Multiple sequence alignment - TraesCS7A01G155300

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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 TraesCS7A01G155300 chr7A 100.000 3818 0 0 1 3818 108443491 108439674 0.000000e+00 7051
1 TraesCS7A01G155300 chr7A 86.922 1017 88 19 2431 3419 108360916 108359917 0.000000e+00 1099
2 TraesCS7A01G155300 chr7A 99.324 592 3 1 1 591 108450264 108449673 0.000000e+00 1070
3 TraesCS7A01G155300 chr7A 97.983 595 6 4 1 591 482049240 482049832 0.000000e+00 1027
4 TraesCS7A01G155300 chr7A 97.980 594 7 4 1 591 482056039 482056630 0.000000e+00 1026
5 TraesCS7A01G155300 chr7A 92.694 219 15 1 3601 3818 108359922 108359704 7.960000e-82 315
6 TraesCS7A01G155300 chr7A 85.593 236 30 4 1059 1293 20094928 20094696 1.060000e-60 244
7 TraesCS7A01G155300 chr7B 91.015 946 39 12 1309 2249 62062358 62061454 0.000000e+00 1234
8 TraesCS7A01G155300 chr7B 84.375 800 63 26 2514 3281 62060892 62060123 0.000000e+00 728
9 TraesCS7A01G155300 chr7B 85.455 495 57 8 3322 3814 62060118 62059637 5.690000e-138 501
10 TraesCS7A01G155300 chr7B 89.494 257 22 3 2260 2513 62061485 62061231 1.710000e-83 320
11 TraesCS7A01G155300 chr7D 92.337 783 40 10 1283 2055 104131305 104130533 0.000000e+00 1096
12 TraesCS7A01G155300 chr7D 88.958 806 40 16 2057 2843 104128492 104127717 0.000000e+00 950
13 TraesCS7A01G155300 chr7D 89.709 515 47 6 3309 3818 104101830 104101317 0.000000e+00 652
14 TraesCS7A01G155300 chr7D 83.456 677 77 19 627 1281 562396298 562396961 7.060000e-167 597
15 TraesCS7A01G155300 chr7D 83.515 643 79 12 630 1255 454676882 454676250 3.310000e-160 575
16 TraesCS7A01G155300 chr7D 82.055 691 89 16 627 1293 104368480 104369159 1.200000e-154 556
17 TraesCS7A01G155300 chr7D 84.886 569 59 14 745 1290 602082887 602082323 2.000000e-152 549
18 TraesCS7A01G155300 chr2B 99.324 592 3 1 1 591 482789071 482788480 0.000000e+00 1070
19 TraesCS7A01G155300 chr2B 98.986 592 5 1 1 591 482782299 482781708 0.000000e+00 1059
20 TraesCS7A01G155300 chr1B 98.314 593 8 2 1 591 516936373 516936965 0.000000e+00 1038
21 TraesCS7A01G155300 chr1B 84.226 691 81 12 621 1290 679233766 679234449 0.000000e+00 647
22 TraesCS7A01G155300 chr3B 97.815 595 9 2 1 593 670496725 670496133 0.000000e+00 1024
23 TraesCS7A01G155300 chr6B 97.804 592 12 1 1 591 404475202 404475793 0.000000e+00 1020
24 TraesCS7A01G155300 chr5A 97.808 593 10 2 1 592 393460316 393460906 0.000000e+00 1020
25 TraesCS7A01G155300 chr5A 83.639 654 77 13 627 1260 54458837 54458194 4.250000e-164 588
26 TraesCS7A01G155300 chr3A 83.965 686 82 14 627 1290 584028653 584027974 1.940000e-177 632
27 TraesCS7A01G155300 chr3A 84.665 626 75 9 653 1259 740696105 740696728 4.220000e-169 604
28 TraesCS7A01G155300 chr6A 84.292 643 79 8 632 1257 454098564 454097927 3.260000e-170 608
29 TraesCS7A01G155300 chr6A 82.514 366 43 6 947 1292 109797079 109796715 6.200000e-78 302
30 TraesCS7A01G155300 chr5D 84.399 641 77 14 627 1246 520768098 520768736 3.260000e-170 608
31 TraesCS7A01G155300 chr5D 84.838 587 70 9 722 1290 348517557 348516972 1.190000e-159 573
32 TraesCS7A01G155300 chr6D 83.535 662 83 9 653 1290 451957703 451958362 2.540000e-166 595
33 TraesCS7A01G155300 chr1D 88.264 409 47 1 652 1059 246075256 246074848 4.430000e-134 488
34 TraesCS7A01G155300 chr3D 82.863 496 62 11 813 1286 562923661 562924155 1.270000e-114 424
35 TraesCS7A01G155300 chr3D 82.683 410 49 5 900 1289 417156864 417156457 1.020000e-90 344
36 TraesCS7A01G155300 chr4D 80.695 518 90 9 3210 3721 116275777 116276290 9.940000e-106 394


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 TraesCS7A01G155300 chr7A 108439674 108443491 3817 True 7051.00 7051 100.00000 1 3818 1 chr7A.!!$R2 3817
1 TraesCS7A01G155300 chr7A 108449673 108450264 591 True 1070.00 1070 99.32400 1 591 1 chr7A.!!$R3 590
2 TraesCS7A01G155300 chr7A 482049240 482049832 592 False 1027.00 1027 97.98300 1 591 1 chr7A.!!$F1 590
3 TraesCS7A01G155300 chr7A 482056039 482056630 591 False 1026.00 1026 97.98000 1 591 1 chr7A.!!$F2 590
4 TraesCS7A01G155300 chr7A 108359704 108360916 1212 True 707.00 1099 89.80800 2431 3818 2 chr7A.!!$R4 1387
5 TraesCS7A01G155300 chr7B 62059637 62062358 2721 True 695.75 1234 87.58475 1309 3814 4 chr7B.!!$R1 2505
6 TraesCS7A01G155300 chr7D 104127717 104131305 3588 True 1023.00 1096 90.64750 1283 2843 2 chr7D.!!$R4 1560
7 TraesCS7A01G155300 chr7D 104101317 104101830 513 True 652.00 652 89.70900 3309 3818 1 chr7D.!!$R1 509
8 TraesCS7A01G155300 chr7D 562396298 562396961 663 False 597.00 597 83.45600 627 1281 1 chr7D.!!$F2 654
9 TraesCS7A01G155300 chr7D 454676250 454676882 632 True 575.00 575 83.51500 630 1255 1 chr7D.!!$R2 625
10 TraesCS7A01G155300 chr7D 104368480 104369159 679 False 556.00 556 82.05500 627 1293 1 chr7D.!!$F1 666
11 TraesCS7A01G155300 chr7D 602082323 602082887 564 True 549.00 549 84.88600 745 1290 1 chr7D.!!$R3 545
12 TraesCS7A01G155300 chr2B 482788480 482789071 591 True 1070.00 1070 99.32400 1 591 1 chr2B.!!$R2 590
13 TraesCS7A01G155300 chr2B 482781708 482782299 591 True 1059.00 1059 98.98600 1 591 1 chr2B.!!$R1 590
14 TraesCS7A01G155300 chr1B 516936373 516936965 592 False 1038.00 1038 98.31400 1 591 1 chr1B.!!$F1 590
15 TraesCS7A01G155300 chr1B 679233766 679234449 683 False 647.00 647 84.22600 621 1290 1 chr1B.!!$F2 669
16 TraesCS7A01G155300 chr3B 670496133 670496725 592 True 1024.00 1024 97.81500 1 593 1 chr3B.!!$R1 592
17 TraesCS7A01G155300 chr6B 404475202 404475793 591 False 1020.00 1020 97.80400 1 591 1 chr6B.!!$F1 590
18 TraesCS7A01G155300 chr5A 393460316 393460906 590 False 1020.00 1020 97.80800 1 592 1 chr5A.!!$F1 591
19 TraesCS7A01G155300 chr5A 54458194 54458837 643 True 588.00 588 83.63900 627 1260 1 chr5A.!!$R1 633
20 TraesCS7A01G155300 chr3A 584027974 584028653 679 True 632.00 632 83.96500 627 1290 1 chr3A.!!$R1 663
21 TraesCS7A01G155300 chr3A 740696105 740696728 623 False 604.00 604 84.66500 653 1259 1 chr3A.!!$F1 606
22 TraesCS7A01G155300 chr6A 454097927 454098564 637 True 608.00 608 84.29200 632 1257 1 chr6A.!!$R2 625
23 TraesCS7A01G155300 chr5D 520768098 520768736 638 False 608.00 608 84.39900 627 1246 1 chr5D.!!$F1 619
24 TraesCS7A01G155300 chr5D 348516972 348517557 585 True 573.00 573 84.83800 722 1290 1 chr5D.!!$R1 568
25 TraesCS7A01G155300 chr6D 451957703 451958362 659 False 595.00 595 83.53500 653 1290 1 chr6D.!!$F1 637
26 TraesCS7A01G155300 chr4D 116275777 116276290 513 False 394.00 394 80.69500 3210 3721 1 chr4D.!!$F1 511

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
677 685 0.808755 CCGAGAAATTTTGGTCCCCG 59.191 55.0 0.00 0.00 0.00 5.73 F
1771 1826 0.165295 GCAAAGGCGTACGTTCCTTC 59.835 55.0 22.31 11.06 41.54 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 2039 0.297820 CGACTTAATTCGAGGCACGC 59.702 55.0 9.42 0.0 41.78 5.34 R
3611 6108 0.174845 TCGACCACCCATGAATCGAC 59.825 55.0 0.00 0.0 37.94 4.20 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
593 598 4.853468 TCTGCTATGTTCCCCAACAATA 57.147 40.909 0.00 0.00 45.78 1.90
594 599 5.186256 TCTGCTATGTTCCCCAACAATAA 57.814 39.130 0.00 0.00 45.78 1.40
595 600 5.575157 TCTGCTATGTTCCCCAACAATAAA 58.425 37.500 0.00 0.00 45.78 1.40
596 601 6.013379 TCTGCTATGTTCCCCAACAATAAAA 58.987 36.000 0.00 0.00 45.78 1.52
597 602 6.152661 TCTGCTATGTTCCCCAACAATAAAAG 59.847 38.462 0.00 0.00 45.78 2.27
598 603 5.777732 TGCTATGTTCCCCAACAATAAAAGT 59.222 36.000 0.00 0.00 45.78 2.66
599 604 6.099341 GCTATGTTCCCCAACAATAAAAGTG 58.901 40.000 0.00 0.00 45.78 3.16
600 605 6.071616 GCTATGTTCCCCAACAATAAAAGTGA 60.072 38.462 0.00 0.00 45.78 3.41
601 606 6.933514 ATGTTCCCCAACAATAAAAGTGAT 57.066 33.333 0.00 0.00 45.78 3.06
602 607 6.739331 TGTTCCCCAACAATAAAAGTGATT 57.261 33.333 0.00 0.00 39.69 2.57
603 608 6.754193 TGTTCCCCAACAATAAAAGTGATTC 58.246 36.000 0.00 0.00 39.69 2.52
604 609 5.993748 TCCCCAACAATAAAAGTGATTCC 57.006 39.130 0.00 0.00 0.00 3.01
605 610 5.398236 TCCCCAACAATAAAAGTGATTCCA 58.602 37.500 0.00 0.00 0.00 3.53
606 611 6.022315 TCCCCAACAATAAAAGTGATTCCAT 58.978 36.000 0.00 0.00 0.00 3.41
607 612 6.500049 TCCCCAACAATAAAAGTGATTCCATT 59.500 34.615 0.00 0.00 0.00 3.16
608 613 7.676043 TCCCCAACAATAAAAGTGATTCCATTA 59.324 33.333 0.00 0.00 0.00 1.90
609 614 7.981225 CCCCAACAATAAAAGTGATTCCATTAG 59.019 37.037 0.00 0.00 0.00 1.73
610 615 8.531146 CCCAACAATAAAAGTGATTCCATTAGT 58.469 33.333 0.00 0.00 0.00 2.24
611 616 9.927668 CCAACAATAAAAGTGATTCCATTAGTT 57.072 29.630 0.00 0.00 0.00 2.24
650 658 2.636778 TTCTTGTGCCGCTGTCGTCA 62.637 55.000 0.00 0.00 0.00 4.35
659 667 2.240500 GCTGTCGTCATCGCCATCC 61.241 63.158 0.00 0.00 36.96 3.51
677 685 0.808755 CCGAGAAATTTTGGTCCCCG 59.191 55.000 0.00 0.00 0.00 5.73
738 747 3.328050 ACCTCGGATCTTCAAAACCTCTT 59.672 43.478 0.00 0.00 0.00 2.85
763 772 1.200716 CTTCGTCAACGCCTAGTGGTA 59.799 52.381 0.00 0.00 39.60 3.25
774 783 5.357257 ACGCCTAGTGGTAATCATAGTTTG 58.643 41.667 0.00 0.00 35.27 2.93
938 956 5.813717 TGAAATCTTTCATCGACATCATGC 58.186 37.500 1.28 0.00 41.88 4.06
959 977 8.090214 TCATGCTGAAGATATATTGATTCGACA 58.910 33.333 0.00 0.00 0.00 4.35
973 991 3.462483 TTCGACAACCTGCACTTCTAA 57.538 42.857 0.00 0.00 0.00 2.10
1010 1030 5.180492 GGTCCAAGTACGTTCATCAATCAAA 59.820 40.000 0.00 0.00 0.00 2.69
1086 1124 4.034048 GTGAAAGAGTGACAACATCGTTGT 59.966 41.667 12.05 12.05 37.82 3.32
1088 1127 5.123186 TGAAAGAGTGACAACATCGTTGTTT 59.877 36.000 13.30 3.48 43.57 2.83
1166 1209 1.538047 ACTACCGCGAAGAAGGTGTA 58.462 50.000 8.23 0.00 40.08 2.90
1238 1284 8.940397 TTTCCTTGAATCTTAGGTTCAAATCT 57.060 30.769 19.48 0.00 42.91 2.40
1260 1309 8.718102 ATCTGTGTACCTGTAATTGTTATGAC 57.282 34.615 0.00 0.00 0.00 3.06
1354 1405 5.052481 TGTATGCTTTCTTCTCATCCATCG 58.948 41.667 0.00 0.00 0.00 3.84
1366 1417 1.137479 CATCCATCGCCAGCCAAAAAT 59.863 47.619 0.00 0.00 0.00 1.82
1367 1418 1.265236 TCCATCGCCAGCCAAAAATT 58.735 45.000 0.00 0.00 0.00 1.82
1400 1453 4.954092 AAAAAGGCAGAAATAGAGCGAG 57.046 40.909 0.00 0.00 0.00 5.03
1406 1459 2.547642 GCAGAAATAGAGCGAGCATCCT 60.548 50.000 0.00 0.00 0.00 3.24
1414 1467 8.485976 AAATAGAGCGAGCATCCTTAATAATC 57.514 34.615 0.00 0.00 0.00 1.75
1419 1472 4.556233 CGAGCATCCTTAATAATCGACCA 58.444 43.478 0.00 0.00 30.08 4.02
1430 1483 8.144478 CCTTAATAATCGACCAATGAGAAGAGA 58.856 37.037 0.00 0.00 0.00 3.10
1533 1588 0.909133 TGCAGGTACCAGCAGGATGA 60.909 55.000 26.51 4.24 39.69 2.92
1535 1590 0.904649 CAGGTACCAGCAGGATGACA 59.095 55.000 15.94 0.00 39.69 3.58
1595 1650 3.394874 CGGTGTGCGTCGACAGTG 61.395 66.667 17.16 0.00 0.00 3.66
1599 1654 3.406361 GTGCGTCGACAGTGGCAG 61.406 66.667 17.16 0.00 35.85 4.85
1656 1711 4.388499 GCTCGCGGGGAACAGGAA 62.388 66.667 8.71 0.00 0.00 3.36
1694 1749 1.848932 CGTCCTCGTCCACGTCAAGA 61.849 60.000 0.00 0.00 40.80 3.02
1771 1826 0.165295 GCAAAGGCGTACGTTCCTTC 59.835 55.000 22.31 11.06 41.54 3.46
1772 1827 0.794473 CAAAGGCGTACGTTCCTTCC 59.206 55.000 22.31 12.30 41.54 3.46
1773 1828 0.683412 AAAGGCGTACGTTCCTTCCT 59.317 50.000 22.31 14.17 41.54 3.36
1774 1829 0.683412 AAGGCGTACGTTCCTTCCTT 59.317 50.000 18.13 16.28 38.21 3.36
1810 1869 0.384725 CGGTGCACGCAGAGAAAAAG 60.385 55.000 11.45 0.00 34.82 2.27
1815 1874 3.240631 GTGCACGCAGAGAAAAAGAAAAC 59.759 43.478 0.00 0.00 0.00 2.43
1816 1875 2.789339 GCACGCAGAGAAAAAGAAAACC 59.211 45.455 0.00 0.00 0.00 3.27
1817 1876 3.733684 GCACGCAGAGAAAAAGAAAACCA 60.734 43.478 0.00 0.00 0.00 3.67
1981 2041 3.654365 CGAAGGTACGTACGTGCG 58.346 61.111 28.40 28.40 36.87 5.34
1989 2049 4.746951 CGTACGTGCGTGCCTCGA 62.747 66.667 18.32 0.00 42.86 4.04
2008 2068 0.037975 AATTAAGTCGTCGCCGTGGT 60.038 50.000 0.00 0.00 35.01 4.16
2017 2077 2.174969 TCGCCGTGGTGTGTGTTTC 61.175 57.895 0.00 0.00 0.00 2.78
2256 4355 2.279784 CCGAGGCGGCTGAGAATC 60.280 66.667 19.63 0.00 41.17 2.52
2274 4373 0.107361 TCTCTGGTCGGAGATACGCA 60.107 55.000 5.47 0.00 40.67 5.24
2418 4520 1.227999 TGTAGCACAGCGGCAAGAAC 61.228 55.000 1.45 0.00 35.83 3.01
2446 4548 3.206150 CCCGGATGATTTTGGTGAGTAG 58.794 50.000 0.73 0.00 0.00 2.57
2447 4549 3.206150 CCGGATGATTTTGGTGAGTAGG 58.794 50.000 0.00 0.00 0.00 3.18
2449 4551 4.513442 CGGATGATTTTGGTGAGTAGGAA 58.487 43.478 0.00 0.00 0.00 3.36
2450 4552 4.572389 CGGATGATTTTGGTGAGTAGGAAG 59.428 45.833 0.00 0.00 0.00 3.46
2451 4553 5.501156 GGATGATTTTGGTGAGTAGGAAGT 58.499 41.667 0.00 0.00 0.00 3.01
2452 4554 6.629515 CGGATGATTTTGGTGAGTAGGAAGTA 60.630 42.308 0.00 0.00 0.00 2.24
2453 4555 7.110155 GGATGATTTTGGTGAGTAGGAAGTAA 58.890 38.462 0.00 0.00 0.00 2.24
2454 4556 7.281100 GGATGATTTTGGTGAGTAGGAAGTAAG 59.719 40.741 0.00 0.00 0.00 2.34
2496 4598 5.027206 TCTAATAGTCGAGCCGTAATTCG 57.973 43.478 0.00 0.00 38.13 3.34
2514 4954 6.486253 AATTCGTCCATGCATGATATGTAC 57.514 37.500 28.31 13.52 0.00 2.90
2515 4955 3.574614 TCGTCCATGCATGATATGTACG 58.425 45.455 28.31 22.54 0.00 3.67
2519 4959 5.619086 CGTCCATGCATGATATGTACGAGTA 60.619 44.000 28.31 0.00 0.00 2.59
2520 4960 5.802451 GTCCATGCATGATATGTACGAGTAG 59.198 44.000 28.31 5.90 0.00 2.57
2522 4962 6.657541 TCCATGCATGATATGTACGAGTAGTA 59.342 38.462 28.31 0.00 0.00 1.82
2598 5054 5.181748 GGAGCTGCTCCTACATAATATTGG 58.818 45.833 35.51 0.00 46.41 3.16
2618 5074 4.380531 TGGAACTCCGAGCAATATGAATC 58.619 43.478 0.00 0.00 39.43 2.52
2622 5078 3.068165 ACTCCGAGCAATATGAATCGACA 59.932 43.478 0.00 0.00 37.35 4.35
2651 5107 2.819608 CCTGTTACATTCAACACCCTGG 59.180 50.000 0.00 0.00 34.75 4.45
2654 5110 4.282496 TGTTACATTCAACACCCTGGTTT 58.718 39.130 0.00 0.00 33.55 3.27
2669 5125 4.998672 CCCTGGTTTACGAACAGTGATAAA 59.001 41.667 0.00 0.00 37.51 1.40
2683 5139 3.071892 AGTGATAAACCGTCCCTTGTTCA 59.928 43.478 0.00 0.00 0.00 3.18
2684 5140 4.007659 GTGATAAACCGTCCCTTGTTCAT 58.992 43.478 0.00 0.00 0.00 2.57
2685 5141 4.006989 TGATAAACCGTCCCTTGTTCATG 58.993 43.478 0.00 0.00 0.00 3.07
2686 5142 2.358322 AAACCGTCCCTTGTTCATGT 57.642 45.000 0.00 0.00 0.00 3.21
2687 5143 1.604604 AACCGTCCCTTGTTCATGTG 58.395 50.000 0.00 0.00 0.00 3.21
2721 5178 3.881688 AGCACCATCAAGATTGTCTATGC 59.118 43.478 0.00 0.00 0.00 3.14
2734 5191 2.427812 TGTCTATGCCAAATGCCACATG 59.572 45.455 0.00 0.00 40.16 3.21
2808 5265 7.186021 ACAATCTTCGACGAAACAAATACTT 57.814 32.000 12.03 0.00 0.00 2.24
2851 5308 9.508642 TGAACTAAAACCATGACATGTGTTATA 57.491 29.630 14.26 1.01 0.00 0.98
2858 5315 4.024893 CCATGACATGTGTTATAGAACGGC 60.025 45.833 14.26 0.00 38.51 5.68
2866 5323 3.793492 GTGTTATAGAACGGCGGAAGTAC 59.207 47.826 13.24 0.83 38.51 2.73
2867 5324 3.696051 TGTTATAGAACGGCGGAAGTACT 59.304 43.478 13.24 3.56 38.51 2.73
2872 5329 2.804527 AGAACGGCGGAAGTACTTTTTC 59.195 45.455 13.24 1.32 0.00 2.29
2878 5335 3.538780 GCGGAAGTACTTTTTCGTTGTC 58.461 45.455 10.02 0.00 0.00 3.18
2880 5337 3.805971 CGGAAGTACTTTTTCGTTGTCCT 59.194 43.478 10.02 0.00 0.00 3.85
2882 5339 5.463061 CGGAAGTACTTTTTCGTTGTCCTAA 59.537 40.000 10.02 0.00 0.00 2.69
2957 5441 0.391263 ACCGAGCAAATTCCGTCTCC 60.391 55.000 0.00 0.00 0.00 3.71
2960 5444 1.404181 CGAGCAAATTCCGTCTCCTGA 60.404 52.381 0.00 0.00 0.00 3.86
3170 5657 7.865530 TTACATGTAGGGAATTATGCTCCTA 57.134 36.000 5.56 0.00 33.11 2.94
3179 5666 6.268847 AGGGAATTATGCTCCTAGTACAAGAG 59.731 42.308 0.00 0.00 33.11 2.85
3283 5771 3.641437 GTACAAATTGCTCTTGTGCCA 57.359 42.857 8.35 0.00 37.56 4.92
3401 5891 2.224066 CCCGGGCTTTGTAGACATCTAG 60.224 54.545 8.08 0.00 0.00 2.43
3441 5932 1.414181 CCTAATCCAGCCATCTCACGT 59.586 52.381 0.00 0.00 0.00 4.49
3583 6079 3.815809 CCAGCCCATTTATCTAACCGAA 58.184 45.455 0.00 0.00 0.00 4.30
3595 6091 3.028850 TCTAACCGAACATAGTCCAGGG 58.971 50.000 0.00 0.00 0.00 4.45
3596 6092 1.946984 AACCGAACATAGTCCAGGGA 58.053 50.000 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
579 584 6.239458 GGAATCACTTTTATTGTTGGGGAACA 60.239 38.462 0.00 0.00 0.00 3.18
603 608 9.369904 CCCTTTGTTTCATATTTGAACTAATGG 57.630 33.333 0.00 8.09 41.50 3.16
604 609 9.927668 ACCCTTTGTTTCATATTTGAACTAATG 57.072 29.630 0.00 0.92 41.50 1.90
623 628 0.597377 GCGGCACAAGAAACCCTTTG 60.597 55.000 0.00 0.00 31.42 2.77
625 630 1.152756 AGCGGCACAAGAAACCCTT 60.153 52.632 1.45 0.00 34.91 3.95
650 658 2.358898 CCAAAATTTCTCGGATGGCGAT 59.641 45.455 0.00 0.00 0.00 4.58
694 702 2.032528 CCACCTCTCAGCGCCAAA 59.967 61.111 2.29 0.00 0.00 3.28
738 747 2.223876 ACTAGGCGTTGACGAAGAACAA 60.224 45.455 7.85 0.00 43.02 2.83
774 783 8.729805 AGAATGAGATGAAGTTTATTCTCACC 57.270 34.615 12.71 9.37 45.22 4.02
938 956 8.706936 CAGGTTGTCGAATCAATATATCTTCAG 58.293 37.037 0.00 0.00 0.00 3.02
959 977 2.912956 TGATCCCTTAGAAGTGCAGGTT 59.087 45.455 0.00 0.00 0.00 3.50
1034 1055 2.490328 TTTTGAAAGCGCCTTGAGTG 57.510 45.000 2.29 0.00 0.00 3.51
1086 1124 8.303876 GGTAAAGAGGTTGCAATTAGATTGAAA 58.696 33.333 0.59 0.00 42.83 2.69
1088 1127 6.093495 CGGTAAAGAGGTTGCAATTAGATTGA 59.907 38.462 0.59 0.00 42.83 2.57
1147 1187 1.538047 TACACCTTCTTCGCGGTAGT 58.462 50.000 6.13 0.00 30.91 2.73
1216 1261 7.175641 ACACAGATTTGAACCTAAGATTCAAGG 59.824 37.037 0.00 4.08 44.57 3.61
1238 1284 6.770542 TGGTCATAACAATTACAGGTACACA 58.229 36.000 0.00 0.00 0.00 3.72
1354 1405 3.433274 GCAACTCTAAATTTTTGGCTGGC 59.567 43.478 0.00 0.00 0.00 4.85
1393 1446 4.218635 TCGATTATTAAGGATGCTCGCTCT 59.781 41.667 0.00 0.00 0.00 4.09
1400 1453 6.650807 TCTCATTGGTCGATTATTAAGGATGC 59.349 38.462 0.00 0.00 0.00 3.91
1406 1459 7.653713 GCTCTCTTCTCATTGGTCGATTATTAA 59.346 37.037 0.00 0.00 0.00 1.40
1414 1467 1.135257 ACGCTCTCTTCTCATTGGTCG 60.135 52.381 0.00 0.00 0.00 4.79
1419 1472 2.277969 CATGCACGCTCTCTTCTCATT 58.722 47.619 0.00 0.00 0.00 2.57
1485 1540 1.192803 GGTCGGTCTCCCACCTTCTT 61.193 60.000 0.00 0.00 44.21 2.52
1533 1588 1.333636 CGCCTCTTCCAGATCCCTGT 61.334 60.000 0.00 0.00 38.74 4.00
1535 1590 2.439104 GCGCCTCTTCCAGATCCCT 61.439 63.158 0.00 0.00 0.00 4.20
1595 1650 3.426568 GCTCACGCTGTTCCTGCC 61.427 66.667 0.00 0.00 0.00 4.85
1618 1673 2.920912 TCCTCGACGGCCCACTTT 60.921 61.111 0.00 0.00 0.00 2.66
1771 1826 2.398554 CCGGCGTGTGGATGAAAGG 61.399 63.158 6.01 0.00 0.00 3.11
1772 1827 3.039202 GCCGGCGTGTGGATGAAAG 62.039 63.158 12.58 0.00 0.00 2.62
1773 1828 3.053291 GCCGGCGTGTGGATGAAA 61.053 61.111 12.58 0.00 0.00 2.69
1798 1857 6.255453 TCAAATTGGTTTTCTTTTTCTCTGCG 59.745 34.615 0.00 0.00 0.00 5.18
1810 1869 5.050159 GCACCTTCACATCAAATTGGTTTTC 60.050 40.000 0.00 0.00 0.00 2.29
1815 1874 3.663995 TGCACCTTCACATCAAATTGG 57.336 42.857 0.00 0.00 0.00 3.16
1816 1875 3.369756 GCATGCACCTTCACATCAAATTG 59.630 43.478 14.21 0.00 0.00 2.32
1817 1876 3.007074 TGCATGCACCTTCACATCAAATT 59.993 39.130 18.46 0.00 0.00 1.82
1885 1945 2.437895 TCGACGATCGACCTGGCT 60.438 61.111 24.34 0.00 44.82 4.75
1978 2038 1.355971 GACTTAATTCGAGGCACGCA 58.644 50.000 0.00 0.00 42.26 5.24
1979 2039 0.297820 CGACTTAATTCGAGGCACGC 59.702 55.000 9.42 0.00 41.78 5.34
1980 2040 1.582502 GACGACTTAATTCGAGGCACG 59.417 52.381 20.45 0.00 41.78 5.34
1981 2041 1.582502 CGACGACTTAATTCGAGGCAC 59.417 52.381 20.45 6.63 41.78 5.01
2008 2068 1.552226 GACGACGACAGAAACACACA 58.448 50.000 0.00 0.00 0.00 3.72
2017 2077 0.784978 GAGAACGACGACGACGACAG 60.785 60.000 25.15 7.04 42.66 3.51
2065 4164 0.682209 CATGAACCTTCTGGCAGGGG 60.682 60.000 15.73 18.53 38.42 4.79
2256 4355 0.738975 TTGCGTATCTCCGACCAGAG 59.261 55.000 0.00 0.00 35.04 3.35
2400 4502 0.951040 AGTTCTTGCCGCTGTGCTAC 60.951 55.000 0.00 0.00 0.00 3.58
2402 4504 1.963338 GAGTTCTTGCCGCTGTGCT 60.963 57.895 0.00 0.00 0.00 4.40
2418 4520 1.745087 CAAAATCATCCGGGTGTGGAG 59.255 52.381 15.92 0.00 42.45 3.86
2446 4548 9.436957 TCTCAAATAGATTGTGTTCTTACTTCC 57.563 33.333 0.00 0.00 40.11 3.46
2496 4598 4.560128 ACTCGTACATATCATGCATGGAC 58.440 43.478 25.97 8.22 34.42 4.02
2514 4954 6.655062 TGCAAAGAACAAATGTTACTACTCG 58.345 36.000 0.00 0.00 38.56 4.18
2515 4955 7.861630 TCTGCAAAGAACAAATGTTACTACTC 58.138 34.615 0.00 0.00 38.56 2.59
2519 4959 5.922544 GCATCTGCAAAGAACAAATGTTACT 59.077 36.000 0.00 0.00 38.57 2.24
2520 4960 5.922544 AGCATCTGCAAAGAACAAATGTTAC 59.077 36.000 4.79 0.00 45.16 2.50
2522 4962 4.952460 AGCATCTGCAAAGAACAAATGTT 58.048 34.783 4.79 0.00 45.16 2.71
2580 5036 6.518369 CGGAGTTCCAATATTATGTAGGAGCA 60.518 42.308 7.90 0.00 32.75 4.26
2581 5037 5.869888 CGGAGTTCCAATATTATGTAGGAGC 59.130 44.000 0.00 0.00 35.14 4.70
2582 5038 7.228314 TCGGAGTTCCAATATTATGTAGGAG 57.772 40.000 0.00 0.00 35.14 3.69
2590 5046 7.676004 TCATATTGCTCGGAGTTCCAATATTA 58.324 34.615 18.63 12.66 38.26 0.98
2598 5054 4.149046 GTCGATTCATATTGCTCGGAGTTC 59.851 45.833 6.90 0.00 0.00 3.01
2618 5074 2.479837 TGTAACAGGCTCTTGTTGTCG 58.520 47.619 7.51 0.00 41.18 4.35
2622 5078 4.887071 TGTTGAATGTAACAGGCTCTTGTT 59.113 37.500 3.00 3.00 43.34 2.83
2651 5107 5.388786 GGACGGTTTATCACTGTTCGTAAAC 60.389 44.000 9.33 9.33 45.87 2.01
2654 5110 3.367292 GGGACGGTTTATCACTGTTCGTA 60.367 47.826 0.00 0.00 45.87 3.43
2669 5125 0.472471 ACACATGAACAAGGGACGGT 59.528 50.000 0.00 0.00 0.00 4.83
2685 5141 2.698803 TGGTGCTATGTGACATGACAC 58.301 47.619 19.48 19.48 40.68 3.67
2686 5142 3.055240 TGATGGTGCTATGTGACATGACA 60.055 43.478 8.61 3.26 0.00 3.58
2687 5143 3.534554 TGATGGTGCTATGTGACATGAC 58.465 45.455 8.61 2.23 0.00 3.06
2721 5178 4.400251 ACTGAATACTCATGTGGCATTTGG 59.600 41.667 0.00 0.00 0.00 3.28
2734 5191 5.938125 ACATGGTACCACAAACTGAATACTC 59.062 40.000 19.09 0.00 0.00 2.59
2808 5265 3.581332 AGTTCAAACTATGGAACGGAGGA 59.419 43.478 0.00 0.00 46.09 3.71
2851 5308 2.538512 AAAAGTACTTCCGCCGTTCT 57.461 45.000 8.95 0.00 0.00 3.01
2858 5315 3.805971 AGGACAACGAAAAAGTACTTCCG 59.194 43.478 8.95 14.57 0.00 4.30
2866 5323 7.011828 TGAAAGACTTAGGACAACGAAAAAG 57.988 36.000 0.00 0.00 0.00 2.27
2867 5324 6.988622 TGAAAGACTTAGGACAACGAAAAA 57.011 33.333 0.00 0.00 0.00 1.94
2872 5329 8.557029 AGTATTTTTGAAAGACTTAGGACAACG 58.443 33.333 0.00 0.00 0.00 4.10
2900 5384 3.718434 TCCCAGATGCATGTCTAGGATTT 59.282 43.478 2.46 0.00 32.18 2.17
2957 5441 7.280205 ACGTCATAAGCCTAAAAATAAGGTCAG 59.720 37.037 0.00 0.00 36.43 3.51
2960 5444 9.052759 CATACGTCATAAGCCTAAAAATAAGGT 57.947 33.333 0.00 0.00 36.43 3.50
3170 5657 1.059913 ACCTGCCAAGCTCTTGTACT 58.940 50.000 8.60 0.00 38.85 2.73
3179 5666 2.203480 TGAACCCACCTGCCAAGC 60.203 61.111 0.00 0.00 0.00 4.01
3234 5722 4.348486 TGCACCTCCAAGCCAAATTATTA 58.652 39.130 0.00 0.00 0.00 0.98
3246 5734 2.107378 TGTACCTCAAATGCACCTCCAA 59.893 45.455 0.00 0.00 0.00 3.53
3283 5771 1.600636 CCGCTGGTGTCCATGTGTT 60.601 57.895 0.00 0.00 30.82 3.32
3379 5867 0.463833 GATGTCTACAAAGCCCGGGG 60.464 60.000 25.28 9.31 0.00 5.73
3441 5932 0.322456 ATGGCCAGAAACGCTAAGCA 60.322 50.000 13.05 0.00 0.00 3.91
3488 5979 7.669722 AGCCTCTTAGGACAACAAATTTAATGA 59.330 33.333 8.83 0.00 37.67 2.57
3497 5988 1.699634 AGCAGCCTCTTAGGACAACAA 59.300 47.619 0.00 0.00 37.67 2.83
3531 6026 3.329520 ACCCAGTTAACCATAGTGCTTCA 59.670 43.478 0.88 0.00 0.00 3.02
3611 6108 0.174845 TCGACCACCCATGAATCGAC 59.825 55.000 0.00 0.00 37.94 4.20
3781 6279 0.745486 CACCAAGGCGCATGATGAGA 60.745 55.000 10.83 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.