Multiple sequence alignment - TraesCS1A01G143800

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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 TraesCS1A01G143800 chr1A 100.000 4727 0 0 1 4727 248617856 248613130 0.000000e+00 8730.0
1 TraesCS1A01G143800 chr1A 88.434 709 71 5 76 783 367438890 367439588 0.000000e+00 845.0
2 TraesCS1A01G143800 chr1A 85.477 661 79 10 1 659 561699651 561700296 0.000000e+00 673.0
3 TraesCS1A01G143800 chr1A 92.138 318 18 1 1 318 320340623 320340933 4.340000e-120 442.0
4 TraesCS1A01G143800 chr1A 98.438 128 1 1 1544 1671 459527246 459527372 1.710000e-54 224.0
5 TraesCS1A01G143800 chr1D 86.886 1487 89 53 3319 4727 198022132 198020674 0.000000e+00 1568.0
6 TraesCS1A01G143800 chr1D 92.308 858 53 11 2292 3141 198023293 198022441 0.000000e+00 1206.0
7 TraesCS1A01G143800 chr1D 92.867 701 26 5 852 1549 198025007 198024328 0.000000e+00 996.0
8 TraesCS1A01G143800 chr1D 94.249 626 32 4 1670 2293 198024332 198023709 0.000000e+00 953.0
9 TraesCS1A01G143800 chr1D 94.891 137 6 1 1537 1673 255827749 255827884 3.710000e-51 213.0
10 TraesCS1A01G143800 chr1D 97.059 34 1 0 781 814 316301200 316301233 1.840000e-04 58.4
11 TraesCS1A01G143800 chr1B 92.018 1140 47 13 2022 3145 277963531 277962420 0.000000e+00 1561.0
12 TraesCS1A01G143800 chr1B 92.977 954 35 14 3798 4727 277960677 277959732 0.000000e+00 1362.0
13 TraesCS1A01G143800 chr1B 90.438 617 44 5 897 1507 277964542 277963935 0.000000e+00 798.0
14 TraesCS1A01G143800 chr1B 95.294 425 19 1 3275 3698 277962304 277961880 0.000000e+00 673.0
15 TraesCS1A01G143800 chr1B 96.517 201 6 1 1687 1887 277963911 277963712 9.800000e-87 331.0
16 TraesCS1A01G143800 chr1B 80.952 84 3 4 3724 3806 277961830 277961759 2.000000e-03 54.7
17 TraesCS1A01G143800 chr2D 91.083 785 56 7 1 783 50494676 50493904 0.000000e+00 1050.0
18 TraesCS1A01G143800 chr2D 90.816 784 62 5 1 783 586775663 586776437 0.000000e+00 1040.0
19 TraesCS1A01G143800 chr2D 90.677 783 57 4 1 780 367988611 367989380 0.000000e+00 1027.0
20 TraesCS1A01G143800 chr2D 96.970 33 1 0 783 815 21460156 21460188 6.610000e-04 56.5
21 TraesCS1A01G143800 chr5D 90.561 784 62 5 1 783 174804499 174805271 0.000000e+00 1027.0
22 TraesCS1A01G143800 chr5D 94.245 139 8 0 1538 1676 85596245 85596383 3.710000e-51 213.0
23 TraesCS1A01G143800 chr4D 90.561 784 60 3 1 783 293373003 293372233 0.000000e+00 1026.0
24 TraesCS1A01G143800 chr4D 89.936 785 61 7 1 783 439178084 439177316 0.000000e+00 996.0
25 TraesCS1A01G143800 chr4D 97.674 129 3 0 1544 1672 94261237 94261365 6.160000e-54 222.0
26 TraesCS1A01G143800 chr4D 96.947 131 4 0 1543 1673 492804281 492804411 2.210000e-53 220.0
27 TraesCS1A01G143800 chr4A 88.648 784 78 6 1 783 578220176 578219403 0.000000e+00 944.0
28 TraesCS1A01G143800 chr6A 88.250 783 80 7 1 782 60086332 60087103 0.000000e+00 926.0
29 TraesCS1A01G143800 chr6A 97.059 34 1 0 782 815 473050364 473050397 1.840000e-04 58.4
30 TraesCS1A01G143800 chr2B 87.500 784 88 8 1 783 385090537 385089763 0.000000e+00 896.0
31 TraesCS1A01G143800 chr2B 100.000 28 0 0 788 815 377525564 377525591 9.000000e-03 52.8
32 TraesCS1A01G143800 chr6D 92.456 570 36 2 1 570 126849087 126849649 0.000000e+00 808.0
33 TraesCS1A01G143800 chr6D 96.923 130 4 0 1543 1672 263622124 263622253 7.960000e-53 219.0
34 TraesCS1A01G143800 chr6D 95.556 135 6 0 1539 1673 160470778 160470644 2.860000e-52 217.0
35 TraesCS1A01G143800 chr7D 97.656 128 3 0 1545 1672 154193123 154192996 2.210000e-53 220.0
36 TraesCS1A01G143800 chr3D 95.000 140 5 2 1532 1671 210622560 210622423 7.960000e-53 219.0
37 TraesCS1A01G143800 chr7A 97.059 34 1 0 782 815 463455820 463455787 1.840000e-04 58.4
38 TraesCS1A01G143800 chr5B 97.059 34 1 0 786 819 87237425 87237392 1.840000e-04 58.4
39 TraesCS1A01G143800 chr3B 96.970 33 1 0 786 818 507293376 507293344 6.610000e-04 56.5
40 TraesCS1A01G143800 chr3A 92.308 39 3 0 782 820 623993302 623993340 6.610000e-04 56.5


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 TraesCS1A01G143800 chr1A 248613130 248617856 4726 True 8730.000000 8730 100.0000 1 4727 1 chr1A.!!$R1 4726
1 TraesCS1A01G143800 chr1A 367438890 367439588 698 False 845.000000 845 88.4340 76 783 1 chr1A.!!$F2 707
2 TraesCS1A01G143800 chr1A 561699651 561700296 645 False 673.000000 673 85.4770 1 659 1 chr1A.!!$F4 658
3 TraesCS1A01G143800 chr1D 198020674 198025007 4333 True 1180.750000 1568 91.5775 852 4727 4 chr1D.!!$R1 3875
4 TraesCS1A01G143800 chr1B 277959732 277964542 4810 True 796.616667 1561 91.3660 897 4727 6 chr1B.!!$R1 3830
5 TraesCS1A01G143800 chr2D 50493904 50494676 772 True 1050.000000 1050 91.0830 1 783 1 chr2D.!!$R1 782
6 TraesCS1A01G143800 chr2D 586775663 586776437 774 False 1040.000000 1040 90.8160 1 783 1 chr2D.!!$F3 782
7 TraesCS1A01G143800 chr2D 367988611 367989380 769 False 1027.000000 1027 90.6770 1 780 1 chr2D.!!$F2 779
8 TraesCS1A01G143800 chr5D 174804499 174805271 772 False 1027.000000 1027 90.5610 1 783 1 chr5D.!!$F2 782
9 TraesCS1A01G143800 chr4D 293372233 293373003 770 True 1026.000000 1026 90.5610 1 783 1 chr4D.!!$R1 782
10 TraesCS1A01G143800 chr4D 439177316 439178084 768 True 996.000000 996 89.9360 1 783 1 chr4D.!!$R2 782
11 TraesCS1A01G143800 chr4A 578219403 578220176 773 True 944.000000 944 88.6480 1 783 1 chr4A.!!$R1 782
12 TraesCS1A01G143800 chr6A 60086332 60087103 771 False 926.000000 926 88.2500 1 782 1 chr6A.!!$F1 781
13 TraesCS1A01G143800 chr2B 385089763 385090537 774 True 896.000000 896 87.5000 1 783 1 chr2B.!!$R1 782
14 TraesCS1A01G143800 chr6D 126849087 126849649 562 False 808.000000 808 92.4560 1 570 1 chr6D.!!$F1 569

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
799 812 0.377203 GGCGAACGAAATGGGTCATC 59.623 55.000 0.00 0.0 0.00 2.92 F
800 813 0.377203 GCGAACGAAATGGGTCATCC 59.623 55.000 0.00 0.0 0.00 3.51 F
1168 1187 0.693049 TCCTGCTCTTTCTTCCACCC 59.307 55.000 0.00 0.0 0.00 4.61 F
1667 1686 0.774908 AGAATTTTGGGACGGTGGGA 59.225 50.000 0.00 0.0 0.00 4.37 F
1668 1687 1.173913 GAATTTTGGGACGGTGGGAG 58.826 55.000 0.00 0.0 0.00 4.30 F
1679 1698 1.920532 GGTGGGAGTATTCACCCCC 59.079 63.158 2.42 0.0 45.60 5.40 F
3552 4288 1.532523 TCCATTGCTTTCACGCATCA 58.467 45.000 0.00 0.0 40.04 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2181 2285 0.175760 TGAGCACGCTTAGTCCATCC 59.824 55.000 0.00 0.0 0.00 3.51 R
2678 3215 0.607489 CATATAGGGCCCTGCAGCAC 60.607 60.000 35.81 0.0 35.96 4.40 R
3037 3576 0.676151 CCTCTGGTCCAAGAGCAAGC 60.676 60.000 11.04 0.0 42.08 4.01 R
3400 4123 0.792640 ATCTCAAACACGCTCGCTTG 59.207 50.000 0.00 0.0 0.00 4.01 R
3401 4124 1.512926 AATCTCAAACACGCTCGCTT 58.487 45.000 0.00 0.0 0.00 4.68 R
3663 4406 2.000429 AATTGGCAGAAGCGAAATGC 58.000 45.000 0.00 0.0 41.84 3.56 R
4377 6298 1.140252 AGTAACACCCACAAGCTCGTT 59.860 47.619 0.00 0.0 0.00 3.85 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
28 35 1.448893 GCGTTAAGGTCGATGGGCA 60.449 57.895 0.00 0.00 0.00 5.36
114 121 1.515954 CTGCGGGTAGACGTGGAAT 59.484 57.895 0.00 0.00 35.98 3.01
250 258 3.746547 GGGTTTACCCCTAGGTCCT 57.253 57.895 8.29 0.00 46.45 3.85
251 259 2.875102 GGGTTTACCCCTAGGTCCTA 57.125 55.000 8.29 0.00 46.45 2.94
252 260 2.687297 GGGTTTACCCCTAGGTCCTAG 58.313 57.143 17.97 17.97 46.45 3.02
269 277 2.288702 CCTAGCATGTAGAGCGCATCTT 60.289 50.000 11.47 0.00 39.64 2.40
272 280 2.158986 AGCATGTAGAGCGCATCTTTCT 60.159 45.455 11.47 5.65 39.64 2.52
632 642 2.450476 GGAGAAAATGATGGTGGCTGT 58.550 47.619 0.00 0.00 0.00 4.40
669 682 2.707849 GGGAAGGAGTAGACGCGCA 61.708 63.158 5.73 0.00 0.00 6.09
710 723 3.124921 CCGACGCAAATCCGGCTT 61.125 61.111 0.00 0.00 36.62 4.35
718 731 5.061920 ACGCAAATCCGGCTTAAAATTAA 57.938 34.783 0.00 0.00 0.00 1.40
730 743 6.859017 GGCTTAAAATTAAGTCGGAAATGGA 58.141 36.000 12.99 0.00 41.63 3.41
734 747 6.995511 AAAATTAAGTCGGAAATGGATCGA 57.004 33.333 0.00 0.00 0.00 3.59
793 806 4.859784 GTTGGGCGAACGAAATGG 57.140 55.556 0.00 0.00 0.00 3.16
794 807 1.211709 GTTGGGCGAACGAAATGGG 59.788 57.895 0.00 0.00 0.00 4.00
795 808 1.228306 TTGGGCGAACGAAATGGGT 60.228 52.632 0.00 0.00 0.00 4.51
796 809 1.238625 TTGGGCGAACGAAATGGGTC 61.239 55.000 0.00 0.00 0.00 4.46
797 810 1.673009 GGGCGAACGAAATGGGTCA 60.673 57.895 0.00 0.00 0.00 4.02
798 811 1.029947 GGGCGAACGAAATGGGTCAT 61.030 55.000 0.00 0.00 0.00 3.06
799 812 0.377203 GGCGAACGAAATGGGTCATC 59.623 55.000 0.00 0.00 0.00 2.92
800 813 0.377203 GCGAACGAAATGGGTCATCC 59.623 55.000 0.00 0.00 0.00 3.51
812 825 1.106285 GGTCATCCCATTGGAGTTGC 58.894 55.000 3.62 0.00 46.08 4.17
813 826 1.341383 GGTCATCCCATTGGAGTTGCT 60.341 52.381 3.62 0.00 46.08 3.91
814 827 2.019984 GTCATCCCATTGGAGTTGCTC 58.980 52.381 3.62 0.00 46.08 4.26
826 839 3.467374 GAGTTGCTCCAAGGATCTAGG 57.533 52.381 0.00 0.00 0.00 3.02
827 840 3.034635 GAGTTGCTCCAAGGATCTAGGA 58.965 50.000 0.00 0.00 0.00 2.94
837 850 8.108378 CTCCAAGGATCTAGGAGTATATAGGA 57.892 42.308 15.88 0.00 43.11 2.94
838 851 8.108378 TCCAAGGATCTAGGAGTATATAGGAG 57.892 42.308 0.00 0.00 0.00 3.69
839 852 7.689409 TCCAAGGATCTAGGAGTATATAGGAGT 59.311 40.741 0.00 0.00 0.00 3.85
840 853 7.777910 CCAAGGATCTAGGAGTATATAGGAGTG 59.222 44.444 0.00 0.00 0.00 3.51
841 854 8.333235 CAAGGATCTAGGAGTATATAGGAGTGT 58.667 40.741 0.00 0.00 0.00 3.55
842 855 8.471302 AGGATCTAGGAGTATATAGGAGTGTT 57.529 38.462 0.00 0.00 0.00 3.32
843 856 9.577337 AGGATCTAGGAGTATATAGGAGTGTTA 57.423 37.037 0.00 0.00 0.00 2.41
850 863 9.245481 AGGAGTATATAGGAGTGTTATACTTGC 57.755 37.037 0.00 0.00 40.53 4.01
890 903 8.231161 CGAAGAAAAGGGAAAAGAAGTCTAATC 58.769 37.037 0.00 0.00 0.00 1.75
908 921 1.677633 CGGGGCCCTAAAACCAGTG 60.678 63.158 24.38 0.00 0.00 3.66
1132 1151 0.969894 CCAGTCCCTCAAACTCGACT 59.030 55.000 0.00 0.00 36.00 4.18
1168 1187 0.693049 TCCTGCTCTTTCTTCCACCC 59.307 55.000 0.00 0.00 0.00 4.61
1188 1207 2.360854 CCCCTCTACCTCTCCTCCATTT 60.361 54.545 0.00 0.00 0.00 2.32
1190 1209 4.451460 CCCCTCTACCTCTCCTCCATTTAT 60.451 50.000 0.00 0.00 0.00 1.40
1194 1213 6.957020 CCTCTACCTCTCCTCCATTTATGTAT 59.043 42.308 0.00 0.00 0.00 2.29
1195 1214 7.093552 CCTCTACCTCTCCTCCATTTATGTATG 60.094 44.444 0.00 0.00 0.00 2.39
1213 1232 6.419484 TGTATGTACAAGGTAGCAGCATAT 57.581 37.500 0.00 0.00 32.40 1.78
1236 1255 5.784177 TCAGTGAAAGGTTTAGTGCTAGAG 58.216 41.667 0.00 0.00 0.00 2.43
1388 1407 9.123709 TCATAAAAATTTGCTTTGTAGTTAGCG 57.876 29.630 0.00 0.00 40.26 4.26
1410 1429 3.440872 GCACAACAAACATATAACGGGGA 59.559 43.478 0.00 0.00 0.00 4.81
1434 1453 5.843673 TTGGTTGTAGCTGAAAATTGTGA 57.156 34.783 0.00 0.00 0.00 3.58
1488 1507 5.785243 ACTGTCTCCTACTGTTTTAGCTTC 58.215 41.667 0.00 0.00 36.96 3.86
1497 1516 3.432252 ACTGTTTTAGCTTCATCGAACCG 59.568 43.478 0.00 0.00 0.00 4.44
1499 1518 4.558178 TGTTTTAGCTTCATCGAACCGTA 58.442 39.130 0.00 0.00 0.00 4.02
1546 1565 8.825667 AACCATGTGTTTTCCATGTTTAATAC 57.174 30.769 0.00 0.00 38.39 1.89
1547 1566 8.189119 ACCATGTGTTTTCCATGTTTAATACT 57.811 30.769 0.00 0.00 38.39 2.12
1548 1567 8.303876 ACCATGTGTTTTCCATGTTTAATACTC 58.696 33.333 0.00 0.00 38.39 2.59
1549 1568 7.759433 CCATGTGTTTTCCATGTTTAATACTCC 59.241 37.037 0.00 0.00 38.39 3.85
1550 1569 6.904498 TGTGTTTTCCATGTTTAATACTCCG 58.096 36.000 0.00 0.00 0.00 4.63
1551 1570 6.487331 TGTGTTTTCCATGTTTAATACTCCGT 59.513 34.615 0.00 0.00 0.00 4.69
1552 1571 7.019418 GTGTTTTCCATGTTTAATACTCCGTC 58.981 38.462 0.00 0.00 0.00 4.79
1553 1572 6.149807 TGTTTTCCATGTTTAATACTCCGTCC 59.850 38.462 0.00 0.00 0.00 4.79
1554 1573 5.423704 TTCCATGTTTAATACTCCGTCCA 57.576 39.130 0.00 0.00 0.00 4.02
1555 1574 5.623956 TCCATGTTTAATACTCCGTCCAT 57.376 39.130 0.00 0.00 0.00 3.41
1556 1575 5.607477 TCCATGTTTAATACTCCGTCCATC 58.393 41.667 0.00 0.00 0.00 3.51
1557 1576 4.755123 CCATGTTTAATACTCCGTCCATCC 59.245 45.833 0.00 0.00 0.00 3.51
1558 1577 4.411256 TGTTTAATACTCCGTCCATCCC 57.589 45.455 0.00 0.00 0.00 3.85
1559 1578 3.775866 TGTTTAATACTCCGTCCATCCCA 59.224 43.478 0.00 0.00 0.00 4.37
1560 1579 4.225492 TGTTTAATACTCCGTCCATCCCAA 59.775 41.667 0.00 0.00 0.00 4.12
1561 1580 5.187687 GTTTAATACTCCGTCCATCCCAAA 58.812 41.667 0.00 0.00 0.00 3.28
1562 1581 5.438698 TTAATACTCCGTCCATCCCAAAA 57.561 39.130 0.00 0.00 0.00 2.44
1563 1582 4.519906 AATACTCCGTCCATCCCAAAAT 57.480 40.909 0.00 0.00 0.00 1.82
1564 1583 2.899303 ACTCCGTCCATCCCAAAATT 57.101 45.000 0.00 0.00 0.00 1.82
1565 1584 2.723273 ACTCCGTCCATCCCAAAATTC 58.277 47.619 0.00 0.00 0.00 2.17
1566 1585 2.308866 ACTCCGTCCATCCCAAAATTCT 59.691 45.455 0.00 0.00 0.00 2.40
1567 1586 3.245264 ACTCCGTCCATCCCAAAATTCTT 60.245 43.478 0.00 0.00 0.00 2.52
1568 1587 3.088532 TCCGTCCATCCCAAAATTCTTG 58.911 45.455 0.00 0.00 0.00 3.02
1569 1588 2.825532 CCGTCCATCCCAAAATTCTTGT 59.174 45.455 0.00 0.00 0.00 3.16
1570 1589 3.119495 CCGTCCATCCCAAAATTCTTGTC 60.119 47.826 0.00 0.00 0.00 3.18
1571 1590 3.758554 CGTCCATCCCAAAATTCTTGTCT 59.241 43.478 0.00 0.00 0.00 3.41
1572 1591 4.218417 CGTCCATCCCAAAATTCTTGTCTT 59.782 41.667 0.00 0.00 0.00 3.01
1573 1592 5.414454 CGTCCATCCCAAAATTCTTGTCTTA 59.586 40.000 0.00 0.00 0.00 2.10
1574 1593 6.403636 CGTCCATCCCAAAATTCTTGTCTTAG 60.404 42.308 0.00 0.00 0.00 2.18
1575 1594 6.659242 GTCCATCCCAAAATTCTTGTCTTAGA 59.341 38.462 0.00 0.00 0.00 2.10
1576 1595 7.340487 GTCCATCCCAAAATTCTTGTCTTAGAT 59.660 37.037 0.00 0.00 0.00 1.98
1577 1596 7.895429 TCCATCCCAAAATTCTTGTCTTAGATT 59.105 33.333 0.00 0.00 0.00 2.40
1578 1597 8.534496 CCATCCCAAAATTCTTGTCTTAGATTT 58.466 33.333 0.00 0.00 0.00 2.17
1579 1598 9.362539 CATCCCAAAATTCTTGTCTTAGATTTG 57.637 33.333 0.00 0.00 29.84 2.32
1580 1599 8.477419 TCCCAAAATTCTTGTCTTAGATTTGT 57.523 30.769 0.00 0.00 28.79 2.83
1581 1600 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
1582 1601 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
1590 1609 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
1591 1610 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
1593 1612 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
1594 1613 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
1601 1620 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
1602 1621 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
1603 1622 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
1604 1623 7.919091 TGTCTAAATACGGATGTATCAAGTCAC 59.081 37.037 0.00 0.00 40.42 3.67
1605 1624 7.113124 GTCTAAATACGGATGTATCAAGTCACG 59.887 40.741 0.00 0.00 40.42 4.35
1606 1625 4.913335 ATACGGATGTATCAAGTCACGT 57.087 40.909 0.00 0.00 36.56 4.49
1607 1626 3.587797 ACGGATGTATCAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
1608 1627 3.921677 ACGGATGTATCAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
1609 1628 4.312443 ACGGATGTATCAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
1610 1629 5.472148 ACGGATGTATCAAGTCACGTTTTA 58.528 37.500 0.00 0.00 0.00 1.52
1611 1630 5.575606 ACGGATGTATCAAGTCACGTTTTAG 59.424 40.000 0.00 0.00 0.00 1.85
1612 1631 5.575606 CGGATGTATCAAGTCACGTTTTAGT 59.424 40.000 0.00 0.00 0.00 2.24
1613 1632 6.748658 CGGATGTATCAAGTCACGTTTTAGTA 59.251 38.462 0.00 0.00 0.00 1.82
1614 1633 7.434307 CGGATGTATCAAGTCACGTTTTAGTAT 59.566 37.037 0.00 0.00 0.00 2.12
1615 1634 9.095065 GGATGTATCAAGTCACGTTTTAGTATT 57.905 33.333 0.00 0.00 0.00 1.89
1625 1644 9.962783 AGTCACGTTTTAGTATTAGATACATCC 57.037 33.333 0.00 0.00 38.21 3.51
1626 1645 8.899776 GTCACGTTTTAGTATTAGATACATCCG 58.100 37.037 0.00 0.00 38.21 4.18
1627 1646 8.623903 TCACGTTTTAGTATTAGATACATCCGT 58.376 33.333 0.00 0.00 38.21 4.69
1628 1647 9.882996 CACGTTTTAGTATTAGATACATCCGTA 57.117 33.333 0.00 0.00 38.21 4.02
1646 1665 9.439500 ACATCCGTATCTAGACTAATCTAAGAC 57.561 37.037 0.00 0.00 36.98 3.01
1647 1666 9.438228 CATCCGTATCTAGACTAATCTAAGACA 57.562 37.037 0.00 0.00 36.98 3.41
1649 1668 9.491675 TCCGTATCTAGACTAATCTAAGACAAG 57.508 37.037 0.00 0.00 36.98 3.16
1650 1669 9.491675 CCGTATCTAGACTAATCTAAGACAAGA 57.508 37.037 0.00 0.00 36.98 3.02
1658 1677 9.454859 AGACTAATCTAAGACAAGAATTTTGGG 57.545 33.333 5.68 0.00 31.46 4.12
1659 1678 9.449719 GACTAATCTAAGACAAGAATTTTGGGA 57.550 33.333 5.68 0.00 0.00 4.37
1660 1679 9.232473 ACTAATCTAAGACAAGAATTTTGGGAC 57.768 33.333 5.68 0.00 0.00 4.46
1661 1680 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
1662 1681 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
1663 1682 3.223674 AGACAAGAATTTTGGGACGGT 57.776 42.857 0.00 0.00 0.00 4.83
1664 1683 2.884639 AGACAAGAATTTTGGGACGGTG 59.115 45.455 0.00 0.00 0.00 4.94
1665 1684 1.960689 ACAAGAATTTTGGGACGGTGG 59.039 47.619 0.00 0.00 0.00 4.61
1666 1685 1.272212 CAAGAATTTTGGGACGGTGGG 59.728 52.381 0.00 0.00 0.00 4.61
1667 1686 0.774908 AGAATTTTGGGACGGTGGGA 59.225 50.000 0.00 0.00 0.00 4.37
1668 1687 1.173913 GAATTTTGGGACGGTGGGAG 58.826 55.000 0.00 0.00 0.00 4.30
1679 1698 1.920532 GGTGGGAGTATTCACCCCC 59.079 63.158 2.42 0.00 45.60 5.40
1804 1823 5.995282 CGATAATGTTTAGGGGAATAGCACA 59.005 40.000 0.00 0.00 0.00 4.57
1838 1857 8.526978 TCTATGCCAAAATTATGCAACAGTTTA 58.473 29.630 0.00 0.00 38.69 2.01
1893 1912 7.582719 TGCAATAGGAGTTCCCAGTTAAATAT 58.417 34.615 0.00 0.00 37.41 1.28
1896 1915 9.220767 CAATAGGAGTTCCCAGTTAAATATAGC 57.779 37.037 0.00 0.00 37.41 2.97
1950 1969 6.240894 ACTGTTGTCATGTGGTCTTCATATT 58.759 36.000 0.00 0.00 0.00 1.28
2014 2033 3.909732 CTGAGAGGTAGGAAGTCCAGAT 58.090 50.000 0.00 0.00 38.89 2.90
2150 2254 5.998363 GGACCCATACACTTGAATTAGGATC 59.002 44.000 0.00 0.00 0.00 3.36
2181 2285 6.543831 GCCCTACATATAATAATTCAGCTGGG 59.456 42.308 15.13 1.31 0.00 4.45
2269 2373 4.400251 TGATGGAAATCATGCAAGTTCCTC 59.600 41.667 16.27 12.04 42.49 3.71
2335 2864 6.505044 AAAGTAACACCGAAGAACTTGTTT 57.495 33.333 0.00 0.00 34.15 2.83
2451 2984 3.305950 GCTGCATCTCAGGTACCTCTATG 60.306 52.174 12.84 16.04 43.06 2.23
2452 2985 3.894427 CTGCATCTCAGGTACCTCTATGT 59.106 47.826 12.84 0.00 39.15 2.29
2539 3076 5.946942 ATCTGCATTCCTCTTTGAGTAGA 57.053 39.130 0.00 0.00 0.00 2.59
2541 3078 7.609097 ATCTGCATTCCTCTTTGAGTAGATA 57.391 36.000 0.00 0.00 0.00 1.98
2559 3096 4.781934 AGATAAATGGCCCTGTACTTGTC 58.218 43.478 0.00 0.00 0.00 3.18
2608 3145 2.296190 CTCAAAGGTTTGCCAGGTAACC 59.704 50.000 14.68 14.68 43.31 2.85
2619 3156 2.735126 GCCAGGTAACCGATTTGCATTG 60.735 50.000 0.00 0.00 37.17 2.82
2707 3244 4.351111 CAGGGCCCTATATGTAAGTCCTTT 59.649 45.833 28.13 0.00 0.00 3.11
2815 3353 6.544928 TGCTTTCAGATATCCAGTCTAACA 57.455 37.500 0.00 0.00 0.00 2.41
2921 3460 5.551760 ATGGCTACTCAATTCTTGTTTCG 57.448 39.130 0.00 0.00 0.00 3.46
2958 3497 4.002982 TGACTTGGTGAACTCATGCATAC 58.997 43.478 0.00 0.00 0.00 2.39
3115 3654 7.587037 AAGATGTCACTTCTTGGAATTTTCA 57.413 32.000 5.16 0.00 32.30 2.69
3131 3671 7.148423 TGGAATTTTCATCTGAAGTATGACGTG 60.148 37.037 0.00 0.00 33.18 4.49
3149 3774 4.353777 ACGTGTATGCCATATCCCTCTAT 58.646 43.478 0.00 0.00 0.00 1.98
3159 3784 6.384015 TGCCATATCCCTCTATAACCTGTATG 59.616 42.308 0.00 0.00 0.00 2.39
3171 3796 2.795329 ACCTGTATGCCTTGGAACTTG 58.205 47.619 0.00 0.00 0.00 3.16
3233 3954 9.997482 GTAGTTTTTACATTCAACACAGAGAAA 57.003 29.630 0.00 0.00 0.00 2.52
3251 3972 8.421784 ACAGAGAAACACTGTTATCTTGTTAGA 58.578 33.333 6.78 0.00 44.69 2.10
3252 3973 9.429359 CAGAGAAACACTGTTATCTTGTTAGAT 57.571 33.333 6.78 0.00 43.51 1.98
3278 3999 6.800072 TTTTTGAGGGGTTGTTATCTTGTT 57.200 33.333 0.00 0.00 0.00 2.83
3279 4000 7.899648 TTTTTGAGGGGTTGTTATCTTGTTA 57.100 32.000 0.00 0.00 0.00 2.41
3280 4001 7.519032 TTTTGAGGGGTTGTTATCTTGTTAG 57.481 36.000 0.00 0.00 0.00 2.34
3299 4020 9.713740 CTTGTTAGATTATCTTTCTTCATGTGC 57.286 33.333 0.00 0.00 0.00 4.57
3315 4036 4.646945 TCATGTGCACCTTGGTTAAAGAAA 59.353 37.500 15.69 0.00 38.24 2.52
3317 4038 3.764434 TGTGCACCTTGGTTAAAGAAACA 59.236 39.130 15.69 0.00 40.08 2.83
3369 4091 5.671329 GCGTTATTTCAGCAAGGACAGTAAG 60.671 44.000 0.00 0.00 0.00 2.34
3382 4104 3.318275 GGACAGTAAGATCTGACGCCATA 59.682 47.826 4.46 0.00 38.63 2.74
3400 4123 8.628882 ACGCCATATTTTAGTAAGAAAAATGC 57.371 30.769 4.49 0.06 37.19 3.56
3401 4124 8.247562 ACGCCATATTTTAGTAAGAAAAATGCA 58.752 29.630 0.00 0.00 37.19 3.96
3407 4143 7.851822 TTTTAGTAAGAAAAATGCAAGCGAG 57.148 32.000 0.00 0.00 0.00 5.03
3552 4288 1.532523 TCCATTGCTTTCACGCATCA 58.467 45.000 0.00 0.00 40.04 3.07
3579 4315 3.560636 ATTATGTACTGACAGGTGGGC 57.439 47.619 7.51 0.00 39.50 5.36
3622 4365 4.461781 AGATGCCCAAGTCAGAAAAGAATG 59.538 41.667 0.00 0.00 0.00 2.67
3669 4412 2.294233 TGCACTGGTGAAAGAGCATTTC 59.706 45.455 4.79 7.31 38.60 2.17
3698 4441 4.701651 TGCCAATTATGAAGTTCAGAGTGG 59.298 41.667 23.65 23.65 35.83 4.00
3700 4443 4.946157 CCAATTATGAAGTTCAGAGTGGCT 59.054 41.667 19.27 2.71 29.47 4.75
3701 4444 5.416952 CCAATTATGAAGTTCAGAGTGGCTT 59.583 40.000 19.27 2.09 29.47 4.35
3702 4445 6.320171 CAATTATGAAGTTCAGAGTGGCTTG 58.680 40.000 11.91 4.67 0.00 4.01
3727 4479 3.963665 TCGTTTTCAAGCACCAAATGAG 58.036 40.909 0.00 0.00 0.00 2.90
3733 4485 3.719924 TCAAGCACCAAATGAGCAAAAG 58.280 40.909 0.00 0.00 0.00 2.27
3734 4486 3.384146 TCAAGCACCAAATGAGCAAAAGA 59.616 39.130 0.00 0.00 0.00 2.52
3745 4529 7.148918 CCAAATGAGCAAAAGATTTCGTGTTAG 60.149 37.037 0.00 0.00 0.00 2.34
3768 4552 6.655078 GAGAATCTTCCAAGCTCTCTCTAT 57.345 41.667 0.00 0.00 34.52 1.98
3769 4553 7.759489 GAGAATCTTCCAAGCTCTCTCTATA 57.241 40.000 0.00 0.00 34.52 1.31
3809 5683 5.301551 TGCAACTTTTGGTGACTGTTATGAT 59.698 36.000 0.00 0.00 40.19 2.45
3820 5694 5.295292 GTGACTGTTATGATCAGATTGTGGG 59.705 44.000 0.09 0.00 36.81 4.61
3842 5716 6.016360 TGGGTGTACTGAATTTTTGTCAGATG 60.016 38.462 8.36 0.00 44.44 2.90
3843 5717 6.206634 GGGTGTACTGAATTTTTGTCAGATGA 59.793 38.462 8.36 0.00 44.44 2.92
3845 5719 7.752239 GGTGTACTGAATTTTTGTCAGATGATG 59.248 37.037 8.36 0.00 44.44 3.07
3903 5783 6.317140 GCCAATTATGAAGTTCAGAGTGATGA 59.683 38.462 11.91 0.00 0.00 2.92
3917 5797 8.853077 TCAGAGTGATGAACAAATTAGTGAAT 57.147 30.769 0.00 0.00 0.00 2.57
3918 5798 8.939929 TCAGAGTGATGAACAAATTAGTGAATC 58.060 33.333 0.00 0.00 0.00 2.52
3919 5799 8.944029 CAGAGTGATGAACAAATTAGTGAATCT 58.056 33.333 0.00 0.00 0.00 2.40
3920 5800 8.944029 AGAGTGATGAACAAATTAGTGAATCTG 58.056 33.333 0.00 0.00 0.00 2.90
3961 5872 8.463930 TCTTTCACACTACAATCCAGATTTTT 57.536 30.769 0.00 0.00 0.00 1.94
3981 5892 2.026014 CACCAAACACACGCTGGC 59.974 61.111 0.00 0.00 33.19 4.85
3983 5894 2.332514 CCAAACACACGCTGGCTG 59.667 61.111 0.00 0.00 0.00 4.85
3984 5895 2.353839 CAAACACACGCTGGCTGC 60.354 61.111 6.26 6.26 38.57 5.25
4018 5930 3.767278 GCAGAAGGCAGCAAAGAATAAG 58.233 45.455 0.00 0.00 43.97 1.73
4019 5931 3.192212 GCAGAAGGCAGCAAAGAATAAGT 59.808 43.478 0.00 0.00 43.97 2.24
4028 5949 7.177392 AGGCAGCAAAGAATAAGTTAACTCATT 59.823 33.333 8.95 6.08 0.00 2.57
4190 6111 2.047274 CGTGGGAACTGCACCGAT 60.047 61.111 0.00 0.00 0.00 4.18
4218 6139 0.961358 CTCCCACGACGTCTCCTTCT 60.961 60.000 14.70 0.00 0.00 2.85
4377 6298 7.555914 TCCCAGATCGAACATTTGATGATTTTA 59.444 33.333 0.00 0.00 31.50 1.52
4403 6324 1.802365 CTTGTGGGTGTTACTTACCGC 59.198 52.381 0.00 0.00 39.14 5.68
4557 6478 8.157476 GTGTCAAATACTGGTAGGGATATCATT 58.843 37.037 4.83 0.00 0.00 2.57
4624 6545 4.577677 TTCTTGGCACTGGCGGCA 62.578 61.111 12.58 12.58 42.47 5.69
4702 6626 3.052082 CTGTCGGCAGCCAAGTGG 61.052 66.667 13.30 0.00 35.77 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.096003 CCCGTGCCCATCGACCTT 62.096 66.667 0.00 0.00 0.00 3.50
146 153 2.803155 GATGGTGCTGCCCGACTCAA 62.803 60.000 0.00 0.00 36.04 3.02
246 254 0.385751 TGCGCTCTACATGCTAGGAC 59.614 55.000 9.73 0.00 0.00 3.85
247 255 1.270826 GATGCGCTCTACATGCTAGGA 59.729 52.381 9.73 0.00 0.00 2.94
248 256 1.271934 AGATGCGCTCTACATGCTAGG 59.728 52.381 9.73 0.00 30.26 3.02
249 257 2.721274 AGATGCGCTCTACATGCTAG 57.279 50.000 9.73 0.00 30.26 3.42
250 258 3.068732 AGAAAGATGCGCTCTACATGCTA 59.931 43.478 9.73 0.00 32.41 3.49
251 259 2.158986 AGAAAGATGCGCTCTACATGCT 60.159 45.455 9.73 0.00 32.41 3.79
252 260 2.208431 AGAAAGATGCGCTCTACATGC 58.792 47.619 9.73 0.00 32.41 4.06
291 299 1.518903 GCAGCTGGAGTTCACCAACC 61.519 60.000 17.12 0.00 39.59 3.77
600 609 7.107542 CCATCATTTTCTCCCATTTTTCACAT 58.892 34.615 0.00 0.00 0.00 3.21
603 612 6.465948 CACCATCATTTTCTCCCATTTTTCA 58.534 36.000 0.00 0.00 0.00 2.69
669 682 2.126463 CACGAGATGGACACGCGT 60.126 61.111 5.58 5.58 43.43 6.01
674 687 2.571757 GCGGACACGAGATGGACA 59.428 61.111 0.00 0.00 44.60 4.02
710 723 7.912383 GTCGATCCATTTCCGACTTAATTTTA 58.088 34.615 0.00 0.00 46.24 1.52
730 743 1.373246 TTTTTCGTCCGCGGTCGAT 60.373 52.632 39.49 0.00 35.87 3.59
734 747 3.340253 CCGTTTTTCGTCCGCGGT 61.340 61.111 27.15 0.00 37.87 5.68
793 806 1.106285 GCAACTCCAATGGGATGACC 58.894 55.000 0.00 0.00 43.91 4.02
794 807 2.019984 GAGCAACTCCAATGGGATGAC 58.980 52.381 0.00 0.00 43.91 3.06
795 808 2.425143 GAGCAACTCCAATGGGATGA 57.575 50.000 0.00 0.00 43.91 2.92
806 819 3.034635 TCCTAGATCCTTGGAGCAACTC 58.965 50.000 7.69 0.00 31.05 3.01
807 820 3.037549 CTCCTAGATCCTTGGAGCAACT 58.962 50.000 7.69 1.70 43.80 3.16
808 821 3.467374 CTCCTAGATCCTTGGAGCAAC 57.533 52.381 7.69 0.00 43.80 4.17
813 826 7.689409 ACTCCTATATACTCCTAGATCCTTGGA 59.311 40.741 0.00 0.00 34.54 3.53
814 827 7.777910 CACTCCTATATACTCCTAGATCCTTGG 59.222 44.444 0.00 0.00 0.00 3.61
815 828 8.333235 ACACTCCTATATACTCCTAGATCCTTG 58.667 40.741 0.00 0.00 0.00 3.61
816 829 8.471302 ACACTCCTATATACTCCTAGATCCTT 57.529 38.462 0.00 0.00 0.00 3.36
817 830 8.471302 AACACTCCTATATACTCCTAGATCCT 57.529 38.462 0.00 0.00 0.00 3.24
824 837 9.245481 GCAAGTATAACACTCCTATATACTCCT 57.755 37.037 5.45 0.00 40.30 3.69
825 838 9.021807 TGCAAGTATAACACTCCTATATACTCC 57.978 37.037 5.45 2.37 40.30 3.85
830 843 9.338622 GGTTTTGCAAGTATAACACTCCTATAT 57.661 33.333 12.47 0.00 36.04 0.86
831 844 7.493320 CGGTTTTGCAAGTATAACACTCCTATA 59.507 37.037 12.47 0.00 36.04 1.31
832 845 6.315393 CGGTTTTGCAAGTATAACACTCCTAT 59.685 38.462 12.47 0.00 36.04 2.57
833 846 5.640357 CGGTTTTGCAAGTATAACACTCCTA 59.360 40.000 12.47 0.00 36.04 2.94
834 847 4.454504 CGGTTTTGCAAGTATAACACTCCT 59.545 41.667 12.47 0.00 36.04 3.69
835 848 4.719040 CGGTTTTGCAAGTATAACACTCC 58.281 43.478 12.47 0.00 36.04 3.85
836 849 4.083484 AGCGGTTTTGCAAGTATAACACTC 60.083 41.667 12.47 2.87 36.04 3.51
837 850 3.818773 AGCGGTTTTGCAAGTATAACACT 59.181 39.130 12.47 7.18 40.05 3.55
838 851 4.155310 AGCGGTTTTGCAAGTATAACAC 57.845 40.909 12.47 5.37 37.31 3.32
839 852 5.943706 TTAGCGGTTTTGCAAGTATAACA 57.056 34.783 12.47 0.00 37.31 2.41
840 853 6.183359 CGTTTTAGCGGTTTTGCAAGTATAAC 60.183 38.462 0.00 0.82 37.31 1.89
841 854 5.852229 CGTTTTAGCGGTTTTGCAAGTATAA 59.148 36.000 0.00 0.00 37.31 0.98
842 855 5.178996 TCGTTTTAGCGGTTTTGCAAGTATA 59.821 36.000 0.00 0.00 37.31 1.47
843 856 4.023878 TCGTTTTAGCGGTTTTGCAAGTAT 60.024 37.500 0.00 0.00 37.31 2.12
844 857 3.311871 TCGTTTTAGCGGTTTTGCAAGTA 59.688 39.130 0.00 0.00 37.31 2.24
845 858 2.097791 TCGTTTTAGCGGTTTTGCAAGT 59.902 40.909 0.00 0.00 37.31 3.16
846 859 2.722071 TCGTTTTAGCGGTTTTGCAAG 58.278 42.857 0.00 0.00 37.31 4.01
847 860 2.846039 TCGTTTTAGCGGTTTTGCAA 57.154 40.000 0.00 0.00 37.31 4.08
848 861 2.355132 TCTTCGTTTTAGCGGTTTTGCA 59.645 40.909 0.00 0.00 37.31 4.08
849 862 2.989641 TCTTCGTTTTAGCGGTTTTGC 58.010 42.857 0.00 0.00 0.00 3.68
850 863 5.051973 CCTTTTCTTCGTTTTAGCGGTTTTG 60.052 40.000 0.00 0.00 0.00 2.44
890 903 1.677633 CACTGGTTTTAGGGCCCCG 60.678 63.158 21.43 0.97 0.00 5.73
922 935 2.441532 GGATCCGAGGGTCCACGA 60.442 66.667 16.26 0.00 34.57 4.35
985 998 2.577644 CATGATGCGGTGTTGCGC 60.578 61.111 0.00 0.00 37.81 6.09
987 1000 1.226101 CGACATGATGCGGTGTTGC 60.226 57.895 0.00 0.00 0.00 4.17
1041 1060 2.048503 CCCGTCACGAAGGTCACC 60.049 66.667 0.00 0.00 0.00 4.02
1153 1172 0.034960 GAGGGGGTGGAAGAAAGAGC 60.035 60.000 0.00 0.00 0.00 4.09
1168 1187 2.785357 AATGGAGGAGAGGTAGAGGG 57.215 55.000 0.00 0.00 0.00 4.30
1188 1207 5.862678 TGCTGCTACCTTGTACATACATA 57.137 39.130 0.00 0.00 35.89 2.29
1190 1209 4.753516 ATGCTGCTACCTTGTACATACA 57.246 40.909 0.00 0.00 0.00 2.29
1194 1213 4.405680 ACTGATATGCTGCTACCTTGTACA 59.594 41.667 0.00 0.00 0.00 2.90
1195 1214 4.747108 CACTGATATGCTGCTACCTTGTAC 59.253 45.833 0.00 0.00 0.00 2.90
1213 1232 5.304614 ACTCTAGCACTAAACCTTTCACTGA 59.695 40.000 0.00 0.00 0.00 3.41
1236 1255 2.436173 AGCAAGTCCTAGGCATCCTTAC 59.564 50.000 2.96 0.00 34.61 2.34
1371 1390 2.614520 TGTGCGCTAACTACAAAGCAAA 59.385 40.909 9.73 0.00 38.70 3.68
1388 1407 3.440872 TCCCCGTTATATGTTTGTTGTGC 59.559 43.478 0.00 0.00 0.00 4.57
1410 1429 6.815089 TCACAATTTTCAGCTACAACCAATT 58.185 32.000 0.00 0.00 0.00 2.32
1434 1453 6.183347 AGCTGTGAAGCAACTATTCCTAATT 58.817 36.000 0.00 0.00 37.25 1.40
1488 1507 1.387756 GTGGAAACGTACGGTTCGATG 59.612 52.381 32.91 0.00 42.36 3.84
1497 1516 7.467557 TTTATCATTATCCGTGGAAACGTAC 57.532 36.000 0.00 0.00 0.00 3.67
1499 1518 6.183360 GGTTTTATCATTATCCGTGGAAACGT 60.183 38.462 0.00 0.00 0.00 3.99
1546 1565 3.004752 AGAATTTTGGGATGGACGGAG 57.995 47.619 0.00 0.00 0.00 4.63
1547 1566 3.088532 CAAGAATTTTGGGATGGACGGA 58.911 45.455 0.00 0.00 0.00 4.69
1548 1567 2.825532 ACAAGAATTTTGGGATGGACGG 59.174 45.455 0.00 0.00 0.00 4.79
1549 1568 3.758554 AGACAAGAATTTTGGGATGGACG 59.241 43.478 5.68 0.00 0.00 4.79
1550 1569 5.728637 AAGACAAGAATTTTGGGATGGAC 57.271 39.130 5.68 0.00 0.00 4.02
1551 1570 6.789268 TCTAAGACAAGAATTTTGGGATGGA 58.211 36.000 5.68 0.00 0.00 3.41
1552 1571 7.651027 ATCTAAGACAAGAATTTTGGGATGG 57.349 36.000 5.68 0.00 0.00 3.51
1553 1572 9.362539 CAAATCTAAGACAAGAATTTTGGGATG 57.637 33.333 5.68 0.00 28.49 3.51
1554 1573 9.093458 ACAAATCTAAGACAAGAATTTTGGGAT 57.907 29.630 0.00 0.00 33.04 3.85
1555 1574 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
1556 1575 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
1564 1583 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
1565 1584 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
1567 1586 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
1568 1587 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
1575 1594 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
1576 1595 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
1577 1596 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
1578 1597 7.919091 GTGACTTGATACATCCGTATTTAGACA 59.081 37.037 0.00 0.00 38.48 3.41
1579 1598 7.113124 CGTGACTTGATACATCCGTATTTAGAC 59.887 40.741 0.00 0.00 38.48 2.59
1580 1599 7.136772 CGTGACTTGATACATCCGTATTTAGA 58.863 38.462 0.00 0.00 38.48 2.10
1581 1600 6.916387 ACGTGACTTGATACATCCGTATTTAG 59.084 38.462 0.00 0.00 38.48 1.85
1582 1601 6.798482 ACGTGACTTGATACATCCGTATTTA 58.202 36.000 0.00 0.00 38.48 1.40
1583 1602 5.657474 ACGTGACTTGATACATCCGTATTT 58.343 37.500 0.00 0.00 38.48 1.40
1584 1603 5.258456 ACGTGACTTGATACATCCGTATT 57.742 39.130 0.00 0.00 38.48 1.89
1585 1604 4.913335 ACGTGACTTGATACATCCGTAT 57.087 40.909 0.00 0.00 41.16 3.06
1586 1605 4.707030 AACGTGACTTGATACATCCGTA 57.293 40.909 0.00 0.00 0.00 4.02
1587 1606 3.587797 AACGTGACTTGATACATCCGT 57.412 42.857 0.00 0.00 0.00 4.69
1588 1607 4.921470 AAAACGTGACTTGATACATCCG 57.079 40.909 0.00 0.00 0.00 4.18
1589 1608 6.963049 ACTAAAACGTGACTTGATACATCC 57.037 37.500 0.00 0.00 0.00 3.51
1599 1618 9.962783 GGATGTATCTAATACTAAAACGTGACT 57.037 33.333 0.00 0.00 36.70 3.41
1600 1619 8.899776 CGGATGTATCTAATACTAAAACGTGAC 58.100 37.037 0.00 0.00 36.70 3.67
1601 1620 8.623903 ACGGATGTATCTAATACTAAAACGTGA 58.376 33.333 0.00 0.00 36.70 4.35
1602 1621 8.792831 ACGGATGTATCTAATACTAAAACGTG 57.207 34.615 0.00 0.00 36.70 4.49
1620 1639 9.439500 GTCTTAGATTAGTCTAGATACGGATGT 57.561 37.037 0.00 0.00 38.17 3.06
1621 1640 9.438228 TGTCTTAGATTAGTCTAGATACGGATG 57.562 37.037 0.00 0.00 38.17 3.51
1623 1642 9.491675 CTTGTCTTAGATTAGTCTAGATACGGA 57.508 37.037 0.00 0.00 38.17 4.69
1624 1643 9.491675 TCTTGTCTTAGATTAGTCTAGATACGG 57.508 37.037 0.00 0.00 38.17 4.02
1632 1651 9.454859 CCCAAAATTCTTGTCTTAGATTAGTCT 57.545 33.333 0.00 0.00 38.52 3.24
1633 1652 9.449719 TCCCAAAATTCTTGTCTTAGATTAGTC 57.550 33.333 0.00 0.00 0.00 2.59
1634 1653 9.232473 GTCCCAAAATTCTTGTCTTAGATTAGT 57.768 33.333 0.00 0.00 0.00 2.24
1635 1654 8.391106 CGTCCCAAAATTCTTGTCTTAGATTAG 58.609 37.037 0.00 0.00 0.00 1.73
1636 1655 7.335924 CCGTCCCAAAATTCTTGTCTTAGATTA 59.664 37.037 0.00 0.00 0.00 1.75
1637 1656 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
1638 1657 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
1639 1658 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
1640 1659 4.760204 ACCGTCCCAAAATTCTTGTCTTAG 59.240 41.667 0.00 0.00 0.00 2.18
1641 1660 4.517453 CACCGTCCCAAAATTCTTGTCTTA 59.483 41.667 0.00 0.00 0.00 2.10
1642 1661 3.317993 CACCGTCCCAAAATTCTTGTCTT 59.682 43.478 0.00 0.00 0.00 3.01
1643 1662 2.884639 CACCGTCCCAAAATTCTTGTCT 59.115 45.455 0.00 0.00 0.00 3.41
1644 1663 2.030274 CCACCGTCCCAAAATTCTTGTC 60.030 50.000 0.00 0.00 0.00 3.18
1645 1664 1.960689 CCACCGTCCCAAAATTCTTGT 59.039 47.619 0.00 0.00 0.00 3.16
1646 1665 1.272212 CCCACCGTCCCAAAATTCTTG 59.728 52.381 0.00 0.00 0.00 3.02
1647 1666 1.146152 TCCCACCGTCCCAAAATTCTT 59.854 47.619 0.00 0.00 0.00 2.52
1648 1667 0.774908 TCCCACCGTCCCAAAATTCT 59.225 50.000 0.00 0.00 0.00 2.40
1649 1668 1.173913 CTCCCACCGTCCCAAAATTC 58.826 55.000 0.00 0.00 0.00 2.17
1650 1669 0.481128 ACTCCCACCGTCCCAAAATT 59.519 50.000 0.00 0.00 0.00 1.82
1651 1670 1.364269 TACTCCCACCGTCCCAAAAT 58.636 50.000 0.00 0.00 0.00 1.82
1652 1671 1.364269 ATACTCCCACCGTCCCAAAA 58.636 50.000 0.00 0.00 0.00 2.44
1653 1672 1.279846 GAATACTCCCACCGTCCCAAA 59.720 52.381 0.00 0.00 0.00 3.28
1654 1673 0.906775 GAATACTCCCACCGTCCCAA 59.093 55.000 0.00 0.00 0.00 4.12
1655 1674 0.252330 TGAATACTCCCACCGTCCCA 60.252 55.000 0.00 0.00 0.00 4.37
1656 1675 0.177373 GTGAATACTCCCACCGTCCC 59.823 60.000 0.00 0.00 0.00 4.46
1657 1676 0.177373 GGTGAATACTCCCACCGTCC 59.823 60.000 0.00 0.00 42.73 4.79
1658 1677 3.754766 GGTGAATACTCCCACCGTC 57.245 57.895 0.00 0.00 42.73 4.79
1666 1685 5.582689 CAAGATTTTGGGGGTGAATACTC 57.417 43.478 0.00 0.00 0.00 2.59
1804 1823 7.093814 TGCATAATTTTGGCATAGAAAGTCAGT 60.094 33.333 0.00 0.00 31.58 3.41
1838 1857 1.639108 GTTCCCTCCAAACATACCCCT 59.361 52.381 0.00 0.00 0.00 4.79
1893 1912 2.637382 TGAATCACAAGTCCACTGGCTA 59.363 45.455 0.00 0.00 0.00 3.93
1896 1915 3.189910 CACATGAATCACAAGTCCACTGG 59.810 47.826 0.00 0.00 0.00 4.00
1969 1988 9.507329 CAGCCAGTAATAATACCAGAATACAAT 57.493 33.333 0.00 0.00 32.08 2.71
1986 2005 3.245658 ACTTCCTACCTCTCAGCCAGTAA 60.246 47.826 0.00 0.00 0.00 2.24
1993 2012 3.374042 TCTGGACTTCCTACCTCTCAG 57.626 52.381 0.00 0.00 36.82 3.35
2080 2183 5.728637 TCGTCACTGCTATGGATCATAAT 57.271 39.130 0.00 0.00 0.00 1.28
2088 2191 0.537188 AGGGTTCGTCACTGCTATGG 59.463 55.000 0.00 0.00 0.00 2.74
2150 2254 9.334947 CTGAATTATTATATGTAGGGCATCAGG 57.665 37.037 0.00 0.00 38.94 3.86
2181 2285 0.175760 TGAGCACGCTTAGTCCATCC 59.824 55.000 0.00 0.00 0.00 3.51
2494 3029 9.736023 AGATTCATTAACAAGAGTTCAAACAAC 57.264 29.630 0.00 0.00 39.15 3.32
2539 3076 3.199071 TCGACAAGTACAGGGCCATTTAT 59.801 43.478 6.18 0.00 0.00 1.40
2541 3078 1.349688 TCGACAAGTACAGGGCCATTT 59.650 47.619 6.18 0.00 0.00 2.32
2559 3096 3.056821 TGAAACATAGACAGGTGTCCTCG 60.057 47.826 6.50 0.00 45.85 4.63
2608 3145 7.043192 AGTGAAAAGAAAGAACAATGCAAATCG 60.043 33.333 0.00 0.00 0.00 3.34
2673 3210 2.598394 GGCCCTGCAGCACAAAGA 60.598 61.111 8.66 0.00 0.00 2.52
2678 3215 0.607489 CATATAGGGCCCTGCAGCAC 60.607 60.000 35.81 0.00 35.96 4.40
2707 3244 5.957771 ATGTTATAGTGCCTGGAGAAGAA 57.042 39.130 0.00 0.00 0.00 2.52
2815 3353 8.112183 ACATCCAGATAAGGAACAAAGAGATTT 58.888 33.333 0.00 0.00 41.92 2.17
2921 3460 7.703328 TCACCAAGTCAAACATTAGAAAGAAC 58.297 34.615 0.00 0.00 0.00 3.01
3037 3576 0.676151 CCTCTGGTCCAAGAGCAAGC 60.676 60.000 11.04 0.00 42.08 4.01
3115 3654 4.099419 TGGCATACACGTCATACTTCAGAT 59.901 41.667 0.00 0.00 0.00 2.90
3131 3671 6.384305 ACAGGTTATAGAGGGATATGGCATAC 59.616 42.308 9.83 4.10 0.00 2.39
3149 3774 4.202524 ACAAGTTCCAAGGCATACAGGTTA 60.203 41.667 0.00 0.00 0.00 2.85
3159 3784 5.705609 TCAGAAAATACAAGTTCCAAGGC 57.294 39.130 0.00 0.00 0.00 4.35
3205 3830 9.391006 TCTCTGTGTTGAATGTAAAAACTACTT 57.609 29.630 0.00 0.00 0.00 2.24
3208 3833 9.997482 GTTTCTCTGTGTTGAATGTAAAAACTA 57.003 29.630 0.00 0.00 0.00 2.24
3209 3834 8.519526 TGTTTCTCTGTGTTGAATGTAAAAACT 58.480 29.630 0.00 0.00 0.00 2.66
3210 3835 8.583765 GTGTTTCTCTGTGTTGAATGTAAAAAC 58.416 33.333 0.00 0.00 0.00 2.43
3222 3943 6.823689 ACAAGATAACAGTGTTTCTCTGTGTT 59.176 34.615 14.90 0.00 44.03 3.32
3225 3946 8.421784 TCTAACAAGATAACAGTGTTTCTCTGT 58.578 33.333 14.90 16.75 46.30 3.41
3255 3976 6.800072 AACAAGATAACAACCCCTCAAAAA 57.200 33.333 0.00 0.00 0.00 1.94
3256 3977 7.291566 TCTAACAAGATAACAACCCCTCAAAA 58.708 34.615 0.00 0.00 0.00 2.44
3257 3978 6.843752 TCTAACAAGATAACAACCCCTCAAA 58.156 36.000 0.00 0.00 0.00 2.69
3258 3979 6.442541 TCTAACAAGATAACAACCCCTCAA 57.557 37.500 0.00 0.00 0.00 3.02
3259 3980 6.636454 ATCTAACAAGATAACAACCCCTCA 57.364 37.500 0.00 0.00 0.00 3.86
3260 3981 9.274206 GATAATCTAACAAGATAACAACCCCTC 57.726 37.037 0.00 0.00 0.00 4.30
3261 3982 9.004231 AGATAATCTAACAAGATAACAACCCCT 57.996 33.333 0.00 0.00 0.00 4.79
3262 3983 9.628500 AAGATAATCTAACAAGATAACAACCCC 57.372 33.333 0.00 0.00 0.00 4.95
3273 3994 9.713740 GCACATGAAGAAAGATAATCTAACAAG 57.286 33.333 0.00 0.00 0.00 3.16
3274 3995 9.230122 TGCACATGAAGAAAGATAATCTAACAA 57.770 29.630 0.00 0.00 0.00 2.83
3275 3996 8.668353 GTGCACATGAAGAAAGATAATCTAACA 58.332 33.333 13.17 0.00 0.00 2.41
3276 3997 8.125448 GGTGCACATGAAGAAAGATAATCTAAC 58.875 37.037 20.43 0.00 0.00 2.34
3277 3998 8.049117 AGGTGCACATGAAGAAAGATAATCTAA 58.951 33.333 20.43 0.00 0.00 2.10
3278 3999 7.568349 AGGTGCACATGAAGAAAGATAATCTA 58.432 34.615 20.43 0.00 0.00 1.98
3279 4000 6.421485 AGGTGCACATGAAGAAAGATAATCT 58.579 36.000 20.43 0.00 0.00 2.40
3280 4001 6.690194 AGGTGCACATGAAGAAAGATAATC 57.310 37.500 20.43 0.00 0.00 1.75
3299 4020 6.142818 TGATGTGTTTCTTTAACCAAGGTG 57.857 37.500 0.00 0.00 35.81 4.00
3317 4038 6.315642 CAGAACAGATCAAAGTGCTATGATGT 59.684 38.462 0.00 0.00 36.45 3.06
3369 4091 8.589335 TTCTTACTAAAATATGGCGTCAGATC 57.411 34.615 0.00 0.00 0.00 2.75
3382 4104 7.062255 GCTCGCTTGCATTTTTCTTACTAAAAT 59.938 33.333 0.00 0.00 36.03 1.82
3400 4123 0.792640 ATCTCAAACACGCTCGCTTG 59.207 50.000 0.00 0.00 0.00 4.01
3401 4124 1.512926 AATCTCAAACACGCTCGCTT 58.487 45.000 0.00 0.00 0.00 4.68
3407 4143 3.120165 GGAGAAGGAAATCTCAAACACGC 60.120 47.826 6.64 0.00 46.24 5.34
3552 4288 5.412594 CACCTGTCAGTACATAATTGCAAGT 59.587 40.000 4.94 4.58 34.37 3.16
3558 4294 3.265737 TGCCCACCTGTCAGTACATAATT 59.734 43.478 0.00 0.00 34.37 1.40
3579 4315 6.091849 GCATCTCAGCATACCTGTATTACATG 59.908 42.308 0.00 0.00 42.38 3.21
3622 4365 4.159506 AGCTCTCGCCCTATGAGATATTTC 59.840 45.833 0.00 0.00 41.39 2.17
3663 4406 2.000429 AATTGGCAGAAGCGAAATGC 58.000 45.000 0.00 0.00 41.84 3.56
3669 4412 4.142622 TGAACTTCATAATTGGCAGAAGCG 60.143 41.667 11.93 0.00 43.41 4.68
3700 4443 4.377839 TGGTGCTTGAAAACGAATTCAA 57.622 36.364 15.75 15.75 44.68 2.69
3701 4444 4.377839 TTGGTGCTTGAAAACGAATTCA 57.622 36.364 6.22 0.00 37.53 2.57
3702 4445 5.461737 TCATTTGGTGCTTGAAAACGAATTC 59.538 36.000 0.00 0.00 0.00 2.17
3727 4479 7.522374 AGATTCTCTAACACGAAATCTTTTGC 58.478 34.615 0.00 0.00 0.00 3.68
3733 4485 7.596749 TTGGAAGATTCTCTAACACGAAATC 57.403 36.000 0.00 0.00 0.00 2.17
3734 4486 6.092807 GCTTGGAAGATTCTCTAACACGAAAT 59.907 38.462 0.00 0.00 0.00 2.17
3745 4529 6.655078 ATAGAGAGAGCTTGGAAGATTCTC 57.345 41.667 10.87 10.87 37.98 2.87
3760 4544 7.658167 CAGGAGAAACGAGTACATATAGAGAGA 59.342 40.741 0.00 0.00 0.00 3.10
3761 4545 7.572353 GCAGGAGAAACGAGTACATATAGAGAG 60.572 44.444 0.00 0.00 0.00 3.20
3762 4546 6.205076 GCAGGAGAAACGAGTACATATAGAGA 59.795 42.308 0.00 0.00 0.00 3.10
3763 4547 6.017026 TGCAGGAGAAACGAGTACATATAGAG 60.017 42.308 0.00 0.00 0.00 2.43
3764 4548 5.826208 TGCAGGAGAAACGAGTACATATAGA 59.174 40.000 0.00 0.00 0.00 1.98
3765 4549 6.073327 TGCAGGAGAAACGAGTACATATAG 57.927 41.667 0.00 0.00 0.00 1.31
3766 4550 6.096423 AGTTGCAGGAGAAACGAGTACATATA 59.904 38.462 0.00 0.00 38.40 0.86
3767 4551 5.105310 AGTTGCAGGAGAAACGAGTACATAT 60.105 40.000 0.00 0.00 38.40 1.78
3768 4552 4.219944 AGTTGCAGGAGAAACGAGTACATA 59.780 41.667 0.00 0.00 38.40 2.29
3769 4553 3.006967 AGTTGCAGGAGAAACGAGTACAT 59.993 43.478 0.00 0.00 38.40 2.29
3809 5683 4.908601 ATTCAGTACACCCACAATCTGA 57.091 40.909 0.00 0.00 0.00 3.27
3820 5694 8.292448 ACATCATCTGACAAAAATTCAGTACAC 58.708 33.333 0.00 0.00 41.22 2.90
3868 5748 6.259550 ACTTCATAATTGGCAAAGAGACAC 57.740 37.500 3.01 0.00 32.34 3.67
3903 5783 6.183360 TGGCAAACCAGATTCACTAATTTGTT 60.183 34.615 0.00 0.00 42.67 2.83
3920 5800 2.908688 AAGAATGGTGTTGGCAAACC 57.091 45.000 18.66 18.66 35.25 3.27
3961 5872 1.372838 CCAGCGTGTGTTTGGTGTGA 61.373 55.000 0.00 0.00 31.88 3.58
4190 6111 1.596934 GTCGTGGGAGCTGGATTCA 59.403 57.895 0.00 0.00 0.00 2.57
4218 6139 2.264480 CGGCGGTGGAGATGACAA 59.736 61.111 0.00 0.00 0.00 3.18
4323 6244 1.466167 CCGTTCAGCCACTGATTCTTG 59.534 52.381 0.00 0.00 40.39 3.02
4377 6298 1.140252 AGTAACACCCACAAGCTCGTT 59.860 47.619 0.00 0.00 0.00 3.85
4403 6324 3.073735 AGGGAGAGCGCACAGAGG 61.074 66.667 11.47 0.00 0.00 3.69
4463 6384 1.977854 TGTTCTTTGCTAGCTCTGGGA 59.022 47.619 17.23 4.49 0.00 4.37
4534 6455 8.275187 ACAATGATATCCCTACCAGTATTTGA 57.725 34.615 0.00 0.00 0.00 2.69
4557 6478 3.489908 GCTGCTGAGATCTCGATGTAACA 60.490 47.826 17.76 6.99 0.00 2.41


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

AutoCloner maintained by Alex Coulton.