Multiple sequence alignment - TraesCS3B01G198400

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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 TraesCS3B01G198400 chr3B 100.000 3939 0 0 1 3939 226005889 226001951 0.000000e+00 7275.0
1 TraesCS3B01G198400 chr3B 79.633 1090 186 26 1115 2183 260842258 260843332 0.000000e+00 750.0
2 TraesCS3B01G198400 chr3B 94.350 354 17 3 3587 3939 556431063 556430712 1.250000e-149 540.0
3 TraesCS3B01G198400 chr3B 77.752 854 129 32 2604 3401 225798186 225797338 5.960000e-128 468.0
4 TraesCS3B01G198400 chr3B 74.416 985 199 42 1170 2129 85224444 85223488 1.340000e-99 374.0
5 TraesCS3B01G198400 chr3A 96.625 1600 28 5 684 2268 174542004 174543592 0.000000e+00 2632.0
6 TraesCS3B01G198400 chr3A 95.822 742 26 5 2728 3467 174544030 174544768 0.000000e+00 1194.0
7 TraesCS3B01G198400 chr3A 91.982 449 8 7 2255 2700 174543625 174544048 4.350000e-169 604.0
8 TraesCS3B01G198400 chr3A 77.604 893 129 38 2606 3437 175239528 175240410 3.560000e-130 475.0
9 TraesCS3B01G198400 chr3A 76.113 988 188 39 1171 2137 65480648 65479688 1.280000e-129 473.0
10 TraesCS3B01G198400 chr3A 96.296 54 1 1 2256 2308 709450632 709450685 1.950000e-13 87.9
11 TraesCS3B01G198400 chr3D 96.357 1153 34 6 2322 3473 155684732 155685877 0.000000e+00 1890.0
12 TraesCS3B01G198400 chr3D 95.626 846 36 1 1129 1974 155675005 155675849 0.000000e+00 1356.0
13 TraesCS3B01G198400 chr3D 79.143 1074 198 16 1113 2173 182320192 182321252 0.000000e+00 719.0
14 TraesCS3B01G198400 chr3D 79.553 939 168 18 1263 2183 182334363 182335295 0.000000e+00 649.0
15 TraesCS3B01G198400 chr3D 97.826 368 8 0 1962 2329 155683898 155684265 1.540000e-178 636.0
16 TraesCS3B01G198400 chr3D 88.362 464 27 11 688 1136 155674294 155674745 2.080000e-147 532.0
17 TraesCS3B01G198400 chr3D 94.253 348 19 1 3592 3939 14116761 14116415 7.490000e-147 531.0
18 TraesCS3B01G198400 chr3D 78.628 889 124 39 2606 3437 155952843 155953722 2.700000e-146 529.0
19 TraesCS3B01G198400 chr3D 76.393 987 185 42 1171 2136 55084843 55083884 4.570000e-134 488.0
20 TraesCS3B01G198400 chr3D 76.234 993 184 45 1168 2137 55742321 55743284 2.750000e-131 479.0
21 TraesCS3B01G198400 chr3D 99.174 121 1 0 3475 3595 586880126 586880006 6.630000e-53 219.0
22 TraesCS3B01G198400 chr3D 72.310 827 176 42 1160 1962 55577502 55578299 3.990000e-50 209.0
23 TraesCS3B01G198400 chr3D 91.781 146 7 3 3480 3624 14116932 14116791 8.630000e-47 198.0
24 TraesCS3B01G198400 chr3D 97.727 44 1 0 1267 1310 148252447 148252404 4.220000e-10 76.8
25 TraesCS3B01G198400 chr3D 100.000 29 0 0 684 712 525636254 525636226 2.000000e-03 54.7
26 TraesCS3B01G198400 chr1B 95.000 680 30 3 2 680 268798277 268797601 0.000000e+00 1064.0
27 TraesCS3B01G198400 chr1B 94.298 684 33 5 2 683 584562226 584562905 0.000000e+00 1042.0
28 TraesCS3B01G198400 chr5D 94.729 683 31 4 2 683 398866613 398867291 0.000000e+00 1057.0
29 TraesCS3B01G198400 chr5D 94.559 680 31 5 2 680 372334432 372333758 0.000000e+00 1046.0
30 TraesCS3B01G198400 chr5D 91.026 156 13 1 1952 2106 390512388 390512543 3.990000e-50 209.0
31 TraesCS3B01G198400 chr5D 97.521 121 3 0 3475 3595 50997804 50997684 1.430000e-49 207.0
32 TraesCS3B01G198400 chr4B 94.453 685 33 4 2 684 645056849 645056168 0.000000e+00 1050.0
33 TraesCS3B01G198400 chr4B 78.558 1096 193 26 1118 2183 397010503 397009420 0.000000e+00 684.0
34 TraesCS3B01G198400 chr4B 96.045 354 12 2 3587 3939 326091185 326090833 3.410000e-160 575.0
35 TraesCS3B01G198400 chr1D 94.084 693 32 7 1 690 453349019 453348333 0.000000e+00 1044.0
36 TraesCS3B01G198400 chr1D 97.541 122 2 1 3475 3595 109570235 109570114 1.430000e-49 207.0
37 TraesCS3B01G198400 chr7D 94.290 683 34 4 2 683 555003068 555002390 0.000000e+00 1040.0
38 TraesCS3B01G198400 chr7D 95.198 354 15 2 3587 3939 22918562 22918914 3.440000e-155 558.0
39 TraesCS3B01G198400 chr5B 94.169 686 35 4 2 685 148988501 148987819 0.000000e+00 1040.0
40 TraesCS3B01G198400 chr5B 98.347 121 2 0 3475 3595 243769209 243769329 3.080000e-51 213.0
41 TraesCS3B01G198400 chr5B 96.721 122 4 0 3474 3595 113686231 113686110 1.860000e-48 204.0
42 TraesCS3B01G198400 chr5B 100.000 30 0 0 684 713 533512934 533512963 5.500000e-04 56.5
43 TraesCS3B01G198400 chr2B 93.768 690 39 3 1 688 752840976 752841663 0.000000e+00 1033.0
44 TraesCS3B01G198400 chr2B 92.017 476 24 6 3477 3939 65491422 65490948 0.000000e+00 656.0
45 TraesCS3B01G198400 chr2B 92.500 40 1 2 684 721 779908597 779908558 5.500000e-04 56.5
46 TraesCS3B01G198400 chr4D 78.221 1102 192 28 1118 2183 319328542 319327453 0.000000e+00 662.0
47 TraesCS3B01G198400 chr4A 78.071 1099 199 29 1115 2183 154354622 154355708 0.000000e+00 656.0
48 TraesCS3B01G198400 chr4A 94.068 354 18 3 3587 3939 663366057 663366408 5.790000e-148 534.0
49 TraesCS3B01G198400 chr7B 95.480 354 14 2 3587 3939 680266958 680267310 7.390000e-157 564.0
50 TraesCS3B01G198400 chr7B 95.198 354 15 2 3587 3939 697060244 697060596 3.440000e-155 558.0
51 TraesCS3B01G198400 chrUn 94.350 354 18 2 3587 3939 88797328 88797680 3.460000e-150 542.0
52 TraesCS3B01G198400 chr5A 92.715 151 9 2 3475 3624 78480193 78480044 2.380000e-52 217.0
53 TraesCS3B01G198400 chr5A 98.347 121 2 0 3475 3595 531651898 531651778 3.080000e-51 213.0
54 TraesCS3B01G198400 chr2D 96.748 123 4 0 3473 3595 177447313 177447435 5.160000e-49 206.0
55 TraesCS3B01G198400 chr6B 90.698 43 3 1 684 726 688035851 688035810 5.500000e-04 56.5
56 TraesCS3B01G198400 chr2A 100.000 30 0 0 684 713 776592685 776592714 5.500000e-04 56.5
57 TraesCS3B01G198400 chr1A 100.000 30 0 0 684 713 357414434 357414463 5.500000e-04 56.5


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 TraesCS3B01G198400 chr3B 226001951 226005889 3938 True 7275.000000 7275 100.000000 1 3939 1 chr3B.!!$R3 3938
1 TraesCS3B01G198400 chr3B 260842258 260843332 1074 False 750.000000 750 79.633000 1115 2183 1 chr3B.!!$F1 1068
2 TraesCS3B01G198400 chr3B 225797338 225798186 848 True 468.000000 468 77.752000 2604 3401 1 chr3B.!!$R2 797
3 TraesCS3B01G198400 chr3B 85223488 85224444 956 True 374.000000 374 74.416000 1170 2129 1 chr3B.!!$R1 959
4 TraesCS3B01G198400 chr3A 174542004 174544768 2764 False 1476.666667 2632 94.809667 684 3467 3 chr3A.!!$F3 2783
5 TraesCS3B01G198400 chr3A 175239528 175240410 882 False 475.000000 475 77.604000 2606 3437 1 chr3A.!!$F1 831
6 TraesCS3B01G198400 chr3A 65479688 65480648 960 True 473.000000 473 76.113000 1171 2137 1 chr3A.!!$R1 966
7 TraesCS3B01G198400 chr3D 155683898 155685877 1979 False 1263.000000 1890 97.091500 1962 3473 2 chr3D.!!$F7 1511
8 TraesCS3B01G198400 chr3D 155674294 155675849 1555 False 944.000000 1356 91.994000 688 1974 2 chr3D.!!$F6 1286
9 TraesCS3B01G198400 chr3D 182320192 182321252 1060 False 719.000000 719 79.143000 1113 2173 1 chr3D.!!$F4 1060
10 TraesCS3B01G198400 chr3D 182334363 182335295 932 False 649.000000 649 79.553000 1263 2183 1 chr3D.!!$F5 920
11 TraesCS3B01G198400 chr3D 155952843 155953722 879 False 529.000000 529 78.628000 2606 3437 1 chr3D.!!$F3 831
12 TraesCS3B01G198400 chr3D 55083884 55084843 959 True 488.000000 488 76.393000 1171 2136 1 chr3D.!!$R1 965
13 TraesCS3B01G198400 chr3D 55742321 55743284 963 False 479.000000 479 76.234000 1168 2137 1 chr3D.!!$F2 969
14 TraesCS3B01G198400 chr3D 14116415 14116932 517 True 364.500000 531 93.017000 3480 3939 2 chr3D.!!$R5 459
15 TraesCS3B01G198400 chr3D 55577502 55578299 797 False 209.000000 209 72.310000 1160 1962 1 chr3D.!!$F1 802
16 TraesCS3B01G198400 chr1B 268797601 268798277 676 True 1064.000000 1064 95.000000 2 680 1 chr1B.!!$R1 678
17 TraesCS3B01G198400 chr1B 584562226 584562905 679 False 1042.000000 1042 94.298000 2 683 1 chr1B.!!$F1 681
18 TraesCS3B01G198400 chr5D 398866613 398867291 678 False 1057.000000 1057 94.729000 2 683 1 chr5D.!!$F2 681
19 TraesCS3B01G198400 chr5D 372333758 372334432 674 True 1046.000000 1046 94.559000 2 680 1 chr5D.!!$R2 678
20 TraesCS3B01G198400 chr4B 645056168 645056849 681 True 1050.000000 1050 94.453000 2 684 1 chr4B.!!$R3 682
21 TraesCS3B01G198400 chr4B 397009420 397010503 1083 True 684.000000 684 78.558000 1118 2183 1 chr4B.!!$R2 1065
22 TraesCS3B01G198400 chr1D 453348333 453349019 686 True 1044.000000 1044 94.084000 1 690 1 chr1D.!!$R2 689
23 TraesCS3B01G198400 chr7D 555002390 555003068 678 True 1040.000000 1040 94.290000 2 683 1 chr7D.!!$R1 681
24 TraesCS3B01G198400 chr5B 148987819 148988501 682 True 1040.000000 1040 94.169000 2 685 1 chr5B.!!$R2 683
25 TraesCS3B01G198400 chr2B 752840976 752841663 687 False 1033.000000 1033 93.768000 1 688 1 chr2B.!!$F1 687
26 TraesCS3B01G198400 chr4D 319327453 319328542 1089 True 662.000000 662 78.221000 1118 2183 1 chr4D.!!$R1 1065
27 TraesCS3B01G198400 chr4A 154354622 154355708 1086 False 656.000000 656 78.071000 1115 2183 1 chr4A.!!$F1 1068

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
251 253 0.818296 GAGGTGTATCAGTGGCGACT 59.182 55.000 0.00 0.0 0.00 4.18 F
528 530 1.377202 GCGCCCCTTCATCAACTGA 60.377 57.895 0.00 0.0 0.00 3.41 F
1230 1516 1.381872 CATCCTCACCGTCTCCCCT 60.382 63.158 0.00 0.0 0.00 4.79 F
1320 1609 2.234296 CCTCCTCCAAGCCACCCTT 61.234 63.158 0.00 0.0 0.00 3.95 F
2253 2593 2.611292 GGAGAACTGAATTCCATCTGCG 59.389 50.000 2.27 0.0 38.16 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1381 1670 2.126189 GTAGCGCGGTTCGGAGTT 60.126 61.111 19.09 0.00 38.94 3.01 R
1552 1850 2.202987 GGAGAGGAGCGTGGCATG 60.203 66.667 1.31 1.31 0.00 4.06 R
2552 3432 0.455815 TCAGCATCGACTACGCACAT 59.544 50.000 0.00 0.00 39.58 3.21 R
2553 3433 0.455815 ATCAGCATCGACTACGCACA 59.544 50.000 0.00 0.00 39.58 4.57 R
3267 4258 0.467384 CAGCATTCCATCCGAGGAGT 59.533 55.000 0.00 0.00 39.25 3.85 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.126831 CTGCAGTGTCGTTTCTCTCTTT 58.873 45.455 5.25 0.00 0.00 2.52
104 106 1.207811 TCTTGCATGGAGCTTCGATGA 59.792 47.619 1.89 0.00 45.94 2.92
169 171 2.920384 TGGTCGGCAGGTGCTACA 60.920 61.111 1.26 0.00 41.70 2.74
181 183 2.347697 GTGCTACACACGACAGATCA 57.652 50.000 0.00 0.00 40.07 2.92
187 189 3.401033 ACACACGACAGATCATCCAAA 57.599 42.857 0.00 0.00 0.00 3.28
197 199 5.874093 ACAGATCATCCAAAGACTTCAAGT 58.126 37.500 0.00 0.00 0.00 3.16
219 221 1.067142 GTGTCGGCTGGTGATACTTGA 60.067 52.381 0.00 0.00 0.00 3.02
251 253 0.818296 GAGGTGTATCAGTGGCGACT 59.182 55.000 0.00 0.00 0.00 4.18
291 293 3.059982 CGCAGGAAGGAGGTGTCA 58.940 61.111 0.00 0.00 0.00 3.58
353 355 3.603532 AGGTTGATGCATCAGTACAGTG 58.396 45.455 27.25 0.00 38.19 3.66
401 403 4.074526 GCGGCCTCTGAGAGCACA 62.075 66.667 6.17 0.00 0.00 4.57
528 530 1.377202 GCGCCCCTTCATCAACTGA 60.377 57.895 0.00 0.00 0.00 3.41
577 579 4.256920 AGACGACGGCTTTAGTCTTACTA 58.743 43.478 0.00 0.00 40.64 1.82
578 580 4.094146 AGACGACGGCTTTAGTCTTACTAC 59.906 45.833 0.00 0.00 40.64 2.73
636 639 4.000557 GTGGCCGTATGCATCGCG 62.001 66.667 0.19 9.63 43.89 5.87
714 718 2.867647 GCCTCCAAAAGCAATTTTCGCT 60.868 45.455 0.00 0.00 42.98 4.93
729 733 8.523464 GCAATTTTCGCTATGTTATACACTTTG 58.477 33.333 0.00 0.00 0.00 2.77
799 803 7.338710 TCTTCTCTTGGAGAAAGACAAAGAAA 58.661 34.615 10.55 0.00 46.18 2.52
806 810 4.152580 GGAGAAAGACAAAGAAAGGCTACG 59.847 45.833 0.00 0.00 0.00 3.51
883 887 3.659092 CGTTCAAAGGCTGCCGCA 61.659 61.111 13.96 0.00 38.10 5.69
977 981 1.532794 CTCTCCCATCCTCCCCTCG 60.533 68.421 0.00 0.00 0.00 4.63
1230 1516 1.381872 CATCCTCACCGTCTCCCCT 60.382 63.158 0.00 0.00 0.00 4.79
1320 1609 2.234296 CCTCCTCCAAGCCACCCTT 61.234 63.158 0.00 0.00 0.00 3.95
1621 1919 4.849329 GCGTCCACTACCCGCTCG 62.849 72.222 0.00 0.00 43.81 5.03
1647 1945 3.849951 ATCTTCGCGCCCATCGGT 61.850 61.111 0.00 0.00 38.94 4.69
2206 2546 6.323739 ACAACAACAATCACCAGGTTAATTCT 59.676 34.615 0.00 0.00 0.00 2.40
2225 2565 4.989279 TCTCATCACATTCATCACGAGA 57.011 40.909 0.00 0.00 0.00 4.04
2253 2593 2.611292 GGAGAACTGAATTCCATCTGCG 59.389 50.000 2.27 0.00 38.16 5.18
2357 3217 9.843334 GCCTATAACTGACATACTAGTTGATAC 57.157 37.037 0.00 0.00 37.66 2.24
2362 3222 8.988064 AACTGACATACTAGTTGATACAGTTG 57.012 34.615 24.41 9.55 41.98 3.16
2365 3225 8.117813 TGACATACTAGTTGATACAGTTGACA 57.882 34.615 0.00 0.00 0.00 3.58
2384 3244 3.858247 ACACACTATAAAAGACGAGGGC 58.142 45.455 0.00 0.00 0.00 5.19
2543 3423 4.212004 CGATGTTGTATGCCTTGATGGTAG 59.788 45.833 0.00 0.00 38.35 3.18
2544 3424 3.884895 TGTTGTATGCCTTGATGGTAGG 58.115 45.455 0.00 0.00 38.35 3.18
2545 3425 3.521531 TGTTGTATGCCTTGATGGTAGGA 59.478 43.478 0.00 0.00 38.35 2.94
2546 3426 4.165950 TGTTGTATGCCTTGATGGTAGGAT 59.834 41.667 0.00 0.00 38.35 3.24
2547 3427 4.623932 TGTATGCCTTGATGGTAGGATC 57.376 45.455 0.00 0.00 38.35 3.36
2548 3428 4.234550 TGTATGCCTTGATGGTAGGATCT 58.765 43.478 0.00 0.00 38.35 2.75
2549 3429 5.402630 TGTATGCCTTGATGGTAGGATCTA 58.597 41.667 0.00 0.00 38.35 1.98
2550 3430 5.843969 TGTATGCCTTGATGGTAGGATCTAA 59.156 40.000 0.00 0.00 38.35 2.10
2551 3431 4.963318 TGCCTTGATGGTAGGATCTAAG 57.037 45.455 0.00 0.00 38.35 2.18
2552 3432 4.556697 TGCCTTGATGGTAGGATCTAAGA 58.443 43.478 0.00 0.00 38.35 2.10
2553 3433 5.158141 TGCCTTGATGGTAGGATCTAAGAT 58.842 41.667 0.00 0.00 38.35 2.40
2554 3434 5.012458 TGCCTTGATGGTAGGATCTAAGATG 59.988 44.000 0.00 0.00 38.35 2.90
2555 3435 5.012561 GCCTTGATGGTAGGATCTAAGATGT 59.987 44.000 0.00 0.00 38.35 3.06
2556 3436 6.462500 CCTTGATGGTAGGATCTAAGATGTG 58.538 44.000 0.00 0.00 34.56 3.21
2557 3437 5.474578 TGATGGTAGGATCTAAGATGTGC 57.525 43.478 0.00 0.00 0.00 4.57
2558 3438 4.021981 TGATGGTAGGATCTAAGATGTGCG 60.022 45.833 0.00 0.00 0.00 5.34
2559 3439 3.296854 TGGTAGGATCTAAGATGTGCGT 58.703 45.455 0.00 0.00 0.00 5.24
2560 3440 4.466827 TGGTAGGATCTAAGATGTGCGTA 58.533 43.478 0.00 0.00 0.00 4.42
2662 3544 6.935771 AGTTGTACTAGTATCATCGGAGTAGG 59.064 42.308 5.75 0.00 0.00 3.18
2700 3651 7.149202 TCCCCATATATAGCTCTGTTTTGTT 57.851 36.000 0.00 0.00 0.00 2.83
2701 3652 7.582719 TCCCCATATATAGCTCTGTTTTGTTT 58.417 34.615 0.00 0.00 0.00 2.83
2702 3653 7.502226 TCCCCATATATAGCTCTGTTTTGTTTG 59.498 37.037 0.00 0.00 0.00 2.93
2703 3654 7.141363 CCCATATATAGCTCTGTTTTGTTTGC 58.859 38.462 0.00 0.00 0.00 3.68
2704 3655 7.201812 CCCATATATAGCTCTGTTTTGTTTGCA 60.202 37.037 0.00 0.00 0.00 4.08
2705 3656 8.355169 CCATATATAGCTCTGTTTTGTTTGCAT 58.645 33.333 0.00 0.00 0.00 3.96
2706 3657 9.740239 CATATATAGCTCTGTTTTGTTTGCATT 57.260 29.630 0.00 0.00 0.00 3.56
2711 3662 7.790823 AGCTCTGTTTTGTTTGCATTTATTT 57.209 28.000 0.00 0.00 0.00 1.40
2712 3663 7.854534 AGCTCTGTTTTGTTTGCATTTATTTC 58.145 30.769 0.00 0.00 0.00 2.17
2713 3664 7.041848 AGCTCTGTTTTGTTTGCATTTATTTCC 60.042 33.333 0.00 0.00 0.00 3.13
2714 3665 7.489574 TCTGTTTTGTTTGCATTTATTTCCC 57.510 32.000 0.00 0.00 0.00 3.97
2715 3666 6.201806 TCTGTTTTGTTTGCATTTATTTCCCG 59.798 34.615 0.00 0.00 0.00 5.14
2716 3667 5.817816 TGTTTTGTTTGCATTTATTTCCCGT 59.182 32.000 0.00 0.00 0.00 5.28
2717 3668 6.316390 TGTTTTGTTTGCATTTATTTCCCGTT 59.684 30.769 0.00 0.00 0.00 4.44
2718 3669 5.914085 TTGTTTGCATTTATTTCCCGTTG 57.086 34.783 0.00 0.00 0.00 4.10
2719 3670 3.743396 TGTTTGCATTTATTTCCCGTTGC 59.257 39.130 0.00 0.00 0.00 4.17
2720 3671 3.951775 TTGCATTTATTTCCCGTTGCT 57.048 38.095 0.00 0.00 0.00 3.91
2721 3672 5.164954 GTTTGCATTTATTTCCCGTTGCTA 58.835 37.500 0.00 0.00 0.00 3.49
2722 3673 4.630894 TGCATTTATTTCCCGTTGCTAG 57.369 40.909 0.00 0.00 0.00 3.42
2723 3674 3.380004 TGCATTTATTTCCCGTTGCTAGG 59.620 43.478 0.00 0.00 0.00 3.02
2724 3675 3.630312 GCATTTATTTCCCGTTGCTAGGA 59.370 43.478 0.00 0.00 0.00 2.94
2725 3676 4.097286 GCATTTATTTCCCGTTGCTAGGAA 59.903 41.667 0.00 0.00 40.41 3.36
2726 3677 5.733373 GCATTTATTTCCCGTTGCTAGGAAG 60.733 44.000 0.00 0.00 42.91 3.46
2727 3678 4.829872 TTATTTCCCGTTGCTAGGAAGA 57.170 40.909 0.00 0.00 42.91 2.87
2728 3679 3.933861 ATTTCCCGTTGCTAGGAAGAT 57.066 42.857 0.00 0.00 42.91 2.40
2729 3680 6.488769 TTATTTCCCGTTGCTAGGAAGATA 57.511 37.500 0.00 0.00 42.91 1.98
2730 3681 5.568620 ATTTCCCGTTGCTAGGAAGATAT 57.431 39.130 0.00 0.00 42.91 1.63
2731 3682 6.681729 ATTTCCCGTTGCTAGGAAGATATA 57.318 37.500 0.00 0.00 42.91 0.86
2732 3683 6.681729 TTTCCCGTTGCTAGGAAGATATAT 57.318 37.500 0.00 0.00 42.91 0.86
2733 3684 7.786046 TTTCCCGTTGCTAGGAAGATATATA 57.214 36.000 0.00 0.00 42.91 0.86
2734 3685 7.973048 TTCCCGTTGCTAGGAAGATATATAT 57.027 36.000 0.00 0.00 37.23 0.86
2735 3686 7.584122 TCCCGTTGCTAGGAAGATATATATC 57.416 40.000 13.95 13.95 0.00 1.63
2736 3687 7.355101 TCCCGTTGCTAGGAAGATATATATCT 58.645 38.462 17.93 17.93 44.54 1.98
2737 3688 7.502895 TCCCGTTGCTAGGAAGATATATATCTC 59.497 40.741 22.64 16.02 41.96 2.75
2738 3689 7.285629 CCCGTTGCTAGGAAGATATATATCTCA 59.714 40.741 22.64 13.61 41.96 3.27
2739 3690 8.349245 CCGTTGCTAGGAAGATATATATCTCAG 58.651 40.741 22.64 17.43 41.96 3.35
2740 3691 8.898761 CGTTGCTAGGAAGATATATATCTCAGT 58.101 37.037 22.64 9.90 41.96 3.41
3071 4033 9.558648 GCAACTCTAGTAGTACTAAGTTTTCTC 57.441 37.037 22.13 14.10 37.50 2.87
3080 4042 5.705905 AGTACTAAGTTTTCTCATGCCCAAC 59.294 40.000 0.00 0.00 0.00 3.77
3144 4108 3.200605 TGGAGCGCATGGGATATGATATT 59.799 43.478 14.90 0.00 0.00 1.28
3200 4164 1.670380 GGAGTTCTTCACTGAGACGCC 60.670 57.143 0.00 0.00 35.01 5.68
3267 4258 6.183360 TGGTATCGGTCGCTTAGTTTGTATTA 60.183 38.462 0.00 0.00 0.00 0.98
3401 4392 6.744537 CAGTGATTTATTGCTTCTTCCTTTCG 59.255 38.462 0.00 0.00 0.00 3.46
3406 4397 1.800805 TGCTTCTTCCTTTCGCTCAG 58.199 50.000 0.00 0.00 0.00 3.35
3414 4405 4.273480 TCTTCCTTTCGCTCAGAGTTTTTG 59.727 41.667 0.00 0.00 0.00 2.44
3468 4459 6.200286 GCTATTTGCATTGTTGATCATCCTTG 59.800 38.462 0.00 0.00 42.31 3.61
3473 4464 5.100259 GCATTGTTGATCATCCTTGAACTG 58.900 41.667 0.00 0.00 34.96 3.16
3474 4465 4.771590 TTGTTGATCATCCTTGAACTGC 57.228 40.909 0.00 0.00 34.96 4.40
3475 4466 3.084039 TGTTGATCATCCTTGAACTGCC 58.916 45.455 0.00 0.00 34.96 4.85
3476 4467 2.424956 GTTGATCATCCTTGAACTGCCC 59.575 50.000 0.00 0.00 34.96 5.36
3477 4468 1.303309 GATCATCCTTGAACTGCCCG 58.697 55.000 0.00 0.00 34.96 6.13
3478 4469 0.620556 ATCATCCTTGAACTGCCCGT 59.379 50.000 0.00 0.00 34.96 5.28
3559 4550 2.359967 CGAACCTCCCCCACTCCTC 61.360 68.421 0.00 0.00 0.00 3.71
3560 4551 1.996187 GAACCTCCCCCACTCCTCC 60.996 68.421 0.00 0.00 0.00 4.30
3561 4552 2.478722 GAACCTCCCCCACTCCTCCT 62.479 65.000 0.00 0.00 0.00 3.69
3566 4557 2.641746 CCCCCACTCCTCCTCCTCT 61.642 68.421 0.00 0.00 0.00 3.69
3703 4756 2.034879 CCTTGCGATCTGGTGCGTT 61.035 57.895 0.00 0.00 0.00 4.84
3704 4757 1.133253 CTTGCGATCTGGTGCGTTG 59.867 57.895 0.00 0.00 0.00 4.10
3706 4759 4.505217 GCGATCTGGTGCGTTGCG 62.505 66.667 0.00 0.00 0.00 4.85
3857 4910 1.993701 TTGTCTGGCCCTTGACAGCA 61.994 55.000 18.35 7.03 42.98 4.41
3868 4921 0.882927 TTGACAGCACGGGCAACTAC 60.883 55.000 14.57 0.00 44.61 2.73
3917 4970 4.101790 CGATGGCGGCGCTTTTGT 62.102 61.111 32.30 12.98 0.00 2.83
3920 4973 2.747507 GATGGCGGCGCTTTTGTGTT 62.748 55.000 32.30 7.44 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.800604 GCTCCAAAGAGAGAAACGACACT 60.801 47.826 0.00 0.00 43.39 3.55
26 27 0.955428 GCTCCACAAACGATGCTCCA 60.955 55.000 0.00 0.00 0.00 3.86
104 106 3.708403 TCAGGCATGACTTGACATCTT 57.292 42.857 0.00 0.00 34.87 2.40
139 141 1.003355 CGACCAGGCATGACCAAGT 60.003 57.895 0.00 0.00 43.14 3.16
169 171 3.259374 AGTCTTTGGATGATCTGTCGTGT 59.741 43.478 0.00 0.00 0.00 4.49
181 183 4.273480 CGACACAACTTGAAGTCTTTGGAT 59.727 41.667 0.00 0.00 0.00 3.41
187 189 1.139058 AGCCGACACAACTTGAAGTCT 59.861 47.619 0.00 0.00 0.00 3.24
197 199 0.973632 AGTATCACCAGCCGACACAA 59.026 50.000 0.00 0.00 0.00 3.33
251 253 1.087202 AAACAGCTGAACACGTCGCA 61.087 50.000 23.35 0.00 0.00 5.10
353 355 1.648467 GCCACCGCTCCATCTTCAAC 61.648 60.000 0.00 0.00 0.00 3.18
401 403 4.250305 GGCACACACTGGTCCGGT 62.250 66.667 0.00 0.00 0.00 5.28
528 530 4.267349 ACAAACTGTCGCTACACCTATT 57.733 40.909 0.00 0.00 0.00 1.73
577 579 8.567948 CACAAGACCTTACAAAATCAATACAGT 58.432 33.333 0.00 0.00 0.00 3.55
578 580 8.783093 TCACAAGACCTTACAAAATCAATACAG 58.217 33.333 0.00 0.00 0.00 2.74
636 639 3.830192 CGGCCTTTGCATCTGGGC 61.830 66.667 14.03 14.03 43.42 5.36
637 640 3.142838 CCGGCCTTTGCATCTGGG 61.143 66.667 0.00 0.00 40.13 4.45
692 696 2.867647 GCGAAAATTGCTTTTGGAGGCT 60.868 45.455 0.00 0.00 34.73 4.58
694 698 3.030668 AGCGAAAATTGCTTTTGGAGG 57.969 42.857 0.00 0.00 40.48 4.30
729 733 8.084073 TGAAACATGATTGAGACTGAATTTTCC 58.916 33.333 0.00 0.00 0.00 3.13
1381 1670 2.126189 GTAGCGCGGTTCGGAGTT 60.126 61.111 19.09 0.00 38.94 3.01
1552 1850 2.202987 GGAGAGGAGCGTGGCATG 60.203 66.667 1.31 1.31 0.00 4.06
1554 1852 2.604686 AAGGAGAGGAGCGTGGCA 60.605 61.111 0.00 0.00 0.00 4.92
2206 2546 4.082026 ACTGTCTCGTGATGAATGTGATGA 60.082 41.667 0.00 0.00 0.00 2.92
2225 2565 5.825593 TGGAATTCAGTTCTCCTAACTGT 57.174 39.130 15.37 0.00 45.75 3.55
2276 2662 6.772716 AGATAAAGAATCCGTGCATTTACCAT 59.227 34.615 0.00 0.00 34.90 3.55
2357 3217 6.089551 CCTCGTCTTTTATAGTGTGTCAACTG 59.910 42.308 0.00 0.00 0.00 3.16
2358 3218 6.157211 CCTCGTCTTTTATAGTGTGTCAACT 58.843 40.000 0.00 0.00 0.00 3.16
2362 3222 3.864003 GCCCTCGTCTTTTATAGTGTGTC 59.136 47.826 0.00 0.00 0.00 3.67
2365 3225 4.820894 AAGCCCTCGTCTTTTATAGTGT 57.179 40.909 0.00 0.00 0.00 3.55
2543 3423 3.250280 TCGACTACGCACATCTTAGATCC 59.750 47.826 0.00 0.00 39.58 3.36
2544 3424 4.469625 TCGACTACGCACATCTTAGATC 57.530 45.455 0.00 0.00 39.58 2.75
2545 3425 4.788690 CATCGACTACGCACATCTTAGAT 58.211 43.478 0.00 0.00 39.58 1.98
2546 3426 3.548214 GCATCGACTACGCACATCTTAGA 60.548 47.826 0.00 0.00 39.58 2.10
2547 3427 2.721603 GCATCGACTACGCACATCTTAG 59.278 50.000 0.00 0.00 39.58 2.18
2548 3428 2.357952 AGCATCGACTACGCACATCTTA 59.642 45.455 0.00 0.00 39.58 2.10
2549 3429 1.135139 AGCATCGACTACGCACATCTT 59.865 47.619 0.00 0.00 39.58 2.40
2550 3430 0.741326 AGCATCGACTACGCACATCT 59.259 50.000 0.00 0.00 39.58 2.90
2551 3431 0.848942 CAGCATCGACTACGCACATC 59.151 55.000 0.00 0.00 39.58 3.06
2552 3432 0.455815 TCAGCATCGACTACGCACAT 59.544 50.000 0.00 0.00 39.58 3.21
2553 3433 0.455815 ATCAGCATCGACTACGCACA 59.544 50.000 0.00 0.00 39.58 4.57
2554 3434 0.848942 CATCAGCATCGACTACGCAC 59.151 55.000 0.00 0.00 39.58 5.34
2555 3435 0.455815 ACATCAGCATCGACTACGCA 59.544 50.000 0.00 0.00 39.58 5.24
2556 3436 2.401017 TACATCAGCATCGACTACGC 57.599 50.000 0.00 0.00 39.58 4.42
2557 3437 3.914966 GGAATACATCAGCATCGACTACG 59.085 47.826 0.00 0.00 41.26 3.51
2558 3438 5.127693 AGGAATACATCAGCATCGACTAC 57.872 43.478 0.00 0.00 0.00 2.73
2559 3439 5.301805 TCAAGGAATACATCAGCATCGACTA 59.698 40.000 0.00 0.00 0.00 2.59
2560 3440 4.100035 TCAAGGAATACATCAGCATCGACT 59.900 41.667 0.00 0.00 0.00 4.18
2645 3525 4.202430 TGACTGCCTACTCCGATGATACTA 60.202 45.833 0.00 0.00 0.00 1.82
2658 3540 3.597255 GGGAAAAGTACTGACTGCCTAC 58.403 50.000 0.00 0.00 35.52 3.18
2662 3544 2.561478 TGGGGAAAAGTACTGACTGC 57.439 50.000 0.00 0.00 35.52 4.40
2700 3651 3.951775 AGCAACGGGAAATAAATGCAA 57.048 38.095 0.00 0.00 36.30 4.08
2701 3652 3.380004 CCTAGCAACGGGAAATAAATGCA 59.620 43.478 0.00 0.00 36.30 3.96
2702 3653 3.630312 TCCTAGCAACGGGAAATAAATGC 59.370 43.478 0.00 0.00 0.00 3.56
2703 3654 5.588648 TCTTCCTAGCAACGGGAAATAAATG 59.411 40.000 0.00 0.00 40.53 2.32
2704 3655 5.751586 TCTTCCTAGCAACGGGAAATAAAT 58.248 37.500 0.00 0.00 40.53 1.40
2705 3656 5.168647 TCTTCCTAGCAACGGGAAATAAA 57.831 39.130 0.00 0.00 40.53 1.40
2706 3657 4.829872 TCTTCCTAGCAACGGGAAATAA 57.170 40.909 0.00 0.00 40.53 1.40
2707 3658 6.681729 ATATCTTCCTAGCAACGGGAAATA 57.318 37.500 0.00 0.00 40.53 1.40
2708 3659 3.933861 ATCTTCCTAGCAACGGGAAAT 57.066 42.857 0.00 0.00 40.53 2.17
2709 3660 6.681729 ATATATCTTCCTAGCAACGGGAAA 57.318 37.500 0.00 0.00 40.53 3.13
2710 3661 7.839705 AGATATATATCTTCCTAGCAACGGGAA 59.160 37.037 17.93 0.00 39.96 3.97
2711 3662 7.355101 AGATATATATCTTCCTAGCAACGGGA 58.645 38.462 17.93 0.00 39.96 5.14
2712 3663 7.285629 TGAGATATATATCTTCCTAGCAACGGG 59.714 40.741 23.14 0.00 42.79 5.28
2713 3664 8.226819 TGAGATATATATCTTCCTAGCAACGG 57.773 38.462 23.14 0.00 42.79 4.44
2714 3665 8.898761 ACTGAGATATATATCTTCCTAGCAACG 58.101 37.037 23.14 9.46 42.79 4.10
2721 3672 9.196139 GGCACTAACTGAGATATATATCTTCCT 57.804 37.037 23.14 12.48 42.79 3.36
2722 3673 8.972127 TGGCACTAACTGAGATATATATCTTCC 58.028 37.037 23.14 13.66 42.79 3.46
2725 3676 9.706529 TGATGGCACTAACTGAGATATATATCT 57.293 33.333 22.62 22.62 45.26 1.98
2732 3683 9.851686 AAAATTATGATGGCACTAACTGAGATA 57.148 29.630 0.00 0.00 0.00 1.98
2733 3684 8.757982 AAAATTATGATGGCACTAACTGAGAT 57.242 30.769 0.00 0.00 0.00 2.75
2734 3685 8.579850 AAAAATTATGATGGCACTAACTGAGA 57.420 30.769 0.00 0.00 0.00 3.27
2735 3686 7.917505 GGAAAAATTATGATGGCACTAACTGAG 59.082 37.037 0.00 0.00 0.00 3.35
2736 3687 7.395772 TGGAAAAATTATGATGGCACTAACTGA 59.604 33.333 0.00 0.00 0.00 3.41
2737 3688 7.546358 TGGAAAAATTATGATGGCACTAACTG 58.454 34.615 0.00 0.00 0.00 3.16
2738 3689 7.716799 TGGAAAAATTATGATGGCACTAACT 57.283 32.000 0.00 0.00 0.00 2.24
2741 3692 9.585369 TCATATGGAAAAATTATGATGGCACTA 57.415 29.630 2.13 0.00 0.00 2.74
2742 3693 8.362639 GTCATATGGAAAAATTATGATGGCACT 58.637 33.333 2.13 0.00 31.02 4.40
2743 3694 8.362639 AGTCATATGGAAAAATTATGATGGCAC 58.637 33.333 2.13 0.00 31.02 5.01
2744 3695 8.361889 CAGTCATATGGAAAAATTATGATGGCA 58.638 33.333 2.13 0.00 31.02 4.92
3071 4033 3.368739 GGATCAAAGGAAAGTTGGGCATG 60.369 47.826 0.00 0.00 0.00 4.06
3080 4042 5.990120 AATTCACCTGGATCAAAGGAAAG 57.010 39.130 18.08 9.02 38.27 2.62
3144 4108 1.543208 GGCATGTCACCAGAACAGACA 60.543 52.381 0.00 0.00 45.26 3.41
3200 4164 6.299604 CAAAGACGACATGTTAAGCTACTTG 58.700 40.000 0.00 0.00 0.00 3.16
3267 4258 0.467384 CAGCATTCCATCCGAGGAGT 59.533 55.000 0.00 0.00 39.25 3.85
3401 4392 4.540824 GATCAACACCAAAAACTCTGAGC 58.459 43.478 4.19 0.00 0.00 4.26
3406 4397 4.041723 CCAACGATCAACACCAAAAACTC 58.958 43.478 0.00 0.00 0.00 3.01
3414 4405 2.604614 GCTCAAACCAACGATCAACACC 60.605 50.000 0.00 0.00 0.00 4.16
3468 4459 1.153881 GGAGACGTACGGGCAGTTC 60.154 63.158 21.06 6.71 0.00 3.01
3473 4464 3.525545 GGAGGGAGACGTACGGGC 61.526 72.222 21.06 11.21 0.00 6.13
3474 4465 2.832201 GGGAGGGAGACGTACGGG 60.832 72.222 21.06 0.00 0.00 5.28
3475 4466 3.207669 CGGGAGGGAGACGTACGG 61.208 72.222 21.06 1.43 0.00 4.02
3476 4467 2.124983 TCGGGAGGGAGACGTACG 60.125 66.667 15.01 15.01 0.00 3.67
3477 4468 2.479750 GCTCGGGAGGGAGACGTAC 61.480 68.421 0.00 0.00 36.08 3.67
3478 4469 2.124403 GCTCGGGAGGGAGACGTA 60.124 66.667 0.00 0.00 36.08 3.57
3559 4550 3.532155 CGGCGAGGGAAGAGGAGG 61.532 72.222 0.00 0.00 0.00 4.30
3560 4551 4.214327 GCGGCGAGGGAAGAGGAG 62.214 72.222 12.98 0.00 0.00 3.69
3680 4733 1.992277 ACCAGATCGCAAGGCCTCT 60.992 57.895 5.23 0.00 38.47 3.69
3804 4857 4.479993 ATCTGCCCAGCTGCCGAC 62.480 66.667 8.66 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.