Multiple sequence alignment - TraesCS4A01G458400

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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 TraesCS4A01G458400 chr4A 100.000 4710 0 0 1 4710 723640957 723636248 0.000000e+00 8698.0
1 TraesCS4A01G458400 chr4A 86.330 1346 84 30 3461 4710 723141758 723140417 0.000000e+00 1375.0
2 TraesCS4A01G458400 chr4A 93.462 520 29 1 2830 3344 723142358 723141839 0.000000e+00 767.0
3 TraesCS4A01G458400 chr4A 84.894 470 53 7 1943 2405 723203783 723203325 4.300000e-125 459.0
4 TraesCS4A01G458400 chr4A 88.293 205 24 0 3132 3336 723206169 723205965 3.640000e-61 246.0
5 TraesCS4A01G458400 chr4A 83.041 171 18 6 2881 3042 723203225 723203057 1.370000e-30 145.0
6 TraesCS4A01G458400 chr4A 97.101 69 1 1 4643 4710 723474774 723474842 1.070000e-21 115.0
7 TraesCS4A01G458400 chr4A 79.394 165 23 7 2944 3107 739660948 739660794 6.450000e-19 106.0
8 TraesCS4A01G458400 chr4A 79.394 165 23 7 2944 3107 742067727 742067573 6.450000e-19 106.0
9 TraesCS4A01G458400 chr7A 90.221 3886 274 54 606 4419 12908318 12912169 0.000000e+00 4974.0
10 TraesCS4A01G458400 chr7A 83.219 292 23 10 3437 3703 12973970 12974260 1.310000e-60 244.0
11 TraesCS4A01G458400 chr7A 83.534 249 16 12 1 241 12907684 12907915 4.780000e-50 209.0
12 TraesCS4A01G458400 chr7A 88.166 169 20 0 3453 3621 12981875 12982043 7.990000e-48 202.0
13 TraesCS4A01G458400 chr7A 81.379 145 26 1 3772 3916 12979797 12979940 2.980000e-22 117.0
14 TraesCS4A01G458400 chr7A 95.000 60 1 2 3750 3808 12982112 12982170 5.020000e-15 93.5
15 TraesCS4A01G458400 chr7A 90.323 62 6 0 3750 3811 2740798 2740737 1.090000e-11 82.4
16 TraesCS4A01G458400 chr7A 100.000 28 0 0 3787 3814 12982244 12982271 9.000000e-03 52.8
17 TraesCS4A01G458400 chr7D 92.537 2747 165 20 606 3335 13474835 13477558 0.000000e+00 3901.0
18 TraesCS4A01G458400 chr7D 81.493 1340 104 62 3447 4710 13477617 13478888 0.000000e+00 968.0
19 TraesCS4A01G458400 chr7D 84.365 307 33 7 3956 4258 2888188 2888483 2.140000e-73 287.0
20 TraesCS4A01G458400 chr7D 81.301 369 51 11 3460 3811 2887670 2888037 2.770000e-72 283.0
21 TraesCS4A01G458400 chr7D 82.965 317 41 8 3954 4259 13488344 13488658 1.670000e-69 274.0
22 TraesCS4A01G458400 chr7D 82.661 248 13 16 1 241 13474192 13474416 4.810000e-45 193.0
23 TraesCS4A01G458400 chr7D 85.271 129 18 1 275 403 13474415 13474542 1.060000e-26 132.0
24 TraesCS4A01G458400 chr7D 89.655 58 4 2 3879 3934 2888131 2888188 6.540000e-09 73.1
25 TraesCS4A01G458400 chrUn 100.000 404 0 0 3150 3553 367671452 367671855 0.000000e+00 747.0


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 TraesCS4A01G458400 chr4A 723636248 723640957 4709 True 8698.000000 8698 100.000000 1 4710 1 chr4A.!!$R1 4709
1 TraesCS4A01G458400 chr4A 723140417 723142358 1941 True 1071.000000 1375 89.896000 2830 4710 2 chr4A.!!$R4 1880
2 TraesCS4A01G458400 chr4A 723203057 723206169 3112 True 283.333333 459 85.409333 1943 3336 3 chr4A.!!$R5 1393
3 TraesCS4A01G458400 chr7A 12907684 12912169 4485 False 2591.500000 4974 86.877500 1 4419 2 chr7A.!!$F2 4418
4 TraesCS4A01G458400 chr7D 13474192 13478888 4696 False 1298.500000 3901 85.490500 1 4710 4 chr7D.!!$F3 4709
5 TraesCS4A01G458400 chr7D 2887670 2888483 813 False 214.366667 287 85.107000 3460 4258 3 chr7D.!!$F2 798

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
414 427 0.036732 TTTCTTGTGCTGGCCGAGAT 59.963 50.0 0.0 0.0 0.00 2.75 F
557 594 0.104672 TGGAGGAAACTGTGGGAGGA 60.105 55.0 0.0 0.0 44.43 3.71 F
909 1029 0.167470 CCTGCAATCACACAGCGAAG 59.833 55.0 0.0 0.0 32.37 3.79 F
992 1115 0.249868 TCTTGCAGGTGACAGGAACG 60.250 55.0 0.0 0.0 0.00 3.95 F
2755 2893 0.036388 TGTAGCAACCTAGCAGCACC 60.036 55.0 0.0 0.0 36.85 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 1965 1.113517 ACTGTACCTGTGCCTCGTGT 61.114 55.000 0.00 0.0 0.00 4.49 R
2247 2377 2.634940 ACTACTTTCTTCCAGCAGAGCA 59.365 45.455 0.00 0.0 0.00 4.26 R
2755 2893 2.231529 AGCATCTACGGCTGTACTAGG 58.768 52.381 0.00 0.0 40.80 3.02 R
2952 3098 2.084546 GTTATTCTTGGCGGAACTGCT 58.915 47.619 5.60 0.0 34.52 4.24 R
4420 4916 0.388778 TTGTTGCGCTGCCATCATTG 60.389 50.000 9.73 0.0 0.00 2.82 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
71 74 8.879427 ATAATATAACCAGCCTAAACAATCCC 57.121 34.615 0.00 0.00 0.00 3.85
72 75 2.990740 AACCAGCCTAAACAATCCCA 57.009 45.000 0.00 0.00 0.00 4.37
74 77 2.738743 ACCAGCCTAAACAATCCCATG 58.261 47.619 0.00 0.00 0.00 3.66
75 78 2.034124 CCAGCCTAAACAATCCCATGG 58.966 52.381 4.14 4.14 0.00 3.66
76 79 2.034124 CAGCCTAAACAATCCCATGGG 58.966 52.381 26.30 26.30 0.00 4.00
114 119 2.239400 CCCCTTTCTTCTCCAACCAAC 58.761 52.381 0.00 0.00 0.00 3.77
126 131 1.272212 CCAACCAACCCAATTCTTCGG 59.728 52.381 0.00 0.00 0.00 4.30
132 137 3.478540 CCCAATTCTTCGGGGACTC 57.521 57.895 0.00 0.00 45.08 3.36
133 138 0.107165 CCCAATTCTTCGGGGACTCC 60.107 60.000 0.00 0.00 45.08 3.85
198 208 2.885861 CTTCCTCACCTCGTCCGG 59.114 66.667 0.00 0.00 0.00 5.14
247 259 4.404098 GGAAAGCGCCGAGGGGAA 62.404 66.667 2.29 0.00 34.06 3.97
248 260 2.359478 GAAAGCGCCGAGGGGAAA 60.359 61.111 2.29 0.00 34.06 3.13
249 261 2.359975 AAAGCGCCGAGGGGAAAG 60.360 61.111 2.29 0.00 34.06 2.62
250 262 3.192103 AAAGCGCCGAGGGGAAAGT 62.192 57.895 2.29 0.00 34.06 2.66
251 263 3.901797 AAGCGCCGAGGGGAAAGTG 62.902 63.158 2.29 0.00 34.06 3.16
253 265 4.778143 CGCCGAGGGGAAAGTGGG 62.778 72.222 0.00 0.00 34.06 4.61
254 266 4.426313 GCCGAGGGGAAAGTGGGG 62.426 72.222 0.00 0.00 34.06 4.96
255 267 2.933834 CCGAGGGGAAAGTGGGGT 60.934 66.667 0.00 0.00 34.06 4.95
256 268 2.351276 CGAGGGGAAAGTGGGGTG 59.649 66.667 0.00 0.00 0.00 4.61
257 269 2.035783 GAGGGGAAAGTGGGGTGC 59.964 66.667 0.00 0.00 0.00 5.01
258 270 3.920093 GAGGGGAAAGTGGGGTGCG 62.920 68.421 0.00 0.00 0.00 5.34
278 290 3.922640 GCCCCCTAGAGCTCGCTG 61.923 72.222 8.37 2.37 0.00 5.18
279 291 3.922640 CCCCCTAGAGCTCGCTGC 61.923 72.222 8.37 0.00 43.29 5.25
280 292 3.150335 CCCCTAGAGCTCGCTGCA 61.150 66.667 8.37 0.00 45.94 4.41
281 293 2.416678 CCCTAGAGCTCGCTGCAG 59.583 66.667 10.11 10.11 45.94 4.41
299 311 2.399580 CAGGGGGAAGAGGTAAGGTAG 58.600 57.143 0.00 0.00 0.00 3.18
319 331 0.179073 CCTTATCCCACACCAGCTCG 60.179 60.000 0.00 0.00 0.00 5.03
333 345 3.764466 CTCGCTCGCACTCCCCTT 61.764 66.667 0.00 0.00 0.00 3.95
335 347 4.821589 CGCTCGCACTCCCCTTCC 62.822 72.222 0.00 0.00 0.00 3.46
336 348 3.706373 GCTCGCACTCCCCTTCCA 61.706 66.667 0.00 0.00 0.00 3.53
338 350 1.144936 CTCGCACTCCCCTTCCATC 59.855 63.158 0.00 0.00 0.00 3.51
341 353 2.190578 CACTCCCCTTCCATCCGC 59.809 66.667 0.00 0.00 0.00 5.54
342 354 3.470888 ACTCCCCTTCCATCCGCG 61.471 66.667 0.00 0.00 0.00 6.46
369 381 1.592223 GCCGCCGAGCTTAGGATAT 59.408 57.895 12.70 0.00 0.00 1.63
372 384 0.108615 CGCCGAGCTTAGGATATGGG 60.109 60.000 12.70 0.00 0.00 4.00
374 386 1.338200 GCCGAGCTTAGGATATGGGTG 60.338 57.143 12.70 0.00 0.00 4.61
403 416 5.105997 GGAACCCAATCTCATCTTTCTTGTG 60.106 44.000 0.00 0.00 0.00 3.33
404 417 3.760684 ACCCAATCTCATCTTTCTTGTGC 59.239 43.478 0.00 0.00 0.00 4.57
405 418 4.015084 CCCAATCTCATCTTTCTTGTGCT 58.985 43.478 0.00 0.00 0.00 4.40
409 422 1.471684 CTCATCTTTCTTGTGCTGGCC 59.528 52.381 0.00 0.00 0.00 5.36
412 425 0.603707 TCTTTCTTGTGCTGGCCGAG 60.604 55.000 0.00 0.00 0.00 4.63
413 426 0.603707 CTTTCTTGTGCTGGCCGAGA 60.604 55.000 0.00 0.00 0.00 4.04
414 427 0.036732 TTTCTTGTGCTGGCCGAGAT 59.963 50.000 0.00 0.00 0.00 2.75
417 430 0.463295 CTTGTGCTGGCCGAGATGAT 60.463 55.000 0.00 0.00 0.00 2.45
419 432 0.104855 TGTGCTGGCCGAGATGATAC 59.895 55.000 0.00 0.00 0.00 2.24
420 433 0.941463 GTGCTGGCCGAGATGATACG 60.941 60.000 0.00 0.00 0.00 3.06
421 434 2.024319 GCTGGCCGAGATGATACGC 61.024 63.158 0.00 0.00 0.00 4.42
423 457 2.087462 CTGGCCGAGATGATACGCCA 62.087 60.000 0.00 0.00 35.67 5.69
437 471 3.029981 GCCAATCCCCTCCCCCTT 61.030 66.667 0.00 0.00 0.00 3.95
438 472 3.074907 GCCAATCCCCTCCCCCTTC 62.075 68.421 0.00 0.00 0.00 3.46
441 475 0.553333 CAATCCCCTCCCCCTTCTTC 59.447 60.000 0.00 0.00 0.00 2.87
443 477 0.624795 ATCCCCTCCCCCTTCTTCAC 60.625 60.000 0.00 0.00 0.00 3.18
444 478 1.229984 CCCCTCCCCCTTCTTCACT 60.230 63.158 0.00 0.00 0.00 3.41
445 479 1.566298 CCCCTCCCCCTTCTTCACTG 61.566 65.000 0.00 0.00 0.00 3.66
448 482 1.705186 CCTCCCCCTTCTTCACTGAAA 59.295 52.381 0.00 0.00 0.00 2.69
449 483 2.108250 CCTCCCCCTTCTTCACTGAAAA 59.892 50.000 0.00 0.00 0.00 2.29
450 484 3.149981 CTCCCCCTTCTTCACTGAAAAC 58.850 50.000 0.00 0.00 0.00 2.43
455 489 4.401925 CCCTTCTTCACTGAAAACAGGAT 58.598 43.478 10.37 0.00 0.00 3.24
456 490 4.217118 CCCTTCTTCACTGAAAACAGGATG 59.783 45.833 10.37 0.00 46.00 3.51
457 491 4.217118 CCTTCTTCACTGAAAACAGGATGG 59.783 45.833 0.00 1.97 43.62 3.51
458 492 3.754965 TCTTCACTGAAAACAGGATGGG 58.245 45.455 0.00 0.00 43.62 4.00
459 493 3.138283 TCTTCACTGAAAACAGGATGGGT 59.862 43.478 0.00 0.00 43.62 4.51
460 494 3.593442 TCACTGAAAACAGGATGGGTT 57.407 42.857 0.00 0.00 43.62 4.11
513 550 1.358152 CCCTCACTGGTTGGTTCCTA 58.642 55.000 0.00 0.00 0.00 2.94
517 554 0.953960 CACTGGTTGGTTCCTACGGC 60.954 60.000 0.00 0.00 0.00 5.68
523 560 0.693622 TTGGTTCCTACGGCCAATGA 59.306 50.000 2.24 0.00 37.36 2.57
525 562 0.463833 GGTTCCTACGGCCAATGAGG 60.464 60.000 2.24 2.92 41.84 3.86
539 576 3.242969 CCAATGAGGCGATGAATTCAGTG 60.243 47.826 14.54 9.57 35.93 3.66
543 580 1.134280 AGGCGATGAATTCAGTGGAGG 60.134 52.381 14.54 0.75 0.00 4.30
547 584 3.181506 GCGATGAATTCAGTGGAGGAAAC 60.182 47.826 14.54 0.00 0.00 2.78
549 586 4.093998 CGATGAATTCAGTGGAGGAAACTG 59.906 45.833 14.54 0.00 44.43 3.16
550 587 4.437682 TGAATTCAGTGGAGGAAACTGT 57.562 40.909 3.38 0.00 44.42 3.55
551 588 4.136796 TGAATTCAGTGGAGGAAACTGTG 58.863 43.478 3.38 0.00 44.42 3.66
553 590 0.764890 TCAGTGGAGGAAACTGTGGG 59.235 55.000 3.70 0.00 44.42 4.61
554 591 0.764890 CAGTGGAGGAAACTGTGGGA 59.235 55.000 0.00 0.00 44.43 4.37
555 592 1.059913 AGTGGAGGAAACTGTGGGAG 58.940 55.000 0.00 0.00 44.43 4.30
557 594 0.104672 TGGAGGAAACTGTGGGAGGA 60.105 55.000 0.00 0.00 44.43 3.71
560 597 2.844348 GGAGGAAACTGTGGGAGGAATA 59.156 50.000 0.00 0.00 44.43 1.75
562 599 4.445019 GGAGGAAACTGTGGGAGGAATATC 60.445 50.000 0.00 0.00 44.43 1.63
563 600 4.111577 AGGAAACTGTGGGAGGAATATCA 58.888 43.478 0.00 0.00 41.13 2.15
564 601 4.540099 AGGAAACTGTGGGAGGAATATCAA 59.460 41.667 0.00 0.00 41.13 2.57
565 602 5.194537 AGGAAACTGTGGGAGGAATATCAAT 59.805 40.000 0.00 0.00 41.13 2.57
567 604 7.060421 GGAAACTGTGGGAGGAATATCAATTA 58.940 38.462 0.00 0.00 0.00 1.40
568 605 7.229506 GGAAACTGTGGGAGGAATATCAATTAG 59.770 40.741 0.00 0.00 0.00 1.73
569 606 6.831664 ACTGTGGGAGGAATATCAATTAGT 57.168 37.500 0.00 0.00 0.00 2.24
570 607 7.213178 ACTGTGGGAGGAATATCAATTAGTT 57.787 36.000 0.00 0.00 0.00 2.24
571 608 7.643123 ACTGTGGGAGGAATATCAATTAGTTT 58.357 34.615 0.00 0.00 0.00 2.66
575 612 8.214364 GTGGGAGGAATATCAATTAGTTTCTCT 58.786 37.037 0.00 0.00 0.00 3.10
576 613 8.213679 TGGGAGGAATATCAATTAGTTTCTCTG 58.786 37.037 0.00 0.00 0.00 3.35
577 614 7.663493 GGGAGGAATATCAATTAGTTTCTCTGG 59.337 40.741 0.00 0.00 0.00 3.86
585 622 7.466746 TCAATTAGTTTCTCTGGAATTTGGG 57.533 36.000 0.00 0.00 0.00 4.12
586 623 7.010160 TCAATTAGTTTCTCTGGAATTTGGGT 58.990 34.615 0.00 0.00 0.00 4.51
587 624 7.508977 TCAATTAGTTTCTCTGGAATTTGGGTT 59.491 33.333 0.00 0.00 0.00 4.11
588 625 6.648879 TTAGTTTCTCTGGAATTTGGGTTG 57.351 37.500 0.00 0.00 0.00 3.77
589 626 3.321968 AGTTTCTCTGGAATTTGGGTTGC 59.678 43.478 0.00 0.00 0.00 4.17
590 627 1.533625 TCTCTGGAATTTGGGTTGCG 58.466 50.000 0.00 0.00 0.00 4.85
591 628 1.202879 TCTCTGGAATTTGGGTTGCGT 60.203 47.619 0.00 0.00 0.00 5.24
592 629 1.200020 CTCTGGAATTTGGGTTGCGTC 59.800 52.381 0.00 0.00 0.00 5.19
593 630 0.243636 CTGGAATTTGGGTTGCGTCC 59.756 55.000 0.00 0.00 0.00 4.79
600 637 2.351276 GGGTTGCGTCCCACTCAT 59.649 61.111 10.62 0.00 46.30 2.90
601 638 1.303317 GGGTTGCGTCCCACTCATT 60.303 57.895 10.62 0.00 46.30 2.57
602 639 1.305930 GGGTTGCGTCCCACTCATTC 61.306 60.000 10.62 0.00 46.30 2.67
604 641 1.066430 GGTTGCGTCCCACTCATTCTA 60.066 52.381 0.00 0.00 0.00 2.10
617 729 5.212934 CACTCATTCTATGCACATCATTGC 58.787 41.667 0.00 0.00 43.31 3.56
622 734 4.700268 TCTATGCACATCATTGCGTTTT 57.300 36.364 0.00 0.00 46.20 2.43
624 736 4.858140 TCTATGCACATCATTGCGTTTTTG 59.142 37.500 0.00 0.00 46.20 2.44
633 745 3.064134 TCATTGCGTTTTTGTTCTGTCGA 59.936 39.130 0.00 0.00 0.00 4.20
634 746 2.445453 TGCGTTTTTGTTCTGTCGAC 57.555 45.000 9.11 9.11 0.00 4.20
637 749 3.165124 GCGTTTTTGTTCTGTCGACAAA 58.835 40.909 20.49 13.48 43.16 2.83
638 750 3.237433 GCGTTTTTGTTCTGTCGACAAAG 59.763 43.478 20.49 9.16 44.83 2.77
658 770 2.575279 AGAGTGTCAGGCAAGGATGATT 59.425 45.455 0.00 0.00 0.00 2.57
660 772 2.040813 AGTGTCAGGCAAGGATGATTGT 59.959 45.455 0.00 0.00 32.56 2.71
664 777 3.624861 GTCAGGCAAGGATGATTGTACTG 59.375 47.826 0.00 0.00 38.00 2.74
671 788 5.575957 CAAGGATGATTGTACTGATTGCAC 58.424 41.667 0.00 0.00 0.00 4.57
716 833 4.248058 GCAGCTGCCATTCTTGTTTAATT 58.752 39.130 28.76 0.00 34.31 1.40
720 837 5.127682 AGCTGCCATTCTTGTTTAATTAGGG 59.872 40.000 0.00 0.00 0.00 3.53
747 866 0.744281 GGGGAGAGAGAGCTTCTTCG 59.256 60.000 0.00 0.00 35.87 3.79
773 892 4.275810 CCCCCATTATCCATTCATAGCTG 58.724 47.826 0.00 0.00 0.00 4.24
800 919 3.820467 CTGTCACATTCCACTTTGCCTTA 59.180 43.478 0.00 0.00 0.00 2.69
853 972 7.008021 AGTTGCAAAAATTCAATCCTGGTAT 57.992 32.000 0.00 0.00 0.00 2.73
871 991 6.540189 CCTGGTATTGTTTCAGAGTTATGGAG 59.460 42.308 0.00 0.00 0.00 3.86
878 998 1.751351 TCAGAGTTATGGAGCACCTCG 59.249 52.381 0.71 0.00 37.04 4.63
881 1001 3.034635 AGAGTTATGGAGCACCTCGATT 58.965 45.455 0.71 0.00 37.04 3.34
890 1010 3.120165 GGAGCACCTCGATTTGTTCTTTC 60.120 47.826 9.23 0.00 0.00 2.62
909 1029 0.167470 CCTGCAATCACACAGCGAAG 59.833 55.000 0.00 0.00 32.37 3.79
911 1031 0.867746 TGCAATCACACAGCGAAGTC 59.132 50.000 0.00 0.00 0.00 3.01
919 1039 4.377021 TCACACAGCGAAGTCACTTTAAT 58.623 39.130 0.00 0.00 0.00 1.40
922 1042 3.125316 CACAGCGAAGTCACTTTAATCCC 59.875 47.826 0.00 0.00 0.00 3.85
926 1046 3.868754 GCGAAGTCACTTTAATCCCCTGT 60.869 47.826 0.00 0.00 0.00 4.00
928 1048 3.611766 AGTCACTTTAATCCCCTGTCG 57.388 47.619 0.00 0.00 0.00 4.35
929 1049 3.170717 AGTCACTTTAATCCCCTGTCGA 58.829 45.455 0.00 0.00 0.00 4.20
930 1050 3.581332 AGTCACTTTAATCCCCTGTCGAA 59.419 43.478 0.00 0.00 0.00 3.71
943 1063 3.187700 CCTGTCGAATGTTAGTGCTACC 58.812 50.000 0.00 0.00 0.00 3.18
954 1074 1.227380 GTGCTACCGCTCCATCCAG 60.227 63.158 0.00 0.00 36.97 3.86
992 1115 0.249868 TCTTGCAGGTGACAGGAACG 60.250 55.000 0.00 0.00 0.00 3.95
1018 1141 2.803155 GATGCGCCACCTGGAGTTCA 62.803 60.000 4.18 0.00 37.33 3.18
1220 1343 2.982130 GTCCGTGCCATCCTCAGT 59.018 61.111 0.00 0.00 0.00 3.41
1423 1546 1.540267 TAAATTGTTCCGGTGCCTGG 58.460 50.000 0.00 0.00 0.00 4.45
1443 1566 2.202756 CCTGCGCCTCCGAACTAC 60.203 66.667 4.18 0.00 36.29 2.73
1497 1620 6.374333 GGGATTATGCGTGGTATGATAACATT 59.626 38.462 0.00 0.00 37.87 2.71
1518 1641 1.115467 CTCACCGGGAGCTGAGTATT 58.885 55.000 6.32 0.00 36.69 1.89
1572 1695 1.300963 GGACCGGTTTAGGTTCCCC 59.699 63.158 9.42 0.00 46.09 4.81
1599 1722 2.824041 ACGATGTTCCCGCATGGC 60.824 61.111 0.00 0.00 0.00 4.40
1645 1768 3.005050 CGATGCCCTCATACCGTTAACTA 59.995 47.826 3.71 0.00 31.96 2.24
1692 1815 1.499007 ACTGGATGTGGGGTGAGTTTT 59.501 47.619 0.00 0.00 0.00 2.43
1706 1829 5.753438 GGGTGAGTTTTCTTGACAAATTTCC 59.247 40.000 0.00 0.00 0.00 3.13
1733 1856 8.668510 TGATATTGTTTCTTATCTCTGAAGGC 57.331 34.615 0.00 0.00 0.00 4.35
1740 1863 7.038302 TGTTTCTTATCTCTGAAGGCTTTAGGA 60.038 37.037 17.77 13.92 0.00 2.94
1842 1965 2.562298 GTCATTTGCACCAAGGGATTCA 59.438 45.455 0.00 0.00 0.00 2.57
1947 2070 2.019249 GCTAGAGCATTTGACATGGCA 58.981 47.619 0.00 0.00 41.59 4.92
1980 2103 5.085920 AGATGTTTGATCCCATGGAACAAA 58.914 37.500 15.22 17.96 46.83 2.83
1996 2121 5.209977 GGAACAAACTCGGTATGTTTTCAC 58.790 41.667 0.00 0.00 37.41 3.18
2014 2139 7.009083 TGTTTTCACGACATTGTTTCAGATTTG 59.991 33.333 0.00 0.00 0.00 2.32
2152 2282 1.412361 GGCTACTGGATCCTCTCTGGT 60.412 57.143 14.23 5.03 37.07 4.00
2247 2377 2.843113 AGATTGAGGACCTAGCAAAGCT 59.157 45.455 0.00 0.00 43.41 3.74
2398 2528 4.583871 ACTCTGCTTGGTAAGATTTCTGG 58.416 43.478 0.00 0.00 0.00 3.86
2463 2593 4.835615 AGCTCATTATCTGTAGTTCCGGAT 59.164 41.667 4.15 0.00 0.00 4.18
2464 2594 5.047660 AGCTCATTATCTGTAGTTCCGGATC 60.048 44.000 4.15 4.19 0.00 3.36
2470 2600 4.884668 TCTGTAGTTCCGGATCAACTTT 57.115 40.909 12.37 0.00 35.63 2.66
2481 2611 4.440112 CCGGATCAACTTTTATTTCTGGCC 60.440 45.833 0.00 0.00 0.00 5.36
2557 2687 5.507482 CCTCATGCTTGAAATCATAGCTTGG 60.507 44.000 20.10 15.02 36.72 3.61
2569 2706 8.414629 AAATCATAGCTTGGATTTCCTATTCC 57.585 34.615 15.60 0.00 38.93 3.01
2606 2744 6.628919 AATTTAACAGGTTTCGCTAACACT 57.371 33.333 0.00 0.00 38.55 3.55
2660 2798 9.384764 GCTAAGTATCAGTTTATCTTTCCTGTT 57.615 33.333 0.00 0.00 0.00 3.16
2693 2831 8.134895 GGAAACATTGTACAATCTTTTGTCTGA 58.865 33.333 18.25 0.00 42.43 3.27
2716 2854 5.482908 ACTTATGGCTCAGTTCACTTACAG 58.517 41.667 0.00 0.00 0.00 2.74
2755 2893 0.036388 TGTAGCAACCTAGCAGCACC 60.036 55.000 0.00 0.00 36.85 5.01
2765 2903 1.067821 CTAGCAGCACCCTAGTACAGC 59.932 57.143 0.00 0.00 0.00 4.40
2767 2905 1.141881 CAGCACCCTAGTACAGCCG 59.858 63.158 0.00 0.00 0.00 5.52
2784 2922 2.766828 AGCCGTAGATGCTTAGAACCTT 59.233 45.455 0.00 0.00 34.87 3.50
2787 2925 5.105064 AGCCGTAGATGCTTAGAACCTTAAA 60.105 40.000 0.00 0.00 34.87 1.52
2793 2931 9.384764 GTAGATGCTTAGAACCTTAAACTCATT 57.615 33.333 0.00 0.00 0.00 2.57
2952 3098 2.519771 AATGGCCAGAAAGAGCATCA 57.480 45.000 13.05 0.00 37.82 3.07
2964 3110 2.747460 GCATCAGCAGTTCCGCCA 60.747 61.111 0.00 0.00 41.58 5.69
3009 3155 1.272147 GGCATCACCCCTGAGAAGTTT 60.272 52.381 0.00 0.00 0.00 2.66
3018 3164 3.073062 CCCCTGAGAAGTTTGAAGAGGAA 59.927 47.826 0.00 0.00 0.00 3.36
3051 3197 3.917760 GAGCGAGCGGGCCACTAT 61.918 66.667 4.39 0.00 0.00 2.12
3108 3254 2.416547 CAGGAACGTGATGGACATGAAC 59.583 50.000 0.00 0.00 38.72 3.18
3116 3262 2.818274 GGACATGAACGCGGGGAC 60.818 66.667 12.47 0.00 0.00 4.46
3329 3475 6.939163 AGCTTTTATCAGGATAGGTAATGCAG 59.061 38.462 0.00 0.00 0.00 4.41
3357 3503 1.847818 TGGTTTGAGTTCTGTCGTCG 58.152 50.000 0.00 0.00 0.00 5.12
3379 3527 3.983344 GTGTACCTTTTCTGCTGCATTTG 59.017 43.478 1.31 0.00 0.00 2.32
3526 3692 1.043116 AGATGGACCGGATTCTGCGA 61.043 55.000 9.46 0.00 30.86 5.10
3591 3786 2.213499 GAAGATACAAGCCATCACCGG 58.787 52.381 0.00 0.00 0.00 5.28
3682 3877 2.490991 GCCGTCAAAACTTACTGGACT 58.509 47.619 0.00 0.00 0.00 3.85
3716 3929 3.155998 CAAAAGCAGCAATAGTCGTTCG 58.844 45.455 0.00 0.00 0.00 3.95
3726 3939 3.589061 ATAGTCGTTCGACGTCATCTC 57.411 47.619 17.16 1.85 43.14 2.75
3817 4071 9.245481 GGATATATCTGTATATAGTAGGTGGGC 57.755 40.741 12.42 0.00 34.71 5.36
3952 4245 4.941263 TCAACCGTTCCAAGAGGATATTTG 59.059 41.667 0.00 0.00 45.26 2.32
3978 4271 3.220674 AGTTTTGAGAAAGCTGGCTCT 57.779 42.857 14.87 5.49 30.32 4.09
3991 4284 1.671328 CTGGCTCTGATGAATGTGCTG 59.329 52.381 0.00 0.00 0.00 4.41
4002 4295 0.806868 AATGTGCTGCTGTCCGAATG 59.193 50.000 0.00 0.00 0.00 2.67
4107 4408 7.329226 CCAAATACGAAACATCTGCTCAAAAAT 59.671 33.333 0.00 0.00 0.00 1.82
4250 4716 3.689347 TGATAAGCCAAGCTGAATGTGT 58.311 40.909 0.00 0.00 39.62 3.72
4261 4727 3.068590 AGCTGAATGTGTTGGTTTCCAAG 59.931 43.478 1.16 0.00 44.82 3.61
4286 4775 6.433766 CAATCTTCAACAGGAAAGAGAACAC 58.566 40.000 0.00 0.00 34.44 3.32
4336 4829 6.862090 ACTTAACTTACAGTTCATCGTCTGAC 59.138 38.462 0.00 0.00 39.51 3.51
4347 4840 3.192844 TCATCGTCTGACTGAAACCTACC 59.807 47.826 6.21 0.00 0.00 3.18
4357 4853 4.223953 ACTGAAACCTACCAGAAGACTCA 58.776 43.478 0.00 0.00 34.65 3.41
4373 4869 1.837439 ACTCAAGTCACTGAACACCCA 59.163 47.619 0.00 0.00 0.00 4.51
4385 4881 0.673437 AACACCCAAAATGACAGGCG 59.327 50.000 0.00 0.00 0.00 5.52
4407 4903 1.462283 CCGGCAGCATGAAGAATATCG 59.538 52.381 0.00 0.00 39.69 2.92
4419 4915 7.483375 GCATGAAGAATATCGCTACTACTACTG 59.517 40.741 0.00 0.00 0.00 2.74
4420 4916 6.900189 TGAAGAATATCGCTACTACTACTGC 58.100 40.000 0.00 0.00 0.00 4.40
4537 5065 6.730960 TTCCATCAACGGAATACAAAGTAC 57.269 37.500 0.00 0.00 40.20 2.73
4539 5067 4.493545 CCATCAACGGAATACAAAGTACGC 60.494 45.833 0.00 0.00 0.00 4.42
4540 5068 3.651206 TCAACGGAATACAAAGTACGCA 58.349 40.909 0.00 0.00 0.00 5.24
4543 5071 2.733026 ACGGAATACAAAGTACGCACAC 59.267 45.455 0.00 0.00 0.00 3.82
4552 5626 2.029815 TACGCACACGCACACCAT 59.970 55.556 0.00 0.00 45.53 3.55
4573 5647 4.065321 TGCATGGTTTACAAAACTTGGG 57.935 40.909 7.49 0.00 32.98 4.12
4603 5677 2.144730 GCACGGTACACACAACCATTA 58.855 47.619 0.00 0.00 36.78 1.90
4609 5683 7.623770 CACGGTACACACAACCATTATATTAC 58.376 38.462 0.00 0.00 36.78 1.89
4618 5695 6.978080 CACAACCATTATATTACAAACCAGCC 59.022 38.462 0.00 0.00 0.00 4.85
4619 5696 6.665680 ACAACCATTATATTACAAACCAGCCA 59.334 34.615 0.00 0.00 0.00 4.75
4620 5697 6.959639 ACCATTATATTACAAACCAGCCAG 57.040 37.500 0.00 0.00 0.00 4.85
4621 5698 6.431722 ACCATTATATTACAAACCAGCCAGT 58.568 36.000 0.00 0.00 0.00 4.00
4632 5709 3.788227 ACCAGCCAGTTTGATCAACTA 57.212 42.857 7.89 0.00 44.60 2.24
4643 5720 6.017192 CAGTTTGATCAACTATGAACACCACA 60.017 38.462 7.89 0.00 44.60 4.17
4644 5721 5.940192 TTGATCAACTATGAACACCACAC 57.060 39.130 3.38 0.00 37.99 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 9.969001 GGGATTGTTTAGGCTGGTTATATTATA 57.031 33.333 0.00 0.00 0.00 0.98
46 47 8.452868 TGGGATTGTTTAGGCTGGTTATATTAT 58.547 33.333 0.00 0.00 0.00 1.28
47 48 7.817440 TGGGATTGTTTAGGCTGGTTATATTA 58.183 34.615 0.00 0.00 0.00 0.98
48 49 6.678547 TGGGATTGTTTAGGCTGGTTATATT 58.321 36.000 0.00 0.00 0.00 1.28
49 50 6.274322 TGGGATTGTTTAGGCTGGTTATAT 57.726 37.500 0.00 0.00 0.00 0.86
56 57 2.034124 CCCATGGGATTGTTTAGGCTG 58.966 52.381 28.27 0.00 37.50 4.85
67 70 4.731929 ACCAAATCTAGTAACCCATGGGAT 59.268 41.667 38.07 28.40 38.96 3.85
68 71 4.116113 ACCAAATCTAGTAACCCATGGGA 58.884 43.478 38.07 13.74 38.96 4.37
69 72 4.519906 ACCAAATCTAGTAACCCATGGG 57.480 45.455 30.23 30.23 42.03 4.00
70 73 4.887655 GGAACCAAATCTAGTAACCCATGG 59.112 45.833 4.14 4.14 0.00 3.66
114 119 0.107165 GGAGTCCCCGAAGAATTGGG 60.107 60.000 0.00 0.00 44.41 4.12
206 216 4.662961 TGCAGCAGTGTCGACGGG 62.663 66.667 11.62 3.78 0.00 5.28
208 218 3.406361 GGTGCAGCAGTGTCGACG 61.406 66.667 11.86 0.00 0.00 5.12
209 219 3.044305 GGGTGCAGCAGTGTCGAC 61.044 66.667 19.06 9.11 0.00 4.20
211 221 3.046087 CTGGGTGCAGCAGTGTCG 61.046 66.667 19.06 0.00 0.00 4.35
212 222 2.670934 CCTGGGTGCAGCAGTGTC 60.671 66.667 19.06 0.00 0.00 3.67
213 223 4.275508 CCCTGGGTGCAGCAGTGT 62.276 66.667 19.06 0.00 0.00 3.55
216 226 3.512154 TTTCCCCTGGGTGCAGCAG 62.512 63.158 19.06 12.61 36.47 4.24
217 227 3.506743 TTTCCCCTGGGTGCAGCA 61.507 61.111 19.06 0.00 36.47 4.41
218 228 2.677875 CTTTCCCCTGGGTGCAGC 60.678 66.667 12.71 7.55 36.47 5.25
241 253 3.966543 CGCACCCCACTTTCCCCT 61.967 66.667 0.00 0.00 0.00 4.79
261 273 3.922640 CAGCGAGCTCTAGGGGGC 61.923 72.222 12.85 6.53 0.00 5.80
262 274 3.922640 GCAGCGAGCTCTAGGGGG 61.923 72.222 12.85 0.00 41.15 5.40
263 275 3.149338 CTGCAGCGAGCTCTAGGGG 62.149 68.421 12.85 0.00 45.94 4.79
264 276 2.416678 CTGCAGCGAGCTCTAGGG 59.583 66.667 12.85 0.00 45.94 3.53
265 277 2.416678 CCTGCAGCGAGCTCTAGG 59.583 66.667 12.85 7.67 45.94 3.02
266 278 2.416678 CCCTGCAGCGAGCTCTAG 59.583 66.667 12.85 2.30 45.94 2.43
267 279 3.150335 CCCCTGCAGCGAGCTCTA 61.150 66.667 12.85 0.00 45.94 2.43
272 284 3.382803 CTCTTCCCCCTGCAGCGAG 62.383 68.421 8.66 0.00 0.00 5.03
273 285 3.393970 CTCTTCCCCCTGCAGCGA 61.394 66.667 8.66 0.00 0.00 4.93
274 286 4.479993 CCTCTTCCCCCTGCAGCG 62.480 72.222 8.66 0.00 0.00 5.18
275 287 1.562672 TTACCTCTTCCCCCTGCAGC 61.563 60.000 8.66 0.00 0.00 5.25
276 288 0.543749 CTTACCTCTTCCCCCTGCAG 59.456 60.000 6.78 6.78 0.00 4.41
277 289 0.914417 CCTTACCTCTTCCCCCTGCA 60.914 60.000 0.00 0.00 0.00 4.41
278 290 0.914902 ACCTTACCTCTTCCCCCTGC 60.915 60.000 0.00 0.00 0.00 4.85
279 291 2.399580 CTACCTTACCTCTTCCCCCTG 58.600 57.143 0.00 0.00 0.00 4.45
280 292 1.344189 GCTACCTTACCTCTTCCCCCT 60.344 57.143 0.00 0.00 0.00 4.79
281 293 1.129917 GCTACCTTACCTCTTCCCCC 58.870 60.000 0.00 0.00 0.00 5.40
299 311 0.464554 GAGCTGGTGTGGGATAAGGC 60.465 60.000 0.00 0.00 0.00 4.35
319 331 2.932130 GATGGAAGGGGAGTGCGAGC 62.932 65.000 0.00 0.00 0.00 5.03
372 384 3.140325 TGAGATTGGGTTCCTTGACAC 57.860 47.619 0.00 0.00 0.00 3.67
374 386 4.227864 AGATGAGATTGGGTTCCTTGAC 57.772 45.455 0.00 0.00 0.00 3.18
403 416 2.024319 GCGTATCATCTCGGCCAGC 61.024 63.158 2.24 0.00 0.00 4.85
404 417 1.373497 GGCGTATCATCTCGGCCAG 60.373 63.158 2.24 0.00 44.62 4.85
405 418 2.734591 GGCGTATCATCTCGGCCA 59.265 61.111 2.24 0.00 44.62 5.36
409 422 1.673033 GGGGATTGGCGTATCATCTCG 60.673 57.143 2.46 0.00 0.00 4.04
412 425 1.339151 GGAGGGGATTGGCGTATCATC 60.339 57.143 2.46 0.00 0.00 2.92
413 426 0.693049 GGAGGGGATTGGCGTATCAT 59.307 55.000 2.46 0.00 0.00 2.45
414 427 1.415672 GGGAGGGGATTGGCGTATCA 61.416 60.000 2.46 0.00 0.00 2.15
417 430 2.770904 GGGGAGGGGATTGGCGTA 60.771 66.667 0.00 0.00 0.00 4.42
420 433 3.029981 AAGGGGGAGGGGATTGGC 61.030 66.667 0.00 0.00 0.00 4.52
421 434 0.926220 AAGAAGGGGGAGGGGATTGG 60.926 60.000 0.00 0.00 0.00 3.16
423 457 0.123266 TGAAGAAGGGGGAGGGGATT 59.877 55.000 0.00 0.00 0.00 3.01
437 471 3.138283 ACCCATCCTGTTTTCAGTGAAGA 59.862 43.478 5.56 0.00 45.68 2.87
438 472 3.490348 ACCCATCCTGTTTTCAGTGAAG 58.510 45.455 5.56 0.00 45.68 3.02
441 475 4.670896 AAAACCCATCCTGTTTTCAGTG 57.329 40.909 0.00 0.00 45.68 3.66
466 500 4.402056 AGAATCTATCTTTTCGGCGGAA 57.598 40.909 7.21 0.00 33.39 4.30
467 501 4.402056 AAGAATCTATCTTTTCGGCGGA 57.598 40.909 7.21 0.00 46.39 5.54
517 554 2.947652 ACTGAATTCATCGCCTCATTGG 59.052 45.455 8.96 0.00 39.35 3.16
523 560 1.134280 CCTCCACTGAATTCATCGCCT 60.134 52.381 8.96 0.00 0.00 5.52
525 562 2.315925 TCCTCCACTGAATTCATCGC 57.684 50.000 8.96 0.00 0.00 4.58
530 567 3.503748 CCACAGTTTCCTCCACTGAATTC 59.496 47.826 7.06 0.00 43.90 2.17
533 570 1.142870 CCCACAGTTTCCTCCACTGAA 59.857 52.381 7.06 0.00 43.90 3.02
536 573 1.059913 CTCCCACAGTTTCCTCCACT 58.940 55.000 0.00 0.00 0.00 4.00
539 576 1.064825 TTCCTCCCACAGTTTCCTCC 58.935 55.000 0.00 0.00 0.00 4.30
543 580 7.775561 ACTAATTGATATTCCTCCCACAGTTTC 59.224 37.037 0.00 0.00 0.00 2.78
547 584 7.995488 AGAAACTAATTGATATTCCTCCCACAG 59.005 37.037 0.00 0.00 0.00 3.66
549 586 8.214364 AGAGAAACTAATTGATATTCCTCCCAC 58.786 37.037 0.00 0.00 0.00 4.61
550 587 8.213679 CAGAGAAACTAATTGATATTCCTCCCA 58.786 37.037 0.00 0.00 0.00 4.37
551 588 7.663493 CCAGAGAAACTAATTGATATTCCTCCC 59.337 40.741 0.00 0.00 0.00 4.30
553 590 9.838339 TTCCAGAGAAACTAATTGATATTCCTC 57.162 33.333 0.00 0.00 0.00 3.71
560 597 7.675619 ACCCAAATTCCAGAGAAACTAATTGAT 59.324 33.333 0.00 0.00 35.09 2.57
562 599 7.232118 ACCCAAATTCCAGAGAAACTAATTG 57.768 36.000 0.00 0.00 35.09 2.32
563 600 7.670364 CAACCCAAATTCCAGAGAAACTAATT 58.330 34.615 0.00 0.00 35.09 1.40
564 601 6.295292 GCAACCCAAATTCCAGAGAAACTAAT 60.295 38.462 0.00 0.00 35.09 1.73
565 602 5.010617 GCAACCCAAATTCCAGAGAAACTAA 59.989 40.000 0.00 0.00 35.09 2.24
567 604 3.321968 GCAACCCAAATTCCAGAGAAACT 59.678 43.478 0.00 0.00 35.09 2.66
568 605 3.653344 GCAACCCAAATTCCAGAGAAAC 58.347 45.455 0.00 0.00 35.09 2.78
569 606 2.295909 CGCAACCCAAATTCCAGAGAAA 59.704 45.455 0.00 0.00 35.09 2.52
570 607 1.885887 CGCAACCCAAATTCCAGAGAA 59.114 47.619 0.00 0.00 36.15 2.87
571 608 1.202879 ACGCAACCCAAATTCCAGAGA 60.203 47.619 0.00 0.00 0.00 3.10
575 612 2.346597 GGACGCAACCCAAATTCCA 58.653 52.632 0.00 0.00 0.00 3.53
585 622 2.380084 TAGAATGAGTGGGACGCAAC 57.620 50.000 0.00 0.00 44.14 4.17
586 623 2.905075 CATAGAATGAGTGGGACGCAA 58.095 47.619 0.00 0.00 44.14 4.85
587 624 1.473257 GCATAGAATGAGTGGGACGCA 60.473 52.381 0.00 0.00 44.14 5.24
588 625 1.221414 GCATAGAATGAGTGGGACGC 58.779 55.000 0.00 0.00 40.45 5.19
589 626 2.205074 GTGCATAGAATGAGTGGGACG 58.795 52.381 0.00 0.00 0.00 4.79
590 627 3.266510 TGTGCATAGAATGAGTGGGAC 57.733 47.619 0.00 0.00 0.00 4.46
591 628 3.455543 TGATGTGCATAGAATGAGTGGGA 59.544 43.478 0.00 0.00 0.00 4.37
592 629 3.812262 TGATGTGCATAGAATGAGTGGG 58.188 45.455 0.00 0.00 0.00 4.61
593 630 5.758924 CAATGATGTGCATAGAATGAGTGG 58.241 41.667 0.00 0.00 35.78 4.00
594 631 5.212934 GCAATGATGTGCATAGAATGAGTG 58.787 41.667 0.00 0.00 44.29 3.51
595 632 4.024302 CGCAATGATGTGCATAGAATGAGT 60.024 41.667 0.00 0.00 45.19 3.41
596 633 4.024302 ACGCAATGATGTGCATAGAATGAG 60.024 41.667 0.00 0.00 45.19 2.90
597 634 3.878699 ACGCAATGATGTGCATAGAATGA 59.121 39.130 0.00 0.00 45.19 2.57
599 636 4.906065 AACGCAATGATGTGCATAGAAT 57.094 36.364 0.00 0.00 45.19 2.40
600 637 4.700268 AAACGCAATGATGTGCATAGAA 57.300 36.364 0.00 0.00 45.19 2.10
601 638 4.700268 AAAACGCAATGATGTGCATAGA 57.300 36.364 0.00 0.00 45.19 1.98
602 639 4.622313 ACAAAAACGCAATGATGTGCATAG 59.378 37.500 0.00 0.00 45.19 2.23
604 641 3.391965 ACAAAAACGCAATGATGTGCAT 58.608 36.364 0.00 0.00 45.19 3.96
617 729 4.643953 TCTTTGTCGACAGAACAAAAACG 58.356 39.130 19.11 0.00 33.68 3.60
622 734 3.857052 ACACTCTTTGTCGACAGAACAA 58.143 40.909 19.11 9.23 29.79 2.83
633 745 1.490490 TCCTTGCCTGACACTCTTTGT 59.510 47.619 0.00 0.00 43.10 2.83
634 746 2.260844 TCCTTGCCTGACACTCTTTG 57.739 50.000 0.00 0.00 0.00 2.77
637 749 1.649321 TCATCCTTGCCTGACACTCT 58.351 50.000 0.00 0.00 0.00 3.24
638 750 2.681848 CAATCATCCTTGCCTGACACTC 59.318 50.000 0.00 0.00 0.00 3.51
716 833 2.290393 CTCCCCTCCATGCCCCTA 59.710 66.667 0.00 0.00 0.00 3.53
720 837 1.074926 TCTCTCTCCCCTCCATGCC 60.075 63.158 0.00 0.00 0.00 4.40
755 874 4.142447 GCAGGCAGCTATGAATGGATAATG 60.142 45.833 0.00 0.00 41.15 1.90
773 892 0.607489 AGTGGAATGTGACAGCAGGC 60.607 55.000 0.00 0.00 0.00 4.85
843 962 7.557719 CCATAACTCTGAAACAATACCAGGATT 59.442 37.037 0.00 0.00 0.00 3.01
853 972 4.072131 GGTGCTCCATAACTCTGAAACAA 58.928 43.478 0.00 0.00 0.00 2.83
871 991 2.814336 AGGAAAGAACAAATCGAGGTGC 59.186 45.455 0.00 0.00 0.00 5.01
878 998 5.403466 GTGTGATTGCAGGAAAGAACAAATC 59.597 40.000 0.00 0.00 0.00 2.17
881 1001 3.698539 TGTGTGATTGCAGGAAAGAACAA 59.301 39.130 0.00 0.00 0.00 2.83
890 1010 0.167470 CTTCGCTGTGTGATTGCAGG 59.833 55.000 0.00 0.00 33.62 4.85
909 1029 3.604875 TCGACAGGGGATTAAAGTGAC 57.395 47.619 0.00 0.00 0.00 3.67
911 1031 4.261801 ACATTCGACAGGGGATTAAAGTG 58.738 43.478 0.00 0.00 0.00 3.16
919 1039 1.066430 GCACTAACATTCGACAGGGGA 60.066 52.381 0.00 0.00 0.00 4.81
922 1042 3.187700 GGTAGCACTAACATTCGACAGG 58.812 50.000 0.00 0.00 0.00 4.00
926 1046 1.917273 GCGGTAGCACTAACATTCGA 58.083 50.000 0.00 0.00 44.35 3.71
943 1063 1.145598 AGCACATCTGGATGGAGCG 59.854 57.895 14.06 2.51 43.75 5.03
1018 1141 2.507102 CGTCACGCGCATCCTCTT 60.507 61.111 5.73 0.00 0.00 2.85
1071 1194 2.737180 CAGGCGCCGAGGATGTAT 59.263 61.111 23.20 0.00 0.00 2.29
1128 1251 2.716828 CTGCGTCTTGGCGTACACG 61.717 63.158 0.00 0.00 43.27 4.49
1206 1329 2.401766 GGCAACTGAGGATGGCACG 61.402 63.158 8.75 0.00 39.81 5.34
1220 1343 1.533625 CTGGAAATCAAGACGGGCAA 58.466 50.000 0.00 0.00 0.00 4.52
1275 1398 1.372251 CGGGATCATCTCCTTCGCG 60.372 63.158 0.00 0.00 44.28 5.87
1280 1403 2.123251 ACGGCGGGATCATCTCCT 60.123 61.111 13.24 0.00 44.28 3.69
1398 1521 4.157840 AGGCACCGGAACAATTTATCTTTC 59.842 41.667 9.46 0.00 0.00 2.62
1434 1557 2.019807 AGGGGTTCTTGTAGTTCGGA 57.980 50.000 0.00 0.00 0.00 4.55
1443 1566 2.629002 CCACGTGAAGGGGTTCTTG 58.371 57.895 19.30 0.00 39.08 3.02
1518 1641 1.301716 GTTCTGCACGGCCTTCTCA 60.302 57.895 0.00 0.00 0.00 3.27
1572 1695 2.668212 AACATCGTGCCACCACCG 60.668 61.111 0.00 0.00 38.79 4.94
1599 1722 7.263205 GATATCATCGATATAAGCATCAGCG 57.737 40.000 0.00 0.00 39.36 5.18
1645 1768 2.290641 GTGCAGTTCTGATGTTTCCGTT 59.709 45.455 3.84 0.00 0.00 4.44
1733 1856 6.179906 TGCTTCCATCCTAAGATCCTAAAG 57.820 41.667 0.00 0.00 0.00 1.85
1740 1863 4.749166 GCCAGAATGCTTCCATCCTAAGAT 60.749 45.833 0.00 0.00 31.97 2.40
1842 1965 1.113517 ACTGTACCTGTGCCTCGTGT 61.114 55.000 0.00 0.00 0.00 4.49
1947 2070 4.383552 GGGATCAAACATCTAGAGCAGTGT 60.384 45.833 0.00 0.00 0.00 3.55
1980 2103 3.374220 TGTCGTGAAAACATACCGAGT 57.626 42.857 0.00 0.00 0.00 4.18
1996 2121 8.279800 TGTAACTACAAATCTGAAACAATGTCG 58.720 33.333 0.00 0.00 32.40 4.35
2014 2139 5.666969 TGTGTTCAGTGCAATGTAACTAC 57.333 39.130 14.62 15.36 0.00 2.73
2247 2377 2.634940 ACTACTTTCTTCCAGCAGAGCA 59.365 45.455 0.00 0.00 0.00 4.26
2463 2593 4.825085 AGAACGGCCAGAAATAAAAGTTGA 59.175 37.500 2.24 0.00 0.00 3.18
2464 2594 4.917415 CAGAACGGCCAGAAATAAAAGTTG 59.083 41.667 2.24 0.00 0.00 3.16
2470 2600 8.918202 ATATATTTCAGAACGGCCAGAAATAA 57.082 30.769 19.30 13.08 42.66 1.40
2481 2611 7.226720 ACAAACCAGGCTATATATTTCAGAACG 59.773 37.037 0.00 0.00 0.00 3.95
2606 2744 6.535150 CACTTAAGAAGACGCCATTCAGAATA 59.465 38.462 10.09 0.00 0.00 1.75
2693 2831 5.482908 CTGTAAGTGAACTGAGCCATAAGT 58.517 41.667 0.00 0.00 0.00 2.24
2716 2854 3.630312 ACAATGGCGGGTTATTGTATGAC 59.370 43.478 0.00 0.00 43.54 3.06
2755 2893 2.231529 AGCATCTACGGCTGTACTAGG 58.768 52.381 0.00 0.00 40.80 3.02
2765 2903 6.338937 AGTTTAAGGTTCTAAGCATCTACGG 58.661 40.000 0.00 0.00 0.00 4.02
2767 2905 8.950208 ATGAGTTTAAGGTTCTAAGCATCTAC 57.050 34.615 0.00 0.00 0.00 2.59
2784 2922 8.565896 ACAGAGAATGCATTGTAATGAGTTTA 57.434 30.769 18.59 0.00 38.70 2.01
2787 2925 8.743085 ATAACAGAGAATGCATTGTAATGAGT 57.257 30.769 18.59 10.84 38.70 3.41
2816 2954 7.968405 ACACAGTCAGTTTGTTTTCTGATTAAC 59.032 33.333 0.00 0.00 41.67 2.01
2819 2957 6.150976 TCACACAGTCAGTTTGTTTTCTGATT 59.849 34.615 0.00 0.00 41.67 2.57
2952 3098 2.084546 GTTATTCTTGGCGGAACTGCT 58.915 47.619 5.60 0.00 34.52 4.24
2964 3110 4.635699 AACTGAACCTCGGGTTATTCTT 57.364 40.909 8.11 0.00 46.95 2.52
3009 3155 4.522789 GCCCACAACTTATTTTCCTCTTCA 59.477 41.667 0.00 0.00 0.00 3.02
3018 3164 1.812571 CGCTCTGCCCACAACTTATTT 59.187 47.619 0.00 0.00 0.00 1.40
3051 3197 1.906574 AGTGGCGGGATCAGTTTCTTA 59.093 47.619 0.00 0.00 0.00 2.10
3329 3475 4.935808 ACAGAACTCAAACCATCGGTTATC 59.064 41.667 0.00 0.00 46.20 1.75
3357 3503 3.923017 AATGCAGCAGAAAAGGTACAC 57.077 42.857 0.00 0.00 0.00 2.90
3379 3527 8.514136 TTATAACAACTTAAACACAAGCATGC 57.486 30.769 10.51 10.51 0.00 4.06
3526 3692 0.252284 AGATCACCGTCCCTTCAGGT 60.252 55.000 0.00 0.00 39.12 4.00
3591 3786 1.307097 GCTCTTCCATCTCATGCCAC 58.693 55.000 0.00 0.00 0.00 5.01
3716 3929 2.413453 GACTTTTGCAGGAGATGACGTC 59.587 50.000 9.11 9.11 0.00 4.34
3726 3939 2.260844 TCTGTCTGGACTTTTGCAGG 57.739 50.000 2.38 0.00 41.45 4.85
3869 4124 0.580104 ACTACTCGCAACAACGCAAC 59.420 50.000 0.00 0.00 0.00 4.17
3952 4245 4.673841 GCCAGCTTTCTCAAAACTATGAGC 60.674 45.833 0.00 0.00 45.21 4.26
3978 4271 1.456296 GGACAGCAGCACATTCATCA 58.544 50.000 0.00 0.00 0.00 3.07
4002 4295 6.771188 TTCAGACTCTGAAAAAGACGAATC 57.229 37.500 17.58 0.00 45.84 2.52
4204 4514 3.635268 CTGCCTGGGCCACCTCTTC 62.635 68.421 0.00 0.00 41.09 2.87
4250 4716 4.161189 TGTTGAAGATTGCTTGGAAACCAA 59.839 37.500 3.21 3.21 41.69 3.67
4261 4727 5.009010 TGTTCTCTTTCCTGTTGAAGATTGC 59.991 40.000 0.00 0.00 33.63 3.56
4286 4775 0.944386 CCCAACACCAAGTTCAGTCG 59.056 55.000 0.00 0.00 38.74 4.18
4336 4829 4.873746 TGAGTCTTCTGGTAGGTTTCAG 57.126 45.455 0.00 0.00 0.00 3.02
4347 4840 4.505922 GTGTTCAGTGACTTGAGTCTTCTG 59.494 45.833 20.05 20.05 44.99 3.02
4357 4853 4.097892 GTCATTTTGGGTGTTCAGTGACTT 59.902 41.667 0.00 0.00 33.74 3.01
4366 4862 0.673437 CGCCTGTCATTTTGGGTGTT 59.327 50.000 0.00 0.00 0.00 3.32
4367 4863 1.178534 CCGCCTGTCATTTTGGGTGT 61.179 55.000 0.00 0.00 0.00 4.16
4373 4869 3.061848 CCGGCCGCCTGTCATTTT 61.062 61.111 22.85 0.00 0.00 1.82
4385 4881 0.819259 TATTCTTCATGCTGCCGGCC 60.819 55.000 26.77 10.34 40.92 6.13
4407 4903 3.743396 GCCATCATTGCAGTAGTAGTAGC 59.257 47.826 0.00 0.00 0.00 3.58
4419 4915 2.162754 GTTGCGCTGCCATCATTGC 61.163 57.895 9.73 0.00 0.00 3.56
4420 4916 0.388778 TTGTTGCGCTGCCATCATTG 60.389 50.000 9.73 0.00 0.00 2.82
4433 4952 8.795786 TGTACTGATGAGTTTAATTTTGTTGC 57.204 30.769 0.00 0.00 33.21 4.17
4524 5052 2.473376 GCGTGTGCGTACTTTGTATTCC 60.473 50.000 4.97 0.00 40.81 3.01
4552 5626 3.452627 ACCCAAGTTTTGTAAACCATGCA 59.547 39.130 0.00 0.00 0.00 3.96
4556 5630 4.442192 GCATCACCCAAGTTTTGTAAACCA 60.442 41.667 0.00 0.00 0.00 3.67
4573 5647 0.948623 TGTACCGTGCTGTGCATCAC 60.949 55.000 0.00 0.00 41.91 3.06
4589 5663 9.516546 TGGTTTGTAATATAATGGTTGTGTGTA 57.483 29.630 0.00 0.00 0.00 2.90
4620 5697 6.142817 GTGTGGTGTTCATAGTTGATCAAAC 58.857 40.000 10.35 4.21 34.27 2.93
4621 5698 5.825151 TGTGTGGTGTTCATAGTTGATCAAA 59.175 36.000 10.35 0.00 34.27 2.69
4632 5709 1.032014 GCTTGGTGTGTGGTGTTCAT 58.968 50.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.