Multiple sequence alignment - TraesCS7A01G197200

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 TraesCS7A01G197200 chr7A 100.000 4519 0 0 948 5466 157169015 157173533 0.000000e+00 8346.0
1 TraesCS7A01G197200 chr7A 98.528 1359 14 4 2279 3633 115322765 115324121 0.000000e+00 2394.0
2 TraesCS7A01G197200 chr7A 100.000 718 0 0 1 718 157168068 157168785 0.000000e+00 1327.0
3 TraesCS7A01G197200 chr6B 99.416 1370 7 1 2269 3637 383569863 383568494 0.000000e+00 2484.0
4 TraesCS7A01G197200 chr6B 99.002 1302 13 0 2329 3630 494090246 494091547 0.000000e+00 2333.0
5 TraesCS7A01G197200 chr4A 99.559 1362 6 0 2268 3629 127487820 127489181 0.000000e+00 2483.0
6 TraesCS7A01G197200 chr4A 93.033 732 37 6 1 718 718515007 718515738 0.000000e+00 1057.0
7 TraesCS7A01G197200 chr3A 98.968 1356 13 1 2279 3634 25927552 25928906 0.000000e+00 2425.0
8 TraesCS7A01G197200 chr3A 96.250 720 23 2 1 718 80125491 80126208 0.000000e+00 1177.0
9 TraesCS7A01G197200 chr3A 95.278 720 29 2 1 718 456459899 456460615 0.000000e+00 1136.0
10 TraesCS7A01G197200 chr2B 98.755 1365 13 4 2270 3633 790107331 790108692 0.000000e+00 2423.0
11 TraesCS7A01G197200 chr2B 99.770 1305 3 0 2329 3633 753935805 753937109 0.000000e+00 2394.0
12 TraesCS7A01G197200 chr2B 84.078 1275 172 18 1006 2263 25443001 25444261 0.000000e+00 1201.0
13 TraesCS7A01G197200 chr2B 82.506 1269 191 19 1013 2263 547940577 547941832 0.000000e+00 1085.0
14 TraesCS7A01G197200 chr2B 78.726 691 133 9 3722 4411 25444346 25445023 3.000000e-122 449.0
15 TraesCS7A01G197200 chr2B 78.770 683 122 13 3736 4411 25356185 25355519 2.340000e-118 436.0
16 TraesCS7A01G197200 chr2B 76.197 689 142 16 3722 4405 25476104 25475433 1.460000e-90 344.0
17 TraesCS7A01G197200 chr2B 76.502 566 97 20 1009 1562 80984720 80985261 5.390000e-70 276.0
18 TraesCS7A01G197200 chr2B 73.031 749 162 29 3681 4400 80986026 80986763 1.530000e-55 228.0
19 TraesCS7A01G197200 chr1B 99.693 1301 4 0 2329 3629 546702658 546703958 0.000000e+00 2381.0
20 TraesCS7A01G197200 chr5B 99.461 1299 6 1 2329 3627 613640297 613641594 0.000000e+00 2359.0
21 TraesCS7A01G197200 chr7D 97.726 1319 26 2 948 2262 155308697 155310015 0.000000e+00 2266.0
22 TraesCS7A01G197200 chr7D 95.303 1256 25 5 3636 4857 155310017 155311272 0.000000e+00 1962.0
23 TraesCS7A01G197200 chr7D 95.802 405 9 6 5065 5466 155311543 155311942 0.000000e+00 647.0
24 TraesCS7A01G197200 chr7D 96.262 214 6 1 4853 5066 155311304 155311515 3.130000e-92 350.0
25 TraesCS7A01G197200 chr7D 87.879 66 8 0 4969 5034 154179936 154179871 1.630000e-10 78.7
26 TraesCS7A01G197200 chr1A 97.059 714 18 2 1 712 3569329 3570041 0.000000e+00 1199.0
27 TraesCS7A01G197200 chr1A 96.518 718 22 2 1 716 380308875 380309591 0.000000e+00 1184.0
28 TraesCS7A01G197200 chr2A 96.528 720 22 2 1 718 711650492 711649774 0.000000e+00 1188.0
29 TraesCS7A01G197200 chr2A 82.504 1286 184 21 1006 2263 16272567 16273839 0.000000e+00 1090.0
30 TraesCS7A01G197200 chr2A 77.358 689 138 13 3722 4407 16273924 16274597 5.130000e-105 392.0
31 TraesCS7A01G197200 chr2A 83.621 232 35 3 4188 4419 9949965 9949737 1.190000e-51 215.0
32 TraesCS7A01G197200 chr2A 86.792 53 7 0 4982 5034 734801342 734801394 5.910000e-05 60.2
33 TraesCS7A01G197200 chr6A 96.916 681 18 2 40 718 530140285 530139606 0.000000e+00 1138.0
34 TraesCS7A01G197200 chr6A 95.139 720 30 3 1 718 58828981 58828265 0.000000e+00 1131.0
35 TraesCS7A01G197200 chr2D 82.582 1286 189 20 989 2263 13963791 13962530 0.000000e+00 1101.0
36 TraesCS7A01G197200 chr2D 80.904 1283 183 32 1006 2263 14021986 14020741 0.000000e+00 955.0
37 TraesCS7A01G197200 chr2D 79.476 687 125 13 3723 4407 13962444 13961772 1.780000e-129 473.0
38 TraesCS7A01G197200 chr2D 86.364 110 15 0 4311 4420 9524580 9524471 2.670000e-23 121.0
39 TraesCS7A01G197200 chr7B 94.053 723 37 4 1 718 702223897 702224618 0.000000e+00 1092.0
40 TraesCS7A01G197200 chr7B 90.625 64 6 0 4971 5034 116376460 116376397 9.760000e-13 86.1
41 TraesCS7A01G197200 chrUn 80.532 1279 208 23 1012 2262 207757717 207756452 0.000000e+00 944.0
42 TraesCS7A01G197200 chrUn 80.093 1291 188 34 1012 2264 2092698 2091439 0.000000e+00 896.0
43 TraesCS7A01G197200 chrUn 85.251 617 80 4 1013 1619 2146374 2146989 4.650000e-175 625.0
44 TraesCS7A01G197200 chrUn 77.844 668 130 13 3730 4394 2095200 2094548 1.100000e-106 398.0
45 TraesCS7A01G197200 chrUn 76.599 735 151 11 3679 4407 2091395 2090676 8.590000e-103 385.0
46 TraesCS7A01G197200 chrUn 74.906 267 43 16 3768 4013 12260771 12261034 3.480000e-17 100.0
47 TraesCS7A01G197200 chr3B 75.064 1179 241 34 1014 2170 2901078 2902225 2.940000e-137 499.0
48 TraesCS7A01G197200 chr3D 74.904 781 151 32 1014 1769 2785077 2785837 1.140000e-81 315.0
49 TraesCS7A01G197200 chr5D 76.800 250 47 9 1238 1480 443644266 443644511 4.440000e-26 130.0


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 TraesCS7A01G197200 chr7A 157168068 157173533 5465 False 4836.500000 8346 100.000000 1 5466 2 chr7A.!!$F2 5465
1 TraesCS7A01G197200 chr7A 115322765 115324121 1356 False 2394.000000 2394 98.528000 2279 3633 1 chr7A.!!$F1 1354
2 TraesCS7A01G197200 chr6B 383568494 383569863 1369 True 2484.000000 2484 99.416000 2269 3637 1 chr6B.!!$R1 1368
3 TraesCS7A01G197200 chr6B 494090246 494091547 1301 False 2333.000000 2333 99.002000 2329 3630 1 chr6B.!!$F1 1301
4 TraesCS7A01G197200 chr4A 127487820 127489181 1361 False 2483.000000 2483 99.559000 2268 3629 1 chr4A.!!$F1 1361
5 TraesCS7A01G197200 chr4A 718515007 718515738 731 False 1057.000000 1057 93.033000 1 718 1 chr4A.!!$F2 717
6 TraesCS7A01G197200 chr3A 25927552 25928906 1354 False 2425.000000 2425 98.968000 2279 3634 1 chr3A.!!$F1 1355
7 TraesCS7A01G197200 chr3A 80125491 80126208 717 False 1177.000000 1177 96.250000 1 718 1 chr3A.!!$F2 717
8 TraesCS7A01G197200 chr3A 456459899 456460615 716 False 1136.000000 1136 95.278000 1 718 1 chr3A.!!$F3 717
9 TraesCS7A01G197200 chr2B 790107331 790108692 1361 False 2423.000000 2423 98.755000 2270 3633 1 chr2B.!!$F3 1363
10 TraesCS7A01G197200 chr2B 753935805 753937109 1304 False 2394.000000 2394 99.770000 2329 3633 1 chr2B.!!$F2 1304
11 TraesCS7A01G197200 chr2B 547940577 547941832 1255 False 1085.000000 1085 82.506000 1013 2263 1 chr2B.!!$F1 1250
12 TraesCS7A01G197200 chr2B 25443001 25445023 2022 False 825.000000 1201 81.402000 1006 4411 2 chr2B.!!$F4 3405
13 TraesCS7A01G197200 chr2B 25355519 25356185 666 True 436.000000 436 78.770000 3736 4411 1 chr2B.!!$R1 675
14 TraesCS7A01G197200 chr2B 25475433 25476104 671 True 344.000000 344 76.197000 3722 4405 1 chr2B.!!$R2 683
15 TraesCS7A01G197200 chr2B 80984720 80986763 2043 False 252.000000 276 74.766500 1009 4400 2 chr2B.!!$F5 3391
16 TraesCS7A01G197200 chr1B 546702658 546703958 1300 False 2381.000000 2381 99.693000 2329 3629 1 chr1B.!!$F1 1300
17 TraesCS7A01G197200 chr5B 613640297 613641594 1297 False 2359.000000 2359 99.461000 2329 3627 1 chr5B.!!$F1 1298
18 TraesCS7A01G197200 chr7D 155308697 155311942 3245 False 1306.250000 2266 96.273250 948 5466 4 chr7D.!!$F1 4518
19 TraesCS7A01G197200 chr1A 3569329 3570041 712 False 1199.000000 1199 97.059000 1 712 1 chr1A.!!$F1 711
20 TraesCS7A01G197200 chr1A 380308875 380309591 716 False 1184.000000 1184 96.518000 1 716 1 chr1A.!!$F2 715
21 TraesCS7A01G197200 chr2A 711649774 711650492 718 True 1188.000000 1188 96.528000 1 718 1 chr2A.!!$R2 717
22 TraesCS7A01G197200 chr2A 16272567 16274597 2030 False 741.000000 1090 79.931000 1006 4407 2 chr2A.!!$F2 3401
23 TraesCS7A01G197200 chr6A 530139606 530140285 679 True 1138.000000 1138 96.916000 40 718 1 chr6A.!!$R2 678
24 TraesCS7A01G197200 chr6A 58828265 58828981 716 True 1131.000000 1131 95.139000 1 718 1 chr6A.!!$R1 717
25 TraesCS7A01G197200 chr2D 14020741 14021986 1245 True 955.000000 955 80.904000 1006 2263 1 chr2D.!!$R2 1257
26 TraesCS7A01G197200 chr2D 13961772 13963791 2019 True 787.000000 1101 81.029000 989 4407 2 chr2D.!!$R3 3418
27 TraesCS7A01G197200 chr7B 702223897 702224618 721 False 1092.000000 1092 94.053000 1 718 1 chr7B.!!$F1 717
28 TraesCS7A01G197200 chrUn 207756452 207757717 1265 True 944.000000 944 80.532000 1012 2262 1 chrUn.!!$R1 1250
29 TraesCS7A01G197200 chrUn 2146374 2146989 615 False 625.000000 625 85.251000 1013 1619 1 chrUn.!!$F1 606
30 TraesCS7A01G197200 chrUn 2090676 2095200 4524 True 559.666667 896 78.178667 1012 4407 3 chrUn.!!$R2 3395
31 TraesCS7A01G197200 chr3B 2901078 2902225 1147 False 499.000000 499 75.064000 1014 2170 1 chr3B.!!$F1 1156
32 TraesCS7A01G197200 chr3D 2785077 2785837 760 False 315.000000 315 74.904000 1014 1769 1 chr3D.!!$F1 755

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
593 596 0.389948 AGAAACTGGGCGTGATCGAC 60.390 55.0 0.0 0.0 45.48 4.20 F
987 990 0.738389 CAGTCGGCACAAACAAAGGT 59.262 50.0 0.0 0.0 0.00 3.50 F
2263 3880 0.610174 CAGGAAGCACTACTCAGGCA 59.390 55.0 0.0 0.0 0.00 4.75 F
2265 3882 0.898320 GGAAGCACTACTCAGGCAGA 59.102 55.0 0.0 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1780 3373 1.004440 GGACCAGATATCCGGCAGC 60.004 63.158 4.79 0.0 0.00 5.25 R
2889 4510 0.178873 AGAAGCTAGGTGGTGGGGAA 60.179 55.000 0.00 0.0 0.00 3.97 R
4132 5813 0.969149 ACAGTCTGTTGGCGAGATCA 59.031 50.000 0.00 0.0 0.00 2.92 R
4516 6206 5.815581 ACATATATTTACATGTGGCCGGAT 58.184 37.500 5.05 0.0 34.15 4.18 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
133 134 1.079681 TACAACATGCGGTCGTCCC 60.080 57.895 0.00 0.00 0.00 4.46
182 185 6.831664 ACTCAACCATAAACCCTAGATCAT 57.168 37.500 0.00 0.00 0.00 2.45
450 453 2.683867 ACGAGAGTTAGATGGAAGACGG 59.316 50.000 0.00 0.00 46.40 4.79
452 455 1.405821 AGAGTTAGATGGAAGACGGCG 59.594 52.381 4.80 4.80 0.00 6.46
453 456 0.460311 AGTTAGATGGAAGACGGCGG 59.540 55.000 13.24 0.00 0.00 6.13
454 457 1.143183 TTAGATGGAAGACGGCGGC 59.857 57.895 13.24 8.92 0.00 6.53
455 458 2.622903 TTAGATGGAAGACGGCGGCG 62.623 60.000 31.06 31.06 0.00 6.46
456 459 4.508128 GATGGAAGACGGCGGCGA 62.508 66.667 38.93 15.22 0.00 5.54
457 460 4.814294 ATGGAAGACGGCGGCGAC 62.814 66.667 38.93 31.51 0.00 5.19
484 487 4.509737 GAGGGCCGCGGTGTAGAC 62.510 72.222 28.70 8.51 0.00 2.59
510 513 4.527157 CGTAGGTCGACGCGGGAC 62.527 72.222 20.22 20.22 42.86 4.46
536 539 3.554692 GGCGACGTTCAGATGCGG 61.555 66.667 0.00 0.00 0.00 5.69
537 540 2.809601 GCGACGTTCAGATGCGGT 60.810 61.111 0.00 0.00 0.00 5.68
538 541 3.071459 GCGACGTTCAGATGCGGTG 62.071 63.158 0.00 0.00 0.00 4.94
539 542 1.733041 CGACGTTCAGATGCGGTGT 60.733 57.895 0.00 0.00 0.00 4.16
540 543 1.674611 CGACGTTCAGATGCGGTGTC 61.675 60.000 0.00 0.00 0.00 3.67
541 544 1.674611 GACGTTCAGATGCGGTGTCG 61.675 60.000 0.00 0.00 39.81 4.35
543 546 1.080093 GTTCAGATGCGGTGTCGGA 60.080 57.895 0.00 0.00 41.81 4.55
550 553 4.404098 GCGGTGTCGGATGGGGTT 62.404 66.667 0.00 0.00 36.79 4.11
553 556 1.078426 GGTGTCGGATGGGGTTCAG 60.078 63.158 0.00 0.00 0.00 3.02
556 559 1.153628 GTCGGATGGGGTTCAGTCG 60.154 63.158 0.00 0.00 0.00 4.18
557 560 2.186903 CGGATGGGGTTCAGTCGG 59.813 66.667 0.00 0.00 0.00 4.79
558 561 2.124695 GGATGGGGTTCAGTCGGC 60.125 66.667 0.00 0.00 0.00 5.54
559 562 2.511600 GATGGGGTTCAGTCGGCG 60.512 66.667 0.00 0.00 0.00 6.46
560 563 4.096003 ATGGGGTTCAGTCGGCGG 62.096 66.667 7.21 0.00 0.00 6.13
564 567 4.814294 GGTTCAGTCGGCGGCGAT 62.814 66.667 36.75 22.01 0.00 4.58
566 569 4.847516 TTCAGTCGGCGGCGATCG 62.848 66.667 36.75 28.27 42.76 3.69
576 579 1.226575 CGGCGATCGCACAGTTAGA 60.227 57.895 38.00 0.00 44.11 2.10
577 580 0.800683 CGGCGATCGCACAGTTAGAA 60.801 55.000 38.00 0.00 44.11 2.10
578 581 1.355971 GGCGATCGCACAGTTAGAAA 58.644 50.000 38.00 0.00 44.11 2.52
579 582 1.060698 GGCGATCGCACAGTTAGAAAC 59.939 52.381 38.00 14.89 44.11 2.78
580 583 1.993370 GCGATCGCACAGTTAGAAACT 59.007 47.619 33.89 0.00 41.03 2.66
591 594 1.659098 GTTAGAAACTGGGCGTGATCG 59.341 52.381 0.00 0.00 40.37 3.69
593 596 0.389948 AGAAACTGGGCGTGATCGAC 60.390 55.000 0.00 0.00 45.48 4.20
602 605 2.078341 CGTGATCGACGTGCGTGAA 61.078 57.895 0.67 0.00 43.50 3.18
623 626 4.951963 CGGGCGGGCGAGAAGATC 62.952 72.222 0.00 0.00 0.00 2.75
634 637 2.710760 CGAGAAGATCGTGTAGCTGAC 58.289 52.381 0.00 0.00 46.62 3.51
635 638 2.353269 CGAGAAGATCGTGTAGCTGACT 59.647 50.000 0.00 0.00 46.62 3.41
637 640 4.673061 CGAGAAGATCGTGTAGCTGACTTT 60.673 45.833 0.00 0.00 46.62 2.66
638 641 5.140747 AGAAGATCGTGTAGCTGACTTTT 57.859 39.130 0.00 0.00 0.00 2.27
639 642 5.542779 AGAAGATCGTGTAGCTGACTTTTT 58.457 37.500 0.00 0.00 0.00 1.94
655 658 1.504359 TTTTTCCTCTACACGTGCGG 58.496 50.000 17.22 11.27 0.00 5.69
660 663 3.909258 CTCTACACGTGCGGCGGTT 62.909 63.158 17.22 0.00 46.52 4.44
661 664 3.039588 CTACACGTGCGGCGGTTT 61.040 61.111 17.22 0.00 46.52 3.27
663 666 2.108344 CTACACGTGCGGCGGTTTTT 62.108 55.000 17.22 0.00 46.52 1.94
692 695 4.062853 CGTCAAGGTATATAGACGTCGG 57.937 50.000 10.46 0.00 46.17 4.79
694 697 4.376819 CGTCAAGGTATATAGACGTCGGTC 60.377 50.000 10.46 0.00 46.17 4.79
706 709 3.059884 GACGTCGGTCTATACGGTATGA 58.940 50.000 10.86 3.98 43.25 2.15
707 710 3.668447 ACGTCGGTCTATACGGTATGAT 58.332 45.455 10.86 0.00 43.25 2.45
709 712 4.867047 ACGTCGGTCTATACGGTATGATAG 59.133 45.833 10.86 0.87 43.25 2.08
710 713 4.269603 CGTCGGTCTATACGGTATGATAGG 59.730 50.000 10.86 0.00 35.51 2.57
711 714 5.423015 GTCGGTCTATACGGTATGATAGGA 58.577 45.833 10.86 0.86 0.00 2.94
712 715 5.523188 GTCGGTCTATACGGTATGATAGGAG 59.477 48.000 10.86 0.00 0.00 3.69
713 716 4.815308 CGGTCTATACGGTATGATAGGAGG 59.185 50.000 10.86 0.00 0.00 4.30
714 717 5.628666 CGGTCTATACGGTATGATAGGAGGT 60.629 48.000 10.86 0.00 0.00 3.85
715 718 5.589452 GGTCTATACGGTATGATAGGAGGTG 59.411 48.000 10.86 0.00 0.00 4.00
716 719 5.589452 GTCTATACGGTATGATAGGAGGTGG 59.411 48.000 10.86 0.00 0.00 4.61
717 720 2.011122 ACGGTATGATAGGAGGTGGG 57.989 55.000 0.00 0.00 0.00 4.61
976 979 2.225791 CTCGTCCATTCCAGTCGGCA 62.226 60.000 0.00 0.00 0.00 5.69
985 988 1.021202 TCCAGTCGGCACAAACAAAG 58.979 50.000 0.00 0.00 0.00 2.77
987 990 0.738389 CAGTCGGCACAAACAAAGGT 59.262 50.000 0.00 0.00 0.00 3.50
1503 3033 1.002134 CACCCTGGAAAGCATCGGT 60.002 57.895 0.00 0.00 0.00 4.69
1672 3253 4.410400 CCGTGGAGGGGCAGGAAC 62.410 72.222 0.00 0.00 35.97 3.62
1861 3463 2.121963 AGCTCACCCCCAAGGACA 60.122 61.111 0.00 0.00 39.89 4.02
2262 3879 0.610687 ACAGGAAGCACTACTCAGGC 59.389 55.000 0.00 0.00 0.00 4.85
2263 3880 0.610174 CAGGAAGCACTACTCAGGCA 59.390 55.000 0.00 0.00 0.00 4.75
2264 3881 0.901124 AGGAAGCACTACTCAGGCAG 59.099 55.000 0.00 0.00 0.00 4.85
2265 3882 0.898320 GGAAGCACTACTCAGGCAGA 59.102 55.000 0.00 0.00 0.00 4.26
2924 4545 3.009143 AGCTTCTCGGGTGAAAACCTAAT 59.991 43.478 0.00 0.00 0.00 1.73
3702 5356 1.957186 GGCGGCTGTACAAACACGA 60.957 57.895 0.00 0.00 29.20 4.35
3961 5636 1.004440 GGATCGCCCCTACATGCTC 60.004 63.158 0.00 0.00 0.00 4.26
4038 5713 1.134699 GCGGTTGACAGATGATCCTGA 60.135 52.381 6.04 0.00 37.59 3.86
4132 5813 4.049817 AGGGCCTCCGAGAGACGT 62.050 66.667 0.00 0.00 40.78 4.34
4516 6206 6.524933 CGTACATGTTGTGTTTTGAAAGTGAA 59.475 34.615 2.30 0.00 42.29 3.18
4643 6333 5.049336 CGATCACAATGGAGTCGACTAGTAT 60.049 44.000 20.09 10.29 34.46 2.12
4799 6515 2.362397 GTGATTCCTCGCCATCTGTCTA 59.638 50.000 0.00 0.00 0.00 2.59
4800 6516 2.362397 TGATTCCTCGCCATCTGTCTAC 59.638 50.000 0.00 0.00 0.00 2.59
4848 6571 2.597455 CTTCTTCTGGGGAAAAGCCAA 58.403 47.619 0.00 0.00 38.95 4.52
4891 6651 4.301072 ACCTTAGCAAATAGGCTGTGAA 57.699 40.909 0.00 0.00 45.44 3.18
4954 6714 3.149196 AGCAGGTGAGGTTTGTATGTTG 58.851 45.455 0.00 0.00 0.00 3.33
5129 6918 3.322828 TCGGGTACTAGGCAAATATGACC 59.677 47.826 0.00 0.00 33.81 4.02
5200 6990 8.020819 TGACCTTTCTTGAGTATTTATTTTGCG 58.979 33.333 0.00 0.00 0.00 4.85
5357 7159 8.996651 TTGTTTTTCCTTCTCCTTTCTCTTAT 57.003 30.769 0.00 0.00 0.00 1.73
5360 7162 9.900710 GTTTTTCCTTCTCCTTTCTCTTATTTC 57.099 33.333 0.00 0.00 0.00 2.17
5381 7183 8.633075 ATTTCTTTCCGTGTGCATATTATTTG 57.367 30.769 0.00 0.00 0.00 2.32
5427 7229 7.814587 GCTTTGTTCTTGCCTACAATATTTTCT 59.185 33.333 0.00 0.00 34.52 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
182 185 9.783081 ATGCTAAATGATATGAGTCACACATAA 57.217 29.630 0.00 0.00 34.58 1.90
422 425 3.119459 TCCATCTAACTCTCGTCTTGCAC 60.119 47.826 0.00 0.00 0.00 4.57
423 426 3.089284 TCCATCTAACTCTCGTCTTGCA 58.911 45.455 0.00 0.00 0.00 4.08
424 427 3.784701 TCCATCTAACTCTCGTCTTGC 57.215 47.619 0.00 0.00 0.00 4.01
425 428 5.336744 GTCTTCCATCTAACTCTCGTCTTG 58.663 45.833 0.00 0.00 0.00 3.02
428 431 3.242804 CCGTCTTCCATCTAACTCTCGTC 60.243 52.174 0.00 0.00 0.00 4.20
430 433 2.541999 GCCGTCTTCCATCTAACTCTCG 60.542 54.545 0.00 0.00 0.00 4.04
432 435 1.405821 CGCCGTCTTCCATCTAACTCT 59.594 52.381 0.00 0.00 0.00 3.24
433 436 1.536284 CCGCCGTCTTCCATCTAACTC 60.536 57.143 0.00 0.00 0.00 3.01
435 438 1.152383 GCCGCCGTCTTCCATCTAAC 61.152 60.000 0.00 0.00 0.00 2.34
437 440 2.812499 GCCGCCGTCTTCCATCTA 59.188 61.111 0.00 0.00 0.00 1.98
439 442 4.508128 TCGCCGCCGTCTTCCATC 62.508 66.667 0.00 0.00 35.54 3.51
440 443 4.814294 GTCGCCGCCGTCTTCCAT 62.814 66.667 0.00 0.00 35.54 3.41
493 496 4.527157 GTCCCGCGTCGACCTACG 62.527 72.222 10.58 11.40 45.58 3.51
516 519 3.902063 CATCTGAACGTCGCCGCG 61.902 66.667 6.39 6.39 37.70 6.46
517 520 4.210304 GCATCTGAACGTCGCCGC 62.210 66.667 0.00 0.00 37.70 6.53
519 522 3.554692 CCGCATCTGAACGTCGCC 61.555 66.667 0.00 0.00 0.00 5.54
520 523 2.809601 ACCGCATCTGAACGTCGC 60.810 61.111 0.00 0.00 0.00 5.19
521 524 1.674611 GACACCGCATCTGAACGTCG 61.675 60.000 0.00 0.00 0.00 5.12
522 525 1.674611 CGACACCGCATCTGAACGTC 61.675 60.000 0.00 0.00 0.00 4.34
523 526 1.733041 CGACACCGCATCTGAACGT 60.733 57.895 3.33 0.00 0.00 3.99
524 527 2.444624 CCGACACCGCATCTGAACG 61.445 63.158 0.00 0.00 0.00 3.95
526 529 0.460109 CATCCGACACCGCATCTGAA 60.460 55.000 0.00 0.00 0.00 3.02
527 530 1.141665 CATCCGACACCGCATCTGA 59.858 57.895 0.00 0.00 0.00 3.27
529 532 2.501128 CCATCCGACACCGCATCT 59.499 61.111 0.00 0.00 0.00 2.90
530 533 2.588877 CCCATCCGACACCGCATC 60.589 66.667 0.00 0.00 0.00 3.91
531 534 4.175337 CCCCATCCGACACCGCAT 62.175 66.667 0.00 0.00 0.00 4.73
533 536 4.404098 AACCCCATCCGACACCGC 62.404 66.667 0.00 0.00 0.00 5.68
535 538 1.078426 CTGAACCCCATCCGACACC 60.078 63.158 0.00 0.00 0.00 4.16
536 539 0.391263 GACTGAACCCCATCCGACAC 60.391 60.000 0.00 0.00 0.00 3.67
537 540 1.884075 CGACTGAACCCCATCCGACA 61.884 60.000 0.00 0.00 0.00 4.35
538 541 1.153628 CGACTGAACCCCATCCGAC 60.154 63.158 0.00 0.00 0.00 4.79
539 542 2.355986 CCGACTGAACCCCATCCGA 61.356 63.158 0.00 0.00 0.00 4.55
540 543 2.186903 CCGACTGAACCCCATCCG 59.813 66.667 0.00 0.00 0.00 4.18
541 544 2.124695 GCCGACTGAACCCCATCC 60.125 66.667 0.00 0.00 0.00 3.51
543 546 4.096003 CCGCCGACTGAACCCCAT 62.096 66.667 0.00 0.00 0.00 4.00
558 561 0.800683 TTCTAACTGTGCGATCGCCG 60.801 55.000 35.12 24.80 41.09 6.46
559 562 1.060698 GTTTCTAACTGTGCGATCGCC 59.939 52.381 35.12 25.81 41.09 5.54
560 563 1.993370 AGTTTCTAACTGTGCGATCGC 59.007 47.619 32.48 32.48 41.01 4.58
569 572 6.919728 TCGATCACGCCCAGTTTCTAACTG 62.920 50.000 11.62 11.62 46.88 3.16
571 574 1.659098 CGATCACGCCCAGTTTCTAAC 59.341 52.381 0.00 0.00 0.00 2.34
572 575 1.546923 TCGATCACGCCCAGTTTCTAA 59.453 47.619 0.00 0.00 39.58 2.10
573 576 1.135199 GTCGATCACGCCCAGTTTCTA 60.135 52.381 0.00 0.00 39.58 2.10
576 579 1.736645 CGTCGATCACGCCCAGTTT 60.737 57.895 5.07 0.00 42.87 2.66
577 580 2.126071 CGTCGATCACGCCCAGTT 60.126 61.111 5.07 0.00 42.87 3.16
586 589 2.078341 CGTTCACGCACGTCGATCA 61.078 57.895 13.06 0.00 41.67 2.92
606 609 4.951963 GATCTTCTCGCCCGCCCG 62.952 72.222 0.00 0.00 0.00 6.13
607 610 4.951963 CGATCTTCTCGCCCGCCC 62.952 72.222 0.00 0.00 41.14 6.13
616 619 4.792521 AAAGTCAGCTACACGATCTTCT 57.207 40.909 0.00 0.00 0.00 2.85
617 620 5.847670 AAAAAGTCAGCTACACGATCTTC 57.152 39.130 0.00 0.00 0.00 2.87
637 640 0.947180 GCCGCACGTGTAGAGGAAAA 60.947 55.000 18.38 0.00 0.00 2.29
638 641 1.373748 GCCGCACGTGTAGAGGAAA 60.374 57.895 18.38 0.00 0.00 3.13
639 642 2.260434 GCCGCACGTGTAGAGGAA 59.740 61.111 18.38 0.00 0.00 3.36
642 645 3.909258 AACCGCCGCACGTGTAGAG 62.909 63.158 18.38 10.32 41.42 2.43
644 647 2.108344 AAAAACCGCCGCACGTGTAG 62.108 55.000 18.38 11.60 41.42 2.74
646 649 3.510675 AAAAACCGCCGCACGTGT 61.511 55.556 18.38 0.00 41.42 4.49
672 675 5.028428 GACCGACGTCTATATACCTTGAC 57.972 47.826 14.70 0.00 35.99 3.18
685 688 3.059884 TCATACCGTATAGACCGACGTC 58.940 50.000 5.18 5.18 37.36 4.34
686 689 3.111853 TCATACCGTATAGACCGACGT 57.888 47.619 0.00 0.00 37.36 4.34
687 690 4.269603 CCTATCATACCGTATAGACCGACG 59.730 50.000 0.00 0.00 38.79 5.12
688 691 5.423015 TCCTATCATACCGTATAGACCGAC 58.577 45.833 0.00 0.00 0.00 4.79
689 692 5.396101 CCTCCTATCATACCGTATAGACCGA 60.396 48.000 0.00 0.00 0.00 4.69
690 693 4.815308 CCTCCTATCATACCGTATAGACCG 59.185 50.000 0.00 0.00 0.00 4.79
691 694 5.589452 CACCTCCTATCATACCGTATAGACC 59.411 48.000 0.00 0.00 0.00 3.85
692 695 5.589452 CCACCTCCTATCATACCGTATAGAC 59.411 48.000 0.00 0.00 0.00 2.59
694 697 4.888239 CCCACCTCCTATCATACCGTATAG 59.112 50.000 0.00 0.00 0.00 1.31
695 698 4.863548 CCCACCTCCTATCATACCGTATA 58.136 47.826 0.00 0.00 0.00 1.47
696 699 3.709587 CCCACCTCCTATCATACCGTAT 58.290 50.000 0.00 0.00 0.00 3.06
698 701 2.011122 CCCACCTCCTATCATACCGT 57.989 55.000 0.00 0.00 0.00 4.83
976 979 5.105146 TGTTAATTGCTCCACCTTTGTTTGT 60.105 36.000 0.00 0.00 0.00 2.83
985 988 2.102578 AGCCATGTTAATTGCTCCACC 58.897 47.619 0.00 0.00 28.88 4.61
987 990 2.101783 CCAGCCATGTTAATTGCTCCA 58.898 47.619 0.00 0.00 32.63 3.86
1364 2885 1.061131 CGATGTTCTTGTGGATGACGC 59.939 52.381 0.00 0.00 0.00 5.19
1672 3253 2.679837 GCATCATCTTGGTGGTGTACTG 59.320 50.000 0.00 0.00 32.75 2.74
1780 3373 1.004440 GGACCAGATATCCGGCAGC 60.004 63.158 4.79 0.00 0.00 5.25
1788 3381 1.948145 GAGACGACACGGACCAGATAT 59.052 52.381 0.00 0.00 0.00 1.63
2176 3793 4.462394 GCTGGTGAGCAGTGTGAA 57.538 55.556 13.65 0.00 45.46 3.18
2262 3879 2.779033 GGTACGCGGGGGTACTCTG 61.779 68.421 20.70 0.00 41.91 3.35
2263 3880 2.440980 GGTACGCGGGGGTACTCT 60.441 66.667 20.70 0.00 41.91 3.24
2264 3881 3.531207 GGGTACGCGGGGGTACTC 61.531 72.222 20.70 15.72 41.91 2.59
2889 4510 0.178873 AGAAGCTAGGTGGTGGGGAA 60.179 55.000 0.00 0.00 0.00 3.97
3702 5356 2.286523 CCCAGGGAGTTGAGCGTCT 61.287 63.158 0.00 0.00 0.00 4.18
3795 5458 2.172483 CTCCTGGAACTCCACACCCG 62.172 65.000 0.00 0.00 42.01 5.28
3961 5636 2.122636 TTTTGGGGTTGGCCTGGG 60.123 61.111 3.32 0.00 34.45 4.45
4059 5734 5.694006 CGGAACAGATTCTTGATCATACCTC 59.306 44.000 0.00 0.00 37.22 3.85
4132 5813 0.969149 ACAGTCTGTTGGCGAGATCA 59.031 50.000 0.00 0.00 0.00 2.92
4516 6206 5.815581 ACATATATTTACATGTGGCCGGAT 58.184 37.500 5.05 0.00 34.15 4.18
4674 6390 6.582636 TGATTTGGTAGCCTGACAATACTAG 58.417 40.000 0.00 0.00 0.00 2.57
4760 6476 0.662619 ACGCATGTGTCAACAGTTGG 59.337 50.000 13.52 0.00 40.39 3.77
4764 6480 2.413239 GGAATCACGCATGTGTCAACAG 60.413 50.000 9.44 0.00 46.49 3.16
4818 6536 3.200825 TCCCCAGAAGAAGCCATAAAGAG 59.799 47.826 0.00 0.00 0.00 2.85
4858 6581 9.950496 CCTATTTGCTAAGGTATTCATAGTCAT 57.050 33.333 0.00 0.00 0.00 3.06
4877 6637 5.893687 TGCATGTATTTCACAGCCTATTTG 58.106 37.500 0.00 0.00 41.51 2.32
4891 6651 4.156556 AGTGTTGCTCGATTTGCATGTATT 59.843 37.500 0.00 0.00 40.34 1.89
4975 6735 1.178276 GCTCTCCTCCTCAACTCGAA 58.822 55.000 0.00 0.00 0.00 3.71
4976 6736 0.329931 AGCTCTCCTCCTCAACTCGA 59.670 55.000 0.00 0.00 0.00 4.04
4977 6737 1.134175 GAAGCTCTCCTCCTCAACTCG 59.866 57.143 0.00 0.00 0.00 4.18
4978 6738 1.480545 GGAAGCTCTCCTCCTCAACTC 59.519 57.143 7.46 0.00 41.61 3.01
5200 6990 3.186909 GGTGAAGAACAGTTTGCCAAAC 58.813 45.455 12.37 12.37 41.69 2.93
5357 7159 7.821652 TCAAATAATATGCACACGGAAAGAAA 58.178 30.769 0.00 0.00 0.00 2.52
5360 7162 8.633075 AAATCAAATAATATGCACACGGAAAG 57.367 30.769 0.00 0.00 0.00 2.62
5381 7183 9.002600 ACAAAGCATAAAGGGAAAAATGAAATC 57.997 29.630 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.