Multiple sequence alignment - TraesCS7B01G356200

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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 TraesCS7B01G356200 chr7B 100.000 4415 0 0 1 4415 616824262 616819848 0.000000 8154.0
1 TraesCS7B01G356200 chr7B 83.442 2597 337 53 875 3416 616750035 616747477 0.000000 2327.0
2 TraesCS7B01G356200 chr7B 83.282 2578 352 42 879 3403 617485715 617488266 0.000000 2300.0
3 TraesCS7B01G356200 chr7B 83.382 2413 336 31 1058 3420 616903139 616905536 0.000000 2174.0
4 TraesCS7B01G356200 chr7B 82.645 2495 352 44 975 3406 617557978 617555502 0.000000 2134.0
5 TraesCS7B01G356200 chr7B 81.822 2536 376 45 966 3442 616836209 616838718 0.000000 2050.0
6 TraesCS7B01G356200 chr7B 80.918 1960 307 40 1510 3416 617578224 617580169 0.000000 1485.0
7 TraesCS7B01G356200 chr7B 95.939 788 29 2 3626 4412 480853017 480853802 0.000000 1275.0
8 TraesCS7B01G356200 chr7B 86.331 695 70 17 816 1499 617571403 617572083 0.000000 734.0
9 TraesCS7B01G356200 chr7B 100.000 30 0 0 3601 3630 616820902 616820931 0.000617 56.5
10 TraesCS7B01G356200 chr7D 83.073 2623 361 50 879 3445 565643528 565646123 0.000000 2307.0
11 TraesCS7B01G356200 chr7D 83.293 2496 337 38 972 3406 566013939 566016415 0.000000 2226.0
12 TraesCS7B01G356200 chr7D 82.590 2510 347 53 966 3416 566037423 566039901 0.000000 2132.0
13 TraesCS7B01G356200 chr7D 87.785 1318 102 22 11 1319 565616364 565615097 0.000000 1487.0
14 TraesCS7B01G356200 chr7D 90.208 1154 88 14 1455 2608 565615038 565613910 0.000000 1482.0
15 TraesCS7B01G356200 chr7D 92.506 814 47 9 2786 3586 565613910 565613098 0.000000 1153.0
16 TraesCS7B01G356200 chr7D 100.000 28 0 0 3601 3628 565613336 565613363 0.008000 52.8
17 TraesCS7B01G356200 chr7A 82.419 2497 353 43 972 3404 652286408 652288882 0.000000 2100.0
18 TraesCS7B01G356200 chr7A 81.501 2665 381 50 815 3414 652356730 652359347 0.000000 2087.0
19 TraesCS7B01G356200 chr7A 81.079 2632 395 54 855 3416 652337825 652340423 0.000000 2006.0
20 TraesCS7B01G356200 chr7A 81.866 2465 358 45 1001 3420 652195194 652197614 0.000000 1993.0
21 TraesCS7B01G356200 chr7A 81.275 2024 321 26 1429 3405 652163852 652165864 0.000000 1585.0
22 TraesCS7B01G356200 chr7A 80.098 1432 216 35 1457 2835 652232233 652233648 0.000000 1002.0
23 TraesCS7B01G356200 chr3A 96.320 788 26 2 3626 4412 614687058 614687843 0.000000 1291.0
24 TraesCS7B01G356200 chrUn 96.310 786 25 3 3631 4415 272193805 272193023 0.000000 1288.0
25 TraesCS7B01G356200 chrUn 96.310 786 25 3 3631 4415 281138965 281138183 0.000000 1288.0
26 TraesCS7B01G356200 chr4B 95.558 788 32 2 3626 4412 673240241 673241026 0.000000 1258.0
27 TraesCS7B01G356200 chr5B 95.785 783 26 4 3631 4412 440537605 440538381 0.000000 1256.0
28 TraesCS7B01G356200 chr5B 94.784 786 38 2 3628 4412 326999332 327000115 0.000000 1221.0
29 TraesCS7B01G356200 chr1B 95.426 787 25 5 3626 4411 645299266 645300042 0.000000 1243.0
30 TraesCS7B01G356200 chr6B 78.921 1798 279 52 1400 3114 216354942 216356722 0.000000 1129.0


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 TraesCS7B01G356200 chr7B 616819848 616824262 4414 True 8154 8154 100.000000 1 4415 1 chr7B.!!$R2 4414
1 TraesCS7B01G356200 chr7B 616747477 616750035 2558 True 2327 2327 83.442000 875 3416 1 chr7B.!!$R1 2541
2 TraesCS7B01G356200 chr7B 617485715 617488266 2551 False 2300 2300 83.282000 879 3403 1 chr7B.!!$F5 2524
3 TraesCS7B01G356200 chr7B 616903139 616905536 2397 False 2174 2174 83.382000 1058 3420 1 chr7B.!!$F4 2362
4 TraesCS7B01G356200 chr7B 617555502 617557978 2476 True 2134 2134 82.645000 975 3406 1 chr7B.!!$R3 2431
5 TraesCS7B01G356200 chr7B 616836209 616838718 2509 False 2050 2050 81.822000 966 3442 1 chr7B.!!$F3 2476
6 TraesCS7B01G356200 chr7B 617578224 617580169 1945 False 1485 1485 80.918000 1510 3416 1 chr7B.!!$F7 1906
7 TraesCS7B01G356200 chr7B 480853017 480853802 785 False 1275 1275 95.939000 3626 4412 1 chr7B.!!$F1 786
8 TraesCS7B01G356200 chr7B 617571403 617572083 680 False 734 734 86.331000 816 1499 1 chr7B.!!$F6 683
9 TraesCS7B01G356200 chr7D 565643528 565646123 2595 False 2307 2307 83.073000 879 3445 1 chr7D.!!$F2 2566
10 TraesCS7B01G356200 chr7D 566013939 566016415 2476 False 2226 2226 83.293000 972 3406 1 chr7D.!!$F3 2434
11 TraesCS7B01G356200 chr7D 566037423 566039901 2478 False 2132 2132 82.590000 966 3416 1 chr7D.!!$F4 2450
12 TraesCS7B01G356200 chr7D 565613098 565616364 3266 True 1374 1487 90.166333 11 3586 3 chr7D.!!$R1 3575
13 TraesCS7B01G356200 chr7A 652286408 652288882 2474 False 2100 2100 82.419000 972 3404 1 chr7A.!!$F4 2432
14 TraesCS7B01G356200 chr7A 652356730 652359347 2617 False 2087 2087 81.501000 815 3414 1 chr7A.!!$F6 2599
15 TraesCS7B01G356200 chr7A 652337825 652340423 2598 False 2006 2006 81.079000 855 3416 1 chr7A.!!$F5 2561
16 TraesCS7B01G356200 chr7A 652195194 652197614 2420 False 1993 1993 81.866000 1001 3420 1 chr7A.!!$F2 2419
17 TraesCS7B01G356200 chr7A 652163852 652165864 2012 False 1585 1585 81.275000 1429 3405 1 chr7A.!!$F1 1976
18 TraesCS7B01G356200 chr7A 652232233 652233648 1415 False 1002 1002 80.098000 1457 2835 1 chr7A.!!$F3 1378
19 TraesCS7B01G356200 chr3A 614687058 614687843 785 False 1291 1291 96.320000 3626 4412 1 chr3A.!!$F1 786
20 TraesCS7B01G356200 chrUn 272193023 272193805 782 True 1288 1288 96.310000 3631 4415 1 chrUn.!!$R1 784
21 TraesCS7B01G356200 chrUn 281138183 281138965 782 True 1288 1288 96.310000 3631 4415 1 chrUn.!!$R2 784
22 TraesCS7B01G356200 chr4B 673240241 673241026 785 False 1258 1258 95.558000 3626 4412 1 chr4B.!!$F1 786
23 TraesCS7B01G356200 chr5B 440537605 440538381 776 False 1256 1256 95.785000 3631 4412 1 chr5B.!!$F2 781
24 TraesCS7B01G356200 chr5B 326999332 327000115 783 False 1221 1221 94.784000 3628 4412 1 chr5B.!!$F1 784
25 TraesCS7B01G356200 chr1B 645299266 645300042 776 False 1243 1243 95.426000 3626 4411 1 chr1B.!!$F1 785
26 TraesCS7B01G356200 chr6B 216354942 216356722 1780 False 1129 1129 78.921000 1400 3114 1 chr6B.!!$F1 1714

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
765 774 0.108615 CGTCACCATGGTGGAGTCTC 60.109 60.0 38.12 21.70 45.43 3.36 F
771 780 0.253894 CATGGTGGAGTCTCATGCCA 59.746 55.0 1.47 6.92 33.06 4.92 F
1878 1952 0.819259 GCTGGCAACTGTTCTGGACA 60.819 55.0 0.00 0.00 37.92 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 1903 0.320247 AGAACAGTTGCCAGCTCTCG 60.320 55.0 0.00 0.0 0.00 4.04 R
2157 2252 0.395686 AGCAGCTCTTCTGACAAGCA 59.604 50.0 11.68 0.0 45.72 3.91 R
3762 3993 0.107508 CCGTTGTCATGATCCTGGCT 60.108 55.0 0.00 0.0 0.00 4.75 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
27 28 8.846943 TCAGCATGTTTTATTCACTCTTCTTA 57.153 30.769 0.00 0.00 37.40 2.10
55 56 6.314784 GTCTTATGGATGGACTTTTGAAACG 58.685 40.000 0.00 0.00 0.00 3.60
93 94 7.268586 ACGATAGCAGTCTATTTCAATGACTT 58.731 34.615 0.00 0.00 37.41 3.01
94 95 7.223582 ACGATAGCAGTCTATTTCAATGACTTG 59.776 37.037 0.00 0.00 37.41 3.16
113 114 4.767255 GGTCAGCTGAGCCACCCG 62.767 72.222 31.17 0.00 36.62 5.28
193 195 5.808366 ATAAGAGAGACCATTCGCCATAA 57.192 39.130 0.00 0.00 0.00 1.90
194 196 4.487714 AAGAGAGACCATTCGCCATAAA 57.512 40.909 0.00 0.00 0.00 1.40
227 229 3.644884 TCACGTCTTCCTTCTTGTCTC 57.355 47.619 0.00 0.00 0.00 3.36
258 260 4.359706 CTTTTCACACCCTGCTTACAAAC 58.640 43.478 0.00 0.00 0.00 2.93
259 261 3.290948 TTCACACCCTGCTTACAAACT 57.709 42.857 0.00 0.00 0.00 2.66
269 271 5.768164 CCCTGCTTACAAACTTTTCCTTCTA 59.232 40.000 0.00 0.00 0.00 2.10
327 329 5.276461 TCTCGAGCTTAAATGCATCCTTA 57.724 39.130 7.81 0.00 34.99 2.69
384 388 8.672214 AAAACATTTCAAATTGTTTCTGCAAC 57.328 26.923 13.22 0.00 43.33 4.17
414 418 6.307031 TGTTCAACGTTTTACATATGTGCT 57.693 33.333 18.81 0.00 0.00 4.40
456 460 3.795688 TTCCCAAGTCTCTGAGCAAAT 57.204 42.857 0.00 0.00 0.00 2.32
461 465 5.473504 TCCCAAGTCTCTGAGCAAATAAAAC 59.526 40.000 0.00 0.00 0.00 2.43
465 469 7.706179 CCAAGTCTCTGAGCAAATAAAACAAAA 59.294 33.333 0.00 0.00 0.00 2.44
466 470 9.252962 CAAGTCTCTGAGCAAATAAAACAAAAT 57.747 29.630 0.00 0.00 0.00 1.82
467 471 9.468532 AAGTCTCTGAGCAAATAAAACAAAATC 57.531 29.630 0.00 0.00 0.00 2.17
468 472 8.632679 AGTCTCTGAGCAAATAAAACAAAATCA 58.367 29.630 0.00 0.00 0.00 2.57
509 513 7.588497 ATTTTGAAAAGTACTTTGGAGAGCT 57.412 32.000 21.22 3.90 32.36 4.09
532 536 7.820872 AGCTGATTTTGATATTTTCACCCAAAG 59.179 33.333 0.00 0.00 32.84 2.77
549 553 4.430007 CCAAAGCTCCATGAAATGTGATG 58.570 43.478 0.00 0.00 44.81 3.07
567 571 4.484236 TGATGTCATCACGGAAATTTTGC 58.516 39.130 11.62 0.00 33.59 3.68
568 572 3.998099 TGTCATCACGGAAATTTTGCA 57.002 38.095 1.50 0.00 0.00 4.08
569 573 4.517952 TGTCATCACGGAAATTTTGCAT 57.482 36.364 1.50 0.00 0.00 3.96
570 574 4.236147 TGTCATCACGGAAATTTTGCATG 58.764 39.130 1.50 0.00 0.00 4.06
571 575 3.061161 GTCATCACGGAAATTTTGCATGC 59.939 43.478 11.82 11.82 0.00 4.06
572 576 2.808523 TCACGGAAATTTTGCATGCA 57.191 40.000 18.46 18.46 0.00 3.96
573 577 2.674954 TCACGGAAATTTTGCATGCAG 58.325 42.857 21.50 9.11 0.00 4.41
574 578 2.035704 TCACGGAAATTTTGCATGCAGT 59.964 40.909 21.50 9.81 0.00 4.40
575 579 2.801679 CACGGAAATTTTGCATGCAGTT 59.198 40.909 21.50 14.05 0.00 3.16
576 580 3.248125 CACGGAAATTTTGCATGCAGTTT 59.752 39.130 21.50 20.95 0.00 2.66
584 588 5.633996 TTTTGCATGCAGTTTACGAAAAG 57.366 34.783 21.50 0.00 0.00 2.27
586 590 3.626977 TGCATGCAGTTTACGAAAAGTG 58.373 40.909 18.46 2.09 45.21 3.16
589 593 3.602390 TGCAGTTTACGAAAAGTGAGC 57.398 42.857 9.32 0.00 45.24 4.26
591 595 3.002246 TGCAGTTTACGAAAAGTGAGCAG 59.998 43.478 9.32 0.00 45.24 4.24
602 606 4.519540 AAAGTGAGCAGTGTTTGTTGTT 57.480 36.364 0.00 0.00 0.00 2.83
607 611 6.451393 AGTGAGCAGTGTTTGTTGTTAAAAA 58.549 32.000 0.00 0.00 0.00 1.94
658 666 4.873746 TTTATTGTTGGGGCGAATTCAA 57.126 36.364 6.22 0.00 0.00 2.69
666 675 2.896685 TGGGGCGAATTCAATTTCACTT 59.103 40.909 6.22 0.00 0.00 3.16
673 682 7.117667 GGGCGAATTCAATTTCACTTTTTATGT 59.882 33.333 6.22 0.00 0.00 2.29
681 690 6.610075 ATTTCACTTTTTATGTGGGAGCAT 57.390 33.333 0.00 0.00 36.21 3.79
711 720 6.325919 TCAAGATTAGAACGCCATTTTTGT 57.674 33.333 0.00 0.00 0.00 2.83
718 727 0.525761 ACGCCATTTTTGTCCATCGG 59.474 50.000 0.00 0.00 0.00 4.18
734 743 4.080356 TCCATCGGTGATTCCAGATTTTCT 60.080 41.667 0.00 0.00 35.57 2.52
759 768 1.804151 CTTTGTACGTCACCATGGTGG 59.196 52.381 38.12 27.33 45.43 4.61
760 769 1.049402 TTGTACGTCACCATGGTGGA 58.951 50.000 38.12 24.53 45.43 4.02
761 770 0.606096 TGTACGTCACCATGGTGGAG 59.394 55.000 38.12 32.19 45.43 3.86
762 771 0.606604 GTACGTCACCATGGTGGAGT 59.393 55.000 38.12 35.02 45.43 3.85
763 772 0.892755 TACGTCACCATGGTGGAGTC 59.107 55.000 38.12 25.15 45.43 3.36
764 773 0.832135 ACGTCACCATGGTGGAGTCT 60.832 55.000 38.12 18.05 45.43 3.24
765 774 0.108615 CGTCACCATGGTGGAGTCTC 60.109 60.000 38.12 21.70 45.43 3.36
766 775 0.976641 GTCACCATGGTGGAGTCTCA 59.023 55.000 38.12 19.06 45.43 3.27
767 776 1.556911 GTCACCATGGTGGAGTCTCAT 59.443 52.381 38.12 1.34 45.43 2.90
768 777 1.556451 TCACCATGGTGGAGTCTCATG 59.444 52.381 38.12 14.35 45.43 3.07
769 778 0.254178 ACCATGGTGGAGTCTCATGC 59.746 55.000 18.99 0.00 40.96 4.06
770 779 0.465097 CCATGGTGGAGTCTCATGCC 60.465 60.000 2.57 1.23 40.96 4.40
771 780 0.253894 CATGGTGGAGTCTCATGCCA 59.746 55.000 1.47 6.92 33.06 4.92
773 782 4.192000 GTGGAGTCTCATGCCACG 57.808 61.111 1.47 0.00 42.20 4.94
933 949 2.671070 CCACCTCCGCCATTCACT 59.329 61.111 0.00 0.00 0.00 3.41
1202 1239 2.445905 TCTACCTCGGGATCTGGTACAT 59.554 50.000 0.00 0.00 38.20 2.29
1258 1295 3.311110 GCGTGACTCCCCTGTCCA 61.311 66.667 0.00 0.00 36.21 4.02
1311 1348 2.811317 GACGGCAACCTCGAGCTG 60.811 66.667 6.99 7.65 42.73 4.24
1319 1356 1.122019 AACCTCGAGCTGGTTGGTCT 61.122 55.000 6.99 5.25 45.10 3.85
1446 1486 1.111116 ACCTTGTCCTTGTCGACGGA 61.111 55.000 11.62 9.63 35.40 4.69
1452 1492 1.079127 CCTTGTCGACGGAGGCAAT 60.079 57.895 20.61 0.00 35.00 3.56
1518 1558 4.457496 ATGTCGGGAGCGTGGCTG 62.457 66.667 0.00 0.00 39.88 4.85
1548 1588 2.967397 CTCACCGGCGAGTACCAA 59.033 61.111 9.30 0.00 0.00 3.67
1662 1702 1.106285 GGAACCGGTCCAGTACGTAT 58.894 55.000 8.04 0.00 46.97 3.06
1664 1704 2.687935 GGAACCGGTCCAGTACGTATTA 59.312 50.000 8.04 0.00 46.97 0.98
1747 1796 2.033372 TCCTGTTCAACCAGACGTACA 58.967 47.619 0.00 0.00 34.23 2.90
1854 1903 1.511768 GAGGCAGTACGTCTGGGTC 59.488 63.158 14.19 0.00 43.78 4.46
1855 1904 2.181021 GGCAGTACGTCTGGGTCG 59.819 66.667 14.19 0.00 43.78 4.79
1878 1952 0.819259 GCTGGCAACTGTTCTGGACA 60.819 55.000 0.00 0.00 37.92 4.02
1917 1991 2.049433 GTGTACGCGCTCTGTGGT 60.049 61.111 5.73 0.00 0.00 4.16
2000 2074 3.379445 GTCGGAGGCGGACTGGAA 61.379 66.667 0.00 0.00 32.23 3.53
2157 2252 1.415659 AGCAAAGCAGAGTGTGAGTCT 59.584 47.619 0.00 0.00 0.00 3.24
2166 2261 2.035704 AGAGTGTGAGTCTGCTTGTCAG 59.964 50.000 0.00 0.00 44.21 3.51
2217 2319 3.943691 AACGGGGGTTGCGCTGTA 61.944 61.111 9.73 0.00 0.00 2.74
2571 2724 2.126189 GTGTACCGCGGTGTCCTC 60.126 66.667 40.02 22.64 0.00 3.71
2609 2783 1.949525 TGCAGTGAAGAAGCTGGAAAC 59.050 47.619 0.00 0.00 33.62 2.78
2643 2827 2.840974 CGACAAGCAATTCCGGACT 58.159 52.632 1.83 0.00 0.00 3.85
2721 2905 2.729455 TCGTTGGGCGACGAGAAA 59.271 55.556 10.13 0.00 46.09 2.52
3449 3678 3.339695 CGCGCGAATTTTCTTACTAACC 58.660 45.455 28.94 0.00 0.00 2.85
3483 3712 8.078060 TCAGAACATGACAAGTATAGGAATGA 57.922 34.615 0.00 0.00 31.12 2.57
3496 3725 8.172352 AGTATAGGAATGAGTGTACACATCTC 57.828 38.462 27.06 16.38 0.00 2.75
3513 3742 1.156736 CTCGAAGTGCCGACCAAAAT 58.843 50.000 0.00 0.00 34.56 1.82
3586 3817 7.173218 TGTTTTCTCCTATTCACAATGACTGTC 59.827 37.037 0.00 0.00 35.47 3.51
3587 3818 4.998788 TCTCCTATTCACAATGACTGTCG 58.001 43.478 2.98 0.00 35.47 4.35
3588 3819 4.462834 TCTCCTATTCACAATGACTGTCGT 59.537 41.667 2.98 0.00 35.47 4.34
3589 3820 5.650703 TCTCCTATTCACAATGACTGTCGTA 59.349 40.000 2.42 0.00 35.47 3.43
3590 3821 6.152154 TCTCCTATTCACAATGACTGTCGTAA 59.848 38.462 2.42 0.00 35.47 3.18
3591 3822 6.097356 TCCTATTCACAATGACTGTCGTAAC 58.903 40.000 2.42 0.00 35.47 2.50
3592 3823 5.867174 CCTATTCACAATGACTGTCGTAACA 59.133 40.000 2.42 0.00 35.47 2.41
3593 3824 6.367695 CCTATTCACAATGACTGTCGTAACAA 59.632 38.462 2.42 0.00 35.47 2.83
3594 3825 5.398176 TTCACAATGACTGTCGTAACAAC 57.602 39.130 2.42 0.00 35.47 3.32
3595 3826 4.434520 TCACAATGACTGTCGTAACAACA 58.565 39.130 2.42 0.00 35.47 3.33
3596 3827 4.870991 TCACAATGACTGTCGTAACAACAA 59.129 37.500 2.42 0.00 35.47 2.83
3597 3828 5.525745 TCACAATGACTGTCGTAACAACAAT 59.474 36.000 2.42 0.00 35.47 2.71
3598 3829 6.702282 TCACAATGACTGTCGTAACAACAATA 59.298 34.615 2.42 0.00 35.47 1.90
3599 3830 7.386573 TCACAATGACTGTCGTAACAACAATAT 59.613 33.333 2.42 0.00 35.47 1.28
3600 3831 7.688167 CACAATGACTGTCGTAACAACAATATC 59.312 37.037 2.42 0.00 35.47 1.63
3601 3832 7.602644 ACAATGACTGTCGTAACAACAATATCT 59.397 33.333 2.42 0.00 34.24 1.98
3602 3833 6.944557 TGACTGTCGTAACAACAATATCTG 57.055 37.500 2.98 0.00 34.24 2.90
3603 3834 5.867174 TGACTGTCGTAACAACAATATCTGG 59.133 40.000 2.98 0.00 34.24 3.86
3604 3835 6.032956 ACTGTCGTAACAACAATATCTGGA 57.967 37.500 0.00 0.00 34.24 3.86
3605 3836 5.867716 ACTGTCGTAACAACAATATCTGGAC 59.132 40.000 0.00 0.00 34.24 4.02
3606 3837 4.860352 TGTCGTAACAACAATATCTGGACG 59.140 41.667 0.00 0.00 30.70 4.79
3607 3838 4.266976 GTCGTAACAACAATATCTGGACGG 59.733 45.833 0.00 0.00 31.04 4.79
3608 3839 3.000925 CGTAACAACAATATCTGGACGGC 59.999 47.826 0.00 0.00 0.00 5.68
3609 3840 1.651987 ACAACAATATCTGGACGGCG 58.348 50.000 4.80 4.80 0.00 6.46
3610 3841 0.304705 CAACAATATCTGGACGGCGC 59.695 55.000 6.90 0.00 0.00 6.53
3611 3842 0.814010 AACAATATCTGGACGGCGCC 60.814 55.000 19.07 19.07 0.00 6.53
3612 3843 1.961277 CAATATCTGGACGGCGCCC 60.961 63.158 23.46 4.87 0.00 6.13
3613 3844 2.140792 AATATCTGGACGGCGCCCT 61.141 57.895 23.46 9.94 0.00 5.19
3614 3845 2.100879 AATATCTGGACGGCGCCCTC 62.101 60.000 23.46 19.40 0.00 4.30
3742 3973 2.982130 GTGGGCATCTCTGGTCGT 59.018 61.111 0.00 0.00 0.00 4.34
3762 3993 1.304381 GCAGATGGCCAGGGTTCAA 60.304 57.895 13.05 0.00 36.11 2.69
3765 3996 2.037847 ATGGCCAGGGTTCAAGCC 59.962 61.111 13.05 0.00 45.96 4.35
3772 4003 0.329261 CAGGGTTCAAGCCAGGATCA 59.671 55.000 8.71 0.00 38.48 2.92
3846 4078 1.550524 AGTTGTCGAAGGCTCATGCTA 59.449 47.619 0.00 0.00 39.59 3.49
3998 4230 3.236003 AAGTCTTCCACGTCCCCGC 62.236 63.158 0.00 0.00 37.70 6.13
4057 4289 2.203596 AGGAGAACCCGTGGTCGT 60.204 61.111 0.00 0.00 40.87 4.34
4135 4367 1.347817 GCCTCACTTGTCTTCGCTCG 61.348 60.000 0.00 0.00 0.00 5.03
4275 4507 3.860605 TGCTCCCGCAGTGTGTGT 61.861 61.111 2.46 0.00 42.25 3.72
4316 4548 4.589216 CAAGGATTGTTGAAGCTCCAAA 57.411 40.909 0.00 0.00 42.34 3.28
4325 4557 3.478857 TGAAGCTCCAAACGAAGGTTA 57.521 42.857 0.00 0.00 34.62 2.85
4351 4583 1.216977 CGGGGTGTTGCGACATCTA 59.783 57.895 16.95 0.00 37.08 1.98
4412 4644 0.749818 TTGGTTGAGTTTGCGCTCCA 60.750 50.000 9.73 1.73 34.74 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.661954 TCCATAAGACCTATAAGAAGAGTGAAT 57.338 33.333 0.00 0.00 0.00 2.57
15 16 9.661954 ATCCATAAGACCTATAAGAAGAGTGAA 57.338 33.333 0.00 0.00 0.00 3.18
16 17 9.083422 CATCCATAAGACCTATAAGAAGAGTGA 57.917 37.037 0.00 0.00 0.00 3.41
17 18 8.310382 CCATCCATAAGACCTATAAGAAGAGTG 58.690 40.741 0.00 0.00 0.00 3.51
18 19 8.235230 TCCATCCATAAGACCTATAAGAAGAGT 58.765 37.037 0.00 0.00 0.00 3.24
24 25 9.277783 CAAAAGTCCATCCATAAGACCTATAAG 57.722 37.037 0.00 0.00 0.00 1.73
27 28 7.451731 TCAAAAGTCCATCCATAAGACCTAT 57.548 36.000 0.00 0.00 0.00 2.57
55 56 3.474600 TGCTATCGTCTAGTGGGTAGTC 58.525 50.000 0.00 0.00 0.00 2.59
93 94 4.687215 GTGGCTCAGCTGACCGCA 62.687 66.667 28.79 15.77 42.61 5.69
109 110 3.709653 TCAAATACTGAATAGAGGCGGGT 59.290 43.478 0.00 0.00 0.00 5.28
111 112 4.693283 TGTCAAATACTGAATAGAGGCGG 58.307 43.478 0.00 0.00 35.22 6.13
113 114 6.543831 ACCAATGTCAAATACTGAATAGAGGC 59.456 38.462 0.00 0.00 35.22 4.70
172 174 5.607939 TTTATGGCGAATGGTCTCTCTTA 57.392 39.130 0.00 0.00 0.00 2.10
194 196 6.346896 AGGAAGACGTGAAAGAGTAGTTTTT 58.653 36.000 0.00 0.00 0.00 1.94
206 208 3.383505 TGAGACAAGAAGGAAGACGTGAA 59.616 43.478 0.00 0.00 0.00 3.18
227 229 1.202405 GGGTGTGAAAAGGTTGCACTG 60.202 52.381 0.99 0.00 33.83 3.66
269 271 9.300681 CCATACATGGTTAGTTTATTCATCCAT 57.699 33.333 0.00 0.00 43.05 3.41
358 362 9.127006 GTTGCAGAAACAATTTGAAATGTTTTT 57.873 25.926 10.29 3.75 46.60 1.94
389 393 7.325821 CAGCACATATGTAAAACGTTGAACAAT 59.674 33.333 16.96 10.59 0.00 2.71
402 406 7.823799 TCTTCACAGAAATCAGCACATATGTAA 59.176 33.333 8.32 0.00 0.00 2.41
408 412 6.395426 TTTTCTTCACAGAAATCAGCACAT 57.605 33.333 0.00 0.00 46.36 3.21
409 413 5.833406 TTTTCTTCACAGAAATCAGCACA 57.167 34.783 0.00 0.00 46.36 4.57
440 444 8.633075 TTTTGTTTTATTTGCTCAGAGACTTG 57.367 30.769 0.00 0.00 0.00 3.16
443 447 8.801715 TGATTTTGTTTTATTTGCTCAGAGAC 57.198 30.769 0.00 0.00 0.00 3.36
498 502 9.298774 GAAAATATCAAAATCAGCTCTCCAAAG 57.701 33.333 0.00 0.00 0.00 2.77
505 509 6.866480 TGGGTGAAAATATCAAAATCAGCTC 58.134 36.000 0.00 0.00 40.50 4.09
509 513 7.678837 AGCTTTGGGTGAAAATATCAAAATCA 58.321 30.769 0.00 0.00 40.50 2.57
532 536 4.337274 TGATGACATCACATTTCATGGAGC 59.663 41.667 14.24 0.00 33.59 4.70
549 553 3.061161 GCATGCAAAATTTCCGTGATGAC 59.939 43.478 14.21 0.00 0.00 3.06
556 560 4.432762 CGTAAACTGCATGCAAAATTTCCG 60.433 41.667 22.88 18.95 0.00 4.30
565 569 3.313803 TCACTTTTCGTAAACTGCATGCA 59.686 39.130 21.29 21.29 0.00 3.96
566 570 3.884169 TCACTTTTCGTAAACTGCATGC 58.116 40.909 11.82 11.82 0.00 4.06
567 571 3.908382 GCTCACTTTTCGTAAACTGCATG 59.092 43.478 0.00 0.00 0.00 4.06
568 572 3.563808 TGCTCACTTTTCGTAAACTGCAT 59.436 39.130 0.00 0.00 0.00 3.96
569 573 2.939756 TGCTCACTTTTCGTAAACTGCA 59.060 40.909 0.00 0.00 0.00 4.41
570 574 3.002348 ACTGCTCACTTTTCGTAAACTGC 59.998 43.478 0.00 0.00 0.00 4.40
571 575 4.034048 ACACTGCTCACTTTTCGTAAACTG 59.966 41.667 0.00 0.00 0.00 3.16
572 576 4.189231 ACACTGCTCACTTTTCGTAAACT 58.811 39.130 0.00 0.00 0.00 2.66
573 577 4.531659 ACACTGCTCACTTTTCGTAAAC 57.468 40.909 0.00 0.00 0.00 2.01
574 578 5.106475 ACAAACACTGCTCACTTTTCGTAAA 60.106 36.000 0.00 0.00 0.00 2.01
575 579 4.393680 ACAAACACTGCTCACTTTTCGTAA 59.606 37.500 0.00 0.00 0.00 3.18
576 580 3.936453 ACAAACACTGCTCACTTTTCGTA 59.064 39.130 0.00 0.00 0.00 3.43
584 588 6.698359 TTTTTAACAACAAACACTGCTCAC 57.302 33.333 0.00 0.00 0.00 3.51
647 655 5.922739 AAAAAGTGAAATTGAATTCGCCC 57.077 34.783 0.04 0.00 39.97 6.13
651 659 9.487790 TCCCACATAAAAAGTGAAATTGAATTC 57.512 29.630 0.00 0.00 39.30 2.17
658 666 6.610075 ATGCTCCCACATAAAAAGTGAAAT 57.390 33.333 0.00 0.00 39.30 2.17
666 675 4.088634 AGCTCAAATGCTCCCACATAAAA 58.911 39.130 0.00 0.00 39.34 1.52
681 690 3.684788 GGCGTTCTAATCTTGAGCTCAAA 59.315 43.478 28.16 19.21 35.15 2.69
711 720 3.931907 AAATCTGGAATCACCGATGGA 57.068 42.857 0.00 0.00 42.61 3.41
718 727 3.442977 AGCAGCAGAAAATCTGGAATCAC 59.557 43.478 9.25 0.00 44.43 3.06
734 743 0.179070 TGGTGACGTACAAAGCAGCA 60.179 50.000 0.00 0.98 36.53 4.41
759 768 1.103803 TAGTCCGTGGCATGAGACTC 58.896 55.000 24.61 0.00 40.07 3.36
760 769 1.557099 TTAGTCCGTGGCATGAGACT 58.443 50.000 24.42 24.42 42.13 3.24
761 770 2.604046 ATTAGTCCGTGGCATGAGAC 57.396 50.000 8.63 13.33 0.00 3.36
762 771 2.499693 TGAATTAGTCCGTGGCATGAGA 59.500 45.455 8.63 0.84 0.00 3.27
763 772 2.905075 TGAATTAGTCCGTGGCATGAG 58.095 47.619 8.63 0.00 0.00 2.90
764 773 3.006940 GTTGAATTAGTCCGTGGCATGA 58.993 45.455 8.63 0.00 0.00 3.07
765 774 2.223021 CGTTGAATTAGTCCGTGGCATG 60.223 50.000 0.00 0.00 0.00 4.06
766 775 2.006888 CGTTGAATTAGTCCGTGGCAT 58.993 47.619 0.00 0.00 0.00 4.40
767 776 1.434555 CGTTGAATTAGTCCGTGGCA 58.565 50.000 0.00 0.00 0.00 4.92
768 777 0.096454 GCGTTGAATTAGTCCGTGGC 59.904 55.000 0.00 0.00 0.00 5.01
769 778 0.368907 CGCGTTGAATTAGTCCGTGG 59.631 55.000 0.00 0.00 0.00 4.94
770 779 1.058695 GTCGCGTTGAATTAGTCCGTG 59.941 52.381 5.77 0.00 0.00 4.94
771 780 1.336148 TGTCGCGTTGAATTAGTCCGT 60.336 47.619 5.77 0.00 0.00 4.69
772 781 1.320555 CTGTCGCGTTGAATTAGTCCG 59.679 52.381 5.77 0.00 0.00 4.79
773 782 1.060698 GCTGTCGCGTTGAATTAGTCC 59.939 52.381 5.77 0.00 0.00 3.85
885 898 3.497031 TCGTCTCGCGAGCGACAT 61.497 61.111 34.87 0.00 45.69 3.06
933 949 2.742053 GTGCAGTCGAATTTAGAGGCAA 59.258 45.455 7.16 0.00 33.07 4.52
1107 1144 4.357947 GCGGAGACCAGCGTGTCA 62.358 66.667 10.63 0.00 37.73 3.58
1452 1492 1.227823 CCACAGCACGTTGGAGGAA 60.228 57.895 0.00 0.00 0.00 3.36
1518 1558 3.567473 GTGAGCTTGTTCTCGCCC 58.433 61.111 0.00 0.00 37.57 6.13
1609 1649 2.594592 GCTGGTGCCGTTGGAGTT 60.595 61.111 0.00 0.00 0.00 3.01
1612 1652 4.680237 CTCGCTGGTGCCGTTGGA 62.680 66.667 0.00 0.00 35.36 3.53
1633 1673 1.439679 GACCGGTTCCACATGAAGAC 58.560 55.000 9.42 0.00 32.37 3.01
1654 1694 1.537202 GCCGGTCCGATAATACGTACT 59.463 52.381 14.39 0.00 0.00 2.73
1662 1702 1.448189 CCAAACGCCGGTCCGATAA 60.448 57.895 14.39 0.00 0.00 1.75
1664 1704 3.697747 TCCAAACGCCGGTCCGAT 61.698 61.111 14.39 0.00 0.00 4.18
1838 1887 2.181021 CGACCCAGACGTACTGCC 59.819 66.667 8.85 1.93 44.52 4.85
1854 1903 0.320247 AGAACAGTTGCCAGCTCTCG 60.320 55.000 0.00 0.00 0.00 4.04
1855 1904 1.155042 CAGAACAGTTGCCAGCTCTC 58.845 55.000 0.00 0.00 0.00 3.20
1917 1991 3.349808 TCGCAAACGCCGAATGCA 61.350 55.556 16.28 0.00 41.33 3.96
2000 2074 4.127040 CGCTCCAGTCGCTGAGCT 62.127 66.667 1.78 0.00 34.75 4.09
2050 2124 4.651008 GGTCGACCCGTTGCGTGA 62.651 66.667 24.75 0.00 0.00 4.35
2157 2252 0.395686 AGCAGCTCTTCTGACAAGCA 59.604 50.000 11.68 0.00 45.72 3.91
2166 2261 1.025647 CCTGGCAAGAGCAGCTCTTC 61.026 60.000 31.35 24.13 46.42 2.87
2571 2724 1.866880 GCAACTTGGACTTGCTGCTTG 60.867 52.381 0.00 0.00 40.79 4.01
2643 2827 4.007644 CCCAGCGTGCTCACCTCA 62.008 66.667 0.00 0.00 0.00 3.86
2799 2989 2.309528 TCATGATGCTGTACCGTTCC 57.690 50.000 0.00 0.00 0.00 3.62
3050 3240 2.354303 CCAAAGCTATACACGTCCACCA 60.354 50.000 0.00 0.00 0.00 4.17
3116 3310 2.352032 GCCTCCACCTCGCTGTACT 61.352 63.158 0.00 0.00 0.00 2.73
3449 3678 6.605849 ACTTGTCATGTTCTGAAATCGATTG 58.394 36.000 12.25 0.00 35.07 2.67
3483 3712 2.352814 GGCACTTCGAGATGTGTACACT 60.353 50.000 25.60 12.04 38.34 3.55
3496 3725 1.685302 CAATTTTGGTCGGCACTTCG 58.315 50.000 0.00 0.00 0.00 3.79
3513 3742 2.738521 GCGACGGAGAAGCTGCAA 60.739 61.111 1.02 0.00 0.00 4.08
3586 3817 3.000925 GCCGTCCAGATATTGTTGTTACG 59.999 47.826 0.00 0.00 0.00 3.18
3587 3818 3.000925 CGCCGTCCAGATATTGTTGTTAC 59.999 47.826 0.00 0.00 0.00 2.50
3588 3819 3.191669 CGCCGTCCAGATATTGTTGTTA 58.808 45.455 0.00 0.00 0.00 2.41
3589 3820 2.006888 CGCCGTCCAGATATTGTTGTT 58.993 47.619 0.00 0.00 0.00 2.83
3590 3821 1.651987 CGCCGTCCAGATATTGTTGT 58.348 50.000 0.00 0.00 0.00 3.32
3591 3822 0.304705 GCGCCGTCCAGATATTGTTG 59.695 55.000 0.00 0.00 0.00 3.33
3592 3823 0.814010 GGCGCCGTCCAGATATTGTT 60.814 55.000 12.58 0.00 0.00 2.83
3593 3824 1.227556 GGCGCCGTCCAGATATTGT 60.228 57.895 12.58 0.00 0.00 2.71
3594 3825 1.961277 GGGCGCCGTCCAGATATTG 60.961 63.158 22.54 0.00 0.00 1.90
3595 3826 2.100879 GAGGGCGCCGTCCAGATATT 62.101 60.000 33.69 3.83 0.00 1.28
3596 3827 2.524394 AGGGCGCCGTCCAGATAT 60.524 61.111 22.54 0.00 0.00 1.63
3597 3828 3.224324 GAGGGCGCCGTCCAGATA 61.224 66.667 33.69 0.00 0.00 1.98
3611 3842 4.007644 TCGTGCAGGTGCTGGAGG 62.008 66.667 6.26 0.00 42.66 4.30
3612 3843 2.740055 GTCGTGCAGGTGCTGGAG 60.740 66.667 6.26 0.00 42.66 3.86
3613 3844 4.662961 CGTCGTGCAGGTGCTGGA 62.663 66.667 6.26 0.00 42.66 3.86
3614 3845 4.662961 TCGTCGTGCAGGTGCTGG 62.663 66.667 6.26 0.00 42.66 4.85
3615 3846 3.406361 GTCGTCGTGCAGGTGCTG 61.406 66.667 6.26 0.00 42.66 4.41
3617 3848 4.994201 TCGTCGTCGTGCAGGTGC 62.994 66.667 6.26 0.00 38.33 5.01
3618 3849 3.097728 GTCGTCGTCGTGCAGGTG 61.098 66.667 6.26 0.82 38.33 4.00
3619 3850 4.678269 CGTCGTCGTCGTGCAGGT 62.678 66.667 6.26 0.00 38.33 4.00
3621 3852 4.379143 TCCGTCGTCGTCGTGCAG 62.379 66.667 10.76 0.00 38.33 4.41
3622 3853 4.379143 CTCCGTCGTCGTCGTGCA 62.379 66.667 10.76 0.00 38.33 4.57
3623 3854 3.978867 CTCTCCGTCGTCGTCGTGC 62.979 68.421 10.76 0.00 38.33 5.34
3624 3855 2.096030 CTCTCCGTCGTCGTCGTG 59.904 66.667 10.76 3.95 38.33 4.35
3742 3973 1.304381 GAACCCTGGCCATCTGCAA 60.304 57.895 5.51 0.00 43.89 4.08
3762 3993 0.107508 CCGTTGTCATGATCCTGGCT 60.108 55.000 0.00 0.00 0.00 4.75
3765 3996 0.460109 TCGCCGTTGTCATGATCCTG 60.460 55.000 0.00 0.00 0.00 3.86
3772 4003 0.673333 TGCAGAATCGCCGTTGTCAT 60.673 50.000 0.00 0.00 0.00 3.06
3826 4058 0.322975 AGCATGAGCCTTCGACAACT 59.677 50.000 0.00 0.00 43.56 3.16
3870 4102 1.942657 GATCGCAAGGATAGCAGCAAA 59.057 47.619 0.00 0.00 34.82 3.68
3960 4192 0.245539 GCTGCAAGGCACATGACAAT 59.754 50.000 0.00 0.00 33.79 2.71
3998 4230 1.134280 AGACCTCGCATCATGAAAGGG 60.134 52.381 16.57 12.96 0.00 3.95
4057 4289 0.383949 GAGCCAAGCAACGGAAACAA 59.616 50.000 0.00 0.00 0.00 2.83
4135 4367 2.283676 TCCCTCTCACGGTGTCCC 60.284 66.667 8.17 0.00 0.00 4.46
4274 4506 0.034616 AGACTCAGGAGCTTGCACAC 59.965 55.000 0.00 0.00 0.00 3.82
4275 4507 0.034476 CAGACTCAGGAGCTTGCACA 59.966 55.000 0.00 0.00 0.00 4.57
4316 4548 2.419574 CCCCGATCAACATAACCTTCGT 60.420 50.000 0.00 0.00 0.00 3.85
4325 4557 1.305219 CGCAACACCCCGATCAACAT 61.305 55.000 0.00 0.00 0.00 2.71
4351 4583 6.512903 CGAAATGAGACAAGCATAGCATCATT 60.513 38.462 0.00 0.00 37.47 2.57


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

AutoCloner maintained by Alex Coulton.