Multiple sequence alignment - TraesCS3A01G467800

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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 TraesCS3A01G467800 chr3A 100.000 4475 0 0 1 4475 700942525 700946999 0.000000e+00 8264.0
1 TraesCS3A01G467800 chr3A 81.905 945 125 22 2873 3774 700893477 700894418 0.000000e+00 756.0
2 TraesCS3A01G467800 chr3A 81.698 754 111 21 3018 3746 701123806 701124557 1.780000e-168 603.0
3 TraesCS3A01G467800 chr3A 80.426 751 93 31 2056 2790 700953017 700953729 1.430000e-144 523.0
4 TraesCS3A01G467800 chr3A 80.702 627 90 18 2187 2789 701139652 701140271 4.080000e-125 459.0
5 TraesCS3A01G467800 chr3A 84.016 488 60 11 2261 2732 701123304 701123789 1.900000e-123 453.0
6 TraesCS3A01G467800 chr3A 86.992 369 38 6 2877 3239 700909030 700909394 1.500000e-109 407.0
7 TraesCS3A01G467800 chr3A 86.475 244 26 6 2191 2432 700908503 700908741 1.230000e-65 261.0
8 TraesCS3A01G467800 chr3A 79.357 373 39 19 1507 1847 701139287 701139653 1.250000e-55 228.0
9 TraesCS3A01G467800 chr3A 84.783 230 28 3 3548 3774 700911725 700911950 1.620000e-54 224.0
10 TraesCS3A01G467800 chr3A 82.000 250 24 13 2873 3121 701140251 701140480 4.570000e-45 193.0
11 TraesCS3A01G467800 chr3A 94.167 120 7 0 866 985 700959236 700959355 2.750000e-42 183.0
12 TraesCS3A01G467800 chr3A 90.977 133 12 0 3546 3678 701140899 701141031 3.560000e-41 180.0
13 TraesCS3A01G467800 chr3A 90.370 135 8 5 801 935 700891041 700891170 5.950000e-39 172.0
14 TraesCS3A01G467800 chr3A 82.836 134 15 7 805 935 701137972 701138100 3.660000e-21 113.0
15 TraesCS3A01G467800 chr3A 91.379 58 3 2 800 855 700890990 700891047 1.330000e-10 78.7
16 TraesCS3A01G467800 chr3A 89.655 58 6 0 2111 2168 700908446 700908503 1.730000e-09 75.0
17 TraesCS3A01G467800 chr3B 89.757 1484 97 23 1974 3445 755709689 755711129 0.000000e+00 1847.0
18 TraesCS3A01G467800 chr3B 90.012 811 41 11 981 1759 755708147 755708949 0.000000e+00 1013.0
19 TraesCS3A01G467800 chr3B 90.566 689 44 8 3788 4475 103402006 103401338 0.000000e+00 893.0
20 TraesCS3A01G467800 chr3B 81.398 844 103 38 1968 2791 754719781 754720590 1.360000e-179 640.0
21 TraesCS3A01G467800 chr3B 82.216 776 96 21 3039 3774 755575764 755576537 8.170000e-177 630.0
22 TraesCS3A01G467800 chr3B 79.947 758 89 40 2056 2790 755604956 755605673 2.400000e-137 499.0
23 TraesCS3A01G467800 chr3B 84.356 505 71 5 3018 3514 755771291 755771795 5.200000e-134 488.0
24 TraesCS3A01G467800 chr3B 79.745 706 92 7 2850 3514 755659986 755660681 8.770000e-127 464.0
25 TraesCS3A01G467800 chr3B 84.874 476 53 12 2309 2766 754770970 754771444 3.150000e-126 462.0
26 TraesCS3A01G467800 chr3B 80.878 638 76 24 3150 3745 755606046 755606679 1.130000e-125 460.0
27 TraesCS3A01G467800 chr3B 85.542 415 43 11 2378 2784 755575242 755575647 6.920000e-113 418.0
28 TraesCS3A01G467800 chr3B 93.309 269 18 0 3506 3774 755722087 755722355 9.020000e-107 398.0
29 TraesCS3A01G467800 chr3B 82.068 474 48 17 1508 1953 754719126 754719590 1.970000e-98 370.0
30 TraesCS3A01G467800 chr3B 87.789 303 24 7 674 976 755707803 755708092 4.290000e-90 342.0
31 TraesCS3A01G467800 chr3B 91.005 189 11 3 1754 1942 755709271 755709453 2.670000e-62 250.0
32 TraesCS3A01G467800 chr3B 91.241 137 11 1 3546 3681 756081689 756081553 7.640000e-43 185.0
33 TraesCS3A01G467800 chr3B 82.775 209 21 11 3538 3746 755660749 755660942 5.950000e-39 172.0
34 TraesCS3A01G467800 chr3B 88.060 134 15 1 1623 1756 755658038 755658170 1.670000e-34 158.0
35 TraesCS3A01G467800 chr3B 75.414 423 47 33 589 979 755603794 755604191 7.750000e-33 152.0
36 TraesCS3A01G467800 chr3B 83.444 151 20 4 2873 3021 755575632 755575779 7.810000e-28 135.0
37 TraesCS3A01G467800 chr3B 92.308 52 2 2 1528 1579 755657423 755657472 6.210000e-09 73.1
38 TraesCS3A01G467800 chr3B 95.349 43 2 0 1528 1570 754770567 754770609 8.030000e-08 69.4
39 TraesCS3A01G467800 chr6D 94.493 690 19 3 3786 4475 59625181 59625851 0.000000e+00 1046.0
40 TraesCS3A01G467800 chr4D 94.331 688 21 2 3788 4475 432947859 432947190 0.000000e+00 1038.0
41 TraesCS3A01G467800 chr4B 94.323 687 16 4 3789 4475 434460703 434461366 0.000000e+00 1031.0
42 TraesCS3A01G467800 chr4B 75.938 320 41 20 1492 1796 649490979 649491277 1.010000e-26 132.0
43 TraesCS3A01G467800 chr6A 94.323 687 5 7 3789 4475 55703472 55704124 0.000000e+00 1022.0
44 TraesCS3A01G467800 chr6A 96.545 521 18 0 15 535 222690428 222690948 0.000000e+00 863.0
45 TraesCS3A01G467800 chr7D 91.486 693 37 16 3788 4475 360329418 360330093 0.000000e+00 933.0
46 TraesCS3A01G467800 chr7B 91.105 697 39 11 3789 4475 524724264 524724947 0.000000e+00 922.0
47 TraesCS3A01G467800 chr2A 97.552 531 12 1 15 545 610714615 610715144 0.000000e+00 907.0
48 TraesCS3A01G467800 chr2A 92.235 528 20 8 3788 4313 525610270 525609762 0.000000e+00 728.0
49 TraesCS3A01G467800 chr2A 100.000 71 0 0 4405 4475 525609780 525609710 1.010000e-26 132.0
50 TraesCS3A01G467800 chr5A 96.905 517 16 0 19 535 311004012 311004528 0.000000e+00 867.0
51 TraesCS3A01G467800 chr5A 96.545 521 18 0 15 535 472460512 472461032 0.000000e+00 863.0
52 TraesCS3A01G467800 chr5A 96.367 523 19 0 15 537 685009981 685010503 0.000000e+00 861.0
53 TraesCS3A01G467800 chr5A 76.037 217 32 14 2876 3088 688244013 688244213 1.330000e-15 95.3
54 TraesCS3A01G467800 chr7A 96.045 531 21 0 15 545 330459537 330459007 0.000000e+00 865.0
55 TraesCS3A01G467800 chr7A 96.374 524 17 2 15 538 655300057 655300578 0.000000e+00 861.0
56 TraesCS3A01G467800 chr4A 96.212 528 19 1 15 542 183855693 183856219 0.000000e+00 863.0
57 TraesCS3A01G467800 chr4A 86.773 688 52 23 3789 4475 578535646 578536295 0.000000e+00 730.0
58 TraesCS3A01G467800 chr1A 96.360 522 18 1 15 536 516081231 516081751 0.000000e+00 857.0
59 TraesCS3A01G467800 chr3D 88.777 695 40 13 3789 4475 110402087 110401423 0.000000e+00 817.0
60 TraesCS3A01G467800 chr3D 86.311 694 63 18 3789 4472 565393844 565393173 0.000000e+00 726.0
61 TraesCS3A01G467800 chr3D 82.750 829 109 17 2876 3673 566422738 566421913 0.000000e+00 708.0
62 TraesCS3A01G467800 chr3D 82.464 844 97 35 1968 2791 566132229 566131417 0.000000e+00 691.0
63 TraesCS3A01G467800 chr3D 80.199 803 100 32 2876 3642 566300242 566299463 8.460000e-152 547.0
64 TraesCS3A01G467800 chr3D 84.100 478 58 11 3205 3681 566101124 566100664 3.180000e-121 446.0
65 TraesCS3A01G467800 chr3D 83.436 489 62 12 2261 2732 566300746 566300260 1.910000e-118 436.0
66 TraesCS3A01G467800 chr3D 80.143 559 70 9 2998 3519 566392607 566392053 3.270000e-101 379.0
67 TraesCS3A01G467800 chr3D 83.533 334 35 12 1635 1953 566132745 566132417 1.220000e-75 294.0
68 TraesCS3A01G467800 chr3D 80.000 430 49 17 1511 1914 566301189 566300771 2.640000e-72 283.0
69 TraesCS3A01G467800 chr3D 85.792 183 19 6 801 982 566423889 566423713 2.130000e-43 187.0
70 TraesCS3A01G467800 chr3D 93.043 115 6 2 867 979 566302059 566301945 2.770000e-37 167.0
71 TraesCS3A01G467800 chr3D 81.773 203 22 11 3544 3746 566391986 566391799 5.990000e-34 156.0
72 TraesCS3A01G467800 chr3D 83.041 171 16 5 2876 3045 566131436 566131278 4.670000e-30 143.0
73 TraesCS3A01G467800 chr3D 86.275 102 10 2 1511 1611 566137700 566137602 1.700000e-19 108.0
74 TraesCS3A01G467800 chr3D 97.917 48 1 0 808 855 566423930 566423883 2.870000e-12 84.2
75 TraesCS3A01G467800 chr3D 92.308 52 2 2 1528 1579 566394260 566394211 6.210000e-09 73.1
76 TraesCS3A01G467800 chr5B 85.408 233 21 8 4249 4475 419843796 419843571 3.480000e-56 230.0
77 TraesCS3A01G467800 chrUn 90.511 137 12 1 3546 3681 408041165 408041301 3.560000e-41 180.0


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 TraesCS3A01G467800 chr3A 700942525 700946999 4474 False 8264.000000 8264 100.000000 1 4475 1 chr3A.!!$F1 4474
1 TraesCS3A01G467800 chr3A 701123304 701124557 1253 False 528.000000 603 82.857000 2261 3746 2 chr3A.!!$F6 1485
2 TraesCS3A01G467800 chr3A 700953017 700953729 712 False 523.000000 523 80.426000 2056 2790 1 chr3A.!!$F2 734
3 TraesCS3A01G467800 chr3A 700890990 700894418 3428 False 335.566667 756 87.884667 800 3774 3 chr3A.!!$F4 2974
4 TraesCS3A01G467800 chr3A 700908446 700911950 3504 False 241.750000 407 86.976250 2111 3774 4 chr3A.!!$F5 1663
5 TraesCS3A01G467800 chr3A 701137972 701141031 3059 False 234.600000 459 83.174400 805 3678 5 chr3A.!!$F7 2873
6 TraesCS3A01G467800 chr3B 103401338 103402006 668 True 893.000000 893 90.566000 3788 4475 1 chr3B.!!$R1 687
7 TraesCS3A01G467800 chr3B 755707803 755711129 3326 False 863.000000 1847 89.640750 674 3445 4 chr3B.!!$F8 2771
8 TraesCS3A01G467800 chr3B 754719126 754720590 1464 False 505.000000 640 81.733000 1508 2791 2 chr3B.!!$F3 1283
9 TraesCS3A01G467800 chr3B 755771291 755771795 504 False 488.000000 488 84.356000 3018 3514 1 chr3B.!!$F2 496
10 TraesCS3A01G467800 chr3B 755575242 755576537 1295 False 394.333333 630 83.734000 2378 3774 3 chr3B.!!$F5 1396
11 TraesCS3A01G467800 chr3B 755603794 755606679 2885 False 370.333333 499 78.746333 589 3745 3 chr3B.!!$F6 3156
12 TraesCS3A01G467800 chr3B 754770567 754771444 877 False 265.700000 462 90.111500 1528 2766 2 chr3B.!!$F4 1238
13 TraesCS3A01G467800 chr3B 755657423 755660942 3519 False 216.775000 464 85.722000 1528 3746 4 chr3B.!!$F7 2218
14 TraesCS3A01G467800 chr6D 59625181 59625851 670 False 1046.000000 1046 94.493000 3786 4475 1 chr6D.!!$F1 689
15 TraesCS3A01G467800 chr4D 432947190 432947859 669 True 1038.000000 1038 94.331000 3788 4475 1 chr4D.!!$R1 687
16 TraesCS3A01G467800 chr4B 434460703 434461366 663 False 1031.000000 1031 94.323000 3789 4475 1 chr4B.!!$F1 686
17 TraesCS3A01G467800 chr6A 55703472 55704124 652 False 1022.000000 1022 94.323000 3789 4475 1 chr6A.!!$F1 686
18 TraesCS3A01G467800 chr6A 222690428 222690948 520 False 863.000000 863 96.545000 15 535 1 chr6A.!!$F2 520
19 TraesCS3A01G467800 chr7D 360329418 360330093 675 False 933.000000 933 91.486000 3788 4475 1 chr7D.!!$F1 687
20 TraesCS3A01G467800 chr7B 524724264 524724947 683 False 922.000000 922 91.105000 3789 4475 1 chr7B.!!$F1 686
21 TraesCS3A01G467800 chr2A 610714615 610715144 529 False 907.000000 907 97.552000 15 545 1 chr2A.!!$F1 530
22 TraesCS3A01G467800 chr2A 525609710 525610270 560 True 430.000000 728 96.117500 3788 4475 2 chr2A.!!$R1 687
23 TraesCS3A01G467800 chr5A 311004012 311004528 516 False 867.000000 867 96.905000 19 535 1 chr5A.!!$F1 516
24 TraesCS3A01G467800 chr5A 472460512 472461032 520 False 863.000000 863 96.545000 15 535 1 chr5A.!!$F2 520
25 TraesCS3A01G467800 chr5A 685009981 685010503 522 False 861.000000 861 96.367000 15 537 1 chr5A.!!$F3 522
26 TraesCS3A01G467800 chr7A 330459007 330459537 530 True 865.000000 865 96.045000 15 545 1 chr7A.!!$R1 530
27 TraesCS3A01G467800 chr7A 655300057 655300578 521 False 861.000000 861 96.374000 15 538 1 chr7A.!!$F1 523
28 TraesCS3A01G467800 chr4A 183855693 183856219 526 False 863.000000 863 96.212000 15 542 1 chr4A.!!$F1 527
29 TraesCS3A01G467800 chr4A 578535646 578536295 649 False 730.000000 730 86.773000 3789 4475 1 chr4A.!!$F2 686
30 TraesCS3A01G467800 chr1A 516081231 516081751 520 False 857.000000 857 96.360000 15 536 1 chr1A.!!$F1 521
31 TraesCS3A01G467800 chr3D 110401423 110402087 664 True 817.000000 817 88.777000 3789 4475 1 chr3D.!!$R1 686
32 TraesCS3A01G467800 chr3D 565393173 565393844 671 True 726.000000 726 86.311000 3789 4472 1 chr3D.!!$R2 683
33 TraesCS3A01G467800 chr3D 566131278 566132745 1467 True 376.000000 691 83.012667 1635 3045 3 chr3D.!!$R5 1410
34 TraesCS3A01G467800 chr3D 566299463 566302059 2596 True 358.250000 547 84.169500 867 3642 4 chr3D.!!$R6 2775
35 TraesCS3A01G467800 chr3D 566421913 566423930 2017 True 326.400000 708 88.819667 801 3673 3 chr3D.!!$R8 2872
36 TraesCS3A01G467800 chr3D 566391799 566394260 2461 True 202.700000 379 84.741333 1528 3746 3 chr3D.!!$R7 2218

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
893 953 0.108585 CATACCCATCACCTTCCCCG 59.891 60.000 0.0 0.0 0.00 5.73 F
2274 6165 0.887247 TGTGGGTGTATGTGCAATGC 59.113 50.000 0.0 0.0 0.00 3.56 F
2996 7701 1.202976 AGAGATTTGTTGGCACAGGCT 60.203 47.619 0.0 0.0 42.39 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2802 7480 1.440938 AACAGTTTTACCGCTGCGCA 61.441 50.000 18.00 10.98 36.26 6.09 R
3451 10337 0.389948 AAGAACGAAGCCAGTAGCCG 60.390 55.000 0.00 0.00 45.47 5.52 R
4119 11093 1.404035 CTGCTGCTCATGCTTGCATTA 59.596 47.619 5.24 0.00 43.56 1.90 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
41 42 5.362263 GTTGTGTCCCACTACTCAGTTTTA 58.638 41.667 2.43 0.00 37.20 1.52
124 125 3.126343 GCCATCGTTCCGTTAGATGTTTT 59.874 43.478 4.33 0.00 39.89 2.43
256 257 3.579302 TGGCCCCACTTGTCAGGG 61.579 66.667 0.00 0.00 45.04 4.45
453 454 3.263261 TGAACACGTGTCTAACAAAGCA 58.737 40.909 23.61 6.39 0.00 3.91
469 470 4.883006 ACAAAGCAATGGCATTTTTGAGTT 59.117 33.333 29.99 14.64 44.61 3.01
477 478 5.793026 TGGCATTTTTGAGTTGTTGAAAC 57.207 34.783 0.00 0.00 0.00 2.78
505 506 2.375174 TGGCAAAACTGAGTAGTGGGAT 59.625 45.455 0.00 0.00 37.19 3.85
538 539 7.913674 TGGCATAAATGATAAAAACCCAAAC 57.086 32.000 0.00 0.00 0.00 2.93
546 547 8.725405 AATGATAAAAACCCAAACGAAAAAGT 57.275 26.923 0.00 0.00 0.00 2.66
547 548 7.758613 TGATAAAAACCCAAACGAAAAAGTC 57.241 32.000 0.00 0.00 0.00 3.01
548 549 7.321153 TGATAAAAACCCAAACGAAAAAGTCA 58.679 30.769 0.00 0.00 0.00 3.41
549 550 7.489757 TGATAAAAACCCAAACGAAAAAGTCAG 59.510 33.333 0.00 0.00 0.00 3.51
550 551 3.793797 AACCCAAACGAAAAAGTCAGG 57.206 42.857 0.00 0.00 0.00 3.86
551 552 2.730382 ACCCAAACGAAAAAGTCAGGT 58.270 42.857 0.00 0.00 0.00 4.00
552 553 3.093814 ACCCAAACGAAAAAGTCAGGTT 58.906 40.909 0.00 0.00 0.00 3.50
553 554 4.271661 ACCCAAACGAAAAAGTCAGGTTA 58.728 39.130 0.00 0.00 0.00 2.85
554 555 4.891168 ACCCAAACGAAAAAGTCAGGTTAT 59.109 37.500 0.00 0.00 0.00 1.89
555 556 5.219633 CCCAAACGAAAAAGTCAGGTTATG 58.780 41.667 0.00 0.00 0.00 1.90
556 557 5.221165 CCCAAACGAAAAAGTCAGGTTATGT 60.221 40.000 0.00 0.00 0.00 2.29
557 558 6.016943 CCCAAACGAAAAAGTCAGGTTATGTA 60.017 38.462 0.00 0.00 0.00 2.29
558 559 7.075741 CCAAACGAAAAAGTCAGGTTATGTAG 58.924 38.462 0.00 0.00 0.00 2.74
559 560 5.857822 ACGAAAAAGTCAGGTTATGTAGC 57.142 39.130 0.00 0.00 0.00 3.58
560 561 5.548406 ACGAAAAAGTCAGGTTATGTAGCT 58.452 37.500 0.00 0.00 34.10 3.32
561 562 6.694447 ACGAAAAAGTCAGGTTATGTAGCTA 58.306 36.000 0.00 0.00 32.12 3.32
562 563 7.156673 ACGAAAAAGTCAGGTTATGTAGCTAA 58.843 34.615 0.00 0.00 32.12 3.09
563 564 7.658575 ACGAAAAAGTCAGGTTATGTAGCTAAA 59.341 33.333 0.00 0.00 32.12 1.85
564 565 7.955864 CGAAAAAGTCAGGTTATGTAGCTAAAC 59.044 37.037 0.00 0.00 32.12 2.01
565 566 8.919777 AAAAAGTCAGGTTATGTAGCTAAACT 57.080 30.769 0.00 0.00 33.44 2.66
566 567 7.907214 AAAGTCAGGTTATGTAGCTAAACTG 57.093 36.000 5.76 5.76 44.36 3.16
571 572 8.492673 TCAGGTTATGTAGCTAAACTGAAATG 57.507 34.615 11.45 0.00 46.99 2.32
572 573 8.318412 TCAGGTTATGTAGCTAAACTGAAATGA 58.682 33.333 11.45 1.28 46.99 2.57
573 574 8.946085 CAGGTTATGTAGCTAAACTGAAATGAA 58.054 33.333 6.18 0.00 45.34 2.57
574 575 9.515226 AGGTTATGTAGCTAAACTGAAATGAAA 57.485 29.630 0.00 0.00 31.41 2.69
579 580 7.136119 TGTAGCTAAACTGAAATGAAAAACCG 58.864 34.615 0.00 0.00 0.00 4.44
580 581 4.982295 AGCTAAACTGAAATGAAAAACCGC 59.018 37.500 0.00 0.00 0.00 5.68
581 582 4.149922 GCTAAACTGAAATGAAAAACCGCC 59.850 41.667 0.00 0.00 0.00 6.13
582 583 4.400529 AAACTGAAATGAAAAACCGCCT 57.599 36.364 0.00 0.00 0.00 5.52
583 584 3.369546 ACTGAAATGAAAAACCGCCTG 57.630 42.857 0.00 0.00 0.00 4.85
584 585 2.061028 CTGAAATGAAAAACCGCCTGC 58.939 47.619 0.00 0.00 0.00 4.85
585 586 1.410517 TGAAATGAAAAACCGCCTGCA 59.589 42.857 0.00 0.00 0.00 4.41
586 587 1.792367 GAAATGAAAAACCGCCTGCAC 59.208 47.619 0.00 0.00 0.00 4.57
587 588 0.749649 AATGAAAAACCGCCTGCACA 59.250 45.000 0.00 0.00 0.00 4.57
588 589 0.749649 ATGAAAAACCGCCTGCACAA 59.250 45.000 0.00 0.00 0.00 3.33
589 590 0.532573 TGAAAAACCGCCTGCACAAA 59.467 45.000 0.00 0.00 0.00 2.83
590 591 1.066858 TGAAAAACCGCCTGCACAAAA 60.067 42.857 0.00 0.00 0.00 2.44
591 592 2.003301 GAAAAACCGCCTGCACAAAAA 58.997 42.857 0.00 0.00 0.00 1.94
592 593 2.323968 AAAACCGCCTGCACAAAAAT 57.676 40.000 0.00 0.00 0.00 1.82
593 594 1.580815 AAACCGCCTGCACAAAAATG 58.419 45.000 0.00 0.00 0.00 2.32
594 595 0.879839 AACCGCCTGCACAAAAATGC 60.880 50.000 0.00 0.00 46.32 3.56
604 605 5.309323 TGCACAAAAATGCTGGTATACTC 57.691 39.130 2.25 0.00 46.28 2.59
605 606 4.142708 TGCACAAAAATGCTGGTATACTCG 60.143 41.667 2.25 0.00 46.28 4.18
608 609 4.634443 ACAAAAATGCTGGTATACTCGGAC 59.366 41.667 2.25 0.00 0.00 4.79
616 617 1.335689 GGTATACTCGGACGATGTGGC 60.336 57.143 2.25 0.00 0.00 5.01
619 620 1.040893 TACTCGGACGATGTGGCCAT 61.041 55.000 9.72 0.00 0.00 4.40
624 625 0.679640 GGACGATGTGGCCATGGAAA 60.680 55.000 18.40 0.00 31.80 3.13
628 629 2.026641 CGATGTGGCCATGGAAAGAAT 58.973 47.619 18.40 1.10 0.00 2.40
630 631 1.462616 TGTGGCCATGGAAAGAATCG 58.537 50.000 18.40 0.00 0.00 3.34
635 636 1.597663 GCCATGGAAAGAATCGTACCG 59.402 52.381 18.40 0.00 0.00 4.02
656 657 3.490896 CGCGAAATTTCTAGATGCTAGCA 59.509 43.478 21.85 21.85 0.00 3.49
657 658 4.151335 CGCGAAATTTCTAGATGCTAGCAT 59.849 41.667 29.97 29.97 39.69 3.79
658 659 5.346011 CGCGAAATTTCTAGATGCTAGCATA 59.654 40.000 29.64 14.75 36.70 3.14
659 660 6.453527 CGCGAAATTTCTAGATGCTAGCATAG 60.454 42.308 29.64 23.11 43.09 2.23
697 699 2.093658 ACATGGTGGACGGTGAGTAATC 60.094 50.000 0.00 0.00 0.00 1.75
698 700 1.634960 TGGTGGACGGTGAGTAATCA 58.365 50.000 0.00 0.00 0.00 2.57
713 717 5.873732 GAGTAATCACTCCTTGCATTTCAC 58.126 41.667 0.00 0.00 44.72 3.18
715 719 5.645497 AGTAATCACTCCTTGCATTTCACTC 59.355 40.000 0.00 0.00 0.00 3.51
722 726 2.159282 CCTTGCATTTCACTCTGCATCC 60.159 50.000 0.00 0.00 46.87 3.51
731 735 3.295093 TCACTCTGCATCCCAAAAACAA 58.705 40.909 0.00 0.00 0.00 2.83
739 743 1.422531 TCCCAAAAACAAGCAGGCAT 58.577 45.000 0.00 0.00 0.00 4.40
757 763 2.124942 GCAGGCAGGCAGAGGTAC 60.125 66.667 0.00 0.00 0.00 3.34
758 764 2.586792 CAGGCAGGCAGAGGTACC 59.413 66.667 2.73 2.73 0.00 3.34
760 766 3.798511 GGCAGGCAGAGGTACCCC 61.799 72.222 8.74 2.05 0.00 4.95
761 767 3.009115 GCAGGCAGAGGTACCCCA 61.009 66.667 8.74 0.00 0.00 4.96
763 769 2.683933 AGGCAGAGGTACCCCACG 60.684 66.667 8.74 0.00 0.00 4.94
764 770 3.782443 GGCAGAGGTACCCCACGG 61.782 72.222 8.74 2.79 0.00 4.94
768 774 3.782443 GAGGTACCCCACGGCCAG 61.782 72.222 8.74 0.00 0.00 4.85
796 802 5.715439 ACCATCTCATATCAGTTTTCCCA 57.285 39.130 0.00 0.00 0.00 4.37
893 953 0.108585 CATACCCATCACCTTCCCCG 59.891 60.000 0.00 0.00 0.00 5.73
1107 1246 2.022934 GGCGCCTACTTGTACTACTCT 58.977 52.381 22.15 0.00 0.00 3.24
1108 1247 3.209410 GGCGCCTACTTGTACTACTCTA 58.791 50.000 22.15 0.00 0.00 2.43
1111 1250 4.377226 GCGCCTACTTGTACTACTCTATCG 60.377 50.000 0.00 0.00 0.00 2.92
1126 1795 9.469807 ACTACTCTATCGAAATGCTAATTCTTG 57.530 33.333 0.00 0.00 0.00 3.02
1135 1822 7.556275 TCGAAATGCTAATTCTTGTTTCCCTAT 59.444 33.333 0.00 0.00 0.00 2.57
1262 2094 2.024369 AGGACAAGGTTGGGTGACTTTT 60.024 45.455 0.00 0.00 0.00 2.27
1263 2095 3.203487 AGGACAAGGTTGGGTGACTTTTA 59.797 43.478 0.00 0.00 0.00 1.52
1387 2225 1.172812 AGCTCGCCCAAACAGTTTCC 61.173 55.000 0.00 0.00 0.00 3.13
1388 2226 1.172812 GCTCGCCCAAACAGTTTCCT 61.173 55.000 0.00 0.00 0.00 3.36
1429 2277 2.508526 ACACCTGCCTGAGAAAACATC 58.491 47.619 0.00 0.00 0.00 3.06
1442 2290 7.941238 CCTGAGAAAACATCATATATCAACCCT 59.059 37.037 0.00 0.00 0.00 4.34
1485 2334 2.358984 GAGCCGGGTTTAACGCCA 60.359 61.111 8.00 0.00 0.00 5.69
1493 2840 1.609841 GGGTTTAACGCCAGTAGTGCT 60.610 52.381 0.35 0.00 0.00 4.40
1526 2883 5.297776 AGGCCTCATCATTTGATAAACTTCG 59.702 40.000 0.00 0.00 32.72 3.79
1527 2884 5.066505 GGCCTCATCATTTGATAAACTTCGT 59.933 40.000 0.00 0.00 32.72 3.85
1528 2885 6.404734 GGCCTCATCATTTGATAAACTTCGTT 60.405 38.462 0.00 0.00 32.72 3.85
1591 2954 2.097541 GTGTAACTGTTGTTCGACGAGC 60.098 50.000 4.57 4.57 37.59 5.03
1619 2998 2.564062 CCCAACTACTAGTCACCGGAAA 59.436 50.000 9.46 0.00 0.00 3.13
1620 2999 3.007182 CCCAACTACTAGTCACCGGAAAA 59.993 47.826 9.46 0.00 0.00 2.29
1881 5562 5.689383 TTTTCTTCTAAAATGCGAGCTGT 57.311 34.783 0.00 0.00 0.00 4.40
1883 5564 5.779806 TTCTTCTAAAATGCGAGCTGTAC 57.220 39.130 0.00 0.00 0.00 2.90
1885 5566 3.603158 TCTAAAATGCGAGCTGTACCA 57.397 42.857 0.00 0.00 0.00 3.25
1892 5573 5.835113 AATGCGAGCTGTACCAATTTAAT 57.165 34.783 0.00 0.00 0.00 1.40
1903 5585 7.413988 GCTGTACCAATTTAATTTTCCAATGGC 60.414 37.037 0.00 0.00 0.00 4.40
1926 5608 3.726557 TTGGAATCCTGATTGTCAGCT 57.273 42.857 0.00 0.00 42.98 4.24
1966 5722 5.742926 GCTACCGTCTAGTATTCAAGTTGAC 59.257 44.000 4.68 0.00 32.03 3.18
1983 5869 5.445964 AGTTGACCAAGTTAGGAAACATGT 58.554 37.500 0.00 0.00 38.12 3.21
2006 5892 1.118838 TTTTTGTTGAGGCCACCCTG 58.881 50.000 5.01 0.00 43.12 4.45
2029 5915 4.879545 GCGAAGGGTTTATGATCTGGTAAA 59.120 41.667 0.00 0.00 0.00 2.01
2043 5929 6.953520 TGATCTGGTAAAATGGTTTCTGGAAT 59.046 34.615 0.00 0.00 0.00 3.01
2045 5931 6.991938 TCTGGTAAAATGGTTTCTGGAATTG 58.008 36.000 0.00 0.00 0.00 2.32
2046 5932 6.780031 TCTGGTAAAATGGTTTCTGGAATTGA 59.220 34.615 0.00 0.00 0.00 2.57
2047 5933 6.754193 TGGTAAAATGGTTTCTGGAATTGAC 58.246 36.000 0.00 0.00 0.00 3.18
2048 5934 5.861787 GGTAAAATGGTTTCTGGAATTGACG 59.138 40.000 0.00 0.00 0.00 4.35
2050 5936 1.904287 TGGTTTCTGGAATTGACGGG 58.096 50.000 0.00 0.00 0.00 5.28
2051 5937 1.144093 TGGTTTCTGGAATTGACGGGT 59.856 47.619 0.00 0.00 0.00 5.28
2052 5938 2.372504 TGGTTTCTGGAATTGACGGGTA 59.627 45.455 0.00 0.00 0.00 3.69
2053 5939 3.181442 TGGTTTCTGGAATTGACGGGTAA 60.181 43.478 0.00 0.00 0.00 2.85
2054 5940 4.014406 GGTTTCTGGAATTGACGGGTAAT 58.986 43.478 0.00 0.00 0.00 1.89
2057 5943 4.561500 TCTGGAATTGACGGGTAATTGA 57.438 40.909 0.00 0.00 0.00 2.57
2060 5946 6.837312 TCTGGAATTGACGGGTAATTGATAT 58.163 36.000 0.00 0.00 0.00 1.63
2105 5991 3.964909 CAAGTAAACCTTCACTTGGTGC 58.035 45.455 6.57 0.00 45.08 5.01
2106 5992 2.583143 AGTAAACCTTCACTTGGTGCC 58.417 47.619 0.00 0.00 37.93 5.01
2158 6045 0.917333 TGAGGGGCCGGGATTAGTTT 60.917 55.000 2.18 0.00 0.00 2.66
2173 6060 6.183360 GGGATTAGTTTAAAGCTCAATTCCCC 60.183 42.308 0.00 0.00 0.00 4.81
2174 6061 6.379988 GGATTAGTTTAAAGCTCAATTCCCCA 59.620 38.462 0.00 0.00 0.00 4.96
2194 6084 3.047877 GGACGGGGCGAACAACAG 61.048 66.667 0.00 0.00 0.00 3.16
2200 6090 1.654023 GGGGCGAACAACAGCATACC 61.654 60.000 0.00 0.00 34.54 2.73
2201 6091 0.958382 GGGCGAACAACAGCATACCA 60.958 55.000 0.00 0.00 34.54 3.25
2230 6120 6.211584 TCAAAAATGGAACCGGAATATTGGAA 59.788 34.615 9.46 0.00 0.00 3.53
2272 6163 3.554752 GCTTTTGTGGGTGTATGTGCAAT 60.555 43.478 0.00 0.00 0.00 3.56
2274 6165 0.887247 TGTGGGTGTATGTGCAATGC 59.113 50.000 0.00 0.00 0.00 3.56
2276 6167 1.477700 GTGGGTGTATGTGCAATGCAT 59.522 47.619 12.38 0.00 41.91 3.96
2277 6168 1.477295 TGGGTGTATGTGCAATGCATG 59.523 47.619 12.38 0.00 41.91 4.06
2293 6184 6.655062 CAATGCATGCATATGTTTTTCATCC 58.345 36.000 32.36 0.00 37.91 3.51
2403 7026 6.697019 GTGCGCCAATGATTTATATTTTCACT 59.303 34.615 4.18 0.00 0.00 3.41
2435 7059 2.866762 GTCATTGAGACTATGAACCGCC 59.133 50.000 0.00 0.00 44.09 6.13
2477 7113 5.012046 TGTCTACTCTTCAGAATTGCTTGGA 59.988 40.000 0.00 0.00 0.00 3.53
2517 7165 7.268447 GTGTTTTGTTAACATCATCTAACGAGC 59.732 37.037 9.56 0.55 31.84 5.03
2532 7181 2.304092 ACGAGCGTATTATGGTCTCCA 58.696 47.619 12.04 0.00 38.19 3.86
2598 7247 1.876156 GGAGTCTGTTCCTTGCTTGTG 59.124 52.381 0.00 0.00 34.27 3.33
2664 7313 7.202526 CCGGCATAATCTATTGTTCATTGTTT 58.797 34.615 0.00 0.00 0.00 2.83
2665 7314 7.167968 CCGGCATAATCTATTGTTCATTGTTTG 59.832 37.037 0.00 0.00 0.00 2.93
2673 7322 7.432059 TCTATTGTTCATTGTTTGCATTGACA 58.568 30.769 0.00 0.00 35.51 3.58
2674 7323 8.089597 TCTATTGTTCATTGTTTGCATTGACAT 58.910 29.630 0.00 0.00 35.51 3.06
2684 7333 1.737236 TGCATTGACATGGTAAGTCGC 59.263 47.619 0.00 0.00 38.83 5.19
2704 7379 5.287513 GTCGCTCACTTTGTCTCTTCTATTC 59.712 44.000 0.00 0.00 0.00 1.75
2757 7433 2.030371 TGCACTGAAGCAATTGAACCA 58.970 42.857 10.34 1.90 42.46 3.67
2758 7434 2.034939 TGCACTGAAGCAATTGAACCAG 59.965 45.455 10.34 13.58 42.46 4.00
2796 7474 4.530946 AGTTCTTACGAGAAAAGATGGGGA 59.469 41.667 0.00 0.00 43.21 4.81
2802 7480 2.437413 GAGAAAAGATGGGGAGCGTTT 58.563 47.619 0.00 0.00 0.00 3.60
2828 7506 1.766069 CGGTAAAACTGTTGCCTTGC 58.234 50.000 0.00 0.00 0.00 4.01
2908 7600 9.567848 TTACGAAAAATGAAATTCAGGATAAGC 57.432 29.630 1.10 0.00 33.67 3.09
2915 7607 4.142622 TGAAATTCAGGATAAGCGCAACTG 60.143 41.667 11.47 10.22 0.00 3.16
2957 7651 2.461695 TCTTGTTCTGCCTCCCTCTAG 58.538 52.381 0.00 0.00 0.00 2.43
2979 7673 9.357161 TCTAGGAGAATAAGGTAGCTTTAAGAG 57.643 37.037 13.21 1.05 0.00 2.85
2996 7701 1.202976 AGAGATTTGTTGGCACAGGCT 60.203 47.619 0.00 0.00 42.39 4.58
3095 7955 3.433274 GGTTAACCAGCGGTACAGTTTAC 59.567 47.826 20.12 4.25 33.12 2.01
3121 7996 7.364320 CCAAAGGTTCTTTTTCCCTGTTAGAAA 60.364 37.037 0.00 0.00 0.00 2.52
3139 8014 5.176741 AGAAAGGCTGTCATTTCTCTCAT 57.823 39.130 7.57 0.00 40.83 2.90
3233 10113 2.795231 ATCTTGAGCTAGCAAAGGCA 57.205 45.000 22.73 10.61 44.61 4.75
3248 10134 4.760715 GCAAAGGCATATCTGAGTGATCAT 59.239 41.667 0.00 0.00 40.72 2.45
3256 10142 8.828644 GGCATATCTGAGTGATCATATCAATTC 58.171 37.037 12.89 1.99 41.69 2.17
3263 10149 9.274206 CTGAGTGATCATATCAATTCTGAATGT 57.726 33.333 12.89 0.00 41.69 2.71
3340 10226 6.321945 CCTGACAATTTTGATCATGTGGGATA 59.678 38.462 4.44 0.00 0.00 2.59
3451 10337 2.143925 CGTCTGTTTTCTCTGGGTTCC 58.856 52.381 0.00 0.00 0.00 3.62
3461 10347 3.682292 CTGGGTTCCGGCTACTGGC 62.682 68.421 0.00 0.00 40.90 4.85
3613 10553 8.404107 AGTAGCTCATCTTTATTCTAGGAGTC 57.596 38.462 0.00 0.00 0.00 3.36
3627 10567 1.068741 AGGAGTCGATTATGAACGCCC 59.931 52.381 0.00 0.00 0.00 6.13
3634 10574 1.940613 GATTATGAACGCCCTGTGGTC 59.059 52.381 0.00 0.00 0.00 4.02
3762 10725 0.831288 CAAATGGCTGGGACCAACCA 60.831 55.000 15.28 15.28 44.92 3.67
3778 10741 1.508088 CCATTTCTGGTTGCCGAGC 59.492 57.895 0.00 0.00 37.79 5.03
3779 10742 1.243342 CCATTTCTGGTTGCCGAGCA 61.243 55.000 0.00 0.00 37.79 4.26
3780 10743 0.597568 CATTTCTGGTTGCCGAGCAA 59.402 50.000 7.15 7.15 46.80 3.91
4015 10980 9.940166 TTTTATCAAGTGATGATTGATTGATCG 57.060 29.630 6.50 0.00 46.85 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.928116 GGGACACAACGAGTAATGCTAC 59.072 50.000 0.00 0.00 0.00 3.58
7 8 2.563620 TGGGACACAACGAGTAATGCTA 59.436 45.455 0.00 0.00 0.00 3.49
8 9 1.346395 TGGGACACAACGAGTAATGCT 59.654 47.619 0.00 0.00 0.00 3.79
9 10 1.803334 TGGGACACAACGAGTAATGC 58.197 50.000 0.00 0.00 0.00 3.56
41 42 9.841295 TTTTGAGTAGTTGTAACTTCTAATGGT 57.159 29.630 2.20 0.00 36.88 3.55
124 125 5.647658 ACGATGTCTAATGGCATTTTTGAGA 59.352 36.000 19.21 11.95 0.00 3.27
195 196 3.764434 GAGAACTGACATGTGGGTCTAGA 59.236 47.826 13.80 0.00 38.61 2.43
453 454 6.598850 AGTTTCAACAACTCAAAAATGCCATT 59.401 30.769 0.00 0.00 0.00 3.16
469 470 3.569194 TTGCCACTAGGAGTTTCAACA 57.431 42.857 0.00 0.00 36.89 3.33
477 478 3.409026 ACTCAGTTTTGCCACTAGGAG 57.591 47.619 0.00 0.00 36.89 3.69
538 539 7.591006 TTAGCTACATAACCTGACTTTTTCG 57.409 36.000 0.00 0.00 0.00 3.46
545 546 7.900782 TTTCAGTTTAGCTACATAACCTGAC 57.099 36.000 0.00 0.00 0.00 3.51
546 547 8.318412 TCATTTCAGTTTAGCTACATAACCTGA 58.682 33.333 0.00 0.00 0.00 3.86
547 548 8.492673 TCATTTCAGTTTAGCTACATAACCTG 57.507 34.615 0.00 0.00 0.00 4.00
548 549 9.515226 TTTCATTTCAGTTTAGCTACATAACCT 57.485 29.630 0.00 0.00 0.00 3.50
553 554 7.807907 CGGTTTTTCATTTCAGTTTAGCTACAT 59.192 33.333 0.00 0.00 0.00 2.29
554 555 7.136119 CGGTTTTTCATTTCAGTTTAGCTACA 58.864 34.615 0.00 0.00 0.00 2.74
555 556 6.087687 GCGGTTTTTCATTTCAGTTTAGCTAC 59.912 38.462 0.00 0.00 0.00 3.58
556 557 6.146898 GCGGTTTTTCATTTCAGTTTAGCTA 58.853 36.000 0.00 0.00 0.00 3.32
557 558 4.982295 GCGGTTTTTCATTTCAGTTTAGCT 59.018 37.500 0.00 0.00 0.00 3.32
558 559 4.149922 GGCGGTTTTTCATTTCAGTTTAGC 59.850 41.667 0.00 0.00 0.00 3.09
559 560 5.402270 CAGGCGGTTTTTCATTTCAGTTTAG 59.598 40.000 0.00 0.00 0.00 1.85
560 561 5.285651 CAGGCGGTTTTTCATTTCAGTTTA 58.714 37.500 0.00 0.00 0.00 2.01
561 562 4.119136 CAGGCGGTTTTTCATTTCAGTTT 58.881 39.130 0.00 0.00 0.00 2.66
562 563 3.716601 CAGGCGGTTTTTCATTTCAGTT 58.283 40.909 0.00 0.00 0.00 3.16
563 564 2.545742 GCAGGCGGTTTTTCATTTCAGT 60.546 45.455 0.00 0.00 0.00 3.41
564 565 2.061028 GCAGGCGGTTTTTCATTTCAG 58.939 47.619 0.00 0.00 0.00 3.02
565 566 1.410517 TGCAGGCGGTTTTTCATTTCA 59.589 42.857 0.00 0.00 0.00 2.69
566 567 1.792367 GTGCAGGCGGTTTTTCATTTC 59.208 47.619 0.00 0.00 0.00 2.17
567 568 1.137872 TGTGCAGGCGGTTTTTCATTT 59.862 42.857 0.00 0.00 0.00 2.32
568 569 0.749649 TGTGCAGGCGGTTTTTCATT 59.250 45.000 0.00 0.00 0.00 2.57
569 570 0.749649 TTGTGCAGGCGGTTTTTCAT 59.250 45.000 0.00 0.00 0.00 2.57
570 571 0.532573 TTTGTGCAGGCGGTTTTTCA 59.467 45.000 0.00 0.00 0.00 2.69
571 572 1.646189 TTTTGTGCAGGCGGTTTTTC 58.354 45.000 0.00 0.00 0.00 2.29
572 573 2.100605 TTTTTGTGCAGGCGGTTTTT 57.899 40.000 0.00 0.00 0.00 1.94
573 574 1.939255 CATTTTTGTGCAGGCGGTTTT 59.061 42.857 0.00 0.00 0.00 2.43
574 575 1.580815 CATTTTTGTGCAGGCGGTTT 58.419 45.000 0.00 0.00 0.00 3.27
575 576 0.879839 GCATTTTTGTGCAGGCGGTT 60.880 50.000 0.00 0.00 44.43 4.44
576 577 1.300853 GCATTTTTGTGCAGGCGGT 60.301 52.632 0.00 0.00 44.43 5.68
577 578 3.553039 GCATTTTTGTGCAGGCGG 58.447 55.556 0.00 0.00 44.43 6.13
583 584 4.342772 CGAGTATACCAGCATTTTTGTGC 58.657 43.478 0.00 0.00 45.38 4.57
584 585 4.634004 TCCGAGTATACCAGCATTTTTGTG 59.366 41.667 0.00 0.00 0.00 3.33
585 586 4.634443 GTCCGAGTATACCAGCATTTTTGT 59.366 41.667 0.00 0.00 0.00 2.83
586 587 4.260212 CGTCCGAGTATACCAGCATTTTTG 60.260 45.833 0.00 0.00 0.00 2.44
587 588 3.869246 CGTCCGAGTATACCAGCATTTTT 59.131 43.478 0.00 0.00 0.00 1.94
588 589 3.131577 TCGTCCGAGTATACCAGCATTTT 59.868 43.478 0.00 0.00 0.00 1.82
589 590 2.691526 TCGTCCGAGTATACCAGCATTT 59.308 45.455 0.00 0.00 0.00 2.32
590 591 2.304092 TCGTCCGAGTATACCAGCATT 58.696 47.619 0.00 0.00 0.00 3.56
591 592 1.977056 TCGTCCGAGTATACCAGCAT 58.023 50.000 0.00 0.00 0.00 3.79
592 593 1.607148 CATCGTCCGAGTATACCAGCA 59.393 52.381 0.00 0.00 0.00 4.41
593 594 1.607628 ACATCGTCCGAGTATACCAGC 59.392 52.381 0.00 0.00 0.00 4.85
594 595 2.031069 CCACATCGTCCGAGTATACCAG 60.031 54.545 0.00 0.00 0.00 4.00
604 605 2.867793 TTCCATGGCCACATCGTCCG 62.868 60.000 8.16 0.00 34.35 4.79
605 606 0.679640 TTTCCATGGCCACATCGTCC 60.680 55.000 8.16 0.00 34.35 4.79
608 609 1.462616 TTCTTTCCATGGCCACATCG 58.537 50.000 8.16 0.00 34.35 3.84
630 631 3.802685 AGCATCTAGAAATTTCGCGGTAC 59.197 43.478 12.42 3.33 0.00 3.34
635 636 5.604010 ATGCTAGCATCTAGAAATTTCGC 57.396 39.130 24.67 9.36 29.42 4.70
660 661 0.251354 ATGTGCAGTGGGTAGCTCTG 59.749 55.000 0.00 11.29 0.00 3.35
665 667 2.858622 CACCATGTGCAGTGGGTAG 58.141 57.895 19.30 7.67 41.14 3.18
697 699 2.095364 GCAGAGTGAAATGCAAGGAGTG 60.095 50.000 0.00 0.00 42.11 3.51
698 700 2.157738 GCAGAGTGAAATGCAAGGAGT 58.842 47.619 0.00 0.00 42.11 3.85
707 711 4.344679 TGTTTTTGGGATGCAGAGTGAAAT 59.655 37.500 0.00 0.00 0.00 2.17
710 714 2.942804 TGTTTTTGGGATGCAGAGTGA 58.057 42.857 0.00 0.00 0.00 3.41
713 717 2.036217 TGCTTGTTTTTGGGATGCAGAG 59.964 45.455 0.00 0.00 0.00 3.35
715 719 2.409975 CTGCTTGTTTTTGGGATGCAG 58.590 47.619 0.00 0.00 39.98 4.41
722 726 0.869730 GCATGCCTGCTTGTTTTTGG 59.130 50.000 6.36 0.00 45.32 3.28
739 743 2.607442 TACCTCTGCCTGCCTGCA 60.607 61.111 0.00 0.00 39.37 4.41
761 767 4.284550 ATGGTTGGTGCTGGCCGT 62.285 61.111 0.00 0.00 0.00 5.68
763 769 2.036256 AGATGGTTGGTGCTGGCC 59.964 61.111 0.00 0.00 0.00 5.36
764 770 0.682209 ATGAGATGGTTGGTGCTGGC 60.682 55.000 0.00 0.00 0.00 4.85
768 774 3.813443 ACTGATATGAGATGGTTGGTGC 58.187 45.455 0.00 0.00 0.00 5.01
796 802 0.948050 AGGTGATGGGGAGAGGAGAT 59.052 55.000 0.00 0.00 0.00 2.75
893 953 1.805945 CGCTTAGCTCGTGTGGGAC 60.806 63.158 1.76 0.00 0.00 4.46
979 1058 4.554036 GCTCCATGTCCTCGGGCC 62.554 72.222 0.00 0.00 0.00 5.80
985 1124 2.191375 CATGCCGCTCCATGTCCT 59.809 61.111 5.56 0.00 38.19 3.85
1070 1209 2.342279 CGTGGTTGGAGAAGCCGA 59.658 61.111 0.00 0.00 40.66 5.54
1072 1211 3.056328 GCCGTGGTTGGAGAAGCC 61.056 66.667 0.00 0.00 37.10 4.35
1107 1246 7.556275 AGGGAAACAAGAATTAGCATTTCGATA 59.444 33.333 0.00 0.00 0.00 2.92
1108 1247 6.378280 AGGGAAACAAGAATTAGCATTTCGAT 59.622 34.615 0.00 0.00 0.00 3.59
1126 1795 4.908481 AGAGGGAGGACATTATAGGGAAAC 59.092 45.833 0.00 0.00 0.00 2.78
1135 1822 4.993705 AACACAAAGAGGGAGGACATTA 57.006 40.909 0.00 0.00 0.00 1.90
1290 2122 5.127845 CCTGCTTGTCTCTACCTTATTCTCA 59.872 44.000 0.00 0.00 0.00 3.27
1387 2225 6.931840 GTGTAGGATCCTAAGATTTAAGCCAG 59.068 42.308 23.33 0.00 30.90 4.85
1388 2226 6.183361 GGTGTAGGATCCTAAGATTTAAGCCA 60.183 42.308 23.33 9.86 30.90 4.75
1456 2304 0.676736 CCCGGCTCATCTAGTTCTCC 59.323 60.000 0.00 0.00 0.00 3.71
1485 2334 1.484240 GCCTCCTGATTCAGCACTACT 59.516 52.381 8.23 0.00 0.00 2.57
1493 2840 1.883678 TGATGAGGCCTCCTGATTCA 58.116 50.000 29.95 19.77 31.76 2.57
1526 2883 7.275920 AGGTAGTCATGGAGATATGTTTCAAC 58.724 38.462 0.00 0.00 0.00 3.18
1527 2884 7.437713 AGGTAGTCATGGAGATATGTTTCAA 57.562 36.000 0.00 0.00 0.00 2.69
1528 2885 7.125659 TGAAGGTAGTCATGGAGATATGTTTCA 59.874 37.037 0.00 0.00 0.00 2.69
1588 2951 0.400594 AGTAGTTGGGTGGTTGGCTC 59.599 55.000 0.00 0.00 0.00 4.70
1591 2954 2.635915 TGACTAGTAGTTGGGTGGTTGG 59.364 50.000 3.85 0.00 0.00 3.77
1763 4329 6.715264 CACTCAAGTTAAAGTAAACTCCCCAT 59.285 38.462 0.00 0.00 38.76 4.00
1863 5544 3.932710 TGGTACAGCTCGCATTTTAGAAG 59.067 43.478 0.00 0.00 0.00 2.85
1864 5545 3.932822 TGGTACAGCTCGCATTTTAGAA 58.067 40.909 0.00 0.00 0.00 2.10
1881 5562 9.525826 AAATGCCATTGGAAAATTAAATTGGTA 57.474 25.926 6.95 0.00 0.00 3.25
1883 5564 8.690680 CAAATGCCATTGGAAAATTAAATTGG 57.309 30.769 6.95 0.00 0.00 3.16
1903 5585 4.401519 AGCTGACAATCAGGATTCCAAATG 59.598 41.667 5.29 1.25 44.43 2.32
1926 5608 3.674997 GGTAGCAAGAGATTTGGACACA 58.325 45.455 0.00 0.00 0.00 3.72
1983 5869 2.630580 GGGTGGCCTCAACAAAAACATA 59.369 45.455 3.32 0.00 30.63 2.29
2006 5892 2.919228 ACCAGATCATAAACCCTTCGC 58.081 47.619 0.00 0.00 0.00 4.70
2029 5915 2.825532 CCCGTCAATTCCAGAAACCATT 59.174 45.455 0.00 0.00 0.00 3.16
2043 5929 8.210946 AGAGATCAAATATCAATTACCCGTCAA 58.789 33.333 0.00 0.00 0.00 3.18
2045 5931 7.062371 CGAGAGATCAAATATCAATTACCCGTC 59.938 40.741 0.00 0.00 0.00 4.79
2046 5932 6.868864 CGAGAGATCAAATATCAATTACCCGT 59.131 38.462 0.00 0.00 0.00 5.28
2047 5933 6.183360 GCGAGAGATCAAATATCAATTACCCG 60.183 42.308 0.00 0.00 0.00 5.28
2048 5934 6.876257 AGCGAGAGATCAAATATCAATTACCC 59.124 38.462 0.00 0.00 0.00 3.69
2050 5936 9.847706 TCTAGCGAGAGATCAAATATCAATTAC 57.152 33.333 0.00 0.00 0.00 1.89
2052 5938 9.941325 ATTCTAGCGAGAGATCAAATATCAATT 57.059 29.630 0.00 0.00 31.77 2.32
2053 5939 9.941325 AATTCTAGCGAGAGATCAAATATCAAT 57.059 29.630 0.00 0.00 31.77 2.57
2054 5940 9.770097 AAATTCTAGCGAGAGATCAAATATCAA 57.230 29.630 0.00 0.00 31.77 2.57
2060 5946 6.878923 TGGAAAAATTCTAGCGAGAGATCAAA 59.121 34.615 0.00 0.00 31.77 2.69
2105 5991 3.131933 CAGAGTTCTCCCTGACTACATGG 59.868 52.174 0.00 0.00 33.97 3.66
2106 5992 4.019858 TCAGAGTTCTCCCTGACTACATG 58.980 47.826 0.00 0.00 34.78 3.21
2158 6045 2.647299 TCCTGTGGGGAATTGAGCTTTA 59.353 45.455 0.00 0.00 41.91 1.85
2173 6060 3.818121 TTGTTCGCCCCGTCCTGTG 62.818 63.158 0.00 0.00 0.00 3.66
2174 6061 3.552384 TTGTTCGCCCCGTCCTGT 61.552 61.111 0.00 0.00 0.00 4.00
2185 6072 3.188254 TGAACATGGTATGCTGTTGTTCG 59.812 43.478 0.00 0.00 45.67 3.95
2194 6084 5.351189 GGTTCCATTTTTGAACATGGTATGC 59.649 40.000 8.35 0.00 43.05 3.14
2200 6090 4.250116 TCCGGTTCCATTTTTGAACATG 57.750 40.909 0.00 0.00 43.05 3.21
2201 6091 4.946478 TTCCGGTTCCATTTTTGAACAT 57.054 36.364 0.00 0.00 43.05 2.71
2230 6120 8.389603 CAAAAGCACATACACAAAGAAACATTT 58.610 29.630 0.00 0.00 0.00 2.32
2272 6163 5.340439 TGGATGAAAAACATATGCATGCA 57.660 34.783 25.04 25.04 39.56 3.96
2274 6165 6.342906 AGGTTGGATGAAAAACATATGCATG 58.657 36.000 10.16 0.00 39.56 4.06
2276 6167 5.999205 AGGTTGGATGAAAAACATATGCA 57.001 34.783 1.58 0.00 39.56 3.96
2277 6168 6.862209 TGTAGGTTGGATGAAAAACATATGC 58.138 36.000 1.58 0.00 39.56 3.14
2477 7113 4.079253 ACAAAACACACTTGAGTTCCTGT 58.921 39.130 0.00 0.00 0.00 4.00
2517 7165 8.230486 GCTGAAATAAATGGAGACCATAATACG 58.770 37.037 3.64 0.00 44.40 3.06
2532 7181 8.627403 CACCAGATTCATGTAGCTGAAATAAAT 58.373 33.333 17.93 0.00 38.55 1.40
2664 7313 1.737236 GCGACTTACCATGTCAATGCA 59.263 47.619 0.00 0.00 34.37 3.96
2665 7314 2.009774 AGCGACTTACCATGTCAATGC 58.990 47.619 0.00 0.00 34.37 3.56
2673 7322 3.006967 AGACAAAGTGAGCGACTTACCAT 59.993 43.478 4.79 0.00 44.68 3.55
2674 7323 2.364324 AGACAAAGTGAGCGACTTACCA 59.636 45.455 4.79 0.00 44.68 3.25
2684 7333 6.929625 TGGAGAATAGAAGAGACAAAGTGAG 58.070 40.000 0.00 0.00 0.00 3.51
2704 7379 7.171167 CAGTTAATTCAGACATAGCTCATGGAG 59.829 40.741 0.00 0.00 39.13 3.86
2802 7480 1.440938 AACAGTTTTACCGCTGCGCA 61.441 50.000 18.00 10.98 36.26 6.09
2816 7494 3.649986 GTCGCGCAAGGCAACAGT 61.650 61.111 8.75 0.00 43.84 3.55
2915 7607 3.549794 ACTTGGCCAATAGAGAAGCATC 58.450 45.455 20.85 0.00 0.00 3.91
2957 7651 9.839817 AAATCTCTTAAAGCTACCTTATTCTCC 57.160 33.333 0.00 0.00 0.00 3.71
2979 7673 1.200948 GAGAGCCTGTGCCAACAAATC 59.799 52.381 0.00 0.00 38.69 2.17
2996 7701 4.584874 TCGTTGGCTAATTTTGATGGAGA 58.415 39.130 0.00 0.00 0.00 3.71
3082 7942 2.497138 ACCTTTGGTAAACTGTACCGC 58.503 47.619 0.00 0.00 40.39 5.68
3088 7948 6.046593 GGGAAAAAGAACCTTTGGTAAACTG 58.953 40.000 0.00 0.00 33.12 3.16
3095 7955 4.753516 AACAGGGAAAAAGAACCTTTGG 57.246 40.909 0.00 0.00 30.66 3.28
3121 7996 2.842496 TGGATGAGAGAAATGACAGCCT 59.158 45.455 0.00 0.00 39.21 4.58
3139 8014 5.008613 GCTTGTGAGATGTAACAACTTTGGA 59.991 40.000 0.00 0.00 32.98 3.53
3197 8100 5.710984 TCAAGATTCCAAGAACTACTCGAC 58.289 41.667 0.00 0.00 0.00 4.20
3248 10134 5.393352 GCCTGCAACACATTCAGAATTGATA 60.393 40.000 10.52 0.00 32.27 2.15
3256 10142 0.892755 ATGGCCTGCAACACATTCAG 59.107 50.000 3.32 0.00 0.00 3.02
3263 10149 3.942377 ATCGCCATGGCCTGCAACA 62.942 57.895 30.79 6.48 37.98 3.33
3340 10226 1.699054 TATGCCCCGCAGAGCTTCAT 61.699 55.000 0.00 0.00 43.65 2.57
3437 10323 1.002773 GTAGCCGGAACCCAGAGAAAA 59.997 52.381 5.05 0.00 0.00 2.29
3451 10337 0.389948 AAGAACGAAGCCAGTAGCCG 60.390 55.000 0.00 0.00 45.47 5.52
3461 10347 5.025190 CGTGAGATCACTAGAAGAACGAAG 58.975 45.833 10.99 0.00 44.34 3.79
3486 10372 4.320971 GCGACGGCGATTATGAGT 57.679 55.556 18.90 0.00 40.82 3.41
3505 10391 1.958288 ACCCTCCTGACTTAGCATGT 58.042 50.000 0.00 0.00 0.00 3.21
3613 10553 0.937304 CCACAGGGCGTTCATAATCG 59.063 55.000 0.00 0.00 0.00 3.34
3627 10567 3.093717 ACAGTAACTGTTCGACCACAG 57.906 47.619 14.33 14.33 42.59 3.66
3762 10725 3.034924 TTGCTCGGCAACCAGAAAT 57.965 47.368 7.15 0.00 43.99 2.17
3774 10737 4.391830 TGCTTTTTAGGAGTACATTGCTCG 59.608 41.667 0.00 0.00 34.00 5.03
3775 10738 5.631992 GTGCTTTTTAGGAGTACATTGCTC 58.368 41.667 0.00 0.00 31.17 4.26
3776 10739 4.154195 CGTGCTTTTTAGGAGTACATTGCT 59.846 41.667 0.00 0.00 31.17 3.91
3777 10740 4.403453 CGTGCTTTTTAGGAGTACATTGC 58.597 43.478 0.00 0.00 31.17 3.56
3778 10741 4.693566 TCCGTGCTTTTTAGGAGTACATTG 59.306 41.667 0.00 0.00 31.17 2.82
3779 10742 4.694037 GTCCGTGCTTTTTAGGAGTACATT 59.306 41.667 0.00 0.00 32.82 2.71
3780 10743 4.251268 GTCCGTGCTTTTTAGGAGTACAT 58.749 43.478 0.00 0.00 32.82 2.29
3781 10744 3.069872 TGTCCGTGCTTTTTAGGAGTACA 59.930 43.478 0.00 0.00 32.82 2.90
3782 10745 3.431233 GTGTCCGTGCTTTTTAGGAGTAC 59.569 47.826 0.00 0.00 32.82 2.73
3783 10746 3.656559 GTGTCCGTGCTTTTTAGGAGTA 58.343 45.455 0.00 0.00 32.82 2.59
3784 10747 2.490991 GTGTCCGTGCTTTTTAGGAGT 58.509 47.619 0.00 0.00 32.82 3.85
3785 10748 1.459592 CGTGTCCGTGCTTTTTAGGAG 59.540 52.381 0.00 0.00 32.82 3.69
3786 10749 1.504359 CGTGTCCGTGCTTTTTAGGA 58.496 50.000 0.00 0.00 0.00 2.94
4119 11093 1.404035 CTGCTGCTCATGCTTGCATTA 59.596 47.619 5.24 0.00 43.56 1.90


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

AutoCloner maintained by Alex Coulton.