Multiple sequence alignment - TraesCS1D01G008400

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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 TraesCS1D01G008400 chr1D 100.000 2679 0 0 1 2679 4236872 4234194 0.000000e+00 4948.0
1 TraesCS1D01G008400 chr1D 88.450 1013 91 18 678 1683 5131778 5130785 0.000000e+00 1199.0
2 TraesCS1D01G008400 chr1D 89.740 809 79 4 690 1496 74311 73505 0.000000e+00 1031.0
3 TraesCS1D01G008400 chr1D 89.740 770 77 2 680 1448 3971597 3970829 0.000000e+00 983.0
4 TraesCS1D01G008400 chr1D 93.023 430 30 0 3 432 5132196 5131767 1.750000e-176 628.0
5 TraesCS1D01G008400 chr1D 87.879 429 52 0 1 429 74744 74316 3.080000e-139 505.0
6 TraesCS1D01G008400 chr1D 97.414 232 5 1 440 671 481719652 481719422 6.950000e-106 394.0
7 TraesCS1D01G008400 chr1D 82.667 150 20 4 2361 2510 4442353 4442210 7.780000e-26 128.0
8 TraesCS1D01G008400 chr1D 100.000 28 0 0 2229 2256 3237331 3237358 5.000000e-03 52.8
9 TraesCS1D01G008400 chr1B 86.597 1634 137 32 680 2307 5989455 5991012 0.000000e+00 1729.0
10 TraesCS1D01G008400 chr1B 84.018 1802 221 32 680 2462 22151038 22149285 0.000000e+00 1670.0
11 TraesCS1D01G008400 chr1B 87.758 825 93 6 678 1496 6484290 6483468 0.000000e+00 957.0
12 TraesCS1D01G008400 chr1B 87.666 827 93 8 678 1496 5698377 5699202 0.000000e+00 953.0
13 TraesCS1D01G008400 chr1B 84.040 990 120 18 690 1673 5757586 5758543 0.000000e+00 918.0
14 TraesCS1D01G008400 chr1B 91.190 420 35 2 5 423 5697961 5698379 1.080000e-158 569.0
15 TraesCS1D01G008400 chr1B 89.252 428 46 0 3 430 6484708 6484281 1.090000e-148 536.0
16 TraesCS1D01G008400 chr1B 87.674 430 52 1 1 429 5989032 5989461 1.430000e-137 499.0
17 TraesCS1D01G008400 chr1B 89.258 391 27 11 2272 2653 5991046 5991430 2.410000e-130 475.0
18 TraesCS1D01G008400 chr1B 91.241 137 12 0 1562 1698 22666360 22666224 1.270000e-43 187.0
19 TraesCS1D01G008400 chr1A 88.507 1018 86 18 678 1683 4501216 4502214 0.000000e+00 1203.0
20 TraesCS1D01G008400 chr1A 87.549 1020 97 17 691 1699 6337789 6336789 0.000000e+00 1153.0
21 TraesCS1D01G008400 chr1A 91.745 424 35 0 1 424 4500796 4501219 8.260000e-165 590.0
22 TraesCS1D01G008400 chr1A 89.569 441 45 1 3 442 6338221 6337781 2.330000e-155 558.0
23 TraesCS1D01G008400 chr1A 90.261 421 41 0 3 423 5502955 5502535 3.900000e-153 551.0
24 TraesCS1D01G008400 chr1A 89.352 432 46 0 1 432 4505007 4505438 6.520000e-151 544.0
25 TraesCS1D01G008400 chr1A 82.911 474 55 15 2183 2649 4258719 4259173 1.160000e-108 403.0
26 TraesCS1D01G008400 chr1A 90.566 159 9 2 1531 1683 5500521 5500363 3.500000e-49 206.0
27 TraesCS1D01G008400 chr1A 90.566 159 9 2 1531 1683 5501999 5501841 3.500000e-49 206.0
28 TraesCS1D01G008400 chr1A 93.827 81 5 0 1632 1712 4258635 4258715 3.620000e-24 122.0
29 TraesCS1D01G008400 chr3D 98.326 239 3 1 433 671 309917018 309916781 4.120000e-113 418.0
30 TraesCS1D01G008400 chr7D 96.443 253 5 3 431 680 45551415 45551666 5.340000e-112 414.0
31 TraesCS1D01G008400 chr7D 97.490 239 4 2 433 671 579141385 579141149 8.930000e-110 407.0
32 TraesCS1D01G008400 chr5D 96.016 251 4 4 433 680 494654047 494654294 1.160000e-108 403.0
33 TraesCS1D01G008400 chr5D 96.250 240 8 1 432 671 15346775 15347013 2.500000e-105 392.0
34 TraesCS1D01G008400 chr5D 94.606 241 12 1 431 671 11244345 11244584 3.260000e-99 372.0
35 TraesCS1D01G008400 chr6D 93.574 249 13 3 433 680 24947847 24948093 4.210000e-98 368.0
36 TraesCS1D01G008400 chr2A 93.724 239 14 1 433 671 715297683 715297446 9.120000e-95 357.0


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 TraesCS1D01G008400 chr1D 4234194 4236872 2678 True 4948.0 4948 100.000000 1 2679 1 chr1D.!!$R2 2678
1 TraesCS1D01G008400 chr1D 3970829 3971597 768 True 983.0 983 89.740000 680 1448 1 chr1D.!!$R1 768
2 TraesCS1D01G008400 chr1D 5130785 5132196 1411 True 913.5 1199 90.736500 3 1683 2 chr1D.!!$R6 1680
3 TraesCS1D01G008400 chr1D 73505 74744 1239 True 768.0 1031 88.809500 1 1496 2 chr1D.!!$R5 1495
4 TraesCS1D01G008400 chr1B 22149285 22151038 1753 True 1670.0 1670 84.018000 680 2462 1 chr1B.!!$R1 1782
5 TraesCS1D01G008400 chr1B 5757586 5758543 957 False 918.0 918 84.040000 690 1673 1 chr1B.!!$F1 983
6 TraesCS1D01G008400 chr1B 5989032 5991430 2398 False 901.0 1729 87.843000 1 2653 3 chr1B.!!$F3 2652
7 TraesCS1D01G008400 chr1B 5697961 5699202 1241 False 761.0 953 89.428000 5 1496 2 chr1B.!!$F2 1491
8 TraesCS1D01G008400 chr1B 6483468 6484708 1240 True 746.5 957 88.505000 3 1496 2 chr1B.!!$R3 1493
9 TraesCS1D01G008400 chr1A 6336789 6338221 1432 True 855.5 1153 88.559000 3 1699 2 chr1A.!!$R2 1696
10 TraesCS1D01G008400 chr1A 4500796 4505438 4642 False 779.0 1203 89.868000 1 1683 3 chr1A.!!$F2 1682
11 TraesCS1D01G008400 chr1A 5500363 5502955 2592 True 321.0 551 90.464333 3 1683 3 chr1A.!!$R1 1680
12 TraesCS1D01G008400 chr1A 4258635 4259173 538 False 262.5 403 88.369000 1632 2649 2 chr1A.!!$F1 1017

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
467 468 0.029433 GGGAGAAATGATTTCGCGGC 59.971 55.0 13.97 3.19 44.29 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2220 3600 0.472471 TCACCTCACCACCAAACCTC 59.528 55.0 0.0 0.0 0.0 3.85 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
138 139 2.555325 TGCTGCAACTCATTCTTTGGAG 59.445 45.455 0.00 0.00 42.38 3.86
181 182 7.007723 TGGGACTATTTTGTACACCTTGAAAT 58.992 34.615 0.00 1.21 0.00 2.17
182 183 7.507616 TGGGACTATTTTGTACACCTTGAAATT 59.492 33.333 7.56 0.00 0.00 1.82
230 231 2.024176 TCCACTGGCCAGAGAAAGTA 57.976 50.000 39.19 13.44 0.00 2.24
234 235 2.932614 CACTGGCCAGAGAAAGTATTCG 59.067 50.000 39.19 9.14 40.63 3.34
253 254 2.154462 CGAAAGCTTGGTGTCCTTGAT 58.846 47.619 0.00 0.00 0.00 2.57
304 305 2.874086 TGATTGGATATGCACAAGCTCG 59.126 45.455 0.00 0.00 42.74 5.03
345 346 1.949799 AAGGAGTCAGCACCTGAGAT 58.050 50.000 0.00 0.00 41.46 2.75
426 427 5.163581 CCGGCATCTCTCAAGAAAATGAATT 60.164 40.000 0.00 0.00 34.49 2.17
427 428 6.327934 CGGCATCTCTCAAGAAAATGAATTT 58.672 36.000 6.34 0.00 34.49 1.82
428 429 6.810182 CGGCATCTCTCAAGAAAATGAATTTT 59.190 34.615 0.68 0.68 42.24 1.82
429 430 7.201410 CGGCATCTCTCAAGAAAATGAATTTTG 60.201 37.037 5.76 0.00 39.86 2.44
430 431 7.816031 GGCATCTCTCAAGAAAATGAATTTTGA 59.184 33.333 5.76 0.00 39.86 2.69
431 432 9.367444 GCATCTCTCAAGAAAATGAATTTTGAT 57.633 29.630 5.76 0.00 39.86 2.57
436 437 9.647797 TCTCAAGAAAATGAATTTTGATCATGG 57.352 29.630 5.76 0.00 39.86 3.66
437 438 9.647797 CTCAAGAAAATGAATTTTGATCATGGA 57.352 29.630 5.76 0.00 39.86 3.41
447 448 9.033481 TGAATTTTGATCATGGATTAAAATCGC 57.967 29.630 16.84 13.65 42.88 4.58
448 449 7.627585 ATTTTGATCATGGATTAAAATCGCG 57.372 32.000 12.96 0.00 41.22 5.87
449 450 4.747540 TGATCATGGATTAAAATCGCGG 57.252 40.909 6.13 0.00 36.27 6.46
450 451 3.501828 TGATCATGGATTAAAATCGCGGG 59.498 43.478 6.13 0.00 36.27 6.13
451 452 3.201353 TCATGGATTAAAATCGCGGGA 57.799 42.857 6.13 4.03 36.27 5.14
452 453 3.138304 TCATGGATTAAAATCGCGGGAG 58.862 45.455 6.13 0.00 36.27 4.30
453 454 2.992124 TGGATTAAAATCGCGGGAGA 57.008 45.000 6.13 0.00 36.27 3.71
454 455 3.269538 TGGATTAAAATCGCGGGAGAA 57.730 42.857 6.13 0.05 36.27 2.87
455 456 3.611970 TGGATTAAAATCGCGGGAGAAA 58.388 40.909 6.13 0.00 36.27 2.52
456 457 4.204012 TGGATTAAAATCGCGGGAGAAAT 58.796 39.130 6.13 4.88 36.27 2.17
457 458 4.036262 TGGATTAAAATCGCGGGAGAAATG 59.964 41.667 6.13 0.00 36.27 2.32
458 459 4.274950 GGATTAAAATCGCGGGAGAAATGA 59.725 41.667 6.13 0.00 36.27 2.57
459 460 5.048713 GGATTAAAATCGCGGGAGAAATGAT 60.049 40.000 6.13 0.00 36.27 2.45
460 461 5.828299 TTAAAATCGCGGGAGAAATGATT 57.172 34.783 6.13 0.00 0.00 2.57
461 462 4.718940 AAAATCGCGGGAGAAATGATTT 57.281 36.364 6.13 0.00 40.05 2.17
462 463 3.971032 AATCGCGGGAGAAATGATTTC 57.029 42.857 9.82 9.82 39.96 2.17
463 464 1.286501 TCGCGGGAGAAATGATTTCG 58.713 50.000 6.13 2.68 44.29 3.46
464 465 0.316196 CGCGGGAGAAATGATTTCGC 60.316 55.000 12.37 12.37 44.29 4.70
465 466 0.316196 GCGGGAGAAATGATTTCGCG 60.316 55.000 13.97 12.28 46.09 5.87
466 467 0.304705 CGGGAGAAATGATTTCGCGG 59.695 55.000 13.97 6.33 44.29 6.46
467 468 0.029433 GGGAGAAATGATTTCGCGGC 59.971 55.000 13.97 3.19 44.29 6.53
468 469 0.316196 GGAGAAATGATTTCGCGGCG 60.316 55.000 17.70 17.70 44.29 6.46
469 470 0.316196 GAGAAATGATTTCGCGGCGG 60.316 55.000 23.46 3.89 44.29 6.13
470 471 1.939299 GAAATGATTTCGCGGCGGC 60.939 57.895 23.46 6.12 0.00 6.53
471 472 3.409959 AAATGATTTCGCGGCGGCC 62.410 57.895 23.46 9.54 35.02 6.13
472 473 4.856801 ATGATTTCGCGGCGGCCT 62.857 61.111 23.46 6.88 35.02 5.19
486 487 3.174265 GCCTCCCCCAGCAGCTAT 61.174 66.667 0.00 0.00 0.00 2.97
487 488 1.843376 GCCTCCCCCAGCAGCTATA 60.843 63.158 0.00 0.00 0.00 1.31
488 489 1.835927 GCCTCCCCCAGCAGCTATAG 61.836 65.000 0.00 0.00 0.00 1.31
489 490 1.676384 CTCCCCCAGCAGCTATAGC 59.324 63.158 17.33 17.33 42.49 2.97
499 500 2.577059 GCTATAGCGGCCGCCATA 59.423 61.111 44.47 37.39 43.17 2.74
500 501 1.519455 GCTATAGCGGCCGCCATAG 60.519 63.158 42.63 42.63 42.74 2.23
501 502 1.519455 CTATAGCGGCCGCCATAGC 60.519 63.158 39.53 19.64 43.17 2.97
512 513 3.566261 CCATAGCGGGCAATAGCG 58.434 61.111 0.00 0.00 43.41 4.26
513 514 2.034879 CCATAGCGGGCAATAGCGG 61.035 63.158 0.00 0.00 43.41 5.52
514 515 2.358737 ATAGCGGGCAATAGCGGC 60.359 61.111 0.00 0.00 43.41 6.53
515 516 3.177194 ATAGCGGGCAATAGCGGCA 62.177 57.895 1.45 0.00 41.56 5.69
516 517 2.674563 ATAGCGGGCAATAGCGGCAA 62.675 55.000 1.45 0.00 41.56 4.52
517 518 2.878089 TAGCGGGCAATAGCGGCAAA 62.878 55.000 1.45 0.00 41.56 3.68
518 519 3.119193 CGGGCAATAGCGGCAAAT 58.881 55.556 1.45 0.00 43.41 2.32
519 520 1.299316 CGGGCAATAGCGGCAAATG 60.299 57.895 1.45 0.00 43.41 2.32
520 521 1.067916 GGGCAATAGCGGCAAATGG 59.932 57.895 1.45 0.00 43.41 3.16
521 522 1.592400 GGCAATAGCGGCAAATGGC 60.592 57.895 1.45 4.41 43.41 4.40
532 533 3.469899 GGCAAATGGCGGAAAATTTTC 57.530 42.857 20.51 20.51 46.16 2.29
533 534 3.073678 GGCAAATGGCGGAAAATTTTCT 58.926 40.909 25.86 7.25 46.16 2.52
534 535 4.249661 GGCAAATGGCGGAAAATTTTCTA 58.750 39.130 25.86 13.23 46.16 2.10
535 536 4.329801 GGCAAATGGCGGAAAATTTTCTAG 59.670 41.667 25.86 20.92 46.16 2.43
536 537 4.929211 GCAAATGGCGGAAAATTTTCTAGT 59.071 37.500 25.86 10.28 37.35 2.57
537 538 5.163963 GCAAATGGCGGAAAATTTTCTAGTG 60.164 40.000 25.86 16.02 37.35 2.74
538 539 4.718940 ATGGCGGAAAATTTTCTAGTGG 57.281 40.909 25.86 13.62 37.35 4.00
539 540 2.823154 TGGCGGAAAATTTTCTAGTGGG 59.177 45.455 25.86 12.24 37.35 4.61
540 541 3.086282 GGCGGAAAATTTTCTAGTGGGA 58.914 45.455 25.86 0.00 37.35 4.37
541 542 3.128764 GGCGGAAAATTTTCTAGTGGGAG 59.871 47.826 25.86 11.25 37.35 4.30
542 543 4.007659 GCGGAAAATTTTCTAGTGGGAGA 58.992 43.478 25.86 0.00 37.35 3.71
543 544 4.095036 GCGGAAAATTTTCTAGTGGGAGAG 59.905 45.833 25.86 9.27 37.35 3.20
544 545 5.488341 CGGAAAATTTTCTAGTGGGAGAGA 58.512 41.667 25.86 0.00 37.35 3.10
545 546 6.116126 CGGAAAATTTTCTAGTGGGAGAGAT 58.884 40.000 25.86 0.00 37.35 2.75
546 547 6.037610 CGGAAAATTTTCTAGTGGGAGAGATG 59.962 42.308 25.86 1.20 37.35 2.90
547 548 7.112779 GGAAAATTTTCTAGTGGGAGAGATGA 58.887 38.462 25.86 0.00 37.35 2.92
548 549 7.777440 GGAAAATTTTCTAGTGGGAGAGATGAT 59.223 37.037 25.86 0.00 37.35 2.45
549 550 9.183368 GAAAATTTTCTAGTGGGAGAGATGATT 57.817 33.333 21.21 0.00 34.41 2.57
550 551 9.539194 AAAATTTTCTAGTGGGAGAGATGATTT 57.461 29.630 0.00 0.00 0.00 2.17
551 552 8.744568 AATTTTCTAGTGGGAGAGATGATTTC 57.255 34.615 0.00 0.00 0.00 2.17
552 553 7.502060 TTTTCTAGTGGGAGAGATGATTTCT 57.498 36.000 0.00 0.00 37.41 2.52
553 554 6.477053 TTCTAGTGGGAGAGATGATTTCTG 57.523 41.667 0.00 0.00 33.74 3.02
554 555 4.898265 TCTAGTGGGAGAGATGATTTCTGG 59.102 45.833 0.00 0.00 33.74 3.86
555 556 3.729108 AGTGGGAGAGATGATTTCTGGA 58.271 45.455 0.00 0.00 33.74 3.86
556 557 3.710677 AGTGGGAGAGATGATTTCTGGAG 59.289 47.826 0.00 0.00 33.74 3.86
557 558 3.044156 TGGGAGAGATGATTTCTGGAGG 58.956 50.000 0.00 0.00 33.74 4.30
558 559 2.371510 GGGAGAGATGATTTCTGGAGGG 59.628 54.545 0.00 0.00 33.74 4.30
559 560 3.044894 GGAGAGATGATTTCTGGAGGGT 58.955 50.000 0.00 0.00 33.74 4.34
560 561 3.457749 GGAGAGATGATTTCTGGAGGGTT 59.542 47.826 0.00 0.00 33.74 4.11
561 562 4.080072 GGAGAGATGATTTCTGGAGGGTTT 60.080 45.833 0.00 0.00 33.74 3.27
562 563 5.504853 GAGAGATGATTTCTGGAGGGTTTT 58.495 41.667 0.00 0.00 33.74 2.43
563 564 5.259632 AGAGATGATTTCTGGAGGGTTTTG 58.740 41.667 0.00 0.00 33.74 2.44
564 565 3.766051 AGATGATTTCTGGAGGGTTTTGC 59.234 43.478 0.00 0.00 31.79 3.68
565 566 2.247358 TGATTTCTGGAGGGTTTTGCC 58.753 47.619 0.00 0.00 0.00 4.52
566 567 1.202348 GATTTCTGGAGGGTTTTGCCG 59.798 52.381 0.00 0.00 38.44 5.69
567 568 0.183971 TTTCTGGAGGGTTTTGCCGA 59.816 50.000 0.00 0.00 38.44 5.54
568 569 0.404040 TTCTGGAGGGTTTTGCCGAT 59.596 50.000 0.00 0.00 38.44 4.18
569 570 0.404040 TCTGGAGGGTTTTGCCGATT 59.596 50.000 0.00 0.00 38.44 3.34
570 571 1.203001 TCTGGAGGGTTTTGCCGATTT 60.203 47.619 0.00 0.00 38.44 2.17
571 572 1.618343 CTGGAGGGTTTTGCCGATTTT 59.382 47.619 0.00 0.00 38.44 1.82
572 573 2.037121 CTGGAGGGTTTTGCCGATTTTT 59.963 45.455 0.00 0.00 38.44 1.94
596 597 8.463930 TTTTAGCCATTTAGAGGGATATGTTG 57.536 34.615 0.00 0.00 26.40 3.33
597 598 5.912149 AGCCATTTAGAGGGATATGTTGA 57.088 39.130 0.00 0.00 0.00 3.18
598 599 5.874093 AGCCATTTAGAGGGATATGTTGAG 58.126 41.667 0.00 0.00 0.00 3.02
599 600 5.006386 GCCATTTAGAGGGATATGTTGAGG 58.994 45.833 0.00 0.00 0.00 3.86
600 601 5.456763 GCCATTTAGAGGGATATGTTGAGGT 60.457 44.000 0.00 0.00 0.00 3.85
601 602 6.605119 CCATTTAGAGGGATATGTTGAGGTT 58.395 40.000 0.00 0.00 0.00 3.50
602 603 7.062957 CCATTTAGAGGGATATGTTGAGGTTT 58.937 38.462 0.00 0.00 0.00 3.27
603 604 7.561356 CCATTTAGAGGGATATGTTGAGGTTTT 59.439 37.037 0.00 0.00 0.00 2.43
604 605 8.624776 CATTTAGAGGGATATGTTGAGGTTTTC 58.375 37.037 0.00 0.00 0.00 2.29
605 606 4.770795 AGAGGGATATGTTGAGGTTTTCG 58.229 43.478 0.00 0.00 0.00 3.46
606 607 3.279434 AGGGATATGTTGAGGTTTTCGC 58.721 45.455 0.00 0.00 0.00 4.70
607 608 2.031683 GGGATATGTTGAGGTTTTCGCG 59.968 50.000 0.00 0.00 0.00 5.87
608 609 2.031683 GGATATGTTGAGGTTTTCGCGG 59.968 50.000 6.13 0.00 0.00 6.46
609 610 0.800012 TATGTTGAGGTTTTCGCGGC 59.200 50.000 6.13 0.00 0.00 6.53
610 611 1.169661 ATGTTGAGGTTTTCGCGGCA 61.170 50.000 6.13 0.00 0.00 5.69
611 612 1.357334 GTTGAGGTTTTCGCGGCAA 59.643 52.632 6.13 0.00 0.00 4.52
612 613 0.039527 GTTGAGGTTTTCGCGGCAAT 60.040 50.000 6.13 0.00 0.00 3.56
613 614 1.198178 GTTGAGGTTTTCGCGGCAATA 59.802 47.619 6.13 0.00 0.00 1.90
614 615 1.083489 TGAGGTTTTCGCGGCAATAG 58.917 50.000 6.13 0.00 0.00 1.73
615 616 0.248094 GAGGTTTTCGCGGCAATAGC 60.248 55.000 6.13 0.00 41.10 2.97
631 632 2.029073 GCCATAGCTTAGCGGCGA 59.971 61.111 12.98 0.00 34.26 5.54
632 633 2.024319 GCCATAGCTTAGCGGCGAG 61.024 63.158 12.98 0.00 34.26 5.03
633 634 1.373497 CCATAGCTTAGCGGCGAGG 60.373 63.158 12.98 0.00 37.29 4.63
634 635 2.024319 CATAGCTTAGCGGCGAGGC 61.024 63.158 12.98 9.10 37.29 4.70
635 636 2.203771 ATAGCTTAGCGGCGAGGCT 61.204 57.895 21.81 21.81 46.88 4.58
636 637 2.148558 ATAGCTTAGCGGCGAGGCTC 62.149 60.000 21.77 3.87 43.54 4.70
638 639 4.593864 CTTAGCGGCGAGGCTCCC 62.594 72.222 12.98 10.25 43.54 4.30
647 648 2.765807 GAGGCTCCCAGGCAGCTA 60.766 66.667 1.24 0.00 44.19 3.32
648 649 2.040043 AGGCTCCCAGGCAGCTAT 60.040 61.111 1.24 0.00 44.19 2.97
649 650 0.833834 GAGGCTCCCAGGCAGCTATA 60.834 60.000 1.24 0.00 44.19 1.31
650 651 0.835543 AGGCTCCCAGGCAGCTATAG 60.836 60.000 1.24 0.00 44.19 1.31
651 652 1.003959 GCTCCCAGGCAGCTATAGC 60.004 63.158 17.33 17.33 42.49 2.97
674 675 4.928661 CAGCTATCGCGGCTATTTTAAT 57.071 40.909 6.13 0.00 42.32 1.40
675 676 4.886971 CAGCTATCGCGGCTATTTTAATC 58.113 43.478 6.13 0.00 42.32 1.75
676 677 4.627467 CAGCTATCGCGGCTATTTTAATCT 59.373 41.667 6.13 0.00 42.32 2.40
677 678 5.805486 CAGCTATCGCGGCTATTTTAATCTA 59.195 40.000 6.13 0.00 42.32 1.98
678 679 6.477033 CAGCTATCGCGGCTATTTTAATCTAT 59.523 38.462 6.13 0.00 42.32 1.98
679 680 6.477033 AGCTATCGCGGCTATTTTAATCTATG 59.523 38.462 6.13 0.00 42.32 2.23
758 759 7.147880 GGCAGAGTTAGTCCAAGTATCTTCTAA 60.148 40.741 0.00 0.00 0.00 2.10
768 769 5.105146 CCAAGTATCTTCTAACAGTGAGGCT 60.105 44.000 0.00 0.00 0.00 4.58
899 900 3.454082 AGTCTGCCTCCATCCTTAAAGAG 59.546 47.826 0.00 0.00 0.00 2.85
904 905 4.165950 TGCCTCCATCCTTAAAGAGCATAA 59.834 41.667 0.00 0.00 0.00 1.90
911 912 9.866655 TCCATCCTTAAAGAGCATAATTATTGT 57.133 29.630 0.00 0.00 0.00 2.71
933 934 1.815003 GGCTGCAGCAGTATTCAAGTT 59.185 47.619 37.63 0.00 44.36 2.66
936 937 3.425892 GCTGCAGCAGTATTCAAGTTCTG 60.426 47.826 33.36 0.00 41.59 3.02
937 938 3.999001 CTGCAGCAGTATTCAAGTTCTGA 59.001 43.478 14.90 0.00 0.00 3.27
1030 1034 0.756442 ACCAGCAGCAACAACACCAT 60.756 50.000 0.00 0.00 0.00 3.55
1175 1179 0.321653 GGGTTGACATCGCTGGAGTT 60.322 55.000 0.00 0.00 0.00 3.01
1195 1199 1.457643 CTATCGGGAGAGCACCCCA 60.458 63.158 8.50 0.00 46.62 4.96
1218 1223 3.185246 TCGCTGGAATTCCTTGATCTC 57.815 47.619 24.73 5.75 36.82 2.75
1294 1299 8.478877 GGTCTCTCTGGTATCTTGAAATTAGAA 58.521 37.037 0.00 0.00 0.00 2.10
1319 1324 2.105649 GCCCTGCTATAAAGAAGCTCCT 59.894 50.000 0.00 0.00 40.73 3.69
1411 1425 3.003480 GCAGCACGTCCTTCTATCTTTT 58.997 45.455 0.00 0.00 0.00 2.27
1437 1451 5.340403 CACATTTAACAAACAGATGCAGTCG 59.660 40.000 0.00 0.00 0.00 4.18
1472 1490 4.523813 CTTGTACCATGTCAACACGTTTC 58.476 43.478 0.00 0.00 0.00 2.78
1490 1508 4.561213 CGTTTCCAAAAGTTTGTTCTCCAC 59.439 41.667 3.26 0.00 36.45 4.02
1505 1523 5.125900 TGTTCTCCACTATTTGAATGCCATG 59.874 40.000 0.00 0.00 0.00 3.66
1506 1524 3.633525 TCTCCACTATTTGAATGCCATGC 59.366 43.478 0.00 0.00 0.00 4.06
1507 1525 3.634504 TCCACTATTTGAATGCCATGCT 58.365 40.909 0.00 0.00 0.00 3.79
1508 1526 4.790937 TCCACTATTTGAATGCCATGCTA 58.209 39.130 0.00 0.00 0.00 3.49
1509 1527 5.199723 TCCACTATTTGAATGCCATGCTAA 58.800 37.500 0.00 0.00 0.00 3.09
1510 1528 5.067674 TCCACTATTTGAATGCCATGCTAAC 59.932 40.000 0.00 0.00 0.00 2.34
1511 1529 5.163530 CCACTATTTGAATGCCATGCTAACA 60.164 40.000 0.00 0.00 0.00 2.41
1512 1530 6.461927 CCACTATTTGAATGCCATGCTAACAT 60.462 38.462 0.00 0.00 36.79 2.71
1522 1540 2.359981 ATGCTAACATGATGCCTGCT 57.640 45.000 0.00 0.00 34.35 4.24
1525 1543 4.622260 TGCTAACATGATGCCTGCTATA 57.378 40.909 0.00 0.00 0.00 1.31
1527 1545 5.375773 TGCTAACATGATGCCTGCTATAAA 58.624 37.500 0.00 0.00 0.00 1.40
1529 1547 5.106396 GCTAACATGATGCCTGCTATAAAGG 60.106 44.000 0.00 0.00 37.91 3.11
1593 1618 1.009078 TCGCTTGTGATATGTGCAGC 58.991 50.000 0.00 0.00 0.00 5.25
1607 1632 2.035704 TGTGCAGCAACGGAATTCAAAT 59.964 40.909 7.93 0.00 0.00 2.32
1634 1659 2.770164 ACCGAAGACATGGAAGGAAG 57.230 50.000 0.00 0.00 0.00 3.46
1647 1672 2.420269 GGAAGGAAGTACCAAGGCTAGC 60.420 54.545 6.04 6.04 42.04 3.42
1730 3083 2.235650 CTCAAGATGTCAGGAAGCTCCA 59.764 50.000 5.21 0.00 39.61 3.86
1803 3156 0.402504 AGGGCGGAAACCACATGTAA 59.597 50.000 0.00 0.00 0.00 2.41
1805 3158 1.068125 GGGCGGAAACCACATGTAAAC 60.068 52.381 0.00 0.00 0.00 2.01
1811 3164 3.305744 GGAAACCACATGTAAACGGCATT 60.306 43.478 0.00 0.00 0.00 3.56
1839 3192 6.616017 TGCATTCTGTTTGCGTCAAATAATA 58.384 32.000 7.98 0.00 43.10 0.98
1846 3199 9.715123 TCTGTTTGCGTCAAATAATATAATGTG 57.285 29.630 7.98 0.00 35.74 3.21
1877 3230 6.767902 AGGTTACTAATGCCATGATTGTAGTG 59.232 38.462 0.00 0.00 0.00 2.74
1897 3251 3.123621 GTGAACCGACTATGCTGAACTTG 59.876 47.826 0.00 0.00 0.00 3.16
1906 3260 5.238583 ACTATGCTGAACTTGGACTTGTAC 58.761 41.667 0.00 0.00 0.00 2.90
1949 3304 8.924511 AATACGGATGAATTATGTTCCTGAAT 57.075 30.769 0.00 0.00 0.00 2.57
1989 3346 2.643933 TGACTCTGAGCATGAAGACG 57.356 50.000 4.19 0.00 0.00 4.18
2006 3363 6.567050 TGAAGACGTACTTGTGGGTTATATC 58.433 40.000 5.20 0.00 39.13 1.63
2012 3369 5.694910 CGTACTTGTGGGTTATATCATGTCC 59.305 44.000 0.00 0.00 0.00 4.02
2013 3370 5.708736 ACTTGTGGGTTATATCATGTCCA 57.291 39.130 0.00 0.00 0.00 4.02
2022 3379 8.102676 TGGGTTATATCATGTCCAATCACTATG 58.897 37.037 0.00 0.00 0.00 2.23
2025 3382 9.710900 GTTATATCATGTCCAATCACTATGTGA 57.289 33.333 2.77 2.77 46.90 3.58
2045 3402 5.357878 TGTGATGTGATTAATTTCAGGAGGC 59.642 40.000 0.00 0.00 0.00 4.70
2049 3406 2.945008 TGATTAATTTCAGGAGGCAGCG 59.055 45.455 0.00 0.00 0.00 5.18
2109 3486 1.774639 CAGCTGGTGTTGATTTGCAC 58.225 50.000 5.57 0.00 35.07 4.57
2110 3487 1.067364 CAGCTGGTGTTGATTTGCACA 59.933 47.619 5.57 0.00 37.35 4.57
2122 3499 3.758023 TGATTTGCACAGTAGATGGTTGG 59.242 43.478 0.00 0.00 0.00 3.77
2220 3600 0.179065 TGGCATTCGCTGGATGAGAG 60.179 55.000 1.61 0.00 38.60 3.20
2272 3655 4.240096 GCTGTTTTTGTCAATGGATGGAG 58.760 43.478 0.00 0.00 0.00 3.86
2307 3691 4.813161 TGAACTGACTTTTGCTTCTCTCTG 59.187 41.667 0.00 0.00 0.00 3.35
2391 3842 3.053619 ACCGCTTCTTCCCAAGGATTATT 60.054 43.478 0.00 0.00 0.00 1.40
2392 3843 4.165372 ACCGCTTCTTCCCAAGGATTATTA 59.835 41.667 0.00 0.00 0.00 0.98
2435 3889 0.326048 AGCCTCCTGTAGCCAGTCAT 60.326 55.000 0.00 0.00 36.95 3.06
2447 3901 1.093159 CCAGTCATTGCTCTGCTTCC 58.907 55.000 0.00 0.00 0.00 3.46
2483 3937 0.468226 TCAAGCCACAAAGTCCGTCT 59.532 50.000 0.00 0.00 0.00 4.18
2512 3966 2.438075 GGAAGCTGCTGCAGGAGG 60.438 66.667 32.87 16.99 42.74 4.30
2541 3997 1.270907 GAGAGCCCCTGTTTCTCTGA 58.729 55.000 0.00 0.00 37.32 3.27
2552 4008 6.295575 CCCCTGTTTCTCTGATATATGTCTCC 60.296 46.154 0.89 0.00 0.00 3.71
2577 4033 9.125906 CCACAATACTAGTTATATTACGACTGC 57.874 37.037 0.00 0.00 0.00 4.40
2590 4686 3.738830 ACGACTGCAACCTGTTAGTTA 57.261 42.857 0.00 0.00 0.00 2.24
2654 4988 2.972713 ACTGAGTGGACCTGAAGCTAAA 59.027 45.455 0.00 0.00 0.00 1.85
2659 4993 2.485814 GTGGACCTGAAGCTAAAAGCAG 59.514 50.000 1.22 0.00 45.56 4.24
2661 4995 2.744741 GGACCTGAAGCTAAAAGCAGTC 59.255 50.000 1.22 0.00 45.56 3.51
2662 4996 3.558109 GGACCTGAAGCTAAAAGCAGTCT 60.558 47.826 1.22 0.00 45.56 3.24
2664 4998 3.071602 ACCTGAAGCTAAAAGCAGTCTCA 59.928 43.478 1.22 0.00 45.56 3.27
2665 4999 4.260170 CCTGAAGCTAAAAGCAGTCTCAT 58.740 43.478 1.22 0.00 45.56 2.90
2671 5005 4.874966 AGCTAAAAGCAGTCTCATAAGCAG 59.125 41.667 1.22 0.00 45.56 4.24
2673 5007 1.649664 AAGCAGTCTCATAAGCAGCG 58.350 50.000 0.00 0.00 0.00 5.18
2674 5008 0.820226 AGCAGTCTCATAAGCAGCGA 59.180 50.000 0.00 0.00 0.00 4.93
2675 5009 1.205655 AGCAGTCTCATAAGCAGCGAA 59.794 47.619 0.00 0.00 0.00 4.70
2676 5010 2.002586 GCAGTCTCATAAGCAGCGAAA 58.997 47.619 0.00 0.00 0.00 3.46
2677 5011 2.030213 GCAGTCTCATAAGCAGCGAAAG 59.970 50.000 0.00 0.00 0.00 2.62
2678 5012 3.515630 CAGTCTCATAAGCAGCGAAAGA 58.484 45.455 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 5.316987 CACAACTGTAAGAGGGGATTTCTT 58.683 41.667 0.00 0.00 38.40 2.52
138 139 2.510238 CGGCTCTAGTGCACCTGC 60.510 66.667 14.63 12.41 42.50 4.85
181 182 7.973388 GCACAGCACATCTATTAATTACCAAAA 59.027 33.333 0.00 0.00 0.00 2.44
182 183 7.339212 AGCACAGCACATCTATTAATTACCAAA 59.661 33.333 0.00 0.00 0.00 3.28
202 203 1.748122 GGCCAGTGGATGAGCACAG 60.748 63.158 15.20 0.00 0.00 3.66
230 231 2.554032 CAAGGACACCAAGCTTTCGAAT 59.446 45.455 0.00 0.00 0.00 3.34
234 235 3.149196 TCATCAAGGACACCAAGCTTTC 58.851 45.455 0.00 0.00 0.00 2.62
253 254 2.483877 CAGTTTGTAATCGCCAAGCTCA 59.516 45.455 0.00 0.00 32.00 4.26
345 346 7.526142 TTTCTAAGCAAAGAGACTCTAGACA 57.474 36.000 5.14 0.00 0.00 3.41
426 427 5.507149 CCCGCGATTTTAATCCATGATCAAA 60.507 40.000 8.23 0.00 31.68 2.69
427 428 4.023279 CCCGCGATTTTAATCCATGATCAA 60.023 41.667 8.23 0.00 31.68 2.57
428 429 3.501828 CCCGCGATTTTAATCCATGATCA 59.498 43.478 8.23 0.00 31.68 2.92
429 430 3.751175 TCCCGCGATTTTAATCCATGATC 59.249 43.478 8.23 0.00 31.68 2.92
430 431 3.750371 TCCCGCGATTTTAATCCATGAT 58.250 40.909 8.23 0.00 31.68 2.45
431 432 3.138304 CTCCCGCGATTTTAATCCATGA 58.862 45.455 8.23 0.00 31.68 3.07
432 433 3.138304 TCTCCCGCGATTTTAATCCATG 58.862 45.455 8.23 0.00 31.68 3.66
433 434 3.485463 TCTCCCGCGATTTTAATCCAT 57.515 42.857 8.23 0.00 31.68 3.41
434 435 2.992124 TCTCCCGCGATTTTAATCCA 57.008 45.000 8.23 0.00 31.68 3.41
435 436 4.274950 TCATTTCTCCCGCGATTTTAATCC 59.725 41.667 8.23 0.00 31.68 3.01
436 437 5.418310 TCATTTCTCCCGCGATTTTAATC 57.582 39.130 8.23 0.00 0.00 1.75
437 438 6.391227 AATCATTTCTCCCGCGATTTTAAT 57.609 33.333 8.23 0.00 0.00 1.40
438 439 5.828299 AATCATTTCTCCCGCGATTTTAA 57.172 34.783 8.23 0.00 0.00 1.52
439 440 5.503357 CGAAATCATTTCTCCCGCGATTTTA 60.503 40.000 8.23 0.00 36.65 1.52
440 441 4.672409 GAAATCATTTCTCCCGCGATTTT 58.328 39.130 8.23 0.00 36.65 1.82
441 442 3.242739 CGAAATCATTTCTCCCGCGATTT 60.243 43.478 8.23 1.37 38.61 2.17
442 443 2.287915 CGAAATCATTTCTCCCGCGATT 59.712 45.455 8.23 0.00 37.52 3.34
443 444 1.867233 CGAAATCATTTCTCCCGCGAT 59.133 47.619 8.23 0.00 37.52 4.58
444 445 1.286501 CGAAATCATTTCTCCCGCGA 58.713 50.000 8.23 0.00 37.52 5.87
445 446 0.316196 GCGAAATCATTTCTCCCGCG 60.316 55.000 8.50 0.00 37.52 6.46
446 447 0.316196 CGCGAAATCATTTCTCCCGC 60.316 55.000 0.00 6.25 37.52 6.13
447 448 0.304705 CCGCGAAATCATTTCTCCCG 59.695 55.000 8.23 7.85 37.52 5.14
448 449 0.029433 GCCGCGAAATCATTTCTCCC 59.971 55.000 8.23 0.00 37.52 4.30
449 450 0.316196 CGCCGCGAAATCATTTCTCC 60.316 55.000 8.23 0.00 37.52 3.71
450 451 0.316196 CCGCCGCGAAATCATTTCTC 60.316 55.000 15.93 0.00 37.52 2.87
451 452 1.721487 CCGCCGCGAAATCATTTCT 59.279 52.632 15.93 0.00 37.52 2.52
452 453 1.939299 GCCGCCGCGAAATCATTTC 60.939 57.895 15.93 0.00 36.32 2.17
453 454 2.102161 GCCGCCGCGAAATCATTT 59.898 55.556 15.93 0.00 0.00 2.32
454 455 3.887868 GGCCGCCGCGAAATCATT 61.888 61.111 15.93 0.00 35.02 2.57
455 456 4.856801 AGGCCGCCGCGAAATCAT 62.857 61.111 15.93 0.00 35.02 2.45
469 470 1.835927 CTATAGCTGCTGGGGGAGGC 61.836 65.000 13.43 0.00 0.00 4.70
470 471 1.835927 GCTATAGCTGCTGGGGGAGG 61.836 65.000 17.75 0.00 38.21 4.30
471 472 1.676384 GCTATAGCTGCTGGGGGAG 59.324 63.158 17.75 3.32 38.21 4.30
472 473 2.210013 CGCTATAGCTGCTGGGGGA 61.210 63.158 21.98 0.00 39.32 4.81
473 474 2.345244 CGCTATAGCTGCTGGGGG 59.655 66.667 21.98 6.70 39.32 5.40
474 475 2.345244 CCGCTATAGCTGCTGGGG 59.655 66.667 21.98 10.99 39.32 4.96
475 476 2.358003 GCCGCTATAGCTGCTGGG 60.358 66.667 27.86 19.26 45.80 4.45
480 481 2.225791 TATGGCGGCCGCTATAGCTG 62.226 60.000 41.59 16.77 42.29 4.24
481 482 1.982395 TATGGCGGCCGCTATAGCT 60.982 57.895 41.59 28.21 42.29 3.32
482 483 2.577059 TATGGCGGCCGCTATAGC 59.423 61.111 41.59 29.45 42.29 2.97
484 485 2.577059 GCTATGGCGGCCGCTATA 59.423 61.111 41.64 41.64 42.29 1.31
495 496 2.034879 CCGCTATTGCCCGCTATGG 61.035 63.158 0.00 0.00 35.36 2.74
496 497 2.680913 GCCGCTATTGCCCGCTATG 61.681 63.158 0.00 0.00 35.36 2.23
497 498 2.358737 GCCGCTATTGCCCGCTAT 60.359 61.111 0.00 0.00 35.36 2.97
498 499 2.878089 TTTGCCGCTATTGCCCGCTA 62.878 55.000 7.24 0.00 33.61 4.26
499 500 4.794648 TTGCCGCTATTGCCCGCT 62.795 61.111 7.24 0.00 33.61 5.52
500 501 3.137637 ATTTGCCGCTATTGCCCGC 62.138 57.895 0.00 0.00 35.36 6.13
501 502 1.299316 CATTTGCCGCTATTGCCCG 60.299 57.895 0.00 0.00 35.36 6.13
502 503 1.067916 CCATTTGCCGCTATTGCCC 59.932 57.895 0.00 0.00 35.36 5.36
503 504 1.592400 GCCATTTGCCGCTATTGCC 60.592 57.895 0.00 0.00 35.36 4.52
504 505 1.945662 CGCCATTTGCCGCTATTGC 60.946 57.895 0.00 0.00 36.24 3.56
505 506 1.299316 CCGCCATTTGCCGCTATTG 60.299 57.895 0.00 0.00 36.24 1.90
506 507 1.034838 TTCCGCCATTTGCCGCTATT 61.035 50.000 0.00 0.00 36.24 1.73
507 508 1.034838 TTTCCGCCATTTGCCGCTAT 61.035 50.000 0.00 0.00 36.24 2.97
508 509 1.244697 TTTTCCGCCATTTGCCGCTA 61.245 50.000 0.00 0.00 36.24 4.26
509 510 1.887344 ATTTTCCGCCATTTGCCGCT 61.887 50.000 0.00 0.00 36.24 5.52
510 511 1.018752 AATTTTCCGCCATTTGCCGC 61.019 50.000 0.00 0.00 36.24 6.53
511 512 1.437625 AAATTTTCCGCCATTTGCCG 58.562 45.000 0.00 0.00 36.24 5.69
512 513 3.073678 AGAAAATTTTCCGCCATTTGCC 58.926 40.909 24.01 0.00 37.92 4.52
513 514 4.929211 ACTAGAAAATTTTCCGCCATTTGC 59.071 37.500 24.01 0.00 37.92 3.68
514 515 5.348451 CCACTAGAAAATTTTCCGCCATTTG 59.652 40.000 24.01 12.88 37.92 2.32
515 516 5.478407 CCACTAGAAAATTTTCCGCCATTT 58.522 37.500 24.01 9.08 37.92 2.32
516 517 4.081697 CCCACTAGAAAATTTTCCGCCATT 60.082 41.667 24.01 9.72 37.92 3.16
517 518 3.447229 CCCACTAGAAAATTTTCCGCCAT 59.553 43.478 24.01 10.37 37.92 4.40
518 519 2.823154 CCCACTAGAAAATTTTCCGCCA 59.177 45.455 24.01 9.00 37.92 5.69
519 520 3.086282 TCCCACTAGAAAATTTTCCGCC 58.914 45.455 24.01 3.51 37.92 6.13
520 521 4.007659 TCTCCCACTAGAAAATTTTCCGC 58.992 43.478 24.01 3.86 37.92 5.54
521 522 5.488341 TCTCTCCCACTAGAAAATTTTCCG 58.512 41.667 24.01 18.21 37.92 4.30
522 523 7.112779 TCATCTCTCCCACTAGAAAATTTTCC 58.887 38.462 24.01 9.23 37.92 3.13
523 524 8.744568 ATCATCTCTCCCACTAGAAAATTTTC 57.255 34.615 21.00 21.00 37.45 2.29
524 525 9.539194 AAATCATCTCTCCCACTAGAAAATTTT 57.461 29.630 2.28 2.28 0.00 1.82
525 526 9.183368 GAAATCATCTCTCCCACTAGAAAATTT 57.817 33.333 0.00 0.00 0.00 1.82
526 527 8.555729 AGAAATCATCTCTCCCACTAGAAAATT 58.444 33.333 0.00 0.00 30.46 1.82
527 528 7.992033 CAGAAATCATCTCTCCCACTAGAAAAT 59.008 37.037 0.00 0.00 35.73 1.82
528 529 7.334090 CAGAAATCATCTCTCCCACTAGAAAA 58.666 38.462 0.00 0.00 35.73 2.29
529 530 6.126940 CCAGAAATCATCTCTCCCACTAGAAA 60.127 42.308 0.00 0.00 35.73 2.52
530 531 5.365025 CCAGAAATCATCTCTCCCACTAGAA 59.635 44.000 0.00 0.00 35.73 2.10
531 532 4.898265 CCAGAAATCATCTCTCCCACTAGA 59.102 45.833 0.00 0.00 35.73 2.43
532 533 4.898265 TCCAGAAATCATCTCTCCCACTAG 59.102 45.833 0.00 0.00 35.73 2.57
533 534 4.883759 TCCAGAAATCATCTCTCCCACTA 58.116 43.478 0.00 0.00 35.73 2.74
534 535 3.710677 CTCCAGAAATCATCTCTCCCACT 59.289 47.826 0.00 0.00 35.73 4.00
535 536 3.181456 CCTCCAGAAATCATCTCTCCCAC 60.181 52.174 0.00 0.00 35.73 4.61
536 537 3.044156 CCTCCAGAAATCATCTCTCCCA 58.956 50.000 0.00 0.00 35.73 4.37
537 538 2.371510 CCCTCCAGAAATCATCTCTCCC 59.628 54.545 0.00 0.00 35.73 4.30
538 539 3.044894 ACCCTCCAGAAATCATCTCTCC 58.955 50.000 0.00 0.00 35.73 3.71
539 540 4.769345 AACCCTCCAGAAATCATCTCTC 57.231 45.455 0.00 0.00 35.73 3.20
540 541 5.259632 CAAAACCCTCCAGAAATCATCTCT 58.740 41.667 0.00 0.00 35.73 3.10
541 542 4.142293 GCAAAACCCTCCAGAAATCATCTC 60.142 45.833 0.00 0.00 35.73 2.75
542 543 3.766051 GCAAAACCCTCCAGAAATCATCT 59.234 43.478 0.00 0.00 39.68 2.90
543 544 3.118992 GGCAAAACCCTCCAGAAATCATC 60.119 47.826 0.00 0.00 0.00 2.92
544 545 2.833943 GGCAAAACCCTCCAGAAATCAT 59.166 45.455 0.00 0.00 0.00 2.45
545 546 2.247358 GGCAAAACCCTCCAGAAATCA 58.753 47.619 0.00 0.00 0.00 2.57
546 547 1.202348 CGGCAAAACCCTCCAGAAATC 59.798 52.381 0.00 0.00 33.26 2.17
547 548 1.203001 TCGGCAAAACCCTCCAGAAAT 60.203 47.619 0.00 0.00 33.26 2.17
548 549 0.183971 TCGGCAAAACCCTCCAGAAA 59.816 50.000 0.00 0.00 33.26 2.52
549 550 0.404040 ATCGGCAAAACCCTCCAGAA 59.596 50.000 0.00 0.00 33.26 3.02
550 551 0.404040 AATCGGCAAAACCCTCCAGA 59.596 50.000 0.00 0.00 33.26 3.86
551 552 1.256812 AAATCGGCAAAACCCTCCAG 58.743 50.000 0.00 0.00 33.26 3.86
552 553 1.710816 AAAATCGGCAAAACCCTCCA 58.289 45.000 0.00 0.00 33.26 3.86
553 554 2.831685 AAAAATCGGCAAAACCCTCC 57.168 45.000 0.00 0.00 33.26 4.30
570 571 8.912988 CAACATATCCCTCTAAATGGCTAAAAA 58.087 33.333 0.00 0.00 0.00 1.94
571 572 8.278639 TCAACATATCCCTCTAAATGGCTAAAA 58.721 33.333 0.00 0.00 0.00 1.52
572 573 7.811282 TCAACATATCCCTCTAAATGGCTAAA 58.189 34.615 0.00 0.00 0.00 1.85
573 574 7.387265 TCAACATATCCCTCTAAATGGCTAA 57.613 36.000 0.00 0.00 0.00 3.09
574 575 6.013379 CCTCAACATATCCCTCTAAATGGCTA 60.013 42.308 0.00 0.00 0.00 3.93
575 576 5.222007 CCTCAACATATCCCTCTAAATGGCT 60.222 44.000 0.00 0.00 0.00 4.75
576 577 5.006386 CCTCAACATATCCCTCTAAATGGC 58.994 45.833 0.00 0.00 0.00 4.40
577 578 6.192970 ACCTCAACATATCCCTCTAAATGG 57.807 41.667 0.00 0.00 0.00 3.16
578 579 8.525290 AAAACCTCAACATATCCCTCTAAATG 57.475 34.615 0.00 0.00 0.00 2.32
579 580 7.499232 CGAAAACCTCAACATATCCCTCTAAAT 59.501 37.037 0.00 0.00 0.00 1.40
580 581 6.821665 CGAAAACCTCAACATATCCCTCTAAA 59.178 38.462 0.00 0.00 0.00 1.85
581 582 6.346096 CGAAAACCTCAACATATCCCTCTAA 58.654 40.000 0.00 0.00 0.00 2.10
582 583 5.684030 GCGAAAACCTCAACATATCCCTCTA 60.684 44.000 0.00 0.00 0.00 2.43
583 584 4.770795 CGAAAACCTCAACATATCCCTCT 58.229 43.478 0.00 0.00 0.00 3.69
584 585 3.312697 GCGAAAACCTCAACATATCCCTC 59.687 47.826 0.00 0.00 0.00 4.30
585 586 3.279434 GCGAAAACCTCAACATATCCCT 58.721 45.455 0.00 0.00 0.00 4.20
586 587 2.031683 CGCGAAAACCTCAACATATCCC 59.968 50.000 0.00 0.00 0.00 3.85
587 588 2.031683 CCGCGAAAACCTCAACATATCC 59.968 50.000 8.23 0.00 0.00 2.59
588 589 2.538939 GCCGCGAAAACCTCAACATATC 60.539 50.000 8.23 0.00 0.00 1.63
589 590 1.400494 GCCGCGAAAACCTCAACATAT 59.600 47.619 8.23 0.00 0.00 1.78
590 591 0.800012 GCCGCGAAAACCTCAACATA 59.200 50.000 8.23 0.00 0.00 2.29
591 592 1.169661 TGCCGCGAAAACCTCAACAT 61.170 50.000 8.23 0.00 0.00 2.71
592 593 1.377366 TTGCCGCGAAAACCTCAACA 61.377 50.000 8.23 0.00 0.00 3.33
593 594 0.039527 ATTGCCGCGAAAACCTCAAC 60.040 50.000 8.23 0.00 0.00 3.18
594 595 1.466950 CTATTGCCGCGAAAACCTCAA 59.533 47.619 8.23 0.08 0.00 3.02
595 596 1.083489 CTATTGCCGCGAAAACCTCA 58.917 50.000 8.23 0.00 0.00 3.86
596 597 0.248094 GCTATTGCCGCGAAAACCTC 60.248 55.000 8.23 0.00 0.00 3.85
597 598 1.800681 GCTATTGCCGCGAAAACCT 59.199 52.632 8.23 0.00 0.00 3.50
598 599 4.377471 GCTATTGCCGCGAAAACC 57.623 55.556 8.23 0.00 0.00 3.27
614 615 2.024319 CTCGCCGCTAAGCTATGGC 61.024 63.158 8.04 8.04 44.09 4.40
615 616 1.373497 CCTCGCCGCTAAGCTATGG 60.373 63.158 0.00 0.00 0.00 2.74
616 617 2.024319 GCCTCGCCGCTAAGCTATG 61.024 63.158 0.00 0.00 0.00 2.23
617 618 2.148558 GAGCCTCGCCGCTAAGCTAT 62.149 60.000 0.00 0.00 39.87 2.97
618 619 2.833582 AGCCTCGCCGCTAAGCTA 60.834 61.111 0.00 0.00 37.32 3.32
619 620 4.214327 GAGCCTCGCCGCTAAGCT 62.214 66.667 0.00 0.00 39.87 3.74
621 622 4.593864 GGGAGCCTCGCCGCTAAG 62.594 72.222 0.00 0.00 39.87 2.18
630 631 0.833834 TATAGCTGCCTGGGAGCCTC 60.834 60.000 32.88 9.74 37.12 4.70
631 632 0.835543 CTATAGCTGCCTGGGAGCCT 60.836 60.000 32.88 23.53 37.12 4.58
632 633 1.676384 CTATAGCTGCCTGGGAGCC 59.324 63.158 32.88 17.30 37.12 4.70
633 634 1.003959 GCTATAGCTGCCTGGGAGC 60.004 63.158 30.25 30.25 38.21 4.70
634 635 1.291588 CGCTATAGCTGCCTGGGAG 59.708 63.158 21.98 11.32 39.32 4.30
635 636 2.872388 GCGCTATAGCTGCCTGGGA 61.872 63.158 21.98 0.00 39.32 4.37
636 637 2.358003 GCGCTATAGCTGCCTGGG 60.358 66.667 21.98 6.20 39.32 4.45
637 638 1.667191 CTGCGCTATAGCTGCCTGG 60.667 63.158 27.09 17.92 38.89 4.45
638 639 3.948380 CTGCGCTATAGCTGCCTG 58.052 61.111 27.09 19.67 38.89 4.85
656 657 7.987268 TCATAGATTAAAATAGCCGCGATAG 57.013 36.000 8.23 0.00 0.00 2.08
657 658 8.942338 AATCATAGATTAAAATAGCCGCGATA 57.058 30.769 8.23 0.00 0.00 2.92
658 659 7.849804 AATCATAGATTAAAATAGCCGCGAT 57.150 32.000 8.23 0.00 0.00 4.58
659 660 7.667043 AAATCATAGATTAAAATAGCCGCGA 57.333 32.000 8.23 0.00 0.00 5.87
660 661 8.015087 TCAAAATCATAGATTAAAATAGCCGCG 58.985 33.333 0.00 0.00 0.00 6.46
661 662 9.846248 ATCAAAATCATAGATTAAAATAGCCGC 57.154 29.630 0.00 0.00 0.00 6.53
674 675 8.786898 GCTTAATGCACCTATCAAAATCATAGA 58.213 33.333 0.00 0.00 42.31 1.98
675 676 8.790718 AGCTTAATGCACCTATCAAAATCATAG 58.209 33.333 0.00 0.00 45.94 2.23
676 677 8.696043 AGCTTAATGCACCTATCAAAATCATA 57.304 30.769 0.00 0.00 45.94 2.15
677 678 7.592885 AGCTTAATGCACCTATCAAAATCAT 57.407 32.000 0.00 0.00 45.94 2.45
678 679 7.122501 TCAAGCTTAATGCACCTATCAAAATCA 59.877 33.333 0.00 0.00 45.94 2.57
679 680 7.433425 GTCAAGCTTAATGCACCTATCAAAATC 59.567 37.037 0.00 0.00 45.94 2.17
768 769 1.613925 GATACAGCTGGAGGCACGATA 59.386 52.381 19.93 0.00 44.79 2.92
778 779 1.065926 TGGCAACTCTGATACAGCTGG 60.066 52.381 19.93 0.00 37.61 4.85
899 900 4.022935 TGCTGCAGCCTACAATAATTATGC 60.023 41.667 34.64 5.94 41.18 3.14
904 905 3.287867 ACTGCTGCAGCCTACAATAAT 57.712 42.857 34.64 1.57 41.18 1.28
911 912 2.237143 ACTTGAATACTGCTGCAGCCTA 59.763 45.455 34.64 23.43 41.18 3.93
912 913 1.004044 ACTTGAATACTGCTGCAGCCT 59.996 47.619 34.64 22.04 41.18 4.58
936 937 1.377725 CCCACCCAGCTGACATGTC 60.378 63.158 19.27 19.27 0.00 3.06
937 938 2.759114 CCCACCCAGCTGACATGT 59.241 61.111 17.39 0.00 0.00 3.21
1030 1034 4.019860 AGGAAGTAAATGCTCTCTTGCAGA 60.020 41.667 0.00 0.00 46.71 4.26
1132 1136 2.095314 TGTTGCCAATAATGCACAGTCG 60.095 45.455 0.00 0.00 38.72 4.18
1175 1179 2.822215 GGGTGCTCTCCCGATAGAA 58.178 57.895 0.00 0.00 37.93 2.10
1195 1199 2.787473 TCAAGGAATTCCAGCGATGT 57.213 45.000 26.22 0.39 38.89 3.06
1218 1223 1.156736 CCAGGGTACTGCAGTTTTCG 58.843 55.000 27.06 10.12 43.53 3.46
1294 1299 3.393941 AGCTTCTTTATAGCAGGGCAGAT 59.606 43.478 0.00 0.00 41.11 2.90
1295 1300 2.774234 AGCTTCTTTATAGCAGGGCAGA 59.226 45.455 0.00 0.00 41.11 4.26
1356 1370 2.301577 AGCAGGCATCTAGTCGTTTC 57.698 50.000 0.00 0.00 0.00 2.78
1411 1425 5.301551 ACTGCATCTGTTTGTTAAATGTGGA 59.698 36.000 0.00 0.00 0.00 4.02
1437 1451 2.241176 TGGTACAAGGGATGGAATGGAC 59.759 50.000 0.00 0.00 31.92 4.02
1472 1490 7.488322 TCAAATAGTGGAGAACAAACTTTTGG 58.512 34.615 6.65 0.00 42.34 3.28
1505 1523 5.106396 CCTTTATAGCAGGCATCATGTTAGC 60.106 44.000 0.00 0.00 0.00 3.09
1506 1524 6.000219 ACCTTTATAGCAGGCATCATGTTAG 59.000 40.000 0.00 0.00 34.32 2.34
1507 1525 5.940617 ACCTTTATAGCAGGCATCATGTTA 58.059 37.500 0.00 0.00 34.32 2.41
1508 1526 4.796606 ACCTTTATAGCAGGCATCATGTT 58.203 39.130 0.00 0.00 34.32 2.71
1509 1527 4.443978 ACCTTTATAGCAGGCATCATGT 57.556 40.909 0.00 0.00 34.32 3.21
1510 1528 7.105588 TGTATACCTTTATAGCAGGCATCATG 58.894 38.462 0.00 0.00 34.32 3.07
1511 1529 7.257790 TGTATACCTTTATAGCAGGCATCAT 57.742 36.000 0.00 0.00 34.32 2.45
1512 1530 6.680148 TGTATACCTTTATAGCAGGCATCA 57.320 37.500 0.00 0.00 34.32 3.07
1513 1531 9.838339 ATAATGTATACCTTTATAGCAGGCATC 57.162 33.333 0.00 0.00 34.32 3.91
1514 1532 9.618890 CATAATGTATACCTTTATAGCAGGCAT 57.381 33.333 0.00 0.00 34.32 4.40
1515 1533 8.821817 TCATAATGTATACCTTTATAGCAGGCA 58.178 33.333 0.00 0.00 34.32 4.75
1516 1534 9.838339 ATCATAATGTATACCTTTATAGCAGGC 57.162 33.333 0.00 0.00 34.32 4.85
1593 1618 7.327275 TCGGTTTAAATGATTTGAATTCCGTTG 59.673 33.333 17.60 0.00 32.94 4.10
1607 1632 5.414454 CCTTCCATGTCTTCGGTTTAAATGA 59.586 40.000 0.00 0.00 0.00 2.57
1634 1659 1.153429 CACGGGCTAGCCTTGGTAC 60.153 63.158 32.18 14.16 36.10 3.34
1701 1732 4.507710 TCCTGACATCTTGAGATTTTCCG 58.492 43.478 0.00 0.00 31.21 4.30
1730 3083 7.129457 TGATATTCTCCTATTGTGAACAGCT 57.871 36.000 0.00 0.00 29.86 4.24
1733 3086 7.774625 TGCAATGATATTCTCCTATTGTGAACA 59.225 33.333 0.00 0.00 32.75 3.18
1775 3128 1.192428 GTTTCCGCCCTCTTCTCCTA 58.808 55.000 0.00 0.00 0.00 2.94
1811 3164 5.809719 TTGACGCAAACAGAATGCATATA 57.190 34.783 0.00 0.00 44.01 0.86
1839 3192 6.710744 GCATTAGTAACCTAGTGGCACATTAT 59.289 38.462 21.41 0.74 44.52 1.28
1860 3213 3.378112 CGGTTCACTACAATCATGGCATT 59.622 43.478 0.00 0.00 0.00 3.56
1877 3230 2.673368 CCAAGTTCAGCATAGTCGGTTC 59.327 50.000 0.00 0.00 0.00 3.62
1897 3251 6.963049 AATATCAGAACAACGTACAAGTCC 57.037 37.500 0.00 0.00 0.00 3.85
1906 3260 8.122306 TCCGTATTACAAATATCAGAACAACG 57.878 34.615 0.00 0.00 0.00 4.10
1927 3281 8.378565 AGATATTCAGGAACATAATTCATCCGT 58.621 33.333 0.00 0.00 37.05 4.69
1928 3282 8.783833 AGATATTCAGGAACATAATTCATCCG 57.216 34.615 0.00 0.00 37.05 4.18
1972 3327 3.085533 AGTACGTCTTCATGCTCAGAGT 58.914 45.455 0.00 0.00 0.00 3.24
1973 3328 3.773860 AGTACGTCTTCATGCTCAGAG 57.226 47.619 0.00 0.00 0.00 3.35
1975 3330 3.366121 CACAAGTACGTCTTCATGCTCAG 59.634 47.826 0.00 0.00 33.63 3.35
1986 3341 6.278363 ACATGATATAACCCACAAGTACGTC 58.722 40.000 0.00 0.00 0.00 4.34
1989 3346 6.588204 TGGACATGATATAACCCACAAGTAC 58.412 40.000 0.00 0.00 0.00 2.73
2022 3379 5.357878 TGCCTCCTGAAATTAATCACATCAC 59.642 40.000 0.00 0.00 0.00 3.06
2025 3382 4.340381 GCTGCCTCCTGAAATTAATCACAT 59.660 41.667 0.00 0.00 0.00 3.21
2026 3383 3.696051 GCTGCCTCCTGAAATTAATCACA 59.304 43.478 0.00 0.00 0.00 3.58
2045 3402 3.724277 GCAATTTTACAATGTTGCGCTG 58.276 40.909 9.73 0.00 37.76 5.18
2049 3406 4.143052 GCAGGAGCAATTTTACAATGTTGC 60.143 41.667 0.00 0.00 45.37 4.17
2109 3486 8.801882 TCTTTTTATTACCCAACCATCTACTG 57.198 34.615 0.00 0.00 0.00 2.74
2110 3487 9.816787 TTTCTTTTTATTACCCAACCATCTACT 57.183 29.630 0.00 0.00 0.00 2.57
2145 3522 1.197264 GCAGCAGAGCAAACAGAGAAG 59.803 52.381 0.00 0.00 0.00 2.85
2176 3556 2.174424 AGGATTTCCTTCTGGGCATCTC 59.826 50.000 0.00 0.00 46.09 2.75
2220 3600 0.472471 TCACCTCACCACCAAACCTC 59.528 55.000 0.00 0.00 0.00 3.85
2272 3655 7.897800 GCAAAAGTCAGTTCAAAACAACAATAC 59.102 33.333 0.00 0.00 0.00 1.89
2307 3691 1.098050 CTTCCACTGCTGCATTACCC 58.902 55.000 1.31 0.00 0.00 3.69
2392 3843 7.809806 GCTGCAGAGATAACAAACACTAAAAAT 59.190 33.333 20.43 0.00 0.00 1.82
2435 3889 3.018856 CAATACCATGGAAGCAGAGCAA 58.981 45.455 21.47 0.00 0.00 3.91
2447 3901 5.104374 GGCTTGATGACAAACAATACCATG 58.896 41.667 10.32 0.00 35.49 3.66
2483 3937 4.373116 GCTTCCCACGGCGACAGA 62.373 66.667 16.62 3.29 0.00 3.41
2519 3973 1.229209 AGAAACAGGGGCTCTCGGA 60.229 57.895 0.00 0.00 0.00 4.55
2552 4008 9.673454 TGCAGTCGTAATATAACTAGTATTGTG 57.327 33.333 0.00 0.00 0.00 3.33
2561 4017 5.974108 ACAGGTTGCAGTCGTAATATAACT 58.026 37.500 0.00 0.00 0.00 2.24
2566 4022 5.395682 ACTAACAGGTTGCAGTCGTAATA 57.604 39.130 0.00 0.00 0.00 0.98
2571 4027 3.650139 ACTAACTAACAGGTTGCAGTCG 58.350 45.455 0.00 0.00 0.00 4.18
2577 4033 6.756221 AGTAGGTGAACTAACTAACAGGTTG 58.244 40.000 0.00 0.00 32.37 3.77
2654 4988 1.205655 TCGCTGCTTATGAGACTGCTT 59.794 47.619 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.