Multiple sequence alignment - TraesCS2A01G557200

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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 TraesCS2A01G557200 chr2A 100.000 5424 0 0 1 5424 760859021 760853598 0.000000e+00 10017.0
1 TraesCS2A01G557200 chr2A 87.455 2774 217 47 2111 4831 759032888 759030193 0.000000e+00 3073.0
2 TraesCS2A01G557200 chr2A 92.603 1852 95 18 677 2501 759101803 759099967 0.000000e+00 2623.0
3 TraesCS2A01G557200 chr2A 85.224 1428 162 24 1648 3070 760919922 760918539 0.000000e+00 1423.0
4 TraesCS2A01G557200 chr2A 84.219 1280 163 24 2194 3453 760916668 760915408 0.000000e+00 1208.0
5 TraesCS2A01G557200 chr2A 87.723 448 41 4 829 1270 760923323 760922884 1.350000e-140 510.0
6 TraesCS2A01G557200 chr2A 80.729 576 92 13 3963 4534 760917741 760917181 1.080000e-116 431.0
7 TraesCS2A01G557200 chr2A 79.605 608 100 14 3940 4535 758756103 758756698 1.090000e-111 414.0
8 TraesCS2A01G557200 chr2A 93.774 257 15 1 1379 1635 760920160 760919905 8.520000e-103 385.0
9 TraesCS2A01G557200 chr2A 88.073 327 33 4 3160 3483 758755246 758755569 3.070000e-102 383.0
10 TraesCS2A01G557200 chr2A 80.443 271 36 14 824 1082 761027509 761027774 1.990000e-44 191.0
11 TraesCS2A01G557200 chr2A 75.238 420 64 23 4956 5342 759030121 759029709 4.350000e-36 163.0
12 TraesCS2A01G557200 chr2A 92.222 90 7 0 526 615 759102542 759102453 1.590000e-25 128.0
13 TraesCS2A01G557200 chr2A 97.778 45 1 0 627 671 760858344 760858300 1.620000e-10 78.7
14 TraesCS2A01G557200 chr2A 97.778 45 1 0 678 722 760858395 760858351 1.620000e-10 78.7
15 TraesCS2A01G557200 chrUn 99.936 3110 1 1 2316 5424 312029495 312032604 0.000000e+00 5731.0
16 TraesCS2A01G557200 chrUn 100.000 105 0 0 5320 5424 372881650 372881546 1.540000e-45 195.0
17 TraesCS2A01G557200 chrUn 80.443 271 36 14 824 1082 319843702 319843967 1.990000e-44 191.0
18 TraesCS2A01G557200 chr2D 91.635 1853 136 5 1647 3483 629452947 629451098 0.000000e+00 2545.0
19 TraesCS2A01G557200 chr2D 88.522 1394 138 7 2108 3483 629583763 629582374 0.000000e+00 1668.0
20 TraesCS2A01G557200 chr2D 84.233 1427 136 49 3865 5278 629450745 629449395 0.000000e+00 1306.0
21 TraesCS2A01G557200 chr2D 84.004 919 108 14 2566 3457 629404217 629403311 0.000000e+00 846.0
22 TraesCS2A01G557200 chr2D 82.604 937 134 15 2549 3457 629559497 629558562 0.000000e+00 800.0
23 TraesCS2A01G557200 chr2D 83.004 912 128 18 2556 3457 629994564 629995458 0.000000e+00 800.0
24 TraesCS2A01G557200 chr2D 87.286 700 47 17 677 1349 629460354 629459670 0.000000e+00 761.0
25 TraesCS2A01G557200 chr2D 84.113 705 93 5 3949 4640 629402962 629402264 0.000000e+00 664.0
26 TraesCS2A01G557200 chr2D 90.385 312 24 5 3540 3850 629451040 629450734 6.540000e-109 405.0
27 TraesCS2A01G557200 chr2D 94.942 257 11 2 1380 1635 629453184 629452929 8.460000e-108 401.0
28 TraesCS2A01G557200 chr2D 83.588 262 34 6 827 1080 629420565 629420305 2.530000e-58 237.0
29 TraesCS2A01G557200 chr2D 77.393 491 50 34 4779 5253 629402186 629401741 9.080000e-58 235.0
30 TraesCS2A01G557200 chr2D 86.364 220 21 4 4701 4920 629574013 629573803 1.170000e-56 231.0
31 TraesCS2A01G557200 chr2D 91.919 99 6 2 3482 3580 629582342 629582246 2.630000e-28 137.0
32 TraesCS2A01G557200 chr2D 91.304 92 7 1 525 615 629461128 629461037 2.050000e-24 124.0
33 TraesCS2A01G557200 chr2D 80.282 142 24 4 680 820 629422045 629421907 2.670000e-18 104.0
34 TraesCS2A01G557200 chr2D 89.583 48 1 3 5330 5374 629580940 629580894 2.110000e-04 58.4
35 TraesCS2A01G557200 chr2D 100.000 28 0 0 3482 3509 629451067 629451040 1.000000e-02 52.8
36 TraesCS2A01G557200 chr2B 94.262 854 43 3 1651 2501 772327952 772327102 0.000000e+00 1301.0
37 TraesCS2A01G557200 chr2B 86.537 1181 106 23 3865 5021 772228549 772227398 0.000000e+00 1251.0
38 TraesCS2A01G557200 chr2B 79.271 1399 219 30 1648 3036 772485592 772484255 0.000000e+00 911.0
39 TraesCS2A01G557200 chr2B 94.497 527 29 0 1 527 212575282 212574756 0.000000e+00 813.0
40 TraesCS2A01G557200 chr2B 79.877 1138 183 31 1943 3070 772353969 772352868 0.000000e+00 791.0
41 TraesCS2A01G557200 chr2B 87.412 707 50 15 677 1356 772334352 772333658 0.000000e+00 776.0
42 TraesCS2A01G557200 chr2B 79.566 1106 134 39 4078 5157 772350861 772349822 0.000000e+00 706.0
43 TraesCS2A01G557200 chr2B 90.335 507 31 12 2992 3483 772229429 772228926 0.000000e+00 649.0
44 TraesCS2A01G557200 chr2B 90.566 371 23 7 3482 3851 772228894 772228535 1.060000e-131 481.0
45 TraesCS2A01G557200 chr2B 87.563 394 36 7 680 1061 772495229 772494837 1.390000e-120 444.0
46 TraesCS2A01G557200 chr2B 81.149 557 91 9 3980 4534 772352055 772351511 8.340000e-118 435.0
47 TraesCS2A01G557200 chr2B 83.058 484 68 7 2570 3052 772602888 772603358 1.400000e-115 427.0
48 TraesCS2A01G557200 chr2B 92.400 250 17 2 1379 1628 772328783 772328536 6.680000e-94 355.0
49 TraesCS2A01G557200 chr2B 82.555 407 66 3 3984 4386 772483462 772483057 2.400000e-93 353.0
50 TraesCS2A01G557200 chr2B 88.435 294 31 2 3160 3450 771959020 771959313 8.640000e-93 351.0
51 TraesCS2A01G557200 chr2B 87.417 302 36 2 3167 3467 772326601 772326301 4.020000e-91 346.0
52 TraesCS2A01G557200 chr2B 86.207 319 41 2 3163 3481 772352859 772352544 5.200000e-90 342.0
53 TraesCS2A01G557200 chr2B 82.804 378 63 2 2121 2497 772602415 772602791 2.420000e-88 337.0
54 TraesCS2A01G557200 chr2B 77.594 424 43 31 4783 5179 772482595 772482197 5.510000e-50 209.0
55 TraesCS2A01G557200 chr2B 94.505 91 5 0 525 615 772335390 772335300 2.040000e-29 141.0
56 TraesCS2A01G557200 chr2B 81.818 77 14 0 4563 4639 772325127 772325051 1.260000e-06 65.8
57 TraesCS2A01G557200 chr2B 86.207 58 8 0 4560 4617 772536958 772536901 4.540000e-06 63.9
58 TraesCS2A01G557200 chr6D 94.687 527 28 0 1 527 450669075 450668549 0.000000e+00 819.0
59 TraesCS2A01G557200 chr3D 94.687 527 28 0 1 527 508062964 508062438 0.000000e+00 819.0
60 TraesCS2A01G557200 chr3D 94.497 527 29 0 1 527 602106941 602107467 0.000000e+00 813.0
61 TraesCS2A01G557200 chr6B 94.318 528 29 1 1 527 77802100 77802627 0.000000e+00 808.0
62 TraesCS2A01G557200 chr7B 94.118 527 31 0 1 527 695709579 695710105 0.000000e+00 802.0
63 TraesCS2A01G557200 chr5B 94.118 527 31 0 1 527 26947013 26946487 0.000000e+00 802.0
64 TraesCS2A01G557200 chr5B 93.939 528 31 1 1 527 10171587 10171060 0.000000e+00 797.0
65 TraesCS2A01G557200 chr5B 84.000 75 12 0 1427 1501 485660384 485660458 7.540000e-09 73.1
66 TraesCS2A01G557200 chr1D 94.106 526 31 0 1 526 31344733 31345258 0.000000e+00 800.0
67 TraesCS2A01G557200 chr7A 86.916 107 13 1 1385 1491 115832585 115832690 9.540000e-23 119.0
68 TraesCS2A01G557200 chr7A 81.169 154 16 7 5033 5178 672009453 672009601 1.600000e-20 111.0
69 TraesCS2A01G557200 chr7A 81.818 143 15 5 5033 5169 501149445 501149582 5.740000e-20 110.0
70 TraesCS2A01G557200 chr4B 84.404 109 17 0 1432 1540 659624382 659624490 2.070000e-19 108.0
71 TraesCS2A01G557200 chr1B 96.154 52 2 0 5373 5424 613737693 613737744 9.680000e-13 86.1


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 TraesCS2A01G557200 chr2A 760853598 760859021 5423 True 3391.466667 10017 98.518667 1 5424 3 chr2A.!!$R3 5423
1 TraesCS2A01G557200 chr2A 759029709 759032888 3179 True 1618.000000 3073 81.346500 2111 5342 2 chr2A.!!$R1 3231
2 TraesCS2A01G557200 chr2A 759099967 759102542 2575 True 1375.500000 2623 92.412500 526 2501 2 chr2A.!!$R2 1975
3 TraesCS2A01G557200 chr2A 760915408 760923323 7915 True 791.400000 1423 86.333800 829 4534 5 chr2A.!!$R4 3705
4 TraesCS2A01G557200 chr2A 758755246 758756698 1452 False 398.500000 414 83.839000 3160 4535 2 chr2A.!!$F2 1375
5 TraesCS2A01G557200 chrUn 312029495 312032604 3109 False 5731.000000 5731 99.936000 2316 5424 1 chrUn.!!$F1 3108
6 TraesCS2A01G557200 chr2D 629449395 629453184 3789 True 941.960000 2545 92.239000 1380 5278 5 chr2D.!!$R5 3898
7 TraesCS2A01G557200 chr2D 629558562 629559497 935 True 800.000000 800 82.604000 2549 3457 1 chr2D.!!$R1 908
8 TraesCS2A01G557200 chr2D 629994564 629995458 894 False 800.000000 800 83.004000 2556 3457 1 chr2D.!!$F1 901
9 TraesCS2A01G557200 chr2D 629580894 629583763 2869 True 621.133333 1668 90.008000 2108 5374 3 chr2D.!!$R7 3266
10 TraesCS2A01G557200 chr2D 629401741 629404217 2476 True 581.666667 846 81.836667 2566 5253 3 chr2D.!!$R3 2687
11 TraesCS2A01G557200 chr2D 629459670 629461128 1458 True 442.500000 761 89.295000 525 1349 2 chr2D.!!$R6 824
12 TraesCS2A01G557200 chr2B 212574756 212575282 526 True 813.000000 813 94.497000 1 527 1 chr2B.!!$R1 526
13 TraesCS2A01G557200 chr2B 772227398 772229429 2031 True 793.666667 1251 89.146000 2992 5021 3 chr2B.!!$R4 2029
14 TraesCS2A01G557200 chr2B 772349822 772353969 4147 True 568.500000 791 81.699750 1943 5157 4 chr2B.!!$R7 3214
15 TraesCS2A01G557200 chr2B 772325051 772328783 3732 True 516.950000 1301 88.974250 1379 4639 4 chr2B.!!$R5 3260
16 TraesCS2A01G557200 chr2B 772482197 772485592 3395 True 491.000000 911 79.806667 1648 5179 3 chr2B.!!$R8 3531
17 TraesCS2A01G557200 chr2B 772333658 772335390 1732 True 458.500000 776 90.958500 525 1356 2 chr2B.!!$R6 831
18 TraesCS2A01G557200 chr2B 772602415 772603358 943 False 382.000000 427 82.931000 2121 3052 2 chr2B.!!$F2 931
19 TraesCS2A01G557200 chr6D 450668549 450669075 526 True 819.000000 819 94.687000 1 527 1 chr6D.!!$R1 526
20 TraesCS2A01G557200 chr3D 508062438 508062964 526 True 819.000000 819 94.687000 1 527 1 chr3D.!!$R1 526
21 TraesCS2A01G557200 chr3D 602106941 602107467 526 False 813.000000 813 94.497000 1 527 1 chr3D.!!$F1 526
22 TraesCS2A01G557200 chr6B 77802100 77802627 527 False 808.000000 808 94.318000 1 527 1 chr6B.!!$F1 526
23 TraesCS2A01G557200 chr7B 695709579 695710105 526 False 802.000000 802 94.118000 1 527 1 chr7B.!!$F1 526
24 TraesCS2A01G557200 chr5B 26946487 26947013 526 True 802.000000 802 94.118000 1 527 1 chr5B.!!$R2 526
25 TraesCS2A01G557200 chr5B 10171060 10171587 527 True 797.000000 797 93.939000 1 527 1 chr5B.!!$R1 526
26 TraesCS2A01G557200 chr1D 31344733 31345258 525 False 800.000000 800 94.106000 1 526 1 chr1D.!!$F1 525

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
654 1805 0.180406 AAACTAGTATGGCCGGCAGG 59.820 55.0 30.85 11.46 41.62 4.85 F
832 1998 0.246635 GCACGAAACTAGCTCCAGGA 59.753 55.0 0.00 0.00 0.00 3.86 F
1934 6295 0.109723 TAGTGGACCACTGGTTTGCC 59.890 55.0 33.24 0.93 45.01 4.52 F
2031 6392 2.608090 GGGCGCTGAACTTATTCTACAC 59.392 50.0 7.64 0.00 35.69 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1533 5324 0.389817 CATCTGACAAGTCCGCGGAA 60.390 55.000 32.93 12.62 0.00 4.30 R
2031 6392 0.592247 GCCGTGATAAAATGCTGCGG 60.592 55.000 0.00 0.00 40.52 5.69 R
2948 7351 6.709846 AGTTTTTCTCTTCTCATCACAGAAGG 59.290 38.462 9.74 2.57 46.61 3.46 R
4826 11205 5.545063 TCAGTTGTTCCAAGTGATACTGA 57.455 39.130 9.77 0.00 35.58 3.41 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 29 1.592669 GGCAGATGCTACGCACGAT 60.593 57.895 4.59 0.00 43.04 3.73
57 58 6.429692 TCTTTCAAAGACTTCAAACTGTGTCA 59.570 34.615 0.00 0.00 31.20 3.58
101 102 0.250234 GCTGAGGTGTATCAGTGGCA 59.750 55.000 5.69 0.00 46.93 4.92
126 127 1.775039 GACGTGCTCAGCTGTTTGCA 61.775 55.000 21.06 21.06 45.94 4.08
150 151 3.637273 GAGGAGGTGCCGTTGGGT 61.637 66.667 0.00 0.00 43.43 4.51
254 255 2.501128 GCGGCCTATGAGAGCACA 59.499 61.111 0.00 0.00 0.00 4.57
331 332 1.066716 ACGTTAGGTTTGGCTGCGATA 60.067 47.619 0.00 0.00 0.00 2.92
338 339 2.032178 GGTTTGGCTGCGATATCTGTTC 59.968 50.000 0.34 0.00 0.00 3.18
497 498 3.961009 ATCGCCCAGATGCAGAGA 58.039 55.556 0.00 0.00 38.36 3.10
499 500 1.332889 ATCGCCCAGATGCAGAGACA 61.333 55.000 0.00 0.00 38.36 3.41
500 501 1.145598 CGCCCAGATGCAGAGACAT 59.854 57.895 0.00 0.00 0.00 3.06
598 600 7.070798 GGTCGTTAGATCTTTATGACTACTCG 58.929 42.308 20.44 0.00 0.00 4.18
602 604 7.746916 CGTTAGATCTTTATGACTACTCGGATG 59.253 40.741 0.00 0.00 0.00 3.51
615 617 4.487714 ACTCGGATGGATCAAGCTTTTA 57.512 40.909 0.00 0.00 0.00 1.52
616 618 5.041191 ACTCGGATGGATCAAGCTTTTAT 57.959 39.130 0.00 0.00 0.00 1.40
617 619 5.440610 ACTCGGATGGATCAAGCTTTTATT 58.559 37.500 0.00 0.00 0.00 1.40
619 621 6.708054 ACTCGGATGGATCAAGCTTTTATTAG 59.292 38.462 0.00 0.00 0.00 1.73
620 622 6.591935 TCGGATGGATCAAGCTTTTATTAGT 58.408 36.000 0.00 0.00 0.00 2.24
621 623 7.732025 TCGGATGGATCAAGCTTTTATTAGTA 58.268 34.615 0.00 0.00 0.00 1.82
622 624 8.208224 TCGGATGGATCAAGCTTTTATTAGTAA 58.792 33.333 0.00 0.00 0.00 2.24
623 625 8.836413 CGGATGGATCAAGCTTTTATTAGTAAA 58.164 33.333 0.00 0.00 0.00 2.01
629 1780 9.569167 GATCAAGCTTTTATTAGTAAAACCACC 57.431 33.333 0.00 0.00 35.45 4.61
641 1792 9.955102 ATTAGTAAAACCACCCTCTTAAACTAG 57.045 33.333 0.00 0.00 0.00 2.57
642 1793 7.384524 AGTAAAACCACCCTCTTAAACTAGT 57.615 36.000 0.00 0.00 0.00 2.57
644 1795 9.109246 AGTAAAACCACCCTCTTAAACTAGTAT 57.891 33.333 0.00 0.00 0.00 2.12
646 1797 5.952347 ACCACCCTCTTAAACTAGTATGG 57.048 43.478 0.00 0.00 0.00 2.74
654 1805 0.180406 AAACTAGTATGGCCGGCAGG 59.820 55.000 30.85 11.46 41.62 4.85
655 1806 0.689745 AACTAGTATGGCCGGCAGGA 60.690 55.000 30.85 12.11 41.02 3.86
668 1819 2.105124 GCAGGAGAGCCAAATGAGC 58.895 57.895 0.00 0.00 36.29 4.26
669 1820 0.679002 GCAGGAGAGCCAAATGAGCA 60.679 55.000 0.00 0.00 36.29 4.26
670 1821 2.022754 GCAGGAGAGCCAAATGAGCAT 61.023 52.381 0.00 0.00 36.29 3.79
671 1822 1.948145 CAGGAGAGCCAAATGAGCATC 59.052 52.381 0.00 0.00 36.29 3.91
672 1823 1.562942 AGGAGAGCCAAATGAGCATCA 59.437 47.619 0.00 0.00 44.12 3.07
673 1824 2.025605 AGGAGAGCCAAATGAGCATCAA 60.026 45.455 0.00 0.00 43.42 2.57
674 1825 4.184909 AGGAGAGCCAAATGAGCATCAAC 61.185 47.826 0.00 0.00 43.42 3.18
681 1832 2.359850 TGAGCATCAACCGCACCC 60.360 61.111 0.00 0.00 45.97 4.61
682 1833 2.045926 GAGCATCAACCGCACCCT 60.046 61.111 0.00 0.00 33.17 4.34
683 1834 2.045926 AGCATCAACCGCACCCTC 60.046 61.111 0.00 0.00 0.00 4.30
684 1835 2.045926 GCATCAACCGCACCCTCT 60.046 61.111 0.00 0.00 0.00 3.69
685 1836 1.675641 GCATCAACCGCACCCTCTT 60.676 57.895 0.00 0.00 0.00 2.85
686 1837 0.392461 GCATCAACCGCACCCTCTTA 60.392 55.000 0.00 0.00 0.00 2.10
687 1838 1.948611 GCATCAACCGCACCCTCTTAA 60.949 52.381 0.00 0.00 0.00 1.85
688 1839 2.432444 CATCAACCGCACCCTCTTAAA 58.568 47.619 0.00 0.00 0.00 1.52
689 1840 2.871096 TCAACCGCACCCTCTTAAAT 57.129 45.000 0.00 0.00 0.00 1.40
690 1841 3.149005 TCAACCGCACCCTCTTAAATT 57.851 42.857 0.00 0.00 0.00 1.82
691 1842 4.289238 TCAACCGCACCCTCTTAAATTA 57.711 40.909 0.00 0.00 0.00 1.40
692 1843 4.258543 TCAACCGCACCCTCTTAAATTAG 58.741 43.478 0.00 0.00 0.00 1.73
693 1844 3.994931 ACCGCACCCTCTTAAATTAGT 57.005 42.857 0.00 0.00 0.00 2.24
694 1845 5.046448 TCAACCGCACCCTCTTAAATTAGTA 60.046 40.000 0.00 0.00 0.00 1.82
695 1846 5.625568 ACCGCACCCTCTTAAATTAGTAT 57.374 39.130 0.00 0.00 0.00 2.12
696 1847 5.365619 ACCGCACCCTCTTAAATTAGTATG 58.634 41.667 0.00 0.00 0.00 2.39
697 1848 4.755123 CCGCACCCTCTTAAATTAGTATGG 59.245 45.833 0.00 0.00 0.00 2.74
698 1849 4.213482 CGCACCCTCTTAAATTAGTATGGC 59.787 45.833 0.00 0.00 0.00 4.40
699 1850 4.519350 GCACCCTCTTAAATTAGTATGGCC 59.481 45.833 0.00 0.00 0.00 5.36
700 1851 4.755123 CACCCTCTTAAATTAGTATGGCCG 59.245 45.833 0.00 0.00 0.00 6.13
701 1852 4.202430 ACCCTCTTAAATTAGTATGGCCGG 60.202 45.833 0.00 0.00 0.00 6.13
702 1853 3.751698 CCTCTTAAATTAGTATGGCCGGC 59.248 47.826 21.18 21.18 0.00 6.13
703 1854 4.385825 CTCTTAAATTAGTATGGCCGGCA 58.614 43.478 30.85 15.30 0.00 5.69
704 1855 4.385825 TCTTAAATTAGTATGGCCGGCAG 58.614 43.478 30.85 12.16 0.00 4.85
705 1856 1.981256 AAATTAGTATGGCCGGCAGG 58.019 50.000 30.85 0.00 41.62 4.85
706 1857 1.136828 AATTAGTATGGCCGGCAGGA 58.863 50.000 30.85 12.11 41.02 3.86
707 1858 0.687354 ATTAGTATGGCCGGCAGGAG 59.313 55.000 30.85 0.00 41.02 3.69
721 1872 2.022754 GCAGGAGAGCCAAATGAGCAT 61.023 52.381 0.00 0.00 36.29 3.79
729 1880 4.110482 GAGCCAAATGAGCATTAGCAAAG 58.890 43.478 15.92 0.00 45.49 2.77
730 1881 2.606272 GCCAAATGAGCATTAGCAAAGC 59.394 45.455 11.20 0.00 45.49 3.51
737 1888 0.659957 GCATTAGCAAAGCGAGGAGG 59.340 55.000 0.00 0.00 41.58 4.30
740 1891 2.386661 TTAGCAAAGCGAGGAGGAAG 57.613 50.000 0.00 0.00 0.00 3.46
749 1900 0.741915 CGAGGAGGAAGCAGTAGACC 59.258 60.000 0.00 0.00 0.00 3.85
780 1931 3.629398 AGCAAACTGAAGAGAAACCACAG 59.371 43.478 0.00 0.00 35.14 3.66
793 1944 2.202932 CACAGAATCCCCCGCTCG 60.203 66.667 0.00 0.00 0.00 5.03
804 1955 1.520787 CCCGCTCGACCACCATTAC 60.521 63.158 0.00 0.00 0.00 1.89
814 1965 0.738389 CCACCATTACCATTCCACGC 59.262 55.000 0.00 0.00 0.00 5.34
822 1973 0.534203 ACCATTCCACGCACGAAACT 60.534 50.000 0.00 0.00 0.00 2.66
832 1998 0.246635 GCACGAAACTAGCTCCAGGA 59.753 55.000 0.00 0.00 0.00 3.86
1053 2224 3.437795 GCATTCGTGCAGGCTGCT 61.438 61.111 36.50 16.51 45.31 4.24
1080 2251 6.183360 GGTTAGTGCTTAGTATTCAGCTCTCT 60.183 42.308 0.00 0.00 39.81 3.10
1081 2252 5.514274 AGTGCTTAGTATTCAGCTCTCTC 57.486 43.478 0.00 0.00 35.44 3.20
1082 2253 4.340950 AGTGCTTAGTATTCAGCTCTCTCC 59.659 45.833 0.00 0.00 35.44 3.71
1083 2254 4.340950 GTGCTTAGTATTCAGCTCTCTCCT 59.659 45.833 0.00 0.00 36.92 3.69
1084 2255 4.340666 TGCTTAGTATTCAGCTCTCTCCTG 59.659 45.833 0.00 0.00 36.92 3.86
1085 2256 4.582656 GCTTAGTATTCAGCTCTCTCCTGA 59.417 45.833 0.00 0.00 37.54 3.86
1195 2367 1.133407 CTCGCCGAAGAAGAAGTAGCT 59.867 52.381 0.00 0.00 0.00 3.32
1212 2384 6.766997 AGTAGCTCCAGTACCTATCTTAGA 57.233 41.667 0.00 0.00 0.00 2.10
1323 4059 2.252855 GCTCTCTCCCGTATCGCG 59.747 66.667 0.00 0.00 40.95 5.87
1324 4060 2.252855 CTCTCTCCCGTATCGCGC 59.747 66.667 0.00 0.00 39.71 6.86
1533 5324 1.215647 GTCGTCTCCTGCATCCGTT 59.784 57.895 0.00 0.00 0.00 4.44
1749 6104 5.104817 GCATGGATTTATATTGGGATTGGGG 60.105 44.000 0.00 0.00 0.00 4.96
1753 6108 7.605651 TGGATTTATATTGGGATTGGGGTTTA 58.394 34.615 0.00 0.00 0.00 2.01
1769 6127 4.019591 GGGGTTTATATATTGGAGCGGACT 60.020 45.833 0.00 0.00 0.00 3.85
1889 6250 3.189910 AGTTATCACTCTGTACGTGCGAA 59.810 43.478 0.00 0.00 32.54 4.70
1890 6251 2.941453 ATCACTCTGTACGTGCGAAT 57.059 45.000 0.00 0.00 32.54 3.34
1892 6253 3.021269 TCACTCTGTACGTGCGAATTT 57.979 42.857 0.00 0.00 32.54 1.82
1925 6286 0.389948 CCTCGCTGTTAGTGGACCAC 60.390 60.000 17.43 17.43 34.10 4.16
1934 6295 0.109723 TAGTGGACCACTGGTTTGCC 59.890 55.000 33.24 0.93 45.01 4.52
2031 6392 2.608090 GGGCGCTGAACTTATTCTACAC 59.392 50.000 7.64 0.00 35.69 2.90
2948 7351 5.227238 CTTGTATCATCCAACAAGTGCTC 57.773 43.478 6.97 0.00 44.83 4.26
2954 7357 2.260844 TCCAACAAGTGCTCCTTCTG 57.739 50.000 0.00 0.00 0.00 3.02
4828 11207 4.825422 CTTCAGCAAGAAGTCAGGTATCA 58.175 43.478 9.94 0.00 46.97 2.15
4975 12379 3.548268 GCAGCGTATCAGTAAGTTCAGAC 59.452 47.826 0.00 0.00 0.00 3.51
4979 12383 4.029704 CGTATCAGTAAGTTCAGACGAGC 58.970 47.826 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 8.830580 CACAGTTTGAAGTCTTTGAAAGATCTA 58.169 33.333 11.20 0.09 40.18 1.98
57 58 1.376466 CTGCCAAGTACCACCAGCT 59.624 57.895 0.00 0.00 0.00 4.24
312 313 1.647346 TATCGCAGCCAAACCTAACG 58.353 50.000 0.00 0.00 0.00 3.18
331 332 2.368875 CTGGGCCTAATACCGAACAGAT 59.631 50.000 4.53 0.00 0.00 2.90
338 339 1.207329 GATAGCCTGGGCCTAATACCG 59.793 57.143 4.53 0.00 43.17 4.02
497 498 1.686236 AAAGGAGGATGACCCCATGT 58.314 50.000 0.00 0.00 36.73 3.21
499 500 2.577970 AGAAAAGGAGGATGACCCCAT 58.422 47.619 0.00 0.00 36.73 4.00
500 501 2.059756 AGAAAAGGAGGATGACCCCA 57.940 50.000 0.00 0.00 36.73 4.96
615 617 9.955102 CTAGTTTAAGAGGGTGGTTTTACTAAT 57.045 33.333 0.00 0.00 0.00 1.73
616 618 8.937835 ACTAGTTTAAGAGGGTGGTTTTACTAA 58.062 33.333 0.00 0.00 0.00 2.24
617 619 8.496534 ACTAGTTTAAGAGGGTGGTTTTACTA 57.503 34.615 0.00 0.00 0.00 1.82
619 621 9.159364 CATACTAGTTTAAGAGGGTGGTTTTAC 57.841 37.037 0.00 0.00 0.00 2.01
620 622 8.323567 CCATACTAGTTTAAGAGGGTGGTTTTA 58.676 37.037 0.00 0.00 0.00 1.52
621 623 7.173032 CCATACTAGTTTAAGAGGGTGGTTTT 58.827 38.462 0.00 0.00 0.00 2.43
622 624 6.718294 CCATACTAGTTTAAGAGGGTGGTTT 58.282 40.000 0.00 0.00 0.00 3.27
623 625 5.338953 GCCATACTAGTTTAAGAGGGTGGTT 60.339 44.000 0.00 0.00 0.00 3.67
624 626 4.163649 GCCATACTAGTTTAAGAGGGTGGT 59.836 45.833 0.00 0.00 0.00 4.16
625 627 4.444449 GGCCATACTAGTTTAAGAGGGTGG 60.444 50.000 0.00 0.00 0.00 4.61
629 1780 3.802675 GCCGGCCATACTAGTTTAAGAGG 60.803 52.174 18.11 0.11 0.00 3.69
641 1792 2.423446 CTCTCCTGCCGGCCATAC 59.577 66.667 26.77 0.00 0.00 2.39
642 1793 3.550431 GCTCTCCTGCCGGCCATA 61.550 66.667 26.77 7.85 0.00 2.74
654 1805 2.098770 GGTTGATGCTCATTTGGCTCTC 59.901 50.000 0.00 0.00 0.00 3.20
655 1806 2.097825 GGTTGATGCTCATTTGGCTCT 58.902 47.619 0.00 0.00 0.00 4.09
661 1812 0.527565 GGTGCGGTTGATGCTCATTT 59.472 50.000 0.00 0.00 0.00 2.32
662 1813 1.315257 GGGTGCGGTTGATGCTCATT 61.315 55.000 0.00 0.00 0.00 2.57
663 1814 1.750399 GGGTGCGGTTGATGCTCAT 60.750 57.895 0.00 0.00 0.00 2.90
664 1815 2.359850 GGGTGCGGTTGATGCTCA 60.360 61.111 0.00 0.00 0.00 4.26
665 1816 2.045926 AGGGTGCGGTTGATGCTC 60.046 61.111 0.00 0.00 0.00 4.26
666 1817 2.045926 GAGGGTGCGGTTGATGCT 60.046 61.111 0.00 0.00 0.00 3.79
667 1818 0.392461 TAAGAGGGTGCGGTTGATGC 60.392 55.000 0.00 0.00 0.00 3.91
668 1819 2.107950 TTAAGAGGGTGCGGTTGATG 57.892 50.000 0.00 0.00 0.00 3.07
669 1820 2.871096 TTTAAGAGGGTGCGGTTGAT 57.129 45.000 0.00 0.00 0.00 2.57
670 1821 2.871096 ATTTAAGAGGGTGCGGTTGA 57.129 45.000 0.00 0.00 0.00 3.18
671 1822 4.007659 ACTAATTTAAGAGGGTGCGGTTG 58.992 43.478 0.00 0.00 0.00 3.77
672 1823 4.296621 ACTAATTTAAGAGGGTGCGGTT 57.703 40.909 0.00 0.00 0.00 4.44
673 1824 3.994931 ACTAATTTAAGAGGGTGCGGT 57.005 42.857 0.00 0.00 0.00 5.68
674 1825 4.755123 CCATACTAATTTAAGAGGGTGCGG 59.245 45.833 0.00 0.00 0.00 5.69
675 1826 4.213482 GCCATACTAATTTAAGAGGGTGCG 59.787 45.833 0.00 0.00 0.00 5.34
676 1827 4.519350 GGCCATACTAATTTAAGAGGGTGC 59.481 45.833 0.00 0.00 0.00 5.01
677 1828 4.755123 CGGCCATACTAATTTAAGAGGGTG 59.245 45.833 2.24 0.00 0.00 4.61
678 1829 4.202430 CCGGCCATACTAATTTAAGAGGGT 60.202 45.833 2.24 0.00 0.00 4.34
679 1830 4.324267 CCGGCCATACTAATTTAAGAGGG 58.676 47.826 2.24 0.00 0.00 4.30
680 1831 3.751698 GCCGGCCATACTAATTTAAGAGG 59.248 47.826 18.11 0.00 0.00 3.69
681 1832 4.385825 TGCCGGCCATACTAATTTAAGAG 58.614 43.478 26.77 0.00 0.00 2.85
682 1833 4.385825 CTGCCGGCCATACTAATTTAAGA 58.614 43.478 26.77 0.00 0.00 2.10
683 1834 3.502211 CCTGCCGGCCATACTAATTTAAG 59.498 47.826 26.77 9.42 0.00 1.85
684 1835 3.136809 TCCTGCCGGCCATACTAATTTAA 59.863 43.478 26.77 0.00 0.00 1.52
685 1836 2.706723 TCCTGCCGGCCATACTAATTTA 59.293 45.455 26.77 0.00 0.00 1.40
686 1837 1.493022 TCCTGCCGGCCATACTAATTT 59.507 47.619 26.77 0.00 0.00 1.82
687 1838 1.072331 CTCCTGCCGGCCATACTAATT 59.928 52.381 26.77 0.00 0.00 1.40
688 1839 0.687354 CTCCTGCCGGCCATACTAAT 59.313 55.000 26.77 0.00 0.00 1.73
689 1840 0.397957 TCTCCTGCCGGCCATACTAA 60.398 55.000 26.77 1.11 0.00 2.24
690 1841 0.827925 CTCTCCTGCCGGCCATACTA 60.828 60.000 26.77 2.02 0.00 1.82
691 1842 2.041922 TCTCCTGCCGGCCATACT 60.042 61.111 26.77 0.00 0.00 2.12
692 1843 2.423446 CTCTCCTGCCGGCCATAC 59.577 66.667 26.77 0.00 0.00 2.39
693 1844 3.550431 GCTCTCCTGCCGGCCATA 61.550 66.667 26.77 7.85 0.00 2.74
701 1852 0.679002 TGCTCATTTGGCTCTCCTGC 60.679 55.000 0.00 0.00 0.00 4.85
702 1853 2.054232 ATGCTCATTTGGCTCTCCTG 57.946 50.000 0.00 0.00 0.00 3.86
703 1854 2.822707 AATGCTCATTTGGCTCTCCT 57.177 45.000 0.00 0.00 0.00 3.69
704 1855 2.292845 GCTAATGCTCATTTGGCTCTCC 59.707 50.000 0.00 0.00 36.03 3.71
705 1856 2.947652 TGCTAATGCTCATTTGGCTCTC 59.052 45.455 15.52 0.00 40.48 3.20
706 1857 3.008835 TGCTAATGCTCATTTGGCTCT 57.991 42.857 15.52 0.00 40.48 4.09
707 1858 3.788333 TTGCTAATGCTCATTTGGCTC 57.212 42.857 15.52 0.49 40.48 4.70
721 1872 1.676014 GCTTCCTCCTCGCTTTGCTAA 60.676 52.381 0.00 0.00 0.00 3.09
729 1880 0.101579 GTCTACTGCTTCCTCCTCGC 59.898 60.000 0.00 0.00 0.00 5.03
730 1881 0.741915 GGTCTACTGCTTCCTCCTCG 59.258 60.000 0.00 0.00 0.00 4.63
737 1888 3.027974 AGTCAAACGGTCTACTGCTTC 57.972 47.619 0.00 0.00 0.00 3.86
740 1891 2.260481 GCTAGTCAAACGGTCTACTGC 58.740 52.381 0.00 0.00 0.00 4.40
780 1931 3.467226 TGGTCGAGCGGGGGATTC 61.467 66.667 10.46 0.00 0.00 2.52
793 1944 2.014128 CGTGGAATGGTAATGGTGGTC 58.986 52.381 0.00 0.00 0.00 4.02
804 1955 1.393539 CTAGTTTCGTGCGTGGAATGG 59.606 52.381 0.00 0.00 0.00 3.16
814 1965 1.272490 TGTCCTGGAGCTAGTTTCGTG 59.728 52.381 0.00 0.00 0.00 4.35
832 1998 1.208052 CGTCAACCTCATCTCCCATGT 59.792 52.381 0.00 0.00 0.00 3.21
1053 2224 4.469945 AGCTGAATACTAAGCACTAACCCA 59.530 41.667 0.00 0.00 42.06 4.51
1080 2251 4.515028 AAGATTGCATTCAGGATCAGGA 57.485 40.909 10.98 0.00 0.00 3.86
1081 2252 5.593679 AAAAGATTGCATTCAGGATCAGG 57.406 39.130 10.98 0.00 0.00 3.86
1082 2253 6.040878 GGAAAAAGATTGCATTCAGGATCAG 58.959 40.000 10.98 0.00 0.00 2.90
1083 2254 5.393352 CGGAAAAAGATTGCATTCAGGATCA 60.393 40.000 10.98 0.00 0.00 2.92
1084 2255 5.039333 CGGAAAAAGATTGCATTCAGGATC 58.961 41.667 10.98 0.00 0.00 3.36
1085 2256 4.142093 CCGGAAAAAGATTGCATTCAGGAT 60.142 41.667 10.98 0.00 38.80 3.24
1195 2367 4.445448 GGACCGTCTAAGATAGGTACTGGA 60.445 50.000 0.00 0.00 41.52 3.86
1246 2419 5.758296 ACTTCACGTCACACTTAACATCAAT 59.242 36.000 0.00 0.00 0.00 2.57
1533 5324 0.389817 CATCTGACAAGTCCGCGGAA 60.390 55.000 32.93 12.62 0.00 4.30
1753 6108 9.003658 CAAGATTTAAAGTCCGCTCCAATATAT 57.996 33.333 0.00 0.00 0.00 0.86
1769 6127 7.916450 CCGACACTTTTGTAACCAAGATTTAAA 59.084 33.333 0.00 0.00 35.47 1.52
1889 6250 1.209747 GAGGACCGCCACTAGGAAAAT 59.790 52.381 0.00 0.00 36.89 1.82
1890 6251 0.611714 GAGGACCGCCACTAGGAAAA 59.388 55.000 0.00 0.00 36.89 2.29
1892 6253 2.050350 CGAGGACCGCCACTAGGAA 61.050 63.158 0.00 0.00 36.89 3.36
1925 6286 1.845809 GACAGACGCAGGCAAACCAG 61.846 60.000 0.00 0.00 39.06 4.00
1934 6295 4.039357 ACGACCCGACAGACGCAG 62.039 66.667 0.00 0.00 41.07 5.18
2031 6392 0.592247 GCCGTGATAAAATGCTGCGG 60.592 55.000 0.00 0.00 40.52 5.69
2948 7351 6.709846 AGTTTTTCTCTTCTCATCACAGAAGG 59.290 38.462 9.74 2.57 46.61 3.46
4823 11202 7.097192 TCAGTTGTTCCAAGTGATACTGATAC 58.903 38.462 9.77 0.00 34.26 2.24
4824 11203 7.239763 TCAGTTGTTCCAAGTGATACTGATA 57.760 36.000 9.77 0.00 34.26 2.15
4825 11204 6.114187 TCAGTTGTTCCAAGTGATACTGAT 57.886 37.500 9.77 0.00 34.26 2.90
4826 11205 5.545063 TCAGTTGTTCCAAGTGATACTGA 57.455 39.130 9.77 0.00 35.58 3.41
4827 11206 5.760253 AGTTCAGTTGTTCCAAGTGATACTG 59.240 40.000 13.56 0.00 32.66 2.74
4828 11207 5.930135 AGTTCAGTTGTTCCAAGTGATACT 58.070 37.500 13.56 14.88 30.51 2.12
4975 12379 3.248363 TGACTGTCAGTGATTTTTGCTCG 59.752 43.478 11.04 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.