Multiple sequence alignment - TraesCS1D01G344300

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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 TraesCS1D01G344300 chr1D 100.000 3088 0 0 1 3088 433059581 433062668 0.000000e+00 5703.0
1 TraesCS1D01G344300 chr1D 86.742 1780 125 55 686 2371 433092279 433094041 0.000000e+00 1877.0
2 TraesCS1D01G344300 chr1D 86.688 954 67 25 1456 2374 433143196 433144124 0.000000e+00 1003.0
3 TraesCS1D01G344300 chr1D 75.550 773 174 12 1316 2082 401921070 401920307 1.750000e-97 366.0
4 TraesCS1D01G344300 chr1D 75.550 773 174 12 1316 2082 402006288 402005525 1.750000e-97 366.0
5 TraesCS1D01G344300 chr1D 75.550 773 174 12 1316 2082 402051332 402050569 1.750000e-97 366.0
6 TraesCS1D01G344300 chr1D 75.550 773 174 12 1316 2082 402107850 402107087 1.750000e-97 366.0
7 TraesCS1D01G344300 chr1D 90.972 144 8 2 141 279 433091820 433091963 4.070000e-44 189.0
8 TraesCS1D01G344300 chr1D 96.429 112 4 0 2620 2731 433062024 433062135 5.260000e-43 185.0
9 TraesCS1D01G344300 chr1D 96.429 112 4 0 2444 2555 433062200 433062311 5.260000e-43 185.0
10 TraesCS1D01G344300 chr1D 85.635 181 19 4 44 224 433127211 433127384 1.890000e-42 183.0
11 TraesCS1D01G344300 chr1D 83.784 148 11 8 675 810 433140755 433140901 8.990000e-26 128.0
12 TraesCS1D01G344300 chr1A 90.299 2639 133 52 1 2555 531365996 531368595 0.000000e+00 3341.0
13 TraesCS1D01G344300 chr1A 91.603 1429 76 24 978 2376 531513133 531514547 0.000000e+00 1934.0
14 TraesCS1D01G344300 chr1A 90.649 385 26 7 2170 2552 531515020 531515396 1.280000e-138 503.0
15 TraesCS1D01G344300 chr1A 92.361 144 6 2 141 279 531501736 531501879 1.880000e-47 200.0
16 TraesCS1D01G344300 chr1A 91.156 147 7 3 138 278 531561211 531561357 8.740000e-46 195.0
17 TraesCS1D01G344300 chr1A 87.730 163 7 6 2620 2772 531368477 531368636 8.800000e-41 178.0
18 TraesCS1D01G344300 chr1A 89.394 132 11 2 535 664 531510307 531510437 2.460000e-36 163.0
19 TraesCS1D01G344300 chr1A 93.204 103 6 1 2806 2907 531515673 531515775 1.920000e-32 150.0
20 TraesCS1D01G344300 chr1A 92.308 91 5 2 2552 2642 548488436 548488348 8.990000e-26 128.0
21 TraesCS1D01G344300 chr1A 90.164 61 5 1 112 172 531509668 531509727 9.180000e-11 78.7
22 TraesCS1D01G344300 chr1B 89.771 1789 116 33 750 2477 584620159 584621941 0.000000e+00 2228.0
23 TraesCS1D01G344300 chr1B 89.856 1735 109 31 750 2423 584574798 584576526 0.000000e+00 2167.0
24 TraesCS1D01G344300 chr1B 88.727 1783 118 38 750 2477 584603553 584605307 0.000000e+00 2104.0
25 TraesCS1D01G344300 chr1B 88.299 1752 132 39 750 2454 584653987 584655712 0.000000e+00 2032.0
26 TraesCS1D01G344300 chr1B 87.263 1743 102 51 686 2343 584778972 584780679 0.000000e+00 1879.0
27 TraesCS1D01G344300 chr1B 90.671 1415 67 24 962 2343 584798089 584799471 0.000000e+00 1821.0
28 TraesCS1D01G344300 chr1B 86.147 1718 97 63 750 2374 584761746 584763415 0.000000e+00 1724.0
29 TraesCS1D01G344300 chr1B 91.667 972 62 9 1521 2477 584566230 584567197 0.000000e+00 1328.0
30 TraesCS1D01G344300 chr1B 88.945 597 33 9 10 605 584563602 584564166 0.000000e+00 706.0
31 TraesCS1D01G344300 chr1B 88.945 597 33 9 10 605 584652316 584652880 0.000000e+00 706.0
32 TraesCS1D01G344300 chr1B 90.705 312 23 3 10 315 584601655 584601966 7.970000e-111 411.0
33 TraesCS1D01G344300 chr1B 87.121 132 14 2 535 664 584875358 584875488 2.480000e-31 147.0
34 TraesCS1D01G344300 chr1B 87.121 132 14 2 535 664 584901761 584901891 2.480000e-31 147.0
35 TraesCS1D01G344300 chr1B 84.667 150 10 6 566 707 584603299 584603443 1.490000e-28 137.0
36 TraesCS1D01G344300 chr1B 84.667 150 10 6 566 707 584653733 584653877 1.490000e-28 137.0
37 TraesCS1D01G344300 chr1B 96.341 82 1 2 2552 2631 61251328 61251247 1.930000e-27 134.0
38 TraesCS1D01G344300 chr1B 95.385 65 2 1 2732 2796 584567483 584567546 5.450000e-18 102.0
39 TraesCS1D01G344300 chr1B 93.846 65 3 1 2732 2796 584605593 584605656 2.530000e-16 97.1
40 TraesCS1D01G344300 chr1B 97.436 39 1 0 2869 2907 584567548 584567586 1.990000e-07 67.6
41 TraesCS1D01G344300 chr1B 97.436 39 1 0 2869 2907 584605658 584605696 1.990000e-07 67.6
42 TraesCS1D01G344300 chr3B 87.584 1482 118 38 861 2303 647944041 647942587 0.000000e+00 1657.0
43 TraesCS1D01G344300 chr3B 87.324 639 49 19 864 1495 647969445 647968832 0.000000e+00 702.0
44 TraesCS1D01G344300 chr3A 87.432 1480 118 37 861 2303 628220333 628218885 0.000000e+00 1640.0
45 TraesCS1D01G344300 chr3A 93.976 166 10 0 2905 3070 731100714 731100879 5.110000e-63 252.0
46 TraesCS1D01G344300 chr3D 85.892 1609 123 57 754 2303 485232665 485231102 0.000000e+00 1618.0
47 TraesCS1D01G344300 chr6A 87.253 557 57 8 962 1514 616689143 616688597 9.400000e-175 623.0
48 TraesCS1D01G344300 chr2B 94.512 164 9 0 2905 3068 214378084 214378247 1.420000e-63 254.0
49 TraesCS1D01G344300 chr2B 92.473 93 5 2 2552 2644 555387930 555388020 6.950000e-27 132.0
50 TraesCS1D01G344300 chr6D 93.491 169 11 0 2902 3070 81746764 81746932 5.110000e-63 252.0
51 TraesCS1D01G344300 chr5D 93.976 166 10 0 2905 3070 321384138 321383973 5.110000e-63 252.0
52 TraesCS1D01G344300 chr6B 93.939 165 10 0 2905 3069 229680783 229680947 1.840000e-62 250.0
53 TraesCS1D01G344300 chr6B 93.939 165 10 0 2906 3070 468734655 468734819 1.840000e-62 250.0
54 TraesCS1D01G344300 chr6B 97.590 83 1 1 2552 2633 252247858 252247776 1.150000e-29 141.0
55 TraesCS1D01G344300 chr5B 93.939 165 10 0 2906 3070 145828182 145828346 1.840000e-62 250.0
56 TraesCS1D01G344300 chr4B 92.982 171 12 0 2898 3068 510313396 510313226 1.840000e-62 250.0
57 TraesCS1D01G344300 chr2D 91.954 174 14 0 2899 3072 240791192 240791019 8.550000e-61 244.0
58 TraesCS1D01G344300 chr7A 97.500 80 1 1 2552 2630 238816486 238816407 5.370000e-28 135.0
59 TraesCS1D01G344300 chr7A 93.407 91 5 1 2552 2641 75869339 75869249 1.930000e-27 134.0
60 TraesCS1D01G344300 chr7A 93.333 90 5 1 2549 2637 171552042 171552131 6.950000e-27 132.0
61 TraesCS1D01G344300 chr4D 95.294 85 3 1 2549 2632 71301605 71301689 1.930000e-27 134.0
62 TraesCS1D01G344300 chr4A 96.296 81 2 1 2549 2628 464953526 464953606 6.950000e-27 132.0
63 TraesCS1D01G344300 chr2A 80.597 134 6 4 621 749 779164732 779164614 5.490000e-13 86.1
64 TraesCS1D01G344300 chrUn 97.436 39 1 0 2869 2907 475893356 475893394 1.990000e-07 67.6
65 TraesCS1D01G344300 chr7D 88.000 50 2 1 610 655 54310133 54310182 4.300000e-04 56.5


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 TraesCS1D01G344300 chr1D 433059581 433062668 3087 False 2024.333333 5703 97.619333 1 3088 3 chr1D.!!$F2 3087
1 TraesCS1D01G344300 chr1D 433091820 433094041 2221 False 1033.000000 1877 88.857000 141 2371 2 chr1D.!!$F3 2230
2 TraesCS1D01G344300 chr1D 433140755 433144124 3369 False 565.500000 1003 85.236000 675 2374 2 chr1D.!!$F4 1699
3 TraesCS1D01G344300 chr1D 401920307 401921070 763 True 366.000000 366 75.550000 1316 2082 1 chr1D.!!$R1 766
4 TraesCS1D01G344300 chr1D 402005525 402006288 763 True 366.000000 366 75.550000 1316 2082 1 chr1D.!!$R2 766
5 TraesCS1D01G344300 chr1D 402050569 402051332 763 True 366.000000 366 75.550000 1316 2082 1 chr1D.!!$R3 766
6 TraesCS1D01G344300 chr1D 402107087 402107850 763 True 366.000000 366 75.550000 1316 2082 1 chr1D.!!$R4 766
7 TraesCS1D01G344300 chr1A 531365996 531368636 2640 False 1759.500000 3341 89.014500 1 2772 2 chr1A.!!$F3 2771
8 TraesCS1D01G344300 chr1A 531509668 531515775 6107 False 565.740000 1934 91.002800 112 2907 5 chr1A.!!$F4 2795
9 TraesCS1D01G344300 chr1B 584620159 584621941 1782 False 2228.000000 2228 89.771000 750 2477 1 chr1B.!!$F2 1727
10 TraesCS1D01G344300 chr1B 584574798 584576526 1728 False 2167.000000 2167 89.856000 750 2423 1 chr1B.!!$F1 1673
11 TraesCS1D01G344300 chr1B 584778972 584780679 1707 False 1879.000000 1879 87.263000 686 2343 1 chr1B.!!$F4 1657
12 TraesCS1D01G344300 chr1B 584798089 584799471 1382 False 1821.000000 1821 90.671000 962 2343 1 chr1B.!!$F5 1381
13 TraesCS1D01G344300 chr1B 584761746 584763415 1669 False 1724.000000 1724 86.147000 750 2374 1 chr1B.!!$F3 1624
14 TraesCS1D01G344300 chr1B 584652316 584655712 3396 False 958.333333 2032 87.303667 10 2454 3 chr1B.!!$F10 2444
15 TraesCS1D01G344300 chr1B 584601655 584605696 4041 False 563.340000 2104 91.076200 10 2907 5 chr1B.!!$F9 2897
16 TraesCS1D01G344300 chr1B 584563602 584567586 3984 False 550.900000 1328 93.358250 10 2907 4 chr1B.!!$F8 2897
17 TraesCS1D01G344300 chr3B 647942587 647944041 1454 True 1657.000000 1657 87.584000 861 2303 1 chr3B.!!$R1 1442
18 TraesCS1D01G344300 chr3B 647968832 647969445 613 True 702.000000 702 87.324000 864 1495 1 chr3B.!!$R2 631
19 TraesCS1D01G344300 chr3A 628218885 628220333 1448 True 1640.000000 1640 87.432000 861 2303 1 chr3A.!!$R1 1442
20 TraesCS1D01G344300 chr3D 485231102 485232665 1563 True 1618.000000 1618 85.892000 754 2303 1 chr3D.!!$R1 1549
21 TraesCS1D01G344300 chr6A 616688597 616689143 546 True 623.000000 623 87.253000 962 1514 1 chr6A.!!$R1 552

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
918 5826 0.824109 AGCATTCTCCACCGATCGAA 59.176 50.0 18.66 1.31 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2531 11625 0.179137 CAGACGACGCAGCCTATTGA 60.179 55.0 0.0 0.0 0.0 2.57 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
36 37 6.044682 CCTTTTCTTCTGCTTCATGTTTTGT 58.955 36.000 0.00 0.00 0.00 2.83
37 38 6.536224 CCTTTTCTTCTGCTTCATGTTTTGTT 59.464 34.615 0.00 0.00 0.00 2.83
39 40 5.581126 TCTTCTGCTTCATGTTTTGTTGT 57.419 34.783 0.00 0.00 0.00 3.32
83 85 1.670083 GCTAACTGTCGGCCGGTTT 60.670 57.895 27.83 15.26 39.73 3.27
112 130 4.416738 GTCACAGCCCTCAGCCCC 62.417 72.222 0.00 0.00 45.47 5.80
181 286 7.221259 GTCTCAGCTAACTAAAAGCTAGCTAAC 59.779 40.741 19.70 0.00 45.50 2.34
202 307 4.245660 ACGATCAGACGTGACAAATGAAT 58.754 39.130 0.00 0.00 44.84 2.57
285 396 3.521560 TCACCTGCTAAAAGCTCATACG 58.478 45.455 0.03 0.00 42.97 3.06
286 397 3.056107 TCACCTGCTAAAAGCTCATACGT 60.056 43.478 0.00 0.00 42.97 3.57
287 398 4.158949 TCACCTGCTAAAAGCTCATACGTA 59.841 41.667 0.00 0.00 42.97 3.57
288 399 4.267928 CACCTGCTAAAAGCTCATACGTAC 59.732 45.833 0.00 0.00 42.97 3.67
289 400 4.159879 ACCTGCTAAAAGCTCATACGTACT 59.840 41.667 0.00 0.00 42.97 2.73
290 401 4.504461 CCTGCTAAAAGCTCATACGTACTG 59.496 45.833 0.00 0.00 42.97 2.74
291 402 3.863424 TGCTAAAAGCTCATACGTACTGC 59.137 43.478 0.00 2.65 42.97 4.40
296 407 3.099267 AGCTCATACGTACTGCCATTC 57.901 47.619 0.00 0.00 0.00 2.67
297 408 2.695666 AGCTCATACGTACTGCCATTCT 59.304 45.455 0.00 0.00 0.00 2.40
368 994 5.772169 CCTCAAAGGAAGTGGAAATTTCTCT 59.228 40.000 17.42 12.88 37.67 3.10
369 995 6.266330 CCTCAAAGGAAGTGGAAATTTCTCTT 59.734 38.462 17.42 19.19 37.67 2.85
540 1713 1.600916 GGAAACACGGAGCTGGCTT 60.601 57.895 0.00 0.00 0.00 4.35
681 2917 8.008279 GCTAGCTGTTTGTTACTACTACAAAAC 58.992 37.037 7.70 0.00 44.42 2.43
687 2955 9.398538 TGTTTGTTACTACTACAAAACATCCTT 57.601 29.630 0.00 0.00 44.42 3.36
806 5523 7.664552 TCCAATGAAGCCAAGATAATCATTT 57.335 32.000 0.00 0.00 38.34 2.32
842 5717 5.586243 GCACATGCCGACCTATATATGAATT 59.414 40.000 0.00 0.00 34.31 2.17
845 5720 7.010830 CACATGCCGACCTATATATGAATTCTG 59.989 40.741 7.05 0.00 0.00 3.02
870 5768 8.225416 TGATCTCGGCCACCTATATATAAGTAT 58.775 37.037 2.24 0.00 0.00 2.12
918 5826 0.824109 AGCATTCTCCACCGATCGAA 59.176 50.000 18.66 1.31 0.00 3.71
1144 7327 3.744719 CGGAGGCCGTCGTCAAGA 61.745 66.667 11.72 0.00 42.73 3.02
1283 7975 1.959042 ACAGCCGATTAGCCAGATTG 58.041 50.000 0.00 0.00 0.00 2.67
1284 7976 1.486310 ACAGCCGATTAGCCAGATTGA 59.514 47.619 0.00 0.00 0.00 2.57
1285 7977 2.105477 ACAGCCGATTAGCCAGATTGAT 59.895 45.455 0.00 0.00 0.00 2.57
1287 7979 4.202357 ACAGCCGATTAGCCAGATTGATTA 60.202 41.667 0.00 0.00 0.00 1.75
1436 8131 2.125512 GACGCCATCAAGGACGCT 60.126 61.111 0.00 0.00 41.22 5.07
1439 8134 2.169789 CGCCATCAAGGACGCTCTG 61.170 63.158 0.00 0.00 41.22 3.35
1607 9921 3.647771 AAGTTCCTGGTCCCGCCC 61.648 66.667 0.00 0.00 36.04 6.13
1844 10158 1.741770 GGTGATGCAGGACGTGGTC 60.742 63.158 0.00 0.00 0.00 4.02
1963 10277 0.324943 AGAATGGTGGTGGAGAACGG 59.675 55.000 0.00 0.00 0.00 4.44
1970 10284 0.958091 TGGTGGAGAACGGCAAAATG 59.042 50.000 0.00 0.00 0.00 2.32
2021 10335 1.077501 CATGGTGAAGATGGCCGGT 60.078 57.895 1.90 0.00 0.00 5.28
2036 10350 0.029035 CCGGTATCGAGGTCAAGACG 59.971 60.000 0.00 0.00 39.00 4.18
2082 10396 4.776647 GCCGCGCAATCAACCACC 62.777 66.667 8.75 0.00 0.00 4.61
2122 10475 1.946855 GCGCACGTACGTGTATGCAA 61.947 55.000 39.56 0.00 46.90 4.08
2123 10476 0.246603 CGCACGTACGTGTATGCAAC 60.247 55.000 39.56 24.46 46.90 4.17
2259 10667 1.810151 GCCAAGCTACGGAATTGTTCA 59.190 47.619 6.28 0.00 0.00 3.18
2269 10677 5.689383 ACGGAATTGTTCATGTATATGGC 57.311 39.130 0.00 0.00 34.97 4.40
2392 11486 5.515886 CCAAAAACCTACTCCTGGATTACCA 60.516 44.000 0.00 0.00 44.76 3.25
2484 11578 7.447374 TGATTTTCCATGTAACAACACTAGG 57.553 36.000 0.00 0.00 0.00 3.02
2486 11580 7.721842 TGATTTTCCATGTAACAACACTAGGAA 59.278 33.333 0.00 0.00 33.34 3.36
2488 11582 4.562082 TCCATGTAACAACACTAGGAACG 58.438 43.478 0.00 0.00 0.00 3.95
2489 11583 4.281435 TCCATGTAACAACACTAGGAACGA 59.719 41.667 0.00 0.00 0.00 3.85
2490 11584 4.992319 CCATGTAACAACACTAGGAACGAA 59.008 41.667 0.00 0.00 0.00 3.85
2491 11585 5.642063 CCATGTAACAACACTAGGAACGAAT 59.358 40.000 0.00 0.00 0.00 3.34
2492 11586 6.814644 CCATGTAACAACACTAGGAACGAATA 59.185 38.462 0.00 0.00 0.00 1.75
2493 11587 7.332430 CCATGTAACAACACTAGGAACGAATAA 59.668 37.037 0.00 0.00 0.00 1.40
2494 11588 8.714179 CATGTAACAACACTAGGAACGAATAAA 58.286 33.333 0.00 0.00 0.00 1.40
2495 11589 8.301730 TGTAACAACACTAGGAACGAATAAAG 57.698 34.615 0.00 0.00 0.00 1.85
2497 11591 5.243207 ACAACACTAGGAACGAATAAAGGG 58.757 41.667 0.00 0.00 0.00 3.95
2498 11592 5.012354 ACAACACTAGGAACGAATAAAGGGA 59.988 40.000 0.00 0.00 0.00 4.20
2499 11593 5.082251 ACACTAGGAACGAATAAAGGGAC 57.918 43.478 0.00 0.00 0.00 4.46
2501 11595 5.954150 ACACTAGGAACGAATAAAGGGACTA 59.046 40.000 0.00 0.00 38.49 2.59
2504 11598 8.636213 CACTAGGAACGAATAAAGGGACTATAA 58.364 37.037 0.00 0.00 38.49 0.98
2505 11599 9.205513 ACTAGGAACGAATAAAGGGACTATAAA 57.794 33.333 0.00 0.00 38.49 1.40
2508 11602 8.935741 AGGAACGAATAAAGGGACTATAAATCT 58.064 33.333 0.00 0.00 38.49 2.40
2509 11603 8.989980 GGAACGAATAAAGGGACTATAAATCTG 58.010 37.037 0.00 0.00 38.49 2.90
2511 11605 6.645415 ACGAATAAAGGGACTATAAATCTGCG 59.355 38.462 0.00 0.00 38.49 5.18
2512 11606 6.866770 CGAATAAAGGGACTATAAATCTGCGA 59.133 38.462 0.00 0.00 38.49 5.10
2513 11607 7.384115 CGAATAAAGGGACTATAAATCTGCGAA 59.616 37.037 0.00 0.00 38.49 4.70
2514 11608 9.220767 GAATAAAGGGACTATAAATCTGCGAAT 57.779 33.333 0.00 0.00 38.49 3.34
2515 11609 8.779354 ATAAAGGGACTATAAATCTGCGAATC 57.221 34.615 0.00 0.00 38.49 2.52
2516 11610 5.808366 AGGGACTATAAATCTGCGAATCA 57.192 39.130 0.00 0.00 36.02 2.57
2517 11611 6.365970 AGGGACTATAAATCTGCGAATCAT 57.634 37.500 0.00 0.00 36.02 2.45
2519 11613 6.014242 AGGGACTATAAATCTGCGAATCATCA 60.014 38.462 0.00 0.00 36.02 3.07
2520 11614 6.650807 GGGACTATAAATCTGCGAATCATCAA 59.349 38.462 0.00 0.00 0.00 2.57
2521 11615 7.335422 GGGACTATAAATCTGCGAATCATCAAT 59.665 37.037 0.00 0.00 0.00 2.57
2522 11616 8.386606 GGACTATAAATCTGCGAATCATCAATC 58.613 37.037 0.00 0.00 0.00 2.67
2523 11617 9.149225 GACTATAAATCTGCGAATCATCAATCT 57.851 33.333 0.00 0.00 0.00 2.40
2524 11618 8.933807 ACTATAAATCTGCGAATCATCAATCTG 58.066 33.333 0.00 0.00 0.00 2.90
2525 11619 7.974482 ATAAATCTGCGAATCATCAATCTGA 57.026 32.000 0.00 0.00 0.00 3.27
2526 11620 6.688637 AAATCTGCGAATCATCAATCTGAA 57.311 33.333 0.00 0.00 0.00 3.02
2527 11621 6.879276 AATCTGCGAATCATCAATCTGAAT 57.121 33.333 0.00 0.00 0.00 2.57
2528 11622 6.879276 ATCTGCGAATCATCAATCTGAATT 57.121 33.333 0.00 0.00 0.00 2.17
2529 11623 6.688637 TCTGCGAATCATCAATCTGAATTT 57.311 33.333 0.00 0.00 0.00 1.82
2531 11625 8.387190 TCTGCGAATCATCAATCTGAATTTAT 57.613 30.769 0.00 0.00 0.00 1.40
2532 11626 8.501580 TCTGCGAATCATCAATCTGAATTTATC 58.498 33.333 0.00 0.00 0.00 1.75
2533 11627 8.156994 TGCGAATCATCAATCTGAATTTATCA 57.843 30.769 0.00 0.00 36.38 2.15
2534 11628 8.623030 TGCGAATCATCAATCTGAATTTATCAA 58.377 29.630 0.00 0.00 37.67 2.57
2540 11634 9.803507 TCATCAATCTGAATTTATCAATAGGCT 57.196 29.630 0.00 0.00 37.67 4.58
2541 11635 9.841880 CATCAATCTGAATTTATCAATAGGCTG 57.158 33.333 0.00 0.00 37.67 4.85
2543 11637 5.929697 TCTGAATTTATCAATAGGCTGCG 57.070 39.130 0.00 0.00 37.67 5.18
2545 11639 5.466728 TCTGAATTTATCAATAGGCTGCGTC 59.533 40.000 0.00 0.00 37.67 5.19
2548 11642 2.417339 TATCAATAGGCTGCGTCGTC 57.583 50.000 0.00 0.00 0.00 4.20
2549 11643 0.747255 ATCAATAGGCTGCGTCGTCT 59.253 50.000 0.00 0.00 0.00 4.18
2550 11644 0.179137 TCAATAGGCTGCGTCGTCTG 60.179 55.000 0.00 0.00 0.00 3.51
2552 11646 3.758088 ATAGGCTGCGTCGTCTGCG 62.758 63.158 0.00 0.00 39.92 5.18
2555 11649 4.122515 GCTGCGTCGTCTGCGTTC 62.123 66.667 0.00 0.00 39.49 3.95
2556 11650 3.470567 CTGCGTCGTCTGCGTTCC 61.471 66.667 0.00 0.00 39.49 3.62
2558 11652 3.033764 GCGTCGTCTGCGTTCCAA 61.034 61.111 0.00 0.00 39.49 3.53
2559 11653 2.591311 GCGTCGTCTGCGTTCCAAA 61.591 57.895 0.00 0.00 39.49 3.28
2560 11654 1.928653 CGTCGTCTGCGTTCCAAAA 59.071 52.632 0.00 0.00 39.49 2.44
2561 11655 0.511221 CGTCGTCTGCGTTCCAAAAT 59.489 50.000 0.00 0.00 39.49 1.82
2562 11656 1.722464 CGTCGTCTGCGTTCCAAAATA 59.278 47.619 0.00 0.00 39.49 1.40
2564 11658 2.991190 GTCGTCTGCGTTCCAAAATAGA 59.009 45.455 0.00 0.00 39.49 1.98
2565 11659 3.617263 GTCGTCTGCGTTCCAAAATAGAT 59.383 43.478 0.00 0.00 39.49 1.98
2566 11660 3.616821 TCGTCTGCGTTCCAAAATAGATG 59.383 43.478 0.00 0.00 39.49 2.90
2567 11661 3.616821 CGTCTGCGTTCCAAAATAGATGA 59.383 43.478 0.00 0.00 0.00 2.92
2568 11662 4.492570 CGTCTGCGTTCCAAAATAGATGAC 60.493 45.833 0.00 0.00 0.00 3.06
2569 11663 3.938963 TCTGCGTTCCAAAATAGATGACC 59.061 43.478 0.00 0.00 0.00 4.02
2570 11664 3.013921 TGCGTTCCAAAATAGATGACCC 58.986 45.455 0.00 0.00 0.00 4.46
2571 11665 3.013921 GCGTTCCAAAATAGATGACCCA 58.986 45.455 0.00 0.00 0.00 4.51
2572 11666 3.442273 GCGTTCCAAAATAGATGACCCAA 59.558 43.478 0.00 0.00 0.00 4.12
2574 11668 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
2576 11670 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
2577 11671 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
2579 11673 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
2580 11674 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
2581 11675 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
2582 11676 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
2583 11677 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
2584 11678 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
2586 11680 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
2587 11681 7.287810 AGATGACCCAACTTTGTACTAACTTT 58.712 34.615 0.00 0.00 0.00 2.66
2588 11682 8.434392 AGATGACCCAACTTTGTACTAACTTTA 58.566 33.333 0.00 0.00 0.00 1.85
2589 11683 9.227777 GATGACCCAACTTTGTACTAACTTTAT 57.772 33.333 0.00 0.00 0.00 1.40
2591 11685 9.492973 TGACCCAACTTTGTACTAACTTTATAC 57.507 33.333 0.00 0.00 0.00 1.47
2592 11686 9.492973 GACCCAACTTTGTACTAACTTTATACA 57.507 33.333 0.00 0.00 0.00 2.29
2593 11687 9.850198 ACCCAACTTTGTACTAACTTTATACAA 57.150 29.630 0.00 0.00 37.10 2.41
2614 11708 9.699410 ATACAAAGTTGGATCATCTATTTTGGA 57.301 29.630 11.01 5.25 0.00 3.53
2615 11709 8.421249 ACAAAGTTGGATCATCTATTTTGGAA 57.579 30.769 11.01 0.00 0.00 3.53
2617 11711 6.683974 AGTTGGATCATCTATTTTGGAACG 57.316 37.500 0.00 0.00 0.00 3.95
2618 11712 5.590259 AGTTGGATCATCTATTTTGGAACGG 59.410 40.000 0.00 0.00 0.00 4.44
2619 11713 5.366482 TGGATCATCTATTTTGGAACGGA 57.634 39.130 0.00 0.00 0.00 4.69
2620 11714 5.368145 TGGATCATCTATTTTGGAACGGAG 58.632 41.667 0.00 0.00 0.00 4.63
2621 11715 4.757149 GGATCATCTATTTTGGAACGGAGG 59.243 45.833 0.00 0.00 0.00 4.30
2622 11716 4.150897 TCATCTATTTTGGAACGGAGGG 57.849 45.455 0.00 0.00 0.00 4.30
2624 11718 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2625 11719 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2628 11722 2.019807 TTTGGAACGGAGGGAGTAGT 57.980 50.000 0.00 0.00 0.00 2.73
2629 11723 2.019807 TTGGAACGGAGGGAGTAGTT 57.980 50.000 0.00 0.00 0.00 2.24
2630 11724 1.553706 TGGAACGGAGGGAGTAGTTC 58.446 55.000 0.00 0.00 41.40 3.01
2647 11741 8.571336 GGAGTAGTTCCATTATGATTTTCCATG 58.429 37.037 0.00 0.00 46.01 3.66
2648 11742 9.125026 GAGTAGTTCCATTATGATTTTCCATGT 57.875 33.333 0.00 0.00 0.00 3.21
2652 11746 9.253832 AGTTCCATTATGATTTTCCATGTAACA 57.746 29.630 0.00 0.00 0.00 2.41
2667 11761 5.642063 CCATGTAACAACACTAGGAACGAAT 59.358 40.000 0.00 0.00 0.00 3.34
2683 11777 7.668492 AGGAACGAATAAAGGGACTATACATC 58.332 38.462 0.00 0.00 38.49 3.06
2686 11780 6.456501 ACGAATAAAGGGACTATACATCTGC 58.543 40.000 0.00 0.00 38.49 4.26
2778 12113 4.124970 TGTCTGCTAATGATCATGAGTGC 58.875 43.478 19.51 15.63 0.00 4.40
2782 12117 2.420642 CTAATGATCATGAGTGCCCCG 58.579 52.381 9.46 0.00 0.00 5.73
2852 12187 6.545504 TTTCCTTCTTCTTTTGACGAGATG 57.454 37.500 0.00 0.00 0.00 2.90
2874 12210 3.389925 AACCACTGGCATGAAACAATG 57.610 42.857 0.00 0.00 0.00 2.82
2916 12252 3.010200 AGTACGAAATACTCCCTCGGT 57.990 47.619 0.00 0.00 40.31 4.69
2917 12253 3.359950 AGTACGAAATACTCCCTCGGTT 58.640 45.455 0.00 0.00 40.31 4.44
2918 12254 2.955477 ACGAAATACTCCCTCGGTTC 57.045 50.000 0.00 0.00 36.90 3.62
2919 12255 1.479730 ACGAAATACTCCCTCGGTTCC 59.520 52.381 0.00 0.00 36.90 3.62
2920 12256 1.755380 CGAAATACTCCCTCGGTTCCT 59.245 52.381 0.00 0.00 0.00 3.36
2921 12257 2.954318 CGAAATACTCCCTCGGTTCCTA 59.046 50.000 0.00 0.00 0.00 2.94
2922 12258 3.382546 CGAAATACTCCCTCGGTTCCTAA 59.617 47.826 0.00 0.00 0.00 2.69
2923 12259 4.142093 CGAAATACTCCCTCGGTTCCTAAA 60.142 45.833 0.00 0.00 0.00 1.85
2924 12260 5.452917 CGAAATACTCCCTCGGTTCCTAAAT 60.453 44.000 0.00 0.00 0.00 1.40
2925 12261 4.957684 ATACTCCCTCGGTTCCTAAATG 57.042 45.455 0.00 0.00 0.00 2.32
2926 12262 2.547990 ACTCCCTCGGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
2927 12263 3.716431 ACTCCCTCGGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
2928 12264 4.098894 ACTCCCTCGGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
2929 12265 4.161754 ACTCCCTCGGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
2930 12266 4.098894 TCCCTCGGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
2931 12267 4.161001 TCCCTCGGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
2932 12268 4.161754 CCCTCGGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
2933 12269 5.338137 CCCTCGGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2934 12270 6.171213 CCTCGGTTCCTAAATGTAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
2935 12271 7.325694 CCTCGGTTCCTAAATGTAAGTCTTTA 58.674 38.462 0.00 0.00 0.00 1.85
2936 12272 7.985752 CCTCGGTTCCTAAATGTAAGTCTTTAT 59.014 37.037 0.00 0.00 0.00 1.40
2969 12305 1.842052 TGTGGACTACATACGGAGCA 58.158 50.000 0.00 0.00 33.42 4.26
2970 12306 2.172679 TGTGGACTACATACGGAGCAA 58.827 47.619 0.00 0.00 33.42 3.91
2971 12307 2.563620 TGTGGACTACATACGGAGCAAA 59.436 45.455 0.00 0.00 33.42 3.68
2972 12308 3.007074 TGTGGACTACATACGGAGCAAAA 59.993 43.478 0.00 0.00 33.42 2.44
2973 12309 4.189231 GTGGACTACATACGGAGCAAAAT 58.811 43.478 0.00 0.00 0.00 1.82
2974 12310 4.034048 GTGGACTACATACGGAGCAAAATG 59.966 45.833 0.00 0.00 0.00 2.32
2975 12311 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
2976 12312 4.873827 GGACTACATACGGAGCAAAATGAA 59.126 41.667 0.00 0.00 0.00 2.57
2977 12313 5.527582 GGACTACATACGGAGCAAAATGAAT 59.472 40.000 0.00 0.00 0.00 2.57
2978 12314 6.363577 ACTACATACGGAGCAAAATGAATG 57.636 37.500 0.00 0.00 0.00 2.67
2979 12315 6.112734 ACTACATACGGAGCAAAATGAATGA 58.887 36.000 0.00 0.00 0.00 2.57
2980 12316 5.895636 ACATACGGAGCAAAATGAATGAA 57.104 34.783 0.00 0.00 0.00 2.57
2981 12317 6.455360 ACATACGGAGCAAAATGAATGAAT 57.545 33.333 0.00 0.00 0.00 2.57
2982 12318 6.498304 ACATACGGAGCAAAATGAATGAATC 58.502 36.000 0.00 0.00 0.00 2.52
2983 12319 4.376340 ACGGAGCAAAATGAATGAATCC 57.624 40.909 0.00 0.00 0.00 3.01
2984 12320 3.763360 ACGGAGCAAAATGAATGAATCCA 59.237 39.130 0.00 0.00 0.00 3.41
2985 12321 4.403432 ACGGAGCAAAATGAATGAATCCAT 59.597 37.500 0.00 0.00 33.66 3.41
2986 12322 5.593909 ACGGAGCAAAATGAATGAATCCATA 59.406 36.000 0.00 0.00 31.59 2.74
2987 12323 5.916883 CGGAGCAAAATGAATGAATCCATAC 59.083 40.000 0.00 0.00 31.59 2.39
2988 12324 6.238842 CGGAGCAAAATGAATGAATCCATACT 60.239 38.462 0.00 0.00 31.59 2.12
2989 12325 7.495055 GGAGCAAAATGAATGAATCCATACTT 58.505 34.615 0.00 0.00 31.59 2.24
2990 12326 8.632679 GGAGCAAAATGAATGAATCCATACTTA 58.367 33.333 0.00 0.00 31.59 2.24
2999 12335 9.970395 TGAATGAATCCATACTTAAAATGCATC 57.030 29.630 0.00 0.00 31.59 3.91
3012 12348 9.944376 ACTTAAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
3028 12364 6.954487 ACATCCGTATGTAGTTCATAGTGA 57.046 37.500 0.00 0.00 44.66 3.41
3029 12365 7.342769 ACATCCGTATGTAGTTCATAGTGAA 57.657 36.000 0.00 0.00 44.66 3.18
3030 12366 7.778083 ACATCCGTATGTAGTTCATAGTGAAA 58.222 34.615 0.00 0.00 44.66 2.69
3031 12367 8.421784 ACATCCGTATGTAGTTCATAGTGAAAT 58.578 33.333 0.00 0.00 44.66 2.17
3032 12368 9.261180 CATCCGTATGTAGTTCATAGTGAAATT 57.739 33.333 0.00 0.00 38.22 1.82
3033 12369 9.832445 ATCCGTATGTAGTTCATAGTGAAATTT 57.168 29.630 0.00 0.00 38.22 1.82
3034 12370 9.661563 TCCGTATGTAGTTCATAGTGAAATTTT 57.338 29.630 0.00 0.00 38.22 1.82
3059 12395 9.976511 TTTACAGAGACATATATTTAGGAACGG 57.023 33.333 0.00 0.00 0.00 4.44
3060 12396 7.834881 ACAGAGACATATATTTAGGAACGGA 57.165 36.000 0.00 0.00 0.00 4.69
3061 12397 7.887381 ACAGAGACATATATTTAGGAACGGAG 58.113 38.462 0.00 0.00 0.00 4.63
3062 12398 7.039644 ACAGAGACATATATTTAGGAACGGAGG 60.040 40.741 0.00 0.00 0.00 4.30
3063 12399 6.437793 AGAGACATATATTTAGGAACGGAGGG 59.562 42.308 0.00 0.00 0.00 4.30
3064 12400 6.320518 AGACATATATTTAGGAACGGAGGGA 58.679 40.000 0.00 0.00 0.00 4.20
3065 12401 6.437793 AGACATATATTTAGGAACGGAGGGAG 59.562 42.308 0.00 0.00 0.00 4.30
3066 12402 6.082707 ACATATATTTAGGAACGGAGGGAGT 58.917 40.000 0.00 0.00 0.00 3.85
3067 12403 7.243824 ACATATATTTAGGAACGGAGGGAGTA 58.756 38.462 0.00 0.00 0.00 2.59
3068 12404 7.899709 ACATATATTTAGGAACGGAGGGAGTAT 59.100 37.037 0.00 0.00 0.00 2.12
3069 12405 9.417561 CATATATTTAGGAACGGAGGGAGTATA 57.582 37.037 0.00 0.00 0.00 1.47
3071 12407 5.859205 TTTAGGAACGGAGGGAGTATAAC 57.141 43.478 0.00 0.00 0.00 1.89
3072 12408 2.675583 AGGAACGGAGGGAGTATAACC 58.324 52.381 0.00 0.00 0.00 2.85
3078 12414 4.170292 CGGAGGGAGTATAACCGTAATG 57.830 50.000 0.00 0.00 38.97 1.90
3079 12415 3.822735 CGGAGGGAGTATAACCGTAATGA 59.177 47.826 0.00 0.00 38.97 2.57
3080 12416 4.279169 CGGAGGGAGTATAACCGTAATGAA 59.721 45.833 0.00 0.00 38.97 2.57
3081 12417 5.047519 CGGAGGGAGTATAACCGTAATGAAT 60.048 44.000 0.00 0.00 38.97 2.57
3082 12418 6.517864 CGGAGGGAGTATAACCGTAATGAATT 60.518 42.308 0.00 0.00 38.97 2.17
3083 12419 7.309377 CGGAGGGAGTATAACCGTAATGAATTA 60.309 40.741 0.00 0.00 38.97 1.40
3084 12420 8.033626 GGAGGGAGTATAACCGTAATGAATTAG 58.966 40.741 0.00 0.00 0.00 1.73
3085 12421 7.384477 AGGGAGTATAACCGTAATGAATTAGC 58.616 38.462 0.00 0.00 0.00 3.09
3086 12422 7.234988 AGGGAGTATAACCGTAATGAATTAGCT 59.765 37.037 0.00 0.00 0.00 3.32
3087 12423 7.876582 GGGAGTATAACCGTAATGAATTAGCTT 59.123 37.037 0.00 0.00 0.00 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 53 1.806542 AGTTAGCGTGTGGAATGCAAG 59.193 47.619 0.00 0.00 43.85 4.01
83 85 4.840005 TGTGACAACCCGCGTGCA 62.840 61.111 4.92 0.00 0.00 4.57
91 93 1.968540 GCTGAGGGCTGTGACAACC 60.969 63.158 0.00 0.00 38.06 3.77
112 130 9.636965 CGTGCATATCATTCGTAATTTATATGG 57.363 33.333 0.00 0.00 31.47 2.74
181 286 4.847365 ATTCATTTGTCACGTCTGATCG 57.153 40.909 0.00 0.00 0.00 3.69
202 307 0.103390 TGCGTCGTCTCTTTGACCAA 59.897 50.000 0.00 0.00 42.49 3.67
285 396 4.336280 AGAAGGGAAAAGAATGGCAGTAC 58.664 43.478 0.00 0.00 0.00 2.73
286 397 4.657814 AGAAGGGAAAAGAATGGCAGTA 57.342 40.909 0.00 0.00 0.00 2.74
287 398 3.532641 AGAAGGGAAAAGAATGGCAGT 57.467 42.857 0.00 0.00 0.00 4.40
288 399 4.879197 AAAGAAGGGAAAAGAATGGCAG 57.121 40.909 0.00 0.00 0.00 4.85
289 400 5.366477 AGAAAAAGAAGGGAAAAGAATGGCA 59.634 36.000 0.00 0.00 0.00 4.92
290 401 5.858381 AGAAAAAGAAGGGAAAAGAATGGC 58.142 37.500 0.00 0.00 0.00 4.40
291 402 6.931281 GGAAGAAAAAGAAGGGAAAAGAATGG 59.069 38.462 0.00 0.00 0.00 3.16
296 407 5.278512 CCTCGGAAGAAAAAGAAGGGAAAAG 60.279 44.000 0.00 0.00 41.32 2.27
297 408 4.583073 CCTCGGAAGAAAAAGAAGGGAAAA 59.417 41.667 0.00 0.00 41.32 2.29
368 994 9.391006 AGAAACGAATAAATATACTTCCAGCAA 57.609 29.630 0.00 0.00 0.00 3.91
369 995 8.958119 AGAAACGAATAAATATACTTCCAGCA 57.042 30.769 0.00 0.00 0.00 4.41
522 1695 1.578206 GAAGCCAGCTCCGTGTTTCC 61.578 60.000 0.00 0.00 0.00 3.13
540 1713 0.393402 ATTGAGCAGCTGATTGGCGA 60.393 50.000 20.43 0.00 37.29 5.54
543 1878 1.598132 CGAGATTGAGCAGCTGATTGG 59.402 52.381 20.43 0.00 0.00 3.16
687 2955 9.825109 TCTTCGGTAATGATATGATACACAAAA 57.175 29.630 0.00 0.00 0.00 2.44
806 5523 3.753797 TCGGCATGTGCTTACAATTAACA 59.246 39.130 4.84 0.00 41.70 2.41
814 5531 2.240493 ATAGGTCGGCATGTGCTTAC 57.760 50.000 4.84 3.71 41.70 2.34
842 5717 2.971901 TATAGGTGGCCGAGATCAGA 57.028 50.000 0.00 0.00 0.00 3.27
845 5720 6.963083 ACTTATATATAGGTGGCCGAGATC 57.037 41.667 6.71 0.00 0.00 2.75
918 5826 6.855763 AGAGAGATCAAATCTGAGAAGTGT 57.144 37.500 0.00 0.00 40.38 3.55
1144 7327 1.630126 ATGGCCTTCTCCATGACGCT 61.630 55.000 3.32 0.00 44.72 5.07
1287 7979 8.722480 TCATCATCAACTCAACGAGATTAATT 57.278 30.769 0.00 0.00 33.32 1.40
1607 9921 2.022129 GTCGCTGAGGTTGGACGTG 61.022 63.158 0.00 0.00 0.00 4.49
1844 10158 2.594303 TCCAGCTTGTTGGGCGTG 60.594 61.111 3.76 0.00 38.81 5.34
1963 10277 3.310307 ACCACCCGGGCATTTTGC 61.310 61.111 24.08 0.00 44.08 3.68
2021 10335 0.395311 AGCCCGTCTTGACCTCGATA 60.395 55.000 0.00 0.00 0.00 2.92
2122 10475 4.320494 GCAAACCATTGAGATCTTTCACGT 60.320 41.667 0.00 0.00 38.94 4.49
2123 10476 4.083110 AGCAAACCATTGAGATCTTTCACG 60.083 41.667 0.00 0.00 38.94 4.35
2209 10616 6.648879 TGAACCAAGGAATAACCAAAGAAG 57.351 37.500 0.00 0.00 42.04 2.85
2259 10667 3.213506 ACATGCACAACGCCATATACAT 58.786 40.909 0.00 0.00 41.33 2.29
2269 10677 2.857748 TCGCTATTAGACATGCACAACG 59.142 45.455 0.00 0.00 0.00 4.10
2286 10694 3.119316 TCAACAAACAACATTGGTTCGCT 60.119 39.130 0.00 0.00 35.55 4.93
2392 11486 2.162208 CGATGTTTTATGCACCAGCTGT 59.838 45.455 13.81 0.00 42.74 4.40
2484 11578 8.496751 GCAGATTTATAGTCCCTTTATTCGTTC 58.503 37.037 0.00 0.00 0.00 3.95
2486 11580 6.645415 CGCAGATTTATAGTCCCTTTATTCGT 59.355 38.462 0.00 0.00 0.00 3.85
2488 11582 8.603242 TTCGCAGATTTATAGTCCCTTTATTC 57.397 34.615 0.00 0.00 35.04 1.75
2489 11583 9.220767 GATTCGCAGATTTATAGTCCCTTTATT 57.779 33.333 0.00 0.00 35.04 1.40
2490 11584 8.375506 TGATTCGCAGATTTATAGTCCCTTTAT 58.624 33.333 0.00 0.00 35.04 1.40
2491 11585 7.732025 TGATTCGCAGATTTATAGTCCCTTTA 58.268 34.615 0.00 0.00 35.04 1.85
2492 11586 6.591935 TGATTCGCAGATTTATAGTCCCTTT 58.408 36.000 0.00 0.00 35.04 3.11
2493 11587 6.174720 TGATTCGCAGATTTATAGTCCCTT 57.825 37.500 0.00 0.00 35.04 3.95
2494 11588 5.808366 TGATTCGCAGATTTATAGTCCCT 57.192 39.130 0.00 0.00 35.04 4.20
2495 11589 6.166279 TGATGATTCGCAGATTTATAGTCCC 58.834 40.000 0.00 0.00 35.04 4.46
2497 11591 9.149225 AGATTGATGATTCGCAGATTTATAGTC 57.851 33.333 0.00 0.00 35.04 2.59
2498 11592 8.933807 CAGATTGATGATTCGCAGATTTATAGT 58.066 33.333 0.00 0.00 35.04 2.12
2499 11593 9.148104 TCAGATTGATGATTCGCAGATTTATAG 57.852 33.333 0.00 0.00 35.04 1.31
2500 11594 9.492973 TTCAGATTGATGATTCGCAGATTTATA 57.507 29.630 0.00 0.00 35.04 0.98
2501 11595 7.974482 TCAGATTGATGATTCGCAGATTTAT 57.026 32.000 0.00 0.00 35.04 1.40
2504 11598 6.879276 ATTCAGATTGATGATTCGCAGATT 57.121 33.333 0.00 0.00 35.04 2.40
2505 11599 6.879276 AATTCAGATTGATGATTCGCAGAT 57.121 33.333 0.00 0.00 35.04 2.90
2506 11600 6.688637 AAATTCAGATTGATGATTCGCAGA 57.311 33.333 0.00 0.00 0.00 4.26
2507 11601 8.287503 TGATAAATTCAGATTGATGATTCGCAG 58.712 33.333 0.00 0.00 0.00 5.18
2508 11602 8.156994 TGATAAATTCAGATTGATGATTCGCA 57.843 30.769 0.00 0.00 0.00 5.10
2509 11603 9.622004 ATTGATAAATTCAGATTGATGATTCGC 57.378 29.630 0.00 0.00 35.27 4.70
2514 11608 9.803507 AGCCTATTGATAAATTCAGATTGATGA 57.196 29.630 0.00 0.00 35.27 2.92
2515 11609 9.841880 CAGCCTATTGATAAATTCAGATTGATG 57.158 33.333 0.00 0.00 35.27 3.07
2516 11610 8.521176 GCAGCCTATTGATAAATTCAGATTGAT 58.479 33.333 0.00 0.00 35.27 2.57
2517 11611 7.308169 CGCAGCCTATTGATAAATTCAGATTGA 60.308 37.037 0.00 0.00 35.27 2.57
2519 11613 6.488006 ACGCAGCCTATTGATAAATTCAGATT 59.512 34.615 0.00 0.00 35.27 2.40
2520 11614 6.000219 ACGCAGCCTATTGATAAATTCAGAT 59.000 36.000 0.00 0.00 35.27 2.90
2521 11615 5.368145 ACGCAGCCTATTGATAAATTCAGA 58.632 37.500 0.00 0.00 35.27 3.27
2522 11616 5.613360 CGACGCAGCCTATTGATAAATTCAG 60.613 44.000 0.00 0.00 35.27 3.02
2523 11617 4.211164 CGACGCAGCCTATTGATAAATTCA 59.789 41.667 0.00 0.00 0.00 2.57
2524 11618 4.211374 ACGACGCAGCCTATTGATAAATTC 59.789 41.667 0.00 0.00 0.00 2.17
2525 11619 4.127171 ACGACGCAGCCTATTGATAAATT 58.873 39.130 0.00 0.00 0.00 1.82
2526 11620 3.728845 ACGACGCAGCCTATTGATAAAT 58.271 40.909 0.00 0.00 0.00 1.40
2527 11621 3.120792 GACGACGCAGCCTATTGATAAA 58.879 45.455 0.00 0.00 0.00 1.40
2528 11622 2.361119 AGACGACGCAGCCTATTGATAA 59.639 45.455 0.00 0.00 0.00 1.75
2529 11623 1.954382 AGACGACGCAGCCTATTGATA 59.046 47.619 0.00 0.00 0.00 2.15
2531 11625 0.179137 CAGACGACGCAGCCTATTGA 60.179 55.000 0.00 0.00 0.00 2.57
2532 11626 1.756375 GCAGACGACGCAGCCTATTG 61.756 60.000 0.00 0.00 0.00 1.90
2533 11627 1.519455 GCAGACGACGCAGCCTATT 60.519 57.895 0.00 0.00 0.00 1.73
2534 11628 2.105128 GCAGACGACGCAGCCTAT 59.895 61.111 0.00 0.00 0.00 2.57
2538 11632 4.122515 GAACGCAGACGACGCAGC 62.123 66.667 0.00 0.00 43.93 5.25
2539 11633 3.470567 GGAACGCAGACGACGCAG 61.471 66.667 0.00 0.00 43.93 5.18
2540 11634 3.776659 TTGGAACGCAGACGACGCA 62.777 57.895 0.00 0.00 43.93 5.24
2541 11635 2.096481 TTTTGGAACGCAGACGACGC 62.096 55.000 0.00 0.00 43.93 5.19
2543 11637 2.991190 TCTATTTTGGAACGCAGACGAC 59.009 45.455 0.00 0.00 43.93 4.34
2548 11642 3.065371 GGGTCATCTATTTTGGAACGCAG 59.935 47.826 0.00 0.00 0.00 5.18
2549 11643 3.013921 GGGTCATCTATTTTGGAACGCA 58.986 45.455 0.00 0.00 0.00 5.24
2550 11644 3.013921 TGGGTCATCTATTTTGGAACGC 58.986 45.455 0.00 0.00 0.00 4.84
2552 11646 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
2553 11647 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
2554 11648 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
2555 11649 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
2556 11650 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
2558 11652 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
2559 11653 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
2560 11654 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
2561 11655 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
2562 11656 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
2565 11659 9.492973 GTATAAAGTTAGTACAAAGTTGGGTCA 57.507 33.333 0.00 0.00 0.00 4.02
2566 11660 9.492973 TGTATAAAGTTAGTACAAAGTTGGGTC 57.507 33.333 0.00 0.00 0.00 4.46
2567 11661 9.850198 TTGTATAAAGTTAGTACAAAGTTGGGT 57.150 29.630 9.39 0.00 35.91 4.51
2588 11682 9.699410 TCCAAAATAGATGATCCAACTTTGTAT 57.301 29.630 0.00 0.00 0.00 2.29
2589 11683 9.527157 TTCCAAAATAGATGATCCAACTTTGTA 57.473 29.630 0.00 0.00 0.00 2.41
2590 11684 8.306761 GTTCCAAAATAGATGATCCAACTTTGT 58.693 33.333 0.00 0.00 0.00 2.83
2591 11685 7.485913 CGTTCCAAAATAGATGATCCAACTTTG 59.514 37.037 0.00 0.00 0.00 2.77
2592 11686 7.362920 CCGTTCCAAAATAGATGATCCAACTTT 60.363 37.037 0.00 0.00 0.00 2.66
2593 11687 6.095440 CCGTTCCAAAATAGATGATCCAACTT 59.905 38.462 0.00 0.00 0.00 2.66
2594 11688 5.590259 CCGTTCCAAAATAGATGATCCAACT 59.410 40.000 0.00 0.00 0.00 3.16
2595 11689 5.588648 TCCGTTCCAAAATAGATGATCCAAC 59.411 40.000 0.00 0.00 0.00 3.77
2596 11690 5.750524 TCCGTTCCAAAATAGATGATCCAA 58.249 37.500 0.00 0.00 0.00 3.53
2597 11691 5.366482 TCCGTTCCAAAATAGATGATCCA 57.634 39.130 0.00 0.00 0.00 3.41
2599 11693 4.757149 CCCTCCGTTCCAAAATAGATGATC 59.243 45.833 0.00 0.00 0.00 2.92
2600 11694 4.412199 TCCCTCCGTTCCAAAATAGATGAT 59.588 41.667 0.00 0.00 0.00 2.45
2601 11695 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2602 11696 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2604 11698 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2605 11699 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2606 11700 4.098894 ACTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
2607 11701 2.910977 ACTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
2608 11702 2.332117 ACTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
2610 11704 1.897802 GAACTACTCCCTCCGTTCCAA 59.102 52.381 0.00 0.00 31.89 3.53
2612 11706 0.822811 GGAACTACTCCCTCCGTTCC 59.177 60.000 4.51 4.51 45.79 3.62
2613 11707 1.553706 TGGAACTACTCCCTCCGTTC 58.446 55.000 0.00 0.00 44.69 3.95
2614 11708 2.249309 ATGGAACTACTCCCTCCGTT 57.751 50.000 0.00 0.00 44.69 4.44
2615 11709 2.249309 AATGGAACTACTCCCTCCGT 57.751 50.000 0.00 0.00 44.69 4.69
2617 11711 6.441088 AATCATAATGGAACTACTCCCTCC 57.559 41.667 0.00 0.00 44.69 4.30
2618 11712 7.445707 GGAAAATCATAATGGAACTACTCCCTC 59.554 40.741 0.00 0.00 44.69 4.30
2619 11713 7.091993 TGGAAAATCATAATGGAACTACTCCCT 60.092 37.037 0.00 0.00 44.69 4.20
2620 11714 7.060421 TGGAAAATCATAATGGAACTACTCCC 58.940 38.462 0.00 0.00 44.69 4.30
2621 11715 8.571336 CATGGAAAATCATAATGGAACTACTCC 58.429 37.037 0.00 0.00 45.64 3.85
2622 11716 9.125026 ACATGGAAAATCATAATGGAACTACTC 57.875 33.333 0.00 0.00 0.00 2.59
2628 11722 9.868277 GTTGTTACATGGAAAATCATAATGGAA 57.132 29.630 0.00 0.00 0.00 3.53
2629 11723 9.029368 TGTTGTTACATGGAAAATCATAATGGA 57.971 29.630 0.00 0.00 0.00 3.41
2630 11724 9.086336 GTGTTGTTACATGGAAAATCATAATGG 57.914 33.333 0.00 0.00 36.50 3.16
2634 11728 9.173021 CCTAGTGTTGTTACATGGAAAATCATA 57.827 33.333 0.00 0.00 36.50 2.15
2635 11729 7.888021 TCCTAGTGTTGTTACATGGAAAATCAT 59.112 33.333 0.00 0.00 36.50 2.45
2636 11730 7.227873 TCCTAGTGTTGTTACATGGAAAATCA 58.772 34.615 0.00 0.00 36.50 2.57
2638 11732 7.308348 CGTTCCTAGTGTTGTTACATGGAAAAT 60.308 37.037 0.00 0.00 39.88 1.82
2639 11733 6.017770 CGTTCCTAGTGTTGTTACATGGAAAA 60.018 38.462 0.00 0.00 39.88 2.29
2640 11734 5.467399 CGTTCCTAGTGTTGTTACATGGAAA 59.533 40.000 0.00 0.00 39.88 3.13
2641 11735 4.992319 CGTTCCTAGTGTTGTTACATGGAA 59.008 41.667 0.00 0.00 37.99 3.53
2643 11737 4.562082 TCGTTCCTAGTGTTGTTACATGG 58.438 43.478 0.00 0.00 36.50 3.66
2645 11739 8.836268 TTTATTCGTTCCTAGTGTTGTTACAT 57.164 30.769 0.00 0.00 36.50 2.29
2647 11741 7.148523 CCCTTTATTCGTTCCTAGTGTTGTTAC 60.149 40.741 0.00 0.00 0.00 2.50
2648 11742 6.875195 CCCTTTATTCGTTCCTAGTGTTGTTA 59.125 38.462 0.00 0.00 0.00 2.41
2650 11744 5.012354 TCCCTTTATTCGTTCCTAGTGTTGT 59.988 40.000 0.00 0.00 0.00 3.32
2652 11746 5.247792 AGTCCCTTTATTCGTTCCTAGTGTT 59.752 40.000 0.00 0.00 0.00 3.32
2667 11761 6.266786 TGATTCGCAGATGTATAGTCCCTTTA 59.733 38.462 0.00 0.00 35.04 1.85
2710 11805 2.105128 GCAGACGACGCAGCCTAT 59.895 61.111 0.00 0.00 0.00 2.57
2819 12154 8.246180 TCAAAAGAAGAAGGAAATATGTCATGC 58.754 33.333 0.00 0.00 0.00 4.06
2852 12187 4.236935 CATTGTTTCATGCCAGTGGTTAC 58.763 43.478 11.74 0.00 0.00 2.50
2907 12243 4.161754 ACTTACATTTAGGAACCGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
2908 12244 4.098894 ACTTACATTTAGGAACCGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2909 12245 4.161754 AGACTTACATTTAGGAACCGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
2910 12246 5.340439 AGACTTACATTTAGGAACCGAGG 57.660 43.478 0.00 0.00 0.00 4.63
2911 12247 8.943909 ATAAAGACTTACATTTAGGAACCGAG 57.056 34.615 0.00 0.00 0.00 4.63
2948 12284 3.558033 TGCTCCGTATGTAGTCCACATA 58.442 45.455 0.00 0.00 46.34 2.29
2950 12286 1.842052 TGCTCCGTATGTAGTCCACA 58.158 50.000 0.00 0.00 42.69 4.17
2951 12287 2.953466 TTGCTCCGTATGTAGTCCAC 57.047 50.000 0.00 0.00 0.00 4.02
2952 12288 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
2953 12289 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
2954 12290 6.257849 TCATTCATTTTGCTCCGTATGTAGTC 59.742 38.462 0.00 0.00 0.00 2.59
2955 12291 6.112734 TCATTCATTTTGCTCCGTATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
2956 12292 6.603237 TCATTCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
2957 12293 6.993786 TTCATTCATTTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
2958 12294 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
2959 12295 5.916883 GGATTCATTCATTTTGCTCCGTATG 59.083 40.000 0.00 0.00 0.00 2.39
2960 12296 5.593909 TGGATTCATTCATTTTGCTCCGTAT 59.406 36.000 0.00 0.00 0.00 3.06
2961 12297 4.946772 TGGATTCATTCATTTTGCTCCGTA 59.053 37.500 0.00 0.00 0.00 4.02
2962 12298 3.763360 TGGATTCATTCATTTTGCTCCGT 59.237 39.130 0.00 0.00 0.00 4.69
2963 12299 4.374843 TGGATTCATTCATTTTGCTCCG 57.625 40.909 0.00 0.00 0.00 4.63
2964 12300 7.047460 AGTATGGATTCATTCATTTTGCTCC 57.953 36.000 0.00 0.00 34.96 4.70
2973 12309 9.970395 GATGCATTTTAAGTATGGATTCATTCA 57.030 29.630 0.00 0.00 34.69 2.57
2986 12322 9.944376 ACGGATGTATATAGATGCATTTTAAGT 57.056 29.630 11.19 0.00 38.38 2.24
2990 12326 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
2993 12329 9.355916 ACTACATACGGATGTATATAGATGCAT 57.644 33.333 20.64 0.00 45.42 3.96
2994 12330 8.747538 ACTACATACGGATGTATATAGATGCA 57.252 34.615 20.64 0.00 45.42 3.96
2995 12331 9.666626 GAACTACATACGGATGTATATAGATGC 57.333 37.037 20.64 0.00 45.42 3.91
3002 12338 9.729281 TCACTATGAACTACATACGGATGTATA 57.271 33.333 20.64 10.04 45.42 1.47
3003 12339 8.631480 TCACTATGAACTACATACGGATGTAT 57.369 34.615 20.64 7.28 45.42 2.29
3004 12340 8.454570 TTCACTATGAACTACATACGGATGTA 57.545 34.615 19.32 19.32 38.17 2.29
3005 12341 7.342769 TTCACTATGAACTACATACGGATGT 57.657 36.000 19.12 19.12 39.44 3.06
3006 12342 8.818141 ATTTCACTATGAACTACATACGGATG 57.182 34.615 5.94 5.94 35.89 3.51
3007 12343 9.832445 AAATTTCACTATGAACTACATACGGAT 57.168 29.630 0.00 0.00 35.89 4.18
3008 12344 9.661563 AAAATTTCACTATGAACTACATACGGA 57.338 29.630 0.00 0.00 35.89 4.69
3033 12369 9.976511 CCGTTCCTAAATATATGTCTCTGTAAA 57.023 33.333 0.00 0.00 0.00 2.01
3034 12370 9.358406 TCCGTTCCTAAATATATGTCTCTGTAA 57.642 33.333 0.00 0.00 0.00 2.41
3035 12371 8.929260 TCCGTTCCTAAATATATGTCTCTGTA 57.071 34.615 0.00 0.00 0.00 2.74
3036 12372 7.039644 CCTCCGTTCCTAAATATATGTCTCTGT 60.040 40.741 0.00 0.00 0.00 3.41
3037 12373 7.316640 CCTCCGTTCCTAAATATATGTCTCTG 58.683 42.308 0.00 0.00 0.00 3.35
3038 12374 6.437793 CCCTCCGTTCCTAAATATATGTCTCT 59.562 42.308 0.00 0.00 0.00 3.10
3039 12375 6.436532 TCCCTCCGTTCCTAAATATATGTCTC 59.563 42.308 0.00 0.00 0.00 3.36
3040 12376 6.320518 TCCCTCCGTTCCTAAATATATGTCT 58.679 40.000 0.00 0.00 0.00 3.41
3041 12377 6.210984 ACTCCCTCCGTTCCTAAATATATGTC 59.789 42.308 0.00 0.00 0.00 3.06
3042 12378 6.082707 ACTCCCTCCGTTCCTAAATATATGT 58.917 40.000 0.00 0.00 0.00 2.29
3043 12379 6.607004 ACTCCCTCCGTTCCTAAATATATG 57.393 41.667 0.00 0.00 0.00 1.78
3045 12381 9.247861 GTTATACTCCCTCCGTTCCTAAATATA 57.752 37.037 0.00 0.00 0.00 0.86
3046 12382 7.179872 GGTTATACTCCCTCCGTTCCTAAATAT 59.820 40.741 0.00 0.00 0.00 1.28
3047 12383 6.494835 GGTTATACTCCCTCCGTTCCTAAATA 59.505 42.308 0.00 0.00 0.00 1.40
3048 12384 5.306419 GGTTATACTCCCTCCGTTCCTAAAT 59.694 44.000 0.00 0.00 0.00 1.40
3049 12385 4.651045 GGTTATACTCCCTCCGTTCCTAAA 59.349 45.833 0.00 0.00 0.00 1.85
3050 12386 4.218312 GGTTATACTCCCTCCGTTCCTAA 58.782 47.826 0.00 0.00 0.00 2.69
3051 12387 3.748668 CGGTTATACTCCCTCCGTTCCTA 60.749 52.174 0.00 0.00 36.99 2.94
3052 12388 2.675583 GGTTATACTCCCTCCGTTCCT 58.324 52.381 0.00 0.00 0.00 3.36
3053 12389 1.339291 CGGTTATACTCCCTCCGTTCC 59.661 57.143 0.00 0.00 36.99 3.62
3054 12390 2.789491 CGGTTATACTCCCTCCGTTC 57.211 55.000 0.00 0.00 36.99 3.95
3057 12393 3.822735 TCATTACGGTTATACTCCCTCCG 59.177 47.826 0.00 0.00 45.53 4.63
3058 12394 5.796424 TTCATTACGGTTATACTCCCTCC 57.204 43.478 0.00 0.00 0.00 4.30
3059 12395 7.544915 GCTAATTCATTACGGTTATACTCCCTC 59.455 40.741 0.00 0.00 0.00 4.30
3060 12396 7.234988 AGCTAATTCATTACGGTTATACTCCCT 59.765 37.037 0.00 0.00 0.00 4.20
3061 12397 7.384477 AGCTAATTCATTACGGTTATACTCCC 58.616 38.462 0.00 0.00 0.00 4.30
3062 12398 8.828688 AAGCTAATTCATTACGGTTATACTCC 57.171 34.615 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.