Multiple sequence alignment - TraesCS4B01G262100

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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 TraesCS4B01G262100 chr4B 100.000 3161 0 0 1 3161 531105185 531108345 0.000000e+00 5838.0
1 TraesCS4B01G262100 chr4B 80.000 130 10 9 2538 2651 531107783 531107912 7.270000e-12 82.4
2 TraesCS4B01G262100 chr3B 94.177 2576 114 17 595 3161 85166161 85163613 0.000000e+00 3893.0
3 TraesCS4B01G262100 chr3B 84.887 794 103 12 597 1379 813214386 813213599 0.000000e+00 785.0
4 TraesCS4B01G262100 chr3B 87.097 713 49 20 1958 2642 380899470 380900167 0.000000e+00 767.0
5 TraesCS4B01G262100 chr3B 87.776 499 44 10 2665 3154 296180383 296179893 4.580000e-158 568.0
6 TraesCS4B01G262100 chr3B 92.063 63 3 1 2590 2650 85164094 85164032 1.560000e-13 87.9
7 TraesCS4B01G262100 chr5B 89.293 1569 102 28 1600 3161 526431658 526433167 0.000000e+00 1906.0
8 TraesCS4B01G262100 chr5B 90.223 1258 73 20 1399 2653 536796202 536794992 0.000000e+00 1596.0
9 TraesCS4B01G262100 chr5B 90.819 806 56 13 599 1393 536797175 536796377 0.000000e+00 1062.0
10 TraesCS4B01G262100 chr5B 89.763 801 68 8 602 1393 692427110 692427905 0.000000e+00 1013.0
11 TraesCS4B01G262100 chr5B 89.231 260 25 2 599 857 526437950 526437693 3.930000e-84 322.0
12 TraesCS4B01G262100 chr5B 92.718 206 13 2 314 517 70464042 70464247 2.380000e-76 296.0
13 TraesCS4B01G262100 chr5B 89.894 188 17 1 1399 1586 692428047 692428232 1.130000e-59 241.0
14 TraesCS4B01G262100 chr5B 83.333 246 28 10 288 522 357123971 357123728 6.870000e-52 215.0
15 TraesCS4B01G262100 chr5D 88.435 1565 115 34 1600 3146 369015472 369013956 0.000000e+00 1827.0
16 TraesCS4B01G262100 chr5D 93.340 1081 62 6 1600 2672 557816169 557817247 0.000000e+00 1589.0
17 TraesCS4B01G262100 chr5D 91.685 445 34 2 2720 3161 557817241 557817685 5.790000e-172 614.0
18 TraesCS4B01G262100 chr5D 92.430 251 14 3 1 246 60187219 60186969 1.390000e-93 353.0
19 TraesCS4B01G262100 chr5D 92.140 229 16 2 290 517 60186855 60186628 3.930000e-84 322.0
20 TraesCS4B01G262100 chr4D 87.885 1560 120 35 1600 3140 46607245 46608754 0.000000e+00 1770.0
21 TraesCS4B01G262100 chr4D 94.477 851 43 3 1600 2446 43370969 43371819 0.000000e+00 1308.0
22 TraesCS4B01G262100 chr4D 84.608 1046 98 31 2133 3161 346226242 346225243 0.000000e+00 981.0
23 TraesCS4B01G262100 chr4D 87.154 794 90 9 598 1390 43361882 43362664 0.000000e+00 891.0
24 TraesCS4B01G262100 chr4D 88.973 263 24 4 597 857 346207172 346207431 1.410000e-83 320.0
25 TraesCS4B01G262100 chr2D 92.047 1031 65 12 1600 2614 585731837 585730808 0.000000e+00 1434.0
26 TraesCS4B01G262100 chr2D 87.438 804 76 12 599 1393 585733052 585732265 0.000000e+00 902.0
27 TraesCS4B01G262100 chr2D 90.426 94 4 4 2519 2608 103015567 103015475 5.540000e-23 119.0
28 TraesCS4B01G262100 chr2D 80.503 159 7 16 2426 2583 345269433 345269568 2.010000e-17 100.0
29 TraesCS4B01G262100 chr2D 78.659 164 7 15 2426 2589 639469837 639469702 2.020000e-12 84.2
30 TraesCS4B01G262100 chr2D 97.674 43 0 1 2526 2568 103015600 103015559 4.370000e-09 73.1
31 TraesCS4B01G262100 chr6B 95.765 850 32 3 1600 2446 564055281 564054433 0.000000e+00 1367.0
32 TraesCS4B01G262100 chr6B 87.916 811 74 18 599 1393 564056460 564055658 0.000000e+00 933.0
33 TraesCS4B01G262100 chr6B 88.931 262 23 5 598 857 696550330 696550587 5.090000e-83 318.0
34 TraesCS4B01G262100 chr6B 86.667 195 21 4 1392 1584 620695338 620695529 8.880000e-51 211.0
35 TraesCS4B01G262100 chr3D 94.941 850 40 2 1600 2446 603108907 603108058 0.000000e+00 1328.0
36 TraesCS4B01G262100 chr3A 88.219 1095 83 23 1607 2669 23142203 23141123 0.000000e+00 1266.0
37 TraesCS4B01G262100 chr3A 87.776 499 44 10 2665 3154 674546773 674546283 4.580000e-158 568.0
38 TraesCS4B01G262100 chr3A 91.489 235 12 6 284 517 681059538 681059765 1.830000e-82 316.0
39 TraesCS4B01G262100 chr3A 87.029 239 16 7 1 224 681059101 681059339 4.050000e-64 255.0
40 TraesCS4B01G262100 chr3A 88.393 112 12 1 15 125 636860262 636860373 1.980000e-27 134.0
41 TraesCS4B01G262100 chr1B 91.078 807 50 11 599 1393 148152747 148153543 0.000000e+00 1072.0
42 TraesCS4B01G262100 chr1B 90.852 798 57 12 600 1393 229996893 229997678 0.000000e+00 1055.0
43 TraesCS4B01G262100 chr1B 95.455 528 23 1 1399 1926 229997853 229998379 0.000000e+00 841.0
44 TraesCS4B01G262100 chr1B 90.446 471 38 4 2677 3140 230019396 230019866 5.790000e-172 614.0
45 TraesCS4B01G262100 chr1B 93.254 252 15 1 599 850 230024844 230024595 1.380000e-98 370.0
46 TraesCS4B01G262100 chr1B 89.388 245 25 1 1 244 357654939 357655183 1.100000e-79 307.0
47 TraesCS4B01G262100 chr1B 84.642 293 17 1 2354 2646 230019178 230019442 1.870000e-67 267.0
48 TraesCS4B01G262100 chr1B 96.460 113 4 0 1553 1665 148153753 148153865 1.500000e-43 187.0
49 TraesCS4B01G262100 chr1D 88.447 805 77 10 599 1393 422072811 422073609 0.000000e+00 957.0
50 TraesCS4B01G262100 chr1D 84.772 197 22 7 1392 1585 422073788 422073979 1.160000e-44 191.0
51 TraesCS4B01G262100 chr7A 87.311 528 43 15 2624 3140 134463956 134464470 1.630000e-162 582.0
52 TraesCS4B01G262100 chr7A 88.958 480 42 9 2666 3138 675424443 675424918 1.630000e-162 582.0
53 TraesCS4B01G262100 chr7A 89.744 273 19 1 1 264 80580370 80580642 1.090000e-89 340.0
54 TraesCS4B01G262100 chr7A 86.972 284 19 7 1 267 619625507 619625225 1.420000e-78 303.0
55 TraesCS4B01G262100 chr7A 89.831 236 14 8 292 525 619625063 619624836 8.570000e-76 294.0
56 TraesCS4B01G262100 chr7A 82.500 240 29 10 288 516 343955588 343955825 6.920000e-47 198.0
57 TraesCS4B01G262100 chr2B 87.776 499 44 10 2665 3154 626097582 626097092 4.580000e-158 568.0
58 TraesCS4B01G262100 chr2B 89.474 285 29 1 1 284 793041740 793041456 3.000000e-95 359.0
59 TraesCS4B01G262100 chr2B 86.224 196 22 4 1392 1585 646600521 646600713 1.150000e-49 207.0
60 TraesCS4B01G262100 chr7B 95.219 251 12 0 1 251 703163516 703163766 6.350000e-107 398.0
61 TraesCS4B01G262100 chr7B 94.118 221 7 4 301 519 703164210 703164426 6.540000e-87 331.0
62 TraesCS4B01G262100 chr7B 82.661 248 29 11 288 523 49083312 49083067 1.150000e-49 207.0
63 TraesCS4B01G262100 chr4A 87.805 246 14 8 1 231 139191484 139191728 1.120000e-69 274.0
64 TraesCS4B01G262100 chr4A 92.432 185 6 6 334 518 139192281 139192457 1.120000e-64 257.0
65 TraesCS4B01G262100 chr4A 94.737 76 4 0 520 595 34300683 34300758 5.540000e-23 119.0
66 TraesCS4B01G262100 chr6D 92.021 188 13 1 1399 1586 460813856 460813671 2.420000e-66 263.0
67 TraesCS4B01G262100 chr6A 90.957 188 15 1 1399 1586 68885937 68886122 5.230000e-63 252.0


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 TraesCS4B01G262100 chr4B 531105185 531108345 3160 False 2960.20 5838 90.0000 1 3161 2 chr4B.!!$F1 3160
1 TraesCS4B01G262100 chr3B 85163613 85166161 2548 True 1990.45 3893 93.1200 595 3161 2 chr3B.!!$R3 2566
2 TraesCS4B01G262100 chr3B 813213599 813214386 787 True 785.00 785 84.8870 597 1379 1 chr3B.!!$R2 782
3 TraesCS4B01G262100 chr3B 380899470 380900167 697 False 767.00 767 87.0970 1958 2642 1 chr3B.!!$F1 684
4 TraesCS4B01G262100 chr5B 526431658 526433167 1509 False 1906.00 1906 89.2930 1600 3161 1 chr5B.!!$F2 1561
5 TraesCS4B01G262100 chr5B 536794992 536797175 2183 True 1329.00 1596 90.5210 599 2653 2 chr5B.!!$R3 2054
6 TraesCS4B01G262100 chr5B 692427110 692428232 1122 False 627.00 1013 89.8285 602 1586 2 chr5B.!!$F3 984
7 TraesCS4B01G262100 chr5D 369013956 369015472 1516 True 1827.00 1827 88.4350 1600 3146 1 chr5D.!!$R1 1546
8 TraesCS4B01G262100 chr5D 557816169 557817685 1516 False 1101.50 1589 92.5125 1600 3161 2 chr5D.!!$F1 1561
9 TraesCS4B01G262100 chr5D 60186628 60187219 591 True 337.50 353 92.2850 1 517 2 chr5D.!!$R2 516
10 TraesCS4B01G262100 chr4D 46607245 46608754 1509 False 1770.00 1770 87.8850 1600 3140 1 chr4D.!!$F3 1540
11 TraesCS4B01G262100 chr4D 43370969 43371819 850 False 1308.00 1308 94.4770 1600 2446 1 chr4D.!!$F2 846
12 TraesCS4B01G262100 chr4D 346225243 346226242 999 True 981.00 981 84.6080 2133 3161 1 chr4D.!!$R1 1028
13 TraesCS4B01G262100 chr4D 43361882 43362664 782 False 891.00 891 87.1540 598 1390 1 chr4D.!!$F1 792
14 TraesCS4B01G262100 chr2D 585730808 585733052 2244 True 1168.00 1434 89.7425 599 2614 2 chr2D.!!$R3 2015
15 TraesCS4B01G262100 chr6B 564054433 564056460 2027 True 1150.00 1367 91.8405 599 2446 2 chr6B.!!$R1 1847
16 TraesCS4B01G262100 chr3D 603108058 603108907 849 True 1328.00 1328 94.9410 1600 2446 1 chr3D.!!$R1 846
17 TraesCS4B01G262100 chr3A 23141123 23142203 1080 True 1266.00 1266 88.2190 1607 2669 1 chr3A.!!$R1 1062
18 TraesCS4B01G262100 chr3A 681059101 681059765 664 False 285.50 316 89.2590 1 517 2 chr3A.!!$F2 516
19 TraesCS4B01G262100 chr1B 229996893 229998379 1486 False 948.00 1055 93.1535 600 1926 2 chr1B.!!$F3 1326
20 TraesCS4B01G262100 chr1B 148152747 148153865 1118 False 629.50 1072 93.7690 599 1665 2 chr1B.!!$F2 1066
21 TraesCS4B01G262100 chr1B 230019178 230019866 688 False 440.50 614 87.5440 2354 3140 2 chr1B.!!$F4 786
22 TraesCS4B01G262100 chr1D 422072811 422073979 1168 False 574.00 957 86.6095 599 1585 2 chr1D.!!$F1 986
23 TraesCS4B01G262100 chr7A 134463956 134464470 514 False 582.00 582 87.3110 2624 3140 1 chr7A.!!$F2 516
24 TraesCS4B01G262100 chr7A 619624836 619625507 671 True 298.50 303 88.4015 1 525 2 chr7A.!!$R1 524
25 TraesCS4B01G262100 chr7B 703163516 703164426 910 False 364.50 398 94.6685 1 519 2 chr7B.!!$F1 518
26 TraesCS4B01G262100 chr4A 139191484 139192457 973 False 265.50 274 90.1185 1 518 2 chr4A.!!$F2 517

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
904 1379 0.476338 CTCATCCTCTCCCTCCTCGA 59.524 60.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2878 4060 1.983224 CCGGGCAAGAAGAAGAGGA 59.017 57.895 0.0 0.0 0.0 3.71 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
47 48 2.808543 GAGGTCGTTCTCTTGCAATTGT 59.191 45.455 7.40 0.00 0.00 2.71
85 86 2.301296 CACCTTATCTCCATCATCGCCT 59.699 50.000 0.00 0.00 0.00 5.52
281 351 3.050275 GCGGCTCCGGATAATGGC 61.050 66.667 3.57 3.89 40.19 4.40
286 356 1.069765 CTCCGGATAATGGCTGCGT 59.930 57.895 3.57 0.00 0.00 5.24
287 357 0.946221 CTCCGGATAATGGCTGCGTC 60.946 60.000 3.57 0.00 0.00 5.19
288 358 2.310233 CCGGATAATGGCTGCGTCG 61.310 63.158 0.00 0.00 0.00 5.12
415 865 1.391157 ATGGCTTGTTGCGTGGTTGT 61.391 50.000 0.00 0.00 44.05 3.32
426 876 1.918543 GCGTGGTTGTCAGCGTTAAAC 60.919 52.381 0.00 0.00 0.00 2.01
427 877 1.328069 CGTGGTTGTCAGCGTTAAACA 59.672 47.619 0.00 0.00 0.00 2.83
428 878 2.032377 CGTGGTTGTCAGCGTTAAACAT 60.032 45.455 0.00 0.00 0.00 2.71
430 880 4.318903 CGTGGTTGTCAGCGTTAAACATAA 60.319 41.667 0.00 0.00 0.00 1.90
443 893 7.704899 AGCGTTAAACATAAAATGATTAAGGGC 59.295 33.333 16.84 14.69 40.55 5.19
483 933 4.646040 TGGATGGATGTGATTGTTTGGATC 59.354 41.667 0.00 0.00 0.00 3.36
489 939 1.478105 GTGATTGTTTGGATCTGCCCC 59.522 52.381 0.00 0.00 34.97 5.80
493 943 0.620556 TGTTTGGATCTGCCCCTCTC 59.379 55.000 0.00 0.00 34.97 3.20
496 946 1.207791 TTGGATCTGCCCCTCTCTTC 58.792 55.000 0.00 0.00 34.97 2.87
505 955 6.240549 TCTGCCCCTCTCTTCTTTTTATAG 57.759 41.667 0.00 0.00 0.00 1.31
511 961 7.501844 CCCCTCTCTTCTTTTTATAGTGGTAG 58.498 42.308 0.00 0.00 0.00 3.18
529 979 8.478775 AGTGGTAGTAGATAGATGTATTTGCA 57.521 34.615 0.00 0.00 0.00 4.08
530 980 8.924303 AGTGGTAGTAGATAGATGTATTTGCAA 58.076 33.333 0.00 0.00 0.00 4.08
531 981 9.197694 GTGGTAGTAGATAGATGTATTTGCAAG 57.802 37.037 0.00 0.00 0.00 4.01
532 982 7.872993 TGGTAGTAGATAGATGTATTTGCAAGC 59.127 37.037 0.00 0.00 0.00 4.01
533 983 7.332182 GGTAGTAGATAGATGTATTTGCAAGCC 59.668 40.741 0.00 0.00 0.00 4.35
534 984 6.830912 AGTAGATAGATGTATTTGCAAGCCA 58.169 36.000 0.00 0.00 0.00 4.75
535 985 7.456725 AGTAGATAGATGTATTTGCAAGCCAT 58.543 34.615 0.00 3.26 0.00 4.40
536 986 6.814506 AGATAGATGTATTTGCAAGCCATC 57.185 37.500 19.38 19.38 33.71 3.51
537 987 3.976793 AGATGTATTTGCAAGCCATCG 57.023 42.857 20.17 0.00 37.56 3.84
538 988 3.544684 AGATGTATTTGCAAGCCATCGA 58.455 40.909 20.17 0.00 37.56 3.59
539 989 3.562973 AGATGTATTTGCAAGCCATCGAG 59.437 43.478 20.17 0.00 37.56 4.04
540 990 2.710377 TGTATTTGCAAGCCATCGAGT 58.290 42.857 0.00 0.00 0.00 4.18
541 991 2.419673 TGTATTTGCAAGCCATCGAGTG 59.580 45.455 0.00 0.00 0.00 3.51
553 1003 4.665833 CCATCGAGTGGTTACCTAATGA 57.334 45.455 2.07 0.00 43.44 2.57
554 1004 4.621991 CCATCGAGTGGTTACCTAATGAG 58.378 47.826 2.07 0.00 43.44 2.90
555 1005 4.341235 CCATCGAGTGGTTACCTAATGAGA 59.659 45.833 2.07 0.00 43.44 3.27
556 1006 4.978083 TCGAGTGGTTACCTAATGAGAC 57.022 45.455 2.07 0.00 0.00 3.36
557 1007 4.338012 TCGAGTGGTTACCTAATGAGACA 58.662 43.478 2.07 0.00 0.00 3.41
558 1008 4.954202 TCGAGTGGTTACCTAATGAGACAT 59.046 41.667 2.07 0.00 0.00 3.06
559 1009 6.124340 TCGAGTGGTTACCTAATGAGACATA 58.876 40.000 2.07 0.00 0.00 2.29
560 1010 6.776116 TCGAGTGGTTACCTAATGAGACATAT 59.224 38.462 2.07 0.00 0.00 1.78
561 1011 7.287005 TCGAGTGGTTACCTAATGAGACATATT 59.713 37.037 2.07 0.00 0.00 1.28
562 1012 7.382488 CGAGTGGTTACCTAATGAGACATATTG 59.618 40.741 2.07 0.00 0.00 1.90
563 1013 7.509546 AGTGGTTACCTAATGAGACATATTGG 58.490 38.462 2.07 0.00 0.00 3.16
564 1014 7.347222 AGTGGTTACCTAATGAGACATATTGGA 59.653 37.037 2.07 0.00 0.00 3.53
565 1015 7.657761 GTGGTTACCTAATGAGACATATTGGAG 59.342 40.741 2.07 0.00 0.00 3.86
566 1016 7.567250 TGGTTACCTAATGAGACATATTGGAGA 59.433 37.037 2.07 0.00 0.00 3.71
567 1017 8.091449 GGTTACCTAATGAGACATATTGGAGAG 58.909 40.741 0.00 0.00 0.00 3.20
568 1018 8.861086 GTTACCTAATGAGACATATTGGAGAGA 58.139 37.037 0.00 0.00 0.00 3.10
569 1019 7.537596 ACCTAATGAGACATATTGGAGAGAG 57.462 40.000 0.00 0.00 0.00 3.20
570 1020 7.301420 ACCTAATGAGACATATTGGAGAGAGA 58.699 38.462 0.00 0.00 0.00 3.10
571 1021 7.786943 ACCTAATGAGACATATTGGAGAGAGAA 59.213 37.037 0.00 0.00 0.00 2.87
572 1022 8.646004 CCTAATGAGACATATTGGAGAGAGAAA 58.354 37.037 0.00 0.00 0.00 2.52
575 1025 8.905660 ATGAGACATATTGGAGAGAGAAATTG 57.094 34.615 0.00 0.00 0.00 2.32
576 1026 8.082672 TGAGACATATTGGAGAGAGAAATTGA 57.917 34.615 0.00 0.00 0.00 2.57
577 1027 8.202811 TGAGACATATTGGAGAGAGAAATTGAG 58.797 37.037 0.00 0.00 0.00 3.02
578 1028 7.507829 AGACATATTGGAGAGAGAAATTGAGG 58.492 38.462 0.00 0.00 0.00 3.86
579 1029 7.127032 AGACATATTGGAGAGAGAAATTGAGGT 59.873 37.037 0.00 0.00 0.00 3.85
580 1030 8.324191 ACATATTGGAGAGAGAAATTGAGGTA 57.676 34.615 0.00 0.00 0.00 3.08
581 1031 8.772250 ACATATTGGAGAGAGAAATTGAGGTAA 58.228 33.333 0.00 0.00 0.00 2.85
582 1032 9.270640 CATATTGGAGAGAGAAATTGAGGTAAG 57.729 37.037 0.00 0.00 0.00 2.34
583 1033 6.688073 TTGGAGAGAGAAATTGAGGTAAGT 57.312 37.500 0.00 0.00 0.00 2.24
584 1034 6.042638 TGGAGAGAGAAATTGAGGTAAGTG 57.957 41.667 0.00 0.00 0.00 3.16
585 1035 5.780282 TGGAGAGAGAAATTGAGGTAAGTGA 59.220 40.000 0.00 0.00 0.00 3.41
586 1036 6.441924 TGGAGAGAGAAATTGAGGTAAGTGAT 59.558 38.462 0.00 0.00 0.00 3.06
587 1037 7.038017 TGGAGAGAGAAATTGAGGTAAGTGATT 60.038 37.037 0.00 0.00 0.00 2.57
588 1038 7.279758 GGAGAGAGAAATTGAGGTAAGTGATTG 59.720 40.741 0.00 0.00 0.00 2.67
589 1039 7.911651 AGAGAGAAATTGAGGTAAGTGATTGA 58.088 34.615 0.00 0.00 0.00 2.57
590 1040 8.378565 AGAGAGAAATTGAGGTAAGTGATTGAA 58.621 33.333 0.00 0.00 0.00 2.69
591 1041 8.924511 AGAGAAATTGAGGTAAGTGATTGAAA 57.075 30.769 0.00 0.00 0.00 2.69
592 1042 9.354673 AGAGAAATTGAGGTAAGTGATTGAAAA 57.645 29.630 0.00 0.00 0.00 2.29
593 1043 9.965824 GAGAAATTGAGGTAAGTGATTGAAAAA 57.034 29.630 0.00 0.00 0.00 1.94
621 1071 9.596308 AAGGAGTATTTAACCAAAAACTACCAT 57.404 29.630 0.00 0.00 0.00 3.55
652 1102 4.514066 GGAAACGTGACAGAAAACTACCAT 59.486 41.667 0.00 0.00 0.00 3.55
657 1107 6.698380 ACGTGACAGAAAACTACCATTCTAT 58.302 36.000 0.00 0.00 34.24 1.98
728 1179 1.732917 CAAGTCACAAAAGCGGCCA 59.267 52.632 2.24 0.00 0.00 5.36
730 1181 0.751643 AAGTCACAAAAGCGGCCACT 60.752 50.000 2.24 0.00 0.00 4.00
731 1182 0.751643 AGTCACAAAAGCGGCCACTT 60.752 50.000 2.24 0.22 0.00 3.16
904 1379 0.476338 CTCATCCTCTCCCTCCTCGA 59.524 60.000 0.00 0.00 0.00 4.04
931 1412 1.063266 ACTCACTCCTCCTCATCCTCC 60.063 57.143 0.00 0.00 0.00 4.30
945 1426 1.221909 TCCTCCCCCTCTCACTGCTA 61.222 60.000 0.00 0.00 0.00 3.49
1038 1519 1.527380 GGAGAGCTCGGACGAGGAT 60.527 63.158 21.57 3.08 42.19 3.24
1406 2121 6.316640 TGTGTTTTGCTGTTAGCTGTTAACTA 59.683 34.615 14.18 2.40 42.97 2.24
1505 2250 6.458232 AAATAAGGTGTGTTGTGTGCTTAA 57.542 33.333 0.00 0.00 0.00 1.85
1562 2307 6.428159 AGCATTTAAGTAAGCATAGGATTCCG 59.572 38.462 0.00 0.00 0.00 4.30
1710 2499 1.632920 TGGGACATGTACCATGAGCAA 59.367 47.619 26.78 0.54 39.06 3.91
2162 3163 7.649533 TCAAGGCAATAATGAATGAGTGAAT 57.350 32.000 0.00 0.00 0.00 2.57
2389 3418 9.856488 CTAAGTGAGTACTCATGCTAAGTTAAA 57.144 33.333 27.54 0.00 42.18 1.52
2630 3771 7.171630 AGCAAGTAGTACTAAACATAGTGCT 57.828 36.000 13.56 13.56 43.63 4.40
2675 3844 3.411446 TCAAACTGAACATAGTGCCTGG 58.589 45.455 0.00 0.00 0.00 4.45
2727 3896 7.175797 AGTGCCTACATACATAGATAGTGCTA 58.824 38.462 0.00 0.00 0.00 3.49
2730 3899 7.450323 TGCCTACATACATAGATAGTGCTAACA 59.550 37.037 0.00 0.00 0.00 2.41
2878 4060 4.602259 CACCACAGTCACGGCCGT 62.602 66.667 28.70 28.70 0.00 5.68
2993 4175 2.825387 GGCAGCGCATCCACATCA 60.825 61.111 11.47 0.00 0.00 3.07
3006 4188 1.548081 CACATCAATTGGGAGGTGCA 58.452 50.000 5.42 0.00 41.82 4.57
3040 4224 2.721167 CGTCGAGGATGGGAGCCAA 61.721 63.158 0.00 0.00 36.95 4.52
3043 4227 1.198094 TCGAGGATGGGAGCCAACAA 61.198 55.000 0.00 0.00 36.95 2.83
3054 4238 1.405105 GAGCCAACAACTGCACTTCAA 59.595 47.619 0.00 0.00 0.00 2.69
3140 4326 1.822506 TCATCGTCAGAGGACTCGTT 58.177 50.000 0.00 0.00 42.05 3.85
3146 4332 2.225963 CGTCAGAGGACTCGTTGTTAGT 59.774 50.000 0.00 0.00 42.05 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 3.170717 AGTAGGTGAAGGAAATGACGGA 58.829 45.455 0.00 0.00 0.00 4.69
131 132 2.803817 CCTTACGGGTAGGCCGCAT 61.804 63.158 0.00 0.00 34.97 4.73
132 133 3.463585 CCTTACGGGTAGGCCGCA 61.464 66.667 0.00 0.00 34.97 5.69
136 137 1.821258 CCTGTCCTTACGGGTAGGC 59.179 63.158 0.00 0.00 45.83 3.93
274 344 1.069765 CCTCCGACGCAGCCATTAT 59.930 57.895 0.00 0.00 0.00 1.28
281 351 4.135153 CCACCTCCTCCGACGCAG 62.135 72.222 0.00 0.00 0.00 5.18
286 356 4.075793 CCCCTCCACCTCCTCCGA 62.076 72.222 0.00 0.00 0.00 4.55
383 833 2.352651 ACAAGCCATCAACAATCGATCG 59.647 45.455 9.36 9.36 0.00 3.69
390 840 0.743688 ACGCAACAAGCCATCAACAA 59.256 45.000 0.00 0.00 41.38 2.83
395 845 0.664166 CAACCACGCAACAAGCCATC 60.664 55.000 0.00 0.00 41.38 3.51
396 846 1.363443 CAACCACGCAACAAGCCAT 59.637 52.632 0.00 0.00 41.38 4.40
415 865 9.781834 CCTTAATCATTTTATGTTTAACGCTGA 57.218 29.630 0.00 0.00 33.36 4.26
430 880 8.991275 TCAAAATCTAATGGCCCTTAATCATTT 58.009 29.630 0.00 3.61 33.72 2.32
443 893 7.770366 TCCATCCATCATCAAAATCTAATGG 57.230 36.000 0.00 0.00 35.95 3.16
483 933 5.819901 CACTATAAAAAGAAGAGAGGGGCAG 59.180 44.000 0.00 0.00 0.00 4.85
505 955 9.197694 CTTGCAAATACATCTATCTACTACCAC 57.802 37.037 0.00 0.00 0.00 4.16
511 961 7.412346 CGATGGCTTGCAAATACATCTATCTAC 60.412 40.741 23.69 7.58 36.97 2.59
517 967 3.544684 TCGATGGCTTGCAAATACATCT 58.455 40.909 23.69 4.23 36.97 2.90
518 968 3.313526 ACTCGATGGCTTGCAAATACATC 59.686 43.478 19.73 19.73 36.26 3.06
519 969 3.065786 CACTCGATGGCTTGCAAATACAT 59.934 43.478 0.00 5.24 0.00 2.29
520 970 2.419673 CACTCGATGGCTTGCAAATACA 59.580 45.455 0.00 0.00 0.00 2.29
521 971 2.223340 CCACTCGATGGCTTGCAAATAC 60.223 50.000 0.00 0.00 43.24 1.89
522 972 2.016318 CCACTCGATGGCTTGCAAATA 58.984 47.619 0.00 0.00 43.24 1.40
523 973 0.813184 CCACTCGATGGCTTGCAAAT 59.187 50.000 0.00 0.00 43.24 2.32
524 974 2.256391 CCACTCGATGGCTTGCAAA 58.744 52.632 0.00 0.00 43.24 3.68
525 975 3.985877 CCACTCGATGGCTTGCAA 58.014 55.556 0.00 0.00 43.24 4.08
533 983 5.163550 TGTCTCATTAGGTAACCACTCGATG 60.164 44.000 0.00 0.00 37.17 3.84
534 984 4.954202 TGTCTCATTAGGTAACCACTCGAT 59.046 41.667 0.00 0.00 37.17 3.59
535 985 4.338012 TGTCTCATTAGGTAACCACTCGA 58.662 43.478 0.00 0.00 37.17 4.04
536 986 4.713824 TGTCTCATTAGGTAACCACTCG 57.286 45.455 0.00 0.00 37.17 4.18
537 987 7.657761 CCAATATGTCTCATTAGGTAACCACTC 59.342 40.741 0.00 0.00 37.17 3.51
538 988 7.347222 TCCAATATGTCTCATTAGGTAACCACT 59.653 37.037 0.00 0.00 37.17 4.00
539 989 7.506114 TCCAATATGTCTCATTAGGTAACCAC 58.494 38.462 0.00 0.00 37.17 4.16
540 990 7.567250 TCTCCAATATGTCTCATTAGGTAACCA 59.433 37.037 0.00 0.00 37.17 3.67
541 991 7.963532 TCTCCAATATGTCTCATTAGGTAACC 58.036 38.462 0.00 0.00 37.17 2.85
542 992 8.861086 TCTCTCCAATATGTCTCATTAGGTAAC 58.139 37.037 0.00 0.00 0.00 2.50
543 993 9.083422 CTCTCTCCAATATGTCTCATTAGGTAA 57.917 37.037 0.00 0.00 0.00 2.85
544 994 8.448816 TCTCTCTCCAATATGTCTCATTAGGTA 58.551 37.037 0.00 0.00 0.00 3.08
545 995 7.301420 TCTCTCTCCAATATGTCTCATTAGGT 58.699 38.462 0.00 0.00 0.00 3.08
546 996 7.773489 TCTCTCTCCAATATGTCTCATTAGG 57.227 40.000 0.00 0.00 0.00 2.69
549 999 9.339850 CAATTTCTCTCTCCAATATGTCTCATT 57.660 33.333 0.00 0.00 0.00 2.57
550 1000 8.712103 TCAATTTCTCTCTCCAATATGTCTCAT 58.288 33.333 0.00 0.00 0.00 2.90
551 1001 8.082672 TCAATTTCTCTCTCCAATATGTCTCA 57.917 34.615 0.00 0.00 0.00 3.27
552 1002 7.656948 CCTCAATTTCTCTCTCCAATATGTCTC 59.343 40.741 0.00 0.00 0.00 3.36
553 1003 7.127032 ACCTCAATTTCTCTCTCCAATATGTCT 59.873 37.037 0.00 0.00 0.00 3.41
554 1004 7.278875 ACCTCAATTTCTCTCTCCAATATGTC 58.721 38.462 0.00 0.00 0.00 3.06
555 1005 7.205515 ACCTCAATTTCTCTCTCCAATATGT 57.794 36.000 0.00 0.00 0.00 2.29
556 1006 9.270640 CTTACCTCAATTTCTCTCTCCAATATG 57.729 37.037 0.00 0.00 0.00 1.78
557 1007 8.997734 ACTTACCTCAATTTCTCTCTCCAATAT 58.002 33.333 0.00 0.00 0.00 1.28
558 1008 8.260818 CACTTACCTCAATTTCTCTCTCCAATA 58.739 37.037 0.00 0.00 0.00 1.90
559 1009 7.038017 TCACTTACCTCAATTTCTCTCTCCAAT 60.038 37.037 0.00 0.00 0.00 3.16
560 1010 6.270000 TCACTTACCTCAATTTCTCTCTCCAA 59.730 38.462 0.00 0.00 0.00 3.53
561 1011 5.780282 TCACTTACCTCAATTTCTCTCTCCA 59.220 40.000 0.00 0.00 0.00 3.86
562 1012 6.287589 TCACTTACCTCAATTTCTCTCTCC 57.712 41.667 0.00 0.00 0.00 3.71
563 1013 8.037758 TCAATCACTTACCTCAATTTCTCTCTC 58.962 37.037 0.00 0.00 0.00 3.20
564 1014 7.911651 TCAATCACTTACCTCAATTTCTCTCT 58.088 34.615 0.00 0.00 0.00 3.10
565 1015 8.553459 TTCAATCACTTACCTCAATTTCTCTC 57.447 34.615 0.00 0.00 0.00 3.20
566 1016 8.924511 TTTCAATCACTTACCTCAATTTCTCT 57.075 30.769 0.00 0.00 0.00 3.10
567 1017 9.965824 TTTTTCAATCACTTACCTCAATTTCTC 57.034 29.630 0.00 0.00 0.00 2.87
568 1018 9.750125 GTTTTTCAATCACTTACCTCAATTTCT 57.250 29.630 0.00 0.00 0.00 2.52
569 1019 9.528018 TGTTTTTCAATCACTTACCTCAATTTC 57.472 29.630 0.00 0.00 0.00 2.17
570 1020 9.883142 TTGTTTTTCAATCACTTACCTCAATTT 57.117 25.926 0.00 0.00 0.00 1.82
571 1021 9.533253 CTTGTTTTTCAATCACTTACCTCAATT 57.467 29.630 0.00 0.00 35.35 2.32
572 1022 8.143835 CCTTGTTTTTCAATCACTTACCTCAAT 58.856 33.333 0.00 0.00 35.35 2.57
573 1023 7.340743 TCCTTGTTTTTCAATCACTTACCTCAA 59.659 33.333 0.00 0.00 35.35 3.02
574 1024 6.831353 TCCTTGTTTTTCAATCACTTACCTCA 59.169 34.615 0.00 0.00 35.35 3.86
575 1025 7.013369 ACTCCTTGTTTTTCAATCACTTACCTC 59.987 37.037 0.00 0.00 35.35 3.85
576 1026 6.833933 ACTCCTTGTTTTTCAATCACTTACCT 59.166 34.615 0.00 0.00 35.35 3.08
577 1027 7.039313 ACTCCTTGTTTTTCAATCACTTACC 57.961 36.000 0.00 0.00 35.35 2.85
583 1033 9.974980 GGTTAAATACTCCTTGTTTTTCAATCA 57.025 29.630 0.00 0.00 35.35 2.57
584 1034 9.974980 TGGTTAAATACTCCTTGTTTTTCAATC 57.025 29.630 0.00 0.00 35.35 2.67
593 1043 8.853126 GGTAGTTTTTGGTTAAATACTCCTTGT 58.147 33.333 0.00 0.00 38.47 3.16
621 1071 3.979948 TCTGTCACGTTTCCGTCAAATA 58.020 40.909 0.00 0.00 46.28 1.40
652 1102 7.432838 GGTAGTTTTTCGCACAAAAACATAGAA 59.567 33.333 24.83 10.23 46.78 2.10
657 1107 4.806330 TGGTAGTTTTTCGCACAAAAACA 58.194 34.783 24.83 14.19 46.78 2.83
716 1167 0.248866 CGAAAAGTGGCCGCTTTTGT 60.249 50.000 45.52 31.52 45.40 2.83
728 1179 2.357760 TTAGCGCGGGCGAAAAGT 60.358 55.556 19.46 2.61 46.35 2.66
730 1181 3.795342 GCTTAGCGCGGGCGAAAA 61.795 61.111 19.60 13.90 46.35 2.29
904 1379 0.033601 AGGAGGAGTGAGTGAGCGAT 60.034 55.000 0.00 0.00 0.00 4.58
931 1412 1.110442 CAGAGTAGCAGTGAGAGGGG 58.890 60.000 0.00 0.00 0.00 4.79
945 1426 0.818296 GACGGTGGTATGCTCAGAGT 59.182 55.000 0.00 0.00 0.00 3.24
1017 1498 1.450491 CTCGTCCGAGCTCTCCTCA 60.450 63.158 12.85 0.00 40.78 3.86
1038 1519 4.828939 GGATCCATTGAAACCATGCAGATA 59.171 41.667 6.95 0.00 0.00 1.98
1253 1736 1.195115 AGCTACCATCTTCTTCGGCA 58.805 50.000 0.00 0.00 0.00 5.69
1313 1796 6.833041 TCAAGATTTAGTACCTGGTTCACAA 58.167 36.000 3.84 0.00 0.00 3.33
1453 2184 8.140628 CAGCAGAGATAAATTCAGCTAACTCTA 58.859 37.037 0.00 0.00 33.18 2.43
1461 2192 5.998454 TTAGCAGCAGAGATAAATTCAGC 57.002 39.130 0.00 0.00 0.00 4.26
1710 2499 2.107726 GTCCTTCACCCTACCCAAGTTT 59.892 50.000 0.00 0.00 0.00 2.66
1987 2776 5.185442 TGTTTTGAATGATATCTGCTTGGCA 59.815 36.000 3.98 0.00 36.92 4.92
2162 3163 6.585695 TTACTTAACCAACACAACAACCAA 57.414 33.333 0.00 0.00 0.00 3.67
2211 3214 3.949754 ACCTAACATGCATCACATTCCAG 59.050 43.478 0.00 0.00 36.64 3.86
2583 3685 6.471841 GCTATCTATGTCAGACTATGAATGCG 59.528 42.308 1.31 0.00 40.43 4.73
2675 3844 9.915629 ATGTTTAGTACTACTTGCTATCTATGC 57.084 33.333 0.91 0.00 0.00 3.14
2727 3896 3.617284 AGTTCCTCGGTTCAGTTTTGTT 58.383 40.909 0.00 0.00 0.00 2.83
2730 3899 4.814771 CAGTAAGTTCCTCGGTTCAGTTTT 59.185 41.667 0.00 0.00 0.00 2.43
2878 4060 1.983224 CCGGGCAAGAAGAAGAGGA 59.017 57.895 0.00 0.00 0.00 3.71
2993 4175 0.324645 GGGACATGCACCTCCCAATT 60.325 55.000 21.21 0.00 45.22 2.32
3031 4215 1.827789 GTGCAGTTGTTGGCTCCCA 60.828 57.895 0.00 0.00 0.00 4.37
3040 4224 0.940126 CGAGCTTGAAGTGCAGTTGT 59.060 50.000 12.53 0.00 0.00 3.32
3043 4227 0.941463 CGACGAGCTTGAAGTGCAGT 60.941 55.000 8.31 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.