Multiple sequence alignment - TraesCS1A01G343000

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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 TraesCS1A01G343000 chr1A 100.000 7063 0 0 1 7063 531716134 531723196 0.000000e+00 13044
1 TraesCS1A01G343000 chr1B 92.562 5028 241 60 722 5687 585325876 585330832 0.000000e+00 7090
2 TraesCS1A01G343000 chr1B 87.317 1364 116 37 5724 7046 585330986 585332333 0.000000e+00 1507
3 TraesCS1A01G343000 chr1D 93.647 4691 186 57 2431 7046 433365185 433369838 0.000000e+00 6909
4 TraesCS1A01G343000 chr1D 90.390 1873 112 39 575 2433 433363323 433365141 0.000000e+00 2399
5 TraesCS1A01G343000 chr1D 81.947 493 77 9 12 498 42128531 42128045 2.370000e-109 407
6 TraesCS1A01G343000 chr5A 86.136 3628 406 66 2653 6225 691440052 691436467 0.000000e+00 3823
7 TraesCS1A01G343000 chr5A 81.161 844 133 20 1240 2074 691441363 691440537 0.000000e+00 654
8 TraesCS1A01G343000 chr5A 78.161 348 64 9 1711 2054 382776138 382775799 2.000000e-50 211
9 TraesCS1A01G343000 chr5A 78.723 282 56 4 5767 6046 396502711 396502990 1.210000e-42 185
10 TraesCS1A01G343000 chr5A 98.571 70 1 0 1021 1090 691441616 691441547 2.680000e-24 124
11 TraesCS1A01G343000 chrUn 86.427 3529 385 67 2653 6123 126753063 126756555 0.000000e+00 3777
12 TraesCS1A01G343000 chrUn 81.371 875 123 28 1210 2071 126751720 126752567 0.000000e+00 676
13 TraesCS1A01G343000 chrUn 98.571 70 1 0 1021 1090 126751499 126751568 2.680000e-24 124
14 TraesCS1A01G343000 chr4B 84.657 3904 455 95 2435 6250 653144800 653148647 0.000000e+00 3759
15 TraesCS1A01G343000 chr4B 98.571 70 1 0 1021 1090 653143495 653143564 2.680000e-24 124
16 TraesCS1A01G343000 chr3D 81.895 1784 238 50 3931 5671 481911874 481910133 0.000000e+00 1426
17 TraesCS1A01G343000 chr3D 78.839 1309 227 36 2624 3908 481913521 481912239 0.000000e+00 837
18 TraesCS1A01G343000 chr3D 79.801 604 108 7 1232 1830 481926277 481925683 1.820000e-115 427
19 TraesCS1A01G343000 chr3D 84.293 382 51 8 5719 6095 481909621 481909244 1.450000e-96 364
20 TraesCS1A01G343000 chr3D 77.686 363 71 8 1711 2071 141456601 141456955 5.550000e-51 213
21 TraesCS1A01G343000 chr6D 81.511 503 90 3 1 500 20134544 20135046 1.830000e-110 411
22 TraesCS1A01G343000 chr6D 75.956 366 74 7 1711 2074 450265545 450265192 7.280000e-40 176
23 TraesCS1A01G343000 chr6D 82.123 179 32 0 1287 1465 147220846 147220668 3.410000e-33 154
24 TraesCS1A01G343000 chr7D 80.435 552 95 11 1 548 136414365 136414907 6.590000e-110 409
25 TraesCS1A01G343000 chr7D 81.579 494 88 3 10 500 628135039 628134546 8.530000e-109 405
26 TraesCS1A01G343000 chr7B 80.284 563 91 15 10 563 104298875 104298324 2.370000e-109 407
27 TraesCS1A01G343000 chr7B 80.754 504 90 7 1 500 339619011 339619511 3.090000e-103 387
28 TraesCS1A01G343000 chr2A 80.108 558 94 12 10 561 66767739 66767193 3.970000e-107 399
29 TraesCS1A01G343000 chr2A 78.161 348 64 9 1711 2054 444664856 444664517 2.000000e-50 211
30 TraesCS1A01G343000 chr2D 81.339 493 88 4 11 499 112538270 112538762 1.430000e-106 398
31 TraesCS1A01G343000 chr6B 80.037 541 97 7 10 548 508533381 508532850 2.390000e-104 390
32 TraesCS1A01G343000 chr5D 79.538 303 60 2 5745 6046 299404596 299404897 1.540000e-51 215
33 TraesCS1A01G343000 chr5B 79.208 303 61 2 5745 6046 340622801 340623102 7.180000e-50 209
34 TraesCS1A01G343000 chr5B 82.386 176 31 0 1287 1462 52305912 52306087 3.410000e-33 154
35 TraesCS1A01G343000 chr5B 75.499 351 67 12 1711 2059 645087697 645088030 3.410000e-33 154
36 TraesCS1A01G343000 chr7A 77.746 346 68 7 1711 2054 133638226 133637888 3.340000e-48 204
37 TraesCS1A01G343000 chr3B 81.250 176 33 0 1287 1462 702359949 702360124 7.390000e-30 143


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 TraesCS1A01G343000 chr1A 531716134 531723196 7062 False 13044.000000 13044 100.000000 1 7063 1 chr1A.!!$F1 7062
1 TraesCS1A01G343000 chr1B 585325876 585332333 6457 False 4298.500000 7090 89.939500 722 7046 2 chr1B.!!$F1 6324
2 TraesCS1A01G343000 chr1D 433363323 433369838 6515 False 4654.000000 6909 92.018500 575 7046 2 chr1D.!!$F1 6471
3 TraesCS1A01G343000 chr5A 691436467 691441616 5149 True 1533.666667 3823 88.622667 1021 6225 3 chr5A.!!$R2 5204
4 TraesCS1A01G343000 chrUn 126751499 126756555 5056 False 1525.666667 3777 88.789667 1021 6123 3 chrUn.!!$F1 5102
5 TraesCS1A01G343000 chr4B 653143495 653148647 5152 False 1941.500000 3759 91.614000 1021 6250 2 chr4B.!!$F1 5229
6 TraesCS1A01G343000 chr3D 481909244 481913521 4277 True 875.666667 1426 81.675667 2624 6095 3 chr3D.!!$R2 3471
7 TraesCS1A01G343000 chr3D 481925683 481926277 594 True 427.000000 427 79.801000 1232 1830 1 chr3D.!!$R1 598
8 TraesCS1A01G343000 chr6D 20134544 20135046 502 False 411.000000 411 81.511000 1 500 1 chr6D.!!$F1 499
9 TraesCS1A01G343000 chr7D 136414365 136414907 542 False 409.000000 409 80.435000 1 548 1 chr7D.!!$F1 547
10 TraesCS1A01G343000 chr7B 104298324 104298875 551 True 407.000000 407 80.284000 10 563 1 chr7B.!!$R1 553
11 TraesCS1A01G343000 chr7B 339619011 339619511 500 False 387.000000 387 80.754000 1 500 1 chr7B.!!$F1 499
12 TraesCS1A01G343000 chr2A 66767193 66767739 546 True 399.000000 399 80.108000 10 561 1 chr2A.!!$R1 551
13 TraesCS1A01G343000 chr6B 508532850 508533381 531 True 390.000000 390 80.037000 10 548 1 chr6B.!!$R1 538


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
965 1016 0.031585 TTTGGAGACGACGACCAGTG 59.968 55.000 0.00 0.0 35.08 3.66 F
1110 1199 0.107945 CCCTTCTCTCCGCCTTCTTG 60.108 60.000 0.00 0.0 0.00 3.02 F
1658 1853 0.679002 CCCTCTCATGCCACACAAGG 60.679 60.000 0.00 0.0 0.00 3.61 F
2000 2222 1.466167 CCTCAGTGTCGCTCCAATTTG 59.534 52.381 0.00 0.0 0.00 2.32 F
3595 3996 0.645868 GATTTCGTACAGGTCTGCGC 59.354 55.000 0.00 0.0 0.00 6.09 F
4861 5634 4.588951 ACGAGTATGGCCTTGATCTAATGA 59.411 41.667 3.32 0.0 0.00 2.57 F
5533 6364 2.806818 CCATCTCCTCATTGCTTCGATG 59.193 50.000 0.00 0.0 0.00 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2312 2552 1.295423 GTCGCCTGCTACTCCCAAA 59.705 57.895 0.00 0.00 0.00 3.28 R
2450 2748 3.494048 CCTGGTCAGCTGATATGTTCCTC 60.494 52.174 21.47 2.96 0.00 3.71 R
3219 3597 0.952984 AGAAGAGTGCGCCAAGAAGC 60.953 55.000 4.18 0.00 0.00 3.86 R
3706 4107 0.317160 TTAGTGACAGACCTGTGGCG 59.683 55.000 7.47 0.00 45.05 5.69 R
4869 5655 3.090037 AGTGTGCACGGAGAGTTATACT 58.910 45.455 13.13 2.73 36.20 2.12 R
5771 7200 0.679640 TGCCCCCGTATCTTGCTTTG 60.680 55.000 0.00 0.00 0.00 2.77 R
6809 8309 1.894756 CTGCAAAACCGTTCCCCGA 60.895 57.895 0.00 0.00 39.56 5.14 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
53 55 3.869065 CGGAGGGCACTGTTTTTAGATA 58.131 45.455 0.00 0.00 0.00 1.98
56 59 5.357032 CGGAGGGCACTGTTTTTAGATATTT 59.643 40.000 0.00 0.00 0.00 1.40
84 87 5.673514 AGTTTTGTTAAGGTTCGTGTCCTA 58.326 37.500 0.00 0.00 34.56 2.94
105 108 0.539669 TCAGGAAGACGAGGCAGTGA 60.540 55.000 0.00 0.00 0.00 3.41
121 124 2.941453 GTGACGGCTCACTGAAGATA 57.059 50.000 9.05 0.00 43.26 1.98
122 125 3.232213 GTGACGGCTCACTGAAGATAA 57.768 47.619 9.05 0.00 43.26 1.75
123 126 3.786635 GTGACGGCTCACTGAAGATAAT 58.213 45.455 9.05 0.00 43.26 1.28
160 164 4.376170 GCCCCCATTCCGGTGGTT 62.376 66.667 10.05 0.00 37.57 3.67
162 166 2.760477 CCCCATTCCGGTGGTTCA 59.240 61.111 10.05 0.00 37.57 3.18
178 182 2.292569 GGTTCATCTAGCATCGTCGGTA 59.707 50.000 0.00 0.00 0.00 4.02
197 201 2.521105 AGACGTGTTAAGGTGTGTCC 57.479 50.000 0.00 0.00 0.00 4.02
202 206 1.055551 TGTTAAGGTGTGTCCCCGGT 61.056 55.000 0.00 0.00 36.75 5.28
220 224 2.648059 GGTGGATCTGTCTTTGATGGG 58.352 52.381 0.00 0.00 0.00 4.00
227 231 3.565307 TCTGTCTTTGATGGGTTTGCTT 58.435 40.909 0.00 0.00 0.00 3.91
230 234 1.969923 TCTTTGATGGGTTTGCTTGGG 59.030 47.619 0.00 0.00 0.00 4.12
235 239 0.108396 ATGGGTTTGCTTGGGTTTGC 59.892 50.000 0.00 0.00 0.00 3.68
249 253 1.798813 GGTTTGCTCATCGTTCGTCTT 59.201 47.619 0.00 0.00 0.00 3.01
251 255 2.432206 TTGCTCATCGTTCGTCTTCA 57.568 45.000 0.00 0.00 0.00 3.02
267 271 3.565482 GTCTTCATTTGTGTGCCTTCAGA 59.435 43.478 0.00 0.00 0.00 3.27
306 310 1.437573 CTACTCTTCATCGGCGGCA 59.562 57.895 10.53 0.00 0.00 5.69
307 311 0.179111 CTACTCTTCATCGGCGGCAA 60.179 55.000 10.53 0.00 0.00 4.52
322 326 1.066908 CGGCAATTGTTGTTCTGGTGT 59.933 47.619 7.40 0.00 0.00 4.16
323 327 2.481104 CGGCAATTGTTGTTCTGGTGTT 60.481 45.455 7.40 0.00 0.00 3.32
329 333 5.923733 ATTGTTGTTCTGGTGTTTTGGTA 57.076 34.783 0.00 0.00 0.00 3.25
333 337 5.354792 TGTTGTTCTGGTGTTTTGGTACTAC 59.645 40.000 0.00 0.00 0.00 2.73
334 338 5.100344 TGTTCTGGTGTTTTGGTACTACA 57.900 39.130 0.00 0.00 0.00 2.74
339 343 2.224695 GGTGTTTTGGTACTACAGGGCT 60.225 50.000 0.00 0.00 0.00 5.19
344 348 5.163174 TGTTTTGGTACTACAGGGCTTTAGT 60.163 40.000 0.00 0.00 33.11 2.24
350 354 5.765182 GGTACTACAGGGCTTTAGTACGATA 59.235 44.000 17.07 0.00 46.32 2.92
361 365 5.230936 GCTTTAGTACGATAACTTTCCGACC 59.769 44.000 0.00 0.00 0.00 4.79
366 370 2.159462 ACGATAACTTTCCGACCGTCTC 60.159 50.000 0.00 0.00 0.00 3.36
376 381 1.668047 CCGACCGTCTCCTACAACAAC 60.668 57.143 0.00 0.00 0.00 3.32
404 409 2.443016 CTCTGACGAGGGAGGGGG 60.443 72.222 0.00 0.00 33.51 5.40
433 439 2.684843 GGCACCTTCAGCTCGCTTG 61.685 63.158 0.00 0.00 0.00 4.01
443 449 1.206072 GCTCGCTTGAGTGCTTGTG 59.794 57.895 0.00 0.00 42.01 3.33
445 451 0.601046 CTCGCTTGAGTGCTTGTGGA 60.601 55.000 0.00 0.00 34.89 4.02
503 509 9.840427 ATTTTTATTATTTCTGGTGTTCGACTG 57.160 29.630 0.00 0.00 0.00 3.51
504 510 7.972832 TTTATTATTTCTGGTGTTCGACTGT 57.027 32.000 0.00 0.00 0.00 3.55
505 511 7.972832 TTATTATTTCTGGTGTTCGACTGTT 57.027 32.000 0.00 0.00 0.00 3.16
506 512 5.917541 TTATTTCTGGTGTTCGACTGTTC 57.082 39.130 0.00 0.00 0.00 3.18
508 514 0.742505 TCTGGTGTTCGACTGTTCGT 59.257 50.000 0.00 0.00 46.01 3.85
509 515 1.135527 TCTGGTGTTCGACTGTTCGTT 59.864 47.619 0.00 0.00 46.01 3.85
510 516 2.358582 TCTGGTGTTCGACTGTTCGTTA 59.641 45.455 0.00 0.00 46.01 3.18
511 517 3.005050 TCTGGTGTTCGACTGTTCGTTAT 59.995 43.478 0.00 0.00 46.01 1.89
512 518 4.216042 TCTGGTGTTCGACTGTTCGTTATA 59.784 41.667 0.00 0.00 46.01 0.98
513 519 4.229096 TGGTGTTCGACTGTTCGTTATAC 58.771 43.478 0.00 0.00 46.01 1.47
514 520 3.609807 GGTGTTCGACTGTTCGTTATACC 59.390 47.826 0.00 0.00 46.01 2.73
515 521 3.299020 GTGTTCGACTGTTCGTTATACCG 59.701 47.826 0.00 0.00 46.01 4.02
516 522 2.178474 TCGACTGTTCGTTATACCGC 57.822 50.000 0.00 0.00 46.01 5.68
517 523 1.194495 CGACTGTTCGTTATACCGCC 58.806 55.000 0.00 0.00 40.61 6.13
518 524 1.564207 GACTGTTCGTTATACCGCCC 58.436 55.000 0.00 0.00 0.00 6.13
519 525 1.135721 GACTGTTCGTTATACCGCCCT 59.864 52.381 0.00 0.00 0.00 5.19
520 526 1.134907 ACTGTTCGTTATACCGCCCTG 60.135 52.381 0.00 0.00 0.00 4.45
521 527 1.135527 CTGTTCGTTATACCGCCCTGA 59.864 52.381 0.00 0.00 0.00 3.86
522 528 1.758280 TGTTCGTTATACCGCCCTGAT 59.242 47.619 0.00 0.00 0.00 2.90
523 529 2.168936 TGTTCGTTATACCGCCCTGATT 59.831 45.455 0.00 0.00 0.00 2.57
524 530 2.519377 TCGTTATACCGCCCTGATTG 57.481 50.000 0.00 0.00 0.00 2.67
525 531 2.033372 TCGTTATACCGCCCTGATTGA 58.967 47.619 0.00 0.00 0.00 2.57
526 532 2.431419 TCGTTATACCGCCCTGATTGAA 59.569 45.455 0.00 0.00 0.00 2.69
527 533 3.070446 TCGTTATACCGCCCTGATTGAAT 59.930 43.478 0.00 0.00 0.00 2.57
528 534 4.281435 TCGTTATACCGCCCTGATTGAATA 59.719 41.667 0.00 0.00 0.00 1.75
529 535 5.046878 TCGTTATACCGCCCTGATTGAATAT 60.047 40.000 0.00 0.00 0.00 1.28
530 536 5.063438 CGTTATACCGCCCTGATTGAATATG 59.937 44.000 0.00 0.00 0.00 1.78
531 537 4.908601 ATACCGCCCTGATTGAATATGA 57.091 40.909 0.00 0.00 0.00 2.15
532 538 3.131709 ACCGCCCTGATTGAATATGAG 57.868 47.619 0.00 0.00 0.00 2.90
533 539 2.439507 ACCGCCCTGATTGAATATGAGT 59.560 45.455 0.00 0.00 0.00 3.41
534 540 3.646162 ACCGCCCTGATTGAATATGAGTA 59.354 43.478 0.00 0.00 0.00 2.59
535 541 4.248859 CCGCCCTGATTGAATATGAGTAG 58.751 47.826 0.00 0.00 0.00 2.57
536 542 4.021104 CCGCCCTGATTGAATATGAGTAGA 60.021 45.833 0.00 0.00 0.00 2.59
537 543 5.337894 CCGCCCTGATTGAATATGAGTAGAT 60.338 44.000 0.00 0.00 0.00 1.98
538 544 5.809562 CGCCCTGATTGAATATGAGTAGATC 59.190 44.000 0.00 0.00 0.00 2.75
539 545 5.809562 GCCCTGATTGAATATGAGTAGATCG 59.190 44.000 0.00 0.00 0.00 3.69
540 546 6.350528 GCCCTGATTGAATATGAGTAGATCGA 60.351 42.308 0.00 0.00 0.00 3.59
541 547 7.606349 CCCTGATTGAATATGAGTAGATCGAA 58.394 38.462 0.00 0.00 0.00 3.71
542 548 8.090831 CCCTGATTGAATATGAGTAGATCGAAA 58.909 37.037 0.00 0.00 0.00 3.46
543 549 9.138062 CCTGATTGAATATGAGTAGATCGAAAG 57.862 37.037 0.00 0.00 0.00 2.62
544 550 9.689976 CTGATTGAATATGAGTAGATCGAAAGT 57.310 33.333 0.00 0.00 0.00 2.66
582 588 6.432607 ACAAGAGTGACTTATTATCGTCGA 57.567 37.500 0.00 0.00 37.03 4.20
584 590 5.080642 AGAGTGACTTATTATCGTCGACG 57.919 43.478 31.30 31.30 41.45 5.12
592 598 0.794229 TTATCGTCGACGTGAACGGC 60.794 55.000 34.40 2.72 45.58 5.68
606 612 3.307242 GTGAACGGCTAGCAATCTTACAG 59.693 47.826 18.24 0.00 0.00 2.74
647 654 3.190337 GCAGCTTGTTTGCCTCTTG 57.810 52.632 0.00 0.00 35.54 3.02
651 658 3.524541 CAGCTTGTTTGCCTCTTGTTTT 58.475 40.909 0.00 0.00 0.00 2.43
672 680 3.377434 TTTGACACAGTTCGTTCAACG 57.623 42.857 2.64 2.64 44.19 4.10
682 690 3.893720 GTTCGTTCAACGGACTCTAGAA 58.106 45.455 14.49 0.00 46.16 2.10
690 698 5.311265 TCAACGGACTCTAGAAGACAAGTA 58.689 41.667 0.00 0.00 0.00 2.24
691 699 5.180868 TCAACGGACTCTAGAAGACAAGTAC 59.819 44.000 0.00 0.00 0.00 2.73
692 700 4.909001 ACGGACTCTAGAAGACAAGTACT 58.091 43.478 0.00 0.00 0.00 2.73
698 706 6.117488 ACTCTAGAAGACAAGTACTAGGAGC 58.883 44.000 0.00 0.00 34.80 4.70
704 712 3.940221 AGACAAGTACTAGGAGCACTACG 59.060 47.826 0.00 0.00 0.00 3.51
705 713 2.422832 ACAAGTACTAGGAGCACTACGC 59.577 50.000 0.00 0.00 42.91 4.42
719 727 3.360533 CACTACGCGTAGAACTACATGG 58.639 50.000 43.57 20.66 36.97 3.66
745 754 1.146263 GGCCCACATAGGTTCCGAG 59.854 63.158 0.00 0.00 34.66 4.63
752 761 3.684788 CCACATAGGTTCCGAGAAACTTG 59.315 47.826 9.09 9.51 0.00 3.16
762 771 5.215252 TCCGAGAAACTTGAGAAGTCAAT 57.785 39.130 0.00 0.00 41.96 2.57
765 774 5.466728 CCGAGAAACTTGAGAAGTCAATCAA 59.533 40.000 0.00 0.00 41.96 2.57
767 776 6.848296 CGAGAAACTTGAGAAGTCAATCAAAC 59.152 38.462 0.00 0.00 41.96 2.93
768 777 7.465916 CGAGAAACTTGAGAAGTCAATCAAACA 60.466 37.037 0.00 0.00 41.96 2.83
769 778 8.055279 AGAAACTTGAGAAGTCAATCAAACAA 57.945 30.769 0.00 0.00 41.96 2.83
770 779 8.522830 AGAAACTTGAGAAGTCAATCAAACAAA 58.477 29.630 0.00 0.00 41.96 2.83
771 780 9.139174 GAAACTTGAGAAGTCAATCAAACAAAA 57.861 29.630 0.00 0.00 41.96 2.44
772 781 9.487790 AAACTTGAGAAGTCAATCAAACAAAAA 57.512 25.926 0.00 0.00 41.96 1.94
814 823 8.602472 TTGCTAATAATCACATTTAACCCCTT 57.398 30.769 0.00 0.00 0.00 3.95
815 824 8.006298 TGCTAATAATCACATTTAACCCCTTG 57.994 34.615 0.00 0.00 0.00 3.61
839 859 2.507407 TGTCTCTAAATTGCACCCCC 57.493 50.000 0.00 0.00 0.00 5.40
840 860 1.707989 TGTCTCTAAATTGCACCCCCA 59.292 47.619 0.00 0.00 0.00 4.96
842 862 1.005450 TCTCTAAATTGCACCCCCACC 59.995 52.381 0.00 0.00 0.00 4.61
844 864 1.304547 TAAATTGCACCCCCACCGG 60.305 57.895 0.00 0.00 0.00 5.28
881 907 1.377987 ACACCACACCACACCACAC 60.378 57.895 0.00 0.00 0.00 3.82
882 908 2.118404 CACCACACCACACCACACC 61.118 63.158 0.00 0.00 0.00 4.16
883 909 2.273776 CCACACCACACCACACCA 59.726 61.111 0.00 0.00 0.00 4.17
884 910 2.118404 CCACACCACACCACACCAC 61.118 63.158 0.00 0.00 0.00 4.16
885 911 2.118404 CACACCACACCACACCACC 61.118 63.158 0.00 0.00 0.00 4.61
886 912 2.899838 CACCACACCACACCACCG 60.900 66.667 0.00 0.00 0.00 4.94
954 980 3.883489 AGGCGGCTATAAAATTTGGAGAC 59.117 43.478 11.03 0.00 0.00 3.36
965 1016 0.031585 TTTGGAGACGACGACCAGTG 59.968 55.000 0.00 0.00 35.08 3.66
992 1043 2.546795 CCATCTTTCTCCTCCGAATCCG 60.547 54.545 0.00 0.00 0.00 4.18
1018 1073 4.316823 TGGACTCCTCCACCGGCT 62.317 66.667 0.00 0.00 42.15 5.52
1019 1074 3.462678 GGACTCCTCCACCGGCTC 61.463 72.222 0.00 0.00 36.42 4.70
1102 1191 1.040339 CCAGGTCTCCCTTCTCTCCG 61.040 65.000 0.00 0.00 39.89 4.63
1110 1199 0.107945 CCCTTCTCTCCGCCTTCTTG 60.108 60.000 0.00 0.00 0.00 3.02
1111 1200 0.742635 CCTTCTCTCCGCCTTCTTGC 60.743 60.000 0.00 0.00 0.00 4.01
1188 1280 3.361644 CGTGAACTGATTTGAATTTGCCG 59.638 43.478 0.00 0.00 0.00 5.69
1190 1282 4.382754 GTGAACTGATTTGAATTTGCCGAC 59.617 41.667 0.00 0.00 0.00 4.79
1194 1286 5.600696 ACTGATTTGAATTTGCCGACTTTT 58.399 33.333 0.00 0.00 0.00 2.27
1204 1296 4.647424 TTGCCGACTTTTTCTGATTTGT 57.353 36.364 0.00 0.00 0.00 2.83
1304 1492 2.493973 CTCCTCTGCGTCCTGCTC 59.506 66.667 0.00 0.00 46.63 4.26
1640 1835 2.501261 GCCGAAAGTATGTTATCCCCC 58.499 52.381 0.00 0.00 0.00 5.40
1655 1850 2.605607 CCCCCTCTCATGCCACACA 61.606 63.158 0.00 0.00 0.00 3.72
1658 1853 0.679002 CCCTCTCATGCCACACAAGG 60.679 60.000 0.00 0.00 0.00 3.61
1702 1911 5.991328 TCGTTCATAATTCAGGCTCAATC 57.009 39.130 0.00 0.00 0.00 2.67
1703 1912 5.674525 TCGTTCATAATTCAGGCTCAATCT 58.325 37.500 0.00 0.00 0.00 2.40
1704 1913 6.115446 TCGTTCATAATTCAGGCTCAATCTT 58.885 36.000 0.00 0.00 0.00 2.40
1705 1914 6.258727 TCGTTCATAATTCAGGCTCAATCTTC 59.741 38.462 0.00 0.00 0.00 2.87
1708 1917 5.525012 TCATAATTCAGGCTCAATCTTCGTG 59.475 40.000 0.00 0.00 0.00 4.35
1893 2115 3.365364 CGAAGCTTTTGGTTGGATCTGTC 60.365 47.826 0.00 0.00 40.61 3.51
1895 2117 3.416156 AGCTTTTGGTTGGATCTGTCTC 58.584 45.455 0.00 0.00 0.00 3.36
1935 2157 1.996191 CGCCAGAGTTTAGACAGCTTC 59.004 52.381 0.00 0.00 0.00 3.86
1961 2183 2.369394 CCAGCATTTACTCCAGGGAAC 58.631 52.381 0.00 0.00 0.00 3.62
2000 2222 1.466167 CCTCAGTGTCGCTCCAATTTG 59.534 52.381 0.00 0.00 0.00 2.32
2014 2236 4.499183 TCCAATTTGTCGCAAACAGTTTT 58.501 34.783 7.08 0.00 39.58 2.43
2015 2237 4.328440 TCCAATTTGTCGCAAACAGTTTTG 59.672 37.500 7.08 7.50 44.42 2.44
2130 2352 5.376625 ACATGCTTTCTGAACAAGGAGTTA 58.623 37.500 0.00 0.00 41.51 2.24
2144 2380 5.869888 ACAAGGAGTTAGTTAAGATGAAGCG 59.130 40.000 0.00 0.00 0.00 4.68
2154 2390 5.872070 AGTTAAGATGAAGCGAGGAGAAAAG 59.128 40.000 0.00 0.00 0.00 2.27
2233 2473 6.470235 CCTCATGTTTCTAAGCTTTAATTGCG 59.530 38.462 3.20 0.00 35.28 4.85
2284 2524 4.660789 ACAAGCTGCTTTGTTGATTTCT 57.339 36.364 13.10 0.00 38.05 2.52
2366 2606 6.933514 ATTGGACCTTGTAAAATGGTGATT 57.066 33.333 0.00 0.00 36.47 2.57
2380 2620 8.574196 AAAATGGTGATTTTAGAGTGTTTTCG 57.426 30.769 0.00 0.00 39.53 3.46
2392 2635 5.123227 AGAGTGTTTTCGGTCTTCATCAAA 58.877 37.500 0.00 0.00 0.00 2.69
2423 2666 3.812609 TCAGCTTCGTTGCTTGAATGTTA 59.187 39.130 2.47 0.00 41.98 2.41
2424 2667 4.274705 TCAGCTTCGTTGCTTGAATGTTAA 59.725 37.500 2.47 0.00 41.98 2.01
2425 2668 5.048782 TCAGCTTCGTTGCTTGAATGTTAAT 60.049 36.000 2.47 0.00 41.98 1.40
2428 2671 5.402270 GCTTCGTTGCTTGAATGTTAATTGT 59.598 36.000 0.00 0.00 0.00 2.71
2429 2672 6.580791 GCTTCGTTGCTTGAATGTTAATTGTA 59.419 34.615 0.00 0.00 0.00 2.41
2430 2673 7.273381 GCTTCGTTGCTTGAATGTTAATTGTAT 59.727 33.333 0.00 0.00 0.00 2.29
2431 2674 9.128107 CTTCGTTGCTTGAATGTTAATTGTATT 57.872 29.630 0.00 0.00 0.00 1.89
2433 2676 9.767684 TCGTTGCTTGAATGTTAATTGTATTAG 57.232 29.630 0.00 0.00 0.00 1.73
2618 2972 4.233632 TGAGAATATGCCATTGGTGACA 57.766 40.909 4.26 0.00 39.83 3.58
2651 3013 2.990740 TTTTGTATCCCTTGGGTGCT 57.009 45.000 5.51 0.00 0.00 4.40
2862 3232 4.141367 TGAAGTGGTACCATTGGTTCTTCA 60.141 41.667 27.14 27.14 36.60 3.02
2868 3238 5.600484 TGGTACCATTGGTTCTTCATGTTTT 59.400 36.000 14.78 0.00 37.09 2.43
2992 3366 4.778904 TGCGTTTACTGAAATTGCACTAC 58.221 39.130 0.00 0.00 35.27 2.73
3219 3597 7.589954 ACGAAATTAAAATTTGACCTGTCTTCG 59.410 33.333 5.44 4.60 38.64 3.79
3595 3996 0.645868 GATTTCGTACAGGTCTGCGC 59.354 55.000 0.00 0.00 0.00 6.09
3706 4107 6.354622 CGTCGTTCTTTTCTTCAGTCAAAATC 59.645 38.462 0.00 0.00 0.00 2.17
3894 4297 8.483758 TGAGGATAATAGTTTCCCAAGTAAGTC 58.516 37.037 0.00 0.00 32.05 3.01
3899 4302 7.981102 AATAGTTTCCCAAGTAAGTCACTTC 57.019 36.000 0.00 0.00 44.48 3.01
3922 4675 9.831737 CTTCCTTATTTATGTTTGACAACTCTG 57.168 33.333 0.00 0.00 33.58 3.35
4362 5123 6.704289 TCCCTTGCATATTTCTCAAAGATG 57.296 37.500 0.00 0.21 41.69 2.90
4407 5173 4.718961 AGGCCCTGACAATATATGTGTTC 58.281 43.478 0.00 0.00 44.12 3.18
4861 5634 4.588951 ACGAGTATGGCCTTGATCTAATGA 59.411 41.667 3.32 0.00 0.00 2.57
4869 5655 8.945195 ATGGCCTTGATCTAATGATATTTTCA 57.055 30.769 3.32 0.00 39.12 2.69
5031 5817 7.885399 ACTGAAGGTATAGTTCTGCAATTTCTT 59.115 33.333 0.00 0.00 0.00 2.52
5061 5855 6.149308 TCTGCACCAGTATCTATTGTTGTTTG 59.851 38.462 0.00 0.00 32.61 2.93
5123 5922 3.276857 CCATGCAGCAATAGTTCAGACT 58.723 45.455 0.00 0.00 39.97 3.24
5327 6154 6.371825 CCAAAGTACTTACCTGATTCCTGTTC 59.628 42.308 8.92 0.00 0.00 3.18
5329 6156 6.532988 AGTACTTACCTGATTCCTGTTCTC 57.467 41.667 0.00 0.00 0.00 2.87
5336 6165 4.006319 CCTGATTCCTGTTCTCTTTCCAC 58.994 47.826 0.00 0.00 0.00 4.02
5344 6173 2.880268 TGTTCTCTTTCCACATGCACAG 59.120 45.455 0.00 0.00 0.00 3.66
5533 6364 2.806818 CCATCTCCTCATTGCTTCGATG 59.193 50.000 0.00 0.00 0.00 3.84
5686 6523 9.461312 AAATTACCTATTCACTTGTATGAAGCA 57.539 29.630 0.00 0.00 41.76 3.91
5687 6524 7.843490 TTACCTATTCACTTGTATGAAGCAC 57.157 36.000 0.00 0.00 41.76 4.40
5688 6525 5.804639 ACCTATTCACTTGTATGAAGCACA 58.195 37.500 0.00 0.00 41.76 4.57
5689 6526 5.877012 ACCTATTCACTTGTATGAAGCACAG 59.123 40.000 0.00 0.00 41.76 3.66
5690 6527 6.108687 CCTATTCACTTGTATGAAGCACAGA 58.891 40.000 0.00 0.00 41.76 3.41
5691 6528 6.595326 CCTATTCACTTGTATGAAGCACAGAA 59.405 38.462 0.00 0.00 41.76 3.02
5692 6529 7.281774 CCTATTCACTTGTATGAAGCACAGAAT 59.718 37.037 0.00 0.00 41.76 2.40
5697 6534 5.410746 ACTTGTATGAAGCACAGAATGACAG 59.589 40.000 0.00 0.00 39.69 3.51
5705 7009 4.960938 AGCACAGAATGACAGAACTACAA 58.039 39.130 0.00 0.00 39.69 2.41
5721 7025 9.811655 CAGAACTACAATTTGTGTAACTGTATG 57.188 33.333 12.30 0.00 42.23 2.39
5742 7171 8.172484 TGTATGCTACTTTATTAAACACTTGCG 58.828 33.333 0.00 0.00 0.00 4.85
5819 7248 5.503846 CGTGTTCACAATGACAACATCTTCA 60.504 40.000 3.87 0.00 35.50 3.02
6141 7579 6.355638 GTGTATGAGACTTGTTTGAACTTCG 58.644 40.000 0.00 0.00 0.00 3.79
6144 7582 4.689071 TGAGACTTGTTTGAACTTCGCTA 58.311 39.130 0.00 0.00 0.00 4.26
6147 7585 6.365247 TGAGACTTGTTTGAACTTCGCTATAC 59.635 38.462 0.00 0.00 0.00 1.47
6148 7586 5.345202 AGACTTGTTTGAACTTCGCTATACG 59.655 40.000 0.00 0.00 45.62 3.06
6149 7587 4.387862 ACTTGTTTGAACTTCGCTATACGG 59.612 41.667 0.00 0.00 43.89 4.02
6172 7610 4.159244 AGTTTTGGTTAGTGTGGCACTA 57.841 40.909 19.83 5.03 43.46 2.74
6174 7612 2.851263 TTGGTTAGTGTGGCACTAGG 57.149 50.000 19.83 0.00 45.83 3.02
6246 7684 3.241493 TGGCAATTCCAGTGTACCG 57.759 52.632 0.00 0.00 40.72 4.02
6252 7690 3.936453 GCAATTCCAGTGTACCGTATTCA 59.064 43.478 0.00 0.00 0.00 2.57
6431 7870 8.846943 AAACTGAACAAAATATGAAATTCCCC 57.153 30.769 0.00 0.00 0.00 4.81
6432 7871 6.946340 ACTGAACAAAATATGAAATTCCCCC 58.054 36.000 0.00 0.00 0.00 5.40
6434 7873 7.017056 ACTGAACAAAATATGAAATTCCCCCAA 59.983 33.333 0.00 0.00 0.00 4.12
6435 7874 7.749666 TGAACAAAATATGAAATTCCCCCAAA 58.250 30.769 0.00 0.00 0.00 3.28
6436 7875 8.220559 TGAACAAAATATGAAATTCCCCCAAAA 58.779 29.630 0.00 0.00 0.00 2.44
6437 7876 9.072375 GAACAAAATATGAAATTCCCCCAAAAA 57.928 29.630 0.00 0.00 0.00 1.94
6731 8231 0.320771 AATGTCGACCTCACCTGTGC 60.321 55.000 14.12 0.00 0.00 4.57
6732 8232 1.471829 ATGTCGACCTCACCTGTGCA 61.472 55.000 14.12 0.00 0.00 4.57
6752 8252 3.841643 CATTTCTGCATCCCTCAACAAC 58.158 45.455 0.00 0.00 0.00 3.32
6809 8309 2.097466 CGTGCGGCAAATAGGAAATTCT 59.903 45.455 3.23 0.00 0.00 2.40
6891 8391 7.585579 TTTATCCACCGGTTTTCTAGTTTTT 57.414 32.000 2.97 0.00 0.00 1.94
6930 8433 7.279090 ACAAAATTTTCTAGGGTTTGTTTTCGG 59.721 33.333 0.00 0.00 38.85 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.442272 CCGAGATCCACCGGGTCT 60.442 66.667 6.32 3.23 41.89 3.85
56 59 6.679843 ACACGAACCTTAACAAAACTCAAAA 58.320 32.000 0.00 0.00 0.00 2.44
84 87 0.540830 ACTGCCTCGTCTTCCTGAGT 60.541 55.000 0.00 0.00 0.00 3.41
105 108 6.267928 ACCTTATATTATCTTCAGTGAGCCGT 59.732 38.462 0.00 0.00 0.00 5.68
112 115 8.361139 CGGTGAGAACCTTATATTATCTTCAGT 58.639 37.037 0.00 0.00 0.00 3.41
121 124 6.053650 GGCTAAACGGTGAGAACCTTATATT 58.946 40.000 0.00 0.00 0.00 1.28
122 125 5.454329 GGGCTAAACGGTGAGAACCTTATAT 60.454 44.000 0.00 0.00 0.00 0.86
123 126 4.141869 GGGCTAAACGGTGAGAACCTTATA 60.142 45.833 0.00 0.00 0.00 0.98
135 138 1.305287 GGAATGGGGGCTAAACGGT 59.695 57.895 0.00 0.00 0.00 4.83
140 143 3.003230 CACCGGAATGGGGGCTAA 58.997 61.111 9.46 0.00 44.64 3.09
160 164 2.806818 GTCTACCGACGATGCTAGATGA 59.193 50.000 0.00 0.00 0.00 2.92
178 182 1.069668 GGGACACACCTTAACACGTCT 59.930 52.381 0.00 0.00 38.98 4.18
186 190 2.218454 CCACCGGGGACACACCTTA 61.218 63.158 4.41 0.00 40.01 2.69
197 201 0.613260 TCAAAGACAGATCCACCGGG 59.387 55.000 6.32 0.00 0.00 5.73
202 206 4.081406 CAAACCCATCAAAGACAGATCCA 58.919 43.478 0.00 0.00 0.00 3.41
209 213 2.289010 CCCAAGCAAACCCATCAAAGAC 60.289 50.000 0.00 0.00 0.00 3.01
220 224 2.407090 GATGAGCAAACCCAAGCAAAC 58.593 47.619 0.00 0.00 0.00 2.93
227 231 0.250124 ACGAACGATGAGCAAACCCA 60.250 50.000 0.14 0.00 0.00 4.51
230 234 2.475111 TGAAGACGAACGATGAGCAAAC 59.525 45.455 0.14 0.00 0.00 2.93
235 239 4.150627 ACACAAATGAAGACGAACGATGAG 59.849 41.667 0.14 0.00 0.00 2.90
249 253 3.256383 CCAATCTGAAGGCACACAAATGA 59.744 43.478 0.00 0.00 0.00 2.57
251 255 3.499338 TCCAATCTGAAGGCACACAAAT 58.501 40.909 0.00 0.00 0.00 2.32
267 271 3.139077 GCGTAAATCGGAAGGATCCAAT 58.861 45.455 15.82 1.38 46.97 3.16
306 310 5.159273 ACCAAAACACCAGAACAACAATT 57.841 34.783 0.00 0.00 0.00 2.32
307 311 4.817318 ACCAAAACACCAGAACAACAAT 57.183 36.364 0.00 0.00 0.00 2.71
322 326 5.571791 ACTAAAGCCCTGTAGTACCAAAA 57.428 39.130 0.00 0.00 0.00 2.44
323 327 5.336690 CGTACTAAAGCCCTGTAGTACCAAA 60.337 44.000 21.59 0.00 45.16 3.28
329 333 5.890419 AGTTATCGTACTAAAGCCCTGTAGT 59.110 40.000 3.78 3.78 34.89 2.73
333 337 5.522824 GGAAAGTTATCGTACTAAAGCCCTG 59.477 44.000 0.00 0.00 0.00 4.45
334 338 5.668471 GGAAAGTTATCGTACTAAAGCCCT 58.332 41.667 0.00 0.00 0.00 5.19
339 343 5.106317 ACGGTCGGAAAGTTATCGTACTAAA 60.106 40.000 0.00 0.00 0.00 1.85
344 348 3.009723 AGACGGTCGGAAAGTTATCGTA 58.990 45.455 1.89 0.00 0.00 3.43
350 354 1.543358 GTAGGAGACGGTCGGAAAGTT 59.457 52.381 1.89 0.00 0.00 2.66
361 365 4.025145 GGACAAAAGTTGTTGTAGGAGACG 60.025 45.833 0.00 0.00 45.52 4.18
366 370 2.287368 GCCGGACAAAAGTTGTTGTAGG 60.287 50.000 5.05 13.91 45.52 3.18
376 381 0.319555 TCGTCAGAGCCGGACAAAAG 60.320 55.000 5.05 0.00 34.97 2.27
415 421 2.359230 AAGCGAGCTGAAGGTGCC 60.359 61.111 0.00 0.00 0.00 5.01
418 424 0.320247 CACTCAAGCGAGCTGAAGGT 60.320 55.000 0.00 0.00 43.66 3.50
424 430 1.070445 ACAAGCACTCAAGCGAGCT 59.930 52.632 0.00 0.00 43.66 4.09
433 439 0.874607 AACGACGTCCACAAGCACTC 60.875 55.000 10.58 0.00 0.00 3.51
443 449 2.679837 TGTAGACCATCTAACGACGTCC 59.320 50.000 10.58 0.00 29.58 4.79
445 451 3.603532 TCTGTAGACCATCTAACGACGT 58.396 45.455 0.00 0.00 29.58 4.34
500 506 1.134907 CAGGGCGGTATAACGAACAGT 60.135 52.381 15.85 0.00 35.47 3.55
501 507 1.135527 TCAGGGCGGTATAACGAACAG 59.864 52.381 15.85 2.46 35.47 3.16
502 508 1.184431 TCAGGGCGGTATAACGAACA 58.816 50.000 15.85 0.00 35.47 3.18
503 509 2.521105 ATCAGGGCGGTATAACGAAC 57.479 50.000 15.85 5.51 35.47 3.95
504 510 2.431419 TCAATCAGGGCGGTATAACGAA 59.569 45.455 15.85 0.00 35.47 3.85
505 511 2.033372 TCAATCAGGGCGGTATAACGA 58.967 47.619 15.85 0.00 35.47 3.85
506 512 2.519377 TCAATCAGGGCGGTATAACG 57.481 50.000 5.62 5.62 0.00 3.18
507 513 6.170506 TCATATTCAATCAGGGCGGTATAAC 58.829 40.000 0.00 0.00 0.00 1.89
508 514 6.013725 ACTCATATTCAATCAGGGCGGTATAA 60.014 38.462 0.00 0.00 0.00 0.98
509 515 5.483937 ACTCATATTCAATCAGGGCGGTATA 59.516 40.000 0.00 0.00 0.00 1.47
510 516 4.287067 ACTCATATTCAATCAGGGCGGTAT 59.713 41.667 0.00 0.00 0.00 2.73
511 517 3.646162 ACTCATATTCAATCAGGGCGGTA 59.354 43.478 0.00 0.00 0.00 4.02
512 518 2.439507 ACTCATATTCAATCAGGGCGGT 59.560 45.455 0.00 0.00 0.00 5.68
513 519 3.131709 ACTCATATTCAATCAGGGCGG 57.868 47.619 0.00 0.00 0.00 6.13
514 520 5.139435 TCTACTCATATTCAATCAGGGCG 57.861 43.478 0.00 0.00 0.00 6.13
515 521 5.809562 CGATCTACTCATATTCAATCAGGGC 59.190 44.000 0.00 0.00 0.00 5.19
516 522 7.163001 TCGATCTACTCATATTCAATCAGGG 57.837 40.000 0.00 0.00 0.00 4.45
517 523 9.138062 CTTTCGATCTACTCATATTCAATCAGG 57.862 37.037 0.00 0.00 0.00 3.86
518 524 9.689976 ACTTTCGATCTACTCATATTCAATCAG 57.310 33.333 0.00 0.00 0.00 2.90
552 558 9.878599 CGATAATAAGTCACTCTTGTTTGTTTT 57.121 29.630 0.00 0.00 38.23 2.43
553 559 9.052759 ACGATAATAAGTCACTCTTGTTTGTTT 57.947 29.630 0.00 0.00 38.23 2.83
554 560 8.603242 ACGATAATAAGTCACTCTTGTTTGTT 57.397 30.769 0.00 0.00 38.23 2.83
555 561 7.061905 CGACGATAATAAGTCACTCTTGTTTGT 59.938 37.037 0.00 0.00 38.23 2.83
556 562 7.272731 TCGACGATAATAAGTCACTCTTGTTTG 59.727 37.037 0.00 0.00 38.23 2.93
557 563 7.272948 GTCGACGATAATAAGTCACTCTTGTTT 59.727 37.037 0.00 0.00 38.23 2.83
558 564 6.746364 GTCGACGATAATAAGTCACTCTTGTT 59.254 38.462 0.00 0.00 39.92 2.83
559 565 6.256686 GTCGACGATAATAAGTCACTCTTGT 58.743 40.000 0.00 0.00 37.23 3.16
560 566 5.392874 CGTCGACGATAATAAGTCACTCTTG 59.607 44.000 33.35 0.00 43.02 3.02
561 567 5.064452 ACGTCGACGATAATAAGTCACTCTT 59.936 40.000 41.52 12.33 43.02 2.85
562 568 4.569966 ACGTCGACGATAATAAGTCACTCT 59.430 41.667 41.52 12.73 43.02 3.24
563 569 4.665292 CACGTCGACGATAATAAGTCACTC 59.335 45.833 41.52 0.00 43.02 3.51
564 570 4.330894 TCACGTCGACGATAATAAGTCACT 59.669 41.667 41.52 13.89 43.02 3.41
565 571 4.581493 TCACGTCGACGATAATAAGTCAC 58.419 43.478 41.52 0.00 43.02 3.67
566 572 4.863152 TCACGTCGACGATAATAAGTCA 57.137 40.909 41.52 2.11 43.02 3.41
567 573 4.142028 CGTTCACGTCGACGATAATAAGTC 59.858 45.833 41.52 20.05 41.53 3.01
568 574 4.024438 CGTTCACGTCGACGATAATAAGT 58.976 43.478 41.52 16.22 41.53 2.24
569 575 3.416674 CCGTTCACGTCGACGATAATAAG 59.583 47.826 41.52 24.91 41.53 1.73
570 576 3.353524 CCGTTCACGTCGACGATAATAA 58.646 45.455 41.52 23.38 41.53 1.40
571 577 2.850631 GCCGTTCACGTCGACGATAATA 60.851 50.000 41.52 19.36 41.53 0.98
572 578 1.818850 CCGTTCACGTCGACGATAAT 58.181 50.000 41.52 19.00 41.53 1.28
573 579 0.794229 GCCGTTCACGTCGACGATAA 60.794 55.000 41.52 29.54 41.53 1.75
582 588 0.246635 AGATTGCTAGCCGTTCACGT 59.753 50.000 13.29 0.00 37.74 4.49
584 590 3.259064 TGTAAGATTGCTAGCCGTTCAC 58.741 45.455 13.29 4.01 0.00 3.18
606 612 5.404946 CCACACATTCTTGATTTGATGGTC 58.595 41.667 0.00 0.00 0.00 4.02
651 658 3.425094 CCGTTGAACGAACTGTGTCAAAA 60.425 43.478 20.47 0.00 46.05 2.44
654 662 1.135053 TCCGTTGAACGAACTGTGTCA 60.135 47.619 20.47 0.00 46.05 3.58
672 680 6.652053 TCCTAGTACTTGTCTTCTAGAGTCC 58.348 44.000 0.00 0.00 33.81 3.85
677 685 5.883673 AGTGCTCCTAGTACTTGTCTTCTAG 59.116 44.000 0.00 0.00 37.96 2.43
680 688 5.447548 CGTAGTGCTCCTAGTACTTGTCTTC 60.448 48.000 0.00 0.00 37.96 2.87
682 690 3.940221 CGTAGTGCTCCTAGTACTTGTCT 59.060 47.826 0.00 0.00 37.96 3.41
690 698 1.134580 TCTACGCGTAGTGCTCCTAGT 60.135 52.381 37.32 4.20 45.12 2.57
691 699 1.579698 TCTACGCGTAGTGCTCCTAG 58.420 55.000 37.32 18.23 45.12 3.02
692 700 1.667724 GTTCTACGCGTAGTGCTCCTA 59.332 52.381 37.32 19.49 45.12 2.94
704 712 1.202268 ACTCGCCATGTAGTTCTACGC 60.202 52.381 5.66 2.91 0.00 4.42
705 713 2.451132 CACTCGCCATGTAGTTCTACG 58.549 52.381 5.66 0.00 0.00 3.51
734 742 5.246429 ACTTCTCAAGTTTCTCGGAACCTAT 59.754 40.000 0.00 0.00 39.04 2.57
745 754 8.687824 TTTGTTTGATTGACTTCTCAAGTTTC 57.312 30.769 0.00 0.00 43.03 2.78
769 778 4.143284 GCAAAACAAAAGTCGTCCGTTTTT 60.143 37.500 0.00 0.00 37.61 1.94
770 779 3.365520 GCAAAACAAAAGTCGTCCGTTTT 59.634 39.130 0.00 0.00 39.64 2.43
771 780 2.918600 GCAAAACAAAAGTCGTCCGTTT 59.081 40.909 0.00 0.00 0.00 3.60
772 781 2.162809 AGCAAAACAAAAGTCGTCCGTT 59.837 40.909 0.00 0.00 0.00 4.44
773 782 1.741145 AGCAAAACAAAAGTCGTCCGT 59.259 42.857 0.00 0.00 0.00 4.69
774 783 2.468532 AGCAAAACAAAAGTCGTCCG 57.531 45.000 0.00 0.00 0.00 4.79
775 784 7.806014 TGATTATTAGCAAAACAAAAGTCGTCC 59.194 33.333 0.00 0.00 0.00 4.79
776 785 8.627428 GTGATTATTAGCAAAACAAAAGTCGTC 58.373 33.333 0.00 0.00 0.00 4.20
777 786 8.132362 TGTGATTATTAGCAAAACAAAAGTCGT 58.868 29.630 0.00 0.00 0.00 4.34
778 787 8.500837 TGTGATTATTAGCAAAACAAAAGTCG 57.499 30.769 0.00 0.00 0.00 4.18
785 794 9.646427 GGGTTAAATGTGATTATTAGCAAAACA 57.354 29.630 0.00 0.00 0.00 2.83
786 795 9.093970 GGGGTTAAATGTGATTATTAGCAAAAC 57.906 33.333 0.00 0.00 0.00 2.43
787 796 9.041354 AGGGGTTAAATGTGATTATTAGCAAAA 57.959 29.630 0.00 0.00 0.00 2.44
788 797 8.602472 AGGGGTTAAATGTGATTATTAGCAAA 57.398 30.769 0.00 0.00 0.00 3.68
814 823 4.947388 GGGTGCAATTTAGAGACATTACCA 59.053 41.667 0.00 0.00 0.00 3.25
815 824 4.338400 GGGGTGCAATTTAGAGACATTACC 59.662 45.833 0.00 0.00 0.00 2.85
839 859 1.447489 CTTCTCTCTGCAGCCGGTG 60.447 63.158 9.47 0.89 0.00 4.94
840 860 2.654079 CCTTCTCTCTGCAGCCGGT 61.654 63.158 9.47 0.00 0.00 5.28
842 862 2.511145 GCCTTCTCTCTGCAGCCG 60.511 66.667 9.47 2.34 0.00 5.52
844 864 1.744741 GGTGCCTTCTCTCTGCAGC 60.745 63.158 9.47 0.00 44.83 5.25
954 980 2.179517 GAGCTCCACTGGTCGTCG 59.820 66.667 0.87 0.00 0.00 5.12
965 1016 1.416030 GGAGGAGAAAGATGGAGCTCC 59.584 57.143 26.78 26.78 45.70 4.70
992 1043 1.452833 GAGGAGTCCATTGCTGGCC 60.453 63.158 12.86 0.00 42.80 5.36
1102 1191 1.809547 GAAACAGAGGAGCAAGAAGGC 59.190 52.381 0.00 0.00 0.00 4.35
1110 1199 2.037772 TGGAAGTGAGAAACAGAGGAGC 59.962 50.000 0.00 0.00 0.00 4.70
1111 1200 4.252073 CATGGAAGTGAGAAACAGAGGAG 58.748 47.826 0.00 0.00 0.00 3.69
1172 1264 6.421801 AGAAAAAGTCGGCAAATTCAAATCAG 59.578 34.615 0.00 0.00 0.00 2.90
1188 1280 4.976116 CGGGACAACAAATCAGAAAAAGTC 59.024 41.667 0.00 0.00 0.00 3.01
1190 1282 4.932146 ACGGGACAACAAATCAGAAAAAG 58.068 39.130 0.00 0.00 0.00 2.27
1194 1286 3.490078 GCAAACGGGACAACAAATCAGAA 60.490 43.478 0.00 0.00 0.00 3.02
1204 1296 1.034838 ACAGCAAGCAAACGGGACAA 61.035 50.000 0.00 0.00 0.00 3.18
1640 1835 0.325933 TCCTTGTGTGGCATGAGAGG 59.674 55.000 0.00 0.00 0.00 3.69
1655 1850 1.590932 GCGCATGTCATCATCTCCTT 58.409 50.000 0.30 0.00 31.15 3.36
1658 1853 2.445565 TAGGCGCATGTCATCATCTC 57.554 50.000 10.83 0.00 31.15 2.75
1702 1911 1.112459 GTTCAAAAGCACGCACGAAG 58.888 50.000 0.00 0.00 0.00 3.79
1703 1912 0.587737 CGTTCAAAAGCACGCACGAA 60.588 50.000 0.00 0.00 0.00 3.85
1704 1913 1.011684 CGTTCAAAAGCACGCACGA 60.012 52.632 0.00 0.00 0.00 4.35
1705 1914 2.003443 CCGTTCAAAAGCACGCACG 61.003 57.895 0.00 0.00 34.98 5.34
1708 1917 2.010817 CTGCCGTTCAAAAGCACGC 61.011 57.895 0.00 0.00 34.98 5.34
1893 2115 1.379176 TGTCCGAGCCCTGAGAGAG 60.379 63.158 0.00 0.00 0.00 3.20
1895 2117 2.888863 GTGTCCGAGCCCTGAGAG 59.111 66.667 0.00 0.00 0.00 3.20
1935 2157 3.494048 CCTGGAGTAAATGCTGGCTCTAG 60.494 52.174 0.00 0.00 36.66 2.43
1961 2183 5.977635 TGAGGTTGGACAATATACAGAGTG 58.022 41.667 0.00 0.00 0.00 3.51
2000 2222 2.553079 TGACCAAAACTGTTTGCGAC 57.447 45.000 6.53 1.63 42.44 5.19
2014 2236 3.495983 CGGTATTATCCCAGCATTGACCA 60.496 47.826 0.00 0.00 0.00 4.02
2015 2237 3.074412 CGGTATTATCCCAGCATTGACC 58.926 50.000 0.00 0.00 0.00 4.02
2130 2352 5.407407 TTTCTCCTCGCTTCATCTTAACT 57.593 39.130 0.00 0.00 0.00 2.24
2144 2380 5.047802 TCCAAATGTTCATGCTTTTCTCCTC 60.048 40.000 0.00 0.00 0.00 3.71
2255 2495 4.192429 ACAAAGCAGCTTGTTGTCTTTT 57.808 36.364 8.88 0.00 36.05 2.27
2312 2552 1.295423 GTCGCCTGCTACTCCCAAA 59.705 57.895 0.00 0.00 0.00 3.28
2326 2566 5.746721 GGTCCAATATTTTAAATGTGGTCGC 59.253 40.000 16.54 10.83 0.00 5.19
2366 2606 6.285224 TGATGAAGACCGAAAACACTCTAAA 58.715 36.000 0.00 0.00 0.00 1.85
2392 2635 7.761409 TCAAGCAACGAAGCTGATTATAAATT 58.239 30.769 7.10 0.00 45.89 1.82
2408 2651 9.554724 ACTAATACAATTAACATTCAAGCAACG 57.445 29.630 0.00 0.00 0.00 4.10
2432 2675 9.990868 ATGTTCCTCCTTTGGTAAATATTAACT 57.009 29.630 0.00 0.00 0.00 2.24
2445 2743 4.574013 GTCAGCTGATATGTTCCTCCTTTG 59.426 45.833 21.47 0.00 0.00 2.77
2450 2748 3.494048 CCTGGTCAGCTGATATGTTCCTC 60.494 52.174 21.47 2.96 0.00 3.71
2646 3000 5.299531 GGGAATGGAGAAATTAGTAAGCACC 59.700 44.000 0.00 0.00 0.00 5.01
2651 3013 8.893563 AACATTGGGAATGGAGAAATTAGTAA 57.106 30.769 0.00 0.00 43.21 2.24
2846 3215 6.420604 CACAAAACATGAAGAACCAATGGTAC 59.579 38.462 4.88 0.00 33.12 3.34
2868 3238 7.387673 CCTGTGAAGAGAAACATGTTATACACA 59.612 37.037 12.39 18.26 40.71 3.72
3195 3573 7.595130 AGCGAAGACAGGTCAAATTTTAATTTC 59.405 33.333 1.84 0.00 36.52 2.17
3219 3597 0.952984 AGAAGAGTGCGCCAAGAAGC 60.953 55.000 4.18 0.00 0.00 3.86
3595 3996 7.307694 TGCTGTAATTATTTGCTGTGAAGAAG 58.692 34.615 8.16 0.00 0.00 2.85
3706 4107 0.317160 TTAGTGACAGACCTGTGGCG 59.683 55.000 7.47 0.00 45.05 5.69
3894 4297 9.612620 GAGTTGTCAAACATAAATAAGGAAGTG 57.387 33.333 0.00 0.00 38.88 3.16
3899 4302 9.965824 AAACAGAGTTGTCAAACATAAATAAGG 57.034 29.630 0.00 0.00 38.88 2.69
3926 4679 6.675026 ACATAACTTGTCATGCATATGATGC 58.325 36.000 6.97 4.46 45.78 3.91
4379 5145 6.096705 CACATATATTGTCAGGGCCTTTTCAA 59.903 38.462 1.32 10.28 36.00 2.69
4383 5149 5.129368 ACACATATATTGTCAGGGCCTTT 57.871 39.130 1.32 0.00 36.00 3.11
4861 5634 7.438459 GTGCACGGAGAGTTATACTGAAAATAT 59.562 37.037 0.00 0.00 0.00 1.28
4869 5655 3.090037 AGTGTGCACGGAGAGTTATACT 58.910 45.455 13.13 2.73 36.20 2.12
5031 5817 7.124573 ACAATAGATACTGGTGCAGACATAA 57.875 36.000 0.00 0.00 35.18 1.90
5312 6139 4.844085 TGGAAAGAGAACAGGAATCAGGTA 59.156 41.667 0.00 0.00 0.00 3.08
5327 6154 7.558161 TTATATTCTGTGCATGTGGAAAGAG 57.442 36.000 0.00 0.00 31.20 2.85
5329 6156 7.013559 TCCATTATATTCTGTGCATGTGGAAAG 59.986 37.037 0.00 0.00 0.00 2.62
5336 6165 7.027760 GCAGATTCCATTATATTCTGTGCATG 58.972 38.462 0.00 0.00 36.91 4.06
5430 6261 5.063880 ACACTCCACAGGTTATTTCTTGAC 58.936 41.667 0.00 0.00 0.00 3.18
5533 6364 8.668510 AACATACTTGATGATTCACAGTATCC 57.331 34.615 10.17 0.00 39.06 2.59
5686 6523 7.283127 ACACAAATTGTAGTTCTGTCATTCTGT 59.717 33.333 0.00 0.00 36.32 3.41
5687 6524 7.642669 ACACAAATTGTAGTTCTGTCATTCTG 58.357 34.615 0.00 0.00 36.32 3.02
5688 6525 7.807977 ACACAAATTGTAGTTCTGTCATTCT 57.192 32.000 0.00 0.00 36.32 2.40
5689 6526 9.382244 GTTACACAAATTGTAGTTCTGTCATTC 57.618 33.333 0.00 0.00 41.86 2.67
5690 6527 9.120538 AGTTACACAAATTGTAGTTCTGTCATT 57.879 29.630 0.00 0.00 41.86 2.57
5691 6528 8.559536 CAGTTACACAAATTGTAGTTCTGTCAT 58.440 33.333 0.00 0.00 41.86 3.06
5692 6529 7.551262 ACAGTTACACAAATTGTAGTTCTGTCA 59.449 33.333 19.19 0.77 41.86 3.58
5697 6534 8.504005 AGCATACAGTTACACAAATTGTAGTTC 58.496 33.333 0.00 0.00 41.77 3.01
5721 7025 9.931210 AATATCGCAAGTGTTTAATAAAGTAGC 57.069 29.630 0.00 0.00 39.48 3.58
5742 7171 5.975939 GCAGAACATTGCAGAGGAAAATATC 59.024 40.000 0.00 0.00 43.53 1.63
5771 7200 0.679640 TGCCCCCGTATCTTGCTTTG 60.680 55.000 0.00 0.00 0.00 2.77
5819 7248 1.980765 TCAACCTCCTGCTCATGTTCT 59.019 47.619 0.00 0.00 0.00 3.01
6141 7579 5.640783 ACACTAACCAAAACTTCCGTATAGC 59.359 40.000 0.00 0.00 0.00 2.97
6144 7582 4.758165 CCACACTAACCAAAACTTCCGTAT 59.242 41.667 0.00 0.00 0.00 3.06
6147 7585 2.287368 GCCACACTAACCAAAACTTCCG 60.287 50.000 0.00 0.00 0.00 4.30
6148 7586 2.691011 TGCCACACTAACCAAAACTTCC 59.309 45.455 0.00 0.00 0.00 3.46
6149 7587 3.380320 AGTGCCACACTAACCAAAACTTC 59.620 43.478 0.00 0.00 43.46 3.01
6172 7610 9.810870 TTTACACAATACTAAATTTACACCCCT 57.189 29.630 0.00 0.00 0.00 4.79
6174 7612 9.563898 GCTTTACACAATACTAAATTTACACCC 57.436 33.333 0.00 0.00 0.00 4.61
6209 7647 5.609423 TGCCAGCATCACAAGTAAAATTTT 58.391 33.333 8.75 8.75 0.00 1.82
6210 7648 5.212532 TGCCAGCATCACAAGTAAAATTT 57.787 34.783 0.00 0.00 0.00 1.82
6213 7651 4.870123 ATTGCCAGCATCACAAGTAAAA 57.130 36.364 0.00 0.00 0.00 1.52
6409 7848 6.945218 TGGGGGAATTTCATATTTTGTTCAG 58.055 36.000 0.00 0.00 0.00 3.02
6530 7986 9.114952 GGGAATTCAAATCTTGTTTGGTTTAAA 57.885 29.630 7.93 0.00 0.00 1.52
6532 7988 7.796054 TGGGAATTCAAATCTTGTTTGGTTTA 58.204 30.769 7.93 0.00 0.00 2.01
6654 8154 6.572519 TCTCAAAGTTCCTGAACCATTTTTG 58.427 36.000 6.41 10.17 42.06 2.44
6731 8231 3.256383 TGTTGTTGAGGGATGCAGAAATG 59.744 43.478 0.00 0.00 0.00 2.32
6732 8232 3.499338 TGTTGTTGAGGGATGCAGAAAT 58.501 40.909 0.00 0.00 0.00 2.17
6772 8272 1.940613 GCACGTTGAGGAAAACTGTCT 59.059 47.619 0.00 0.00 0.00 3.41
6809 8309 1.894756 CTGCAAAACCGTTCCCCGA 60.895 57.895 0.00 0.00 39.56 5.14
6909 8412 6.474140 AACCGAAAACAAACCCTAGAAAAT 57.526 33.333 0.00 0.00 0.00 1.82
6913 8416 5.195185 AGAAAACCGAAAACAAACCCTAGA 58.805 37.500 0.00 0.00 0.00 2.43
6916 8419 3.764972 TGAGAAAACCGAAAACAAACCCT 59.235 39.130 0.00 0.00 0.00 4.34



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

AutoCloner maintained by Alex Coulton.