Multiple sequence alignment - TraesCS5B01G062900

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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 TraesCS5B01G062900 chr5B 100.000 6510 0 0 1 6510 70560200 70566709 0.000000e+00 12022.0
1 TraesCS5B01G062900 chr5B 97.698 695 15 1 1 694 324242662 324243356 0.000000e+00 1194.0
2 TraesCS5B01G062900 chr5B 81.129 1240 177 27 3544 4753 70553530 70554742 0.000000e+00 941.0
3 TraesCS5B01G062900 chr5B 84.840 686 80 19 3656 4325 70613233 70613910 0.000000e+00 669.0
4 TraesCS5B01G062900 chr5B 84.875 681 78 18 1452 2120 70552878 70553545 0.000000e+00 664.0
5 TraesCS5B01G062900 chr5B 83.247 770 70 29 4783 5500 70614582 70615344 0.000000e+00 652.0
6 TraesCS5B01G062900 chr5B 83.393 560 72 16 1566 2120 70389347 70389890 3.500000e-137 499.0
7 TraesCS5B01G062900 chr5B 99.262 271 2 0 5499 5769 70570711 70570981 2.110000e-134 490.0
8 TraesCS5B01G062900 chr5B 86.547 446 47 8 4300 4738 70613950 70614389 4.570000e-131 479.0
9 TraesCS5B01G062900 chr5B 81.431 587 94 9 1546 2120 70612505 70613088 3.550000e-127 466.0
10 TraesCS5B01G062900 chr5B 82.046 479 63 13 5019 5493 70555388 70555847 2.850000e-103 387.0
11 TraesCS5B01G062900 chr5B 83.059 425 54 14 3659 4067 70391803 70392225 2.870000e-98 370.0
12 TraesCS5B01G062900 chr5B 79.800 401 42 21 779 1164 70611700 70612076 8.380000e-64 255.0
13 TraesCS5B01G062900 chr5B 88.293 205 21 2 4108 4312 70392386 70392587 6.520000e-60 243.0
14 TraesCS5B01G062900 chr5B 85.477 241 26 6 4783 5022 70626276 70626508 6.520000e-60 243.0
15 TraesCS5B01G062900 chr5B 84.906 212 22 4 949 1152 70550779 70550988 8.560000e-49 206.0
16 TraesCS5B01G062900 chr5B 86.517 89 10 2 5328 5415 70545510 70545597 5.370000e-16 97.1
17 TraesCS5B01G062900 chr5B 88.406 69 8 0 1391 1459 70389272 70389340 4.180000e-12 84.2
18 TraesCS5B01G062900 chr1B 96.207 1450 34 3 2119 3547 525828848 525827399 0.000000e+00 2353.0
19 TraesCS5B01G062900 chr1B 95.084 1424 39 6 2119 3521 70173877 70175290 0.000000e+00 2213.0
20 TraesCS5B01G062900 chr1B 89.029 1030 64 28 5501 6510 1315840 1314840 0.000000e+00 1230.0
21 TraesCS5B01G062900 chr1B 80.303 858 119 26 1279 2120 476875743 476876566 2.600000e-168 603.0
22 TraesCS5B01G062900 chr7D 95.429 1444 41 10 2119 3539 7816030 7817471 0.000000e+00 2278.0
23 TraesCS5B01G062900 chr7D 82.086 1323 171 49 2122 3398 41446348 41447650 0.000000e+00 1070.0
24 TraesCS5B01G062900 chr7D 80.120 669 111 16 3650 4315 580746305 580745656 4.570000e-131 479.0
25 TraesCS5B01G062900 chr7A 94.441 1439 53 9 2119 3535 184634908 184633475 0.000000e+00 2189.0
26 TraesCS5B01G062900 chr7A 97.135 698 18 2 1 697 736019823 736020519 0.000000e+00 1177.0
27 TraesCS5B01G062900 chr7A 95.422 699 30 2 1 697 466206253 466206951 0.000000e+00 1112.0
28 TraesCS5B01G062900 chr6B 93.291 1401 61 10 2119 3489 64193646 64192249 0.000000e+00 2036.0
29 TraesCS5B01G062900 chr7B 92.035 1381 59 15 2114 3471 146984326 146982974 0.000000e+00 1893.0
30 TraesCS5B01G062900 chr7B 89.505 1010 72 23 5499 6507 504397033 504398009 0.000000e+00 1247.0
31 TraesCS5B01G062900 chr7B 93.660 836 49 4 2404 3238 700180899 700181731 0.000000e+00 1247.0
32 TraesCS5B01G062900 chr7B 79.556 1037 160 44 2467 3464 463424016 463422993 0.000000e+00 693.0
33 TraesCS5B01G062900 chr7B 80.415 674 118 10 3650 4318 648394043 648393379 9.740000e-138 501.0
34 TraesCS5B01G062900 chr7B 80.514 662 116 11 3650 4309 646284565 646285215 4.530000e-136 496.0
35 TraesCS5B01G062900 chr7B 76.064 752 123 28 1389 2120 646283742 646284456 8.090000e-89 339.0
36 TraesCS5B01G062900 chr7B 91.083 157 13 1 3376 3532 700183037 700183192 1.840000e-50 211.0
37 TraesCS5B01G062900 chr7B 91.667 96 6 2 5498 5592 110348444 110348538 1.470000e-26 132.0
38 TraesCS5B01G062900 chr7B 96.000 75 2 1 3465 3538 146979628 146979554 3.190000e-23 121.0
39 TraesCS5B01G062900 chr4B 94.127 1226 54 3 2119 3327 452727342 452728566 0.000000e+00 1849.0
40 TraesCS5B01G062900 chr4B 84.940 332 17 10 3007 3326 452729186 452729496 8.200000e-79 305.0
41 TraesCS5B01G062900 chr2B 93.760 1234 59 6 2119 3335 693358632 693359864 0.000000e+00 1836.0
42 TraesCS5B01G062900 chr2B 98.317 1010 16 1 5501 6510 10812512 10811504 0.000000e+00 1770.0
43 TraesCS5B01G062900 chr2B 93.235 1020 41 11 5501 6509 707623398 707624400 0.000000e+00 1476.0
44 TraesCS5B01G062900 chr2B 96.983 696 20 1 1 695 733839091 733838396 0.000000e+00 1168.0
45 TraesCS5B01G062900 chr2B 95.442 702 30 2 1 701 168841805 168841105 0.000000e+00 1118.0
46 TraesCS5B01G062900 chr2B 97.426 272 6 1 5499 5770 10807503 10807233 4.600000e-126 462.0
47 TraesCS5B01G062900 chr2B 88.492 252 10 11 5499 5749 707628386 707628619 2.970000e-73 287.0
48 TraesCS5B01G062900 chr1A 98.047 1024 14 5 5488 6510 584849322 584850340 0.000000e+00 1775.0
49 TraesCS5B01G062900 chr1A 98.524 271 2 1 5499 5769 584854336 584854604 1.640000e-130 477.0
50 TraesCS5B01G062900 chr5D 94.499 1127 56 3 3550 4675 60077255 60076134 0.000000e+00 1733.0
51 TraesCS5B01G062900 chr5D 86.738 1116 84 30 697 1788 60079631 60078556 0.000000e+00 1182.0
52 TraesCS5B01G062900 chr5D 88.553 926 78 16 5604 6510 24073951 24073035 0.000000e+00 1098.0
53 TraesCS5B01G062900 chr5D 82.703 1243 174 21 3544 4753 60086243 60085009 0.000000e+00 1066.0
54 TraesCS5B01G062900 chr5D 91.069 739 48 12 2805 3532 14104510 14105241 0.000000e+00 983.0
55 TraesCS5B01G062900 chr5D 91.382 731 41 7 4783 5494 60073927 60073200 0.000000e+00 981.0
56 TraesCS5B01G062900 chr5D 84.959 738 96 9 1387 2120 60086954 60086228 0.000000e+00 734.0
57 TraesCS5B01G062900 chr5D 85.465 688 75 19 3655 4325 60012545 60011866 0.000000e+00 693.0
58 TraesCS5B01G062900 chr5D 85.714 602 71 12 4783 5381 60011282 60010693 7.170000e-174 621.0
59 TraesCS5B01G062900 chr5D 88.034 468 47 4 4293 4755 60011832 60011369 4.440000e-151 545.0
60 TraesCS5B01G062900 chr5D 93.994 333 20 0 1788 2120 60077578 60077246 7.530000e-139 505.0
61 TraesCS5B01G062900 chr5D 83.063 555 80 12 1566 2120 60254080 60253540 5.860000e-135 492.0
62 TraesCS5B01G062900 chr5D 84.100 478 61 9 5019 5493 60084366 60083901 1.290000e-121 448.0
63 TraesCS5B01G062900 chr5D 82.915 398 56 9 3678 4067 60253269 60252876 1.340000e-91 348.0
64 TraesCS5B01G062900 chr5D 88.710 248 23 4 4067 4313 60252756 60252513 1.370000e-76 298.0
65 TraesCS5B01G062900 chr5D 79.634 437 62 16 1390 1821 60013204 60012790 8.260000e-74 289.0
66 TraesCS5B01G062900 chr5D 90.741 216 18 2 4484 4698 60076111 60075897 2.970000e-73 287.0
67 TraesCS5B01G062900 chr5D 77.978 445 67 17 4783 5209 60084918 60084487 3.900000e-62 250.0
68 TraesCS5B01G062900 chr5D 77.518 427 49 19 751 1164 60013755 60013363 5.110000e-51 213.0
69 TraesCS5B01G062900 chr5D 87.619 105 13 0 1060 1164 60087214 60087110 8.860000e-24 122.0
70 TraesCS5B01G062900 chr5D 89.855 69 7 0 1391 1459 60254155 60254087 8.990000e-14 89.8
71 TraesCS5B01G062900 chr5D 84.270 89 12 2 5328 5415 60138894 60138807 1.160000e-12 86.1
72 TraesCS5B01G062900 chrUn 97.851 698 14 1 1 697 459024406 459025103 0.000000e+00 1205.0
73 TraesCS5B01G062900 chr3B 88.139 1037 71 30 5501 6510 85216099 85217110 0.000000e+00 1186.0
74 TraesCS5B01G062900 chr3B 96.705 698 21 2 1 697 427583896 427583200 0.000000e+00 1160.0
75 TraesCS5B01G062900 chr3B 96.562 698 22 2 1 697 814834917 814835613 0.000000e+00 1155.0
76 TraesCS5B01G062900 chr6D 95.702 698 28 2 1 697 379009603 379008907 0.000000e+00 1122.0
77 TraesCS5B01G062900 chr4A 87.908 918 85 17 5604 6506 426007022 426007928 0.000000e+00 1057.0
78 TraesCS5B01G062900 chr4A 91.555 746 63 0 5761 6506 19591905 19591160 0.000000e+00 1029.0
79 TraesCS5B01G062900 chr1D 80.607 856 116 23 1282 2120 355076109 355076931 3.340000e-172 616.0
80 TraesCS5B01G062900 chr1D 78.414 454 66 21 3100 3528 369905685 369905239 3.870000e-67 267.0
81 TraesCS5B01G062900 chr6A 80.533 750 95 28 1391 2120 495255749 495255031 4.470000e-146 529.0
82 TraesCS5B01G062900 chr5A 83.066 561 73 16 1566 2120 48765813 48765269 2.110000e-134 490.0
83 TraesCS5B01G062900 chr5A 82.670 427 51 13 3656 4067 48765144 48764726 2.230000e-94 357.0
84 TraesCS5B01G062900 chr5A 86.235 247 29 4 4068 4313 48764606 48764364 5.010000e-66 263.0
85 TraesCS5B01G062900 chr5A 89.855 69 7 0 1391 1459 48765888 48765820 8.990000e-14 89.8


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 TraesCS5B01G062900 chr5B 70560200 70566709 6509 False 12022.00 12022 100.00000 1 6510 1 chr5B.!!$F2 6509
1 TraesCS5B01G062900 chr5B 324242662 324243356 694 False 1194.00 1194 97.69800 1 694 1 chr5B.!!$F5 693
2 TraesCS5B01G062900 chr5B 70550779 70555847 5068 False 549.50 941 83.23900 949 5493 4 chr5B.!!$F7 4544
3 TraesCS5B01G062900 chr5B 70611700 70615344 3644 False 504.20 669 83.17300 779 5500 5 chr5B.!!$F8 4721
4 TraesCS5B01G062900 chr5B 70389272 70392587 3315 False 299.05 499 85.78775 1391 4312 4 chr5B.!!$F6 2921
5 TraesCS5B01G062900 chr1B 525827399 525828848 1449 True 2353.00 2353 96.20700 2119 3547 1 chr1B.!!$R2 1428
6 TraesCS5B01G062900 chr1B 70173877 70175290 1413 False 2213.00 2213 95.08400 2119 3521 1 chr1B.!!$F1 1402
7 TraesCS5B01G062900 chr1B 1314840 1315840 1000 True 1230.00 1230 89.02900 5501 6510 1 chr1B.!!$R1 1009
8 TraesCS5B01G062900 chr1B 476875743 476876566 823 False 603.00 603 80.30300 1279 2120 1 chr1B.!!$F2 841
9 TraesCS5B01G062900 chr7D 7816030 7817471 1441 False 2278.00 2278 95.42900 2119 3539 1 chr7D.!!$F1 1420
10 TraesCS5B01G062900 chr7D 41446348 41447650 1302 False 1070.00 1070 82.08600 2122 3398 1 chr7D.!!$F2 1276
11 TraesCS5B01G062900 chr7D 580745656 580746305 649 True 479.00 479 80.12000 3650 4315 1 chr7D.!!$R1 665
12 TraesCS5B01G062900 chr7A 184633475 184634908 1433 True 2189.00 2189 94.44100 2119 3535 1 chr7A.!!$R1 1416
13 TraesCS5B01G062900 chr7A 736019823 736020519 696 False 1177.00 1177 97.13500 1 697 1 chr7A.!!$F2 696
14 TraesCS5B01G062900 chr7A 466206253 466206951 698 False 1112.00 1112 95.42200 1 697 1 chr7A.!!$F1 696
15 TraesCS5B01G062900 chr6B 64192249 64193646 1397 True 2036.00 2036 93.29100 2119 3489 1 chr6B.!!$R1 1370
16 TraesCS5B01G062900 chr7B 504397033 504398009 976 False 1247.00 1247 89.50500 5499 6507 1 chr7B.!!$F2 1008
17 TraesCS5B01G062900 chr7B 146979554 146984326 4772 True 1007.00 1893 94.01750 2114 3538 2 chr7B.!!$R3 1424
18 TraesCS5B01G062900 chr7B 700180899 700183192 2293 False 729.00 1247 92.37150 2404 3532 2 chr7B.!!$F4 1128
19 TraesCS5B01G062900 chr7B 463422993 463424016 1023 True 693.00 693 79.55600 2467 3464 1 chr7B.!!$R1 997
20 TraesCS5B01G062900 chr7B 648393379 648394043 664 True 501.00 501 80.41500 3650 4318 1 chr7B.!!$R2 668
21 TraesCS5B01G062900 chr7B 646283742 646285215 1473 False 417.50 496 78.28900 1389 4309 2 chr7B.!!$F3 2920
22 TraesCS5B01G062900 chr4B 452727342 452729496 2154 False 1077.00 1849 89.53350 2119 3327 2 chr4B.!!$F1 1208
23 TraesCS5B01G062900 chr2B 693358632 693359864 1232 False 1836.00 1836 93.76000 2119 3335 1 chr2B.!!$F1 1216
24 TraesCS5B01G062900 chr2B 10811504 10812512 1008 True 1770.00 1770 98.31700 5501 6510 1 chr2B.!!$R2 1009
25 TraesCS5B01G062900 chr2B 733838396 733839091 695 True 1168.00 1168 96.98300 1 695 1 chr2B.!!$R4 694
26 TraesCS5B01G062900 chr2B 168841105 168841805 700 True 1118.00 1118 95.44200 1 701 1 chr2B.!!$R3 700
27 TraesCS5B01G062900 chr2B 707623398 707628619 5221 False 881.50 1476 90.86350 5499 6509 2 chr2B.!!$F2 1010
28 TraesCS5B01G062900 chr1A 584849322 584854604 5282 False 1126.00 1775 98.28550 5488 6510 2 chr1A.!!$F1 1022
29 TraesCS5B01G062900 chr5D 24073035 24073951 916 True 1098.00 1098 88.55300 5604 6510 1 chr5D.!!$R1 906
30 TraesCS5B01G062900 chr5D 14104510 14105241 731 False 983.00 983 91.06900 2805 3532 1 chr5D.!!$F1 727
31 TraesCS5B01G062900 chr5D 60073200 60079631 6431 True 937.60 1733 91.47080 697 5494 5 chr5D.!!$R4 4797
32 TraesCS5B01G062900 chr5D 60083901 60087214 3313 True 524.00 1066 83.47180 1060 5493 5 chr5D.!!$R5 4433
33 TraesCS5B01G062900 chr5D 60010693 60013755 3062 True 472.20 693 83.27300 751 5381 5 chr5D.!!$R3 4630
34 TraesCS5B01G062900 chr5D 60252513 60254155 1642 True 306.95 492 86.13575 1391 4313 4 chr5D.!!$R6 2922
35 TraesCS5B01G062900 chrUn 459024406 459025103 697 False 1205.00 1205 97.85100 1 697 1 chrUn.!!$F1 696
36 TraesCS5B01G062900 chr3B 85216099 85217110 1011 False 1186.00 1186 88.13900 5501 6510 1 chr3B.!!$F1 1009
37 TraesCS5B01G062900 chr3B 427583200 427583896 696 True 1160.00 1160 96.70500 1 697 1 chr3B.!!$R1 696
38 TraesCS5B01G062900 chr3B 814834917 814835613 696 False 1155.00 1155 96.56200 1 697 1 chr3B.!!$F2 696
39 TraesCS5B01G062900 chr6D 379008907 379009603 696 True 1122.00 1122 95.70200 1 697 1 chr6D.!!$R1 696
40 TraesCS5B01G062900 chr4A 426007022 426007928 906 False 1057.00 1057 87.90800 5604 6506 1 chr4A.!!$F1 902
41 TraesCS5B01G062900 chr4A 19591160 19591905 745 True 1029.00 1029 91.55500 5761 6506 1 chr4A.!!$R1 745
42 TraesCS5B01G062900 chr1D 355076109 355076931 822 False 616.00 616 80.60700 1282 2120 1 chr1D.!!$F1 838
43 TraesCS5B01G062900 chr6A 495255031 495255749 718 True 529.00 529 80.53300 1391 2120 1 chr6A.!!$R1 729
44 TraesCS5B01G062900 chr5A 48764364 48765888 1524 True 299.95 490 85.45650 1391 4313 4 chr5A.!!$R1 2922

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
843 861 0.526096 GTCCTAACCGCACGCGATTA 60.526 55.0 15.93 5.41 42.83 1.75 F
1257 1303 0.234884 GCGTATGCGTGCCCTAAATC 59.765 55.0 4.81 0.00 40.81 2.17 F
1736 3619 0.244994 ACACTCATCCTGCACGACTC 59.755 55.0 0.00 0.00 0.00 3.36 F
1739 3623 0.463204 CTCATCCTGCACGACTCCAT 59.537 55.0 0.00 0.00 0.00 3.41 F
1847 4719 0.745845 GCATTGGCACTGGATCGAGT 60.746 55.0 4.29 4.29 40.72 4.18 F
3765 14113 0.238289 CGGTGGCGATGGAATTATGC 59.762 55.0 0.00 0.00 0.00 3.14 F
4635 15422 0.458716 GGAGACAAGACGTAGGCTGC 60.459 60.0 0.00 0.00 0.00 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2745 5650 1.039856 TTCCAAGCCTGTTCCTTTGC 58.960 50.000 0.00 0.00 0.00 3.68 R
3186 7045 1.302511 GGCGGCTCCTTCTTGTCAA 60.303 57.895 0.00 0.00 0.00 3.18 R
3212 7071 2.752807 GGGGCTCCAAATCGGCCTA 61.753 63.158 0.00 0.00 44.70 3.93 R
3608 11996 3.546724 TCTCTGTAATCTCGAGTCCAGG 58.453 50.000 13.13 8.33 0.00 4.45 R
3791 14145 3.184986 GCAATGTTCATGTTTTGCTCACC 59.815 43.478 13.48 0.00 40.90 4.02 R
4686 15475 0.466007 TTGGCTGCAGTCTTCTTGCA 60.466 50.000 20.86 0.00 37.04 4.08 R
5938 19092 2.512692 TGCCAGGACAAAGCACATAT 57.487 45.000 0.00 0.00 0.00 1.78 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
406 408 2.065799 GTGATATCCATCCCCCACCTT 58.934 52.381 0.00 0.00 0.00 3.50
594 596 1.580815 CCGTTGTTGGCATTTGCTTT 58.419 45.000 2.12 0.00 41.70 3.51
664 667 1.686355 ATCGGTGTTGGTTGCTTTGA 58.314 45.000 0.00 0.00 0.00 2.69
746 757 2.084610 TGAACGCACCTTCAGATCAG 57.915 50.000 0.00 0.00 0.00 2.90
843 861 0.526096 GTCCTAACCGCACGCGATTA 60.526 55.000 15.93 5.41 42.83 1.75
879 897 2.822758 GCATATCACGCGGCTGCAA 61.823 57.895 19.50 2.10 42.97 4.08
891 912 4.623814 CTGCAAGCCCTCGAATGA 57.376 55.556 0.00 0.00 0.00 2.57
917 938 4.514577 ACCGCGCTCGATTCTGGG 62.515 66.667 5.56 0.00 38.10 4.45
924 945 1.646189 GCTCGATTCTGGGTTCTGAC 58.354 55.000 0.00 0.00 0.00 3.51
925 946 1.205893 GCTCGATTCTGGGTTCTGACT 59.794 52.381 0.00 0.00 0.00 3.41
927 948 3.257393 CTCGATTCTGGGTTCTGACTTG 58.743 50.000 0.00 0.00 0.00 3.16
928 949 2.632996 TCGATTCTGGGTTCTGACTTGT 59.367 45.455 0.00 0.00 0.00 3.16
929 950 2.738846 CGATTCTGGGTTCTGACTTGTG 59.261 50.000 0.00 0.00 0.00 3.33
930 951 3.554960 CGATTCTGGGTTCTGACTTGTGA 60.555 47.826 0.00 0.00 0.00 3.58
931 952 3.924114 TTCTGGGTTCTGACTTGTGAA 57.076 42.857 0.00 0.00 0.00 3.18
933 954 3.541632 TCTGGGTTCTGACTTGTGAAAC 58.458 45.455 0.00 0.00 37.35 2.78
1007 1034 0.301687 CGATCCTCGCCGATGTTTTG 59.698 55.000 0.00 0.00 31.14 2.44
1009 1036 0.676466 ATCCTCGCCGATGTTTTGCA 60.676 50.000 0.00 0.00 0.00 4.08
1112 1149 2.062636 AGGGCAGAGGAAGGTTTTGTA 58.937 47.619 0.00 0.00 0.00 2.41
1199 1241 3.069729 AGGTGGCAGAGTTTATATCGGTC 59.930 47.826 0.00 0.00 0.00 4.79
1200 1242 3.181469 GGTGGCAGAGTTTATATCGGTCA 60.181 47.826 0.00 0.00 0.00 4.02
1208 1250 9.209175 GCAGAGTTTATATCGGTCATAAAGAAT 57.791 33.333 0.00 0.00 30.52 2.40
1239 1281 2.798976 TTTGAATCTGTGCAAGGTGC 57.201 45.000 0.00 0.00 45.29 5.01
1257 1303 0.234884 GCGTATGCGTGCCCTAAATC 59.765 55.000 4.81 0.00 40.81 2.17
1268 1318 1.548719 GCCCTAAATCCGTTGCCTTTT 59.451 47.619 0.00 0.00 0.00 2.27
1270 1320 3.193903 GCCCTAAATCCGTTGCCTTTTAA 59.806 43.478 0.00 0.00 0.00 1.52
1271 1321 4.142026 GCCCTAAATCCGTTGCCTTTTAAT 60.142 41.667 0.00 0.00 0.00 1.40
1272 1322 5.068067 GCCCTAAATCCGTTGCCTTTTAATA 59.932 40.000 0.00 0.00 0.00 0.98
1273 1323 6.406065 GCCCTAAATCCGTTGCCTTTTAATAA 60.406 38.462 0.00 0.00 0.00 1.40
1274 1324 7.548967 CCCTAAATCCGTTGCCTTTTAATAAA 58.451 34.615 0.00 0.00 0.00 1.40
1275 1325 7.704899 CCCTAAATCCGTTGCCTTTTAATAAAG 59.295 37.037 0.00 0.00 40.38 1.85
1364 1418 3.599730 TGACCATGTTGAGCAGACTAG 57.400 47.619 0.00 0.00 0.00 2.57
1369 1423 2.732412 TGTTGAGCAGACTAGAGCAC 57.268 50.000 0.00 0.00 0.00 4.40
1380 1434 5.061853 CAGACTAGAGCACGGGTAGTTATA 58.938 45.833 0.00 0.00 0.00 0.98
1385 1439 5.764487 AGAGCACGGGTAGTTATACTTAC 57.236 43.478 0.00 0.00 32.12 2.34
1518 3379 8.887264 ACCATATGACCCTGTTTGTAATTAAA 57.113 30.769 3.65 0.00 0.00 1.52
1531 3396 8.696374 TGTTTGTAATTAAACAGTTCCCATTCA 58.304 29.630 2.98 0.00 43.46 2.57
1600 3466 5.243981 GCTAGTGATGCCATGTTCATCTAT 58.756 41.667 19.52 13.15 40.59 1.98
1731 3614 1.728971 CTTCGAACACTCATCCTGCAC 59.271 52.381 0.00 0.00 0.00 4.57
1734 3617 1.071605 GAACACTCATCCTGCACGAC 58.928 55.000 0.00 0.00 0.00 4.34
1736 3619 0.244994 ACACTCATCCTGCACGACTC 59.755 55.000 0.00 0.00 0.00 3.36
1739 3623 0.463204 CTCATCCTGCACGACTCCAT 59.537 55.000 0.00 0.00 0.00 3.41
1814 4683 4.099633 TGCCAATCATTCCCATGGTTTTA 58.900 39.130 11.73 0.00 30.62 1.52
1847 4719 0.745845 GCATTGGCACTGGATCGAGT 60.746 55.000 4.29 4.29 40.72 4.18
1922 4794 4.237724 TGCTAAATGAAGAGACTGTCGTG 58.762 43.478 1.52 0.00 0.00 4.35
2013 4896 4.016444 TCACAATGTGGCTCCTTAATTCC 58.984 43.478 13.95 0.00 33.87 3.01
2088 4975 2.158696 AGAAGACAAGCTCAAAGGCAGT 60.159 45.455 0.00 0.00 34.17 4.40
2111 4998 3.425577 GTGCCACATACACCATCATTG 57.574 47.619 0.00 0.00 31.67 2.82
2196 5089 1.087202 ACACACAACACGACACGCAT 61.087 50.000 0.00 0.00 0.00 4.73
2260 5153 3.380142 CCCAAACAATTCCAAGACAACG 58.620 45.455 0.00 0.00 0.00 4.10
2413 5314 4.402528 CGCCACCACCCGATCCAA 62.403 66.667 0.00 0.00 0.00 3.53
2706 5610 4.722700 GCACGCCACTCCCACCAT 62.723 66.667 0.00 0.00 0.00 3.55
2745 5650 1.096386 CCCGACACTCTAGAGACCGG 61.096 65.000 28.33 28.33 37.64 5.28
3212 7071 0.972883 GAAGGAGCCGCCAGATCTAT 59.027 55.000 0.00 0.00 40.02 1.98
3544 11932 0.840722 GGGAGGGAGAGGGTGTTTCA 60.841 60.000 0.00 0.00 0.00 2.69
3548 11936 2.507471 GAGGGAGAGGGTGTTTCATCAT 59.493 50.000 0.00 0.00 0.00 2.45
3567 11955 6.539826 TCATCATTGGTGTTATAGAGCAAGTG 59.460 38.462 0.00 0.00 34.50 3.16
3608 11996 2.279784 CGAGCTTCCCATCCGCTC 60.280 66.667 0.00 0.00 44.98 5.03
3653 12090 4.371624 TTCTTGAATCCATGTGTCCACT 57.628 40.909 0.00 0.00 0.00 4.00
3676 14019 9.877178 CACTGTTTCTAGAGGTAGTTAATCATT 57.123 33.333 0.00 0.00 0.00 2.57
3765 14113 0.238289 CGGTGGCGATGGAATTATGC 59.762 55.000 0.00 0.00 0.00 3.14
3791 14145 5.261209 TGTGGAGTTTGACATTTTCTTGG 57.739 39.130 0.00 0.00 0.00 3.61
3824 14178 9.598517 AAAACATGAACATTGCTAAGAAAGAAA 57.401 25.926 0.00 0.00 0.00 2.52
3856 14210 7.978982 AGAAGAAATTCAATCTGATAACCACG 58.021 34.615 0.00 0.00 0.00 4.94
4134 14633 7.010091 GCAAACTGCCGCATTAACTAATATTTT 59.990 33.333 0.00 0.00 37.42 1.82
4380 14947 3.676873 GCAATGCCAATTGGTACCTTGAG 60.677 47.826 24.65 11.28 42.98 3.02
4447 15014 2.143925 GACGAACTTGAAAGTCTGGGG 58.856 52.381 0.00 0.00 38.57 4.96
4472 15039 4.473444 AGCAACTCCAGAAATTCTTTGGA 58.527 39.130 4.26 4.26 38.62 3.53
4529 15096 9.349713 TGGATGTAATTAAACAGTGTTTCTCTT 57.650 29.630 24.06 16.94 31.70 2.85
4544 15325 7.122799 AGTGTTTCTCTTTAAAGTTTTGCTCCT 59.877 33.333 14.74 1.91 0.00 3.69
4565 15346 7.317842 TCCTTGTTATTTGTGTTTCACGTTA 57.682 32.000 0.00 0.00 37.14 3.18
4570 15351 7.285069 TGTTATTTGTGTTTCACGTTATCTCG 58.715 34.615 0.00 0.00 37.14 4.04
4576 15357 4.796830 GTGTTTCACGTTATCTCGCTCATA 59.203 41.667 0.00 0.00 0.00 2.15
4635 15422 0.458716 GGAGACAAGACGTAGGCTGC 60.459 60.000 0.00 0.00 0.00 5.25
4639 15428 2.076863 GACAAGACGTAGGCTGCAAAT 58.923 47.619 2.89 0.00 0.00 2.32
4640 15429 1.806542 ACAAGACGTAGGCTGCAAATG 59.193 47.619 2.89 0.00 0.00 2.32
4686 15475 2.555547 GCAGCGCCCAAGAAACAGT 61.556 57.895 2.29 0.00 0.00 3.55
4688 15477 2.050077 GCGCCCAAGAAACAGTGC 60.050 61.111 0.00 0.00 0.00 4.40
4730 17341 4.095185 CCTCAGAAGGTAGAGAGTAACACG 59.905 50.000 0.00 0.00 37.94 4.49
4777 17439 9.398170 ACTGTGATAAAACAATCGATTTTTCAG 57.602 29.630 8.21 12.48 31.79 3.02
4779 17441 8.356657 TGTGATAAAACAATCGATTTTTCAGGT 58.643 29.630 8.21 0.00 31.79 4.00
4869 17559 4.628333 GCCTTCTTACTGTGCGTGTTATAA 59.372 41.667 0.00 0.00 0.00 0.98
4947 17638 2.886862 AGATGATGAGGACGAAGCTG 57.113 50.000 0.00 0.00 0.00 4.24
4983 17674 7.920738 AGATCGTCTGGCTGTTTATAATTTTC 58.079 34.615 0.00 0.00 0.00 2.29
5111 18181 2.935201 GCAGCCATTAAGACTGAGACTG 59.065 50.000 6.40 0.00 33.10 3.51
5149 18219 4.642466 AGGAAAGAAAGGGAAGAACGAT 57.358 40.909 0.00 0.00 0.00 3.73
5166 18236 1.168714 GATCCAAGCAAAAGAGGCGT 58.831 50.000 0.00 0.00 36.08 5.68
5173 18243 1.215014 GCAAAAGAGGCGTGGCAAAC 61.215 55.000 0.00 0.00 0.00 2.93
5191 18262 4.974721 AAGGCCACGGCACCCTTG 62.975 66.667 10.83 0.00 44.11 3.61
5230 18304 2.038387 ACGAGGACAACAAGTTTGCT 57.962 45.000 0.00 0.00 0.00 3.91
5274 18348 1.954382 GAAAACCGGTGGAAGAAAGCT 59.046 47.619 8.52 0.00 0.00 3.74
5293 18367 1.047596 TTGCTGCCCAGAAGCCAAAA 61.048 50.000 0.00 0.00 40.06 2.44
5316 18390 2.158143 AGACTACCAACAGGAAGAGGGT 60.158 50.000 0.00 0.00 35.66 4.34
5381 18455 1.895798 TGCGAAAGATGAGTGACTCCT 59.104 47.619 10.52 0.00 0.00 3.69
5382 18456 2.094494 TGCGAAAGATGAGTGACTCCTC 60.094 50.000 10.52 9.96 0.00 3.71
5647 18740 4.342378 TCGGATGAGATTACTTGGAGAAGG 59.658 45.833 0.00 0.00 32.95 3.46
5938 19092 9.559732 TTCTCTGACAAAGTGAAAATCAATCTA 57.440 29.630 0.00 0.00 35.88 1.98
6050 19204 7.329588 ACTTTGTACACCAAGTTCCTTTAAG 57.670 36.000 7.06 1.25 33.75 1.85
6063 19217 7.554959 AGTTCCTTTAAGATAGACTGAACCA 57.445 36.000 0.00 0.00 31.31 3.67
6291 19445 6.239036 GCTAAAGTTCAGTCCCAAGTTCAAAT 60.239 38.462 0.00 0.00 0.00 2.32
6359 19513 3.737559 TTGGTAGGTGCATGAAGGAAT 57.262 42.857 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
479 481 1.202154 CCACCGCGTACAAAACAACAA 60.202 47.619 4.92 0.00 0.00 2.83
594 596 8.711457 CAACAAGCTCAAAAGAAAAAGAAGAAA 58.289 29.630 0.00 0.00 0.00 2.52
664 667 2.297880 GGTTTCCCCACGCTTTGTATTT 59.702 45.455 0.00 0.00 0.00 1.40
676 679 7.638655 TTTCTACCGAAAAAGGGTTTCCCCA 62.639 44.000 0.00 0.00 43.64 4.96
727 730 1.941209 GCTGATCTGAAGGTGCGTTCA 60.941 52.381 3.42 7.05 35.16 3.18
728 731 0.723981 GCTGATCTGAAGGTGCGTTC 59.276 55.000 3.42 0.00 0.00 3.95
774 785 0.975135 TGGTAACCAATCGTCCCGAA 59.025 50.000 0.00 0.00 39.99 4.30
879 897 1.726853 CTCGTTTTCATTCGAGGGCT 58.273 50.000 6.67 0.00 46.26 5.19
909 930 4.008074 TCACAAGTCAGAACCCAGAATC 57.992 45.455 0.00 0.00 0.00 2.52
928 949 0.874175 CGGTGCTCGTGAGTGTTTCA 60.874 55.000 0.00 0.00 0.00 2.69
929 950 1.853319 CGGTGCTCGTGAGTGTTTC 59.147 57.895 0.00 0.00 0.00 2.78
930 951 2.244651 GCGGTGCTCGTGAGTGTTT 61.245 57.895 0.00 0.00 41.72 2.83
931 952 2.661866 GCGGTGCTCGTGAGTGTT 60.662 61.111 0.00 0.00 41.72 3.32
933 954 4.662961 TGGCGGTGCTCGTGAGTG 62.663 66.667 0.00 0.00 41.72 3.51
1007 1034 0.678048 GGGACTGAGGTCATGGTTGC 60.678 60.000 0.00 0.00 43.77 4.17
1009 1036 1.630878 GAAGGGACTGAGGTCATGGTT 59.369 52.381 0.00 0.00 43.77 3.67
1112 1149 5.252630 ACCAGATTCTTCTTGAAGGAGGAAT 59.747 40.000 0.00 4.61 42.16 3.01
1222 1264 0.534877 ACGCACCTTGCACAGATTCA 60.535 50.000 0.00 0.00 45.36 2.57
1223 1265 1.438651 TACGCACCTTGCACAGATTC 58.561 50.000 0.00 0.00 45.36 2.52
1225 1267 1.372582 CATACGCACCTTGCACAGAT 58.627 50.000 0.00 0.00 45.36 2.90
1227 1269 1.135315 GCATACGCACCTTGCACAG 59.865 57.895 0.00 0.00 45.36 3.66
1228 1270 2.676029 CGCATACGCACCTTGCACA 61.676 57.895 0.00 0.00 45.36 4.57
1229 1271 2.098298 CGCATACGCACCTTGCAC 59.902 61.111 0.00 0.00 45.36 4.57
1231 1273 2.098298 CACGCATACGCACCTTGC 59.902 61.111 0.00 0.00 45.53 4.01
1249 1295 5.592104 ATTAAAAGGCAACGGATTTAGGG 57.408 39.130 0.00 0.00 46.39 3.53
1268 1318 5.423610 TGCAGCCAATAAAAGCCCTTTATTA 59.576 36.000 11.73 0.00 44.77 0.98
1270 1320 3.774216 TGCAGCCAATAAAAGCCCTTTAT 59.226 39.130 0.00 0.00 41.16 1.40
1271 1321 3.169099 TGCAGCCAATAAAAGCCCTTTA 58.831 40.909 0.00 0.00 34.00 1.85
1272 1322 1.977129 TGCAGCCAATAAAAGCCCTTT 59.023 42.857 0.00 0.00 0.00 3.11
1273 1323 1.551883 CTGCAGCCAATAAAAGCCCTT 59.448 47.619 0.00 0.00 0.00 3.95
1274 1324 1.188863 CTGCAGCCAATAAAAGCCCT 58.811 50.000 0.00 0.00 0.00 5.19
1275 1325 0.176449 CCTGCAGCCAATAAAAGCCC 59.824 55.000 8.66 0.00 0.00 5.19
1276 1326 0.897621 ACCTGCAGCCAATAAAAGCC 59.102 50.000 8.66 0.00 0.00 4.35
1277 1327 1.404583 CCACCTGCAGCCAATAAAAGC 60.405 52.381 8.66 0.00 0.00 3.51
1326 1380 2.032549 GTCATCATGGTACGCTGATTGC 60.033 50.000 6.16 0.77 32.23 3.56
1364 1418 5.277047 GTGTAAGTATAACTACCCGTGCTC 58.723 45.833 0.00 0.00 0.00 4.26
1369 1423 5.455392 CATCCGTGTAAGTATAACTACCCG 58.545 45.833 0.00 0.00 0.00 5.28
1380 1434 1.899814 TCTTGAGCCATCCGTGTAAGT 59.100 47.619 0.00 0.00 0.00 2.24
1385 1439 2.489329 ACAAAATCTTGAGCCATCCGTG 59.511 45.455 0.00 0.00 36.33 4.94
1518 3379 3.508793 CAGCAAAGATGAATGGGAACTGT 59.491 43.478 0.00 0.00 0.00 3.55
1529 3394 5.512753 TTGTAAACAAGCAGCAAAGATGA 57.487 34.783 0.00 0.00 0.00 2.92
1531 3396 5.156355 CGATTGTAAACAAGCAGCAAAGAT 58.844 37.500 11.24 0.00 41.91 2.40
1570 3436 1.186200 TGGCATCACTAGCGTCTTCT 58.814 50.000 0.00 0.00 0.00 2.85
1580 3446 5.072193 TGGTATAGATGAACATGGCATCACT 59.928 40.000 24.00 16.11 43.50 3.41
1600 3466 3.901844 GGGTGATAGGTGCTAATCTGGTA 59.098 47.826 0.00 0.00 0.00 3.25
1847 4719 4.080751 GGGTTGTAGTTTGGGACATAGCTA 60.081 45.833 0.00 0.00 39.30 3.32
2111 4998 5.381174 AAAGCCTTTTTCGGTATAACACC 57.619 39.130 0.00 0.00 44.75 4.16
2112 4999 5.084055 CGAAAGCCTTTTTCGGTATAACAC 58.916 41.667 12.72 0.00 45.17 3.32
2113 5000 5.285798 CGAAAGCCTTTTTCGGTATAACA 57.714 39.130 12.72 0.00 45.17 2.41
2196 5089 3.433598 GCACCTATGTATCTTGCCTTGGA 60.434 47.826 0.00 0.00 0.00 3.53
2260 5153 4.457834 AGTGTGCCTAGTGTGTATCTTC 57.542 45.455 0.00 0.00 0.00 2.87
2413 5314 4.210331 CCCGGATGAAAATCTTGATCCTT 58.790 43.478 0.73 0.00 41.73 3.36
2642 5546 1.043116 CGGGCTAGTCTCCATGGTCA 61.043 60.000 12.58 0.00 0.00 4.02
2745 5650 1.039856 TTCCAAGCCTGTTCCTTTGC 58.960 50.000 0.00 0.00 0.00 3.68
3186 7045 1.302511 GGCGGCTCCTTCTTGTCAA 60.303 57.895 0.00 0.00 0.00 3.18
3212 7071 2.752807 GGGGCTCCAAATCGGCCTA 61.753 63.158 0.00 0.00 44.70 3.93
3544 11932 5.824624 CCACTTGCTCTATAACACCAATGAT 59.175 40.000 0.00 0.00 0.00 2.45
3548 11936 4.901197 TCCACTTGCTCTATAACACCAA 57.099 40.909 0.00 0.00 0.00 3.67
3567 11955 8.455682 TCGGTAATTTTAAGTTTCATGTCATCC 58.544 33.333 0.00 0.00 0.00 3.51
3608 11996 3.546724 TCTCTGTAATCTCGAGTCCAGG 58.453 50.000 13.13 8.33 0.00 4.45
3676 14019 9.230122 TGAAACACAAGATAATGAGCTATTTGA 57.770 29.630 0.00 0.00 0.00 2.69
3765 14113 5.762045 AGAAAATGTCAAACTCCACATTCG 58.238 37.500 0.00 0.00 41.42 3.34
3791 14145 3.184986 GCAATGTTCATGTTTTGCTCACC 59.815 43.478 13.48 0.00 40.90 4.02
3824 14178 4.874966 CAGATTGAATTTCTTCTCGAGGCT 59.125 41.667 13.56 0.00 32.29 4.58
3856 14210 5.824904 AGTGCATGTTTGATGTTCCTATC 57.175 39.130 0.00 0.00 0.00 2.08
4000 14373 8.653036 AACTCTGTAAGTACTGAAGAGGTAAT 57.347 34.615 23.41 11.16 38.95 1.89
4007 14381 8.756864 GTTTGAAGAACTCTGTAAGTACTGAAG 58.243 37.037 0.00 0.00 37.17 3.02
4134 14633 1.164411 CATTACTTCCTGCACGGCAA 58.836 50.000 0.35 0.00 38.41 4.52
4353 14920 2.754946 ACCAATTGGCATTGCAAGAG 57.245 45.000 24.79 0.80 38.88 2.85
4357 14924 1.935799 AGGTACCAATTGGCATTGCA 58.064 45.000 24.79 0.01 38.88 4.08
4380 14947 1.478916 GCTCCTGTACCTTCTCCAGAC 59.521 57.143 0.00 0.00 0.00 3.51
4447 15014 5.693555 CCAAAGAATTTCTGGAGTTGCTTTC 59.306 40.000 0.00 0.00 35.03 2.62
4529 15096 9.092876 CACAAATAACAAGGAGCAAAACTTTAA 57.907 29.630 0.00 0.00 0.00 1.52
4544 15325 7.794810 CGAGATAACGTGAAACACAAATAACAA 59.205 33.333 0.00 0.00 35.74 2.83
4565 15346 8.535335 ACCTGTATCAAAATATATGAGCGAGAT 58.465 33.333 0.00 0.00 0.00 2.75
4570 15351 7.678947 AGCACCTGTATCAAAATATATGAGC 57.321 36.000 0.00 0.00 0.00 4.26
4576 15357 6.742109 GCATCAAGCACCTGTATCAAAATAT 58.258 36.000 0.00 0.00 44.79 1.28
4635 15422 3.797039 TCTCGCCTATGGAGTTCATTTG 58.203 45.455 0.00 0.00 37.30 2.32
4639 15428 1.757118 CCTTCTCGCCTATGGAGTTCA 59.243 52.381 0.00 0.00 33.26 3.18
4640 15429 1.757699 ACCTTCTCGCCTATGGAGTTC 59.242 52.381 0.00 0.00 33.26 3.01
4686 15475 0.466007 TTGGCTGCAGTCTTCTTGCA 60.466 50.000 20.86 0.00 37.04 4.08
4688 15477 1.000938 GGTTTGGCTGCAGTCTTCTTG 60.001 52.381 20.86 0.00 0.00 3.02
4777 17439 5.520649 TGCAGGTTTCGTTTCAAAATTTACC 59.479 36.000 0.00 0.00 0.00 2.85
4779 17441 5.233263 GCTGCAGGTTTCGTTTCAAAATTTA 59.767 36.000 17.12 0.00 0.00 1.40
4892 17582 8.720562 GCACTTGCCTATGAAATTGTTAATTTT 58.279 29.630 1.55 0.00 36.81 1.82
4947 17638 3.303760 GCCAGACGATCTTTTAGTTCGAC 59.696 47.826 12.53 7.55 39.16 4.20
4983 17674 1.279496 TGTTCTGGAGGGGAGTCATG 58.721 55.000 0.00 0.00 0.00 3.07
5111 18181 0.676151 CCTTCCTGCTGTCCTTCTGC 60.676 60.000 0.00 0.00 40.62 4.26
5149 18219 2.330254 CACGCCTCTTTTGCTTGGA 58.670 52.632 0.00 0.00 0.00 3.53
5173 18243 4.974721 AAGGGTGCCGTGGCCTTG 62.975 66.667 8.69 0.00 41.09 3.61
5191 18262 0.959553 TCTCACCAGACAACTCGGTC 59.040 55.000 0.00 0.00 38.08 4.79
5230 18304 2.866156 CTCAACTTGCACTTCTTCGACA 59.134 45.455 0.00 0.00 0.00 4.35
5293 18367 3.328050 CCCTCTTCCTGTTGGTAGTCTTT 59.672 47.826 0.00 0.00 33.18 2.52
5399 18473 2.203195 TGTCTGCGCAACCAAGCT 60.203 55.556 13.05 0.00 0.00 3.74
5421 18513 2.091389 AGAGGAGCCTCAGCATCTTCTA 60.091 50.000 18.16 0.00 44.99 2.10
5647 18740 4.998051 ACCATCTCTATCTCCTTCTCCTC 58.002 47.826 0.00 0.00 0.00 3.71
5810 18964 6.040842 TGCCTACAAGAAGCTTTGAAGATTTT 59.959 34.615 0.00 0.00 34.31 1.82
5938 19092 2.512692 TGCCAGGACAAAGCACATAT 57.487 45.000 0.00 0.00 0.00 1.78
6063 19217 7.095187 GGCTAACGCTACAGCTGAAATAATATT 60.095 37.037 23.35 6.57 37.91 1.28
6291 19445 6.859508 CGTATAGTTCGGTATGTGAAGCATAA 59.140 38.462 0.00 0.00 41.29 1.90
6359 19513 5.888691 TTGCTGTTAACAAAGTCTGTCAA 57.111 34.783 10.03 3.61 37.23 3.18


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

AutoCloner maintained by Alex Coulton.