Multiple sequence alignment - TraesCS1B01G026700

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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 TraesCS1B01G026700 chr1B 100.000 2850 0 0 1 2850 12977339 12974490 0.000000e+00 5264.0
1 TraesCS1B01G026700 chr1B 89.653 1904 128 31 987 2848 13448749 13446873 0.000000e+00 2361.0
2 TraesCS1B01G026700 chr1B 91.324 1337 66 24 977 2285 12388448 12387134 0.000000e+00 1781.0
3 TraesCS1B01G026700 chr1B 88.223 1384 100 26 938 2285 12739005 12737649 0.000000e+00 1594.0
4 TraesCS1B01G026700 chr1B 81.919 1261 142 43 1048 2285 12754827 12753630 0.000000e+00 987.0
5 TraesCS1B01G026700 chr1B 79.514 576 95 15 1 574 308294584 308294030 3.440000e-104 388.0
6 TraesCS1B01G026700 chr1B 89.761 293 28 1 1598 1890 13046567 13046857 9.640000e-100 374.0
7 TraesCS1B01G026700 chr1B 91.364 220 19 0 733 952 12403499 12403280 4.610000e-78 302.0
8 TraesCS1B01G026700 chr1B 79.841 377 62 12 2291 2660 481304716 481304347 2.180000e-66 263.0
9 TraesCS1B01G026700 chr1B 86.893 206 20 4 730 935 13448951 13448753 1.030000e-54 224.0
10 TraesCS1B01G026700 chr1B 94.643 56 3 0 767 822 12397508 12397563 1.410000e-13 87.9
11 TraesCS1B01G026700 chr1B 95.745 47 2 0 769 815 13448835 13448789 3.040000e-10 76.8
12 TraesCS1B01G026700 chr1D 90.141 1420 110 13 850 2243 9365018 9363603 0.000000e+00 1820.0
13 TraesCS1B01G026700 chr1D 83.868 998 112 27 1300 2285 9395592 9394632 0.000000e+00 905.0
14 TraesCS1B01G026700 chr1D 82.920 1048 104 33 1048 2062 9400542 9399537 0.000000e+00 874.0
15 TraesCS1B01G026700 chr1D 86.453 812 90 12 1486 2285 9367448 9366645 0.000000e+00 872.0
16 TraesCS1B01G026700 chr1D 82.653 196 24 9 2463 2652 462485670 462485861 6.320000e-37 165.0
17 TraesCS1B01G026700 chr1D 96.774 93 3 0 723 815 9365061 9364969 3.800000e-34 156.0
18 TraesCS1B01G026700 chr1D 91.379 58 4 1 901 958 9400681 9400625 8.470000e-11 78.7
19 TraesCS1B01G026700 chr1A 88.188 1253 100 23 1048 2285 10607672 10606453 0.000000e+00 1450.0
20 TraesCS1B01G026700 chr1A 83.101 574 92 5 1 572 73113134 73112564 4.210000e-143 518.0
21 TraesCS1B01G026700 chr1A 85.333 225 22 8 723 947 10607967 10607754 3.700000e-54 222.0
22 TraesCS1B01G026700 chr1A 100.000 30 0 0 786 815 10607830 10607801 3.970000e-04 56.5
23 TraesCS1B01G026700 chr4A 82.087 575 97 5 1 574 730899014 730898445 1.190000e-133 486.0
24 TraesCS1B01G026700 chr4A 80.423 378 49 13 2288 2654 668107501 668107138 6.050000e-67 265.0
25 TraesCS1B01G026700 chr7B 81.993 572 97 5 4 574 107084932 107085498 5.520000e-132 481.0
26 TraesCS1B01G026700 chr4B 82.850 379 38 17 2288 2655 235376067 235376429 5.930000e-82 315.0
27 TraesCS1B01G026700 chr4B 79.753 405 46 20 2283 2660 148916984 148916589 7.830000e-66 261.0
28 TraesCS1B01G026700 chr4B 81.423 253 44 3 323 574 566985126 566984876 1.340000e-48 204.0
29 TraesCS1B01G026700 chr4D 81.795 390 49 13 2283 2660 105123965 105123586 9.920000e-80 307.0
30 TraesCS1B01G026700 chr2B 81.414 382 43 21 2289 2658 148243742 148244107 1.290000e-73 287.0
31 TraesCS1B01G026700 chr7D 80.000 370 63 9 2289 2656 53482400 53482040 2.180000e-66 263.0
32 TraesCS1B01G026700 chr3D 79.847 392 52 17 2288 2657 7104533 7104919 7.830000e-66 261.0
33 TraesCS1B01G026700 chr3D 92.806 139 5 3 587 725 457417303 457417436 2.240000e-46 196.0
34 TraesCS1B01G026700 chr6A 79.427 384 57 14 2286 2660 484851716 484852086 4.710000e-63 252.0
35 TraesCS1B01G026700 chr5D 78.814 354 45 18 2289 2622 442891580 442891923 8.000000e-51 211.0
36 TraesCS1B01G026700 chr5D 89.344 122 10 3 2289 2410 354506936 354507054 1.770000e-32 150.0
37 TraesCS1B01G026700 chr3A 85.500 200 23 5 2462 2660 108489832 108490026 1.340000e-48 204.0
38 TraesCS1B01G026700 chr3A 90.000 130 8 2 587 716 600330625 600330749 2.270000e-36 163.0
39 TraesCS1B01G026700 chr2A 77.436 390 56 17 2288 2658 617735662 617736038 1.340000e-48 204.0
40 TraesCS1B01G026700 chr7A 82.812 192 29 3 2462 2652 735449264 735449076 4.880000e-38 169.0
41 TraesCS1B01G026700 chr7A 80.952 210 36 2 2444 2652 44928193 44928399 2.270000e-36 163.0


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 TraesCS1B01G026700 chr1B 12974490 12977339 2849 True 5264.000000 5264 100.000000 1 2850 1 chr1B.!!$R5 2849
1 TraesCS1B01G026700 chr1B 12387134 12388448 1314 True 1781.000000 1781 91.324000 977 2285 1 chr1B.!!$R1 1308
2 TraesCS1B01G026700 chr1B 12737649 12739005 1356 True 1594.000000 1594 88.223000 938 2285 1 chr1B.!!$R3 1347
3 TraesCS1B01G026700 chr1B 12753630 12754827 1197 True 987.000000 987 81.919000 1048 2285 1 chr1B.!!$R4 1237
4 TraesCS1B01G026700 chr1B 13446873 13448951 2078 True 887.266667 2361 90.763667 730 2848 3 chr1B.!!$R8 2118
5 TraesCS1B01G026700 chr1B 308294030 308294584 554 True 388.000000 388 79.514000 1 574 1 chr1B.!!$R6 573
6 TraesCS1B01G026700 chr1D 9363603 9367448 3845 True 949.333333 1820 91.122667 723 2285 3 chr1D.!!$R1 1562
7 TraesCS1B01G026700 chr1D 9394632 9400681 6049 True 619.233333 905 86.055667 901 2285 3 chr1D.!!$R2 1384
8 TraesCS1B01G026700 chr1A 10606453 10607967 1514 True 576.166667 1450 91.173667 723 2285 3 chr1A.!!$R2 1562
9 TraesCS1B01G026700 chr1A 73112564 73113134 570 True 518.000000 518 83.101000 1 572 1 chr1A.!!$R1 571
10 TraesCS1B01G026700 chr4A 730898445 730899014 569 True 486.000000 486 82.087000 1 574 1 chr4A.!!$R2 573
11 TraesCS1B01G026700 chr7B 107084932 107085498 566 False 481.000000 481 81.993000 4 574 1 chr7B.!!$F1 570

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
622 623 0.038455 GCGAGCTATAGAGGGAGGGA 59.962 60.0 3.21 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2318 8815 1.010419 CATTTTTGGCACGCAGGAGC 61.01 55.0 0.0 0.0 37.42 4.7 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
28 29 1.229658 AGTGGAAGGAGGGTGGAGG 60.230 63.158 0.00 0.00 0.00 4.30
34 35 2.049792 AAGGAGGGTGGAGGACTGGT 62.050 60.000 0.00 0.00 0.00 4.00
94 95 0.178987 GAGTCTAGATCGAGGGGGCA 60.179 60.000 2.78 0.00 0.00 5.36
122 123 3.993382 GGGATTTATACCCGCGACA 57.007 52.632 8.23 0.00 37.85 4.35
125 126 1.069668 GGATTTATACCCGCGACACCT 59.930 52.381 8.23 0.00 0.00 4.00
233 234 4.192453 TGCAACCCCGGGTCGTTT 62.192 61.111 21.85 3.70 33.12 3.60
296 297 4.025401 CCCGCAGCCAAACGTGAC 62.025 66.667 0.00 0.00 0.00 3.67
298 299 4.368808 CGCAGCCAAACGTGACGG 62.369 66.667 10.66 0.00 0.00 4.79
299 300 4.025401 GCAGCCAAACGTGACGGG 62.025 66.667 10.66 1.63 0.00 5.28
300 301 4.025401 CAGCCAAACGTGACGGGC 62.025 66.667 14.51 14.51 46.77 6.13
303 304 3.656045 CCAAACGTGACGGGCCAC 61.656 66.667 10.66 0.00 0.00 5.01
304 305 3.656045 CAAACGTGACGGGCCACC 61.656 66.667 10.66 0.00 33.67 4.61
314 315 4.419921 GGGCCACCGGGTTCGATT 62.420 66.667 6.32 0.00 39.00 3.34
315 316 3.131478 GGCCACCGGGTTCGATTG 61.131 66.667 6.32 0.00 39.00 2.67
316 317 3.810896 GCCACCGGGTTCGATTGC 61.811 66.667 6.32 0.00 39.00 3.56
318 319 3.496131 CACCGGGTTCGATTGCCG 61.496 66.667 6.32 0.00 39.00 5.69
320 321 4.770874 CCGGGTTCGATTGCCGGT 62.771 66.667 1.90 0.00 38.96 5.28
321 322 3.496131 CGGGTTCGATTGCCGGTG 61.496 66.667 1.90 0.00 39.00 4.94
322 323 3.810896 GGGTTCGATTGCCGGTGC 61.811 66.667 1.90 0.00 39.14 5.01
350 351 3.866582 GAGGCCACCGGGATCCTG 61.867 72.222 14.26 14.26 35.59 3.86
351 352 4.741239 AGGCCACCGGGATCCTGT 62.741 66.667 19.51 10.50 35.59 4.00
352 353 4.176752 GGCCACCGGGATCCTGTC 62.177 72.222 19.51 5.47 35.59 3.51
362 363 2.355010 GGATCCTGTCCCAAATCCTG 57.645 55.000 3.84 0.00 41.50 3.86
363 364 1.133668 GGATCCTGTCCCAAATCCTGG 60.134 57.143 3.84 0.00 45.97 4.45
364 365 0.259938 ATCCTGTCCCAAATCCTGGC 59.740 55.000 0.00 0.00 44.90 4.85
365 366 1.139498 TCCTGTCCCAAATCCTGGCA 61.139 55.000 0.00 0.00 44.90 4.92
366 367 0.251742 CCTGTCCCAAATCCTGGCAA 60.252 55.000 0.00 0.00 44.90 4.52
367 368 1.631405 CTGTCCCAAATCCTGGCAAA 58.369 50.000 0.00 0.00 44.90 3.68
392 393 5.920193 AAACATGGGAATGGAACTATGTG 57.080 39.130 0.00 0.00 0.00 3.21
393 394 3.902218 ACATGGGAATGGAACTATGTGG 58.098 45.455 0.00 0.00 0.00 4.17
394 395 2.435372 TGGGAATGGAACTATGTGGC 57.565 50.000 0.00 0.00 0.00 5.01
396 397 1.064017 GGGAATGGAACTATGTGGCCA 60.064 52.381 0.00 0.00 34.45 5.36
397 398 2.622977 GGGAATGGAACTATGTGGCCAA 60.623 50.000 7.24 0.00 33.51 4.52
400 401 2.897271 TGGAACTATGTGGCCAATGT 57.103 45.000 7.24 0.41 0.00 2.71
401 402 2.722094 TGGAACTATGTGGCCAATGTC 58.278 47.619 7.24 0.00 0.00 3.06
402 403 1.670811 GGAACTATGTGGCCAATGTCG 59.329 52.381 7.24 0.00 0.00 4.35
403 404 2.627945 GAACTATGTGGCCAATGTCGA 58.372 47.619 7.24 0.00 0.00 4.20
404 405 3.206150 GAACTATGTGGCCAATGTCGAT 58.794 45.455 7.24 0.00 0.00 3.59
406 407 2.092968 ACTATGTGGCCAATGTCGATGT 60.093 45.455 7.24 0.00 0.00 3.06
408 409 1.164411 TGTGGCCAATGTCGATGTTC 58.836 50.000 7.24 0.00 0.00 3.18
409 410 1.271325 TGTGGCCAATGTCGATGTTCT 60.271 47.619 7.24 0.00 0.00 3.01
410 411 1.398390 GTGGCCAATGTCGATGTTCTC 59.602 52.381 7.24 0.00 0.00 2.87
418 419 2.107141 CGATGTTCTCGCCCTCCC 59.893 66.667 0.00 0.00 41.14 4.30
419 420 2.427245 CGATGTTCTCGCCCTCCCT 61.427 63.158 0.00 0.00 41.14 4.20
422 423 1.333636 ATGTTCTCGCCCTCCCTCAG 61.334 60.000 0.00 0.00 0.00 3.35
439 440 3.554692 GGAACTGCGCGTCCATCG 61.555 66.667 17.10 0.00 43.12 3.84
440 441 2.809601 GAACTGCGCGTCCATCGT 60.810 61.111 8.43 0.00 42.13 3.73
448 449 4.082523 CGTCCATCGTGCACCCCT 62.083 66.667 12.15 0.00 34.52 4.79
449 450 2.125106 GTCCATCGTGCACCCCTC 60.125 66.667 12.15 0.00 0.00 4.30
451 452 3.402681 CCATCGTGCACCCCTCCT 61.403 66.667 12.15 0.00 0.00 3.69
452 453 2.187946 CATCGTGCACCCCTCCTC 59.812 66.667 12.15 0.00 0.00 3.71
453 454 3.461773 ATCGTGCACCCCTCCTCG 61.462 66.667 12.15 0.00 0.00 4.63
454 455 4.988716 TCGTGCACCCCTCCTCGT 62.989 66.667 12.15 0.00 0.00 4.18
455 456 4.436998 CGTGCACCCCTCCTCGTC 62.437 72.222 12.15 0.00 0.00 4.20
456 457 4.436998 GTGCACCCCTCCTCGTCG 62.437 72.222 5.22 0.00 0.00 5.12
458 459 3.827898 GCACCCCTCCTCGTCGAG 61.828 72.222 15.53 15.53 0.00 4.04
468 469 1.803943 CTCGTCGAGGAGAACCAGG 59.196 63.158 26.94 1.74 38.94 4.45
469 470 2.182030 CGTCGAGGAGAACCAGGC 59.818 66.667 0.00 0.00 38.94 4.85
470 471 2.182030 GTCGAGGAGAACCAGGCG 59.818 66.667 0.00 0.00 38.94 5.52
472 473 3.068691 CGAGGAGAACCAGGCGGA 61.069 66.667 2.43 0.00 38.94 5.54
473 474 2.896443 GAGGAGAACCAGGCGGAG 59.104 66.667 2.43 0.00 38.94 4.63
475 476 4.821589 GGAGAACCAGGCGGAGCG 62.822 72.222 2.43 0.00 46.39 5.03
488 489 2.951745 GAGCGCATCGTGTCGGAG 60.952 66.667 11.47 0.00 0.00 4.63
489 490 3.396911 GAGCGCATCGTGTCGGAGA 62.397 63.158 11.47 0.00 0.00 3.71
490 491 2.506217 GCGCATCGTGTCGGAGAA 60.506 61.111 0.30 0.00 39.69 2.87
491 492 2.789203 GCGCATCGTGTCGGAGAAC 61.789 63.158 0.30 0.00 39.69 3.01
492 493 2.497092 CGCATCGTGTCGGAGAACG 61.497 63.158 6.79 6.79 39.69 3.95
504 505 1.140407 GGAGAACGATCTTGCCGACG 61.140 60.000 0.00 0.00 35.54 5.12
505 506 0.456312 GAGAACGATCTTGCCGACGT 60.456 55.000 0.00 0.00 40.64 4.34
506 507 0.456312 AGAACGATCTTGCCGACGTC 60.456 55.000 5.18 5.18 38.00 4.34
507 508 1.730593 GAACGATCTTGCCGACGTCG 61.731 60.000 30.33 30.33 38.00 5.12
509 510 1.513373 CGATCTTGCCGACGTCGAA 60.513 57.895 37.65 23.57 43.02 3.71
510 511 1.730593 CGATCTTGCCGACGTCGAAC 61.731 60.000 37.65 27.78 43.02 3.95
524 525 3.614143 GAACGTGATCGATCGGGC 58.386 61.111 20.03 11.72 40.62 6.13
525 526 2.278596 AACGTGATCGATCGGGCG 60.279 61.111 24.82 24.82 40.62 6.13
526 527 3.768185 AACGTGATCGATCGGGCGG 62.768 63.158 27.67 15.98 40.62 6.13
530 531 3.038417 GATCGATCGGGCGGCAAG 61.038 66.667 16.41 4.04 0.00 4.01
531 532 4.609018 ATCGATCGGGCGGCAAGG 62.609 66.667 16.41 0.00 0.00 3.61
535 536 3.164269 ATCGGGCGGCAAGGAGAT 61.164 61.111 12.47 4.37 0.00 2.75
536 537 3.170490 ATCGGGCGGCAAGGAGATC 62.170 63.158 12.47 0.00 0.00 2.75
537 538 4.918201 CGGGCGGCAAGGAGATCC 62.918 72.222 12.47 0.00 0.00 3.36
538 539 4.918201 GGGCGGCAAGGAGATCCG 62.918 72.222 12.47 0.00 45.46 4.18
545 546 2.831742 AAGGAGATCCGCCGCGTA 60.832 61.111 12.58 0.00 42.08 4.42
546 547 2.420568 AAGGAGATCCGCCGCGTAA 61.421 57.895 12.58 0.00 42.08 3.18
547 548 2.351336 AAGGAGATCCGCCGCGTAAG 62.351 60.000 12.58 0.00 42.08 2.34
549 550 1.657794 GAGATCCGCCGCGTAAGTC 60.658 63.158 12.58 4.13 41.68 3.01
550 551 3.022914 GATCCGCCGCGTAAGTCG 61.023 66.667 12.58 0.00 43.12 4.18
578 579 4.251760 CGTATCGCCTGCCATCTC 57.748 61.111 0.00 0.00 0.00 2.75
579 580 1.373497 CGTATCGCCTGCCATCTCC 60.373 63.158 0.00 0.00 0.00 3.71
580 581 1.004440 GTATCGCCTGCCATCTCCC 60.004 63.158 0.00 0.00 0.00 4.30
581 582 1.459348 TATCGCCTGCCATCTCCCA 60.459 57.895 0.00 0.00 0.00 4.37
583 584 1.925285 ATCGCCTGCCATCTCCCAAA 61.925 55.000 0.00 0.00 0.00 3.28
584 585 1.454479 CGCCTGCCATCTCCCAAAT 60.454 57.895 0.00 0.00 0.00 2.32
586 587 2.024590 GCCTGCCATCTCCCAAATGC 62.025 60.000 0.00 0.00 0.00 3.56
588 589 0.396695 CTGCCATCTCCCAAATGCCT 60.397 55.000 0.00 0.00 0.00 4.75
589 590 0.685131 TGCCATCTCCCAAATGCCTG 60.685 55.000 0.00 0.00 0.00 4.85
591 592 1.688772 CCATCTCCCAAATGCCTGAG 58.311 55.000 0.00 0.00 0.00 3.35
592 593 1.213678 CCATCTCCCAAATGCCTGAGA 59.786 52.381 0.00 0.00 38.17 3.27
593 594 2.158505 CCATCTCCCAAATGCCTGAGAT 60.159 50.000 0.00 0.00 43.50 2.75
595 596 1.492176 TCTCCCAAATGCCTGAGATCC 59.508 52.381 0.00 0.00 0.00 3.36
596 597 0.181114 TCCCAAATGCCTGAGATCCG 59.819 55.000 0.00 0.00 0.00 4.18
597 598 1.450531 CCCAAATGCCTGAGATCCGC 61.451 60.000 0.00 0.00 0.00 5.54
598 599 1.645455 CAAATGCCTGAGATCCGCG 59.355 57.895 0.00 0.00 0.00 6.46
599 600 0.811219 CAAATGCCTGAGATCCGCGA 60.811 55.000 8.23 0.00 0.00 5.87
600 601 0.531532 AAATGCCTGAGATCCGCGAG 60.532 55.000 8.23 0.00 0.00 5.03
620 621 2.176140 CGCGAGCTATAGAGGGAGG 58.824 63.158 0.00 0.00 0.00 4.30
621 622 1.309499 CGCGAGCTATAGAGGGAGGG 61.309 65.000 0.00 0.00 0.00 4.30
622 623 0.038455 GCGAGCTATAGAGGGAGGGA 59.962 60.000 3.21 0.00 0.00 4.20
623 624 1.828979 CGAGCTATAGAGGGAGGGAC 58.171 60.000 3.21 0.00 0.00 4.46
624 625 1.828979 GAGCTATAGAGGGAGGGACG 58.171 60.000 3.21 0.00 0.00 4.79
625 626 0.406361 AGCTATAGAGGGAGGGACGG 59.594 60.000 3.21 0.00 0.00 4.79
626 627 0.404812 GCTATAGAGGGAGGGACGGA 59.595 60.000 3.21 0.00 0.00 4.69
627 628 1.614850 GCTATAGAGGGAGGGACGGAG 60.615 61.905 3.21 0.00 0.00 4.63
628 629 1.004979 CTATAGAGGGAGGGACGGAGG 59.995 61.905 0.00 0.00 0.00 4.30
629 630 0.701659 ATAGAGGGAGGGACGGAGGA 60.702 60.000 0.00 0.00 0.00 3.71
630 631 1.354168 TAGAGGGAGGGACGGAGGAG 61.354 65.000 0.00 0.00 0.00 3.69
631 632 3.742248 GAGGGAGGGACGGAGGAGG 62.742 73.684 0.00 0.00 0.00 4.30
633 634 2.442458 GGAGGGACGGAGGAGGAC 60.442 72.222 0.00 0.00 0.00 3.85
634 635 2.359404 GAGGGACGGAGGAGGACA 59.641 66.667 0.00 0.00 0.00 4.02
635 636 1.755008 GAGGGACGGAGGAGGACAG 60.755 68.421 0.00 0.00 0.00 3.51
636 637 2.212794 GAGGGACGGAGGAGGACAGA 62.213 65.000 0.00 0.00 0.00 3.41
637 638 1.305046 GGGACGGAGGAGGACAGAA 60.305 63.158 0.00 0.00 0.00 3.02
638 639 0.688087 GGGACGGAGGAGGACAGAAT 60.688 60.000 0.00 0.00 0.00 2.40
639 640 0.461961 GGACGGAGGAGGACAGAATG 59.538 60.000 0.00 0.00 46.00 2.67
640 641 0.461961 GACGGAGGAGGACAGAATGG 59.538 60.000 0.00 0.00 43.62 3.16
641 642 0.041238 ACGGAGGAGGACAGAATGGA 59.959 55.000 0.00 0.00 43.62 3.41
642 643 0.461961 CGGAGGAGGACAGAATGGAC 59.538 60.000 0.00 0.00 43.62 4.02
644 645 0.461961 GAGGAGGACAGAATGGACCG 59.538 60.000 0.00 0.00 43.62 4.79
646 647 0.902531 GGAGGACAGAATGGACCGAA 59.097 55.000 0.00 0.00 43.62 4.30
647 648 1.134670 GGAGGACAGAATGGACCGAAG 60.135 57.143 0.00 0.00 43.62 3.79
660 661 2.202492 CGAAGGAGCACGACGAGG 60.202 66.667 0.00 0.00 0.00 4.63
662 663 1.585006 GAAGGAGCACGACGAGGAA 59.415 57.895 0.00 0.00 0.00 3.36
663 664 0.456995 GAAGGAGCACGACGAGGAAG 60.457 60.000 0.00 0.00 0.00 3.46
664 665 1.878656 AAGGAGCACGACGAGGAAGG 61.879 60.000 0.00 0.00 0.00 3.46
666 667 1.153997 GAGCACGACGAGGAAGGTC 60.154 63.158 0.00 0.00 0.00 3.85
668 669 1.444553 GCACGACGAGGAAGGTCAG 60.445 63.158 0.00 0.00 34.04 3.51
669 670 1.957562 CACGACGAGGAAGGTCAGT 59.042 57.895 0.00 0.00 34.04 3.41
670 671 0.314302 CACGACGAGGAAGGTCAGTT 59.686 55.000 0.00 0.00 34.04 3.16
672 673 1.411612 ACGACGAGGAAGGTCAGTTTT 59.588 47.619 0.00 0.00 34.04 2.43
673 674 2.159000 ACGACGAGGAAGGTCAGTTTTT 60.159 45.455 0.00 0.00 34.04 1.94
674 675 3.068590 ACGACGAGGAAGGTCAGTTTTTA 59.931 43.478 0.00 0.00 34.04 1.52
675 676 4.243270 CGACGAGGAAGGTCAGTTTTTAT 58.757 43.478 0.00 0.00 34.04 1.40
676 677 4.091509 CGACGAGGAAGGTCAGTTTTTATG 59.908 45.833 0.00 0.00 34.04 1.90
678 679 6.105397 ACGAGGAAGGTCAGTTTTTATGTA 57.895 37.500 0.00 0.00 0.00 2.29
679 680 6.164176 ACGAGGAAGGTCAGTTTTTATGTAG 58.836 40.000 0.00 0.00 0.00 2.74
680 681 5.581085 CGAGGAAGGTCAGTTTTTATGTAGG 59.419 44.000 0.00 0.00 0.00 3.18
682 683 6.712276 AGGAAGGTCAGTTTTTATGTAGGAG 58.288 40.000 0.00 0.00 0.00 3.69
683 684 6.500751 AGGAAGGTCAGTTTTTATGTAGGAGA 59.499 38.462 0.00 0.00 0.00 3.71
684 685 6.819146 GGAAGGTCAGTTTTTATGTAGGAGAG 59.181 42.308 0.00 0.00 0.00 3.20
685 686 5.735766 AGGTCAGTTTTTATGTAGGAGAGC 58.264 41.667 0.00 0.00 0.00 4.09
686 687 5.485708 AGGTCAGTTTTTATGTAGGAGAGCT 59.514 40.000 0.00 0.00 0.00 4.09
687 688 5.813157 GGTCAGTTTTTATGTAGGAGAGCTC 59.187 44.000 5.27 5.27 0.00 4.09
696 697 3.715015 GGAGAGCTCCTTCGGGTT 58.285 61.111 10.93 0.00 46.16 4.11
698 699 0.325272 GGAGAGCTCCTTCGGGTTTT 59.675 55.000 10.93 0.00 46.16 2.43
765 2431 7.817478 ACATATCATCCAATAAAATCTACGCGA 59.183 33.333 15.93 0.00 0.00 5.87
825 2491 2.281761 AAGGTGGAGCGTGCCTTG 60.282 61.111 4.54 0.00 40.71 3.61
832 2498 2.749044 AGCGTGCCTTGCCATCTG 60.749 61.111 0.00 0.00 0.00 2.90
849 2515 4.201753 CCATCTGCAGTAGTCAAATCAACG 60.202 45.833 14.67 0.00 0.00 4.10
852 2518 1.201921 GCAGTAGTCAAATCAACGCGG 60.202 52.381 12.47 0.00 0.00 6.46
853 2519 1.076332 AGTAGTCAAATCAACGCGGC 58.924 50.000 12.47 0.00 0.00 6.53
854 2520 0.793861 GTAGTCAAATCAACGCGGCA 59.206 50.000 12.47 0.00 0.00 5.69
855 2521 1.396996 GTAGTCAAATCAACGCGGCAT 59.603 47.619 12.47 0.00 0.00 4.40
859 2525 1.444212 AAATCAACGCGGCATGCAC 60.444 52.632 21.36 10.08 46.97 4.57
875 2548 0.598065 GCACCAAGCCACCAACTAAG 59.402 55.000 0.00 0.00 37.23 2.18
884 2557 2.878117 GCCACCAACTAAGCCATGTGTA 60.878 50.000 0.00 0.00 0.00 2.90
1001 2700 1.940613 ACAACTGTCGTCAAGCTTTCC 59.059 47.619 0.00 0.00 0.00 3.13
1097 2835 0.970427 TCACGCCCACATGCTCTCTA 60.970 55.000 0.00 0.00 0.00 2.43
1108 2846 2.649331 TGCTCTCTACGTGTAAAGCC 57.351 50.000 0.00 0.00 0.00 4.35
1169 2921 2.491621 TGCTCTCGCATCAGTCCG 59.508 61.111 0.00 0.00 42.25 4.79
1176 2928 2.767445 CGCATCAGTCCGTCGGGTA 61.767 63.158 12.29 0.00 33.83 3.69
1179 2931 0.750546 CATCAGTCCGTCGGGTAGGA 60.751 60.000 12.29 4.93 33.83 2.94
1211 2963 2.044946 GAAGCCCGGCATTCCACT 60.045 61.111 13.15 0.00 0.00 4.00
1268 3024 4.141620 CCAGTCCCTGCTACATATTCAGTT 60.142 45.833 0.00 0.00 0.00 3.16
2049 8523 8.778358 AGTTAAAGAATCTATCATCAAATCCGC 58.222 33.333 0.00 0.00 0.00 5.54
2064 8538 6.791303 TCAAATCCGCTACAAAATGGTAATC 58.209 36.000 0.00 0.00 0.00 1.75
2172 8665 5.974158 CACCAAAAATGTCAACATCGTGTTA 59.026 36.000 0.00 0.00 38.77 2.41
2337 8834 1.010419 GCTCCTGCGTGCCAAAAATG 61.010 55.000 0.00 0.00 0.00 2.32
2343 8840 2.411904 TGCGTGCCAAAAATGGATTTC 58.588 42.857 0.00 0.00 0.00 2.17
2439 8945 3.447229 AGGGGAAATTTTTGACCTATGCG 59.553 43.478 0.00 0.00 0.00 4.73
2494 9000 7.749539 ACACTTAATTTTGTTTTTCTCACCG 57.250 32.000 0.00 0.00 0.00 4.94
2523 9030 1.347062 TGCTATCCCGTATGGCATGA 58.653 50.000 10.98 0.00 46.08 3.07
2554 9061 4.771114 TGGGCACTTGCTACACTAATAT 57.229 40.909 0.38 0.00 41.70 1.28
2636 9144 8.792830 TTTACTATTCATTAGGGAGCATATGC 57.207 34.615 20.36 20.36 35.13 3.14
2637 9145 6.633325 ACTATTCATTAGGGAGCATATGCT 57.367 37.500 29.97 29.97 42.49 3.79
2657 9165 1.025041 CCCTAGAGCCAAAAATCCGC 58.975 55.000 0.00 0.00 0.00 5.54
2664 9172 1.068816 AGCCAAAAATCCGCGTACAAC 60.069 47.619 4.92 0.00 0.00 3.32
2668 9176 3.180782 CCAAAAATCCGCGTACAACAAAC 59.819 43.478 4.92 0.00 0.00 2.93
2684 9192 9.583765 GTACAACAAACACTAAATTTAAACCCA 57.416 29.630 0.00 0.00 0.00 4.51
2687 9195 8.599774 CAACAAACACTAAATTTAAACCCACTG 58.400 33.333 0.00 0.00 0.00 3.66
2694 9202 7.007723 ACTAAATTTAAACCCACTGTGGATGA 58.992 34.615 27.94 6.96 40.96 2.92
2732 9240 9.679661 TTGAGTATTTAATCTCATGTTTAGGCA 57.320 29.630 7.52 0.00 39.85 4.75
2738 9246 5.511234 AATCTCATGTTTAGGCAATCTGC 57.489 39.130 0.00 0.00 44.08 4.26
2837 9345 5.755409 AAAAATTAACATTGGGGAGGGTC 57.245 39.130 0.00 0.00 0.00 4.46
2848 9356 2.364448 GAGGGTCCTTCGAGGCCT 60.364 66.667 3.86 3.86 34.61 5.19
2849 9357 2.364448 AGGGTCCTTCGAGGCCTC 60.364 66.667 23.79 23.79 34.61 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.072211 CCGAAAAACCCTAGAACCAGTC 58.928 50.000 0.00 0.00 0.00 3.51
34 35 1.878948 CGGCACCGAAAAACCCTAGAA 60.879 52.381 2.01 0.00 42.83 2.10
94 95 5.631119 CGGGTATAAATCCCAAATCCTTCT 58.369 41.667 1.91 0.00 44.81 2.85
122 123 0.613292 ATGAGAGGAGCGACACAGGT 60.613 55.000 0.00 0.00 0.00 4.00
125 126 1.893062 CCATGAGAGGAGCGACACA 59.107 57.895 0.00 0.00 0.00 3.72
152 153 2.110213 GCCCACGTGGACAGTGAA 59.890 61.111 36.07 0.00 41.83 3.18
157 158 3.899981 GATGCTGCCCACGTGGACA 62.900 63.158 36.07 29.41 37.39 4.02
216 217 4.192453 AAACGACCCGGGGTTGCA 62.192 61.111 29.89 0.00 40.62 4.08
220 221 3.944945 GGTCAAACGACCCGGGGT 61.945 66.667 27.92 21.21 46.36 4.95
279 280 4.025401 GTCACGTTTGGCTGCGGG 62.025 66.667 0.00 0.00 0.00 6.13
280 281 4.368808 CGTCACGTTTGGCTGCGG 62.369 66.667 0.00 0.00 0.00 5.69
281 282 4.368808 CCGTCACGTTTGGCTGCG 62.369 66.667 0.00 0.00 0.00 5.18
282 283 4.025401 CCCGTCACGTTTGGCTGC 62.025 66.667 0.00 0.00 0.00 5.25
286 287 3.656045 GTGGCCCGTCACGTTTGG 61.656 66.667 0.00 0.00 0.00 3.28
287 288 3.656045 GGTGGCCCGTCACGTTTG 61.656 66.667 0.00 0.00 38.46 2.93
298 299 3.131478 CAATCGAACCCGGTGGCC 61.131 66.667 0.00 0.00 36.24 5.36
299 300 3.810896 GCAATCGAACCCGGTGGC 61.811 66.667 0.00 0.00 38.84 5.01
300 301 3.131478 GGCAATCGAACCCGGTGG 61.131 66.667 0.00 0.00 36.24 4.61
301 302 3.496131 CGGCAATCGAACCCGGTG 61.496 66.667 12.31 0.00 42.43 4.94
304 305 3.496131 CACCGGCAATCGAACCCG 61.496 66.667 0.00 12.97 42.43 5.28
306 307 3.810896 GGCACCGGCAATCGAACC 61.811 66.667 0.00 0.00 43.71 3.62
333 334 3.866582 CAGGATCCCGGTGGCCTC 61.867 72.222 8.55 0.00 0.00 4.70
334 335 4.741239 ACAGGATCCCGGTGGCCT 62.741 66.667 8.55 0.00 29.31 5.19
335 336 4.176752 GACAGGATCCCGGTGGCC 62.177 72.222 8.55 0.00 30.91 5.36
336 337 4.176752 GGACAGGATCCCGGTGGC 62.177 72.222 8.55 1.79 42.46 5.01
344 345 2.355010 CCAGGATTTGGGACAGGATC 57.645 55.000 0.00 0.00 43.75 3.36
372 373 3.902218 CCACATAGTTCCATTCCCATGT 58.098 45.455 0.00 0.00 0.00 3.21
374 375 2.424812 GGCCACATAGTTCCATTCCCAT 60.425 50.000 0.00 0.00 0.00 4.00
376 377 1.064017 TGGCCACATAGTTCCATTCCC 60.064 52.381 0.00 0.00 0.00 3.97
377 378 2.435372 TGGCCACATAGTTCCATTCC 57.565 50.000 0.00 0.00 0.00 3.01
378 379 3.701040 ACATTGGCCACATAGTTCCATTC 59.299 43.478 3.88 0.00 0.00 2.67
379 380 3.701040 GACATTGGCCACATAGTTCCATT 59.299 43.478 3.88 0.00 0.00 3.16
380 381 3.290710 GACATTGGCCACATAGTTCCAT 58.709 45.455 3.88 0.00 0.00 3.41
382 383 1.670811 CGACATTGGCCACATAGTTCC 59.329 52.381 3.88 0.00 0.00 3.62
383 384 2.627945 TCGACATTGGCCACATAGTTC 58.372 47.619 3.88 0.00 0.00 3.01
387 388 2.708216 ACATCGACATTGGCCACATA 57.292 45.000 3.88 0.00 0.00 2.29
390 391 1.398390 GAGAACATCGACATTGGCCAC 59.602 52.381 3.88 0.00 0.00 5.01
402 403 1.330655 TGAGGGAGGGCGAGAACATC 61.331 60.000 0.00 0.00 0.00 3.06
403 404 1.306141 TGAGGGAGGGCGAGAACAT 60.306 57.895 0.00 0.00 0.00 2.71
404 405 1.984570 CTGAGGGAGGGCGAGAACA 60.985 63.158 0.00 0.00 0.00 3.18
406 407 2.364317 CCTGAGGGAGGGCGAGAA 60.364 66.667 0.00 0.00 38.36 2.87
408 409 2.364317 TTCCTGAGGGAGGGCGAG 60.364 66.667 0.00 0.00 43.06 5.03
409 410 2.683933 GTTCCTGAGGGAGGGCGA 60.684 66.667 0.00 0.00 43.06 5.54
410 411 2.685380 AGTTCCTGAGGGAGGGCG 60.685 66.667 0.00 0.00 43.06 6.13
411 412 2.993853 CAGTTCCTGAGGGAGGGC 59.006 66.667 0.00 0.00 43.06 5.19
413 414 2.581354 CGCAGTTCCTGAGGGAGG 59.419 66.667 0.00 0.00 43.29 4.30
415 416 4.069232 CGCGCAGTTCCTGAGGGA 62.069 66.667 8.75 0.00 44.14 4.20
416 417 4.379243 ACGCGCAGTTCCTGAGGG 62.379 66.667 5.73 9.77 46.01 4.30
417 418 2.811317 GACGCGCAGTTCCTGAGG 60.811 66.667 5.73 0.00 32.10 3.86
418 419 2.811317 GGACGCGCAGTTCCTGAG 60.811 66.667 5.73 0.00 34.50 3.35
419 420 2.835701 GATGGACGCGCAGTTCCTGA 62.836 60.000 17.83 2.53 32.44 3.86
422 423 3.554692 CGATGGACGCGCAGTTCC 61.555 66.667 5.73 10.63 34.51 3.62
424 425 3.112075 CACGATGGACGCGCAGTT 61.112 61.111 5.73 0.00 46.94 3.16
431 432 4.082523 AGGGGTGCACGATGGACG 62.083 66.667 11.45 0.00 39.79 4.79
432 433 2.125106 GAGGGGTGCACGATGGAC 60.125 66.667 11.45 0.00 38.03 4.02
433 434 3.399181 GGAGGGGTGCACGATGGA 61.399 66.667 11.45 0.00 0.00 3.41
434 435 3.391665 GAGGAGGGGTGCACGATGG 62.392 68.421 11.45 0.00 0.00 3.51
435 436 2.187946 GAGGAGGGGTGCACGATG 59.812 66.667 11.45 0.00 0.00 3.84
439 440 4.436998 CGACGAGGAGGGGTGCAC 62.437 72.222 8.80 8.80 0.00 4.57
440 441 4.671590 TCGACGAGGAGGGGTGCA 62.672 66.667 0.00 0.00 0.00 4.57
441 442 3.827898 CTCGACGAGGAGGGGTGC 61.828 72.222 17.27 0.00 0.00 5.01
451 452 2.341101 GCCTGGTTCTCCTCGACGA 61.341 63.158 0.00 0.00 34.23 4.20
452 453 2.182030 GCCTGGTTCTCCTCGACG 59.818 66.667 0.00 0.00 34.23 5.12
453 454 2.182030 CGCCTGGTTCTCCTCGAC 59.818 66.667 0.00 0.00 34.23 4.20
454 455 3.068691 CCGCCTGGTTCTCCTCGA 61.069 66.667 0.00 0.00 34.23 4.04
455 456 3.068691 TCCGCCTGGTTCTCCTCG 61.069 66.667 0.00 0.00 36.30 4.63
456 457 2.896443 CTCCGCCTGGTTCTCCTC 59.104 66.667 0.00 0.00 36.30 3.71
458 459 4.821589 CGCTCCGCCTGGTTCTCC 62.822 72.222 0.00 0.00 36.30 3.71
470 471 4.492160 TCCGACACGATGCGCTCC 62.492 66.667 9.73 0.00 0.00 4.70
472 473 2.989881 TTCTCCGACACGATGCGCT 61.990 57.895 9.73 0.00 0.00 5.92
473 474 2.506217 TTCTCCGACACGATGCGC 60.506 61.111 0.00 0.00 0.00 6.09
474 475 2.497092 CGTTCTCCGACACGATGCG 61.497 63.158 0.00 0.00 38.76 4.73
475 476 1.154093 TCGTTCTCCGACACGATGC 60.154 57.895 0.00 0.00 41.60 3.91
484 485 1.138883 TCGGCAAGATCGTTCTCCG 59.861 57.895 14.41 14.41 39.52 4.63
486 487 0.456312 ACGTCGGCAAGATCGTTCTC 60.456 55.000 0.00 0.00 34.63 2.87
488 489 1.730593 CGACGTCGGCAAGATCGTTC 61.731 60.000 29.70 0.00 36.97 3.95
489 490 1.800315 CGACGTCGGCAAGATCGTT 60.800 57.895 29.70 0.00 36.97 3.85
490 491 2.191354 TTCGACGTCGGCAAGATCGT 62.191 55.000 35.05 8.06 38.56 3.73
491 492 1.513373 TTCGACGTCGGCAAGATCG 60.513 57.895 35.05 9.66 40.29 3.69
492 493 1.730593 CGTTCGACGTCGGCAAGATC 61.731 60.000 35.05 14.96 40.29 2.75
493 494 1.800315 CGTTCGACGTCGGCAAGAT 60.800 57.895 35.05 0.00 40.29 2.40
507 508 2.293627 CGCCCGATCGATCACGTTC 61.294 63.158 24.40 7.90 40.69 3.95
509 510 4.266070 CCGCCCGATCGATCACGT 62.266 66.667 24.40 0.00 40.69 4.49
512 513 3.790334 CTTGCCGCCCGATCGATCA 62.790 63.158 24.40 1.30 0.00 2.92
517 518 3.170490 ATCTCCTTGCCGCCCGATC 62.170 63.158 0.00 0.00 0.00 3.69
518 519 3.164269 ATCTCCTTGCCGCCCGAT 61.164 61.111 0.00 0.00 0.00 4.18
521 522 4.918201 CGGATCTCCTTGCCGCCC 62.918 72.222 0.00 0.00 38.46 6.13
527 528 2.622903 TTACGCGGCGGATCTCCTTG 62.623 60.000 27.37 0.00 0.00 3.61
530 531 2.354773 CTTACGCGGCGGATCTCC 60.355 66.667 27.37 0.00 0.00 3.71
531 532 1.657794 GACTTACGCGGCGGATCTC 60.658 63.158 27.37 11.59 0.00 2.75
532 533 2.412112 GACTTACGCGGCGGATCT 59.588 61.111 27.37 7.96 0.00 2.75
533 534 3.022914 CGACTTACGCGGCGGATC 61.023 66.667 27.37 12.76 34.51 3.36
561 562 1.373497 GGAGATGGCAGGCGATACG 60.373 63.158 0.00 0.00 0.00 3.06
562 563 1.004440 GGGAGATGGCAGGCGATAC 60.004 63.158 0.00 0.00 0.00 2.24
563 564 1.053835 TTGGGAGATGGCAGGCGATA 61.054 55.000 0.00 0.00 0.00 2.92
565 566 1.925285 ATTTGGGAGATGGCAGGCGA 61.925 55.000 0.00 0.00 0.00 5.54
566 567 1.454479 ATTTGGGAGATGGCAGGCG 60.454 57.895 0.00 0.00 0.00 5.52
567 568 2.024590 GCATTTGGGAGATGGCAGGC 62.025 60.000 0.00 0.00 0.00 4.85
568 569 1.397390 GGCATTTGGGAGATGGCAGG 61.397 60.000 5.87 0.00 46.06 4.85
569 570 2.121645 GGCATTTGGGAGATGGCAG 58.878 57.895 5.87 0.00 46.06 4.85
570 571 4.360643 GGCATTTGGGAGATGGCA 57.639 55.556 5.87 0.00 46.06 4.92
571 572 0.396139 TCAGGCATTTGGGAGATGGC 60.396 55.000 2.81 2.81 46.86 4.40
572 573 1.213678 TCTCAGGCATTTGGGAGATGG 59.786 52.381 0.00 0.00 31.82 3.51
573 574 2.723322 TCTCAGGCATTTGGGAGATG 57.277 50.000 0.00 0.00 31.82 2.90
574 575 2.107901 GGATCTCAGGCATTTGGGAGAT 59.892 50.000 0.00 0.00 46.69 2.75
575 576 1.492176 GGATCTCAGGCATTTGGGAGA 59.508 52.381 0.00 0.00 40.37 3.71
576 577 1.813092 CGGATCTCAGGCATTTGGGAG 60.813 57.143 0.00 0.00 29.52 4.30
577 578 0.181114 CGGATCTCAGGCATTTGGGA 59.819 55.000 0.00 0.00 30.84 4.37
578 579 1.450531 GCGGATCTCAGGCATTTGGG 61.451 60.000 0.00 0.00 0.00 4.12
579 580 1.779025 CGCGGATCTCAGGCATTTGG 61.779 60.000 0.00 0.00 0.00 3.28
580 581 0.811219 TCGCGGATCTCAGGCATTTG 60.811 55.000 6.13 0.00 0.00 2.32
581 582 0.531532 CTCGCGGATCTCAGGCATTT 60.532 55.000 6.13 0.00 0.00 2.32
583 584 2.733301 CTCGCGGATCTCAGGCAT 59.267 61.111 6.13 0.00 0.00 4.40
584 585 3.531207 CCTCGCGGATCTCAGGCA 61.531 66.667 6.13 0.00 0.00 4.75
597 598 1.133664 CTCTATAGCTCGCGCCTCG 59.866 63.158 0.00 0.00 36.60 4.63
598 599 1.504446 CCTCTATAGCTCGCGCCTC 59.496 63.158 0.00 0.00 36.60 4.70
599 600 1.974343 CCCTCTATAGCTCGCGCCT 60.974 63.158 0.00 2.26 36.60 5.52
600 601 1.928706 CTCCCTCTATAGCTCGCGCC 61.929 65.000 0.00 0.00 36.60 6.53
601 602 1.504446 CTCCCTCTATAGCTCGCGC 59.496 63.158 0.00 0.00 0.00 6.86
603 604 0.038455 TCCCTCCCTCTATAGCTCGC 59.962 60.000 0.00 0.00 0.00 5.03
604 605 1.828979 GTCCCTCCCTCTATAGCTCG 58.171 60.000 0.00 0.00 0.00 5.03
607 608 0.404812 TCCGTCCCTCCCTCTATAGC 59.595 60.000 0.00 0.00 0.00 2.97
612 613 2.617538 TCCTCCGTCCCTCCCTCT 60.618 66.667 0.00 0.00 0.00 3.69
613 614 2.123640 CTCCTCCGTCCCTCCCTC 60.124 72.222 0.00 0.00 0.00 4.30
615 616 3.752167 TCCTCCTCCGTCCCTCCC 61.752 72.222 0.00 0.00 0.00 4.30
616 617 2.442458 GTCCTCCTCCGTCCCTCC 60.442 72.222 0.00 0.00 0.00 4.30
617 618 1.755008 CTGTCCTCCTCCGTCCCTC 60.755 68.421 0.00 0.00 0.00 4.30
618 619 1.801302 TTCTGTCCTCCTCCGTCCCT 61.801 60.000 0.00 0.00 0.00 4.20
619 620 0.688087 ATTCTGTCCTCCTCCGTCCC 60.688 60.000 0.00 0.00 0.00 4.46
620 621 0.461961 CATTCTGTCCTCCTCCGTCC 59.538 60.000 0.00 0.00 0.00 4.79
621 622 0.461961 CCATTCTGTCCTCCTCCGTC 59.538 60.000 0.00 0.00 0.00 4.79
622 623 0.041238 TCCATTCTGTCCTCCTCCGT 59.959 55.000 0.00 0.00 0.00 4.69
623 624 0.461961 GTCCATTCTGTCCTCCTCCG 59.538 60.000 0.00 0.00 0.00 4.63
624 625 0.833949 GGTCCATTCTGTCCTCCTCC 59.166 60.000 0.00 0.00 0.00 4.30
625 626 0.461961 CGGTCCATTCTGTCCTCCTC 59.538 60.000 0.00 0.00 0.00 3.71
626 627 0.041238 TCGGTCCATTCTGTCCTCCT 59.959 55.000 0.00 0.00 0.00 3.69
627 628 0.902531 TTCGGTCCATTCTGTCCTCC 59.097 55.000 0.00 0.00 0.00 4.30
628 629 1.134670 CCTTCGGTCCATTCTGTCCTC 60.135 57.143 0.00 0.00 0.00 3.71
629 630 0.905357 CCTTCGGTCCATTCTGTCCT 59.095 55.000 0.00 0.00 0.00 3.85
630 631 0.902531 TCCTTCGGTCCATTCTGTCC 59.097 55.000 0.00 0.00 0.00 4.02
631 632 1.740718 GCTCCTTCGGTCCATTCTGTC 60.741 57.143 0.00 0.00 0.00 3.51
633 634 0.250234 TGCTCCTTCGGTCCATTCTG 59.750 55.000 0.00 0.00 0.00 3.02
634 635 0.250513 GTGCTCCTTCGGTCCATTCT 59.749 55.000 0.00 0.00 0.00 2.40
635 636 1.084370 CGTGCTCCTTCGGTCCATTC 61.084 60.000 0.00 0.00 0.00 2.67
636 637 1.079127 CGTGCTCCTTCGGTCCATT 60.079 57.895 0.00 0.00 0.00 3.16
637 638 1.982395 TCGTGCTCCTTCGGTCCAT 60.982 57.895 0.00 0.00 0.00 3.41
638 639 2.599281 TCGTGCTCCTTCGGTCCA 60.599 61.111 0.00 0.00 0.00 4.02
639 640 2.126031 GTCGTGCTCCTTCGGTCC 60.126 66.667 0.00 0.00 0.00 4.46
640 641 2.504244 CGTCGTGCTCCTTCGGTC 60.504 66.667 0.00 0.00 0.00 4.79
641 642 2.979197 CTCGTCGTGCTCCTTCGGT 61.979 63.158 0.00 0.00 0.00 4.69
642 643 2.202492 CTCGTCGTGCTCCTTCGG 60.202 66.667 0.00 0.00 0.00 4.30
644 645 0.456995 CTTCCTCGTCGTGCTCCTTC 60.457 60.000 0.00 0.00 0.00 3.46
646 647 2.344203 CCTTCCTCGTCGTGCTCCT 61.344 63.158 0.00 0.00 0.00 3.69
647 648 2.182030 CCTTCCTCGTCGTGCTCC 59.818 66.667 0.00 0.00 0.00 4.70
650 651 1.444553 CTGACCTTCCTCGTCGTGC 60.445 63.158 0.00 0.00 32.68 5.34
651 652 0.314302 AACTGACCTTCCTCGTCGTG 59.686 55.000 0.00 0.00 32.68 4.35
653 654 2.150397 AAAACTGACCTTCCTCGTCG 57.850 50.000 0.00 0.00 32.68 5.12
654 655 4.995487 ACATAAAAACTGACCTTCCTCGTC 59.005 41.667 0.00 0.00 0.00 4.20
655 656 4.969484 ACATAAAAACTGACCTTCCTCGT 58.031 39.130 0.00 0.00 0.00 4.18
656 657 5.581085 CCTACATAAAAACTGACCTTCCTCG 59.419 44.000 0.00 0.00 0.00 4.63
657 658 6.708285 TCCTACATAAAAACTGACCTTCCTC 58.292 40.000 0.00 0.00 0.00 3.71
658 659 6.500751 TCTCCTACATAAAAACTGACCTTCCT 59.499 38.462 0.00 0.00 0.00 3.36
659 660 6.708285 TCTCCTACATAAAAACTGACCTTCC 58.292 40.000 0.00 0.00 0.00 3.46
660 661 6.314152 GCTCTCCTACATAAAAACTGACCTTC 59.686 42.308 0.00 0.00 0.00 3.46
662 663 5.485708 AGCTCTCCTACATAAAAACTGACCT 59.514 40.000 0.00 0.00 0.00 3.85
663 664 5.735766 AGCTCTCCTACATAAAAACTGACC 58.264 41.667 0.00 0.00 0.00 4.02
664 665 5.813157 GGAGCTCTCCTACATAAAAACTGAC 59.187 44.000 14.64 0.00 46.16 3.51
698 699 7.112779 ACTCTCCTTCTCTCTCAAAACAAAAA 58.887 34.615 0.00 0.00 0.00 1.94
701 702 5.878406 ACTCTCCTTCTCTCTCAAAACAA 57.122 39.130 0.00 0.00 0.00 2.83
703 704 6.647481 GGTAAACTCTCCTTCTCTCTCAAAAC 59.353 42.308 0.00 0.00 0.00 2.43
706 707 5.394738 TGGTAAACTCTCCTTCTCTCTCAA 58.605 41.667 0.00 0.00 0.00 3.02
707 708 4.999310 TGGTAAACTCTCCTTCTCTCTCA 58.001 43.478 0.00 0.00 0.00 3.27
708 709 7.833285 ATATGGTAAACTCTCCTTCTCTCTC 57.167 40.000 0.00 0.00 0.00 3.20
776 2442 2.247358 CATGGGTTAGTTGGTGGCTTT 58.753 47.619 0.00 0.00 0.00 3.51
825 2491 3.273434 TGATTTGACTACTGCAGATGGC 58.727 45.455 23.35 14.96 45.13 4.40
832 2498 1.201921 CCGCGTTGATTTGACTACTGC 60.202 52.381 4.92 0.00 0.00 4.40
834 2500 1.076332 GCCGCGTTGATTTGACTACT 58.924 50.000 4.92 0.00 0.00 2.57
835 2501 0.793861 TGCCGCGTTGATTTGACTAC 59.206 50.000 4.92 0.00 0.00 2.73
837 2503 0.168788 CATGCCGCGTTGATTTGACT 59.831 50.000 4.92 0.00 0.00 3.41
840 2506 1.444042 TGCATGCCGCGTTGATTTG 60.444 52.632 16.68 0.00 46.97 2.32
852 2518 2.870119 TTGGTGGCTTGGTGCATGC 61.870 57.895 11.82 11.82 45.15 4.06
853 2519 1.005867 GTTGGTGGCTTGGTGCATG 60.006 57.895 0.00 0.00 45.15 4.06
854 2520 0.112218 TAGTTGGTGGCTTGGTGCAT 59.888 50.000 0.00 0.00 45.15 3.96
855 2521 0.106469 TTAGTTGGTGGCTTGGTGCA 60.106 50.000 0.00 0.00 45.15 4.57
859 2525 0.539438 TGGCTTAGTTGGTGGCTTGG 60.539 55.000 0.00 0.00 0.00 3.61
875 2548 2.037121 ACCTTGGCTTTTTACACATGGC 59.963 45.455 0.00 0.00 32.99 4.40
884 2557 3.383505 GTCAAGTACCACCTTGGCTTTTT 59.616 43.478 0.00 0.00 42.43 1.94
985 2678 1.497991 TTCGGAAAGCTTGACGACAG 58.502 50.000 20.98 4.17 34.82 3.51
1001 2700 9.567917 CATATGTTTCACACGTAAATCTATTCG 57.432 33.333 0.00 0.00 30.28 3.34
1097 2835 1.599797 GGCACCAGGCTTTACACGT 60.600 57.895 0.00 0.00 44.01 4.49
1168 2920 1.509923 GTGGAGTTCCTACCCGACG 59.490 63.158 0.00 0.00 36.82 5.12
1169 2921 1.611474 GGGTGGAGTTCCTACCCGAC 61.611 65.000 17.42 0.81 42.89 4.79
1176 2928 3.712218 GCTTCTTATAGGGTGGAGTTCCT 59.288 47.826 0.00 0.00 36.82 3.36
1179 2931 2.778270 GGGCTTCTTATAGGGTGGAGTT 59.222 50.000 0.00 0.00 0.00 3.01
1211 2963 1.494721 GGGAGGTTGATGCCTAATGGA 59.505 52.381 0.00 0.00 39.34 3.41
1268 3024 0.316841 GGCGAGGATTGGTTGCAAAA 59.683 50.000 0.00 0.00 0.00 2.44
1338 3094 1.664649 CAGCTGCAAGGACGACGAA 60.665 57.895 0.00 0.00 0.00 3.85
2049 8523 7.176690 ACTGGGTTTGAGATTACCATTTTGTAG 59.823 37.037 0.00 0.00 36.10 2.74
2064 8538 5.535753 AAAGAATTTGGACTGGGTTTGAG 57.464 39.130 0.00 0.00 36.60 3.02
2146 8639 4.803088 CACGATGTTGACATTTTTGGTGTT 59.197 37.500 0.00 0.00 36.57 3.32
2318 8815 1.010419 CATTTTTGGCACGCAGGAGC 61.010 55.000 0.00 0.00 37.42 4.70
2326 8823 5.747951 TTTGTGAAATCCATTTTTGGCAC 57.252 34.783 0.00 0.00 0.00 5.01
2363 8860 6.792250 CGACAATGAACACATCTAGTTTTGTC 59.208 38.462 10.99 10.99 40.19 3.18
2413 8910 7.564793 GCATAGGTCAAAAATTTCCCCTAAAT 58.435 34.615 0.00 0.00 39.56 1.40
2418 8915 3.445805 TCGCATAGGTCAAAAATTTCCCC 59.554 43.478 0.00 0.00 0.00 4.81
2453 8959 4.689612 AGTGTAACATATGGCCTTCGAT 57.310 40.909 3.32 0.00 41.43 3.59
2459 8965 8.996024 AACAAAATTAAGTGTAACATATGGCC 57.004 30.769 7.80 0.00 41.43 5.36
2490 8996 1.863454 GATAGCAGTGCTTCATCGGTG 59.137 52.381 25.23 0.00 40.44 4.94
2491 8997 1.202580 GGATAGCAGTGCTTCATCGGT 60.203 52.381 25.23 0.00 40.44 4.69
2492 8998 1.506493 GGATAGCAGTGCTTCATCGG 58.494 55.000 25.23 0.00 40.44 4.18
2494 9000 1.202580 ACGGGATAGCAGTGCTTCATC 60.203 52.381 25.23 20.04 40.44 2.92
2523 9030 4.089408 AGCAAGTGCCCATGAAAATTTT 57.911 36.364 2.28 2.28 43.38 1.82
2533 9040 4.163268 TCATATTAGTGTAGCAAGTGCCCA 59.837 41.667 0.00 0.00 43.38 5.36
2535 9042 5.584649 TGTTCATATTAGTGTAGCAAGTGCC 59.415 40.000 0.00 0.00 43.38 5.01
2536 9043 6.662414 TGTTCATATTAGTGTAGCAAGTGC 57.338 37.500 0.00 0.00 42.49 4.40
2636 9144 2.565841 CGGATTTTTGGCTCTAGGGAG 58.434 52.381 0.00 0.00 42.18 4.30
2637 9145 1.408266 GCGGATTTTTGGCTCTAGGGA 60.408 52.381 0.00 0.00 0.00 4.20
2638 9146 1.025041 GCGGATTTTTGGCTCTAGGG 58.975 55.000 0.00 0.00 0.00 3.53
2639 9147 0.657840 CGCGGATTTTTGGCTCTAGG 59.342 55.000 0.00 0.00 0.00 3.02
2640 9148 1.369625 ACGCGGATTTTTGGCTCTAG 58.630 50.000 12.47 0.00 0.00 2.43
2641 9149 2.273557 GTACGCGGATTTTTGGCTCTA 58.726 47.619 12.47 0.00 0.00 2.43
2642 9150 1.084289 GTACGCGGATTTTTGGCTCT 58.916 50.000 12.47 0.00 0.00 4.09
2643 9151 0.800012 TGTACGCGGATTTTTGGCTC 59.200 50.000 12.47 0.00 0.00 4.70
2644 9152 1.068816 GTTGTACGCGGATTTTTGGCT 60.069 47.619 12.47 0.00 0.00 4.75
2645 9153 1.333115 GTTGTACGCGGATTTTTGGC 58.667 50.000 12.47 0.00 0.00 4.52
2652 9160 1.873698 AGTGTTTGTTGTACGCGGAT 58.126 45.000 12.47 0.00 0.00 4.18
2657 9165 8.744923 GGGTTTAAATTTAGTGTTTGTTGTACG 58.255 33.333 0.00 0.00 0.00 3.67
2664 9172 7.223777 CCACAGTGGGTTTAAATTTAGTGTTTG 59.776 37.037 12.40 0.00 32.67 2.93
2668 9176 6.642707 TCCACAGTGGGTTTAAATTTAGTG 57.357 37.500 20.14 1.27 38.32 2.74
2684 9192 6.888088 TCAAATTGATCTCAATCATCCACAGT 59.112 34.615 5.92 0.00 45.06 3.55
2687 9195 7.330900 ACTCAAATTGATCTCAATCATCCAC 57.669 36.000 5.92 0.00 45.06 4.02
2716 9224 5.511234 GCAGATTGCCTAAACATGAGATT 57.489 39.130 0.00 0.00 37.42 2.40
2830 9338 3.471806 GGCCTCGAAGGACCCTCC 61.472 72.222 0.00 0.00 37.46 4.30


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

AutoCloner maintained by Alex Coulton.