Multiple sequence alignment - TraesCS5B01G299800

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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 TraesCS5B01G299800 chr5B 100.000 3586 0 0 1 3586 484646009 484642424 0.000000e+00 6623.0
1 TraesCS5B01G299800 chr5B 90.945 1005 57 15 1699 2686 485427483 485428470 0.000000e+00 1321.0
2 TraesCS5B01G299800 chr5B 97.696 738 17 0 971 1708 485426281 485427018 0.000000e+00 1269.0
3 TraesCS5B01G299800 chr5B 90.179 112 9 2 890 999 485426153 485426264 1.040000e-30 145.0
4 TraesCS5B01G299800 chr5A 95.068 2271 81 21 852 3101 510883554 510885814 0.000000e+00 3544.0
5 TraesCS5B01G299800 chr5A 95.005 1081 52 2 895 1973 510015745 510014665 0.000000e+00 1696.0
6 TraesCS5B01G299800 chr5A 91.538 650 47 6 2044 2686 510013550 510012902 0.000000e+00 889.0
7 TraesCS5B01G299800 chr5A 84.600 487 52 20 1 476 510881976 510882450 2.520000e-126 462.0
8 TraesCS5B01G299800 chr5A 86.713 429 30 14 3085 3510 510885828 510886232 5.460000e-123 451.0
9 TraesCS5B01G299800 chr5A 94.828 58 1 2 1966 2022 510013604 510013548 4.930000e-14 89.8
10 TraesCS5B01G299800 chr5D 96.229 2042 64 10 971 3007 403155631 403153598 0.000000e+00 3332.0
11 TraesCS5B01G299800 chr5D 94.593 1757 64 18 852 2588 404188271 404190016 0.000000e+00 2689.0
12 TraesCS5B01G299800 chr5D 92.308 182 12 2 623 803 404188092 404188272 1.280000e-64 257.0
13 TraesCS5B01G299800 chr5D 87.000 200 24 2 3008 3206 403153479 403153281 1.300000e-54 224.0
14 TraesCS5B01G299800 chr5D 82.500 280 23 8 3227 3505 403144254 403144000 4.660000e-54 222.0
15 TraesCS5B01G299800 chr1D 92.284 972 73 2 999 1969 220420140 220421110 0.000000e+00 1378.0
16 TraesCS5B01G299800 chr1D 87.661 543 46 11 2065 2586 220421178 220421720 2.370000e-171 612.0
17 TraesCS5B01G299800 chr1B 91.367 973 80 4 999 1969 315390942 315389972 0.000000e+00 1328.0
18 TraesCS5B01G299800 chr1B 87.432 549 48 11 2065 2592 315389901 315389353 2.370000e-171 612.0
19 TraesCS5B01G299800 chr2D 90.539 983 82 4 988 1969 336653636 336654608 0.000000e+00 1290.0
20 TraesCS5B01G299800 chr2D 91.837 98 8 0 2482 2579 336668094 336668191 1.740000e-28 137.0
21 TraesCS5B01G299800 chr2A 89.908 981 77 9 988 1967 446997993 446998952 0.000000e+00 1243.0
22 TraesCS5B01G299800 chr2A 86.813 546 49 13 2065 2588 446999067 446999611 3.990000e-164 588.0
23 TraesCS5B01G299800 chr3B 85.132 982 131 9 999 1968 811505824 811504846 0.000000e+00 990.0
24 TraesCS5B01G299800 chr1A 87.661 543 47 10 2064 2588 284321584 284322124 6.580000e-172 614.0


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 TraesCS5B01G299800 chr5B 484642424 484646009 3585 True 6623.000000 6623 100.000000 1 3586 1 chr5B.!!$R1 3585
1 TraesCS5B01G299800 chr5B 485426153 485428470 2317 False 911.666667 1321 92.940000 890 2686 3 chr5B.!!$F1 1796
2 TraesCS5B01G299800 chr5A 510881976 510886232 4256 False 1485.666667 3544 88.793667 1 3510 3 chr5A.!!$F1 3509
3 TraesCS5B01G299800 chr5A 510012902 510015745 2843 True 891.600000 1696 93.790333 895 2686 3 chr5A.!!$R1 1791
4 TraesCS5B01G299800 chr5D 403153281 403155631 2350 True 1778.000000 3332 91.614500 971 3206 2 chr5D.!!$R2 2235
5 TraesCS5B01G299800 chr5D 404188092 404190016 1924 False 1473.000000 2689 93.450500 623 2588 2 chr5D.!!$F1 1965
6 TraesCS5B01G299800 chr1D 220420140 220421720 1580 False 995.000000 1378 89.972500 999 2586 2 chr1D.!!$F1 1587
7 TraesCS5B01G299800 chr1B 315389353 315390942 1589 True 970.000000 1328 89.399500 999 2592 2 chr1B.!!$R1 1593
8 TraesCS5B01G299800 chr2D 336653636 336654608 972 False 1290.000000 1290 90.539000 988 1969 1 chr2D.!!$F1 981
9 TraesCS5B01G299800 chr2A 446997993 446999611 1618 False 915.500000 1243 88.360500 988 2588 2 chr2A.!!$F1 1600
10 TraesCS5B01G299800 chr3B 811504846 811505824 978 True 990.000000 990 85.132000 999 1968 1 chr3B.!!$R1 969
11 TraesCS5B01G299800 chr1A 284321584 284322124 540 False 614.000000 614 87.661000 2064 2588 1 chr1A.!!$F1 524

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
807 1656 0.033504 ATTCGTGCGTCCAACTGACT 59.966 50.0 0.00 0.0 42.13 3.41 F
1536 2460 0.252103 ACTTCTCCTACCTCGGCCAA 60.252 55.0 2.24 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2474 5052 0.322456 GCATCTTGTACACCCCAGCA 60.322 55.0 0.0 0.0 0.0 4.41 R
3127 5865 0.104487 TGCTCGACGTGTAAACCCAA 59.896 50.0 0.0 0.0 0.0 4.12 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
31 33 6.947258 CCAGTTTTCTATTTGGCTTTGTTTG 58.053 36.000 0.00 0.00 0.00 2.93
32 34 6.538381 CCAGTTTTCTATTTGGCTTTGTTTGT 59.462 34.615 0.00 0.00 0.00 2.83
33 35 7.065683 CCAGTTTTCTATTTGGCTTTGTTTGTT 59.934 33.333 0.00 0.00 0.00 2.83
34 36 9.092876 CAGTTTTCTATTTGGCTTTGTTTGTTA 57.907 29.630 0.00 0.00 0.00 2.41
35 37 9.830975 AGTTTTCTATTTGGCTTTGTTTGTTAT 57.169 25.926 0.00 0.00 0.00 1.89
130 135 9.236691 TCAAATTCTTGAACTTCTTCAAATTCG 57.763 29.630 0.00 0.00 44.18 3.34
131 136 7.629027 AATTCTTGAACTTCTTCAAATTCGC 57.371 32.000 0.00 0.00 44.18 4.70
132 137 6.377327 TTCTTGAACTTCTTCAAATTCGCT 57.623 33.333 0.00 0.00 44.18 4.93
133 138 7.490962 TTCTTGAACTTCTTCAAATTCGCTA 57.509 32.000 0.00 0.00 44.18 4.26
151 156 9.853555 AATTCGCTAACATTTGTGAATTCATTA 57.146 25.926 12.12 4.26 43.98 1.90
153 158 9.502145 TTCGCTAACATTTGTGAATTCATTATC 57.498 29.630 12.12 0.00 29.93 1.75
322 333 1.806542 TGAGCACTTTCTCAAATCCGC 59.193 47.619 0.00 0.00 39.89 5.54
332 343 8.164153 CACTTTCTCAAATCCGCAAATATTTTG 58.836 33.333 0.00 0.00 0.00 2.44
333 344 6.645700 TTCTCAAATCCGCAAATATTTTGC 57.354 33.333 13.54 13.54 41.71 3.68
340 351 3.862267 TCCGCAAATATTTTGCAAATCCG 59.138 39.130 20.97 0.00 45.14 4.18
344 355 5.164012 CGCAAATATTTTGCAAATCCGTGAA 60.164 36.000 20.97 0.00 45.14 3.18
345 356 6.014898 GCAAATATTTTGCAAATCCGTGAAC 58.985 36.000 13.65 0.00 44.34 3.18
496 507 8.050325 TCAATAGAATAAAAAGGACCATCCGAA 58.950 33.333 0.00 0.00 42.75 4.30
497 508 8.682710 CAATAGAATAAAAAGGACCATCCGAAA 58.317 33.333 0.00 0.00 42.75 3.46
498 509 8.996651 ATAGAATAAAAAGGACCATCCGAAAT 57.003 30.769 0.00 0.00 42.75 2.17
500 511 8.134202 AGAATAAAAAGGACCATCCGAAATTT 57.866 30.769 0.00 0.00 42.75 1.82
501 512 8.593679 AGAATAAAAAGGACCATCCGAAATTTT 58.406 29.630 0.00 8.01 42.75 1.82
502 513 9.863845 GAATAAAAAGGACCATCCGAAATTTTA 57.136 29.630 0.00 10.48 42.75 1.52
505 516 8.966069 AAAAAGGACCATCCGAAATTTTAAAA 57.034 26.923 2.51 2.51 42.75 1.52
527 538 3.850122 AAAACAGCCGATTTTCCTAGC 57.150 42.857 0.00 0.00 0.00 3.42
528 539 2.489938 AACAGCCGATTTTCCTAGCA 57.510 45.000 0.00 0.00 0.00 3.49
529 540 2.489938 ACAGCCGATTTTCCTAGCAA 57.510 45.000 0.00 0.00 0.00 3.91
530 541 2.790433 ACAGCCGATTTTCCTAGCAAA 58.210 42.857 0.00 0.00 0.00 3.68
531 542 3.153919 ACAGCCGATTTTCCTAGCAAAA 58.846 40.909 0.00 0.00 0.00 2.44
540 551 2.218953 TCCTAGCAAAATCGGTAGCG 57.781 50.000 8.29 8.29 35.98 4.26
541 552 1.752498 TCCTAGCAAAATCGGTAGCGA 59.248 47.619 20.51 20.51 35.98 4.93
542 553 2.166870 TCCTAGCAAAATCGGTAGCGAA 59.833 45.455 22.11 5.00 35.98 4.70
543 554 2.284417 CCTAGCAAAATCGGTAGCGAAC 59.716 50.000 22.11 8.61 35.98 3.95
545 556 1.732259 AGCAAAATCGGTAGCGAACAG 59.268 47.619 22.11 12.31 0.00 3.16
546 557 1.202031 GCAAAATCGGTAGCGAACAGG 60.202 52.381 22.11 12.34 0.00 4.00
547 558 1.084289 AAAATCGGTAGCGAACAGGC 58.916 50.000 22.11 0.00 0.00 4.85
548 559 1.082117 AAATCGGTAGCGAACAGGCG 61.082 55.000 22.11 0.00 38.18 5.52
556 567 2.095843 CGAACAGGCGCGTTAAGC 59.904 61.111 8.43 0.00 43.95 3.09
567 578 3.851620 CGTTAAGCGCCGTATAGGA 57.148 52.632 2.29 0.00 45.00 2.94
568 579 1.682982 CGTTAAGCGCCGTATAGGAG 58.317 55.000 2.29 0.00 45.00 3.69
569 580 1.665161 CGTTAAGCGCCGTATAGGAGG 60.665 57.143 2.29 0.00 45.00 4.30
570 581 1.610522 GTTAAGCGCCGTATAGGAGGA 59.389 52.381 2.29 0.00 45.00 3.71
572 583 1.179814 AAGCGCCGTATAGGAGGAGG 61.180 60.000 2.29 0.00 45.00 4.30
573 584 1.902432 GCGCCGTATAGGAGGAGGT 60.902 63.158 0.00 0.00 45.00 3.85
575 586 0.250814 CGCCGTATAGGAGGAGGTCT 60.251 60.000 0.00 0.00 45.00 3.85
576 587 1.536940 GCCGTATAGGAGGAGGTCTC 58.463 60.000 0.00 0.00 45.00 3.36
585 596 4.709690 GGAGGTCTCCCTACCAGG 57.290 66.667 5.73 0.00 42.86 4.45
586 597 1.762858 GGAGGTCTCCCTACCAGGC 60.763 68.421 5.73 0.00 42.86 4.85
589 600 3.075005 GTCTCCCTACCAGGCGCA 61.075 66.667 10.83 0.00 32.73 6.09
590 601 2.041922 TCTCCCTACCAGGCGCAT 60.042 61.111 10.83 0.00 32.73 4.73
594 605 1.378514 CCCTACCAGGCGCATTGTT 60.379 57.895 10.83 0.00 32.73 2.83
595 606 0.107410 CCCTACCAGGCGCATTGTTA 60.107 55.000 10.83 0.00 32.73 2.41
597 608 1.603802 CCTACCAGGCGCATTGTTATG 59.396 52.381 10.83 0.00 34.76 1.90
598 609 2.288666 CTACCAGGCGCATTGTTATGT 58.711 47.619 10.83 3.05 34.12 2.29
599 610 1.544724 ACCAGGCGCATTGTTATGTT 58.455 45.000 10.83 0.00 34.12 2.71
600 611 1.892474 ACCAGGCGCATTGTTATGTTT 59.108 42.857 10.83 0.00 34.12 2.83
601 612 2.261345 CCAGGCGCATTGTTATGTTTG 58.739 47.619 10.83 0.00 34.12 2.93
602 613 1.655099 CAGGCGCATTGTTATGTTTGC 59.345 47.619 10.83 0.00 34.12 3.68
603 614 0.998669 GGCGCATTGTTATGTTTGCC 59.001 50.000 10.83 0.00 38.52 4.52
604 615 1.404047 GGCGCATTGTTATGTTTGCCT 60.404 47.619 10.83 0.00 40.45 4.75
606 617 3.506810 GCGCATTGTTATGTTTGCCTAA 58.493 40.909 0.30 0.00 34.12 2.69
607 618 3.923461 GCGCATTGTTATGTTTGCCTAAA 59.077 39.130 0.30 0.00 34.12 1.85
609 620 5.107298 GCGCATTGTTATGTTTGCCTAAAAA 60.107 36.000 0.30 0.00 34.12 1.94
658 727 0.668535 AACGCTCTGCTTTTGTTCCC 59.331 50.000 0.00 0.00 0.00 3.97
665 1513 2.616842 TCTGCTTTTGTTCCCTCGTTTC 59.383 45.455 0.00 0.00 0.00 2.78
666 1514 2.357637 CTGCTTTTGTTCCCTCGTTTCA 59.642 45.455 0.00 0.00 0.00 2.69
694 1543 1.082117 GCCCCATGTACGAGTCGTTG 61.082 60.000 25.19 15.84 41.54 4.10
739 1588 3.281727 ACGTATTACTCCTACCCGTCA 57.718 47.619 0.00 0.00 0.00 4.35
784 1633 1.108776 TTCTGCTACGGCGATAAGGT 58.891 50.000 16.62 0.00 42.25 3.50
789 1638 2.363038 TGCTACGGCGATAAGGTTGTAT 59.637 45.455 16.62 0.00 42.25 2.29
795 1644 2.033151 GGCGATAAGGTTGTATTCGTGC 60.033 50.000 0.00 0.00 0.00 5.34
797 1646 2.855963 CGATAAGGTTGTATTCGTGCGT 59.144 45.455 0.00 0.00 0.00 5.24
801 1650 1.149987 GGTTGTATTCGTGCGTCCAA 58.850 50.000 0.00 0.00 0.00 3.53
802 1651 1.136169 GGTTGTATTCGTGCGTCCAAC 60.136 52.381 0.00 0.00 33.27 3.77
803 1652 1.796459 GTTGTATTCGTGCGTCCAACT 59.204 47.619 0.00 0.00 31.79 3.16
804 1653 1.424403 TGTATTCGTGCGTCCAACTG 58.576 50.000 0.00 0.00 0.00 3.16
805 1654 1.000052 TGTATTCGTGCGTCCAACTGA 60.000 47.619 0.00 0.00 0.00 3.41
806 1655 1.389106 GTATTCGTGCGTCCAACTGAC 59.611 52.381 0.00 0.00 40.81 3.51
807 1656 0.033504 ATTCGTGCGTCCAACTGACT 59.966 50.000 0.00 0.00 42.13 3.41
808 1657 0.874175 TTCGTGCGTCCAACTGACTG 60.874 55.000 0.00 0.00 42.13 3.51
809 1658 1.591594 CGTGCGTCCAACTGACTGT 60.592 57.895 0.00 0.00 42.13 3.55
810 1659 0.318360 CGTGCGTCCAACTGACTGTA 60.318 55.000 0.00 0.00 42.13 2.74
811 1660 1.668919 CGTGCGTCCAACTGACTGTAT 60.669 52.381 0.00 0.00 42.13 2.29
812 1661 2.414957 CGTGCGTCCAACTGACTGTATA 60.415 50.000 0.00 0.00 42.13 1.47
813 1662 3.179830 GTGCGTCCAACTGACTGTATAG 58.820 50.000 0.00 0.00 42.13 1.31
814 1663 2.194271 GCGTCCAACTGACTGTATAGC 58.806 52.381 0.00 0.00 42.13 2.97
815 1664 2.810650 CGTCCAACTGACTGTATAGCC 58.189 52.381 0.00 0.00 42.13 3.93
816 1665 2.165641 CGTCCAACTGACTGTATAGCCA 59.834 50.000 0.00 0.00 42.13 4.75
817 1666 3.735208 CGTCCAACTGACTGTATAGCCAG 60.735 52.174 1.19 1.19 42.13 4.85
818 1667 2.168521 TCCAACTGACTGTATAGCCAGC 59.831 50.000 2.67 0.00 37.88 4.85
819 1668 2.093500 CCAACTGACTGTATAGCCAGCA 60.093 50.000 2.67 0.00 37.88 4.41
820 1669 2.932614 CAACTGACTGTATAGCCAGCAC 59.067 50.000 2.67 0.00 37.88 4.40
821 1670 1.135139 ACTGACTGTATAGCCAGCACG 59.865 52.381 2.67 0.00 37.88 5.34
822 1671 1.135139 CTGACTGTATAGCCAGCACGT 59.865 52.381 0.00 0.00 35.83 4.49
823 1672 1.548719 TGACTGTATAGCCAGCACGTT 59.451 47.619 0.00 0.00 35.83 3.99
824 1673 1.927174 GACTGTATAGCCAGCACGTTG 59.073 52.381 0.00 0.00 35.83 4.10
825 1674 1.275291 ACTGTATAGCCAGCACGTTGT 59.725 47.619 0.00 0.00 35.83 3.32
826 1675 2.289444 ACTGTATAGCCAGCACGTTGTT 60.289 45.455 0.00 0.00 35.83 2.83
827 1676 2.073056 TGTATAGCCAGCACGTTGTTG 58.927 47.619 0.00 0.00 0.00 3.33
828 1677 2.289133 TGTATAGCCAGCACGTTGTTGA 60.289 45.455 0.00 0.00 29.49 3.18
829 1678 2.113860 ATAGCCAGCACGTTGTTGAT 57.886 45.000 0.00 0.00 29.49 2.57
830 1679 1.890876 TAGCCAGCACGTTGTTGATT 58.109 45.000 0.00 0.00 29.49 2.57
831 1680 1.890876 AGCCAGCACGTTGTTGATTA 58.109 45.000 0.00 0.00 29.49 1.75
832 1681 1.535462 AGCCAGCACGTTGTTGATTAC 59.465 47.619 0.00 0.00 29.49 1.89
833 1682 1.401018 GCCAGCACGTTGTTGATTACC 60.401 52.381 0.00 0.00 29.49 2.85
834 1683 1.136085 CCAGCACGTTGTTGATTACCG 60.136 52.381 0.00 0.00 29.49 4.02
835 1684 1.529438 CAGCACGTTGTTGATTACCGT 59.471 47.619 0.00 0.00 29.49 4.83
836 1685 2.032377 CAGCACGTTGTTGATTACCGTT 60.032 45.455 0.00 0.00 29.49 4.44
837 1686 2.222445 AGCACGTTGTTGATTACCGTTC 59.778 45.455 0.00 0.00 0.00 3.95
838 1687 2.663606 GCACGTTGTTGATTACCGTTCC 60.664 50.000 0.00 0.00 0.00 3.62
839 1688 1.794116 ACGTTGTTGATTACCGTTCCG 59.206 47.619 0.00 0.00 0.00 4.30
840 1689 1.794116 CGTTGTTGATTACCGTTCCGT 59.206 47.619 0.00 0.00 0.00 4.69
841 1690 2.985809 CGTTGTTGATTACCGTTCCGTA 59.014 45.455 0.00 0.00 0.00 4.02
842 1691 3.059834 CGTTGTTGATTACCGTTCCGTAG 59.940 47.826 0.00 0.00 0.00 3.51
843 1692 4.236935 GTTGTTGATTACCGTTCCGTAGA 58.763 43.478 0.00 0.00 0.00 2.59
844 1693 4.517952 TGTTGATTACCGTTCCGTAGAA 57.482 40.909 0.00 0.00 0.00 2.10
845 1694 5.075858 TGTTGATTACCGTTCCGTAGAAT 57.924 39.130 0.00 0.00 33.67 2.40
846 1695 5.104374 TGTTGATTACCGTTCCGTAGAATC 58.896 41.667 0.00 0.00 33.67 2.52
847 1696 4.311816 TGATTACCGTTCCGTAGAATCC 57.688 45.455 0.00 0.00 33.67 3.01
848 1697 3.700539 TGATTACCGTTCCGTAGAATCCA 59.299 43.478 0.00 0.00 33.67 3.41
849 1698 4.342951 TGATTACCGTTCCGTAGAATCCAT 59.657 41.667 0.00 0.00 33.67 3.41
850 1699 2.596904 ACCGTTCCGTAGAATCCATG 57.403 50.000 0.00 0.00 33.67 3.66
875 1724 3.365265 GGCAACAGCCTTCCCGTG 61.365 66.667 0.00 0.00 45.21 4.94
965 1823 3.254470 AGATCGATCGCTAGCTAGCTA 57.746 47.619 36.02 29.00 46.85 3.32
967 1825 2.745515 TCGATCGCTAGCTAGCTAGA 57.254 50.000 42.59 28.97 46.56 2.43
968 1826 2.612604 TCGATCGCTAGCTAGCTAGAG 58.387 52.381 42.59 39.32 46.56 2.43
969 1827 1.062002 CGATCGCTAGCTAGCTAGAGC 59.938 57.143 42.59 33.47 46.56 4.09
1224 2127 4.802051 GGCCCCAAGATCAGCGCA 62.802 66.667 11.47 0.00 0.00 6.09
1536 2460 0.252103 ACTTCTCCTACCTCGGCCAA 60.252 55.000 2.24 0.00 0.00 4.52
2241 4795 2.664081 AAGCAGAAGGAGGCGGAGG 61.664 63.158 0.00 0.00 34.54 4.30
2375 4929 0.602106 CGGAGATGGCTCGCATCAAT 60.602 55.000 0.00 0.00 42.25 2.57
2423 4977 4.202440 CCCAAGATCAGCATCTGGAGTAAT 60.202 45.833 0.00 0.00 38.55 1.89
2594 5175 0.606401 CTGCCAACTGATCACCGGTT 60.606 55.000 2.97 0.00 44.86 4.44
2610 5191 1.063488 GTTTGGTGCGCACTCGTTT 59.937 52.632 36.84 0.00 38.14 3.60
2611 5192 1.063327 TTTGGTGCGCACTCGTTTG 59.937 52.632 36.84 0.00 38.14 2.93
2612 5193 1.649390 TTTGGTGCGCACTCGTTTGT 61.649 50.000 36.84 0.00 38.14 2.83
2614 5195 2.052237 GTGCGCACTCGTTTGTGG 60.052 61.111 32.55 1.39 38.31 4.17
2615 5196 3.947841 TGCGCACTCGTTTGTGGC 61.948 61.111 5.66 8.99 38.31 5.01
2694 5283 5.564063 CGTCACACTAGGTGTTAATGTCAGA 60.564 44.000 10.08 0.00 45.08 3.27
2726 5315 6.879276 TTTCGGGTACATACATTTGTTGAA 57.121 33.333 0.00 0.00 0.00 2.69
2890 5479 7.490962 TGAACAGATTTTTCACGTTGTCTAT 57.509 32.000 0.00 0.00 0.00 1.98
3010 5717 4.689612 AGGATTAGTAATGCGTGATGGT 57.310 40.909 8.55 0.00 34.03 3.55
3080 5788 9.726232 CAAAATTCACTCGATTCACATATGATT 57.274 29.630 10.38 0.00 33.85 2.57
3139 5877 2.948323 GGCCGTTGGGTTTACACG 59.052 61.111 0.00 0.00 34.97 4.49
3143 5881 0.597118 CCGTTGGGTTTACACGTCGA 60.597 55.000 0.00 0.00 0.00 4.20
3182 5920 4.207165 AGTATTGTGTGTGGAGCAGTTTT 58.793 39.130 0.00 0.00 0.00 2.43
3211 5949 5.100943 CCTTTTAGGTCGTGTTAGCTACTC 58.899 45.833 0.00 0.00 0.00 2.59
3212 5950 5.105837 CCTTTTAGGTCGTGTTAGCTACTCT 60.106 44.000 0.00 0.00 0.00 3.24
3214 5952 5.972107 TTAGGTCGTGTTAGCTACTCTTT 57.028 39.130 0.00 0.00 0.00 2.52
3215 5953 7.452880 TTTAGGTCGTGTTAGCTACTCTTTA 57.547 36.000 0.00 0.00 0.00 1.85
3219 5960 7.705214 AGGTCGTGTTAGCTACTCTTTATTAG 58.295 38.462 0.00 0.00 0.00 1.73
3244 5985 9.523168 AGTACTTCCTATACTTGGATGATACTC 57.477 37.037 0.00 0.00 34.20 2.59
3245 5986 7.784470 ACTTCCTATACTTGGATGATACTCC 57.216 40.000 0.00 0.00 34.20 3.85
3246 5987 6.434652 ACTTCCTATACTTGGATGATACTCCG 59.565 42.308 0.00 0.00 38.21 4.63
3247 5988 6.135819 TCCTATACTTGGATGATACTCCGA 57.864 41.667 0.00 0.00 38.21 4.55
3248 5989 5.944599 TCCTATACTTGGATGATACTCCGAC 59.055 44.000 0.00 0.00 38.21 4.79
3249 5990 5.710567 CCTATACTTGGATGATACTCCGACA 59.289 44.000 0.00 0.00 38.21 4.35
3250 5991 3.802948 ACTTGGATGATACTCCGACAC 57.197 47.619 0.00 0.00 38.21 3.67
3251 5992 3.366396 ACTTGGATGATACTCCGACACT 58.634 45.455 0.00 0.00 38.21 3.55
3252 5993 3.381908 ACTTGGATGATACTCCGACACTC 59.618 47.826 0.00 0.00 38.21 3.51
3269 6010 2.303452 TCAACCGTTTGAGCGTCAC 58.697 52.632 0.00 0.00 36.79 3.67
3278 6019 3.245284 CGTTTGAGCGTCACTAATATGGG 59.755 47.826 0.00 0.00 0.00 4.00
3280 6021 4.955811 TTGAGCGTCACTAATATGGGAT 57.044 40.909 0.00 0.00 0.00 3.85
3290 6031 6.708054 GTCACTAATATGGGATGGAGAAAGTG 59.292 42.308 0.00 0.00 33.60 3.16
3293 6034 7.941238 CACTAATATGGGATGGAGAAAGTGAAT 59.059 37.037 0.00 0.00 34.05 2.57
3294 6035 8.506083 ACTAATATGGGATGGAGAAAGTGAATT 58.494 33.333 0.00 0.00 0.00 2.17
3295 6036 9.359653 CTAATATGGGATGGAGAAAGTGAATTT 57.640 33.333 0.00 0.00 0.00 1.82
3296 6037 8.613922 AATATGGGATGGAGAAAGTGAATTTT 57.386 30.769 0.00 0.00 0.00 1.82
3297 6038 5.982890 TGGGATGGAGAAAGTGAATTTTC 57.017 39.130 0.00 0.00 37.34 2.29
3299 6040 6.077322 TGGGATGGAGAAAGTGAATTTTCTT 58.923 36.000 2.78 0.00 45.00 2.52
3300 6041 6.554605 TGGGATGGAGAAAGTGAATTTTCTTT 59.445 34.615 2.78 8.02 45.00 2.52
3301 6042 7.093354 GGGATGGAGAAAGTGAATTTTCTTTC 58.907 38.462 19.48 19.48 45.00 2.62
3332 6073 8.819643 AATATAACAGAACTTCTAATCCGAGC 57.180 34.615 0.00 0.00 0.00 5.03
3336 6077 4.098196 ACAGAACTTCTAATCCGAGCTACC 59.902 45.833 0.00 0.00 0.00 3.18
3337 6078 3.637694 AGAACTTCTAATCCGAGCTACCC 59.362 47.826 0.00 0.00 0.00 3.69
3352 6093 3.850173 AGCTACCCCTCTTTTCATTACCA 59.150 43.478 0.00 0.00 0.00 3.25
3380 6121 4.461992 ACGAAAATACAACACCAGTTCG 57.538 40.909 0.00 0.00 41.46 3.95
3407 6148 5.843019 ATAGGAAGTGAGAAAGGGAAACA 57.157 39.130 0.00 0.00 0.00 2.83
3449 6190 7.581011 ACTATGAAACAAAAATTTGATCGCC 57.419 32.000 12.54 0.00 40.55 5.54
3453 6194 1.000283 ACAAAAATTTGATCGCCGCCA 60.000 42.857 12.54 0.00 40.55 5.69
3454 6195 1.655099 CAAAAATTTGATCGCCGCCAG 59.345 47.619 0.00 0.00 40.55 4.85
3510 6253 4.036380 TGACATGCAGCATTGATCAAGATC 59.964 41.667 14.54 5.40 38.29 2.75
3511 6254 4.207955 ACATGCAGCATTGATCAAGATCT 58.792 39.130 14.54 7.57 38.60 2.75
3512 6255 4.645136 ACATGCAGCATTGATCAAGATCTT 59.355 37.500 14.54 0.88 38.60 2.40
3513 6256 5.127194 ACATGCAGCATTGATCAAGATCTTT 59.873 36.000 14.54 0.00 38.60 2.52
3514 6257 5.244785 TGCAGCATTGATCAAGATCTTTC 57.755 39.130 14.54 2.52 38.60 2.62
3515 6258 4.948004 TGCAGCATTGATCAAGATCTTTCT 59.052 37.500 14.54 0.00 38.60 2.52
3516 6259 5.066117 TGCAGCATTGATCAAGATCTTTCTC 59.934 40.000 14.54 6.18 38.60 2.87
3517 6260 5.297278 GCAGCATTGATCAAGATCTTTCTCT 59.703 40.000 14.54 0.00 38.60 3.10
3518 6261 6.183360 GCAGCATTGATCAAGATCTTTCTCTT 60.183 38.462 14.54 0.00 38.60 2.85
3519 6262 7.411274 CAGCATTGATCAAGATCTTTCTCTTC 58.589 38.462 14.54 0.00 38.60 2.87
3520 6263 7.281324 CAGCATTGATCAAGATCTTTCTCTTCT 59.719 37.037 14.54 0.00 38.60 2.85
3521 6264 7.830201 AGCATTGATCAAGATCTTTCTCTTCTT 59.170 33.333 14.54 0.00 38.60 2.52
3522 6265 8.460428 GCATTGATCAAGATCTTTCTCTTCTTT 58.540 33.333 14.54 0.00 38.60 2.52
3543 6286 2.265739 TGCGGGTGAGCACTGATC 59.734 61.111 0.16 0.00 42.92 2.92
3544 6287 2.265739 GCGGGTGAGCACTGATCA 59.734 61.111 0.00 0.00 37.05 2.92
3545 6288 1.375908 GCGGGTGAGCACTGATCAA 60.376 57.895 0.00 0.00 37.05 2.57
3546 6289 1.364626 GCGGGTGAGCACTGATCAAG 61.365 60.000 0.00 0.00 37.05 3.02
3547 6290 0.247460 CGGGTGAGCACTGATCAAGA 59.753 55.000 0.00 0.00 26.97 3.02
3548 6291 1.134580 CGGGTGAGCACTGATCAAGAT 60.135 52.381 0.00 0.00 26.97 2.40
3549 6292 2.559440 GGGTGAGCACTGATCAAGATC 58.441 52.381 0.00 1.36 38.29 2.75
3550 6293 2.093288 GGGTGAGCACTGATCAAGATCA 60.093 50.000 11.87 11.87 44.83 2.92
3581 6324 7.527084 AGATTCTGTAATTCGAGTGCTTAAC 57.473 36.000 0.00 0.00 0.00 2.01
3582 6325 7.097192 AGATTCTGTAATTCGAGTGCTTAACA 58.903 34.615 0.00 0.00 0.00 2.41
3583 6326 6.706055 TTCTGTAATTCGAGTGCTTAACAG 57.294 37.500 0.00 0.00 0.00 3.16
3584 6327 5.779922 TCTGTAATTCGAGTGCTTAACAGT 58.220 37.500 0.00 0.00 33.39 3.55
3585 6328 6.916440 TCTGTAATTCGAGTGCTTAACAGTA 58.084 36.000 0.00 0.00 29.71 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 11 9.830975 ATAACAAACAAAGCCAAATAGAAAACT 57.169 25.926 0.00 0.00 0.00 2.66
95 99 8.606602 AGAAGTTCAAGAATTTGATTTTTGTGC 58.393 29.630 5.50 0.00 42.60 4.57
123 128 8.005662 TGAATTCACAAATGTTAGCGAATTTG 57.994 30.769 3.38 12.07 45.25 2.32
124 129 8.761575 ATGAATTCACAAATGTTAGCGAATTT 57.238 26.923 11.07 0.00 34.23 1.82
127 132 9.502145 GATAATGAATTCACAAATGTTAGCGAA 57.498 29.630 11.07 0.00 0.00 4.70
129 134 9.507280 AAGATAATGAATTCACAAATGTTAGCG 57.493 29.630 11.07 0.00 0.00 4.26
226 231 7.276878 TCGGGAATTTGAAGAAAGTTTGAAAAC 59.723 33.333 0.00 0.00 39.17 2.43
231 237 4.681483 GCTCGGGAATTTGAAGAAAGTTTG 59.319 41.667 0.00 0.00 0.00 2.93
248 254 3.059166 CACAAAAATGAAAAGGCTCGGG 58.941 45.455 0.00 0.00 0.00 5.14
287 296 9.333724 AGAAAGTGCTCATTCATTTGAAAAATT 57.666 25.926 6.53 0.00 37.61 1.82
298 309 4.154737 CGGATTTGAGAAAGTGCTCATTCA 59.845 41.667 6.53 0.00 43.84 2.57
300 311 3.119708 GCGGATTTGAGAAAGTGCTCATT 60.120 43.478 0.00 0.00 43.84 2.57
305 316 2.704725 TTGCGGATTTGAGAAAGTGC 57.295 45.000 0.00 0.00 0.00 4.40
322 333 7.114882 TGTTCACGGATTTGCAAAATATTTG 57.885 32.000 17.19 9.94 0.00 2.32
332 343 7.344910 TGAAATAAAATGTTCACGGATTTGC 57.655 32.000 0.00 0.00 0.00 3.68
476 487 8.771920 AAAATTTCGGATGGTCCTTTTTATTC 57.228 30.769 0.00 0.00 33.30 1.75
480 491 8.966069 TTTTAAAATTTCGGATGGTCCTTTTT 57.034 26.923 0.00 0.00 33.30 1.94
481 492 8.966069 TTTTTAAAATTTCGGATGGTCCTTTT 57.034 26.923 0.55 0.00 33.30 2.27
507 518 3.153919 TGCTAGGAAAATCGGCTGTTTT 58.846 40.909 5.79 5.79 0.00 2.43
508 519 2.790433 TGCTAGGAAAATCGGCTGTTT 58.210 42.857 0.00 0.00 0.00 2.83
509 520 2.489938 TGCTAGGAAAATCGGCTGTT 57.510 45.000 0.00 0.00 0.00 3.16
510 521 2.489938 TTGCTAGGAAAATCGGCTGT 57.510 45.000 0.00 0.00 0.00 4.40
512 523 4.639135 GATTTTGCTAGGAAAATCGGCT 57.361 40.909 33.04 16.51 40.62 5.52
517 528 4.035208 CGCTACCGATTTTGCTAGGAAAAT 59.965 41.667 28.56 28.56 38.07 1.82
518 529 3.372822 CGCTACCGATTTTGCTAGGAAAA 59.627 43.478 22.26 22.26 36.29 2.29
520 531 2.166870 TCGCTACCGATTTTGCTAGGAA 59.833 45.455 0.00 0.00 38.82 3.36
521 532 1.752498 TCGCTACCGATTTTGCTAGGA 59.248 47.619 0.00 0.00 38.82 2.94
522 533 2.218953 TCGCTACCGATTTTGCTAGG 57.781 50.000 0.00 0.00 38.82 3.02
525 536 1.732259 CTGTTCGCTACCGATTTTGCT 59.268 47.619 0.00 0.00 43.97 3.91
526 537 1.202031 CCTGTTCGCTACCGATTTTGC 60.202 52.381 0.00 0.00 43.97 3.68
527 538 1.202031 GCCTGTTCGCTACCGATTTTG 60.202 52.381 0.00 0.00 43.97 2.44
528 539 1.084289 GCCTGTTCGCTACCGATTTT 58.916 50.000 0.00 0.00 43.97 1.82
529 540 1.082117 CGCCTGTTCGCTACCGATTT 61.082 55.000 0.00 0.00 43.97 2.17
530 541 1.518572 CGCCTGTTCGCTACCGATT 60.519 57.895 0.00 0.00 43.97 3.34
531 542 2.104331 CGCCTGTTCGCTACCGAT 59.896 61.111 0.00 0.00 43.97 4.18
550 561 1.610522 TCCTCCTATACGGCGCTTAAC 59.389 52.381 6.90 0.00 0.00 2.01
552 563 1.531423 CTCCTCCTATACGGCGCTTA 58.469 55.000 6.90 0.00 0.00 3.09
553 564 1.179814 CCTCCTCCTATACGGCGCTT 61.180 60.000 6.90 0.00 0.00 4.68
554 565 1.604023 CCTCCTCCTATACGGCGCT 60.604 63.158 6.90 0.00 0.00 5.92
555 566 1.864725 GACCTCCTCCTATACGGCGC 61.865 65.000 6.90 0.00 0.00 6.53
556 567 0.250814 AGACCTCCTCCTATACGGCG 60.251 60.000 4.80 4.80 0.00 6.46
572 583 1.972660 AATGCGCCTGGTAGGGAGAC 61.973 60.000 4.18 0.00 35.37 3.36
573 584 1.689233 AATGCGCCTGGTAGGGAGA 60.689 57.895 4.18 0.00 35.37 3.71
575 586 1.847798 AACAATGCGCCTGGTAGGGA 61.848 55.000 4.18 0.00 35.37 4.20
576 587 0.107410 TAACAATGCGCCTGGTAGGG 60.107 55.000 4.18 0.00 35.37 3.53
577 588 1.603802 CATAACAATGCGCCTGGTAGG 59.396 52.381 4.18 3.13 38.80 3.18
579 590 2.411628 ACATAACAATGCGCCTGGTA 57.588 45.000 4.18 5.79 0.00 3.25
580 591 1.544724 AACATAACAATGCGCCTGGT 58.455 45.000 4.18 3.15 0.00 4.00
581 592 2.261345 CAAACATAACAATGCGCCTGG 58.739 47.619 4.18 0.00 0.00 4.45
582 593 1.655099 GCAAACATAACAATGCGCCTG 59.345 47.619 4.18 4.75 0.00 4.85
583 594 1.404047 GGCAAACATAACAATGCGCCT 60.404 47.619 4.18 0.00 39.66 5.52
584 595 0.998669 GGCAAACATAACAATGCGCC 59.001 50.000 4.18 0.00 39.66 6.53
585 596 1.994916 AGGCAAACATAACAATGCGC 58.005 45.000 0.00 0.00 39.66 6.09
586 597 6.459257 TTTTTAGGCAAACATAACAATGCG 57.541 33.333 0.00 0.00 39.66 4.73
609 620 4.236935 CAGAACATAACAATGCGCCTTTT 58.763 39.130 4.18 1.74 0.00 2.27
610 621 3.836949 CAGAACATAACAATGCGCCTTT 58.163 40.909 4.18 0.00 0.00 3.11
611 622 2.415893 GCAGAACATAACAATGCGCCTT 60.416 45.455 4.18 0.00 0.00 4.35
612 623 1.133025 GCAGAACATAACAATGCGCCT 59.867 47.619 4.18 0.00 0.00 5.52
613 624 1.548986 GCAGAACATAACAATGCGCC 58.451 50.000 4.18 0.00 0.00 6.53
614 625 1.548986 GGCAGAACATAACAATGCGC 58.451 50.000 0.00 0.00 37.76 6.09
615 626 1.531677 CCGGCAGAACATAACAATGCG 60.532 52.381 0.00 0.00 37.76 4.73
616 627 1.472480 ACCGGCAGAACATAACAATGC 59.528 47.619 0.00 0.00 36.16 3.56
617 628 3.190327 TGAACCGGCAGAACATAACAATG 59.810 43.478 0.00 0.00 0.00 2.82
618 629 3.417101 TGAACCGGCAGAACATAACAAT 58.583 40.909 0.00 0.00 0.00 2.71
621 632 2.412325 CGTTGAACCGGCAGAACATAAC 60.412 50.000 0.00 0.00 0.00 1.89
665 1513 3.814268 CATGGGGCGGCTTCGTTG 61.814 66.667 9.56 0.63 36.07 4.10
666 1514 2.961893 TACATGGGGCGGCTTCGTT 61.962 57.895 9.56 0.00 36.07 3.85
694 1543 1.341209 CAAGCTGAAAACCAGGAACCC 59.659 52.381 0.00 0.00 43.13 4.11
770 1619 3.667261 CGAATACAACCTTATCGCCGTAG 59.333 47.826 0.00 0.00 0.00 3.51
784 1633 1.795872 CAGTTGGACGCACGAATACAA 59.204 47.619 0.00 0.00 0.00 2.41
789 1638 4.021650 GTCAGTTGGACGCACGAA 57.978 55.556 0.00 0.00 36.65 3.85
803 1652 1.182667 ACGTGCTGGCTATACAGTCA 58.817 50.000 0.00 0.00 40.59 3.41
804 1653 1.927174 CAACGTGCTGGCTATACAGTC 59.073 52.381 0.00 0.00 40.59 3.51
805 1654 1.275291 ACAACGTGCTGGCTATACAGT 59.725 47.619 0.00 0.00 40.59 3.55
806 1655 2.010145 ACAACGTGCTGGCTATACAG 57.990 50.000 0.00 0.00 41.41 2.74
807 1656 2.073056 CAACAACGTGCTGGCTATACA 58.927 47.619 0.00 0.00 0.00 2.29
808 1657 2.343101 TCAACAACGTGCTGGCTATAC 58.657 47.619 0.00 0.00 0.00 1.47
809 1658 2.753055 TCAACAACGTGCTGGCTATA 57.247 45.000 0.00 0.00 0.00 1.31
810 1659 2.113860 ATCAACAACGTGCTGGCTAT 57.886 45.000 0.00 0.00 0.00 2.97
811 1660 1.890876 AATCAACAACGTGCTGGCTA 58.109 45.000 0.00 0.00 0.00 3.93
812 1661 1.535462 GTAATCAACAACGTGCTGGCT 59.465 47.619 0.00 0.00 0.00 4.75
813 1662 1.401018 GGTAATCAACAACGTGCTGGC 60.401 52.381 0.00 0.00 0.00 4.85
814 1663 1.136085 CGGTAATCAACAACGTGCTGG 60.136 52.381 0.00 0.00 0.00 4.85
815 1664 1.529438 ACGGTAATCAACAACGTGCTG 59.471 47.619 0.00 0.00 36.32 4.41
816 1665 1.873698 ACGGTAATCAACAACGTGCT 58.126 45.000 0.00 0.00 36.32 4.40
817 1666 2.567067 GAACGGTAATCAACAACGTGC 58.433 47.619 0.00 0.00 37.87 5.34
818 1667 3.177605 GGAACGGTAATCAACAACGTG 57.822 47.619 0.00 0.00 37.87 4.49
834 1683 3.114065 GTCGTCATGGATTCTACGGAAC 58.886 50.000 2.98 0.00 36.08 3.62
835 1684 2.756207 TGTCGTCATGGATTCTACGGAA 59.244 45.455 2.98 0.00 36.08 4.30
836 1685 2.371306 TGTCGTCATGGATTCTACGGA 58.629 47.619 2.98 0.00 36.08 4.69
837 1686 2.863401 TGTCGTCATGGATTCTACGG 57.137 50.000 2.98 0.00 36.08 4.02
838 1687 3.116300 CCTTGTCGTCATGGATTCTACG 58.884 50.000 8.58 0.00 40.11 3.51
839 1688 2.866762 GCCTTGTCGTCATGGATTCTAC 59.133 50.000 16.75 0.00 40.11 2.59
840 1689 2.499693 TGCCTTGTCGTCATGGATTCTA 59.500 45.455 16.75 0.00 40.11 2.10
841 1690 1.278985 TGCCTTGTCGTCATGGATTCT 59.721 47.619 16.75 0.00 40.11 2.40
842 1691 1.737838 TGCCTTGTCGTCATGGATTC 58.262 50.000 16.75 2.24 40.11 2.52
843 1692 1.812571 GTTGCCTTGTCGTCATGGATT 59.187 47.619 16.75 0.00 40.11 3.01
844 1693 1.271325 TGTTGCCTTGTCGTCATGGAT 60.271 47.619 16.75 0.00 40.11 3.41
845 1694 0.107643 TGTTGCCTTGTCGTCATGGA 59.892 50.000 16.75 1.86 40.11 3.41
846 1695 0.518636 CTGTTGCCTTGTCGTCATGG 59.481 55.000 9.70 9.70 40.49 3.66
847 1696 0.110056 GCTGTTGCCTTGTCGTCATG 60.110 55.000 0.00 0.00 0.00 3.07
848 1697 2.247790 GCTGTTGCCTTGTCGTCAT 58.752 52.632 0.00 0.00 0.00 3.06
849 1698 3.731136 GCTGTTGCCTTGTCGTCA 58.269 55.556 0.00 0.00 0.00 4.35
875 1724 7.147811 GCCCATATATATAGGAGTATAGCAGGC 60.148 44.444 11.02 3.45 0.00 4.85
880 1729 9.249053 CTGTGGCCCATATATATAGGAGTATAG 57.751 40.741 11.02 1.33 0.00 1.31
920 1772 2.182825 CGAGAAGATAACCACGTTCCG 58.817 52.381 0.00 0.00 0.00 4.30
965 1823 1.602323 CGGCGGATCTCTAGGCTCT 60.602 63.158 0.00 0.00 0.00 4.09
967 1825 0.963355 GATCGGCGGATCTCTAGGCT 60.963 60.000 23.04 0.00 44.66 4.58
968 1826 1.509004 GATCGGCGGATCTCTAGGC 59.491 63.158 23.04 0.00 44.66 3.93
969 1827 0.673956 TCGATCGGCGGATCTCTAGG 60.674 60.000 26.04 13.88 45.66 3.02
1536 2460 3.044305 GCGTCCTGCTGCGTCTTT 61.044 61.111 0.00 0.00 41.73 2.52
2258 4812 1.692519 ACGTACTCTGTCTTGGCCTTT 59.307 47.619 3.32 0.00 0.00 3.11
2474 5052 0.322456 GCATCTTGTACACCCCAGCA 60.322 55.000 0.00 0.00 0.00 4.41
2477 5055 0.618458 GGAGCATCTTGTACACCCCA 59.382 55.000 0.00 0.00 33.73 4.96
2594 5175 2.109739 ACAAACGAGTGCGCACCAA 61.110 52.632 35.51 0.00 42.48 3.67
2610 5191 2.557805 GTCGAGACGTACGCCACA 59.442 61.111 16.72 0.00 0.00 4.17
2694 5283 5.177326 TGTATGTACCCGAAAAACGCTATT 58.823 37.500 0.00 0.00 41.07 1.73
2726 5315 3.110447 ACGCCAAACATGAAGCAAAAT 57.890 38.095 0.00 0.00 0.00 1.82
3010 5717 8.795842 ACCAAATGTAAAAGGATTATACGACA 57.204 30.769 0.00 0.00 0.00 4.35
3080 5788 6.751514 ACGCATGTTTGTCTGGATTTAATA 57.248 33.333 0.00 0.00 0.00 0.98
3127 5865 0.104487 TGCTCGACGTGTAAACCCAA 59.896 50.000 0.00 0.00 0.00 4.12
3139 5877 0.723981 GTGCCTGATCTTTGCTCGAC 59.276 55.000 0.00 0.00 0.00 4.20
3143 5881 2.283145 ACTTGTGCCTGATCTTTGCT 57.717 45.000 0.00 0.00 0.00 3.91
3219 5960 8.741841 GGAGTATCATCCAAGTATAGGAAGTAC 58.258 40.741 0.00 0.00 38.93 2.73
3234 5975 3.491104 GGTTGAGTGTCGGAGTATCATCC 60.491 52.174 0.00 0.00 36.25 3.51
3235 5976 3.707793 GGTTGAGTGTCGGAGTATCATC 58.292 50.000 0.00 0.00 36.25 2.92
3236 5977 2.099263 CGGTTGAGTGTCGGAGTATCAT 59.901 50.000 0.00 0.00 36.25 2.45
3237 5978 1.471287 CGGTTGAGTGTCGGAGTATCA 59.529 52.381 0.00 0.00 36.25 2.15
3238 5979 1.471684 ACGGTTGAGTGTCGGAGTATC 59.528 52.381 0.00 0.00 0.00 2.24
3239 5980 1.542492 ACGGTTGAGTGTCGGAGTAT 58.458 50.000 0.00 0.00 0.00 2.12
3240 5981 1.321474 AACGGTTGAGTGTCGGAGTA 58.679 50.000 0.00 0.00 0.00 2.59
3241 5982 0.462789 AAACGGTTGAGTGTCGGAGT 59.537 50.000 0.00 0.00 0.00 3.85
3242 5983 0.859232 CAAACGGTTGAGTGTCGGAG 59.141 55.000 7.64 0.00 36.83 4.63
3243 5984 0.460722 TCAAACGGTTGAGTGTCGGA 59.539 50.000 12.93 0.00 38.88 4.55
3244 5985 2.980562 TCAAACGGTTGAGTGTCGG 58.019 52.632 12.93 0.00 38.88 4.79
3251 5992 0.179094 AGTGACGCTCAAACGGTTGA 60.179 50.000 16.40 16.40 41.57 3.18
3252 5993 1.493772 TAGTGACGCTCAAACGGTTG 58.506 50.000 6.93 6.93 37.37 3.77
3269 6010 8.930846 AATTCACTTTCTCCATCCCATATTAG 57.069 34.615 0.00 0.00 0.00 1.73
3306 6047 9.262358 GCTCGGATTAGAAGTTCTGTTATATTT 57.738 33.333 15.90 0.00 0.00 1.40
3322 6063 2.296073 AGAGGGGTAGCTCGGATTAG 57.704 55.000 0.00 0.00 0.00 1.73
3332 6073 4.640647 GCTTGGTAATGAAAAGAGGGGTAG 59.359 45.833 0.00 0.00 0.00 3.18
3336 6077 6.564328 GTTATGCTTGGTAATGAAAAGAGGG 58.436 40.000 0.00 0.00 0.00 4.30
3337 6078 6.093495 TCGTTATGCTTGGTAATGAAAAGAGG 59.907 38.462 0.00 0.00 0.00 3.69
3352 6093 6.016610 ACTGGTGTTGTATTTTCGTTATGCTT 60.017 34.615 0.00 0.00 0.00 3.91
3380 6121 6.301169 TCCCTTTCTCACTTCCTATTTCTC 57.699 41.667 0.00 0.00 0.00 2.87
3407 6148 7.899178 TCATAGTATGTGTTTCGATTGTTGT 57.101 32.000 9.94 0.00 0.00 3.32
3441 6182 1.153449 CCTTACTGGCGGCGATCAA 60.153 57.895 12.98 0.00 0.00 2.57
3449 6190 4.142600 CCAAGAATCTTTTCCTTACTGGCG 60.143 45.833 0.00 0.00 35.26 5.69
3453 6194 4.998051 TGGCCAAGAATCTTTTCCTTACT 58.002 39.130 0.61 0.00 31.84 2.24
3454 6195 5.921962 ATGGCCAAGAATCTTTTCCTTAC 57.078 39.130 10.96 0.00 31.84 2.34
3522 6265 0.749818 TCAGTGCTCACCCGCAAAAA 60.750 50.000 0.00 0.00 42.32 1.94
3523 6266 0.537143 ATCAGTGCTCACCCGCAAAA 60.537 50.000 0.00 0.00 42.32 2.44
3524 6267 0.955428 GATCAGTGCTCACCCGCAAA 60.955 55.000 0.00 0.00 42.32 3.68
3525 6268 1.375908 GATCAGTGCTCACCCGCAA 60.376 57.895 0.00 0.00 42.32 4.85
3526 6269 2.110757 TTGATCAGTGCTCACCCGCA 62.111 55.000 0.00 0.00 37.62 5.69
3527 6270 1.364626 CTTGATCAGTGCTCACCCGC 61.365 60.000 0.00 0.00 0.00 6.13
3528 6271 0.247460 TCTTGATCAGTGCTCACCCG 59.753 55.000 0.00 0.00 0.00 5.28
3529 6272 2.093288 TGATCTTGATCAGTGCTCACCC 60.093 50.000 9.02 0.00 0.00 4.61
3530 6273 3.196463 CTGATCTTGATCAGTGCTCACC 58.804 50.000 24.67 0.00 42.24 4.02
3555 6298 9.250624 GTTAAGCACTCGAATTACAGAATCTAT 57.749 33.333 0.00 0.00 0.00 1.98
3556 6299 8.248253 TGTTAAGCACTCGAATTACAGAATCTA 58.752 33.333 0.00 0.00 0.00 1.98
3557 6300 7.097192 TGTTAAGCACTCGAATTACAGAATCT 58.903 34.615 0.00 0.00 0.00 2.40
3558 6301 7.063544 ACTGTTAAGCACTCGAATTACAGAATC 59.936 37.037 0.00 0.00 0.00 2.52
3559 6302 6.874134 ACTGTTAAGCACTCGAATTACAGAAT 59.126 34.615 0.00 0.00 0.00 2.40
3560 6303 6.220930 ACTGTTAAGCACTCGAATTACAGAA 58.779 36.000 0.00 0.00 0.00 3.02
3561 6304 5.779922 ACTGTTAAGCACTCGAATTACAGA 58.220 37.500 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.