Multiple sequence alignment - TraesCS6B01G230400

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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 TraesCS6B01G230400 chr6B 100.000 4733 0 0 1 4733 372570754 372575486 0.000000e+00 8741.0
1 TraesCS6B01G230400 chr6B 90.233 645 57 6 1 643 632317412 632316772 0.000000e+00 837.0
2 TraesCS6B01G230400 chr6B 87.138 622 64 10 1 621 457473595 457472989 0.000000e+00 691.0
3 TraesCS6B01G230400 chr6B 93.103 145 9 1 1718 1861 207511028 207510884 1.330000e-50 211.0
4 TraesCS6B01G230400 chr6A 97.572 1318 25 3 1843 3159 366036564 366035253 0.000000e+00 2250.0
5 TraesCS6B01G230400 chr6A 95.046 969 30 4 3161 4121 366032608 366031650 0.000000e+00 1507.0
6 TraesCS6B01G230400 chr6A 97.086 755 9 7 760 1507 366037460 366036712 0.000000e+00 1260.0
7 TraesCS6B01G230400 chr6A 95.777 592 17 2 4142 4733 366031588 366031005 0.000000e+00 948.0
8 TraesCS6B01G230400 chr6A 93.333 135 4 4 1590 1720 366036695 366036562 1.340000e-45 195.0
9 TraesCS6B01G230400 chr6A 98.361 61 1 0 741 801 366037519 366037459 1.800000e-19 108.0
10 TraesCS6B01G230400 chr6D 96.970 1320 25 6 1843 3159 256723104 256724411 0.000000e+00 2202.0
11 TraesCS6B01G230400 chr6D 95.253 990 18 6 3156 4133 256724462 256725434 0.000000e+00 1541.0
12 TraesCS6B01G230400 chr6D 97.856 653 7 4 861 1507 256722310 256722961 0.000000e+00 1122.0
13 TraesCS6B01G230400 chr6D 97.566 493 4 2 4244 4733 256726424 256726911 0.000000e+00 837.0
14 TraesCS6B01G230400 chr6D 96.648 179 4 2 694 871 256712518 256712695 3.580000e-76 296.0
15 TraesCS6B01G230400 chr6D 94.444 126 4 1 4142 4267 256725499 256725621 1.740000e-44 191.0
16 TraesCS6B01G230400 chr6D 95.726 117 4 1 1604 1720 256722991 256723106 2.250000e-43 187.0
17 TraesCS6B01G230400 chr2B 89.934 606 51 9 51 654 589099685 589099088 0.000000e+00 773.0
18 TraesCS6B01G230400 chr2B 93.878 147 9 0 1197 1343 497852975 497853121 6.160000e-54 222.0
19 TraesCS6B01G230400 chr2B 97.656 128 3 0 1718 1845 270452381 270452508 2.220000e-53 220.0
20 TraesCS6B01G230400 chr2B 96.212 132 5 0 1719 1850 335525596 335525465 2.870000e-52 217.0
21 TraesCS6B01G230400 chr2B 94.161 137 8 0 1717 1853 551567867 551568003 4.800000e-50 209.0
22 TraesCS6B01G230400 chr2B 90.000 90 5 3 1508 1596 720236279 720236365 3.870000e-21 113.0
23 TraesCS6B01G230400 chr2B 86.275 102 9 4 1508 1606 55859790 55859691 6.480000e-19 106.0
24 TraesCS6B01G230400 chr2B 100.000 48 0 0 1001 1048 497852784 497852831 6.520000e-14 89.8
25 TraesCS6B01G230400 chr4B 88.290 649 67 9 1 645 312107289 312107932 0.000000e+00 769.0
26 TraesCS6B01G230400 chr4B 87.539 642 73 6 1 640 584095896 584096532 0.000000e+00 736.0
27 TraesCS6B01G230400 chr3B 87.727 660 74 7 1 654 317258186 317257528 0.000000e+00 763.0
28 TraesCS6B01G230400 chr3B 88.117 446 49 4 1 446 332350612 332351053 1.170000e-145 527.0
29 TraesCS6B01G230400 chr3B 88.235 272 27 4 375 645 137321389 137321656 2.130000e-83 320.0
30 TraesCS6B01G230400 chr3B 86.420 81 9 2 1508 1587 45768847 45768926 2.350000e-13 87.9
31 TraesCS6B01G230400 chr3B 86.420 81 9 2 1508 1587 45838989 45839068 2.350000e-13 87.9
32 TraesCS6B01G230400 chr3B 86.420 81 9 2 1508 1587 45876270 45876349 2.350000e-13 87.9
33 TraesCS6B01G230400 chr7B 88.889 621 62 7 34 653 222669797 222669183 0.000000e+00 758.0
34 TraesCS6B01G230400 chr7B 89.726 584 54 6 2 583 622483635 622484214 0.000000e+00 741.0
35 TraesCS6B01G230400 chr7B 91.096 146 13 0 1198 1343 732774854 732774709 1.040000e-46 198.0
36 TraesCS6B01G230400 chr7B 90.361 83 6 2 1508 1589 745107321 745107402 1.800000e-19 108.0
37 TraesCS6B01G230400 chr7A 94.012 167 7 3 2908 3073 451519972 451519808 2.830000e-62 250.0
38 TraesCS6B01G230400 chr7A 94.444 162 6 3 2908 3068 494786990 494786831 3.660000e-61 246.0
39 TraesCS6B01G230400 chr7A 99.225 129 1 0 1719 1847 598218301 598218429 2.850000e-57 233.0
40 TraesCS6B01G230400 chr7A 83.333 156 17 3 1197 1343 622334351 622334506 8.260000e-28 135.0
41 TraesCS6B01G230400 chr5D 94.444 162 6 3 2908 3068 464292349 464292508 3.660000e-61 246.0
42 TraesCS6B01G230400 chr7D 92.941 170 9 3 2905 3073 397554913 397555080 1.320000e-60 244.0
43 TraesCS6B01G230400 chr7D 92.771 83 4 2 1508 1589 111408131 111408212 8.320000e-23 119.0
44 TraesCS6B01G230400 chr7D 90.667 75 6 1 1514 1588 156200223 156200150 1.080000e-16 99.0
45 TraesCS6B01G230400 chr7D 94.231 52 3 0 1001 1052 540631503 540631554 3.930000e-11 80.5
46 TraesCS6B01G230400 chr2D 93.373 166 8 3 2904 3068 299891719 299891556 4.730000e-60 243.0
47 TraesCS6B01G230400 chr2D 94.558 147 8 0 1197 1343 423872637 423872783 1.330000e-55 228.0
48 TraesCS6B01G230400 chr2D 98.077 52 1 0 1001 1052 423872448 423872499 1.810000e-14 91.6
49 TraesCS6B01G230400 chr1D 93.373 166 8 3 2904 3068 225704950 225704787 4.730000e-60 243.0
50 TraesCS6B01G230400 chr3D 92.857 168 9 3 2906 3072 187836306 187836471 1.700000e-59 241.0
51 TraesCS6B01G230400 chrUn 98.425 127 2 0 1719 1845 79340138 79340264 1.710000e-54 224.0
52 TraesCS6B01G230400 chr5B 97.015 134 3 1 1719 1852 356725620 356725488 1.710000e-54 224.0
53 TraesCS6B01G230400 chr2A 93.878 147 9 0 1197 1343 564503357 564503211 6.160000e-54 222.0
54 TraesCS6B01G230400 chr2A 98.077 52 1 0 1001 1052 564503563 564503512 1.810000e-14 91.6
55 TraesCS6B01G230400 chr1B 97.656 128 3 0 1719 1846 563885347 563885220 2.220000e-53 220.0
56 TraesCS6B01G230400 chr1B 91.837 147 11 1 1719 1864 332086458 332086312 2.230000e-48 204.0
57 TraesCS6B01G230400 chr1B 84.946 93 9 3 1508 1596 345408196 345408287 6.520000e-14 89.8


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 TraesCS6B01G230400 chr6B 372570754 372575486 4732 False 8741.000000 8741 100.000000 1 4733 1 chr6B.!!$F1 4732
1 TraesCS6B01G230400 chr6B 632316772 632317412 640 True 837.000000 837 90.233000 1 643 1 chr6B.!!$R3 642
2 TraesCS6B01G230400 chr6B 457472989 457473595 606 True 691.000000 691 87.138000 1 621 1 chr6B.!!$R2 620
3 TraesCS6B01G230400 chr6A 366031005 366037519 6514 True 1044.666667 2250 96.195833 741 4733 6 chr6A.!!$R1 3992
4 TraesCS6B01G230400 chr6D 256722310 256726911 4601 False 1013.333333 2202 96.302500 861 4733 6 chr6D.!!$F2 3872
5 TraesCS6B01G230400 chr2B 589099088 589099685 597 True 773.000000 773 89.934000 51 654 1 chr2B.!!$R3 603
6 TraesCS6B01G230400 chr4B 312107289 312107932 643 False 769.000000 769 88.290000 1 645 1 chr4B.!!$F1 644
7 TraesCS6B01G230400 chr4B 584095896 584096532 636 False 736.000000 736 87.539000 1 640 1 chr4B.!!$F2 639
8 TraesCS6B01G230400 chr3B 317257528 317258186 658 True 763.000000 763 87.727000 1 654 1 chr3B.!!$R1 653
9 TraesCS6B01G230400 chr7B 222669183 222669797 614 True 758.000000 758 88.889000 34 653 1 chr7B.!!$R1 619
10 TraesCS6B01G230400 chr7B 622483635 622484214 579 False 741.000000 741 89.726000 2 583 1 chr7B.!!$F1 581

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
224 231 0.103755 GGGAAATCTACGACGGGGTC 59.896 60.0 0.00 0.00 0.00 4.46 F
717 731 0.105778 GACTGTAGCCTGGCTCCATC 59.894 60.0 27.16 14.89 40.44 3.51 F
725 739 0.107017 CCTGGCTCCATCGTCCAAAT 60.107 55.0 0.00 0.00 0.00 2.32 F
727 741 0.617935 TGGCTCCATCGTCCAAATCA 59.382 50.0 0.00 0.00 0.00 2.57 F
729 743 0.659957 GCTCCATCGTCCAAATCAGC 59.340 55.0 0.00 0.00 0.00 4.26 F
1737 1815 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.0 5.23 0.00 44.66 2.17 F
1740 1818 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.00 44.66 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1721 1799 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 R
1722 1800 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30 R
1723 1801 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30 R
1725 1803 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69 R
1823 1901 2.040178 ACTCCCTCCATCCGACAATAC 58.960 52.381 0.00 0.00 0.00 1.89 R
3657 6384 1.453928 GGGGACAGCATAGCCAACC 60.454 63.158 0.00 0.00 0.00 3.77 R
3903 6630 6.127647 ACAAATGAATAGCCACACCATTACAG 60.128 38.462 0.00 0.00 0.00 2.74 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
84 89 2.092968 TCTTCAAACACCTGCTGACAGT 60.093 45.455 3.99 0.00 42.81 3.55
172 177 4.943705 GGCAGAGGAGAATAAACATGAACA 59.056 41.667 0.00 0.00 0.00 3.18
176 181 4.922206 AGGAGAATAAACATGAACAGCCA 58.078 39.130 0.00 0.00 0.00 4.75
224 231 0.103755 GGGAAATCTACGACGGGGTC 59.896 60.000 0.00 0.00 0.00 4.46
292 303 1.486310 TCTGACCTGTGAGCTTGTTGT 59.514 47.619 0.00 0.00 0.00 3.32
527 539 0.176680 GATCGAGCCACACACCAGAT 59.823 55.000 0.00 0.00 0.00 2.90
537 549 2.584064 CACCAGATGTGCGGGCTA 59.416 61.111 0.00 0.00 38.34 3.93
672 686 7.759489 TTTTAAAGGTGAATCATGTGCTAGT 57.241 32.000 0.00 0.00 0.00 2.57
673 687 7.759489 TTTAAAGGTGAATCATGTGCTAGTT 57.241 32.000 0.00 0.00 0.00 2.24
674 688 7.759489 TTAAAGGTGAATCATGTGCTAGTTT 57.241 32.000 0.00 0.00 0.00 2.66
675 689 6.655078 AAAGGTGAATCATGTGCTAGTTTT 57.345 33.333 0.00 0.00 0.00 2.43
676 690 6.655078 AAGGTGAATCATGTGCTAGTTTTT 57.345 33.333 0.00 0.00 0.00 1.94
707 721 7.717568 TCTCAGTAATAAATGAGACTGTAGCC 58.282 38.462 1.71 0.00 45.31 3.93
708 722 7.561722 TCTCAGTAATAAATGAGACTGTAGCCT 59.438 37.037 1.71 0.00 45.31 4.58
709 723 7.492524 TCAGTAATAAATGAGACTGTAGCCTG 58.507 38.462 0.00 0.00 40.19 4.85
710 724 6.703607 CAGTAATAAATGAGACTGTAGCCTGG 59.296 42.308 0.00 0.00 35.61 4.45
711 725 2.409948 AAATGAGACTGTAGCCTGGC 57.590 50.000 11.65 11.65 0.00 4.85
712 726 1.577736 AATGAGACTGTAGCCTGGCT 58.422 50.000 26.52 26.52 43.41 4.75
713 727 1.118838 ATGAGACTGTAGCCTGGCTC 58.881 55.000 27.16 16.93 43.20 4.70
714 728 0.972983 TGAGACTGTAGCCTGGCTCC 60.973 60.000 27.16 15.48 42.46 4.70
715 729 0.972983 GAGACTGTAGCCTGGCTCCA 60.973 60.000 27.16 19.87 38.42 3.86
716 730 0.326048 AGACTGTAGCCTGGCTCCAT 60.326 55.000 27.16 10.05 40.44 3.41
717 731 0.105778 GACTGTAGCCTGGCTCCATC 59.894 60.000 27.16 14.89 40.44 3.51
718 732 1.068753 CTGTAGCCTGGCTCCATCG 59.931 63.158 27.16 5.20 40.44 3.84
719 733 1.680522 CTGTAGCCTGGCTCCATCGT 61.681 60.000 27.16 1.30 40.44 3.73
720 734 1.068250 GTAGCCTGGCTCCATCGTC 59.932 63.158 27.16 4.58 40.44 4.20
721 735 2.134287 TAGCCTGGCTCCATCGTCC 61.134 63.158 27.16 0.00 40.44 4.79
722 736 2.871795 TAGCCTGGCTCCATCGTCCA 62.872 60.000 27.16 0.22 40.44 4.02
723 737 2.989639 CCTGGCTCCATCGTCCAA 59.010 61.111 0.00 0.00 0.00 3.53
724 738 1.299648 CCTGGCTCCATCGTCCAAA 59.700 57.895 0.00 0.00 0.00 3.28
725 739 0.107017 CCTGGCTCCATCGTCCAAAT 60.107 55.000 0.00 0.00 0.00 2.32
726 740 1.303309 CTGGCTCCATCGTCCAAATC 58.697 55.000 0.00 0.00 0.00 2.17
727 741 0.617935 TGGCTCCATCGTCCAAATCA 59.382 50.000 0.00 0.00 0.00 2.57
728 742 1.303309 GGCTCCATCGTCCAAATCAG 58.697 55.000 0.00 0.00 0.00 2.90
729 743 0.659957 GCTCCATCGTCCAAATCAGC 59.340 55.000 0.00 0.00 0.00 4.26
730 744 2.013563 GCTCCATCGTCCAAATCAGCA 61.014 52.381 0.00 0.00 0.00 4.41
731 745 2.358957 CTCCATCGTCCAAATCAGCAA 58.641 47.619 0.00 0.00 0.00 3.91
732 746 2.749076 CTCCATCGTCCAAATCAGCAAA 59.251 45.455 0.00 0.00 0.00 3.68
733 747 3.153130 TCCATCGTCCAAATCAGCAAAA 58.847 40.909 0.00 0.00 0.00 2.44
734 748 3.191162 TCCATCGTCCAAATCAGCAAAAG 59.809 43.478 0.00 0.00 0.00 2.27
735 749 3.191162 CCATCGTCCAAATCAGCAAAAGA 59.809 43.478 0.00 0.00 0.00 2.52
736 750 4.321156 CCATCGTCCAAATCAGCAAAAGAA 60.321 41.667 0.00 0.00 0.00 2.52
737 751 4.909696 TCGTCCAAATCAGCAAAAGAAA 57.090 36.364 0.00 0.00 0.00 2.52
738 752 4.606961 TCGTCCAAATCAGCAAAAGAAAC 58.393 39.130 0.00 0.00 0.00 2.78
739 753 4.097135 TCGTCCAAATCAGCAAAAGAAACA 59.903 37.500 0.00 0.00 0.00 2.83
747 761 3.130340 TCAGCAAAAGAAACACCTGGAAC 59.870 43.478 0.00 0.00 0.00 3.62
915 970 3.420482 CCCGCAATTCCCCTCCCT 61.420 66.667 0.00 0.00 0.00 4.20
982 1037 2.772691 GCTCCTCCGATCCGTTCGT 61.773 63.158 4.59 0.00 46.65 3.85
1505 1566 7.395190 TTGCTTTATTGTCTTGTCATATGCT 57.605 32.000 0.00 0.00 0.00 3.79
1506 1567 8.504812 TTGCTTTATTGTCTTGTCATATGCTA 57.495 30.769 0.00 0.00 0.00 3.49
1507 1568 7.919690 TGCTTTATTGTCTTGTCATATGCTAC 58.080 34.615 0.00 0.00 0.00 3.58
1508 1569 7.770433 TGCTTTATTGTCTTGTCATATGCTACT 59.230 33.333 0.00 0.00 0.00 2.57
1509 1570 8.279103 GCTTTATTGTCTTGTCATATGCTACTC 58.721 37.037 0.00 0.00 0.00 2.59
1510 1571 8.662781 TTTATTGTCTTGTCATATGCTACTCC 57.337 34.615 0.00 0.00 0.00 3.85
1511 1572 5.939764 TTGTCTTGTCATATGCTACTCCT 57.060 39.130 0.00 0.00 0.00 3.69
1512 1573 5.521906 TGTCTTGTCATATGCTACTCCTC 57.478 43.478 0.00 0.00 0.00 3.71
1513 1574 4.342378 TGTCTTGTCATATGCTACTCCTCC 59.658 45.833 0.00 0.00 0.00 4.30
1514 1575 3.898123 TCTTGTCATATGCTACTCCTCCC 59.102 47.826 0.00 0.00 0.00 4.30
1515 1576 3.328535 TGTCATATGCTACTCCTCCCA 57.671 47.619 0.00 0.00 0.00 4.37
1516 1577 3.861846 TGTCATATGCTACTCCTCCCAT 58.138 45.455 0.00 0.00 0.00 4.00
1517 1578 3.580022 TGTCATATGCTACTCCTCCCATG 59.420 47.826 0.00 0.00 0.00 3.66
1518 1579 3.834813 GTCATATGCTACTCCTCCCATGA 59.165 47.826 0.00 0.00 0.00 3.07
1519 1580 4.469227 GTCATATGCTACTCCTCCCATGAT 59.531 45.833 0.00 0.00 0.00 2.45
1520 1581 4.468868 TCATATGCTACTCCTCCCATGATG 59.531 45.833 0.00 0.00 0.00 3.07
1521 1582 2.180946 TGCTACTCCTCCCATGATGT 57.819 50.000 0.00 0.00 0.00 3.06
1522 1583 3.328535 TGCTACTCCTCCCATGATGTA 57.671 47.619 0.00 0.00 0.00 2.29
1523 1584 3.653164 TGCTACTCCTCCCATGATGTAA 58.347 45.455 0.00 0.00 0.00 2.41
1524 1585 3.643320 TGCTACTCCTCCCATGATGTAAG 59.357 47.826 0.00 0.00 0.00 2.34
1525 1586 3.898123 GCTACTCCTCCCATGATGTAAGA 59.102 47.826 0.00 0.00 0.00 2.10
1526 1587 4.262249 GCTACTCCTCCCATGATGTAAGAC 60.262 50.000 0.00 0.00 0.00 3.01
1527 1588 2.695666 ACTCCTCCCATGATGTAAGACG 59.304 50.000 0.00 0.00 0.00 4.18
1528 1589 2.695666 CTCCTCCCATGATGTAAGACGT 59.304 50.000 0.00 0.00 0.00 4.34
1529 1590 3.104512 TCCTCCCATGATGTAAGACGTT 58.895 45.455 0.00 0.00 0.00 3.99
1530 1591 3.517901 TCCTCCCATGATGTAAGACGTTT 59.482 43.478 0.00 0.00 0.00 3.60
1531 1592 4.019681 TCCTCCCATGATGTAAGACGTTTT 60.020 41.667 0.00 0.00 0.00 2.43
1532 1593 4.700213 CCTCCCATGATGTAAGACGTTTTT 59.300 41.667 0.00 0.00 0.00 1.94
1577 1638 6.753107 AAAAAGTCTTACATTATGGGACGG 57.247 37.500 0.00 0.00 32.86 4.79
1578 1639 5.687166 AAAGTCTTACATTATGGGACGGA 57.313 39.130 0.00 0.00 32.86 4.69
1579 1640 4.939052 AGTCTTACATTATGGGACGGAG 57.061 45.455 0.00 0.00 32.86 4.63
1580 1641 3.641906 AGTCTTACATTATGGGACGGAGG 59.358 47.826 0.00 0.00 32.86 4.30
1581 1642 3.640029 GTCTTACATTATGGGACGGAGGA 59.360 47.826 0.00 0.00 0.00 3.71
1582 1643 4.100498 GTCTTACATTATGGGACGGAGGAA 59.900 45.833 0.00 0.00 0.00 3.36
1583 1644 4.344102 TCTTACATTATGGGACGGAGGAAG 59.656 45.833 0.00 0.00 0.00 3.46
1599 1660 8.164058 ACGGAGGAAGTAGTTTACAGTATATC 57.836 38.462 0.00 0.00 0.00 1.63
1600 1661 7.997803 ACGGAGGAAGTAGTTTACAGTATATCT 59.002 37.037 0.00 0.00 0.00 1.98
1601 1662 9.499479 CGGAGGAAGTAGTTTACAGTATATCTA 57.501 37.037 0.00 0.00 0.00 1.98
1684 1762 3.829601 TGGCACGGATTCTAAAAACCAAT 59.170 39.130 0.00 0.00 0.00 3.16
1709 1787 4.162320 TCCATCTCTCTATTGGTCACCAAC 59.838 45.833 12.79 0.00 46.95 3.77
1720 1798 5.515884 ATTGGTCACCAACTTCCGTTGTAC 61.516 45.833 12.79 0.00 46.95 2.90
1721 1799 7.665122 ATTGGTCACCAACTTCCGTTGTACT 62.665 44.000 12.79 0.00 46.95 2.73
1725 1803 2.833631 CAACTTCCGTTGTACTCCCT 57.166 50.000 0.00 0.00 44.27 4.20
1726 1804 2.685100 CAACTTCCGTTGTACTCCCTC 58.315 52.381 0.00 0.00 44.27 4.30
1727 1805 1.264295 ACTTCCGTTGTACTCCCTCC 58.736 55.000 0.00 0.00 0.00 4.30
1728 1806 0.172803 CTTCCGTTGTACTCCCTCCG 59.827 60.000 0.00 0.00 0.00 4.63
1729 1807 0.540365 TTCCGTTGTACTCCCTCCGT 60.540 55.000 0.00 0.00 0.00 4.69
1730 1808 0.962356 TCCGTTGTACTCCCTCCGTC 60.962 60.000 0.00 0.00 0.00 4.79
1731 1809 1.509923 CGTTGTACTCCCTCCGTCC 59.490 63.158 0.00 0.00 0.00 4.79
1732 1810 1.509923 GTTGTACTCCCTCCGTCCG 59.490 63.158 0.00 0.00 0.00 4.79
1733 1811 1.679977 TTGTACTCCCTCCGTCCGG 60.680 63.158 0.00 0.00 0.00 5.14
1734 1812 2.141011 TTGTACTCCCTCCGTCCGGA 62.141 60.000 0.00 0.00 42.90 5.14
1735 1813 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
1736 1814 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
1737 1815 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1738 1816 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1739 1817 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1740 1818 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1741 1819 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1742 1820 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1743 1821 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1744 1822 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1745 1823 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
1746 1824 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
1747 1825 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
1748 1826 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
1749 1827 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
1750 1828 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
1751 1829 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
1752 1830 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
1753 1831 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
1754 1832 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
1755 1833 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
1756 1834 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
1757 1835 7.433131 CGGAAATACTTGTCATCAAAATGGATG 59.567 37.037 0.00 0.00 44.78 3.51
1766 1844 5.881923 CATCAAAATGGATGAAAGGGGAT 57.118 39.130 0.00 0.00 46.00 3.85
1767 1845 5.607477 CATCAAAATGGATGAAAGGGGATG 58.393 41.667 0.00 0.00 46.00 3.51
1768 1846 4.686891 TCAAAATGGATGAAAGGGGATGT 58.313 39.130 0.00 0.00 0.00 3.06
1769 1847 5.836705 TCAAAATGGATGAAAGGGGATGTA 58.163 37.500 0.00 0.00 0.00 2.29
1770 1848 6.442961 TCAAAATGGATGAAAGGGGATGTAT 58.557 36.000 0.00 0.00 0.00 2.29
1771 1849 6.550854 TCAAAATGGATGAAAGGGGATGTATC 59.449 38.462 0.00 0.00 0.00 2.24
1772 1850 5.937492 AATGGATGAAAGGGGATGTATCT 57.063 39.130 0.00 0.00 0.00 1.98
1773 1851 7.406620 AAATGGATGAAAGGGGATGTATCTA 57.593 36.000 0.00 0.00 0.00 1.98
1774 1852 6.633325 ATGGATGAAAGGGGATGTATCTAG 57.367 41.667 0.00 0.00 0.00 2.43
1775 1853 5.726560 TGGATGAAAGGGGATGTATCTAGA 58.273 41.667 0.00 0.00 0.00 2.43
1776 1854 5.544176 TGGATGAAAGGGGATGTATCTAGAC 59.456 44.000 0.00 0.00 0.00 2.59
1777 1855 5.336849 GGATGAAAGGGGATGTATCTAGACG 60.337 48.000 0.00 0.00 0.00 4.18
1778 1856 4.543689 TGAAAGGGGATGTATCTAGACGT 58.456 43.478 0.00 0.00 0.00 4.34
1779 1857 5.698104 TGAAAGGGGATGTATCTAGACGTA 58.302 41.667 0.00 0.00 0.00 3.57
1780 1858 6.312529 TGAAAGGGGATGTATCTAGACGTAT 58.687 40.000 0.00 0.00 0.00 3.06
1781 1859 6.781014 TGAAAGGGGATGTATCTAGACGTATT 59.219 38.462 0.00 0.00 0.00 1.89
1782 1860 7.289317 TGAAAGGGGATGTATCTAGACGTATTT 59.711 37.037 0.00 0.00 0.00 1.40
1783 1861 7.613551 AAGGGGATGTATCTAGACGTATTTT 57.386 36.000 0.00 0.00 0.00 1.82
1784 1862 8.716674 AAGGGGATGTATCTAGACGTATTTTA 57.283 34.615 0.00 0.00 0.00 1.52
1785 1863 8.350852 AGGGGATGTATCTAGACGTATTTTAG 57.649 38.462 0.00 0.00 0.00 1.85
1786 1864 7.949006 AGGGGATGTATCTAGACGTATTTTAGT 59.051 37.037 0.00 0.00 0.00 2.24
1787 1865 8.583296 GGGGATGTATCTAGACGTATTTTAGTT 58.417 37.037 0.00 0.00 0.00 2.24
1788 1866 9.623350 GGGATGTATCTAGACGTATTTTAGTTC 57.377 37.037 0.00 0.00 0.00 3.01
1820 1898 9.696917 ACATCTCTTTTTATTCATTTTGGTGAC 57.303 29.630 0.00 0.00 0.00 3.67
1821 1899 9.695526 CATCTCTTTTTATTCATTTTGGTGACA 57.304 29.630 0.00 0.00 39.83 3.58
1840 1918 2.838736 CAAGTATTGTCGGATGGAGGG 58.161 52.381 0.00 0.00 42.34 4.30
1841 1919 2.434336 CAAGTATTGTCGGATGGAGGGA 59.566 50.000 0.00 0.00 42.34 4.20
1842 1920 2.320781 AGTATTGTCGGATGGAGGGAG 58.679 52.381 0.00 0.00 0.00 4.30
1843 1921 2.040178 GTATTGTCGGATGGAGGGAGT 58.960 52.381 0.00 0.00 0.00 3.85
1844 1922 2.471815 ATTGTCGGATGGAGGGAGTA 57.528 50.000 0.00 0.00 0.00 2.59
1849 1927 4.489737 TGTCGGATGGAGGGAGTAATATT 58.510 43.478 0.00 0.00 0.00 1.28
1939 2017 4.245660 TGCATTTCTTGAGACGGTCTAAG 58.754 43.478 11.27 13.95 0.00 2.18
2156 2236 7.700656 AGTTACATAACAAGTTTTGCTGTTGAC 59.299 33.333 4.67 1.99 38.62 3.18
2223 2303 2.919772 TCTGTAGTCCAGGATCCACA 57.080 50.000 15.82 7.35 41.83 4.17
2230 2310 1.906574 GTCCAGGATCCACAGTGGTTA 59.093 52.381 19.65 0.90 39.03 2.85
2444 2524 0.399949 TGGTCCTTCCACCTGACTGT 60.400 55.000 0.00 0.00 41.93 3.55
2712 2792 6.419710 GTGGGATTACACTTTTTAGTTTGTGC 59.580 38.462 0.00 0.00 38.32 4.57
2733 2813 4.405358 TGCCCAAAAAGAAAACTCACATCT 59.595 37.500 0.00 0.00 0.00 2.90
2833 2913 6.939730 TCTAATGAGGTGAGTGTTAAATTGCA 59.060 34.615 0.00 0.00 0.00 4.08
2836 2916 5.069318 TGAGGTGAGTGTTAAATTGCATGA 58.931 37.500 0.00 0.00 0.00 3.07
2927 3008 8.611051 ACTTGTACTCCTCTGTTCCTAAATAT 57.389 34.615 0.00 0.00 0.00 1.28
2928 3009 9.710818 ACTTGTACTCCTCTGTTCCTAAATATA 57.289 33.333 0.00 0.00 0.00 0.86
3068 3149 7.021998 ACTTATATTTAGGAATGGAGGGAGC 57.978 40.000 0.00 0.00 0.00 4.70
3141 3222 4.497300 CTTTGGGGATATGTTGCTTGTTG 58.503 43.478 0.00 0.00 0.00 3.33
3179 5903 8.432805 CAAGAGGGTATCTTATCAGGTTGTAAT 58.567 37.037 0.00 0.00 46.91 1.89
3257 5982 7.959175 TCTGTGTTAGTAGTAATTGGAAGTGT 58.041 34.615 0.00 0.00 0.00 3.55
3351 6076 9.513906 TGAGTCTCCAGTTATATATTCTCTCTG 57.486 37.037 0.00 0.00 0.00 3.35
3413 6138 1.538047 TGTCATTGGCAGCTCCTTTC 58.462 50.000 0.00 0.00 35.26 2.62
3528 6255 5.455056 TCTAAGAACGTCTCTTCTGCTTT 57.545 39.130 13.76 0.00 43.66 3.51
3563 6290 7.773690 ACAGTAGTTGTTTTCATTTCCTGTAGT 59.226 33.333 0.00 0.00 36.31 2.73
3572 6299 5.164620 TCATTTCCTGTAGTGCTGATTGA 57.835 39.130 0.00 0.00 0.00 2.57
3586 6313 3.431486 GCTGATTGACTAGGCTAGCACTT 60.431 47.826 21.26 9.99 0.00 3.16
3657 6384 3.707793 GCTGTAGTCCTACGGAATCAAG 58.292 50.000 15.78 0.60 43.37 3.02
3756 6483 5.186409 AGCAAGTTTACGACCAAGTCCTATA 59.814 40.000 0.00 0.00 0.00 1.31
3867 6594 3.920446 TGTCTACACTGCGCAATCTTTA 58.080 40.909 13.05 0.00 0.00 1.85
3903 6630 8.723942 ACATCTATAGTTTCTGTCCATTTGTC 57.276 34.615 0.00 0.00 0.00 3.18
3905 6632 8.824781 CATCTATAGTTTCTGTCCATTTGTCTG 58.175 37.037 0.00 0.00 0.00 3.51
3917 6651 3.367292 CCATTTGTCTGTAATGGTGTGGC 60.367 47.826 6.47 0.00 44.51 5.01
4006 6740 3.953612 TCCATGTCACAATATTTGCCCTC 59.046 43.478 0.00 0.00 0.00 4.30
4070 6804 8.323140 GCTTGTTGTTGATGATGCATTTAATAC 58.677 33.333 0.00 0.00 0.00 1.89
4133 6869 7.136772 TGTCGGATATTACTCATACTTTGTCG 58.863 38.462 0.00 0.00 0.00 4.35
4134 6870 6.581542 GTCGGATATTACTCATACTTTGTCGG 59.418 42.308 0.00 0.00 0.00 4.79
4135 6871 6.487668 TCGGATATTACTCATACTTTGTCGGA 59.512 38.462 0.00 0.00 0.00 4.55
4136 6872 7.013559 TCGGATATTACTCATACTTTGTCGGAA 59.986 37.037 0.00 0.00 0.00 4.30
4138 6874 7.924412 GGATATTACTCATACTTTGTCGGAACA 59.076 37.037 0.00 0.00 0.00 3.18
4139 6875 9.477484 GATATTACTCATACTTTGTCGGAACAT 57.523 33.333 0.00 0.00 34.73 2.71
4166 6961 8.514504 ACCAGATAAATTTCCTAGAAATGGGAT 58.485 33.333 3.46 0.00 0.00 3.85
4182 6977 8.274322 AGAAATGGGATTCATGACACAGTAATA 58.726 33.333 0.00 0.00 35.99 0.98
4183 6978 8.821686 AAATGGGATTCATGACACAGTAATAA 57.178 30.769 0.00 0.00 35.99 1.40
4184 6979 9.425248 AAATGGGATTCATGACACAGTAATAAT 57.575 29.630 0.00 0.00 35.99 1.28
4185 6980 8.627208 ATGGGATTCATGACACAGTAATAATC 57.373 34.615 0.00 0.00 34.22 1.75
4186 6981 7.572814 TGGGATTCATGACACAGTAATAATCA 58.427 34.615 0.00 0.00 0.00 2.57
4240 7035 5.435557 CGCAATATAAAGCTAGCACACTTC 58.564 41.667 18.83 0.00 0.00 3.01
4267 7888 4.402155 ACATCAGTCAAACACCAACAACAT 59.598 37.500 0.00 0.00 0.00 2.71
4268 7889 5.592282 ACATCAGTCAAACACCAACAACATA 59.408 36.000 0.00 0.00 0.00 2.29
4269 7890 6.096141 ACATCAGTCAAACACCAACAACATAA 59.904 34.615 0.00 0.00 0.00 1.90
4270 7891 5.885881 TCAGTCAAACACCAACAACATAAC 58.114 37.500 0.00 0.00 0.00 1.89
4271 7892 5.416013 TCAGTCAAACACCAACAACATAACA 59.584 36.000 0.00 0.00 0.00 2.41
4538 8162 7.645340 GCCAGTGATAGTGCATAAACAAAATAG 59.355 37.037 0.00 0.00 0.00 1.73
4709 8333 5.321927 GGTAACAGGATTCTTCCCTTTCAA 58.678 41.667 0.00 0.00 43.76 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.036346 GCAGAACAGAGCAATTTTGGGT 59.964 45.455 0.00 0.00 0.00 4.51
172 177 0.617413 CTGGATCCACAGTTCTGGCT 59.383 55.000 11.44 0.00 33.81 4.75
224 231 2.136878 CCATCCACTCTCCCTCCCG 61.137 68.421 0.00 0.00 0.00 5.14
228 235 2.243221 CAAATTCCCATCCACTCTCCCT 59.757 50.000 0.00 0.00 0.00 4.20
229 236 2.659428 CAAATTCCCATCCACTCTCCC 58.341 52.381 0.00 0.00 0.00 4.30
230 237 2.659428 CCAAATTCCCATCCACTCTCC 58.341 52.381 0.00 0.00 0.00 3.71
231 238 2.242196 TCCCAAATTCCCATCCACTCTC 59.758 50.000 0.00 0.00 0.00 3.20
232 239 2.287584 TCCCAAATTCCCATCCACTCT 58.712 47.619 0.00 0.00 0.00 3.24
292 303 1.670674 CCCATCGACGGAAAAAGACGA 60.671 52.381 0.00 0.00 39.63 4.20
527 539 2.510411 CCATCCATAGCCCGCACA 59.490 61.111 0.00 0.00 0.00 4.57
570 582 0.036765 GTGGCATAGACACGGACCAA 60.037 55.000 0.00 0.00 29.47 3.67
680 694 9.757227 GCTACAGTCTCATTTATTACTGAGAAT 57.243 33.333 8.21 0.43 46.89 2.40
681 695 8.198109 GGCTACAGTCTCATTTATTACTGAGAA 58.802 37.037 8.21 0.00 46.89 2.87
682 696 7.561722 AGGCTACAGTCTCATTTATTACTGAGA 59.438 37.037 8.21 0.00 44.20 3.27
683 697 7.651304 CAGGCTACAGTCTCATTTATTACTGAG 59.349 40.741 8.21 0.00 41.47 3.35
684 698 7.417911 CCAGGCTACAGTCTCATTTATTACTGA 60.418 40.741 8.21 0.00 41.47 3.41
685 699 6.703607 CCAGGCTACAGTCTCATTTATTACTG 59.296 42.308 0.00 0.00 43.90 2.74
686 700 6.686632 GCCAGGCTACAGTCTCATTTATTACT 60.687 42.308 3.29 0.00 0.00 2.24
687 701 5.467063 GCCAGGCTACAGTCTCATTTATTAC 59.533 44.000 3.29 0.00 0.00 1.89
688 702 5.366768 AGCCAGGCTACAGTCTCATTTATTA 59.633 40.000 14.18 0.00 36.99 0.98
689 703 4.164988 AGCCAGGCTACAGTCTCATTTATT 59.835 41.667 14.18 0.00 36.99 1.40
690 704 3.713764 AGCCAGGCTACAGTCTCATTTAT 59.286 43.478 14.18 0.00 36.99 1.40
691 705 3.107601 AGCCAGGCTACAGTCTCATTTA 58.892 45.455 14.18 0.00 36.99 1.40
692 706 1.912043 AGCCAGGCTACAGTCTCATTT 59.088 47.619 14.18 0.00 36.99 2.32
693 707 1.484240 GAGCCAGGCTACAGTCTCATT 59.516 52.381 16.16 0.00 39.88 2.57
694 708 1.118838 GAGCCAGGCTACAGTCTCAT 58.881 55.000 16.16 0.00 39.88 2.90
695 709 0.972983 GGAGCCAGGCTACAGTCTCA 60.973 60.000 20.17 0.00 39.71 3.27
696 710 0.972983 TGGAGCCAGGCTACAGTCTC 60.973 60.000 24.04 3.94 45.48 3.36
697 711 1.079256 TGGAGCCAGGCTACAGTCT 59.921 57.895 24.04 0.00 45.48 3.24
698 712 3.713650 TGGAGCCAGGCTACAGTC 58.286 61.111 24.04 5.58 45.48 3.51
702 716 1.068250 GACGATGGAGCCAGGCTAC 59.932 63.158 18.16 18.16 39.88 3.58
703 717 2.134287 GGACGATGGAGCCAGGCTA 61.134 63.158 16.16 0.00 39.88 3.93
704 718 3.474570 GGACGATGGAGCCAGGCT 61.475 66.667 16.12 16.12 43.88 4.58
705 719 2.819984 TTTGGACGATGGAGCCAGGC 62.820 60.000 1.84 1.84 32.47 4.85
706 720 0.107017 ATTTGGACGATGGAGCCAGG 60.107 55.000 0.00 0.00 32.47 4.45
707 721 1.303309 GATTTGGACGATGGAGCCAG 58.697 55.000 0.00 0.00 32.47 4.85
708 722 0.617935 TGATTTGGACGATGGAGCCA 59.382 50.000 0.00 0.00 0.00 4.75
709 723 1.303309 CTGATTTGGACGATGGAGCC 58.697 55.000 0.00 0.00 0.00 4.70
710 724 0.659957 GCTGATTTGGACGATGGAGC 59.340 55.000 0.00 0.00 0.00 4.70
711 725 2.028420 TGCTGATTTGGACGATGGAG 57.972 50.000 0.00 0.00 0.00 3.86
712 726 2.488204 TTGCTGATTTGGACGATGGA 57.512 45.000 0.00 0.00 0.00 3.41
713 727 3.191162 TCTTTTGCTGATTTGGACGATGG 59.809 43.478 0.00 0.00 0.00 3.51
714 728 4.424061 TCTTTTGCTGATTTGGACGATG 57.576 40.909 0.00 0.00 0.00 3.84
715 729 5.221224 TGTTTCTTTTGCTGATTTGGACGAT 60.221 36.000 0.00 0.00 0.00 3.73
716 730 4.097135 TGTTTCTTTTGCTGATTTGGACGA 59.903 37.500 0.00 0.00 0.00 4.20
717 731 4.207019 GTGTTTCTTTTGCTGATTTGGACG 59.793 41.667 0.00 0.00 0.00 4.79
718 732 4.507756 GGTGTTTCTTTTGCTGATTTGGAC 59.492 41.667 0.00 0.00 0.00 4.02
719 733 4.405358 AGGTGTTTCTTTTGCTGATTTGGA 59.595 37.500 0.00 0.00 0.00 3.53
720 734 4.508861 CAGGTGTTTCTTTTGCTGATTTGG 59.491 41.667 0.00 0.00 0.00 3.28
721 735 4.508861 CCAGGTGTTTCTTTTGCTGATTTG 59.491 41.667 0.00 0.00 0.00 2.32
722 736 4.405358 TCCAGGTGTTTCTTTTGCTGATTT 59.595 37.500 0.00 0.00 0.00 2.17
723 737 3.960102 TCCAGGTGTTTCTTTTGCTGATT 59.040 39.130 0.00 0.00 0.00 2.57
724 738 3.565307 TCCAGGTGTTTCTTTTGCTGAT 58.435 40.909 0.00 0.00 0.00 2.90
725 739 3.011566 TCCAGGTGTTTCTTTTGCTGA 57.988 42.857 0.00 0.00 0.00 4.26
726 740 3.447742 GTTCCAGGTGTTTCTTTTGCTG 58.552 45.455 0.00 0.00 0.00 4.41
727 741 2.430694 GGTTCCAGGTGTTTCTTTTGCT 59.569 45.455 0.00 0.00 0.00 3.91
728 742 2.167487 TGGTTCCAGGTGTTTCTTTTGC 59.833 45.455 0.00 0.00 0.00 3.68
729 743 3.699038 TCTGGTTCCAGGTGTTTCTTTTG 59.301 43.478 17.37 0.00 35.01 2.44
730 744 3.976015 TCTGGTTCCAGGTGTTTCTTTT 58.024 40.909 17.37 0.00 35.01 2.27
731 745 3.662759 TCTGGTTCCAGGTGTTTCTTT 57.337 42.857 17.37 0.00 35.01 2.52
732 746 3.498661 GGATCTGGTTCCAGGTGTTTCTT 60.499 47.826 17.37 0.00 35.72 2.52
733 747 2.040412 GGATCTGGTTCCAGGTGTTTCT 59.960 50.000 17.37 0.00 35.72 2.52
734 748 2.224769 TGGATCTGGTTCCAGGTGTTTC 60.225 50.000 17.37 8.03 40.90 2.78
735 749 1.780309 TGGATCTGGTTCCAGGTGTTT 59.220 47.619 17.37 0.27 40.90 2.83
736 750 1.444933 TGGATCTGGTTCCAGGTGTT 58.555 50.000 17.37 2.45 40.90 3.32
737 751 3.180449 TGGATCTGGTTCCAGGTGT 57.820 52.632 17.37 5.70 40.90 4.16
825 879 3.075005 GAGAGGCAGCCCACGGTA 61.075 66.667 8.22 0.00 0.00 4.02
915 970 5.785423 TCTGATTGGTTTAAGAGAAGGGAGA 59.215 40.000 0.00 0.00 0.00 3.71
1165 1221 2.764251 AAAGCAATCACGACGCGCAC 62.764 55.000 5.73 0.00 0.00 5.34
1166 1222 2.111932 AAAAGCAATCACGACGCGCA 62.112 50.000 5.73 0.00 0.00 6.09
1453 1514 0.248012 TGCTTCATTTACTCCGCGGA 59.752 50.000 29.03 29.03 0.00 5.54
1457 1518 5.760253 AGGAATGTATGCTTCATTTACTCCG 59.240 40.000 0.00 0.00 35.94 4.63
1505 1566 3.889538 CGTCTTACATCATGGGAGGAGTA 59.110 47.826 0.00 0.00 0.00 2.59
1506 1567 2.695666 CGTCTTACATCATGGGAGGAGT 59.304 50.000 0.00 0.00 0.00 3.85
1507 1568 2.695666 ACGTCTTACATCATGGGAGGAG 59.304 50.000 0.00 0.00 0.00 3.69
1508 1569 2.747177 ACGTCTTACATCATGGGAGGA 58.253 47.619 0.00 0.00 0.00 3.71
1509 1570 3.543680 AACGTCTTACATCATGGGAGG 57.456 47.619 0.00 0.00 0.00 4.30
1510 1571 5.880054 AAAAACGTCTTACATCATGGGAG 57.120 39.130 0.00 0.00 0.00 4.30
1554 1615 6.478129 TCCGTCCCATAATGTAAGACTTTTT 58.522 36.000 0.00 0.00 0.00 1.94
1555 1616 6.057321 TCCGTCCCATAATGTAAGACTTTT 57.943 37.500 0.00 0.00 0.00 2.27
1556 1617 5.396436 CCTCCGTCCCATAATGTAAGACTTT 60.396 44.000 0.00 0.00 0.00 2.66
1557 1618 4.101119 CCTCCGTCCCATAATGTAAGACTT 59.899 45.833 0.00 0.00 0.00 3.01
1558 1619 3.641906 CCTCCGTCCCATAATGTAAGACT 59.358 47.826 0.00 0.00 0.00 3.24
1559 1620 3.640029 TCCTCCGTCCCATAATGTAAGAC 59.360 47.826 0.00 0.00 0.00 3.01
1560 1621 3.918566 TCCTCCGTCCCATAATGTAAGA 58.081 45.455 0.00 0.00 0.00 2.10
1561 1622 4.101119 ACTTCCTCCGTCCCATAATGTAAG 59.899 45.833 0.00 0.00 0.00 2.34
1562 1623 4.035112 ACTTCCTCCGTCCCATAATGTAA 58.965 43.478 0.00 0.00 0.00 2.41
1563 1624 3.649843 ACTTCCTCCGTCCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
1564 1625 2.478292 ACTTCCTCCGTCCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
1565 1626 3.641906 ACTACTTCCTCCGTCCCATAATG 59.358 47.826 0.00 0.00 0.00 1.90
1566 1627 3.924922 ACTACTTCCTCCGTCCCATAAT 58.075 45.455 0.00 0.00 0.00 1.28
1567 1628 3.393426 ACTACTTCCTCCGTCCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
1568 1629 3.393426 AACTACTTCCTCCGTCCCATA 57.607 47.619 0.00 0.00 0.00 2.74
1569 1630 2.249309 AACTACTTCCTCCGTCCCAT 57.751 50.000 0.00 0.00 0.00 4.00
1570 1631 2.019807 AAACTACTTCCTCCGTCCCA 57.980 50.000 0.00 0.00 0.00 4.37
1571 1632 2.827921 TGTAAACTACTTCCTCCGTCCC 59.172 50.000 0.00 0.00 0.00 4.46
1572 1633 3.509184 ACTGTAAACTACTTCCTCCGTCC 59.491 47.826 0.00 0.00 0.00 4.79
1573 1634 4.780275 ACTGTAAACTACTTCCTCCGTC 57.220 45.455 0.00 0.00 0.00 4.79
1574 1635 7.997803 AGATATACTGTAAACTACTTCCTCCGT 59.002 37.037 0.00 0.00 0.00 4.69
1575 1636 8.393671 AGATATACTGTAAACTACTTCCTCCG 57.606 38.462 0.00 0.00 0.00 4.63
1599 1660 7.390440 CCAGAGAGAGTGATCCATAACTACTAG 59.610 44.444 0.00 0.00 0.00 2.57
1600 1661 7.147284 ACCAGAGAGAGTGATCCATAACTACTA 60.147 40.741 0.00 0.00 0.00 1.82
1601 1662 6.068010 CCAGAGAGAGTGATCCATAACTACT 58.932 44.000 0.00 0.00 0.00 2.57
1602 1663 5.830991 ACCAGAGAGAGTGATCCATAACTAC 59.169 44.000 0.00 0.00 0.00 2.73
1603 1664 6.019656 ACCAGAGAGAGTGATCCATAACTA 57.980 41.667 0.00 0.00 0.00 2.24
1604 1665 4.877773 ACCAGAGAGAGTGATCCATAACT 58.122 43.478 0.00 0.00 0.00 2.24
1605 1666 4.646945 TGACCAGAGAGAGTGATCCATAAC 59.353 45.833 0.00 0.00 0.00 1.89
1606 1667 4.871822 TGACCAGAGAGAGTGATCCATAA 58.128 43.478 0.00 0.00 0.00 1.90
1684 1762 4.782691 TGGTGACCAATAGAGAGATGGAAA 59.217 41.667 0.00 0.00 37.66 3.13
1709 1787 0.172803 CGGAGGGAGTACAACGGAAG 59.827 60.000 0.00 0.00 0.00 3.46
1720 1798 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
1721 1799 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1722 1800 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1723 1801 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1724 1802 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
1725 1803 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
1726 1804 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
1727 1805 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
1728 1806 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
1729 1807 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
1730 1808 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
1731 1809 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
1732 1810 8.469200 TCATCCATTTTGATGACAAGTATTTCC 58.531 33.333 0.00 0.00 44.65 3.13
1744 1822 5.129815 ACATCCCCTTTCATCCATTTTGATG 59.870 40.000 0.00 0.00 42.84 3.07
1745 1823 5.282946 ACATCCCCTTTCATCCATTTTGAT 58.717 37.500 0.00 0.00 0.00 2.57
1746 1824 4.686891 ACATCCCCTTTCATCCATTTTGA 58.313 39.130 0.00 0.00 0.00 2.69
1747 1825 6.552350 AGATACATCCCCTTTCATCCATTTTG 59.448 38.462 0.00 0.00 0.00 2.44
1748 1826 6.686544 AGATACATCCCCTTTCATCCATTTT 58.313 36.000 0.00 0.00 0.00 1.82
1749 1827 6.285329 AGATACATCCCCTTTCATCCATTT 57.715 37.500 0.00 0.00 0.00 2.32
1750 1828 5.937492 AGATACATCCCCTTTCATCCATT 57.063 39.130 0.00 0.00 0.00 3.16
1751 1829 6.214412 GTCTAGATACATCCCCTTTCATCCAT 59.786 42.308 0.00 0.00 0.00 3.41
1752 1830 5.544176 GTCTAGATACATCCCCTTTCATCCA 59.456 44.000 0.00 0.00 0.00 3.41
1753 1831 5.336849 CGTCTAGATACATCCCCTTTCATCC 60.337 48.000 0.00 0.00 0.00 3.51
1754 1832 5.244178 ACGTCTAGATACATCCCCTTTCATC 59.756 44.000 0.00 0.00 0.00 2.92
1755 1833 5.148502 ACGTCTAGATACATCCCCTTTCAT 58.851 41.667 0.00 0.00 0.00 2.57
1756 1834 4.543689 ACGTCTAGATACATCCCCTTTCA 58.456 43.478 0.00 0.00 0.00 2.69
1757 1835 6.837471 ATACGTCTAGATACATCCCCTTTC 57.163 41.667 0.00 0.00 0.00 2.62
1758 1836 7.613551 AAATACGTCTAGATACATCCCCTTT 57.386 36.000 0.00 0.00 0.00 3.11
1759 1837 7.613551 AAAATACGTCTAGATACATCCCCTT 57.386 36.000 0.00 0.00 0.00 3.95
1760 1838 7.949006 ACTAAAATACGTCTAGATACATCCCCT 59.051 37.037 0.00 0.00 0.00 4.79
1761 1839 8.120140 ACTAAAATACGTCTAGATACATCCCC 57.880 38.462 0.00 0.00 0.00 4.81
1762 1840 9.623350 GAACTAAAATACGTCTAGATACATCCC 57.377 37.037 0.00 0.00 0.00 3.85
1794 1872 9.696917 GTCACCAAAATGAATAAAAAGAGATGT 57.303 29.630 0.00 0.00 0.00 3.06
1795 1873 9.695526 TGTCACCAAAATGAATAAAAAGAGATG 57.304 29.630 0.00 0.00 0.00 2.90
1797 1875 9.748708 CTTGTCACCAAAATGAATAAAAAGAGA 57.251 29.630 0.00 0.00 0.00 3.10
1798 1876 9.533253 ACTTGTCACCAAAATGAATAAAAAGAG 57.467 29.630 0.00 0.00 0.00 2.85
1820 1898 2.434336 TCCCTCCATCCGACAATACTTG 59.566 50.000 0.00 0.00 0.00 3.16
1821 1899 2.700897 CTCCCTCCATCCGACAATACTT 59.299 50.000 0.00 0.00 0.00 2.24
1822 1900 2.320781 CTCCCTCCATCCGACAATACT 58.679 52.381 0.00 0.00 0.00 2.12
1823 1901 2.040178 ACTCCCTCCATCCGACAATAC 58.960 52.381 0.00 0.00 0.00 1.89
1824 1902 2.471815 ACTCCCTCCATCCGACAATA 57.528 50.000 0.00 0.00 0.00 1.90
1825 1903 2.471815 TACTCCCTCCATCCGACAAT 57.528 50.000 0.00 0.00 0.00 2.71
1826 1904 2.241281 TTACTCCCTCCATCCGACAA 57.759 50.000 0.00 0.00 0.00 3.18
1827 1905 2.471815 ATTACTCCCTCCATCCGACA 57.528 50.000 0.00 0.00 0.00 4.35
1828 1906 5.485209 AAATATTACTCCCTCCATCCGAC 57.515 43.478 0.00 0.00 0.00 4.79
1829 1907 7.808279 ATTAAATATTACTCCCTCCATCCGA 57.192 36.000 0.00 0.00 0.00 4.55
1939 2017 5.064441 ACACCTTGGTGAATACGTACTAC 57.936 43.478 24.67 0.00 0.00 2.73
1970 2049 7.422399 TGCAGTCAAACCATTAGAACTTTAAC 58.578 34.615 0.00 0.00 0.00 2.01
2156 2236 4.678509 TGCCAATTTAGTTAAGCAGTCG 57.321 40.909 0.00 0.00 0.00 4.18
2223 2303 4.989168 GTGAAGTCGAACTCAATAACCACT 59.011 41.667 0.00 0.00 0.00 4.00
2230 2310 3.321497 GCTCTGTGAAGTCGAACTCAAT 58.679 45.455 0.00 0.00 0.00 2.57
2444 2524 3.803340 AGTTTCCCTCCTGAAGTATGGA 58.197 45.455 0.00 0.00 0.00 3.41
2712 2792 7.848223 AAAAGATGTGAGTTTTCTTTTTGGG 57.152 32.000 4.51 0.00 43.55 4.12
3059 3140 3.806949 AAAACTGTTATGCTCCCTCCA 57.193 42.857 0.00 0.00 0.00 3.86
3141 3222 2.559785 CCTCTTGGGTGTCACATGC 58.440 57.895 5.12 0.00 0.00 4.06
3179 5903 6.843752 TGTCCTCCTACCAAAACTTAAATGA 58.156 36.000 0.00 0.00 0.00 2.57
3413 6138 2.543777 ATGGGGTATCGAATGGAACG 57.456 50.000 0.00 0.00 0.00 3.95
3563 6290 2.110578 TGCTAGCCTAGTCAATCAGCA 58.889 47.619 13.29 0.00 35.33 4.41
3572 6299 2.661718 GAGGAGAAGTGCTAGCCTAGT 58.338 52.381 13.29 0.00 0.00 2.57
3586 6313 2.929301 ACATTAGTTTGGGGGAGGAGA 58.071 47.619 0.00 0.00 0.00 3.71
3657 6384 1.453928 GGGGACAGCATAGCCAACC 60.454 63.158 0.00 0.00 0.00 3.77
3903 6630 6.127647 ACAAATGAATAGCCACACCATTACAG 60.128 38.462 0.00 0.00 0.00 2.74
3905 6632 6.207691 ACAAATGAATAGCCACACCATTAC 57.792 37.500 0.00 0.00 0.00 1.89
3976 6710 0.392863 TTGTGACATGGATCAGGGCG 60.393 55.000 0.00 0.00 0.00 6.13
4006 6740 1.667236 TACTGCGCAATGGAAGGATG 58.333 50.000 13.05 0.00 0.00 3.51
4070 6804 6.403636 GGTTGTGACTATTGCTATTGGACAAG 60.404 42.308 8.62 0.00 0.00 3.16
4133 6869 9.847224 TTCTAGGAAATTTATCTGGTATGTTCC 57.153 33.333 0.00 0.00 34.71 3.62
4138 6874 9.813826 CCCATTTCTAGGAAATTTATCTGGTAT 57.186 33.333 3.15 0.00 0.00 2.73
4139 6875 9.009675 TCCCATTTCTAGGAAATTTATCTGGTA 57.990 33.333 3.15 0.00 0.00 3.25
4140 6876 7.882755 TCCCATTTCTAGGAAATTTATCTGGT 58.117 34.615 3.15 0.00 0.00 4.00
4240 7035 4.096231 TGTTGGTGTTTGACTGATGTTCTG 59.904 41.667 0.00 0.00 0.00 3.02
4267 7888 7.611467 AGCTGTTCTTGATGTGGAATTATGTTA 59.389 33.333 0.00 0.00 0.00 2.41
4268 7889 6.435277 AGCTGTTCTTGATGTGGAATTATGTT 59.565 34.615 0.00 0.00 0.00 2.71
4269 7890 5.948162 AGCTGTTCTTGATGTGGAATTATGT 59.052 36.000 0.00 0.00 0.00 2.29
4270 7891 6.263344 CAGCTGTTCTTGATGTGGAATTATG 58.737 40.000 5.25 0.00 0.00 1.90
4271 7892 5.359009 CCAGCTGTTCTTGATGTGGAATTAT 59.641 40.000 13.81 0.00 0.00 1.28
4538 8162 7.724305 TTGGTATTAGTGTCTTTCTGTGTTC 57.276 36.000 0.00 0.00 0.00 3.18
4709 8333 3.323115 TCTGAAGACTGTCAAGCTCACAT 59.677 43.478 10.88 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.