Multiple sequence alignment - TraesCS7A01G460100

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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 TraesCS7A01G460100 chr7A 100.000 2502 0 0 1 2502 655452829 655450328 0.000000e+00 4621.0
1 TraesCS7A01G460100 chr7A 95.060 668 31 2 1788 2454 41184865 41185531 0.000000e+00 1050.0
2 TraesCS7A01G460100 chr7A 82.240 991 109 30 637 1608 654503691 654502749 0.000000e+00 793.0
3 TraesCS7A01G460100 chr7A 80.134 1047 141 25 577 1595 656982026 656983033 0.000000e+00 719.0
4 TraesCS7A01G460100 chr7A 80.317 315 59 3 18 331 236511562 236511874 4.160000e-58 235.0
5 TraesCS7A01G460100 chr7D 93.829 1183 55 8 442 1607 568185936 568184755 0.000000e+00 1764.0
6 TraesCS7A01G460100 chr7D 81.262 1046 130 26 577 1595 568324165 568323159 0.000000e+00 785.0
7 TraesCS7A01G460100 chr7D 90.778 347 31 1 1 347 568186611 568186266 1.750000e-126 462.0
8 TraesCS7A01G460100 chr7D 81.416 339 59 4 1 338 620121979 620122314 8.820000e-70 274.0
9 TraesCS7A01G460100 chr7D 94.231 156 9 0 1607 1762 322700370 322700215 3.220000e-59 239.0
10 TraesCS7A01G460100 chr3A 96.041 682 27 0 1788 2469 651224401 651223720 0.000000e+00 1110.0
11 TraesCS7A01G460100 chrUn 93.421 684 43 2 1788 2469 431841961 431842644 0.000000e+00 1013.0
12 TraesCS7A01G460100 chrUn 91.787 694 47 7 1799 2487 31654387 31655075 0.000000e+00 957.0
13 TraesCS7A01G460100 chr7B 91.888 715 54 3 398 1109 622838421 622837708 0.000000e+00 996.0
14 TraesCS7A01G460100 chr7B 96.017 477 16 1 1105 1578 622832941 622832465 0.000000e+00 773.0
15 TraesCS7A01G460100 chr7B 79.906 1060 139 29 572 1595 623934254 623933233 0.000000e+00 710.0
16 TraesCS7A01G460100 chr7B 81.432 377 65 5 1 375 586098461 586098088 1.120000e-78 303.0
17 TraesCS7A01G460100 chr7B 86.585 82 7 3 450 529 743660855 743660934 1.230000e-13 87.9
18 TraesCS7A01G460100 chr1B 90.517 696 58 5 1799 2491 684086129 684086819 0.000000e+00 913.0
19 TraesCS7A01G460100 chr1B 90.972 432 34 2 1797 2226 522202270 522201842 6.000000e-161 577.0
20 TraesCS7A01G460100 chr1A 90.922 694 41 13 1788 2469 428188683 428188000 0.000000e+00 913.0
21 TraesCS7A01G460100 chr1A 94.231 156 9 0 1607 1762 316422487 316422642 3.220000e-59 239.0
22 TraesCS7A01G460100 chr4A 88.872 674 55 5 1797 2469 223670960 223670306 0.000000e+00 811.0
23 TraesCS7A01G460100 chr4A 88.707 673 54 6 1797 2467 85032010 85032662 0.000000e+00 802.0
24 TraesCS7A01G460100 chr4A 82.474 97 15 1 450 546 725799865 725799959 1.590000e-12 84.2
25 TraesCS7A01G460100 chr6B 87.591 685 48 17 1797 2469 2357759 2358418 0.000000e+00 760.0
26 TraesCS7A01G460100 chr6B 82.114 369 59 6 2 367 192356668 192357032 2.420000e-80 309.0
27 TraesCS7A01G460100 chr6B 86.747 83 7 3 450 530 432480830 432480750 3.430000e-14 89.8
28 TraesCS7A01G460100 chr6D 82.322 379 60 6 1 375 41173408 41173783 3.100000e-84 322.0
29 TraesCS7A01G460100 chr6D 93.590 156 10 0 1607 1762 120414195 120414040 1.500000e-57 233.0
30 TraesCS7A01G460100 chr5B 81.720 372 63 5 6 375 540915807 540916175 3.130000e-79 305.0
31 TraesCS7A01G460100 chr5A 83.385 325 53 1 13 337 533951579 533951902 1.450000e-77 300.0
32 TraesCS7A01G460100 chr5A 95.513 156 7 0 1607 1762 72968709 72968554 1.490000e-62 250.0
33 TraesCS7A01G460100 chr6A 81.522 368 59 9 1 364 12985043 12984681 6.770000e-76 294.0
34 TraesCS7A01G460100 chr6A 87.500 80 10 0 450 529 551695838 551695759 2.650000e-15 93.5
35 TraesCS7A01G460100 chr2A 81.351 370 62 6 1 368 672424501 672424137 6.770000e-76 294.0
36 TraesCS7A01G460100 chr2A 93.590 156 10 0 1607 1762 466160505 466160660 1.500000e-57 233.0
37 TraesCS7A01G460100 chr2A 87.273 55 7 0 398 452 416913819 416913873 2.080000e-06 63.9
38 TraesCS7A01G460100 chr3D 84.672 274 37 4 1 273 301975200 301975469 4.100000e-68 268.0
39 TraesCS7A01G460100 chr3D 87.654 81 10 0 450 530 519155665 519155745 7.370000e-16 95.3
40 TraesCS7A01G460100 chr2D 93.671 158 8 1 1607 1762 618626300 618626457 4.160000e-58 235.0
41 TraesCS7A01G460100 chr2D 93.548 155 9 1 1607 1761 596061139 596060986 1.940000e-56 230.0
42 TraesCS7A01G460100 chr2D 90.566 53 5 0 398 450 467227942 467227994 1.240000e-08 71.3
43 TraesCS7A01G460100 chr1D 93.631 157 9 1 1607 1762 472264237 472264393 1.500000e-57 233.0
44 TraesCS7A01G460100 chr1D 86.250 80 11 0 449 528 127191669 127191590 1.230000e-13 87.9
45 TraesCS7A01G460100 chr1D 86.250 80 11 0 450 529 153222725 153222804 1.230000e-13 87.9
46 TraesCS7A01G460100 chr4D 92.949 156 11 0 1607 1762 154760585 154760740 6.960000e-56 228.0
47 TraesCS7A01G460100 chr3B 74.742 194 37 9 262 446 166130538 166130728 2.670000e-10 76.8
48 TraesCS7A01G460100 chr2B 94.286 35 2 0 341 375 443944478 443944444 1.000000e-03 54.7
49 TraesCS7A01G460100 chr2B 96.875 32 1 0 341 372 785744340 785744371 1.000000e-03 54.7


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 TraesCS7A01G460100 chr7A 655450328 655452829 2501 True 4621 4621 100.0000 1 2502 1 chr7A.!!$R2 2501
1 TraesCS7A01G460100 chr7A 41184865 41185531 666 False 1050 1050 95.0600 1788 2454 1 chr7A.!!$F1 666
2 TraesCS7A01G460100 chr7A 654502749 654503691 942 True 793 793 82.2400 637 1608 1 chr7A.!!$R1 971
3 TraesCS7A01G460100 chr7A 656982026 656983033 1007 False 719 719 80.1340 577 1595 1 chr7A.!!$F3 1018
4 TraesCS7A01G460100 chr7D 568184755 568186611 1856 True 1113 1764 92.3035 1 1607 2 chr7D.!!$R3 1606
5 TraesCS7A01G460100 chr7D 568323159 568324165 1006 True 785 785 81.2620 577 1595 1 chr7D.!!$R2 1018
6 TraesCS7A01G460100 chr3A 651223720 651224401 681 True 1110 1110 96.0410 1788 2469 1 chr3A.!!$R1 681
7 TraesCS7A01G460100 chrUn 431841961 431842644 683 False 1013 1013 93.4210 1788 2469 1 chrUn.!!$F2 681
8 TraesCS7A01G460100 chrUn 31654387 31655075 688 False 957 957 91.7870 1799 2487 1 chrUn.!!$F1 688
9 TraesCS7A01G460100 chr7B 622837708 622838421 713 True 996 996 91.8880 398 1109 1 chr7B.!!$R3 711
10 TraesCS7A01G460100 chr7B 623933233 623934254 1021 True 710 710 79.9060 572 1595 1 chr7B.!!$R4 1023
11 TraesCS7A01G460100 chr1B 684086129 684086819 690 False 913 913 90.5170 1799 2491 1 chr1B.!!$F1 692
12 TraesCS7A01G460100 chr1A 428188000 428188683 683 True 913 913 90.9220 1788 2469 1 chr1A.!!$R1 681
13 TraesCS7A01G460100 chr4A 223670306 223670960 654 True 811 811 88.8720 1797 2469 1 chr4A.!!$R1 672
14 TraesCS7A01G460100 chr4A 85032010 85032662 652 False 802 802 88.7070 1797 2467 1 chr4A.!!$F1 670
15 TraesCS7A01G460100 chr6B 2357759 2358418 659 False 760 760 87.5910 1797 2469 1 chr6B.!!$F1 672

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
377 378 0.03601 CATCTGTGTCTGTGGACCCC 60.036 60.0 0.0 0.0 41.47 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1725 2025 0.107848 GGTACAGGTGCGCCATTAGT 60.108 55.0 20.59 13.38 37.19 2.24 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
20 21 2.666026 GGCTTAAGCACACTCTTTTGC 58.334 47.619 27.83 3.13 44.36 3.68
87 88 1.128188 AATATGCCTCCGGGACTCCC 61.128 60.000 0.00 3.63 41.09 4.30
108 109 2.898738 AGTCTGATGAGCGGGCTG 59.101 61.111 0.00 0.00 36.19 4.85
133 134 5.352569 CCAGACATGGTGAAGACAAATAGAC 59.647 44.000 0.00 0.00 42.17 2.59
135 136 5.249393 AGACATGGTGAAGACAAATAGACCT 59.751 40.000 0.00 0.00 0.00 3.85
136 137 5.248640 ACATGGTGAAGACAAATAGACCTG 58.751 41.667 0.00 0.00 0.00 4.00
139 140 3.559171 GGTGAAGACAAATAGACCTGCCA 60.559 47.826 0.00 0.00 0.00 4.92
162 163 2.553172 GGCCGGATGTAGACTAGTGTAG 59.447 54.545 5.05 0.00 0.00 2.74
164 165 3.631227 GCCGGATGTAGACTAGTGTAGTT 59.369 47.826 5.05 0.00 39.59 2.24
181 182 3.992943 AGTTTATCCGTGTCATGGGAA 57.007 42.857 11.31 3.54 35.60 3.97
303 304 0.322098 TTGCACGAATTCCATCCGGT 60.322 50.000 0.00 0.00 0.00 5.28
307 308 1.810151 CACGAATTCCATCCGGTTTGT 59.190 47.619 0.00 0.00 0.00 2.83
331 332 9.486497 TGTTGCATAAATGTTTGAAATGTATGT 57.514 25.926 0.00 0.00 30.73 2.29
337 338 4.517952 TGTTTGAAATGTATGTGGGCAG 57.482 40.909 0.00 0.00 0.00 4.85
347 348 1.046472 ATGTGGGCAGCATTGGATGG 61.046 55.000 0.00 0.00 0.00 3.51
350 351 3.908081 GGCAGCATTGGATGGCGG 61.908 66.667 0.00 0.00 46.20 6.13
351 352 3.142838 GCAGCATTGGATGGCGGT 61.143 61.111 0.00 0.00 34.54 5.68
352 353 3.113745 CAGCATTGGATGGCGGTC 58.886 61.111 0.00 0.00 34.54 4.79
353 354 1.452651 CAGCATTGGATGGCGGTCT 60.453 57.895 0.00 0.00 34.54 3.85
354 355 1.153086 AGCATTGGATGGCGGTCTC 60.153 57.895 0.00 0.00 34.54 3.36
355 356 2.189499 GCATTGGATGGCGGTCTCC 61.189 63.158 0.00 0.00 0.00 3.71
356 357 1.526917 CATTGGATGGCGGTCTCCC 60.527 63.158 0.00 0.00 0.00 4.30
366 367 2.982130 GGTCTCCCGCATCTGTGT 59.018 61.111 0.00 0.00 0.00 3.72
367 368 1.153549 GGTCTCCCGCATCTGTGTC 60.154 63.158 0.00 0.00 0.00 3.67
368 369 1.608717 GGTCTCCCGCATCTGTGTCT 61.609 60.000 0.00 0.00 0.00 3.41
369 370 0.459237 GTCTCCCGCATCTGTGTCTG 60.459 60.000 0.00 0.00 0.00 3.51
370 371 0.900182 TCTCCCGCATCTGTGTCTGT 60.900 55.000 0.00 0.00 0.00 3.41
371 372 0.738762 CTCCCGCATCTGTGTCTGTG 60.739 60.000 0.00 0.00 0.00 3.66
372 373 1.742880 CCCGCATCTGTGTCTGTGG 60.743 63.158 0.00 0.00 41.67 4.17
373 374 1.293179 CCGCATCTGTGTCTGTGGA 59.707 57.895 0.00 0.00 44.15 4.02
374 375 1.016130 CCGCATCTGTGTCTGTGGAC 61.016 60.000 0.00 0.00 44.15 4.02
375 376 1.016130 CGCATCTGTGTCTGTGGACC 61.016 60.000 0.00 0.00 41.47 4.46
376 377 0.674895 GCATCTGTGTCTGTGGACCC 60.675 60.000 0.00 0.00 41.47 4.46
377 378 0.036010 CATCTGTGTCTGTGGACCCC 60.036 60.000 0.00 0.00 41.47 4.95
378 379 0.178891 ATCTGTGTCTGTGGACCCCT 60.179 55.000 0.00 0.00 41.47 4.79
379 380 0.832135 TCTGTGTCTGTGGACCCCTC 60.832 60.000 0.00 0.00 41.47 4.30
380 381 1.831652 CTGTGTCTGTGGACCCCTCC 61.832 65.000 0.00 0.00 41.47 4.30
381 382 2.203938 TGTCTGTGGACCCCTCCC 60.204 66.667 0.00 0.00 41.47 4.30
382 383 3.009714 GTCTGTGGACCCCTCCCC 61.010 72.222 0.00 0.00 35.34 4.81
383 384 4.348495 TCTGTGGACCCCTCCCCC 62.348 72.222 0.00 0.00 35.34 5.40
403 404 1.977009 CCCCCTCCTTTTTGTCCGC 60.977 63.158 0.00 0.00 0.00 5.54
422 423 3.467226 GACGGATGCGGGAGGGAA 61.467 66.667 12.44 0.00 0.00 3.97
428 429 0.740737 GATGCGGGAGGGAATTTGTG 59.259 55.000 0.00 0.00 0.00 3.33
436 437 0.105246 AGGGAATTTGTGGGTTGCCA 60.105 50.000 0.00 0.00 38.18 4.92
461 697 4.761739 TGAAGATGTCCTTACTTGCCTTTG 59.238 41.667 0.00 0.00 34.68 2.77
499 735 7.158697 GCCAAGGGTAATTTTGTCATAACTTT 58.841 34.615 0.00 0.00 0.00 2.66
535 771 2.846206 TCTTGGTCACCATGCTAGGAAT 59.154 45.455 0.00 0.00 31.53 3.01
551 787 5.517655 GCTAGGAATGGAGGGAGTAGATAGT 60.518 48.000 0.00 0.00 0.00 2.12
552 788 6.297126 GCTAGGAATGGAGGGAGTAGATAGTA 60.297 46.154 0.00 0.00 0.00 1.82
553 789 6.147437 AGGAATGGAGGGAGTAGATAGTAG 57.853 45.833 0.00 0.00 0.00 2.57
554 790 5.858408 AGGAATGGAGGGAGTAGATAGTAGA 59.142 44.000 0.00 0.00 0.00 2.59
555 791 6.511083 AGGAATGGAGGGAGTAGATAGTAGAT 59.489 42.308 0.00 0.00 0.00 1.98
556 792 6.831868 GGAATGGAGGGAGTAGATAGTAGATC 59.168 46.154 0.00 0.00 0.00 2.75
557 793 6.979018 ATGGAGGGAGTAGATAGTAGATCA 57.021 41.667 0.00 0.00 0.00 2.92
559 795 5.852807 TGGAGGGAGTAGATAGTAGATCAGT 59.147 44.000 0.00 0.00 0.00 3.41
560 796 6.013206 TGGAGGGAGTAGATAGTAGATCAGTC 60.013 46.154 0.00 0.00 0.00 3.51
561 797 6.045072 AGGGAGTAGATAGTAGATCAGTCG 57.955 45.833 0.00 0.00 0.00 4.18
562 798 5.781306 AGGGAGTAGATAGTAGATCAGTCGA 59.219 44.000 0.00 0.00 0.00 4.20
565 803 7.093814 GGGAGTAGATAGTAGATCAGTCGACTA 60.094 44.444 19.57 7.46 43.60 2.59
608 846 4.858935 ACCATCAATTTGACACAAGAACG 58.141 39.130 0.15 0.00 0.00 3.95
670 914 9.878667 TTACCATCAATTTGATACTACGAGAAA 57.121 29.630 11.44 0.00 34.28 2.52
756 1000 7.875041 AGATATCGAAATCAACTACTCCATTGG 59.125 37.037 0.00 0.00 0.00 3.16
784 1030 2.666272 TTGGTTGCATCCACTTACCA 57.334 45.000 16.21 8.07 37.20 3.25
929 1175 3.221771 TGAAAACTTGCACTATGGCTGT 58.778 40.909 0.00 0.00 34.04 4.40
951 1197 7.339721 GCTGTTATATATAGAGGCTGAGTGGTA 59.660 40.741 0.00 0.00 0.00 3.25
988 1234 4.346734 AACACATACCGACAGTACTACG 57.653 45.455 12.65 12.65 32.46 3.51
1229 1475 3.988379 TTCAAAAGACATCCACTGTGC 57.012 42.857 1.29 0.00 38.54 4.57
1341 1594 2.020720 CACACTTGTGCAGGTTGGTAA 58.979 47.619 0.10 0.00 39.39 2.85
1515 1812 4.475016 AGGTGCCTAGACCTTCAATGTAAT 59.525 41.667 0.00 0.00 44.53 1.89
1608 1908 8.677148 AGTGTATTTGTCTTTGATGTGTAACT 57.323 30.769 0.00 0.00 38.04 2.24
1609 1909 9.772973 AGTGTATTTGTCTTTGATGTGTAACTA 57.227 29.630 0.00 0.00 38.04 2.24
1611 1911 9.772973 TGTATTTGTCTTTGATGTGTAACTAGT 57.227 29.630 0.00 0.00 38.04 2.57
1632 1932 9.734984 ACTAGTTAAAACTATTAATGGCACACT 57.265 29.630 3.16 0.00 40.45 3.55
1633 1933 9.988350 CTAGTTAAAACTATTAATGGCACACTG 57.012 33.333 3.16 0.00 40.45 3.66
1634 1934 8.404107 AGTTAAAACTATTAATGGCACACTGT 57.596 30.769 0.00 0.00 38.49 3.55
1635 1935 8.296713 AGTTAAAACTATTAATGGCACACTGTG 58.703 33.333 6.19 6.19 38.49 3.66
1644 1944 4.318021 CACACTGTGCGCTGGTGC 62.318 66.667 21.06 0.00 34.70 5.01
1658 1958 4.616181 GCTGGTGCGTCATTAATAGTTT 57.384 40.909 0.00 0.00 0.00 2.66
1659 1959 4.981794 GCTGGTGCGTCATTAATAGTTTT 58.018 39.130 0.00 0.00 0.00 2.43
1660 1960 4.793216 GCTGGTGCGTCATTAATAGTTTTG 59.207 41.667 0.00 0.00 0.00 2.44
1661 1961 5.303747 TGGTGCGTCATTAATAGTTTTGG 57.696 39.130 0.00 0.00 0.00 3.28
1662 1962 5.004448 TGGTGCGTCATTAATAGTTTTGGA 58.996 37.500 0.00 0.00 0.00 3.53
1663 1963 5.473846 TGGTGCGTCATTAATAGTTTTGGAA 59.526 36.000 0.00 0.00 0.00 3.53
1664 1964 6.016192 TGGTGCGTCATTAATAGTTTTGGAAA 60.016 34.615 0.00 0.00 0.00 3.13
1665 1965 6.864165 GGTGCGTCATTAATAGTTTTGGAAAA 59.136 34.615 0.00 0.00 0.00 2.29
1666 1966 7.382759 GGTGCGTCATTAATAGTTTTGGAAAAA 59.617 33.333 0.00 0.00 0.00 1.94
1667 1967 8.921670 GTGCGTCATTAATAGTTTTGGAAAAAT 58.078 29.630 0.00 0.00 0.00 1.82
1700 2000 3.034721 AGTAATGGTACACCGTGTGTG 57.965 47.619 14.66 4.58 46.84 3.82
1720 2020 2.700722 TGGTGCGCCATTAGTAATGA 57.299 45.000 22.03 1.55 41.46 2.57
1721 2021 2.560504 TGGTGCGCCATTAGTAATGAG 58.439 47.619 22.03 16.14 41.46 2.90
1722 2022 1.873591 GGTGCGCCATTAGTAATGAGG 59.126 52.381 22.03 14.32 41.46 3.86
1723 2023 2.484770 GGTGCGCCATTAGTAATGAGGA 60.485 50.000 22.03 14.25 41.46 3.71
1724 2024 2.544267 GTGCGCCATTAGTAATGAGGAC 59.456 50.000 22.03 20.20 41.46 3.85
1725 2025 2.169561 TGCGCCATTAGTAATGAGGACA 59.830 45.455 22.03 12.31 41.46 4.02
1726 2026 2.544267 GCGCCATTAGTAATGAGGACAC 59.456 50.000 22.03 5.52 41.46 3.67
1727 2027 3.741388 GCGCCATTAGTAATGAGGACACT 60.741 47.826 22.03 0.00 41.46 3.55
1728 2028 4.500887 GCGCCATTAGTAATGAGGACACTA 60.501 45.833 22.03 0.00 41.46 2.74
1729 2029 5.597806 CGCCATTAGTAATGAGGACACTAA 58.402 41.667 22.03 0.00 41.46 2.24
1730 2030 6.223852 CGCCATTAGTAATGAGGACACTAAT 58.776 40.000 22.03 0.00 43.09 1.73
1734 2034 4.060038 AGTAATGAGGACACTAATGGCG 57.940 45.455 0.00 0.00 32.81 5.69
1735 2035 1.668419 AATGAGGACACTAATGGCGC 58.332 50.000 0.00 0.00 32.81 6.53
1736 2036 0.541392 ATGAGGACACTAATGGCGCA 59.459 50.000 10.83 0.00 32.81 6.09
1737 2037 0.391130 TGAGGACACTAATGGCGCAC 60.391 55.000 10.83 0.00 32.81 5.34
1738 2038 1.078426 AGGACACTAATGGCGCACC 60.078 57.895 10.83 0.00 32.81 5.01
1739 2039 1.078426 GGACACTAATGGCGCACCT 60.078 57.895 10.83 0.00 32.81 4.00
1740 2040 1.369091 GGACACTAATGGCGCACCTG 61.369 60.000 10.83 0.00 32.81 4.00
1741 2041 0.673644 GACACTAATGGCGCACCTGT 60.674 55.000 10.83 0.44 36.63 4.00
1742 2042 0.611200 ACACTAATGGCGCACCTGTA 59.389 50.000 10.83 0.00 36.63 2.74
1743 2043 1.006832 CACTAATGGCGCACCTGTAC 58.993 55.000 10.83 0.00 36.63 2.90
1744 2044 0.107848 ACTAATGGCGCACCTGTACC 60.108 55.000 10.83 0.00 36.63 3.34
1745 2045 0.178068 CTAATGGCGCACCTGTACCT 59.822 55.000 10.83 0.00 36.63 3.08
1746 2046 0.107897 TAATGGCGCACCTGTACCTG 60.108 55.000 10.83 0.00 36.63 4.00
1747 2047 2.819984 AATGGCGCACCTGTACCTGG 62.820 60.000 10.83 0.00 36.63 4.45
1748 2048 4.016706 GGCGCACCTGTACCTGGT 62.017 66.667 10.83 4.05 36.11 4.00
1752 2052 2.742372 CACCTGTACCTGGTGCGC 60.742 66.667 18.19 0.00 44.09 6.09
1753 2053 4.016706 ACCTGTACCTGGTGCGCC 62.017 66.667 10.11 10.11 34.44 6.53
1754 2054 4.015406 CCTGTACCTGGTGCGCCA 62.015 66.667 19.93 19.93 43.73 5.69
1755 2055 2.742372 CTGTACCTGGTGCGCCAC 60.742 66.667 16.89 6.26 40.46 5.01
1756 2056 3.238497 TGTACCTGGTGCGCCACT 61.238 61.111 16.89 5.89 40.46 4.00
1757 2057 2.742372 GTACCTGGTGCGCCACTG 60.742 66.667 16.89 12.24 40.46 3.66
1758 2058 4.697756 TACCTGGTGCGCCACTGC 62.698 66.667 16.89 0.00 40.46 4.40
1760 2060 4.393155 CCTGGTGCGCCACTGCTA 62.393 66.667 16.89 0.00 40.46 3.49
1761 2061 2.124983 CTGGTGCGCCACTGCTAT 60.125 61.111 16.89 0.00 40.46 2.97
1762 2062 2.436469 TGGTGCGCCACTGCTATG 60.436 61.111 16.89 0.00 40.46 2.23
1763 2063 3.204827 GGTGCGCCACTGCTATGG 61.205 66.667 12.58 2.66 43.26 2.74
1802 2102 7.895962 TCCTAGTAGTATAACTCATGCATGGAT 59.104 37.037 25.97 15.85 0.00 3.41
1883 2191 7.590279 ACTAACCCAACTTTTATGTTTGATCG 58.410 34.615 0.00 0.00 0.00 3.69
1994 2302 1.139058 AGTTAGGAGCGTATTGGCCTG 59.861 52.381 3.32 0.00 32.04 4.85
2128 2439 7.744087 TGCTAATTCACAACATCTAGTTTGT 57.256 32.000 0.00 0.00 38.74 2.83
2140 2451 8.950210 CAACATCTAGTTTGTCTTGTTGGATAT 58.050 33.333 5.85 0.00 39.94 1.63
2165 2476 1.529865 GTTGGAGTAGTTTGCGTGGTC 59.470 52.381 0.00 0.00 0.00 4.02
2316 2630 3.268013 ACAATTGACTTTGCGTAGTGC 57.732 42.857 13.59 0.00 46.70 4.40
2425 2746 4.951715 ACTTAAAAGGGGACGAAACAAAGT 59.048 37.500 0.00 0.00 0.00 2.66
2441 2763 2.362077 CAAAGTGGGACCAAACCAAGAG 59.638 50.000 0.00 0.00 40.24 2.85
2444 2766 2.986728 AGTGGGACCAAACCAAGAGTAT 59.013 45.455 0.00 0.00 40.24 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 1.971505 CTTCCCTATGTCCGGCTGCA 61.972 60.000 0.50 0.00 0.00 4.41
87 88 2.584418 CCGCTCATCAGACTGCCG 60.584 66.667 0.00 0.00 0.00 5.69
111 112 5.249393 AGGTCTATTTGTCTTCACCATGTCT 59.751 40.000 0.00 0.00 0.00 3.41
119 120 3.674997 GTGGCAGGTCTATTTGTCTTCA 58.325 45.455 0.00 0.00 0.00 3.02
135 136 4.155733 CTACATCCGGCCGTGGCA 62.156 66.667 26.12 8.17 44.11 4.92
136 137 3.845259 TCTACATCCGGCCGTGGC 61.845 66.667 26.12 1.16 41.06 5.01
139 140 0.106819 ACTAGTCTACATCCGGCCGT 60.107 55.000 26.12 7.98 0.00 5.68
147 148 7.555554 ACACGGATAAACTACACTAGTCTACAT 59.444 37.037 0.00 0.00 38.26 2.29
148 149 6.881065 ACACGGATAAACTACACTAGTCTACA 59.119 38.462 0.00 0.00 38.26 2.74
162 163 3.315191 CCATTCCCATGACACGGATAAAC 59.685 47.826 0.00 0.00 31.07 2.01
164 165 2.774809 TCCATTCCCATGACACGGATAA 59.225 45.455 0.00 0.00 31.07 1.75
251 252 7.686938 CGGACTTCATATAAACAAGACGAAAAC 59.313 37.037 0.00 0.00 0.00 2.43
295 296 3.584406 TTTATGCAACAAACCGGATGG 57.416 42.857 9.46 0.00 42.84 3.51
299 300 4.747108 TCAAACATTTATGCAACAAACCGG 59.253 37.500 0.00 0.00 0.00 5.28
307 308 8.933807 CCACATACATTTCAAACATTTATGCAA 58.066 29.630 0.00 0.00 0.00 4.08
331 332 2.760799 GCCATCCAATGCTGCCCA 60.761 61.111 0.00 0.00 0.00 5.36
337 338 2.189499 GGAGACCGCCATCCAATGC 61.189 63.158 0.00 0.00 35.54 3.56
350 351 0.459237 CAGACACAGATGCGGGAGAC 60.459 60.000 0.00 0.00 0.00 3.36
351 352 0.900182 ACAGACACAGATGCGGGAGA 60.900 55.000 0.00 0.00 0.00 3.71
352 353 0.738762 CACAGACACAGATGCGGGAG 60.739 60.000 0.00 0.00 0.00 4.30
353 354 1.293179 CACAGACACAGATGCGGGA 59.707 57.895 0.00 0.00 0.00 5.14
354 355 1.742880 CCACAGACACAGATGCGGG 60.743 63.158 0.00 0.00 0.00 6.13
355 356 1.016130 GTCCACAGACACAGATGCGG 61.016 60.000 0.00 0.00 42.99 5.69
356 357 1.016130 GGTCCACAGACACAGATGCG 61.016 60.000 0.00 0.00 45.48 4.73
357 358 0.674895 GGGTCCACAGACACAGATGC 60.675 60.000 0.00 0.00 46.44 3.91
358 359 3.540211 GGGTCCACAGACACAGATG 57.460 57.895 0.00 0.00 46.44 2.90
363 364 2.593956 GGGAGGGGTCCACAGACAC 61.594 68.421 0.00 0.00 46.47 3.67
364 365 2.203938 GGGAGGGGTCCACAGACA 60.204 66.667 0.00 0.00 45.48 3.41
365 366 3.009714 GGGGAGGGGTCCACAGAC 61.010 72.222 0.00 0.00 42.73 3.51
366 367 4.348495 GGGGGAGGGGTCCACAGA 62.348 72.222 0.00 0.00 34.04 3.41
385 386 1.977009 GCGGACAAAAAGGAGGGGG 60.977 63.158 0.00 0.00 0.00 5.40
386 387 2.332654 CGCGGACAAAAAGGAGGGG 61.333 63.158 0.00 0.00 0.00 4.79
387 388 2.332654 CCGCGGACAAAAAGGAGGG 61.333 63.158 24.07 0.00 0.00 4.30
388 389 1.302192 TCCGCGGACAAAAAGGAGG 60.302 57.895 27.28 0.00 0.00 4.30
389 390 1.866925 GTCCGCGGACAAAAAGGAG 59.133 57.895 44.88 8.87 44.02 3.69
390 391 1.957186 CGTCCGCGGACAAAAAGGA 60.957 57.895 46.26 16.11 44.77 3.36
391 392 2.554272 CGTCCGCGGACAAAAAGG 59.446 61.111 46.26 30.57 44.77 3.11
415 416 0.608130 GCAACCCACAAATTCCCTCC 59.392 55.000 0.00 0.00 0.00 4.30
416 417 0.608130 GGCAACCCACAAATTCCCTC 59.392 55.000 0.00 0.00 0.00 4.30
420 421 3.399440 TCAATGGCAACCCACAAATTC 57.601 42.857 0.00 0.00 45.77 2.17
422 423 2.971330 TCTTCAATGGCAACCCACAAAT 59.029 40.909 0.00 0.00 45.77 2.32
428 429 1.478105 GGACATCTTCAATGGCAACCC 59.522 52.381 0.00 0.00 0.00 4.11
436 437 5.184892 AGGCAAGTAAGGACATCTTCAAT 57.815 39.130 0.00 0.00 36.93 2.57
461 697 2.158827 ACCCTTGGCAAATTTGTTGGTC 60.159 45.455 19.03 2.38 0.00 4.02
499 735 8.544622 TGGTGACCAAGACACATAATTCTATAA 58.455 33.333 0.00 0.00 39.65 0.98
504 740 5.677091 GCATGGTGACCAAGACACATAATTC 60.677 44.000 9.06 0.00 36.95 2.17
514 750 1.951209 TCCTAGCATGGTGACCAAGA 58.049 50.000 9.06 0.00 36.95 3.02
535 771 5.852807 ACTGATCTACTATCTACTCCCTCCA 59.147 44.000 0.00 0.00 0.00 3.86
551 787 5.066593 AGATGCATGTAGTCGACTGATCTA 58.933 41.667 28.12 4.38 0.00 1.98
552 788 3.888323 AGATGCATGTAGTCGACTGATCT 59.112 43.478 28.12 18.39 0.00 2.75
553 789 4.235939 AGATGCATGTAGTCGACTGATC 57.764 45.455 28.12 17.26 0.00 2.92
554 790 4.319839 CGTAGATGCATGTAGTCGACTGAT 60.320 45.833 28.12 16.20 0.00 2.90
555 791 3.002348 CGTAGATGCATGTAGTCGACTGA 59.998 47.826 28.12 14.57 0.00 3.41
556 792 3.242772 ACGTAGATGCATGTAGTCGACTG 60.243 47.826 28.12 13.10 0.00 3.51
557 793 2.943690 ACGTAGATGCATGTAGTCGACT 59.056 45.455 23.66 23.66 0.00 4.18
559 795 4.153655 GGATACGTAGATGCATGTAGTCGA 59.846 45.833 17.24 5.24 0.00 4.20
560 796 4.154375 AGGATACGTAGATGCATGTAGTCG 59.846 45.833 2.46 8.16 46.39 4.18
561 797 5.630661 AGGATACGTAGATGCATGTAGTC 57.369 43.478 2.46 0.64 46.39 2.59
562 798 6.406692 AAAGGATACGTAGATGCATGTAGT 57.593 37.500 2.46 7.50 46.39 2.73
565 803 5.069914 TGGTAAAGGATACGTAGATGCATGT 59.930 40.000 2.46 1.37 46.39 3.21
608 846 2.938956 AATGTAGCTAGGTGCATCCC 57.061 50.000 23.08 0.00 45.94 3.85
733 977 5.758296 GCCAATGGAGTAGTTGATTTCGATA 59.242 40.000 2.05 0.00 0.00 2.92
756 1000 6.938472 AAGTGGATGCAACCAATTTTGTTGC 61.938 40.000 21.29 25.27 44.09 4.17
874 1120 8.750515 TTGCTCATAGATGAATTAATTGGACA 57.249 30.769 5.17 0.00 36.18 4.02
886 1132 4.100653 CAGACTCCCTTTGCTCATAGATGA 59.899 45.833 0.00 0.00 35.16 2.92
929 1175 8.612145 TCTGTACCACTCAGCCTCTATATATAA 58.388 37.037 0.00 0.00 33.48 0.98
951 1197 4.085357 TGTGTTTATGCAGGACTTCTGT 57.915 40.909 0.00 0.00 45.08 3.41
988 1234 3.747193 CGTTGGTCATGTTCTATGTTGC 58.253 45.455 0.00 0.00 0.00 4.17
1245 1491 0.744281 TCACAGTCAGTTCGTGAGCA 59.256 50.000 0.00 0.00 35.13 4.26
1341 1594 7.860373 GTGTGTGTGTGTACAAATATGACAATT 59.140 33.333 0.00 0.00 38.82 2.32
1434 1723 4.806247 CACGGTAACCTGCAAAATTTTCAA 59.194 37.500 0.00 0.00 0.00 2.69
1608 1908 9.509956 ACAGTGTGCCATTAATAGTTTTAACTA 57.490 29.630 0.00 4.92 44.84 2.24
1609 1909 8.296713 CACAGTGTGCCATTAATAGTTTTAACT 58.703 33.333 10.97 0.29 42.91 2.24
1610 1910 8.447787 CACAGTGTGCCATTAATAGTTTTAAC 57.552 34.615 10.97 0.00 0.00 2.01
1627 1927 4.318021 GCACCAGCGCACAGTGTG 62.318 66.667 19.27 19.27 36.51 3.82
1637 1937 4.616181 AAACTATTAATGACGCACCAGC 57.384 40.909 0.00 0.00 37.42 4.85
1638 1938 5.123186 TCCAAAACTATTAATGACGCACCAG 59.877 40.000 0.00 0.00 0.00 4.00
1639 1939 5.004448 TCCAAAACTATTAATGACGCACCA 58.996 37.500 0.00 0.00 0.00 4.17
1640 1940 5.554822 TCCAAAACTATTAATGACGCACC 57.445 39.130 0.00 0.00 0.00 5.01
1641 1941 7.861176 TTTTCCAAAACTATTAATGACGCAC 57.139 32.000 0.00 0.00 0.00 5.34
1670 1970 6.431852 ACGGTGTACCATTACTAGCAATTTTT 59.568 34.615 1.50 0.00 35.14 1.94
1671 1971 5.941647 ACGGTGTACCATTACTAGCAATTTT 59.058 36.000 1.50 0.00 35.14 1.82
1672 1972 5.353123 CACGGTGTACCATTACTAGCAATTT 59.647 40.000 0.00 0.00 35.14 1.82
1673 1973 4.873827 CACGGTGTACCATTACTAGCAATT 59.126 41.667 0.00 0.00 35.14 2.32
1674 1974 4.081309 ACACGGTGTACCATTACTAGCAAT 60.081 41.667 12.96 0.00 35.14 3.56
1675 1975 3.258872 ACACGGTGTACCATTACTAGCAA 59.741 43.478 12.96 0.00 35.14 3.91
1676 1976 2.827322 ACACGGTGTACCATTACTAGCA 59.173 45.455 12.96 0.00 35.14 3.49
1677 1977 3.184541 CACACGGTGTACCATTACTAGC 58.815 50.000 14.30 0.00 35.14 3.42
1678 1978 4.171005 CACACACGGTGTACCATTACTAG 58.829 47.826 14.30 0.00 45.65 2.57
1679 1979 4.177165 CACACACGGTGTACCATTACTA 57.823 45.455 14.30 0.00 45.65 1.82
1680 1980 3.034721 CACACACGGTGTACCATTACT 57.965 47.619 14.30 0.00 45.65 2.24
1702 2002 1.873591 CCTCATTACTAATGGCGCACC 59.126 52.381 10.83 0.00 39.38 5.01
1703 2003 2.544267 GTCCTCATTACTAATGGCGCAC 59.456 50.000 10.83 0.00 39.38 5.34
1704 2004 2.169561 TGTCCTCATTACTAATGGCGCA 59.830 45.455 10.83 0.00 39.38 6.09
1705 2005 2.544267 GTGTCCTCATTACTAATGGCGC 59.456 50.000 0.00 0.00 39.38 6.53
1706 2006 4.060038 AGTGTCCTCATTACTAATGGCG 57.940 45.455 8.62 1.84 39.38 5.69
1710 2010 6.223852 CGCCATTAGTGTCCTCATTACTAAT 58.776 40.000 0.00 0.00 44.25 1.73
1711 2011 5.597806 CGCCATTAGTGTCCTCATTACTAA 58.402 41.667 0.00 0.00 40.12 2.24
1712 2012 4.500887 GCGCCATTAGTGTCCTCATTACTA 60.501 45.833 0.00 0.00 0.00 1.82
1713 2013 3.741388 GCGCCATTAGTGTCCTCATTACT 60.741 47.826 0.00 0.00 0.00 2.24
1714 2014 2.544267 GCGCCATTAGTGTCCTCATTAC 59.456 50.000 0.00 0.00 0.00 1.89
1715 2015 2.169561 TGCGCCATTAGTGTCCTCATTA 59.830 45.455 4.18 0.00 0.00 1.90
1716 2016 1.065491 TGCGCCATTAGTGTCCTCATT 60.065 47.619 4.18 0.00 0.00 2.57
1717 2017 0.541392 TGCGCCATTAGTGTCCTCAT 59.459 50.000 4.18 0.00 0.00 2.90
1718 2018 0.391130 GTGCGCCATTAGTGTCCTCA 60.391 55.000 4.18 0.00 0.00 3.86
1719 2019 1.090052 GGTGCGCCATTAGTGTCCTC 61.090 60.000 12.58 0.00 34.09 3.71
1720 2020 1.078426 GGTGCGCCATTAGTGTCCT 60.078 57.895 12.58 0.00 34.09 3.85
1721 2021 1.078426 AGGTGCGCCATTAGTGTCC 60.078 57.895 20.59 0.00 37.19 4.02
1722 2022 0.673644 ACAGGTGCGCCATTAGTGTC 60.674 55.000 20.59 0.00 37.19 3.67
1723 2023 0.611200 TACAGGTGCGCCATTAGTGT 59.389 50.000 20.59 15.76 37.19 3.55
1724 2024 1.006832 GTACAGGTGCGCCATTAGTG 58.993 55.000 20.59 10.11 37.19 2.74
1725 2025 0.107848 GGTACAGGTGCGCCATTAGT 60.108 55.000 20.59 13.38 37.19 2.24
1726 2026 0.178068 AGGTACAGGTGCGCCATTAG 59.822 55.000 20.59 7.78 37.19 1.73
1727 2027 0.107897 CAGGTACAGGTGCGCCATTA 60.108 55.000 20.59 5.89 37.19 1.90
1728 2028 1.377202 CAGGTACAGGTGCGCCATT 60.377 57.895 20.59 7.01 37.19 3.16
1729 2029 2.268920 CAGGTACAGGTGCGCCAT 59.731 61.111 20.59 8.81 37.19 4.40
1730 2030 4.015406 CCAGGTACAGGTGCGCCA 62.015 66.667 20.59 0.00 37.19 5.69
1737 2037 4.015406 TGGCGCACCAGGTACAGG 62.015 66.667 10.83 0.00 42.67 4.00
1763 2063 7.721409 ATACTACTAGGAAAAGGGCTATAGC 57.279 40.000 16.78 16.78 41.14 2.97
1766 2066 9.311676 GAGTTATACTACTAGGAAAAGGGCTAT 57.688 37.037 0.00 0.00 0.00 2.97
1767 2067 8.284435 TGAGTTATACTACTAGGAAAAGGGCTA 58.716 37.037 0.00 0.00 0.00 3.93
1768 2068 7.130775 TGAGTTATACTACTAGGAAAAGGGCT 58.869 38.462 0.00 0.00 0.00 5.19
1769 2069 7.357429 TGAGTTATACTACTAGGAAAAGGGC 57.643 40.000 0.00 0.00 0.00 5.19
1770 2070 7.873505 GCATGAGTTATACTACTAGGAAAAGGG 59.126 40.741 0.00 0.00 0.00 3.95
1771 2071 8.421784 TGCATGAGTTATACTACTAGGAAAAGG 58.578 37.037 0.00 0.00 0.00 3.11
1772 2072 9.988815 ATGCATGAGTTATACTACTAGGAAAAG 57.011 33.333 0.00 0.00 0.00 2.27
1773 2073 9.764363 CATGCATGAGTTATACTACTAGGAAAA 57.236 33.333 22.59 0.00 0.00 2.29
1774 2074 8.367911 CCATGCATGAGTTATACTACTAGGAAA 58.632 37.037 28.31 0.00 0.00 3.13
1775 2075 7.728532 TCCATGCATGAGTTATACTACTAGGAA 59.271 37.037 28.31 0.00 0.00 3.36
1776 2076 7.238710 TCCATGCATGAGTTATACTACTAGGA 58.761 38.462 28.31 7.68 0.00 2.94
1777 2077 7.468141 TCCATGCATGAGTTATACTACTAGG 57.532 40.000 28.31 5.24 0.00 3.02
1778 2078 8.526978 ACATCCATGCATGAGTTATACTACTAG 58.473 37.037 28.31 5.90 0.00 2.57
1779 2079 8.422577 ACATCCATGCATGAGTTATACTACTA 57.577 34.615 28.31 0.00 0.00 1.82
1780 2080 7.308450 ACATCCATGCATGAGTTATACTACT 57.692 36.000 28.31 0.00 0.00 2.57
1781 2081 9.658799 AATACATCCATGCATGAGTTATACTAC 57.341 33.333 28.31 0.00 0.00 2.73
1871 2179 3.927854 TGTTCCCGACGATCAAACATAA 58.072 40.909 0.00 0.00 0.00 1.90
1994 2302 1.479323 TGCTCCGTTGTCACCTATACC 59.521 52.381 0.00 0.00 0.00 2.73
2128 2439 3.772572 TCCAACCTCGATATCCAACAAGA 59.227 43.478 0.00 0.00 0.00 3.02
2140 2451 1.336517 CGCAAACTACTCCAACCTCGA 60.337 52.381 0.00 0.00 0.00 4.04
2165 2476 0.321564 TGGCGGGAGTCAAACTCATG 60.322 55.000 9.16 2.22 46.79 3.07
2410 2731 0.179012 TCCCACTTTGTTTCGTCCCC 60.179 55.000 0.00 0.00 0.00 4.81
2425 2746 3.256704 AGATACTCTTGGTTTGGTCCCA 58.743 45.455 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.