Multiple sequence alignment - TraesCS3B01G581900

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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 TraesCS3B01G581900 chr3B 100.000 5358 0 0 1 5358 810324719 810330076 0.000000e+00 9895.0
1 TraesCS3B01G581900 chr3B 95.455 594 23 4 1 591 808964163 808963571 0.000000e+00 944.0
2 TraesCS3B01G581900 chr3A 91.599 3845 190 47 845 4627 732665098 732668871 0.000000e+00 5188.0
3 TraesCS3B01G581900 chr3A 87.615 759 50 21 4618 5358 732670850 732671582 0.000000e+00 841.0
4 TraesCS3B01G581900 chr3A 92.727 110 7 1 739 847 732665020 732665129 2.000000e-34 158.0
5 TraesCS3B01G581900 chr3D 94.681 1974 89 6 1623 3583 603418642 603416672 0.000000e+00 3049.0
6 TraesCS3B01G581900 chr3D 95.017 1766 56 13 3596 5358 603415240 603413504 0.000000e+00 2745.0
7 TraesCS3B01G581900 chr3D 86.007 829 57 27 844 1632 603419745 603418936 0.000000e+00 833.0
8 TraesCS3B01G581900 chr3D 90.909 110 9 1 739 847 603419822 603419713 4.320000e-31 147.0
9 TraesCS3B01G581900 chr5B 97.639 593 11 3 1 591 536221108 536220517 0.000000e+00 1014.0
10 TraesCS3B01G581900 chr5B 83.234 167 14 11 291 447 371388723 371388561 2.010000e-29 141.0
11 TraesCS3B01G581900 chr7B 95.110 593 26 3 1 591 678643265 678643856 0.000000e+00 931.0
12 TraesCS3B01G581900 chr7B 94.276 594 30 4 1 591 705694015 705694607 0.000000e+00 905.0
13 TraesCS3B01G581900 chr4B 85.016 614 44 15 1 591 554014276 554014864 1.000000e-161 580.0
14 TraesCS3B01G581900 chr1A 82.931 621 50 26 1 591 112367741 112367147 4.790000e-140 508.0
15 TraesCS3B01G581900 chr1A 94.964 139 6 1 592 729 140362706 140362844 3.250000e-52 217.0
16 TraesCS3B01G581900 chr4A 82.126 621 49 29 1 591 173699818 173699230 4.860000e-130 475.0
17 TraesCS3B01G581900 chr4A 94.326 141 6 2 595 734 207758565 207758426 1.170000e-51 215.0
18 TraesCS3B01G581900 chr4A 86.806 144 11 6 311 447 202219684 202219542 2.580000e-33 154.0
19 TraesCS3B01G581900 chr4D 78.641 515 64 23 7 479 449191702 449192212 3.140000e-77 300.0
20 TraesCS3B01G581900 chr1D 76.245 522 66 33 6 474 106514418 106513902 1.940000e-54 224.0
21 TraesCS3B01G581900 chr5D 76.096 502 69 29 22 479 537328676 537329170 1.170000e-51 215.0
22 TraesCS3B01G581900 chr6D 89.888 89 7 2 636 724 327980026 327980112 4.390000e-21 113.0
23 TraesCS3B01G581900 chr2B 86.667 90 11 1 640 729 5975593 5975505 1.230000e-16 99.0
24 TraesCS3B01G581900 chr5A 100.000 28 0 0 477 504 698155447 698155420 1.000000e-02 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G581900 chr3B 810324719 810330076 5357 False 9895.000000 9895 100.0000 1 5358 1 chr3B.!!$F1 5357
1 TraesCS3B01G581900 chr3B 808963571 808964163 592 True 944.000000 944 95.4550 1 591 1 chr3B.!!$R1 590
2 TraesCS3B01G581900 chr3A 732665020 732671582 6562 False 2062.333333 5188 90.6470 739 5358 3 chr3A.!!$F1 4619
3 TraesCS3B01G581900 chr3D 603413504 603419822 6318 True 1693.500000 3049 91.6535 739 5358 4 chr3D.!!$R1 4619
4 TraesCS3B01G581900 chr5B 536220517 536221108 591 True 1014.000000 1014 97.6390 1 591 1 chr5B.!!$R2 590
5 TraesCS3B01G581900 chr7B 678643265 678643856 591 False 931.000000 931 95.1100 1 591 1 chr7B.!!$F1 590
6 TraesCS3B01G581900 chr7B 705694015 705694607 592 False 905.000000 905 94.2760 1 591 1 chr7B.!!$F2 590
7 TraesCS3B01G581900 chr4B 554014276 554014864 588 False 580.000000 580 85.0160 1 591 1 chr4B.!!$F1 590
8 TraesCS3B01G581900 chr1A 112367147 112367741 594 True 508.000000 508 82.9310 1 591 1 chr1A.!!$R1 590
9 TraesCS3B01G581900 chr4A 173699230 173699818 588 True 475.000000 475 82.1260 1 591 1 chr4A.!!$R1 590
10 TraesCS3B01G581900 chr4D 449191702 449192212 510 False 300.000000 300 78.6410 7 479 1 chr4D.!!$F1 472
11 TraesCS3B01G581900 chr1D 106513902 106514418 516 True 224.000000 224 76.2450 6 474 1 chr1D.!!$R1 468

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
725 829 0.249741 TAAAGGCGCGGCTTAGGATC 60.250 55.000 42.43 7.22 0.00 3.36 F
1460 1596 0.104120 CTGAACCGCGTCCATCCATA 59.896 55.000 4.92 0.00 0.00 2.74 F
1461 1597 0.104120 TGAACCGCGTCCATCCATAG 59.896 55.000 4.92 0.00 0.00 2.23 F
1660 2121 0.108472 GCCCTCTTTCATTTGGCAGC 60.108 55.000 0.00 0.00 41.76 5.25 F
1825 2286 0.185901 AGGTGAGGCTGCTTTTTGGA 59.814 50.000 0.00 0.00 0.00 3.53 F
1862 2323 0.235665 GAACGGCTCATGTGTGTGTG 59.764 55.000 0.00 0.00 0.00 3.82 F
1968 2438 0.613572 TAGAGGTGTGCCATCCGTGA 60.614 55.000 0.00 0.00 37.19 4.35 F
2665 3145 1.068588 TGTAGTATCATGGCTCACCGC 59.931 52.381 0.00 0.00 39.70 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 2304 0.235665 CACACACACATGAGCCGTTC 59.764 55.000 0.0 0.0 0.00 3.95 R
2923 3404 0.031994 CAGGAAAAAGGTTGCACGGG 59.968 55.000 0.0 0.0 0.00 5.28 R
3058 3539 0.859232 GGCGTATGTATGGTTCTGCG 59.141 55.000 0.0 0.0 0.00 5.18 R
3420 3902 1.003580 AGTGGAGTGCTTATGTGGGTG 59.996 52.381 0.0 0.0 0.00 4.61 R
3808 5711 5.419542 TCTATAGGCACAACACAGATTGTC 58.580 41.667 0.0 0.0 40.89 3.18 R
3898 5801 8.415950 TGGTCAAGGCAAAATAAATAGAGAAA 57.584 30.769 0.0 0.0 0.00 2.52 R
3951 5854 0.459237 CCTTGAGCACTACCTCTGCG 60.459 60.000 0.0 0.0 39.79 5.18 R
4648 8539 0.321298 CCGTTTCGACCTCCCACAAT 60.321 55.000 0.0 0.0 0.00 2.71 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
601 705 7.841915 AAAAACATTCCAAACGTCATCTTTT 57.158 28.000 0.00 0.00 0.00 2.27
602 706 7.841915 AAAACATTCCAAACGTCATCTTTTT 57.158 28.000 0.00 0.00 0.00 1.94
630 734 3.865224 TTTTCGTTCTTAACAGCGTCC 57.135 42.857 0.00 0.00 0.00 4.79
631 735 1.787012 TTCGTTCTTAACAGCGTCCC 58.213 50.000 0.00 0.00 0.00 4.46
632 736 0.387622 TCGTTCTTAACAGCGTCCCG 60.388 55.000 0.00 0.00 0.00 5.14
633 737 0.387622 CGTTCTTAACAGCGTCCCGA 60.388 55.000 0.00 0.00 0.00 5.14
634 738 1.787012 GTTCTTAACAGCGTCCCGAA 58.213 50.000 0.00 0.00 0.00 4.30
635 739 1.458445 GTTCTTAACAGCGTCCCGAAC 59.542 52.381 0.00 0.00 0.00 3.95
654 758 3.343421 GTCGCGTCGGCCTTGTTT 61.343 61.111 5.77 0.00 35.02 2.83
655 759 3.342627 TCGCGTCGGCCTTGTTTG 61.343 61.111 5.77 0.00 35.02 2.93
656 760 4.383602 CGCGTCGGCCTTGTTTGG 62.384 66.667 0.00 0.00 35.02 3.28
657 761 4.038080 GCGTCGGCCTTGTTTGGG 62.038 66.667 0.00 0.00 0.00 4.12
663 767 4.007644 GCCTTGTTTGGGCCAGGC 62.008 66.667 16.86 16.86 43.49 4.85
674 778 3.015145 GCCAGGCCTAGGTGGGAA 61.015 66.667 17.85 0.00 34.06 3.97
675 779 2.998949 CCAGGCCTAGGTGGGAAC 59.001 66.667 3.98 0.00 36.00 3.62
711 815 3.642755 CCATAGCGGCGCTAAAGG 58.357 61.111 40.67 36.79 44.62 3.11
712 816 2.607892 CCATAGCGGCGCTAAAGGC 61.608 63.158 40.67 8.03 44.62 4.35
721 825 3.014856 GCTAAAGGCGCGGCTTAG 58.985 61.111 42.43 34.79 0.00 2.18
722 826 2.534903 GCTAAAGGCGCGGCTTAGG 61.535 63.158 42.43 34.88 0.00 2.69
723 827 1.143183 CTAAAGGCGCGGCTTAGGA 59.857 57.895 42.43 29.50 0.00 2.94
724 828 0.249911 CTAAAGGCGCGGCTTAGGAT 60.250 55.000 42.43 30.42 0.00 3.24
725 829 0.249741 TAAAGGCGCGGCTTAGGATC 60.250 55.000 42.43 7.22 0.00 3.36
726 830 1.972660 AAAGGCGCGGCTTAGGATCT 61.973 55.000 42.43 26.21 0.00 2.75
727 831 2.356433 GGCGCGGCTTAGGATCTC 60.356 66.667 27.05 0.00 0.00 2.75
728 832 2.356433 GCGCGGCTTAGGATCTCC 60.356 66.667 8.83 0.00 0.00 3.71
729 833 2.340443 CGCGGCTTAGGATCTCCC 59.660 66.667 0.00 0.00 36.42 4.30
730 834 2.340443 GCGGCTTAGGATCTCCCG 59.660 66.667 0.00 0.00 40.87 5.14
731 835 2.340443 CGGCTTAGGATCTCCCGC 59.660 66.667 0.00 0.00 40.87 6.13
732 836 2.340443 GGCTTAGGATCTCCCGCG 59.660 66.667 0.00 0.00 40.87 6.46
733 837 2.356433 GCTTAGGATCTCCCGCGC 60.356 66.667 0.00 0.00 40.87 6.86
734 838 2.862223 GCTTAGGATCTCCCGCGCT 61.862 63.158 5.56 0.00 40.87 5.92
735 839 1.287503 CTTAGGATCTCCCGCGCTC 59.712 63.158 5.56 0.00 40.87 5.03
736 840 2.465097 CTTAGGATCTCCCGCGCTCG 62.465 65.000 5.56 0.00 40.87 5.03
761 865 4.204012 TCTGAAACAGAAAAATCCGTGGT 58.796 39.130 0.00 0.00 37.57 4.16
765 869 3.982576 ACAGAAAAATCCGTGGTGTTC 57.017 42.857 0.00 0.00 0.00 3.18
767 871 2.546368 CAGAAAAATCCGTGGTGTTCGA 59.454 45.455 0.00 0.00 0.00 3.71
780 885 4.314440 TTCGAGCTTGCTGGGCGT 62.314 61.111 0.00 0.00 34.52 5.68
851 956 3.804193 CGAAAGCGAAGGCCCAGC 61.804 66.667 0.00 2.10 41.24 4.85
852 957 2.360475 GAAAGCGAAGGCCCAGCT 60.360 61.111 10.95 10.95 43.90 4.24
853 958 2.360475 AAAGCGAAGGCCCAGCTC 60.360 61.111 16.15 0.11 40.78 4.09
854 959 3.927481 AAAGCGAAGGCCCAGCTCC 62.927 63.158 16.15 0.00 40.78 4.70
857 962 4.821589 CGAAGGCCCAGCTCCGAC 62.822 72.222 0.00 0.00 0.00 4.79
858 963 4.475135 GAAGGCCCAGCTCCGACC 62.475 72.222 0.00 0.00 0.00 4.79
947 1061 3.188786 GCTCGCTCGCGTGGATTT 61.189 61.111 5.77 0.00 40.74 2.17
948 1062 2.998667 CTCGCTCGCGTGGATTTC 59.001 61.111 5.77 0.00 40.74 2.17
949 1063 2.849966 CTCGCTCGCGTGGATTTCG 61.850 63.158 5.77 2.13 40.74 3.46
950 1064 3.179265 CGCTCGCGTGGATTTCGT 61.179 61.111 5.77 0.00 34.35 3.85
951 1065 2.395690 GCTCGCGTGGATTTCGTG 59.604 61.111 5.77 0.00 39.65 4.35
952 1066 2.092291 GCTCGCGTGGATTTCGTGA 61.092 57.895 5.77 0.00 43.70 4.35
1043 1161 3.368501 CCCCTCCTCCCTCCTCCA 61.369 72.222 0.00 0.00 0.00 3.86
1321 1457 2.396157 GGGTGTTCGACGGAATGCC 61.396 63.158 0.00 0.00 34.05 4.40
1345 1481 1.007734 GTCGTGCCGAGTCTGTTCA 60.008 57.895 0.00 0.00 36.23 3.18
1348 1484 1.668151 GTGCCGAGTCTGTTCACCC 60.668 63.158 0.00 0.00 0.00 4.61
1355 1491 1.079750 GTCTGTTCACCCGGAGAGC 60.080 63.158 0.73 3.04 0.00 4.09
1357 1493 2.525629 TGTTCACCCGGAGAGCCA 60.526 61.111 0.73 0.00 0.00 4.75
1377 1513 2.615912 CAAGGCCAGATAAGTTAGCTGC 59.384 50.000 20.38 15.52 40.69 5.25
1399 1535 2.335369 GACGGCGTCACTGACAGT 59.665 61.111 33.07 1.07 32.09 3.55
1404 1540 0.319555 GGCGTCACTGACAGTGCTAA 60.320 55.000 27.53 10.71 45.54 3.09
1419 1555 9.317936 TGACAGTGCTAAATATTTCACTAGATG 57.682 33.333 17.51 11.32 37.66 2.90
1436 1572 3.501349 AGATGATACCAGTAGCGGTCAT 58.499 45.455 0.00 0.00 40.67 3.06
1440 1576 0.973496 TACCAGTAGCGGTCATGCCA 60.973 55.000 0.00 0.00 40.67 4.92
1446 1582 0.391130 TAGCGGTCATGCCACTGAAC 60.391 55.000 0.00 0.00 36.97 3.18
1449 1585 2.690778 GGTCATGCCACTGAACCGC 61.691 63.158 1.78 0.00 37.17 5.68
1450 1586 2.741985 TCATGCCACTGAACCGCG 60.742 61.111 0.00 0.00 0.00 6.46
1451 1587 3.049674 CATGCCACTGAACCGCGT 61.050 61.111 4.92 0.00 0.00 6.01
1452 1588 2.742372 ATGCCACTGAACCGCGTC 60.742 61.111 4.92 0.00 0.00 5.19
1453 1589 4.980805 TGCCACTGAACCGCGTCC 62.981 66.667 4.92 0.00 0.00 4.79
1454 1590 4.980805 GCCACTGAACCGCGTCCA 62.981 66.667 4.92 0.00 0.00 4.02
1456 1592 2.100631 CCACTGAACCGCGTCCATC 61.101 63.158 4.92 0.00 0.00 3.51
1457 1593 2.100631 CACTGAACCGCGTCCATCC 61.101 63.158 4.92 0.00 0.00 3.51
1459 1595 1.153369 CTGAACCGCGTCCATCCAT 60.153 57.895 4.92 0.00 0.00 3.41
1460 1596 0.104120 CTGAACCGCGTCCATCCATA 59.896 55.000 4.92 0.00 0.00 2.74
1461 1597 0.104120 TGAACCGCGTCCATCCATAG 59.896 55.000 4.92 0.00 0.00 2.23
1465 1615 1.004560 CGCGTCCATCCATAGCCAT 60.005 57.895 0.00 0.00 0.00 4.40
1493 1643 3.679083 GCTTATTTGAGTCGGTAGTGGCT 60.679 47.826 0.00 0.00 0.00 4.75
1501 1651 1.755380 GTCGGTAGTGGCTTCCTACAT 59.245 52.381 10.28 0.00 37.18 2.29
1504 1654 2.691526 CGGTAGTGGCTTCCTACATACA 59.308 50.000 10.28 0.00 37.18 2.29
1505 1655 3.321111 CGGTAGTGGCTTCCTACATACAT 59.679 47.826 10.28 0.00 37.18 2.29
1506 1656 4.521639 CGGTAGTGGCTTCCTACATACATA 59.478 45.833 10.28 0.00 37.18 2.29
1507 1657 5.185249 CGGTAGTGGCTTCCTACATACATAT 59.815 44.000 10.28 0.00 37.18 1.78
1508 1658 6.625300 CGGTAGTGGCTTCCTACATACATATC 60.625 46.154 10.28 0.00 37.18 1.63
1509 1659 6.210784 GGTAGTGGCTTCCTACATACATATCA 59.789 42.308 10.28 0.00 37.18 2.15
1539 1689 8.239314 TCAATTTCTCTCTATTTGTTGTCATGC 58.761 33.333 0.00 0.00 0.00 4.06
1540 1690 7.692460 ATTTCTCTCTATTTGTTGTCATGCA 57.308 32.000 0.00 0.00 0.00 3.96
1541 1691 7.509141 TTTCTCTCTATTTGTTGTCATGCAA 57.491 32.000 0.00 0.00 34.16 4.08
1543 1693 5.645067 TCTCTCTATTTGTTGTCATGCAAGG 59.355 40.000 0.00 0.00 37.83 3.61
1544 1694 4.156556 TCTCTATTTGTTGTCATGCAAGGC 59.843 41.667 0.00 0.00 37.83 4.35
1545 1695 3.825585 TCTATTTGTTGTCATGCAAGGCA 59.174 39.130 0.00 0.00 44.86 4.75
1547 1697 2.975732 TTGTTGTCATGCAAGGCAAA 57.024 40.000 10.97 0.00 43.62 3.68
1548 1698 2.512485 TGTTGTCATGCAAGGCAAAG 57.488 45.000 10.97 0.00 43.62 2.77
1550 1700 2.629137 TGTTGTCATGCAAGGCAAAGAT 59.371 40.909 10.97 0.00 43.62 2.40
1551 1701 3.248266 GTTGTCATGCAAGGCAAAGATC 58.752 45.455 10.97 0.00 43.62 2.75
1552 1702 1.469703 TGTCATGCAAGGCAAAGATCG 59.530 47.619 0.00 0.00 43.62 3.69
1553 1703 1.470098 GTCATGCAAGGCAAAGATCGT 59.530 47.619 0.00 0.00 43.62 3.73
1555 1705 1.469703 CATGCAAGGCAAAGATCGTCA 59.530 47.619 0.00 0.00 43.62 4.35
1557 1707 2.161855 TGCAAGGCAAAGATCGTCAAT 58.838 42.857 0.00 0.00 34.76 2.57
1558 1708 2.557924 TGCAAGGCAAAGATCGTCAATT 59.442 40.909 0.00 0.00 34.76 2.32
1559 1709 3.755905 TGCAAGGCAAAGATCGTCAATTA 59.244 39.130 0.00 0.00 34.76 1.40
1560 1710 4.098416 GCAAGGCAAAGATCGTCAATTAC 58.902 43.478 0.00 0.00 0.00 1.89
1561 1711 7.588305 TGCAAGGCAAAGATCGTCAATTACG 62.588 44.000 0.00 0.00 44.15 3.18
1586 1736 4.478206 TTCTCTTTAGGTCCTGATGCAG 57.522 45.455 0.00 0.00 0.00 4.41
1660 2121 0.108472 GCCCTCTTTCATTTGGCAGC 60.108 55.000 0.00 0.00 41.76 5.25
1825 2286 0.185901 AGGTGAGGCTGCTTTTTGGA 59.814 50.000 0.00 0.00 0.00 3.53
1843 2304 8.885494 TTTTTGGAGGTGTATCTTTGAATTTG 57.115 30.769 0.00 0.00 0.00 2.32
1862 2323 0.235665 GAACGGCTCATGTGTGTGTG 59.764 55.000 0.00 0.00 0.00 3.82
1872 2342 3.685756 TCATGTGTGTGTGCATCATGTAG 59.314 43.478 0.00 0.00 39.00 2.74
1873 2343 3.124578 TGTGTGTGTGCATCATGTAGT 57.875 42.857 0.00 0.00 0.00 2.73
1874 2344 3.475575 TGTGTGTGTGCATCATGTAGTT 58.524 40.909 0.00 0.00 0.00 2.24
1875 2345 4.636249 TGTGTGTGTGCATCATGTAGTTA 58.364 39.130 0.00 0.00 0.00 2.24
1876 2346 5.059833 TGTGTGTGTGCATCATGTAGTTAA 58.940 37.500 0.00 0.00 0.00 2.01
1877 2347 5.704978 TGTGTGTGTGCATCATGTAGTTAAT 59.295 36.000 0.00 0.00 0.00 1.40
1878 2348 6.023435 GTGTGTGTGCATCATGTAGTTAATG 58.977 40.000 0.00 0.00 0.00 1.90
1879 2349 5.704978 TGTGTGTGCATCATGTAGTTAATGT 59.295 36.000 0.00 0.00 0.00 2.71
1880 2350 6.876257 TGTGTGTGCATCATGTAGTTAATGTA 59.124 34.615 0.00 0.00 0.00 2.29
1894 2364 8.306038 TGTAGTTAATGTAATTACGTGGTCTGT 58.694 33.333 11.06 0.00 38.79 3.41
1895 2365 7.823149 AGTTAATGTAATTACGTGGTCTGTC 57.177 36.000 11.06 0.00 38.79 3.51
1968 2438 0.613572 TAGAGGTGTGCCATCCGTGA 60.614 55.000 0.00 0.00 37.19 4.35
2012 2482 8.684520 TGGTTATTTATTGGGTTACGTTTATGG 58.315 33.333 0.00 0.00 0.00 2.74
2024 2494 6.799925 GGTTACGTTTATGGACAATGAAACTG 59.200 38.462 0.00 0.00 31.11 3.16
2048 2518 9.217278 CTGATTCATTCCAAATAGATAGACTGG 57.783 37.037 0.00 0.00 0.00 4.00
2049 2519 7.663081 TGATTCATTCCAAATAGATAGACTGGC 59.337 37.037 0.00 0.00 0.00 4.85
2118 2588 4.687018 TCAACACTTGAATTGCAATGCATC 59.313 37.500 20.94 11.46 35.97 3.91
2142 2612 5.396772 CCCAAGCCAGAGTTCTCATGTTATA 60.397 44.000 2.64 0.00 0.00 0.98
2186 2656 9.371136 TCTTCTCTAGTAAAATAATGTGCTGTG 57.629 33.333 0.00 0.00 0.00 3.66
2203 2673 3.922850 GCTGTGCATTTAAAAAGGAGAGC 59.077 43.478 14.94 14.94 0.00 4.09
2289 2759 2.182030 GGTCTTGACCGCTCCTCG 59.818 66.667 3.87 0.00 38.08 4.63
2312 2782 4.000988 GCGGATTACATCGGGTATGAATT 58.999 43.478 0.00 0.00 39.07 2.17
2452 2932 3.073062 ACACATTTTGGTAGGAGCAGAGT 59.927 43.478 0.00 0.00 0.00 3.24
2471 2951 6.671190 CAGAGTGTGCTTGTTATTTGATTCA 58.329 36.000 0.00 0.00 0.00 2.57
2535 3015 1.080298 TTGTGCCCATTACGTAAGCG 58.920 50.000 14.25 7.30 45.62 4.68
2665 3145 1.068588 TGTAGTATCATGGCTCACCGC 59.931 52.381 0.00 0.00 39.70 5.68
2695 3175 3.722147 CGTAAGCACATCCTAATCTGCT 58.278 45.455 0.00 0.00 38.60 4.24
2899 3380 8.420374 AGTAACCACATGATTTGTCGTTATAG 57.580 34.615 0.00 0.00 41.76 1.31
2923 3404 4.677673 AATAATTTGGGGCTGAATCTGC 57.322 40.909 3.37 3.37 0.00 4.26
2949 3430 2.742774 CAACCTTTTTCCTGCTTTCCG 58.257 47.619 0.00 0.00 0.00 4.30
3058 3539 4.631813 ACTGCATTCCGTATTTCAGAAGTC 59.368 41.667 0.00 0.00 0.00 3.01
3094 3575 1.986575 GCCGAAGAGCAATCAGGCAC 61.987 60.000 7.50 0.00 43.65 5.01
3294 3775 5.357878 TGGTGCTTATGAATGGTTCTTGATC 59.642 40.000 0.00 0.00 0.00 2.92
3402 3884 2.647297 GCTCCTTGCAACTGTGGC 59.353 61.111 0.00 0.00 42.31 5.01
3420 3902 2.438021 TGGCTAATGGGACTACATGACC 59.562 50.000 0.00 0.00 0.00 4.02
3570 4052 5.484173 TGCATCTATTTAAGCTGGTTTCG 57.516 39.130 0.00 0.00 0.00 3.46
3594 5495 5.715279 GGGTTCTAGCTTTATTTTTCTGGGT 59.285 40.000 0.00 0.00 0.00 4.51
3776 5679 5.105473 TGTTGGCCTCTAGTTATAGTGTGTC 60.105 44.000 3.32 0.00 0.00 3.67
4029 5932 1.039856 ATAACCCAAATGCCCGCATC 58.960 50.000 2.00 0.00 35.31 3.91
4047 5950 1.740297 TCCTCGAGACAGTGAGCTAC 58.260 55.000 15.71 0.00 0.00 3.58
4056 5959 1.000163 ACAGTGAGCTACAACGAGGTG 60.000 52.381 0.00 0.00 0.00 4.00
4107 6010 1.079197 TGCCGTCACACTATGCCAG 60.079 57.895 0.00 0.00 0.00 4.85
4192 6095 6.464834 CGTCGATTTTAATCTTGGTGCTTAAC 59.535 38.462 0.00 0.00 33.24 2.01
4216 6119 1.268032 GCAGTTGTCGTGTTCAACCTG 60.268 52.381 5.38 5.12 44.02 4.00
4297 6200 3.065925 GCTGCACAAGGAATCTGGAATAC 59.934 47.826 0.00 0.00 0.00 1.89
4318 6221 2.380410 CGAAAGCACGGAGGGTTCG 61.380 63.158 0.00 0.00 0.00 3.95
4399 6302 7.286775 GTCTCCCTAGCTGGATTATAGAATAGG 59.713 44.444 0.00 0.00 38.35 2.57
4424 6327 3.635836 AGCTATCCAAGTAGTACCGGTTC 59.364 47.826 15.04 8.12 0.00 3.62
4452 6355 6.320171 TGTAATACTCGAAGAAGAGAAACCG 58.680 40.000 0.62 0.00 40.57 4.44
4456 6359 1.067776 TCGAAGAAGAGAAACCGCTCC 60.068 52.381 0.00 0.00 35.49 4.70
4502 6405 4.563061 TGCTGCTATGCTGTGTATGATAG 58.437 43.478 0.00 0.00 0.00 2.08
4503 6406 4.281688 TGCTGCTATGCTGTGTATGATAGA 59.718 41.667 0.00 0.00 0.00 1.98
4504 6407 5.221501 TGCTGCTATGCTGTGTATGATAGAA 60.222 40.000 0.00 0.00 0.00 2.10
4505 6408 5.873712 GCTGCTATGCTGTGTATGATAGAAT 59.126 40.000 0.00 0.00 0.00 2.40
4539 6442 1.210478 GTCTCCTGTGGCATGTATGGT 59.790 52.381 0.00 0.00 0.00 3.55
4540 6443 2.434336 GTCTCCTGTGGCATGTATGGTA 59.566 50.000 0.00 0.00 0.00 3.25
4541 6444 3.071602 GTCTCCTGTGGCATGTATGGTAT 59.928 47.826 0.00 0.00 0.00 2.73
4542 6445 3.071457 TCTCCTGTGGCATGTATGGTATG 59.929 47.826 0.00 0.00 0.00 2.39
4543 6446 2.106338 TCCTGTGGCATGTATGGTATGG 59.894 50.000 0.00 0.00 0.00 2.74
4583 6486 4.148128 ACTTCTATTGCTCCTGATGGTG 57.852 45.455 0.00 0.00 34.23 4.17
4632 8523 7.417003 GGTTTCTAGTCTGGTTTCCTCTCTATC 60.417 44.444 0.00 0.00 0.00 2.08
4648 8539 9.101325 TCCTCTCTATCTTCTTTACTGGAAAAA 57.899 33.333 0.00 0.00 0.00 1.94
4661 8552 2.228822 CTGGAAAAATTGTGGGAGGTCG 59.771 50.000 0.00 0.00 0.00 4.79
4666 8557 1.519408 AATTGTGGGAGGTCGAAACG 58.481 50.000 0.00 0.00 0.00 3.60
4806 8697 6.742109 AGAAAAGAGAATGTCCAATGTTGTG 58.258 36.000 0.00 0.00 0.00 3.33
4910 8802 5.486526 TCCAAATGACCCACATATTTTTGC 58.513 37.500 0.00 0.00 38.38 3.68
4948 8847 7.659390 TGCCCAAAAGTAAATGTTATTTTCAGG 59.341 33.333 0.00 0.00 0.00 3.86
5064 8964 5.163854 CCGCAACTGTAATCTAAAAGGAGTG 60.164 44.000 0.00 0.00 0.00 3.51
5127 9027 4.811969 ATGATGTAACTTACCACCGACA 57.188 40.909 0.00 0.00 0.00 4.35
5139 9039 2.104111 ACCACCGACAAATTCAGTGAGA 59.896 45.455 0.00 0.00 34.90 3.27
5214 9114 1.981495 AGAGGACAGGGTTCTCCTTTG 59.019 52.381 1.07 0.00 45.47 2.77
5323 9232 7.254117 GGACATATCGCAATAATATCGTTCCTG 60.254 40.741 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
609 713 3.002553 GGGACGCTGTTAAGAACGAAAAA 59.997 43.478 2.11 0.00 0.00 1.94
610 714 2.545106 GGGACGCTGTTAAGAACGAAAA 59.455 45.455 2.11 0.00 0.00 2.29
611 715 2.137523 GGGACGCTGTTAAGAACGAAA 58.862 47.619 2.11 0.00 0.00 3.46
612 716 1.787012 GGGACGCTGTTAAGAACGAA 58.213 50.000 2.11 0.00 0.00 3.85
613 717 3.502237 GGGACGCTGTTAAGAACGA 57.498 52.632 2.11 0.00 0.00 3.85
637 741 3.343421 AAACAAGGCCGACGCGAC 61.343 61.111 15.93 5.54 35.02 5.19
638 742 3.342627 CAAACAAGGCCGACGCGA 61.343 61.111 15.93 0.00 35.02 5.87
639 743 4.383602 CCAAACAAGGCCGACGCG 62.384 66.667 3.53 3.53 35.02 6.01
640 744 4.038080 CCCAAACAAGGCCGACGC 62.038 66.667 0.00 0.00 0.00 5.19
641 745 4.038080 GCCCAAACAAGGCCGACG 62.038 66.667 0.00 0.00 45.16 5.12
647 751 3.313524 GGCCTGGCCCAAACAAGG 61.314 66.667 27.77 0.00 44.06 3.61
657 761 3.015145 TTCCCACCTAGGCCTGGC 61.015 66.667 17.99 11.05 35.39 4.85
658 762 2.680370 GGTTCCCACCTAGGCCTGG 61.680 68.421 17.99 13.68 40.44 4.45
659 763 2.998949 GGTTCCCACCTAGGCCTG 59.001 66.667 17.99 0.87 40.44 4.85
660 764 2.687566 CGGTTCCCACCTAGGCCT 60.688 66.667 11.78 11.78 41.64 5.19
661 765 4.484872 GCGGTTCCCACCTAGGCC 62.485 72.222 9.30 0.00 41.64 5.19
662 766 4.832608 CGCGGTTCCCACCTAGGC 62.833 72.222 9.30 0.00 41.64 3.93
663 767 3.387947 ACGCGGTTCCCACCTAGG 61.388 66.667 12.47 7.41 41.64 3.02
664 768 2.125673 CACGCGGTTCCCACCTAG 60.126 66.667 12.47 0.00 41.64 3.02
665 769 3.697747 CCACGCGGTTCCCACCTA 61.698 66.667 12.47 0.00 41.64 3.08
694 798 2.607892 GCCTTTAGCGCCGCTATGG 61.608 63.158 24.89 24.89 41.01 2.74
695 799 2.939022 GCCTTTAGCGCCGCTATG 59.061 61.111 20.79 15.10 41.01 2.23
704 808 2.534903 CCTAAGCCGCGCCTTTAGC 61.535 63.158 7.95 0.17 38.52 3.09
705 809 0.249911 ATCCTAAGCCGCGCCTTTAG 60.250 55.000 7.95 11.03 0.00 1.85
706 810 0.249741 GATCCTAAGCCGCGCCTTTA 60.250 55.000 7.95 1.36 0.00 1.85
707 811 1.523938 GATCCTAAGCCGCGCCTTT 60.524 57.895 7.95 0.05 0.00 3.11
708 812 2.109181 GATCCTAAGCCGCGCCTT 59.891 61.111 7.72 7.72 0.00 4.35
709 813 2.840102 AGATCCTAAGCCGCGCCT 60.840 61.111 0.00 0.00 0.00 5.52
710 814 2.356433 GAGATCCTAAGCCGCGCC 60.356 66.667 0.00 0.00 0.00 6.53
711 815 2.356433 GGAGATCCTAAGCCGCGC 60.356 66.667 0.00 0.00 0.00 6.86
712 816 2.340443 GGGAGATCCTAAGCCGCG 59.660 66.667 0.00 0.00 35.95 6.46
713 817 2.340443 CGGGAGATCCTAAGCCGC 59.660 66.667 0.00 0.00 35.95 6.53
714 818 2.340443 GCGGGAGATCCTAAGCCG 59.660 66.667 0.00 0.00 35.95 5.52
715 819 2.340443 CGCGGGAGATCCTAAGCC 59.660 66.667 0.00 0.00 35.95 4.35
716 820 2.356433 GCGCGGGAGATCCTAAGC 60.356 66.667 8.83 2.17 35.95 3.09
717 821 1.287503 GAGCGCGGGAGATCCTAAG 59.712 63.158 8.83 0.00 35.95 2.18
718 822 2.552819 CGAGCGCGGGAGATCCTAA 61.553 63.158 8.83 0.00 35.95 2.69
719 823 2.978565 CGAGCGCGGGAGATCCTA 60.979 66.667 8.83 0.00 35.95 2.94
729 833 2.215478 CTGTTTCAGAACCGAGCGCG 62.215 60.000 0.00 0.00 34.80 6.86
730 834 0.944311 TCTGTTTCAGAACCGAGCGC 60.944 55.000 0.00 0.00 37.57 5.92
731 835 1.497991 TTCTGTTTCAGAACCGAGCG 58.502 50.000 7.92 0.00 44.27 5.03
761 865 2.669569 GCCCAGCAAGCTCGAACA 60.670 61.111 0.00 0.00 0.00 3.18
765 869 4.093952 CAACGCCCAGCAAGCTCG 62.094 66.667 0.00 0.00 0.00 5.03
780 885 2.034687 GCCAAGAGAGCAGCCCAA 59.965 61.111 0.00 0.00 0.00 4.12
786 891 4.069232 CGACGGGCCAAGAGAGCA 62.069 66.667 4.39 0.00 0.00 4.26
860 965 4.445545 GTGCCTTCGCTTTCGCCG 62.446 66.667 0.00 0.00 35.36 6.46
861 966 4.445545 CGTGCCTTCGCTTTCGCC 62.446 66.667 0.00 0.00 35.36 5.54
892 997 2.734591 GGACGGCATCGGATAGCA 59.265 61.111 12.28 0.00 41.39 3.49
944 1058 4.381932 GGAATGGGAATTGCTTCACGAAAT 60.382 41.667 0.00 0.00 37.63 2.17
945 1059 3.056891 GGAATGGGAATTGCTTCACGAAA 60.057 43.478 0.00 0.00 37.63 3.46
946 1060 2.491693 GGAATGGGAATTGCTTCACGAA 59.508 45.455 0.00 0.00 37.63 3.85
947 1061 2.091541 GGAATGGGAATTGCTTCACGA 58.908 47.619 0.00 0.00 37.63 4.35
948 1062 1.134946 GGGAATGGGAATTGCTTCACG 59.865 52.381 0.00 0.00 37.63 4.35
949 1063 2.178580 TGGGAATGGGAATTGCTTCAC 58.821 47.619 0.00 0.00 35.20 3.18
950 1064 2.619697 TGGGAATGGGAATTGCTTCA 57.380 45.000 0.00 0.00 32.70 3.02
951 1065 3.181462 GGAATGGGAATGGGAATTGCTTC 60.181 47.826 0.00 0.00 0.00 3.86
952 1066 2.773661 GGAATGGGAATGGGAATTGCTT 59.226 45.455 0.00 0.00 0.00 3.91
1223 1359 1.369568 GGAAAAACGAACCGTGCGG 60.370 57.895 9.29 9.29 39.99 5.69
1233 1369 2.035259 CCGCGAAAACAAAGGAAAAACG 60.035 45.455 8.23 0.00 0.00 3.60
1335 1471 0.528470 CTCTCCGGGTGAACAGACTC 59.472 60.000 0.00 0.00 0.00 3.36
1336 1472 1.536943 GCTCTCCGGGTGAACAGACT 61.537 60.000 0.00 0.00 0.00 3.24
1337 1473 1.079750 GCTCTCCGGGTGAACAGAC 60.080 63.158 0.00 0.00 0.00 3.51
1338 1474 2.283529 GGCTCTCCGGGTGAACAGA 61.284 63.158 0.00 0.00 0.00 3.41
1339 1475 2.111999 TTGGCTCTCCGGGTGAACAG 62.112 60.000 0.00 0.00 34.14 3.16
1348 1484 1.402896 TATCTGGCCTTGGCTCTCCG 61.403 60.000 11.71 0.00 34.14 4.63
1355 1491 3.209410 CAGCTAACTTATCTGGCCTTGG 58.791 50.000 3.32 0.00 0.00 3.61
1357 1493 2.239654 TGCAGCTAACTTATCTGGCCTT 59.760 45.455 3.32 0.00 0.00 4.35
1363 1499 1.757118 TCCGCTGCAGCTAACTTATCT 59.243 47.619 34.22 0.00 39.32 1.98
1419 1555 1.605712 GGCATGACCGCTACTGGTATC 60.606 57.143 0.00 0.00 44.01 2.24
1423 1559 1.815421 GTGGCATGACCGCTACTGG 60.815 63.158 0.00 0.00 46.20 4.00
1436 1572 4.980805 GGACGCGGTTCAGTGGCA 62.981 66.667 12.47 0.00 0.00 4.92
1440 1576 1.899437 ATGGATGGACGCGGTTCAGT 61.899 55.000 12.47 0.00 0.00 3.41
1446 1582 2.357517 GGCTATGGATGGACGCGG 60.358 66.667 12.47 0.00 0.00 6.46
1449 1585 1.406069 GCCTATGGCTATGGATGGACG 60.406 57.143 0.73 0.00 46.69 4.79
1450 1586 2.409948 GCCTATGGCTATGGATGGAC 57.590 55.000 0.73 0.00 46.69 4.02
1465 1615 2.500098 ACCGACTCAAATAAGCTGCCTA 59.500 45.455 0.00 0.00 0.00 3.93
1477 1627 0.606604 GGAAGCCACTACCGACTCAA 59.393 55.000 0.00 0.00 0.00 3.02
1480 1630 1.272313 TGTAGGAAGCCACTACCGACT 60.272 52.381 7.38 0.00 39.99 4.18
1521 1671 4.156556 GCCTTGCATGACAACAAATAGAGA 59.843 41.667 0.00 0.00 33.68 3.10
1524 1674 4.177165 TGCCTTGCATGACAACAAATAG 57.823 40.909 0.00 0.00 33.68 1.73
1537 1687 1.603456 TTGACGATCTTTGCCTTGCA 58.397 45.000 0.00 0.00 36.47 4.08
1538 1688 2.927553 ATTGACGATCTTTGCCTTGC 57.072 45.000 0.00 0.00 0.00 4.01
1552 1702 7.063191 GGACCTAAAGAGAAAGTCGTAATTGAC 59.937 40.741 0.00 0.00 39.21 3.18
1553 1703 7.039223 AGGACCTAAAGAGAAAGTCGTAATTGA 60.039 37.037 0.00 0.00 0.00 2.57
1555 1705 7.039223 TCAGGACCTAAAGAGAAAGTCGTAATT 60.039 37.037 0.00 0.00 0.00 1.40
1557 1707 5.771666 TCAGGACCTAAAGAGAAAGTCGTAA 59.228 40.000 0.00 0.00 0.00 3.18
1558 1708 5.319453 TCAGGACCTAAAGAGAAAGTCGTA 58.681 41.667 0.00 0.00 0.00 3.43
1559 1709 4.150359 TCAGGACCTAAAGAGAAAGTCGT 58.850 43.478 0.00 0.00 0.00 4.34
1560 1710 4.785511 TCAGGACCTAAAGAGAAAGTCG 57.214 45.455 0.00 0.00 0.00 4.18
1561 1711 4.873259 GCATCAGGACCTAAAGAGAAAGTC 59.127 45.833 0.00 0.00 0.00 3.01
1562 1712 4.287067 TGCATCAGGACCTAAAGAGAAAGT 59.713 41.667 0.00 0.00 0.00 2.66
1563 1713 4.836825 TGCATCAGGACCTAAAGAGAAAG 58.163 43.478 0.00 0.00 0.00 2.62
1564 1714 4.287067 ACTGCATCAGGACCTAAAGAGAAA 59.713 41.667 0.00 0.00 35.51 2.52
1571 1721 3.107601 AGCTAACTGCATCAGGACCTAA 58.892 45.455 0.00 0.00 45.94 2.69
1586 1736 0.670546 TCGACAGGCAAGCAGCTAAC 60.671 55.000 0.00 0.00 44.79 2.34
1660 2121 2.308344 CATCAGCGATGCCTGACTG 58.692 57.895 0.00 0.00 44.00 3.51
1780 2241 4.036380 GGGTCAATGTTTTCCGTATGATCC 59.964 45.833 0.00 0.00 31.53 3.36
1825 2286 5.335661 GCCGTTCAAATTCAAAGATACACCT 60.336 40.000 0.00 0.00 0.00 4.00
1843 2304 0.235665 CACACACACATGAGCCGTTC 59.764 55.000 0.00 0.00 0.00 3.95
1862 2323 9.580916 CACGTAATTACATTAACTACATGATGC 57.419 33.333 15.67 0.00 0.00 3.91
1872 2342 6.689547 CGACAGACCACGTAATTACATTAAC 58.310 40.000 15.67 4.18 0.00 2.01
1873 2343 5.289193 GCGACAGACCACGTAATTACATTAA 59.711 40.000 15.67 0.00 0.00 1.40
1874 2344 4.799949 GCGACAGACCACGTAATTACATTA 59.200 41.667 15.67 0.00 0.00 1.90
1875 2345 3.615496 GCGACAGACCACGTAATTACATT 59.385 43.478 15.67 0.00 0.00 2.71
1876 2346 3.184541 GCGACAGACCACGTAATTACAT 58.815 45.455 15.67 0.00 0.00 2.29
1877 2347 2.030096 TGCGACAGACCACGTAATTACA 60.030 45.455 15.67 0.00 0.00 2.41
1878 2348 2.597305 CTGCGACAGACCACGTAATTAC 59.403 50.000 5.47 5.47 32.44 1.89
1879 2349 2.416296 CCTGCGACAGACCACGTAATTA 60.416 50.000 8.20 0.00 32.44 1.40
1880 2350 1.671850 CCTGCGACAGACCACGTAATT 60.672 52.381 8.20 0.00 32.44 1.40
1885 2355 1.007336 GTAACCTGCGACAGACCACG 61.007 60.000 8.20 0.00 32.44 4.94
1894 2364 1.832883 ATTGCCATTGTAACCTGCGA 58.167 45.000 0.00 0.00 0.00 5.10
1895 2365 2.261345 CAATTGCCATTGTAACCTGCG 58.739 47.619 2.36 0.00 35.86 5.18
2000 2470 7.577979 TCAGTTTCATTGTCCATAAACGTAAC 58.422 34.615 0.00 0.00 37.02 2.50
2024 2494 7.663081 TGCCAGTCTATCTATTTGGAATGAATC 59.337 37.037 0.00 0.00 0.00 2.52
2071 2541 7.608376 TGAATTAATACCATCAGACCGAAACAA 59.392 33.333 0.00 0.00 0.00 2.83
2118 2588 1.004044 ACATGAGAACTCTGGCTTGGG 59.996 52.381 0.00 0.00 0.00 4.12
2172 2642 8.505625 CCTTTTTAAATGCACAGCACATTATTT 58.494 29.630 0.00 0.00 43.04 1.40
2186 2656 5.409214 TGCAATTGCTCTCCTTTTTAAATGC 59.591 36.000 29.37 0.00 42.66 3.56
2289 2759 1.274167 TCATACCCGATGTAATCCGCC 59.726 52.381 0.00 0.00 41.39 6.13
2312 2782 6.112734 CAGTTTACAACAGGCATGGAGTATA 58.887 40.000 2.31 0.00 0.00 1.47
2352 2822 3.825328 AGGCTATTTGGCAGGTTGATAG 58.175 45.455 0.00 0.00 44.55 2.08
2452 2932 5.170021 GGCATGAATCAAATAACAAGCACA 58.830 37.500 0.00 0.00 0.00 4.57
2602 3082 8.721019 AAAGTTGGCATGAATTATGGTTTATG 57.279 30.769 0.00 0.00 37.26 1.90
2644 3124 2.864097 GCGGTGAGCCATGATACTACAG 60.864 54.545 0.00 0.00 40.81 2.74
2665 3145 1.089481 ATGTGCTTACGCGATGGGTG 61.089 55.000 15.93 0.00 39.65 4.61
2673 3153 2.221981 GCAGATTAGGATGTGCTTACGC 59.778 50.000 1.76 0.00 46.09 4.42
2801 3281 7.041303 GGTTATAAATTACAGGTAGCCTTGAGC 60.041 40.741 0.00 0.00 44.25 4.26
2861 3342 7.367285 TCATGTGGTTACTTAACAAGAAATGC 58.633 34.615 1.72 0.00 37.92 3.56
2899 3380 5.985530 GCAGATTCAGCCCCAAATTATTTAC 59.014 40.000 0.00 0.00 0.00 2.01
2923 3404 0.031994 CAGGAAAAAGGTTGCACGGG 59.968 55.000 0.00 0.00 0.00 5.28
2949 3430 2.035066 GTGGCCATCATACTGAATTGGC 59.965 50.000 9.72 11.57 46.54 4.52
3058 3539 0.859232 GGCGTATGTATGGTTCTGCG 59.141 55.000 0.00 0.00 0.00 5.18
3148 3629 1.129998 GCAGCAGCTGTATCAGTTGTG 59.870 52.381 23.60 11.21 43.05 3.33
3258 3739 6.254281 TCATAAGCACCAGTTTTTCTAAGC 57.746 37.500 0.00 0.00 0.00 3.09
3294 3775 1.354040 GCATGAGAAGACACTGGACG 58.646 55.000 0.00 0.00 0.00 4.79
3396 3878 3.134623 TCATGTAGTCCCATTAGCCACAG 59.865 47.826 0.00 0.00 0.00 3.66
3402 3884 3.181454 GGGTGGTCATGTAGTCCCATTAG 60.181 52.174 11.65 0.00 35.43 1.73
3420 3902 1.003580 AGTGGAGTGCTTATGTGGGTG 59.996 52.381 0.00 0.00 0.00 4.61
3518 4000 5.601313 TCTCTAACCTACTTGTTGGACTGTT 59.399 40.000 8.14 0.00 33.01 3.16
3531 4013 8.894768 ATAGATGCATTGTTTCTCTAACCTAC 57.105 34.615 0.00 0.00 35.81 3.18
3570 4052 5.715279 ACCCAGAAAAATAAAGCTAGAACCC 59.285 40.000 0.00 0.00 0.00 4.11
3808 5711 5.419542 TCTATAGGCACAACACAGATTGTC 58.580 41.667 0.00 0.00 40.89 3.18
3898 5801 8.415950 TGGTCAAGGCAAAATAAATAGAGAAA 57.584 30.769 0.00 0.00 0.00 2.52
3899 5802 8.593945 ATGGTCAAGGCAAAATAAATAGAGAA 57.406 30.769 0.00 0.00 0.00 2.87
3903 5806 9.305925 GAAGAATGGTCAAGGCAAAATAAATAG 57.694 33.333 0.00 0.00 0.00 1.73
3905 5808 7.910584 AGAAGAATGGTCAAGGCAAAATAAAT 58.089 30.769 0.00 0.00 0.00 1.40
3951 5854 0.459237 CCTTGAGCACTACCTCTGCG 60.459 60.000 0.00 0.00 39.79 5.18
3978 5881 2.285776 CGCATCATACACACCATCAACG 60.286 50.000 0.00 0.00 0.00 4.10
4029 5932 1.454201 TGTAGCTCACTGTCTCGAGG 58.546 55.000 13.56 0.00 0.00 4.63
4047 5950 3.506810 GTCTCTTGAGATCACCTCGTTG 58.493 50.000 3.50 0.00 44.92 4.10
4056 5959 6.239008 CCATTACTGAGAGGTCTCTTGAGATC 60.239 46.154 8.44 3.17 43.25 2.75
4107 6010 3.000727 CGTACCAGGAATGTTGTTCTCC 58.999 50.000 0.00 0.00 0.00 3.71
4131 6034 2.802787 AGCCTCAGAAACCGATATCG 57.197 50.000 18.31 18.31 39.44 2.92
4192 6095 2.823196 TGAACACGACAACTGCAAAG 57.177 45.000 0.00 0.00 0.00 2.77
4216 6119 1.786579 GCGATGTTTCCAGTGTTTTGC 59.213 47.619 0.00 0.00 0.00 3.68
4318 6221 4.768583 AGATCTTGTCTTCTTGATCCAGC 58.231 43.478 0.00 0.00 36.82 4.85
4399 6302 4.582240 ACCGGTACTACTTGGATAGCTAAC 59.418 45.833 4.49 0.00 0.00 2.34
4424 6327 9.959775 GTTTCTCTTCTTCGAGTATTACAATTG 57.040 33.333 3.24 3.24 32.83 2.32
4452 6355 2.096819 TGCGAATTTTTATGTCCGGAGC 59.903 45.455 3.06 0.00 0.00 4.70
4456 6359 5.856455 AGTTTTCTGCGAATTTTTATGTCCG 59.144 36.000 0.00 0.00 0.00 4.79
4539 6442 8.041143 AGTATTATTTAGGTTCAGCCACCATA 57.959 34.615 0.46 0.00 39.62 2.74
4540 6443 6.911308 AGTATTATTTAGGTTCAGCCACCAT 58.089 36.000 0.46 0.00 39.62 3.55
4541 6444 6.321821 AGTATTATTTAGGTTCAGCCACCA 57.678 37.500 0.46 0.00 39.62 4.17
4542 6445 7.054751 AGAAGTATTATTTAGGTTCAGCCACC 58.945 38.462 0.00 0.00 40.61 4.61
4543 6446 9.780186 ATAGAAGTATTATTTAGGTTCAGCCAC 57.220 33.333 0.00 0.00 40.61 5.01
4632 8523 7.049799 TCCCACAATTTTTCCAGTAAAGAAG 57.950 36.000 0.00 0.00 0.00 2.85
4648 8539 0.321298 CCGTTTCGACCTCCCACAAT 60.321 55.000 0.00 0.00 0.00 2.71
4707 8598 8.789762 TGTAATATCAAATGGCATTGATCTCAG 58.210 33.333 14.47 0.00 44.64 3.35
4708 8599 8.694581 TGTAATATCAAATGGCATTGATCTCA 57.305 30.769 14.47 11.74 44.64 3.27
4806 8697 3.901844 TCCCTCCATGGTATTGTACTAGC 59.098 47.826 12.58 0.00 0.00 3.42
4910 8802 4.754322 ACTTTTGGGCAACTTGTTACTTG 58.246 39.130 0.00 0.00 0.00 3.16
4948 8847 6.655062 TGTCAAATGTCATGTACGTTTTCTC 58.345 36.000 0.00 7.01 43.34 2.87
5111 9011 5.467735 ACTGAATTTGTCGGTGGTAAGTTAC 59.532 40.000 4.32 4.32 44.65 2.50
5127 9027 4.869297 CGCATCTTCTCTCTCACTGAATTT 59.131 41.667 0.00 0.00 0.00 1.82
5139 9039 6.376978 CAAAGTTTGAAATCGCATCTTCTCT 58.623 36.000 10.19 0.00 0.00 3.10
5184 9084 3.354467 ACCCTGTCCTCTTTAGTACTCG 58.646 50.000 0.00 0.00 0.00 4.18
5214 9114 9.476202 AAGGCATTTACTGTTTTTGAATCTTAC 57.524 29.630 0.00 0.00 0.00 2.34
5323 9232 4.346418 AGATTATCACCCATGTGGAGAGAC 59.654 45.833 0.00 0.00 42.98 3.36


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

AutoCloner maintained by Alex Coulton.