Multiple sequence alignment - TraesCS5A01G182200

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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 TraesCS5A01G182200 chr5A 100.000 6042 0 0 1 6042 382067561 382073602 0.000000e+00 11158.0
1 TraesCS5A01G182200 chr5A 76.190 147 31 4 5502 5646 536677089 536676945 2.340000e-09 75.0
2 TraesCS5A01G182200 chr5B 90.793 4540 263 66 18 4510 328103392 328107823 0.000000e+00 5925.0
3 TraesCS5A01G182200 chr5B 89.641 1419 102 17 4639 6036 328108060 328109454 0.000000e+00 1764.0
4 TraesCS5A01G182200 chr5B 95.327 107 4 1 4495 4601 328107842 328107947 1.040000e-37 169.0
5 TraesCS5A01G182200 chr5D 90.993 2498 134 48 2 2466 288544905 288547344 0.000000e+00 3282.0
6 TraesCS5A01G182200 chr5D 89.649 2338 145 23 3772 6042 288548537 288550844 0.000000e+00 2887.0
7 TraesCS5A01G182200 chr5D 91.140 1140 71 14 2513 3642 288547338 288548457 0.000000e+00 1519.0
8 TraesCS5A01G182200 chr3A 90.572 891 65 10 1296 2171 512327924 512328810 0.000000e+00 1162.0
9 TraesCS5A01G182200 chr3A 90.244 164 13 1 2393 2553 509865416 509865253 1.710000e-50 211.0
10 TraesCS5A01G182200 chr3A 77.707 157 29 6 5494 5646 8796880 8797034 2.320000e-14 91.6
11 TraesCS5A01G182200 chr3A 87.500 64 5 2 2170 2233 512329042 512329102 3.020000e-08 71.3
12 TraesCS5A01G182200 chr3D 89.944 537 43 6 1642 2172 392350332 392350863 0.000000e+00 682.0
13 TraesCS5A01G182200 chr3D 97.619 42 1 0 2170 2211 392351083 392351124 8.400000e-09 73.1
14 TraesCS5A01G182200 chr4B 92.357 157 8 2 2404 2556 106227409 106227565 2.830000e-53 220.0
15 TraesCS5A01G182200 chr4B 78.358 134 26 3 5515 5646 521734968 521734836 3.880000e-12 84.2
16 TraesCS5A01G182200 chr7B 92.208 154 9 3 2404 2554 369872719 369872872 1.320000e-51 215.0
17 TraesCS5A01G182200 chr1A 92.208 154 9 1 2404 2554 395177601 395177448 1.320000e-51 215.0
18 TraesCS5A01G182200 chr7D 91.083 157 10 2 2400 2553 34757021 34756866 6.140000e-50 209.0
19 TraesCS5A01G182200 chr7D 89.571 163 13 2 2404 2562 436459777 436459615 2.850000e-48 204.0
20 TraesCS5A01G182200 chr1B 90.683 161 9 4 2404 2561 632021077 632020920 6.140000e-50 209.0
21 TraesCS5A01G182200 chr4A 89.697 165 14 1 2396 2557 460230641 460230805 2.210000e-49 207.0
22 TraesCS5A01G182200 chr4A 79.054 148 28 3 5501 5646 658069022 658069168 1.390000e-16 99.0
23 TraesCS5A01G182200 chr4A 78.378 148 29 3 5501 5646 658108002 658108148 6.450000e-15 93.5
24 TraesCS5A01G182200 chr7A 81.955 133 23 1 5515 5646 680258170 680258038 1.780000e-20 111.0
25 TraesCS5A01G182200 chr7A 83.516 91 14 1 5560 5650 6349896 6349807 3.880000e-12 84.2


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 TraesCS5A01G182200 chr5A 382067561 382073602 6041 False 11158.000000 11158 100.000000 1 6042 1 chr5A.!!$F1 6041
1 TraesCS5A01G182200 chr5B 328103392 328109454 6062 False 2619.333333 5925 91.920333 18 6036 3 chr5B.!!$F1 6018
2 TraesCS5A01G182200 chr5D 288544905 288550844 5939 False 2562.666667 3282 90.594000 2 6042 3 chr5D.!!$F1 6040
3 TraesCS5A01G182200 chr3A 512327924 512329102 1178 False 616.650000 1162 89.036000 1296 2233 2 chr3A.!!$F2 937
4 TraesCS5A01G182200 chr3D 392350332 392351124 792 False 377.550000 682 93.781500 1642 2211 2 chr3D.!!$F1 569

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
475 482 0.095245 CGCATCACTAAAGCACACCG 59.905 55.0 0.00 0.00 0.00 4.94 F
476 483 0.179189 GCATCACTAAAGCACACCGC 60.179 55.0 0.00 0.00 42.91 5.68 F
634 654 0.320160 GCCGTAGTTCTCCGTGGTTT 60.320 55.0 0.00 0.00 0.00 3.27 F
776 798 0.461870 TGAACTGATCCGGCGATTGG 60.462 55.0 9.30 0.00 0.00 3.16 F
2399 2708 0.626277 TGGGGCCCCAGCTACTTATT 60.626 55.0 41.29 0.00 41.89 1.40 F
3013 3327 0.108585 TGGCCTTCCGATGCTTATCC 59.891 55.0 3.32 0.00 34.14 2.59 F
3106 3420 0.388134 GCTGGTGTGCATTGCTCTTG 60.388 55.0 10.49 0.45 0.00 3.02 F
3595 3915 0.453390 GCAGGTTAGTGGCTGCATTC 59.547 55.0 0.50 0.00 41.89 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2365 2674 1.748591 GCCCCATTCTCCAGTGTGATC 60.749 57.143 0.00 0.00 0.00 2.92 R
2375 2684 2.078665 TAGCTGGGGCCCCATTCTC 61.079 63.158 44.00 29.63 46.15 2.87 R
2564 2876 1.284198 AGGCCATGCAACTCAGAGAAT 59.716 47.619 5.01 0.00 0.00 2.40 R
2567 2879 1.661341 GTAGGCCATGCAACTCAGAG 58.339 55.000 5.01 0.00 0.00 3.35 R
3372 3692 0.320050 TTAGCGACACCATCACTGCA 59.680 50.000 0.00 0.00 0.00 4.41 R
4457 4781 0.411848 CAAATTAGGGGTGTGGGGGT 59.588 55.000 0.00 0.00 0.00 4.95 R
4659 5109 1.522668 GGTGTACAAGCTGTGCATCA 58.477 50.000 0.00 0.00 44.34 3.07 R
5496 5984 0.391263 CAACCTACCTTGACCGCTCC 60.391 60.000 0.00 0.00 0.00 4.70 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
92 94 3.484407 CATCCTCTAGCAAGAAATGGGG 58.516 50.000 0.00 0.00 0.00 4.96
109 111 1.009829 GGGATCAGATTGCACGTGTC 58.990 55.000 18.38 10.14 0.00 3.67
155 158 1.941975 CGGAAAATATAAACGCGGGGT 59.058 47.619 12.47 0.00 0.00 4.95
208 211 2.058057 CACCAAAATTTACTGCGCACC 58.942 47.619 5.66 0.00 0.00 5.01
209 212 1.335506 ACCAAAATTTACTGCGCACCG 60.336 47.619 5.66 0.00 0.00 4.94
287 291 1.595093 CCCAGAAATCACAACGGGCC 61.595 60.000 0.00 0.00 0.00 5.80
310 314 0.841289 CCGCCATTAAACCCTAGGGA 59.159 55.000 35.38 12.63 38.96 4.20
311 315 1.202770 CCGCCATTAAACCCTAGGGAG 60.203 57.143 35.38 15.04 38.96 4.30
312 316 1.766496 CGCCATTAAACCCTAGGGAGA 59.234 52.381 35.38 15.54 38.96 3.71
313 317 2.171870 CGCCATTAAACCCTAGGGAGAA 59.828 50.000 35.38 22.81 38.96 2.87
340 344 2.352388 CCCGAAAGAAACCGATGCTTA 58.648 47.619 0.00 0.00 0.00 3.09
366 373 1.078567 GAGAGGGAGTGCAGCTTGG 60.079 63.158 0.00 0.00 0.00 3.61
367 374 2.749441 GAGGGAGTGCAGCTTGGC 60.749 66.667 0.00 0.00 0.00 4.52
368 375 4.357279 AGGGAGTGCAGCTTGGCC 62.357 66.667 0.00 0.00 0.00 5.36
369 376 4.666253 GGGAGTGCAGCTTGGCCA 62.666 66.667 0.00 0.00 0.00 5.36
370 377 3.060615 GGAGTGCAGCTTGGCCAG 61.061 66.667 5.11 1.08 0.00 4.85
371 378 2.282040 GAGTGCAGCTTGGCCAGT 60.282 61.111 5.11 0.00 0.00 4.00
372 379 2.596631 AGTGCAGCTTGGCCAGTG 60.597 61.111 5.11 6.49 0.00 3.66
470 477 3.769739 ATATCCCGCATCACTAAAGCA 57.230 42.857 0.00 0.00 0.00 3.91
472 479 0.323302 TCCCGCATCACTAAAGCACA 59.677 50.000 0.00 0.00 0.00 4.57
474 481 0.447801 CCGCATCACTAAAGCACACC 59.552 55.000 0.00 0.00 0.00 4.16
475 482 0.095245 CGCATCACTAAAGCACACCG 59.905 55.000 0.00 0.00 0.00 4.94
476 483 0.179189 GCATCACTAAAGCACACCGC 60.179 55.000 0.00 0.00 42.91 5.68
477 484 1.155889 CATCACTAAAGCACACCGCA 58.844 50.000 0.00 0.00 46.13 5.69
478 485 1.129251 CATCACTAAAGCACACCGCAG 59.871 52.381 0.00 0.00 46.13 5.18
530 537 2.506438 CTTTCGTCGTCCTCGCCC 60.506 66.667 0.00 0.00 36.96 6.13
583 590 1.739049 CATCCCAGCGACCTCTCTC 59.261 63.158 0.00 0.00 0.00 3.20
584 591 1.826054 ATCCCAGCGACCTCTCTCG 60.826 63.158 0.00 0.00 36.70 4.04
590 610 4.180946 CGACCTCTCTCGCACCCG 62.181 72.222 0.00 0.00 0.00 5.28
604 624 3.917760 CCCGTCCATCCCTCTCGC 61.918 72.222 0.00 0.00 0.00 5.03
609 629 3.917760 CCATCCCTCTCGCCGTCC 61.918 72.222 0.00 0.00 0.00 4.79
610 630 2.835431 CATCCCTCTCGCCGTCCT 60.835 66.667 0.00 0.00 0.00 3.85
611 631 1.528542 CATCCCTCTCGCCGTCCTA 60.529 63.158 0.00 0.00 0.00 2.94
612 632 0.896019 CATCCCTCTCGCCGTCCTAT 60.896 60.000 0.00 0.00 0.00 2.57
613 633 0.609681 ATCCCTCTCGCCGTCCTATC 60.610 60.000 0.00 0.00 0.00 2.08
614 634 1.228306 CCCTCTCGCCGTCCTATCT 60.228 63.158 0.00 0.00 0.00 1.98
617 637 2.136196 CTCTCGCCGTCCTATCTGCC 62.136 65.000 0.00 0.00 0.00 4.85
618 638 3.544167 CTCGCCGTCCTATCTGCCG 62.544 68.421 0.00 0.00 0.00 5.69
620 640 2.549198 CGCCGTCCTATCTGCCGTA 61.549 63.158 0.00 0.00 0.00 4.02
624 644 1.001597 CCGTCCTATCTGCCGTAGTTC 60.002 57.143 0.00 0.00 0.00 3.01
625 645 1.948145 CGTCCTATCTGCCGTAGTTCT 59.052 52.381 0.00 0.00 0.00 3.01
626 646 2.031857 CGTCCTATCTGCCGTAGTTCTC 60.032 54.545 0.00 0.00 0.00 2.87
627 647 2.293955 GTCCTATCTGCCGTAGTTCTCC 59.706 54.545 0.00 0.00 0.00 3.71
628 648 1.267261 CCTATCTGCCGTAGTTCTCCG 59.733 57.143 0.00 0.00 0.00 4.63
629 649 1.948145 CTATCTGCCGTAGTTCTCCGT 59.052 52.381 0.00 0.00 0.00 4.69
630 650 0.456221 ATCTGCCGTAGTTCTCCGTG 59.544 55.000 0.00 0.00 0.00 4.94
631 651 1.153823 CTGCCGTAGTTCTCCGTGG 60.154 63.158 0.00 0.00 0.00 4.94
632 652 1.874345 CTGCCGTAGTTCTCCGTGGT 61.874 60.000 0.00 0.00 0.00 4.16
633 653 1.291272 GCCGTAGTTCTCCGTGGTT 59.709 57.895 0.00 0.00 0.00 3.67
634 654 0.320160 GCCGTAGTTCTCCGTGGTTT 60.320 55.000 0.00 0.00 0.00 3.27
635 655 1.706443 CCGTAGTTCTCCGTGGTTTC 58.294 55.000 0.00 0.00 0.00 2.78
636 656 1.334054 CGTAGTTCTCCGTGGTTTCG 58.666 55.000 0.00 0.00 0.00 3.46
637 657 1.335324 CGTAGTTCTCCGTGGTTTCGT 60.335 52.381 0.00 0.00 0.00 3.85
638 658 2.747436 GTAGTTCTCCGTGGTTTCGTT 58.253 47.619 0.00 0.00 0.00 3.85
639 659 1.578583 AGTTCTCCGTGGTTTCGTTG 58.421 50.000 0.00 0.00 0.00 4.10
640 660 0.584876 GTTCTCCGTGGTTTCGTTGG 59.415 55.000 0.00 0.00 0.00 3.77
641 661 1.161563 TTCTCCGTGGTTTCGTTGGC 61.162 55.000 0.00 0.00 0.00 4.52
642 662 2.592287 TCCGTGGTTTCGTTGGCC 60.592 61.111 0.00 0.00 0.00 5.36
643 663 3.666253 CCGTGGTTTCGTTGGCCC 61.666 66.667 0.00 0.00 0.00 5.80
650 670 2.631580 TTTCGTTGGCCCGCAATCC 61.632 57.895 0.00 0.00 0.00 3.01
676 696 1.524621 CTTGGGCTCCTGGTATGCG 60.525 63.158 0.00 0.00 0.00 4.73
677 697 2.257409 CTTGGGCTCCTGGTATGCGT 62.257 60.000 0.00 0.00 0.00 5.24
703 724 2.923121 TGCTCTGTCACTCAAAGCTTT 58.077 42.857 5.69 5.69 40.46 3.51
757 778 4.517285 TCTTCAGTCTTCTTGTTGTTGCT 58.483 39.130 0.00 0.00 0.00 3.91
768 789 1.872952 TGTTGTTGCTGAACTGATCCG 59.127 47.619 0.00 0.00 32.79 4.18
776 798 0.461870 TGAACTGATCCGGCGATTGG 60.462 55.000 9.30 0.00 0.00 3.16
788 810 2.286418 CGGCGATTGGTAGCTCAAAATC 60.286 50.000 0.00 0.00 0.00 2.17
793 815 5.276270 CGATTGGTAGCTCAAAATCATTGG 58.724 41.667 12.85 0.00 0.00 3.16
809 831 4.619973 TCATTGGTGTTCATTTTGCAGAC 58.380 39.130 0.00 0.00 0.00 3.51
820 842 1.398692 TTTGCAGACTGGTTTGGGAC 58.601 50.000 4.26 0.00 0.00 4.46
853 877 3.289836 TCCTTGATCTCTCTGCTCTCTG 58.710 50.000 0.00 0.00 0.00 3.35
857 881 2.689471 TGATCTCTCTGCTCTCTGCTTC 59.311 50.000 0.00 0.00 43.37 3.86
866 890 2.566279 TGCTCTCTGCTTCTCATCTTGT 59.434 45.455 0.00 0.00 43.37 3.16
870 894 4.818642 TCTCTGCTTCTCATCTTGTTCTG 58.181 43.478 0.00 0.00 0.00 3.02
872 896 3.008330 CTGCTTCTCATCTTGTTCTGGG 58.992 50.000 0.00 0.00 0.00 4.45
916 940 3.118112 TCTGAGGAAATCTTGGGCATCTC 60.118 47.826 0.00 0.00 0.00 2.75
933 957 1.539869 TCTGCTGCCTTTCCCCTCT 60.540 57.895 0.00 0.00 0.00 3.69
934 958 1.077858 CTGCTGCCTTTCCCCTCTC 60.078 63.158 0.00 0.00 0.00 3.20
938 962 2.286502 GCCTTTCCCCTCTCCCCT 60.287 66.667 0.00 0.00 0.00 4.79
944 968 1.841334 TTCCCCTCTCCCCTTTTCAA 58.159 50.000 0.00 0.00 0.00 2.69
956 980 2.295909 CCCTTTTCAATCAACCAAGCGA 59.704 45.455 0.00 0.00 0.00 4.93
993 1017 1.000163 TGAGCAGAGGAACAGTTCGAC 60.000 52.381 7.22 4.03 0.00 4.20
1011 1035 2.354704 CGACTGGGAAATGGCTGAAGTA 60.355 50.000 0.00 0.00 0.00 2.24
1080 1104 4.106197 GGTTTGAGTACTGCATAGACTCG 58.894 47.826 0.00 0.00 42.10 4.18
1117 1141 3.118847 TCTGTGCCATCTCATCTCTCAAC 60.119 47.826 0.00 0.00 0.00 3.18
1118 1142 2.093288 TGTGCCATCTCATCTCTCAACC 60.093 50.000 0.00 0.00 0.00 3.77
1142 1166 2.092699 TGGCATGTTGGATCAATCGGTA 60.093 45.455 0.00 0.00 0.00 4.02
1144 1168 3.189287 GGCATGTTGGATCAATCGGTATC 59.811 47.826 0.00 0.00 0.00 2.24
1198 1222 0.897621 GAGAGGCAATTGGTTTGGGG 59.102 55.000 7.72 0.00 35.75 4.96
1201 1225 1.001974 GAGGCAATTGGTTTGGGGTTC 59.998 52.381 7.72 0.00 35.75 3.62
1261 1285 2.041081 CCCCACAATGTTGGTTCCTCTA 59.959 50.000 2.71 0.00 34.44 2.43
1534 1569 3.324846 CCTCTCCATAATCCATGACCGAA 59.675 47.826 0.00 0.00 36.69 4.30
1674 1729 9.920946 ATCCATGTTATACATTTCAGTTTACCT 57.079 29.630 0.00 0.00 36.53 3.08
1828 1889 4.223032 CCCACTTCTCCTTTAACTGCTAGA 59.777 45.833 0.00 0.00 0.00 2.43
1829 1890 5.280011 CCCACTTCTCCTTTAACTGCTAGAA 60.280 44.000 0.00 0.00 0.00 2.10
1983 2046 6.426633 TGTTCATATACTGGACCAAATATGCG 59.573 38.462 21.50 8.47 31.61 4.73
2036 2108 0.639943 TACTATCCTGGTCCCTGCCA 59.360 55.000 0.00 0.00 36.97 4.92
2129 2201 3.634568 TGCCGATGTGTTAAACAAAGG 57.365 42.857 0.00 0.00 43.61 3.11
2298 2607 2.501723 CCTTTTCGAGAGAGGATTCCCA 59.498 50.000 0.00 0.00 43.69 4.37
2344 2653 8.713271 CCTTACTTTTGTTCTGTTTAGCTCTAG 58.287 37.037 0.00 0.00 0.00 2.43
2360 2669 5.858381 AGCTCTAGTCACTTTGATGTTTGA 58.142 37.500 0.00 0.00 0.00 2.69
2365 2674 7.919690 TCTAGTCACTTTGATGTTTGAAACTG 58.080 34.615 9.69 0.00 0.00 3.16
2375 2684 4.898829 TGTTTGAAACTGATCACACTGG 57.101 40.909 9.69 0.00 32.52 4.00
2384 2693 1.561076 TGATCACACTGGAGAATGGGG 59.439 52.381 0.00 0.00 0.00 4.96
2399 2708 0.626277 TGGGGCCCCAGCTACTTATT 60.626 55.000 41.29 0.00 41.89 1.40
2401 2710 1.478837 GGGGCCCCAGCTACTTATTTC 60.479 57.143 37.61 1.86 39.73 2.17
2431 2740 6.055588 CCCTCCGTTCACAAATATAAGATGT 58.944 40.000 0.00 0.00 0.00 3.06
2499 2808 4.035091 TGTTTGTTCACTCATTTCAGTCCG 59.965 41.667 0.00 0.00 0.00 4.79
2510 2819 3.770263 TTTCAGTCCGTATGTAGTCCG 57.230 47.619 0.00 0.00 0.00 4.79
2511 2820 1.019673 TCAGTCCGTATGTAGTCCGC 58.980 55.000 0.00 0.00 0.00 5.54
2554 2866 9.537192 CATATATTTGTTAACGGAGGAAGTACA 57.463 33.333 0.26 0.00 0.00 2.90
2564 2876 7.571080 AACGGAGGAAGTACAATTTTAAACA 57.429 32.000 0.00 0.00 0.00 2.83
2567 2879 8.294577 ACGGAGGAAGTACAATTTTAAACATTC 58.705 33.333 0.00 0.00 0.00 2.67
2604 2916 6.100569 TGGCCTACCTTGCTAGTTTGATAATA 59.899 38.462 3.32 0.00 36.63 0.98
2682 2994 3.221771 TGATTGGCACTTTAGCAACACT 58.778 40.909 0.00 0.00 35.83 3.55
2726 3038 5.541845 TGCTACATATGGTAAGATGCACTC 58.458 41.667 7.80 0.00 28.08 3.51
2874 3186 6.450545 TCATATTTACTCAGGCAAGATCTCG 58.549 40.000 0.00 0.00 0.00 4.04
2885 3198 4.705507 AGGCAAGATCTCGTACTCTGTTAA 59.294 41.667 0.00 0.00 0.00 2.01
2894 3207 4.553323 TCGTACTCTGTTAACTTGCCTTC 58.447 43.478 7.22 0.00 0.00 3.46
2902 3216 7.122799 ACTCTGTTAACTTGCCTTCTTTTTCTT 59.877 33.333 7.22 0.00 0.00 2.52
2903 3217 7.257722 TCTGTTAACTTGCCTTCTTTTTCTTG 58.742 34.615 7.22 0.00 0.00 3.02
2904 3218 6.930731 TGTTAACTTGCCTTCTTTTTCTTGT 58.069 32.000 7.22 0.00 0.00 3.16
3013 3327 0.108585 TGGCCTTCCGATGCTTATCC 59.891 55.000 3.32 0.00 34.14 2.59
3025 3339 5.296780 CCGATGCTTATCCTATTTGTTGTGT 59.703 40.000 0.00 0.00 0.00 3.72
3085 3399 3.519510 TCCGATTTTGGAGAGGTTCTCAT 59.480 43.478 8.23 0.00 45.12 2.90
3106 3420 0.388134 GCTGGTGTGCATTGCTCTTG 60.388 55.000 10.49 0.45 0.00 3.02
3136 3450 1.825090 TGCCCACATTCTAACAGCAG 58.175 50.000 0.00 0.00 0.00 4.24
3162 3476 2.940410 TGCATATCATCACACTGCACTG 59.060 45.455 0.00 0.00 37.88 3.66
3201 3515 2.299297 CAGGACAGACCGTTCTAACCTT 59.701 50.000 4.79 0.00 44.74 3.50
3210 3524 5.950549 AGACCGTTCTAACCTTATCTCTTCA 59.049 40.000 0.00 0.00 0.00 3.02
3238 3556 2.432206 GTTTGTAAACCGGCTTGCAT 57.568 45.000 9.25 0.00 32.82 3.96
3240 3558 4.104696 GTTTGTAAACCGGCTTGCATAT 57.895 40.909 9.25 0.00 32.82 1.78
3243 3561 3.550820 TGTAAACCGGCTTGCATATCAT 58.449 40.909 4.09 0.00 0.00 2.45
3246 3564 3.441496 AACCGGCTTGCATATCATTTG 57.559 42.857 0.00 0.00 0.00 2.32
3372 3692 3.440151 GCATTCGGCATGATGGCT 58.560 55.556 17.13 0.00 43.97 4.75
3404 3724 4.321082 GGTGTCGCTAATAGAGGTACCATC 60.321 50.000 15.94 8.88 0.00 3.51
3416 3736 4.580995 AGAGGTACCATCTCATACTTGTCG 59.419 45.833 15.94 0.00 33.92 4.35
3436 3756 6.560711 TGTCGAATACATGATTTCTCGAAGA 58.439 36.000 0.00 0.00 31.43 2.87
3586 3906 0.744414 CATCGGGTGGCAGGTTAGTG 60.744 60.000 0.00 0.00 0.00 2.74
3588 3908 2.361230 GGGTGGCAGGTTAGTGGC 60.361 66.667 0.00 0.00 43.25 5.01
3595 3915 0.453390 GCAGGTTAGTGGCTGCATTC 59.547 55.000 0.50 0.00 41.89 2.67
3598 3918 1.065126 AGGTTAGTGGCTGCATTCTCC 60.065 52.381 0.50 0.00 0.00 3.71
3601 3921 3.181450 GGTTAGTGGCTGCATTCTCCTAT 60.181 47.826 0.50 0.00 0.00 2.57
3603 3923 2.121948 AGTGGCTGCATTCTCCTATCA 58.878 47.619 0.50 0.00 0.00 2.15
3610 3930 5.512060 GGCTGCATTCTCCTATCATCTTGTA 60.512 44.000 0.50 0.00 0.00 2.41
3616 3936 7.930865 GCATTCTCCTATCATCTTGTAGAGTTT 59.069 37.037 0.00 0.00 0.00 2.66
3620 3940 8.816894 TCTCCTATCATCTTGTAGAGTTTTGTT 58.183 33.333 0.00 0.00 0.00 2.83
3650 3970 7.907389 TGTTAAGTCCAGTAGTTCTCATGAAT 58.093 34.615 0.00 0.00 34.40 2.57
3656 3976 5.877012 TCCAGTAGTTCTCATGAATTTGAGC 59.123 40.000 0.00 0.00 42.37 4.26
3682 4002 7.439157 TCAACTAGAATTGTCAGTGATTTGG 57.561 36.000 0.00 0.00 0.00 3.28
3687 4007 8.695456 ACTAGAATTGTCAGTGATTTGGTTTTT 58.305 29.630 0.00 0.00 0.00 1.94
3716 4036 6.350027 GGTTGTAGTCTTGTAGAACTACTCCC 60.350 46.154 12.25 8.84 37.00 4.30
3719 4039 7.337167 TGTAGTCTTGTAGAACTACTCCCTAG 58.663 42.308 12.25 0.00 37.00 3.02
3724 4044 4.853007 TGTAGAACTACTCCCTAGTCACC 58.147 47.826 12.25 0.00 34.26 4.02
3725 4045 4.290459 TGTAGAACTACTCCCTAGTCACCA 59.710 45.833 12.25 0.00 34.26 4.17
3742 4063 5.710099 AGTCACCACTGAACTTTTCTGAAAA 59.290 36.000 14.31 14.31 33.42 2.29
3762 4083 9.853921 CTGAAAAGAAATGAAACTTTACAATGC 57.146 29.630 0.00 0.00 0.00 3.56
3763 4084 9.376075 TGAAAAGAAATGAAACTTTACAATGCA 57.624 25.926 0.00 0.00 0.00 3.96
3766 4087 9.545105 AAAGAAATGAAACTTTACAATGCATGA 57.455 25.926 0.00 0.00 0.00 3.07
3767 4088 9.715121 AAGAAATGAAACTTTACAATGCATGAT 57.285 25.926 0.00 0.00 0.00 2.45
3768 4089 9.146984 AGAAATGAAACTTTACAATGCATGATG 57.853 29.630 0.00 0.00 0.00 3.07
3769 4090 9.142515 GAAATGAAACTTTACAATGCATGATGA 57.857 29.630 0.00 0.00 0.00 2.92
3770 4091 8.470040 AATGAAACTTTACAATGCATGATGAC 57.530 30.769 0.00 0.00 0.00 3.06
3870 4192 5.174395 GCATCTGAGCTTTCACTCTAAGAA 58.826 41.667 0.00 0.00 37.58 2.52
3906 4228 6.438108 TGGCATGCCTAATATTATGCAGAATT 59.562 34.615 35.53 9.98 45.73 2.17
4011 4333 7.809238 TGGTTTCATGATCTTCTTCTCCATAT 58.191 34.615 0.00 0.00 0.00 1.78
4127 4449 4.119136 CACTTTTTGCTTCCATTCCGTTT 58.881 39.130 0.00 0.00 0.00 3.60
4139 4461 4.876679 TCCATTCCGTTTACAATATTCGCA 59.123 37.500 0.00 0.00 0.00 5.10
4163 4485 6.542005 CAGCCATATACTGTGTTATGTTTGGA 59.458 38.462 10.01 0.00 0.00 3.53
4244 4566 8.855110 CCTGAGTTCTCTAGCTAGATTTGAATA 58.145 37.037 23.48 12.40 0.00 1.75
4249 4571 6.673106 TCTCTAGCTAGATTTGAATAGCACG 58.327 40.000 23.48 7.58 45.54 5.34
4287 4611 4.681978 GTGTCTCCAGCGGCGGTT 62.682 66.667 9.73 0.00 0.00 4.44
4302 4626 1.420430 CGGTTGGGCTATCCTTCCTA 58.580 55.000 0.00 0.00 36.20 2.94
4305 4629 2.508300 GGTTGGGCTATCCTTCCTACAA 59.492 50.000 0.00 0.00 36.20 2.41
4341 4665 2.799412 CTCTATGCGCAACCTCTTCATC 59.201 50.000 17.11 0.00 0.00 2.92
4348 4672 1.197721 GCAACCTCTTCATCGTTGGTG 59.802 52.381 0.00 0.00 37.84 4.17
4396 4720 5.579564 ACCAGAGTACTTTTCTCGGTATC 57.420 43.478 0.00 0.00 37.21 2.24
4421 4745 2.117206 TGCTCAAAATGGCCCGGT 59.883 55.556 0.00 0.00 0.00 5.28
4450 4774 1.087771 GGCTGGATGGGTTCGTAACG 61.088 60.000 0.00 0.00 0.00 3.18
4456 4780 2.611224 GGATGGGTTCGTAACGTCACTT 60.611 50.000 0.00 0.00 0.00 3.16
4457 4781 3.367292 GGATGGGTTCGTAACGTCACTTA 60.367 47.826 0.00 0.00 0.00 2.24
4469 4793 1.848895 TCACTTACCCCCACACCCC 60.849 63.158 0.00 0.00 0.00 4.95
4522 4885 5.409826 GTCCACTGTCTCGAGATTTGAATTT 59.590 40.000 19.90 0.00 0.00 1.82
4533 4896 9.350357 CTCGAGATTTGAATTTGAAATGACATT 57.650 29.630 6.58 0.00 0.00 2.71
4750 5200 6.418819 CCTTGTCAATGTTGTCAAAATGTCTC 59.581 38.462 6.81 0.00 36.19 3.36
4819 5270 5.715439 TTGAATTGTATCATCCCTGACCT 57.285 39.130 0.00 0.00 33.22 3.85
4921 5372 3.445450 ACAACACGCTAGATGTCAGAGAT 59.555 43.478 0.00 0.00 0.00 2.75
4945 5396 1.925888 GAAGGACAGGGGGATGCAT 59.074 57.895 0.00 0.00 0.00 3.96
5103 5554 4.692155 CCAAATGAAGAAACCTTTGCATCC 59.308 41.667 0.00 0.00 0.00 3.51
5116 5567 0.106769 TGCATCCCAATACGGCATGT 60.107 50.000 0.00 0.00 0.00 3.21
5135 5586 6.765036 GGCATGTTTCTGAATTCTGATAGAGA 59.235 38.462 14.89 1.67 0.00 3.10
5243 5694 9.864034 GTCCGATTGTACATAGATATTTGTTTG 57.136 33.333 0.00 0.00 0.00 2.93
5312 5781 3.189080 TCTCATGAAACATTTGCGGACAG 59.811 43.478 0.00 0.00 0.00 3.51
5331 5800 2.031314 CAGATGAGGCACATTGTTAGCG 59.969 50.000 0.00 0.00 39.56 4.26
5418 5887 6.014327 AGTGAAATGTGCCATTAATCCTTGTT 60.014 34.615 1.52 0.00 0.00 2.83
5458 5934 1.227089 GCTCAGATCATGTCGGCGT 60.227 57.895 6.85 0.00 0.00 5.68
5496 5984 6.098017 CCCTTGTAAGAGTTAGTCGGTTTAG 58.902 44.000 0.00 0.00 0.00 1.85
5555 6043 0.754472 AGTTTTCCCTCGTGAACCGA 59.246 50.000 0.00 0.00 45.00 4.69
5558 6046 1.803334 TTTCCCTCGTGAACCGATTG 58.197 50.000 0.00 0.00 46.23 2.67
5633 6121 6.540083 ACTAAGTTATTGGCCTAAAGTGTGT 58.460 36.000 3.32 0.00 0.00 3.72
5634 6122 5.705609 AAGTTATTGGCCTAAAGTGTGTG 57.294 39.130 3.32 0.00 0.00 3.82
5646 6134 6.401394 CCTAAAGTGTGTGATCAGATTGAGA 58.599 40.000 0.00 0.00 0.00 3.27
5663 6158 8.697067 CAGATTGAGATTTTTAAAACTGTGCAG 58.303 33.333 0.00 0.00 0.00 4.41
5705 6200 6.484288 ACCAATGACTCATTTCACTCCATTA 58.516 36.000 1.17 0.00 31.05 1.90
5711 6206 6.667848 TGACTCATTTCACTCCATTACTCCTA 59.332 38.462 0.00 0.00 0.00 2.94
5718 6213 3.068307 CACTCCATTACTCCTAAGACCGG 59.932 52.174 0.00 0.00 0.00 5.28
5738 6239 0.168788 CACACATCGGTTGTCATGCC 59.831 55.000 0.00 0.00 36.00 4.40
5762 6263 6.762661 CCCACTTTTGATGAAGAAACAACAAT 59.237 34.615 0.00 0.00 33.86 2.71
5786 6293 3.843893 AGTAAAAGTGTACACCCCGTT 57.156 42.857 22.28 13.05 0.00 4.44
5802 6309 1.303317 GTTGCGGGATCCAACCACT 60.303 57.895 15.23 0.00 37.25 4.00
5806 6313 2.334977 TGCGGGATCCAACCACTATAT 58.665 47.619 15.23 0.00 0.00 0.86
5829 6336 3.826157 GTCATGTCTTGGGTTTTCATCCA 59.174 43.478 0.00 0.00 0.00 3.41
5845 6352 7.904558 TTTCATCCAGATAGTATGTCTGAGT 57.095 36.000 5.24 0.00 44.57 3.41
5873 6380 5.906113 TTAAAACAGTGCCTTCAACAAGA 57.094 34.783 0.00 0.00 0.00 3.02
5881 6388 2.159448 TGCCTTCAACAAGAACACAACG 60.159 45.455 0.00 0.00 31.61 4.10
5888 6395 4.095185 TCAACAAGAACACAACGGGTAAAG 59.905 41.667 0.00 0.00 0.00 1.85
5919 6426 1.468520 GCCAAGCGCAACTATCAAAGA 59.531 47.619 11.47 0.00 37.47 2.52
5923 6430 2.205074 AGCGCAACTATCAAAGATCGG 58.795 47.619 11.47 0.00 0.00 4.18
5940 6447 2.885616 TCGGACCTAGAGTTTTCACCT 58.114 47.619 0.00 0.00 0.00 4.00
5942 6449 3.006537 TCGGACCTAGAGTTTTCACCTTG 59.993 47.826 0.00 0.00 0.00 3.61
5948 6455 4.223032 CCTAGAGTTTTCACCTTGGAGCTA 59.777 45.833 0.00 0.00 0.00 3.32
5959 6466 3.137913 ACCTTGGAGCTAGATACTCGGTA 59.862 47.826 2.67 0.00 34.87 4.02
5967 6474 6.134040 AGCTAGATACTCGGTACTCAAAAC 57.866 41.667 0.00 0.00 0.00 2.43
5971 6478 2.902705 ACTCGGTACTCAAAACAGCA 57.097 45.000 0.00 0.00 0.00 4.41
5976 6483 2.294074 GGTACTCAAAACAGCACCACA 58.706 47.619 0.00 0.00 0.00 4.17
5991 6498 1.898574 CACAAAGCCGAAGCCACCT 60.899 57.895 0.00 0.00 41.25 4.00
6038 6545 3.952628 GAAGGCGTCACGGAAGGGG 62.953 68.421 0.00 0.00 33.12 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.183830 TGTTTAATTGCTCTTCTTGTTGTTTG 57.816 30.769 0.00 0.00 0.00 2.93
6 7 7.174253 TCCGTATTGTTTAATTGCTCTTCTTGT 59.826 33.333 0.00 0.00 0.00 3.16
84 86 2.033801 CGTGCAATCTGATCCCCATTTC 59.966 50.000 0.00 0.00 0.00 2.17
92 94 1.929836 GAGGACACGTGCAATCTGATC 59.070 52.381 17.22 2.44 0.00 2.92
109 111 2.271800 GTGTGGCGTTATCTTCAGAGG 58.728 52.381 0.00 0.00 0.00 3.69
233 236 3.451178 TCGGATCAGAGGTTTTAAGGAGG 59.549 47.826 0.00 0.00 0.00 4.30
287 291 2.884639 CCTAGGGTTTAATGGCGGATTG 59.115 50.000 0.00 0.00 0.00 2.67
310 314 0.395312 TTCTTTCGGGGCGTTCTTCT 59.605 50.000 0.00 0.00 0.00 2.85
311 315 1.069432 GTTTCTTTCGGGGCGTTCTTC 60.069 52.381 0.00 0.00 0.00 2.87
312 316 0.949397 GTTTCTTTCGGGGCGTTCTT 59.051 50.000 0.00 0.00 0.00 2.52
313 317 0.887836 GGTTTCTTTCGGGGCGTTCT 60.888 55.000 0.00 0.00 0.00 3.01
340 344 2.115911 CACTCCCTCTCGCTACGCT 61.116 63.158 0.00 0.00 0.00 5.07
366 373 2.439156 GGATGAGTGGGCACTGGC 60.439 66.667 0.00 0.00 42.66 4.85
367 374 2.262774 GAGGGATGAGTGGGCACTGG 62.263 65.000 0.00 0.00 42.66 4.00
368 375 1.222936 GAGGGATGAGTGGGCACTG 59.777 63.158 0.00 0.00 42.66 3.66
369 376 2.362369 CGAGGGATGAGTGGGCACT 61.362 63.158 0.00 0.00 45.84 4.40
370 377 2.187946 CGAGGGATGAGTGGGCAC 59.812 66.667 0.00 0.00 0.00 5.01
371 378 3.785859 GCGAGGGATGAGTGGGCA 61.786 66.667 0.00 0.00 0.00 5.36
372 379 3.785859 TGCGAGGGATGAGTGGGC 61.786 66.667 0.00 0.00 0.00 5.36
530 537 1.750778 AGTAGCCGCAATGGGAATTTG 59.249 47.619 0.00 0.00 38.63 2.32
583 590 4.530857 GAGGGATGGACGGGTGCG 62.531 72.222 0.00 0.00 0.00 5.34
584 591 3.083997 AGAGGGATGGACGGGTGC 61.084 66.667 0.00 0.00 0.00 5.01
587 607 3.917760 GCGAGAGGGATGGACGGG 61.918 72.222 0.00 0.00 0.00 5.28
590 610 3.140225 GACGGCGAGAGGGATGGAC 62.140 68.421 16.62 0.00 0.00 4.02
604 624 1.001597 GAACTACGGCAGATAGGACGG 60.002 57.143 0.00 0.00 45.67 4.79
609 629 1.948145 ACGGAGAACTACGGCAGATAG 59.052 52.381 11.16 0.00 42.25 2.08
610 630 1.674441 CACGGAGAACTACGGCAGATA 59.326 52.381 11.16 0.00 42.25 1.98
611 631 0.456221 CACGGAGAACTACGGCAGAT 59.544 55.000 11.16 0.00 42.25 2.90
612 632 1.592400 CCACGGAGAACTACGGCAGA 61.592 60.000 11.16 0.00 42.25 4.26
613 633 1.153823 CCACGGAGAACTACGGCAG 60.154 63.158 11.16 0.91 42.25 4.85
614 634 1.466025 AACCACGGAGAACTACGGCA 61.466 55.000 11.16 0.00 42.25 5.69
617 637 1.334054 CGAAACCACGGAGAACTACG 58.666 55.000 4.82 4.82 43.89 3.51
618 638 2.428888 ACGAAACCACGGAGAACTAC 57.571 50.000 0.00 0.00 37.61 2.73
620 640 1.578583 CAACGAAACCACGGAGAACT 58.421 50.000 0.00 0.00 37.61 3.01
624 644 2.613506 GGCCAACGAAACCACGGAG 61.614 63.158 0.00 0.00 37.61 4.63
625 645 2.592287 GGCCAACGAAACCACGGA 60.592 61.111 0.00 0.00 37.61 4.69
626 646 3.666253 GGGCCAACGAAACCACGG 61.666 66.667 4.39 0.00 37.61 4.94
627 647 4.020378 CGGGCCAACGAAACCACG 62.020 66.667 4.39 0.00 39.31 4.94
628 648 4.337060 GCGGGCCAACGAAACCAC 62.337 66.667 4.39 0.00 35.47 4.16
629 649 4.877619 TGCGGGCCAACGAAACCA 62.878 61.111 4.39 0.00 35.47 3.67
630 650 2.812542 GATTGCGGGCCAACGAAACC 62.813 60.000 4.39 0.00 33.56 3.27
631 651 1.443702 GATTGCGGGCCAACGAAAC 60.444 57.895 4.39 0.00 33.56 2.78
632 652 2.631580 GGATTGCGGGCCAACGAAA 61.632 57.895 4.39 0.00 35.99 3.46
633 653 3.059386 GGATTGCGGGCCAACGAA 61.059 61.111 4.39 0.00 35.99 3.85
636 656 3.336715 GAACGGATTGCGGGCCAAC 62.337 63.158 4.39 0.00 35.99 3.77
637 657 3.059386 GAACGGATTGCGGGCCAA 61.059 61.111 4.39 0.00 37.94 4.52
676 696 1.942657 TGAGTGACAGAGCAAGCAAAC 59.057 47.619 0.00 0.00 0.00 2.93
677 697 2.330440 TGAGTGACAGAGCAAGCAAA 57.670 45.000 0.00 0.00 0.00 3.68
703 724 1.425066 ACTCAAGATGGTCCCAAAGCA 59.575 47.619 0.00 0.00 40.26 3.91
709 730 1.902508 TCTGTCACTCAAGATGGTCCC 59.097 52.381 0.00 0.00 0.00 4.46
713 734 6.638610 AGAAATAGTCTGTCACTCAAGATGG 58.361 40.000 0.00 0.00 36.43 3.51
746 767 3.607775 CGGATCAGTTCAGCAACAACAAG 60.608 47.826 0.00 0.00 34.60 3.16
757 778 0.461870 CCAATCGCCGGATCAGTTCA 60.462 55.000 5.05 0.00 30.81 3.18
768 789 2.682856 TGATTTTGAGCTACCAATCGCC 59.317 45.455 0.00 0.00 0.00 5.54
776 798 6.012658 TGAACACCAATGATTTTGAGCTAC 57.987 37.500 0.00 0.00 0.00 3.58
788 810 4.446385 CAGTCTGCAAAATGAACACCAATG 59.554 41.667 0.00 0.00 0.00 2.82
793 815 3.715628 ACCAGTCTGCAAAATGAACAC 57.284 42.857 0.00 0.00 0.00 3.32
823 845 4.022935 CAGAGAGATCAAGGAATCCTCTCG 60.023 50.000 0.56 0.00 36.33 4.04
853 877 3.064900 ACCCAGAACAAGATGAGAAGC 57.935 47.619 0.00 0.00 0.00 3.86
857 881 3.754965 TGGAAACCCAGAACAAGATGAG 58.245 45.455 0.00 0.00 0.00 2.90
870 894 7.985184 AGAAGAAAAATGTTAAACTGGAAACCC 59.015 33.333 0.00 0.00 0.00 4.11
872 896 9.581099 TCAGAAGAAAAATGTTAAACTGGAAAC 57.419 29.630 0.00 0.00 0.00 2.78
884 908 7.256083 CCCAAGATTTCCTCAGAAGAAAAATGT 60.256 37.037 0.00 0.00 36.83 2.71
916 940 1.077858 GAGAGGGGAAAGGCAGCAG 60.078 63.158 0.00 0.00 0.00 4.24
933 957 2.632512 GCTTGGTTGATTGAAAAGGGGA 59.367 45.455 0.00 0.00 0.00 4.81
934 958 2.610232 CGCTTGGTTGATTGAAAAGGGG 60.610 50.000 0.00 0.00 0.00 4.79
938 962 6.102663 TCTTTTTCGCTTGGTTGATTGAAAA 58.897 32.000 0.00 0.00 34.56 2.29
944 968 5.200368 ACAATCTTTTTCGCTTGGTTGAT 57.800 34.783 0.00 0.00 0.00 2.57
993 1017 4.321974 GGTTTTACTTCAGCCATTTCCCAG 60.322 45.833 0.00 0.00 0.00 4.45
1011 1035 1.702957 TGGACCATCTCTTCCGGTTTT 59.297 47.619 0.00 0.00 34.24 2.43
1080 1104 1.065126 CACAGACCCCAGGAAGGATTC 60.065 57.143 0.00 0.00 46.67 2.52
1117 1141 0.887247 TTGATCCAACATGCCAACGG 59.113 50.000 0.00 0.00 0.00 4.44
1118 1142 2.792196 CGATTGATCCAACATGCCAACG 60.792 50.000 0.00 0.00 0.00 4.10
1142 1166 8.960591 CACAAATATTCAGGGTAAGAAACAGAT 58.039 33.333 0.00 0.00 0.00 2.90
1144 1168 7.362920 CCCACAAATATTCAGGGTAAGAAACAG 60.363 40.741 10.28 0.00 34.75 3.16
1261 1285 4.320546 TCTCACATCATTTCCACCCATT 57.679 40.909 0.00 0.00 0.00 3.16
1294 1318 6.076981 AGGAGTGTAGCAAACATGAAAAAG 57.923 37.500 0.00 0.00 41.10 2.27
1300 1326 3.149196 ACCAAGGAGTGTAGCAAACATG 58.851 45.455 0.00 0.00 41.10 3.21
1674 1729 5.473504 GGAACCTCTGCAGATAGAACAAAAA 59.526 40.000 18.63 0.00 0.00 1.94
1903 1964 6.258230 TCAAGCAAATAATCTGTCAGGTTG 57.742 37.500 8.70 0.00 35.16 3.77
1949 2012 8.271458 TGGTCCAGTATATGAACACATGTTAAT 58.729 33.333 0.00 0.00 38.56 1.40
1983 2046 7.656707 AAAGCAACAACAAATATCCACAATC 57.343 32.000 0.00 0.00 0.00 2.67
2129 2201 3.689161 GCTTTTGGATATTTTTGCCCACC 59.311 43.478 0.00 0.00 0.00 4.61
2298 2607 2.027100 GGCCACTAGAGCTTTTACCACT 60.027 50.000 0.00 0.00 0.00 4.00
2344 2653 7.166473 GTGATCAGTTTCAAACATCAAAGTGAC 59.834 37.037 2.41 1.55 42.16 3.67
2360 2669 4.330250 CCATTCTCCAGTGTGATCAGTTT 58.670 43.478 0.00 0.00 0.00 2.66
2365 2674 1.748591 GCCCCATTCTCCAGTGTGATC 60.749 57.143 0.00 0.00 0.00 2.92
2375 2684 2.078665 TAGCTGGGGCCCCATTCTC 61.079 63.158 44.00 29.63 46.15 2.87
2384 2693 5.037383 AGTAAGAAATAAGTAGCTGGGGC 57.963 43.478 0.00 0.00 39.06 5.80
2399 2708 2.600790 TGTGAACGGAGGGAGTAAGAA 58.399 47.619 0.00 0.00 0.00 2.52
2401 2710 3.396260 TTTGTGAACGGAGGGAGTAAG 57.604 47.619 0.00 0.00 0.00 2.34
2457 2766 8.597662 ACAAACACACTAAAACGTGTCTATAT 57.402 30.769 0.00 0.00 45.74 0.86
2473 2782 5.640732 ACTGAAATGAGTGAACAAACACAC 58.359 37.500 0.00 0.00 42.45 3.82
2499 2808 6.649141 TGGATATTTCAATGCGGACTACATAC 59.351 38.462 0.00 0.00 0.00 2.39
2539 2851 8.674263 TGTTTAAAATTGTACTTCCTCCGTTA 57.326 30.769 0.00 0.00 0.00 3.18
2554 2866 9.199982 CATGCAACTCAGAGAATGTTTAAAATT 57.800 29.630 3.79 0.00 0.00 1.82
2564 2876 1.284198 AGGCCATGCAACTCAGAGAAT 59.716 47.619 5.01 0.00 0.00 2.40
2567 2879 1.661341 GTAGGCCATGCAACTCAGAG 58.339 55.000 5.01 0.00 0.00 3.35
2572 2884 3.271250 CAAGGTAGGCCATGCAACT 57.729 52.632 5.01 0.00 37.19 3.16
2627 2939 6.071616 TCCATGCTCCAAATAAACTTTGGTAC 60.072 38.462 14.53 9.56 46.75 3.34
2705 3017 6.753180 ACTGAGTGCATCTTACCATATGTAG 58.247 40.000 1.24 0.00 0.00 2.74
2719 3031 4.767578 AATGATCTGGTACTGAGTGCAT 57.232 40.909 2.55 0.00 40.25 3.96
2777 3089 8.804743 CATATTTTCAGTGACATTGAAGATTGC 58.195 33.333 17.95 0.00 36.07 3.56
2860 3172 2.685388 CAGAGTACGAGATCTTGCCTGA 59.315 50.000 10.09 0.00 0.00 3.86
2874 3186 6.862711 AAAGAAGGCAAGTTAACAGAGTAC 57.137 37.500 8.61 0.00 0.00 2.73
2885 3198 7.875554 TGTTTTTACAAGAAAAAGAAGGCAAGT 59.124 29.630 0.00 0.00 30.95 3.16
2894 3207 9.914923 GGTGCTAAATGTTTTTACAAGAAAAAG 57.085 29.630 0.00 0.00 30.95 2.27
2902 3216 7.517614 TCTCATGGTGCTAAATGTTTTTACA 57.482 32.000 0.00 0.00 0.00 2.41
2903 3217 8.986477 AATCTCATGGTGCTAAATGTTTTTAC 57.014 30.769 0.00 0.00 0.00 2.01
3013 3327 9.573133 GAGATATTGGGAAAACACAACAAATAG 57.427 33.333 0.00 0.00 0.00 1.73
3025 3339 6.889177 TGTACATGCTTGAGATATTGGGAAAA 59.111 34.615 6.60 0.00 0.00 2.29
3136 3450 2.615447 CAGTGTGATGATATGCACCACC 59.385 50.000 0.00 0.00 34.19 4.61
3147 3461 0.179051 TGTGCAGTGCAGTGTGATGA 60.179 50.000 20.42 0.61 40.08 2.92
3162 3476 0.890542 TGCAACTGATCTGGGTGTGC 60.891 55.000 4.49 8.29 0.00 4.57
3201 3515 9.679661 TTTACAAACCATAATGCTGAAGAGATA 57.320 29.630 0.00 0.00 0.00 1.98
3235 3553 7.707464 TGATGTGGAAATGAACAAATGATATGC 59.293 33.333 0.00 0.00 0.00 3.14
3330 3650 1.273048 TCTGCATTGAATGTTGGTGCC 59.727 47.619 7.05 0.00 35.03 5.01
3372 3692 0.320050 TTAGCGACACCATCACTGCA 59.680 50.000 0.00 0.00 0.00 4.41
3404 3724 9.254133 AGAAATCATGTATTCGACAAGTATGAG 57.746 33.333 0.00 0.00 42.78 2.90
3467 3787 6.956371 CTGAAGAACTCAAATGGTTTCAACCC 60.956 42.308 6.25 0.00 40.07 4.11
3586 3906 3.699411 AGATGATAGGAGAATGCAGCC 57.301 47.619 0.00 0.00 0.00 4.85
3588 3908 6.990798 TCTACAAGATGATAGGAGAATGCAG 58.009 40.000 0.00 0.00 0.00 4.41
3650 3970 6.712095 ACTGACAATTCTAGTTGATGCTCAAA 59.288 34.615 0.40 0.00 38.22 2.69
3656 3976 7.966753 CCAAATCACTGACAATTCTAGTTGATG 59.033 37.037 0.40 0.00 33.37 3.07
3687 4007 6.639632 AGTTCTACAAGACTACAACCGTAA 57.360 37.500 0.00 0.00 0.00 3.18
3688 4008 6.936900 AGTAGTTCTACAAGACTACAACCGTA 59.063 38.462 14.02 0.00 34.37 4.02
3689 4009 5.767168 AGTAGTTCTACAAGACTACAACCGT 59.233 40.000 14.02 0.00 34.37 4.83
3690 4010 6.251655 AGTAGTTCTACAAGACTACAACCG 57.748 41.667 14.02 0.00 34.37 4.44
3691 4011 6.350027 GGGAGTAGTTCTACAAGACTACAACC 60.350 46.154 14.02 14.60 34.37 3.77
3692 4012 6.433716 AGGGAGTAGTTCTACAAGACTACAAC 59.566 42.308 14.02 8.52 34.37 3.32
3693 4013 6.550163 AGGGAGTAGTTCTACAAGACTACAA 58.450 40.000 14.02 0.00 34.37 2.41
3694 4014 6.137104 AGGGAGTAGTTCTACAAGACTACA 57.863 41.667 14.02 0.00 34.37 2.74
3695 4015 7.337938 ACTAGGGAGTAGTTCTACAAGACTAC 58.662 42.308 11.73 5.72 39.06 2.73
3696 4016 7.181665 TGACTAGGGAGTAGTTCTACAAGACTA 59.818 40.741 11.73 7.66 42.48 2.59
3697 4017 6.012683 TGACTAGGGAGTAGTTCTACAAGACT 60.013 42.308 11.73 7.06 42.48 3.24
3698 4018 6.093909 GTGACTAGGGAGTAGTTCTACAAGAC 59.906 46.154 11.73 0.96 42.48 3.01
3699 4019 6.179040 GTGACTAGGGAGTAGTTCTACAAGA 58.821 44.000 11.73 0.00 42.48 3.02
3700 4020 5.357596 GGTGACTAGGGAGTAGTTCTACAAG 59.642 48.000 11.73 4.58 42.48 3.16
3701 4021 5.222192 TGGTGACTAGGGAGTAGTTCTACAA 60.222 44.000 11.73 0.00 42.48 2.41
3706 4026 3.444388 CAGTGGTGACTAGGGAGTAGTTC 59.556 52.174 0.00 0.00 42.48 3.01
3716 4036 5.601662 TCAGAAAAGTTCAGTGGTGACTAG 58.398 41.667 0.00 0.00 30.10 2.57
3719 4039 5.560966 TTTCAGAAAAGTTCAGTGGTGAC 57.439 39.130 0.00 0.00 30.10 3.67
3742 4063 9.146984 CATCATGCATTGTAAAGTTTCATTTCT 57.853 29.630 0.00 0.00 0.00 2.52
3753 4074 4.217983 TGCACAGTCATCATGCATTGTAAA 59.782 37.500 0.00 0.00 44.17 2.01
3754 4075 3.757493 TGCACAGTCATCATGCATTGTAA 59.243 39.130 0.00 0.00 44.17 2.41
3755 4076 3.345414 TGCACAGTCATCATGCATTGTA 58.655 40.909 0.00 0.00 44.17 2.41
3756 4077 2.164338 TGCACAGTCATCATGCATTGT 58.836 42.857 0.00 0.00 44.17 2.71
3757 4078 2.931512 TGCACAGTCATCATGCATTG 57.068 45.000 0.00 0.00 44.17 2.82
3761 4082 2.223502 CCTGAATGCACAGTCATCATGC 60.224 50.000 0.77 0.00 34.73 4.06
3762 4083 2.357952 CCCTGAATGCACAGTCATCATG 59.642 50.000 0.77 0.00 34.73 3.07
3763 4084 2.240414 TCCCTGAATGCACAGTCATCAT 59.760 45.455 0.77 0.00 34.73 2.45
3764 4085 1.629861 TCCCTGAATGCACAGTCATCA 59.370 47.619 0.77 0.00 34.73 3.07
3765 4086 2.408271 TCCCTGAATGCACAGTCATC 57.592 50.000 0.77 0.00 34.73 2.92
3766 4087 2.885135 TTCCCTGAATGCACAGTCAT 57.115 45.000 0.77 0.00 34.73 3.06
3767 4088 2.885135 ATTCCCTGAATGCACAGTCA 57.115 45.000 0.46 0.46 36.30 3.41
3768 4089 3.209410 CCTATTCCCTGAATGCACAGTC 58.791 50.000 3.87 0.00 36.30 3.51
3769 4090 2.578021 ACCTATTCCCTGAATGCACAGT 59.422 45.455 3.87 0.00 36.30 3.55
3770 4091 3.287867 ACCTATTCCCTGAATGCACAG 57.712 47.619 0.00 0.00 33.95 3.66
3870 4192 0.604578 GGCATGCCACAACAGAACAT 59.395 50.000 32.08 0.00 35.81 2.71
3906 4228 2.892215 TCTCACTGCATTGCATCCAAAA 59.108 40.909 12.53 0.00 38.13 2.44
4011 4333 7.827729 GGCTCAAGAGAAACCTTAATTACCTAA 59.172 37.037 0.32 0.00 0.00 2.69
4033 4355 2.680913 AAATGCGTGCTCGTGGCTC 61.681 57.895 10.18 0.00 42.39 4.70
4124 4446 7.957484 CAGTATATGGCTGCGAATATTGTAAAC 59.043 37.037 10.52 4.62 0.00 2.01
4127 4449 6.589907 CACAGTATATGGCTGCGAATATTGTA 59.410 38.462 10.52 0.00 37.47 2.41
4139 4461 6.658849 TCCAAACATAACACAGTATATGGCT 58.341 36.000 9.32 0.00 34.52 4.75
4249 4571 7.160633 ACACAACAAACGAGCAAAATTATTC 57.839 32.000 0.00 0.00 0.00 1.75
4287 4611 4.044308 TGAATTGTAGGAAGGATAGCCCA 58.956 43.478 0.00 0.00 37.41 5.36
4302 4626 6.349611 GCATAGAGTTCATGTTGGTGAATTGT 60.350 38.462 0.00 0.00 39.99 2.71
4305 4629 4.333649 CGCATAGAGTTCATGTTGGTGAAT 59.666 41.667 0.00 0.00 39.99 2.57
4341 4665 4.342772 CAAGAAAGAGTGAAACACCAACG 58.657 43.478 0.00 0.00 41.43 4.10
4348 4672 5.408604 TCGATAAGCCAAGAAAGAGTGAAAC 59.591 40.000 0.00 0.00 0.00 2.78
4396 4720 1.068055 GCCATTTTGAGCACCTGTCAG 60.068 52.381 0.00 0.00 0.00 3.51
4421 4745 1.672030 CATCCAGCCTTCGTGTGCA 60.672 57.895 0.00 0.00 0.00 4.57
4450 4774 1.377612 GGGTGTGGGGGTAAGTGAC 59.622 63.158 0.00 0.00 0.00 3.67
4456 4780 1.641714 CAAATTAGGGGTGTGGGGGTA 59.358 52.381 0.00 0.00 0.00 3.69
4457 4781 0.411848 CAAATTAGGGGTGTGGGGGT 59.588 55.000 0.00 0.00 0.00 4.95
4469 4793 8.142551 GTGGGAGTCCATACTAGTACAAATTAG 58.857 40.741 12.30 0.00 46.09 1.73
4533 4896 8.461222 CAGATACTAGATTGGACATTTTTGCAA 58.539 33.333 0.00 0.00 0.00 4.08
4653 5103 3.570926 ACAAGCTGTGCATCATCTTTG 57.429 42.857 0.00 0.00 31.24 2.77
4659 5109 1.522668 GGTGTACAAGCTGTGCATCA 58.477 50.000 0.00 0.00 44.34 3.07
4717 5167 6.000840 TGACAACATTGACAAGGCACTATTA 58.999 36.000 0.00 0.00 38.49 0.98
4725 5175 6.275335 AGACATTTTGACAACATTGACAAGG 58.725 36.000 8.97 0.00 42.03 3.61
4750 5200 2.435069 AGGACTCTTGCATGGAGATGAG 59.565 50.000 19.63 8.05 35.10 2.90
4819 5270 4.565022 TGTAGTCATTGAACTGCATCGAA 58.435 39.130 0.00 0.00 37.02 3.71
4945 5396 4.323477 CGGAACCGCTCCCACCAA 62.323 66.667 0.00 0.00 41.87 3.67
5103 5554 4.637483 ATTCAGAAACATGCCGTATTGG 57.363 40.909 0.00 0.00 42.50 3.16
5135 5586 7.027874 TCTCTACTTCTCTTCTCCTCTTCTT 57.972 40.000 0.00 0.00 0.00 2.52
5243 5694 7.178712 ACTAGCATTAATTCATTGTCTACGC 57.821 36.000 0.00 0.00 0.00 4.42
5312 5781 1.331756 CCGCTAACAATGTGCCTCATC 59.668 52.381 0.00 0.00 35.48 2.92
5331 5800 1.895131 TCTACGGTGGGTTCAACTACC 59.105 52.381 4.87 4.87 37.47 3.18
5418 5887 0.879839 CATATCGCGGATGTGTGCCA 60.880 55.000 6.13 0.00 0.00 4.92
5458 5934 6.065374 TCTTACAAGGGTCTTATTGCAACAA 58.935 36.000 0.00 0.00 0.00 2.83
5496 5984 0.391263 CAACCTACCTTGACCGCTCC 60.391 60.000 0.00 0.00 0.00 4.70
5552 6040 3.631686 TGATCAAATAAGGCCACAATCGG 59.368 43.478 5.01 0.00 0.00 4.18
5597 6085 8.963725 GGCCAATAACTTAGTAAGTGGTTAAAT 58.036 33.333 16.22 1.67 41.91 1.40
5601 6089 6.135819 AGGCCAATAACTTAGTAAGTGGTT 57.864 37.500 16.22 10.96 41.91 3.67
5612 6100 5.381757 TCACACACTTTAGGCCAATAACTT 58.618 37.500 5.01 0.00 0.00 2.66
5646 6134 5.508200 TCCGACTGCACAGTTTTAAAAAT 57.492 34.783 4.52 0.00 42.66 1.82
5663 6158 3.869065 TGGTCCATTTACTCAATCCGAC 58.131 45.455 0.00 0.00 0.00 4.79
5705 6200 0.830444 TGTGTGCCGGTCTTAGGAGT 60.830 55.000 1.90 0.00 0.00 3.85
5711 6206 2.047274 CCGATGTGTGCCGGTCTT 60.047 61.111 1.90 0.00 40.78 3.01
5718 6213 0.454957 GCATGACAACCGATGTGTGC 60.455 55.000 0.00 10.33 44.12 4.57
5738 6239 7.775397 ATTGTTGTTTCTTCATCAAAAGTGG 57.225 32.000 0.00 0.00 32.99 4.00
5762 6263 4.100808 ACGGGGTGTACACTTTTACTTGTA 59.899 41.667 24.55 0.00 0.00 2.41
5786 6293 1.796017 TATAGTGGTTGGATCCCGCA 58.204 50.000 9.90 0.00 34.86 5.69
5802 6309 7.502226 GGATGAAAACCCAAGACATGACATATA 59.498 37.037 0.00 0.00 0.00 0.86
5806 6313 3.826157 GGATGAAAACCCAAGACATGACA 59.174 43.478 0.00 0.00 0.00 3.58
5845 6352 6.600032 TGTTGAAGGCACTGTTTTAAAGTCTA 59.400 34.615 0.00 0.00 40.86 2.59
5852 6359 5.184096 TGTTCTTGTTGAAGGCACTGTTTTA 59.816 36.000 0.00 0.00 40.86 1.52
5859 6366 3.179048 GTTGTGTTCTTGTTGAAGGCAC 58.821 45.455 0.00 0.00 36.69 5.01
5873 6380 1.026584 GGTGCTTTACCCGTTGTGTT 58.973 50.000 0.00 0.00 44.15 3.32
5888 6395 2.126346 GCTTGGCAATGACGGTGC 60.126 61.111 0.00 0.00 41.45 5.01
5911 6418 7.123697 TGAAAACTCTAGGTCCGATCTTTGATA 59.876 37.037 0.00 0.00 0.00 2.15
5915 6422 5.480205 GTGAAAACTCTAGGTCCGATCTTT 58.520 41.667 0.00 0.00 0.00 2.52
5919 6426 3.442076 AGGTGAAAACTCTAGGTCCGAT 58.558 45.455 0.00 0.00 0.00 4.18
5923 6430 4.570930 CTCCAAGGTGAAAACTCTAGGTC 58.429 47.826 0.00 0.00 0.00 3.85
5940 6447 4.141551 TGAGTACCGAGTATCTAGCTCCAA 60.142 45.833 0.00 0.00 0.00 3.53
5942 6449 4.005487 TGAGTACCGAGTATCTAGCTCC 57.995 50.000 0.00 0.00 0.00 4.70
5948 6455 4.219944 TGCTGTTTTGAGTACCGAGTATCT 59.780 41.667 0.00 0.00 0.00 1.98
5959 6466 2.417243 GCTTTGTGGTGCTGTTTTGAGT 60.417 45.455 0.00 0.00 0.00 3.41
5967 6474 1.283793 CTTCGGCTTTGTGGTGCTG 59.716 57.895 0.00 0.00 36.94 4.41
5971 6478 2.193536 GTGGCTTCGGCTTTGTGGT 61.194 57.895 0.00 0.00 41.44 4.16
5976 6483 1.152756 ACAAGGTGGCTTCGGCTTT 60.153 52.632 0.00 0.00 41.44 3.51
5991 6498 2.110213 GGGGTGACAGCGACACAA 59.890 61.111 11.55 0.00 39.65 3.33


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

AutoCloner maintained by Alex Coulton.