Multiple sequence alignment - TraesCS6A01G012800

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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 TraesCS6A01G012800 chr6A 100.000 4781 0 0 1 4781 5899731 5904511 0.000000e+00 8829
1 TraesCS6A01G012800 chr6A 87.533 2671 284 30 2120 4778 5917830 5920463 0.000000e+00 3042
2 TraesCS6A01G012800 chr6A 85.824 1954 249 25 2139 4083 5940823 5942757 0.000000e+00 2049
3 TraesCS6A01G012800 chr6A 82.483 1587 191 34 668 2228 5939243 5940768 0.000000e+00 1310
4 TraesCS6A01G012800 chr6A 84.115 661 87 8 1637 2295 5917082 5917726 1.460000e-174 623
5 TraesCS6A01G012800 chr6A 79.062 640 112 17 1534 2156 6699204 6699838 2.060000e-113 420
6 TraesCS6A01G012800 chr6D 89.598 1865 192 2 2194 4057 6353176 6355039 0.000000e+00 2368
7 TraesCS6A01G012800 chr6D 87.627 2061 201 34 2725 4778 6465693 6467706 0.000000e+00 2344
8 TraesCS6A01G012800 chr6D 87.526 1892 228 5 2194 4083 6371580 6373465 0.000000e+00 2180
9 TraesCS6A01G012800 chr6D 86.182 1954 242 25 2139 4083 6426456 6428390 0.000000e+00 2087
10 TraesCS6A01G012800 chr6D 86.671 1688 214 9 2179 3860 6497689 6499371 0.000000e+00 1860
11 TraesCS6A01G012800 chr6D 83.468 1482 188 31 829 2295 6441657 6443096 0.000000e+00 1327
12 TraesCS6A01G012800 chr6D 82.438 1600 195 34 653 2228 6424864 6426401 0.000000e+00 1319
13 TraesCS6A01G012800 chr6D 80.813 1574 292 7 2211 3779 7033393 7034961 0.000000e+00 1225
14 TraesCS6A01G012800 chr6D 88.394 853 72 6 636 1480 6351272 6352105 0.000000e+00 1002
15 TraesCS6A01G012800 chr6D 84.107 862 94 11 978 1836 6370241 6371062 0.000000e+00 793
16 TraesCS6A01G012800 chr6D 84.082 735 87 14 3705 4436 6505056 6505763 0.000000e+00 682
17 TraesCS6A01G012800 chr6D 88.619 536 55 3 948 1477 6496245 6496780 0.000000e+00 647
18 TraesCS6A01G012800 chr6D 86.667 540 63 6 1886 2425 6371065 6371595 1.480000e-164 590
19 TraesCS6A01G012800 chr6D 80.000 640 106 18 1534 2156 7032776 7033410 2.030000e-123 453
20 TraesCS6A01G012800 chr6D 89.714 350 36 0 1533 1882 6352206 6352555 9.440000e-122 448
21 TraesCS6A01G012800 chr6D 89.296 355 36 2 1530 1882 6496792 6497146 1.220000e-120 444
22 TraesCS6A01G012800 chr6D 81.174 494 76 10 993 1473 7032265 7032754 9.710000e-102 381
23 TraesCS6A01G012800 chr6D 86.010 193 11 1 636 828 6370035 6370211 4.880000e-45 193
24 TraesCS6A01G012800 chr6D 90.654 107 10 0 4469 4575 460745087 460744981 4.990000e-30 143
25 TraesCS6A01G012800 chr6B 85.868 1677 220 12 2190 3860 11793680 11795345 0.000000e+00 1768
26 TraesCS6A01G012800 chr6B 92.844 1076 53 7 669 1744 11592527 11593578 0.000000e+00 1539
27 TraesCS6A01G012800 chr6B 88.798 1223 132 4 2641 3860 11599601 11600821 0.000000e+00 1495
28 TraesCS6A01G012800 chr6B 86.098 820 101 12 3621 4436 11795645 11796455 0.000000e+00 870
29 TraesCS6A01G012800 chr6B 84.793 868 104 19 3621 4468 11601123 11601982 0.000000e+00 846
30 TraesCS6A01G012800 chr6B 84.783 782 91 15 657 1421 11792014 11792784 0.000000e+00 760
31 TraesCS6A01G012800 chr6B 84.709 412 60 2 2196 2607 11599192 11599600 4.450000e-110 409
32 TraesCS6A01G012800 chr6B 87.324 355 45 0 1528 1882 11792780 11793134 1.600000e-109 407
33 TraesCS6A01G012800 chr6B 79.947 379 58 11 2015 2391 11593572 11593934 3.670000e-66 263
34 TraesCS6A01G012800 chr6B 85.022 227 27 5 657 881 11764531 11764752 1.730000e-54 224
35 TraesCS6A01G012800 chr6B 86.893 206 19 3 4583 4781 11798667 11798871 1.730000e-54 224
36 TraesCS6A01G012800 chr2A 91.523 637 47 7 4 634 288962247 288962882 0.000000e+00 870
37 TraesCS6A01G012800 chr2B 90.402 646 49 7 2 634 118293137 118293782 0.000000e+00 837
38 TraesCS6A01G012800 chr4B 90.015 651 51 8 2 638 666758271 666757621 0.000000e+00 830
39 TraesCS6A01G012800 chr1D 87.403 643 67 10 2 634 476232646 476232008 0.000000e+00 726
40 TraesCS6A01G012800 chr3B 87.031 640 69 10 4 633 389321044 389321679 0.000000e+00 710
41 TraesCS6A01G012800 chr1A 86.801 644 73 7 2 633 40983388 40982745 0.000000e+00 708
42 TraesCS6A01G012800 chr4D 86.656 652 68 13 3 639 68767138 68766491 0.000000e+00 704
43 TraesCS6A01G012800 chr4D 87.719 114 12 2 4462 4575 21147727 21147838 1.080000e-26 132
44 TraesCS6A01G012800 chr5B 86.533 646 73 9 2 633 354991259 354991904 0.000000e+00 699
45 TraesCS6A01G012800 chr7B 86.314 643 75 9 2 635 1810354 1809716 0.000000e+00 688
46 TraesCS6A01G012800 chr4A 90.741 108 10 0 4468 4575 469243058 469242951 1.390000e-30 145
47 TraesCS6A01G012800 chr1B 89.091 110 10 2 4467 4575 459922168 459922276 8.350000e-28 135
48 TraesCS6A01G012800 chr3D 88.288 111 13 0 4465 4575 23865901 23865791 3.000000e-27 134
49 TraesCS6A01G012800 chr5A 87.611 113 14 0 4462 4574 653299433 653299545 1.080000e-26 132
50 TraesCS6A01G012800 chr2D 85.124 121 16 2 4469 4588 593512488 593512607 6.500000e-24 122


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 TraesCS6A01G012800 chr6A 5899731 5904511 4780 False 8829.000000 8829 100.000000 1 4781 1 chr6A.!!$F1 4780
1 TraesCS6A01G012800 chr6A 5917082 5920463 3381 False 1832.500000 3042 85.824000 1637 4778 2 chr6A.!!$F3 3141
2 TraesCS6A01G012800 chr6A 5939243 5942757 3514 False 1679.500000 2049 84.153500 668 4083 2 chr6A.!!$F4 3415
3 TraesCS6A01G012800 chr6A 6699204 6699838 634 False 420.000000 420 79.062000 1534 2156 1 chr6A.!!$F2 622
4 TraesCS6A01G012800 chr6D 6465693 6467706 2013 False 2344.000000 2344 87.627000 2725 4778 1 chr6D.!!$F2 2053
5 TraesCS6A01G012800 chr6D 6424864 6428390 3526 False 1703.000000 2087 84.310000 653 4083 2 chr6D.!!$F6 3430
6 TraesCS6A01G012800 chr6D 6441657 6443096 1439 False 1327.000000 1327 83.468000 829 2295 1 chr6D.!!$F1 1466
7 TraesCS6A01G012800 chr6D 6351272 6355039 3767 False 1272.666667 2368 89.235333 636 4057 3 chr6D.!!$F4 3421
8 TraesCS6A01G012800 chr6D 6496245 6499371 3126 False 983.666667 1860 88.195333 948 3860 3 chr6D.!!$F7 2912
9 TraesCS6A01G012800 chr6D 6370035 6373465 3430 False 939.000000 2180 86.077500 636 4083 4 chr6D.!!$F5 3447
10 TraesCS6A01G012800 chr6D 7032265 7034961 2696 False 686.333333 1225 80.662333 993 3779 3 chr6D.!!$F8 2786
11 TraesCS6A01G012800 chr6D 6505056 6505763 707 False 682.000000 682 84.082000 3705 4436 1 chr6D.!!$F3 731
12 TraesCS6A01G012800 chr6B 11599192 11601982 2790 False 916.666667 1495 86.100000 2196 4468 3 chr6B.!!$F3 2272
13 TraesCS6A01G012800 chr6B 11592527 11593934 1407 False 901.000000 1539 86.395500 669 2391 2 chr6B.!!$F2 1722
14 TraesCS6A01G012800 chr6B 11792014 11798871 6857 False 805.800000 1768 86.193200 657 4781 5 chr6B.!!$F4 4124
15 TraesCS6A01G012800 chr2A 288962247 288962882 635 False 870.000000 870 91.523000 4 634 1 chr2A.!!$F1 630
16 TraesCS6A01G012800 chr2B 118293137 118293782 645 False 837.000000 837 90.402000 2 634 1 chr2B.!!$F1 632
17 TraesCS6A01G012800 chr4B 666757621 666758271 650 True 830.000000 830 90.015000 2 638 1 chr4B.!!$R1 636
18 TraesCS6A01G012800 chr1D 476232008 476232646 638 True 726.000000 726 87.403000 2 634 1 chr1D.!!$R1 632
19 TraesCS6A01G012800 chr3B 389321044 389321679 635 False 710.000000 710 87.031000 4 633 1 chr3B.!!$F1 629
20 TraesCS6A01G012800 chr1A 40982745 40983388 643 True 708.000000 708 86.801000 2 633 1 chr1A.!!$R1 631
21 TraesCS6A01G012800 chr4D 68766491 68767138 647 True 704.000000 704 86.656000 3 639 1 chr4D.!!$R1 636
22 TraesCS6A01G012800 chr5B 354991259 354991904 645 False 699.000000 699 86.533000 2 633 1 chr5B.!!$F1 631
23 TraesCS6A01G012800 chr7B 1809716 1810354 638 True 688.000000 688 86.314000 2 635 1 chr7B.!!$R1 633

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
408 410 0.752658 CGATGGGAGATGGTAGCACA 59.247 55.000 0.0 0.0 0.0 4.57 F
1716 1871 0.401738 ACCAATCCCTCACACACCTG 59.598 55.000 0.0 0.0 0.0 4.00 F
1818 1973 0.608640 CAAGCCTCAAGTACCTCGGT 59.391 55.000 0.0 0.0 0.0 4.69 F
2104 2289 1.002134 AGAATGGGGCACTTGACCG 60.002 57.895 0.0 0.0 47.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 2152 0.616111 TCCAGAGGAGAGGCTTCCAC 60.616 60.0 15.14 10.34 39.84 4.02 R
3092 3704 0.034756 AAATTTTCCCACTTGGCCGC 59.965 50.0 0.00 0.00 0.00 6.53 R
3668 4280 0.670854 GGCGACTCTCCACACTTTCC 60.671 60.0 0.00 0.00 0.00 3.13 R
4086 5790 0.324943 TTAGTTCCACTCCTGCCAGC 59.675 55.0 0.00 0.00 0.00 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 146 8.486210 TCACATAGCATTTAACATTACTCCTCT 58.514 33.333 0.00 0.00 0.00 3.69
248 249 4.769488 TGTGCTTTATTATGGGCAGTTTGA 59.231 37.500 0.00 0.00 35.29 2.69
275 276 7.899973 ACTGCAGAAATGATTTGGTCTTTAAT 58.100 30.769 23.35 0.00 0.00 1.40
316 318 1.195115 TGCAGGTTATCTTCCGAGCT 58.805 50.000 0.00 0.00 34.06 4.09
341 343 1.468565 CGTTGATCCGTATGTGGTCGT 60.469 52.381 0.00 0.00 0.00 4.34
376 378 2.353610 GGCCAGGGAGCATTTGGTG 61.354 63.158 0.00 0.00 34.43 4.17
381 383 1.067295 AGGGAGCATTTGGTGACTGA 58.933 50.000 0.00 0.00 0.00 3.41
408 410 0.752658 CGATGGGAGATGGTAGCACA 59.247 55.000 0.00 0.00 0.00 4.57
441 443 1.312371 CGGTTTGGATGGCGGTCATT 61.312 55.000 0.00 0.00 35.97 2.57
452 454 6.069673 TGGATGGCGGTCATTTAATAGGATAT 60.070 38.462 0.00 0.00 35.97 1.63
523 529 6.699575 ATTACTGTTTTGCTCTTTGTGAGT 57.300 33.333 0.00 0.00 44.41 3.41
563 580 5.935945 TGGAGACTTGTGTTGGATCTTTTA 58.064 37.500 0.00 0.00 0.00 1.52
595 612 2.183478 TAGGGCCGTATGCATCATTG 57.817 50.000 0.19 0.00 43.89 2.82
926 978 4.920112 CCACCCGACGTTGCACCA 62.920 66.667 0.00 0.00 0.00 4.17
1008 1070 4.856801 GCCACCGCCATGGATCGT 62.857 66.667 18.40 4.24 43.02 3.73
1125 1202 2.415608 CGAGAGGGACGCCTTGCTA 61.416 63.158 0.00 0.00 0.00 3.49
1127 1204 1.305381 AGAGGGACGCCTTGCTAGT 60.305 57.895 0.00 0.00 0.00 2.57
1233 1316 3.198236 CTGCAGCAACACAACCGGG 62.198 63.158 6.32 0.00 0.00 5.73
1243 1326 1.378514 ACAACCGGGCATGTCATCC 60.379 57.895 6.32 0.00 0.00 3.51
1382 1465 3.288092 GTGTTCCAGAGTTCTTGGGTTT 58.712 45.455 0.00 0.00 0.00 3.27
1462 1617 0.610174 TCAGCTAGGCAACCTGTCAG 59.390 55.000 0.00 0.00 34.61 3.51
1519 1674 9.685276 ATTTCAACAATATGAGTATGGTCTCAA 57.315 29.630 0.62 0.00 45.65 3.02
1520 1675 8.492673 TTCAACAATATGAGTATGGTCTCAAC 57.507 34.615 0.62 0.00 45.65 3.18
1521 1676 6.756542 TCAACAATATGAGTATGGTCTCAACG 59.243 38.462 0.62 0.00 45.65 4.10
1522 1677 5.601662 ACAATATGAGTATGGTCTCAACGG 58.398 41.667 0.62 0.00 45.65 4.44
1523 1678 5.362717 ACAATATGAGTATGGTCTCAACGGA 59.637 40.000 0.62 0.00 45.65 4.69
1524 1679 3.802948 ATGAGTATGGTCTCAACGGAC 57.197 47.619 0.62 0.00 45.65 4.79
1525 1680 2.521126 TGAGTATGGTCTCAACGGACA 58.479 47.619 0.00 0.00 40.82 4.02
1526 1681 3.096852 TGAGTATGGTCTCAACGGACAT 58.903 45.455 0.00 0.00 40.82 3.06
1527 1682 3.130516 TGAGTATGGTCTCAACGGACATC 59.869 47.826 0.00 0.00 40.82 3.06
1528 1683 3.366396 AGTATGGTCTCAACGGACATCT 58.634 45.455 0.00 0.00 37.91 2.90
1529 1684 2.969628 ATGGTCTCAACGGACATCTC 57.030 50.000 0.00 0.00 37.91 2.75
1530 1685 1.627864 TGGTCTCAACGGACATCTCA 58.372 50.000 0.00 0.00 37.91 3.27
1531 1686 2.179427 TGGTCTCAACGGACATCTCAT 58.821 47.619 0.00 0.00 37.91 2.90
1580 1735 2.642171 ACCCATCTACCTCTGTTGGA 57.358 50.000 0.00 0.00 0.00 3.53
1716 1871 0.401738 ACCAATCCCTCACACACCTG 59.598 55.000 0.00 0.00 0.00 4.00
1749 1904 7.180051 ACAAATCTTCAGTACCTTGATCTCTCT 59.820 37.037 0.00 0.00 0.00 3.10
1751 1906 4.952957 TCTTCAGTACCTTGATCTCTCTGG 59.047 45.833 0.00 0.00 0.00 3.86
1756 1911 4.641094 AGTACCTTGATCTCTCTGGTAACG 59.359 45.833 0.00 0.00 42.51 3.18
1818 1973 0.608640 CAAGCCTCAAGTACCTCGGT 59.391 55.000 0.00 0.00 0.00 4.69
1892 2047 3.134081 TCATCCCTCCAACGGTTAGAATC 59.866 47.826 0.00 0.00 0.00 2.52
1941 2126 9.903682 ACAATGACAGTAGATTTGAAAAATCTG 57.096 29.630 20.35 10.60 37.54 2.90
1963 2148 6.097696 TCTGTGTGATTTGGAATACCTATCGA 59.902 38.462 0.00 0.00 37.04 3.59
1967 2152 6.710295 TGTGATTTGGAATACCTATCGATTGG 59.290 38.462 22.18 22.18 37.04 3.16
1989 2174 1.209261 GGAAGCCTCTCCTCTGGAAAG 59.791 57.143 0.00 0.00 32.21 2.62
2028 2213 7.664082 AGATAAATTGCCTAGATGTTCATCG 57.336 36.000 7.08 0.00 0.00 3.84
2104 2289 1.002134 AGAATGGGGCACTTGACCG 60.002 57.895 0.00 0.00 47.00 4.79
2113 2298 2.161609 GGGCACTTGACCGACTTATTTG 59.838 50.000 0.00 0.00 30.66 2.32
2129 2314 6.956047 ACTTATTTGTGTTCGACCTTTCTTC 58.044 36.000 0.00 0.00 0.00 2.87
2145 2330 6.663523 ACCTTTCTTCCAATAACATTACTGGG 59.336 38.462 0.00 0.00 31.25 4.45
2229 2625 2.961062 TCTTACTGGAGTTATACCGCCC 59.039 50.000 0.00 0.00 0.00 6.13
2250 2646 2.681344 CGGGTTGGGAAATTACACTAGC 59.319 50.000 0.00 0.00 0.00 3.42
2253 2649 5.503002 GGGTTGGGAAATTACACTAGCTTA 58.497 41.667 0.00 0.00 0.00 3.09
2295 2907 4.130118 GCAACCATCTTACTGGACCTATG 58.870 47.826 0.00 0.00 39.73 2.23
2306 2918 1.223077 TGGACCTATGCTACCAGGGAT 59.777 52.381 0.00 0.00 36.15 3.85
2307 2919 1.625818 GGACCTATGCTACCAGGGATG 59.374 57.143 0.00 0.00 36.15 3.51
2327 2939 1.818850 GCGAGTTGCACTGCATTATG 58.181 50.000 4.10 0.00 45.45 1.90
2328 2940 1.818850 CGAGTTGCACTGCATTATGC 58.181 50.000 10.65 10.65 45.29 3.14
2329 2941 1.399440 CGAGTTGCACTGCATTATGCT 59.601 47.619 18.44 0.00 45.31 3.79
2330 2942 2.538333 CGAGTTGCACTGCATTATGCTC 60.538 50.000 18.44 3.95 45.31 4.26
2331 2943 2.681848 GAGTTGCACTGCATTATGCTCT 59.318 45.455 18.44 13.87 45.31 4.09
2408 3020 5.163280 ACTGCACTAGTTTGTGGTACCTTTA 60.163 40.000 14.36 0.00 35.67 1.85
2464 3076 2.946329 TCTAAGATCAGTCTGCTCGGTC 59.054 50.000 0.00 0.00 34.13 4.79
2466 3078 1.102154 AGATCAGTCTGCTCGGTCAG 58.898 55.000 0.00 0.00 32.13 3.51
2520 3132 3.161067 AGATGGTATGATCACGGAGGAG 58.839 50.000 0.00 0.00 0.00 3.69
2600 3212 1.608283 GCCTCTGCCGTTAGAGTTTGT 60.608 52.381 10.97 0.00 42.09 2.83
2639 3251 9.620259 AGTAGAATTGACTTTATCCTCCAATTC 57.380 33.333 14.64 14.64 46.42 2.17
2661 3273 4.166725 TCTTTCACTGGGCATATTCCTGAT 59.833 41.667 5.96 0.00 0.00 2.90
2673 3285 9.077885 GGGCATATTCCTGATTCTATTTGTAAA 57.922 33.333 0.00 0.00 0.00 2.01
2705 3317 6.653989 ACCTACTTGTCTTGGATTTATCAGG 58.346 40.000 0.00 0.00 0.00 3.86
2718 3330 6.101734 TGGATTTATCAGGCAACCTTCTAGAT 59.898 38.462 0.00 0.00 37.17 1.98
2775 3387 3.333680 TGGTTTTCCTCCTCTTAAGCCAT 59.666 43.478 0.00 0.00 41.38 4.40
2790 3402 9.396022 CTCTTAAGCCATAATAAGTTTTCTGGA 57.604 33.333 0.00 0.00 32.27 3.86
2901 3513 2.800544 CGGAGACTTGGTATATTTGCGG 59.199 50.000 0.00 0.00 0.00 5.69
2983 3595 2.510768 ACACCTTCGTCAACTGAGTC 57.489 50.000 0.00 0.00 0.00 3.36
3055 3667 1.276989 CAGCAATGGCCCAGAAACATT 59.723 47.619 0.00 0.00 42.56 2.71
3065 3677 3.569701 GCCCAGAAACATTCAAAGAGACA 59.430 43.478 0.00 0.00 0.00 3.41
3105 3717 2.925706 TACAGCGGCCAAGTGGGA 60.926 61.111 2.24 0.00 40.01 4.37
3122 3734 8.204160 CCAAGTGGGAAAATTTAGAGAAGTTTT 58.796 33.333 0.00 0.00 37.23 2.43
3129 3741 9.574458 GGAAAATTTAGAGAAGTTTTGCCTATC 57.426 33.333 0.00 0.00 36.92 2.08
3132 3744 7.923414 ATTTAGAGAAGTTTTGCCTATCGTT 57.077 32.000 0.00 0.00 0.00 3.85
3213 3825 1.697432 TCACTCAACCACCTAACAGGG 59.303 52.381 0.00 0.00 40.58 4.45
3228 3840 2.287584 ACAGGGGAAATTCCAGATGGA 58.712 47.619 14.68 0.00 43.73 3.41
3252 3864 8.483758 GGAATTACCTCTCTTAATGGACTGTTA 58.516 37.037 0.00 0.00 35.41 2.41
3327 3939 5.824624 TGGAGCTATGAAATCACTTGAATCC 59.175 40.000 0.00 0.00 0.00 3.01
3375 3987 6.121776 TCTAGTGAAATCCCAACAAGCTTA 57.878 37.500 0.00 0.00 0.00 3.09
3380 3992 4.706476 TGAAATCCCAACAAGCTTATCAGG 59.294 41.667 0.00 0.00 0.00 3.86
3668 4280 4.298332 GTGTTTTGCACCCTATTGTTCAG 58.702 43.478 0.00 0.00 42.10 3.02
3684 4296 3.181465 TGTTCAGGAAAGTGTGGAGAGTC 60.181 47.826 0.00 0.00 0.00 3.36
3904 5600 4.810191 AGTATGCGTTCTTTTCTCTCCT 57.190 40.909 0.00 0.00 0.00 3.69
3989 5692 4.511527 AGTCATGATGAACTCACATGGTC 58.488 43.478 0.00 11.80 40.86 4.02
4033 5736 5.008217 TCCTTTTGTGTTGATGGTTCGTAAG 59.992 40.000 0.00 0.00 0.00 2.34
4086 5790 4.652822 ACTGTTAAGCTTTTAGTGAGGGG 58.347 43.478 3.20 0.00 0.00 4.79
4097 5801 4.664267 TGAGGGGCTGGCAGGAGT 62.664 66.667 17.64 0.00 0.00 3.85
4166 5872 7.255555 CGAGGGATCATCCATCTCTATAGATTG 60.256 44.444 16.26 4.55 43.15 2.67
4258 5964 2.762327 GGGGACAACACGAGTAGGATAA 59.238 50.000 0.00 0.00 0.00 1.75
4291 5997 3.485378 CACACATGTAACCAGTTTTTGCG 59.515 43.478 0.00 0.00 0.00 4.85
4301 6007 2.197324 TTTTTGCGGTGGCTCCCT 59.803 55.556 0.00 0.00 40.82 4.20
4399 6107 6.486657 ACTGAAATTTGTAGCTAAAGCAGTGA 59.513 34.615 4.54 0.00 45.16 3.41
4400 6108 7.013274 ACTGAAATTTGTAGCTAAAGCAGTGAA 59.987 33.333 4.54 0.00 45.16 3.18
4463 6179 5.934402 AGAACGTCCTTCCATTACACTAT 57.066 39.130 0.00 0.00 0.00 2.12
4478 6194 8.630917 CCATTACACTATTATATACTCCCTCCG 58.369 40.741 0.00 0.00 0.00 4.63
4479 6195 9.404848 CATTACACTATTATATACTCCCTCCGA 57.595 37.037 0.00 0.00 0.00 4.55
4532 8091 9.687210 TTCAATACGGACTACATATGAATGTAC 57.313 33.333 10.38 4.86 44.66 2.90
4539 8098 9.508567 CGGACTACATATGAATGTACATAGATG 57.491 37.037 9.21 9.93 44.66 2.90
4553 8112 7.221450 TGTACATAGATGTATTTTAGGGTGCC 58.779 38.462 5.69 0.00 44.25 5.01
4556 8115 4.706842 AGATGTATTTTAGGGTGCCGAT 57.293 40.909 0.00 0.00 0.00 4.18
4558 8117 5.063880 AGATGTATTTTAGGGTGCCGATTC 58.936 41.667 0.00 0.00 0.00 2.52
4559 8118 4.223556 TGTATTTTAGGGTGCCGATTCA 57.776 40.909 0.00 0.00 0.00 2.57
4560 8119 3.942748 TGTATTTTAGGGTGCCGATTCAC 59.057 43.478 0.00 0.00 36.28 3.18
4561 8120 2.871096 TTTTAGGGTGCCGATTCACT 57.129 45.000 0.00 0.00 37.16 3.41
4562 8121 2.396590 TTTAGGGTGCCGATTCACTC 57.603 50.000 0.00 0.00 37.71 3.51
4564 8123 1.496060 TAGGGTGCCGATTCACTCAT 58.504 50.000 5.38 0.00 39.86 2.90
4566 8125 1.004745 AGGGTGCCGATTCACTCATTT 59.995 47.619 5.38 0.00 39.86 2.32
4569 8128 2.253603 GTGCCGATTCACTCATTTTGC 58.746 47.619 0.00 0.00 34.29 3.68
4570 8129 2.095059 GTGCCGATTCACTCATTTTGCT 60.095 45.455 0.00 0.00 34.29 3.91
4572 8131 2.478539 GCCGATTCACTCATTTTGCTCC 60.479 50.000 0.00 0.00 0.00 4.70
4573 8132 2.223112 CCGATTCACTCATTTTGCTCCG 60.223 50.000 0.00 0.00 0.00 4.63
4574 8133 2.416547 CGATTCACTCATTTTGCTCCGT 59.583 45.455 0.00 0.00 0.00 4.69
4687 8461 9.261180 CATTATCTAACCATAGTCGTCAATGTT 57.739 33.333 0.00 0.00 0.00 2.71
4762 8542 3.814842 CAGCACATCACTAACTGAAACCA 59.185 43.478 0.00 0.00 30.60 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.133627 TGTCCAATTTTGTTTTGCCAAATTATG 58.866 29.630 0.00 0.00 34.50 1.90
17 18 6.306987 ACATCTTGTAGAACCTGTCCAATTT 58.693 36.000 0.00 0.00 0.00 1.82
110 111 0.535335 ATGCTATGTGAACCGTCCGT 59.465 50.000 0.00 0.00 0.00 4.69
145 146 6.317642 CCCAAATAACGTGGTGATAGAATTCA 59.682 38.462 8.44 0.00 34.01 2.57
176 177 5.104941 TGTGTCGAAATCTATCCCATCAAGT 60.105 40.000 0.00 0.00 0.00 3.16
248 249 5.796424 AGACCAAATCATTTCTGCAGTTT 57.204 34.783 14.67 2.57 0.00 2.66
376 378 2.297597 CTCCCATCGGGTAGATTCAGTC 59.702 54.545 0.00 0.00 44.74 3.51
381 383 2.260822 CCATCTCCCATCGGGTAGATT 58.739 52.381 9.83 0.00 44.74 2.40
408 410 4.668636 TCCAAACCGGTTGAAAATATCCT 58.331 39.130 23.08 0.00 39.87 3.24
530 536 6.458342 CCAACACAAGTCTCCAAGTCTTAAAC 60.458 42.308 0.00 0.00 0.00 2.01
533 539 4.407621 TCCAACACAAGTCTCCAAGTCTTA 59.592 41.667 0.00 0.00 0.00 2.10
534 540 3.199946 TCCAACACAAGTCTCCAAGTCTT 59.800 43.478 0.00 0.00 0.00 3.01
563 580 8.104566 TGCATACGGCCCTAATTATTAATAAGT 58.895 33.333 13.15 12.75 43.89 2.24
595 612 2.124403 CCCCAGCCTCTGCATCAC 60.124 66.667 0.00 0.00 41.13 3.06
650 667 8.585881 GGAGTGTGTTGCTAGGAGATTATATAA 58.414 37.037 0.00 0.00 0.00 0.98
719 738 3.534056 GATGCCATGGCCTGCACC 61.534 66.667 33.44 12.16 40.88 5.01
778 808 6.126883 ACCAGTCATATTTTCCGGTCAAGATA 60.127 38.462 0.00 0.00 0.00 1.98
818 859 4.842574 AGTTTTTCCATGGCAAGTGTTTT 58.157 34.783 6.96 0.00 0.00 2.43
1008 1070 1.959226 GACGAACTTGGCAGGCGAA 60.959 57.895 0.00 0.00 0.00 4.70
1125 1202 2.574006 TGATGCCTTGCTTGAAGACT 57.426 45.000 0.00 0.00 32.82 3.24
1127 1204 3.423749 TCATTGATGCCTTGCTTGAAGA 58.576 40.909 0.00 0.00 32.82 2.87
1225 1308 1.378514 GGATGACATGCCCGGTTGT 60.379 57.895 0.00 0.38 0.00 3.32
1243 1326 1.580845 CTTCCGCCAAGGTCAAGCTG 61.581 60.000 0.00 0.00 41.99 4.24
1382 1465 5.013079 TCAAGATGCCTCAGGTTCTTTAAGA 59.987 40.000 8.01 0.00 29.47 2.10
1462 1617 6.538263 AGGATAAATCAAGGTATTCCAGCTC 58.462 40.000 0.00 0.00 32.46 4.09
1508 1663 3.130516 TGAGATGTCCGTTGAGACCATAC 59.869 47.826 0.00 0.00 35.83 2.39
1509 1664 3.361786 TGAGATGTCCGTTGAGACCATA 58.638 45.455 0.00 0.00 35.83 2.74
1510 1665 2.179427 TGAGATGTCCGTTGAGACCAT 58.821 47.619 0.00 0.00 35.83 3.55
1511 1666 1.627864 TGAGATGTCCGTTGAGACCA 58.372 50.000 0.00 0.00 35.83 4.02
1512 1667 2.544685 CATGAGATGTCCGTTGAGACC 58.455 52.381 0.00 0.00 35.83 3.85
1513 1668 2.166459 TCCATGAGATGTCCGTTGAGAC 59.834 50.000 0.00 0.00 37.28 3.36
1514 1669 2.456577 TCCATGAGATGTCCGTTGAGA 58.543 47.619 0.00 0.00 0.00 3.27
1515 1670 2.967599 TCCATGAGATGTCCGTTGAG 57.032 50.000 0.00 0.00 0.00 3.02
1516 1671 3.183793 CATCCATGAGATGTCCGTTGA 57.816 47.619 13.19 0.00 46.32 3.18
1525 1680 4.035814 TCTGTTGAGACCATCCATGAGAT 58.964 43.478 0.00 0.00 34.66 2.75
1526 1681 3.196469 GTCTGTTGAGACCATCCATGAGA 59.804 47.826 0.00 0.00 42.66 3.27
1527 1682 3.529533 GTCTGTTGAGACCATCCATGAG 58.470 50.000 0.00 0.00 42.66 2.90
1528 1683 3.616956 GTCTGTTGAGACCATCCATGA 57.383 47.619 0.00 0.00 42.66 3.07
1666 1821 3.876274 AAGCGAGCACTCAGAAAGATA 57.124 42.857 0.00 0.00 0.00 1.98
1716 1871 5.552178 AGGTACTGAAGATTTGTGAGGTTC 58.448 41.667 0.00 0.00 37.18 3.62
1749 1904 1.612199 GGATGGCCAAAGTCGTTACCA 60.612 52.381 10.96 0.00 0.00 3.25
1751 1906 1.816074 TGGATGGCCAAAGTCGTTAC 58.184 50.000 10.96 0.00 42.49 2.50
1818 1973 5.133941 CCATACAGAGAGGTACTAGCAAGA 58.866 45.833 0.00 0.00 41.55 3.02
1870 2025 2.241281 TCTAACCGTTGGAGGGATGA 57.759 50.000 0.00 0.00 35.02 2.92
1892 2047 2.351726 GCTTTGTTACCCATGTAGCTCG 59.648 50.000 0.00 0.00 0.00 5.03
1941 2126 7.307989 CCAATCGATAGGTATTCCAAATCACAC 60.308 40.741 0.00 0.00 35.89 3.82
1963 2148 0.915364 GAGGAGAGGCTTCCACCAAT 59.085 55.000 15.14 0.00 39.84 3.16
1967 2152 0.616111 TCCAGAGGAGAGGCTTCCAC 60.616 60.000 15.14 10.34 39.84 4.02
2028 2213 4.745649 AGCTCAAGTACCGTAATCTGTTC 58.254 43.478 0.00 0.00 0.00 3.18
2104 2289 6.541111 AGAAAGGTCGAACACAAATAAGTC 57.459 37.500 1.87 0.00 0.00 3.01
2113 2298 5.237779 TGTTATTGGAAGAAAGGTCGAACAC 59.762 40.000 1.87 0.00 0.00 3.32
2129 2314 6.243148 GGTATACCCCCAGTAATGTTATTGG 58.757 44.000 11.17 7.19 39.47 3.16
2145 2330 2.167900 CCTTATGCCTAGCGGTATACCC 59.832 54.545 16.47 9.09 37.56 3.69
2229 2625 2.681344 GCTAGTGTAATTTCCCAACCCG 59.319 50.000 0.00 0.00 0.00 5.28
2243 2639 7.948034 AGAGAAAGATACTGTAAGCTAGTGT 57.052 36.000 0.00 0.00 37.60 3.55
2250 2646 8.539770 TGCTTGAAAGAGAAAGATACTGTAAG 57.460 34.615 0.00 0.00 42.29 2.34
2253 2649 6.205658 GGTTGCTTGAAAGAGAAAGATACTGT 59.794 38.462 0.00 0.00 0.00 3.55
2295 2907 1.972660 AACTCGCCATCCCTGGTAGC 61.973 60.000 0.00 0.00 45.10 3.58
2320 2932 4.880696 AGAAAGGTCAAGAGAGCATAATGC 59.119 41.667 0.00 0.00 44.60 3.56
2327 2939 3.393089 TGTCAGAAAGGTCAAGAGAGC 57.607 47.619 0.00 0.00 42.53 4.09
2328 2940 4.697514 TGTTGTCAGAAAGGTCAAGAGAG 58.302 43.478 0.00 0.00 0.00 3.20
2329 2941 4.753516 TGTTGTCAGAAAGGTCAAGAGA 57.246 40.909 0.00 0.00 0.00 3.10
2330 2942 7.678947 ATATTGTTGTCAGAAAGGTCAAGAG 57.321 36.000 0.00 0.00 0.00 2.85
2331 2943 8.999431 GTAATATTGTTGTCAGAAAGGTCAAGA 58.001 33.333 0.00 0.00 0.00 3.02
2385 2997 3.402628 AGGTACCACAAACTAGTGCAG 57.597 47.619 15.94 0.00 38.18 4.41
2398 3010 8.445361 AGGTTCTTAGAAAGATAAAGGTACCA 57.555 34.615 15.94 0.00 37.38 3.25
2408 3020 6.498651 TCCAGTGAGAAGGTTCTTAGAAAGAT 59.501 38.462 0.00 0.00 37.73 2.40
2464 3076 0.314302 AGGTCGAGTTCGGTCAACTG 59.686 55.000 1.26 0.00 46.10 3.16
2466 3078 2.593257 CTAAGGTCGAGTTCGGTCAAC 58.407 52.381 1.26 0.00 40.29 3.18
2472 3084 7.595502 AGATTATTATTGCTAAGGTCGAGTTCG 59.404 37.037 0.00 0.00 41.45 3.95
2506 3118 0.689080 AGGTGCTCCTCCGTGATCAT 60.689 55.000 0.18 0.00 40.58 2.45
2538 3150 9.575868 TGTGATAAATCCAGGTGTTTTAAGTTA 57.424 29.630 0.00 0.00 0.00 2.24
2639 3251 3.889815 TCAGGAATATGCCCAGTGAAAG 58.110 45.455 0.00 0.00 0.00 2.62
2673 3285 4.597507 TCCAAGACAAGTAGGTTCCTCAAT 59.402 41.667 0.00 0.00 0.00 2.57
2705 3317 4.479786 AGTTCTCCATCTAGAAGGTTGC 57.520 45.455 13.54 3.82 36.19 4.17
2718 3330 3.309296 AGAACACTGAGGAAGTTCTCCA 58.691 45.455 10.15 0.63 46.47 3.86
2790 3402 7.234355 AGTTCTTAAGTGATGATGGGAACTTT 58.766 34.615 1.63 0.00 38.94 2.66
2901 3513 6.476706 AGAAATTGTGACTTAGCTGCAAAAAC 59.523 34.615 1.02 0.00 0.00 2.43
2958 3570 4.124238 TCAGTTGACGAAGGTGTTTAAGG 58.876 43.478 0.00 0.00 0.00 2.69
2983 3595 8.128322 ACACCAGATATACTATTTCCTGCTAG 57.872 38.462 0.00 0.00 0.00 3.42
3055 3667 2.890945 TGTCGACCTCATGTCTCTTTGA 59.109 45.455 14.12 0.00 42.13 2.69
3065 3677 5.253330 ACCATTTAAACATGTCGACCTCAT 58.747 37.500 14.12 0.00 0.00 2.90
3083 3695 0.960364 CACTTGGCCGCTGTACCATT 60.960 55.000 0.00 0.00 35.42 3.16
3092 3704 0.034756 AAATTTTCCCACTTGGCCGC 59.965 50.000 0.00 0.00 0.00 6.53
3105 3717 8.793592 ACGATAGGCAAAACTTCTCTAAATTTT 58.206 29.630 0.00 0.00 43.77 1.82
3122 3734 2.169561 TGGTGCTTCATAACGATAGGCA 59.830 45.455 0.00 0.00 43.77 4.75
3129 3741 4.749245 AAGTTCTTGGTGCTTCATAACG 57.251 40.909 0.00 0.00 0.00 3.18
3132 3744 7.552687 CCATACTTAAGTTCTTGGTGCTTCATA 59.447 37.037 14.49 0.00 0.00 2.15
3252 3864 8.591114 ATTGATTCCATGAGAAGTTCAGATTT 57.409 30.769 5.50 0.00 39.68 2.17
3327 3939 1.352083 TGTTCCTTGAGAGGTCCAGG 58.648 55.000 0.00 0.00 43.97 4.45
3355 3967 5.324409 TGATAAGCTTGTTGGGATTTCACT 58.676 37.500 9.86 0.00 0.00 3.41
3375 3987 7.406104 AGGAGCTTAAATAAGTCAAACCTGAT 58.594 34.615 0.00 0.00 35.75 2.90
3380 3992 7.175119 AGTCCAAGGAGCTTAAATAAGTCAAAC 59.825 37.037 0.00 0.00 35.75 2.93
3668 4280 0.670854 GGCGACTCTCCACACTTTCC 60.671 60.000 0.00 0.00 0.00 3.13
3684 4296 2.678336 GTCAAAGAGGTGGAAATAGGCG 59.322 50.000 0.00 0.00 0.00 5.52
3760 5455 1.961793 TAACTTGTTGTCGCCTTGCT 58.038 45.000 0.00 0.00 0.00 3.91
3889 5585 5.379732 AGTCTACAGGAGAGAAAAGAACG 57.620 43.478 0.00 0.00 33.72 3.95
3904 5600 7.436118 ACCAAAGTTCGTATTACAAGTCTACA 58.564 34.615 0.00 0.00 0.00 2.74
3989 5692 7.929941 AAGGAACTAGAGCTGGAAAATTAAG 57.070 36.000 0.00 0.00 38.49 1.85
4033 5736 3.976169 TCACAAAACATTGGCTTACAGC 58.024 40.909 0.00 0.00 41.46 4.40
4042 5745 7.095060 ACAGTATAGCAGACTCACAAAACATTG 60.095 37.037 0.00 0.00 0.00 2.82
4086 5790 0.324943 TTAGTTCCACTCCTGCCAGC 59.675 55.000 0.00 0.00 0.00 4.85
4097 5801 3.255642 GTGCTTCATGGCTTTTAGTTCCA 59.744 43.478 0.00 0.00 0.00 3.53
4113 5819 5.090083 TGTTAGTTCGTTTTGTTGTGCTTC 58.910 37.500 0.00 0.00 0.00 3.86
4166 5872 1.859080 GCCGTAATGTGACGATTCCTC 59.141 52.381 0.00 0.00 45.82 3.71
4258 5964 4.219725 GGTTACATGTGTGCCCTTGTATTT 59.780 41.667 9.11 0.00 0.00 1.40
4291 5997 3.631250 TCATTTCAAATAGGGAGCCACC 58.369 45.455 0.00 0.00 38.08 4.61
4301 6007 4.746466 ACACCCACCCTTCATTTCAAATA 58.254 39.130 0.00 0.00 0.00 1.40
4356 6064 9.778741 AATTTCAGTTGTCATCTTGTCTAACTA 57.221 29.630 0.00 0.00 0.00 2.24
4374 6082 6.486657 TCACTGCTTTAGCTACAAATTTCAGT 59.513 34.615 3.10 0.16 42.66 3.41
4492 6208 8.755977 AGTCCGTATTGAAATCTCTAAAAGGTA 58.244 33.333 0.00 0.00 0.00 3.08
4530 8089 6.268158 TCGGCACCCTAAAATACATCTATGTA 59.732 38.462 5.33 5.33 46.21 2.29
4532 8091 5.547465 TCGGCACCCTAAAATACATCTATG 58.453 41.667 0.00 0.00 0.00 2.23
4536 8095 4.819630 TGAATCGGCACCCTAAAATACATC 59.180 41.667 0.00 0.00 0.00 3.06
4539 8098 4.196971 AGTGAATCGGCACCCTAAAATAC 58.803 43.478 0.00 0.00 39.59 1.89
4541 8100 3.279434 GAGTGAATCGGCACCCTAAAAT 58.721 45.455 0.00 0.00 39.59 1.82
4546 8105 0.620556 AATGAGTGAATCGGCACCCT 59.379 50.000 0.00 0.00 39.59 4.34
4547 8106 1.463674 AAATGAGTGAATCGGCACCC 58.536 50.000 0.00 0.00 39.59 4.61
4548 8107 2.867429 CAAAATGAGTGAATCGGCACC 58.133 47.619 0.00 0.00 39.59 5.01
4549 8108 2.095059 AGCAAAATGAGTGAATCGGCAC 60.095 45.455 0.00 0.00 39.05 5.01
4551 8110 2.478539 GGAGCAAAATGAGTGAATCGGC 60.479 50.000 0.00 0.00 0.00 5.54
4553 8112 2.416547 ACGGAGCAAAATGAGTGAATCG 59.583 45.455 0.00 0.00 0.00 3.34
4556 8115 2.807967 CTCACGGAGCAAAATGAGTGAA 59.192 45.455 0.00 0.00 38.02 3.18
4558 8117 1.466167 CCTCACGGAGCAAAATGAGTG 59.534 52.381 7.14 0.00 37.47 3.51
4559 8118 1.611673 CCCTCACGGAGCAAAATGAGT 60.612 52.381 7.14 0.00 37.47 3.41
4560 8119 1.089920 CCCTCACGGAGCAAAATGAG 58.910 55.000 0.00 0.00 38.65 2.90
4561 8120 0.690192 TCCCTCACGGAGCAAAATGA 59.310 50.000 0.00 0.00 34.86 2.57
4562 8121 3.248043 TCCCTCACGGAGCAAAATG 57.752 52.632 0.00 0.00 34.86 2.32
4570 8129 2.673258 TGCATAATACTCCCTCACGGA 58.327 47.619 0.00 0.00 38.83 4.69
4572 8131 4.631131 TGAATGCATAATACTCCCTCACG 58.369 43.478 0.00 0.00 0.00 4.35
4573 8132 5.468072 CACTGAATGCATAATACTCCCTCAC 59.532 44.000 0.00 0.00 0.00 3.51
4574 8133 5.366477 TCACTGAATGCATAATACTCCCTCA 59.634 40.000 0.00 0.00 0.00 3.86
4602 8375 9.678260 GATAAGCTCTGGGAAATATATGAACAT 57.322 33.333 0.00 0.00 0.00 2.71
4687 8461 5.886609 TCATTTATTTTCTCTGTCCACCCA 58.113 37.500 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.