Multiple sequence alignment - TraesCS2D01G055700

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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 TraesCS2D01G055700 chr2D 100.000 3579 0 0 1 3579 22249492 22245914 0.000000e+00 6610
1 TraesCS2D01G055700 chr2D 86.272 1741 174 28 933 2671 605778174 605776497 0.000000e+00 1831
2 TraesCS2D01G055700 chr2D 87.361 1345 148 8 933 2276 22311538 22310215 0.000000e+00 1522
3 TraesCS2D01G055700 chr2D 87.370 1346 147 8 933 2276 22333638 22332314 0.000000e+00 1522
4 TraesCS2D01G055700 chr2D 89.440 625 60 6 315 935 22312197 22311575 0.000000e+00 784
5 TraesCS2D01G055700 chr2D 89.150 553 47 12 2171 2719 22359691 22359148 0.000000e+00 676
6 TraesCS2D01G055700 chr2D 88.530 558 49 11 2171 2719 22313491 22312940 0.000000e+00 662
7 TraesCS2D01G055700 chr2D 88.530 558 49 11 2171 2719 22335591 22335040 0.000000e+00 662
8 TraesCS2D01G055700 chr2D 87.201 586 54 15 2349 2924 22310188 22309614 0.000000e+00 647
9 TraesCS2D01G055700 chr2D 87.053 587 53 17 2349 2924 22332287 22331713 3.010000e-180 641
10 TraesCS2D01G055700 chr2D 87.578 161 16 2 3419 3579 22290454 22290298 2.190000e-42 183
11 TraesCS2D01G055700 chrUn 88.332 2931 280 26 1 2917 203453588 203450706 0.000000e+00 3461
12 TraesCS2D01G055700 chrUn 88.316 2927 276 28 1 2917 227693498 227696368 0.000000e+00 3450
13 TraesCS2D01G055700 chrUn 88.255 2929 278 28 1 2917 12742591 12739717 0.000000e+00 3443
14 TraesCS2D01G055700 chrUn 88.091 2897 275 29 30 2917 203474035 203471200 0.000000e+00 3374
15 TraesCS2D01G055700 chrUn 86.792 2173 225 20 748 2917 227678609 227680722 0.000000e+00 2366
16 TraesCS2D01G055700 chrUn 88.605 1799 176 16 1 1792 232603578 232605354 0.000000e+00 2159
17 TraesCS2D01G055700 chrUn 88.605 1799 176 16 1 1792 337160773 337162549 0.000000e+00 2159
18 TraesCS2D01G055700 chrUn 88.520 1777 177 14 30 1800 374042145 374040390 0.000000e+00 2126
19 TraesCS2D01G055700 chrUn 88.687 1485 129 15 1436 2917 395639257 395637809 0.000000e+00 1775
20 TraesCS2D01G055700 chrUn 87.703 1171 134 4 933 2102 16841824 16840663 0.000000e+00 1356
21 TraesCS2D01G055700 chrUn 87.745 1175 125 12 933 2102 16881407 16880247 0.000000e+00 1354
22 TraesCS2D01G055700 chrUn 86.678 1171 146 6 933 2102 16838009 16836848 0.000000e+00 1290
23 TraesCS2D01G055700 chrUn 83.196 1339 155 10 933 2266 12803751 12802478 0.000000e+00 1162
24 TraesCS2D01G055700 chrUn 91.856 749 51 9 1 743 271558450 271557706 0.000000e+00 1037
25 TraesCS2D01G055700 chrUn 93.888 589 31 5 1 585 462951211 462951798 0.000000e+00 883
26 TraesCS2D01G055700 chrUn 88.191 669 50 9 2920 3579 12801675 12801027 0.000000e+00 771
27 TraesCS2D01G055700 chrUn 88.742 604 59 5 1499 2102 16887821 16887227 0.000000e+00 730
28 TraesCS2D01G055700 chrUn 90.805 435 37 2 2920 3354 203450667 203450236 2.400000e-161 579
29 TraesCS2D01G055700 chrUn 90.805 435 37 2 2920 3354 327240073 327240504 2.400000e-161 579
30 TraesCS2D01G055700 chrUn 90.575 435 38 2 2920 3354 12739679 12739248 1.110000e-159 573
31 TraesCS2D01G055700 chrUn 90.575 435 38 2 2920 3354 227696406 227696837 1.110000e-159 573
32 TraesCS2D01G055700 chrUn 88.578 464 52 1 1629 2092 12807690 12807228 2.410000e-156 562
33 TraesCS2D01G055700 chrUn 90.115 435 40 2 2920 3354 203471162 203470731 2.410000e-156 562
34 TraesCS2D01G055700 chrUn 89.885 435 41 2 2920 3354 276627925 276628356 1.120000e-154 556
35 TraesCS2D01G055700 chrUn 89.655 435 42 2 2920 3354 227680760 227681191 5.220000e-153 551
36 TraesCS2D01G055700 chrUn 91.304 345 26 2 3010 3354 16790109 16789769 5.410000e-128 468
37 TraesCS2D01G055700 chrUn 84.320 338 29 9 3252 3579 16855949 16855626 3.470000e-80 309
38 TraesCS2D01G055700 chrUn 84.874 238 21 8 3352 3579 248388991 248388759 3.600000e-55 226
39 TraesCS2D01G055700 chrUn 83.544 237 26 5 3352 3579 12782837 12782605 3.620000e-50 209
40 TraesCS2D01G055700 chrUn 83.122 237 27 5 3352 3579 319282819 319282587 1.680000e-48 204
41 TraesCS2D01G055700 chr6B 81.340 209 32 6 2717 2921 8165146 8164941 2.860000e-36 163
42 TraesCS2D01G055700 chr2B 80.465 215 40 2 2708 2921 712009569 712009356 2.860000e-36 163
43 TraesCS2D01G055700 chr2B 81.340 209 32 7 2717 2921 763459093 763459298 2.860000e-36 163


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 TraesCS2D01G055700 chr2D 22245914 22249492 3578 True 6610.000000 6610 100.0000 1 3579 1 chr2D.!!$R1 3578
1 TraesCS2D01G055700 chr2D 605776497 605778174 1677 True 1831.000000 1831 86.2720 933 2671 1 chr2D.!!$R4 1738
2 TraesCS2D01G055700 chr2D 22331713 22335591 3878 True 941.666667 1522 87.6510 933 2924 3 chr2D.!!$R6 1991
3 TraesCS2D01G055700 chr2D 22309614 22313491 3877 True 903.750000 1522 88.1330 315 2924 4 chr2D.!!$R5 2609
4 TraesCS2D01G055700 chr2D 22359148 22359691 543 True 676.000000 676 89.1500 2171 2719 1 chr2D.!!$R3 548
5 TraesCS2D01G055700 chrUn 232603578 232605354 1776 False 2159.000000 2159 88.6050 1 1792 1 chrUn.!!$F1 1791
6 TraesCS2D01G055700 chrUn 337160773 337162549 1776 False 2159.000000 2159 88.6050 1 1792 1 chrUn.!!$F4 1791
7 TraesCS2D01G055700 chrUn 374040390 374042145 1755 True 2126.000000 2126 88.5200 30 1800 1 chrUn.!!$R9 1770
8 TraesCS2D01G055700 chrUn 203450236 203453588 3352 True 2020.000000 3461 89.5685 1 3354 2 chrUn.!!$R14 3353
9 TraesCS2D01G055700 chrUn 227693498 227696837 3339 False 2011.500000 3450 89.4455 1 3354 2 chrUn.!!$F7 3353
10 TraesCS2D01G055700 chrUn 12739248 12742591 3343 True 2008.000000 3443 89.4150 1 3354 2 chrUn.!!$R11 3353
11 TraesCS2D01G055700 chrUn 203470731 203474035 3304 True 1968.000000 3374 89.1030 30 3354 2 chrUn.!!$R15 3324
12 TraesCS2D01G055700 chrUn 395637809 395639257 1448 True 1775.000000 1775 88.6870 1436 2917 1 chrUn.!!$R10 1481
13 TraesCS2D01G055700 chrUn 227678609 227681191 2582 False 1458.500000 2366 88.2235 748 3354 2 chrUn.!!$F6 2606
14 TraesCS2D01G055700 chrUn 16880247 16881407 1160 True 1354.000000 1354 87.7450 933 2102 1 chrUn.!!$R4 1169
15 TraesCS2D01G055700 chrUn 16836848 16841824 4976 True 1323.000000 1356 87.1905 933 2102 2 chrUn.!!$R13 1169
16 TraesCS2D01G055700 chrUn 271557706 271558450 744 True 1037.000000 1037 91.8560 1 743 1 chrUn.!!$R7 742
17 TraesCS2D01G055700 chrUn 462951211 462951798 587 False 883.000000 883 93.8880 1 585 1 chrUn.!!$F5 584
18 TraesCS2D01G055700 chrUn 12801027 12807690 6663 True 831.666667 1162 86.6550 933 3579 3 chrUn.!!$R12 2646
19 TraesCS2D01G055700 chrUn 16887227 16887821 594 True 730.000000 730 88.7420 1499 2102 1 chrUn.!!$R5 603

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
890 1878 0.254747 CGCCAAAGGGGACAAGGATA 59.745 55.0 0.0 0.0 40.01 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2815 9786 0.599204 ACTTACAACACGCACTCGGG 60.599 55.0 0.0 0.0 46.41 5.14 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
40 41 5.178096 TCAGTTGCTCCCATTCTGATTAA 57.822 39.130 0.00 0.00 31.88 1.40
54 55 3.876914 TCTGATTAAATGTCCCACATCGC 59.123 43.478 0.00 0.00 37.97 4.58
59 60 1.959042 AATGTCCCACATCGCTCATC 58.041 50.000 0.00 0.00 37.97 2.92
139 140 2.353803 CCTAAGGTTTCTCAGTCCACCG 60.354 54.545 0.00 0.00 34.19 4.94
288 290 4.019591 AGTCCACATTACCCCAGTAAAGAC 60.020 45.833 0.00 0.00 41.68 3.01
661 904 5.227569 AGTGTATCATTGAACACACCTCA 57.772 39.130 21.87 0.00 46.71 3.86
686 929 1.215647 AGCGTTGTCGGTGGATCTC 59.784 57.895 0.00 0.00 46.08 2.75
698 941 2.698797 GGTGGATCTCGGAAATGGACTA 59.301 50.000 0.00 0.00 0.00 2.59
700 943 4.372656 GTGGATCTCGGAAATGGACTAAG 58.627 47.826 0.00 0.00 0.00 2.18
705 948 0.814010 CGGAAATGGACTAAGCGGGG 60.814 60.000 0.00 0.00 0.00 5.73
860 1848 7.600375 ACCTTATCACACTTCTATATTCATGCG 59.400 37.037 0.00 0.00 0.00 4.73
861 1849 7.814587 CCTTATCACACTTCTATATTCATGCGA 59.185 37.037 0.00 0.00 0.00 5.10
890 1878 0.254747 CGCCAAAGGGGACAAGGATA 59.745 55.000 0.00 0.00 40.01 2.59
895 1883 4.401925 CCAAAGGGGACAAGGATATGATC 58.598 47.826 0.00 0.00 40.01 2.92
982 4057 1.144057 CCAGCCATGGTAGGACGTC 59.856 63.158 14.67 7.13 42.17 4.34
1003 4078 4.790962 CGTGCCCTCCAGCTGCAT 62.791 66.667 8.66 0.00 37.34 3.96
1106 4181 2.490509 ACGACGAACTACACCATCATCA 59.509 45.455 0.00 0.00 0.00 3.07
1110 4185 4.832248 ACGAACTACACCATCATCAATGT 58.168 39.130 0.00 0.00 33.13 2.71
1184 4259 4.823276 CCGCTCAGTGGCTTCTAG 57.177 61.111 0.00 0.00 0.00 2.43
1191 4266 1.359474 TCAGTGGCTTCTAGTCCTCCT 59.641 52.381 0.00 0.00 0.00 3.69
1209 4284 0.321122 CTCCTCTTTGCCAAGCGTCT 60.321 55.000 0.00 0.00 0.00 4.18
1282 4357 1.830279 ACGAGTTCCTATCCGTCACA 58.170 50.000 0.00 0.00 0.00 3.58
1283 4358 1.471684 ACGAGTTCCTATCCGTCACAC 59.528 52.381 0.00 0.00 0.00 3.82
1287 4362 0.528924 TTCCTATCCGTCACACGTGG 59.471 55.000 21.57 9.11 40.58 4.94
1389 4464 2.579873 CATCGAGCCCCTCAATTTCAT 58.420 47.619 0.00 0.00 0.00 2.57
1395 4470 2.018644 GCCCCTCAATTTCATGAGCGA 61.019 52.381 0.00 0.00 44.43 4.93
1470 4545 2.104792 AGTTTGTAGAAGTGGCTGCTCA 59.895 45.455 0.00 0.00 0.00 4.26
1495 4570 4.502604 CCTCACGACAGGAAAGGAAAAGTA 60.503 45.833 0.00 0.00 35.20 2.24
1510 4585 1.285280 AAGTACAGGCCCATGCTACA 58.715 50.000 0.00 0.00 37.74 2.74
1568 4643 0.598680 GCTATCGCCGAAGCTCATGT 60.599 55.000 12.06 0.00 35.80 3.21
1599 4674 3.998672 GGAGGCCGACCACAACGA 61.999 66.667 15.42 0.00 39.06 3.85
1693 4771 4.776647 GCACGCGGGTTGGCAATC 62.777 66.667 11.45 1.27 0.00 2.67
1750 4828 3.234353 AGAGATCAGGGATATCGTTGCA 58.766 45.455 0.00 0.00 35.69 4.08
1801 4879 2.350895 CGGATGGTGAAGTGGGCA 59.649 61.111 0.00 0.00 0.00 5.36
1897 4975 4.415150 ATGGTGACCGGCTGCAGG 62.415 66.667 17.47 17.47 0.00 4.85
1915 4995 1.437547 AGGAGGGAGTACAGGGTTTCT 59.562 52.381 0.00 0.00 0.00 2.52
1919 4999 4.325658 GGAGGGAGTACAGGGTTTCTAGTA 60.326 50.000 0.00 0.00 0.00 1.82
1928 5008 6.547930 ACAGGGTTTCTAGTAAGAAGGATC 57.452 41.667 0.00 0.00 42.60 3.36
2035 5119 8.877808 TTGTGACATGTGATATCTACAGAATC 57.122 34.615 1.15 6.73 0.00 2.52
2115 9015 7.540055 GCCTGAACTTCTTGTTATCATTTTGAG 59.460 37.037 0.00 0.00 39.30 3.02
2116 9016 8.571336 CCTGAACTTCTTGTTATCATTTTGAGT 58.429 33.333 0.00 0.00 39.30 3.41
2117 9017 9.956720 CTGAACTTCTTGTTATCATTTTGAGTT 57.043 29.630 0.00 0.00 39.30 3.01
2118 9018 9.734620 TGAACTTCTTGTTATCATTTTGAGTTG 57.265 29.630 0.00 0.00 39.30 3.16
2119 9019 9.736023 GAACTTCTTGTTATCATTTTGAGTTGT 57.264 29.630 0.00 0.00 39.30 3.32
2121 9021 9.520204 ACTTCTTGTTATCATTTTGAGTTGTTG 57.480 29.630 0.00 0.00 0.00 3.33
2122 9022 9.520204 CTTCTTGTTATCATTTTGAGTTGTTGT 57.480 29.630 0.00 0.00 0.00 3.32
2123 9023 9.868277 TTCTTGTTATCATTTTGAGTTGTTGTT 57.132 25.926 0.00 0.00 0.00 2.83
2124 9024 9.299963 TCTTGTTATCATTTTGAGTTGTTGTTG 57.700 29.630 0.00 0.00 0.00 3.33
2125 9025 8.994429 TTGTTATCATTTTGAGTTGTTGTTGT 57.006 26.923 0.00 0.00 0.00 3.32
2126 9026 8.994429 TGTTATCATTTTGAGTTGTTGTTGTT 57.006 26.923 0.00 0.00 0.00 2.83
2127 9027 8.867935 TGTTATCATTTTGAGTTGTTGTTGTTG 58.132 29.630 0.00 0.00 0.00 3.33
2128 9028 8.868916 GTTATCATTTTGAGTTGTTGTTGTTGT 58.131 29.630 0.00 0.00 0.00 3.32
2129 9029 7.903995 ATCATTTTGAGTTGTTGTTGTTGTT 57.096 28.000 0.00 0.00 0.00 2.83
2159 9059 5.126545 TGTTGTTATCCTACTGTGCGATAGT 59.873 40.000 0.00 0.00 39.35 2.12
2185 9085 4.793071 TGTTTCATCTTATGCCACAAACG 58.207 39.130 0.00 0.00 30.38 3.60
2190 9090 1.810151 TCTTATGCCACAAACGGAAGC 59.190 47.619 0.00 0.00 0.00 3.86
2296 9227 6.388278 AGTTGTTCTTGTTATCGTACTCCTC 58.612 40.000 0.00 0.00 0.00 3.71
2384 9315 3.655276 ATTACCACAGAACGTTCGACT 57.345 42.857 21.87 2.48 0.00 4.18
2385 9316 2.693797 TACCACAGAACGTTCGACTC 57.306 50.000 21.87 0.00 0.00 3.36
2386 9317 1.030457 ACCACAGAACGTTCGACTCT 58.970 50.000 21.87 1.34 0.00 3.24
2430 9376 1.221635 CCCTCTCTCTCCCTCTCTCA 58.778 60.000 0.00 0.00 0.00 3.27
2441 9387 1.133792 CCCTCTCTCACCTCTCTCTCC 60.134 61.905 0.00 0.00 0.00 3.71
2442 9388 1.133792 CCTCTCTCACCTCTCTCTCCC 60.134 61.905 0.00 0.00 0.00 4.30
2443 9389 0.923358 TCTCTCACCTCTCTCTCCCC 59.077 60.000 0.00 0.00 0.00 4.81
2444 9390 0.926293 CTCTCACCTCTCTCTCCCCT 59.074 60.000 0.00 0.00 0.00 4.79
2445 9391 0.923358 TCTCACCTCTCTCTCCCCTC 59.077 60.000 0.00 0.00 0.00 4.30
2446 9392 0.926293 CTCACCTCTCTCTCCCCTCT 59.074 60.000 0.00 0.00 0.00 3.69
2447 9393 2.131854 CTCACCTCTCTCTCCCCTCTA 58.868 57.143 0.00 0.00 0.00 2.43
2448 9394 1.847737 TCACCTCTCTCTCCCCTCTAC 59.152 57.143 0.00 0.00 0.00 2.59
2452 9398 1.423921 CTCTCTCTCCCCTCTACCTCC 59.576 61.905 0.00 0.00 0.00 4.30
2456 9402 1.000041 TCTCCCCTCTACCTCCCTCC 61.000 65.000 0.00 0.00 0.00 4.30
2457 9403 1.230853 TCCCCTCTACCTCCCTCCA 60.231 63.158 0.00 0.00 0.00 3.86
2520 9481 5.755861 CGAGAAGAAATCATAACCTCTTCCC 59.244 44.000 6.97 0.00 43.12 3.97
2545 9510 0.243095 ACCTTAGCACGACGACTTCC 59.757 55.000 0.00 0.00 0.00 3.46
2563 9528 2.778299 TCCCGATTGTCTTCCAACTTG 58.222 47.619 0.00 0.00 35.44 3.16
2610 9578 2.335316 TTTGTGGCGTATACATCCCC 57.665 50.000 3.32 0.00 0.00 4.81
2649 9617 8.587952 ACAAAGTGCAAGTAAATGGATAAAAC 57.412 30.769 0.00 0.00 0.00 2.43
2674 9642 6.652205 TCCTTTATCCCAACTGTTTAGGAT 57.348 37.500 20.06 20.06 41.90 3.24
2696 9667 9.077885 AGGATAAACAAATGAAAGCTAAACTCA 57.922 29.630 0.00 0.00 0.00 3.41
2771 9742 0.537188 ATAGGCTGTTCTGTGACGGG 59.463 55.000 0.00 0.00 0.00 5.28
2798 9769 1.153823 CCGCCTCCGTTGTAGACAG 60.154 63.158 0.00 0.00 0.00 3.51
2815 9786 4.612932 GACAGATGGCAGATGTCTTTTC 57.387 45.455 21.29 3.87 40.14 2.29
2827 9798 0.878961 GTCTTTTCCCGAGTGCGTGT 60.879 55.000 0.00 0.00 35.23 4.49
2834 9805 0.599204 CCCGAGTGCGTGTTGTAAGT 60.599 55.000 0.00 0.00 35.23 2.24
2836 9807 0.429736 CGAGTGCGTGTTGTAAGTCG 59.570 55.000 0.00 0.00 0.00 4.18
2847 9819 1.504359 TGTAAGTCGGGTGCTTTTCG 58.496 50.000 0.00 0.00 0.00 3.46
2857 9829 3.114065 GGGTGCTTTTCGAGTAGATACG 58.886 50.000 0.52 0.00 0.00 3.06
2860 9832 3.790288 GTGCTTTTCGAGTAGATACGGTC 59.210 47.826 0.52 0.00 0.00 4.79
2874 10033 8.834733 AGTAGATACGGTCTTATCCCTATAAGT 58.165 37.037 5.34 0.00 43.45 2.24
2917 10079 4.093743 TCGGCTTATAGATGGCCATAAGA 58.906 43.478 24.19 12.11 45.50 2.10
2921 10083 4.865365 GCTTATAGATGGCCATAAGACGAC 59.135 45.833 24.19 9.72 37.04 4.34
2937 10149 0.100861 CGACTCGGCTTAGAGGAACC 59.899 60.000 8.69 0.00 42.31 3.62
2945 10157 2.892784 CTTAGAGGAACCTAAGCCGG 57.107 55.000 0.00 0.00 39.15 6.13
2994 10206 1.310904 GCTAACACACGGGAAAACCA 58.689 50.000 0.00 0.00 40.22 3.67
3151 10363 9.438291 GAAATTTGAGAATACGTACCATGATTG 57.562 33.333 0.00 0.00 0.00 2.67
3191 10403 3.818586 CATGCAATGTGGGGTTGAC 57.181 52.632 0.00 0.00 40.20 3.18
3230 10442 2.223525 GCAGCAGAGCATTTCCAATCTC 60.224 50.000 0.00 0.00 0.00 2.75
3258 10470 3.006677 GGGGGAAGGCTGTATGCA 58.993 61.111 0.00 0.00 45.15 3.96
3274 10486 0.689080 TGCATCCTCCTCCCAGAGTC 60.689 60.000 0.00 0.00 31.53 3.36
3322 10534 0.037882 CACGGTGAGCTGATGTGACT 60.038 55.000 0.74 0.00 32.39 3.41
3330 10542 1.959899 GCTGATGTGACTGAACGGCG 61.960 60.000 4.80 4.80 0.00 6.46
3331 10543 0.388520 CTGATGTGACTGAACGGCGA 60.389 55.000 16.62 0.00 0.00 5.54
3414 10626 3.607370 GAGGGACCAGCGGTTCACC 62.607 68.421 8.07 8.09 35.25 4.02
3415 10627 4.717313 GGGACCAGCGGTTCACCC 62.717 72.222 8.07 7.52 35.25 4.61
3416 10628 4.717313 GGACCAGCGGTTCACCCC 62.717 72.222 1.80 0.00 35.25 4.95
3417 10629 3.948719 GACCAGCGGTTCACCCCA 61.949 66.667 1.80 0.00 35.25 4.96
3418 10630 3.256960 ACCAGCGGTTCACCCCAT 61.257 61.111 0.00 0.00 27.29 4.00
3419 10631 2.751436 CCAGCGGTTCACCCCATG 60.751 66.667 0.00 0.00 0.00 3.66
3420 10632 3.443045 CAGCGGTTCACCCCATGC 61.443 66.667 0.00 0.00 0.00 4.06
3422 10634 2.755469 GCGGTTCACCCCATGCAT 60.755 61.111 0.00 0.00 0.00 3.96
3443 10664 1.227002 CCTTCCTAGCGAACGCCTC 60.227 63.158 15.44 0.00 43.17 4.70
3469 10690 0.741915 CTCCCTGAGCTTAGACGTCC 59.258 60.000 13.01 0.00 0.00 4.79
3473 10694 0.179161 CTGAGCTTAGACGTCCGGTG 60.179 60.000 13.01 1.43 0.00 4.94
3474 10695 0.892358 TGAGCTTAGACGTCCGGTGT 60.892 55.000 13.01 0.51 0.00 4.16
3475 10696 1.089920 GAGCTTAGACGTCCGGTGTA 58.910 55.000 13.01 0.00 0.00 2.90
3476 10697 0.807496 AGCTTAGACGTCCGGTGTAC 59.193 55.000 13.01 0.00 0.00 2.90
3477 10698 0.522076 GCTTAGACGTCCGGTGTACG 60.522 60.000 13.01 12.19 45.64 3.67
3532 10753 4.271816 CCTCGTGGGAGCCGATCG 62.272 72.222 8.51 8.51 39.06 3.69
3533 10754 3.209812 CTCGTGGGAGCCGATCGA 61.210 66.667 18.66 0.00 33.27 3.59
3534 10755 2.518587 TCGTGGGAGCCGATCGAT 60.519 61.111 18.66 4.31 0.00 3.59
3535 10756 2.355126 CGTGGGAGCCGATCGATG 60.355 66.667 18.66 1.12 0.00 3.84
3543 10764 3.233980 CCGATCGATGGCCTGGGA 61.234 66.667 18.66 0.00 0.00 4.37
3544 10765 2.341543 CGATCGATGGCCTGGGAG 59.658 66.667 10.26 0.00 0.00 4.30
3545 10766 2.203082 CGATCGATGGCCTGGGAGA 61.203 63.158 10.26 0.00 0.00 3.71
3546 10767 1.539560 CGATCGATGGCCTGGGAGAT 61.540 60.000 10.26 1.68 0.00 2.75
3547 10768 1.561643 GATCGATGGCCTGGGAGATA 58.438 55.000 0.54 0.00 0.00 1.98
3548 10769 1.205893 GATCGATGGCCTGGGAGATAC 59.794 57.143 0.54 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.475751 GGATGAGCGATGTGGGACATT 60.476 52.381 0.00 0.00 44.52 2.71
59 60 3.492421 AAAACATAGTTGCGCTCATGG 57.508 42.857 9.73 0.00 0.00 3.66
98 99 2.738314 GGCCATGTGCAAAATCAACTTC 59.262 45.455 0.00 0.00 43.89 3.01
165 166 3.686241 ACATGATGACTCAATCACCAACG 59.314 43.478 0.00 0.00 41.24 4.10
272 273 3.920841 ACCAAGGTCTTTACTGGGGTAAT 59.079 43.478 0.00 0.00 37.69 1.89
320 558 9.995957 CATATGAATGTCTCTACTACTTATCCG 57.004 37.037 0.00 0.00 0.00 4.18
478 720 1.211949 CAATGGGTCGGATGGGTTAGT 59.788 52.381 0.00 0.00 0.00 2.24
601 844 6.704493 TGACGTTTAATGGATGCTAGGAATAC 59.296 38.462 0.00 0.00 0.00 1.89
686 929 0.814010 CCCCGCTTAGTCCATTTCCG 60.814 60.000 0.00 0.00 0.00 4.30
698 941 1.743995 GTGTACGAATGCCCCGCTT 60.744 57.895 0.00 0.00 0.00 4.68
700 943 2.125269 AGTGTACGAATGCCCCGC 60.125 61.111 0.00 0.00 0.00 6.13
705 948 1.594862 GATGCTGGAGTGTACGAATGC 59.405 52.381 0.00 0.00 0.00 3.56
860 1848 3.573489 CTTTGGCGAACGCGGTGTC 62.573 63.158 12.47 3.59 43.06 3.67
861 1849 3.645975 CTTTGGCGAACGCGGTGT 61.646 61.111 12.47 0.00 43.06 4.16
890 1878 1.493871 CTCCAGCCCCTTCTTGATCAT 59.506 52.381 0.00 0.00 0.00 2.45
895 1883 0.911525 TCCTCTCCAGCCCCTTCTTG 60.912 60.000 0.00 0.00 0.00 3.02
1003 4078 2.053865 CGGTGCGGGGGTAGTCTTA 61.054 63.158 0.00 0.00 0.00 2.10
1044 4119 2.184322 GGCACATCTCGGCGAAGA 59.816 61.111 12.13 11.19 0.00 2.87
1076 4151 2.746412 TAGTTCGTCGTGGTCCCGGA 62.746 60.000 0.73 0.00 0.00 5.14
1106 4181 1.025812 CTCTCCGTCCGAGCTACATT 58.974 55.000 0.00 0.00 38.62 2.71
1110 4185 0.183014 ATTCCTCTCCGTCCGAGCTA 59.817 55.000 0.00 0.00 38.62 3.32
1159 4234 4.731612 CACTGAGCGGCGTCAGCT 62.732 66.667 27.42 17.35 46.90 4.24
1171 4246 1.359474 AGGAGGACTAGAAGCCACTGA 59.641 52.381 0.00 0.00 0.00 3.41
1183 4258 0.178891 TGGCAAAGAGGAGGAGGACT 60.179 55.000 0.00 0.00 0.00 3.85
1184 4259 0.693049 TTGGCAAAGAGGAGGAGGAC 59.307 55.000 0.00 0.00 0.00 3.85
1191 4266 0.603707 CAGACGCTTGGCAAAGAGGA 60.604 55.000 4.56 0.00 37.51 3.71
1383 4458 1.394917 GTGCTTCGTCGCTCATGAAAT 59.605 47.619 0.00 0.00 29.09 2.17
1389 4464 0.168348 GACTAGTGCTTCGTCGCTCA 59.832 55.000 0.00 0.00 0.00 4.26
1395 4470 2.085320 AGACGATGACTAGTGCTTCGT 58.915 47.619 23.25 23.25 45.05 3.85
1470 4545 1.938585 TCCTTTCCTGTCGTGAGGAT 58.061 50.000 6.09 0.00 41.97 3.24
1495 4570 0.625316 TCATTGTAGCATGGGCCTGT 59.375 50.000 4.53 0.00 42.56 4.00
1510 4585 4.814294 GCGTCGGCCCTCGTCATT 62.814 66.667 14.19 0.00 40.32 2.57
1568 4643 2.583441 CCTCCTGCTCCGTCACCAA 61.583 63.158 0.00 0.00 0.00 3.67
1599 4674 2.798148 GAACCGGCCCATGAACTCGT 62.798 60.000 0.00 0.00 0.00 4.18
1686 4761 4.812476 CCGACCGCTCGATTGCCA 62.812 66.667 0.71 0.00 43.06 4.92
1693 4771 3.350909 TTCCATGTCCGACCGCTCG 62.351 63.158 0.00 0.00 39.83 5.03
1780 4858 1.296392 CCACTTCACCATCCGCTCA 59.704 57.895 0.00 0.00 0.00 4.26
1897 4975 3.710724 ACTAGAAACCCTGTACTCCCTC 58.289 50.000 0.00 0.00 0.00 4.30
1928 5008 2.082231 CCAGTGGATGAAGAAGCACAG 58.918 52.381 1.68 0.00 0.00 3.66
1995 5078 3.134623 TGTCACAATATCTGGCGATCCTT 59.865 43.478 0.00 0.00 0.00 3.36
2035 5119 8.385111 GCATGAAATTGTTGTAATGAATTGAGG 58.615 33.333 0.00 0.00 0.00 3.86
2047 8946 7.731882 TTCATCAAATGCATGAAATTGTTGT 57.268 28.000 0.00 0.00 37.33 3.32
2115 9015 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
2116 9016 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
2117 9017 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
2118 9018 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
2119 9019 7.095607 GGATAACAACAACAACAACAACAACAA 60.096 33.333 0.00 0.00 0.00 2.83
2120 9020 6.366332 GGATAACAACAACAACAACAACAACA 59.634 34.615 0.00 0.00 0.00 3.33
2121 9021 6.588373 AGGATAACAACAACAACAACAACAAC 59.412 34.615 0.00 0.00 0.00 3.32
2122 9022 6.692486 AGGATAACAACAACAACAACAACAA 58.308 32.000 0.00 0.00 0.00 2.83
2123 9023 6.274157 AGGATAACAACAACAACAACAACA 57.726 33.333 0.00 0.00 0.00 3.33
2124 9024 7.431084 CAGTAGGATAACAACAACAACAACAAC 59.569 37.037 0.00 0.00 0.00 3.32
2125 9025 7.121463 ACAGTAGGATAACAACAACAACAACAA 59.879 33.333 0.00 0.00 0.00 2.83
2126 9026 6.600032 ACAGTAGGATAACAACAACAACAACA 59.400 34.615 0.00 0.00 0.00 3.33
2127 9027 6.910433 CACAGTAGGATAACAACAACAACAAC 59.090 38.462 0.00 0.00 0.00 3.32
2128 9028 6.459024 GCACAGTAGGATAACAACAACAACAA 60.459 38.462 0.00 0.00 0.00 2.83
2129 9029 5.008217 GCACAGTAGGATAACAACAACAACA 59.992 40.000 0.00 0.00 0.00 3.33
2159 9059 5.781210 TGTGGCATAAGATGAAACAACAA 57.219 34.783 0.00 0.00 0.00 2.83
2185 9085 4.037923 TGTCTTGAACATTTTCCAGCTTCC 59.962 41.667 0.00 0.00 31.20 3.46
2263 9194 7.643764 ACGATAACAAGAACAACTCAAAATGTG 59.356 33.333 0.00 0.00 0.00 3.21
2296 9227 4.616802 GTGGCATAAGATGAAACAACAACG 59.383 41.667 0.00 0.00 0.00 4.10
2384 9315 3.714798 GGAGGAAGGTAGAGAGAGAGAGA 59.285 52.174 0.00 0.00 0.00 3.10
2385 9316 3.181443 GGGAGGAAGGTAGAGAGAGAGAG 60.181 56.522 0.00 0.00 0.00 3.20
2386 9317 2.781174 GGGAGGAAGGTAGAGAGAGAGA 59.219 54.545 0.00 0.00 0.00 3.10
2430 9376 1.228190 GGTAGAGGGGAGAGAGAGGT 58.772 60.000 0.00 0.00 0.00 3.85
2441 9387 0.863956 AGATGGAGGGAGGTAGAGGG 59.136 60.000 0.00 0.00 0.00 4.30
2442 9388 1.786441 AGAGATGGAGGGAGGTAGAGG 59.214 57.143 0.00 0.00 0.00 3.69
2443 9389 2.716424 AGAGAGATGGAGGGAGGTAGAG 59.284 54.545 0.00 0.00 0.00 2.43
2444 9390 2.714250 GAGAGAGATGGAGGGAGGTAGA 59.286 54.545 0.00 0.00 0.00 2.59
2445 9391 2.716424 AGAGAGAGATGGAGGGAGGTAG 59.284 54.545 0.00 0.00 0.00 3.18
2446 9392 2.445145 CAGAGAGAGATGGAGGGAGGTA 59.555 54.545 0.00 0.00 0.00 3.08
2447 9393 1.217689 CAGAGAGAGATGGAGGGAGGT 59.782 57.143 0.00 0.00 0.00 3.85
2448 9394 1.999648 CAGAGAGAGATGGAGGGAGG 58.000 60.000 0.00 0.00 0.00 4.30
2452 9398 2.967201 AGAATGCAGAGAGAGATGGAGG 59.033 50.000 0.00 0.00 0.00 4.30
2520 9481 0.806102 CGTCGTGCTAAGGTCCCATG 60.806 60.000 0.00 0.00 0.00 3.66
2545 9510 2.504367 ACCAAGTTGGAAGACAATCGG 58.496 47.619 28.80 0.00 40.96 4.18
2610 9578 4.338118 TGCACTTTGTTCCTCTAAACCAAG 59.662 41.667 0.00 0.00 37.70 3.61
2649 9617 6.481643 TCCTAAACAGTTGGGATAAAGGAAG 58.518 40.000 4.61 0.00 39.34 3.46
2696 9667 5.310857 ACAGGGTCTAAAAGAGGTCTCAAAT 59.689 40.000 0.55 0.00 0.00 2.32
2777 9748 1.378911 TCTACAACGGAGGCGGCTA 60.379 57.895 13.24 0.00 0.00 3.93
2798 9769 1.672881 CGGGAAAAGACATCTGCCATC 59.327 52.381 0.00 0.00 0.00 3.51
2815 9786 0.599204 ACTTACAACACGCACTCGGG 60.599 55.000 0.00 0.00 46.41 5.14
2827 9798 1.868498 CGAAAAGCACCCGACTTACAA 59.132 47.619 0.00 0.00 0.00 2.41
2834 9805 1.250328 TCTACTCGAAAAGCACCCGA 58.750 50.000 0.00 0.00 0.00 5.14
2836 9807 3.114065 CGTATCTACTCGAAAAGCACCC 58.886 50.000 0.00 0.00 0.00 4.61
2847 9819 9.328845 CTTATAGGGATAAGACCGTATCTACTC 57.671 40.741 0.00 0.00 45.16 2.59
2857 9829 5.124297 GCTCTCGACTTATAGGGATAAGACC 59.876 48.000 10.83 3.06 45.16 3.85
2860 9832 6.827586 AAGCTCTCGACTTATAGGGATAAG 57.172 41.667 3.66 3.66 46.91 1.73
2917 10079 0.810016 GTTCCTCTAAGCCGAGTCGT 59.190 55.000 12.31 0.00 0.00 4.34
2921 10083 3.719173 CTTAGGTTCCTCTAAGCCGAG 57.281 52.381 0.00 0.00 39.53 4.63
2994 10206 6.653020 TCACACATGCACTATAGGAAAATCT 58.347 36.000 4.43 0.00 0.00 2.40
3004 10216 4.022155 TGCACAAAATCACACATGCACTAT 60.022 37.500 0.00 0.00 38.11 2.12
3061 10273 2.940994 TGCACCCTGCTTGTTTACTA 57.059 45.000 0.00 0.00 45.31 1.82
3155 10367 1.133181 TGTGCTCCAGATTGGGGACA 61.133 55.000 0.00 3.38 41.85 4.02
3191 10403 1.222115 GCTTCGGGCTATTGGCTACG 61.222 60.000 0.10 3.98 41.46 3.51
3258 10470 1.063266 GTCAGACTCTGGGAGGAGGAT 60.063 57.143 6.20 0.00 37.63 3.24
3274 10486 2.740055 AAGGCTTGAGCGCGTCAG 60.740 61.111 8.43 0.00 43.26 3.51
3308 10520 1.337167 CCGTTCAGTCACATCAGCTCA 60.337 52.381 0.00 0.00 0.00 4.26
3322 10534 2.357034 GTTCTGGCTCGCCGTTCA 60.357 61.111 3.14 0.00 39.42 3.18
3330 10542 0.381089 GATGCATGCTGTTCTGGCTC 59.619 55.000 20.33 0.00 0.00 4.70
3331 10543 0.034380 AGATGCATGCTGTTCTGGCT 60.034 50.000 20.33 1.68 0.00 4.75
3395 10607 2.525629 TGAACCGCTGGTCCCTCA 60.526 61.111 0.69 0.00 33.12 3.86
3414 10626 0.538977 CTAGGAAGGGCATGCATGGG 60.539 60.000 27.34 4.09 0.00 4.00
3415 10627 1.177256 GCTAGGAAGGGCATGCATGG 61.177 60.000 27.34 10.03 0.00 3.66
3416 10628 1.512996 CGCTAGGAAGGGCATGCATG 61.513 60.000 22.70 22.70 0.00 4.06
3417 10629 1.228063 CGCTAGGAAGGGCATGCAT 60.228 57.895 21.36 4.13 0.00 3.96
3418 10630 1.909459 TTCGCTAGGAAGGGCATGCA 61.909 55.000 21.36 0.00 35.68 3.96
3419 10631 1.153168 TTCGCTAGGAAGGGCATGC 60.153 57.895 9.90 9.90 35.68 4.06
3420 10632 1.154205 CGTTCGCTAGGAAGGGCATG 61.154 60.000 0.00 0.00 36.98 4.06
3422 10634 2.577059 CGTTCGCTAGGAAGGGCA 59.423 61.111 0.00 0.00 36.98 5.36
3443 10664 1.339610 CTAAGCTCAGGGAGTGGATCG 59.660 57.143 0.00 0.00 31.39 3.69
3469 10690 2.278596 CGAGGCCATCGTACACCG 60.279 66.667 5.01 0.00 46.62 4.94
3477 10698 1.817099 CCTCAACAGCGAGGCCATC 60.817 63.158 5.01 0.00 45.95 3.51
3478 10699 2.270205 CCTCAACAGCGAGGCCAT 59.730 61.111 5.01 0.00 45.95 4.40
3483 10704 1.734477 CGTCCACCTCAACAGCGAG 60.734 63.158 0.00 0.00 0.00 5.03
3484 10705 2.338620 CGTCCACCTCAACAGCGA 59.661 61.111 0.00 0.00 0.00 4.93
3485 10706 2.507110 ATCCGTCCACCTCAACAGCG 62.507 60.000 0.00 0.00 0.00 5.18
3486 10707 0.741221 GATCCGTCCACCTCAACAGC 60.741 60.000 0.00 0.00 0.00 4.40
3487 10708 0.458543 CGATCCGTCCACCTCAACAG 60.459 60.000 0.00 0.00 0.00 3.16
3531 10752 1.290324 CGTATCTCCCAGGCCATCG 59.710 63.158 5.01 0.00 0.00 3.84
3532 10753 1.674057 CCGTATCTCCCAGGCCATC 59.326 63.158 5.01 0.00 0.00 3.51
3533 10754 2.520536 GCCGTATCTCCCAGGCCAT 61.521 63.158 5.01 0.00 43.54 4.40
3534 10755 3.161450 GCCGTATCTCCCAGGCCA 61.161 66.667 5.01 0.00 43.54 5.36
3537 10758 1.742768 GTGAGCCGTATCTCCCAGG 59.257 63.158 0.00 0.00 32.22 4.45
3538 10759 1.043116 TGGTGAGCCGTATCTCCCAG 61.043 60.000 3.58 0.00 37.67 4.45
3539 10760 1.001120 TGGTGAGCCGTATCTCCCA 59.999 57.895 3.58 0.00 37.67 4.37
3541 10762 1.442148 GGTGGTGAGCCGTATCTCC 59.558 63.158 0.00 0.00 37.67 3.71
3542 10763 1.065928 CGGTGGTGAGCCGTATCTC 59.934 63.158 0.00 0.00 43.84 2.75
3543 10764 3.207354 CGGTGGTGAGCCGTATCT 58.793 61.111 0.00 0.00 43.84 1.98
3560 10781 1.218316 GACCTGATGACCCCGACAC 59.782 63.158 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.