Multiple sequence alignment - TraesCS1B01G337900

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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 TraesCS1B01G337900 chr1B 100.000 4605 0 0 1 4605 565852903 565848299 0.000000e+00 8504.0
1 TraesCS1B01G337900 chr1B 91.541 3310 178 44 1304 4578 565811677 565808435 0.000000e+00 4468.0
2 TraesCS1B01G337900 chr1B 88.986 345 25 5 959 1302 565820433 565820101 9.220000e-112 414.0
3 TraesCS1B01G337900 chr1D 92.926 2884 145 32 1610 4478 418242138 418239299 0.000000e+00 4141.0
4 TraesCS1B01G337900 chr1D 85.400 637 43 31 954 1550 418243070 418242444 2.350000e-172 616.0
5 TraesCS1B01G337900 chr1A 91.002 2556 144 28 2078 4605 515590020 515587523 0.000000e+00 3367.0
6 TraesCS1B01G337900 chr1A 88.813 1171 78 23 954 2094 515591335 515590188 0.000000e+00 1387.0
7 TraesCS1B01G337900 chr1A 88.889 153 17 0 3283 3435 515650121 515649969 6.080000e-44 189.0
8 TraesCS1B01G337900 chr1A 84.034 119 12 5 648 765 426625139 426625027 1.750000e-19 108.0
9 TraesCS1B01G337900 chr1A 88.060 67 6 2 705 770 336540678 336540743 1.370000e-10 78.7
10 TraesCS1B01G337900 chr1A 90.698 43 4 0 1561 1603 558255425 558255383 1.790000e-04 58.4
11 TraesCS1B01G337900 chr4B 87.972 2012 166 39 2346 4347 109922128 109924073 0.000000e+00 2305.0
12 TraesCS1B01G337900 chr4B 93.850 748 38 7 1563 2304 109921382 109922127 0.000000e+00 1120.0
13 TraesCS1B01G337900 chr4B 86.256 211 16 5 954 1163 109920851 109921049 2.790000e-52 217.0
14 TraesCS1B01G337900 chr4B 97.368 38 1 0 1427 1464 109921318 109921355 1.070000e-06 65.8
15 TraesCS1B01G337900 chr7D 75.794 661 117 33 1 639 54969468 54968829 1.250000e-75 294.0
16 TraesCS1B01G337900 chr7D 76.109 586 117 20 1 574 55226320 55226894 7.540000e-73 285.0
17 TraesCS1B01G337900 chr7D 79.070 258 40 10 317 570 25322462 25322709 1.020000e-36 165.0
18 TraesCS1B01G337900 chr7D 79.832 238 31 14 331 562 153126228 153126002 1.720000e-34 158.0
19 TraesCS1B01G337900 chr7D 89.286 84 7 1 690 773 221588126 221588045 2.270000e-18 104.0
20 TraesCS1B01G337900 chr7D 76.705 176 35 4 287 461 215793828 215793658 4.910000e-15 93.5
21 TraesCS1B01G337900 chr4D 80.501 359 57 12 187 540 426786342 426786692 3.530000e-66 263.0
22 TraesCS1B01G337900 chr4D 74.720 447 76 24 329 752 46591698 46592130 1.020000e-36 165.0
23 TraesCS1B01G337900 chr5B 74.118 595 97 33 186 770 457937483 457936936 4.700000e-45 193.0
24 TraesCS1B01G337900 chr5B 77.992 259 49 5 326 582 465228618 465228366 6.170000e-34 156.0
25 TraesCS1B01G337900 chr5B 93.182 44 3 0 1482 1525 595315182 595315139 1.070000e-06 65.8
26 TraesCS1B01G337900 chr2A 80.913 241 36 10 337 575 632948401 632948169 1.020000e-41 182.0
27 TraesCS1B01G337900 chr2A 77.528 178 29 7 16 189 57986839 57987009 3.790000e-16 97.1
28 TraesCS1B01G337900 chr2A 94.595 37 2 0 1563 1599 692757174 692757138 1.790000e-04 58.4
29 TraesCS1B01G337900 chr6B 79.121 273 45 10 330 599 487000465 487000202 1.320000e-40 178.0
30 TraesCS1B01G337900 chr6B 72.080 548 105 39 328 860 184722222 184721708 2.250000e-23 121.0
31 TraesCS1B01G337900 chr6D 73.455 550 106 33 292 835 444465993 444466508 2.200000e-38 171.0
32 TraesCS1B01G337900 chr5A 78.855 227 42 6 337 561 530881355 530881577 1.030000e-31 148.0
33 TraesCS1B01G337900 chr2D 74.691 324 52 20 537 836 377111626 377111309 2.910000e-22 117.0
34 TraesCS1B01G337900 chr2D 97.059 34 1 0 1561 1594 150379349 150379316 1.790000e-04 58.4
35 TraesCS1B01G337900 chr2B 85.714 105 11 3 669 770 212944690 212944587 1.750000e-19 108.0
36 TraesCS1B01G337900 chr2B 79.104 134 16 7 647 770 631328351 631328220 1.060000e-11 82.4
37 TraesCS1B01G337900 chr3B 94.872 39 2 0 1561 1599 27165183 27165145 1.380000e-05 62.1


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 TraesCS1B01G337900 chr1B 565848299 565852903 4604 True 8504.00 8504 100.0000 1 4605 1 chr1B.!!$R3 4604
1 TraesCS1B01G337900 chr1B 565808435 565811677 3242 True 4468.00 4468 91.5410 1304 4578 1 chr1B.!!$R1 3274
2 TraesCS1B01G337900 chr1D 418239299 418243070 3771 True 2378.50 4141 89.1630 954 4478 2 chr1D.!!$R1 3524
3 TraesCS1B01G337900 chr1A 515587523 515591335 3812 True 2377.00 3367 89.9075 954 4605 2 chr1A.!!$R4 3651
4 TraesCS1B01G337900 chr4B 109920851 109924073 3222 False 926.95 2305 91.3615 954 4347 4 chr4B.!!$F1 3393
5 TraesCS1B01G337900 chr7D 54968829 54969468 639 True 294.00 294 75.7940 1 639 1 chr7D.!!$R1 638
6 TraesCS1B01G337900 chr7D 55226320 55226894 574 False 285.00 285 76.1090 1 574 1 chr7D.!!$F2 573

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
921 936 0.179070 GTCCCTTCAGGCGAGGATTC 60.179 60.0 6.24 0.00 36.33 2.52 F
1308 1334 0.163146 CGCTCGCTCGTATCGTATGA 59.837 55.0 0.00 0.00 0.00 2.15 F
2417 2987 0.386113 CTGCGAAGGGCTAGTCCTAC 59.614 60.0 18.33 10.15 44.05 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 2232 0.687354 AAGCTGGTTCTGGACATCGT 59.313 50.0 0.00 0.0 0.00 3.73 R
2931 3504 0.394565 AGGAGATATGAGCGGCAACC 59.605 55.0 1.45 0.0 0.00 3.77 R
4321 4933 0.440371 CGAGCAAGCGTCTCTTTTCC 59.560 55.0 0.00 0.0 31.27 3.13 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
32 33 5.827666 TCTTGTTTTTCTCGGTTTCATTCC 58.172 37.500 0.00 0.00 0.00 3.01
50 52 6.355747 TCATTCCTTTGCATTGGTTTCTTTT 58.644 32.000 5.56 0.00 0.00 2.27
51 53 6.260493 TCATTCCTTTGCATTGGTTTCTTTTG 59.740 34.615 5.56 0.00 0.00 2.44
55 57 6.432472 TCCTTTGCATTGGTTTCTTTTGTTTT 59.568 30.769 5.56 0.00 0.00 2.43
63 76 9.676195 CATTGGTTTCTTTTGTTTTTGTTTTCT 57.324 25.926 0.00 0.00 0.00 2.52
84 97 9.737427 TTTTCTTTGTTTTTCTTTTTGGTTTCC 57.263 25.926 0.00 0.00 0.00 3.13
90 103 6.151817 TGTTTTTCTTTTTGGTTTCCATTGGG 59.848 34.615 2.09 0.00 31.53 4.12
91 104 5.443230 TTTCTTTTTGGTTTCCATTGGGT 57.557 34.783 2.09 0.00 31.53 4.51
97 110 5.443230 TTTGGTTTCCATTGGGTTTCTTT 57.557 34.783 2.09 0.00 31.53 2.52
98 111 4.414337 TGGTTTCCATTGGGTTTCTTTG 57.586 40.909 2.09 0.00 34.93 2.77
101 114 5.425539 TGGTTTCCATTGGGTTTCTTTGTTA 59.574 36.000 2.09 0.00 34.93 2.41
105 118 6.353404 TCCATTGGGTTTCTTTGTTATTCC 57.647 37.500 2.09 0.00 34.93 3.01
108 121 7.730784 TCCATTGGGTTTCTTTGTTATTCCTTA 59.269 33.333 2.09 0.00 34.93 2.69
109 122 8.539544 CCATTGGGTTTCTTTGTTATTCCTTAT 58.460 33.333 0.00 0.00 0.00 1.73
142 156 9.893305 TCAATTTTTATCGGTTTCTTCTTTCTC 57.107 29.630 0.00 0.00 0.00 2.87
148 162 3.875134 TCGGTTTCTTCTTTCTCCAACAC 59.125 43.478 0.00 0.00 0.00 3.32
193 208 9.903682 ACAGATTCAACATTTTTGATACTTCAG 57.096 29.630 0.00 0.00 32.27 3.02
194 209 8.857216 CAGATTCAACATTTTTGATACTTCAGC 58.143 33.333 0.00 0.00 32.27 4.26
196 211 9.195411 GATTCAACATTTTTGATACTTCAGCAA 57.805 29.630 0.00 0.00 32.27 3.91
197 212 9.715121 ATTCAACATTTTTGATACTTCAGCAAT 57.285 25.926 0.00 0.00 31.36 3.56
334 349 9.730420 ACATTTTCCTAATACGCATTTAACATC 57.270 29.630 0.00 0.00 0.00 3.06
335 350 9.950680 CATTTTCCTAATACGCATTTAACATCT 57.049 29.630 0.00 0.00 0.00 2.90
338 353 9.997482 TTTCCTAATACGCATTTAACATCTTTC 57.003 29.630 0.00 0.00 0.00 2.62
339 354 8.725405 TCCTAATACGCATTTAACATCTTTCA 57.275 30.769 0.00 0.00 0.00 2.69
340 355 9.168451 TCCTAATACGCATTTAACATCTTTCAA 57.832 29.630 0.00 0.00 0.00 2.69
341 356 9.781834 CCTAATACGCATTTAACATCTTTCAAA 57.218 29.630 0.00 0.00 0.00 2.69
347 362 9.128107 ACGCATTTAACATCTTTCAAATACAAG 57.872 29.630 0.00 0.00 0.00 3.16
348 363 9.128107 CGCATTTAACATCTTTCAAATACAAGT 57.872 29.630 0.00 0.00 0.00 3.16
367 382 7.734538 ACAAGTTTAACATTTTCTGAACACG 57.265 32.000 0.00 0.00 0.00 4.49
368 383 7.309920 ACAAGTTTAACATTTTCTGAACACGT 58.690 30.769 0.00 0.00 0.00 4.49
369 384 7.272515 ACAAGTTTAACATTTTCTGAACACGTG 59.727 33.333 15.48 15.48 0.00 4.49
370 385 6.262601 AGTTTAACATTTTCTGAACACGTGG 58.737 36.000 21.57 1.33 0.00 4.94
371 386 5.821516 TTAACATTTTCTGAACACGTGGT 57.178 34.783 21.57 14.94 0.00 4.16
372 387 3.963383 ACATTTTCTGAACACGTGGTC 57.037 42.857 26.70 26.70 0.00 4.02
373 388 3.275143 ACATTTTCTGAACACGTGGTCA 58.725 40.909 32.71 32.71 39.87 4.02
374 389 3.692101 ACATTTTCTGAACACGTGGTCAA 59.308 39.130 33.93 21.47 41.85 3.18
375 390 3.750639 TTTTCTGAACACGTGGTCAAC 57.249 42.857 33.93 10.84 41.85 3.18
376 391 2.388310 TTCTGAACACGTGGTCAACA 57.612 45.000 33.93 21.93 41.85 3.33
377 392 2.613026 TCTGAACACGTGGTCAACAT 57.387 45.000 33.93 1.81 41.85 2.71
378 393 2.912771 TCTGAACACGTGGTCAACATT 58.087 42.857 33.93 11.32 41.85 2.71
379 394 3.275143 TCTGAACACGTGGTCAACATTT 58.725 40.909 33.93 10.55 41.85 2.32
380 395 3.692101 TCTGAACACGTGGTCAACATTTT 59.308 39.130 33.93 9.80 41.85 1.82
381 396 4.156922 TCTGAACACGTGGTCAACATTTTT 59.843 37.500 33.93 9.03 41.85 1.94
593 608 8.977505 ACATATTTGAAGTTTTCCAAACGATTG 58.022 29.630 0.00 0.00 35.42 2.67
594 609 9.190858 CATATTTGAAGTTTTCCAAACGATTGA 57.809 29.630 7.03 0.00 38.94 2.57
595 610 9.927668 ATATTTGAAGTTTTCCAAACGATTGAT 57.072 25.926 7.03 0.00 38.94 2.57
596 611 7.462109 TTTGAAGTTTTCCAAACGATTGATG 57.538 32.000 7.03 0.00 38.94 3.07
597 612 6.384258 TGAAGTTTTCCAAACGATTGATGA 57.616 33.333 7.03 0.00 38.94 2.92
598 613 6.800543 TGAAGTTTTCCAAACGATTGATGAA 58.199 32.000 7.03 0.24 38.94 2.57
599 614 6.695278 TGAAGTTTTCCAAACGATTGATGAAC 59.305 34.615 7.03 7.99 38.94 3.18
600 615 5.212194 AGTTTTCCAAACGATTGATGAACG 58.788 37.500 7.03 0.00 38.94 3.95
601 616 4.822036 TTTCCAAACGATTGATGAACGT 57.178 36.364 7.03 0.00 38.94 3.99
603 618 5.926214 TTCCAAACGATTGATGAACGTTA 57.074 34.783 7.03 0.00 46.74 3.18
604 619 6.489127 TTCCAAACGATTGATGAACGTTAT 57.511 33.333 7.03 0.00 46.74 1.89
605 620 6.489127 TCCAAACGATTGATGAACGTTATT 57.511 33.333 7.03 0.00 46.74 1.40
606 621 7.598189 TCCAAACGATTGATGAACGTTATTA 57.402 32.000 7.03 0.00 46.74 0.98
607 622 8.030744 TCCAAACGATTGATGAACGTTATTAA 57.969 30.769 7.03 0.00 46.74 1.40
608 623 8.504815 TCCAAACGATTGATGAACGTTATTAAA 58.495 29.630 7.03 0.00 46.74 1.52
609 624 9.119329 CCAAACGATTGATGAACGTTATTAAAA 57.881 29.630 7.03 0.00 46.74 1.52
651 666 9.672673 TTTTTGAATACATTTCCAACCTTTTCA 57.327 25.926 0.00 0.00 0.00 2.69
652 667 9.672673 TTTTGAATACATTTCCAACCTTTTCAA 57.327 25.926 0.00 0.00 0.00 2.69
653 668 9.672673 TTTGAATACATTTCCAACCTTTTCAAA 57.327 25.926 0.00 0.00 37.88 2.69
654 669 9.844257 TTGAATACATTTCCAACCTTTTCAAAT 57.156 25.926 0.00 0.00 30.23 2.32
655 670 9.270640 TGAATACATTTCCAACCTTTTCAAATG 57.729 29.630 0.00 0.00 39.38 2.32
656 671 7.671495 ATACATTTCCAACCTTTTCAAATGC 57.329 32.000 0.00 0.00 37.78 3.56
657 672 5.683681 ACATTTCCAACCTTTTCAAATGCT 58.316 33.333 0.00 0.00 37.78 3.79
658 673 6.121590 ACATTTCCAACCTTTTCAAATGCTT 58.878 32.000 0.00 0.00 37.78 3.91
659 674 6.038492 ACATTTCCAACCTTTTCAAATGCTTG 59.962 34.615 0.00 0.00 37.78 4.01
660 675 5.350504 TTCCAACCTTTTCAAATGCTTGA 57.649 34.783 0.00 0.00 39.87 3.02
661 676 5.549742 TCCAACCTTTTCAAATGCTTGAT 57.450 34.783 0.00 0.00 41.22 2.57
662 677 6.662865 TCCAACCTTTTCAAATGCTTGATA 57.337 33.333 0.00 0.00 41.22 2.15
663 678 7.060383 TCCAACCTTTTCAAATGCTTGATAA 57.940 32.000 0.00 0.00 41.22 1.75
664 679 7.678837 TCCAACCTTTTCAAATGCTTGATAAT 58.321 30.769 0.00 0.00 41.22 1.28
665 680 8.156165 TCCAACCTTTTCAAATGCTTGATAATT 58.844 29.630 0.00 0.00 41.22 1.40
666 681 8.785946 CCAACCTTTTCAAATGCTTGATAATTT 58.214 29.630 0.00 0.00 41.22 1.82
695 710 9.712305 TTTTCAAATACCTGTTCAACTTTTTCA 57.288 25.926 0.00 0.00 0.00 2.69
696 711 8.696410 TTCAAATACCTGTTCAACTTTTTCAC 57.304 30.769 0.00 0.00 0.00 3.18
697 712 7.831753 TCAAATACCTGTTCAACTTTTTCACA 58.168 30.769 0.00 0.00 0.00 3.58
698 713 7.757624 TCAAATACCTGTTCAACTTTTTCACAC 59.242 33.333 0.00 0.00 0.00 3.82
699 714 6.767524 ATACCTGTTCAACTTTTTCACACA 57.232 33.333 0.00 0.00 0.00 3.72
700 715 5.059404 ACCTGTTCAACTTTTTCACACAG 57.941 39.130 0.00 0.00 0.00 3.66
701 716 4.764823 ACCTGTTCAACTTTTTCACACAGA 59.235 37.500 0.00 0.00 33.44 3.41
702 717 5.418840 ACCTGTTCAACTTTTTCACACAGAT 59.581 36.000 0.00 0.00 33.44 2.90
703 718 6.071391 ACCTGTTCAACTTTTTCACACAGATT 60.071 34.615 0.00 0.00 33.44 2.40
704 719 6.254157 CCTGTTCAACTTTTTCACACAGATTG 59.746 38.462 0.00 0.00 33.44 2.67
705 720 6.686630 TGTTCAACTTTTTCACACAGATTGT 58.313 32.000 0.00 0.00 39.97 2.71
706 721 7.821652 TGTTCAACTTTTTCACACAGATTGTA 58.178 30.769 0.00 0.00 35.67 2.41
707 722 8.465999 TGTTCAACTTTTTCACACAGATTGTAT 58.534 29.630 0.00 0.00 35.67 2.29
708 723 9.944663 GTTCAACTTTTTCACACAGATTGTATA 57.055 29.630 0.00 0.00 35.67 1.47
737 752 9.872757 TTTTTCGTATACATGAGAAACAGTTTC 57.127 29.630 17.11 17.11 39.96 2.78
754 769 9.787435 AAACAGTTTCTCTATACACATTTACCA 57.213 29.630 0.00 0.00 0.00 3.25
755 770 9.959721 AACAGTTTCTCTATACACATTTACCAT 57.040 29.630 0.00 0.00 0.00 3.55
756 771 9.959721 ACAGTTTCTCTATACACATTTACCATT 57.040 29.630 0.00 0.00 0.00 3.16
777 792 9.442047 ACCATTTTTGAAATACTTGTTTCACAA 57.558 25.926 1.03 0.00 45.04 3.33
842 857 9.982291 TTATTCAGAATAATTGCAACTACGAAC 57.018 29.630 11.05 0.00 0.00 3.95
843 858 7.428282 TTCAGAATAATTGCAACTACGAACA 57.572 32.000 0.00 0.00 0.00 3.18
844 859 7.428282 TCAGAATAATTGCAACTACGAACAA 57.572 32.000 0.00 0.00 0.00 2.83
845 860 7.866729 TCAGAATAATTGCAACTACGAACAAA 58.133 30.769 0.00 0.00 0.00 2.83
846 861 8.346300 TCAGAATAATTGCAACTACGAACAAAA 58.654 29.630 0.00 0.00 0.00 2.44
847 862 8.629986 CAGAATAATTGCAACTACGAACAAAAG 58.370 33.333 0.00 0.00 0.00 2.27
848 863 8.349983 AGAATAATTGCAACTACGAACAAAAGT 58.650 29.630 0.00 0.00 0.00 2.66
849 864 9.601971 GAATAATTGCAACTACGAACAAAAGTA 57.398 29.630 0.00 0.00 0.00 2.24
850 865 9.953697 AATAATTGCAACTACGAACAAAAGTAA 57.046 25.926 0.00 0.00 0.00 2.24
851 866 9.953697 ATAATTGCAACTACGAACAAAAGTAAA 57.046 25.926 0.00 0.00 0.00 2.01
852 867 8.690680 AATTGCAACTACGAACAAAAGTAAAA 57.309 26.923 0.00 0.00 0.00 1.52
853 868 8.690680 ATTGCAACTACGAACAAAAGTAAAAA 57.309 26.923 0.00 0.00 0.00 1.94
874 889 1.029681 AAAAACGAGGTTGTGGCTCC 58.970 50.000 0.00 0.00 0.00 4.70
875 890 0.822121 AAAACGAGGTTGTGGCTCCC 60.822 55.000 0.00 0.00 0.00 4.30
876 891 3.530910 AACGAGGTTGTGGCTCCCG 62.531 63.158 0.00 0.00 0.00 5.14
877 892 4.003788 CGAGGTTGTGGCTCCCGT 62.004 66.667 0.00 0.00 0.00 5.28
878 893 2.430367 GAGGTTGTGGCTCCCGTT 59.570 61.111 0.00 0.00 0.00 4.44
879 894 1.671379 GAGGTTGTGGCTCCCGTTC 60.671 63.158 0.00 0.00 0.00 3.95
880 895 3.047877 GGTTGTGGCTCCCGTTCG 61.048 66.667 0.00 0.00 0.00 3.95
881 896 2.280592 GTTGTGGCTCCCGTTCGT 60.281 61.111 0.00 0.00 0.00 3.85
882 897 2.029964 TTGTGGCTCCCGTTCGTC 59.970 61.111 0.00 0.00 0.00 4.20
883 898 2.504274 TTGTGGCTCCCGTTCGTCT 61.504 57.895 0.00 0.00 0.00 4.18
884 899 2.432628 GTGGCTCCCGTTCGTCTG 60.433 66.667 0.00 0.00 0.00 3.51
885 900 3.691342 TGGCTCCCGTTCGTCTGG 61.691 66.667 0.00 0.00 0.00 3.86
888 903 3.382832 CTCCCGTTCGTCTGGGCT 61.383 66.667 4.09 0.00 45.60 5.19
889 904 3.649277 CTCCCGTTCGTCTGGGCTG 62.649 68.421 4.09 0.00 45.60 4.85
890 905 4.760047 CCCGTTCGTCTGGGCTGG 62.760 72.222 0.00 0.00 38.90 4.85
908 923 4.016706 CCCAACTCGGCGTCCCTT 62.017 66.667 6.85 0.00 0.00 3.95
909 924 2.434359 CCAACTCGGCGTCCCTTC 60.434 66.667 6.85 0.00 0.00 3.46
910 925 2.342279 CAACTCGGCGTCCCTTCA 59.658 61.111 6.85 0.00 0.00 3.02
911 926 1.738099 CAACTCGGCGTCCCTTCAG 60.738 63.158 6.85 0.00 0.00 3.02
912 927 2.943978 AACTCGGCGTCCCTTCAGG 61.944 63.158 6.85 0.00 0.00 3.86
913 928 4.821589 CTCGGCGTCCCTTCAGGC 62.822 72.222 6.85 0.00 34.51 4.85
916 931 4.821589 GGCGTCCCTTCAGGCGAG 62.822 72.222 0.00 0.00 37.34 5.03
917 932 4.821589 GCGTCCCTTCAGGCGAGG 62.822 72.222 0.00 0.00 37.34 4.63
918 933 3.068691 CGTCCCTTCAGGCGAGGA 61.069 66.667 6.24 0.00 37.34 3.71
919 934 2.427245 CGTCCCTTCAGGCGAGGAT 61.427 63.158 6.24 0.00 37.34 3.24
920 935 1.908483 GTCCCTTCAGGCGAGGATT 59.092 57.895 6.24 0.00 36.33 3.01
921 936 0.179070 GTCCCTTCAGGCGAGGATTC 60.179 60.000 6.24 0.00 36.33 2.52
922 937 1.147153 CCCTTCAGGCGAGGATTCC 59.853 63.158 6.24 0.00 36.33 3.01
923 938 1.147153 CCTTCAGGCGAGGATTCCC 59.853 63.158 0.00 0.00 36.33 3.97
924 939 1.227380 CTTCAGGCGAGGATTCCCG 60.227 63.158 0.00 4.23 37.58 5.14
925 940 2.650813 CTTCAGGCGAGGATTCCCGG 62.651 65.000 13.24 0.00 37.58 5.73
930 945 4.547367 CGAGGATTCCCGGCACCC 62.547 72.222 0.00 0.00 37.58 4.61
931 946 4.191015 GAGGATTCCCGGCACCCC 62.191 72.222 0.00 0.00 37.58 4.95
933 948 4.506255 GGATTCCCGGCACCCCAG 62.506 72.222 0.00 0.00 0.00 4.45
1003 1019 2.885676 CGCTTCGATTCGGCCATGG 61.886 63.158 7.63 7.63 0.00 3.66
1163 1182 1.507742 TGACCTCTGGCCATCCCTATA 59.492 52.381 5.51 0.00 0.00 1.31
1165 1184 3.339742 TGACCTCTGGCCATCCCTATATA 59.660 47.826 5.51 0.00 0.00 0.86
1166 1185 4.015258 TGACCTCTGGCCATCCCTATATAT 60.015 45.833 5.51 0.00 0.00 0.86
1167 1186 4.561752 ACCTCTGGCCATCCCTATATATC 58.438 47.826 5.51 0.00 0.00 1.63
1169 1188 5.440072 ACCTCTGGCCATCCCTATATATCTA 59.560 44.000 5.51 0.00 0.00 1.98
1192 1211 5.080642 TGTTTCAGCATGCAAAATTTTCG 57.919 34.783 21.98 0.00 34.76 3.46
1236 1255 0.524862 AGCTGCAAAATTCCTGCTCG 59.475 50.000 1.02 6.18 40.59 5.03
1246 1265 1.870055 TTCCTGCTCGTCGGGTACAC 61.870 60.000 0.00 0.00 42.13 2.90
1255 1274 3.198068 TCGTCGGGTACACTAGTGTATC 58.802 50.000 32.53 31.44 46.36 2.24
1256 1275 3.118629 TCGTCGGGTACACTAGTGTATCT 60.119 47.826 34.21 15.66 46.36 1.98
1260 1282 6.815641 CGTCGGGTACACTAGTGTATCTATAT 59.184 42.308 34.21 13.40 46.36 0.86
1261 1283 7.976175 CGTCGGGTACACTAGTGTATCTATATA 59.024 40.741 34.21 18.60 46.36 0.86
1302 1328 0.524816 TTTGTCCGCTCGCTCGTATC 60.525 55.000 0.00 0.00 0.00 2.24
1303 1329 2.425448 GTCCGCTCGCTCGTATCG 60.425 66.667 0.00 0.00 0.00 2.92
1305 1331 1.592400 TCCGCTCGCTCGTATCGTA 60.592 57.895 0.00 0.00 0.00 3.43
1306 1332 0.947660 TCCGCTCGCTCGTATCGTAT 60.948 55.000 0.00 0.00 0.00 3.06
1307 1333 0.789753 CCGCTCGCTCGTATCGTATG 60.790 60.000 0.00 0.00 0.00 2.39
1308 1334 0.163146 CGCTCGCTCGTATCGTATGA 59.837 55.000 0.00 0.00 0.00 2.15
1311 1337 2.841329 GCTCGCTCGTATCGTATGATTC 59.159 50.000 2.02 0.00 35.99 2.52
1325 1351 6.345298 TCGTATGATTCCTGATGTTTAAGCA 58.655 36.000 0.00 0.00 0.00 3.91
1332 1358 5.063180 TCCTGATGTTTAAGCATGCAAAG 57.937 39.130 21.98 0.16 0.00 2.77
1342 1368 7.010367 TGTTTAAGCATGCAAAGTTTTCTTCAG 59.990 33.333 21.98 0.00 39.48 3.02
1382 1408 7.612633 AGAATCAAATGCCCAAAATATGCTTTT 59.387 29.630 0.00 0.00 34.06 2.27
1383 1409 7.706100 ATCAAATGCCCAAAATATGCTTTTT 57.294 28.000 0.00 0.00 32.21 1.94
1420 1495 3.710326 TCGATCAATAGCAGCGTAGTT 57.290 42.857 0.00 0.00 0.00 2.24
1421 1496 4.823790 TCGATCAATAGCAGCGTAGTTA 57.176 40.909 0.00 0.00 0.00 2.24
1422 1497 5.372547 TCGATCAATAGCAGCGTAGTTAT 57.627 39.130 0.00 0.00 0.00 1.89
1423 1498 5.391449 TCGATCAATAGCAGCGTAGTTATC 58.609 41.667 0.00 0.00 0.00 1.75
1424 1499 5.181433 TCGATCAATAGCAGCGTAGTTATCT 59.819 40.000 0.00 0.00 0.00 1.98
1425 1500 5.284897 CGATCAATAGCAGCGTAGTTATCTG 59.715 44.000 0.00 0.00 0.00 2.90
1460 1595 3.883830 AGCAGCGCTAATATATCAGCT 57.116 42.857 10.99 8.67 36.99 4.24
1555 1690 2.416431 GGGACGATTAATACGGATCGGG 60.416 54.545 10.05 0.00 46.90 5.14
1590 1725 6.653273 AATCAGCGACGATTAATATGGATG 57.347 37.500 0.00 0.00 33.82 3.51
1641 2022 7.223777 GGTTTACAGAATTTGCAAGCTTTGTAA 59.776 33.333 17.35 17.35 33.37 2.41
1680 2063 4.610945 CTGGTTTCAGTTCCAACATGTTC 58.389 43.478 8.48 0.00 36.30 3.18
1708 2091 2.812836 TGGCATGATGAACTGATGGT 57.187 45.000 0.00 0.00 0.00 3.55
1709 2092 3.090210 TGGCATGATGAACTGATGGTT 57.910 42.857 0.00 0.00 41.40 3.67
1721 2104 5.652014 TGAACTGATGGTTTCTTCTTGTTGT 59.348 36.000 0.00 0.00 38.41 3.32
1747 2130 5.957798 TCAGAGCCAGCTATGAAAAATTTG 58.042 37.500 14.22 0.00 40.72 2.32
1849 2232 7.054124 AGTTCTTCACTGTTTCTATTCAACCA 58.946 34.615 0.00 0.00 32.83 3.67
1980 2365 6.743575 ATACTGTTGTACTGCTGATTTTCC 57.256 37.500 0.00 0.00 0.00 3.13
2001 2386 5.063880 TCCTTTTCTGTACTTCTTTCAGCC 58.936 41.667 0.00 0.00 0.00 4.85
2160 2729 2.621338 GATGAGTTGGATTGTCTGCGA 58.379 47.619 0.00 0.00 0.00 5.10
2222 2791 2.178912 ACACCGGTCAGTTAATGTGG 57.821 50.000 2.59 0.00 0.00 4.17
2342 2912 3.898509 GCACACGCAGCCCAAACA 61.899 61.111 0.00 0.00 38.36 2.83
2347 2917 0.595588 CACGCAGCCCAAACATGTTA 59.404 50.000 12.39 0.00 0.00 2.41
2402 2972 9.935682 TCTTTTCTTCTATAAAAATATGCTGCG 57.064 29.630 0.00 0.00 0.00 5.18
2417 2987 0.386113 CTGCGAAGGGCTAGTCCTAC 59.614 60.000 18.33 10.15 44.05 3.18
2563 3134 6.135290 TGTGCATATTAAGAGCATTGAACC 57.865 37.500 0.00 0.00 40.78 3.62
2783 3355 1.388547 ACACCTCAACGCAACATGTT 58.611 45.000 4.92 4.92 0.00 2.71
2931 3504 6.823497 TGTACTTAAAATAGGATTCCCGGAG 58.177 40.000 0.73 0.00 37.58 4.63
3012 3585 3.177228 ACAGCCTGAAGGTCAAGTCTAT 58.823 45.455 0.00 0.00 37.57 1.98
3122 3695 0.951558 GTCGAGGCTTTTTGGCAAGA 59.048 50.000 0.00 0.00 44.55 3.02
3375 3951 8.814038 AAGCTTAAATTTGACATCACCTCTAT 57.186 30.769 0.00 0.00 0.00 1.98
3399 3975 4.497984 TGTGCGCAAGGGGTGTGT 62.498 61.111 14.00 0.00 40.09 3.72
3416 3992 1.966451 GTGAGGAGGTTTGTGCCCG 60.966 63.158 0.00 0.00 0.00 6.13
3421 4012 1.304134 GAGGTTTGTGCCCGGGAAT 60.304 57.895 29.31 0.00 0.00 3.01
3465 4056 2.646930 GCCTGATGTTGTGATGGATGA 58.353 47.619 0.00 0.00 0.00 2.92
3491 4082 3.886123 CCGGAACCAAAGACATATTCCT 58.114 45.455 0.00 0.00 37.31 3.36
3528 4119 7.410800 TCATTTCACAGAAATGTTCATTTGC 57.589 32.000 23.87 7.30 38.44 3.68
3533 4124 5.534278 TCACAGAAATGTTCATTTGCCAGTA 59.466 36.000 14.29 0.00 0.00 2.74
3548 4139 6.710597 TTGCCAGTAGTAAAGTATCGATCT 57.289 37.500 0.00 0.00 0.00 2.75
3608 4199 0.034756 CATGGGGCCGTATTGATCGA 59.965 55.000 0.00 0.00 0.00 3.59
3620 4211 6.512741 GCCGTATTGATCGATGGTATGTTTTT 60.513 38.462 0.54 0.00 0.00 1.94
3710 4302 1.937223 TCTGTGTTAACGCCAGTTGTG 59.063 47.619 16.23 0.00 41.35 3.33
3799 4391 4.136796 TCCTTGTTCCAGATCAAGTTGTG 58.863 43.478 14.35 0.00 39.25 3.33
3884 4476 1.077089 GCGCCGTTTGGAGTACTCTC 61.077 60.000 21.88 12.69 37.39 3.20
3885 4477 0.242825 CGCCGTTTGGAGTACTCTCA 59.757 55.000 21.88 15.01 42.05 3.27
3886 4478 1.135083 CGCCGTTTGGAGTACTCTCAT 60.135 52.381 21.88 0.00 42.05 2.90
3887 4479 2.271800 GCCGTTTGGAGTACTCTCATG 58.728 52.381 21.88 11.19 42.05 3.07
3888 4480 2.353803 GCCGTTTGGAGTACTCTCATGT 60.354 50.000 21.88 0.00 42.05 3.21
3889 4481 3.254060 CCGTTTGGAGTACTCTCATGTG 58.746 50.000 21.88 8.36 42.05 3.21
3891 4483 4.382040 CCGTTTGGAGTACTCTCATGTGAT 60.382 45.833 21.88 0.00 42.05 3.06
3894 4486 3.981212 TGGAGTACTCTCATGTGATCCA 58.019 45.455 21.88 11.88 42.05 3.41
3895 4487 3.956848 TGGAGTACTCTCATGTGATCCAG 59.043 47.826 21.88 0.00 42.05 3.86
3896 4488 3.243704 GGAGTACTCTCATGTGATCCAGC 60.244 52.174 21.88 0.00 42.05 4.85
3897 4489 3.636300 GAGTACTCTCATGTGATCCAGCT 59.364 47.826 15.91 0.00 40.18 4.24
3898 4490 4.029520 AGTACTCTCATGTGATCCAGCTT 58.970 43.478 0.00 0.00 0.00 3.74
3899 4491 3.996921 ACTCTCATGTGATCCAGCTTT 57.003 42.857 0.00 0.00 0.00 3.51
3900 4492 5.658634 AGTACTCTCATGTGATCCAGCTTTA 59.341 40.000 0.00 0.00 0.00 1.85
3901 4493 4.764172 ACTCTCATGTGATCCAGCTTTAC 58.236 43.478 0.00 0.00 0.00 2.01
3902 4494 4.125703 CTCTCATGTGATCCAGCTTTACC 58.874 47.826 0.00 0.00 0.00 2.85
3903 4495 3.776969 TCTCATGTGATCCAGCTTTACCT 59.223 43.478 0.00 0.00 0.00 3.08
4008 4608 7.802738 TCTCGTTGACGTTGAAATCAAATATT 58.197 30.769 3.25 0.00 36.62 1.28
4076 4678 2.706190 AGGGTGTCTAGTGTCTGCTTTT 59.294 45.455 0.00 0.00 0.00 2.27
4079 4681 4.021368 GGGTGTCTAGTGTCTGCTTTTAGA 60.021 45.833 0.00 0.00 0.00 2.10
4261 4872 6.385176 TGATCTTGATTTGGATGGACTAGAGT 59.615 38.462 0.00 0.00 0.00 3.24
4295 4906 2.266055 GGGACCGTTGCTCTCCTG 59.734 66.667 0.00 0.00 0.00 3.86
4303 4914 3.004734 ACCGTTGCTCTCCTGAATTTTTG 59.995 43.478 0.00 0.00 0.00 2.44
4308 4920 3.058016 TGCTCTCCTGAATTTTTGCTTCG 60.058 43.478 0.00 0.00 0.00 3.79
4309 4921 3.496155 CTCTCCTGAATTTTTGCTTCGC 58.504 45.455 0.00 0.00 0.00 4.70
4310 4922 3.149196 TCTCCTGAATTTTTGCTTCGCT 58.851 40.909 0.00 0.00 0.00 4.93
4311 4923 3.569701 TCTCCTGAATTTTTGCTTCGCTT 59.430 39.130 0.00 0.00 0.00 4.68
4448 5061 0.318955 GTTCAACAGCCCACACATGC 60.319 55.000 0.00 0.00 0.00 4.06
4450 5063 2.985282 AACAGCCCACACATGCGG 60.985 61.111 0.00 0.00 0.00 5.69
4465 5078 2.028925 CGGTGCAAACCCAAAGGC 59.971 61.111 0.00 0.00 36.11 4.35
4478 5091 1.396653 CAAAGGCCCCTATGCTCAAG 58.603 55.000 0.00 0.00 0.00 3.02
4480 5093 0.921256 AAGGCCCCTATGCTCAAGGT 60.921 55.000 0.00 0.00 31.70 3.50
4524 5153 2.443016 CGGTCCCCTCCCTGAGAG 60.443 72.222 0.00 0.00 42.83 3.20
4590 5219 2.831526 TCAATGATCGACAAGTCCTGGA 59.168 45.455 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.096282 AGGAATGAAACCGAGAAAAACAAGAA 59.904 34.615 0.00 0.00 0.00 2.52
12 13 5.845391 AAGGAATGAAACCGAGAAAAACA 57.155 34.783 0.00 0.00 0.00 2.83
14 15 5.047188 GCAAAGGAATGAAACCGAGAAAAA 58.953 37.500 0.00 0.00 0.00 1.94
16 17 3.634448 TGCAAAGGAATGAAACCGAGAAA 59.366 39.130 0.00 0.00 0.00 2.52
21 22 2.995258 CCAATGCAAAGGAATGAAACCG 59.005 45.455 1.70 0.00 0.00 4.44
32 33 7.594386 ACAAAAACAAAAGAAACCAATGCAAAG 59.406 29.630 0.00 0.00 0.00 2.77
63 76 8.084684 CCAATGGAAACCAAAAAGAAAAACAAA 58.915 29.630 0.00 0.00 36.95 2.83
72 85 5.436175 AGAAACCCAATGGAAACCAAAAAG 58.564 37.500 0.00 0.00 36.95 2.27
83 96 6.358974 AGGAATAACAAAGAAACCCAATGG 57.641 37.500 0.00 0.00 37.80 3.16
84 97 9.942850 AATAAGGAATAACAAAGAAACCCAATG 57.057 29.630 0.00 0.00 0.00 2.82
116 129 9.893305 GAGAAAGAAGAAACCGATAAAAATTGA 57.107 29.630 0.00 0.00 0.00 2.57
117 130 9.129209 GGAGAAAGAAGAAACCGATAAAAATTG 57.871 33.333 0.00 0.00 0.00 2.32
118 131 8.856103 TGGAGAAAGAAGAAACCGATAAAAATT 58.144 29.630 0.00 0.00 0.00 1.82
119 132 8.404107 TGGAGAAAGAAGAAACCGATAAAAAT 57.596 30.769 0.00 0.00 0.00 1.82
130 144 4.258543 ACACGTGTTGGAGAAAGAAGAAA 58.741 39.130 17.22 0.00 0.00 2.52
135 149 4.761975 AGTTAACACGTGTTGGAGAAAGA 58.238 39.130 37.43 16.96 38.90 2.52
136 150 5.479716 AAGTTAACACGTGTTGGAGAAAG 57.520 39.130 37.43 2.25 38.90 2.62
170 185 8.746922 TGCTGAAGTATCAAAAATGTTGAATC 57.253 30.769 0.00 0.00 34.49 2.52
308 323 9.730420 GATGTTAAATGCGTATTAGGAAAATGT 57.270 29.630 0.00 0.00 0.00 2.71
309 324 9.950680 AGATGTTAAATGCGTATTAGGAAAATG 57.049 29.630 0.00 0.00 0.00 2.32
312 327 9.997482 GAAAGATGTTAAATGCGTATTAGGAAA 57.003 29.630 0.00 0.00 0.00 3.13
313 328 9.168451 TGAAAGATGTTAAATGCGTATTAGGAA 57.832 29.630 0.00 0.00 0.00 3.36
314 329 8.725405 TGAAAGATGTTAAATGCGTATTAGGA 57.275 30.769 0.00 0.00 0.00 2.94
315 330 9.781834 TTTGAAAGATGTTAAATGCGTATTAGG 57.218 29.630 0.00 0.00 0.00 2.69
321 336 9.128107 CTTGTATTTGAAAGATGTTAAATGCGT 57.872 29.630 0.00 0.00 30.84 5.24
322 337 9.128107 ACTTGTATTTGAAAGATGTTAAATGCG 57.872 29.630 0.00 0.00 30.84 4.73
341 356 9.445786 CGTGTTCAGAAAATGTTAAACTTGTAT 57.554 29.630 0.00 0.00 0.00 2.29
342 357 8.452534 ACGTGTTCAGAAAATGTTAAACTTGTA 58.547 29.630 0.00 0.00 0.00 2.41
343 358 7.272515 CACGTGTTCAGAAAATGTTAAACTTGT 59.727 33.333 7.58 0.00 0.00 3.16
344 359 7.253618 CCACGTGTTCAGAAAATGTTAAACTTG 60.254 37.037 15.65 0.00 0.00 3.16
345 360 6.750039 CCACGTGTTCAGAAAATGTTAAACTT 59.250 34.615 15.65 0.00 0.00 2.66
346 361 6.127842 ACCACGTGTTCAGAAAATGTTAAACT 60.128 34.615 15.65 0.00 0.00 2.66
347 362 6.031471 ACCACGTGTTCAGAAAATGTTAAAC 58.969 36.000 15.65 0.00 0.00 2.01
348 363 6.127980 TGACCACGTGTTCAGAAAATGTTAAA 60.128 34.615 12.19 0.00 0.00 1.52
349 364 5.354513 TGACCACGTGTTCAGAAAATGTTAA 59.645 36.000 12.19 0.00 0.00 2.01
350 365 4.876679 TGACCACGTGTTCAGAAAATGTTA 59.123 37.500 12.19 0.00 0.00 2.41
351 366 3.692101 TGACCACGTGTTCAGAAAATGTT 59.308 39.130 12.19 0.00 0.00 2.71
352 367 3.275143 TGACCACGTGTTCAGAAAATGT 58.725 40.909 12.19 0.00 0.00 2.71
353 368 3.961477 TGACCACGTGTTCAGAAAATG 57.039 42.857 12.19 0.00 0.00 2.32
354 369 3.692101 TGTTGACCACGTGTTCAGAAAAT 59.308 39.130 15.65 0.00 0.00 1.82
355 370 3.075148 TGTTGACCACGTGTTCAGAAAA 58.925 40.909 15.65 0.00 0.00 2.29
356 371 2.701107 TGTTGACCACGTGTTCAGAAA 58.299 42.857 15.65 3.41 0.00 2.52
357 372 2.388310 TGTTGACCACGTGTTCAGAA 57.612 45.000 15.65 5.86 0.00 3.02
358 373 2.613026 ATGTTGACCACGTGTTCAGA 57.387 45.000 15.65 7.53 0.00 3.27
359 374 3.691049 AAATGTTGACCACGTGTTCAG 57.309 42.857 15.65 1.83 0.00 3.02
360 375 4.442375 AAAAATGTTGACCACGTGTTCA 57.558 36.364 12.19 12.19 0.00 3.18
567 582 8.977505 CAATCGTTTGGAAAACTTCAAATATGT 58.022 29.630 0.00 0.00 35.66 2.29
568 583 9.190858 TCAATCGTTTGGAAAACTTCAAATATG 57.809 29.630 6.39 0.00 35.66 1.78
569 584 9.927668 ATCAATCGTTTGGAAAACTTCAAATAT 57.072 25.926 6.39 0.00 35.66 1.28
570 585 9.190858 CATCAATCGTTTGGAAAACTTCAAATA 57.809 29.630 6.39 0.00 35.66 1.40
571 586 7.925483 TCATCAATCGTTTGGAAAACTTCAAAT 59.075 29.630 6.39 0.00 35.66 2.32
572 587 7.261325 TCATCAATCGTTTGGAAAACTTCAAA 58.739 30.769 6.39 0.00 33.44 2.69
573 588 6.800543 TCATCAATCGTTTGGAAAACTTCAA 58.199 32.000 6.39 0.00 33.44 2.69
574 589 6.384258 TCATCAATCGTTTGGAAAACTTCA 57.616 33.333 6.39 0.00 33.44 3.02
575 590 6.129457 CGTTCATCAATCGTTTGGAAAACTTC 60.129 38.462 6.39 0.00 33.44 3.01
576 591 5.685511 CGTTCATCAATCGTTTGGAAAACTT 59.314 36.000 6.39 0.00 33.44 2.66
577 592 5.212194 CGTTCATCAATCGTTTGGAAAACT 58.788 37.500 6.39 0.00 33.44 2.66
578 593 4.973663 ACGTTCATCAATCGTTTGGAAAAC 59.026 37.500 6.39 7.20 34.07 2.43
579 594 5.176407 ACGTTCATCAATCGTTTGGAAAA 57.824 34.783 6.39 0.00 34.07 2.29
580 595 4.822036 ACGTTCATCAATCGTTTGGAAA 57.178 36.364 6.39 0.00 34.07 3.13
581 596 4.822036 AACGTTCATCAATCGTTTGGAA 57.178 36.364 6.39 0.97 43.56 3.53
582 597 6.489127 AATAACGTTCATCAATCGTTTGGA 57.511 33.333 2.82 0.00 43.56 3.53
583 598 8.662369 TTTAATAACGTTCATCAATCGTTTGG 57.338 30.769 2.82 0.00 43.56 3.28
625 640 9.672673 TGAAAAGGTTGGAAATGTATTCAAAAA 57.327 25.926 0.00 0.00 0.00 1.94
626 641 9.672673 TTGAAAAGGTTGGAAATGTATTCAAAA 57.327 25.926 0.00 0.00 32.99 2.44
627 642 9.672673 TTTGAAAAGGTTGGAAATGTATTCAAA 57.327 25.926 0.00 0.00 40.13 2.69
628 643 9.844257 ATTTGAAAAGGTTGGAAATGTATTCAA 57.156 25.926 0.00 0.00 33.79 2.69
629 644 9.270640 CATTTGAAAAGGTTGGAAATGTATTCA 57.729 29.630 0.00 0.00 32.00 2.57
630 645 8.229811 GCATTTGAAAAGGTTGGAAATGTATTC 58.770 33.333 0.00 0.00 36.70 1.75
631 646 7.938490 AGCATTTGAAAAGGTTGGAAATGTATT 59.062 29.630 0.00 0.00 36.70 1.89
632 647 7.452562 AGCATTTGAAAAGGTTGGAAATGTAT 58.547 30.769 0.00 0.00 36.70 2.29
633 648 6.825610 AGCATTTGAAAAGGTTGGAAATGTA 58.174 32.000 0.00 0.00 36.70 2.29
634 649 5.683681 AGCATTTGAAAAGGTTGGAAATGT 58.316 33.333 0.00 0.00 36.70 2.71
635 650 6.260493 TCAAGCATTTGAAAAGGTTGGAAATG 59.740 34.615 20.28 0.00 40.26 2.32
636 651 6.355747 TCAAGCATTTGAAAAGGTTGGAAAT 58.644 32.000 20.28 0.00 40.26 2.17
637 652 5.738909 TCAAGCATTTGAAAAGGTTGGAAA 58.261 33.333 20.28 3.77 40.26 3.13
638 653 5.350504 TCAAGCATTTGAAAAGGTTGGAA 57.649 34.783 20.28 4.37 40.26 3.53
639 654 5.549742 ATCAAGCATTTGAAAAGGTTGGA 57.450 34.783 20.28 10.72 45.82 3.53
640 655 7.910441 ATTATCAAGCATTTGAAAAGGTTGG 57.090 32.000 20.28 6.68 45.82 3.77
669 684 9.712305 TGAAAAAGTTGAACAGGTATTTGAAAA 57.288 25.926 0.00 0.00 0.00 2.29
670 685 9.145865 GTGAAAAAGTTGAACAGGTATTTGAAA 57.854 29.630 0.00 0.00 0.00 2.69
671 686 8.307483 TGTGAAAAAGTTGAACAGGTATTTGAA 58.693 29.630 0.00 0.00 0.00 2.69
672 687 7.757624 GTGTGAAAAAGTTGAACAGGTATTTGA 59.242 33.333 0.00 0.00 0.00 2.69
673 688 7.543868 TGTGTGAAAAAGTTGAACAGGTATTTG 59.456 33.333 0.00 0.00 0.00 2.32
674 689 7.607250 TGTGTGAAAAAGTTGAACAGGTATTT 58.393 30.769 0.00 0.00 0.00 1.40
675 690 7.122055 TCTGTGTGAAAAAGTTGAACAGGTATT 59.878 33.333 0.00 0.00 35.42 1.89
676 691 6.601613 TCTGTGTGAAAAAGTTGAACAGGTAT 59.398 34.615 0.00 0.00 35.42 2.73
677 692 5.941058 TCTGTGTGAAAAAGTTGAACAGGTA 59.059 36.000 0.00 0.00 35.42 3.08
678 693 4.764823 TCTGTGTGAAAAAGTTGAACAGGT 59.235 37.500 0.00 0.00 35.42 4.00
679 694 5.309323 TCTGTGTGAAAAAGTTGAACAGG 57.691 39.130 0.00 0.00 35.42 4.00
680 695 6.808212 ACAATCTGTGTGAAAAAGTTGAACAG 59.192 34.615 0.00 0.00 39.72 3.16
681 696 6.686630 ACAATCTGTGTGAAAAAGTTGAACA 58.313 32.000 0.00 0.00 39.72 3.18
682 697 8.856490 ATACAATCTGTGTGAAAAAGTTGAAC 57.144 30.769 0.00 0.00 41.89 3.18
711 726 9.872757 GAAACTGTTTCTCATGTATACGAAAAA 57.127 29.630 22.55 1.18 36.73 1.94
712 727 9.268268 AGAAACTGTTTCTCATGTATACGAAAA 57.732 29.630 25.82 0.00 46.62 2.29
713 728 8.827177 AGAAACTGTTTCTCATGTATACGAAA 57.173 30.769 25.82 0.00 46.62 3.46
728 743 9.787435 TGGTAAATGTGTATAGAGAAACTGTTT 57.213 29.630 5.29 5.29 0.00 2.83
729 744 9.959721 ATGGTAAATGTGTATAGAGAAACTGTT 57.040 29.630 0.00 0.00 0.00 3.16
730 745 9.959721 AATGGTAAATGTGTATAGAGAAACTGT 57.040 29.630 0.00 0.00 0.00 3.55
816 831 9.982291 GTTCGTAGTTGCAATTATTCTGAATAA 57.018 29.630 21.38 21.38 37.71 1.40
817 832 9.157104 TGTTCGTAGTTGCAATTATTCTGAATA 57.843 29.630 0.59 6.01 0.00 1.75
818 833 8.039603 TGTTCGTAGTTGCAATTATTCTGAAT 57.960 30.769 0.59 8.14 0.00 2.57
819 834 7.428282 TGTTCGTAGTTGCAATTATTCTGAA 57.572 32.000 0.59 3.95 0.00 3.02
820 835 7.428282 TTGTTCGTAGTTGCAATTATTCTGA 57.572 32.000 0.59 0.00 0.00 3.27
821 836 8.500837 TTTTGTTCGTAGTTGCAATTATTCTG 57.499 30.769 0.59 0.00 0.00 3.02
822 837 8.349983 ACTTTTGTTCGTAGTTGCAATTATTCT 58.650 29.630 0.59 0.00 0.00 2.40
823 838 8.502161 ACTTTTGTTCGTAGTTGCAATTATTC 57.498 30.769 0.59 0.00 0.00 1.75
824 839 9.953697 TTACTTTTGTTCGTAGTTGCAATTATT 57.046 25.926 0.59 0.00 0.00 1.40
825 840 9.953697 TTTACTTTTGTTCGTAGTTGCAATTAT 57.046 25.926 0.59 0.00 0.00 1.28
826 841 9.784680 TTTTACTTTTGTTCGTAGTTGCAATTA 57.215 25.926 0.59 0.00 0.00 1.40
827 842 8.690680 TTTTACTTTTGTTCGTAGTTGCAATT 57.309 26.923 0.59 0.00 0.00 2.32
828 843 8.690680 TTTTTACTTTTGTTCGTAGTTGCAAT 57.309 26.923 0.59 0.00 0.00 3.56
855 870 1.029681 GGAGCCACAACCTCGTTTTT 58.970 50.000 0.00 0.00 0.00 1.94
856 871 0.822121 GGGAGCCACAACCTCGTTTT 60.822 55.000 0.00 0.00 0.00 2.43
857 872 1.228154 GGGAGCCACAACCTCGTTT 60.228 57.895 0.00 0.00 0.00 3.60
858 873 2.430367 GGGAGCCACAACCTCGTT 59.570 61.111 0.00 0.00 0.00 3.85
859 874 4.003788 CGGGAGCCACAACCTCGT 62.004 66.667 0.00 0.00 0.00 4.18
860 875 3.530910 AACGGGAGCCACAACCTCG 62.531 63.158 0.00 0.00 0.00 4.63
861 876 1.671379 GAACGGGAGCCACAACCTC 60.671 63.158 0.00 0.00 0.00 3.85
862 877 2.430367 GAACGGGAGCCACAACCT 59.570 61.111 0.00 0.00 0.00 3.50
863 878 3.047877 CGAACGGGAGCCACAACC 61.048 66.667 0.00 0.00 0.00 3.77
864 879 2.280592 ACGAACGGGAGCCACAAC 60.281 61.111 0.00 0.00 0.00 3.32
865 880 2.029964 GACGAACGGGAGCCACAA 59.970 61.111 0.00 0.00 0.00 3.33
866 881 2.915659 AGACGAACGGGAGCCACA 60.916 61.111 0.00 0.00 0.00 4.17
867 882 2.432628 CAGACGAACGGGAGCCAC 60.433 66.667 0.00 0.00 0.00 5.01
868 883 3.691342 CCAGACGAACGGGAGCCA 61.691 66.667 0.00 0.00 35.91 4.75
869 884 4.452733 CCCAGACGAACGGGAGCC 62.453 72.222 2.14 0.00 46.34 4.70
871 886 3.382832 AGCCCAGACGAACGGGAG 61.383 66.667 11.23 1.49 46.34 4.30
872 887 3.691342 CAGCCCAGACGAACGGGA 61.691 66.667 11.23 0.00 46.34 5.14
873 888 4.760047 CCAGCCCAGACGAACGGG 62.760 72.222 0.00 0.00 46.15 5.28
891 906 3.952628 GAAGGGACGCCGAGTTGGG 62.953 68.421 0.00 0.00 38.63 4.12
892 907 2.434359 GAAGGGACGCCGAGTTGG 60.434 66.667 0.00 0.00 42.50 3.77
893 908 1.738099 CTGAAGGGACGCCGAGTTG 60.738 63.158 0.00 0.00 0.00 3.16
894 909 2.657237 CTGAAGGGACGCCGAGTT 59.343 61.111 0.00 0.00 0.00 3.01
895 910 3.382832 CCTGAAGGGACGCCGAGT 61.383 66.667 0.00 0.00 37.23 4.18
896 911 4.821589 GCCTGAAGGGACGCCGAG 62.822 72.222 0.00 0.00 37.23 4.63
899 914 4.821589 CTCGCCTGAAGGGACGCC 62.822 72.222 0.00 0.00 37.23 5.68
900 915 4.821589 CCTCGCCTGAAGGGACGC 62.822 72.222 0.00 0.00 37.23 5.19
901 916 1.961180 AATCCTCGCCTGAAGGGACG 61.961 60.000 0.00 0.00 37.23 4.79
902 917 0.179070 GAATCCTCGCCTGAAGGGAC 60.179 60.000 0.00 0.00 37.23 4.46
903 918 1.338136 GGAATCCTCGCCTGAAGGGA 61.338 60.000 0.00 0.00 37.23 4.20
904 919 1.147153 GGAATCCTCGCCTGAAGGG 59.853 63.158 0.00 0.00 35.18 3.95
905 920 1.147153 GGGAATCCTCGCCTGAAGG 59.853 63.158 0.00 0.00 38.53 3.46
906 921 1.227380 CGGGAATCCTCGCCTGAAG 60.227 63.158 0.00 0.00 32.05 3.02
907 922 2.731571 CCGGGAATCCTCGCCTGAA 61.732 63.158 0.00 0.00 32.05 3.02
908 923 3.154473 CCGGGAATCCTCGCCTGA 61.154 66.667 0.00 0.00 32.05 3.86
909 924 4.918201 GCCGGGAATCCTCGCCTG 62.918 72.222 2.18 0.00 0.00 4.85
913 928 4.547367 GGGTGCCGGGAATCCTCG 62.547 72.222 2.18 0.97 0.00 4.63
914 929 4.191015 GGGGTGCCGGGAATCCTC 62.191 72.222 3.74 1.67 0.00 3.71
916 931 4.506255 CTGGGGTGCCGGGAATCC 62.506 72.222 2.18 6.20 0.00 3.01
944 959 3.649277 ATCGGTGGCGTCTCTGTGC 62.649 63.158 0.00 0.00 0.00 4.57
945 960 1.517257 GATCGGTGGCGTCTCTGTG 60.517 63.158 0.00 0.00 0.00 3.66
946 961 2.711922 GGATCGGTGGCGTCTCTGT 61.712 63.158 0.00 0.00 0.00 3.41
947 962 2.105128 GGATCGGTGGCGTCTCTG 59.895 66.667 0.00 0.00 0.00 3.35
948 963 3.148279 GGGATCGGTGGCGTCTCT 61.148 66.667 0.00 0.00 0.00 3.10
949 964 3.432051 CTGGGATCGGTGGCGTCTC 62.432 68.421 0.00 0.00 0.00 3.36
950 965 3.461773 CTGGGATCGGTGGCGTCT 61.462 66.667 0.00 0.00 0.00 4.18
980 996 2.878991 CCGAATCGAAGCGACGCA 60.879 61.111 23.70 0.35 39.18 5.24
1003 1019 4.200283 CAGGCTCGTCTCCGGAGC 62.200 72.222 27.39 19.70 36.87 4.70
1123 1142 1.005924 ACCAATAAGGGCCCTCTGTTG 59.994 52.381 28.84 26.80 43.89 3.33
1163 1182 9.826574 AAATTTTGCATGCTGAAACATAGATAT 57.173 25.926 20.33 0.00 0.00 1.63
1165 1184 8.556213 AAAATTTTGCATGCTGAAACATAGAT 57.444 26.923 20.33 0.00 0.00 1.98
1166 1185 7.148771 CGAAAATTTTGCATGCTGAAACATAGA 60.149 33.333 20.33 0.00 0.00 1.98
1167 1186 6.951530 CGAAAATTTTGCATGCTGAAACATAG 59.048 34.615 20.33 7.78 0.00 2.23
1169 1188 5.236911 ACGAAAATTTTGCATGCTGAAACAT 59.763 32.000 20.33 9.65 0.00 2.71
1261 1283 9.196139 ACAAACAATTAGTAGCTCTCTCTCTAT 57.804 33.333 0.00 0.00 0.00 1.98
1264 1286 6.754675 GGACAAACAATTAGTAGCTCTCTCTC 59.245 42.308 0.00 0.00 0.00 3.20
1266 1288 5.517054 CGGACAAACAATTAGTAGCTCTCTC 59.483 44.000 0.00 0.00 0.00 3.20
1268 1290 4.033014 GCGGACAAACAATTAGTAGCTCTC 59.967 45.833 0.00 0.00 0.00 3.20
1273 1295 3.241995 GCGAGCGGACAAACAATTAGTAG 60.242 47.826 0.00 0.00 0.00 2.57
1283 1309 0.524816 GATACGAGCGAGCGGACAAA 60.525 55.000 0.00 0.00 35.12 2.83
1302 1328 6.603237 TGCTTAAACATCAGGAATCATACG 57.397 37.500 0.00 0.00 0.00 3.06
1303 1329 6.860023 GCATGCTTAAACATCAGGAATCATAC 59.140 38.462 11.37 0.00 0.00 2.39
1305 1331 5.361571 TGCATGCTTAAACATCAGGAATCAT 59.638 36.000 20.33 0.00 0.00 2.45
1306 1332 4.705991 TGCATGCTTAAACATCAGGAATCA 59.294 37.500 20.33 0.00 0.00 2.57
1307 1333 5.252969 TGCATGCTTAAACATCAGGAATC 57.747 39.130 20.33 0.00 0.00 2.52
1308 1334 5.664294 TTGCATGCTTAAACATCAGGAAT 57.336 34.783 20.33 0.00 0.00 3.01
1311 1337 4.813027 ACTTTGCATGCTTAAACATCAGG 58.187 39.130 20.33 1.91 0.00 3.86
1325 1351 5.596836 TCCAACTGAAGAAAACTTTGCAT 57.403 34.783 0.00 0.00 0.00 3.96
1332 1358 9.052759 TCTAGTTTACATCCAACTGAAGAAAAC 57.947 33.333 0.00 0.00 35.95 2.43
1342 1368 7.702348 GGCATTTGATTCTAGTTTACATCCAAC 59.298 37.037 0.00 0.00 0.00 3.77
1398 1424 4.244425 ACTACGCTGCTATTGATCGAAT 57.756 40.909 0.00 0.00 0.00 3.34
1420 1495 7.429633 GCTGCTATTAAGAACTCTCACAGATA 58.570 38.462 0.00 0.00 0.00 1.98
1421 1496 6.279882 GCTGCTATTAAGAACTCTCACAGAT 58.720 40.000 0.00 0.00 0.00 2.90
1422 1497 5.655488 GCTGCTATTAAGAACTCTCACAGA 58.345 41.667 0.00 0.00 0.00 3.41
1423 1498 4.502282 CGCTGCTATTAAGAACTCTCACAG 59.498 45.833 0.00 0.00 0.00 3.66
1424 1499 4.424626 CGCTGCTATTAAGAACTCTCACA 58.575 43.478 0.00 0.00 0.00 3.58
1425 1500 3.244111 GCGCTGCTATTAAGAACTCTCAC 59.756 47.826 0.00 0.00 0.00 3.51
1460 1595 9.677567 GTATTAAAATTGTGAAAGAACAGCAGA 57.322 29.630 0.00 0.00 0.00 4.26
1535 1670 2.416431 CCCCGATCCGTATTAATCGTCC 60.416 54.545 0.00 0.00 42.41 4.79
1555 1690 3.391049 GTCGCTGATTTAGTACATCCCC 58.609 50.000 0.00 0.00 0.00 4.81
1590 1725 7.770897 CCATAGACATAATAAATGCTACCTCCC 59.229 40.741 0.00 0.00 0.00 4.30
1641 2022 6.721208 TGAAACCAGCAAATAGGAGAAAGAAT 59.279 34.615 0.00 0.00 0.00 2.40
1680 2063 7.092137 TCAGTTCATCATGCCAATAGAAAAG 57.908 36.000 0.00 0.00 0.00 2.27
1708 2091 4.130118 GCTCTGAGGACAACAAGAAGAAA 58.870 43.478 6.83 0.00 0.00 2.52
1709 2092 3.495100 GGCTCTGAGGACAACAAGAAGAA 60.495 47.826 6.83 0.00 0.00 2.52
1721 2104 2.165357 TTCATAGCTGGCTCTGAGGA 57.835 50.000 6.83 0.00 32.18 3.71
1747 2130 8.424918 TCTCTGATTTCTTCCATATACTTGTCC 58.575 37.037 0.00 0.00 0.00 4.02
1849 2232 0.687354 AAGCTGGTTCTGGACATCGT 59.313 50.000 0.00 0.00 0.00 3.73
1980 2365 4.216472 GGGGCTGAAAGAAGTACAGAAAAG 59.784 45.833 0.00 0.00 34.07 2.27
2001 2386 1.834188 ATCGTTTGCTTGTAAGGGGG 58.166 50.000 0.00 0.00 0.00 5.40
2160 2729 8.816894 TCTCTAGGACAGTTGAAGATGTAATTT 58.183 33.333 0.00 0.00 0.00 1.82
2402 2972 3.770388 AGACAAAGTAGGACTAGCCCTTC 59.230 47.826 1.70 0.00 37.74 3.46
2441 3011 7.390162 GGCTCTTCTAAGCTGCATTATTCTAAT 59.610 37.037 1.02 0.00 42.13 1.73
2499 3069 4.022416 TGACTGCATTGGTTGTACAATTCC 60.022 41.667 12.26 9.85 38.94 3.01
2674 3246 6.623986 GCATCCTCGTAGATTACAGGATAGTG 60.624 46.154 14.31 9.16 40.98 2.74
2675 3247 5.416326 GCATCCTCGTAGATTACAGGATAGT 59.584 44.000 14.31 0.00 40.98 2.12
2802 3374 6.845758 ATAACTAGCACTACTGTTACACCA 57.154 37.500 0.00 0.00 30.14 4.17
2931 3504 0.394565 AGGAGATATGAGCGGCAACC 59.605 55.000 1.45 0.00 0.00 3.77
3012 3585 1.153269 TCAGCGTTGTCACTGCCAA 60.153 52.632 0.00 0.00 33.80 4.52
3122 3695 1.384191 GGAAGTCCACTGGGCCAAT 59.616 57.895 8.04 0.00 35.64 3.16
3375 3951 1.078497 CCCTTGCGCACAGTATCCA 60.078 57.895 11.12 0.00 0.00 3.41
3399 3975 2.429930 CGGGCACAAACCTCCTCA 59.570 61.111 0.00 0.00 0.00 3.86
3465 4056 0.472471 TGTCTTTGGTTCCGGCTCTT 59.528 50.000 0.00 0.00 0.00 2.85
3491 4082 5.885352 TCTGTGAAATGAAAGTGAGGAAACA 59.115 36.000 0.00 0.00 0.00 2.83
3528 4119 7.133513 GTCACAGATCGATACTTTACTACTGG 58.866 42.308 0.00 0.00 0.00 4.00
3533 4124 5.585445 ACTCGTCACAGATCGATACTTTACT 59.415 40.000 0.00 0.00 35.57 2.24
3548 4139 2.473816 CTCAGCTTTGAACTCGTCACA 58.526 47.619 0.00 0.00 35.39 3.58
3620 4211 2.158534 ACATAACCACTGGTGCAGGAAA 60.159 45.455 0.00 0.00 35.34 3.13
3661 4253 7.219484 AGGAAAATCAAGACACATAAGGTTG 57.781 36.000 0.00 0.00 0.00 3.77
3668 4260 7.286316 ACAGAAAGAAGGAAAATCAAGACACAT 59.714 33.333 0.00 0.00 0.00 3.21
3710 4302 0.586802 GGAGTTTTCACCGCAGTCAC 59.413 55.000 0.00 0.00 0.00 3.67
3799 4391 6.017109 TGACTAACAAGAAGAAGAACAATGCC 60.017 38.462 0.00 0.00 0.00 4.40
3884 4476 4.460382 ACAAAGGTAAAGCTGGATCACATG 59.540 41.667 0.00 0.00 0.00 3.21
3885 4477 4.460382 CACAAAGGTAAAGCTGGATCACAT 59.540 41.667 0.00 0.00 0.00 3.21
3886 4478 3.820467 CACAAAGGTAAAGCTGGATCACA 59.180 43.478 0.00 0.00 0.00 3.58
3887 4479 3.821033 ACACAAAGGTAAAGCTGGATCAC 59.179 43.478 0.00 0.00 0.00 3.06
3888 4480 4.098914 ACACAAAGGTAAAGCTGGATCA 57.901 40.909 0.00 0.00 0.00 2.92
3889 4481 9.726438 ATATATACACAAAGGTAAAGCTGGATC 57.274 33.333 0.00 0.00 0.00 3.36
3891 4483 9.914834 AAATATATACACAAAGGTAAAGCTGGA 57.085 29.630 0.00 0.00 0.00 3.86
3900 4492 9.528489 ACCAGAACAAAATATATACACAAAGGT 57.472 29.630 0.00 0.00 0.00 3.50
3901 4493 9.787532 CACCAGAACAAAATATATACACAAAGG 57.212 33.333 0.00 0.00 0.00 3.11
4008 4608 4.408596 ACAAAAAGGAAAATCAGCCCTTCA 59.591 37.500 0.00 0.00 39.21 3.02
4076 4678 2.656002 AGCAGCTACTTCCATCGTCTA 58.344 47.619 0.00 0.00 0.00 2.59
4079 4681 1.550524 TGAAGCAGCTACTTCCATCGT 59.449 47.619 21.45 0.00 44.50 3.73
4261 4872 4.201679 CGACAGCGGTATCGGCCA 62.202 66.667 7.53 0.00 34.67 5.36
4276 4887 3.379445 GGAGAGCAACGGTCCCGA 61.379 66.667 13.54 0.00 42.83 5.14
4321 4933 0.440371 CGAGCAAGCGTCTCTTTTCC 59.560 55.000 0.00 0.00 31.27 3.13
4448 5061 2.028925 GCCTTTGGGTTTGCACCG 59.971 61.111 0.00 0.00 45.39 4.94
4450 5063 2.425592 GGGCCTTTGGGTTTGCAC 59.574 61.111 0.84 0.00 34.45 4.57
4465 5078 2.173356 TCATCAACCTTGAGCATAGGGG 59.827 50.000 4.15 0.00 41.08 4.79
4494 5123 1.602237 GGACCGTGGTCATGTCCAT 59.398 57.895 20.02 0.00 46.29 3.41
4524 5153 1.733718 GCATTCTTCGGCTTCTTTGGC 60.734 52.381 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.