Multiple sequence alignment - TraesCS5B01G570600

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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 TraesCS5B01G570600 chr5B 100.000 3374 0 0 1 3374 712205743 712209116 0.000000e+00 6231.0
1 TraesCS5B01G570600 chr5B 90.188 958 76 11 1787 2738 711930996 711931941 0.000000e+00 1232.0
2 TraesCS5B01G570600 chr5B 88.518 958 106 2 1788 2741 711962439 711963396 0.000000e+00 1157.0
3 TraesCS5B01G570600 chr5B 96.577 555 17 2 2746 3300 610061741 610062293 0.000000e+00 918.0
4 TraesCS5B01G570600 chr5B 84.976 832 95 18 977 1787 711414176 711413354 0.000000e+00 817.0
5 TraesCS5B01G570600 chr5B 97.281 331 9 0 987 1317 711354091 711353761 2.270000e-156 562.0
6 TraesCS5B01G570600 chr5B 91.860 344 26 2 965 1308 711930368 711930709 2.350000e-131 479.0
7 TraesCS5B01G570600 chr5B 83.621 348 30 9 1461 1787 711735615 711735956 5.470000e-78 302.0
8 TraesCS5B01G570600 chr5B 88.073 109 10 2 1435 1543 711353649 711353544 3.530000e-25 126.0
9 TraesCS5B01G570600 chr5B 81.818 88 4 4 1341 1428 711353761 711353686 2.810000e-06 63.9
10 TraesCS5B01G570600 chr5D 92.506 894 67 0 1835 2728 552860505 552859612 0.000000e+00 1280.0
11 TraesCS5B01G570600 chr5D 90.842 950 79 5 1787 2735 561896547 561897489 0.000000e+00 1266.0
12 TraesCS5B01G570600 chr5D 91.199 909 76 3 1835 2741 561923924 561924830 0.000000e+00 1232.0
13 TraesCS5B01G570600 chr5D 82.783 848 87 30 977 1787 561645345 561644520 0.000000e+00 702.0
14 TraesCS5B01G570600 chr5D 89.013 537 40 4 790 1308 561895707 561896242 0.000000e+00 647.0
15 TraesCS5B01G570600 chr5D 88.889 360 35 3 953 1308 556541129 556540771 4.000000e-119 438.0
16 TraesCS5B01G570600 chr5D 82.653 392 38 4 1030 1421 551878547 551878908 1.510000e-83 320.0
17 TraesCS5B01G570600 chr5D 81.137 387 59 8 999 1381 552861278 552860902 7.080000e-77 298.0
18 TraesCS5B01G570600 chr5D 84.861 251 34 4 426 674 561895290 561895538 2.010000e-62 250.0
19 TraesCS5B01G570600 chr5D 88.462 104 11 1 690 792 561895578 561895681 1.270000e-24 124.0
20 TraesCS5B01G570600 chr5D 94.444 36 1 1 644 679 525738258 525738224 2.000000e-03 54.7
21 TraesCS5B01G570600 chr7B 90.578 934 82 2 1789 2722 1305243 1306170 0.000000e+00 1232.0
22 TraesCS5B01G570600 chr7B 91.348 890 75 2 1831 2719 834441 833553 0.000000e+00 1216.0
23 TraesCS5B01G570600 chr7B 89.811 952 84 10 1783 2730 1036856 1035914 0.000000e+00 1208.0
24 TraesCS5B01G570600 chr7B 91.196 886 76 2 1835 2719 890357 889473 0.000000e+00 1203.0
25 TraesCS5B01G570600 chr7B 83.983 949 83 26 426 1308 891649 890704 0.000000e+00 846.0
26 TraesCS5B01G570600 chr7B 98.069 259 5 0 95 353 478905076 478904818 5.130000e-123 451.0
27 TraesCS5B01G570600 chr7B 97.338 263 6 1 95 357 478908553 478908292 2.390000e-121 446.0
28 TraesCS5B01G570600 chr7B 86.217 341 36 3 987 1317 1304695 1305034 3.200000e-95 359.0
29 TraesCS5B01G570600 chr7B 92.683 123 9 0 1435 1557 1348345 1348467 9.620000e-41 178.0
30 TraesCS5B01G570600 chr7B 88.172 93 8 3 3 95 891958 891869 1.280000e-19 108.0
31 TraesCS5B01G570600 chr7B 83.478 115 14 5 481 592 120747431 120747543 5.960000e-18 102.0
32 TraesCS5B01G570600 chr7B 83.871 93 12 3 501 592 42867962 42868052 6.000000e-13 86.1
33 TraesCS5B01G570600 chr7B 95.918 49 2 0 1379 1427 1348253 1348301 2.790000e-11 80.5
34 TraesCS5B01G570600 chr3B 97.143 560 15 1 2746 3305 564755268 564754710 0.000000e+00 944.0
35 TraesCS5B01G570600 chr3B 96.223 556 20 1 2745 3300 684079265 684078711 0.000000e+00 909.0
36 TraesCS5B01G570600 chr3B 94.836 581 26 4 2745 3324 788163439 788162862 0.000000e+00 904.0
37 TraesCS5B01G570600 chr4A 96.577 555 18 1 2746 3300 686728931 686728378 0.000000e+00 918.0
38 TraesCS5B01G570600 chr6B 96.071 560 21 1 2746 3305 31328233 31327675 0.000000e+00 911.0
39 TraesCS5B01G570600 chr4B 95.017 582 25 4 2746 3325 664084879 664084300 0.000000e+00 911.0
40 TraesCS5B01G570600 chr4B 94.492 581 29 3 2745 3324 600364823 600364245 0.000000e+00 893.0
41 TraesCS5B01G570600 chr4B 83.158 95 10 6 501 592 396447876 396447785 7.760000e-12 82.4
42 TraesCS5B01G570600 chr2B 96.383 553 19 1 2748 3300 746811628 746812179 0.000000e+00 909.0
43 TraesCS5B01G570600 chr7D 97.297 259 7 0 95 353 240909928 240910186 1.110000e-119 440.0
44 TraesCS5B01G570600 chr7D 96.947 262 5 2 96 357 240906445 240906703 1.440000e-118 436.0
45 TraesCS5B01G570600 chr2A 96.538 260 8 1 95 353 28562451 28562192 2.410000e-116 429.0
46 TraesCS5B01G570600 chr2A 95.817 263 9 2 96 357 28656409 28656148 1.120000e-114 424.0
47 TraesCS5B01G570600 chr2A 95.076 264 11 2 95 357 28581275 28581013 6.740000e-112 414.0
48 TraesCS5B01G570600 chr2A 93.561 264 14 3 95 357 28566034 28565773 1.140000e-104 390.0
49 TraesCS5B01G570600 chr6D 94.231 260 11 3 95 353 26701637 26701381 8.770000e-106 394.0
50 TraesCS5B01G570600 chr1A 88.462 78 7 2 511 587 217607713 217607637 3.580000e-15 93.5
51 TraesCS5B01G570600 chr1A 100.000 29 0 0 642 670 393966578 393966550 2.000000e-03 54.7
52 TraesCS5B01G570600 chr4D 87.013 77 10 0 515 591 309631327 309631403 1.670000e-13 87.9
53 TraesCS5B01G570600 chr6A 83.871 93 11 4 509 601 568499443 568499531 6.000000e-13 86.1
54 TraesCS5B01G570600 chr2D 81.651 109 13 7 501 605 596007809 596007914 2.160000e-12 84.2


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 TraesCS5B01G570600 chr5B 712205743 712209116 3373 False 6231.000000 6231 100.000000 1 3374 1 chr5B.!!$F4 3373
1 TraesCS5B01G570600 chr5B 711962439 711963396 957 False 1157.000000 1157 88.518000 1788 2741 1 chr5B.!!$F3 953
2 TraesCS5B01G570600 chr5B 610061741 610062293 552 False 918.000000 918 96.577000 2746 3300 1 chr5B.!!$F1 554
3 TraesCS5B01G570600 chr5B 711930368 711931941 1573 False 855.500000 1232 91.024000 965 2738 2 chr5B.!!$F5 1773
4 TraesCS5B01G570600 chr5B 711413354 711414176 822 True 817.000000 817 84.976000 977 1787 1 chr5B.!!$R1 810
5 TraesCS5B01G570600 chr5B 711353544 711354091 547 True 250.633333 562 89.057333 987 1543 3 chr5B.!!$R2 556
6 TraesCS5B01G570600 chr5D 561923924 561924830 906 False 1232.000000 1232 91.199000 1835 2741 1 chr5D.!!$F2 906
7 TraesCS5B01G570600 chr5D 552859612 552861278 1666 True 789.000000 1280 86.821500 999 2728 2 chr5D.!!$R4 1729
8 TraesCS5B01G570600 chr5D 561644520 561645345 825 True 702.000000 702 82.783000 977 1787 1 chr5D.!!$R3 810
9 TraesCS5B01G570600 chr5D 561895290 561897489 2199 False 571.750000 1266 88.294500 426 2735 4 chr5D.!!$F3 2309
10 TraesCS5B01G570600 chr7B 833553 834441 888 True 1216.000000 1216 91.348000 1831 2719 1 chr7B.!!$R1 888
11 TraesCS5B01G570600 chr7B 1035914 1036856 942 True 1208.000000 1208 89.811000 1783 2730 1 chr7B.!!$R2 947
12 TraesCS5B01G570600 chr7B 1304695 1306170 1475 False 795.500000 1232 88.397500 987 2722 2 chr7B.!!$F3 1735
13 TraesCS5B01G570600 chr7B 889473 891958 2485 True 719.000000 1203 87.783667 3 2719 3 chr7B.!!$R3 2716
14 TraesCS5B01G570600 chr7B 478904818 478908553 3735 True 448.500000 451 97.703500 95 357 2 chr7B.!!$R4 262
15 TraesCS5B01G570600 chr3B 564754710 564755268 558 True 944.000000 944 97.143000 2746 3305 1 chr3B.!!$R1 559
16 TraesCS5B01G570600 chr3B 684078711 684079265 554 True 909.000000 909 96.223000 2745 3300 1 chr3B.!!$R2 555
17 TraesCS5B01G570600 chr3B 788162862 788163439 577 True 904.000000 904 94.836000 2745 3324 1 chr3B.!!$R3 579
18 TraesCS5B01G570600 chr4A 686728378 686728931 553 True 918.000000 918 96.577000 2746 3300 1 chr4A.!!$R1 554
19 TraesCS5B01G570600 chr6B 31327675 31328233 558 True 911.000000 911 96.071000 2746 3305 1 chr6B.!!$R1 559
20 TraesCS5B01G570600 chr4B 664084300 664084879 579 True 911.000000 911 95.017000 2746 3325 1 chr4B.!!$R3 579
21 TraesCS5B01G570600 chr4B 600364245 600364823 578 True 893.000000 893 94.492000 2745 3324 1 chr4B.!!$R2 579
22 TraesCS5B01G570600 chr2B 746811628 746812179 551 False 909.000000 909 96.383000 2748 3300 1 chr2B.!!$F1 552
23 TraesCS5B01G570600 chr7D 240906445 240910186 3741 False 438.000000 440 97.122000 95 357 2 chr7D.!!$F1 262
24 TraesCS5B01G570600 chr2A 28562192 28566034 3842 True 409.500000 429 95.049500 95 357 2 chr2A.!!$R3 262

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
642 797 0.039180 TCCGGAGAGCCTGTGTTCTA 59.961 55.0 0.00 0.00 31.48 2.10 F
849 1064 0.303493 CAATTATTGCCCCGTCGACG 59.697 55.0 30.33 30.33 39.44 5.12 F
1549 2184 0.321830 TGATGCTGCTGCTGCTGTTA 60.322 50.0 27.67 11.62 39.81 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2011 3092 0.540923 CTGCTTCCTCCTTCTCCAGG 59.459 60.000 0.00 0.00 45.64 4.45 R
2319 3635 1.006102 AGGCTTGTCGTCTTCACCG 60.006 57.895 0.00 0.00 0.00 4.94 R
2400 3716 1.733402 CTGTTTTGGCTGCCAACGGA 61.733 55.000 32.36 16.62 43.82 4.69 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
37 38 5.402270 GTGTTGCATCTTCCATGTGTTTTAC 59.598 40.000 0.00 0.00 0.00 2.01
39 40 4.148079 TGCATCTTCCATGTGTTTTACCA 58.852 39.130 0.00 0.00 0.00 3.25
42 43 5.048083 GCATCTTCCATGTGTTTTACCAGAA 60.048 40.000 0.00 0.00 0.00 3.02
45 46 5.763204 TCTTCCATGTGTTTTACCAGAAGTC 59.237 40.000 0.00 0.00 33.68 3.01
46 47 5.304686 TCCATGTGTTTTACCAGAAGTCT 57.695 39.130 0.00 0.00 0.00 3.24
47 48 5.063204 TCCATGTGTTTTACCAGAAGTCTG 58.937 41.667 1.05 1.05 43.40 3.51
69 70 7.444487 GTCTGTGTTTATCTACAAAACCTTCCT 59.556 37.037 0.00 0.00 36.26 3.36
70 71 7.996644 TCTGTGTTTATCTACAAAACCTTCCTT 59.003 33.333 0.00 0.00 36.26 3.36
72 73 8.973182 TGTGTTTATCTACAAAACCTTCCTTTT 58.027 29.630 0.00 0.00 36.26 2.27
176 178 1.156736 CTCCAACTACAAAGGGCACG 58.843 55.000 0.00 0.00 0.00 5.34
292 294 1.521616 CTCTGCTTCCTCCTCCTGC 59.478 63.158 0.00 0.00 0.00 4.85
377 379 4.630894 TTGGATGATTCCGAAATTTCCG 57.369 40.909 12.54 6.41 45.89 4.30
385 387 9.329913 GATGATTCCGAAATTTCCGTATAAATG 57.670 33.333 12.54 0.00 0.00 2.32
388 390 6.055231 TCCGAAATTTCCGTATAAATGCAG 57.945 37.500 12.54 0.00 0.00 4.41
392 394 1.975660 TTCCGTATAAATGCAGCCCC 58.024 50.000 0.00 0.00 0.00 5.80
396 398 2.146342 CGTATAAATGCAGCCCCTGAG 58.854 52.381 0.00 0.00 32.44 3.35
429 431 8.250143 AGATATGTTCTCACACATATACACCA 57.750 34.615 6.36 0.00 46.16 4.17
432 434 4.530553 TGTTCTCACACATATACACCACCT 59.469 41.667 0.00 0.00 0.00 4.00
433 435 5.717654 TGTTCTCACACATATACACCACCTA 59.282 40.000 0.00 0.00 0.00 3.08
513 667 6.312529 TCTATATCATGTACTTCCCCGTCTT 58.687 40.000 0.00 0.00 0.00 3.01
525 679 5.936372 ACTTCCCCGTCTTAAAATAAGTGTC 59.064 40.000 0.00 0.00 0.00 3.67
576 730 9.872721 AAAGCTAGTATAAAGTTAAGACACCTC 57.127 33.333 0.00 0.00 0.00 3.85
626 780 8.662369 TTTCGTTATGTTTTCAATTATGTCCG 57.338 30.769 0.00 0.00 0.00 4.79
632 786 4.394920 TGTTTTCAATTATGTCCGGAGAGC 59.605 41.667 3.06 0.00 0.00 4.09
633 787 2.910688 TCAATTATGTCCGGAGAGCC 57.089 50.000 3.06 0.00 0.00 4.70
642 797 0.039180 TCCGGAGAGCCTGTGTTCTA 59.961 55.000 0.00 0.00 31.48 2.10
690 871 3.254892 GAAACAGGAGACCGACATTCTC 58.745 50.000 0.00 0.00 39.11 2.87
692 873 2.096248 ACAGGAGACCGACATTCTCTC 58.904 52.381 0.00 0.00 39.67 3.20
693 874 2.291282 ACAGGAGACCGACATTCTCTCT 60.291 50.000 0.00 0.00 39.67 3.10
695 876 3.948473 CAGGAGACCGACATTCTCTCTAA 59.052 47.826 0.00 0.00 39.67 2.10
696 877 4.399618 CAGGAGACCGACATTCTCTCTAAA 59.600 45.833 0.00 0.00 39.67 1.85
720 901 2.916934 ACCTTTCAGCAGGGGTGTATTA 59.083 45.455 0.00 0.00 38.42 0.98
721 902 3.527665 ACCTTTCAGCAGGGGTGTATTAT 59.472 43.478 0.00 0.00 38.42 1.28
728 909 6.964464 TCAGCAGGGGTGTATTATTAAAAGA 58.036 36.000 0.00 0.00 32.43 2.52
781 962 4.509616 TGTATCCATAGGTTGGTCAAACG 58.490 43.478 0.00 0.00 46.52 3.60
783 964 3.773418 TCCATAGGTTGGTCAAACGAA 57.227 42.857 0.00 0.00 46.52 3.85
794 1004 3.634448 TGGTCAAACGAATCAAACCACAT 59.366 39.130 0.00 0.00 32.08 3.21
805 1015 1.662629 CAAACCACATCGCTAGAGCTG 59.337 52.381 0.00 0.00 39.32 4.24
823 1033 4.379243 CAGCTTCCACCGGCGTCT 62.379 66.667 6.01 0.00 0.00 4.18
826 1041 2.098831 GCTTCCACCGGCGTCTAAC 61.099 63.158 6.01 0.00 0.00 2.34
844 1059 1.075600 CCCCCAATTATTGCCCCGT 60.076 57.895 0.00 0.00 0.00 5.28
849 1064 0.303493 CAATTATTGCCCCGTCGACG 59.697 55.000 30.33 30.33 39.44 5.12
885 1104 2.632544 CGGAGTGCAGACGGGTGTA 61.633 63.158 0.00 0.00 0.00 2.90
887 1106 1.663739 GAGTGCAGACGGGTGTACA 59.336 57.895 9.53 0.00 35.65 2.90
896 1115 3.047877 GGGTGTACAGTGGCGTGC 61.048 66.667 0.00 0.00 0.00 5.34
897 1116 2.280524 GGTGTACAGTGGCGTGCA 60.281 61.111 0.00 0.00 0.00 4.57
947 1166 4.293648 CACACGACACCGCTCCCA 62.294 66.667 0.00 0.00 39.95 4.37
948 1167 3.311110 ACACGACACCGCTCCCAT 61.311 61.111 0.00 0.00 39.95 4.00
949 1168 2.815211 CACGACACCGCTCCCATG 60.815 66.667 0.00 0.00 39.95 3.66
951 1170 4.758251 CGACACCGCTCCCATGCA 62.758 66.667 0.00 0.00 0.00 3.96
952 1171 2.821366 GACACCGCTCCCATGCAG 60.821 66.667 0.00 0.00 0.00 4.41
958 1177 2.747460 GCTCCCATGCAGCGTTGA 60.747 61.111 2.38 0.00 0.00 3.18
1333 1896 4.918201 GGCCGGATCTGAAGGGCG 62.918 72.222 5.05 0.00 46.50 6.13
1353 1931 0.674581 TTGTCCGCCATCAAGCTCTG 60.675 55.000 0.00 0.00 0.00 3.35
1374 1952 2.202756 GCCGGTAGTGCTCTTCGG 60.203 66.667 19.31 19.31 39.98 4.30
1383 1961 2.743928 GCTCTTCGGCACACCCTG 60.744 66.667 0.00 0.00 0.00 4.45
1433 2032 1.555075 GCCTACACCCAAGAGTGATGA 59.445 52.381 0.00 0.00 40.34 2.92
1437 2036 1.340405 ACACCCAAGAGTGATGATGCC 60.340 52.381 0.00 0.00 40.34 4.40
1532 2167 2.618816 GCAAGAGGAATGGTGGTGATGA 60.619 50.000 0.00 0.00 0.00 2.92
1533 2168 3.894759 CAAGAGGAATGGTGGTGATGAT 58.105 45.455 0.00 0.00 0.00 2.45
1534 2169 3.572632 AGAGGAATGGTGGTGATGATG 57.427 47.619 0.00 0.00 0.00 3.07
1549 2184 0.321830 TGATGCTGCTGCTGCTGTTA 60.322 50.000 27.67 11.62 39.81 2.41
1623 2371 1.202615 TCTGCTAGTGCTGATGATGGC 60.203 52.381 0.00 0.00 41.21 4.40
1681 2701 4.627467 CCAGAGAAATCAAGTCCGTGTTAG 59.373 45.833 0.00 0.00 0.00 2.34
1724 2744 0.881118 TTGGTCTCCAATTTGCTCGC 59.119 50.000 0.00 0.00 38.75 5.03
1745 2771 1.470098 CACTATCCCAAGCAACAGCAC 59.530 52.381 0.00 0.00 0.00 4.40
1772 2804 4.873129 CGTCCCACATCGGCCTCG 62.873 72.222 0.00 0.00 37.82 4.63
1778 2810 2.680352 ACATCGGCCTCGGACTGT 60.680 61.111 0.00 0.00 36.95 3.55
1796 2861 3.891366 ACTGTTTCCATGACTTTTGAGGG 59.109 43.478 0.00 0.00 0.00 4.30
1799 2864 5.147032 TGTTTCCATGACTTTTGAGGGAAT 58.853 37.500 0.00 0.00 34.65 3.01
1809 2874 4.218417 ACTTTTGAGGGAATTGTCAATCGG 59.782 41.667 0.00 0.00 32.79 4.18
1815 2880 2.287915 GGGAATTGTCAATCGGATCACG 59.712 50.000 0.00 0.00 46.11 4.35
1899 2980 5.808366 AGACAACTTTCACCACTCATCTA 57.192 39.130 0.00 0.00 0.00 1.98
2080 3164 7.479352 TTAGATCATCTCCAGAGATCCATTC 57.521 40.000 7.20 3.22 45.78 2.67
2085 3169 1.411977 CTCCAGAGATCCATTCTGCGT 59.588 52.381 5.18 0.00 40.54 5.24
2086 3170 1.833630 TCCAGAGATCCATTCTGCGTT 59.166 47.619 5.18 0.00 40.54 4.84
2249 3565 4.785346 AGGTAGCAGACATGATGGAAAT 57.215 40.909 0.00 0.00 0.00 2.17
2288 3604 2.301870 TGCGAGGTTTGGAGTCTAATGT 59.698 45.455 0.00 0.00 0.00 2.71
2400 3716 3.295973 TGCAAACAAGCTAAAGGGTTCT 58.704 40.909 0.00 0.00 32.86 3.01
2496 3812 2.205022 AGCATCAGTGGCTAAAGCAA 57.795 45.000 4.07 0.00 44.36 3.91
2742 4061 3.217242 CGATTGGGGTGATCGATCC 57.783 57.895 22.31 13.23 46.93 3.36
2743 4062 0.681733 CGATTGGGGTGATCGATCCT 59.318 55.000 22.31 0.00 46.93 3.24
2852 4171 0.261991 ATGACTAGGCGGGAGGAGAA 59.738 55.000 0.00 0.00 0.00 2.87
3078 4397 6.839124 ATCACAAGCATTTGGTCTTCATTA 57.161 33.333 0.00 0.00 38.66 1.90
3312 5730 5.560966 AAAGAACGAACTCTGAAAAAGCA 57.439 34.783 0.00 0.00 0.00 3.91
3313 5731 4.802876 AGAACGAACTCTGAAAAAGCAG 57.197 40.909 0.00 0.00 37.24 4.24
3314 5732 4.442706 AGAACGAACTCTGAAAAAGCAGA 58.557 39.130 0.00 0.00 42.31 4.26
3315 5733 4.876107 AGAACGAACTCTGAAAAAGCAGAA 59.124 37.500 0.00 0.00 43.75 3.02
3317 5735 5.560966 ACGAACTCTGAAAAAGCAGAAAA 57.439 34.783 0.00 0.00 43.75 2.29
3318 5736 5.573146 ACGAACTCTGAAAAAGCAGAAAAG 58.427 37.500 0.00 0.00 43.75 2.27
3319 5737 5.354234 ACGAACTCTGAAAAAGCAGAAAAGA 59.646 36.000 0.00 0.00 43.75 2.52
3320 5738 6.128007 ACGAACTCTGAAAAAGCAGAAAAGAA 60.128 34.615 0.00 0.00 43.75 2.52
3321 5739 6.747280 CGAACTCTGAAAAAGCAGAAAAGAAA 59.253 34.615 0.00 0.00 43.75 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.072508 GGAAGATGCAACACAAGTAGATTTCA 60.073 38.462 0.00 0.00 0.00 2.69
39 40 8.211629 AGGTTTTGTAGATAAACACAGACTTCT 58.788 33.333 0.00 0.00 37.25 2.85
42 43 7.444487 GGAAGGTTTTGTAGATAAACACAGACT 59.556 37.037 0.00 0.00 37.25 3.24
45 46 7.745620 AGGAAGGTTTTGTAGATAAACACAG 57.254 36.000 0.00 0.00 37.25 3.66
46 47 8.528044 AAAGGAAGGTTTTGTAGATAAACACA 57.472 30.769 0.00 0.00 37.25 3.72
47 48 9.811995 AAAAAGGAAGGTTTTGTAGATAAACAC 57.188 29.630 0.00 0.00 37.25 3.32
84 85 2.749621 GGTCGCTGACAAAATCCTTCAT 59.250 45.455 10.14 0.00 33.68 2.57
85 86 2.151202 GGTCGCTGACAAAATCCTTCA 58.849 47.619 10.14 0.00 33.68 3.02
86 87 2.151202 TGGTCGCTGACAAAATCCTTC 58.849 47.619 10.14 0.00 33.68 3.46
88 89 2.496899 ATGGTCGCTGACAAAATCCT 57.503 45.000 10.14 0.00 33.68 3.24
89 90 3.270877 AGTATGGTCGCTGACAAAATCC 58.729 45.455 10.14 0.00 33.68 3.01
90 91 5.050091 CCATAGTATGGTCGCTGACAAAATC 60.050 44.000 19.60 0.00 45.54 2.17
91 92 4.816385 CCATAGTATGGTCGCTGACAAAAT 59.184 41.667 19.60 4.40 45.54 1.82
92 93 4.188462 CCATAGTATGGTCGCTGACAAAA 58.812 43.478 19.60 0.00 45.54 2.44
93 94 3.792401 CCATAGTATGGTCGCTGACAAA 58.208 45.455 19.60 0.06 45.54 2.83
377 379 3.492102 TCTCAGGGGCTGCATTTATAC 57.508 47.619 0.50 0.00 0.00 1.47
385 387 0.322816 TCAACATTCTCAGGGGCTGC 60.323 55.000 0.00 0.00 0.00 5.25
388 390 2.725221 ATCTCAACATTCTCAGGGGC 57.275 50.000 0.00 0.00 0.00 5.80
415 417 6.411376 TCCTTTTAGGTGGTGTATATGTGTG 58.589 40.000 0.00 0.00 36.53 3.82
422 424 7.504926 TTGTATCTCCTTTTAGGTGGTGTAT 57.495 36.000 0.00 0.00 36.53 2.29
423 425 6.938698 TTGTATCTCCTTTTAGGTGGTGTA 57.061 37.500 0.00 0.00 36.53 2.90
424 426 5.836024 TTGTATCTCCTTTTAGGTGGTGT 57.164 39.130 0.00 0.00 36.53 4.16
493 646 6.795144 TTTAAGACGGGGAAGTACATGATA 57.205 37.500 0.00 0.00 0.00 2.15
504 657 5.246656 TGAGACACTTATTTTAAGACGGGGA 59.753 40.000 1.47 0.00 0.00 4.81
505 658 5.484715 TGAGACACTTATTTTAAGACGGGG 58.515 41.667 1.47 0.00 0.00 5.73
560 714 7.229907 GTCCCAAAATGAGGTGTCTTAACTTTA 59.770 37.037 0.00 0.00 0.00 1.85
562 716 5.535030 GTCCCAAAATGAGGTGTCTTAACTT 59.465 40.000 0.00 0.00 0.00 2.66
567 721 2.504367 CGTCCCAAAATGAGGTGTCTT 58.496 47.619 0.00 0.00 0.00 3.01
574 728 2.717639 ATCCTCCGTCCCAAAATGAG 57.282 50.000 0.00 0.00 0.00 2.90
576 730 3.820557 ACATATCCTCCGTCCCAAAATG 58.179 45.455 0.00 0.00 0.00 2.32
583 737 5.295152 ACGAAAAATACATATCCTCCGTCC 58.705 41.667 0.00 0.00 0.00 4.79
614 768 2.103094 CAGGCTCTCCGGACATAATTGA 59.897 50.000 0.00 0.00 37.47 2.57
615 769 2.158900 ACAGGCTCTCCGGACATAATTG 60.159 50.000 0.00 0.00 37.47 2.32
616 770 2.119495 ACAGGCTCTCCGGACATAATT 58.881 47.619 0.00 0.00 37.47 1.40
620 774 1.194781 AACACAGGCTCTCCGGACAT 61.195 55.000 0.00 0.00 37.47 3.06
622 776 1.079750 GAACACAGGCTCTCCGGAC 60.080 63.158 0.00 0.00 37.47 4.79
625 779 2.952978 ACTATAGAACACAGGCTCTCCG 59.047 50.000 6.78 0.00 37.47 4.63
626 780 3.702045 ACACTATAGAACACAGGCTCTCC 59.298 47.826 6.78 0.00 0.00 3.71
659 814 8.647796 TGTCGGTCTCCTGTTTCATAATATAAT 58.352 33.333 0.00 0.00 0.00 1.28
674 829 2.818751 AGAGAGAATGTCGGTCTCCT 57.181 50.000 0.00 0.00 42.17 3.69
695 876 1.762370 CACCCCTGCTGAAAGGTTTTT 59.238 47.619 0.00 0.00 35.34 1.94
696 877 1.342975 ACACCCCTGCTGAAAGGTTTT 60.343 47.619 0.00 0.00 35.34 2.43
728 909 5.191323 TGGGACCCAAAATGATAATGCAAAT 59.809 36.000 12.05 0.00 0.00 2.32
740 921 7.404396 TGGATACAAATTATTGGGACCCAAAAT 59.596 33.333 29.61 23.54 46.31 1.82
741 922 6.730977 TGGATACAAATTATTGGGACCCAAAA 59.269 34.615 29.61 22.51 46.31 2.44
742 923 6.264528 TGGATACAAATTATTGGGACCCAAA 58.735 36.000 29.61 15.09 46.31 3.28
781 962 3.001736 GCTCTAGCGATGTGGTTTGATTC 59.998 47.826 0.00 0.00 0.00 2.52
783 964 2.555199 GCTCTAGCGATGTGGTTTGAT 58.445 47.619 0.00 0.00 0.00 2.57
823 1033 1.411787 CGGGGCAATAATTGGGGGTTA 60.412 52.381 0.00 0.00 0.00 2.85
826 1041 1.075600 ACGGGGCAATAATTGGGGG 60.076 57.895 0.00 0.00 0.00 5.40
881 1100 1.831389 CTGTGCACGCCACTGTACAC 61.831 60.000 13.13 0.00 44.92 2.90
887 1106 2.901840 CCAACTGTGCACGCCACT 60.902 61.111 13.13 0.00 44.92 4.00
896 1115 1.003233 GGGTACTCTTCCCCAACTGTG 59.997 57.143 0.00 0.00 40.88 3.66
897 1116 1.132495 AGGGTACTCTTCCCCAACTGT 60.132 52.381 0.00 0.00 45.64 3.55
947 1166 2.434884 CTCGGGTCAACGCTGCAT 60.435 61.111 0.00 0.00 0.00 3.96
951 1170 4.421479 CGAGCTCGGGTCAACGCT 62.421 66.667 28.40 0.00 35.37 5.07
1317 1880 3.682292 AACGCCCTTCAGATCCGGC 62.682 63.158 0.00 0.00 38.07 6.13
1333 1896 0.674895 AGAGCTTGATGGCGGACAAC 60.675 55.000 0.00 0.00 37.29 3.32
1374 1952 4.982701 AAGCTGCCCAGGGTGTGC 62.983 66.667 7.55 9.30 0.00 4.57
1383 1961 2.335712 GCACTGTACCAAGCTGCCC 61.336 63.158 0.00 0.00 0.00 5.36
1532 2167 1.310933 GGTAACAGCAGCAGCAGCAT 61.311 55.000 12.92 0.42 45.49 3.79
1533 2168 1.968017 GGTAACAGCAGCAGCAGCA 60.968 57.895 12.92 0.00 45.49 4.41
1534 2169 2.873288 GGTAACAGCAGCAGCAGC 59.127 61.111 3.17 0.46 45.49 5.25
1549 2184 3.948719 ATCACCACCAACGCCGGT 61.949 61.111 1.90 0.00 41.07 5.28
1592 2233 2.548920 GCACTAGCAGAGTTGGAGTTGT 60.549 50.000 0.00 0.00 41.58 3.32
1623 2371 3.120234 TGTCAAAATGCAGCGTATCACTG 60.120 43.478 0.00 0.00 38.22 3.66
1681 2701 2.439156 GTGGGACTGCATGCCCTC 60.439 66.667 16.68 15.28 44.96 4.30
1706 2726 0.960364 GGCGAGCAAATTGGAGACCA 60.960 55.000 0.00 0.00 0.00 4.02
1724 2744 1.098050 GCTGTTGCTTGGGATAGTGG 58.902 55.000 0.00 0.00 36.03 4.00
1760 2792 2.202797 CAGTCCGAGGCCGATGTG 60.203 66.667 0.00 0.00 38.22 3.21
1778 2810 5.602145 ACAATTCCCTCAAAAGTCATGGAAA 59.398 36.000 0.00 0.00 35.66 3.13
1796 2861 3.001330 GTCCGTGATCCGATTGACAATTC 59.999 47.826 1.39 0.00 39.56 2.17
1799 2864 1.273886 TGTCCGTGATCCGATTGACAA 59.726 47.619 5.32 0.00 39.56 3.18
1809 2874 1.741770 GGCACCAGTGTCCGTGATC 60.742 63.158 2.57 0.00 31.36 2.92
1815 2880 2.186826 GTGTGTGGCACCAGTGTCC 61.187 63.158 16.26 2.45 42.10 4.02
1899 2980 7.093814 TGCTTTTTAGTCCTTGCATCATTGTAT 60.094 33.333 0.00 0.00 0.00 2.29
2010 3091 0.911525 TGCTTCCTCCTTCTCCAGGG 60.912 60.000 0.00 0.00 44.12 4.45
2011 3092 0.540923 CTGCTTCCTCCTTCTCCAGG 59.459 60.000 0.00 0.00 45.64 4.45
2015 3096 1.153469 CCGCTGCTTCCTCCTTCTC 60.153 63.158 0.00 0.00 0.00 2.87
2067 3151 1.938577 CAACGCAGAATGGATCTCTGG 59.061 52.381 11.28 5.44 40.62 3.86
2080 3164 3.325870 TCTTGGACTTGATACAACGCAG 58.674 45.455 0.00 0.00 0.00 5.18
2085 3169 5.997746 CAGAAACCTCTTGGACTTGATACAA 59.002 40.000 0.00 0.00 37.04 2.41
2086 3170 5.306937 TCAGAAACCTCTTGGACTTGATACA 59.693 40.000 0.00 0.00 37.04 2.29
2249 3565 2.359214 CGCAGCTCTAGTGGATCAACTA 59.641 50.000 9.67 9.67 0.00 2.24
2319 3635 1.006102 AGGCTTGTCGTCTTCACCG 60.006 57.895 0.00 0.00 0.00 4.94
2378 3694 3.897505 AGAACCCTTTAGCTTGTTTGCAT 59.102 39.130 0.00 0.00 34.99 3.96
2400 3716 1.733402 CTGTTTTGGCTGCCAACGGA 61.733 55.000 32.36 16.62 43.82 4.69
2424 3740 3.914426 AGGTCCTTGTGTAATAGCCTG 57.086 47.619 0.00 0.00 0.00 4.85
2544 3860 5.359009 GCATTTCTTCAGATCAAATGGGAGA 59.641 40.000 14.04 2.22 37.78 3.71
2741 4060 4.530946 TGACCCTTTTTCTACTAGTGGAGG 59.469 45.833 9.07 9.13 0.00 4.30
2742 4061 5.740290 TGACCCTTTTTCTACTAGTGGAG 57.260 43.478 9.07 0.00 0.00 3.86
2743 4062 6.503560 TTTGACCCTTTTTCTACTAGTGGA 57.496 37.500 4.58 4.58 0.00 4.02
2852 4171 5.968528 TTGCAATGAACCGGTATTAAAGT 57.031 34.783 8.00 0.00 0.00 2.66
3078 4397 5.600484 CCCTCAGATCCTACACATAGAGTTT 59.400 44.000 0.00 0.00 0.00 2.66
3292 5710 4.442706 TCTGCTTTTTCAGAGTTCGTTCT 58.557 39.130 0.00 0.00 38.11 3.01
3296 5714 5.810525 TCTTTTCTGCTTTTTCAGAGTTCG 58.189 37.500 0.00 0.00 43.23 3.95


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

AutoCloner maintained by Alex Coulton.