Multiple sequence alignment - TraesCS7A01G228100

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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 TraesCS7A01G228100 chr7A 100.000 2216 0 0 1 2216 198660113 198662328 0.000000e+00 4093.0
1 TraesCS7A01G228100 chr7A 96.333 300 10 1 1518 1816 616469990 616469691 1.980000e-135 492.0
2 TraesCS7A01G228100 chr6A 97.365 683 17 1 3 684 490308477 490307795 0.000000e+00 1160.0
3 TraesCS7A01G228100 chr6A 94.888 313 14 2 1518 1828 65071077 65071389 2.560000e-134 488.0
4 TraesCS7A01G228100 chr4B 88.903 811 55 21 685 1475 638224892 638224097 0.000000e+00 966.0
5 TraesCS7A01G228100 chr4B 86.284 401 31 3 1817 2216 638223764 638223387 4.400000e-112 414.0
6 TraesCS7A01G228100 chr4B 100.000 34 0 0 1476 1509 638223798 638223765 1.840000e-06 63.9
7 TraesCS7A01G228100 chr7B 88.779 811 56 21 685 1475 547953953 547953158 0.000000e+00 961.0
8 TraesCS7A01G228100 chr7B 89.197 361 29 4 685 1037 470702153 470701795 2.020000e-120 442.0
9 TraesCS7A01G228100 chr7B 86.250 400 32 2 1817 2216 547952826 547952450 1.580000e-111 412.0
10 TraesCS7A01G228100 chr7B 100.000 34 0 0 1476 1509 547952860 547952827 1.840000e-06 63.9
11 TraesCS7A01G228100 chr2B 88.764 801 56 14 685 1475 394355141 394355917 0.000000e+00 950.0
12 TraesCS7A01G228100 chr2B 84.179 670 86 10 686 1339 707719103 707719768 1.120000e-177 632.0
13 TraesCS7A01G228100 chr2B 82.133 694 79 20 777 1456 110676796 110677458 8.940000e-154 553.0
14 TraesCS7A01G228100 chr2B 90.773 401 33 2 1817 2214 394356175 394356574 1.160000e-147 532.0
15 TraesCS7A01G228100 chr2B 85.204 196 18 3 1824 2018 707724635 707724820 8.080000e-45 191.0
16 TraesCS7A01G228100 chr2B 100.000 34 0 0 1476 1509 394356141 394356174 1.840000e-06 63.9
17 TraesCS7A01G228100 chr4A 87.654 729 52 19 761 1475 658359455 658360159 0.000000e+00 813.0
18 TraesCS7A01G228100 chr4A 92.211 398 29 2 1817 2214 658360417 658360812 1.490000e-156 562.0
19 TraesCS7A01G228100 chr4A 94.551 312 15 2 1518 1828 57414034 57414344 4.280000e-132 481.0
20 TraesCS7A01G228100 chr4A 98.765 81 1 0 685 765 658357982 658358062 6.380000e-31 145.0
21 TraesCS7A01G228100 chr7D 86.812 690 81 10 1 684 558153807 558153122 0.000000e+00 761.0
22 TraesCS7A01G228100 chr7D 83.168 202 32 2 1021 1222 312046154 312045955 1.350000e-42 183.0
23 TraesCS7A01G228100 chr7D 85.556 90 12 1 1092 1181 39092424 39092336 2.340000e-15 93.5
24 TraesCS7A01G228100 chr6B 88.203 551 48 8 685 1222 42466112 42466658 1.860000e-180 641.0
25 TraesCS7A01G228100 chr6B 91.960 398 31 1 1817 2214 377154387 377153991 6.910000e-155 556.0
26 TraesCS7A01G228100 chr6B 96.333 300 10 1 1518 1816 547713657 547713956 1.980000e-135 492.0
27 TraesCS7A01G228100 chr6B 83.152 368 47 14 326 684 654503091 654503452 2.740000e-84 322.0
28 TraesCS7A01G228100 chr6B 89.328 253 21 6 434 684 141659772 141659524 1.650000e-81 313.0
29 TraesCS7A01G228100 chr6B 82.240 366 34 12 1118 1475 377154987 377154645 1.000000e-73 287.0
30 TraesCS7A01G228100 chr6B 88.500 200 20 1 2020 2216 42467978 42468177 2.840000e-59 239.0
31 TraesCS7A01G228100 chr6B 86.139 202 17 3 1819 2019 42467391 42467582 8.020000e-50 207.0
32 TraesCS7A01G228100 chr6B 100.000 34 0 0 1476 1509 42467355 42467388 1.840000e-06 63.9
33 TraesCS7A01G228100 chr6B 100.000 34 0 0 1476 1509 377154421 377154388 1.840000e-06 63.9
34 TraesCS7A01G228100 chr2A 96.667 300 9 1 1518 1816 597847822 597848121 4.250000e-137 497.0
35 TraesCS7A01G228100 chr2A 96.656 299 9 1 1518 1815 18596988 18596690 1.530000e-136 496.0
36 TraesCS7A01G228100 chr2A 95.987 299 11 1 1518 1815 15845684 15845386 3.310000e-133 484.0
37 TraesCS7A01G228100 chr2A 94.551 312 15 2 1518 1828 486909061 486908751 4.280000e-132 481.0
38 TraesCS7A01G228100 chr2A 85.670 321 37 9 373 687 12203594 12203911 1.640000e-86 329.0
39 TraesCS7A01G228100 chr2A 82.114 369 51 13 327 684 26918048 26918412 3.580000e-78 302.0
40 TraesCS7A01G228100 chr2A 87.273 110 12 1 697 806 115438830 115438937 8.310000e-25 124.0
41 TraesCS7A01G228100 chr1A 96.656 299 9 1 1518 1815 382255931 382256229 1.530000e-136 496.0
42 TraesCS7A01G228100 chr5B 84.615 377 49 9 314 684 445190794 445191167 1.250000e-97 366.0
43 TraesCS7A01G228100 chr5B 79.499 439 60 17 807 1219 595056504 595056070 3.600000e-73 285.0
44 TraesCS7A01G228100 chr5B 84.733 131 19 1 1092 1222 144856239 144856368 1.790000e-26 130.0
45 TraesCS7A01G228100 chrUn 84.298 363 48 8 330 684 110693451 110693090 1.630000e-91 346.0
46 TraesCS7A01G228100 chrUn 87.273 110 12 1 697 806 150892333 150892440 8.310000e-25 124.0
47 TraesCS7A01G228100 chr3A 80.795 453 70 16 246 687 8130712 8130266 2.730000e-89 339.0
48 TraesCS7A01G228100 chr1B 87.500 88 10 1 1075 1162 390441432 390441346 1.400000e-17 100.0
49 TraesCS7A01G228100 chr5D 94.872 39 2 0 1299 1337 209732711 209732673 6.610000e-06 62.1


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 TraesCS7A01G228100 chr7A 198660113 198662328 2215 False 4093.000000 4093 100.000000 1 2216 1 chr7A.!!$F1 2215
1 TraesCS7A01G228100 chr6A 490307795 490308477 682 True 1160.000000 1160 97.365000 3 684 1 chr6A.!!$R1 681
2 TraesCS7A01G228100 chr4B 638223387 638224892 1505 True 481.300000 966 91.729000 685 2216 3 chr4B.!!$R1 1531
3 TraesCS7A01G228100 chr7B 547952450 547953953 1503 True 478.966667 961 91.676333 685 2216 3 chr7B.!!$R2 1531
4 TraesCS7A01G228100 chr2B 707719103 707719768 665 False 632.000000 632 84.179000 686 1339 1 chr2B.!!$F2 653
5 TraesCS7A01G228100 chr2B 110676796 110677458 662 False 553.000000 553 82.133000 777 1456 1 chr2B.!!$F1 679
6 TraesCS7A01G228100 chr2B 394355141 394356574 1433 False 515.300000 950 93.179000 685 2214 3 chr2B.!!$F4 1529
7 TraesCS7A01G228100 chr4A 658357982 658360812 2830 False 506.666667 813 92.876667 685 2214 3 chr4A.!!$F2 1529
8 TraesCS7A01G228100 chr7D 558153122 558153807 685 True 761.000000 761 86.812000 1 684 1 chr7D.!!$R3 683
9 TraesCS7A01G228100 chr6B 377153991 377154987 996 True 302.300000 556 91.400000 1118 2214 3 chr6B.!!$R2 1096
10 TraesCS7A01G228100 chr6B 42466112 42468177 2065 False 287.725000 641 90.710500 685 2216 4 chr6B.!!$F3 1531

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
794 2199 0.544697 ACGTTGGAGTTGAGTTGGGT 59.455 50.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 3713 0.110486 GAGCCCTTTGGTTCACAGGA 59.89 55.0 1.99 0.0 41.28 3.86 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
49 50 2.375174 TCCACACTTCCTTTAGCATGGT 59.625 45.455 1.62 1.62 0.00 3.55
121 123 1.878088 TGCGACGTCTCTAAGTCTTGT 59.122 47.619 14.70 0.00 35.38 3.16
273 276 0.958382 CCGGATCCAGGCGAAACAAA 60.958 55.000 13.41 0.00 0.00 2.83
279 282 0.608035 CCAGGCGAAACAAAGGGCTA 60.608 55.000 0.00 0.00 34.92 3.93
593 601 1.202382 GCTCCGCGTTACAGATTAGGT 60.202 52.381 4.92 0.00 0.00 3.08
636 644 2.618045 GCCCTGGCACAAATGTAGTACT 60.618 50.000 2.58 0.00 38.70 2.73
716 724 8.387015 AGAGGTTTCTCTCGTGAGATCGATTAT 61.387 40.741 17.24 1.80 46.79 1.28
794 2199 0.544697 ACGTTGGAGTTGAGTTGGGT 59.455 50.000 0.00 0.00 0.00 4.51
870 2276 1.675310 CTGGATCTGGCCGTGCAAA 60.675 57.895 0.00 0.00 0.00 3.68
895 2301 2.561419 TCGGAGAAGGAGAACGAAACAT 59.439 45.455 0.00 0.00 0.00 2.71
897 2303 3.614150 CGGAGAAGGAGAACGAAACATGA 60.614 47.826 0.00 0.00 0.00 3.07
933 2343 5.947228 GTCAAAGGAGATGACACAATTCA 57.053 39.130 2.01 0.00 45.13 2.57
1016 2426 2.106332 GATGTCGGCCGGAATCGT 59.894 61.111 27.83 14.51 33.95 3.73
1073 2493 1.755384 GGGTCGGGGAAGATGATCC 59.245 63.158 0.00 0.00 38.86 3.36
1192 2612 1.832883 CTCGGGAGATGGAGATCGAT 58.167 55.000 0.00 0.00 38.80 3.59
1211 2699 1.079612 CGAGCCATGACAGACAGCA 60.080 57.895 0.00 0.00 0.00 4.41
1212 2700 1.082679 CGAGCCATGACAGACAGCAG 61.083 60.000 0.00 0.00 0.00 4.24
1213 2701 0.036577 GAGCCATGACAGACAGCAGT 60.037 55.000 0.00 0.00 0.00 4.40
1214 2702 1.205655 GAGCCATGACAGACAGCAGTA 59.794 52.381 0.00 0.00 0.00 2.74
1215 2703 1.206610 AGCCATGACAGACAGCAGTAG 59.793 52.381 0.00 0.00 0.00 2.57
1216 2704 1.741732 GCCATGACAGACAGCAGTAGG 60.742 57.143 0.00 0.00 0.00 3.18
1217 2705 1.134580 CCATGACAGACAGCAGTAGGG 60.135 57.143 0.00 0.00 0.00 3.53
1218 2706 1.827344 CATGACAGACAGCAGTAGGGA 59.173 52.381 0.00 0.00 0.00 4.20
1219 2707 1.550327 TGACAGACAGCAGTAGGGAG 58.450 55.000 0.00 0.00 0.00 4.30
1220 2708 0.174617 GACAGACAGCAGTAGGGAGC 59.825 60.000 0.00 0.00 0.00 4.70
1221 2709 0.542938 ACAGACAGCAGTAGGGAGCA 60.543 55.000 0.00 0.00 0.00 4.26
1222 2710 0.829333 CAGACAGCAGTAGGGAGCAT 59.171 55.000 0.00 0.00 0.00 3.79
1223 2711 0.829333 AGACAGCAGTAGGGAGCATG 59.171 55.000 0.00 0.00 0.00 4.06
1224 2712 0.826715 GACAGCAGTAGGGAGCATGA 59.173 55.000 0.00 0.00 0.00 3.07
1225 2713 0.539051 ACAGCAGTAGGGAGCATGAC 59.461 55.000 0.00 0.00 0.00 3.06
1226 2714 0.538584 CAGCAGTAGGGAGCATGACA 59.461 55.000 0.00 0.00 0.00 3.58
1227 2715 0.829333 AGCAGTAGGGAGCATGACAG 59.171 55.000 0.00 0.00 0.00 3.51
1228 2716 0.826715 GCAGTAGGGAGCATGACAGA 59.173 55.000 0.00 0.00 0.00 3.41
1229 2717 1.415659 GCAGTAGGGAGCATGACAGAT 59.584 52.381 0.00 0.00 0.00 2.90
1230 2718 2.630098 GCAGTAGGGAGCATGACAGATA 59.370 50.000 0.00 0.00 0.00 1.98
1231 2719 3.305950 GCAGTAGGGAGCATGACAGATAG 60.306 52.174 0.00 0.00 0.00 2.08
1232 2720 4.148079 CAGTAGGGAGCATGACAGATAGA 58.852 47.826 0.00 0.00 0.00 1.98
1248 2736 0.039180 TAGAGGTCGGGAGCAACTCA 59.961 55.000 0.32 0.00 31.08 3.41
1255 2743 1.613630 GGGAGCAACTCAGAGGGGA 60.614 63.158 1.53 0.00 31.08 4.81
1442 3133 2.399356 GCTTGCCGTCCTAAGCCAC 61.399 63.158 0.00 0.00 42.57 5.01
1509 3499 0.830648 CCGTCCCTGCATCTCCTAAA 59.169 55.000 0.00 0.00 0.00 1.85
1511 3501 2.632996 CCGTCCCTGCATCTCCTAAATA 59.367 50.000 0.00 0.00 0.00 1.40
1512 3502 3.555168 CCGTCCCTGCATCTCCTAAATAC 60.555 52.174 0.00 0.00 0.00 1.89
1513 3503 3.322254 CGTCCCTGCATCTCCTAAATACT 59.678 47.826 0.00 0.00 0.00 2.12
1515 3505 5.685075 CGTCCCTGCATCTCCTAAATACTTT 60.685 44.000 0.00 0.00 0.00 2.66
1516 3506 5.529060 GTCCCTGCATCTCCTAAATACTTTG 59.471 44.000 0.00 0.00 0.00 2.77
1517 3507 5.191722 TCCCTGCATCTCCTAAATACTTTGT 59.808 40.000 0.00 0.00 0.00 2.83
1518 3508 5.888161 CCCTGCATCTCCTAAATACTTTGTT 59.112 40.000 0.00 0.00 0.00 2.83
1519 3509 6.378280 CCCTGCATCTCCTAAATACTTTGTTT 59.622 38.462 0.00 0.00 0.00 2.83
1520 3510 7.253422 CCTGCATCTCCTAAATACTTTGTTTG 58.747 38.462 0.00 0.00 0.00 2.93
1521 3511 7.156876 TGCATCTCCTAAATACTTTGTTTGG 57.843 36.000 0.00 0.00 0.00 3.28
1522 3512 6.719370 TGCATCTCCTAAATACTTTGTTTGGT 59.281 34.615 0.00 0.00 0.00 3.67
1523 3513 7.232534 TGCATCTCCTAAATACTTTGTTTGGTT 59.767 33.333 0.00 0.00 0.00 3.67
1524 3514 7.755373 GCATCTCCTAAATACTTTGTTTGGTTC 59.245 37.037 0.00 0.00 0.00 3.62
1525 3515 8.792633 CATCTCCTAAATACTTTGTTTGGTTCA 58.207 33.333 0.00 0.00 0.00 3.18
1526 3516 8.934023 TCTCCTAAATACTTTGTTTGGTTCAT 57.066 30.769 0.00 0.00 0.00 2.57
1529 3519 9.238368 TCCTAAATACTTTGTTTGGTTCATAGG 57.762 33.333 0.00 0.00 0.00 2.57
1530 3520 9.238368 CCTAAATACTTTGTTTGGTTCATAGGA 57.762 33.333 0.00 0.00 0.00 2.94
1534 3524 8.980481 ATACTTTGTTTGGTTCATAGGATAGG 57.020 34.615 0.00 0.00 0.00 2.57
1535 3525 7.027874 ACTTTGTTTGGTTCATAGGATAGGA 57.972 36.000 0.00 0.00 0.00 2.94
1536 3526 7.643123 ACTTTGTTTGGTTCATAGGATAGGAT 58.357 34.615 0.00 0.00 28.27 3.24
1537 3527 8.116026 ACTTTGTTTGGTTCATAGGATAGGATT 58.884 33.333 0.00 0.00 28.27 3.01
1538 3528 9.627123 CTTTGTTTGGTTCATAGGATAGGATTA 57.373 33.333 0.00 0.00 28.27 1.75
1540 3530 9.793259 TTGTTTGGTTCATAGGATAGGATTATC 57.207 33.333 0.00 0.00 35.87 1.75
1541 3531 8.944138 TGTTTGGTTCATAGGATAGGATTATCA 58.056 33.333 0.00 0.00 37.92 2.15
1542 3532 9.965902 GTTTGGTTCATAGGATAGGATTATCAT 57.034 33.333 0.00 0.00 37.92 2.45
1545 3535 9.439461 TGGTTCATAGGATAGGATTATCATAGG 57.561 37.037 0.00 0.00 36.37 2.57
1546 3536 9.661954 GGTTCATAGGATAGGATTATCATAGGA 57.338 37.037 0.00 1.09 39.88 2.94
1564 3554 9.621239 ATCATAGGAATAGGAATCTTGTAGGAA 57.379 33.333 0.00 0.00 0.00 3.36
1565 3555 9.447279 TCATAGGAATAGGAATCTTGTAGGAAA 57.553 33.333 0.00 0.00 0.00 3.13
1568 3558 8.337118 AGGAATAGGAATCTTGTAGGAAATGA 57.663 34.615 0.00 0.00 0.00 2.57
1569 3559 8.435982 AGGAATAGGAATCTTGTAGGAAATGAG 58.564 37.037 0.00 0.00 0.00 2.90
1570 3560 8.432805 GGAATAGGAATCTTGTAGGAAATGAGA 58.567 37.037 0.00 0.00 0.00 3.27
1572 3562 9.790344 AATAGGAATCTTGTAGGAAATGAGATG 57.210 33.333 0.00 0.00 0.00 2.90
1573 3563 7.443302 AGGAATCTTGTAGGAAATGAGATGA 57.557 36.000 0.00 0.00 0.00 2.92
1574 3564 7.278875 AGGAATCTTGTAGGAAATGAGATGAC 58.721 38.462 0.00 0.00 0.00 3.06
1575 3565 7.050377 GGAATCTTGTAGGAAATGAGATGACA 58.950 38.462 0.00 0.00 0.00 3.58
1576 3566 7.718753 GGAATCTTGTAGGAAATGAGATGACAT 59.281 37.037 0.00 0.00 0.00 3.06
1577 3567 9.118300 GAATCTTGTAGGAAATGAGATGACATT 57.882 33.333 0.00 0.00 41.43 2.71
1580 3570 9.770097 TCTTGTAGGAAATGAGATGACATTATC 57.230 33.333 0.00 0.00 39.19 1.75
1581 3571 9.775854 CTTGTAGGAAATGAGATGACATTATCT 57.224 33.333 0.00 0.00 39.19 1.98
1617 3607 9.527157 TGAATAGGAATAGGAAACAAAATGTCA 57.473 29.630 0.00 0.00 0.00 3.58
1622 3612 8.096414 AGGAATAGGAAACAAAATGTCATTTGG 58.904 33.333 11.54 11.06 43.10 3.28
1623 3613 7.877612 GGAATAGGAAACAAAATGTCATTTGGT 59.122 33.333 11.90 11.90 41.83 3.67
1643 3633 5.984233 GGTTGACACCAAAGGAATTTTTC 57.016 39.130 0.00 0.00 43.61 2.29
1644 3634 4.814234 GGTTGACACCAAAGGAATTTTTCC 59.186 41.667 0.00 0.00 45.80 3.13
1645 3635 5.627968 GGTTGACACCAAAGGAATTTTTCCA 60.628 40.000 8.87 0.00 46.88 3.53
1646 3636 6.911529 GGTTGACACCAAAGGAATTTTTCCAT 60.912 38.462 8.87 0.00 46.88 3.41
1647 3637 8.334633 GGTTGACACCAAAGGAATTTTTCCATT 61.335 37.037 8.87 0.31 46.88 3.16
1658 3648 6.765915 GAATTTTTCCATTGAGTCTAGGCT 57.234 37.500 0.00 0.00 0.00 4.58
1659 3649 6.765915 AATTTTTCCATTGAGTCTAGGCTC 57.234 37.500 17.74 17.74 36.12 4.70
1660 3650 5.505181 TTTTTCCATTGAGTCTAGGCTCT 57.495 39.130 24.20 2.95 36.51 4.09
1661 3651 5.505181 TTTTCCATTGAGTCTAGGCTCTT 57.495 39.130 24.20 9.92 36.51 2.85
1662 3652 5.505181 TTTCCATTGAGTCTAGGCTCTTT 57.495 39.130 24.20 9.56 36.51 2.52
1663 3653 5.505181 TTCCATTGAGTCTAGGCTCTTTT 57.495 39.130 24.20 7.12 36.51 2.27
1664 3654 5.505181 TCCATTGAGTCTAGGCTCTTTTT 57.495 39.130 24.20 4.72 36.51 1.94
1696 3686 8.826765 TCCTATGAAATATGGAGGATAGAAACC 58.173 37.037 0.00 0.00 31.25 3.27
1697 3687 8.605947 CCTATGAAATATGGAGGATAGAAACCA 58.394 37.037 0.00 0.00 36.83 3.67
1700 3690 8.924511 TGAAATATGGAGGATAGAAACCAATC 57.075 34.615 0.00 0.00 36.00 2.67
1701 3691 7.944554 TGAAATATGGAGGATAGAAACCAATCC 59.055 37.037 0.00 0.00 41.77 3.01
1730 3720 4.855340 GGAATAGAAACCCATTCCTGTGA 58.145 43.478 6.17 0.00 44.56 3.58
1731 3721 5.261216 GGAATAGAAACCCATTCCTGTGAA 58.739 41.667 6.17 0.00 44.56 3.18
1732 3722 5.125578 GGAATAGAAACCCATTCCTGTGAAC 59.874 44.000 6.17 0.00 44.56 3.18
1733 3723 2.876581 AGAAACCCATTCCTGTGAACC 58.123 47.619 0.00 0.00 38.94 3.62
1734 3724 2.176798 AGAAACCCATTCCTGTGAACCA 59.823 45.455 0.00 0.00 38.94 3.67
1735 3725 2.765689 AACCCATTCCTGTGAACCAA 57.234 45.000 0.00 0.00 32.13 3.67
1736 3726 2.765689 ACCCATTCCTGTGAACCAAA 57.234 45.000 0.00 0.00 32.13 3.28
1737 3727 2.597455 ACCCATTCCTGTGAACCAAAG 58.403 47.619 0.00 0.00 32.13 2.77
1738 3728 1.895131 CCCATTCCTGTGAACCAAAGG 59.105 52.381 0.00 0.00 40.12 3.11
1739 3729 1.895131 CCATTCCTGTGAACCAAAGGG 59.105 52.381 3.53 0.00 39.27 3.95
1740 3730 1.273327 CATTCCTGTGAACCAAAGGGC 59.727 52.381 3.53 0.00 39.27 5.19
1741 3731 0.555769 TTCCTGTGAACCAAAGGGCT 59.444 50.000 3.53 0.00 39.27 5.19
1742 3732 0.110486 TCCTGTGAACCAAAGGGCTC 59.890 55.000 3.53 0.00 39.27 4.70
1743 3733 0.111253 CCTGTGAACCAAAGGGCTCT 59.889 55.000 0.00 0.00 35.31 4.09
1744 3734 1.351017 CCTGTGAACCAAAGGGCTCTA 59.649 52.381 0.00 0.00 35.31 2.43
1745 3735 2.224769 CCTGTGAACCAAAGGGCTCTAA 60.225 50.000 0.00 0.00 35.31 2.10
1746 3736 3.486383 CTGTGAACCAAAGGGCTCTAAA 58.514 45.455 0.00 0.00 37.90 1.85
1747 3737 3.486383 TGTGAACCAAAGGGCTCTAAAG 58.514 45.455 0.00 0.00 37.90 1.85
1748 3738 2.820197 GTGAACCAAAGGGCTCTAAAGG 59.180 50.000 0.00 0.00 37.90 3.11
1749 3739 2.714250 TGAACCAAAGGGCTCTAAAGGA 59.286 45.455 5.94 0.00 37.90 3.36
1750 3740 3.139397 TGAACCAAAGGGCTCTAAAGGAA 59.861 43.478 5.94 0.00 37.90 3.36
1751 3741 3.895704 ACCAAAGGGCTCTAAAGGAAA 57.104 42.857 5.94 0.00 37.90 3.13
1752 3742 4.193240 ACCAAAGGGCTCTAAAGGAAAA 57.807 40.909 5.94 0.00 37.90 2.29
1753 3743 4.552674 ACCAAAGGGCTCTAAAGGAAAAA 58.447 39.130 5.94 0.00 37.90 1.94
1808 3798 8.807948 TCTATGAAATTCCTCTAAACCAAAGG 57.192 34.615 0.00 0.00 0.00 3.11
1809 3799 8.611257 TCTATGAAATTCCTCTAAACCAAAGGA 58.389 33.333 0.00 0.00 37.42 3.36
1810 3800 7.709149 ATGAAATTCCTCTAAACCAAAGGAG 57.291 36.000 0.00 0.00 40.21 3.69
1811 3801 6.010219 TGAAATTCCTCTAAACCAAAGGAGG 58.990 40.000 0.00 0.00 44.69 4.30
1812 3802 3.434940 TTCCTCTAAACCAAAGGAGGC 57.565 47.619 0.00 0.00 43.46 4.70
1813 3803 1.633945 TCCTCTAAACCAAAGGAGGCC 59.366 52.381 0.00 0.00 43.46 5.19
1814 3804 1.636003 CCTCTAAACCAAAGGAGGCCT 59.364 52.381 3.86 3.86 38.82 5.19
1859 3849 0.623723 TTGTCCCCTAATGGCCTCAC 59.376 55.000 3.32 0.00 0.00 3.51
1990 3980 9.764363 TTGTAGTGGCATATAGTATTCTTTCAG 57.236 33.333 0.00 0.00 0.00 3.02
2011 4004 5.045215 CAGTCCAAATTAATTGATGCGCAT 58.955 37.500 25.66 25.66 41.85 4.73
2030 4418 9.760077 ATGCGCATTTAGTATAACTTTAGTACT 57.240 29.630 19.28 0.00 33.55 2.73
2049 4437 4.617253 ACTGAATTGTACTAGGTGTGCA 57.383 40.909 0.00 0.00 39.46 4.57
2086 4477 8.696374 TGGATCGAAGAGAGTATCAAATTTACT 58.304 33.333 0.00 0.00 43.63 2.24
2161 4552 2.351244 CGCCTAGGACTGCACTCCA 61.351 63.158 14.75 1.00 31.94 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.182568 TGGATTCCATTGTATGCCATATAGAGA 59.817 37.037 0.00 0.00 0.00 3.10
24 25 3.686016 TGCTAAAGGAAGTGTGGATTCC 58.314 45.455 0.00 0.00 45.56 3.01
49 50 3.039588 GCGGTTTCTCGCGGACAA 61.040 61.111 6.13 0.00 46.23 3.18
142 145 2.509111 CACGCATGCTAGCCACGA 60.509 61.111 22.78 1.63 0.00 4.35
273 276 1.613630 CAGACACACCCCTAGCCCT 60.614 63.158 0.00 0.00 0.00 5.19
279 282 2.038762 AACCCCAGACACACCCCT 60.039 61.111 0.00 0.00 0.00 4.79
395 399 0.537653 TCTCCACCAACACGACACAA 59.462 50.000 0.00 0.00 0.00 3.33
446 451 1.525923 CCCCATCTGTCAGCCTCTG 59.474 63.158 0.00 0.00 0.00 3.35
636 644 5.829062 TTTGAGGCTAGGGTAACAACTTA 57.171 39.130 0.00 0.00 39.74 2.24
794 2199 3.379057 TCCGATTTACTACGTGATGCTCA 59.621 43.478 0.00 0.00 0.00 4.26
870 2276 0.882474 CGTTCTCCTTCTCCGACAGT 59.118 55.000 0.00 0.00 0.00 3.55
895 2301 0.322187 TGACTCTCCGTCCATCGTCA 60.322 55.000 0.00 0.00 42.13 4.35
897 2303 1.202582 CTTTGACTCTCCGTCCATCGT 59.797 52.381 0.00 0.00 42.13 3.73
922 2332 1.333308 CGTGTTGGCTGAATTGTGTCA 59.667 47.619 0.00 0.00 0.00 3.58
987 2397 2.900167 CGACATCGGGTCCGCGATA 61.900 63.158 17.19 0.00 43.95 2.92
1192 2612 1.216444 GCTGTCTGTCATGGCTCGA 59.784 57.895 0.00 0.00 0.00 4.04
1211 2699 4.406456 CTCTATCTGTCATGCTCCCTACT 58.594 47.826 0.00 0.00 0.00 2.57
1212 2700 3.509575 CCTCTATCTGTCATGCTCCCTAC 59.490 52.174 0.00 0.00 0.00 3.18
1213 2701 3.141083 ACCTCTATCTGTCATGCTCCCTA 59.859 47.826 0.00 0.00 0.00 3.53
1214 2702 2.090831 ACCTCTATCTGTCATGCTCCCT 60.091 50.000 0.00 0.00 0.00 4.20
1215 2703 2.298729 GACCTCTATCTGTCATGCTCCC 59.701 54.545 0.00 0.00 0.00 4.30
1216 2704 2.030363 CGACCTCTATCTGTCATGCTCC 60.030 54.545 0.00 0.00 0.00 4.70
1217 2705 2.030363 CCGACCTCTATCTGTCATGCTC 60.030 54.545 0.00 0.00 0.00 4.26
1218 2706 1.959985 CCGACCTCTATCTGTCATGCT 59.040 52.381 0.00 0.00 0.00 3.79
1219 2707 1.000283 CCCGACCTCTATCTGTCATGC 60.000 57.143 0.00 0.00 0.00 4.06
1220 2708 2.556189 CTCCCGACCTCTATCTGTCATG 59.444 54.545 0.00 0.00 0.00 3.07
1221 2709 2.870175 CTCCCGACCTCTATCTGTCAT 58.130 52.381 0.00 0.00 0.00 3.06
1222 2710 1.751032 GCTCCCGACCTCTATCTGTCA 60.751 57.143 0.00 0.00 0.00 3.58
1223 2711 0.955905 GCTCCCGACCTCTATCTGTC 59.044 60.000 0.00 0.00 0.00 3.51
1224 2712 0.259065 TGCTCCCGACCTCTATCTGT 59.741 55.000 0.00 0.00 0.00 3.41
1225 2713 1.067821 GTTGCTCCCGACCTCTATCTG 59.932 57.143 0.00 0.00 0.00 2.90
1226 2714 1.063567 AGTTGCTCCCGACCTCTATCT 60.064 52.381 0.00 0.00 0.00 1.98
1227 2715 1.338655 GAGTTGCTCCCGACCTCTATC 59.661 57.143 0.00 0.00 0.00 2.08
1228 2716 1.342076 TGAGTTGCTCCCGACCTCTAT 60.342 52.381 0.00 0.00 0.00 1.98
1229 2717 0.039180 TGAGTTGCTCCCGACCTCTA 59.961 55.000 0.00 0.00 0.00 2.43
1230 2718 1.228894 TGAGTTGCTCCCGACCTCT 60.229 57.895 0.00 0.00 0.00 3.69
1231 2719 1.216710 CTGAGTTGCTCCCGACCTC 59.783 63.158 0.00 0.00 0.00 3.85
1232 2720 1.228894 TCTGAGTTGCTCCCGACCT 60.229 57.895 0.00 0.00 0.00 3.85
1248 2736 4.835891 CTACCGGCCGTCCCCTCT 62.836 72.222 26.12 0.00 0.00 3.69
1277 2945 4.559063 CCGCTGCCTGCTATGCCT 62.559 66.667 0.00 0.00 40.11 4.75
1278 2946 4.864334 ACCGCTGCCTGCTATGCC 62.864 66.667 0.00 0.00 40.11 4.40
1280 2948 2.963854 CGACCGCTGCCTGCTATG 60.964 66.667 0.00 0.00 40.11 2.23
1305 2984 3.827898 CGACTGCCGACTCCTCCC 61.828 72.222 0.00 0.00 41.76 4.30
1334 3017 4.141937 CCTCTCATTTCGTCCCAATCACTA 60.142 45.833 0.00 0.00 0.00 2.74
1422 3111 3.490890 GCTTAGGACGGCAAGCAG 58.509 61.111 8.39 0.00 45.20 4.24
1442 3133 2.566824 CCATTGGGACGTTCAAGGG 58.433 57.895 17.36 17.36 39.24 3.95
1471 3162 0.966179 GAAAATGCCCCTTGGACGTT 59.034 50.000 0.00 0.00 0.00 3.99
1509 3499 8.778059 TCCTATCCTATGAACCAAACAAAGTAT 58.222 33.333 0.00 0.00 0.00 2.12
1511 3501 7.027874 TCCTATCCTATGAACCAAACAAAGT 57.972 36.000 0.00 0.00 0.00 2.66
1512 3502 8.525290 AATCCTATCCTATGAACCAAACAAAG 57.475 34.615 0.00 0.00 0.00 2.77
1515 3505 8.944138 TGATAATCCTATCCTATGAACCAAACA 58.056 33.333 0.00 0.00 34.10 2.83
1516 3506 9.965902 ATGATAATCCTATCCTATGAACCAAAC 57.034 33.333 0.00 0.00 34.10 2.93
1519 3509 9.439461 CCTATGATAATCCTATCCTATGAACCA 57.561 37.037 0.00 0.00 34.10 3.67
1520 3510 9.661954 TCCTATGATAATCCTATCCTATGAACC 57.338 37.037 0.00 0.00 34.10 3.62
1538 3528 9.621239 TTCCTACAAGATTCCTATTCCTATGAT 57.379 33.333 0.00 0.00 0.00 2.45
1539 3529 9.447279 TTTCCTACAAGATTCCTATTCCTATGA 57.553 33.333 0.00 0.00 0.00 2.15
1542 3532 9.447279 TCATTTCCTACAAGATTCCTATTCCTA 57.553 33.333 0.00 0.00 0.00 2.94
1543 3533 8.337118 TCATTTCCTACAAGATTCCTATTCCT 57.663 34.615 0.00 0.00 0.00 3.36
1544 3534 8.432805 TCTCATTTCCTACAAGATTCCTATTCC 58.567 37.037 0.00 0.00 0.00 3.01
1546 3536 9.790344 CATCTCATTTCCTACAAGATTCCTATT 57.210 33.333 0.00 0.00 0.00 1.73
1547 3537 9.163894 TCATCTCATTTCCTACAAGATTCCTAT 57.836 33.333 0.00 0.00 0.00 2.57
1548 3538 8.424918 GTCATCTCATTTCCTACAAGATTCCTA 58.575 37.037 0.00 0.00 0.00 2.94
1549 3539 7.092712 TGTCATCTCATTTCCTACAAGATTCCT 60.093 37.037 0.00 0.00 0.00 3.36
1550 3540 7.050377 TGTCATCTCATTTCCTACAAGATTCC 58.950 38.462 0.00 0.00 0.00 3.01
1551 3541 8.674263 ATGTCATCTCATTTCCTACAAGATTC 57.326 34.615 0.00 0.00 0.00 2.52
1554 3544 9.770097 GATAATGTCATCTCATTTCCTACAAGA 57.230 33.333 0.00 0.00 38.68 3.02
1555 3545 9.775854 AGATAATGTCATCTCATTTCCTACAAG 57.224 33.333 0.00 0.00 38.68 3.16
1556 3546 9.770097 GAGATAATGTCATCTCATTTCCTACAA 57.230 33.333 7.98 0.00 46.84 2.41
1591 3581 9.527157 TGACATTTTGTTTCCTATTCCTATTCA 57.473 29.630 0.00 0.00 0.00 2.57
1596 3586 8.096414 CCAAATGACATTTTGTTTCCTATTCCT 58.904 33.333 10.77 0.00 35.30 3.36
1597 3587 7.877612 ACCAAATGACATTTTGTTTCCTATTCC 59.122 33.333 10.77 0.00 35.30 3.01
1598 3588 8.831715 ACCAAATGACATTTTGTTTCCTATTC 57.168 30.769 10.77 0.00 35.30 1.75
1599 3589 9.054922 CAACCAAATGACATTTTGTTTCCTATT 57.945 29.630 21.56 3.46 36.38 1.73
1600 3590 8.428063 TCAACCAAATGACATTTTGTTTCCTAT 58.572 29.630 21.56 4.04 36.38 2.57
1601 3591 7.786030 TCAACCAAATGACATTTTGTTTCCTA 58.214 30.769 21.56 9.70 36.38 2.94
1602 3592 6.648192 TCAACCAAATGACATTTTGTTTCCT 58.352 32.000 21.56 4.92 36.38 3.36
1603 3593 6.917217 TCAACCAAATGACATTTTGTTTCC 57.083 33.333 21.56 0.00 36.38 3.13
1621 3611 4.814234 GGAAAAATTCCTTTGGTGTCAACC 59.186 41.667 1.86 0.00 46.57 3.77
1622 3612 5.984233 GGAAAAATTCCTTTGGTGTCAAC 57.016 39.130 1.86 0.00 46.57 3.18
1633 3623 8.285329 GAGCCTAGACTCAATGGAAAAATTCCT 61.285 40.741 10.28 0.00 42.21 3.36
1634 3624 6.183360 GAGCCTAGACTCAATGGAAAAATTCC 60.183 42.308 0.51 2.12 42.14 3.01
1635 3625 6.601217 AGAGCCTAGACTCAATGGAAAAATTC 59.399 38.462 8.89 0.00 39.26 2.17
1636 3626 6.488715 AGAGCCTAGACTCAATGGAAAAATT 58.511 36.000 8.89 0.00 39.26 1.82
1637 3627 6.072199 AGAGCCTAGACTCAATGGAAAAAT 57.928 37.500 8.89 0.00 39.26 1.82
1638 3628 5.505181 AGAGCCTAGACTCAATGGAAAAA 57.495 39.130 8.89 0.00 39.26 1.94
1639 3629 5.505181 AAGAGCCTAGACTCAATGGAAAA 57.495 39.130 8.89 0.00 39.26 2.29
1640 3630 5.505181 AAAGAGCCTAGACTCAATGGAAA 57.495 39.130 8.89 0.00 39.26 3.13
1641 3631 5.505181 AAAAGAGCCTAGACTCAATGGAA 57.495 39.130 8.89 0.00 39.26 3.53
1642 3632 5.505181 AAAAAGAGCCTAGACTCAATGGA 57.495 39.130 8.89 0.00 39.26 3.41
1670 3660 8.826765 GGTTTCTATCCTCCATATTTCATAGGA 58.173 37.037 0.00 0.00 40.50 2.94
1671 3661 8.605947 TGGTTTCTATCCTCCATATTTCATAGG 58.394 37.037 0.00 0.00 0.00 2.57
1674 3664 9.525826 GATTGGTTTCTATCCTCCATATTTCAT 57.474 33.333 0.00 0.00 0.00 2.57
1675 3665 7.944554 GGATTGGTTTCTATCCTCCATATTTCA 59.055 37.037 0.00 0.00 40.55 2.69
1676 3666 8.341892 GGATTGGTTTCTATCCTCCATATTTC 57.658 38.462 0.00 0.00 40.55 2.17
1709 3699 5.125578 GGTTCACAGGAATGGGTTTCTATTC 59.874 44.000 0.00 0.00 39.30 1.75
1710 3700 5.016831 GGTTCACAGGAATGGGTTTCTATT 58.983 41.667 0.00 0.00 35.05 1.73
1711 3701 4.044065 TGGTTCACAGGAATGGGTTTCTAT 59.956 41.667 0.00 0.00 35.05 1.98
1712 3702 3.396276 TGGTTCACAGGAATGGGTTTCTA 59.604 43.478 0.00 0.00 35.05 2.10
1713 3703 2.176798 TGGTTCACAGGAATGGGTTTCT 59.823 45.455 0.00 0.00 35.05 2.52
1714 3704 2.593026 TGGTTCACAGGAATGGGTTTC 58.407 47.619 0.00 0.00 35.05 2.78
1715 3705 2.765689 TGGTTCACAGGAATGGGTTT 57.234 45.000 0.00 0.00 35.05 3.27
1716 3706 2.765689 TTGGTTCACAGGAATGGGTT 57.234 45.000 0.00 0.00 35.05 4.11
1717 3707 2.597455 CTTTGGTTCACAGGAATGGGT 58.403 47.619 0.00 0.00 35.05 4.51
1718 3708 1.895131 CCTTTGGTTCACAGGAATGGG 59.105 52.381 0.00 0.00 33.52 4.00
1719 3709 1.895131 CCCTTTGGTTCACAGGAATGG 59.105 52.381 1.99 0.00 33.52 3.16
1720 3710 1.273327 GCCCTTTGGTTCACAGGAATG 59.727 52.381 1.99 0.00 33.52 2.67
1721 3711 1.147817 AGCCCTTTGGTTCACAGGAAT 59.852 47.619 1.99 0.00 33.52 3.01
1722 3712 0.555769 AGCCCTTTGGTTCACAGGAA 59.444 50.000 1.99 0.00 33.52 3.36
1723 3713 0.110486 GAGCCCTTTGGTTCACAGGA 59.890 55.000 1.99 0.00 41.28 3.86
1724 3714 0.111253 AGAGCCCTTTGGTTCACAGG 59.889 55.000 0.00 0.00 43.89 4.00
1725 3715 2.859165 TAGAGCCCTTTGGTTCACAG 57.141 50.000 0.00 0.00 43.89 3.66
1726 3716 3.486383 CTTTAGAGCCCTTTGGTTCACA 58.514 45.455 0.00 0.00 43.89 3.58
1727 3717 2.820197 CCTTTAGAGCCCTTTGGTTCAC 59.180 50.000 0.00 0.00 43.89 3.18
1728 3718 2.714250 TCCTTTAGAGCCCTTTGGTTCA 59.286 45.455 0.00 0.00 43.89 3.18
1729 3719 3.434940 TCCTTTAGAGCCCTTTGGTTC 57.565 47.619 0.00 0.00 41.91 3.62
1730 3720 3.895704 TTCCTTTAGAGCCCTTTGGTT 57.104 42.857 0.00 0.00 0.00 3.67
1731 3721 3.895704 TTTCCTTTAGAGCCCTTTGGT 57.104 42.857 0.00 0.00 0.00 3.67
1782 3772 9.243105 CCTTTGGTTTAGAGGAATTTCATAGAA 57.757 33.333 0.00 0.00 32.11 2.10
1783 3773 8.611257 TCCTTTGGTTTAGAGGAATTTCATAGA 58.389 33.333 0.00 0.00 36.67 1.98
1784 3774 8.807948 TCCTTTGGTTTAGAGGAATTTCATAG 57.192 34.615 0.00 0.00 36.67 2.23
1785 3775 8.807948 CTCCTTTGGTTTAGAGGAATTTCATA 57.192 34.615 0.00 0.00 39.00 2.15
1786 3776 7.709149 CTCCTTTGGTTTAGAGGAATTTCAT 57.291 36.000 0.00 0.00 39.00 2.57
1794 3784 2.041755 AAGGCCTCCTTTGGTTTAGAGG 59.958 50.000 5.23 0.43 41.69 3.69
1795 3785 3.441500 AAGGCCTCCTTTGGTTTAGAG 57.558 47.619 5.23 0.00 41.69 2.43
1845 3835 1.338136 ACCGAGTGAGGCCATTAGGG 61.338 60.000 5.01 0.72 40.85 3.53
1859 3849 7.433708 TTCAAATATGCCATTGTATACCGAG 57.566 36.000 0.00 0.00 0.00 4.63
1982 3972 7.541783 CGCATCAATTAATTTGGACTGAAAGAA 59.458 33.333 0.00 0.00 35.06 2.52
1990 3980 5.971895 AATGCGCATCAATTAATTTGGAC 57.028 34.783 25.53 0.00 35.92 4.02
2005 3995 9.027129 CAGTACTAAAGTTATACTAAATGCGCA 57.973 33.333 14.96 14.96 0.00 6.09
2030 4418 3.244387 TGCTGCACACCTAGTACAATTCA 60.244 43.478 0.00 0.00 0.00 2.57
2042 4430 3.924144 TCCAAATTATTTGCTGCACACC 58.076 40.909 11.82 0.00 39.31 4.16
2049 4437 6.825721 ACTCTCTTCGATCCAAATTATTTGCT 59.174 34.615 11.82 1.94 39.31 3.91
2086 4477 6.635021 AGGGAGAAGCCTATTAGATTTAGGA 58.365 40.000 0.96 0.00 38.86 2.94
2147 4538 1.990060 GGCCTGGAGTGCAGTCCTA 60.990 63.158 34.80 22.34 37.52 2.94
2161 4552 4.103928 ATCCTACCGGGGTGGCCT 62.104 66.667 6.32 0.00 43.94 5.19


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

AutoCloner maintained by Alex Coulton.