Multiple sequence alignment - TraesCS7B01G019300

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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 TraesCS7B01G019300 chr7B 100.000 3981 0 0 1 3981 16523409 16527389 0.000000e+00 7352.0
1 TraesCS7B01G019300 chr7B 83.780 746 90 15 2485 3210 16828140 16828874 0.000000e+00 678.0
2 TraesCS7B01G019300 chr7B 84.819 718 46 26 1 698 658145809 658145135 0.000000e+00 664.0
3 TraesCS7B01G019300 chr7B 86.131 548 65 7 2616 3159 16734044 16734584 7.420000e-162 580.0
4 TraesCS7B01G019300 chr7B 87.066 518 45 10 780 1285 16732142 16732649 2.080000e-157 566.0
5 TraesCS7B01G019300 chr7B 87.707 423 32 8 880 1285 15935302 15935721 3.600000e-130 475.0
6 TraesCS7B01G019300 chr7B 93.309 269 12 5 2352 2616 16525494 16525760 3.730000e-105 392.0
7 TraesCS7B01G019300 chr7B 93.309 269 12 5 2086 2352 16525760 16526024 3.730000e-105 392.0
8 TraesCS7B01G019300 chr7B 81.875 480 58 14 2740 3207 29607066 29606604 1.040000e-100 377.0
9 TraesCS7B01G019300 chr7B 84.225 355 30 11 1695 2030 16733058 16733405 4.960000e-84 322.0
10 TraesCS7B01G019300 chr7B 82.703 370 39 13 3406 3769 16734779 16735129 5.000000e-79 305.0
11 TraesCS7B01G019300 chr7B 84.746 295 42 2 2852 3146 17215320 17215611 3.890000e-75 292.0
12 TraesCS7B01G019300 chr7B 80.982 326 49 7 2852 3169 16953180 16953500 3.070000e-61 246.0
13 TraesCS7B01G019300 chr7B 79.620 368 45 18 2484 2826 69170025 69169663 1.850000e-58 237.0
14 TraesCS7B01G019300 chr7B 82.888 187 26 4 1284 1470 16732702 16732882 3.180000e-36 163.0
15 TraesCS7B01G019300 chr7B 83.088 136 7 8 1285 1418 16951368 16951489 4.210000e-20 110.0
16 TraesCS7B01G019300 chr7B 95.385 65 2 1 592 656 624462553 624462616 7.040000e-18 102.0
17 TraesCS7B01G019300 chr7B 79.518 166 14 10 3607 3772 16829077 16829222 2.530000e-17 100.0
18 TraesCS7B01G019300 chr7B 91.667 72 3 3 596 666 471089601 471089532 3.270000e-16 97.1
19 TraesCS7B01G019300 chr7B 79.528 127 14 5 1285 1411 16826731 16826845 3.300000e-11 80.5
20 TraesCS7B01G019300 chr7B 100.000 31 0 0 1585 1615 16732979 16733009 1.550000e-04 58.4
21 TraesCS7B01G019300 chr7A 93.037 2743 88 27 1284 3981 77915566 77918250 0.000000e+00 3912.0
22 TraesCS7B01G019300 chr7A 95.914 514 15 2 778 1285 77915000 77915513 0.000000e+00 828.0
23 TraesCS7B01G019300 chr7A 81.016 1122 144 44 2659 3770 78078774 78077712 0.000000e+00 828.0
24 TraesCS7B01G019300 chr7A 89.530 468 31 10 834 1285 78080838 78080373 9.590000e-161 577.0
25 TraesCS7B01G019300 chr7A 86.207 522 40 16 785 1285 77706602 77707112 1.630000e-148 536.0
26 TraesCS7B01G019300 chr7A 86.947 452 31 13 862 1285 77731710 77732161 2.150000e-132 483.0
27 TraesCS7B01G019300 chr7A 82.328 481 52 17 2754 3218 84025714 84025251 1.740000e-103 387.0
28 TraesCS7B01G019300 chr7A 92.509 267 16 3 2352 2616 77916350 77916614 2.900000e-101 379.0
29 TraesCS7B01G019300 chr7A 85.467 289 15 6 2086 2352 77916614 77916897 3.920000e-70 276.0
30 TraesCS7B01G019300 chr7A 92.763 152 6 3 1900 2048 78134563 78134414 8.660000e-52 215.0
31 TraesCS7B01G019300 chr7A 88.000 150 12 3 3531 3674 78132631 78132482 5.290000e-39 172.0
32 TraesCS7B01G019300 chr7A 91.304 92 8 0 2252 2343 78078864 78078773 4.180000e-25 126.0
33 TraesCS7B01G019300 chr7A 98.039 51 1 0 3719 3769 78132467 78132417 5.480000e-14 89.8
34 TraesCS7B01G019300 chr7A 78.947 133 16 5 1285 1417 78080319 78080199 3.300000e-11 80.5
35 TraesCS7B01G019300 chr7D 93.564 1880 65 16 2145 3981 73369383 73371249 0.000000e+00 2750.0
36 TraesCS7B01G019300 chr7D 92.032 866 28 11 1284 2146 73368319 73369146 0.000000e+00 1179.0
37 TraesCS7B01G019300 chr7D 96.685 543 12 2 749 1285 73367724 73368266 0.000000e+00 898.0
38 TraesCS7B01G019300 chr7D 79.690 1354 157 66 2442 3770 73563610 73562350 0.000000e+00 869.0
39 TraesCS7B01G019300 chr7D 84.334 683 75 17 2485 3153 73610998 73610334 1.210000e-179 640.0
40 TraesCS7B01G019300 chr7D 89.423 520 36 10 780 1291 73178009 73178517 4.340000e-179 638.0
41 TraesCS7B01G019300 chr7D 83.779 524 48 21 778 1285 73217955 73218457 2.800000e-126 462.0
42 TraesCS7B01G019300 chr7D 84.016 513 41 10 784 1285 73565517 73565035 4.690000e-124 455.0
43 TraesCS7B01G019300 chr7D 83.206 524 43 10 783 1285 73612955 73612456 4.720000e-119 438.0
44 TraesCS7B01G019300 chr7D 83.733 375 32 12 1695 2048 73612154 73611788 1.070000e-85 327.0
45 TraesCS7B01G019300 chr7D 85.135 296 15 7 2086 2352 73369586 73369881 3.920000e-70 276.0
46 TraesCS7B01G019300 chr7D 90.821 207 15 3 2411 2616 73369383 73369586 1.410000e-69 274.0
47 TraesCS7B01G019300 chr7D 84.211 190 23 5 1285 1474 73612402 73612220 1.140000e-40 178.0
48 TraesCS7B01G019300 chr7D 93.069 101 7 0 2252 2352 73563523 73563423 8.910000e-32 148.0
49 TraesCS7B01G019300 chr7D 98.039 51 1 0 3719 3769 73609839 73609789 5.480000e-14 89.8
50 TraesCS7B01G019300 chr2B 92.068 706 29 9 1 698 58870176 58869490 0.000000e+00 968.0
51 TraesCS7B01G019300 chr2B 90.754 703 43 13 1 698 49406919 49406234 0.000000e+00 918.0
52 TraesCS7B01G019300 chr2B 89.744 702 52 9 1 698 716760 716075 0.000000e+00 880.0
53 TraesCS7B01G019300 chr2B 83.505 194 22 5 2527 2713 675714294 675714484 5.290000e-39 172.0
54 TraesCS7B01G019300 chr2B 77.083 288 54 8 1756 2035 55698593 55698310 5.330000e-34 156.0
55 TraesCS7B01G019300 chr2B 78.099 242 50 3 1795 2035 54786528 54786289 2.480000e-32 150.0
56 TraesCS7B01G019300 chr2B 91.667 72 2 4 596 665 794322556 794322487 3.270000e-16 97.1
57 TraesCS7B01G019300 chr4B 92.023 702 35 11 1 698 608389175 608389859 0.000000e+00 966.0
58 TraesCS7B01G019300 chr4B 87.941 340 16 13 2145 2484 14523341 14523027 1.040000e-100 377.0
59 TraesCS7B01G019300 chr4B 89.855 207 18 2 2411 2616 14523341 14523137 3.050000e-66 263.0
60 TraesCS7B01G019300 chr4B 80.707 368 41 16 2484 2826 144285451 144285813 3.950000e-65 259.0
61 TraesCS7B01G019300 chr4B 94.118 85 4 1 2062 2146 14523661 14523578 1.160000e-25 128.0
62 TraesCS7B01G019300 chr4B 91.667 72 2 4 596 665 57520722 57520791 3.270000e-16 97.1
63 TraesCS7B01G019300 chr1B 90.043 703 49 10 1 698 539879164 539879850 0.000000e+00 891.0
64 TraesCS7B01G019300 chr1B 87.585 443 43 4 2485 2917 15262823 15262383 1.650000e-138 503.0
65 TraesCS7B01G019300 chr1B 87.075 147 11 1 2214 2352 15262830 15262684 4.120000e-35 159.0
66 TraesCS7B01G019300 chr1B 92.857 70 4 1 596 665 105706305 105706237 2.530000e-17 100.0
67 TraesCS7B01G019300 chr5B 93.548 589 30 4 1 586 605831123 605830540 0.000000e+00 870.0
68 TraesCS7B01G019300 chr5B 91.864 590 23 5 1 586 118430727 118431295 0.000000e+00 800.0
69 TraesCS7B01G019300 chr5B 97.727 44 1 0 655 698 118431338 118431381 4.270000e-10 76.8
70 TraesCS7B01G019300 chr3B 90.014 701 30 10 1 698 159462825 159463488 0.000000e+00 870.0
71 TraesCS7B01G019300 chr3B 89.527 592 48 8 1 586 154449432 154448849 0.000000e+00 737.0
72 TraesCS7B01G019300 chr3B 77.828 221 30 18 490 694 528713648 528713865 6.990000e-23 119.0
73 TraesCS7B01G019300 chr3B 96.923 65 2 0 592 656 575240019 575240083 4.210000e-20 110.0
74 TraesCS7B01G019300 chr6B 90.981 632 36 12 71 698 370149668 370150282 0.000000e+00 832.0
75 TraesCS7B01G019300 chr6B 91.667 72 2 4 596 665 525940407 525940476 3.270000e-16 97.1
76 TraesCS7B01G019300 chr6A 91.155 554 18 8 3192 3726 5281318 5281859 0.000000e+00 723.0
77 TraesCS7B01G019300 chr6A 93.455 275 14 2 3707 3981 5289000 5289270 4.790000e-109 405.0
78 TraesCS7B01G019300 chr6A 86.636 217 15 9 2067 2271 5281037 5281251 1.110000e-55 228.0
79 TraesCS7B01G019300 chr3D 82.843 204 24 6 2521 2716 482834926 482834726 5.290000e-39 172.0
80 TraesCS7B01G019300 chr2D 77.083 288 55 7 1756 2035 33580386 33580102 5.330000e-34 156.0
81 TraesCS7B01G019300 chr2D 78.462 195 15 9 1282 1476 33580686 33580519 7.040000e-18 102.0
82 TraesCS7B01G019300 chr2D 76.684 193 18 9 1284 1476 33373741 33373576 9.170000e-12 82.4
83 TraesCS7B01G019300 chr2D 77.181 149 19 8 1284 1432 32992440 32992307 5.520000e-09 73.1
84 TraesCS7B01G019300 chr2D 80.392 102 11 5 1375 1476 33314881 33314789 7.140000e-08 69.4
85 TraesCS7B01G019300 chr2A 76.389 288 57 7 1756 2035 36411055 36410771 1.150000e-30 145.0
86 TraesCS7B01G019300 chrUn 96.721 61 2 0 596 656 329542852 329542912 7.040000e-18 102.0
87 TraesCS7B01G019300 chr6D 100.000 36 0 0 2485 2520 450337420 450337455 2.570000e-07 67.6
88 TraesCS7B01G019300 chr4D 84.615 65 5 5 559 621 477736556 477736495 4.300000e-05 60.2


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 TraesCS7B01G019300 chr7B 16523409 16527389 3980 False 2712.000000 7352 95.539333 1 3981 3 chr7B.!!$F4 3980
1 TraesCS7B01G019300 chr7B 658145135 658145809 674 True 664.000000 664 84.819000 1 698 1 chr7B.!!$R4 697
2 TraesCS7B01G019300 chr7B 16732142 16735129 2987 False 332.400000 580 87.168833 780 3769 6 chr7B.!!$F5 2989
3 TraesCS7B01G019300 chr7B 16826731 16829222 2491 False 286.166667 678 80.942000 1285 3772 3 chr7B.!!$F6 2487
4 TraesCS7B01G019300 chr7A 77915000 77918250 3250 False 1348.750000 3912 91.731750 778 3981 4 chr7A.!!$F3 3203
5 TraesCS7B01G019300 chr7A 77706602 77707112 510 False 536.000000 536 86.207000 785 1285 1 chr7A.!!$F1 500
6 TraesCS7B01G019300 chr7A 78077712 78080838 3126 True 402.875000 828 85.199250 834 3770 4 chr7A.!!$R2 2936
7 TraesCS7B01G019300 chr7D 73367724 73371249 3525 False 1075.400000 2750 91.647400 749 3981 5 chr7D.!!$F3 3232
8 TraesCS7B01G019300 chr7D 73178009 73178517 508 False 638.000000 638 89.423000 780 1291 1 chr7D.!!$F1 511
9 TraesCS7B01G019300 chr7D 73562350 73565517 3167 True 490.666667 869 85.591667 784 3770 3 chr7D.!!$R1 2986
10 TraesCS7B01G019300 chr7D 73217955 73218457 502 False 462.000000 462 83.779000 778 1285 1 chr7D.!!$F2 507
11 TraesCS7B01G019300 chr7D 73609789 73612955 3166 True 334.560000 640 86.704600 783 3769 5 chr7D.!!$R2 2986
12 TraesCS7B01G019300 chr2B 58869490 58870176 686 True 968.000000 968 92.068000 1 698 1 chr2B.!!$R5 697
13 TraesCS7B01G019300 chr2B 49406234 49406919 685 True 918.000000 918 90.754000 1 698 1 chr2B.!!$R2 697
14 TraesCS7B01G019300 chr2B 716075 716760 685 True 880.000000 880 89.744000 1 698 1 chr2B.!!$R1 697
15 TraesCS7B01G019300 chr4B 608389175 608389859 684 False 966.000000 966 92.023000 1 698 1 chr4B.!!$F3 697
16 TraesCS7B01G019300 chr4B 14523027 14523661 634 True 256.000000 377 90.638000 2062 2616 3 chr4B.!!$R1 554
17 TraesCS7B01G019300 chr1B 539879164 539879850 686 False 891.000000 891 90.043000 1 698 1 chr1B.!!$F1 697
18 TraesCS7B01G019300 chr5B 605830540 605831123 583 True 870.000000 870 93.548000 1 586 1 chr5B.!!$R1 585
19 TraesCS7B01G019300 chr5B 118430727 118431381 654 False 438.400000 800 94.795500 1 698 2 chr5B.!!$F1 697
20 TraesCS7B01G019300 chr3B 159462825 159463488 663 False 870.000000 870 90.014000 1 698 1 chr3B.!!$F1 697
21 TraesCS7B01G019300 chr3B 154448849 154449432 583 True 737.000000 737 89.527000 1 586 1 chr3B.!!$R1 585
22 TraesCS7B01G019300 chr6B 370149668 370150282 614 False 832.000000 832 90.981000 71 698 1 chr6B.!!$F1 627
23 TraesCS7B01G019300 chr6A 5281037 5281859 822 False 475.500000 723 88.895500 2067 3726 2 chr6A.!!$F2 1659

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
712 740 1.083489 CGTTGAGCGGCAAATAGGAA 58.917 50.000 1.45 0.00 38.44 3.36 F
713 741 1.466950 CGTTGAGCGGCAAATAGGAAA 59.533 47.619 1.45 0.00 38.44 3.13 F
1579 1769 0.039256 TCTTGCCAAATGTGCGCTTC 60.039 50.000 9.73 2.14 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1765 0.538287 AAGAACTGCACCCAGGAAGC 60.538 55.0 0.0 0.0 43.53 3.86 R
1587 1777 0.594796 GCAACCAACGGCAAGAACTG 60.595 55.0 0.0 0.0 0.00 3.16 R
3223 4407 0.037605 ACTACTACAACCGCTGCACC 60.038 55.0 0.0 0.0 0.00 5.01 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
478 503 4.871933 ACATTTTCCAAGAAAGGCGAAT 57.128 36.364 0.00 0.00 0.00 3.34
589 617 3.636282 AAAAACCGATTCAGGAAACCG 57.364 42.857 2.26 0.00 34.73 4.44
590 618 2.554370 AAACCGATTCAGGAAACCGA 57.446 45.000 8.19 0.00 34.73 4.69
591 619 2.781681 AACCGATTCAGGAAACCGAT 57.218 45.000 8.19 0.00 34.73 4.18
592 620 2.781681 ACCGATTCAGGAAACCGATT 57.218 45.000 8.19 0.00 34.73 3.34
593 621 2.629051 ACCGATTCAGGAAACCGATTC 58.371 47.619 8.19 0.00 37.31 2.52
594 622 2.027561 ACCGATTCAGGAAACCGATTCA 60.028 45.455 8.19 0.00 39.98 2.57
595 623 2.609459 CCGATTCAGGAAACCGATTCAG 59.391 50.000 8.19 0.00 39.98 3.02
596 624 2.609459 CGATTCAGGAAACCGATTCAGG 59.391 50.000 3.81 0.00 39.98 3.86
597 625 3.678806 CGATTCAGGAAACCGATTCAGGA 60.679 47.826 3.81 0.00 39.98 3.86
598 626 3.780804 TTCAGGAAACCGATTCAGGAA 57.219 42.857 3.81 3.87 39.98 3.36
620 648 3.258971 CTTCTAGAAGGTTCCAGCTGG 57.741 52.381 27.87 27.87 34.87 4.85
621 649 2.327325 TCTAGAAGGTTCCAGCTGGT 57.673 50.000 31.58 12.98 36.34 4.00
622 650 2.621070 TCTAGAAGGTTCCAGCTGGTT 58.379 47.619 31.58 18.94 36.34 3.67
623 651 2.979678 TCTAGAAGGTTCCAGCTGGTTT 59.020 45.455 31.58 20.51 36.34 3.27
624 652 2.755952 AGAAGGTTCCAGCTGGTTTT 57.244 45.000 31.58 20.18 36.34 2.43
625 653 3.032265 AGAAGGTTCCAGCTGGTTTTT 57.968 42.857 31.58 20.50 36.34 1.94
711 739 2.762360 CGTTGAGCGGCAAATAGGA 58.238 52.632 1.45 0.00 38.44 2.94
712 740 1.083489 CGTTGAGCGGCAAATAGGAA 58.917 50.000 1.45 0.00 38.44 3.36
713 741 1.466950 CGTTGAGCGGCAAATAGGAAA 59.533 47.619 1.45 0.00 38.44 3.13
714 742 2.097466 CGTTGAGCGGCAAATAGGAAAT 59.903 45.455 1.45 0.00 38.44 2.17
715 743 3.427503 CGTTGAGCGGCAAATAGGAAATT 60.428 43.478 1.45 0.00 38.44 1.82
716 744 4.105486 GTTGAGCGGCAAATAGGAAATTC 58.895 43.478 1.45 0.00 38.44 2.17
717 745 2.687935 TGAGCGGCAAATAGGAAATTCC 59.312 45.455 3.29 3.29 36.58 3.01
718 746 1.676006 AGCGGCAAATAGGAAATTCCG 59.324 47.619 6.35 0.00 42.75 4.30
719 747 2.119671 CGGCAAATAGGAAATTCCGC 57.880 50.000 6.35 3.38 42.75 5.54
720 748 1.676006 CGGCAAATAGGAAATTCCGCT 59.324 47.619 6.35 0.00 42.75 5.52
721 749 2.541588 CGGCAAATAGGAAATTCCGCTG 60.542 50.000 6.35 4.92 42.75 5.18
722 750 2.687935 GGCAAATAGGAAATTCCGCTGA 59.312 45.455 6.35 0.00 42.75 4.26
723 751 3.319122 GGCAAATAGGAAATTCCGCTGAT 59.681 43.478 6.35 0.00 42.75 2.90
724 752 4.293415 GCAAATAGGAAATTCCGCTGATG 58.707 43.478 6.35 5.15 42.75 3.07
725 753 4.794003 GCAAATAGGAAATTCCGCTGATGG 60.794 45.833 6.35 0.00 42.75 3.51
726 754 1.967319 TAGGAAATTCCGCTGATGGC 58.033 50.000 6.35 0.00 42.75 4.40
735 763 3.272334 GCTGATGGCGCCGGTTAG 61.272 66.667 23.90 19.28 0.00 2.34
736 764 2.588877 CTGATGGCGCCGGTTAGG 60.589 66.667 23.90 5.73 44.97 2.69
737 765 3.078196 TGATGGCGCCGGTTAGGA 61.078 61.111 23.90 1.41 45.00 2.94
738 766 2.280186 GATGGCGCCGGTTAGGAG 60.280 66.667 23.90 0.00 45.00 3.69
739 767 3.809374 GATGGCGCCGGTTAGGAGG 62.809 68.421 23.90 0.00 45.00 4.30
741 769 4.222847 GGCGCCGGTTAGGAGGAG 62.223 72.222 12.58 0.00 45.00 3.69
742 770 4.893601 GCGCCGGTTAGGAGGAGC 62.894 72.222 1.90 0.00 45.27 4.70
743 771 3.148279 CGCCGGTTAGGAGGAGCT 61.148 66.667 1.90 0.00 45.00 4.09
744 772 2.816012 GCCGGTTAGGAGGAGCTC 59.184 66.667 4.71 4.71 45.00 4.09
914 977 3.683937 GCCGCAACCAACAGCCAT 61.684 61.111 0.00 0.00 0.00 4.40
1550 1738 1.863454 CATTCGCCCGAGAGAAATCTG 59.137 52.381 0.00 0.00 35.32 2.90
1575 1765 1.001487 TCTGTTCTTGCCAAATGTGCG 60.001 47.619 0.00 0.00 0.00 5.34
1576 1766 0.597118 TGTTCTTGCCAAATGTGCGC 60.597 50.000 0.00 0.00 0.00 6.09
1577 1767 0.318955 GTTCTTGCCAAATGTGCGCT 60.319 50.000 9.73 0.00 0.00 5.92
1579 1769 0.039256 TCTTGCCAAATGTGCGCTTC 60.039 50.000 9.73 2.14 0.00 3.86
1580 1770 1.006337 TTGCCAAATGTGCGCTTCC 60.006 52.632 9.73 0.00 0.00 3.46
1581 1771 1.462731 TTGCCAAATGTGCGCTTCCT 61.463 50.000 9.73 0.00 0.00 3.36
1582 1772 1.444895 GCCAAATGTGCGCTTCCTG 60.445 57.895 9.73 0.00 0.00 3.86
1583 1773 1.213537 CCAAATGTGCGCTTCCTGG 59.786 57.895 9.73 5.31 0.00 4.45
1584 1774 1.213537 CAAATGTGCGCTTCCTGGG 59.786 57.895 9.73 0.00 0.00 4.45
1585 1775 1.228552 AAATGTGCGCTTCCTGGGT 60.229 52.632 9.73 0.00 0.00 4.51
1586 1776 1.526575 AAATGTGCGCTTCCTGGGTG 61.527 55.000 9.73 0.00 0.00 4.61
1638 1828 5.827568 ATCGCATTTGTGATTGTGTTTTC 57.172 34.783 0.82 0.00 42.06 2.29
1639 1829 4.676546 TCGCATTTGTGATTGTGTTTTCA 58.323 34.783 0.00 0.00 0.00 2.69
1640 1830 4.739228 TCGCATTTGTGATTGTGTTTTCAG 59.261 37.500 0.00 0.00 0.00 3.02
1649 1839 5.294306 GTGATTGTGTTTTCAGTCAGTCAGA 59.706 40.000 0.00 0.00 35.40 3.27
2030 2269 3.620903 AGGACCCCTGGTGAGAGA 58.379 61.111 0.00 0.00 35.25 3.10
2032 2271 1.990614 GGACCCCTGGTGAGAGACC 60.991 68.421 0.00 0.00 46.37 3.85
2033 2272 1.079438 GACCCCTGGTGAGAGACCT 59.921 63.158 0.00 0.00 46.32 3.85
2036 2275 1.079256 CCCTGGTGAGAGACCTCCA 59.921 63.158 0.00 0.00 46.32 3.86
2323 3432 6.163476 TGTGGATTTATCAGTCTGTGTACAC 58.837 40.000 19.36 19.36 0.00 2.90
2324 3433 6.163476 GTGGATTTATCAGTCTGTGTACACA 58.837 40.000 26.37 26.37 39.32 3.72
2372 3481 8.406172 TGAAGTGCTTCAAAAACAGTTTATTC 57.594 30.769 11.72 0.00 45.56 1.75
2397 3506 8.826710 TCAAAGTGTTATAGTCTGACAAAACAG 58.173 33.333 17.33 9.80 39.02 3.16
2434 3552 8.840833 TTTAGATACTGTTTACTGCATGAACA 57.159 30.769 0.00 8.71 35.62 3.18
2536 3686 8.182227 ACTGTTGTAGAAAAGCAAAAGTAGTTC 58.818 33.333 0.00 0.00 40.29 3.01
2604 3754 4.926832 TGTACACAGTGTAAATGATGGTCG 59.073 41.667 15.24 0.00 34.21 4.79
2636 3786 7.732996 TGAAGCTAGTAGAAACTACTGGTTTT 58.267 34.615 18.72 14.61 46.77 2.43
2656 3811 7.712797 GGTTTTCCAAATTTCTGTCTTGAGTA 58.287 34.615 0.00 0.00 40.31 2.59
2777 3934 9.862371 TTTGCAGAGAAGATACTAAGTTTCTAG 57.138 33.333 0.00 0.00 30.49 2.43
2921 4103 0.321919 TCTGCTGCCTAACTGCCTTG 60.322 55.000 0.00 0.00 42.24 3.61
2956 4138 0.249784 CAGCCTATGATGAGCTGCGT 60.250 55.000 0.00 0.00 46.60 5.24
2971 4153 1.040893 TGCGTCACCCGGATGTCTAT 61.041 55.000 0.73 0.00 36.94 1.98
3220 4404 3.565482 TGATTGAGAACTGTGGAAAGTGC 59.435 43.478 0.00 0.00 0.00 4.40
3223 4407 1.795286 GAGAACTGTGGAAAGTGCTCG 59.205 52.381 0.00 0.00 41.86 5.03
3246 4430 1.927174 GCAGCGGTTGTAGTAGTCATG 59.073 52.381 0.00 0.00 0.00 3.07
3253 4437 3.927142 GGTTGTAGTAGTCATGTGAGTGC 59.073 47.826 0.66 0.00 0.00 4.40
3628 4870 9.313118 AGTTCATTACATTGTTTTCAGGTTTTC 57.687 29.630 0.00 0.00 0.00 2.29
3674 4916 6.096705 TGTTTTGATGTCTTGTTTGACCAGAT 59.903 34.615 0.00 0.00 36.21 2.90
3775 5028 4.038402 CACTGATTTGGTGGCTCTCTTTTT 59.962 41.667 0.00 0.00 0.00 1.94
3805 5058 7.558161 TTGCCAGTAATTAGTTGATGATCTG 57.442 36.000 0.00 0.00 0.00 2.90
3840 5093 3.429881 GTGGCTTCAAATTTTAGCTGTGC 59.570 43.478 17.19 5.88 35.30 4.57
3858 5111 2.096013 GTGCGGTCCTTTCTAATCTTGC 59.904 50.000 0.00 0.00 0.00 4.01
3912 5165 8.792830 TTTGTTCTTAAGATCCATAGTTCAGG 57.207 34.615 5.89 0.00 0.00 3.86
3928 5181 3.301794 TCAGGGATGTTCATTCATGGG 57.698 47.619 6.00 0.00 0.00 4.00
3972 5225 6.491062 TGATGAGTTTGTCCAAATCACAATCT 59.509 34.615 0.00 0.00 36.78 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
586 614 3.709587 TCTAGAAGGTTCCTGAATCGGT 58.290 45.455 0.00 0.00 0.00 4.69
587 615 4.688021 CTTCTAGAAGGTTCCTGAATCGG 58.312 47.826 22.67 0.00 34.87 4.18
622 650 2.468915 AGGTTCCCAAAACCGGAAAAA 58.531 42.857 9.46 0.00 44.82 1.94
623 651 2.162264 AGGTTCCCAAAACCGGAAAA 57.838 45.000 9.46 0.00 44.82 2.29
624 652 2.033372 GAAGGTTCCCAAAACCGGAAA 58.967 47.619 9.46 0.00 44.82 3.13
625 653 1.215924 AGAAGGTTCCCAAAACCGGAA 59.784 47.619 9.46 0.00 44.82 4.30
626 654 0.848053 AGAAGGTTCCCAAAACCGGA 59.152 50.000 9.46 0.00 44.82 5.14
627 655 2.039348 TCTAGAAGGTTCCCAAAACCGG 59.961 50.000 0.00 0.00 44.82 5.28
628 656 3.412237 TCTAGAAGGTTCCCAAAACCG 57.588 47.619 0.00 0.00 44.82 4.44
698 726 1.676006 CGGAATTTCCTATTTGCCGCT 59.324 47.619 13.45 0.00 33.30 5.52
699 727 2.119671 CGGAATTTCCTATTTGCCGC 57.880 50.000 13.45 0.00 33.30 6.53
700 728 1.676006 AGCGGAATTTCCTATTTGCCG 59.324 47.619 13.45 0.00 40.17 5.69
701 729 2.687935 TCAGCGGAATTTCCTATTTGCC 59.312 45.455 13.45 0.00 33.30 4.52
702 730 4.293415 CATCAGCGGAATTTCCTATTTGC 58.707 43.478 13.45 8.71 33.30 3.68
703 731 4.794003 GCCATCAGCGGAATTTCCTATTTG 60.794 45.833 13.45 6.47 33.30 2.32
704 732 3.319122 GCCATCAGCGGAATTTCCTATTT 59.681 43.478 13.45 0.00 33.30 1.40
705 733 2.887152 GCCATCAGCGGAATTTCCTATT 59.113 45.455 13.45 0.00 33.30 1.73
706 734 2.508526 GCCATCAGCGGAATTTCCTAT 58.491 47.619 13.45 0.00 33.30 2.57
707 735 1.967319 GCCATCAGCGGAATTTCCTA 58.033 50.000 13.45 0.00 33.30 2.94
708 736 2.799176 GCCATCAGCGGAATTTCCT 58.201 52.632 13.45 0.00 33.30 3.36
718 746 3.272334 CTAACCGGCGCCATCAGC 61.272 66.667 28.98 0.00 38.52 4.26
719 747 2.588877 CCTAACCGGCGCCATCAG 60.589 66.667 28.98 16.63 0.00 2.90
720 748 3.078196 TCCTAACCGGCGCCATCA 61.078 61.111 28.98 7.07 0.00 3.07
721 749 2.280186 CTCCTAACCGGCGCCATC 60.280 66.667 28.98 0.00 0.00 3.51
722 750 3.861797 CCTCCTAACCGGCGCCAT 61.862 66.667 28.98 14.62 0.00 4.40
724 752 4.222847 CTCCTCCTAACCGGCGCC 62.223 72.222 19.07 19.07 0.00 6.53
725 753 4.893601 GCTCCTCCTAACCGGCGC 62.894 72.222 0.00 0.00 0.00 6.53
726 754 3.140225 GAGCTCCTCCTAACCGGCG 62.140 68.421 0.00 0.00 0.00 6.46
727 755 2.798364 GGAGCTCCTCCTAACCGGC 61.798 68.421 26.25 0.00 46.41 6.13
728 756 3.539842 GGAGCTCCTCCTAACCGG 58.460 66.667 26.25 0.00 46.41 5.28
828 857 3.068691 CCGTCCAGGGCTTCGAGA 61.069 66.667 0.00 0.00 35.97 4.04
1550 1738 3.181476 ACATTTGGCAAGAACAGAACCAC 60.181 43.478 0.00 0.00 0.00 4.16
1575 1765 0.538287 AAGAACTGCACCCAGGAAGC 60.538 55.000 0.00 0.00 43.53 3.86
1576 1766 1.242076 CAAGAACTGCACCCAGGAAG 58.758 55.000 0.00 0.00 43.53 3.46
1577 1767 3.419793 CAAGAACTGCACCCAGGAA 57.580 52.632 0.00 0.00 43.53 3.36
1587 1777 0.594796 GCAACCAACGGCAAGAACTG 60.595 55.000 0.00 0.00 0.00 3.16
1615 1805 5.752472 TGAAAACACAATCACAAATGCGATT 59.248 32.000 0.00 0.00 32.04 3.34
1637 1827 6.166984 ACTCTGAATTTTCTGACTGACTGA 57.833 37.500 0.00 0.00 32.70 3.41
1638 1828 9.814899 ATATACTCTGAATTTTCTGACTGACTG 57.185 33.333 0.00 0.00 32.70 3.51
1718 1918 1.609210 TCCCAGCATCACGGACAGA 60.609 57.895 0.00 0.00 0.00 3.41
2030 2269 3.772025 CACTTGTTAGGAGATCTGGAGGT 59.228 47.826 0.00 0.00 0.00 3.85
2032 2271 5.667539 TTCACTTGTTAGGAGATCTGGAG 57.332 43.478 0.00 0.00 0.00 3.86
2033 2272 5.306937 TGTTTCACTTGTTAGGAGATCTGGA 59.693 40.000 0.00 0.00 0.00 3.86
2036 2275 6.426646 ACTGTTTCACTTGTTAGGAGATCT 57.573 37.500 0.00 0.00 0.00 2.75
2178 3239 2.224548 GCACCCCACTAACAAAGACTCT 60.225 50.000 0.00 0.00 0.00 3.24
2323 3432 5.760253 AGAGTTCAGACCAACATTTACACTG 59.240 40.000 0.00 0.00 0.00 3.66
2324 3433 5.760253 CAGAGTTCAGACCAACATTTACACT 59.240 40.000 0.00 0.00 0.00 3.55
2333 3442 2.545946 GCACTTCAGAGTTCAGACCAAC 59.454 50.000 0.00 0.00 32.54 3.77
2372 3481 8.612619 ACTGTTTTGTCAGACTATAACACTTTG 58.387 33.333 1.31 1.66 38.63 2.77
2536 3686 1.271871 TGGCACCTACTGTTCCCATTG 60.272 52.381 0.00 0.00 27.60 2.82
2604 3754 6.275494 AGTTTCTACTAGCTTCAGAGTTCC 57.725 41.667 0.00 0.00 31.21 3.62
2635 3785 8.924511 ATCTTACTCAAGACAGAAATTTGGAA 57.075 30.769 0.00 0.00 43.50 3.53
2647 3798 8.690680 ACGAACTGAAATATCTTACTCAAGAC 57.309 34.615 0.00 0.00 43.50 3.01
2654 3809 8.056571 CGAAATGGACGAACTGAAATATCTTAC 58.943 37.037 0.00 0.00 0.00 2.34
2656 3811 6.594159 ACGAAATGGACGAACTGAAATATCTT 59.406 34.615 0.00 0.00 34.70 2.40
2662 3817 5.231702 TGATACGAAATGGACGAACTGAAA 58.768 37.500 0.00 0.00 34.70 2.69
2777 3934 9.937175 GATACTATCTGAATTTTGTTAACAGGC 57.063 33.333 8.56 0.00 0.00 4.85
2848 4013 8.133627 AGATCAAGAAGTCAAAACATGAAACAG 58.866 33.333 0.00 0.00 40.50 3.16
2856 4021 7.572523 ATGACAAGATCAAGAAGTCAAAACA 57.427 32.000 0.00 0.00 41.93 2.83
2956 4138 2.430694 CTGTGAATAGACATCCGGGTGA 59.569 50.000 24.73 0.00 0.00 4.02
2971 4153 5.714333 AGCTCTGATCTTTCTCTACTGTGAA 59.286 40.000 0.00 0.00 0.00 3.18
3220 4404 2.048597 TACAACCGCTGCACCGAG 60.049 61.111 2.22 0.00 0.00 4.63
3222 4406 1.076533 CTACTACAACCGCTGCACCG 61.077 60.000 0.00 0.00 0.00 4.94
3223 4407 0.037605 ACTACTACAACCGCTGCACC 60.038 55.000 0.00 0.00 0.00 5.01
3253 4437 4.015084 AGAAATGAATGCCAGAAGAGTGG 58.985 43.478 0.00 0.00 41.01 4.00
3628 4870 6.259550 ACAAAAAGAAGGCAGCTTATGTAG 57.740 37.500 0.00 0.00 0.00 2.74
3805 5058 3.873910 TGAAGCCACATAGCTAAACTCC 58.126 45.455 0.00 0.00 44.11 3.85
3840 5093 4.003648 ACAAGCAAGATTAGAAAGGACCG 58.996 43.478 0.00 0.00 0.00 4.79
3912 5165 7.555087 TGTTTATTTCCCATGAATGAACATCC 58.445 34.615 10.20 0.00 37.77 3.51
3915 5168 6.817641 GCATGTTTATTTCCCATGAATGAACA 59.182 34.615 14.34 14.34 42.93 3.18


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

AutoCloner maintained by Alex Coulton.