Multiple sequence alignment - TraesCS7B01G227600

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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 TraesCS7B01G227600 chr7B 100.000 2768 0 0 1 2768 427823689 427820922 0.000000e+00 5112
1 TraesCS7B01G227600 chr7B 88.591 298 32 2 2472 2767 125382505 125382802 7.290000e-96 361
2 TraesCS7B01G227600 chr7B 94.565 92 5 0 545 636 80090432 80090523 2.870000e-30 143
3 TraesCS7B01G227600 chr7B 93.478 92 6 0 544 635 663485612 663485703 1.340000e-28 137
4 TraesCS7B01G227600 chr7D 93.049 1827 73 30 639 2444 413442834 413441041 0.000000e+00 2621
5 TraesCS7B01G227600 chr7D 92.059 340 13 1 208 547 413443151 413442826 1.500000e-127 466
6 TraesCS7B01G227600 chr7D 90.135 223 12 6 1 222 413443387 413443174 5.840000e-72 281
7 TraesCS7B01G227600 chr7A 91.274 1845 82 33 639 2444 475167071 475165267 0.000000e+00 2442
8 TraesCS7B01G227600 chr7A 92.701 548 24 3 1 547 475167595 475167063 0.000000e+00 776
9 TraesCS7B01G227600 chr5B 91.275 298 24 2 2472 2767 304669576 304669873 3.320000e-109 405
10 TraesCS7B01G227600 chr5B 96.629 89 3 0 548 636 578828496 578828584 6.180000e-32 148
11 TraesCS7B01G227600 chr5B 94.382 89 5 0 548 636 34558165 34558253 1.340000e-28 137
12 TraesCS7B01G227600 chr2B 95.556 90 3 1 548 636 582314998 582315087 2.870000e-30 143
13 TraesCS7B01G227600 chr2B 94.382 89 3 1 548 636 391452329 391452415 4.810000e-28 135
14 TraesCS7B01G227600 chr2B 94.382 89 3 1 548 636 474281061 474280975 4.810000e-28 135
15 TraesCS7B01G227600 chr2B 94.382 89 3 1 548 636 650478327 650478241 4.810000e-28 135
16 TraesCS7B01G227600 chr2B 94.318 88 5 0 549 636 798983540 798983453 4.810000e-28 135


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 TraesCS7B01G227600 chr7B 427820922 427823689 2767 True 5112.000000 5112 100.000000 1 2768 1 chr7B.!!$R1 2767
1 TraesCS7B01G227600 chr7D 413441041 413443387 2346 True 1122.666667 2621 91.747667 1 2444 3 chr7D.!!$R1 2443
2 TraesCS7B01G227600 chr7A 475165267 475167595 2328 True 1609.000000 2442 91.987500 1 2444 2 chr7A.!!$R1 2443

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
767 809 0.613777 AGTCCATCCCGAACTTGGTC 59.386 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2625 2704 0.10212 GATGTGACCAGAGCGAGAGG 59.898 60.0 0.0 0.0 0.0 3.69 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
48 49 1.609208 ATCCTGCAACAACACACCTC 58.391 50.000 0.00 0.00 0.00 3.85
72 73 6.094881 TCCGAATCAAAAATTAATCGAAGCCT 59.905 34.615 0.00 0.00 32.38 4.58
93 95 5.462405 CCTCTTAGCTAGGCTACAAATACG 58.538 45.833 0.00 0.00 41.12 3.06
175 177 3.332034 ACCGCCACTGATAAAACACTAC 58.668 45.455 0.00 0.00 0.00 2.73
222 261 2.014857 GCCCGACTAATCCTGGAAAAC 58.985 52.381 0.00 0.00 0.00 2.43
270 309 4.503991 GGAAGCTTCTTCTGTTCTTGGAGA 60.504 45.833 25.05 0.00 0.00 3.71
311 350 3.812609 CCAGCCGCAATATACATACACAA 59.187 43.478 0.00 0.00 0.00 3.33
312 351 4.274705 CCAGCCGCAATATACATACACAAA 59.725 41.667 0.00 0.00 0.00 2.83
313 352 5.204833 CAGCCGCAATATACATACACAAAC 58.795 41.667 0.00 0.00 0.00 2.93
314 353 4.878971 AGCCGCAATATACATACACAAACA 59.121 37.500 0.00 0.00 0.00 2.83
315 354 4.967575 GCCGCAATATACATACACAAACAC 59.032 41.667 0.00 0.00 0.00 3.32
316 355 5.447954 GCCGCAATATACATACACAAACACA 60.448 40.000 0.00 0.00 0.00 3.72
317 356 6.547283 CCGCAATATACATACACAAACACAA 58.453 36.000 0.00 0.00 0.00 3.33
318 357 7.192913 CCGCAATATACATACACAAACACAAT 58.807 34.615 0.00 0.00 0.00 2.71
319 358 7.375808 CCGCAATATACATACACAAACACAATC 59.624 37.037 0.00 0.00 0.00 2.67
320 359 7.110079 CGCAATATACATACACAAACACAATCG 59.890 37.037 0.00 0.00 0.00 3.34
321 360 8.119845 GCAATATACATACACAAACACAATCGA 58.880 33.333 0.00 0.00 0.00 3.59
322 361 9.636965 CAATATACATACACAAACACAATCGAG 57.363 33.333 0.00 0.00 0.00 4.04
323 362 9.594478 AATATACATACACAAACACAATCGAGA 57.406 29.630 0.00 0.00 0.00 4.04
324 363 5.591643 ACATACACAAACACAATCGAGAC 57.408 39.130 0.00 0.00 0.00 3.36
389 428 6.040278 TCAGTGCTAGTCAAATCTCAGATAGG 59.960 42.308 0.00 0.00 0.00 2.57
447 486 4.675161 TGGCGCCTTCCCATGCAA 62.675 61.111 29.70 0.00 0.00 4.08
526 566 5.394224 AAGTTAGCTAGTGAGAGGTGAAC 57.606 43.478 0.00 0.00 0.00 3.18
543 583 9.588096 AGAGGTGAACAAAAGGTTTCTTTATAT 57.412 29.630 0.00 0.00 41.92 0.86
544 584 9.626045 GAGGTGAACAAAAGGTTTCTTTATATG 57.374 33.333 0.00 0.00 41.92 1.78
545 585 9.362151 AGGTGAACAAAAGGTTTCTTTATATGA 57.638 29.630 0.00 0.00 41.92 2.15
569 609 9.230122 TGATCAAAAATGCTAGACATACAAAGA 57.770 29.630 0.00 0.00 38.34 2.52
589 629 8.871686 CAAAGATTTGTAAAAGCCTGTAAACT 57.128 30.769 0.00 0.00 33.59 2.66
590 630 9.959749 CAAAGATTTGTAAAAGCCTGTAAACTA 57.040 29.630 0.00 0.00 33.59 2.24
603 643 9.515226 AAGCCTGTAAACTATTTTCATCTAACA 57.485 29.630 0.00 0.00 0.00 2.41
604 644 9.515226 AGCCTGTAAACTATTTTCATCTAACAA 57.485 29.630 0.00 0.00 0.00 2.83
605 645 9.556030 GCCTGTAAACTATTTTCATCTAACAAC 57.444 33.333 0.00 0.00 0.00 3.32
613 653 9.295825 ACTATTTTCATCTAACAACCAATCACA 57.704 29.630 0.00 0.00 0.00 3.58
616 656 8.641499 TTTTCATCTAACAACCAATCACAAAC 57.359 30.769 0.00 0.00 0.00 2.93
617 657 6.325919 TCATCTAACAACCAATCACAAACC 57.674 37.500 0.00 0.00 0.00 3.27
618 658 6.068010 TCATCTAACAACCAATCACAAACCT 58.932 36.000 0.00 0.00 0.00 3.50
619 659 6.206634 TCATCTAACAACCAATCACAAACCTC 59.793 38.462 0.00 0.00 0.00 3.85
620 660 5.690865 TCTAACAACCAATCACAAACCTCT 58.309 37.500 0.00 0.00 0.00 3.69
621 661 6.126409 TCTAACAACCAATCACAAACCTCTT 58.874 36.000 0.00 0.00 0.00 2.85
622 662 7.284074 TCTAACAACCAATCACAAACCTCTTA 58.716 34.615 0.00 0.00 0.00 2.10
623 663 5.767816 ACAACCAATCACAAACCTCTTAC 57.232 39.130 0.00 0.00 0.00 2.34
624 664 4.583073 ACAACCAATCACAAACCTCTTACC 59.417 41.667 0.00 0.00 0.00 2.85
625 665 3.763057 ACCAATCACAAACCTCTTACCC 58.237 45.455 0.00 0.00 0.00 3.69
626 666 3.089284 CCAATCACAAACCTCTTACCCC 58.911 50.000 0.00 0.00 0.00 4.95
627 667 3.089284 CAATCACAAACCTCTTACCCCC 58.911 50.000 0.00 0.00 0.00 5.40
628 668 2.127651 TCACAAACCTCTTACCCCCT 57.872 50.000 0.00 0.00 0.00 4.79
629 669 1.702957 TCACAAACCTCTTACCCCCTG 59.297 52.381 0.00 0.00 0.00 4.45
630 670 1.702957 CACAAACCTCTTACCCCCTGA 59.297 52.381 0.00 0.00 0.00 3.86
631 671 2.308866 CACAAACCTCTTACCCCCTGAT 59.691 50.000 0.00 0.00 0.00 2.90
632 672 2.993863 ACAAACCTCTTACCCCCTGATT 59.006 45.455 0.00 0.00 0.00 2.57
633 673 3.401342 ACAAACCTCTTACCCCCTGATTT 59.599 43.478 0.00 0.00 0.00 2.17
634 674 4.140782 ACAAACCTCTTACCCCCTGATTTT 60.141 41.667 0.00 0.00 0.00 1.82
635 675 4.317530 AACCTCTTACCCCCTGATTTTC 57.682 45.455 0.00 0.00 0.00 2.29
636 676 2.581246 ACCTCTTACCCCCTGATTTTCC 59.419 50.000 0.00 0.00 0.00 3.13
637 677 2.421529 CCTCTTACCCCCTGATTTTCCG 60.422 54.545 0.00 0.00 0.00 4.30
638 678 2.238898 CTCTTACCCCCTGATTTTCCGT 59.761 50.000 0.00 0.00 0.00 4.69
639 679 2.645797 TCTTACCCCCTGATTTTCCGTT 59.354 45.455 0.00 0.00 0.00 4.44
640 680 3.845398 TCTTACCCCCTGATTTTCCGTTA 59.155 43.478 0.00 0.00 0.00 3.18
641 681 4.475747 TCTTACCCCCTGATTTTCCGTTAT 59.524 41.667 0.00 0.00 0.00 1.89
642 682 5.666718 TCTTACCCCCTGATTTTCCGTTATA 59.333 40.000 0.00 0.00 0.00 0.98
673 713 2.154854 TCGAGTGCTTTCTTGACCTG 57.845 50.000 0.00 0.00 0.00 4.00
767 809 0.613777 AGTCCATCCCGAACTTGGTC 59.386 55.000 0.00 0.00 0.00 4.02
768 810 0.739813 GTCCATCCCGAACTTGGTCG 60.740 60.000 0.53 0.53 40.77 4.79
769 811 2.106683 CCATCCCGAACTTGGTCGC 61.107 63.158 2.14 0.00 39.74 5.19
770 812 2.125673 ATCCCGAACTTGGTCGCG 60.126 61.111 0.00 0.00 39.74 5.87
817 859 5.419155 TCAGCTGCCACCTCTATATATACAC 59.581 44.000 9.47 0.00 0.00 2.90
818 860 5.420421 CAGCTGCCACCTCTATATATACACT 59.580 44.000 0.00 0.00 0.00 3.55
924 971 2.024414 TCGATCCATCTCTGCTTTCGA 58.976 47.619 0.00 0.00 0.00 3.71
937 984 2.879942 CTTTCGATTCAACGCCGGCG 62.880 60.000 44.88 44.88 46.03 6.46
1112 1163 0.534412 AAGGACTCGCACAGGATCAG 59.466 55.000 0.00 0.00 0.00 2.90
1254 1305 3.317436 ATCCTCCTCACTCCCGCCA 62.317 63.158 0.00 0.00 0.00 5.69
1301 1352 2.357517 CTTCCCGCAGCAGTCGTT 60.358 61.111 0.00 0.00 0.00 3.85
1634 1688 4.424711 ATTCCATGGCCACGGCGT 62.425 61.111 14.62 6.77 43.06 5.68
1646 1700 3.462383 CGGCGTGTTAACCGGTAC 58.538 61.111 8.00 3.41 45.74 3.34
1647 1701 1.080569 CGGCGTGTTAACCGGTACT 60.081 57.895 8.00 0.00 45.74 2.73
1800 1854 2.048222 TGCGTGTGGTCAGCTAGC 60.048 61.111 6.62 6.62 0.00 3.42
1860 1926 4.929819 TTGATTTCCATCTCCATGCATG 57.070 40.909 20.19 20.19 0.00 4.06
1861 1927 2.626266 TGATTTCCATCTCCATGCATGC 59.374 45.455 21.69 11.82 0.00 4.06
1863 1929 0.107066 TTCCATCTCCATGCATGCGT 60.107 50.000 21.69 10.53 0.00 5.24
1864 1930 0.533531 TCCATCTCCATGCATGCGTC 60.534 55.000 21.69 0.00 0.00 5.19
1865 1931 1.568025 CATCTCCATGCATGCGTCG 59.432 57.895 21.69 3.27 0.00 5.12
1867 1933 3.945434 CTCCATGCATGCGTCGCC 61.945 66.667 21.69 0.00 0.00 5.54
1883 1949 4.463879 CCCGTCTGCAGGGCTGAG 62.464 72.222 15.13 0.00 42.77 3.35
1895 1961 3.801983 GCAGGGCTGAGAGAATTAGTAGC 60.802 52.174 0.00 0.00 0.00 3.58
1930 1996 7.375053 GGAGAGAAACAGGATTAGTAGCTATG 58.625 42.308 0.00 0.00 0.00 2.23
1946 2013 8.924511 AGTAGCTATGTATACATTTGGCATTT 57.075 30.769 22.90 11.67 37.76 2.32
1991 2058 8.747666 CGAAGACATTAAGAGCAAGTTAGATAC 58.252 37.037 0.00 0.00 0.00 2.24
1992 2059 9.587772 GAAGACATTAAGAGCAAGTTAGATACA 57.412 33.333 0.00 0.00 0.00 2.29
1993 2060 9.593134 AAGACATTAAGAGCAAGTTAGATACAG 57.407 33.333 0.00 0.00 0.00 2.74
1994 2061 8.754080 AGACATTAAGAGCAAGTTAGATACAGT 58.246 33.333 0.00 0.00 0.00 3.55
2039 2106 1.202651 GGTACTGCTCATTACCCGCAT 60.203 52.381 5.42 0.00 32.34 4.73
2040 2107 1.867233 GTACTGCTCATTACCCGCATG 59.133 52.381 0.00 0.00 32.62 4.06
2041 2108 1.097547 ACTGCTCATTACCCGCATGC 61.098 55.000 7.91 7.91 32.62 4.06
2042 2109 1.077858 TGCTCATTACCCGCATGCA 60.078 52.632 19.57 0.00 0.00 3.96
2121 2189 3.198068 AGTCAGCTGGTATATGTTTGCG 58.802 45.455 15.13 0.00 0.00 4.85
2131 2199 2.201921 TATGTTTGCGCCCCAACTTA 57.798 45.000 4.18 5.42 31.97 2.24
2132 2200 1.333177 ATGTTTGCGCCCCAACTTAA 58.667 45.000 4.18 0.00 31.97 1.85
2133 2201 1.333177 TGTTTGCGCCCCAACTTAAT 58.667 45.000 4.18 0.00 31.97 1.40
2134 2202 1.689273 TGTTTGCGCCCCAACTTAATT 59.311 42.857 4.18 0.00 31.97 1.40
2193 2261 7.429374 TCATATGGAAGACTCTCAACTGATT 57.571 36.000 2.13 0.00 0.00 2.57
2253 2324 4.774124 ACATAATGCTCAGTGCTGTATGT 58.226 39.130 13.50 13.50 42.20 2.29
2255 2326 3.623906 AATGCTCAGTGCTGTATGTCT 57.376 42.857 0.00 0.00 43.37 3.41
2267 2338 8.239314 CAGTGCTGTATGTCTTTCATTTGTAAT 58.761 33.333 0.00 0.00 37.91 1.89
2277 2348 9.308000 TGTCTTTCATTTGTAATAGAAATGGGT 57.692 29.630 18.70 0.00 40.01 4.51
2342 2417 1.128507 CTCATGTTTACGCGTGCATGT 59.871 47.619 31.93 14.60 39.54 3.21
2360 2439 6.733725 GTGCATGTTCACGATTGATATATTCG 59.266 38.462 4.18 4.18 37.96 3.34
2364 2443 9.129209 CATGTTCACGATTGATATATTCGTAGT 57.871 33.333 9.89 0.00 41.80 2.73
2376 2455 7.554476 TGATATATTCGTAGTGCATCTCTAGCT 59.446 37.037 0.00 0.00 0.00 3.32
2381 2460 3.365868 CGTAGTGCATCTCTAGCTGATCC 60.366 52.174 0.00 0.00 0.00 3.36
2393 2472 7.911651 TCTCTAGCTGATCCCCTTATAATTTG 58.088 38.462 0.00 0.00 0.00 2.32
2395 2474 5.669798 AGCTGATCCCCTTATAATTTGGT 57.330 39.130 0.00 0.00 0.00 3.67
2413 2492 4.730949 TGGTCCCTTACATCTTAACTCG 57.269 45.455 0.00 0.00 0.00 4.18
2444 2523 6.500684 TGATCAGCTAAACAATGGTTCTTC 57.499 37.500 0.00 0.00 35.82 2.87
2445 2524 6.240894 TGATCAGCTAAACAATGGTTCTTCT 58.759 36.000 0.00 0.00 35.82 2.85
2446 2525 6.716628 TGATCAGCTAAACAATGGTTCTTCTT 59.283 34.615 0.00 0.00 35.82 2.52
2447 2526 6.317789 TCAGCTAAACAATGGTTCTTCTTG 57.682 37.500 0.00 0.00 35.82 3.02
2448 2527 5.241506 TCAGCTAAACAATGGTTCTTCTTGG 59.758 40.000 0.00 0.00 35.82 3.61
2449 2528 4.021981 AGCTAAACAATGGTTCTTCTTGGC 60.022 41.667 0.00 0.00 35.82 4.52
2450 2529 4.021981 GCTAAACAATGGTTCTTCTTGGCT 60.022 41.667 0.00 0.00 35.82 4.75
2451 2530 4.590850 AAACAATGGTTCTTCTTGGCTC 57.409 40.909 0.00 0.00 35.82 4.70
2452 2531 2.519013 ACAATGGTTCTTCTTGGCTCC 58.481 47.619 0.00 0.00 0.00 4.70
2453 2532 1.821136 CAATGGTTCTTCTTGGCTCCC 59.179 52.381 0.00 0.00 0.00 4.30
2454 2533 0.332972 ATGGTTCTTCTTGGCTCCCC 59.667 55.000 0.00 0.00 0.00 4.81
2455 2534 1.000771 GGTTCTTCTTGGCTCCCCC 60.001 63.158 0.00 0.00 0.00 5.40
2456 2535 1.501654 GGTTCTTCTTGGCTCCCCCT 61.502 60.000 0.00 0.00 0.00 4.79
2457 2536 0.034960 GTTCTTCTTGGCTCCCCCTC 60.035 60.000 0.00 0.00 0.00 4.30
2458 2537 0.475632 TTCTTCTTGGCTCCCCCTCA 60.476 55.000 0.00 0.00 0.00 3.86
2459 2538 0.475632 TCTTCTTGGCTCCCCCTCAA 60.476 55.000 0.00 0.00 0.00 3.02
2460 2539 0.405585 CTTCTTGGCTCCCCCTCAAA 59.594 55.000 0.00 0.00 0.00 2.69
2461 2540 0.405585 TTCTTGGCTCCCCCTCAAAG 59.594 55.000 0.00 0.00 0.00 2.77
2462 2541 1.000396 CTTGGCTCCCCCTCAAAGG 60.000 63.158 0.00 0.00 34.30 3.11
2463 2542 1.465188 TTGGCTCCCCCTCAAAGGA 60.465 57.895 0.00 0.00 37.67 3.36
2468 2547 3.027533 TCCCCCTCAAAGGAGATGG 57.972 57.895 0.00 0.00 44.26 3.51
2469 2548 1.228510 CCCCCTCAAAGGAGATGGC 59.771 63.158 0.00 0.00 44.26 4.40
2470 2549 1.284841 CCCCCTCAAAGGAGATGGCT 61.285 60.000 0.00 0.00 44.26 4.75
2471 2550 0.182299 CCCCTCAAAGGAGATGGCTC 59.818 60.000 0.00 0.00 44.26 4.70
2479 2558 2.851588 GAGATGGCTCCCCTCCCC 60.852 72.222 0.00 0.00 35.01 4.81
2480 2559 4.523282 AGATGGCTCCCCTCCCCC 62.523 72.222 0.00 0.00 0.00 5.40
2511 2590 4.749310 CGACGCCTGCTTCTGGCT 62.749 66.667 11.88 1.15 44.56 4.75
2512 2591 2.817396 GACGCCTGCTTCTGGCTC 60.817 66.667 11.88 6.01 44.56 4.70
2513 2592 4.400961 ACGCCTGCTTCTGGCTCC 62.401 66.667 11.88 0.00 44.56 4.70
2515 2594 4.400961 GCCTGCTTCTGGCTCCGT 62.401 66.667 7.37 0.00 43.62 4.69
2516 2595 2.125350 CCTGCTTCTGGCTCCGTC 60.125 66.667 0.00 0.00 42.39 4.79
2517 2596 2.654079 CCTGCTTCTGGCTCCGTCT 61.654 63.158 0.00 0.00 42.39 4.18
2518 2597 1.153667 CTGCTTCTGGCTCCGTCTC 60.154 63.158 0.00 0.00 42.39 3.36
2519 2598 2.202676 GCTTCTGGCTCCGTCTCG 60.203 66.667 0.00 0.00 38.06 4.04
2549 2628 4.821589 CCTTGCGCGTCCTCCCTC 62.822 72.222 8.43 0.00 0.00 4.30
2550 2629 4.821589 CTTGCGCGTCCTCCCTCC 62.822 72.222 8.43 0.00 0.00 4.30
2555 2634 4.467107 GCGTCCTCCCTCCTCCCT 62.467 72.222 0.00 0.00 0.00 4.20
2556 2635 2.123640 CGTCCTCCCTCCTCCCTC 60.124 72.222 0.00 0.00 0.00 4.30
2557 2636 2.284151 GTCCTCCCTCCTCCCTCC 59.716 72.222 0.00 0.00 0.00 4.30
2558 2637 3.036959 TCCTCCCTCCTCCCTCCC 61.037 72.222 0.00 0.00 0.00 4.30
2559 2638 4.179599 CCTCCCTCCTCCCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
2560 2639 3.039526 CTCCCTCCTCCCTCCCCT 61.040 72.222 0.00 0.00 0.00 4.79
2561 2640 3.036959 TCCCTCCTCCCTCCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
2562 2641 4.179599 CCCTCCTCCCTCCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
2563 2642 4.548513 CCTCCTCCCTCCCCTCCG 62.549 77.778 0.00 0.00 0.00 4.63
2574 2653 4.824515 CCCTCCGCGGACTCCTCT 62.825 72.222 27.28 0.00 33.16 3.69
2575 2654 3.522731 CCTCCGCGGACTCCTCTG 61.523 72.222 27.28 12.94 33.16 3.35
2576 2655 3.522731 CTCCGCGGACTCCTCTGG 61.523 72.222 27.28 8.25 0.00 3.86
2580 2659 3.844090 GCGGACTCCTCTGGGCTC 61.844 72.222 0.00 0.00 0.00 4.70
2581 2660 3.151022 CGGACTCCTCTGGGCTCC 61.151 72.222 0.00 0.00 0.00 4.70
2582 2661 3.151022 GGACTCCTCTGGGCTCCG 61.151 72.222 0.00 0.00 0.00 4.63
2583 2662 3.844090 GACTCCTCTGGGCTCCGC 61.844 72.222 0.00 0.00 0.00 5.54
2584 2663 4.390556 ACTCCTCTGGGCTCCGCT 62.391 66.667 0.00 0.00 0.00 5.52
2585 2664 3.535962 CTCCTCTGGGCTCCGCTC 61.536 72.222 0.00 0.00 0.00 5.03
2617 2696 3.478274 GCTCCCCTCTGCTCCCTG 61.478 72.222 0.00 0.00 0.00 4.45
2618 2697 2.767496 CTCCCCTCTGCTCCCTGG 60.767 72.222 0.00 0.00 0.00 4.45
2619 2698 4.421554 TCCCCTCTGCTCCCTGGG 62.422 72.222 6.33 6.33 39.37 4.45
2622 2701 3.478274 CCTCTGCTCCCTGGGCTC 61.478 72.222 8.22 2.24 0.00 4.70
2623 2702 3.478274 CTCTGCTCCCTGGGCTCC 61.478 72.222 8.22 0.00 0.00 4.70
2635 2714 4.851214 GGCTCCCCCTCTCGCTCT 62.851 72.222 0.00 0.00 0.00 4.09
2636 2715 3.535962 GCTCCCCCTCTCGCTCTG 61.536 72.222 0.00 0.00 0.00 3.35
2637 2716 2.837291 CTCCCCCTCTCGCTCTGG 60.837 72.222 0.00 0.00 0.00 3.86
2638 2717 3.670629 CTCCCCCTCTCGCTCTGGT 62.671 68.421 0.00 0.00 0.00 4.00
2639 2718 3.151022 CCCCCTCTCGCTCTGGTC 61.151 72.222 0.00 0.00 0.00 4.02
2640 2719 2.363018 CCCCTCTCGCTCTGGTCA 60.363 66.667 0.00 0.00 0.00 4.02
2641 2720 2.716017 CCCCTCTCGCTCTGGTCAC 61.716 68.421 0.00 0.00 0.00 3.67
2642 2721 1.979155 CCCTCTCGCTCTGGTCACA 60.979 63.158 0.00 0.00 0.00 3.58
2643 2722 1.326213 CCCTCTCGCTCTGGTCACAT 61.326 60.000 0.00 0.00 0.00 3.21
2644 2723 0.102120 CCTCTCGCTCTGGTCACATC 59.898 60.000 0.00 0.00 0.00 3.06
2645 2724 0.248417 CTCTCGCTCTGGTCACATCG 60.248 60.000 0.00 0.00 0.00 3.84
2646 2725 1.875813 CTCGCTCTGGTCACATCGC 60.876 63.158 0.00 0.00 0.00 4.58
2647 2726 2.887568 CGCTCTGGTCACATCGCC 60.888 66.667 0.00 0.00 0.00 5.54
2648 2727 2.512515 GCTCTGGTCACATCGCCC 60.513 66.667 0.00 0.00 0.00 6.13
2649 2728 2.187946 CTCTGGTCACATCGCCCC 59.812 66.667 0.00 0.00 0.00 5.80
2650 2729 2.284625 TCTGGTCACATCGCCCCT 60.285 61.111 0.00 0.00 0.00 4.79
2651 2730 2.187946 CTGGTCACATCGCCCCTC 59.812 66.667 0.00 0.00 0.00 4.30
2652 2731 2.284625 TGGTCACATCGCCCCTCT 60.285 61.111 0.00 0.00 0.00 3.69
2653 2732 1.903877 CTGGTCACATCGCCCCTCTT 61.904 60.000 0.00 0.00 0.00 2.85
2654 2733 1.153349 GGTCACATCGCCCCTCTTC 60.153 63.158 0.00 0.00 0.00 2.87
2655 2734 1.519455 GTCACATCGCCCCTCTTCG 60.519 63.158 0.00 0.00 0.00 3.79
2656 2735 2.202932 CACATCGCCCCTCTTCGG 60.203 66.667 0.00 0.00 0.00 4.30
2669 2748 4.674281 CCTCTTCGGGCTAATAAGTTCT 57.326 45.455 0.00 0.00 0.00 3.01
2670 2749 4.372656 CCTCTTCGGGCTAATAAGTTCTG 58.627 47.826 0.00 0.00 0.00 3.02
2671 2750 4.372656 CTCTTCGGGCTAATAAGTTCTGG 58.627 47.826 0.00 0.00 0.00 3.86
2672 2751 3.134081 TCTTCGGGCTAATAAGTTCTGGG 59.866 47.826 0.00 0.00 0.00 4.45
2673 2752 1.140252 TCGGGCTAATAAGTTCTGGGC 59.860 52.381 0.00 0.00 0.00 5.36
2674 2753 1.594331 GGGCTAATAAGTTCTGGGCG 58.406 55.000 0.00 0.00 0.00 6.13
2675 2754 0.945099 GGCTAATAAGTTCTGGGCGC 59.055 55.000 0.00 0.00 0.00 6.53
2676 2755 1.475213 GGCTAATAAGTTCTGGGCGCT 60.475 52.381 7.64 0.00 0.00 5.92
2677 2756 1.599542 GCTAATAAGTTCTGGGCGCTG 59.400 52.381 7.64 1.03 0.00 5.18
2678 2757 2.213499 CTAATAAGTTCTGGGCGCTGG 58.787 52.381 7.64 0.00 0.00 4.85
2679 2758 0.618458 AATAAGTTCTGGGCGCTGGA 59.382 50.000 7.64 0.00 0.00 3.86
2680 2759 0.839946 ATAAGTTCTGGGCGCTGGAT 59.160 50.000 7.64 0.00 0.00 3.41
2681 2760 0.618458 TAAGTTCTGGGCGCTGGATT 59.382 50.000 7.64 3.65 0.00 3.01
2682 2761 0.678048 AAGTTCTGGGCGCTGGATTC 60.678 55.000 7.64 0.00 0.00 2.52
2683 2762 2.125147 TTCTGGGCGCTGGATTCG 60.125 61.111 7.64 0.00 0.00 3.34
2684 2763 3.680620 TTCTGGGCGCTGGATTCGG 62.681 63.158 7.64 0.00 0.00 4.30
2685 2764 4.161295 CTGGGCGCTGGATTCGGA 62.161 66.667 7.64 0.00 0.00 4.55
2686 2765 3.466791 CTGGGCGCTGGATTCGGAT 62.467 63.158 7.64 0.00 0.00 4.18
2687 2766 2.974698 GGGCGCTGGATTCGGATG 60.975 66.667 7.64 0.00 0.00 3.51
2688 2767 2.974698 GGCGCTGGATTCGGATGG 60.975 66.667 7.64 0.00 0.00 3.51
2689 2768 3.654020 GCGCTGGATTCGGATGGC 61.654 66.667 0.00 0.00 0.00 4.40
2690 2769 2.109799 CGCTGGATTCGGATGGCT 59.890 61.111 0.00 0.00 0.00 4.75
2691 2770 1.958205 CGCTGGATTCGGATGGCTC 60.958 63.158 0.00 0.00 0.00 4.70
2692 2771 1.599240 GCTGGATTCGGATGGCTCC 60.599 63.158 0.00 0.00 38.29 4.70
2709 2788 3.827898 CGGGTCGGAGTCTGAGGC 61.828 72.222 0.58 0.00 0.00 4.70
2710 2789 3.462678 GGGTCGGAGTCTGAGGCC 61.463 72.222 0.58 0.00 0.00 5.19
2711 2790 3.462678 GGTCGGAGTCTGAGGCCC 61.463 72.222 0.58 0.00 0.00 5.80
2712 2791 3.462678 GTCGGAGTCTGAGGCCCC 61.463 72.222 0.58 0.00 0.00 5.80
2713 2792 3.673597 TCGGAGTCTGAGGCCCCT 61.674 66.667 0.00 0.00 0.00 4.79
2714 2793 2.685380 CGGAGTCTGAGGCCCCTT 60.685 66.667 0.00 0.00 0.00 3.95
2715 2794 2.726351 CGGAGTCTGAGGCCCCTTC 61.726 68.421 0.00 0.00 0.00 3.46
2716 2795 1.306568 GGAGTCTGAGGCCCCTTCT 60.307 63.158 0.00 0.00 0.00 2.85
2717 2796 0.912006 GGAGTCTGAGGCCCCTTCTT 60.912 60.000 0.00 0.00 0.00 2.52
2718 2797 0.539518 GAGTCTGAGGCCCCTTCTTC 59.460 60.000 0.00 0.00 0.00 2.87
2719 2798 0.912006 AGTCTGAGGCCCCTTCTTCC 60.912 60.000 0.00 0.00 0.00 3.46
2720 2799 1.616628 TCTGAGGCCCCTTCTTCCC 60.617 63.158 0.00 0.00 0.00 3.97
2721 2800 2.614013 TGAGGCCCCTTCTTCCCC 60.614 66.667 0.00 0.00 0.00 4.81
2722 2801 2.286502 GAGGCCCCTTCTTCCCCT 60.287 66.667 0.00 0.00 0.00 4.79
2723 2802 2.286502 AGGCCCCTTCTTCCCCTC 60.287 66.667 0.00 0.00 0.00 4.30
2724 2803 3.421386 GGCCCCTTCTTCCCCTCC 61.421 72.222 0.00 0.00 0.00 4.30
2725 2804 3.421386 GCCCCTTCTTCCCCTCCC 61.421 72.222 0.00 0.00 0.00 4.30
2726 2805 2.461637 CCCCTTCTTCCCCTCCCT 59.538 66.667 0.00 0.00 0.00 4.20
2727 2806 2.003548 CCCCTTCTTCCCCTCCCTG 61.004 68.421 0.00 0.00 0.00 4.45
2728 2807 2.684499 CCCTTCTTCCCCTCCCTGC 61.684 68.421 0.00 0.00 0.00 4.85
2729 2808 2.684499 CCTTCTTCCCCTCCCTGCC 61.684 68.421 0.00 0.00 0.00 4.85
2730 2809 2.614013 TTCTTCCCCTCCCTGCCC 60.614 66.667 0.00 0.00 0.00 5.36
2748 2827 4.516195 GGTCCCGGCTCGCTCTTC 62.516 72.222 0.00 0.00 0.00 2.87
2749 2828 4.516195 GTCCCGGCTCGCTCTTCC 62.516 72.222 0.00 0.00 0.00 3.46
2755 2834 4.821589 GCTCGCTCTTCCCCGGTG 62.822 72.222 0.00 0.00 0.00 4.94
2756 2835 4.148825 CTCGCTCTTCCCCGGTGG 62.149 72.222 0.00 0.82 0.00 4.61
2759 2838 4.785453 GCTCTTCCCCGGTGGCTG 62.785 72.222 0.00 0.00 0.00 4.85
2760 2839 4.785453 CTCTTCCCCGGTGGCTGC 62.785 72.222 0.00 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 6.265577 AGGCTTCGATTAATTTTTGATTCGG 58.734 36.000 0.00 0.00 0.00 4.30
72 73 5.135383 TCCGTATTTGTAGCCTAGCTAAGA 58.865 41.667 0.00 0.00 43.07 2.10
83 84 6.879276 TCCAGATACTCTCCGTATTTGTAG 57.121 41.667 0.00 0.00 38.42 2.74
93 95 9.084533 AGAGTTAACATATTCCAGATACTCTCC 57.915 37.037 8.61 0.00 0.00 3.71
175 177 7.364200 TGGACTTAAACAACGGTTGATTATTG 58.636 34.615 26.39 19.68 37.30 1.90
222 261 7.801315 CCACGGTTGATTAATATTTAATCCGTG 59.199 37.037 25.78 25.78 41.34 4.94
270 309 2.826128 TGGTTGCTCTGTCGTTCTCTAT 59.174 45.455 0.00 0.00 0.00 1.98
295 334 8.119845 TCGATTGTGTTTGTGTATGTATATTGC 58.880 33.333 0.00 0.00 0.00 3.56
319 358 3.961477 ATTCATGTCTCTCGAGTCTCG 57.039 47.619 16.33 16.33 42.10 4.04
320 359 8.390354 CAGATATATTCATGTCTCTCGAGTCTC 58.610 40.741 13.13 4.59 30.78 3.36
321 360 8.100164 TCAGATATATTCATGTCTCTCGAGTCT 58.900 37.037 13.13 0.00 30.78 3.24
322 361 8.175069 GTCAGATATATTCATGTCTCTCGAGTC 58.825 40.741 13.13 5.30 30.78 3.36
323 362 7.120579 GGTCAGATATATTCATGTCTCTCGAGT 59.879 40.741 13.13 0.00 30.78 4.18
324 363 7.415095 GGGTCAGATATATTCATGTCTCTCGAG 60.415 44.444 5.93 5.93 30.78 4.04
389 428 1.821136 CAATCCCCCTCTGTTTCTTGC 59.179 52.381 0.00 0.00 0.00 4.01
543 583 9.230122 TCTTTGTATGTCTAGCATTTTTGATCA 57.770 29.630 0.00 0.00 38.94 2.92
564 604 8.871686 AGTTTACAGGCTTTTACAAATCTTTG 57.128 30.769 1.19 1.19 43.62 2.77
577 617 9.515226 TGTTAGATGAAAATAGTTTACAGGCTT 57.485 29.630 0.00 0.00 0.00 4.35
578 618 9.515226 TTGTTAGATGAAAATAGTTTACAGGCT 57.485 29.630 0.00 0.00 0.00 4.58
579 619 9.556030 GTTGTTAGATGAAAATAGTTTACAGGC 57.444 33.333 0.00 0.00 0.00 4.85
587 627 9.295825 TGTGATTGGTTGTTAGATGAAAATAGT 57.704 29.630 0.00 0.00 0.00 2.12
590 630 9.260002 GTTTGTGATTGGTTGTTAGATGAAAAT 57.740 29.630 0.00 0.00 0.00 1.82
591 631 7.708752 GGTTTGTGATTGGTTGTTAGATGAAAA 59.291 33.333 0.00 0.00 0.00 2.29
592 632 7.069331 AGGTTTGTGATTGGTTGTTAGATGAAA 59.931 33.333 0.00 0.00 0.00 2.69
593 633 6.549364 AGGTTTGTGATTGGTTGTTAGATGAA 59.451 34.615 0.00 0.00 0.00 2.57
594 634 6.068010 AGGTTTGTGATTGGTTGTTAGATGA 58.932 36.000 0.00 0.00 0.00 2.92
595 635 6.207417 AGAGGTTTGTGATTGGTTGTTAGATG 59.793 38.462 0.00 0.00 0.00 2.90
596 636 6.306987 AGAGGTTTGTGATTGGTTGTTAGAT 58.693 36.000 0.00 0.00 0.00 1.98
597 637 5.690865 AGAGGTTTGTGATTGGTTGTTAGA 58.309 37.500 0.00 0.00 0.00 2.10
598 638 6.391227 AAGAGGTTTGTGATTGGTTGTTAG 57.609 37.500 0.00 0.00 0.00 2.34
599 639 6.263617 GGTAAGAGGTTTGTGATTGGTTGTTA 59.736 38.462 0.00 0.00 0.00 2.41
600 640 5.068591 GGTAAGAGGTTTGTGATTGGTTGTT 59.931 40.000 0.00 0.00 0.00 2.83
601 641 4.583073 GGTAAGAGGTTTGTGATTGGTTGT 59.417 41.667 0.00 0.00 0.00 3.32
602 642 4.022329 GGGTAAGAGGTTTGTGATTGGTTG 60.022 45.833 0.00 0.00 0.00 3.77
603 643 4.149598 GGGTAAGAGGTTTGTGATTGGTT 58.850 43.478 0.00 0.00 0.00 3.67
604 644 3.499745 GGGGTAAGAGGTTTGTGATTGGT 60.500 47.826 0.00 0.00 0.00 3.67
605 645 3.089284 GGGGTAAGAGGTTTGTGATTGG 58.911 50.000 0.00 0.00 0.00 3.16
606 646 3.089284 GGGGGTAAGAGGTTTGTGATTG 58.911 50.000 0.00 0.00 0.00 2.67
607 647 2.993863 AGGGGGTAAGAGGTTTGTGATT 59.006 45.455 0.00 0.00 0.00 2.57
608 648 2.308866 CAGGGGGTAAGAGGTTTGTGAT 59.691 50.000 0.00 0.00 0.00 3.06
609 649 1.702957 CAGGGGGTAAGAGGTTTGTGA 59.297 52.381 0.00 0.00 0.00 3.58
610 650 1.702957 TCAGGGGGTAAGAGGTTTGTG 59.297 52.381 0.00 0.00 0.00 3.33
611 651 2.127651 TCAGGGGGTAAGAGGTTTGT 57.872 50.000 0.00 0.00 0.00 2.83
612 652 3.739401 AATCAGGGGGTAAGAGGTTTG 57.261 47.619 0.00 0.00 0.00 2.93
613 653 4.510386 GGAAAATCAGGGGGTAAGAGGTTT 60.510 45.833 0.00 0.00 0.00 3.27
614 654 3.011369 GGAAAATCAGGGGGTAAGAGGTT 59.989 47.826 0.00 0.00 0.00 3.50
615 655 2.581246 GGAAAATCAGGGGGTAAGAGGT 59.419 50.000 0.00 0.00 0.00 3.85
616 656 2.421529 CGGAAAATCAGGGGGTAAGAGG 60.422 54.545 0.00 0.00 0.00 3.69
617 657 2.238898 ACGGAAAATCAGGGGGTAAGAG 59.761 50.000 0.00 0.00 0.00 2.85
618 658 2.271777 ACGGAAAATCAGGGGGTAAGA 58.728 47.619 0.00 0.00 0.00 2.10
619 659 2.801077 ACGGAAAATCAGGGGGTAAG 57.199 50.000 0.00 0.00 0.00 2.34
620 660 4.866327 ATAACGGAAAATCAGGGGGTAA 57.134 40.909 0.00 0.00 0.00 2.85
621 661 5.607592 TCATATAACGGAAAATCAGGGGGTA 59.392 40.000 0.00 0.00 0.00 3.69
622 662 4.414182 TCATATAACGGAAAATCAGGGGGT 59.586 41.667 0.00 0.00 0.00 4.95
623 663 4.980573 TCATATAACGGAAAATCAGGGGG 58.019 43.478 0.00 0.00 0.00 5.40
624 664 8.677300 CAATATCATATAACGGAAAATCAGGGG 58.323 37.037 0.00 0.00 0.00 4.79
625 665 8.184192 GCAATATCATATAACGGAAAATCAGGG 58.816 37.037 0.00 0.00 0.00 4.45
626 666 8.729756 TGCAATATCATATAACGGAAAATCAGG 58.270 33.333 0.00 0.00 0.00 3.86
630 670 9.773328 CGATTGCAATATCATATAACGGAAAAT 57.227 29.630 12.97 0.00 0.00 1.82
631 671 8.994170 TCGATTGCAATATCATATAACGGAAAA 58.006 29.630 12.97 0.00 0.00 2.29
632 672 8.541133 TCGATTGCAATATCATATAACGGAAA 57.459 30.769 12.97 0.00 0.00 3.13
633 673 7.817478 ACTCGATTGCAATATCATATAACGGAA 59.183 33.333 12.97 0.00 0.00 4.30
634 674 7.275560 CACTCGATTGCAATATCATATAACGGA 59.724 37.037 12.97 0.00 0.00 4.69
635 675 7.394099 CACTCGATTGCAATATCATATAACGG 58.606 38.462 12.97 5.37 0.00 4.44
636 676 6.896613 GCACTCGATTGCAATATCATATAACG 59.103 38.462 21.45 8.41 42.49 3.18
637 677 7.968246 AGCACTCGATTGCAATATCATATAAC 58.032 34.615 26.86 0.00 45.62 1.89
638 678 8.552083 AAGCACTCGATTGCAATATCATATAA 57.448 30.769 26.86 0.00 45.62 0.98
639 679 8.552083 AAAGCACTCGATTGCAATATCATATA 57.448 30.769 26.86 0.00 45.62 0.86
640 680 7.389884 AGAAAGCACTCGATTGCAATATCATAT 59.610 33.333 26.86 2.79 45.62 1.78
641 681 6.707608 AGAAAGCACTCGATTGCAATATCATA 59.292 34.615 26.86 0.00 45.62 2.15
642 682 5.530171 AGAAAGCACTCGATTGCAATATCAT 59.470 36.000 26.86 4.21 45.62 2.45
673 713 1.666700 TGCGAATTATGGGCGTGTAAC 59.333 47.619 0.00 0.00 0.00 2.50
840 887 2.502876 CAGCAGTAGTACGTACGTGTG 58.497 52.381 30.25 18.57 36.66 3.82
937 984 2.609183 ATAGCTTGTCGACGTCGCCC 62.609 60.000 32.19 23.76 39.60 6.13
978 1025 2.726180 GATCGGTCGATCGGTGCG 60.726 66.667 19.53 3.63 41.09 5.34
990 1041 1.252175 ACTCCTCCATGATCGATCGG 58.748 55.000 20.03 15.69 0.00 4.18
998 1049 1.341089 ACGCTGAGTACTCCTCCATGA 60.341 52.381 20.11 0.00 39.65 3.07
1494 1548 1.696336 GGAGATAGGATGCTTGGCAGA 59.304 52.381 0.00 0.00 43.65 4.26
1500 1554 0.394565 GCACCGGAGATAGGATGCTT 59.605 55.000 9.46 0.00 0.00 3.91
1584 1638 1.696832 GCTCGCCGAACAGGTTGATC 61.697 60.000 0.00 0.00 43.70 2.92
1725 1779 6.539103 GGTTGTTGAAGAGATCCCAATAGTAC 59.461 42.308 0.00 0.00 0.00 2.73
1800 1854 0.731417 AGTAGTAGCCACGCGTGTAG 59.269 55.000 34.81 22.81 0.00 2.74
1850 1916 3.945434 GGCGACGCATGCATGGAG 61.945 66.667 27.34 16.28 0.00 3.86
1867 1933 3.368190 CTCTCAGCCCTGCAGACGG 62.368 68.421 17.39 10.24 0.00 4.79
1869 1935 0.540923 ATTCTCTCAGCCCTGCAGAC 59.459 55.000 17.39 6.97 0.00 3.51
1870 1936 1.283347 AATTCTCTCAGCCCTGCAGA 58.717 50.000 17.39 0.00 0.00 4.26
1871 1937 2.170187 ACTAATTCTCTCAGCCCTGCAG 59.830 50.000 6.78 6.78 0.00 4.41
1872 1938 2.191400 ACTAATTCTCTCAGCCCTGCA 58.809 47.619 0.00 0.00 0.00 4.41
1873 1939 2.998316 ACTAATTCTCTCAGCCCTGC 57.002 50.000 0.00 0.00 0.00 4.85
1874 1940 3.640967 AGCTACTAATTCTCTCAGCCCTG 59.359 47.826 0.00 0.00 0.00 4.45
1875 1941 3.922375 AGCTACTAATTCTCTCAGCCCT 58.078 45.455 0.00 0.00 0.00 5.19
1876 1942 4.681074 AAGCTACTAATTCTCTCAGCCC 57.319 45.455 0.00 0.00 0.00 5.19
1930 1996 8.355169 ACATCTCATCAAATGCCAAATGTATAC 58.645 33.333 0.00 0.00 0.00 1.47
1946 2013 3.490348 TCGCTCCTATCACATCTCATCA 58.510 45.455 0.00 0.00 0.00 3.07
1991 2058 8.836413 GCTGACTTAGGCTATCTATATCTACTG 58.164 40.741 0.00 0.00 0.00 2.74
1992 2059 8.778059 AGCTGACTTAGGCTATCTATATCTACT 58.222 37.037 0.00 0.00 37.00 2.57
1993 2060 8.836413 CAGCTGACTTAGGCTATCTATATCTAC 58.164 40.741 8.42 0.00 37.00 2.59
1994 2061 7.996066 CCAGCTGACTTAGGCTATCTATATCTA 59.004 40.741 17.39 0.00 37.00 1.98
1995 2062 6.833416 CCAGCTGACTTAGGCTATCTATATCT 59.167 42.308 17.39 0.00 37.00 1.98
1996 2063 6.605594 ACCAGCTGACTTAGGCTATCTATATC 59.394 42.308 17.39 0.00 37.00 1.63
1997 2064 6.498538 ACCAGCTGACTTAGGCTATCTATAT 58.501 40.000 17.39 0.00 37.00 0.86
1998 2065 5.893500 ACCAGCTGACTTAGGCTATCTATA 58.106 41.667 17.39 0.00 37.00 1.31
2082 2149 3.515502 TGACTAAGGTAGCAAGCAGACAT 59.484 43.478 0.00 0.00 0.00 3.06
2121 2189 2.233676 CACCTCCAAATTAAGTTGGGGC 59.766 50.000 28.98 0.00 46.37 5.80
2224 2294 5.340010 GCACTGAGCATTATGTATGTCTG 57.660 43.478 0.00 0.00 44.79 3.51
2297 2372 7.440856 AGGTAATTACTTTACGAAAACCACGAA 59.559 33.333 15.05 0.00 41.01 3.85
2309 2384 7.842721 CGCGTAAACATGAGGTAATTACTTTAC 59.157 37.037 15.05 16.62 39.64 2.01
2360 2439 3.056891 GGGATCAGCTAGAGATGCACTAC 60.057 52.174 15.45 0.00 35.77 2.73
2364 2443 1.132913 AGGGGATCAGCTAGAGATGCA 60.133 52.381 15.45 0.00 35.77 3.96
2376 2455 4.988221 AGGGACCAAATTATAAGGGGATCA 59.012 41.667 6.80 0.00 0.00 2.92
2381 2460 7.526918 AGATGTAAGGGACCAAATTATAAGGG 58.473 38.462 0.00 0.00 0.00 3.95
2393 2472 4.732672 ACGAGTTAAGATGTAAGGGACC 57.267 45.455 0.00 0.00 0.00 4.46
2433 2512 1.821136 GGGAGCCAAGAAGAACCATTG 59.179 52.381 0.00 0.00 0.00 2.82
2444 2523 1.000396 CCTTTGAGGGGGAGCCAAG 60.000 63.158 0.00 0.00 0.00 3.61
2445 2524 1.465188 TCCTTTGAGGGGGAGCCAA 60.465 57.895 0.00 0.00 35.59 4.52
2446 2525 1.925455 CTCCTTTGAGGGGGAGCCA 60.925 63.158 0.00 0.00 41.92 4.75
2447 2526 0.990818 ATCTCCTTTGAGGGGGAGCC 60.991 60.000 4.31 0.00 46.22 4.70
2448 2527 0.182299 CATCTCCTTTGAGGGGGAGC 59.818 60.000 4.31 0.00 46.22 4.70
2450 2529 1.281925 GCCATCTCCTTTGAGGGGGA 61.282 60.000 0.00 0.00 36.18 4.81
2451 2530 1.228510 GCCATCTCCTTTGAGGGGG 59.771 63.158 0.00 0.00 36.18 5.40
2452 2531 0.182299 GAGCCATCTCCTTTGAGGGG 59.818 60.000 0.00 0.00 38.25 4.79
2453 2532 3.796764 GAGCCATCTCCTTTGAGGG 57.203 57.895 0.00 0.00 40.50 4.30
2462 2541 2.851588 GGGGAGGGGAGCCATCTC 60.852 72.222 0.00 0.00 33.52 2.75
2463 2542 4.523282 GGGGGAGGGGAGCCATCT 62.523 72.222 0.00 0.00 34.44 2.90
2502 2581 2.202676 CGAGACGGAGCCAGAAGC 60.203 66.667 0.00 0.00 44.25 3.86
2532 2611 4.821589 GAGGGAGGACGCGCAAGG 62.822 72.222 5.73 0.00 38.28 3.61
2533 2612 4.821589 GGAGGGAGGACGCGCAAG 62.822 72.222 5.73 0.00 43.44 4.01
2538 2617 4.467107 AGGGAGGAGGGAGGACGC 62.467 72.222 0.00 0.00 0.00 5.19
2539 2618 2.123640 GAGGGAGGAGGGAGGACG 60.124 72.222 0.00 0.00 0.00 4.79
2540 2619 2.284151 GGAGGGAGGAGGGAGGAC 59.716 72.222 0.00 0.00 0.00 3.85
2541 2620 3.036959 GGGAGGGAGGAGGGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
2542 2621 4.179599 GGGGAGGGAGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
2543 2622 3.039526 AGGGGAGGGAGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
2544 2623 3.036959 GAGGGGAGGGAGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
2545 2624 4.179599 GGAGGGGAGGGAGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
2546 2625 4.548513 CGGAGGGGAGGGAGGAGG 62.549 77.778 0.00 0.00 0.00 4.30
2557 2636 4.824515 AGAGGAGTCCGCGGAGGG 62.825 72.222 31.97 0.00 41.52 4.30
2558 2637 3.522731 CAGAGGAGTCCGCGGAGG 61.523 72.222 31.97 8.36 42.97 4.30
2559 2638 3.522731 CCAGAGGAGTCCGCGGAG 61.523 72.222 31.97 15.18 0.00 4.63
2563 2642 3.844090 GAGCCCAGAGGAGTCCGC 61.844 72.222 4.46 4.46 33.47 5.54
2564 2643 3.151022 GGAGCCCAGAGGAGTCCG 61.151 72.222 2.76 0.00 33.47 4.79
2565 2644 3.151022 CGGAGCCCAGAGGAGTCC 61.151 72.222 0.00 0.00 35.38 3.85
2600 2679 3.478274 CAGGGAGCAGAGGGGAGC 61.478 72.222 0.00 0.00 0.00 4.70
2601 2680 2.767496 CCAGGGAGCAGAGGGGAG 60.767 72.222 0.00 0.00 0.00 4.30
2602 2681 4.421554 CCCAGGGAGCAGAGGGGA 62.422 72.222 0.00 0.00 41.49 4.81
2605 2684 3.478274 GAGCCCAGGGAGCAGAGG 61.478 72.222 10.89 0.00 0.00 3.69
2606 2685 3.478274 GGAGCCCAGGGAGCAGAG 61.478 72.222 10.89 0.00 0.00 3.35
2618 2697 4.851214 AGAGCGAGAGGGGGAGCC 62.851 72.222 0.00 0.00 0.00 4.70
2619 2698 3.535962 CAGAGCGAGAGGGGGAGC 61.536 72.222 0.00 0.00 0.00 4.70
2620 2699 2.837291 CCAGAGCGAGAGGGGGAG 60.837 72.222 0.00 0.00 0.00 4.30
2621 2700 3.663815 GACCAGAGCGAGAGGGGGA 62.664 68.421 0.00 0.00 0.00 4.81
2622 2701 3.151022 GACCAGAGCGAGAGGGGG 61.151 72.222 0.00 0.00 0.00 5.40
2623 2702 2.363018 TGACCAGAGCGAGAGGGG 60.363 66.667 0.00 0.00 0.00 4.79
2624 2703 1.326213 ATGTGACCAGAGCGAGAGGG 61.326 60.000 0.00 0.00 0.00 4.30
2625 2704 0.102120 GATGTGACCAGAGCGAGAGG 59.898 60.000 0.00 0.00 0.00 3.69
2626 2705 0.248417 CGATGTGACCAGAGCGAGAG 60.248 60.000 0.00 0.00 0.00 3.20
2627 2706 1.803289 CGATGTGACCAGAGCGAGA 59.197 57.895 0.00 0.00 0.00 4.04
2628 2707 1.875813 GCGATGTGACCAGAGCGAG 60.876 63.158 8.95 0.00 0.00 5.03
2629 2708 2.181777 GCGATGTGACCAGAGCGA 59.818 61.111 8.95 0.00 0.00 4.93
2630 2709 2.887568 GGCGATGTGACCAGAGCG 60.888 66.667 0.37 0.37 0.00 5.03
2637 2716 1.519455 CGAAGAGGGGCGATGTGAC 60.519 63.158 0.00 0.00 0.00 3.67
2638 2717 2.721167 CCGAAGAGGGGCGATGTGA 61.721 63.158 0.00 0.00 35.97 3.58
2639 2718 2.202932 CCGAAGAGGGGCGATGTG 60.203 66.667 0.00 0.00 35.97 3.21
2648 2727 4.372656 CAGAACTTATTAGCCCGAAGAGG 58.627 47.826 0.00 0.00 40.63 3.69
2649 2728 4.372656 CCAGAACTTATTAGCCCGAAGAG 58.627 47.826 0.00 0.00 0.00 2.85
2650 2729 3.134081 CCCAGAACTTATTAGCCCGAAGA 59.866 47.826 0.00 0.00 0.00 2.87
2651 2730 3.467803 CCCAGAACTTATTAGCCCGAAG 58.532 50.000 0.00 0.00 0.00 3.79
2652 2731 2.420967 GCCCAGAACTTATTAGCCCGAA 60.421 50.000 0.00 0.00 0.00 4.30
2653 2732 1.140252 GCCCAGAACTTATTAGCCCGA 59.860 52.381 0.00 0.00 0.00 5.14
2654 2733 1.594331 GCCCAGAACTTATTAGCCCG 58.406 55.000 0.00 0.00 0.00 6.13
2655 2734 1.594331 CGCCCAGAACTTATTAGCCC 58.406 55.000 0.00 0.00 0.00 5.19
2656 2735 0.945099 GCGCCCAGAACTTATTAGCC 59.055 55.000 0.00 0.00 0.00 3.93
2657 2736 1.599542 CAGCGCCCAGAACTTATTAGC 59.400 52.381 2.29 0.00 0.00 3.09
2658 2737 2.158957 TCCAGCGCCCAGAACTTATTAG 60.159 50.000 2.29 0.00 0.00 1.73
2659 2738 1.834896 TCCAGCGCCCAGAACTTATTA 59.165 47.619 2.29 0.00 0.00 0.98
2660 2739 0.618458 TCCAGCGCCCAGAACTTATT 59.382 50.000 2.29 0.00 0.00 1.40
2661 2740 0.839946 ATCCAGCGCCCAGAACTTAT 59.160 50.000 2.29 0.00 0.00 1.73
2662 2741 0.618458 AATCCAGCGCCCAGAACTTA 59.382 50.000 2.29 0.00 0.00 2.24
2663 2742 0.678048 GAATCCAGCGCCCAGAACTT 60.678 55.000 2.29 0.00 0.00 2.66
2664 2743 1.078143 GAATCCAGCGCCCAGAACT 60.078 57.895 2.29 0.00 0.00 3.01
2665 2744 2.464459 CGAATCCAGCGCCCAGAAC 61.464 63.158 2.29 0.00 0.00 3.01
2666 2745 2.125147 CGAATCCAGCGCCCAGAA 60.125 61.111 2.29 0.00 0.00 3.02
2667 2746 4.161295 CCGAATCCAGCGCCCAGA 62.161 66.667 2.29 0.00 0.00 3.86
2668 2747 3.466791 ATCCGAATCCAGCGCCCAG 62.467 63.158 2.29 0.00 0.00 4.45
2669 2748 3.479203 ATCCGAATCCAGCGCCCA 61.479 61.111 2.29 0.00 0.00 5.36
2670 2749 2.974698 CATCCGAATCCAGCGCCC 60.975 66.667 2.29 0.00 0.00 6.13
2671 2750 2.974698 CCATCCGAATCCAGCGCC 60.975 66.667 2.29 0.00 0.00 6.53
2672 2751 3.654020 GCCATCCGAATCCAGCGC 61.654 66.667 0.00 0.00 0.00 5.92
2673 2752 1.958205 GAGCCATCCGAATCCAGCG 60.958 63.158 0.00 0.00 0.00 5.18
2674 2753 1.599240 GGAGCCATCCGAATCCAGC 60.599 63.158 0.00 0.00 35.37 4.85
2675 2754 4.787871 GGAGCCATCCGAATCCAG 57.212 61.111 0.00 0.00 35.37 3.86
2692 2771 3.827898 GCCTCAGACTCCGACCCG 61.828 72.222 0.00 0.00 0.00 5.28
2693 2772 3.462678 GGCCTCAGACTCCGACCC 61.463 72.222 0.00 0.00 0.00 4.46
2694 2773 3.462678 GGGCCTCAGACTCCGACC 61.463 72.222 0.84 0.00 0.00 4.79
2695 2774 3.462678 GGGGCCTCAGACTCCGAC 61.463 72.222 0.84 0.00 0.00 4.79
2696 2775 3.239627 AAGGGGCCTCAGACTCCGA 62.240 63.158 4.79 0.00 0.00 4.55
2697 2776 2.685380 AAGGGGCCTCAGACTCCG 60.685 66.667 4.79 0.00 0.00 4.63
2698 2777 0.912006 AAGAAGGGGCCTCAGACTCC 60.912 60.000 4.79 0.00 0.00 3.85
2699 2778 0.539518 GAAGAAGGGGCCTCAGACTC 59.460 60.000 4.79 0.00 0.00 3.36
2700 2779 0.912006 GGAAGAAGGGGCCTCAGACT 60.912 60.000 4.79 0.00 0.00 3.24
2701 2780 1.604915 GGAAGAAGGGGCCTCAGAC 59.395 63.158 4.79 0.00 0.00 3.51
2702 2781 1.616628 GGGAAGAAGGGGCCTCAGA 60.617 63.158 4.79 0.00 0.00 3.27
2703 2782 2.684499 GGGGAAGAAGGGGCCTCAG 61.684 68.421 4.79 0.00 0.00 3.35
2704 2783 2.614013 GGGGAAGAAGGGGCCTCA 60.614 66.667 4.79 0.00 0.00 3.86
2705 2784 2.286502 AGGGGAAGAAGGGGCCTC 60.287 66.667 0.84 0.00 0.00 4.70
2706 2785 2.286502 GAGGGGAAGAAGGGGCCT 60.287 66.667 0.84 0.00 0.00 5.19
2707 2786 3.421386 GGAGGGGAAGAAGGGGCC 61.421 72.222 0.00 0.00 0.00 5.80
2708 2787 3.421386 GGGAGGGGAAGAAGGGGC 61.421 72.222 0.00 0.00 0.00 5.80
2709 2788 2.003548 CAGGGAGGGGAAGAAGGGG 61.004 68.421 0.00 0.00 0.00 4.79
2710 2789 2.684499 GCAGGGAGGGGAAGAAGGG 61.684 68.421 0.00 0.00 0.00 3.95
2711 2790 2.684499 GGCAGGGAGGGGAAGAAGG 61.684 68.421 0.00 0.00 0.00 3.46
2712 2791 2.684499 GGGCAGGGAGGGGAAGAAG 61.684 68.421 0.00 0.00 0.00 2.85
2713 2792 2.614013 GGGCAGGGAGGGGAAGAA 60.614 66.667 0.00 0.00 0.00 2.52
2731 2810 4.516195 GAAGAGCGAGCCGGGACC 62.516 72.222 2.18 0.00 0.00 4.46
2732 2811 4.516195 GGAAGAGCGAGCCGGGAC 62.516 72.222 2.18 0.00 0.00 4.46
2738 2817 4.821589 CACCGGGGAAGAGCGAGC 62.822 72.222 6.32 0.00 0.00 5.03
2739 2818 4.148825 CCACCGGGGAAGAGCGAG 62.149 72.222 4.41 0.00 40.01 5.03
2742 2821 4.785453 CAGCCACCGGGGAAGAGC 62.785 72.222 4.41 0.00 40.01 4.09
2743 2822 4.785453 GCAGCCACCGGGGAAGAG 62.785 72.222 4.41 0.00 40.01 2.85


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

AutoCloner maintained by Alex Coulton.