Multiple sequence alignment - TraesCS4D01G262600

Loading Multiple Alignment...

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 TraesCS4D01G262600 chr4D 100.000 3649 0 0 1 3649 433698373 433702021 0.000000e+00 6739.0
1 TraesCS4D01G262600 chr4D 88.889 108 10 2 3423 3529 446987574 446987468 8.220000e-27 132.0
2 TraesCS4D01G262600 chr4D 85.047 107 16 0 3423 3529 437968911 437968805 3.850000e-20 110.0
3 TraesCS4D01G262600 chr4D 85.047 107 14 2 3426 3530 54279783 54279677 1.390000e-19 108.0
4 TraesCS4D01G262600 chr4D 89.189 74 7 1 2685 2757 463708873 463708800 1.400000e-14 91.6
5 TraesCS4D01G262600 chr4A 93.074 3061 136 33 1 3036 35150015 35153024 0.000000e+00 4409.0
6 TraesCS4D01G262600 chr4A 90.460 587 41 7 3063 3649 35162584 35163155 0.000000e+00 760.0
7 TraesCS4D01G262600 chr4A 91.837 196 15 1 1 196 319834375 319834569 4.640000e-69 272.0
8 TraesCS4D01G262600 chr4A 83.333 282 47 0 3129 3410 530762891 530763172 1.010000e-65 261.0
9 TraesCS4D01G262600 chr4A 85.202 223 26 4 3130 3349 57170902 57170684 4.740000e-54 222.0
10 TraesCS4D01G262600 chr4A 86.408 103 11 1 3028 3130 235253 235154 3.850000e-20 110.0
11 TraesCS4D01G262600 chr4B 89.179 2569 157 57 322 2840 532254619 532257116 0.000000e+00 3092.0
12 TraesCS4D01G262600 chr4B 84.211 665 79 14 2839 3501 532257202 532257842 1.110000e-174 623.0
13 TraesCS4D01G262600 chr4B 86.139 101 11 1 3030 3130 37379148 37379051 4.980000e-19 106.0
14 TraesCS4D01G262600 chr2B 86.729 1168 103 23 1534 2680 451890801 451891937 0.000000e+00 1251.0
15 TraesCS4D01G262600 chr2B 91.220 205 17 1 1 205 383640183 383639980 9.980000e-71 278.0
16 TraesCS4D01G262600 chr2B 91.237 194 15 2 1 194 283168913 283168722 2.790000e-66 263.0
17 TraesCS4D01G262600 chr2B 94.574 129 7 0 1322 1450 451890640 451890768 2.220000e-47 200.0
18 TraesCS4D01G262600 chr2B 88.350 103 9 1 3028 3130 294203215 294203116 1.780000e-23 121.0
19 TraesCS4D01G262600 chr2A 85.947 1167 116 23 1534 2680 516025020 516026158 0.000000e+00 1203.0
20 TraesCS4D01G262600 chr2A 90.909 198 16 2 1 198 12284485 12284290 7.770000e-67 265.0
21 TraesCS4D01G262600 chr2A 88.235 153 11 7 1305 1450 516024834 516024986 3.740000e-40 176.0
22 TraesCS4D01G262600 chr2A 86.139 101 11 1 3030 3130 697374704 697374801 4.980000e-19 106.0
23 TraesCS4D01G262600 chr2A 89.189 74 7 1 2682 2754 138912563 138912636 1.400000e-14 91.6
24 TraesCS4D01G262600 chr2D 87.565 957 71 22 1743 2678 380577853 380578782 0.000000e+00 1064.0
25 TraesCS4D01G262600 chr2D 80.738 488 62 22 988 1450 380577084 380577564 5.800000e-93 351.0
26 TraesCS4D01G262600 chr2D 87.568 185 18 5 1534 1716 380577598 380577779 3.690000e-50 209.0
27 TraesCS4D01G262600 chr6D 86.331 278 36 2 2752 3028 395990369 395990093 5.920000e-78 302.0
28 TraesCS4D01G262600 chr6D 91.327 196 16 1 1 196 414926841 414927035 2.160000e-67 267.0
29 TraesCS4D01G262600 chr7D 85.866 283 39 1 2750 3032 41436325 41436044 2.130000e-77 300.0
30 TraesCS4D01G262600 chr7D 83.630 281 45 1 3130 3410 60338600 60338879 2.790000e-66 263.0
31 TraesCS4D01G262600 chr7D 84.109 258 41 0 3153 3410 320263784 320264041 2.180000e-62 250.0
32 TraesCS4D01G262600 chr6B 85.714 280 38 2 2754 3032 170346728 170347006 9.910000e-76 294.0
33 TraesCS4D01G262600 chr5D 84.806 283 41 2 2750 3032 127153156 127153436 2.140000e-72 283.0
34 TraesCS4D01G262600 chr5D 81.651 109 20 0 3423 3531 84389611 84389503 1.400000e-14 91.6
35 TraesCS4D01G262600 chr3A 85.252 278 37 3 2752 3028 737898790 737898516 2.140000e-72 283.0
36 TraesCS4D01G262600 chr3A 86.408 103 11 1 3028 3130 649799106 649799205 3.850000e-20 110.0
37 TraesCS4D01G262600 chr3A 90.789 76 6 1 2683 2757 121649758 121649683 2.320000e-17 100.0
38 TraesCS4D01G262600 chr3A 91.549 71 5 1 2685 2754 10362895 10362965 3.000000e-16 97.1
39 TraesCS4D01G262600 chr1D 84.946 279 42 0 2754 3032 271661043 271661321 2.140000e-72 283.0
40 TraesCS4D01G262600 chr1D 82.857 280 46 1 2755 3032 290980988 290980709 2.180000e-62 250.0
41 TraesCS4D01G262600 chr1D 87.379 103 10 1 3028 3130 375254993 375255092 8.280000e-22 115.0
42 TraesCS4D01G262600 chr3B 85.660 265 36 1 2755 3017 189846193 189846457 9.980000e-71 278.0
43 TraesCS4D01G262600 chr3B 89.041 73 8 0 2685 2757 741347739 741347667 1.400000e-14 91.6
44 TraesCS4D01G262600 chr3D 84.155 284 42 3 2750 3032 606312820 606313101 4.640000e-69 272.0
45 TraesCS4D01G262600 chr3D 90.816 196 17 1 1 196 179355583 179355777 1.010000e-65 261.0
46 TraesCS4D01G262600 chr1B 91.837 196 14 2 1 195 636833417 636833223 4.640000e-69 272.0
47 TraesCS4D01G262600 chr1B 91.237 194 16 1 1 194 66377849 66377657 2.790000e-66 263.0
48 TraesCS4D01G262600 chr7B 91.282 195 15 2 1 194 713117879 713117686 7.770000e-67 265.0
49 TraesCS4D01G262600 chrUn 82.206 281 48 1 3128 3408 9856572 9856850 1.310000e-59 241.0
50 TraesCS4D01G262600 chrUn 81.570 293 52 1 3128 3420 308415095 308414805 1.310000e-59 241.0
51 TraesCS4D01G262600 chr7A 82.403 233 38 2 3178 3410 384603464 384603235 2.220000e-47 200.0
52 TraesCS4D01G262600 chr7A 91.781 73 5 1 2683 2754 33210940 33210868 2.320000e-17 100.0
53 TraesCS4D01G262600 chr7A 91.781 73 5 1 2683 2754 509811813 509811885 2.320000e-17 100.0
54 TraesCS4D01G262600 chr6A 87.850 107 13 0 3423 3529 60027903 60028009 3.830000e-25 126.0
55 TraesCS4D01G262600 chr6A 85.437 103 12 1 3028 3130 470142312 470142411 1.790000e-18 104.0
56 TraesCS4D01G262600 chr5A 87.156 109 14 0 3423 3531 552544544 552544436 1.380000e-24 124.0
57 TraesCS4D01G262600 chr5A 84.545 110 15 2 3423 3531 702987264 702987156 1.390000e-19 108.0
58 TraesCS4D01G262600 chr5A 91.176 68 5 1 2682 2748 328662366 328662433 1.400000e-14 91.6


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 TraesCS4D01G262600 chr4D 433698373 433702021 3648 False 6739.000000 6739 100.000000 1 3649 1 chr4D.!!$F1 3648
1 TraesCS4D01G262600 chr4A 35150015 35153024 3009 False 4409.000000 4409 93.074000 1 3036 1 chr4A.!!$F1 3035
2 TraesCS4D01G262600 chr4A 35162584 35163155 571 False 760.000000 760 90.460000 3063 3649 1 chr4A.!!$F2 586
3 TraesCS4D01G262600 chr4B 532254619 532257842 3223 False 1857.500000 3092 86.695000 322 3501 2 chr4B.!!$F1 3179
4 TraesCS4D01G262600 chr2B 451890640 451891937 1297 False 725.500000 1251 90.651500 1322 2680 2 chr2B.!!$F1 1358
5 TraesCS4D01G262600 chr2A 516024834 516026158 1324 False 689.500000 1203 87.091000 1305 2680 2 chr2A.!!$F3 1375
6 TraesCS4D01G262600 chr2D 380577084 380578782 1698 False 541.333333 1064 85.290333 988 2678 3 chr2D.!!$F1 1690

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
87 88 0.603439 TTTCGGTCCACGTTTAGGCC 60.603 55.000 0.00 0.0 44.69 5.19 F
91 92 1.004679 GTCCACGTTTAGGCCCGAA 60.005 57.895 0.00 0.0 0.00 4.30 F
92 93 1.017701 GTCCACGTTTAGGCCCGAAG 61.018 60.000 0.00 0.0 0.00 3.79 F
344 346 1.069049 GCTCTTGCATGGTGGTTGTTT 59.931 47.619 0.00 0.0 39.41 2.83 F
1676 1750 0.100682 CCAGGTCGGTCGTCATACTG 59.899 60.000 0.00 0.0 0.00 2.74 F
2329 2463 0.546988 AGAAAGGGCCCCTCTACGTT 60.547 55.000 21.43 0.0 30.89 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 1564 0.104671 TATTAAGTACCGCCACCGCC 59.895 55.000 0.0 0.0 0.0 6.13 R
1495 1565 1.796459 CATATTAAGTACCGCCACCGC 59.204 52.381 0.0 0.0 0.0 5.68 R
1496 1566 3.102052 ACATATTAAGTACCGCCACCG 57.898 47.619 0.0 0.0 0.0 4.94 R
2329 2463 1.191489 TGAGAGGTCCGAACATGGCA 61.191 55.000 0.0 0.0 0.0 4.92 R
2502 2643 0.240945 GCACCAAGTACGCTGCAAAT 59.759 50.000 0.0 0.0 0.0 2.32 R
3274 3526 0.695803 GACCCACCTCCATCCCTCAT 60.696 60.000 0.0 0.0 0.0 2.90 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
73 74 5.576447 ATTAAATTGTAGCCCACTTTCGG 57.424 39.130 0.00 0.00 29.73 4.30
85 86 1.796459 CACTTTCGGTCCACGTTTAGG 59.204 52.381 0.00 0.00 44.69 2.69
86 87 0.794473 CTTTCGGTCCACGTTTAGGC 59.206 55.000 0.00 0.00 44.69 3.93
87 88 0.603439 TTTCGGTCCACGTTTAGGCC 60.603 55.000 0.00 0.00 44.69 5.19
88 89 2.435410 CGGTCCACGTTTAGGCCC 60.435 66.667 0.00 0.00 37.93 5.80
89 90 2.435410 GGTCCACGTTTAGGCCCG 60.435 66.667 0.00 0.00 0.00 6.13
90 91 2.658422 GTCCACGTTTAGGCCCGA 59.342 61.111 0.00 0.00 0.00 5.14
91 92 1.004679 GTCCACGTTTAGGCCCGAA 60.005 57.895 0.00 0.00 0.00 4.30
92 93 1.017701 GTCCACGTTTAGGCCCGAAG 61.018 60.000 0.00 0.00 0.00 3.79
109 110 1.338136 AAGGAGCCATACGTGAGGGG 61.338 60.000 0.00 0.00 0.00 4.79
134 135 7.279313 GGGAGTGTTGACGTATAAATGTATTGT 59.721 37.037 0.00 0.00 0.00 2.71
153 154 9.593565 TGTATTGTCTAGTCTCTTCCATCATAT 57.406 33.333 0.00 0.00 0.00 1.78
196 197 6.866770 TGACTAAAGCATGTACTTCTACACAC 59.133 38.462 0.00 0.00 35.63 3.82
200 201 3.119459 AGCATGTACTTCTACACACTCCG 60.119 47.826 0.00 0.00 35.63 4.63
204 205 1.617322 ACTTCTACACACTCCGAGCA 58.383 50.000 0.00 0.00 0.00 4.26
221 223 1.967066 AGCACCGGAGAGGAGATAATG 59.033 52.381 9.46 0.00 45.00 1.90
241 243 4.733077 TGGGTGACAAGGAAATAGGAAA 57.267 40.909 0.00 0.00 0.00 3.13
252 254 3.186613 GGAAATAGGAAATCGACGATGGC 59.813 47.826 11.83 6.39 0.00 4.40
292 294 2.943449 GGAAACCCTACACGAGAGAG 57.057 55.000 0.00 0.00 0.00 3.20
297 299 4.522722 AACCCTACACGAGAGAGAAAAG 57.477 45.455 0.00 0.00 0.00 2.27
310 312 5.133221 AGAGAGAAAAGCTTTTTGCAGGTA 58.867 37.500 24.58 0.00 45.94 3.08
329 331 6.357367 CAGGTAACCCATATTAGTTGCTCTT 58.643 40.000 3.68 0.00 37.17 2.85
344 346 1.069049 GCTCTTGCATGGTGGTTGTTT 59.931 47.619 0.00 0.00 39.41 2.83
345 347 2.295909 GCTCTTGCATGGTGGTTGTTTA 59.704 45.455 0.00 0.00 39.41 2.01
349 351 4.586421 TCTTGCATGGTGGTTGTTTAATCA 59.414 37.500 0.00 0.00 0.00 2.57
410 412 1.139058 GGCCATGTCCGAGTAGTGAAT 59.861 52.381 0.00 0.00 0.00 2.57
417 419 4.527944 TGTCCGAGTAGTGAATGAGAGAT 58.472 43.478 0.00 0.00 0.00 2.75
495 515 7.667984 TGTTTACGTACATACATACACATCG 57.332 36.000 0.00 0.00 0.00 3.84
519 540 1.559219 TGGCTGCACACATGTATACCT 59.441 47.619 0.00 0.00 0.00 3.08
766 788 5.363101 CATTACCAGTGCTATGATGTCAGT 58.637 41.667 0.00 0.00 0.00 3.41
963 997 1.133853 GGCATCCTCATTCCTGAGCTT 60.134 52.381 0.00 0.00 46.39 3.74
973 1007 3.456380 TTCCTGAGCTTTTAGCCCATT 57.544 42.857 0.00 0.00 43.77 3.16
982 1016 2.425143 TTTAGCCCATTCCTGAGCTG 57.575 50.000 0.00 0.00 36.79 4.24
1017 1051 2.567169 TGACATGAGGATCGTTGGAGTT 59.433 45.455 0.00 0.00 38.61 3.01
1236 1270 5.998454 AATATCCTCGCTCATTTGTGAAG 57.002 39.130 0.00 0.00 0.00 3.02
1295 1336 4.095782 TCTGCCAGAACACAGTTGTTAAAC 59.904 41.667 0.00 0.00 46.43 2.01
1484 1554 5.997385 TCGATAGAAGAAAAACCAAGTTGC 58.003 37.500 0.00 0.00 46.15 4.17
1486 1556 6.262273 TCGATAGAAGAAAAACCAAGTTGCTT 59.738 34.615 0.00 0.00 46.15 3.91
1487 1557 7.442969 TCGATAGAAGAAAAACCAAGTTGCTTA 59.557 33.333 0.00 0.00 46.15 3.09
1488 1558 8.237267 CGATAGAAGAAAAACCAAGTTGCTTAT 58.763 33.333 0.00 0.00 39.76 1.73
1489 1559 9.914131 GATAGAAGAAAAACCAAGTTGCTTATT 57.086 29.630 0.00 0.00 0.00 1.40
1492 1562 7.860872 AGAAGAAAAACCAAGTTGCTTATTACG 59.139 33.333 0.00 0.00 0.00 3.18
1493 1563 7.034685 AGAAAAACCAAGTTGCTTATTACGT 57.965 32.000 0.00 0.00 0.00 3.57
1494 1564 6.915843 AGAAAAACCAAGTTGCTTATTACGTG 59.084 34.615 0.00 0.00 0.00 4.49
1495 1565 4.759516 AACCAAGTTGCTTATTACGTGG 57.240 40.909 0.00 0.00 37.66 4.94
1496 1566 2.486592 ACCAAGTTGCTTATTACGTGGC 59.513 45.455 0.00 0.00 35.63 5.01
1497 1567 2.475519 CCAAGTTGCTTATTACGTGGCG 60.476 50.000 0.00 0.00 0.00 5.69
1498 1568 1.365699 AGTTGCTTATTACGTGGCGG 58.634 50.000 0.00 0.00 0.00 6.13
1499 1569 1.081094 GTTGCTTATTACGTGGCGGT 58.919 50.000 0.00 0.00 0.00 5.68
1500 1570 1.080298 TTGCTTATTACGTGGCGGTG 58.920 50.000 0.00 0.00 0.00 4.94
1501 1571 0.741574 TGCTTATTACGTGGCGGTGG 60.742 55.000 0.00 0.00 0.00 4.61
1502 1572 2.011453 CTTATTACGTGGCGGTGGC 58.989 57.895 0.00 0.00 38.90 5.01
1503 1573 1.758319 CTTATTACGTGGCGGTGGCG 61.758 60.000 0.00 0.00 41.24 5.69
1504 1574 3.719883 TATTACGTGGCGGTGGCGG 62.720 63.158 0.00 0.00 41.24 6.13
1511 1581 2.265424 GGCGGTGGCGGTACTTAA 59.735 61.111 0.00 0.00 41.24 1.85
1519 1589 4.025480 CGGTGGCGGTACTTAATATGTTTC 60.025 45.833 0.00 0.00 0.00 2.78
1676 1750 0.100682 CCAGGTCGGTCGTCATACTG 59.899 60.000 0.00 0.00 0.00 2.74
1694 1768 8.753175 GTCATACTGACCACGAATTTCTATAAC 58.247 37.037 0.00 0.00 41.37 1.89
1699 1773 7.492669 ACTGACCACGAATTTCTATAACATCTG 59.507 37.037 0.00 0.00 0.00 2.90
1793 1919 1.377725 CAGAAAGCCCAGCGGTCAT 60.378 57.895 0.00 0.00 0.00 3.06
1808 1934 3.814268 CATGCGAAACTGGCGGGG 61.814 66.667 0.00 0.00 0.00 5.73
2329 2463 0.546988 AGAAAGGGCCCCTCTACGTT 60.547 55.000 21.43 0.00 30.89 3.99
2502 2643 1.006337 GTGCGCTGCCATTTTTCCA 60.006 52.632 9.73 0.00 0.00 3.53
2646 2787 0.259938 GGGCAAGGAGTCCATTCCAT 59.740 55.000 12.86 0.00 43.39 3.41
2674 2818 5.941948 AACCGTGAAGTTAATGAGGAAAG 57.058 39.130 0.00 0.00 0.00 2.62
2717 2862 8.546322 TCATGGTGAGAGTAACTTAGACTAGTA 58.454 37.037 0.00 0.00 0.00 1.82
2759 2904 6.836527 AGTCTATGTTACTACCTTCAGAGCAT 59.163 38.462 0.00 0.00 0.00 3.79
2760 2905 7.343316 AGTCTATGTTACTACCTTCAGAGCATT 59.657 37.037 0.00 0.00 0.00 3.56
2774 2919 7.443575 CCTTCAGAGCATTGTTAATAGCATAGT 59.556 37.037 0.00 0.00 0.00 2.12
2781 2926 8.906867 AGCATTGTTAATAGCATAGTCAACAAT 58.093 29.630 5.01 5.01 43.61 2.71
2814 2959 4.512944 GGAGTTGCCATGTCACATATAGTG 59.487 45.833 0.00 0.00 42.54 2.74
2890 3122 7.509141 TTAATGCATGATCCATCGTACATTT 57.491 32.000 11.00 0.13 39.36 2.32
2895 3127 5.220835 GCATGATCCATCGTACATTTTCACA 60.221 40.000 0.00 0.00 0.00 3.58
2898 3130 6.784176 TGATCCATCGTACATTTTCACAATG 58.216 36.000 0.00 0.00 0.00 2.82
2933 3170 1.723870 CTGCAGCCGGCTGTTAATC 59.276 57.895 46.58 33.52 45.24 1.75
2978 3215 6.361433 TCTCCTCTTCTATCTCATCGAACTT 58.639 40.000 0.00 0.00 0.00 2.66
2983 3220 6.730175 TCTTCTATCTCATCGAACTTAGCAC 58.270 40.000 0.00 0.00 0.00 4.40
3022 3259 9.964354 TTAATCCTTATAGCATGCTGATTGTAT 57.036 29.630 30.42 16.38 0.00 2.29
3121 3358 6.500684 TTCTTAAAAAGCTCTATGTGCTGG 57.499 37.500 0.00 0.00 41.03 4.85
3122 3359 5.560724 TCTTAAAAAGCTCTATGTGCTGGT 58.439 37.500 0.00 0.00 41.03 4.00
3123 3360 6.707290 TCTTAAAAAGCTCTATGTGCTGGTA 58.293 36.000 0.00 0.00 41.03 3.25
3124 3361 7.165485 TCTTAAAAAGCTCTATGTGCTGGTAA 58.835 34.615 0.00 0.00 41.03 2.85
3125 3362 7.829211 TCTTAAAAAGCTCTATGTGCTGGTAAT 59.171 33.333 0.00 0.00 41.03 1.89
3133 3370 6.533367 GCTCTATGTGCTGGTAATATAAGAGC 59.467 42.308 0.00 0.00 36.30 4.09
3136 3376 8.428852 TCTATGTGCTGGTAATATAAGAGCAAA 58.571 33.333 0.00 0.00 41.15 3.68
3211 3451 7.169158 ACTGAGTTGAAAGAGATAGAAGAGG 57.831 40.000 0.00 0.00 0.00 3.69
3212 3452 6.951198 ACTGAGTTGAAAGAGATAGAAGAGGA 59.049 38.462 0.00 0.00 0.00 3.71
3213 3453 7.122650 ACTGAGTTGAAAGAGATAGAAGAGGAG 59.877 40.741 0.00 0.00 0.00 3.69
3214 3454 7.178573 TGAGTTGAAAGAGATAGAAGAGGAGA 58.821 38.462 0.00 0.00 0.00 3.71
3248 3500 1.338389 GGCTACAAACTAACAGCCGGA 60.338 52.381 5.05 0.00 43.80 5.14
3274 3526 4.392921 GCACATGCTCCTAGAGACTTTA 57.607 45.455 0.00 0.00 38.21 1.85
3299 3551 1.141053 GGATGGAGGTGGGTCATGTAC 59.859 57.143 0.00 0.00 0.00 2.90
3410 3662 4.394729 CAGCTCCCTGTACTTTTAACCAA 58.605 43.478 0.00 0.00 34.31 3.67
3411 3663 4.215613 CAGCTCCCTGTACTTTTAACCAAC 59.784 45.833 0.00 0.00 34.31 3.77
3414 3666 5.382616 CTCCCTGTACTTTTAACCAACCTT 58.617 41.667 0.00 0.00 0.00 3.50
3525 3777 5.182380 GCTAAGCTACTCCCACTATGACTAG 59.818 48.000 0.00 0.00 0.00 2.57
3545 3797 1.073177 CCTTACCGTACACTTTGCCG 58.927 55.000 0.00 0.00 0.00 5.69
3548 3800 0.668096 TACCGTACACTTTGCCGCAG 60.668 55.000 0.00 0.00 0.00 5.18
3569 3821 6.441274 GCAGTCAAGATTCTTTCAATTGTGA 58.559 36.000 5.13 0.21 0.00 3.58
3596 3848 1.530323 ACGCCACCAACCTAACATTC 58.470 50.000 0.00 0.00 0.00 2.67
3607 3859 6.659242 ACCAACCTAACATTCCACATTCTTAG 59.341 38.462 0.00 0.00 0.00 2.18
3609 3861 7.148239 CCAACCTAACATTCCACATTCTTAGTC 60.148 40.741 0.00 0.00 0.00 2.59
3623 3875 6.371825 ACATTCTTAGTCGAGGGTTGAAAATC 59.628 38.462 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.898123 GACCTCTTGGCTCTGATACCATA 59.102 47.826 0.91 0.00 35.42 2.74
39 40 1.847999 CAATTTAATTGCGCCAGCTCG 59.152 47.619 4.18 0.00 45.42 5.03
40 41 2.879826 ACAATTTAATTGCGCCAGCTC 58.120 42.857 16.57 0.00 43.98 4.09
73 74 1.004679 TTCGGGCCTAAACGTGGAC 60.005 57.895 0.84 0.00 0.00 4.02
85 86 2.280186 CGTATGGCTCCTTCGGGC 60.280 66.667 0.00 0.00 34.44 6.13
86 87 1.227263 CACGTATGGCTCCTTCGGG 60.227 63.158 0.00 0.00 0.00 5.14
87 88 0.249073 CTCACGTATGGCTCCTTCGG 60.249 60.000 0.00 0.00 0.00 4.30
88 89 0.249073 CCTCACGTATGGCTCCTTCG 60.249 60.000 0.00 0.00 0.00 3.79
89 90 0.105039 CCCTCACGTATGGCTCCTTC 59.895 60.000 0.00 0.00 0.00 3.46
90 91 1.338136 CCCCTCACGTATGGCTCCTT 61.338 60.000 0.00 0.00 0.00 3.36
91 92 1.762460 CCCCTCACGTATGGCTCCT 60.762 63.158 0.00 0.00 0.00 3.69
92 93 2.808206 CCCCCTCACGTATGGCTCC 61.808 68.421 0.00 0.00 0.00 4.70
93 94 1.749334 CTCCCCCTCACGTATGGCTC 61.749 65.000 0.00 0.00 0.00 4.70
94 95 1.762460 CTCCCCCTCACGTATGGCT 60.762 63.158 0.00 0.00 0.00 4.75
95 96 2.064581 ACTCCCCCTCACGTATGGC 61.065 63.158 0.00 0.00 0.00 4.40
96 97 0.976073 ACACTCCCCCTCACGTATGG 60.976 60.000 0.00 0.00 0.00 2.74
97 98 0.902531 AACACTCCCCCTCACGTATG 59.097 55.000 0.00 0.00 0.00 2.39
98 99 0.902531 CAACACTCCCCCTCACGTAT 59.097 55.000 0.00 0.00 0.00 3.06
99 100 0.178955 TCAACACTCCCCCTCACGTA 60.179 55.000 0.00 0.00 0.00 3.57
102 103 1.004918 CGTCAACACTCCCCCTCAC 60.005 63.158 0.00 0.00 0.00 3.51
105 106 2.537633 TATACGTCAACACTCCCCCT 57.462 50.000 0.00 0.00 0.00 4.79
109 110 8.193250 ACAATACATTTATACGTCAACACTCC 57.807 34.615 0.00 0.00 0.00 3.85
134 135 5.882040 ACCGATATGATGGAAGAGACTAGA 58.118 41.667 0.00 0.00 0.00 2.43
163 164 2.031157 ACATGCTTTAGTCAACGCAACC 60.031 45.455 0.00 0.00 41.62 3.77
169 170 7.384115 TGTGTAGAAGTACATGCTTTAGTCAAC 59.616 37.037 0.00 0.00 41.29 3.18
177 178 4.618460 CGGAGTGTGTAGAAGTACATGCTT 60.618 45.833 0.00 0.00 41.29 3.91
184 185 2.486982 GTGCTCGGAGTGTGTAGAAGTA 59.513 50.000 6.90 0.00 0.00 2.24
200 201 1.693627 TTATCTCCTCTCCGGTGCTC 58.306 55.000 0.00 0.00 0.00 4.26
204 205 1.220750 ACCCATTATCTCCTCTCCGGT 59.779 52.381 0.00 0.00 0.00 5.28
221 223 4.335594 CGATTTCCTATTTCCTTGTCACCC 59.664 45.833 0.00 0.00 0.00 4.61
241 243 1.371758 CGATTCCGCCATCGTCGAT 60.372 57.895 0.75 0.75 41.03 3.59
252 254 0.741326 TTCTCTGAGAGGCGATTCCG 59.259 55.000 9.97 0.00 40.77 4.30
292 294 3.807622 GGGTTACCTGCAAAAAGCTTTTC 59.192 43.478 24.04 13.46 45.94 2.29
297 299 4.736126 ATATGGGTTACCTGCAAAAAGC 57.264 40.909 0.00 0.00 38.15 3.51
329 331 4.944619 TTGATTAAACAACCACCATGCA 57.055 36.364 0.00 0.00 0.00 3.96
349 351 9.100197 TCCTCTTTTAGCCCAATTAGAAAATTT 57.900 29.630 0.00 0.00 32.87 1.82
410 412 0.909610 AAACCGGGCCTGATCTCTCA 60.910 55.000 15.09 0.00 0.00 3.27
417 419 2.909965 GCACAAAACCGGGCCTGA 60.910 61.111 15.09 0.00 0.00 3.86
495 515 2.791383 TACATGTGTGCAGCCAAAAC 57.209 45.000 9.11 0.00 0.00 2.43
519 540 8.580720 GTCTCTTGATGATACTCATAAGGCTAA 58.419 37.037 0.00 0.00 37.20 3.09
547 568 8.190888 TCGTCAATTTTAAAATGTGTTTGCTT 57.809 26.923 14.04 0.00 0.00 3.91
963 997 1.683011 GCAGCTCAGGAATGGGCTAAA 60.683 52.381 1.64 0.00 33.43 1.85
973 1007 0.898326 TCCTTACGTGCAGCTCAGGA 60.898 55.000 0.00 0.00 34.80 3.86
982 1016 1.328680 CATGTCATGCTCCTTACGTGC 59.671 52.381 0.00 0.00 0.00 5.34
1295 1336 4.556135 CGCATTAGTCAGCAACAAATCTTG 59.444 41.667 0.00 0.00 0.00 3.02
1479 1549 1.338389 ACCGCCACGTAATAAGCAACT 60.338 47.619 0.00 0.00 0.00 3.16
1484 1554 1.758319 CGCCACCGCCACGTAATAAG 61.758 60.000 0.00 0.00 0.00 1.73
1486 1556 2.202770 CGCCACCGCCACGTAATA 60.203 61.111 0.00 0.00 0.00 0.98
1492 1562 2.784889 TTAAGTACCGCCACCGCCAC 62.785 60.000 0.00 0.00 0.00 5.01
1493 1563 1.901654 ATTAAGTACCGCCACCGCCA 61.902 55.000 0.00 0.00 0.00 5.69
1494 1564 0.104671 TATTAAGTACCGCCACCGCC 59.895 55.000 0.00 0.00 0.00 6.13
1495 1565 1.796459 CATATTAAGTACCGCCACCGC 59.204 52.381 0.00 0.00 0.00 5.68
1496 1566 3.102052 ACATATTAAGTACCGCCACCG 57.898 47.619 0.00 0.00 0.00 4.94
1497 1567 5.121105 AGAAACATATTAAGTACCGCCACC 58.879 41.667 0.00 0.00 0.00 4.61
1498 1568 6.314400 TGAAGAAACATATTAAGTACCGCCAC 59.686 38.462 0.00 0.00 0.00 5.01
1499 1569 6.314400 GTGAAGAAACATATTAAGTACCGCCA 59.686 38.462 0.00 0.00 0.00 5.69
1500 1570 6.314400 TGTGAAGAAACATATTAAGTACCGCC 59.686 38.462 0.00 0.00 0.00 6.13
1501 1571 7.298507 TGTGAAGAAACATATTAAGTACCGC 57.701 36.000 0.00 0.00 0.00 5.68
1519 1589 8.453320 TGACTCTGCATTTTTATGTATGTGAAG 58.547 33.333 0.00 0.00 0.00 3.02
1528 1598 6.198650 TCATGGTGACTCTGCATTTTTATG 57.801 37.500 0.00 0.00 0.00 1.90
1676 1750 8.420374 TTCAGATGTTATAGAAATTCGTGGTC 57.580 34.615 0.00 0.00 0.00 4.02
1678 1752 9.869844 GAATTCAGATGTTATAGAAATTCGTGG 57.130 33.333 0.00 0.00 0.00 4.94
1699 1773 9.050601 CAGTATTCACTATCCAGAAAGGAATTC 57.949 37.037 0.00 0.00 41.13 2.17
2329 2463 1.191489 TGAGAGGTCCGAACATGGCA 61.191 55.000 0.00 0.00 0.00 4.92
2393 2527 1.685224 ACATTCCGATGTGCAGGGT 59.315 52.632 0.00 0.00 44.64 4.34
2502 2643 0.240945 GCACCAAGTACGCTGCAAAT 59.759 50.000 0.00 0.00 0.00 2.32
2640 2781 3.454812 ACTTCACGGTTAGCCTATGGAAT 59.545 43.478 0.00 0.00 0.00 3.01
2646 2787 5.394883 CCTCATTAACTTCACGGTTAGCCTA 60.395 44.000 0.00 0.00 33.90 3.93
2674 2818 6.043411 CACCATGACTAGCCTAAAGTCTTAC 58.957 44.000 0.00 0.00 43.13 2.34
2695 2840 8.961294 TGATACTAGTCTAAGTTACTCTCACC 57.039 38.462 0.00 0.00 0.00 4.02
2717 2862 9.955102 AACATAGACTAATGTCATATGCATGAT 57.045 29.630 10.16 0.00 43.03 2.45
2732 2877 7.832685 TGCTCTGAAGGTAGTAACATAGACTAA 59.167 37.037 0.00 0.00 31.33 2.24
2759 2904 8.836413 GCCTATTGTTGACTATGCTATTAACAA 58.164 33.333 0.00 0.00 40.78 2.83
2760 2905 8.210946 AGCCTATTGTTGACTATGCTATTAACA 58.789 33.333 0.00 0.00 0.00 2.41
2774 2919 5.997746 GCAACTCCATATAGCCTATTGTTGA 59.002 40.000 0.00 0.00 35.65 3.18
2876 3108 6.757897 ACATTGTGAAAATGTACGATGGAT 57.242 33.333 0.00 0.00 41.10 3.41
2933 3170 3.096092 AGAGAAGGGAAGCAGACTGTAG 58.904 50.000 3.99 0.00 0.00 2.74
2994 3231 9.305555 ACAATCAGCATGCTATAAGGATTAAAT 57.694 29.630 22.19 10.33 31.12 1.40
3103 3340 9.627123 TTATATTACCAGCACATAGAGCTTTTT 57.373 29.630 0.00 0.00 41.14 1.94
3108 3345 6.533367 GCTCTTATATTACCAGCACATAGAGC 59.467 42.308 0.00 0.00 36.30 4.09
3110 3347 7.539034 TGCTCTTATATTACCAGCACATAGA 57.461 36.000 0.00 0.00 35.17 1.98
3133 3370 9.151471 CCCGTCTATATCACCTTATTGTATTTG 57.849 37.037 0.00 0.00 0.00 2.32
3136 3376 6.668283 AGCCCGTCTATATCACCTTATTGTAT 59.332 38.462 0.00 0.00 0.00 2.29
3203 3443 6.381498 TCTTGTCTTCTCTCTCCTCTTCTA 57.619 41.667 0.00 0.00 0.00 2.10
3204 3444 5.255397 TCTTGTCTTCTCTCTCCTCTTCT 57.745 43.478 0.00 0.00 0.00 2.85
3205 3445 4.399303 CCTCTTGTCTTCTCTCTCCTCTTC 59.601 50.000 0.00 0.00 0.00 2.87
3206 3446 4.344104 CCTCTTGTCTTCTCTCTCCTCTT 58.656 47.826 0.00 0.00 0.00 2.85
3207 3447 3.309121 CCCTCTTGTCTTCTCTCTCCTCT 60.309 52.174 0.00 0.00 0.00 3.69
3208 3448 3.023832 CCCTCTTGTCTTCTCTCTCCTC 58.976 54.545 0.00 0.00 0.00 3.71
3209 3449 2.888069 GCCCTCTTGTCTTCTCTCTCCT 60.888 54.545 0.00 0.00 0.00 3.69
3210 3450 1.480545 GCCCTCTTGTCTTCTCTCTCC 59.519 57.143 0.00 0.00 0.00 3.71
3211 3451 2.456577 AGCCCTCTTGTCTTCTCTCTC 58.543 52.381 0.00 0.00 0.00 3.20
3212 3452 2.621556 AGCCCTCTTGTCTTCTCTCT 57.378 50.000 0.00 0.00 0.00 3.10
3213 3453 3.093057 TGTAGCCCTCTTGTCTTCTCTC 58.907 50.000 0.00 0.00 0.00 3.20
3214 3454 3.176924 TGTAGCCCTCTTGTCTTCTCT 57.823 47.619 0.00 0.00 0.00 3.10
3274 3526 0.695803 GACCCACCTCCATCCCTCAT 60.696 60.000 0.00 0.00 0.00 2.90
3375 3627 2.896685 AGGGAGCTGCTGACTATATGAC 59.103 50.000 7.01 0.00 0.00 3.06
3410 3662 9.154847 GTTTGGAGTAACATACGTATTAAAGGT 57.845 33.333 5.03 0.00 0.00 3.50
3411 3663 9.153721 TGTTTGGAGTAACATACGTATTAAAGG 57.846 33.333 5.03 0.00 33.31 3.11
3414 3666 8.313292 AGGTGTTTGGAGTAACATACGTATTAA 58.687 33.333 5.03 0.00 39.93 1.40
3420 3672 4.817517 AGAGGTGTTTGGAGTAACATACG 58.182 43.478 0.00 0.00 39.93 3.06
3489 3741 7.562454 TGGGAGTAGCTTAGCTAGTAACATAAA 59.438 37.037 20.13 1.82 43.78 1.40
3507 3759 4.107127 AGGCTAGTCATAGTGGGAGTAG 57.893 50.000 0.00 0.00 39.97 2.57
3525 3777 0.800631 GGCAAAGTGTACGGTAAGGC 59.199 55.000 0.00 0.00 0.00 4.35
3545 3797 6.441274 TCACAATTGAAAGAATCTTGACTGC 58.559 36.000 13.59 0.00 0.00 4.40
3548 3800 9.125906 CTTCATCACAATTGAAAGAATCTTGAC 57.874 33.333 13.59 0.00 34.61 3.18
3596 3848 3.056107 TCAACCCTCGACTAAGAATGTGG 60.056 47.826 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.