Multiple sequence alignment - TraesCS4B01G313200

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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 TraesCS4B01G313200 chr4B 100.000 2480 0 0 1 2480 603036996 603039475 0.000000e+00 4580.0
1 TraesCS4B01G313200 chr4B 93.397 1257 55 14 313 1550 603147725 603148972 0.000000e+00 1836.0
2 TraesCS4B01G313200 chr4B 86.008 1651 128 42 1 1591 602894631 602893024 0.000000e+00 1674.0
3 TraesCS4B01G313200 chr4B 89.959 976 71 12 627 1591 602874061 602873102 0.000000e+00 1234.0
4 TraesCS4B01G313200 chr4B 87.697 317 17 6 1 296 603147352 603147667 1.410000e-92 350.0
5 TraesCS4B01G313200 chr4B 92.386 197 13 2 723 917 603028903 603028707 1.880000e-71 279.0
6 TraesCS4B01G313200 chr4B 91.011 178 12 4 67 241 602883932 602883756 1.150000e-58 237.0
7 TraesCS4B01G313200 chr4B 82.143 280 40 5 320 592 602874338 602874062 5.330000e-57 231.0
8 TraesCS4B01G313200 chr4B 96.000 75 3 0 1 75 602889380 602889306 3.350000e-24 122.0
9 TraesCS4B01G313200 chr4B 97.674 43 1 0 247 289 602882147 602882105 9.510000e-10 75.0
10 TraesCS4B01G313200 chr4D 92.823 1254 60 15 313 1550 477558294 477559533 0.000000e+00 1790.0
11 TraesCS4B01G313200 chr4D 92.240 915 60 10 721 1631 477543849 477542942 0.000000e+00 1286.0
12 TraesCS4B01G313200 chr4D 93.727 271 15 2 1 269 477555792 477556062 2.970000e-109 405.0
13 TraesCS4B01G313200 chr4D 89.362 47 5 0 1664 1710 308952772 308952818 2.660000e-05 60.2
14 TraesCS4B01G313200 chr4A 91.507 836 59 9 724 1550 684470866 684471698 0.000000e+00 1140.0
15 TraesCS4B01G313200 chr4A 80.194 929 92 44 20 898 684450531 684449645 1.630000e-171 612.0
16 TraesCS4B01G313200 chr2D 89.938 646 61 3 1837 2480 69277482 69276839 0.000000e+00 830.0
17 TraesCS4B01G313200 chr2D 84.398 673 65 17 1839 2480 107526392 107527055 2.090000e-175 625.0
18 TraesCS4B01G313200 chr2D 82.488 651 76 18 1839 2480 554073441 554074062 1.010000e-148 536.0
19 TraesCS4B01G313200 chr1A 82.359 992 127 35 682 1651 372316441 372315476 0.000000e+00 819.0
20 TraesCS4B01G313200 chr1B 82.359 992 124 32 680 1651 401992740 401991780 0.000000e+00 815.0
21 TraesCS4B01G313200 chr1B 81.930 974 129 31 693 1651 402039924 402038983 0.000000e+00 780.0
22 TraesCS4B01G313200 chr3D 86.119 670 57 12 1839 2480 182326168 182326829 0.000000e+00 689.0
23 TraesCS4B01G313200 chr3D 81.250 192 29 5 325 511 8288283 8288094 5.530000e-32 148.0
24 TraesCS4B01G313200 chr3D 78.367 245 42 10 330 566 67054841 67055082 5.530000e-32 148.0
25 TraesCS4B01G313200 chr3D 82.667 75 12 1 365 438 295261749 295261675 5.730000e-07 65.8
26 TraesCS4B01G313200 chr5D 85.907 667 65 17 1837 2480 105095782 105096442 0.000000e+00 684.0
27 TraesCS4B01G313200 chr5B 84.932 657 80 10 1835 2480 38514666 38514018 0.000000e+00 647.0
28 TraesCS4B01G313200 chr5B 80.091 658 95 24 1839 2480 56954508 56953871 8.080000e-125 457.0
29 TraesCS4B01G313200 chr5B 96.774 31 1 0 1663 1693 521025836 521025806 4.000000e-03 52.8
30 TraesCS4B01G313200 chr2B 84.187 664 79 18 1837 2479 153216474 153215816 2.710000e-174 621.0
31 TraesCS4B01G313200 chr2B 83.901 646 85 10 1839 2480 90188419 90187789 1.270000e-167 599.0
32 TraesCS4B01G313200 chr2B 85.938 64 7 1 1649 1710 117636098 117636161 1.590000e-07 67.6
33 TraesCS4B01G313200 chr6B 87.221 493 51 6 1837 2328 560206542 560207023 3.600000e-153 551.0
34 TraesCS4B01G313200 chr6B 87.018 493 53 5 1837 2328 540573377 540572895 1.680000e-151 545.0
35 TraesCS4B01G313200 chr6B 78.392 199 22 15 329 522 51349272 51349090 2.610000e-20 110.0
36 TraesCS4B01G313200 chr1D 82.508 646 90 17 1839 2480 362782777 362783403 1.680000e-151 545.0
37 TraesCS4B01G313200 chr1D 81.098 656 99 20 1836 2480 190152397 190153038 3.680000e-138 501.0
38 TraesCS4B01G313200 chr6D 80.704 653 98 20 1837 2480 82471412 82470779 1.330000e-132 483.0
39 TraesCS4B01G313200 chr6D 87.755 49 4 2 1644 1690 122379117 122379069 3.450000e-04 56.5
40 TraesCS4B01G313200 chr3A 81.928 581 81 15 1914 2480 143379207 143379777 1.040000e-128 470.0
41 TraesCS4B01G313200 chr3A 85.057 87 13 0 365 451 9358358 9358444 3.400000e-14 89.8
42 TraesCS4B01G313200 chr3A 76.536 179 31 7 352 522 624913571 624913396 1.220000e-13 87.9
43 TraesCS4B01G313200 chr7A 79.331 658 102 27 1839 2480 441978436 441977797 4.900000e-117 431.0
44 TraesCS4B01G313200 chr7A 88.889 54 6 0 1655 1708 161646529 161646476 1.590000e-07 67.6
45 TraesCS4B01G313200 chr3B 100.000 28 0 0 1663 1690 40291453 40291480 4.000000e-03 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 TraesCS4B01G313200 chr4B 603036996 603039475 2479 False 4580.0 4580 100.000 1 2480 1 chr4B.!!$F1 2479
1 TraesCS4B01G313200 chr4B 603147352 603148972 1620 False 1093.0 1836 90.547 1 1550 2 chr4B.!!$F2 1549
2 TraesCS4B01G313200 chr4B 602889306 602894631 5325 True 898.0 1674 91.004 1 1591 2 chr4B.!!$R4 1590
3 TraesCS4B01G313200 chr4B 602873102 602874338 1236 True 732.5 1234 86.051 320 1591 2 chr4B.!!$R2 1271
4 TraesCS4B01G313200 chr4D 477542942 477543849 907 True 1286.0 1286 92.240 721 1631 1 chr4D.!!$R1 910
5 TraesCS4B01G313200 chr4D 477555792 477559533 3741 False 1097.5 1790 93.275 1 1550 2 chr4D.!!$F2 1549
6 TraesCS4B01G313200 chr4A 684470866 684471698 832 False 1140.0 1140 91.507 724 1550 1 chr4A.!!$F1 826
7 TraesCS4B01G313200 chr4A 684449645 684450531 886 True 612.0 612 80.194 20 898 1 chr4A.!!$R1 878
8 TraesCS4B01G313200 chr2D 69276839 69277482 643 True 830.0 830 89.938 1837 2480 1 chr2D.!!$R1 643
9 TraesCS4B01G313200 chr2D 107526392 107527055 663 False 625.0 625 84.398 1839 2480 1 chr2D.!!$F1 641
10 TraesCS4B01G313200 chr2D 554073441 554074062 621 False 536.0 536 82.488 1839 2480 1 chr2D.!!$F2 641
11 TraesCS4B01G313200 chr1A 372315476 372316441 965 True 819.0 819 82.359 682 1651 1 chr1A.!!$R1 969
12 TraesCS4B01G313200 chr1B 401991780 401992740 960 True 815.0 815 82.359 680 1651 1 chr1B.!!$R1 971
13 TraesCS4B01G313200 chr1B 402038983 402039924 941 True 780.0 780 81.930 693 1651 1 chr1B.!!$R2 958
14 TraesCS4B01G313200 chr3D 182326168 182326829 661 False 689.0 689 86.119 1839 2480 1 chr3D.!!$F2 641
15 TraesCS4B01G313200 chr5D 105095782 105096442 660 False 684.0 684 85.907 1837 2480 1 chr5D.!!$F1 643
16 TraesCS4B01G313200 chr5B 38514018 38514666 648 True 647.0 647 84.932 1835 2480 1 chr5B.!!$R1 645
17 TraesCS4B01G313200 chr5B 56953871 56954508 637 True 457.0 457 80.091 1839 2480 1 chr5B.!!$R2 641
18 TraesCS4B01G313200 chr2B 153215816 153216474 658 True 621.0 621 84.187 1837 2479 1 chr2B.!!$R2 642
19 TraesCS4B01G313200 chr2B 90187789 90188419 630 True 599.0 599 83.901 1839 2480 1 chr2B.!!$R1 641
20 TraesCS4B01G313200 chr1D 362782777 362783403 626 False 545.0 545 82.508 1839 2480 1 chr1D.!!$F2 641
21 TraesCS4B01G313200 chr1D 190152397 190153038 641 False 501.0 501 81.098 1836 2480 1 chr1D.!!$F1 644
22 TraesCS4B01G313200 chr6D 82470779 82471412 633 True 483.0 483 80.704 1837 2480 1 chr6D.!!$R1 643
23 TraesCS4B01G313200 chr3A 143379207 143379777 570 False 470.0 470 81.928 1914 2480 1 chr3A.!!$F2 566
24 TraesCS4B01G313200 chr7A 441977797 441978436 639 True 431.0 431 79.331 1839 2480 1 chr7A.!!$R2 641

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
434 2648 0.521291 TGTTTAGTTGGCGAGCATGC 59.479 50.0 10.51 10.51 0.0 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 4101 0.170339 GACCAGGGGAATTTTTCGCG 59.83 55.0 0.0 0.0 42.92 5.87 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
70 71 1.134965 GCCTAGCTAGGACACACACAG 60.135 57.143 38.74 12.28 46.63 3.66
138 140 4.843220 AAATCAGCCAAAGTTCTCACTG 57.157 40.909 0.00 0.00 31.60 3.66
147 150 5.880332 GCCAAAGTTCTCACTGGTATCAATA 59.120 40.000 0.00 0.00 31.60 1.90
155 158 9.178758 GTTCTCACTGGTATCAATAAAAAGGAT 57.821 33.333 0.00 0.00 0.00 3.24
179 182 9.149225 GATAGTGATTAGTGCCTGATTAATCTG 57.851 37.037 16.24 14.95 35.35 2.90
218 221 7.738847 TCAATCCAGATGACTATCAAAGCATA 58.261 34.615 0.00 0.00 35.70 3.14
219 222 8.212995 TCAATCCAGATGACTATCAAAGCATAA 58.787 33.333 0.00 0.00 35.70 1.90
284 2452 4.883585 GCTCAATATTGGTCTCACATGGAA 59.116 41.667 15.36 0.00 0.00 3.53
369 2582 6.455360 TGATTTCAGATTCTTTACCATGGC 57.545 37.500 13.04 0.00 0.00 4.40
434 2648 0.521291 TGTTTAGTTGGCGAGCATGC 59.479 50.000 10.51 10.51 0.00 4.06
457 2675 6.127196 TGCCAAATCCATCCCAGTTTATTTAC 60.127 38.462 0.00 0.00 0.00 2.01
536 2757 9.754382 ATTGCCATAAAATGTCAGATTTATCAC 57.246 29.630 4.29 2.05 31.17 3.06
554 2775 7.599630 TTATCACGCCTAAATTTCTAACGTT 57.400 32.000 5.88 5.88 0.00 3.99
714 2939 1.200020 GTGTAGCATGACAAGGTTGGC 59.800 52.381 0.00 0.00 36.50 4.52
715 2940 1.073763 TGTAGCATGACAAGGTTGGCT 59.926 47.619 0.00 0.00 37.03 4.75
717 2942 2.584835 AGCATGACAAGGTTGGCTAA 57.415 45.000 0.00 0.00 37.03 3.09
718 2943 2.162681 AGCATGACAAGGTTGGCTAAC 58.837 47.619 4.02 4.02 37.03 2.34
719 2944 1.885887 GCATGACAAGGTTGGCTAACA 59.114 47.619 15.34 0.00 38.58 2.41
807 3042 2.403252 AAACCATCGGTCCTGATCAC 57.597 50.000 0.00 0.00 33.12 3.06
836 3077 2.675844 TCTCGCCGTATCAAACAAATGG 59.324 45.455 0.00 0.00 0.00 3.16
939 3193 2.858745 ACTACGCCAAACAGTTCCATT 58.141 42.857 0.00 0.00 0.00 3.16
962 3222 2.181954 TGCATGCACGCATCCATATA 57.818 45.000 18.46 0.00 36.86 0.86
1227 3519 2.190578 GGCGGGCAGTGCTCTATT 59.809 61.111 14.31 0.00 0.00 1.73
1374 3668 4.662961 CTGTGCACCGCCGTCAGA 62.663 66.667 15.69 0.00 0.00 3.27
1401 3695 1.071385 GTCCTCGGCATCCATCTCAAT 59.929 52.381 0.00 0.00 0.00 2.57
1468 3762 1.300620 CCGTCCGAGTTCACTTGCA 60.301 57.895 0.00 0.00 0.00 4.08
1499 3798 3.479269 GACGCGTACTGCTGCACC 61.479 66.667 13.97 0.00 43.27 5.01
1538 3837 2.347755 GCTTTCCATCCGTACTTCGTTC 59.652 50.000 0.00 0.00 37.94 3.95
1591 3891 8.042515 CCATTTCCACATTTGAATCCTTGTAAT 58.957 33.333 0.00 0.00 0.00 1.89
1594 3894 9.921637 TTTCCACATTTGAATCCTTGTAATAAC 57.078 29.630 0.00 0.00 0.00 1.89
1635 3935 1.890876 TGCACACAACCATGTACTCC 58.109 50.000 0.00 0.00 37.82 3.85
1643 3943 5.175859 CACAACCATGTACTCCTCGTATTT 58.824 41.667 0.00 0.00 37.82 1.40
1672 3972 2.279186 AAAAAGGCCGTGCGTTGC 60.279 55.556 0.00 0.00 36.74 4.17
1674 3974 2.564553 AAAAAGGCCGTGCGTTGCAA 62.565 50.000 0.00 0.00 41.47 4.08
1675 3975 3.766496 AAAGGCCGTGCGTTGCAAC 62.766 57.895 19.89 19.89 41.47 4.17
1706 4006 4.908601 AATAACACACACTCCTCATCCA 57.091 40.909 0.00 0.00 0.00 3.41
1707 4007 4.908601 ATAACACACACTCCTCATCCAA 57.091 40.909 0.00 0.00 0.00 3.53
1708 4008 3.795688 AACACACACTCCTCATCCAAT 57.204 42.857 0.00 0.00 0.00 3.16
1711 4011 3.840666 ACACACACTCCTCATCCAATAGT 59.159 43.478 0.00 0.00 0.00 2.12
1712 4012 4.081420 ACACACACTCCTCATCCAATAGTC 60.081 45.833 0.00 0.00 0.00 2.59
1713 4013 4.161189 CACACACTCCTCATCCAATAGTCT 59.839 45.833 0.00 0.00 0.00 3.24
1714 4014 4.404073 ACACACTCCTCATCCAATAGTCTC 59.596 45.833 0.00 0.00 0.00 3.36
1715 4015 4.648762 CACACTCCTCATCCAATAGTCTCT 59.351 45.833 0.00 0.00 0.00 3.10
1716 4016 5.830457 CACACTCCTCATCCAATAGTCTCTA 59.170 44.000 0.00 0.00 0.00 2.43
1717 4017 5.830991 ACACTCCTCATCCAATAGTCTCTAC 59.169 44.000 0.00 0.00 0.00 2.59
1718 4018 6.068010 CACTCCTCATCCAATAGTCTCTACT 58.932 44.000 0.00 0.00 39.91 2.57
1719 4019 7.147284 ACACTCCTCATCCAATAGTCTCTACTA 60.147 40.741 0.00 0.00 42.35 1.82
1734 4034 8.934023 AGTCTCTACTATTAAAGGAGGATCTG 57.066 38.462 0.00 0.00 36.71 2.90
1735 4035 7.450323 AGTCTCTACTATTAAAGGAGGATCTGC 59.550 40.741 0.00 0.00 36.71 4.26
1739 4039 2.981859 TTAAAGGAGGATCTGCCGTC 57.018 50.000 0.00 0.00 43.43 4.79
1740 4040 0.744874 TAAAGGAGGATCTGCCGTCG 59.255 55.000 0.00 0.00 43.43 5.12
1741 4041 2.579684 AAAGGAGGATCTGCCGTCGC 62.580 60.000 0.00 0.00 43.43 5.19
1743 4043 4.933064 GAGGATCTGCCGTCGCCG 62.933 72.222 0.00 0.00 43.43 6.46
1745 4045 4.814294 GGATCTGCCGTCGCCGTT 62.814 66.667 0.00 0.00 0.00 4.44
1746 4046 3.554692 GATCTGCCGTCGCCGTTG 61.555 66.667 0.00 0.00 0.00 4.10
1747 4047 4.373116 ATCTGCCGTCGCCGTTGT 62.373 61.111 0.00 0.00 0.00 3.32
1748 4048 3.876589 ATCTGCCGTCGCCGTTGTT 62.877 57.895 0.00 0.00 0.00 2.83
1749 4049 4.368808 CTGCCGTCGCCGTTGTTG 62.369 66.667 0.00 0.00 0.00 3.33
1751 4051 4.659874 GCCGTCGCCGTTGTTGTG 62.660 66.667 0.00 0.00 0.00 3.33
1755 4055 1.553195 CGTCGCCGTTGTTGTGATGA 61.553 55.000 0.00 0.00 32.28 2.92
1756 4056 0.796312 GTCGCCGTTGTTGTGATGAT 59.204 50.000 0.00 0.00 0.00 2.45
1758 4058 0.179192 CGCCGTTGTTGTGATGATGG 60.179 55.000 0.00 0.00 0.00 3.51
1762 4062 2.412716 CCGTTGTTGTGATGATGGTTCG 60.413 50.000 0.00 0.00 0.00 3.95
1763 4063 2.478514 CGTTGTTGTGATGATGGTTCGA 59.521 45.455 0.00 0.00 0.00 3.71
1765 4065 2.422597 TGTTGTGATGATGGTTCGACC 58.577 47.619 0.00 0.00 39.22 4.79
1767 4067 2.672961 TGTGATGATGGTTCGACCTC 57.327 50.000 5.77 2.63 39.58 3.85
1768 4068 1.207089 TGTGATGATGGTTCGACCTCC 59.793 52.381 5.77 0.50 39.58 4.30
1769 4069 0.459899 TGATGATGGTTCGACCTCCG 59.540 55.000 5.77 0.00 39.58 4.63
1770 4070 0.460311 GATGATGGTTCGACCTCCGT 59.540 55.000 5.77 1.13 39.58 4.69
1771 4071 0.460311 ATGATGGTTCGACCTCCGTC 59.540 55.000 12.85 12.85 39.58 4.79
1772 4072 0.611062 TGATGGTTCGACCTCCGTCT 60.611 55.000 17.70 0.00 39.58 4.18
1773 4073 0.100861 GATGGTTCGACCTCCGTCTC 59.899 60.000 12.60 1.08 39.58 3.36
1775 4075 0.824595 TGGTTCGACCTCCGTCTCAA 60.825 55.000 5.77 0.00 39.58 3.02
1776 4076 0.388263 GGTTCGACCTCCGTCTCAAC 60.388 60.000 0.00 0.00 39.75 3.18
1777 4077 0.388263 GTTCGACCTCCGTCTCAACC 60.388 60.000 0.00 0.00 39.75 3.77
1778 4078 1.530013 TTCGACCTCCGTCTCAACCC 61.530 60.000 0.00 0.00 39.75 4.11
1780 4080 1.891616 GACCTCCGTCTCAACCCTC 59.108 63.158 0.00 0.00 35.99 4.30
1781 4081 1.935327 GACCTCCGTCTCAACCCTCG 61.935 65.000 0.00 0.00 35.99 4.63
1782 4082 1.677966 CCTCCGTCTCAACCCTCGA 60.678 63.158 0.00 0.00 0.00 4.04
1783 4083 1.507174 CTCCGTCTCAACCCTCGAC 59.493 63.158 0.00 0.00 0.00 4.20
1784 4084 1.935327 CTCCGTCTCAACCCTCGACC 61.935 65.000 0.00 0.00 0.00 4.79
1787 4087 0.679002 CGTCTCAACCCTCGACCCTA 60.679 60.000 0.00 0.00 0.00 3.53
1788 4088 0.816373 GTCTCAACCCTCGACCCTAC 59.184 60.000 0.00 0.00 0.00 3.18
1789 4089 0.679002 TCTCAACCCTCGACCCTACG 60.679 60.000 0.00 0.00 0.00 3.51
1790 4090 2.183555 CAACCCTCGACCCTACGC 59.816 66.667 0.00 0.00 0.00 4.42
1794 4094 3.885521 CCTCGACCCTACGCCGTC 61.886 72.222 0.00 0.00 0.00 4.79
1795 4095 2.823147 CTCGACCCTACGCCGTCT 60.823 66.667 0.00 0.00 0.00 4.18
1796 4096 2.360350 TCGACCCTACGCCGTCTT 60.360 61.111 0.00 0.00 0.00 3.01
1798 4098 1.080298 CGACCCTACGCCGTCTTTT 60.080 57.895 0.00 0.00 0.00 2.27
1801 4101 1.449070 CCCTACGCCGTCTTTTCCC 60.449 63.158 0.00 0.00 0.00 3.97
1803 4103 2.432972 TACGCCGTCTTTTCCCGC 60.433 61.111 0.00 0.00 0.00 6.13
1806 4106 3.045492 GCCGTCTTTTCCCGCGAA 61.045 61.111 8.23 0.00 0.00 4.70
1807 4107 2.609759 GCCGTCTTTTCCCGCGAAA 61.610 57.895 8.23 0.00 36.18 3.46
1808 4108 1.943293 CCGTCTTTTCCCGCGAAAA 59.057 52.632 8.23 6.61 43.97 2.29
1809 4109 0.308376 CCGTCTTTTCCCGCGAAAAA 59.692 50.000 8.23 13.14 45.12 1.94
1810 4110 1.068816 CCGTCTTTTCCCGCGAAAAAT 60.069 47.619 8.23 0.00 45.12 1.82
1811 4111 2.606065 CCGTCTTTTCCCGCGAAAAATT 60.606 45.455 8.23 0.00 45.12 1.82
1812 4112 2.655001 CGTCTTTTCCCGCGAAAAATTC 59.345 45.455 8.23 8.88 45.12 2.17
1813 4113 2.984471 GTCTTTTCCCGCGAAAAATTCC 59.016 45.455 8.23 1.82 45.12 3.01
1815 4115 0.604073 TTTCCCGCGAAAAATTCCCC 59.396 50.000 8.23 0.00 35.02 4.81
1816 4116 0.251430 TTCCCGCGAAAAATTCCCCT 60.251 50.000 8.23 0.00 0.00 4.79
1817 4117 0.963355 TCCCGCGAAAAATTCCCCTG 60.963 55.000 8.23 0.00 0.00 4.45
1818 4118 1.510844 CCGCGAAAAATTCCCCTGG 59.489 57.895 8.23 0.00 0.00 4.45
1819 4119 1.248101 CCGCGAAAAATTCCCCTGGT 61.248 55.000 8.23 0.00 0.00 4.00
1820 4120 0.170339 CGCGAAAAATTCCCCTGGTC 59.830 55.000 0.00 0.00 0.00 4.02
1821 4121 0.530744 GCGAAAAATTCCCCTGGTCC 59.469 55.000 0.00 0.00 0.00 4.46
1822 4122 0.808755 CGAAAAATTCCCCTGGTCCG 59.191 55.000 0.00 0.00 0.00 4.79
1824 4124 2.735151 GAAAAATTCCCCTGGTCCGAT 58.265 47.619 0.00 0.00 0.00 4.18
1825 4125 2.437085 AAAATTCCCCTGGTCCGATC 57.563 50.000 0.00 0.00 0.00 3.69
1826 4126 0.551396 AAATTCCCCTGGTCCGATCC 59.449 55.000 0.00 0.00 0.00 3.36
1827 4127 0.327576 AATTCCCCTGGTCCGATCCT 60.328 55.000 0.00 0.00 0.00 3.24
1828 4128 0.764752 ATTCCCCTGGTCCGATCCTC 60.765 60.000 0.00 0.00 0.00 3.71
1829 4129 2.844839 CCCCTGGTCCGATCCTCC 60.845 72.222 0.00 0.00 0.00 4.30
1831 4131 1.834822 CCCTGGTCCGATCCTCCTC 60.835 68.421 0.00 0.00 0.00 3.71
1832 4132 1.834822 CCTGGTCCGATCCTCCTCC 60.835 68.421 0.00 0.00 0.00 4.30
1833 4133 2.123854 TGGTCCGATCCTCCTCCG 60.124 66.667 0.00 0.00 0.00 4.63
2032 6269 7.529158 CACAAACAATATATGCACTCTGAACA 58.471 34.615 0.00 0.00 0.00 3.18
2190 6581 2.814336 CCGAGTCGTCCTCATCATCATA 59.186 50.000 12.31 0.00 40.48 2.15
2258 7515 2.161808 GGATCGTCTGAGTCGAAGAACA 59.838 50.000 5.83 0.00 39.69 3.18
2395 7652 2.185867 GCGACATCCTGCGGGTAA 59.814 61.111 12.43 0.00 0.00 2.85
2448 7705 2.818132 CTCGGTGATGAGGAGGCC 59.182 66.667 0.00 0.00 32.18 5.19
2473 7730 3.047877 CGCCAACGGTGTTCCTCC 61.048 66.667 0.00 0.00 34.97 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 150 6.721318 TCAGGCACTAATCACTATCCTTTTT 58.279 36.000 0.00 0.00 36.02 1.94
152 155 8.317679 AGATTAATCAGGCACTAATCACTATCC 58.682 37.037 17.56 0.00 36.02 2.59
155 158 8.023021 ACAGATTAATCAGGCACTAATCACTA 57.977 34.615 17.56 0.00 36.02 2.74
165 168 8.929260 ATCAAATGATACAGATTAATCAGGCA 57.071 30.769 17.56 9.74 35.67 4.75
218 221 1.985159 TGATGTGGGCTCTACAGGTTT 59.015 47.619 0.00 0.00 0.00 3.27
219 222 1.279271 GTGATGTGGGCTCTACAGGTT 59.721 52.381 0.00 0.00 0.00 3.50
284 2452 4.738685 GAGGGTTATGCTACCTACCTACT 58.261 47.826 0.00 0.00 38.30 2.57
358 2567 7.437793 AAATGTTTGATTTGCCATGGTAAAG 57.562 32.000 28.34 0.00 33.60 1.85
369 2582 8.804688 ATTTGCCATGAAAAATGTTTGATTTG 57.195 26.923 0.00 0.00 0.00 2.32
434 2648 6.382570 TGGTAAATAAACTGGGATGGATTTGG 59.617 38.462 0.00 0.00 0.00 3.28
572 2793 7.367285 GCGCAATGGACAAGGAAATAATAATA 58.633 34.615 0.30 0.00 0.00 0.98
603 2824 1.134818 TGGACTTCATTAGCGATGCGT 60.135 47.619 0.00 0.00 35.64 5.24
714 2939 4.395854 TGTTCATGCATGTTAGGCTGTTAG 59.604 41.667 25.43 0.00 0.00 2.34
715 2940 4.331108 TGTTCATGCATGTTAGGCTGTTA 58.669 39.130 25.43 0.00 0.00 2.41
717 2942 2.794103 TGTTCATGCATGTTAGGCTGT 58.206 42.857 25.43 0.00 0.00 4.40
718 2943 3.702330 CATGTTCATGCATGTTAGGCTG 58.298 45.455 25.43 12.88 40.81 4.85
719 2944 2.100252 GCATGTTCATGCATGTTAGGCT 59.900 45.455 25.43 5.18 45.75 4.58
807 3042 2.390938 TGATACGGCGAGATTTTAGCG 58.609 47.619 16.62 0.00 0.00 4.26
836 3077 1.254954 AGGTTGTCCTCTCGGTGTAC 58.745 55.000 0.00 0.00 40.58 2.90
962 3222 4.477213 AGTGTTGTATTTATAGCCAGGGGT 59.523 41.667 0.00 0.00 0.00 4.95
1027 3300 2.797156 CGTGTGCTTGAGTAGGATATGC 59.203 50.000 0.00 0.00 0.00 3.14
1270 3564 2.347490 GACCTTGAGGCCGAGCAA 59.653 61.111 0.00 2.58 39.32 3.91
1401 3695 1.302752 GCTGATGTCCACAGGCACA 60.303 57.895 0.00 0.00 36.09 4.57
1468 3762 1.743995 GCGTCCGTTAATGGCCTGT 60.744 57.895 9.01 0.00 0.00 4.00
1499 3798 0.657368 GCAAATCTTATTCGGCGCCG 60.657 55.000 42.13 42.13 41.35 6.46
1538 3837 5.445939 CGGTTCCACATCTCACGAAAATAAG 60.446 44.000 0.00 0.00 0.00 1.73
1568 3868 9.921637 GTTATTACAAGGATTCAAATGTGGAAA 57.078 29.630 0.00 0.00 0.00 3.13
1616 3916 1.419762 AGGAGTACATGGTTGTGTGCA 59.580 47.619 0.00 0.00 37.20 4.57
1620 3920 2.743636 ACGAGGAGTACATGGTTGTG 57.256 50.000 0.00 0.00 36.53 3.33
1655 3955 2.279186 GCAACGCACGGCCTTTTT 60.279 55.556 0.00 0.00 0.00 1.94
1657 3957 3.522731 TTGCAACGCACGGCCTTT 61.523 55.556 0.00 0.00 38.71 3.11
1658 3958 4.264638 GTTGCAACGCACGGCCTT 62.265 61.111 14.90 0.00 38.71 4.35
1684 3984 5.241403 TGGATGAGGAGTGTGTGTTATTT 57.759 39.130 0.00 0.00 0.00 1.40
1685 3985 4.908601 TGGATGAGGAGTGTGTGTTATT 57.091 40.909 0.00 0.00 0.00 1.40
1686 3986 4.908601 TTGGATGAGGAGTGTGTGTTAT 57.091 40.909 0.00 0.00 0.00 1.89
1687 3987 4.908601 ATTGGATGAGGAGTGTGTGTTA 57.091 40.909 0.00 0.00 0.00 2.41
1688 3988 3.795688 ATTGGATGAGGAGTGTGTGTT 57.204 42.857 0.00 0.00 0.00 3.32
1689 3989 3.840666 ACTATTGGATGAGGAGTGTGTGT 59.159 43.478 0.00 0.00 0.00 3.72
1690 3990 4.161189 AGACTATTGGATGAGGAGTGTGTG 59.839 45.833 0.00 0.00 0.00 3.82
1692 3992 4.648762 AGAGACTATTGGATGAGGAGTGTG 59.351 45.833 0.00 0.00 0.00 3.82
1694 3994 6.068010 AGTAGAGACTATTGGATGAGGAGTG 58.932 44.000 0.00 0.00 32.65 3.51
1711 4011 6.722129 GGCAGATCCTCCTTTAATAGTAGAGA 59.278 42.308 0.00 0.00 0.00 3.10
1712 4012 6.349777 CGGCAGATCCTCCTTTAATAGTAGAG 60.350 46.154 0.00 0.00 0.00 2.43
1713 4013 5.477291 CGGCAGATCCTCCTTTAATAGTAGA 59.523 44.000 0.00 0.00 0.00 2.59
1714 4014 5.244178 ACGGCAGATCCTCCTTTAATAGTAG 59.756 44.000 0.00 0.00 0.00 2.57
1715 4015 5.145564 ACGGCAGATCCTCCTTTAATAGTA 58.854 41.667 0.00 0.00 0.00 1.82
1716 4016 3.967987 ACGGCAGATCCTCCTTTAATAGT 59.032 43.478 0.00 0.00 0.00 2.12
1717 4017 4.561105 GACGGCAGATCCTCCTTTAATAG 58.439 47.826 0.00 0.00 0.00 1.73
1718 4018 3.005472 CGACGGCAGATCCTCCTTTAATA 59.995 47.826 0.00 0.00 0.00 0.98
1719 4019 2.224066 CGACGGCAGATCCTCCTTTAAT 60.224 50.000 0.00 0.00 0.00 1.40
1720 4020 1.136305 CGACGGCAGATCCTCCTTTAA 59.864 52.381 0.00 0.00 0.00 1.52
1721 4021 0.744874 CGACGGCAGATCCTCCTTTA 59.255 55.000 0.00 0.00 0.00 1.85
1722 4022 1.517832 CGACGGCAGATCCTCCTTT 59.482 57.895 0.00 0.00 0.00 3.11
1724 4024 3.532155 GCGACGGCAGATCCTCCT 61.532 66.667 0.00 0.00 39.62 3.69
1725 4025 4.593864 GGCGACGGCAGATCCTCC 62.594 72.222 17.49 0.00 42.47 4.30
1739 4039 0.179192 CCATCATCACAACAACGGCG 60.179 55.000 4.80 4.80 0.00 6.46
1740 4040 0.881118 ACCATCATCACAACAACGGC 59.119 50.000 0.00 0.00 0.00 5.68
1741 4041 2.412716 CGAACCATCATCACAACAACGG 60.413 50.000 0.00 0.00 0.00 4.44
1743 4043 3.364964 GGTCGAACCATCATCACAACAAC 60.365 47.826 0.00 0.00 38.42 3.32
1744 4044 2.811431 GGTCGAACCATCATCACAACAA 59.189 45.455 0.00 0.00 38.42 2.83
1745 4045 2.038426 AGGTCGAACCATCATCACAACA 59.962 45.455 0.00 0.00 41.95 3.33
1746 4046 2.673368 GAGGTCGAACCATCATCACAAC 59.327 50.000 0.00 0.00 41.95 3.32
1747 4047 2.354704 GGAGGTCGAACCATCATCACAA 60.355 50.000 0.00 0.00 41.95 3.33
1748 4048 1.207089 GGAGGTCGAACCATCATCACA 59.793 52.381 0.00 0.00 41.95 3.58
1749 4049 1.802880 CGGAGGTCGAACCATCATCAC 60.803 57.143 0.00 0.00 41.95 3.06
1751 4051 0.460311 ACGGAGGTCGAACCATCATC 59.540 55.000 0.00 0.00 41.95 2.92
1762 4062 1.891616 GAGGGTTGAGACGGAGGTC 59.108 63.158 0.00 0.00 43.76 3.85
1763 4063 1.977544 CGAGGGTTGAGACGGAGGT 60.978 63.158 0.00 0.00 0.00 3.85
1765 4065 1.507174 GTCGAGGGTTGAGACGGAG 59.493 63.158 0.00 0.00 0.00 4.63
1767 4067 2.572284 GGTCGAGGGTTGAGACGG 59.428 66.667 0.00 0.00 35.87 4.79
1768 4068 0.679002 TAGGGTCGAGGGTTGAGACG 60.679 60.000 0.00 0.00 35.87 4.18
1769 4069 0.816373 GTAGGGTCGAGGGTTGAGAC 59.184 60.000 0.00 0.00 0.00 3.36
1770 4070 0.679002 CGTAGGGTCGAGGGTTGAGA 60.679 60.000 0.00 0.00 0.00 3.27
1771 4071 1.807886 CGTAGGGTCGAGGGTTGAG 59.192 63.158 0.00 0.00 0.00 3.02
1772 4072 2.345760 GCGTAGGGTCGAGGGTTGA 61.346 63.158 0.00 0.00 0.00 3.18
1773 4073 2.183555 GCGTAGGGTCGAGGGTTG 59.816 66.667 0.00 0.00 0.00 3.77
1781 4081 0.738762 GGAAAAGACGGCGTAGGGTC 60.739 60.000 14.74 8.65 0.00 4.46
1782 4082 1.294459 GGAAAAGACGGCGTAGGGT 59.706 57.895 14.74 0.00 0.00 4.34
1783 4083 1.449070 GGGAAAAGACGGCGTAGGG 60.449 63.158 14.74 0.00 0.00 3.53
1784 4084 1.808390 CGGGAAAAGACGGCGTAGG 60.808 63.158 14.74 0.00 0.00 3.18
1789 4089 2.120355 TTTTCGCGGGAAAAGACGGC 62.120 55.000 29.78 0.00 44.86 5.68
1790 4090 1.943293 TTTTCGCGGGAAAAGACGG 59.057 52.632 29.78 0.00 44.86 4.79
1796 4096 0.604073 GGGGAATTTTTCGCGGGAAA 59.396 50.000 22.19 22.19 42.92 3.13
1798 4098 0.963355 CAGGGGAATTTTTCGCGGGA 60.963 55.000 6.13 0.00 42.92 5.14
1801 4101 0.170339 GACCAGGGGAATTTTTCGCG 59.830 55.000 0.00 0.00 42.92 5.87
1803 4103 0.808755 CGGACCAGGGGAATTTTTCG 59.191 55.000 0.00 0.00 0.00 3.46
1805 4105 2.623239 GGATCGGACCAGGGGAATTTTT 60.623 50.000 0.00 0.00 0.00 1.94
1806 4106 1.063942 GGATCGGACCAGGGGAATTTT 60.064 52.381 0.00 0.00 0.00 1.82
1807 4107 0.551396 GGATCGGACCAGGGGAATTT 59.449 55.000 0.00 0.00 0.00 1.82
1808 4108 0.327576 AGGATCGGACCAGGGGAATT 60.328 55.000 0.00 0.00 0.00 2.17
1809 4109 0.764752 GAGGATCGGACCAGGGGAAT 60.765 60.000 0.00 0.00 0.00 3.01
1810 4110 1.382695 GAGGATCGGACCAGGGGAA 60.383 63.158 0.00 0.00 0.00 3.97
1811 4111 2.282446 GAGGATCGGACCAGGGGA 59.718 66.667 0.00 0.00 0.00 4.81
1812 4112 2.844839 GGAGGATCGGACCAGGGG 60.845 72.222 0.00 0.00 34.37 4.79
1813 4113 1.834822 GAGGAGGATCGGACCAGGG 60.835 68.421 0.00 0.00 34.37 4.45
1815 4115 2.196925 CGGAGGAGGATCGGACCAG 61.197 68.421 0.00 0.00 34.37 4.00
1816 4116 2.123854 CGGAGGAGGATCGGACCA 60.124 66.667 0.00 0.00 34.37 4.02
1817 4117 3.607661 GCGGAGGAGGATCGGACC 61.608 72.222 0.00 0.00 34.37 4.46
1818 4118 0.894184 TATGCGGAGGAGGATCGGAC 60.894 60.000 0.00 0.00 34.37 4.79
1819 4119 0.178973 TTATGCGGAGGAGGATCGGA 60.179 55.000 0.00 0.00 34.37 4.55
1820 4120 0.244994 CTTATGCGGAGGAGGATCGG 59.755 60.000 0.00 0.00 34.37 4.18
1821 4121 1.201181 CTCTTATGCGGAGGAGGATCG 59.799 57.143 0.00 0.00 34.37 3.69
1822 4122 1.067213 GCTCTTATGCGGAGGAGGATC 60.067 57.143 6.51 0.00 0.00 3.36
1824 4124 0.397114 TGCTCTTATGCGGAGGAGGA 60.397 55.000 6.51 1.67 35.36 3.71
1825 4125 0.683973 ATGCTCTTATGCGGAGGAGG 59.316 55.000 6.51 0.00 34.85 4.30
1826 4126 1.617850 AGATGCTCTTATGCGGAGGAG 59.382 52.381 0.00 1.22 34.85 3.69
1827 4127 1.615883 GAGATGCTCTTATGCGGAGGA 59.384 52.381 0.00 0.00 35.76 3.71
1828 4128 1.337635 GGAGATGCTCTTATGCGGAGG 60.338 57.143 0.00 0.00 35.36 4.30
1829 4129 1.342496 TGGAGATGCTCTTATGCGGAG 59.658 52.381 0.00 0.00 35.36 4.63
1831 4131 1.869767 GTTGGAGATGCTCTTATGCGG 59.130 52.381 0.00 0.00 35.36 5.69
1832 4132 2.543012 CTGTTGGAGATGCTCTTATGCG 59.457 50.000 0.00 0.00 35.36 4.73
1833 4133 2.290093 GCTGTTGGAGATGCTCTTATGC 59.710 50.000 0.00 0.00 0.00 3.14
1879 4179 3.736100 CGCGTGCTGCAAATGGGA 61.736 61.111 2.77 0.00 46.97 4.37
2118 6470 7.571080 TTTTATCGTGTTGGACTAGGTTTTT 57.429 32.000 0.00 0.00 0.00 1.94
2153 6529 3.354467 ACTCGGAGTAGGTTCTAGTTGG 58.646 50.000 9.33 0.00 0.00 3.77
2190 6581 0.597637 CTCGAACAACACCAGCGAGT 60.598 55.000 0.00 0.00 42.35 4.18
2258 7515 1.613255 CGTTAATGCAGGTGGGGAGTT 60.613 52.381 0.00 0.00 0.00 3.01
2297 7554 2.847234 TCGGTGGAAGGCACTGGT 60.847 61.111 0.00 0.00 40.86 4.00


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

AutoCloner maintained by Alex Coulton.