Multiple sequence alignment - TraesCS3B01G006500

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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 TraesCS3B01G006500 chr3B 100.000 3483 0 0 1 3483 3406299 3409781 0.000000e+00 6433.0
1 TraesCS3B01G006500 chr3B 90.273 1357 85 21 55 1379 5324512 5323171 0.000000e+00 1731.0
2 TraesCS3B01G006500 chr3B 87.628 1269 91 27 854 2108 3667380 3666164 0.000000e+00 1413.0
3 TraesCS3B01G006500 chr3B 89.003 1164 73 16 959 2108 5169064 5170186 0.000000e+00 1389.0
4 TraesCS3B01G006500 chr3B 91.088 965 64 13 1899 2862 5322652 5321709 0.000000e+00 1286.0
5 TraesCS3B01G006500 chr3B 82.579 442 69 7 106 543 3610485 3610922 1.960000e-102 383.0
6 TraesCS3B01G006500 chr3B 82.500 440 73 4 106 543 5226207 5225770 1.960000e-102 383.0
7 TraesCS3B01G006500 chr3B 92.647 204 15 0 3280 3483 5321306 5321103 9.450000e-76 294.0
8 TraesCS3B01G006500 chr3B 88.177 203 17 3 2414 2616 3625833 3626028 5.810000e-58 235.0
9 TraesCS3B01G006500 chr3B 83.475 236 23 14 2310 2538 3665866 3665640 4.560000e-49 206.0
10 TraesCS3B01G006500 chr3B 83.404 235 23 14 2311 2538 5170484 5170709 1.640000e-48 204.0
11 TraesCS3B01G006500 chr3B 83.408 223 28 4 540 762 3610958 3611171 7.630000e-47 198.0
12 TraesCS3B01G006500 chr3B 83.636 220 27 4 543 762 5225731 5225521 7.630000e-47 198.0
13 TraesCS3B01G006500 chr3B 81.250 288 15 11 2906 3184 5321594 5321337 2.740000e-46 196.0
14 TraesCS3B01G006500 chr3D 91.109 1136 74 12 937 2071 1337531 1338640 0.000000e+00 1513.0
15 TraesCS3B01G006500 chr3D 95.672 439 13 5 937 1374 1640646 1640213 0.000000e+00 701.0
16 TraesCS3B01G006500 chr3D 85.735 687 69 11 1422 2103 1591396 1592058 0.000000e+00 699.0
17 TraesCS3B01G006500 chr3D 93.925 428 25 1 2983 3409 1339816 1340243 0.000000e+00 645.0
18 TraesCS3B01G006500 chr3D 89.139 488 50 3 57 543 1641539 1641054 3.850000e-169 604.0
19 TraesCS3B01G006500 chr3D 89.234 483 49 3 62 543 1336629 1337109 4.970000e-168 601.0
20 TraesCS3B01G006500 chr3D 90.974 421 22 9 853 1273 1644239 1643835 1.410000e-153 553.0
21 TraesCS3B01G006500 chr3D 90.339 383 22 7 543 915 1641015 1640638 4.040000e-134 488.0
22 TraesCS3B01G006500 chr3D 89.421 397 19 4 540 915 1337145 1337539 2.430000e-131 479.0
23 TraesCS3B01G006500 chr3D 86.455 347 31 11 2215 2553 1338984 1339322 1.980000e-97 366.0
24 TraesCS3B01G006500 chr3D 87.687 268 22 3 2590 2857 1339323 1339579 5.650000e-78 302.0
25 TraesCS3B01G006500 chr3D 87.435 191 19 4 2351 2538 1639106 1638918 7.570000e-52 215.0
26 TraesCS3B01G006500 chr3D 82.353 221 30 1 543 763 1523587 1523798 2.140000e-42 183.0
27 TraesCS3B01G006500 chr3A 90.521 844 42 13 588 1422 7477206 7476392 0.000000e+00 1081.0
28 TraesCS3B01G006500 chr3A 92.926 311 19 3 224 532 7477528 7477219 1.910000e-122 449.0
29 TraesCS3B01G006500 chr3A 90.909 209 14 4 1899 2107 7475900 7475697 3.420000e-70 276.0
30 TraesCS3B01G006500 chr3A 85.864 191 22 4 2351 2538 7475373 7475185 7.630000e-47 198.0
31 TraesCS3B01G006500 chr7D 96.783 373 12 0 994 1366 7302269 7301897 1.060000e-174 623.0
32 TraesCS3B01G006500 chr7D 86.719 128 17 0 1939 2066 7301777 7301650 3.620000e-30 143.0
33 TraesCS3B01G006500 chr7D 93.333 90 6 0 2397 2486 7300734 7300645 2.180000e-27 134.0
34 TraesCS3B01G006500 chr7A 96.515 373 13 0 994 1366 8262589 8262217 4.940000e-173 617.0
35 TraesCS3B01G006500 chr7A 83.509 285 44 3 3111 3393 725193620 725193903 2.670000e-66 263.0
36 TraesCS3B01G006500 chr7A 87.500 128 16 0 1939 2066 8262112 8261985 7.790000e-32 148.0
37 TraesCS3B01G006500 chr4A 95.979 373 15 0 994 1366 732517265 732516893 1.070000e-169 606.0
38 TraesCS3B01G006500 chr5B 80.777 515 77 15 2980 3483 457081716 457082219 1.960000e-102 383.0
39 TraesCS3B01G006500 chr7B 88.189 127 15 0 1940 2066 150374241 150374115 6.020000e-33 152.0
40 TraesCS3B01G006500 chr7B 94.444 36 0 2 7 42 110687169 110687136 2.000000e-03 54.7
41 TraesCS3B01G006500 chr6B 93.333 90 6 0 2397 2486 265677438 265677349 2.180000e-27 134.0
42 TraesCS3B01G006500 chrUn 85.294 68 6 4 55 122 30189147 30189084 2.240000e-07 67.6
43 TraesCS3B01G006500 chr5D 100.000 34 0 0 1 34 259455764 259455797 2.900000e-06 63.9
44 TraesCS3B01G006500 chr2D 100.000 34 0 0 1 34 485994942 485994909 2.900000e-06 63.9
45 TraesCS3B01G006500 chr2B 100.000 33 0 0 2 34 474542100 474542068 1.040000e-05 62.1
46 TraesCS3B01G006500 chr2B 88.679 53 1 1 1 48 11321442 11321390 3.750000e-05 60.2
47 TraesCS3B01G006500 chr6A 88.462 52 2 3 1 48 101544304 101544253 3.750000e-05 60.2
48 TraesCS3B01G006500 chr6D 97.059 34 1 0 1 34 305186081 305186114 1.350000e-04 58.4
49 TraesCS3B01G006500 chr6D 97.059 34 1 0 1 34 377836886 377836853 1.350000e-04 58.4
50 TraesCS3B01G006500 chr6D 97.059 34 1 0 1 34 404335073 404335106 1.350000e-04 58.4


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 TraesCS3B01G006500 chr3B 3406299 3409781 3482 False 6433.00 6433 100.000000 1 3483 1 chr3B.!!$F1 3482
1 TraesCS3B01G006500 chr3B 5321103 5324512 3409 True 876.75 1731 88.814500 55 3483 4 chr3B.!!$R3 3428
2 TraesCS3B01G006500 chr3B 3665640 3667380 1740 True 809.50 1413 85.551500 854 2538 2 chr3B.!!$R1 1684
3 TraesCS3B01G006500 chr3B 5169064 5170709 1645 False 796.50 1389 86.203500 959 2538 2 chr3B.!!$F4 1579
4 TraesCS3B01G006500 chr3B 3610485 3611171 686 False 290.50 383 82.993500 106 762 2 chr3B.!!$F3 656
5 TraesCS3B01G006500 chr3B 5225521 5226207 686 True 290.50 383 83.068000 106 762 2 chr3B.!!$R2 656
6 TraesCS3B01G006500 chr3D 1591396 1592058 662 False 699.00 699 85.735000 1422 2103 1 chr3D.!!$F2 681
7 TraesCS3B01G006500 chr3D 1336629 1340243 3614 False 651.00 1513 89.638500 62 3409 6 chr3D.!!$F3 3347
8 TraesCS3B01G006500 chr3D 1638918 1644239 5321 True 512.20 701 90.711800 57 2538 5 chr3D.!!$R1 2481
9 TraesCS3B01G006500 chr3A 7475185 7477528 2343 True 501.00 1081 90.055000 224 2538 4 chr3A.!!$R1 2314
10 TraesCS3B01G006500 chr7D 7300645 7302269 1624 True 300.00 623 92.278333 994 2486 3 chr7D.!!$R1 1492
11 TraesCS3B01G006500 chr7A 8261985 8262589 604 True 382.50 617 92.007500 994 2066 2 chr7A.!!$R1 1072
12 TraesCS3B01G006500 chr5B 457081716 457082219 503 False 383.00 383 80.777000 2980 3483 1 chr5B.!!$F1 503

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
547 3236 0.033503 TCCAGACATCGGGAGCTACA 60.034 55.0 0.00 0.00 35.30 2.74 F
619 3308 0.814010 AGATGTTAACGCGGGCATCC 60.814 55.0 21.64 10.71 38.67 3.51 F
1497 4269 0.804989 AGCTGCGGCAGAAACATTAC 59.195 50.0 32.72 12.56 41.70 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1388 4160 0.321564 CCGATCTGACTGTTTGGCCA 60.322 55.0 0.00 0.0 0.00 5.36 R
2300 5676 0.512952 GCGACTGCAACACTTGTAGG 59.487 55.0 5.27 0.0 46.05 3.18 R
2715 6687 0.250295 AACAGCAGGCAAAGTAGCGA 60.250 50.0 0.00 0.0 34.64 4.93 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
18 19 2.662150 GACGCGCGGTTTAAGAGAT 58.338 52.632 35.22 8.59 0.00 2.75
19 20 1.831343 GACGCGCGGTTTAAGAGATA 58.169 50.000 35.22 0.00 0.00 1.98
20 21 2.187707 GACGCGCGGTTTAAGAGATAA 58.812 47.619 35.22 0.00 0.00 1.75
22 23 2.995258 ACGCGCGGTTTAAGAGATAAAA 59.005 40.909 35.22 0.00 35.33 1.52
23 24 3.619929 ACGCGCGGTTTAAGAGATAAAAT 59.380 39.130 35.22 2.79 35.33 1.82
24 25 3.960002 CGCGCGGTTTAAGAGATAAAATG 59.040 43.478 24.84 0.00 35.33 2.32
25 26 4.493545 CGCGCGGTTTAAGAGATAAAATGT 60.494 41.667 24.84 0.00 35.33 2.71
26 27 5.329493 GCGCGGTTTAAGAGATAAAATGTT 58.671 37.500 8.83 0.00 35.33 2.71
27 28 5.798434 GCGCGGTTTAAGAGATAAAATGTTT 59.202 36.000 8.83 0.00 35.33 2.83
28 29 6.307077 GCGCGGTTTAAGAGATAAAATGTTTT 59.693 34.615 8.83 0.00 35.33 2.43
29 30 7.653783 CGCGGTTTAAGAGATAAAATGTTTTG 58.346 34.615 0.00 0.00 35.33 2.44
30 31 7.535940 CGCGGTTTAAGAGATAAAATGTTTTGA 59.464 33.333 0.00 0.00 35.33 2.69
31 32 9.187455 GCGGTTTAAGAGATAAAATGTTTTGAA 57.813 29.630 1.16 0.00 35.33 2.69
75 2720 3.245984 TGAGGAGGTGGGAGTGATCTTTA 60.246 47.826 0.00 0.00 0.00 1.85
88 2733 8.315482 GGGAGTGATCTTTAAAAGAAGTACTCT 58.685 37.037 7.64 0.00 41.03 3.24
119 2764 2.168326 TCTTGCGAGATGAAGCACAA 57.832 45.000 0.00 0.00 43.69 3.33
172 2817 2.039746 CCACTTCTAACCCATGACCACA 59.960 50.000 0.00 0.00 0.00 4.17
184 2829 3.561960 CCATGACCACAAATTCCCTCTCA 60.562 47.826 0.00 0.00 0.00 3.27
255 2902 3.988525 GTGCCATTGTTGCCGCCA 61.989 61.111 0.00 0.00 0.00 5.69
257 2904 4.440127 GCCATTGTTGCCGCCAGG 62.440 66.667 0.00 0.00 41.62 4.45
390 3039 0.104304 AGACCATTATGGCGTCGGAC 59.896 55.000 11.72 0.00 42.67 4.79
433 3082 2.738521 CCGTGAAGGTGTCAGCGG 60.739 66.667 0.00 0.00 41.35 5.52
512 3162 7.388500 ACTTACAAATGGGCAAGATTGAAATTG 59.612 33.333 0.00 0.00 0.00 2.32
532 3182 3.995199 TGAACTGTTGAAGTAGCTCCAG 58.005 45.455 0.00 0.00 38.56 3.86
534 3184 3.669251 ACTGTTGAAGTAGCTCCAGAC 57.331 47.619 0.00 0.00 37.36 3.51
547 3236 0.033503 TCCAGACATCGGGAGCTACA 60.034 55.000 0.00 0.00 35.30 2.74
563 3252 2.550978 CTACAACGGAGATCGGCAATT 58.449 47.619 0.00 0.00 44.45 2.32
598 3287 2.611473 CGACAAGGCATATCTAGGCAGG 60.611 54.545 0.00 0.00 34.14 4.85
603 3292 1.558756 GGCATATCTAGGCAGGCAGAT 59.441 52.381 11.77 11.77 34.14 2.90
612 3301 1.060937 GCAGGCAGATGTTAACGCG 59.939 57.895 3.53 3.53 0.00 6.01
619 3308 0.814010 AGATGTTAACGCGGGCATCC 60.814 55.000 21.64 10.71 38.67 3.51
722 3450 0.981183 AGTAACTGATGTTGGGCCGA 59.019 50.000 0.00 0.00 37.59 5.54
957 3701 4.063967 CGCCGCACCACCACTCTA 62.064 66.667 0.00 0.00 0.00 2.43
964 3708 3.379445 CCACCACTCTACCGCCGT 61.379 66.667 0.00 0.00 0.00 5.68
1014 3776 2.482142 GGCGAAGATGAAGACGATCCTT 60.482 50.000 0.00 0.00 0.00 3.36
1424 4196 1.812214 CGGCGAGCTCGATTTAGTGC 61.812 60.000 38.74 18.13 43.02 4.40
1484 4256 2.096218 GTGTTCTTCTGGTTTAGCTGCG 60.096 50.000 0.00 0.00 0.00 5.18
1497 4269 0.804989 AGCTGCGGCAGAAACATTAC 59.195 50.000 32.72 12.56 41.70 1.89
1562 4405 5.683681 ACCATTCTGTATATGTGATGTGCA 58.316 37.500 0.00 0.00 0.00 4.57
1572 4415 4.627611 ATGTGATGTGCATGTAGCTTTC 57.372 40.909 0.00 0.00 45.94 2.62
1649 4534 4.100653 TGAATGCAATTTGTTCACCTTGGA 59.899 37.500 0.00 0.00 36.07 3.53
1752 4642 1.279271 ACAGGGGTCAGTAGCATTGTC 59.721 52.381 0.00 0.00 0.00 3.18
1768 4663 6.998802 AGCATTGTCTACTCTAGTCTTTGTT 58.001 36.000 0.00 0.00 0.00 2.83
1796 4694 1.486310 TGACCCATAGTGCTGCCTAAG 59.514 52.381 0.00 0.00 0.00 2.18
1821 4736 1.072173 ACTTGAGTGTGCTATGCCACA 59.928 47.619 11.50 0.00 42.99 4.17
1872 4790 5.009610 GGTTTGGCTTTTATCTCTTGTGACA 59.990 40.000 0.00 0.00 0.00 3.58
1879 4797 7.275999 GGCTTTTATCTCTTGTGACACTACTAC 59.724 40.741 7.20 0.00 0.00 2.73
1887 4805 6.330278 TCTTGTGACACTACTACATATGTGC 58.670 40.000 18.81 0.00 34.14 4.57
1897 4823 8.450180 CACTACTACATATGTGCATTGTTCAAA 58.550 33.333 18.81 0.00 0.00 2.69
1911 4837 8.874816 TGCATTGTTCAAATCATGTATGAAATG 58.125 29.630 10.57 11.83 40.69 2.32
2227 5497 3.684305 TCTGTCGATGCGATTTGTTTCAT 59.316 39.130 0.00 0.00 38.42 2.57
2263 5589 9.341899 CACTAGTATTTAAGTGAAACATTTGCC 57.658 33.333 0.00 0.00 44.79 4.52
2295 5671 9.166173 TGTCTGAATGAATGAACTATTACTTGG 57.834 33.333 0.00 0.00 0.00 3.61
2296 5672 9.167311 GTCTGAATGAATGAACTATTACTTGGT 57.833 33.333 0.00 0.00 0.00 3.67
2301 5677 9.614792 AATGAATGAACTATTACTTGGTACTCC 57.385 33.333 0.00 0.00 0.00 3.85
2366 5781 5.765182 TGAAGTGACGATCATCTCTATGCTA 59.235 40.000 0.00 0.00 32.76 3.49
2407 6378 1.098050 GCTCGAACCAGAAATGCCAT 58.902 50.000 0.00 0.00 0.00 4.40
2419 6390 5.291178 CAGAAATGCCATGTGAAGAACAAA 58.709 37.500 0.00 0.00 43.61 2.83
2537 6509 5.130350 TGTAGCTTTTAACAGAAACTGCCT 58.870 37.500 0.00 0.00 34.37 4.75
2540 6512 6.901081 AGCTTTTAACAGAAACTGCCTTAT 57.099 33.333 0.00 0.00 34.37 1.73
2611 6583 1.615883 CTGTACTGGATCGATCAGGGG 59.384 57.143 25.93 14.32 36.62 4.79
2629 6601 2.093447 GGGGTGTCATGTAACTGGAGAG 60.093 54.545 0.00 0.00 0.00 3.20
2631 6603 2.622436 GTGTCATGTAACTGGAGAGGC 58.378 52.381 0.00 0.00 0.00 4.70
2658 6630 3.563808 TCCTTGGAGATGTGTTTGTTTCG 59.436 43.478 0.00 0.00 0.00 3.46
2660 6632 2.293170 TGGAGATGTGTTTGTTTCGCA 58.707 42.857 0.00 0.00 0.00 5.10
2690 6662 5.365021 AATACCTCTTGTTATCTGCTGCT 57.635 39.130 0.00 0.00 0.00 4.24
2691 6663 2.983229 ACCTCTTGTTATCTGCTGCTG 58.017 47.619 0.00 0.00 0.00 4.41
2693 6665 2.935201 CCTCTTGTTATCTGCTGCTGTC 59.065 50.000 0.00 0.00 0.00 3.51
2694 6666 3.369261 CCTCTTGTTATCTGCTGCTGTCT 60.369 47.826 0.00 0.00 0.00 3.41
2698 6670 4.754372 TGTTATCTGCTGCTGTCTTTTG 57.246 40.909 0.00 0.00 0.00 2.44
2715 6687 3.608316 TTTGTTTGCTTGAGCCTTGTT 57.392 38.095 0.00 0.00 41.18 2.83
2716 6688 2.869233 TGTTTGCTTGAGCCTTGTTC 57.131 45.000 0.00 0.00 41.18 3.18
2730 6702 0.591170 TTGTTCGCTACTTTGCCTGC 59.409 50.000 0.00 0.00 0.00 4.85
2736 6708 1.128692 CGCTACTTTGCCTGCTGTTAC 59.871 52.381 0.00 0.00 0.00 2.50
2761 6733 2.039746 TGCTACACCTACACTTGCCAAT 59.960 45.455 0.00 0.00 0.00 3.16
2797 6769 1.399714 TTGACGTGTCCTCTGACTGT 58.600 50.000 0.00 0.00 42.28 3.55
2837 6810 1.798813 CACTTGCAGTTTCGTCCCTAC 59.201 52.381 0.00 0.00 0.00 3.18
2862 6835 7.766278 ACTCAGCCAAGTTTTGTATCTATGTAG 59.234 37.037 0.00 0.00 0.00 2.74
2864 6837 8.100791 TCAGCCAAGTTTTGTATCTATGTAGTT 58.899 33.333 0.00 0.00 0.00 2.24
2953 6995 1.616628 ACCTCCATGACTCCACCCC 60.617 63.158 0.00 0.00 0.00 4.95
2954 6996 1.616327 CCTCCATGACTCCACCCCA 60.616 63.158 0.00 0.00 0.00 4.96
2959 7001 3.254024 ATGACTCCACCCCACGCAC 62.254 63.158 0.00 0.00 0.00 5.34
2973 7040 1.374758 CGCACCTCTCCCTTGACAC 60.375 63.158 0.00 0.00 0.00 3.67
2978 7045 2.203788 TCTCCCTTGACACGGCCT 60.204 61.111 0.00 0.00 0.00 5.19
2979 7046 2.046892 CTCCCTTGACACGGCCTG 60.047 66.667 0.00 0.21 0.00 4.85
2981 7048 2.358737 CCCTTGACACGGCCTGAC 60.359 66.667 0.00 0.00 0.00 3.51
2985 7154 1.831389 CTTGACACGGCCTGACAACG 61.831 60.000 13.07 8.22 32.16 4.10
3111 7288 0.669318 CGCCGAAAGCTACAACCAGA 60.669 55.000 0.00 0.00 40.39 3.86
3112 7289 1.519408 GCCGAAAGCTACAACCAGAA 58.481 50.000 0.00 0.00 38.99 3.02
3113 7290 1.197036 GCCGAAAGCTACAACCAGAAC 59.803 52.381 0.00 0.00 38.99 3.01
3114 7291 2.767505 CCGAAAGCTACAACCAGAACT 58.232 47.619 0.00 0.00 0.00 3.01
3115 7292 2.480419 CCGAAAGCTACAACCAGAACTG 59.520 50.000 0.00 0.00 0.00 3.16
3116 7293 2.096218 CGAAAGCTACAACCAGAACTGC 60.096 50.000 0.00 0.00 0.00 4.40
3117 7294 2.938956 AAGCTACAACCAGAACTGCT 57.061 45.000 0.00 0.00 0.00 4.24
3118 7295 2.464157 AGCTACAACCAGAACTGCTC 57.536 50.000 0.00 0.00 0.00 4.26
3119 7296 1.694150 AGCTACAACCAGAACTGCTCA 59.306 47.619 0.00 0.00 0.00 4.26
3120 7297 2.104792 AGCTACAACCAGAACTGCTCAA 59.895 45.455 0.00 0.00 0.00 3.02
3121 7298 2.878406 GCTACAACCAGAACTGCTCAAA 59.122 45.455 0.00 0.00 0.00 2.69
3122 7299 3.304057 GCTACAACCAGAACTGCTCAAAC 60.304 47.826 0.00 0.00 0.00 2.93
3123 7300 2.024414 ACAACCAGAACTGCTCAAACC 58.976 47.619 0.00 0.00 0.00 3.27
3124 7301 2.023673 CAACCAGAACTGCTCAAACCA 58.976 47.619 0.00 0.00 0.00 3.67
3125 7302 1.972872 ACCAGAACTGCTCAAACCAG 58.027 50.000 0.00 0.00 36.41 4.00
3126 7303 1.212935 ACCAGAACTGCTCAAACCAGT 59.787 47.619 0.00 0.00 44.92 4.00
3159 7352 2.564062 CTGGAACCAACTACTACCGGAA 59.436 50.000 9.46 0.00 0.00 4.30
3207 7401 0.675633 AGCGACCTTTTTGCTGCAAT 59.324 45.000 16.77 0.00 44.13 3.56
3208 7402 1.069049 AGCGACCTTTTTGCTGCAATT 59.931 42.857 16.77 0.00 44.13 2.32
3213 7407 1.192980 CCTTTTTGCTGCAATTGTCGC 59.807 47.619 16.77 10.35 0.00 5.19
3250 7444 0.733150 GGCGAGGGAATTTGCTACAC 59.267 55.000 0.00 0.00 0.00 2.90
3289 7483 0.465705 TAGTGCTATGACCTGGCAGC 59.534 55.000 9.56 0.00 42.62 5.25
3309 7504 2.029918 GCCGATTTTCTTTGCTGGAACT 60.030 45.455 0.00 0.00 0.00 3.01
3312 7507 3.004734 CGATTTTCTTTGCTGGAACTGGT 59.995 43.478 0.00 0.00 0.00 4.00
3320 7515 1.974957 TGCTGGAACTGGTTACTAGCA 59.025 47.619 14.22 14.22 36.18 3.49
3445 7640 2.235016 ACCGGCATCAACAAAAGCTAA 58.765 42.857 0.00 0.00 0.00 3.09
3454 7649 5.705609 TCAACAAAAGCTAAATCCACCTC 57.294 39.130 0.00 0.00 0.00 3.85
3474 7669 2.053627 CTTTGTTTTGCTGCGATGGTC 58.946 47.619 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.644805 TTTTATCTCTTAAACCGCGCG 57.355 42.857 25.67 25.67 29.47 6.86
3 4 4.905269 ACATTTTATCTCTTAAACCGCGC 58.095 39.130 0.00 0.00 29.47 6.86
5 6 8.736751 TCAAAACATTTTATCTCTTAAACCGC 57.263 30.769 0.00 0.00 29.47 5.68
42 43 3.245407 CCCACCTCCTCAAAGATCCTTTT 60.245 47.826 0.00 0.00 0.00 2.27
44 45 1.918957 CCCACCTCCTCAAAGATCCTT 59.081 52.381 0.00 0.00 0.00 3.36
45 46 1.081174 TCCCACCTCCTCAAAGATCCT 59.919 52.381 0.00 0.00 0.00 3.24
46 47 1.488393 CTCCCACCTCCTCAAAGATCC 59.512 57.143 0.00 0.00 0.00 3.36
48 49 1.912043 CACTCCCACCTCCTCAAAGAT 59.088 52.381 0.00 0.00 0.00 2.40
49 50 1.132849 TCACTCCCACCTCCTCAAAGA 60.133 52.381 0.00 0.00 0.00 2.52
50 51 1.352083 TCACTCCCACCTCCTCAAAG 58.648 55.000 0.00 0.00 0.00 2.77
51 52 1.909302 GATCACTCCCACCTCCTCAAA 59.091 52.381 0.00 0.00 0.00 2.69
52 53 1.079490 AGATCACTCCCACCTCCTCAA 59.921 52.381 0.00 0.00 0.00 3.02
53 54 0.712979 AGATCACTCCCACCTCCTCA 59.287 55.000 0.00 0.00 0.00 3.86
59 60 6.004574 ACTTCTTTTAAAGATCACTCCCACC 58.995 40.000 8.31 0.00 37.38 4.61
119 2764 5.298347 TGAACCAAACGTCCTTTTTGTTTT 58.702 33.333 0.00 0.00 33.80 2.43
172 2817 1.673168 GCTCGCATGAGAGGGAATTT 58.327 50.000 25.22 0.00 45.57 1.82
184 2829 1.447838 CTACGGTTGTGGCTCGCAT 60.448 57.895 0.00 0.00 0.00 4.73
255 2902 1.380302 GGTTGTGCTGGGATGTCCT 59.620 57.895 0.00 0.00 36.20 3.85
257 2904 2.690778 GCGGTTGTGCTGGGATGTC 61.691 63.158 0.00 0.00 0.00 3.06
301 2948 2.046285 GCGGTTGTGCTGGGCTATT 61.046 57.895 0.00 0.00 0.00 1.73
390 3039 0.678395 CCTCCAGGATCTCCATCGTG 59.322 60.000 0.00 0.00 42.34 4.35
429 3078 1.069823 GTCACCATGATCATCTCCGCT 59.930 52.381 4.86 0.00 0.00 5.52
433 3082 1.270518 CCCCGTCACCATGATCATCTC 60.271 57.143 4.86 0.00 0.00 2.75
467 3116 1.082104 GCTTTGAAGTTGCGGGTCG 60.082 57.895 0.00 0.00 0.00 4.79
512 3162 3.991121 GTCTGGAGCTACTTCAACAGTTC 59.009 47.826 0.00 0.00 36.88 3.01
532 3182 0.527817 CCGTTGTAGCTCCCGATGTC 60.528 60.000 0.00 0.00 0.00 3.06
534 3184 0.249073 CTCCGTTGTAGCTCCCGATG 60.249 60.000 0.00 0.00 0.00 3.84
547 3236 0.251916 TGGAATTGCCGATCTCCGTT 59.748 50.000 0.00 0.00 40.66 4.44
563 3252 2.498481 CCTTGTCGGTATACTTGGTGGA 59.502 50.000 2.25 0.00 0.00 4.02
598 3287 1.714899 ATGCCCGCGTTAACATCTGC 61.715 55.000 4.92 3.54 0.00 4.26
603 3292 1.743623 CAGGATGCCCGCGTTAACA 60.744 57.895 4.92 0.00 37.58 2.41
612 3301 0.465460 TTAATGCGACCAGGATGCCC 60.465 55.000 0.00 0.00 31.97 5.36
619 3308 2.607635 AGCGTTATGTTAATGCGACCAG 59.392 45.455 5.97 0.00 37.26 4.00
722 3450 0.443869 GTGCGTGAATCAATCTGCGT 59.556 50.000 0.00 0.00 34.23 5.24
777 3513 2.291605 GGTTTGGCCCAATACTCCTCTT 60.292 50.000 0.00 0.00 0.00 2.85
846 3585 1.723220 GTCGCTAGGGTTTTCTGTCC 58.277 55.000 6.70 0.00 0.00 4.02
950 3694 4.849329 GCGACGGCGGTAGAGTGG 62.849 72.222 15.06 0.00 38.16 4.00
951 3695 4.849329 GGCGACGGCGGTAGAGTG 62.849 72.222 15.06 0.00 41.24 3.51
964 3708 2.440430 CTTCCTCCTCCTCGGCGA 60.440 66.667 10.14 10.14 0.00 5.54
1050 3812 1.006102 CTTCGCCGACACCTTCACT 60.006 57.895 0.00 0.00 0.00 3.41
1098 3860 1.166531 GCTTGAAGTTGCGGGTCAGT 61.167 55.000 0.00 0.00 0.00 3.41
1387 4159 1.522668 CGATCTGACTGTTTGGCCAA 58.477 50.000 16.05 16.05 0.00 4.52
1388 4160 0.321564 CCGATCTGACTGTTTGGCCA 60.322 55.000 0.00 0.00 0.00 5.36
1389 4161 1.648467 GCCGATCTGACTGTTTGGCC 61.648 60.000 0.00 0.00 38.44 5.36
1444 4216 6.265196 AGAACACATTTTCTATGCACAGGAAA 59.735 34.615 0.00 0.00 33.89 3.13
1445 4217 5.769662 AGAACACATTTTCTATGCACAGGAA 59.230 36.000 0.00 0.00 33.89 3.36
1484 4256 3.437049 GTCCACTCAGTAATGTTTCTGCC 59.563 47.826 0.00 0.00 0.00 4.85
1497 4269 5.163642 ACTGCGTATAAACTAGTCCACTCAG 60.164 44.000 0.00 5.38 0.00 3.35
1516 4359 3.681417 TCATGAACAGAGATTTGACTGCG 59.319 43.478 0.00 0.00 37.61 5.18
1562 4405 3.054139 TGATGGGCAGAAGAAAGCTACAT 60.054 43.478 0.00 0.00 33.46 2.29
1572 4415 1.064166 AGGTGGATTGATGGGCAGAAG 60.064 52.381 0.00 0.00 0.00 2.85
1649 4534 6.707290 CATTATTGGCATCAATGATCCCAAT 58.293 36.000 28.34 28.34 45.42 3.16
1679 4566 7.138692 ACATCTCAAATAAGCTTGACAGAAC 57.861 36.000 9.86 0.00 32.00 3.01
1752 4642 5.723672 TCACCCAACAAAGACTAGAGTAG 57.276 43.478 0.00 0.00 0.00 2.57
1796 4694 3.365364 GGCATAGCACACTCAAGTTTGTC 60.365 47.826 0.00 0.00 0.00 3.18
1821 4736 6.272318 ACATCACAAACGTTCAATGTCAAAT 58.728 32.000 0.00 0.00 0.00 2.32
1872 4790 8.560355 TTTGAACAATGCACATATGTAGTAGT 57.440 30.769 8.32 1.44 0.00 2.73
1879 4797 7.764695 ACATGATTTGAACAATGCACATATG 57.235 32.000 0.00 0.00 0.00 1.78
1887 4805 9.373603 ACCATTTCATACATGATTTGAACAATG 57.626 29.630 0.00 7.10 36.56 2.82
1897 4823 8.985315 AACATCAGTACCATTTCATACATGAT 57.015 30.769 0.00 0.00 36.56 2.45
1911 4837 4.327680 AGGAAAGCAAGAACATCAGTACC 58.672 43.478 0.00 0.00 0.00 3.34
2012 4938 2.686405 GAGCTCAATGTCATTGCCATCA 59.314 45.455 19.02 2.68 40.05 3.07
2294 5670 3.244112 ACTGCAACACTTGTAGGAGTACC 60.244 47.826 5.27 0.00 46.05 3.34
2295 5671 3.988517 GACTGCAACACTTGTAGGAGTAC 59.011 47.826 5.27 0.00 46.05 2.73
2296 5672 3.305131 CGACTGCAACACTTGTAGGAGTA 60.305 47.826 5.27 0.00 46.05 2.59
2297 5673 2.545952 CGACTGCAACACTTGTAGGAGT 60.546 50.000 5.27 0.00 46.05 3.85
2298 5674 2.061773 CGACTGCAACACTTGTAGGAG 58.938 52.381 5.27 0.00 46.05 3.69
2299 5675 1.872237 GCGACTGCAACACTTGTAGGA 60.872 52.381 5.27 0.00 46.05 2.94
2300 5676 0.512952 GCGACTGCAACACTTGTAGG 59.487 55.000 5.27 0.00 46.05 3.18
2407 6378 5.034852 TCCTGATGTCTTTGTTCTTCACA 57.965 39.130 0.00 0.00 0.00 3.58
2419 6390 3.306364 CGTCCAAGAACTTCCTGATGTCT 60.306 47.826 0.00 0.00 0.00 3.41
2578 6550 2.884012 CCAGTACAGATTGCAACCAACA 59.116 45.455 0.00 0.00 32.95 3.33
2584 6556 3.885724 TCGATCCAGTACAGATTGCAA 57.114 42.857 0.00 0.00 0.00 4.08
2611 6583 2.234908 AGCCTCTCCAGTTACATGACAC 59.765 50.000 0.00 0.00 0.00 3.67
2629 6601 1.815003 CACATCTCCAAGGAACAAGCC 59.185 52.381 0.00 0.00 0.00 4.35
2631 6603 4.339247 ACAAACACATCTCCAAGGAACAAG 59.661 41.667 0.00 0.00 0.00 3.16
2690 6662 2.760092 AGGCTCAAGCAAACAAAAGACA 59.240 40.909 4.13 0.00 44.36 3.41
2691 6663 3.443099 AGGCTCAAGCAAACAAAAGAC 57.557 42.857 4.13 0.00 44.36 3.01
2693 6665 3.524541 ACAAGGCTCAAGCAAACAAAAG 58.475 40.909 4.13 0.00 44.36 2.27
2694 6666 3.608316 ACAAGGCTCAAGCAAACAAAA 57.392 38.095 4.13 0.00 44.36 2.44
2698 6670 1.758783 CGAACAAGGCTCAAGCAAAC 58.241 50.000 4.13 0.00 44.36 2.93
2715 6687 0.250295 AACAGCAGGCAAAGTAGCGA 60.250 50.000 0.00 0.00 34.64 4.93
2716 6688 1.128692 GTAACAGCAGGCAAAGTAGCG 59.871 52.381 0.00 0.00 34.64 4.26
2754 6726 3.318839 CACTTGTTCTTCTCCATTGGCAA 59.681 43.478 0.68 0.68 0.00 4.52
2761 6733 4.058124 CGTCAATCACTTGTTCTTCTCCA 58.942 43.478 0.00 0.00 33.87 3.86
2837 6810 6.992063 ACATAGATACAAAACTTGGCTGAG 57.008 37.500 0.00 0.00 34.12 3.35
2871 6844 9.302345 CGAGTAGTCATACACAAACATTTCTAT 57.698 33.333 0.00 0.00 34.07 1.98
2873 6846 7.152645 ACGAGTAGTCATACACAAACATTTCT 58.847 34.615 0.00 0.00 34.07 2.52
2878 6851 7.254522 GGAAAAACGAGTAGTCATACACAAACA 60.255 37.037 0.00 0.00 34.07 2.83
2879 6852 7.042254 AGGAAAAACGAGTAGTCATACACAAAC 60.042 37.037 0.00 0.00 34.07 2.93
2880 6853 6.987992 AGGAAAAACGAGTAGTCATACACAAA 59.012 34.615 0.00 0.00 34.07 2.83
2881 6854 6.518493 AGGAAAAACGAGTAGTCATACACAA 58.482 36.000 0.00 0.00 34.07 3.33
2883 6856 5.575995 GGAGGAAAAACGAGTAGTCATACAC 59.424 44.000 0.00 0.00 34.07 2.90
2884 6857 5.244402 TGGAGGAAAAACGAGTAGTCATACA 59.756 40.000 0.00 0.00 34.07 2.29
2885 6858 5.717119 TGGAGGAAAAACGAGTAGTCATAC 58.283 41.667 0.00 0.00 0.00 2.39
2886 6859 5.988310 TGGAGGAAAAACGAGTAGTCATA 57.012 39.130 0.00 0.00 0.00 2.15
2889 6862 4.142881 GCAATGGAGGAAAAACGAGTAGTC 60.143 45.833 0.00 0.00 0.00 2.59
2891 6864 4.003648 AGCAATGGAGGAAAAACGAGTAG 58.996 43.478 0.00 0.00 0.00 2.57
2892 6865 4.015872 AGCAATGGAGGAAAAACGAGTA 57.984 40.909 0.00 0.00 0.00 2.59
2953 6995 1.374758 GTCAAGGGAGAGGTGCGTG 60.375 63.158 0.00 0.00 0.00 5.34
2954 6996 1.837051 TGTCAAGGGAGAGGTGCGT 60.837 57.895 0.00 0.00 0.00 5.24
2959 7001 2.266055 GCCGTGTCAAGGGAGAGG 59.734 66.667 6.95 0.00 32.77 3.69
2985 7154 3.880846 GCCGCATGTAGCACCTGC 61.881 66.667 4.46 6.52 46.13 4.85
2989 7158 1.779025 CTCATGGCCGCATGTAGCAC 61.779 60.000 10.63 2.27 46.13 4.40
3023 7193 1.077429 GGTTCCAGCATCTCCCCAC 60.077 63.158 0.00 0.00 0.00 4.61
3024 7194 1.139498 TTGGTTCCAGCATCTCCCCA 61.139 55.000 0.00 0.00 0.00 4.96
3113 7290 6.381801 CATTTTTACCTACTGGTTTGAGCAG 58.618 40.000 5.66 5.66 46.05 4.24
3114 7291 5.278758 GCATTTTTACCTACTGGTTTGAGCA 60.279 40.000 0.00 0.00 46.05 4.26
3115 7292 5.048013 AGCATTTTTACCTACTGGTTTGAGC 60.048 40.000 0.00 0.00 46.05 4.26
3116 7293 6.381801 CAGCATTTTTACCTACTGGTTTGAG 58.618 40.000 0.00 0.00 46.05 3.02
3117 7294 5.242838 CCAGCATTTTTACCTACTGGTTTGA 59.757 40.000 0.00 0.00 46.05 2.69
3118 7295 5.242838 TCCAGCATTTTTACCTACTGGTTTG 59.757 40.000 6.73 0.00 46.05 2.93
3119 7296 5.390387 TCCAGCATTTTTACCTACTGGTTT 58.610 37.500 6.73 0.00 46.05 3.27
3120 7297 4.993028 TCCAGCATTTTTACCTACTGGTT 58.007 39.130 6.73 0.00 46.05 3.67
3122 7299 4.157840 GGTTCCAGCATTTTTACCTACTGG 59.842 45.833 0.00 0.00 44.87 4.00
3123 7300 4.764823 TGGTTCCAGCATTTTTACCTACTG 59.235 41.667 0.00 0.00 0.00 2.74
3124 7301 4.993028 TGGTTCCAGCATTTTTACCTACT 58.007 39.130 0.00 0.00 0.00 2.57
3125 7302 5.243060 AGTTGGTTCCAGCATTTTTACCTAC 59.757 40.000 8.28 0.00 33.53 3.18
3126 7303 5.390387 AGTTGGTTCCAGCATTTTTACCTA 58.610 37.500 8.28 0.00 0.00 3.08
3159 7352 1.965643 ACCATTGCTTGTGAATGCAGT 59.034 42.857 0.00 0.00 40.46 4.40
3184 7377 1.827789 AGCAAAAAGGTCGCTGCCA 60.828 52.632 0.00 0.00 35.33 4.92
3250 7444 2.515523 CAGCTCCGCCATGAAGGG 60.516 66.667 0.00 0.00 38.09 3.95
3289 7483 3.568538 CAGTTCCAGCAAAGAAAATCGG 58.431 45.455 0.00 0.00 0.00 4.18
3320 7515 3.596066 ATCGCGTGGTTGCAGCTCT 62.596 57.895 5.77 0.00 34.15 4.09
3445 7640 3.493176 GCAGCAAAACAAAGAGGTGGATT 60.493 43.478 0.00 0.00 0.00 3.01
3454 7649 2.053627 GACCATCGCAGCAAAACAAAG 58.946 47.619 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.