraesCS2A01G494500 chr2D 591575159 591575690 531 False 693.000000 693 90.619000 881 1399 1 chr2D.!!$F1 518
5 TraesCS2A01G494500 chr2D 591597231 591597892 661 False 254.333333 446 91.206333 1 765 3 chr2D.!!$F4 764
6 TraesCS2A01G494500 chr2B 717344853 717348958 4105 False 947.000000 1637 91.209000 565 2059 2 chr2B.!!$F5 1494
7 TraesCS2A01G494500 chr2B 717131283 717132200 917 False 896.000000 896 85.076000 688 1562 1 chr2B.!!$F1 874
8 TraesCS2A01G494500 chr2B 717327345 717328604 1259 False 694.500000 1182 84.803500 150 1562 2 chr2B.!!$F4 1412
9 TraesCS2A01G494500 chr2B 717237220 717237748 528 False 658.000000 658 89.414000 881 1399 1 chr2B.!!$F2 518

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
613 644 0.675633 AGCATTTGCAAAGCCGACTT 59.324 45.0 18.19 0.0 45.16 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2321 6374 0.103208 AGAAATCGCCGGCAGTAGAG 59.897 55.0 28.98 9.08 0.0 2.43 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
39 40 4.020039 TCACCCTATAGCGGTTTTTGAGAA 60.020 41.667 9.48 0.00 0.00 2.87
40 41 4.094442 CACCCTATAGCGGTTTTTGAGAAC 59.906 45.833 9.48 0.00 0.00 3.01
44 58 5.642063 CCTATAGCGGTTTTTGAGAACTTGA 59.358 40.000 0.00 0.00 0.00 3.02
58 72 7.984422 TGAGAACTTGAATGAATCTAGCAAA 57.016 32.000 0.00 0.00 34.68 3.68
59 73 8.394971 TGAGAACTTGAATGAATCTAGCAAAA 57.605 30.769 0.00 0.00 34.68 2.44
60 74 9.017509 TGAGAACTTGAATGAATCTAGCAAAAT 57.982 29.630 0.00 0.00 34.68 1.82
61 75 9.852091 GAGAACTTGAATGAATCTAGCAAAATT 57.148 29.630 0.00 0.00 34.68 1.82
70 84 9.988350 AATGAATCTAGCAAAATTGTTAGTACG 57.012 29.630 14.18 0.00 41.14 3.67
89 103 4.181309 ACGTGAAAGCTTTGGAAAACAA 57.819 36.364 18.30 0.00 37.28 2.83
107 122 8.669243 GGAAAACAACAAAAATCCATAAACACA 58.331 29.630 0.00 0.00 0.00 3.72
178 193 5.531634 TCTTTGCATCCTGTGAAAACAATC 58.468 37.500 0.00 0.00 31.87 2.67
218 233 9.611284 TGCGAAATAAATCATGTAATTCATAGC 57.389 29.630 0.00 0.00 34.67 2.97
264 288 8.862325 TTCTTGCAATTTTAGTATCTCAAGGA 57.138 30.769 0.00 0.00 32.82 3.36
266 290 9.113838 TCTTGCAATTTTAGTATCTCAAGGATC 57.886 33.333 0.00 0.00 35.98 3.36
269 293 9.060347 TGCAATTTTAGTATCTCAAGGATCATC 57.940 33.333 0.00 0.00 35.98 2.92
324 348 6.267635 TCCCATCCCAAATCAATTTCCTTTA 58.732 36.000 0.00 0.00 0.00 1.85
325 349 6.908029 TCCCATCCCAAATCAATTTCCTTTAT 59.092 34.615 0.00 0.00 0.00 1.40
334 364 9.282569 CAAATCAATTTCCTTTATGTCCCAAAA 57.717 29.630 0.00 0.00 0.00 2.44
335 365 9.859152 AAATCAATTTCCTTTATGTCCCAAAAA 57.141 25.926 0.00 0.00 0.00 1.94
371 401 4.209307 TGTGGCGATCATTTTAGTACCA 57.791 40.909 0.00 0.00 0.00 3.25
372 402 4.776349 TGTGGCGATCATTTTAGTACCAT 58.224 39.130 0.00 0.00 0.00 3.55
374 404 5.650266 TGTGGCGATCATTTTAGTACCATTT 59.350 36.000 0.00 0.00 0.00 2.32
396 426 2.606065 GGTGTGTACAAAATGCGGTTCC 60.606 50.000 0.00 0.00 0.00 3.62
407 437 0.878416 TGCGGTTCCATGCAAAGTAC 59.122 50.000 0.00 0.00 38.34 2.73
408 438 1.165270 GCGGTTCCATGCAAAGTACT 58.835 50.000 0.00 0.00 0.00 2.73
409 439 1.130561 GCGGTTCCATGCAAAGTACTC 59.869 52.381 0.00 0.00 0.00 2.59
410 440 1.737793 CGGTTCCATGCAAAGTACTCC 59.262 52.381 0.00 0.00 0.00 3.85
411 441 2.092323 GGTTCCATGCAAAGTACTCCC 58.908 52.381 0.00 0.00 0.00 4.30
412 442 2.290960 GGTTCCATGCAAAGTACTCCCT 60.291 50.000 0.00 0.00 0.00 4.20
413 443 3.010420 GTTCCATGCAAAGTACTCCCTC 58.990 50.000 0.00 0.00 0.00 4.30
414 444 1.559682 TCCATGCAAAGTACTCCCTCC 59.440 52.381 0.00 0.00 0.00 4.30
415 445 1.656652 CATGCAAAGTACTCCCTCCG 58.343 55.000 0.00 0.00 0.00 4.63
416 446 1.066143 CATGCAAAGTACTCCCTCCGT 60.066 52.381 0.00 0.00 0.00 4.69
417 447 1.053424 TGCAAAGTACTCCCTCCGTT 58.947 50.000 0.00 0.00 0.00 4.44
418 448 1.001633 TGCAAAGTACTCCCTCCGTTC 59.998 52.381 0.00 0.00 0.00 3.95
419 449 1.275573 GCAAAGTACTCCCTCCGTTCT 59.724 52.381 0.00 0.00 0.00 3.01
420 450 2.289506 GCAAAGTACTCCCTCCGTTCTT 60.290 50.000 0.00 0.00 0.00 2.52
421 451 3.056322 GCAAAGTACTCCCTCCGTTCTTA 60.056 47.826 0.00 0.00 0.00 2.10
422 452 4.562143 GCAAAGTACTCCCTCCGTTCTTAA 60.562 45.833 0.00 0.00 0.00 1.85
423 453 5.544650 CAAAGTACTCCCTCCGTTCTTAAA 58.455 41.667 0.00 0.00 0.00 1.52
424 454 6.171213 CAAAGTACTCCCTCCGTTCTTAAAT 58.829 40.000 0.00 0.00 0.00 1.40
425 455 7.325694 CAAAGTACTCCCTCCGTTCTTAAATA 58.674 38.462 0.00 0.00 0.00 1.40
426 456 7.672122 AAGTACTCCCTCCGTTCTTAAATAT 57.328 36.000 0.00 0.00 0.00 1.28
427 457 7.672122 AGTACTCCCTCCGTTCTTAAATATT 57.328 36.000 0.00 0.00 0.00 1.28
428 458 8.087303 AGTACTCCCTCCGTTCTTAAATATTT 57.913 34.615 5.89 5.89 0.00 1.40
429 459 8.546322 AGTACTCCCTCCGTTCTTAAATATTTT 58.454 33.333 5.91 0.00 0.00 1.82
430 460 9.170734 GTACTCCCTCCGTTCTTAAATATTTTT 57.829 33.333 5.91 0.00 0.00 1.94
431 461 8.277490 ACTCCCTCCGTTCTTAAATATTTTTC 57.723 34.615 5.91 0.00 0.00 2.29
432 462 8.107729 ACTCCCTCCGTTCTTAAATATTTTTCT 58.892 33.333 5.91 0.00 0.00 2.52
433 463 8.873186 TCCCTCCGTTCTTAAATATTTTTCTT 57.127 30.769 5.91 0.00 0.00 2.52
434 464 9.304335 TCCCTCCGTTCTTAAATATTTTTCTTT 57.696 29.630 5.91 0.00 0.00 2.52
435 465 9.923143 CCCTCCGTTCTTAAATATTTTTCTTTT 57.077 29.630 5.91 0.00 0.00 2.27
463 493 9.337396 AGAAATTTCAACAAGTGACTACATACA 57.663 29.630 19.99 0.00 35.39 2.29
464 494 9.599322 GAAATTTCAACAAGTGACTACATACAG 57.401 33.333 13.40 0.00 35.39 2.74
465 495 8.902540 AATTTCAACAAGTGACTACATACAGA 57.097 30.769 0.00 0.00 35.39 3.41
466 496 7.946655 TTTCAACAAGTGACTACATACAGAG 57.053 36.000 0.00 0.00 35.39 3.35
467 497 6.650427 TCAACAAGTGACTACATACAGAGT 57.350 37.500 0.00 0.00 0.00 3.24
468 498 7.754851 TCAACAAGTGACTACATACAGAGTA 57.245 36.000 0.00 0.00 0.00 2.59
469 499 8.173542 TCAACAAGTGACTACATACAGAGTAA 57.826 34.615 0.00 0.00 0.00 2.24
470 500 8.635328 TCAACAAGTGACTACATACAGAGTAAA 58.365 33.333 0.00 0.00 0.00 2.01
471 501 9.256477 CAACAAGTGACTACATACAGAGTAAAA 57.744 33.333 0.00 0.00 0.00 1.52
472 502 9.998106 AACAAGTGACTACATACAGAGTAAAAT 57.002 29.630 0.00 0.00 0.00 1.82
473 503 9.424319 ACAAGTGACTACATACAGAGTAAAATG 57.576 33.333 0.00 0.00 0.00 2.32
474 504 9.639601 CAAGTGACTACATACAGAGTAAAATGA 57.360 33.333 0.00 0.00 0.00 2.57
475 505 9.862371 AAGTGACTACATACAGAGTAAAATGAG 57.138 33.333 0.00 0.00 0.00 2.90
476 506 9.026121 AGTGACTACATACAGAGTAAAATGAGT 57.974 33.333 0.00 0.00 0.00 3.41
477 507 9.077674 GTGACTACATACAGAGTAAAATGAGTG 57.922 37.037 0.00 0.00 0.00 3.51
478 508 9.020731 TGACTACATACAGAGTAAAATGAGTGA 57.979 33.333 0.00 0.00 0.00 3.41
479 509 9.856488 GACTACATACAGAGTAAAATGAGTGAA 57.144 33.333 0.00 0.00 0.00 3.18
483 513 9.725019 ACATACAGAGTAAAATGAGTGAATCAA 57.275 29.630 0.00 0.00 42.53 2.57
484 514 9.979270 CATACAGAGTAAAATGAGTGAATCAAC 57.021 33.333 0.00 0.00 42.53 3.18
485 515 9.725019 ATACAGAGTAAAATGAGTGAATCAACA 57.275 29.630 0.00 0.00 42.53 3.33
486 516 7.865707 ACAGAGTAAAATGAGTGAATCAACAC 58.134 34.615 0.00 0.00 42.53 3.32
500 530 9.950496 AGTGAATCAACACTCTAAAATATGTCT 57.050 29.630 0.00 0.00 46.36 3.41
505 535 9.836864 ATCAACACTCTAAAATATGTCTATGCA 57.163 29.630 0.00 0.00 0.00 3.96
506 536 9.836864 TCAACACTCTAAAATATGTCTATGCAT 57.163 29.630 3.79 3.79 0.00 3.96
508 538 8.839310 ACACTCTAAAATATGTCTATGCATCC 57.161 34.615 0.19 0.00 0.00 3.51
509 539 8.432013 ACACTCTAAAATATGTCTATGCATCCA 58.568 33.333 0.19 0.00 0.00 3.41
510 540 9.445878 CACTCTAAAATATGTCTATGCATCCAT 57.554 33.333 0.19 7.06 35.44 3.41
516 546 8.429493 AAATATGTCTATGCATCCATATGTCG 57.571 34.615 19.23 0.00 33.66 4.35
517 547 4.871933 TGTCTATGCATCCATATGTCGT 57.128 40.909 0.19 0.00 33.66 4.34
518 548 5.975693 TGTCTATGCATCCATATGTCGTA 57.024 39.130 0.19 0.00 33.66 3.43
519 549 5.954335 TGTCTATGCATCCATATGTCGTAG 58.046 41.667 0.19 3.84 33.66 3.51
520 550 5.476945 TGTCTATGCATCCATATGTCGTAGT 59.523 40.000 0.19 0.00 34.19 2.73
521 551 6.015434 TGTCTATGCATCCATATGTCGTAGTT 60.015 38.462 0.19 0.00 34.19 2.24
522 552 6.528423 GTCTATGCATCCATATGTCGTAGTTC 59.472 42.308 0.19 0.16 34.19 3.01
523 553 4.664150 TGCATCCATATGTCGTAGTTCA 57.336 40.909 1.24 0.00 35.38 3.18
524 554 5.213891 TGCATCCATATGTCGTAGTTCAT 57.786 39.130 1.24 0.00 35.38 2.57
525 555 5.610398 TGCATCCATATGTCGTAGTTCATT 58.390 37.500 1.24 0.00 35.38 2.57
526 556 6.054941 TGCATCCATATGTCGTAGTTCATTT 58.945 36.000 1.24 0.00 35.38 2.32
527 557 6.018016 TGCATCCATATGTCGTAGTTCATTTG 60.018 38.462 1.24 0.00 35.38 2.32
528 558 6.202762 GCATCCATATGTCGTAGTTCATTTGA 59.797 38.462 1.24 0.00 35.38 2.69
529 559 7.254761 GCATCCATATGTCGTAGTTCATTTGAA 60.255 37.037 1.24 0.00 35.38 2.69
530 560 8.611757 CATCCATATGTCGTAGTTCATTTGAAA 58.388 33.333 1.24 0.00 35.58 2.69
531 561 8.731275 TCCATATGTCGTAGTTCATTTGAAAT 57.269 30.769 1.24 0.00 35.58 2.17
532 562 8.826710 TCCATATGTCGTAGTTCATTTGAAATC 58.173 33.333 1.24 0.00 35.58 2.17
533 563 8.830580 CCATATGTCGTAGTTCATTTGAAATCT 58.169 33.333 1.24 0.00 35.58 2.40
534 564 9.855361 CATATGTCGTAGTTCATTTGAAATCTC 57.145 33.333 0.00 0.00 35.58 2.75
535 565 9.823647 ATATGTCGTAGTTCATTTGAAATCTCT 57.176 29.630 0.00 0.00 35.58 3.10
537 567 9.653287 ATGTCGTAGTTCATTTGAAATCTCTAA 57.347 29.630 0.00 0.00 35.58 2.10
538 568 9.483916 TGTCGTAGTTCATTTGAAATCTCTAAA 57.516 29.630 0.00 0.00 35.58 1.85
562 592 6.753107 AAGACAAATATTTAGGAACGGTGG 57.247 37.500 0.00 0.00 0.00 4.61
563 593 5.190677 AGACAAATATTTAGGAACGGTGGG 58.809 41.667 0.00 0.00 0.00 4.61
588 619 8.972127 GGAGTATAAGCAGAACATATATCAGGA 58.028 37.037 0.00 0.00 0.00 3.86
607 638 5.409214 TCAGGATTTTAAGCATTTGCAAAGC 59.591 36.000 18.19 19.01 45.16 3.51
613 644 0.675633 AGCATTTGCAAAGCCGACTT 59.324 45.000 18.19 0.00 45.16 3.01
614 645 0.785979 GCATTTGCAAAGCCGACTTG 59.214 50.000 18.19 9.91 41.59 3.16
703 780 1.482593 GGACAATGATCTCCACGAGGT 59.517 52.381 0.00 0.00 35.89 3.85
822 902 8.883954 TTGCATCATCACAAAGAAAATAAACA 57.116 26.923 0.00 0.00 0.00 2.83
845 925 2.225068 AGCCGAGGAATAATGTCACG 57.775 50.000 0.00 0.00 0.00 4.35
885 967 1.449070 GCACCTACCAACCGCCTAC 60.449 63.158 0.00 0.00 0.00 3.18
976 1069 2.345760 CCCGCCAAAAGCAGAGCAT 61.346 57.895 0.00 0.00 44.04 3.79
979 1072 1.310933 CGCCAAAAGCAGAGCATCCT 61.311 55.000 0.00 0.00 44.04 3.24
980 1073 1.755179 GCCAAAAGCAGAGCATCCTA 58.245 50.000 0.00 0.00 42.97 2.94
1375 1523 3.057548 CGTTGCTGCAGGGCATGA 61.058 61.111 17.12 0.00 42.09 3.07
1387 1535 1.450312 GGCATGACGGTGGAGAAGG 60.450 63.158 0.00 0.00 0.00 3.46
1433 1581 3.272334 CGCGCCTAGGCCATTCAC 61.272 66.667 28.09 9.51 37.98 3.18
1598 1762 4.059459 GGCAAGCGACGACACGTG 62.059 66.667 15.48 15.48 41.37 4.49
1670 1834 2.101770 GTAGTTCGTCGAGGGCGG 59.898 66.667 5.12 0.00 38.28 6.13
1801 4653 2.159734 GCTTGAAGAGCGTGATGACTTG 60.160 50.000 0.00 0.00 42.46 3.16
1802 4654 2.084610 TGAAGAGCGTGATGACTTGG 57.915 50.000 0.00 0.00 0.00 3.61
1803 4655 1.618343 TGAAGAGCGTGATGACTTGGA 59.382 47.619 0.00 0.00 0.00 3.53
1804 4656 2.266554 GAAGAGCGTGATGACTTGGAG 58.733 52.381 0.00 0.00 0.00 3.86
1805 4657 1.550327 AGAGCGTGATGACTTGGAGA 58.450 50.000 0.00 0.00 0.00 3.71
1806 4658 1.476085 AGAGCGTGATGACTTGGAGAG 59.524 52.381 0.00 0.00 0.00 3.20
1807 4659 0.534412 AGCGTGATGACTTGGAGAGG 59.466 55.000 0.00 0.00 0.00 3.69
1808 4660 0.532573 GCGTGATGACTTGGAGAGGA 59.467 55.000 0.00 0.00 0.00 3.71
1809 4661 1.137872 GCGTGATGACTTGGAGAGGAT 59.862 52.381 0.00 0.00 0.00 3.24
1810 4662 2.419297 GCGTGATGACTTGGAGAGGATT 60.419 50.000 0.00 0.00 0.00 3.01
1811 4663 3.181475 GCGTGATGACTTGGAGAGGATTA 60.181 47.826 0.00 0.00 0.00 1.75
1812 4664 4.680708 GCGTGATGACTTGGAGAGGATTAA 60.681 45.833 0.00 0.00 0.00 1.40
1813 4665 5.419542 CGTGATGACTTGGAGAGGATTAAA 58.580 41.667 0.00 0.00 0.00 1.52
1814 4666 6.051717 CGTGATGACTTGGAGAGGATTAAAT 58.948 40.000 0.00 0.00 0.00 1.40
1815 4667 6.201806 CGTGATGACTTGGAGAGGATTAAATC 59.798 42.308 0.00 0.00 0.00 2.17
1830 4682 5.836347 GATTAAATCCACTTCAATCCCTGC 58.164 41.667 0.00 0.00 0.00 4.85
1831 4683 3.463048 AAATCCACTTCAATCCCTGCT 57.537 42.857 0.00 0.00 0.00 4.24
1832 4684 4.591321 AAATCCACTTCAATCCCTGCTA 57.409 40.909 0.00 0.00 0.00 3.49
1833 4685 4.591321 AATCCACTTCAATCCCTGCTAA 57.409 40.909 0.00 0.00 0.00 3.09
1834 4686 4.591321 ATCCACTTCAATCCCTGCTAAA 57.409 40.909 0.00 0.00 0.00 1.85
1835 4687 3.686016 TCCACTTCAATCCCTGCTAAAC 58.314 45.455 0.00 0.00 0.00 2.01
1836 4688 2.755103 CCACTTCAATCCCTGCTAAACC 59.245 50.000 0.00 0.00 0.00 3.27
1837 4689 2.755103 CACTTCAATCCCTGCTAAACCC 59.245 50.000 0.00 0.00 0.00 4.11
1838 4690 2.291605 ACTTCAATCCCTGCTAAACCCC 60.292 50.000 0.00 0.00 0.00 4.95
1839 4691 0.629058 TCAATCCCTGCTAAACCCCC 59.371 55.000 0.00 0.00 0.00 5.40
1840 4692 0.631212 CAATCCCTGCTAAACCCCCT 59.369 55.000 0.00 0.00 0.00 4.79
1841 4693 1.007118 CAATCCCTGCTAAACCCCCTT 59.993 52.381 0.00 0.00 0.00 3.95
1842 4694 0.927029 ATCCCTGCTAAACCCCCTTC 59.073 55.000 0.00 0.00 0.00 3.46
1843 4695 0.476808 TCCCTGCTAAACCCCCTTCA 60.477 55.000 0.00 0.00 0.00 3.02
1844 4696 0.407918 CCCTGCTAAACCCCCTTCAA 59.592 55.000 0.00 0.00 0.00 2.69
1845 4697 1.203125 CCCTGCTAAACCCCCTTCAAA 60.203 52.381 0.00 0.00 0.00 2.69
1846 4698 2.559705 CCCTGCTAAACCCCCTTCAAAT 60.560 50.000 0.00 0.00 0.00 2.32
1847 4699 2.760650 CCTGCTAAACCCCCTTCAAATC 59.239 50.000 0.00 0.00 0.00 2.17
1848 4700 2.760650 CTGCTAAACCCCCTTCAAATCC 59.239 50.000 0.00 0.00 0.00 3.01
1849 4701 2.108168 GCTAAACCCCCTTCAAATCCC 58.892 52.381 0.00 0.00 0.00 3.85
1850 4702 2.292257 GCTAAACCCCCTTCAAATCCCT 60.292 50.000 0.00 0.00 0.00 4.20
1851 4703 2.623418 AAACCCCCTTCAAATCCCTC 57.377 50.000 0.00 0.00 0.00 4.30
1852 4704 1.773541 AACCCCCTTCAAATCCCTCT 58.226 50.000 0.00 0.00 0.00 3.69
1853 4705 1.299939 ACCCCCTTCAAATCCCTCTC 58.700 55.000 0.00 0.00 0.00 3.20
1854 4706 0.553333 CCCCCTTCAAATCCCTCTCC 59.447 60.000 0.00 0.00 0.00 3.71
1855 4707 1.298953 CCCCTTCAAATCCCTCTCCA 58.701 55.000 0.00 0.00 0.00 3.86
1856 4708 1.064389 CCCCTTCAAATCCCTCTCCAC 60.064 57.143 0.00 0.00 0.00 4.02
1857 4709 1.064389 CCCTTCAAATCCCTCTCCACC 60.064 57.143 0.00 0.00 0.00 4.61
1858 4710 1.407437 CCTTCAAATCCCTCTCCACCG 60.407 57.143 0.00 0.00 0.00 4.94
1859 4711 1.555075 CTTCAAATCCCTCTCCACCGA 59.445 52.381 0.00 0.00 0.00 4.69
1860 4712 1.651737 TCAAATCCCTCTCCACCGAA 58.348 50.000 0.00 0.00 0.00 4.30
1861 4713 1.278127 TCAAATCCCTCTCCACCGAAC 59.722 52.381 0.00 0.00 0.00 3.95
1862 4714 1.003118 CAAATCCCTCTCCACCGAACA 59.997 52.381 0.00 0.00 0.00 3.18
1863 4715 0.613777 AATCCCTCTCCACCGAACAC 59.386 55.000 0.00 0.00 0.00 3.32
1864 4716 0.544357 ATCCCTCTCCACCGAACACA 60.544 55.000 0.00 0.00 0.00 3.72
1865 4717 1.185618 TCCCTCTCCACCGAACACAG 61.186 60.000 0.00 0.00 0.00 3.66
1908 4760 7.254218 CCTCTTTCTGAAAACTTTTGTGATTGC 60.254 37.037 4.18 0.00 0.00 3.56
2052 6105 7.341512 TGTTCATGATGTTAATGAGGCCAAATA 59.658 33.333 5.01 0.00 35.54 1.40
2121 6174 1.620822 ACTTTTGCATTTCGGAGGCT 58.379 45.000 0.00 0.00 0.00 4.58
2122 6175 1.541588 ACTTTTGCATTTCGGAGGCTC 59.458 47.619 5.78 5.78 0.00 4.70
2126 6179 1.614996 TGCATTTCGGAGGCTCAAAA 58.385 45.000 17.69 15.67 0.00 2.44
2127 6180 1.269448 TGCATTTCGGAGGCTCAAAAC 59.731 47.619 17.69 6.77 0.00 2.43
2128 6181 1.402852 GCATTTCGGAGGCTCAAAACC 60.403 52.381 17.69 7.41 0.00 3.27
2129 6182 1.202348 CATTTCGGAGGCTCAAAACCC 59.798 52.381 17.69 0.00 0.00 4.11
2139 6192 1.613925 GCTCAAAACCCCTTCTCCAAC 59.386 52.381 0.00 0.00 0.00 3.77
2150 6203 4.080356 CCCCTTCTCCAACAGATGATGTAA 60.080 45.833 0.00 0.00 43.00 2.41
2187 6240 2.947448 AAAATGCATCTCCGCCTTTC 57.053 45.000 0.00 0.00 29.84 2.62
2208 6261 7.094975 CCTTTCGGAGATGTAAAATACAACACA 60.095 37.037 0.00 0.00 42.76 3.72
2239 6292 6.936900 GTGCAAATATACATCTCCACCTACAT 59.063 38.462 0.00 0.00 0.00 2.29
2253 6306 6.406370 TCCACCTACATGAGATGTAAAACTG 58.594 40.000 0.00 0.00 44.44 3.16
2257 6310 3.937814 ACATGAGATGTAAAACTGGCGA 58.062 40.909 0.00 0.00 42.78 5.54
2262 6315 0.604243 ATGTAAAACTGGCGACCGCA 60.604 50.000 16.47 1.97 44.11 5.69
2278 6331 2.639286 CACGCCAACTGCTCAACC 59.361 61.111 0.00 0.00 38.05 3.77
2280 6333 4.389576 CGCCAACTGCTCAACCGC 62.390 66.667 0.00 0.00 38.05 5.68
2281 6334 4.043200 GCCAACTGCTCAACCGCC 62.043 66.667 0.00 0.00 36.87 6.13
2290 6343 0.668535 GCTCAACCGCCTTCAGTTTT 59.331 50.000 0.00 0.00 0.00 2.43
2297 6350 0.661020 CGCCTTCAGTTTTGTTCCGT 59.339 50.000 0.00 0.00 0.00 4.69
2321 6374 3.512516 GCCAGATGGTTGCTCGCC 61.513 66.667 0.00 0.00 37.57 5.54
2324 6377 1.220206 CAGATGGTTGCTCGCCTCT 59.780 57.895 0.00 0.00 0.00 3.69
2327 6380 0.461961 GATGGTTGCTCGCCTCTACT 59.538 55.000 0.00 0.00 0.00 2.57
2344 6397 2.435938 TGCCGGCGATTTCTCACC 60.436 61.111 23.90 0.00 0.00 4.02
2345 6398 2.435938 GCCGGCGATTTCTCACCA 60.436 61.111 12.58 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.516300 TCTCAAAAACCGCTATAGGGTGA 59.484 43.478 15.02 10.48 37.96 4.02
19 20 4.514401 AGTTCTCAAAAACCGCTATAGGG 58.486 43.478 9.79 9.79 35.02 3.53
44 58 9.988350 CGTACTAACAATTTTGCTAGATTCATT 57.012 29.630 7.53 0.00 32.61 2.57
58 72 6.261381 TCCAAAGCTTTCACGTACTAACAATT 59.739 34.615 9.23 0.00 0.00 2.32
59 73 5.761234 TCCAAAGCTTTCACGTACTAACAAT 59.239 36.000 9.23 0.00 0.00 2.71
60 74 5.117584 TCCAAAGCTTTCACGTACTAACAA 58.882 37.500 9.23 0.00 0.00 2.83
61 75 4.695396 TCCAAAGCTTTCACGTACTAACA 58.305 39.130 9.23 0.00 0.00 2.41
70 84 5.854431 TTGTTGTTTTCCAAAGCTTTCAC 57.146 34.783 9.23 2.22 34.07 3.18
107 122 9.270640 TGCAATGCAAGTTGTATTTTATTCTTT 57.729 25.926 15.55 0.00 34.76 2.52
108 123 8.830201 TGCAATGCAAGTTGTATTTTATTCTT 57.170 26.923 15.55 0.00 34.76 2.52
156 171 5.176223 GTGATTGTTTTCACAGGATGCAAAG 59.824 40.000 0.00 0.00 44.38 2.77
239 255 8.862325 TCCTTGAGATACTAAAATTGCAAGAA 57.138 30.769 4.94 0.00 34.89 2.52
334 364 3.477530 GCCACAAAGAGGACACTACTTT 58.522 45.455 0.00 0.00 34.77 2.66
335 365 2.548067 CGCCACAAAGAGGACACTACTT 60.548 50.000 0.00 0.00 0.00 2.24
347 377 5.123186 TGGTACTAAAATGATCGCCACAAAG 59.877 40.000 0.00 0.00 0.00 2.77
371 401 3.068873 ACCGCATTTTGTACACACCAAAT 59.931 39.130 0.00 0.00 31.89 2.32
372 402 2.427453 ACCGCATTTTGTACACACCAAA 59.573 40.909 0.00 0.00 0.00 3.28
374 404 1.681538 ACCGCATTTTGTACACACCA 58.318 45.000 0.00 0.00 0.00 4.17
396 426 1.066143 ACGGAGGGAGTACTTTGCATG 60.066 52.381 0.00 0.00 0.00 4.06
407 437 8.507524 AGAAAAATATTTAAGAACGGAGGGAG 57.492 34.615 0.01 0.00 0.00 4.30
408 438 8.873186 AAGAAAAATATTTAAGAACGGAGGGA 57.127 30.769 0.01 0.00 0.00 4.20
409 439 9.923143 AAAAGAAAAATATTTAAGAACGGAGGG 57.077 29.630 0.01 0.00 0.00 4.30
437 467 9.337396 TGTATGTAGTCACTTGTTGAAATTTCT 57.663 29.630 18.64 0.00 35.39 2.52
438 468 9.599322 CTGTATGTAGTCACTTGTTGAAATTTC 57.401 33.333 11.41 11.41 35.39 2.17
439 469 9.337396 TCTGTATGTAGTCACTTGTTGAAATTT 57.663 29.630 0.00 0.00 35.39 1.82
440 470 8.902540 TCTGTATGTAGTCACTTGTTGAAATT 57.097 30.769 0.00 0.00 35.39 1.82
441 471 8.150945 ACTCTGTATGTAGTCACTTGTTGAAAT 58.849 33.333 0.00 0.00 35.39 2.17
442 472 7.497595 ACTCTGTATGTAGTCACTTGTTGAAA 58.502 34.615 0.00 0.00 35.39 2.69
443 473 7.050970 ACTCTGTATGTAGTCACTTGTTGAA 57.949 36.000 0.00 0.00 35.39 2.69
444 474 6.650427 ACTCTGTATGTAGTCACTTGTTGA 57.350 37.500 0.00 0.00 0.00 3.18
445 475 8.812147 TTTACTCTGTATGTAGTCACTTGTTG 57.188 34.615 0.00 0.00 0.00 3.33
446 476 9.998106 ATTTTACTCTGTATGTAGTCACTTGTT 57.002 29.630 0.00 0.00 0.00 2.83
447 477 9.424319 CATTTTACTCTGTATGTAGTCACTTGT 57.576 33.333 0.00 0.00 0.00 3.16
448 478 9.639601 TCATTTTACTCTGTATGTAGTCACTTG 57.360 33.333 0.00 0.00 0.00 3.16
449 479 9.862371 CTCATTTTACTCTGTATGTAGTCACTT 57.138 33.333 0.00 0.00 0.00 3.16
450 480 9.026121 ACTCATTTTACTCTGTATGTAGTCACT 57.974 33.333 0.00 0.00 0.00 3.41
451 481 9.077674 CACTCATTTTACTCTGTATGTAGTCAC 57.922 37.037 0.00 0.00 0.00 3.67
452 482 9.020731 TCACTCATTTTACTCTGTATGTAGTCA 57.979 33.333 0.00 0.00 0.00 3.41
453 483 9.856488 TTCACTCATTTTACTCTGTATGTAGTC 57.144 33.333 0.00 0.00 0.00 2.59
457 487 9.725019 TTGATTCACTCATTTTACTCTGTATGT 57.275 29.630 0.00 0.00 32.72 2.29
458 488 9.979270 GTTGATTCACTCATTTTACTCTGTATG 57.021 33.333 0.00 0.00 32.72 2.39
459 489 9.725019 TGTTGATTCACTCATTTTACTCTGTAT 57.275 29.630 0.00 0.00 32.72 2.29
460 490 8.988934 GTGTTGATTCACTCATTTTACTCTGTA 58.011 33.333 0.00 0.00 35.68 2.74
461 491 7.716998 AGTGTTGATTCACTCATTTTACTCTGT 59.283 33.333 0.00 0.00 44.07 3.41
462 492 8.092521 AGTGTTGATTCACTCATTTTACTCTG 57.907 34.615 0.00 0.00 44.07 3.35
479 509 9.836864 TGCATAGACATATTTTAGAGTGTTGAT 57.163 29.630 0.00 0.00 0.00 2.57
480 510 9.836864 ATGCATAGACATATTTTAGAGTGTTGA 57.163 29.630 0.00 0.00 0.00 3.18
482 512 9.277783 GGATGCATAGACATATTTTAGAGTGTT 57.722 33.333 0.00 0.00 0.00 3.32
483 513 8.432013 TGGATGCATAGACATATTTTAGAGTGT 58.568 33.333 0.00 0.00 0.00 3.55
484 514 8.837788 TGGATGCATAGACATATTTTAGAGTG 57.162 34.615 0.00 0.00 0.00 3.51
490 520 8.886719 CGACATATGGATGCATAGACATATTTT 58.113 33.333 20.07 13.82 35.08 1.82
491 521 8.043113 ACGACATATGGATGCATAGACATATTT 58.957 33.333 20.07 16.52 35.08 1.40
492 522 7.559486 ACGACATATGGATGCATAGACATATT 58.441 34.615 20.07 14.54 35.08 1.28
493 523 7.117285 ACGACATATGGATGCATAGACATAT 57.883 36.000 18.23 18.23 37.08 1.78
494 524 6.530019 ACGACATATGGATGCATAGACATA 57.470 37.500 12.73 16.08 36.43 2.29
495 525 5.411831 ACGACATATGGATGCATAGACAT 57.588 39.130 12.73 7.69 36.43 3.06
496 526 4.871933 ACGACATATGGATGCATAGACA 57.128 40.909 12.73 0.00 36.43 3.41
497 527 5.955488 ACTACGACATATGGATGCATAGAC 58.045 41.667 12.73 5.74 36.43 2.59
498 528 6.208599 TGAACTACGACATATGGATGCATAGA 59.791 38.462 12.73 0.00 36.43 1.98
499 529 6.389906 TGAACTACGACATATGGATGCATAG 58.610 40.000 12.73 7.43 36.43 2.23
500 530 6.339587 TGAACTACGACATATGGATGCATA 57.660 37.500 9.55 9.55 36.43 3.14
501 531 5.213891 TGAACTACGACATATGGATGCAT 57.786 39.130 7.80 4.68 36.43 3.96
502 532 4.664150 TGAACTACGACATATGGATGCA 57.336 40.909 7.80 0.00 36.43 3.96
503 533 6.202762 TCAAATGAACTACGACATATGGATGC 59.797 38.462 7.80 0.00 36.43 3.91
504 534 7.713764 TCAAATGAACTACGACATATGGATG 57.286 36.000 7.80 0.00 39.16 3.51
505 535 8.731275 TTTCAAATGAACTACGACATATGGAT 57.269 30.769 7.80 0.00 33.13 3.41
506 536 8.731275 ATTTCAAATGAACTACGACATATGGA 57.269 30.769 7.80 0.00 33.13 3.41
507 537 8.830580 AGATTTCAAATGAACTACGACATATGG 58.169 33.333 7.80 0.00 33.13 2.74
508 538 9.855361 GAGATTTCAAATGAACTACGACATATG 57.145 33.333 0.00 0.00 33.13 1.78
509 539 9.823647 AGAGATTTCAAATGAACTACGACATAT 57.176 29.630 0.00 0.00 33.13 1.78
511 541 9.653287 TTAGAGATTTCAAATGAACTACGACAT 57.347 29.630 0.00 0.00 33.13 3.06
512 542 9.483916 TTTAGAGATTTCAAATGAACTACGACA 57.516 29.630 0.00 0.00 33.13 4.35
536 566 8.085909 CCACCGTTCCTAAATATTTGTCTTTTT 58.914 33.333 11.05 0.00 0.00 1.94
537 567 7.309560 CCCACCGTTCCTAAATATTTGTCTTTT 60.310 37.037 11.05 0.00 0.00 2.27
538 568 6.152154 CCCACCGTTCCTAAATATTTGTCTTT 59.848 38.462 11.05 0.00 0.00 2.52
539 569 5.650703 CCCACCGTTCCTAAATATTTGTCTT 59.349 40.000 11.05 0.00 0.00 3.01
540 570 5.045432 TCCCACCGTTCCTAAATATTTGTCT 60.045 40.000 11.05 0.00 0.00 3.41
541 571 5.187687 TCCCACCGTTCCTAAATATTTGTC 58.812 41.667 11.05 0.00 0.00 3.18
542 572 5.182169 TCCCACCGTTCCTAAATATTTGT 57.818 39.130 11.05 0.00 0.00 2.83
543 573 5.190677 ACTCCCACCGTTCCTAAATATTTG 58.809 41.667 11.05 1.40 0.00 2.32
544 574 5.446260 ACTCCCACCGTTCCTAAATATTT 57.554 39.130 5.89 5.89 0.00 1.40
545 575 6.758806 ATACTCCCACCGTTCCTAAATATT 57.241 37.500 0.00 0.00 0.00 1.28
546 576 7.526693 GCTTATACTCCCACCGTTCCTAAATAT 60.527 40.741 0.00 0.00 0.00 1.28
547 577 6.239402 GCTTATACTCCCACCGTTCCTAAATA 60.239 42.308 0.00 0.00 0.00 1.40
548 578 5.454329 GCTTATACTCCCACCGTTCCTAAAT 60.454 44.000 0.00 0.00 0.00 1.40
549 579 4.141869 GCTTATACTCCCACCGTTCCTAAA 60.142 45.833 0.00 0.00 0.00 1.85
550 580 3.385755 GCTTATACTCCCACCGTTCCTAA 59.614 47.826 0.00 0.00 0.00 2.69
551 581 2.961062 GCTTATACTCCCACCGTTCCTA 59.039 50.000 0.00 0.00 0.00 2.94
552 582 1.761198 GCTTATACTCCCACCGTTCCT 59.239 52.381 0.00 0.00 0.00 3.36
553 583 1.483415 TGCTTATACTCCCACCGTTCC 59.517 52.381 0.00 0.00 0.00 3.62
554 584 2.429610 TCTGCTTATACTCCCACCGTTC 59.570 50.000 0.00 0.00 0.00 3.95
555 585 2.463752 TCTGCTTATACTCCCACCGTT 58.536 47.619 0.00 0.00 0.00 4.44
556 586 2.154567 TCTGCTTATACTCCCACCGT 57.845 50.000 0.00 0.00 0.00 4.83
557 587 2.167693 TGTTCTGCTTATACTCCCACCG 59.832 50.000 0.00 0.00 0.00 4.94
558 588 3.906720 TGTTCTGCTTATACTCCCACC 57.093 47.619 0.00 0.00 0.00 4.61
559 589 8.531982 TGATATATGTTCTGCTTATACTCCCAC 58.468 37.037 0.00 0.00 0.00 4.61
560 590 8.664669 TGATATATGTTCTGCTTATACTCCCA 57.335 34.615 0.00 0.00 0.00 4.37
561 591 8.200792 CCTGATATATGTTCTGCTTATACTCCC 58.799 40.741 0.00 0.00 0.00 4.30
562 592 8.972127 TCCTGATATATGTTCTGCTTATACTCC 58.028 37.037 0.00 0.00 0.00 3.85
588 619 4.152223 GTCGGCTTTGCAAATGCTTAAAAT 59.848 37.500 23.53 0.00 45.34 1.82
604 635 1.071699 ACATGTACCACAAGTCGGCTT 59.928 47.619 0.00 0.00 34.82 4.35
607 638 5.290158 GTGTATAACATGTACCACAAGTCGG 59.710 44.000 0.00 0.00 27.55 4.79
613 644 3.927758 GCGTGTGTATAACATGTACCACA 59.072 43.478 0.00 7.21 46.01 4.17
614 645 3.927758 TGCGTGTGTATAACATGTACCAC 59.072 43.478 0.00 4.56 46.01 4.16
649 680 9.656323 TCATTTGTTAGGTACTCCTATGTCTAT 57.344 33.333 0.00 0.00 44.68 1.98
703 780 2.513753 CTGTGCCAGGTAACATTTCCA 58.486 47.619 0.00 0.00 41.41 3.53
799 876 9.142515 TCATGTTTATTTTCTTTGTGATGATGC 57.857 29.630 0.00 0.00 0.00 3.91
822 902 4.130118 GTGACATTATTCCTCGGCTTCAT 58.870 43.478 0.00 0.00 0.00 2.57
845 925 2.027625 CTTCGTCCAGTTGGCCGAC 61.028 63.158 16.08 16.08 45.82 4.79
885 967 2.426752 CGCGGCGTGGAGTTTTTG 60.427 61.111 15.36 0.00 0.00 2.44
961 1054 1.755179 TAGGATGCTCTGCTTTTGGC 58.245 50.000 0.00 0.00 42.22 4.52
976 1069 2.423898 CCTTCTCGCCGGCTTAGGA 61.424 63.158 26.68 15.52 0.00 2.94
979 1072 2.363276 TCCCTTCTCGCCGGCTTA 60.363 61.111 26.68 11.82 0.00 3.09
980 1073 3.775654 CTCCCTTCTCGCCGGCTT 61.776 66.667 26.68 0.00 0.00 4.35
1371 1519 0.458543 CGACCTTCTCCACCGTCATG 60.459 60.000 0.00 0.00 0.00 3.07
1375 1523 1.831286 ACACGACCTTCTCCACCGT 60.831 57.895 0.00 0.00 0.00 4.83
1387 1535 5.538118 TCCATATATTGATCACCACACGAC 58.462 41.667 0.00 0.00 0.00 4.34
1789 4641 0.532573 TCCTCTCCAAGTCATCACGC 59.467 55.000 0.00 0.00 0.00 5.34
1807 4659 5.595952 AGCAGGGATTGAAGTGGATTTAATC 59.404 40.000 0.00 0.00 41.11 1.75
1808 4660 5.522641 AGCAGGGATTGAAGTGGATTTAAT 58.477 37.500 0.00 0.00 30.25 1.40
1809 4661 4.934356 AGCAGGGATTGAAGTGGATTTAA 58.066 39.130 0.00 0.00 0.00 1.52
1810 4662 4.591321 AGCAGGGATTGAAGTGGATTTA 57.409 40.909 0.00 0.00 0.00 1.40
1811 4663 3.463048 AGCAGGGATTGAAGTGGATTT 57.537 42.857 0.00 0.00 0.00 2.17
1812 4664 4.591321 TTAGCAGGGATTGAAGTGGATT 57.409 40.909 0.00 0.00 0.00 3.01
1813 4665 4.273318 GTTTAGCAGGGATTGAAGTGGAT 58.727 43.478 0.00 0.00 0.00 3.41
1814 4666 3.561313 GGTTTAGCAGGGATTGAAGTGGA 60.561 47.826 0.00 0.00 0.00 4.02
1815 4667 2.755103 GGTTTAGCAGGGATTGAAGTGG 59.245 50.000 0.00 0.00 0.00 4.00
1816 4668 2.755103 GGGTTTAGCAGGGATTGAAGTG 59.245 50.000 0.00 0.00 0.00 3.16
1817 4669 2.291605 GGGGTTTAGCAGGGATTGAAGT 60.292 50.000 0.00 0.00 0.00 3.01
1818 4670 2.379005 GGGGTTTAGCAGGGATTGAAG 58.621 52.381 0.00 0.00 0.00 3.02
1819 4671 1.006639 GGGGGTTTAGCAGGGATTGAA 59.993 52.381 0.00 0.00 0.00 2.69
1820 4672 0.629058 GGGGGTTTAGCAGGGATTGA 59.371 55.000 0.00 0.00 0.00 2.57
1821 4673 0.631212 AGGGGGTTTAGCAGGGATTG 59.369 55.000 0.00 0.00 0.00 2.67
1822 4674 1.288037 GAAGGGGGTTTAGCAGGGATT 59.712 52.381 0.00 0.00 0.00 3.01
1823 4675 0.927029 GAAGGGGGTTTAGCAGGGAT 59.073 55.000 0.00 0.00 0.00 3.85
1824 4676 0.476808 TGAAGGGGGTTTAGCAGGGA 60.477 55.000 0.00 0.00 0.00 4.20
1825 4677 0.407918 TTGAAGGGGGTTTAGCAGGG 59.592 55.000 0.00 0.00 0.00 4.45
1826 4678 2.302587 TTTGAAGGGGGTTTAGCAGG 57.697 50.000 0.00 0.00 0.00 4.85
1827 4679 2.760650 GGATTTGAAGGGGGTTTAGCAG 59.239 50.000 0.00 0.00 0.00 4.24
1828 4680 2.558800 GGGATTTGAAGGGGGTTTAGCA 60.559 50.000 0.00 0.00 0.00 3.49
1829 4681 2.108168 GGGATTTGAAGGGGGTTTAGC 58.892 52.381 0.00 0.00 0.00 3.09
1830 4682 3.269643 AGAGGGATTTGAAGGGGGTTTAG 59.730 47.826 0.00 0.00 0.00 1.85
1831 4683 3.268595 GAGAGGGATTTGAAGGGGGTTTA 59.731 47.826 0.00 0.00 0.00 2.01
1832 4684 2.043115 GAGAGGGATTTGAAGGGGGTTT 59.957 50.000 0.00 0.00 0.00 3.27
1833 4685 1.641192 GAGAGGGATTTGAAGGGGGTT 59.359 52.381 0.00 0.00 0.00 4.11
1834 4686 1.299939 GAGAGGGATTTGAAGGGGGT 58.700 55.000 0.00 0.00 0.00 4.95
1835 4687 0.553333 GGAGAGGGATTTGAAGGGGG 59.447 60.000 0.00 0.00 0.00 5.40
1836 4688 1.064389 GTGGAGAGGGATTTGAAGGGG 60.064 57.143 0.00 0.00 0.00 4.79
1837 4689 1.064389 GGTGGAGAGGGATTTGAAGGG 60.064 57.143 0.00 0.00 0.00 3.95
1838 4690 1.407437 CGGTGGAGAGGGATTTGAAGG 60.407 57.143 0.00 0.00 0.00 3.46
1839 4691 1.555075 TCGGTGGAGAGGGATTTGAAG 59.445 52.381 0.00 0.00 0.00 3.02
1840 4692 1.651737 TCGGTGGAGAGGGATTTGAA 58.348 50.000 0.00 0.00 0.00 2.69
1841 4693 1.278127 GTTCGGTGGAGAGGGATTTGA 59.722 52.381 0.00 0.00 0.00 2.69
1842 4694 1.003118 TGTTCGGTGGAGAGGGATTTG 59.997 52.381 0.00 0.00 0.00 2.32
1843 4695 1.003233 GTGTTCGGTGGAGAGGGATTT 59.997 52.381 0.00 0.00 0.00 2.17
1844 4696 0.613777 GTGTTCGGTGGAGAGGGATT 59.386 55.000 0.00 0.00 0.00 3.01
1845 4697 0.544357 TGTGTTCGGTGGAGAGGGAT 60.544 55.000 0.00 0.00 0.00 3.85
1846 4698 1.152419 TGTGTTCGGTGGAGAGGGA 60.152 57.895 0.00 0.00 0.00 4.20
1847 4699 1.293498 CTGTGTTCGGTGGAGAGGG 59.707 63.158 0.00 0.00 0.00 4.30
1848 4700 1.374758 GCTGTGTTCGGTGGAGAGG 60.375 63.158 0.00 0.00 0.00 3.69
1849 4701 1.374758 GGCTGTGTTCGGTGGAGAG 60.375 63.158 0.00 0.00 0.00 3.20
1850 4702 1.837051 AGGCTGTGTTCGGTGGAGA 60.837 57.895 0.00 0.00 0.00 3.71
1851 4703 1.669115 CAGGCTGTGTTCGGTGGAG 60.669 63.158 6.28 0.00 0.00 3.86
1852 4704 1.480212 ATCAGGCTGTGTTCGGTGGA 61.480 55.000 15.27 0.00 0.00 4.02
1853 4705 0.606401 AATCAGGCTGTGTTCGGTGG 60.606 55.000 15.27 0.00 0.00 4.61
1854 4706 0.518636 CAATCAGGCTGTGTTCGGTG 59.481 55.000 15.27 0.02 0.00 4.94
1855 4707 0.108585 ACAATCAGGCTGTGTTCGGT 59.891 50.000 15.27 3.89 0.00 4.69
1856 4708 0.518636 CACAATCAGGCTGTGTTCGG 59.481 55.000 15.27 3.31 39.48 4.30
1862 4714 2.234908 GGACTCTACACAATCAGGCTGT 59.765 50.000 15.27 0.00 0.00 4.40
1863 4715 2.499289 AGGACTCTACACAATCAGGCTG 59.501 50.000 8.58 8.58 0.00 4.85
1864 4716 2.763448 GAGGACTCTACACAATCAGGCT 59.237 50.000 0.00 0.00 0.00 4.58
1865 4717 2.763448 AGAGGACTCTACACAATCAGGC 59.237 50.000 0.00 0.00 38.35 4.85
1908 4760 1.468520 CAAGGATGCAACCAGTTACGG 59.531 52.381 16.21 0.00 0.00 4.02
1974 6027 6.424509 TGCAGCAAGGAACAATTTCTATTTTG 59.575 34.615 0.00 0.00 31.71 2.44
2052 6105 8.535335 TCTATTGAAGATGCTCTAAGACACTTT 58.465 33.333 0.00 0.00 0.00 2.66
2114 6167 0.960861 GAAGGGGTTTTGAGCCTCCG 60.961 60.000 0.00 0.00 0.00 4.63
2115 6168 0.405973 AGAAGGGGTTTTGAGCCTCC 59.594 55.000 0.00 0.00 0.00 4.30
2121 6174 2.512056 TCTGTTGGAGAAGGGGTTTTGA 59.488 45.455 0.00 0.00 0.00 2.69
2122 6175 2.944129 TCTGTTGGAGAAGGGGTTTTG 58.056 47.619 0.00 0.00 0.00 2.44
2126 6179 2.044793 TCATCTGTTGGAGAAGGGGT 57.955 50.000 0.00 0.00 33.12 4.95
2127 6180 2.240667 ACATCATCTGTTGGAGAAGGGG 59.759 50.000 0.00 0.00 32.90 4.79
2128 6181 3.641434 ACATCATCTGTTGGAGAAGGG 57.359 47.619 0.00 0.00 32.90 3.95
2129 6182 6.459298 GCATTTACATCATCTGTTGGAGAAGG 60.459 42.308 0.00 0.00 39.39 3.46
2170 6223 2.397751 CGAAAGGCGGAGATGCATT 58.602 52.632 0.00 0.00 41.16 3.56
2171 6224 4.131376 CGAAAGGCGGAGATGCAT 57.869 55.556 0.00 0.00 36.28 3.96
2180 6233 4.569162 TGTATTTTACATCTCCGAAAGGCG 59.431 41.667 0.00 0.00 42.22 5.52
2181 6234 6.128117 TGTTGTATTTTACATCTCCGAAAGGC 60.128 38.462 0.00 0.00 44.87 4.35
2182 6235 7.094975 TGTGTTGTATTTTACATCTCCGAAAGG 60.095 37.037 0.00 0.00 45.94 3.11
2183 6236 7.802738 TGTGTTGTATTTTACATCTCCGAAAG 58.197 34.615 0.00 0.00 38.68 2.62
2184 6237 7.731882 TGTGTTGTATTTTACATCTCCGAAA 57.268 32.000 0.00 0.00 38.68 3.46
2185 6238 7.201487 CGATGTGTTGTATTTTACATCTCCGAA 60.201 37.037 12.59 0.00 44.37 4.30
2186 6239 6.254804 CGATGTGTTGTATTTTACATCTCCGA 59.745 38.462 12.59 0.00 44.37 4.55
2187 6240 6.410845 CGATGTGTTGTATTTTACATCTCCG 58.589 40.000 12.59 0.00 44.37 4.63
2208 6261 3.664107 AGATGTATATTTGCACCGCGAT 58.336 40.909 8.23 0.00 0.00 4.58
2239 6292 2.695359 GGTCGCCAGTTTTACATCTCA 58.305 47.619 0.00 0.00 0.00 3.27
2270 6323 0.465460 AAACTGAAGGCGGTTGAGCA 60.465 50.000 0.00 0.00 42.66 4.26
2273 6326 1.757682 ACAAAACTGAAGGCGGTTGA 58.242 45.000 0.00 0.00 42.66 3.18
2278 6331 0.661020 ACGGAACAAAACTGAAGGCG 59.339 50.000 0.00 0.00 0.00 5.52
2280 6333 1.263217 CGGACGGAACAAAACTGAAGG 59.737 52.381 0.00 0.00 0.00 3.46
2281 6334 1.333791 GCGGACGGAACAAAACTGAAG 60.334 52.381 0.00 0.00 0.00 3.02
2307 6360 0.461961 GTAGAGGCGAGCAACCATCT 59.538 55.000 0.00 0.00 0.00 2.90
2310 6363 1.591703 CAGTAGAGGCGAGCAACCA 59.408 57.895 0.00 0.00 0.00 3.67
2313 6366 2.579201 GGCAGTAGAGGCGAGCAA 59.421 61.111 0.00 0.00 0.00 3.91
2321 6374 0.103208 AGAAATCGCCGGCAGTAGAG 59.897 55.000 28.98 9.08 0.00 2.43
2324 6377 0.459585 GTGAGAAATCGCCGGCAGTA 60.460 55.000 28.98 11.85 0.00 2.74
2327 6380 2.435938 GGTGAGAAATCGCCGGCA 60.436 61.111 28.98 14.46 0.00 5.69
2344 6397 4.157817 GCGGCAGCAATGTTTCTG 57.842 55.556 3.18 0.00 44.35 3.02


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

AutoCloner maintained by Alex Coulton.