Multiple sequence alignment - TraesCS7B01G312600

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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 TraesCS7B01G312600 chr7B 100.000 4514 0 0 1 4514 558366994 558362481 0.000000e+00 8336.0
1 TraesCS7B01G312600 chr7B 85.580 1595 165 21 1843 3381 558642069 558640484 0.000000e+00 1611.0
2 TraesCS7B01G312600 chr7B 84.927 1579 176 23 1769 3297 556687498 556689064 0.000000e+00 1541.0
3 TraesCS7B01G312600 chr7B 80.342 1460 245 26 1881 3307 558324491 558323041 0.000000e+00 1068.0
4 TraesCS7B01G312600 chr7B 85.294 510 51 14 1236 1724 558642699 558642193 5.210000e-139 505.0
5 TraesCS7B01G312600 chr7D 91.495 1752 122 15 1874 3609 523277254 523275514 0.000000e+00 2385.0
6 TraesCS7B01G312600 chr7D 86.259 1601 159 23 1818 3366 523437321 523438912 0.000000e+00 1681.0
7 TraesCS7B01G312600 chr7D 84.028 1584 189 22 1766 3293 522872681 522874256 0.000000e+00 1465.0
8 TraesCS7B01G312600 chr7D 96.134 595 23 0 2705 3299 523486879 523487473 0.000000e+00 972.0
9 TraesCS7B01G312600 chr7D 91.766 668 49 4 3848 4512 41796280 41795616 0.000000e+00 924.0
10 TraesCS7B01G312600 chr7D 84.072 835 115 3 2491 3307 523269155 523268321 0.000000e+00 789.0
11 TraesCS7B01G312600 chr7D 84.409 821 78 21 3726 4512 518616173 518615369 0.000000e+00 761.0
12 TraesCS7B01G312600 chr7D 86.735 588 43 14 933 1494 523485584 523486162 4.960000e-174 621.0
13 TraesCS7B01G312600 chr7D 79.873 785 115 28 3 766 523484525 523485287 6.650000e-148 534.0
14 TraesCS7B01G312600 chr7D 87.534 369 36 6 1874 2236 523486512 523486876 6.980000e-113 418.0
15 TraesCS7B01G312600 chr7D 83.512 467 40 10 863 1300 523280074 523279616 7.030000e-108 401.0
16 TraesCS7B01G312600 chr7D 94.574 258 14 0 1490 1747 523436921 523437178 2.530000e-107 399.0
17 TraesCS7B01G312600 chr7D 85.638 376 27 13 847 1201 523278227 523277858 1.980000e-98 370.0
18 TraesCS7B01G312600 chr7D 95.175 228 11 0 1494 1721 523277549 523277322 1.190000e-95 361.0
19 TraesCS7B01G312600 chr7D 94.667 225 12 0 1494 1718 523486216 523486440 2.580000e-92 350.0
20 TraesCS7B01G312600 chr7D 83.146 356 49 7 3 354 523279311 523278963 9.430000e-82 315.0
21 TraesCS7B01G312600 chr7D 89.610 231 17 5 1270 1494 523277832 523277603 2.050000e-73 287.0
22 TraesCS7B01G312600 chr7D 74.521 522 81 32 366 846 523278778 523278268 3.590000e-41 180.0
23 TraesCS7B01G312600 chr7A 89.976 1636 123 22 1840 3453 603945303 603943687 0.000000e+00 2074.0
24 TraesCS7B01G312600 chr7A 85.515 1650 168 36 1771 3353 603960432 603958787 0.000000e+00 1657.0
25 TraesCS7B01G312600 chr7A 86.988 830 86 12 2488 3297 603025373 603026200 0.000000e+00 915.0
26 TraesCS7B01G312600 chr7A 81.050 971 145 20 1493 2444 603024254 603025204 0.000000e+00 737.0
27 TraesCS7B01G312600 chr7A 83.866 719 73 20 1068 1747 603961208 603960494 0.000000e+00 645.0
28 TraesCS7B01G312600 chr7A 80.718 529 62 24 129 632 603948432 603947919 4.260000e-100 375.0
29 TraesCS7B01G312600 chr7A 93.013 229 16 0 1494 1722 603945557 603945329 7.240000e-88 335.0
30 TraesCS7B01G312600 chr7A 86.972 284 23 7 1224 1494 603945894 603945612 1.580000e-79 307.0
31 TraesCS7B01G312600 chr7A 88.550 131 11 2 3 133 603948830 603948704 6.050000e-34 156.0
32 TraesCS7B01G312600 chr7A 88.550 131 11 2 3 133 603949086 603948960 6.050000e-34 156.0
33 TraesCS7B01G312600 chr7A 88.550 131 11 2 3 133 603949342 603949216 6.050000e-34 156.0
34 TraesCS7B01G312600 chr6D 91.667 660 46 6 3860 4514 435532519 435533174 0.000000e+00 905.0
35 TraesCS7B01G312600 chr3A 91.018 668 54 4 3848 4512 624183372 624184036 0.000000e+00 896.0
36 TraesCS7B01G312600 chr3A 90.120 668 59 4 3848 4512 746409271 746409934 0.000000e+00 861.0
37 TraesCS7B01G312600 chr3A 90.015 661 51 9 3858 4514 702409250 702408601 0.000000e+00 841.0
38 TraesCS7B01G312600 chr3A 84.455 817 82 16 3720 4513 691302363 691301569 0.000000e+00 763.0
39 TraesCS7B01G312600 chr3A 83.449 574 76 14 3949 4513 577079803 577079240 2.410000e-142 516.0
40 TraesCS7B01G312600 chr3A 90.769 65 6 0 3539 3603 41987606 41987670 2.240000e-13 87.9
41 TraesCS7B01G312600 chr3A 89.706 68 5 2 3536 3603 545208811 545208746 8.050000e-13 86.1
42 TraesCS7B01G312600 chr3A 91.379 58 5 0 3545 3602 647473060 647473003 3.740000e-11 80.5
43 TraesCS7B01G312600 chr1A 91.018 668 53 5 3848 4512 535340781 535341444 0.000000e+00 894.0
44 TraesCS7B01G312600 chr5B 84.982 819 79 22 3715 4514 463233659 463234452 0.000000e+00 791.0
45 TraesCS7B01G312600 chr4D 84.083 823 80 22 3726 4513 473867161 473867967 0.000000e+00 747.0
46 TraesCS7B01G312600 chr4D 90.000 60 5 1 3544 3603 400168882 400168824 4.840000e-10 76.8
47 TraesCS7B01G312600 chr5D 94.000 450 25 2 3848 4295 406986533 406986982 0.000000e+00 680.0
48 TraesCS7B01G312600 chr1D 89.231 260 26 2 4191 4448 391141363 391141104 1.570000e-84 324.0
49 TraesCS7B01G312600 chr4A 95.161 62 3 0 3615 3676 539303886 539303825 1.030000e-16 99.0
50 TraesCS7B01G312600 chrUn 96.429 56 2 0 3620 3675 18147822 18147767 4.810000e-15 93.5
51 TraesCS7B01G312600 chr3B 93.333 60 3 1 3544 3603 737461272 737461330 2.240000e-13 87.9
52 TraesCS7B01G312600 chr3B 93.220 59 3 1 3545 3603 737496522 737496579 8.050000e-13 86.1
53 TraesCS7B01G312600 chr4B 75.263 190 41 5 1985 2171 483698563 483698749 8.050000e-13 86.1
54 TraesCS7B01G312600 chr6B 91.667 60 4 1 3544 3603 456947359 456947417 1.040000e-11 82.4
55 TraesCS7B01G312600 chr2B 92.982 57 3 1 3545 3601 34041370 34041315 1.040000e-11 82.4


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 TraesCS7B01G312600 chr7B 558362481 558366994 4513 True 8336.000000 8336 100.000000 1 4514 1 chr7B.!!$R2 4513
1 TraesCS7B01G312600 chr7B 556687498 556689064 1566 False 1541.000000 1541 84.927000 1769 3297 1 chr7B.!!$F1 1528
2 TraesCS7B01G312600 chr7B 558323041 558324491 1450 True 1068.000000 1068 80.342000 1881 3307 1 chr7B.!!$R1 1426
3 TraesCS7B01G312600 chr7B 558640484 558642699 2215 True 1058.000000 1611 85.437000 1236 3381 2 chr7B.!!$R3 2145
4 TraesCS7B01G312600 chr7D 522872681 522874256 1575 False 1465.000000 1465 84.028000 1766 3293 1 chr7D.!!$F1 1527
5 TraesCS7B01G312600 chr7D 523436921 523438912 1991 False 1040.000000 1681 90.416500 1490 3366 2 chr7D.!!$F2 1876
6 TraesCS7B01G312600 chr7D 41795616 41796280 664 True 924.000000 924 91.766000 3848 4512 1 chr7D.!!$R1 664
7 TraesCS7B01G312600 chr7D 523268321 523269155 834 True 789.000000 789 84.072000 2491 3307 1 chr7D.!!$R3 816
8 TraesCS7B01G312600 chr7D 518615369 518616173 804 True 761.000000 761 84.409000 3726 4512 1 chr7D.!!$R2 786
9 TraesCS7B01G312600 chr7D 523275514 523280074 4560 True 614.142857 2385 86.156714 3 3609 7 chr7D.!!$R4 3606
10 TraesCS7B01G312600 chr7D 523484525 523487473 2948 False 579.000000 972 88.988600 3 3299 5 chr7D.!!$F3 3296
11 TraesCS7B01G312600 chr7A 603958787 603961208 2421 True 1151.000000 1657 84.690500 1068 3353 2 chr7A.!!$R2 2285
12 TraesCS7B01G312600 chr7A 603024254 603026200 1946 False 826.000000 915 84.019000 1493 3297 2 chr7A.!!$F1 1804
13 TraesCS7B01G312600 chr7A 603943687 603949342 5655 True 508.428571 2074 88.047000 3 3453 7 chr7A.!!$R1 3450
14 TraesCS7B01G312600 chr6D 435532519 435533174 655 False 905.000000 905 91.667000 3860 4514 1 chr6D.!!$F1 654
15 TraesCS7B01G312600 chr3A 624183372 624184036 664 False 896.000000 896 91.018000 3848 4512 1 chr3A.!!$F2 664
16 TraesCS7B01G312600 chr3A 746409271 746409934 663 False 861.000000 861 90.120000 3848 4512 1 chr3A.!!$F3 664
17 TraesCS7B01G312600 chr3A 702408601 702409250 649 True 841.000000 841 90.015000 3858 4514 1 chr3A.!!$R5 656
18 TraesCS7B01G312600 chr3A 691301569 691302363 794 True 763.000000 763 84.455000 3720 4513 1 chr3A.!!$R4 793
19 TraesCS7B01G312600 chr3A 577079240 577079803 563 True 516.000000 516 83.449000 3949 4513 1 chr3A.!!$R2 564
20 TraesCS7B01G312600 chr1A 535340781 535341444 663 False 894.000000 894 91.018000 3848 4512 1 chr1A.!!$F1 664
21 TraesCS7B01G312600 chr5B 463233659 463234452 793 False 791.000000 791 84.982000 3715 4514 1 chr5B.!!$F1 799
22 TraesCS7B01G312600 chr4D 473867161 473867967 806 False 747.000000 747 84.083000 3726 4513 1 chr4D.!!$F1 787

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
364 1851 0.250513 AATCACCTCCTTCGTCCTGC 59.749 55.0 0.00 0.0 0.0 4.85 F
1680 4780 0.040058 TCCTACTGCGGAAGGTACCA 59.960 55.0 15.94 0.0 34.3 3.25 F
1991 5221 0.675083 TCGTCTTGTTTGTCGGCCTA 59.325 50.0 0.00 0.0 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 5199 0.041576 GCCGACAAACAAGACGAACC 60.042 55.0 0.0 0.0 0.00 3.62 R
3479 6873 0.179054 GGCTTAACATCGACTCCCCC 60.179 60.0 0.0 0.0 0.00 5.40 R
3704 7099 0.037326 TGCCTGTGTGTAGCTGTAGC 60.037 55.0 0.0 0.0 42.49 3.58 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
34 1048 6.439487 TCTCTTCTATCCTCTCTCCATTGTT 58.561 40.000 0.00 0.00 0.00 2.83
39 1053 6.882656 TCTATCCTCTCTCCATTGTTCAAAG 58.117 40.000 0.00 0.00 0.00 2.77
43 1057 4.006319 CTCTCTCCATTGTTCAAAGGACC 58.994 47.826 5.55 0.00 0.00 4.46
120 1137 4.822350 TGTCCGTTTTGATGAATGGTGTTA 59.178 37.500 0.00 0.00 37.07 2.41
197 1490 0.250553 ATCGTTTTCTTCCCCGCACA 60.251 50.000 0.00 0.00 0.00 4.57
239 1536 2.325761 AGCGTATGTCGTGAACAACTC 58.674 47.619 0.00 0.00 42.37 3.01
249 1546 5.047306 TGTCGTGAACAACTCCAATAGATCT 60.047 40.000 0.00 0.00 34.03 2.75
252 1549 4.268884 GTGAACAACTCCAATAGATCTCGC 59.731 45.833 0.00 0.00 0.00 5.03
256 1553 4.343526 ACAACTCCAATAGATCTCGCATCT 59.656 41.667 0.00 2.68 0.00 2.90
259 1556 4.832266 ACTCCAATAGATCTCGCATCTCTT 59.168 41.667 0.00 0.00 0.00 2.85
271 1581 6.431278 TCTCGCATCTCTTAAAGAACTATCG 58.569 40.000 0.00 0.00 37.61 2.92
354 1668 4.223032 ACGGGATCATGTATAATCACCTCC 59.777 45.833 0.00 0.00 0.00 4.30
356 1670 5.046304 CGGGATCATGTATAATCACCTCCTT 60.046 44.000 0.00 0.00 0.00 3.36
364 1851 0.250513 AATCACCTCCTTCGTCCTGC 59.749 55.000 0.00 0.00 0.00 4.85
381 1870 3.751175 TCCTGCAAGTTTACGGAAAGATG 59.249 43.478 0.00 0.00 0.00 2.90
391 1880 1.075970 GGAAAGATGGCCCTTCCCC 60.076 63.158 0.00 0.00 0.00 4.81
437 1928 4.083643 CGCTTGAAAGTTCATGATGAGTGT 60.084 41.667 10.26 0.00 37.00 3.55
440 1931 3.433274 TGAAAGTTCATGATGAGTGTCGC 59.567 43.478 0.00 0.00 31.01 5.19
442 1933 1.067565 AGTTCATGATGAGTGTCGCGT 60.068 47.619 5.77 0.00 0.00 6.01
476 1967 2.202650 GTCGCCTAACGCCGCTTA 60.203 61.111 0.00 0.00 43.23 3.09
480 1971 2.228914 GCCTAACGCCGCTTAGTCG 61.229 63.158 8.08 0.00 0.00 4.18
483 1974 0.455633 CTAACGCCGCTTAGTCGTGT 60.456 55.000 0.00 0.00 36.49 4.49
488 1979 3.238241 CGCTTAGTCGTGTCGCCG 61.238 66.667 0.00 0.00 0.00 6.46
489 1980 2.177531 GCTTAGTCGTGTCGCCGA 59.822 61.111 0.00 0.00 33.79 5.54
495 1986 2.356433 TCGTGTCGCCGATTTGCA 60.356 55.556 0.00 0.00 30.63 4.08
496 1987 1.956678 TCGTGTCGCCGATTTGCAA 60.957 52.632 0.00 0.00 30.63 4.08
510 2543 2.594592 GCAACCGCACCTCCACTT 60.595 61.111 0.00 0.00 38.36 3.16
514 2547 3.322466 CCGCACCTCCACTTCCCT 61.322 66.667 0.00 0.00 0.00 4.20
525 2558 1.148273 ACTTCCCTGCTTTGTCGCA 59.852 52.632 0.00 0.00 38.40 5.10
536 2569 1.134367 CTTTGTCGCATCGTCCCTCTA 59.866 52.381 0.00 0.00 0.00 2.43
540 2579 2.027751 GCATCGTCCCTCTACCGC 59.972 66.667 0.00 0.00 0.00 5.68
591 2630 4.479993 GCCTCCCATGCTGCGTCT 62.480 66.667 0.00 0.00 0.00 4.18
745 2833 2.174107 CGCACCATGCAGTTCACG 59.826 61.111 1.20 0.00 45.36 4.35
747 2835 1.965930 GCACCATGCAGTTCACGGA 60.966 57.895 0.00 0.00 44.26 4.69
762 2850 1.807981 CGGACACACACACACACGT 60.808 57.895 0.00 0.00 0.00 4.49
763 2851 1.748647 CGGACACACACACACACGTC 61.749 60.000 0.00 0.00 0.00 4.34
764 2852 0.459585 GGACACACACACACACGTCT 60.460 55.000 0.00 0.00 0.00 4.18
846 2988 7.997107 AAACAAATTTTACGGAAAGAGGTTC 57.003 32.000 0.00 0.00 35.28 3.62
849 2991 5.700722 AATTTTACGGAAAGAGGTTCACC 57.299 39.130 0.00 0.00 38.06 4.02
887 3068 1.312815 ACAGGAGCTGTTGAAGTTGC 58.687 50.000 0.00 0.00 42.59 4.17
889 3070 3.067494 ACAGGAGCTGTTGAAGTTGCTC 61.067 50.000 0.00 5.38 42.59 4.26
894 3075 2.035961 AGCTGTTGAAGTTGCTCGTCTA 59.964 45.455 0.00 0.00 0.00 2.59
900 3081 1.989165 GAAGTTGCTCGTCTAGTGCTG 59.011 52.381 0.00 0.00 39.85 4.41
961 3950 8.498054 TCTTTAATCTTTCCTGCATAAGAGTG 57.502 34.615 13.31 2.10 34.17 3.51
962 3951 6.683974 TTAATCTTTCCTGCATAAGAGTGC 57.316 37.500 13.31 0.00 45.25 4.40
1000 3990 1.487976 TGTCCCATTGGAGATGCTCTC 59.512 52.381 3.62 5.01 42.85 3.20
1005 3995 0.392336 ATTGGAGATGCTCTCGGCTC 59.608 55.000 6.97 0.00 44.28 4.70
1013 4004 5.509840 GGAGATGCTCTCGGCTCTTTAATTA 60.510 44.000 6.97 0.00 44.28 1.40
1014 4005 6.107901 AGATGCTCTCGGCTCTTTAATTAT 57.892 37.500 0.00 0.00 42.39 1.28
1015 4006 7.233389 AGATGCTCTCGGCTCTTTAATTATA 57.767 36.000 0.00 0.00 42.39 0.98
1016 4007 7.319646 AGATGCTCTCGGCTCTTTAATTATAG 58.680 38.462 0.00 0.00 42.39 1.31
1023 4014 8.958506 TCTCGGCTCTTTAATTATAGATAGACC 58.041 37.037 6.15 5.62 0.00 3.85
1038 4029 1.076332 AGACCGCGGAAATTTTCTCG 58.924 50.000 35.90 1.74 0.00 4.04
1050 4041 2.679355 TTTTCTCGATGCCAACAACG 57.321 45.000 0.00 0.00 42.84 4.10
1056 4047 1.602323 GATGCCAACAACGTGGGGA 60.602 57.895 0.00 0.00 39.26 4.81
1057 4048 1.586154 GATGCCAACAACGTGGGGAG 61.586 60.000 0.00 0.00 39.26 4.30
1058 4049 2.983592 GCCAACAACGTGGGGAGG 60.984 66.667 0.00 0.00 39.26 4.30
1206 4232 1.153939 CTCTGCCTCCTTCGTCGTG 60.154 63.158 0.00 0.00 0.00 4.35
1223 4255 7.502177 TCGTCGTGATTATTTTCTCTACAAC 57.498 36.000 0.00 0.00 0.00 3.32
1224 4256 7.310664 TCGTCGTGATTATTTTCTCTACAACT 58.689 34.615 0.00 0.00 0.00 3.16
1225 4257 7.484007 TCGTCGTGATTATTTTCTCTACAACTC 59.516 37.037 0.00 0.00 0.00 3.01
1226 4258 7.253684 CGTCGTGATTATTTTCTCTACAACTCC 60.254 40.741 0.00 0.00 0.00 3.85
1280 4313 0.413037 TTCAACCCCTGGCATGGATT 59.587 50.000 10.70 0.00 0.00 3.01
1429 4462 5.730568 GCCGCTCAGTTCTTGGTAATTTATG 60.731 44.000 0.00 0.00 0.00 1.90
1448 4485 0.507358 GTCGCGTTCACCTGTTCTTC 59.493 55.000 5.77 0.00 0.00 2.87
1452 4495 1.719780 GCGTTCACCTGTTCTTCGTAG 59.280 52.381 0.00 0.00 0.00 3.51
1480 4523 8.984891 AAATTCTTTGCGTGATGATTAATTCA 57.015 26.923 0.00 0.00 39.12 2.57
1481 4524 8.984891 AATTCTTTGCGTGATGATTAATTCAA 57.015 26.923 0.00 0.00 38.03 2.69
1482 4525 8.624701 ATTCTTTGCGTGATGATTAATTCAAG 57.375 30.769 0.00 0.00 38.03 3.02
1483 4526 7.144722 TCTTTGCGTGATGATTAATTCAAGT 57.855 32.000 5.39 0.00 38.03 3.16
1484 4527 7.592938 TCTTTGCGTGATGATTAATTCAAGTT 58.407 30.769 5.39 0.00 38.03 2.66
1487 4530 9.684448 TTTGCGTGATGATTAATTCAAGTTTTA 57.316 25.926 5.39 0.00 38.03 1.52
1488 4531 9.684448 TTGCGTGATGATTAATTCAAGTTTTAA 57.316 25.926 5.39 0.00 38.03 1.52
1527 4627 1.376037 GCTACTGCCTGGCGTTCTT 60.376 57.895 14.98 0.00 0.00 2.52
1539 4639 1.424493 GCGTTCTTCGGCATCTCCTG 61.424 60.000 0.00 0.00 40.26 3.86
1680 4780 0.040058 TCCTACTGCGGAAGGTACCA 59.960 55.000 15.94 0.00 34.30 3.25
1742 4842 1.739338 CTTGATCCTCCTCCCGACCG 61.739 65.000 0.00 0.00 0.00 4.79
1819 5020 2.180086 TCTACATCCTGCCTGGTCCTAT 59.820 50.000 0.00 0.00 37.07 2.57
1824 5025 2.492025 TCCTGCCTGGTCCTATTTGAT 58.508 47.619 0.00 0.00 37.07 2.57
1866 5076 4.098416 GCAAGATCGTTAGAATTTGGTGC 58.902 43.478 0.00 0.00 0.00 5.01
1872 5082 2.668279 CGTTAGAATTTGGTGCCTGTGC 60.668 50.000 0.00 0.00 38.26 4.57
1958 5183 1.183030 TCACCTCGTCGGACATGGTT 61.183 55.000 16.25 3.60 36.31 3.67
1969 5199 1.677820 GGACATGGTTACGGTTCAGGG 60.678 57.143 0.00 0.00 0.00 4.45
1983 5213 1.961793 TCAGGGGTTCGTCTTGTTTG 58.038 50.000 0.00 0.00 0.00 2.93
1991 5221 0.675083 TCGTCTTGTTTGTCGGCCTA 59.325 50.000 0.00 0.00 0.00 3.93
2071 5301 2.099831 GTTCGACGACGGCGATCT 59.900 61.111 28.54 0.00 41.64 2.75
2449 5689 5.344884 GTCAGTTACTACAATCCTCTGAGC 58.655 45.833 0.00 0.00 32.41 4.26
2484 5845 5.701290 GTGCTTGGTTACAACTAGACTGATT 59.299 40.000 0.00 0.00 32.14 2.57
2505 5870 4.994907 TTGATATGCTGCTTGCTTGATT 57.005 36.364 0.00 0.00 43.37 2.57
2523 5888 5.344743 TGATTAGATTCTTCGACAAGGCT 57.655 39.130 0.00 0.00 0.00 4.58
2830 6195 3.578515 GACCGGGCTTTCGTTCCGA 62.579 63.158 6.32 0.00 45.96 4.55
3009 6392 4.063967 CAGTACGCGCTGGTGGGA 62.064 66.667 5.73 0.00 33.11 4.37
3243 6626 1.474677 CGCTTCTTCTGGATGATGGCT 60.475 52.381 0.00 0.00 0.00 4.75
3256 6639 1.133513 TGATGGCTGGACTTGGTTGTT 60.134 47.619 0.00 0.00 0.00 2.83
3307 6690 3.519510 CAGGAGGTACAAATCCAGGAAGA 59.480 47.826 12.08 0.00 38.12 2.87
3385 6770 2.679342 GGTGCATGGTGCCCCTAGA 61.679 63.158 0.00 0.00 44.23 2.43
3389 6781 1.849692 TGCATGGTGCCCCTAGATAAA 59.150 47.619 0.00 0.00 44.23 1.40
3407 6799 3.482722 AAAGCACGATTCATCAGCAAG 57.517 42.857 0.00 0.00 32.06 4.01
3411 6803 2.674852 GCACGATTCATCAGCAAGAGAA 59.325 45.455 0.00 0.00 0.00 2.87
3413 6805 4.201891 GCACGATTCATCAGCAAGAGAAAT 60.202 41.667 0.00 0.00 0.00 2.17
3414 6806 5.263948 CACGATTCATCAGCAAGAGAAATG 58.736 41.667 0.00 0.00 0.00 2.32
3415 6807 4.334759 ACGATTCATCAGCAAGAGAAATGG 59.665 41.667 0.00 0.00 0.00 3.16
3416 6808 4.334759 CGATTCATCAGCAAGAGAAATGGT 59.665 41.667 0.00 0.00 0.00 3.55
3438 6832 7.857456 TGGTCCTAAAAAGATCAGCAATAGTA 58.143 34.615 0.00 0.00 0.00 1.82
3477 6871 1.102978 ACTGGGTTCACTTGTGTTGC 58.897 50.000 0.46 0.00 0.00 4.17
3479 6873 1.358759 GGGTTCACTTGTGTTGCGG 59.641 57.895 0.46 0.00 0.00 5.69
3482 6876 1.826054 TTCACTTGTGTTGCGGGGG 60.826 57.895 0.46 0.00 0.00 5.40
3500 6894 0.539986 GGGAGTCGATGTTAAGCCCA 59.460 55.000 0.00 0.00 34.25 5.36
3516 6910 4.423625 AGCCCAGCTAAAAGTCGATAAT 57.576 40.909 0.00 0.00 36.99 1.28
3520 6914 7.097834 AGCCCAGCTAAAAGTCGATAATATAC 58.902 38.462 0.00 0.00 36.99 1.47
3574 6969 8.785329 TTGAATAAAGGGTGAATTTTATTGGC 57.215 30.769 6.87 0.00 38.75 4.52
3592 6987 5.680594 TTGGCTTAAAATGGAGCATCAAT 57.319 34.783 0.00 0.00 40.63 2.57
3594 6989 6.395426 TGGCTTAAAATGGAGCATCAATAG 57.605 37.500 0.00 0.00 40.63 1.73
3595 6990 6.128486 TGGCTTAAAATGGAGCATCAATAGA 58.872 36.000 0.00 0.00 40.63 1.98
3629 7024 7.707774 AAACATGGAAAATGTTTAGAAACGG 57.292 32.000 13.29 0.00 46.63 4.44
3630 7025 5.227152 ACATGGAAAATGTTTAGAAACGGC 58.773 37.500 0.00 0.00 41.74 5.68
3631 7026 3.891324 TGGAAAATGTTTAGAAACGGCG 58.109 40.909 4.80 4.80 41.74 6.46
3632 7027 3.239254 GGAAAATGTTTAGAAACGGCGG 58.761 45.455 13.24 0.00 41.74 6.13
3633 7028 3.058085 GGAAAATGTTTAGAAACGGCGGA 60.058 43.478 13.24 0.00 41.74 5.54
3634 7029 3.547649 AAATGTTTAGAAACGGCGGAC 57.452 42.857 13.24 1.57 41.74 4.79
3635 7030 1.445871 ATGTTTAGAAACGGCGGACC 58.554 50.000 13.24 0.00 41.74 4.46
3648 7043 4.668118 GGACCGGCCGAACGTTCA 62.668 66.667 30.73 0.00 0.00 3.18
3649 7044 3.110178 GACCGGCCGAACGTTCAG 61.110 66.667 30.73 17.60 0.00 3.02
3655 7050 3.110178 CCGAACGTTCAGCCGGTC 61.110 66.667 26.71 0.00 41.09 4.79
3656 7051 2.355363 CGAACGTTCAGCCGGTCA 60.355 61.111 26.71 0.00 44.67 4.02
3657 7052 2.654912 CGAACGTTCAGCCGGTCAC 61.655 63.158 26.71 0.00 44.67 3.67
3658 7053 1.593209 GAACGTTCAGCCGGTCACA 60.593 57.895 23.12 0.00 43.89 3.58
3659 7054 1.828331 GAACGTTCAGCCGGTCACAC 61.828 60.000 23.12 0.00 43.89 3.82
3660 7055 3.041940 CGTTCAGCCGGTCACACC 61.042 66.667 1.90 0.00 34.05 4.16
3669 7064 2.430921 GGTCACACCGCTCACTCG 60.431 66.667 0.00 0.00 0.00 4.18
3670 7065 3.106407 GTCACACCGCTCACTCGC 61.106 66.667 0.00 0.00 0.00 5.03
3671 7066 4.357947 TCACACCGCTCACTCGCC 62.358 66.667 0.00 0.00 0.00 5.54
3672 7067 4.363990 CACACCGCTCACTCGCCT 62.364 66.667 0.00 0.00 0.00 5.52
3673 7068 2.675423 ACACCGCTCACTCGCCTA 60.675 61.111 0.00 0.00 0.00 3.93
3674 7069 2.103143 CACCGCTCACTCGCCTAG 59.897 66.667 0.00 0.00 0.00 3.02
3675 7070 3.827898 ACCGCTCACTCGCCTAGC 61.828 66.667 0.00 0.00 0.00 3.42
3692 7087 3.641492 CGCAGCTACACACAAGCA 58.359 55.556 0.00 0.00 42.62 3.91
3693 7088 1.205064 CGCAGCTACACACAAGCAC 59.795 57.895 0.00 0.00 42.62 4.40
3694 7089 1.224069 CGCAGCTACACACAAGCACT 61.224 55.000 0.00 0.00 42.62 4.40
3695 7090 1.795768 GCAGCTACACACAAGCACTA 58.204 50.000 0.00 0.00 42.62 2.74
3696 7091 2.143122 GCAGCTACACACAAGCACTAA 58.857 47.619 0.00 0.00 42.62 2.24
3697 7092 2.548057 GCAGCTACACACAAGCACTAAA 59.452 45.455 0.00 0.00 42.62 1.85
3698 7093 3.607078 GCAGCTACACACAAGCACTAAAC 60.607 47.826 0.00 0.00 42.62 2.01
3699 7094 2.800544 AGCTACACACAAGCACTAAACG 59.199 45.455 0.00 0.00 42.62 3.60
3700 7095 2.661979 GCTACACACAAGCACTAAACGC 60.662 50.000 0.00 0.00 39.83 4.84
3701 7096 0.303493 ACACACAAGCACTAAACGCG 59.697 50.000 3.53 3.53 0.00 6.01
3702 7097 0.303493 CACACAAGCACTAAACGCGT 59.697 50.000 5.58 5.58 0.00 6.01
3703 7098 0.303493 ACACAAGCACTAAACGCGTG 59.697 50.000 14.98 2.11 43.36 5.34
3704 7099 0.384230 CACAAGCACTAAACGCGTGG 60.384 55.000 14.98 9.19 42.24 4.94
3705 7100 1.440353 CAAGCACTAAACGCGTGGC 60.440 57.895 14.98 12.24 35.55 5.01
3706 7101 1.597027 AAGCACTAAACGCGTGGCT 60.597 52.632 14.98 14.47 33.10 4.75
3707 7102 0.320073 AAGCACTAAACGCGTGGCTA 60.320 50.000 14.98 3.98 33.10 3.93
3708 7103 1.012486 AGCACTAAACGCGTGGCTAC 61.012 55.000 14.98 0.73 33.10 3.58
3709 7104 1.286354 GCACTAAACGCGTGGCTACA 61.286 55.000 14.98 0.00 33.10 2.74
3710 7105 0.713883 CACTAAACGCGTGGCTACAG 59.286 55.000 14.98 6.49 0.00 2.74
3711 7106 1.012486 ACTAAACGCGTGGCTACAGC 61.012 55.000 14.98 4.04 41.14 4.40
3712 7107 0.736325 CTAAACGCGTGGCTACAGCT 60.736 55.000 14.98 0.00 41.70 4.24
3713 7108 0.527113 TAAACGCGTGGCTACAGCTA 59.473 50.000 14.98 0.00 41.70 3.32
3724 7119 1.406069 GCTACAGCTACACACAGGCAT 60.406 52.381 0.00 0.00 38.21 4.40
3790 7194 4.747108 CGTCTTCTTATCCATTCGATGCTT 59.253 41.667 0.00 0.00 31.92 3.91
3808 7212 6.620877 ATGCTTATCCGTATTCCTATCCAA 57.379 37.500 0.00 0.00 0.00 3.53
3973 7394 4.697756 CTTGTCCGCCTCCGCCAA 62.698 66.667 0.00 0.00 0.00 4.52
4252 7687 1.616374 TGTGTGCTACAAGGTCGATGA 59.384 47.619 0.00 0.00 36.06 2.92
4255 7690 2.299013 TGTGCTACAAGGTCGATGACTT 59.701 45.455 0.00 0.00 32.47 3.01
4300 7735 1.527034 GAAGAGTGCTGCATCCAACA 58.473 50.000 5.27 0.00 0.00 3.33
4345 7782 1.898094 TGCACGTTGGAGCTGCAAT 60.898 52.632 24.13 6.05 37.97 3.56
4346 7783 1.286880 GCACGTTGGAGCTGCAATT 59.713 52.632 24.13 11.35 0.00 2.32
4356 7793 0.329261 AGCTGCAATTGGCTACTGGA 59.671 50.000 7.72 0.00 45.15 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 1030 6.054295 CCTTTGAACAATGGAGAGAGGATAG 58.946 44.000 12.22 0.00 37.70 2.08
17 1031 5.726308 TCCTTTGAACAATGGAGAGAGGATA 59.274 40.000 15.08 0.00 39.01 2.59
18 1032 4.537688 TCCTTTGAACAATGGAGAGAGGAT 59.462 41.667 15.08 0.00 39.01 3.24
19 1033 3.909995 TCCTTTGAACAATGGAGAGAGGA 59.090 43.478 15.08 7.61 39.01 3.71
20 1034 4.006319 GTCCTTTGAACAATGGAGAGAGG 58.994 47.826 18.14 7.39 42.84 3.69
34 1048 9.002600 CATATTCATCAAATATCGGTCCTTTGA 57.997 33.333 8.32 8.32 38.28 2.69
39 1053 7.362056 CCAACCATATTCATCAAATATCGGTCC 60.362 40.741 9.95 0.00 38.91 4.46
43 1057 7.236474 CGTCCAACCATATTCATCAAATATCG 58.764 38.462 0.00 0.00 38.28 2.92
120 1137 5.148651 ACGGAAAGTATTAGAGCAACACT 57.851 39.130 0.00 0.00 0.00 3.55
239 1536 7.374272 TCTTTAAGAGATGCGAGATCTATTGG 58.626 38.462 12.50 5.71 32.58 3.16
271 1581 4.409718 TTTGCCCCAACTTTCCTTAAAC 57.590 40.909 0.00 0.00 0.00 2.01
298 1609 1.648504 GTTTACGGAATCGGTGGAGG 58.351 55.000 3.60 0.00 41.39 4.30
299 1610 1.648504 GGTTTACGGAATCGGTGGAG 58.351 55.000 3.60 0.00 41.39 3.86
300 1611 0.249955 GGGTTTACGGAATCGGTGGA 59.750 55.000 3.60 0.00 41.39 4.02
302 1613 1.066716 TCTGGGTTTACGGAATCGGTG 60.067 52.381 3.60 0.00 41.39 4.94
303 1614 1.269012 TCTGGGTTTACGGAATCGGT 58.731 50.000 0.00 0.00 41.39 4.69
305 1616 4.752661 TTTTTCTGGGTTTACGGAATCG 57.247 40.909 0.00 0.00 43.02 3.34
306 1617 9.726232 GTAATATTTTTCTGGGTTTACGGAATC 57.274 33.333 0.00 0.00 35.78 2.52
307 1618 8.400186 CGTAATATTTTTCTGGGTTTACGGAAT 58.600 33.333 0.00 0.00 37.71 3.01
354 1668 1.459592 CCGTAAACTTGCAGGACGAAG 59.540 52.381 1.40 0.00 35.59 3.79
356 1670 0.675083 TCCGTAAACTTGCAGGACGA 59.325 50.000 1.40 0.00 35.59 4.20
364 1851 2.163613 GGGCCATCTTTCCGTAAACTTG 59.836 50.000 4.39 0.00 0.00 3.16
381 1870 3.497332 GTCAAATTATAGGGGAAGGGCC 58.503 50.000 0.00 0.00 0.00 5.80
391 1880 6.510638 GCGGTCTTTTACCCGTCAAATTATAG 60.511 42.308 0.00 0.00 46.62 1.31
466 1957 1.731969 GACACGACTAAGCGGCGTT 60.732 57.895 9.37 0.00 35.90 4.84
470 1961 2.879462 GGCGACACGACTAAGCGG 60.879 66.667 0.00 0.00 35.12 5.52
474 1965 1.342555 CAAATCGGCGACACGACTAA 58.657 50.000 13.76 0.00 46.64 2.24
476 1967 2.380410 GCAAATCGGCGACACGACT 61.380 57.895 13.76 0.00 46.64 4.18
480 1971 4.130857 GTTGCAAATCGGCGACAC 57.869 55.556 13.76 2.12 45.59 3.67
495 1986 2.430367 GGAAGTGGAGGTGCGGTT 59.570 61.111 0.00 0.00 0.00 4.44
496 1987 3.637273 GGGAAGTGGAGGTGCGGT 61.637 66.667 0.00 0.00 0.00 5.68
501 1992 0.111253 CAAAGCAGGGAAGTGGAGGT 59.889 55.000 0.00 0.00 0.00 3.85
507 2540 1.148273 TGCGACAAAGCAGGGAAGT 59.852 52.632 0.00 0.00 42.92 3.01
525 2558 2.905880 CGGCGGTAGAGGGACGAT 60.906 66.667 0.00 0.00 0.00 3.73
612 2651 4.814294 GGTACTGCGGCCGTCCTG 62.814 72.222 28.70 16.93 0.00 3.86
745 2833 0.459585 AGACGTGTGTGTGTGTGTCC 60.460 55.000 0.00 0.00 0.00 4.02
747 2835 0.245266 TGAGACGTGTGTGTGTGTGT 59.755 50.000 0.00 0.00 0.00 3.72
762 2850 0.107703 GGACCCGCATGTCATTGAGA 60.108 55.000 5.13 0.00 36.97 3.27
763 2851 0.107508 AGGACCCGCATGTCATTGAG 60.108 55.000 5.13 0.00 36.97 3.02
764 2852 1.134521 GTAGGACCCGCATGTCATTGA 60.135 52.381 5.13 0.00 36.97 2.57
820 2962 9.518906 GAACCTCTTTCCGTAAAATTTGTTTTA 57.481 29.630 0.00 0.00 0.00 1.52
827 2969 5.382616 AGGTGAACCTCTTTCCGTAAAATT 58.617 37.500 0.00 0.00 44.77 1.82
887 3068 2.645730 AGCTTTCAGCACTAGACGAG 57.354 50.000 0.00 0.00 45.56 4.18
889 3070 2.480416 CCCTAGCTTTCAGCACTAGACG 60.480 54.545 0.00 0.00 45.56 4.18
894 3075 1.078848 CGCCCTAGCTTTCAGCACT 60.079 57.895 0.00 0.00 45.56 4.40
900 3081 6.706716 AGAAAATATCTAACGCCCTAGCTTTC 59.293 38.462 0.00 0.00 36.32 2.62
937 3624 7.192232 GCACTCTTATGCAGGAAAGATTAAAG 58.808 38.462 8.80 1.87 45.39 1.85
951 3638 2.726066 GCGTTTGTCTGCACTCTTATGC 60.726 50.000 0.00 0.00 46.32 3.14
961 3950 0.598065 AATGGGAAGCGTTTGTCTGC 59.402 50.000 0.00 0.00 0.00 4.26
962 3951 1.608590 ACAATGGGAAGCGTTTGTCTG 59.391 47.619 0.00 0.00 0.00 3.51
1000 3990 6.472808 GCGGTCTATCTATAATTAAAGAGCCG 59.527 42.308 0.00 0.00 34.13 5.52
1005 3995 8.752766 TTTCCGCGGTCTATCTATAATTAAAG 57.247 34.615 27.15 0.00 0.00 1.85
1013 4004 5.855045 AGAAAATTTCCGCGGTCTATCTAT 58.145 37.500 27.15 5.90 0.00 1.98
1014 4005 5.272283 AGAAAATTTCCGCGGTCTATCTA 57.728 39.130 27.15 0.00 0.00 1.98
1015 4006 4.120589 GAGAAAATTTCCGCGGTCTATCT 58.879 43.478 27.15 20.57 0.00 1.98
1016 4007 3.060473 CGAGAAAATTTCCGCGGTCTATC 60.060 47.826 27.15 16.35 0.00 2.08
1023 4014 1.456732 GCATCGAGAAAATTTCCGCG 58.543 50.000 0.00 0.00 0.00 6.46
1038 4029 1.586154 CTCCCCACGTTGTTGGCATC 61.586 60.000 0.00 0.00 35.00 3.91
1223 4255 4.566426 AGGGAGAAAGAACATGAAGGAG 57.434 45.455 0.00 0.00 0.00 3.69
1224 4256 5.316987 GAAAGGGAGAAAGAACATGAAGGA 58.683 41.667 0.00 0.00 0.00 3.36
1225 4257 4.154918 CGAAAGGGAGAAAGAACATGAAGG 59.845 45.833 0.00 0.00 0.00 3.46
1226 4258 4.378874 GCGAAAGGGAGAAAGAACATGAAG 60.379 45.833 0.00 0.00 0.00 3.02
1232 4264 1.807142 CAGGCGAAAGGGAGAAAGAAC 59.193 52.381 0.00 0.00 0.00 3.01
1280 4313 6.153067 CCACCAAAATTAACAGCGAAACATA 58.847 36.000 0.00 0.00 0.00 2.29
1373 4406 1.338105 CCACCTGTGCGATTCTTCAGA 60.338 52.381 0.00 0.00 0.00 3.27
1376 4409 1.667724 CATCCACCTGTGCGATTCTTC 59.332 52.381 0.00 0.00 0.00 2.87
1418 4451 3.371591 GGTGAACGCGACATAAATTACCA 59.628 43.478 15.93 0.00 0.00 3.25
1429 4462 0.507358 GAAGAACAGGTGAACGCGAC 59.493 55.000 15.93 7.16 0.00 5.19
1448 4485 6.530567 TCATCACGCAAAGAATTTTACTACG 58.469 36.000 0.00 0.00 35.03 3.51
1476 4519 7.574967 CGGTACCTGCAAGATTAAAACTTGAAT 60.575 37.037 21.68 7.22 44.92 2.57
1478 4521 5.180492 CGGTACCTGCAAGATTAAAACTTGA 59.820 40.000 21.68 10.99 44.92 3.02
1479 4522 5.180492 TCGGTACCTGCAAGATTAAAACTTG 59.820 40.000 10.90 16.37 44.92 3.16
1480 4523 5.310451 TCGGTACCTGCAAGATTAAAACTT 58.690 37.500 10.90 0.00 34.07 2.66
1481 4524 4.901868 TCGGTACCTGCAAGATTAAAACT 58.098 39.130 10.90 0.00 34.07 2.66
1482 4525 4.694037 ACTCGGTACCTGCAAGATTAAAAC 59.306 41.667 10.90 0.00 34.07 2.43
1483 4526 4.901868 ACTCGGTACCTGCAAGATTAAAA 58.098 39.130 10.90 0.00 34.07 1.52
1484 4527 4.546829 ACTCGGTACCTGCAAGATTAAA 57.453 40.909 10.90 0.00 34.07 1.52
1487 4530 2.567615 AGAACTCGGTACCTGCAAGATT 59.432 45.455 10.90 0.00 34.07 2.40
1488 4531 2.093973 CAGAACTCGGTACCTGCAAGAT 60.094 50.000 10.90 0.00 34.07 2.40
1491 4591 3.906660 CAGAACTCGGTACCTGCAA 57.093 52.632 10.90 0.00 0.00 4.08
1539 4639 0.731855 GAGGTACGTGACGAGGTTGC 60.732 60.000 13.70 0.00 0.00 4.17
1680 4780 0.178068 GCAGGATACGACCATGGTGT 59.822 55.000 25.52 21.65 46.39 4.16
1693 4793 1.227380 GACGCCGATGAAGCAGGAT 60.227 57.895 0.00 0.00 0.00 3.24
1742 4842 9.298774 CAGGATGAAAAATTCTTAATTGAGAGC 57.701 33.333 0.00 0.00 39.69 4.09
1866 5076 1.368579 CCTGCCCAAAAAGCACAGG 59.631 57.895 0.00 0.00 41.78 4.00
1872 5082 1.376295 GCATGCCCTGCCCAAAAAG 60.376 57.895 6.36 0.00 45.66 2.27
1950 5175 1.677820 CCCCTGAACCGTAACCATGTC 60.678 57.143 0.00 0.00 0.00 3.06
1958 5183 0.540365 AGACGAACCCCTGAACCGTA 60.540 55.000 0.00 0.00 33.32 4.02
1969 5199 0.041576 GCCGACAAACAAGACGAACC 60.042 55.000 0.00 0.00 0.00 3.62
1983 5213 2.076863 GGCAATCATGTATAGGCCGAC 58.923 52.381 0.00 0.00 30.94 4.79
1991 5221 4.285003 CCCAATCCAATGGCAATCATGTAT 59.715 41.667 0.00 0.00 39.26 2.29
2406 5642 0.738762 CGGAGATCAGTGGTGTGCTG 60.739 60.000 0.00 0.00 35.43 4.41
2449 5689 2.100631 CCAAGCACGCGGAGGTAAG 61.101 63.158 12.47 4.86 0.00 2.34
2505 5870 2.418746 GGCAGCCTTGTCGAAGAATCTA 60.419 50.000 3.29 0.00 39.69 1.98
2607 5972 1.996798 TCTTGAACTCCTCGACCTGT 58.003 50.000 0.00 0.00 0.00 4.00
2931 6296 4.194720 AGGCGCGCCGTCTCTAAG 62.195 66.667 41.70 0.00 37.12 2.18
3009 6392 4.008933 GTGAGCACCTCGCCCACT 62.009 66.667 0.00 0.00 45.38 4.00
3096 6479 3.606662 GCTATCGCGAGGAGCCCA 61.607 66.667 27.09 0.00 44.76 5.36
3213 6596 1.122019 AGAAGAAGCGGTCCAGGTGT 61.122 55.000 0.00 0.00 0.00 4.16
3222 6605 1.590932 CCATCATCCAGAAGAAGCGG 58.409 55.000 0.00 0.00 0.00 5.52
3243 6626 4.531854 TCAGATTCAAACAACCAAGTCCA 58.468 39.130 0.00 0.00 0.00 4.02
3256 6639 1.818060 CCCAAACGCCATCAGATTCAA 59.182 47.619 0.00 0.00 0.00 2.69
3329 6712 3.691342 TTCTCGGCCCACGGTGAG 61.691 66.667 10.28 0.00 44.45 3.51
3375 6760 1.138266 TCGTGCTTTATCTAGGGGCAC 59.862 52.381 0.00 0.00 46.41 5.01
3381 6766 5.693555 TGCTGATGAATCGTGCTTTATCTAG 59.306 40.000 8.74 0.00 32.60 2.43
3382 6767 5.600696 TGCTGATGAATCGTGCTTTATCTA 58.399 37.500 8.74 0.00 32.60 1.98
3385 6770 4.877823 TCTTGCTGATGAATCGTGCTTTAT 59.122 37.500 8.74 0.00 32.60 1.40
3389 6781 2.093816 TCTCTTGCTGATGAATCGTGCT 60.094 45.455 8.74 0.00 32.60 4.40
3407 6799 6.375455 TGCTGATCTTTTTAGGACCATTTCTC 59.625 38.462 0.00 0.00 0.00 2.87
3411 6803 7.836183 ACTATTGCTGATCTTTTTAGGACCATT 59.164 33.333 0.00 0.00 0.00 3.16
3413 6805 6.721318 ACTATTGCTGATCTTTTTAGGACCA 58.279 36.000 0.00 0.00 0.00 4.02
3414 6806 8.732746 TTACTATTGCTGATCTTTTTAGGACC 57.267 34.615 0.00 0.00 0.00 4.46
3415 6807 9.989869 GTTTACTATTGCTGATCTTTTTAGGAC 57.010 33.333 0.00 0.00 0.00 3.85
3416 6808 9.174166 GGTTTACTATTGCTGATCTTTTTAGGA 57.826 33.333 0.00 0.00 0.00 2.94
3438 6832 5.894807 CAGTTCACATTCTTGAAGTGGTTT 58.105 37.500 11.32 0.00 46.60 3.27
3479 6873 0.179054 GGCTTAACATCGACTCCCCC 60.179 60.000 0.00 0.00 0.00 5.40
3482 6876 1.941325 CTGGGCTTAACATCGACTCC 58.059 55.000 0.00 0.00 0.00 3.85
3484 6878 0.905357 AGCTGGGCTTAACATCGACT 59.095 50.000 0.00 0.00 33.89 4.18
3494 6888 2.789409 ATCGACTTTTAGCTGGGCTT 57.211 45.000 0.00 0.00 40.44 4.35
3496 6890 6.872020 TGTATATTATCGACTTTTAGCTGGGC 59.128 38.462 0.00 0.00 0.00 5.36
3516 6910 8.791327 TGAGTTGAGCAAAAATCTCATGTATA 57.209 30.769 0.00 0.00 39.96 1.47
3520 6914 7.884816 AAATGAGTTGAGCAAAAATCTCATG 57.115 32.000 12.10 0.00 40.79 3.07
3573 6968 9.617975 GTATTCTATTGATGCTCCATTTTAAGC 57.382 33.333 0.00 0.00 39.02 3.09
3609 7004 4.481463 CGCCGTTTCTAAACATTTTCCAT 58.519 39.130 6.41 0.00 38.81 3.41
3610 7005 3.304794 CCGCCGTTTCTAAACATTTTCCA 60.305 43.478 6.41 0.00 38.81 3.53
3611 7006 3.058085 TCCGCCGTTTCTAAACATTTTCC 60.058 43.478 6.41 0.00 38.81 3.13
3612 7007 3.910170 GTCCGCCGTTTCTAAACATTTTC 59.090 43.478 6.41 0.00 38.81 2.29
3613 7008 3.304861 GGTCCGCCGTTTCTAAACATTTT 60.305 43.478 6.41 0.00 38.81 1.82
3614 7009 2.227149 GGTCCGCCGTTTCTAAACATTT 59.773 45.455 6.41 0.00 38.81 2.32
3615 7010 1.808343 GGTCCGCCGTTTCTAAACATT 59.192 47.619 6.41 0.00 38.81 2.71
3616 7011 1.445871 GGTCCGCCGTTTCTAAACAT 58.554 50.000 6.41 0.00 38.81 2.71
3617 7012 2.917172 GGTCCGCCGTTTCTAAACA 58.083 52.632 6.41 0.00 38.81 2.83
3631 7026 4.668118 TGAACGTTCGGCCGGTCC 62.668 66.667 27.83 12.43 43.82 4.46
3632 7027 3.110178 CTGAACGTTCGGCCGGTC 61.110 66.667 27.83 17.35 44.68 4.79
3638 7033 3.110178 GACCGGCTGAACGTTCGG 61.110 66.667 28.97 28.97 46.95 4.30
3639 7034 2.355363 TGACCGGCTGAACGTTCG 60.355 61.111 22.48 17.48 0.00 3.95
3640 7035 1.593209 TGTGACCGGCTGAACGTTC 60.593 57.895 21.42 21.42 0.00 3.95
3641 7036 1.885850 GTGTGACCGGCTGAACGTT 60.886 57.895 0.00 0.00 0.00 3.99
3642 7037 2.279918 GTGTGACCGGCTGAACGT 60.280 61.111 0.00 0.00 0.00 3.99
3643 7038 3.041940 GGTGTGACCGGCTGAACG 61.042 66.667 0.00 0.00 0.00 3.95
3652 7047 2.430921 CGAGTGAGCGGTGTGACC 60.431 66.667 0.00 0.00 34.05 4.02
3653 7048 3.106407 GCGAGTGAGCGGTGTGAC 61.106 66.667 0.00 0.00 0.00 3.67
3654 7049 4.357947 GGCGAGTGAGCGGTGTGA 62.358 66.667 0.00 0.00 38.18 3.58
3655 7050 2.874010 CTAGGCGAGTGAGCGGTGTG 62.874 65.000 0.00 0.00 38.18 3.82
3656 7051 2.675423 TAGGCGAGTGAGCGGTGT 60.675 61.111 0.00 0.00 38.18 4.16
3657 7052 2.103143 CTAGGCGAGTGAGCGGTG 59.897 66.667 0.00 0.00 38.18 4.94
3658 7053 3.827898 GCTAGGCGAGTGAGCGGT 61.828 66.667 0.00 0.00 38.18 5.68
3669 7064 2.167861 GTGTGTAGCTGCGCTAGGC 61.168 63.158 16.48 10.76 42.11 3.93
3670 7065 0.389817 TTGTGTGTAGCTGCGCTAGG 60.390 55.000 16.48 0.00 42.11 3.02
3671 7066 0.994995 CTTGTGTGTAGCTGCGCTAG 59.005 55.000 16.48 5.66 42.11 3.42
3672 7067 1.014044 GCTTGTGTGTAGCTGCGCTA 61.014 55.000 16.48 6.23 40.44 4.26
3673 7068 2.320587 GCTTGTGTGTAGCTGCGCT 61.321 57.895 16.48 8.09 43.41 5.92
3674 7069 2.174349 GCTTGTGTGTAGCTGCGC 59.826 61.111 8.58 8.58 35.74 6.09
3675 7070 1.205064 GTGCTTGTGTGTAGCTGCG 59.795 57.895 0.00 0.00 39.38 5.18
3676 7071 1.795768 TAGTGCTTGTGTGTAGCTGC 58.204 50.000 0.00 0.00 39.38 5.25
3677 7072 3.362986 CGTTTAGTGCTTGTGTGTAGCTG 60.363 47.826 0.00 0.00 39.38 4.24
3678 7073 2.800544 CGTTTAGTGCTTGTGTGTAGCT 59.199 45.455 0.00 0.00 39.38 3.32
3679 7074 2.661979 GCGTTTAGTGCTTGTGTGTAGC 60.662 50.000 0.00 0.00 39.10 3.58
3680 7075 2.409752 CGCGTTTAGTGCTTGTGTGTAG 60.410 50.000 0.00 0.00 0.00 2.74
3681 7076 1.523515 CGCGTTTAGTGCTTGTGTGTA 59.476 47.619 0.00 0.00 0.00 2.90
3682 7077 0.303493 CGCGTTTAGTGCTTGTGTGT 59.697 50.000 0.00 0.00 0.00 3.72
3683 7078 0.303493 ACGCGTTTAGTGCTTGTGTG 59.697 50.000 5.58 0.00 0.00 3.82
3684 7079 0.303493 CACGCGTTTAGTGCTTGTGT 59.697 50.000 10.22 0.00 32.52 3.72
3685 7080 0.384230 CCACGCGTTTAGTGCTTGTG 60.384 55.000 10.22 0.00 38.22 3.33
3686 7081 1.938861 CCACGCGTTTAGTGCTTGT 59.061 52.632 10.22 0.00 38.22 3.16
3687 7082 1.440353 GCCACGCGTTTAGTGCTTG 60.440 57.895 10.22 0.00 38.22 4.01
3688 7083 0.320073 TAGCCACGCGTTTAGTGCTT 60.320 50.000 10.22 1.00 38.22 3.91
3689 7084 1.012486 GTAGCCACGCGTTTAGTGCT 61.012 55.000 10.22 15.09 38.22 4.40
3690 7085 1.286354 TGTAGCCACGCGTTTAGTGC 61.286 55.000 10.22 7.74 38.22 4.40
3691 7086 0.713883 CTGTAGCCACGCGTTTAGTG 59.286 55.000 10.22 0.00 39.19 2.74
3692 7087 1.012486 GCTGTAGCCACGCGTTTAGT 61.012 55.000 10.22 0.00 34.31 2.24
3693 7088 0.736325 AGCTGTAGCCACGCGTTTAG 60.736 55.000 10.22 1.93 43.38 1.85
3694 7089 0.527113 TAGCTGTAGCCACGCGTTTA 59.473 50.000 10.22 0.00 43.38 2.01
3695 7090 1.012486 GTAGCTGTAGCCACGCGTTT 61.012 55.000 10.22 0.00 43.38 3.60
3696 7091 1.445582 GTAGCTGTAGCCACGCGTT 60.446 57.895 10.22 0.00 43.38 4.84
3697 7092 2.181021 GTAGCTGTAGCCACGCGT 59.819 61.111 5.58 5.58 43.38 6.01
3698 7093 2.158959 GTGTAGCTGTAGCCACGCG 61.159 63.158 3.53 3.53 43.38 6.01
3699 7094 1.080093 TGTGTAGCTGTAGCCACGC 60.080 57.895 8.68 8.68 42.12 5.34
3700 7095 0.038618 TGTGTGTAGCTGTAGCCACG 60.039 55.000 0.00 0.00 43.38 4.94
3701 7096 1.673033 CCTGTGTGTAGCTGTAGCCAC 60.673 57.143 0.00 3.55 43.38 5.01
3702 7097 0.608130 CCTGTGTGTAGCTGTAGCCA 59.392 55.000 0.00 0.00 43.38 4.75
3703 7098 0.741221 GCCTGTGTGTAGCTGTAGCC 60.741 60.000 0.00 0.00 43.38 3.93
3704 7099 0.037326 TGCCTGTGTGTAGCTGTAGC 60.037 55.000 0.00 0.00 42.49 3.58
3705 7100 2.680312 ATGCCTGTGTGTAGCTGTAG 57.320 50.000 0.00 0.00 0.00 2.74
3706 7101 4.545208 TTAATGCCTGTGTGTAGCTGTA 57.455 40.909 0.00 0.00 0.00 2.74
3707 7102 3.417069 TTAATGCCTGTGTGTAGCTGT 57.583 42.857 0.00 0.00 0.00 4.40
3708 7103 3.424829 CGTTTAATGCCTGTGTGTAGCTG 60.425 47.826 0.00 0.00 0.00 4.24
3709 7104 2.742053 CGTTTAATGCCTGTGTGTAGCT 59.258 45.455 0.00 0.00 0.00 3.32
3710 7105 2.727916 GCGTTTAATGCCTGTGTGTAGC 60.728 50.000 0.00 0.00 0.00 3.58
3711 7106 2.473868 CGCGTTTAATGCCTGTGTGTAG 60.474 50.000 0.00 0.00 0.00 2.74
3712 7107 1.461512 CGCGTTTAATGCCTGTGTGTA 59.538 47.619 0.00 0.00 0.00 2.90
3713 7108 0.237235 CGCGTTTAATGCCTGTGTGT 59.763 50.000 0.00 0.00 0.00 3.72
3714 7109 0.237235 ACGCGTTTAATGCCTGTGTG 59.763 50.000 5.58 0.00 0.00 3.82
3715 7110 0.237235 CACGCGTTTAATGCCTGTGT 59.763 50.000 10.22 0.00 0.00 3.72
3716 7111 0.454285 CCACGCGTTTAATGCCTGTG 60.454 55.000 10.22 6.85 0.00 3.66
3717 7112 1.873165 CCACGCGTTTAATGCCTGT 59.127 52.632 10.22 0.00 0.00 4.00
3718 7113 1.514014 GCCACGCGTTTAATGCCTG 60.514 57.895 10.22 2.61 0.00 4.85
3724 7119 1.649815 CCAACAGCCACGCGTTTAA 59.350 52.632 10.22 0.00 0.00 1.52
3766 7164 4.051922 GCATCGAATGGATAAGAAGACGT 58.948 43.478 0.00 0.00 32.85 4.34
3790 7194 3.765511 CCGGTTGGATAGGAATACGGATA 59.234 47.826 0.00 0.00 42.42 2.59
3889 7304 2.944557 CGCGTCGTCGATCCACAG 60.945 66.667 6.17 0.00 39.71 3.66
3945 7361 2.338984 GGACAAGGCGACGAGTGT 59.661 61.111 0.00 0.00 0.00 3.55
4123 7548 4.864704 TGAAAGGGGTTGTAGCAAAATC 57.135 40.909 0.00 0.00 0.00 2.17
4233 7668 1.993370 GTCATCGACCTTGTAGCACAC 59.007 52.381 0.00 0.00 0.00 3.82
4252 7687 1.192146 TGTAGCTTCCTCCGGCAAGT 61.192 55.000 0.00 0.00 0.00 3.16
4255 7690 1.686325 GGATGTAGCTTCCTCCGGCA 61.686 60.000 0.00 0.00 0.00 5.69
4300 7735 2.882876 CTCCCGACATCGAACGGT 59.117 61.111 21.13 7.67 46.53 4.83
4334 7771 0.329261 AGTAGCCAATTGCAGCTCCA 59.671 50.000 11.83 0.00 44.83 3.86
4345 7782 1.903877 GCAGCTCCTCCAGTAGCCAA 61.904 60.000 0.00 0.00 39.64 4.52
4346 7783 2.362369 GCAGCTCCTCCAGTAGCCA 61.362 63.158 0.00 0.00 39.64 4.75
4356 7793 1.994507 CTCCCCTCTTGCAGCTCCT 60.995 63.158 0.00 0.00 0.00 3.69
4467 7908 1.599071 CTCTGCAGTCGTTGAAGCAAA 59.401 47.619 14.67 0.00 36.44 3.68
4468 7909 1.220529 CTCTGCAGTCGTTGAAGCAA 58.779 50.000 14.67 0.00 36.44 3.91
4480 7921 1.740297 AGCATTTGAGAGCTCTGCAG 58.260 50.000 23.91 7.63 36.00 4.41


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

AutoCloner maintained by Alex Coulton.