Multiple sequence alignment - TraesCS7B01G092900

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 TraesCS7B01G092900 chr7B 100.000 5116 0 0 1 5116 106338842 106343957 0.000000e+00 9448
1 TraesCS7B01G092900 chr7B 94.291 543 25 4 1 539 710242698 710242158 0.000000e+00 826
2 TraesCS7B01G092900 chr7B 89.182 379 25 9 4324 4693 106576752 106577123 4.670000e-125 459
3 TraesCS7B01G092900 chr7B 91.447 304 17 5 4261 4563 106541633 106541928 4.770000e-110 409
4 TraesCS7B01G092900 chr7D 92.366 4624 184 66 547 5110 141189131 141184617 0.000000e+00 6427
5 TraesCS7B01G092900 chr7D 80.220 637 64 30 4389 5005 141343164 141343758 6.120000e-114 422
6 TraesCS7B01G092900 chr7D 84.937 239 10 6 4333 4563 141136524 141136304 8.620000e-53 219
7 TraesCS7B01G092900 chr7D 94.366 71 4 0 4324 4394 141299823 141299893 5.420000e-20 110
8 TraesCS7B01G092900 chr7D 95.455 66 3 0 4046 4111 141297295 141297360 7.010000e-19 106
9 TraesCS7B01G092900 chr7A 91.600 3107 113 46 545 3559 143144216 143147266 0.000000e+00 4156
10 TraesCS7B01G092900 chr7A 92.303 1520 68 20 3593 5097 143147256 143148741 0.000000e+00 2113
11 TraesCS7B01G092900 chr7A 87.228 736 52 23 1290 2010 182095100 182094392 0.000000e+00 800
12 TraesCS7B01G092900 chr7A 81.339 702 74 24 4399 5082 143182700 143183362 7.590000e-143 518
13 TraesCS7B01G092900 chr7A 88.919 370 22 10 4041 4393 143181813 143182180 6.080000e-119 438
14 TraesCS7B01G092900 chr7A 85.294 408 37 9 1292 1686 676403724 676403327 2.870000e-107 399
15 TraesCS7B01G092900 chr2A 87.788 737 57 15 1290 2010 21408699 21409418 0.000000e+00 832
16 TraesCS7B01G092900 chr2A 87.209 602 50 14 1419 2010 282967507 282968091 0.000000e+00 660
17 TraesCS7B01G092900 chr4B 94.280 542 25 4 1 539 551682757 551683295 0.000000e+00 824
18 TraesCS7B01G092900 chr4B 92.037 540 39 3 1 539 434661768 434662304 0.000000e+00 756
19 TraesCS7B01G092900 chr4B 88.051 544 55 9 3 540 649543073 649542534 2.010000e-178 636
20 TraesCS7B01G092900 chr5B 90.388 541 48 3 1 540 608678216 608678753 0.000000e+00 708
21 TraesCS7B01G092900 chr5B 85.366 410 37 9 1290 1686 685116705 685117104 2.220000e-108 403
22 TraesCS7B01G092900 chr5B 83.688 423 46 9 1277 1686 496764081 496764493 1.340000e-100 377
23 TraesCS7B01G092900 chr2B 88.910 523 52 5 21 540 351644676 351645195 1.550000e-179 640
24 TraesCS7B01G092900 chr2B 86.447 546 61 9 3 539 746132345 746131804 2.050000e-163 586
25 TraesCS7B01G092900 chr2B 85.610 410 36 9 1290 1686 171091331 171091730 4.770000e-110 409
26 TraesCS7B01G092900 chr2B 75.810 401 61 24 4742 5116 765091115 765090725 2.450000e-38 171
27 TraesCS7B01G092900 chr1D 86.162 542 64 10 3 539 64205907 64205372 4.440000e-160 575
28 TraesCS7B01G092900 chr1D 86.829 205 23 1 3006 3206 398049939 398049735 5.150000e-55 226
29 TraesCS7B01G092900 chr1D 85.854 205 25 2 3006 3206 398053129 398052925 1.120000e-51 215
30 TraesCS7B01G092900 chr3D 85.978 542 66 9 3 539 177023042 177023578 5.750000e-159 571
31 TraesCS7B01G092900 chr4A 85.372 417 38 9 1283 1686 599536020 599535614 1.330000e-110 411
32 TraesCS7B01G092900 chr3A 85.122 410 38 9 1290 1686 700004672 700004273 1.030000e-106 398
33 TraesCS7B01G092900 chr6B 83.933 417 44 9 1283 1686 91283014 91282608 1.340000e-100 377
34 TraesCS7B01G092900 chr6B 85.507 207 28 2 2977 3182 591233476 591233271 1.120000e-51 215
35 TraesCS7B01G092900 chr6A 85.124 242 27 2 3859 4100 541400181 541399949 6.620000e-59 239
36 TraesCS7B01G092900 chr6A 85.024 207 29 2 2977 3182 541400950 541400745 5.190000e-50 209
37 TraesCS7B01G092900 chr2D 77.419 403 53 25 4742 5116 622935670 622935278 6.710000e-49 206
38 TraesCS7B01G092900 chr1A 85.542 166 22 2 4920 5083 562965706 562965871 6.810000e-39 172


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 TraesCS7B01G092900 chr7B 106338842 106343957 5115 False 9448.0 9448 100.0000 1 5116 1 chr7B.!!$F1 5115
1 TraesCS7B01G092900 chr7B 710242158 710242698 540 True 826.0 826 94.2910 1 539 1 chr7B.!!$R1 538
2 TraesCS7B01G092900 chr7D 141184617 141189131 4514 True 6427.0 6427 92.3660 547 5110 1 chr7D.!!$R2 4563
3 TraesCS7B01G092900 chr7D 141343164 141343758 594 False 422.0 422 80.2200 4389 5005 1 chr7D.!!$F1 616
4 TraesCS7B01G092900 chr7A 143144216 143148741 4525 False 3134.5 4156 91.9515 545 5097 2 chr7A.!!$F1 4552
5 TraesCS7B01G092900 chr7A 182094392 182095100 708 True 800.0 800 87.2280 1290 2010 1 chr7A.!!$R1 720
6 TraesCS7B01G092900 chr7A 143181813 143183362 1549 False 478.0 518 85.1290 4041 5082 2 chr7A.!!$F2 1041
7 TraesCS7B01G092900 chr2A 21408699 21409418 719 False 832.0 832 87.7880 1290 2010 1 chr2A.!!$F1 720
8 TraesCS7B01G092900 chr2A 282967507 282968091 584 False 660.0 660 87.2090 1419 2010 1 chr2A.!!$F2 591
9 TraesCS7B01G092900 chr4B 551682757 551683295 538 False 824.0 824 94.2800 1 539 1 chr4B.!!$F2 538
10 TraesCS7B01G092900 chr4B 434661768 434662304 536 False 756.0 756 92.0370 1 539 1 chr4B.!!$F1 538
11 TraesCS7B01G092900 chr4B 649542534 649543073 539 True 636.0 636 88.0510 3 540 1 chr4B.!!$R1 537
12 TraesCS7B01G092900 chr5B 608678216 608678753 537 False 708.0 708 90.3880 1 540 1 chr5B.!!$F2 539
13 TraesCS7B01G092900 chr2B 351644676 351645195 519 False 640.0 640 88.9100 21 540 1 chr2B.!!$F2 519
14 TraesCS7B01G092900 chr2B 746131804 746132345 541 True 586.0 586 86.4470 3 539 1 chr2B.!!$R1 536
15 TraesCS7B01G092900 chr1D 64205372 64205907 535 True 575.0 575 86.1620 3 539 1 chr1D.!!$R1 536
16 TraesCS7B01G092900 chr1D 398049735 398053129 3394 True 220.5 226 86.3415 3006 3206 2 chr1D.!!$R2 200
17 TraesCS7B01G092900 chr3D 177023042 177023578 536 False 571.0 571 85.9780 3 539 1 chr3D.!!$F1 536
18 TraesCS7B01G092900 chr6A 541399949 541400950 1001 True 224.0 239 85.0740 2977 4100 2 chr6A.!!$R1 1123

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
291 297 0.254178 ATTCAGGCGATGGCAAGACT 59.746 50.000 1.01 0.0 42.47 3.24 F
1204 1222 0.474184 CCGGAGATAGCCAACCCATT 59.526 55.000 0.00 0.0 0.00 3.16 F
1279 1303 0.953727 TGCTGCTGACGCTGATTTTT 59.046 45.000 0.00 0.0 37.28 1.94 F
1554 1594 1.199327 GCATCCATCCATCATGCTTCG 59.801 52.381 0.00 0.0 39.92 3.79 F
2691 2792 0.039764 AGACAGACGACCTCCATCCA 59.960 55.000 0.00 0.0 0.00 3.41 F
2852 2959 0.173708 TCGTGCACCGCATATACACA 59.826 50.000 12.15 0.0 41.91 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1285 1309 0.029567 CTCCGAGATCACCTGCGTAC 59.970 60.000 0.00 0.00 0.00 3.67 R
2361 2442 0.099436 GTTCATCATGTGAAGCCGCC 59.901 55.000 9.93 0.00 46.99 6.13 R
2364 2445 1.063174 GCGAGTTCATCATGTGAAGCC 59.937 52.381 9.93 5.70 46.99 4.35 R
3546 7030 1.152030 AGGTCTCAAGCTGGGTCCA 60.152 57.895 0.00 0.00 0.00 4.02 R
3594 7078 1.133976 AGTGAACTCTTGCAAGCTGGT 60.134 47.619 21.99 14.96 0.00 4.00 R
4736 8830 1.068250 GCCTATGGACCGACTCTGC 59.932 63.158 0.00 0.00 0.00 4.26 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
170 173 2.799126 ATTCCCTAACCATCGTGCAA 57.201 45.000 0.00 0.00 0.00 4.08
200 206 7.558807 TGATCTTCAAATGCCATCTATTTCTGT 59.441 33.333 0.00 0.00 0.00 3.41
274 280 2.293677 TGACGCGCATCAAGACTATT 57.706 45.000 2.46 0.00 0.00 1.73
291 297 0.254178 ATTCAGGCGATGGCAAGACT 59.746 50.000 1.01 0.00 42.47 3.24
319 325 1.497991 CGAGTCGGTGAAGCTTTTGA 58.502 50.000 4.10 0.00 0.00 2.69
455 466 3.288809 ACATTCTCTTTTGCTTTCGCC 57.711 42.857 0.00 0.00 34.43 5.54
465 476 1.803334 TGCTTTCGCCGAGTTGTAAT 58.197 45.000 0.00 0.00 34.43 1.89
468 479 3.184541 GCTTTCGCCGAGTTGTAATCTA 58.815 45.455 0.00 0.00 0.00 1.98
478 489 6.106673 CCGAGTTGTAATCTAATGAACCTGT 58.893 40.000 0.00 0.00 0.00 4.00
570 582 1.311859 CTGTCAGTTTTCAGCTGGCA 58.688 50.000 15.13 0.00 45.00 4.92
575 587 0.663153 AGTTTTCAGCTGGCACGTTC 59.337 50.000 15.13 0.00 0.00 3.95
648 664 1.454847 AGCCCACAAACGCAAAGGA 60.455 52.632 0.00 0.00 0.00 3.36
709 725 1.630333 TCTCCCTCCCTCCCTCCAT 60.630 63.158 0.00 0.00 0.00 3.41
711 727 2.122189 CCCTCCCTCCCTCCATCC 60.122 72.222 0.00 0.00 0.00 3.51
712 728 2.705410 CCTCCCTCCCTCCATCCA 59.295 66.667 0.00 0.00 0.00 3.41
714 730 1.768077 CTCCCTCCCTCCATCCACC 60.768 68.421 0.00 0.00 0.00 4.61
715 731 2.263099 CTCCCTCCCTCCATCCACCT 62.263 65.000 0.00 0.00 0.00 4.00
718 734 1.003442 CTCCCTCCATCCACCTCCA 59.997 63.158 0.00 0.00 0.00 3.86
870 887 2.873133 GCTCCGAGCTTGTATGTAGT 57.127 50.000 13.42 0.00 38.45 2.73
911 929 1.875514 TGACACAACAGCTTGCTCATC 59.124 47.619 0.00 0.00 0.00 2.92
1072 1090 0.809385 GAACGAGATCCACGACCTGA 59.191 55.000 15.07 0.00 34.70 3.86
1161 1179 3.607299 TTCCCTCCCCACCTCGGA 61.607 66.667 0.00 0.00 36.56 4.55
1198 1216 2.140792 GCTCCCCGGAGATAGCCAA 61.141 63.158 15.14 0.00 44.53 4.52
1204 1222 0.474184 CCGGAGATAGCCAACCCATT 59.526 55.000 0.00 0.00 0.00 3.16
1257 1280 3.132289 TCATGGTTTTCTACTAGCTCGGG 59.868 47.826 0.00 0.00 0.00 5.14
1275 1299 2.812609 CGTGCTGCTGACGCTGAT 60.813 61.111 0.00 0.00 37.28 2.90
1276 1300 2.385875 CGTGCTGCTGACGCTGATT 61.386 57.895 0.00 0.00 37.28 2.57
1277 1301 1.871772 GTGCTGCTGACGCTGATTT 59.128 52.632 0.00 0.00 37.28 2.17
1279 1303 0.953727 TGCTGCTGACGCTGATTTTT 59.046 45.000 0.00 0.00 37.28 1.94
1298 1336 4.678509 TTTTTCATGTACGCAGGTGATC 57.321 40.909 0.00 0.00 0.00 2.92
1359 1397 3.845259 GGGCGGCGTCCATCTACA 61.845 66.667 28.11 0.00 0.00 2.74
1400 1438 4.335647 CAGCTGGGCCAGTCCGTT 62.336 66.667 32.80 12.31 33.43 4.44
1534 1574 2.941428 TCAGGTACGCATACGCATATG 58.059 47.619 0.00 0.00 45.53 1.78
1554 1594 1.199327 GCATCCATCCATCATGCTTCG 59.801 52.381 0.00 0.00 39.92 3.79
1567 1607 1.442769 TGCTTCGTGCCTTCATCTTC 58.557 50.000 1.30 0.00 42.00 2.87
1609 1650 2.284855 GCGAATGATACGTCGTTGTTCC 60.285 50.000 1.78 0.00 39.46 3.62
2031 2100 1.329906 GCATGTAGCACTAGCAGCAAG 59.670 52.381 10.05 0.00 45.49 4.01
2119 2196 4.832823 TGGATAAGGCATCTCGATGTAGAA 59.167 41.667 8.54 0.00 40.80 2.10
2120 2197 5.164954 GGATAAGGCATCTCGATGTAGAAC 58.835 45.833 8.54 0.00 40.80 3.01
2121 2198 5.047660 GGATAAGGCATCTCGATGTAGAACT 60.048 44.000 8.54 0.00 40.80 3.01
2233 2310 4.082245 AGGGGTTGACATTCGCTAATTTTG 60.082 41.667 0.00 0.00 0.00 2.44
2240 2317 5.064707 TGACATTCGCTAATTTTGTAGAGGC 59.935 40.000 0.00 0.00 0.00 4.70
2355 2436 4.455877 GTCTAGCGGGCATAATTAGCAAAT 59.544 41.667 8.51 0.00 0.00 2.32
2361 2442 5.050837 GCGGGCATAATTAGCAAATTTGAAG 60.051 40.000 22.31 0.00 36.67 3.02
2364 2445 5.050837 GGCATAATTAGCAAATTTGAAGGCG 60.051 40.000 22.31 3.13 36.67 5.52
2424 2505 1.511958 GTATAAGCTCGACGTTGACGC 59.488 52.381 15.40 15.40 44.43 5.19
2426 2507 2.807631 TAAGCTCGACGTTGACGCCC 62.808 60.000 18.05 2.93 44.43 6.13
2428 2509 2.805353 CTCGACGTTGACGCCCAG 60.805 66.667 0.00 0.00 44.43 4.45
2435 2516 1.479323 ACGTTGACGCCCAGTATATGT 59.521 47.619 3.05 0.00 44.43 2.29
2440 2521 4.783764 TGACGCCCAGTATATGTCTATG 57.216 45.455 0.00 0.00 0.00 2.23
2599 2700 2.324330 TGCGTGTGCCCAAAGATCG 61.324 57.895 0.00 0.00 41.78 3.69
2691 2792 0.039764 AGACAGACGACCTCCATCCA 59.960 55.000 0.00 0.00 0.00 3.41
2726 2827 1.276705 TGCTGGCCATAGACGTAAACA 59.723 47.619 5.51 0.00 0.00 2.83
2760 2864 2.368875 ACGTAAAGGGAGGGAGCATATG 59.631 50.000 0.00 0.00 0.00 1.78
2785 2892 1.202099 TGCATAACAAGGACGGGGGA 61.202 55.000 0.00 0.00 0.00 4.81
2841 2948 2.279918 ACCTTCACGTCGTGCACC 60.280 61.111 20.56 0.00 32.98 5.01
2842 2949 3.403057 CCTTCACGTCGTGCACCG 61.403 66.667 20.56 12.66 32.98 4.94
2843 2950 4.059459 CTTCACGTCGTGCACCGC 62.059 66.667 20.56 3.07 36.19 5.68
2844 2951 4.874977 TTCACGTCGTGCACCGCA 62.875 61.111 20.56 0.00 36.19 5.69
2845 2952 4.656117 TCACGTCGTGCACCGCAT 62.656 61.111 20.56 0.00 41.91 4.73
2846 2953 2.750715 TTCACGTCGTGCACCGCATA 62.751 55.000 20.56 0.00 41.91 3.14
2847 2954 2.164663 CACGTCGTGCACCGCATAT 61.165 57.895 13.22 0.00 41.91 1.78
2848 2955 0.868177 CACGTCGTGCACCGCATATA 60.868 55.000 13.22 0.00 41.91 0.86
2849 2956 0.868602 ACGTCGTGCACCGCATATAC 60.869 55.000 12.15 0.00 41.91 1.47
2850 2957 0.868177 CGTCGTGCACCGCATATACA 60.868 55.000 12.15 0.00 41.91 2.29
2851 2958 0.575390 GTCGTGCACCGCATATACAC 59.425 55.000 12.15 0.00 41.91 2.90
2852 2959 0.173708 TCGTGCACCGCATATACACA 59.826 50.000 12.15 0.00 41.91 3.72
2853 2960 0.300491 CGTGCACCGCATATACACAC 59.700 55.000 12.15 0.00 41.91 3.82
2854 2961 1.364721 GTGCACCGCATATACACACA 58.635 50.000 5.22 0.00 41.91 3.72
2855 2962 1.939934 GTGCACCGCATATACACACAT 59.060 47.619 5.22 0.00 41.91 3.21
2856 2963 3.127589 GTGCACCGCATATACACACATA 58.872 45.455 5.22 0.00 41.91 2.29
2857 2964 3.558006 GTGCACCGCATATACACACATAA 59.442 43.478 5.22 0.00 41.91 1.90
2858 2965 4.213270 GTGCACCGCATATACACACATAAT 59.787 41.667 5.22 0.00 41.91 1.28
2859 2966 5.407084 GTGCACCGCATATACACACATAATA 59.593 40.000 5.22 0.00 41.91 0.98
2860 2967 5.992217 TGCACCGCATATACACACATAATAA 59.008 36.000 0.00 0.00 31.71 1.40
2861 2968 6.073494 TGCACCGCATATACACACATAATAAC 60.073 38.462 0.00 0.00 31.71 1.89
2920 3027 0.457853 GCAGCGTACGTCTCAATCCA 60.458 55.000 17.90 0.00 0.00 3.41
3199 6503 2.363680 ACGTTGATTTGCCACAAATCCA 59.636 40.909 23.29 14.12 36.17 3.41
3264 6582 9.979270 CTCTGTTCTTGTGCTAGTATTAATTTG 57.021 33.333 0.00 0.00 0.00 2.32
3546 7030 4.314740 TTTAATTGCAAAAGTGACGGCT 57.685 36.364 1.71 0.00 0.00 5.52
3628 7112 7.959651 GCAAGAGTTCACTAGTAATGAATTGTG 59.040 37.037 0.00 0.00 38.31 3.33
3674 7158 9.112725 CAAACAGATAGATGACACATTATTCCA 57.887 33.333 0.00 0.00 0.00 3.53
3679 7163 3.202818 AGATGACACATTATTCCAGGCCA 59.797 43.478 5.01 0.00 0.00 5.36
3754 7238 4.219288 AGGAAAGATCAGCCATTGAACAAC 59.781 41.667 0.00 0.00 39.77 3.32
3890 7438 1.123077 CAGGAGGATCGATGAACCCA 58.877 55.000 0.54 0.00 34.37 4.51
4082 7630 4.426112 CGCCTGCAGAGTCAGCGA 62.426 66.667 24.19 0.00 36.47 4.93
4360 7929 3.064207 CGTGTATGTGTATACCATGGGC 58.936 50.000 18.09 3.82 38.71 5.36
4383 7952 3.250280 ACGTAGATAGCGTGAGTACATGG 59.750 47.826 0.00 0.00 41.33 3.66
4510 8595 7.487189 GCATAAGTTTAATATGATGATGCAGCC 59.513 37.037 0.00 0.00 37.64 4.85
4523 8608 2.670934 CAGCCAACGGAGCTTGCT 60.671 61.111 0.00 0.00 38.95 3.91
4524 8609 2.113986 AGCCAACGGAGCTTGCTT 59.886 55.556 0.00 0.00 37.24 3.91
4525 8610 0.955428 CAGCCAACGGAGCTTGCTTA 60.955 55.000 0.00 0.00 38.95 3.09
4526 8611 0.250727 AGCCAACGGAGCTTGCTTAA 60.251 50.000 0.00 0.00 37.24 1.85
4600 8690 1.997669 GAACTCGTGAGGTCATGGAC 58.002 55.000 10.00 0.00 44.39 4.02
4606 8700 1.825474 CGTGAGGTCATGGACTTACCT 59.175 52.381 2.78 2.78 46.33 3.08
4711 8805 1.899814 ACGGGTCTCACTGAGCAAATA 59.100 47.619 0.62 0.00 44.40 1.40
4730 8824 1.941377 AGCAAGCCATCCCAATCAAA 58.059 45.000 0.00 0.00 0.00 2.69
4735 8829 2.674420 AGCCATCCCAATCAAATGGAG 58.326 47.619 4.83 0.00 43.54 3.86
4736 8830 1.690352 GCCATCCCAATCAAATGGAGG 59.310 52.381 4.83 0.00 43.54 4.30
4737 8831 1.690352 CCATCCCAATCAAATGGAGGC 59.310 52.381 0.00 0.00 43.54 4.70
4738 8832 2.390696 CATCCCAATCAAATGGAGGCA 58.609 47.619 0.00 0.00 43.54 4.75
4739 8833 2.148446 TCCCAATCAAATGGAGGCAG 57.852 50.000 0.00 0.00 43.54 4.85
4740 8834 1.640149 TCCCAATCAAATGGAGGCAGA 59.360 47.619 0.00 0.00 43.54 4.26
4741 8835 2.029623 CCCAATCAAATGGAGGCAGAG 58.970 52.381 0.00 0.00 43.54 3.35
4742 8836 2.622452 CCCAATCAAATGGAGGCAGAGT 60.622 50.000 0.00 0.00 43.54 3.24
4792 8887 2.034066 CCAAGGCCTCAAGCGGAA 59.966 61.111 5.23 0.00 45.17 4.30
4915 9026 6.864685 CACACGAACTAGTAATGTTAGGTGAA 59.135 38.462 0.00 0.00 36.40 3.18
4937 9048 7.599998 GTGAATTGATAGGCAACAATGAGTTTT 59.400 33.333 0.00 0.00 39.78 2.43
5039 9153 7.494298 AGTTTCGTGCAAAACCTTTTATTTCAT 59.506 29.630 9.81 0.00 39.46 2.57
5076 9190 7.124052 AGCCCTTGTATACACTAGAAGAAGTA 58.876 38.462 4.68 0.00 30.04 2.24
5079 9193 9.583765 CCCTTGTATACACTAGAAGAAGTAAAC 57.416 37.037 4.68 0.00 30.04 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 168 4.092383 GGCATTTGAAGATCACATTTGCAC 59.908 41.667 18.90 11.04 31.68 4.57
170 173 7.834881 ATAGATGGCATTTGAAGATCACATT 57.165 32.000 0.00 0.00 0.00 2.71
274 280 0.461548 CTAGTCTTGCCATCGCCTGA 59.538 55.000 0.00 0.00 0.00 3.86
455 466 7.456253 CAACAGGTTCATTAGATTACAACTCG 58.544 38.462 0.00 0.00 0.00 4.18
465 476 3.411446 CACAGGCAACAGGTTCATTAGA 58.589 45.455 0.00 0.00 41.41 2.10
468 479 1.331214 CCACAGGCAACAGGTTCATT 58.669 50.000 0.00 0.00 41.41 2.57
540 552 2.839486 AACTGACAGGATGCGAAGAA 57.161 45.000 7.51 0.00 42.53 2.52
541 553 2.839486 AAACTGACAGGATGCGAAGA 57.161 45.000 7.51 0.00 42.53 2.87
542 554 2.807967 TGAAAACTGACAGGATGCGAAG 59.192 45.455 7.51 0.00 42.53 3.79
543 555 2.807967 CTGAAAACTGACAGGATGCGAA 59.192 45.455 7.51 0.00 42.53 4.70
570 582 2.250485 CGAGACACCGTCGAACGT 59.750 61.111 0.00 0.00 40.58 3.99
632 648 0.597377 GCTTCCTTTGCGTTTGTGGG 60.597 55.000 0.00 0.00 0.00 4.61
648 664 3.946201 ACTCCACTGCAGGCGCTT 61.946 61.111 19.93 0.00 39.64 4.68
736 753 3.572584 CGCGTATTTATAGGTGGAGGTC 58.427 50.000 0.00 0.00 0.00 3.85
861 878 0.179111 GCAGGCTCGCACTACATACA 60.179 55.000 4.40 0.00 0.00 2.29
908 926 5.278218 CCCGGACTATGAGATATGATCGATG 60.278 48.000 0.54 0.00 0.00 3.84
911 929 4.200092 TCCCGGACTATGAGATATGATCG 58.800 47.826 0.73 0.00 0.00 3.69
947 965 3.133003 CGACTACCCTTGATGTTGATCCT 59.867 47.826 0.00 0.00 0.00 3.24
956 974 0.033796 TCCGGTCGACTACCCTTGAT 60.034 55.000 16.46 0.00 46.62 2.57
959 977 1.379576 CCTCCGGTCGACTACCCTT 60.380 63.158 16.46 0.00 46.62 3.95
1161 1179 0.389166 CTCGCTCGCTCACCTTCTTT 60.389 55.000 0.00 0.00 0.00 2.52
1235 1257 3.132289 CCCGAGCTAGTAGAAAACCATGA 59.868 47.826 0.00 0.00 0.00 3.07
1277 1301 4.323417 AGATCACCTGCGTACATGAAAAA 58.677 39.130 0.00 0.00 0.00 1.94
1279 1303 3.521560 GAGATCACCTGCGTACATGAAA 58.478 45.455 0.00 0.00 0.00 2.69
1280 1304 2.479560 CGAGATCACCTGCGTACATGAA 60.480 50.000 0.00 0.00 0.00 2.57
1281 1305 1.065551 CGAGATCACCTGCGTACATGA 59.934 52.381 0.00 0.00 0.00 3.07
1282 1306 1.481240 CGAGATCACCTGCGTACATG 58.519 55.000 0.00 0.00 0.00 3.21
1283 1307 0.385751 CCGAGATCACCTGCGTACAT 59.614 55.000 0.00 0.00 0.00 2.29
1285 1309 0.029567 CTCCGAGATCACCTGCGTAC 59.970 60.000 0.00 0.00 0.00 3.67
1286 1310 1.101635 CCTCCGAGATCACCTGCGTA 61.102 60.000 0.00 0.00 0.00 4.42
1287 1311 2.418910 CCTCCGAGATCACCTGCGT 61.419 63.158 0.00 0.00 0.00 5.24
1288 1312 2.415010 CCTCCGAGATCACCTGCG 59.585 66.667 0.00 0.00 0.00 5.18
1298 1336 4.436998 GTCGCCACCACCTCCGAG 62.437 72.222 0.00 0.00 0.00 4.63
1534 1574 1.199327 CGAAGCATGATGGATGGATGC 59.801 52.381 0.00 0.00 42.37 3.91
1554 1594 2.999355 GTGAGACAGAAGATGAAGGCAC 59.001 50.000 0.00 0.00 0.00 5.01
1567 1607 4.739584 CGTCCGTACGTGAGACAG 57.260 61.111 15.21 7.39 44.21 3.51
1609 1650 4.019681 TCATGTTGGTAACCAAGTCCTAGG 60.020 45.833 0.82 0.82 44.82 3.02
1925 1986 5.361285 CCAAGTCTCCAACTAGTGCTATACT 59.639 44.000 0.00 0.00 43.56 2.12
1926 1987 5.360144 TCCAAGTCTCCAACTAGTGCTATAC 59.640 44.000 0.00 0.00 37.17 1.47
1935 2000 4.048970 AGCTACTCCAAGTCTCCAACTA 57.951 45.455 0.00 0.00 37.17 2.24
2119 2196 8.652290 GTTCTTCCCTAATCATGGAATAGTAGT 58.348 37.037 0.00 0.00 39.79 2.73
2120 2197 8.651389 TGTTCTTCCCTAATCATGGAATAGTAG 58.349 37.037 0.00 0.00 39.79 2.57
2121 2198 8.561536 TGTTCTTCCCTAATCATGGAATAGTA 57.438 34.615 0.00 0.00 39.79 1.82
2361 2442 0.099436 GTTCATCATGTGAAGCCGCC 59.901 55.000 9.93 0.00 46.99 6.13
2364 2445 1.063174 GCGAGTTCATCATGTGAAGCC 59.937 52.381 9.93 5.70 46.99 4.35
2424 2505 7.030165 GTGATCGAACATAGACATATACTGGG 58.970 42.308 0.00 0.00 0.00 4.45
2426 2507 9.463443 TTTGTGATCGAACATAGACATATACTG 57.537 33.333 0.00 0.00 0.00 2.74
2435 2516 6.169800 TGGTTGATTTGTGATCGAACATAGA 58.830 36.000 0.00 0.00 0.00 1.98
2440 2521 3.492313 GCTGGTTGATTTGTGATCGAAC 58.508 45.455 0.00 0.00 0.00 3.95
2760 2864 2.226437 CCGTCCTTGTTATGCATATGCC 59.774 50.000 24.54 9.81 41.18 4.40
2770 2874 1.659022 TTGATCCCCCGTCCTTGTTA 58.341 50.000 0.00 0.00 0.00 2.41
2920 3027 2.045926 GCACACGGAGAAGCCCAT 60.046 61.111 0.00 0.00 0.00 4.00
3537 7021 3.314331 CTGGGTCCAGCCGTCACT 61.314 66.667 3.86 0.00 37.24 3.41
3546 7030 1.152030 AGGTCTCAAGCTGGGTCCA 60.152 57.895 0.00 0.00 0.00 4.02
3594 7078 1.133976 AGTGAACTCTTGCAAGCTGGT 60.134 47.619 21.99 14.96 0.00 4.00
3628 7112 8.161699 TGTTTGTAAGGTTCAAAGAATCCTAC 57.838 34.615 0.00 0.00 35.83 3.18
3674 7158 8.436778 TGTATTGTGTTTGTCTATATATGGCCT 58.563 33.333 3.32 0.00 0.00 5.19
3754 7238 1.325640 CGTGTGTGCATAGCTAAGCTG 59.674 52.381 20.60 5.53 40.10 4.24
4082 7630 3.138930 CTCGTCGACGGCCATGGAT 62.139 63.158 35.05 0.00 40.29 3.41
4141 7694 9.148879 ACAGAGCATATATATATAGTTGGGGTC 57.851 37.037 4.90 7.12 0.00 4.46
4279 7846 4.477975 AGCTCGCTCGTACACGGC 62.478 66.667 1.39 3.83 40.29 5.68
4383 7952 3.757745 ATACAAATGCGTTACACCAGC 57.242 42.857 0.00 0.00 0.00 4.85
4510 8595 2.663119 GCAAATTAAGCAAGCTCCGTTG 59.337 45.455 0.00 0.00 0.00 4.10
4523 8608 7.537596 TCCAGATCTTTTTCAGGCAAATTAA 57.462 32.000 0.00 0.00 0.00 1.40
4524 8609 7.451255 TCTTCCAGATCTTTTTCAGGCAAATTA 59.549 33.333 0.00 0.00 0.00 1.40
4525 8610 6.268387 TCTTCCAGATCTTTTTCAGGCAAATT 59.732 34.615 0.00 0.00 0.00 1.82
4526 8611 5.776716 TCTTCCAGATCTTTTTCAGGCAAAT 59.223 36.000 0.00 0.00 0.00 2.32
4711 8805 1.941377 TTTGATTGGGATGGCTTGCT 58.059 45.000 0.00 0.00 0.00 3.91
4730 8824 2.060980 GGACCGACTCTGCCTCCAT 61.061 63.158 0.00 0.00 0.00 3.41
4735 8829 1.742768 CCTATGGACCGACTCTGCC 59.257 63.158 0.00 0.00 0.00 4.85
4736 8830 1.068250 GCCTATGGACCGACTCTGC 59.932 63.158 0.00 0.00 0.00 4.26
4737 8831 1.742768 GGCCTATGGACCGACTCTG 59.257 63.158 0.00 0.00 0.00 3.35
4738 8832 4.279326 GGCCTATGGACCGACTCT 57.721 61.111 0.00 0.00 0.00 3.24
4792 8887 7.228706 GCAATAATAGTATATTTGCGGCCCTAT 59.771 37.037 11.88 0.00 0.00 2.57
4882 8978 6.708949 ACATTACTAGTTCGTGTGTGGATTTT 59.291 34.615 0.00 0.00 0.00 1.82
4915 9026 6.869913 CACAAAACTCATTGTTGCCTATCAAT 59.130 34.615 0.00 0.00 41.44 2.57
4937 9048 1.203063 AGAGACACTGGTAGGCTCACA 60.203 52.381 0.00 0.00 0.00 3.58
5039 9153 3.806949 ACAAGGGCTCCTGTCAATTTA 57.193 42.857 0.00 0.00 32.13 1.40


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

AutoCloner maintained by Alex Coulton.