Multiple sequence alignment - TraesCS1B01G133900

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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 TraesCS1B01G133900 chr1B 100.000 3584 0 0 1 3584 169644869 169641286 0.000000e+00 6619
1 TraesCS1B01G133900 chr1B 82.691 1375 144 48 1296 2619 2557232 2555901 0.000000e+00 1134
2 TraesCS1B01G133900 chr1B 82.691 1375 144 48 1296 2619 2613967 2612636 0.000000e+00 1134
3 TraesCS1B01G133900 chr1B 90.476 609 38 6 1 589 427673056 427673664 0.000000e+00 785
4 TraesCS1B01G133900 chr1B 86.275 612 55 14 1 585 585168622 585168013 3.900000e-179 638
5 TraesCS1B01G133900 chr1B 88.355 541 38 15 72 592 10109374 10108839 8.450000e-176 627
6 TraesCS1B01G133900 chr1B 84.756 164 24 1 2797 2959 522223083 522222920 2.860000e-36 163
7 TraesCS1B01G133900 chr1A 90.054 2242 112 29 602 2767 117194280 117192074 0.000000e+00 2802
8 TraesCS1B01G133900 chr1A 81.996 561 81 11 41 597 533770555 533771099 3.260000e-125 459
9 TraesCS1B01G133900 chr1D 92.483 1051 48 13 746 1790 111016211 111015186 0.000000e+00 1474
10 TraesCS1B01G133900 chr1D 90.882 1009 44 13 1794 2767 111010389 111009394 0.000000e+00 1310
11 TraesCS1B01G133900 chr1D 92.143 280 12 5 1514 1790 111011126 111010854 1.560000e-103 387
12 TraesCS1B01G133900 chr1D 85.492 193 22 4 2799 2989 287619491 287619679 2.820000e-46 196
13 TraesCS1B01G133900 chr1D 97.015 67 1 1 602 668 111035110 111035045 1.050000e-20 111
14 TraesCS1B01G133900 chrUn 82.691 1375 144 48 1296 2619 297916728 297915397 0.000000e+00 1134
15 TraesCS1B01G133900 chr6B 90.744 605 36 7 2 587 599987921 599988524 0.000000e+00 789
16 TraesCS1B01G133900 chr6B 93.919 444 23 1 3141 3584 256480605 256480166 0.000000e+00 667
17 TraesCS1B01G133900 chr6B 82.824 524 75 10 65 587 1156372 1155863 4.220000e-124 455
18 TraesCS1B01G133900 chr6B 94.961 258 13 0 2797 3054 256481298 256481041 4.310000e-109 405
19 TraesCS1B01G133900 chr6B 94.400 250 11 1 1720 1969 444302474 444302228 7.260000e-102 381
20 TraesCS1B01G133900 chr6A 89.604 606 43 2 2 587 83931191 83931796 0.000000e+00 752
21 TraesCS1B01G133900 chr7D 90.674 579 32 3 33 591 52474423 52474999 0.000000e+00 750
22 TraesCS1B01G133900 chr7D 85.875 623 55 14 1 594 193415216 193414598 1.820000e-177 632
23 TraesCS1B01G133900 chr7D 85.668 614 56 17 3 587 178289181 178289791 5.080000e-173 617
24 TraesCS1B01G133900 chr7D 85.227 616 59 21 1 587 576640837 576640225 3.960000e-169 604
25 TraesCS1B01G133900 chr7D 91.398 279 20 4 1774 2052 326033835 326033561 2.610000e-101 379
26 TraesCS1B01G133900 chr4B 81.436 808 101 24 2807 3584 656237945 656238733 1.830000e-172 616
27 TraesCS1B01G133900 chr4B 90.606 330 31 0 1723 2052 121936848 121936519 4.250000e-119 438
28 TraesCS1B01G133900 chr4B 88.945 199 19 1 2334 2532 121936417 121936222 3.570000e-60 243
29 TraesCS1B01G133900 chr7A 83.119 699 93 16 1296 1993 134016519 134015845 6.580000e-172 614
30 TraesCS1B01G133900 chr3B 84.116 554 77 6 38 591 27471636 27472178 3.170000e-145 525
31 TraesCS1B01G133900 chr3B 78.648 281 52 5 1991 2270 73849873 73850146 2.840000e-41 180
32 TraesCS1B01G133900 chr6D 78.846 624 93 22 1 587 472923946 472924567 5.610000e-103 385
33 TraesCS1B01G133900 chr2A 82.710 428 44 18 951 1365 596358568 596358158 1.580000e-93 353
34 TraesCS1B01G133900 chr2D 90.222 225 22 0 1402 1626 22815765 22815541 9.730000e-76 294
35 TraesCS1B01G133900 chr2D 91.716 169 14 0 1402 1570 453570141 453569973 5.980000e-58 235
36 TraesCS1B01G133900 chr2D 80.117 342 41 13 1045 1365 22816100 22815765 2.780000e-56 230
37 TraesCS1B01G133900 chr2D 84.834 211 16 7 1160 1360 453570350 453570146 7.850000e-47 198
38 TraesCS1B01G133900 chr2D 88.000 125 9 5 951 1075 453570521 453570403 3.730000e-30 143
39 TraesCS1B01G133900 chr5B 81.562 320 33 14 292 591 508032116 508031803 1.290000e-59 241
40 TraesCS1B01G133900 chr3D 86.905 168 22 0 2797 2964 584572371 584572204 4.720000e-44 189
41 TraesCS1B01G133900 chr3D 80.000 195 35 3 2797 2989 135545557 135545749 1.340000e-29 141
42 TraesCS1B01G133900 chr3A 86.310 168 23 0 2797 2964 79460429 79460262 2.200000e-42 183
43 TraesCS1B01G133900 chr3A 85.714 168 24 0 2797 2964 664272852 664272685 1.020000e-40 178
44 TraesCS1B01G133900 chr3A 77.465 284 59 4 1988 2270 59434846 59435125 7.960000e-37 165
45 TraesCS1B01G133900 chr3A 84.568 162 25 0 2796 2957 733318319 733318158 1.030000e-35 161
46 TraesCS1B01G133900 chr3A 81.421 183 30 3 2797 2977 340816012 340815832 2.880000e-31 147
47 TraesCS1B01G133900 chr5A 85.816 141 20 0 451 591 692236343 692236203 2.230000e-32 150
48 TraesCS1B01G133900 chr4D 88.430 121 14 0 467 587 75795412 75795292 2.880000e-31 147
49 TraesCS1B01G133900 chr4A 84.138 145 21 2 451 593 4873112 4872968 4.820000e-29 139
50 TraesCS1B01G133900 chr7B 83.453 139 23 0 449 587 434359136 434358998 2.900000e-26 130


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 TraesCS1B01G133900 chr1B 169641286 169644869 3583 True 6619.0 6619 100.0000 1 3584 1 chr1B.!!$R4 3583
1 TraesCS1B01G133900 chr1B 2555901 2557232 1331 True 1134.0 1134 82.6910 1296 2619 1 chr1B.!!$R1 1323
2 TraesCS1B01G133900 chr1B 2612636 2613967 1331 True 1134.0 1134 82.6910 1296 2619 1 chr1B.!!$R2 1323
3 TraesCS1B01G133900 chr1B 427673056 427673664 608 False 785.0 785 90.4760 1 589 1 chr1B.!!$F1 588
4 TraesCS1B01G133900 chr1B 585168013 585168622 609 True 638.0 638 86.2750 1 585 1 chr1B.!!$R6 584
5 TraesCS1B01G133900 chr1B 10108839 10109374 535 True 627.0 627 88.3550 72 592 1 chr1B.!!$R3 520
6 TraesCS1B01G133900 chr1A 117192074 117194280 2206 True 2802.0 2802 90.0540 602 2767 1 chr1A.!!$R1 2165
7 TraesCS1B01G133900 chr1A 533770555 533771099 544 False 459.0 459 81.9960 41 597 1 chr1A.!!$F1 556
8 TraesCS1B01G133900 chr1D 111015186 111016211 1025 True 1474.0 1474 92.4830 746 1790 1 chr1D.!!$R1 1044
9 TraesCS1B01G133900 chr1D 111009394 111011126 1732 True 848.5 1310 91.5125 1514 2767 2 chr1D.!!$R3 1253
10 TraesCS1B01G133900 chrUn 297915397 297916728 1331 True 1134.0 1134 82.6910 1296 2619 1 chrUn.!!$R1 1323
11 TraesCS1B01G133900 chr6B 599987921 599988524 603 False 789.0 789 90.7440 2 587 1 chr6B.!!$F1 585
12 TraesCS1B01G133900 chr6B 256480166 256481298 1132 True 536.0 667 94.4400 2797 3584 2 chr6B.!!$R3 787
13 TraesCS1B01G133900 chr6B 1155863 1156372 509 True 455.0 455 82.8240 65 587 1 chr6B.!!$R1 522
14 TraesCS1B01G133900 chr6A 83931191 83931796 605 False 752.0 752 89.6040 2 587 1 chr6A.!!$F1 585
15 TraesCS1B01G133900 chr7D 52474423 52474999 576 False 750.0 750 90.6740 33 591 1 chr7D.!!$F1 558
16 TraesCS1B01G133900 chr7D 193414598 193415216 618 True 632.0 632 85.8750 1 594 1 chr7D.!!$R1 593
17 TraesCS1B01G133900 chr7D 178289181 178289791 610 False 617.0 617 85.6680 3 587 1 chr7D.!!$F2 584
18 TraesCS1B01G133900 chr7D 576640225 576640837 612 True 604.0 604 85.2270 1 587 1 chr7D.!!$R3 586
19 TraesCS1B01G133900 chr4B 656237945 656238733 788 False 616.0 616 81.4360 2807 3584 1 chr4B.!!$F1 777
20 TraesCS1B01G133900 chr4B 121936222 121936848 626 True 340.5 438 89.7755 1723 2532 2 chr4B.!!$R1 809
21 TraesCS1B01G133900 chr7A 134015845 134016519 674 True 614.0 614 83.1190 1296 1993 1 chr7A.!!$R1 697
22 TraesCS1B01G133900 chr3B 27471636 27472178 542 False 525.0 525 84.1160 38 591 1 chr3B.!!$F1 553
23 TraesCS1B01G133900 chr6D 472923946 472924567 621 False 385.0 385 78.8460 1 587 1 chr6D.!!$F1 586
24 TraesCS1B01G133900 chr2D 22815541 22816100 559 True 262.0 294 85.1695 1045 1626 2 chr2D.!!$R1 581

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
910 983 0.033504 TCGGTCCAAAGTCTGCTGTC 59.966 55.0 0.0 0.0 0.0 3.51 F
1128 1201 0.250467 TGAGAAGCAAGGTGTCTGCC 60.250 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2539 3146 0.032130 ATGAGCACGTCGAACACACT 59.968 50.0 0.0 0.0 0.00 3.55 R
2891 3531 0.531532 CAGATTAGCCACCCTGCGAG 60.532 60.0 0.0 0.0 36.02 5.03 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
80 99 1.608590 CATTGTGGAGCGTGAAGGTTT 59.391 47.619 0.00 0.00 0.00 3.27
130 152 1.101049 CGTTGGGCAGGTTTCTGTGT 61.101 55.000 0.00 0.00 42.78 3.72
184 206 4.333690 AGAGATTCACAGCTTGCTCAAAT 58.666 39.130 0.00 0.00 0.00 2.32
274 299 3.432186 GTGGCGCCACAAGAAAGT 58.568 55.556 46.18 0.00 45.53 2.66
368 393 0.250901 GGTGGTGCATGTGGTCTTCT 60.251 55.000 0.00 0.00 0.00 2.85
385 410 5.182001 GGTCTTCTACCGTGTTACTCTTGTA 59.818 44.000 0.00 0.00 38.88 2.41
424 452 1.148273 GCAGTGTGAGGGTTGGTGA 59.852 57.895 0.00 0.00 0.00 4.02
534 582 4.464244 TCCGTTGATTAATTGGGCAATTCA 59.536 37.500 0.00 0.00 40.99 2.57
549 597 6.127647 TGGGCAATTCACTTCTGCTTAATTAG 60.128 38.462 0.00 0.00 36.32 1.73
660 708 0.816373 GACGGTGACCTCTCTAACCC 59.184 60.000 0.00 0.00 0.00 4.11
661 709 0.408700 ACGGTGACCTCTCTAACCCT 59.591 55.000 0.00 0.00 0.00 4.34
662 710 0.818296 CGGTGACCTCTCTAACCCTG 59.182 60.000 0.00 0.00 0.00 4.45
664 712 2.258109 GGTGACCTCTCTAACCCTGTT 58.742 52.381 0.00 0.00 0.00 3.16
665 713 2.234168 GGTGACCTCTCTAACCCTGTTC 59.766 54.545 0.00 0.00 0.00 3.18
666 714 2.094649 GTGACCTCTCTAACCCTGTTCG 60.095 54.545 0.00 0.00 0.00 3.95
713 782 5.066117 ACAGAGACAAATCGTTAGATCGCTA 59.934 40.000 0.00 0.00 35.74 4.26
735 804 0.593128 AATGAGCCGTGCACTTTCAC 59.407 50.000 16.19 3.07 0.00 3.18
736 805 1.237285 ATGAGCCGTGCACTTTCACC 61.237 55.000 16.19 0.00 33.57 4.02
737 806 1.598130 GAGCCGTGCACTTTCACCT 60.598 57.895 16.19 1.56 33.57 4.00
738 807 1.569479 GAGCCGTGCACTTTCACCTC 61.569 60.000 16.19 7.29 33.57 3.85
739 808 2.617274 GCCGTGCACTTTCACCTCC 61.617 63.158 16.19 0.00 33.57 4.30
740 809 1.071471 CCGTGCACTTTCACCTCCT 59.929 57.895 16.19 0.00 33.57 3.69
741 810 0.535102 CCGTGCACTTTCACCTCCTT 60.535 55.000 16.19 0.00 33.57 3.36
742 811 1.270625 CCGTGCACTTTCACCTCCTTA 60.271 52.381 16.19 0.00 33.57 2.69
743 812 2.615493 CCGTGCACTTTCACCTCCTTAT 60.615 50.000 16.19 0.00 33.57 1.73
744 813 2.673368 CGTGCACTTTCACCTCCTTATC 59.327 50.000 16.19 0.00 33.57 1.75
753 822 3.491342 TCACCTCCTTATCATCTCCGAG 58.509 50.000 0.00 0.00 0.00 4.63
756 825 3.398292 ACCTCCTTATCATCTCCGAGGTA 59.602 47.826 4.78 0.00 46.36 3.08
789 858 1.909302 CTCACCAGGACCACACCTATT 59.091 52.381 0.00 0.00 38.32 1.73
797 866 0.672401 ACCACACCTATTCGGTTGCG 60.672 55.000 0.00 0.00 46.37 4.85
827 896 2.510238 CGAGGCCACTGTGCTAGC 60.510 66.667 8.10 8.10 0.00 3.42
910 983 0.033504 TCGGTCCAAAGTCTGCTGTC 59.966 55.000 0.00 0.00 0.00 3.51
942 1015 2.187946 CCGAGGATCAGCCACCAC 59.812 66.667 0.00 0.00 40.02 4.16
1095 1168 0.621571 ACCAGCAGCCCAAGATAGGA 60.622 55.000 0.00 0.00 0.00 2.94
1128 1201 0.250467 TGAGAAGCAAGGTGTCTGCC 60.250 55.000 0.00 0.00 0.00 4.85
1249 1346 4.634991 GCGATTACGTAAGGTGTTTTCAG 58.365 43.478 14.25 3.12 46.39 3.02
1253 1350 6.183359 CGATTACGTAAGGTGTTTTCAGTCTC 60.183 42.308 14.25 0.46 46.39 3.36
1260 1357 2.538939 GGTGTTTTCAGTCTCACAACGC 60.539 50.000 0.00 0.00 33.17 4.84
1294 1391 2.874664 CGGTTTCGGTCCTGGGTGA 61.875 63.158 0.00 0.00 0.00 4.02
1629 1730 4.085055 CGGTAATCAAGATCAAACGATCCG 60.085 45.833 0.00 0.00 40.26 4.18
1642 1747 2.002586 ACGATCCGAGTGCAAATTCAG 58.997 47.619 0.00 0.00 0.00 3.02
1668 1795 1.971167 CGTGGTGTGGGGTGATTGG 60.971 63.158 0.00 0.00 0.00 3.16
1692 1825 3.450817 TGACATGGTATGATCTTGGACGT 59.549 43.478 0.00 0.00 0.00 4.34
1866 2466 1.679305 GTCCTGAGCTCCGAGTCCA 60.679 63.158 12.15 0.00 0.00 4.02
2079 2681 1.374758 GTGTCCAAGGACTCGCAGG 60.375 63.158 19.20 0.00 44.80 4.85
2105 2707 2.892425 GCCAAGATCCTCGCGGTG 60.892 66.667 6.13 0.00 0.00 4.94
2299 2904 1.153429 CAGCTTACCCCGGTACTGC 60.153 63.158 0.00 9.03 33.49 4.40
2311 2916 3.181501 CCCGGTACTGCACATTAAACATG 60.182 47.826 0.00 0.00 0.00 3.21
2312 2917 3.425404 CGGTACTGCACATTAAACATGC 58.575 45.455 0.00 2.82 39.88 4.06
2439 3046 3.249189 AAGGCTGGCGTGGAGGAA 61.249 61.111 0.00 0.00 0.00 3.36
2539 3146 0.250858 CAACATGCTGGACAGGGACA 60.251 55.000 1.01 0.00 33.23 4.02
2590 3205 6.085555 TCTCCTCCATAACATGATTACGAC 57.914 41.667 0.00 0.00 0.00 4.34
2623 3239 2.621998 GCCAGAGCTATCATGCAAACAT 59.378 45.455 0.00 0.00 34.24 2.71
2624 3240 3.550233 GCCAGAGCTATCATGCAAACATG 60.550 47.826 0.00 0.00 44.81 3.21
2664 3303 3.323403 GGAGAGGATTTCGATGGTCTCAT 59.677 47.826 10.90 0.00 33.52 2.90
2674 3313 4.017126 TCGATGGTCTCATCCGCTTATAT 58.983 43.478 0.00 0.00 45.20 0.86
2680 3319 5.047731 TGGTCTCATCCGCTTATATTCTCTG 60.048 44.000 0.00 0.00 0.00 3.35
2682 3321 6.151312 GGTCTCATCCGCTTATATTCTCTGTA 59.849 42.308 0.00 0.00 0.00 2.74
2686 3325 9.676195 CTCATCCGCTTATATTCTCTGTATATG 57.324 37.037 0.00 0.00 0.00 1.78
2687 3326 8.633561 TCATCCGCTTATATTCTCTGTATATGG 58.366 37.037 0.00 0.00 0.00 2.74
2718 3358 3.108144 CTGGTGCGAGTTTTGAAGTTTG 58.892 45.455 0.00 0.00 0.00 2.93
2744 3384 6.808321 ATTTTCCTTAAGGCTTAATTCCCC 57.192 37.500 19.32 0.00 34.44 4.81
2745 3385 3.965470 TCCTTAAGGCTTAATTCCCCC 57.035 47.619 19.32 0.00 34.44 5.40
2756 3396 5.414454 GGCTTAATTCCCCCAAAAATGTTTC 59.586 40.000 0.00 0.00 0.00 2.78
2767 3407 5.517655 CCCAAAAATGTTTCCCTACTCCCTA 60.518 44.000 0.00 0.00 0.00 3.53
2768 3408 6.194967 CCAAAAATGTTTCCCTACTCCCTAT 58.805 40.000 0.00 0.00 0.00 2.57
2769 3409 6.667848 CCAAAAATGTTTCCCTACTCCCTATT 59.332 38.462 0.00 0.00 0.00 1.73
2770 3410 7.363793 CCAAAAATGTTTCCCTACTCCCTATTG 60.364 40.741 0.00 0.00 0.00 1.90
2771 3411 6.652205 AAATGTTTCCCTACTCCCTATTGA 57.348 37.500 0.00 0.00 0.00 2.57
2772 3412 6.652205 AATGTTTCCCTACTCCCTATTGAA 57.348 37.500 0.00 0.00 0.00 2.69
2773 3413 6.652205 ATGTTTCCCTACTCCCTATTGAAA 57.348 37.500 0.00 0.00 0.00 2.69
2774 3414 5.812286 TGTTTCCCTACTCCCTATTGAAAC 58.188 41.667 0.00 0.00 40.08 2.78
2775 3415 4.748277 TTCCCTACTCCCTATTGAAACG 57.252 45.455 0.00 0.00 0.00 3.60
2776 3416 2.433239 TCCCTACTCCCTATTGAAACGC 59.567 50.000 0.00 0.00 0.00 4.84
2777 3417 2.470821 CCTACTCCCTATTGAAACGCG 58.529 52.381 3.53 3.53 0.00 6.01
2778 3418 2.159142 CCTACTCCCTATTGAAACGCGT 60.159 50.000 5.58 5.58 0.00 6.01
2779 3419 2.005971 ACTCCCTATTGAAACGCGTC 57.994 50.000 14.44 0.25 0.00 5.19
2780 3420 1.549170 ACTCCCTATTGAAACGCGTCT 59.451 47.619 14.44 0.00 0.00 4.18
2781 3421 2.756760 ACTCCCTATTGAAACGCGTCTA 59.243 45.455 14.44 0.00 0.00 2.59
2782 3422 3.383825 ACTCCCTATTGAAACGCGTCTAT 59.616 43.478 14.44 6.14 0.00 1.98
2783 3423 4.581824 ACTCCCTATTGAAACGCGTCTATA 59.418 41.667 14.44 7.06 0.00 1.31
2784 3424 5.243283 ACTCCCTATTGAAACGCGTCTATAT 59.757 40.000 14.44 7.17 0.00 0.86
2785 3425 6.092955 TCCCTATTGAAACGCGTCTATATT 57.907 37.500 14.44 1.36 0.00 1.28
2786 3426 7.040201 ACTCCCTATTGAAACGCGTCTATATTA 60.040 37.037 14.44 0.00 0.00 0.98
2787 3427 7.660112 TCCCTATTGAAACGCGTCTATATTAA 58.340 34.615 14.44 1.73 0.00 1.40
2788 3428 7.811236 TCCCTATTGAAACGCGTCTATATTAAG 59.189 37.037 14.44 3.85 0.00 1.85
2789 3429 7.063074 CCCTATTGAAACGCGTCTATATTAAGG 59.937 40.741 14.44 12.81 0.00 2.69
2790 3430 7.811236 CCTATTGAAACGCGTCTATATTAAGGA 59.189 37.037 14.44 0.00 0.00 3.36
2791 3431 6.817270 TTGAAACGCGTCTATATTAAGGAC 57.183 37.500 14.44 0.00 0.00 3.85
2792 3432 5.893687 TGAAACGCGTCTATATTAAGGACA 58.106 37.500 14.44 0.00 0.00 4.02
2793 3433 5.975344 TGAAACGCGTCTATATTAAGGACAG 59.025 40.000 14.44 0.00 0.00 3.51
2794 3434 5.511234 AACGCGTCTATATTAAGGACAGT 57.489 39.130 14.44 0.00 0.00 3.55
2795 3435 6.624352 AACGCGTCTATATTAAGGACAGTA 57.376 37.500 14.44 0.00 0.00 2.74
2820 3460 1.760613 CCCTACCCTCACAGCGATTTA 59.239 52.381 0.00 0.00 0.00 1.40
2827 3467 3.058501 CCCTCACAGCGATTTACGTTTTT 60.059 43.478 0.00 0.00 44.60 1.94
2842 3482 0.248539 TTTTTGGCCGTCCGTTTTCG 60.249 50.000 0.00 0.00 43.67 3.46
2850 3490 1.415374 CGTCCGTTTTCGTGATCTGT 58.585 50.000 0.00 0.00 42.35 3.41
2891 3531 7.427606 CAGATTTAATGTGAAAAGCGATCTGTC 59.572 37.037 0.00 0.00 35.48 3.51
3036 3676 3.465403 CCCGAGAGCCCAGTCCAG 61.465 72.222 0.00 0.00 0.00 3.86
3063 3703 4.803426 CTCCTGTCGCCTCCGCAC 62.803 72.222 0.00 0.00 34.03 5.34
3090 3730 2.244695 TCTCGTAGGGTTTCTCAAGCA 58.755 47.619 0.00 0.00 31.46 3.91
3093 3733 2.029290 TCGTAGGGTTTCTCAAGCAGAC 60.029 50.000 0.00 0.00 31.46 3.51
3135 3776 4.421554 CTCCTCTGCCCCCTCCCA 62.422 72.222 0.00 0.00 0.00 4.37
3147 4140 3.003173 CTCCCACCGCCTTCTGGA 61.003 66.667 0.00 0.00 34.57 3.86
3153 4146 1.605738 ACCGCCTTCTGGACGTACT 60.606 57.895 0.00 0.00 34.57 2.73
3248 4242 4.514577 CGCCCGATCCACTCGCTT 62.515 66.667 0.00 0.00 46.25 4.68
3362 4356 0.393267 GCCCCTACAACAATGCCGTA 60.393 55.000 0.00 0.00 0.00 4.02
3385 4380 0.828343 CCTCCCTATCGACCCTGACC 60.828 65.000 0.00 0.00 0.00 4.02
3417 4413 0.820074 CCTACCTCGACCTCGCATCT 60.820 60.000 0.00 0.00 39.60 2.90
3441 4437 0.807667 GTCGTCGCTCTACCTCGGTA 60.808 60.000 0.00 0.00 0.00 4.02
3546 4563 7.730364 CCAGTTGGTATTGACTATACAATCC 57.270 40.000 8.90 0.00 40.80 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 99 3.440522 CGAGTGAGAGACTGTAACATCCA 59.559 47.826 0.00 0.00 33.83 3.41
130 152 6.950842 AGAGAATATCATTGACCTTGTCACA 58.049 36.000 0.00 0.00 42.60 3.58
184 206 2.046314 GCTAGCCGCCTCCAAACA 60.046 61.111 2.29 0.00 0.00 2.83
205 227 0.035152 ACAATCGCCTTGCCAGATCA 60.035 50.000 0.00 0.00 38.50 2.92
274 299 1.017701 CATCAAGCAGCTGCAGACGA 61.018 55.000 38.24 26.95 45.16 4.20
368 393 4.012374 CCCTCTACAAGAGTAACACGGTA 58.988 47.826 3.42 0.00 40.72 4.02
385 410 2.568623 ACATCGCAAAGAAACCCTCT 57.431 45.000 0.00 0.00 35.13 3.69
424 452 5.708230 ACAAACATACCCAACACATAACGAT 59.292 36.000 0.00 0.00 0.00 3.73
534 582 5.306532 TCGTCGACTAATTAAGCAGAAGT 57.693 39.130 14.70 0.00 0.00 3.01
549 597 2.839474 CAAAAGATTTGCCTCGTCGAC 58.161 47.619 5.18 5.18 0.00 4.20
591 639 5.390991 GCCATGAGCTAGTTTTGTTGAGTAC 60.391 44.000 0.00 0.00 38.99 2.73
592 640 4.695455 GCCATGAGCTAGTTTTGTTGAGTA 59.305 41.667 0.00 0.00 38.99 2.59
593 641 3.503748 GCCATGAGCTAGTTTTGTTGAGT 59.496 43.478 0.00 0.00 38.99 3.41
594 642 4.088823 GCCATGAGCTAGTTTTGTTGAG 57.911 45.455 0.00 0.00 38.99 3.02
660 708 0.865111 TCCGTGACAAATGCGAACAG 59.135 50.000 0.00 0.00 0.00 3.16
661 709 0.865111 CTCCGTGACAAATGCGAACA 59.135 50.000 0.00 0.00 0.00 3.18
662 710 0.865769 ACTCCGTGACAAATGCGAAC 59.134 50.000 0.00 0.00 0.00 3.95
664 712 1.588674 AAACTCCGTGACAAATGCGA 58.411 45.000 0.00 0.00 0.00 5.10
665 713 2.043411 CAAAACTCCGTGACAAATGCG 58.957 47.619 0.00 0.00 0.00 4.73
666 714 2.393764 CCAAAACTCCGTGACAAATGC 58.606 47.619 0.00 0.00 0.00 3.56
713 782 1.174712 AAAGTGCACGGCTCATTGCT 61.175 50.000 12.01 0.00 42.39 3.91
735 804 2.883026 ACCTCGGAGATGATAAGGAGG 58.117 52.381 6.58 3.47 45.09 4.30
736 805 3.437395 CGTACCTCGGAGATGATAAGGAG 59.563 52.174 6.58 0.00 33.89 3.69
737 806 3.181447 ACGTACCTCGGAGATGATAAGGA 60.181 47.826 6.58 0.00 44.69 3.36
738 807 3.147629 ACGTACCTCGGAGATGATAAGG 58.852 50.000 6.58 0.00 44.69 2.69
797 866 3.423154 CCTCGTTGCCTGCGAACC 61.423 66.667 0.00 0.00 37.93 3.62
827 896 1.162698 CAAGCCATGTGAGTGAGTGG 58.837 55.000 0.00 0.00 34.84 4.00
894 967 1.862806 GCGACAGCAGACTTTGGAC 59.137 57.895 0.00 0.00 44.35 4.02
918 991 2.359169 GCTGATCCTCGGTGGGTGA 61.359 63.158 0.00 0.00 36.20 4.02
942 1015 4.006319 GGATGAGAAGAGGTGTTTTCTGG 58.994 47.826 0.00 0.00 33.97 3.86
1249 1346 2.465920 CGAAGCGCGTTGTGAGAC 59.534 61.111 8.43 0.00 34.64 3.36
1376 1473 1.403814 TGGAGAAGTAGCTCATCCCG 58.596 55.000 0.00 0.00 36.62 5.14
1481 1578 2.282674 AGGTGGTAGCCGTCGTCA 60.283 61.111 0.00 0.00 0.00 4.35
1629 1730 5.565259 CACGAATGTAACTGAATTTGCACTC 59.435 40.000 0.00 0.00 0.00 3.51
1642 1747 1.161843 CCCCACACCACGAATGTAAC 58.838 55.000 0.00 0.00 0.00 2.50
1668 1795 3.812053 GTCCAAGATCATACCATGTCAGC 59.188 47.826 0.00 0.00 0.00 4.26
1692 1825 0.392863 TAGCACGCCACGAGGTAGTA 60.393 55.000 0.00 0.00 37.19 1.82
1792 2386 1.153489 CAGACCAGCTCGATGTGGG 60.153 63.158 15.64 4.88 38.25 4.61
1866 2466 2.125512 GTCGTGGATCGCCTTGCT 60.126 61.111 0.00 0.00 39.67 3.91
2299 2904 7.410800 AGAATGTTGTTGCATGTTTAATGTG 57.589 32.000 0.00 0.00 0.00 3.21
2311 2916 7.381948 TGTGTTCATGATTAAGAATGTTGTTGC 59.618 33.333 0.00 0.00 0.00 4.17
2312 2917 8.800231 TGTGTTCATGATTAAGAATGTTGTTG 57.200 30.769 0.00 0.00 0.00 3.33
2314 2919 9.985730 ATTTGTGTTCATGATTAAGAATGTTGT 57.014 25.926 0.00 0.00 0.00 3.32
2426 3033 3.197790 CGCATTCCTCCACGCCAG 61.198 66.667 0.00 0.00 0.00 4.85
2539 3146 0.032130 ATGAGCACGTCGAACACACT 59.968 50.000 0.00 0.00 0.00 3.55
2590 3205 1.712977 GCTCTGGCTTTGCATCCTCG 61.713 60.000 0.00 0.00 35.22 4.63
2623 3239 6.005066 TCTCCAAATTAATCAGAGGCATCA 57.995 37.500 0.00 0.00 0.00 3.07
2624 3240 5.472820 CCTCTCCAAATTAATCAGAGGCATC 59.527 44.000 14.90 0.00 42.94 3.91
2629 3245 7.712639 TCGAAATCCTCTCCAAATTAATCAGAG 59.287 37.037 0.00 0.00 0.00 3.35
2632 3248 7.229306 CCATCGAAATCCTCTCCAAATTAATCA 59.771 37.037 0.00 0.00 0.00 2.57
2664 3303 8.633561 CATCCATATACAGAGAATATAAGCGGA 58.366 37.037 0.00 0.00 0.00 5.54
2674 3313 5.833667 AGTCGTTCCATCCATATACAGAGAA 59.166 40.000 0.00 0.00 0.00 2.87
2680 3319 4.307432 CACCAGTCGTTCCATCCATATAC 58.693 47.826 0.00 0.00 0.00 1.47
2682 3321 2.485479 GCACCAGTCGTTCCATCCATAT 60.485 50.000 0.00 0.00 0.00 1.78
2686 3325 2.100631 CGCACCAGTCGTTCCATCC 61.101 63.158 0.00 0.00 0.00 3.51
2687 3326 1.078759 CTCGCACCAGTCGTTCCATC 61.079 60.000 0.00 0.00 0.00 3.51
2718 3358 7.769044 GGGGAATTAAGCCTTAAGGAAAATTTC 59.231 37.037 26.21 21.07 37.39 2.17
2739 3379 3.067645 AGGGAAACATTTTTGGGGGAA 57.932 42.857 0.00 0.00 0.00 3.97
2744 3384 4.416516 AGGGAGTAGGGAAACATTTTTGG 58.583 43.478 0.00 0.00 0.00 3.28
2745 3385 7.396055 TCAATAGGGAGTAGGGAAACATTTTTG 59.604 37.037 0.00 0.00 0.00 2.44
2756 3396 2.802057 CGCGTTTCAATAGGGAGTAGGG 60.802 54.545 0.00 0.00 0.00 3.53
2767 3407 6.982141 TGTCCTTAATATAGACGCGTTTCAAT 59.018 34.615 15.53 7.49 33.09 2.57
2768 3408 6.331845 TGTCCTTAATATAGACGCGTTTCAA 58.668 36.000 15.53 0.00 33.09 2.69
2769 3409 5.893687 TGTCCTTAATATAGACGCGTTTCA 58.106 37.500 15.53 1.26 33.09 2.69
2770 3410 5.975939 ACTGTCCTTAATATAGACGCGTTTC 59.024 40.000 15.53 0.11 33.09 2.78
2771 3411 5.899299 ACTGTCCTTAATATAGACGCGTTT 58.101 37.500 15.53 11.28 33.09 3.60
2772 3412 5.511234 ACTGTCCTTAATATAGACGCGTT 57.489 39.130 15.53 6.16 33.09 4.84
2773 3413 6.814506 ATACTGTCCTTAATATAGACGCGT 57.185 37.500 13.85 13.85 33.09 6.01
2774 3414 9.435802 GATTATACTGTCCTTAATATAGACGCG 57.564 37.037 3.53 3.53 33.09 6.01
2775 3415 9.733219 GGATTATACTGTCCTTAATATAGACGC 57.267 37.037 0.00 0.00 33.09 5.19
2781 3421 9.503369 GGGTAGGGATTATACTGTCCTTAATAT 57.497 37.037 0.00 0.00 34.84 1.28
2782 3422 8.694696 AGGGTAGGGATTATACTGTCCTTAATA 58.305 37.037 0.00 0.00 34.84 0.98
2783 3423 7.554560 AGGGTAGGGATTATACTGTCCTTAAT 58.445 38.462 0.00 0.00 34.84 1.40
2784 3424 6.941915 AGGGTAGGGATTATACTGTCCTTAA 58.058 40.000 0.00 0.00 34.84 1.85
2785 3425 6.105139 TGAGGGTAGGGATTATACTGTCCTTA 59.895 42.308 0.00 0.00 34.84 2.69
2786 3426 5.102783 TGAGGGTAGGGATTATACTGTCCTT 60.103 44.000 0.00 0.00 34.84 3.36
2787 3427 4.422592 TGAGGGTAGGGATTATACTGTCCT 59.577 45.833 0.00 0.00 34.84 3.85
2788 3428 4.527427 GTGAGGGTAGGGATTATACTGTCC 59.473 50.000 0.00 0.00 0.00 4.02
2789 3429 5.145564 TGTGAGGGTAGGGATTATACTGTC 58.854 45.833 0.00 0.00 0.00 3.51
2790 3430 5.148502 CTGTGAGGGTAGGGATTATACTGT 58.851 45.833 0.00 0.00 0.00 3.55
2791 3431 4.021016 GCTGTGAGGGTAGGGATTATACTG 60.021 50.000 0.00 0.00 0.00 2.74
2792 3432 4.161102 GCTGTGAGGGTAGGGATTATACT 58.839 47.826 0.00 0.00 0.00 2.12
2793 3433 3.056749 CGCTGTGAGGGTAGGGATTATAC 60.057 52.174 0.00 0.00 0.00 1.47
2794 3434 3.162666 CGCTGTGAGGGTAGGGATTATA 58.837 50.000 0.00 0.00 0.00 0.98
2795 3435 1.971357 CGCTGTGAGGGTAGGGATTAT 59.029 52.381 0.00 0.00 0.00 1.28
2804 3444 0.606604 ACGTAAATCGCTGTGAGGGT 59.393 50.000 0.00 0.00 44.19 4.34
2827 3467 2.718747 ATCACGAAAACGGACGGCCA 62.719 55.000 8.76 0.00 0.00 5.36
2842 3482 2.673368 CGGCCAGAAACTAACAGATCAC 59.327 50.000 2.24 0.00 0.00 3.06
2891 3531 0.531532 CAGATTAGCCACCCTGCGAG 60.532 60.000 0.00 0.00 36.02 5.03
2959 3599 1.146982 AGAAAAGGCCCAGCTTACCAA 59.853 47.619 0.00 0.00 0.00 3.67
3036 3676 3.202467 GACAGGAGAGAGTCGGGC 58.798 66.667 0.00 0.00 0.00 6.13
3085 3725 3.120385 TGCGATGCCGTCTGCTTG 61.120 61.111 0.00 0.00 42.00 4.01
3086 3726 3.121030 GTGCGATGCCGTCTGCTT 61.121 61.111 0.00 0.00 42.00 3.91
3135 3776 1.605738 AGTACGTCCAGAAGGCGGT 60.606 57.895 0.00 0.00 38.29 5.68
3166 4159 0.041386 AAAGGAGAGCCGGGACTAGT 59.959 55.000 2.18 0.00 39.96 2.57
3168 4161 1.687368 GGTAAAGGAGAGCCGGGACTA 60.687 57.143 2.18 0.00 39.96 2.59
3248 4242 4.717629 CGGCGCTGTCAAGGTCGA 62.718 66.667 8.45 0.00 0.00 4.20
3362 4356 2.521224 GGTCGATAGGGAGGGCGT 60.521 66.667 0.00 0.00 0.00 5.68
3385 4380 2.125106 GTAGGGTGAAGCAGCGGG 60.125 66.667 0.00 0.00 32.08 6.13
3417 4413 2.393768 GGTAGAGCGACGACGTCCA 61.394 63.158 21.63 0.04 41.98 4.02
3441 4437 3.230134 TCCACAAGGCATACAAAAGCTT 58.770 40.909 0.00 0.00 33.74 3.74
3546 4563 6.781138 ACATTACAATTACCACACATTAGCG 58.219 36.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.