Multiple sequence alignment - TraesCS1A01G412300

Loading Multiple Alignment...

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 TraesCS1A01G412300 chr1A 100.000 3356 0 0 1 3356 572675235 572678590 0.000000e+00 6198.0
1 TraesCS1A01G412300 chr1A 87.855 1375 134 17 1013 2371 572361110 572359753 0.000000e+00 1583.0
2 TraesCS1A01G412300 chr1A 95.506 89 3 1 2547 2635 583302839 583302752 1.260000e-29 141.0
3 TraesCS1A01G412300 chr1D 93.022 1734 72 23 706 2414 476763259 476764968 0.000000e+00 2486.0
4 TraesCS1A01G412300 chr1D 83.026 1031 116 30 1363 2371 476592636 476591643 0.000000e+00 880.0
5 TraesCS1A01G412300 chr1D 96.617 266 9 0 3091 3356 476765314 476765579 3.070000e-120 442.0
6 TraesCS1A01G412300 chr1D 91.259 286 25 0 1013 1298 476592920 476592635 1.130000e-104 390.0
7 TraesCS1A01G412300 chr1D 86.364 352 38 8 219 564 476754759 476755106 3.160000e-100 375.0
8 TraesCS1A01G412300 chr1D 85.764 288 12 6 2635 2893 476765031 476765318 9.170000e-71 278.0
9 TraesCS1A01G412300 chr1D 89.840 187 12 4 1 182 476754572 476754756 2.010000e-57 233.0
10 TraesCS1A01G412300 chr1D 92.632 95 6 1 2548 2642 321677924 321678017 5.840000e-28 135.0
11 TraesCS1A01G412300 chr1D 83.761 117 19 0 1727 1843 476759006 476758890 9.840000e-21 111.0
12 TraesCS1A01G412300 chr1D 91.429 70 5 1 2481 2550 476764961 476765029 9.910000e-16 95.3
13 TraesCS1A01G412300 chr1B 91.102 1787 100 12 672 2417 664016278 664018046 0.000000e+00 2364.0
14 TraesCS1A01G412300 chr1B 87.437 1385 134 25 1006 2371 662942312 662940949 0.000000e+00 1557.0
15 TraesCS1A01G412300 chr1B 88.553 463 38 6 136 593 664015467 664015919 6.330000e-152 547.0
16 TraesCS1A01G412300 chr1B 87.896 347 20 7 2071 2417 664082921 664083245 4.060000e-104 388.0
17 TraesCS1A01G412300 chr1B 87.288 118 11 4 2543 2660 352885047 352884934 7.560000e-27 132.0
18 TraesCS1A01G412300 chr1B 82.906 117 20 0 1727 1843 659956224 659956108 4.580000e-19 106.0
19 TraesCS1A01G412300 chr5A 86.543 1397 144 17 1013 2371 674545253 674543863 0.000000e+00 1498.0
20 TraesCS1A01G412300 chr7D 93.237 207 12 2 2889 3094 98997898 98997693 1.510000e-78 303.0
21 TraesCS1A01G412300 chr7D 87.864 206 18 6 2890 3094 91690004 91689805 5.600000e-58 235.0
22 TraesCS1A01G412300 chr4A 90.000 210 17 2 2885 3094 733630324 733630529 5.520000e-68 268.0
23 TraesCS1A01G412300 chr4A 88.235 204 13 7 2891 3094 574771660 574771468 2.010000e-57 233.0
24 TraesCS1A01G412300 chr7A 89.623 212 17 4 2884 3094 93256723 93256516 7.140000e-67 265.0
25 TraesCS1A01G412300 chr7A 88.991 109 10 2 2549 2655 126927402 126927294 2.100000e-27 134.0
26 TraesCS1A01G412300 chr2D 87.793 213 14 5 2890 3093 119841069 119841278 4.330000e-59 239.0
27 TraesCS1A01G412300 chr2D 90.385 104 7 3 2540 2642 601266046 601266147 2.100000e-27 134.0
28 TraesCS1A01G412300 chr2D 83.333 114 19 0 1730 1843 39315506 39315393 4.580000e-19 106.0
29 TraesCS1A01G412300 chr3A 88.235 204 13 7 2891 3094 224963145 224963337 2.010000e-57 233.0
30 TraesCS1A01G412300 chr6A 84.804 204 18 5 2891 3094 486004182 486004372 3.420000e-45 193.0
31 TraesCS1A01G412300 chr6D 83.415 205 20 7 2890 3094 345388374 345388564 9.570000e-41 178.0
32 TraesCS1A01G412300 chr2B 94.737 95 3 2 2551 2644 551988778 551988685 2.700000e-31 147.0
33 TraesCS1A01G412300 chr2B 91.176 102 6 3 2548 2648 635384196 635384097 5.840000e-28 135.0
34 TraesCS1A01G412300 chr3D 90.385 104 7 3 2546 2649 123309491 123309591 2.100000e-27 134.0
35 TraesCS1A01G412300 chr5D 89.524 105 10 1 2546 2650 234053027 234053130 7.560000e-27 132.0
36 TraesCS1A01G412300 chr4D 80.110 181 28 3 1397 1569 278296850 278296670 9.770000e-26 128.0
37 TraesCS1A01G412300 chr4B 83.761 117 19 0 1727 1843 238161274 238161390 9.840000e-21 111.0


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 TraesCS1A01G412300 chr1A 572675235 572678590 3355 False 6198.000 6198 100.0000 1 3356 1 chr1A.!!$F1 3355
1 TraesCS1A01G412300 chr1A 572359753 572361110 1357 True 1583.000 1583 87.8550 1013 2371 1 chr1A.!!$R1 1358
2 TraesCS1A01G412300 chr1D 476763259 476765579 2320 False 825.325 2486 91.7080 706 3356 4 chr1D.!!$F3 2650
3 TraesCS1A01G412300 chr1D 476591643 476592920 1277 True 635.000 880 87.1425 1013 2371 2 chr1D.!!$R2 1358
4 TraesCS1A01G412300 chr1D 476754572 476755106 534 False 304.000 375 88.1020 1 564 2 chr1D.!!$F2 563
5 TraesCS1A01G412300 chr1B 662940949 662942312 1363 True 1557.000 1557 87.4370 1006 2371 1 chr1B.!!$R3 1365
6 TraesCS1A01G412300 chr1B 664015467 664018046 2579 False 1455.500 2364 89.8275 136 2417 2 chr1B.!!$F2 2281
7 TraesCS1A01G412300 chr5A 674543863 674545253 1390 True 1498.000 1498 86.5430 1013 2371 1 chr5A.!!$R1 1358

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
28 29 0.250124 TTGGAACGGTGTTGCGAGAT 60.250 50.0 0.00 0.0 0.00 2.75 F
661 926 0.320073 TGAGTTTGCGAACCTACGGG 60.320 55.0 13.41 0.0 36.39 5.28 F
981 1286 0.873743 GCCGCACAGAGCTAAGCTAG 60.874 60.0 0.00 0.0 39.88 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1001 1309 0.758734 CCCTTGCTCCGATATGTCCA 59.241 55.000 0.00 0.00 0.00 4.02 R
1917 2275 1.068474 CGTCGAACCGCTTCTTGAAT 58.932 50.000 0.00 0.00 0.00 2.57 R
2901 3306 1.963515 AGGCAAATCTTTTGCTTCGGT 59.036 42.857 20.56 2.95 44.36 4.69 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
28 29 0.250124 TTGGAACGGTGTTGCGAGAT 60.250 50.000 0.00 0.00 0.00 2.75
33 34 1.374125 CGGTGTTGCGAGATGGTGA 60.374 57.895 0.00 0.00 0.00 4.02
40 41 3.435327 TGTTGCGAGATGGTGAATGTAAC 59.565 43.478 0.00 0.00 0.00 2.50
46 47 5.611374 CGAGATGGTGAATGTAACCCTATT 58.389 41.667 0.00 0.00 36.83 1.73
47 48 5.466728 CGAGATGGTGAATGTAACCCTATTG 59.533 44.000 0.00 0.00 36.83 1.90
48 49 6.575244 AGATGGTGAATGTAACCCTATTGA 57.425 37.500 0.00 0.00 36.83 2.57
49 50 6.357367 AGATGGTGAATGTAACCCTATTGAC 58.643 40.000 0.00 0.00 36.83 3.18
82 87 3.326006 TCTGAAGTGAAATCAGGAGCACT 59.674 43.478 3.92 0.00 43.58 4.40
108 113 9.582648 TGAGTTCCTTAGTTAAAAATAAAGGCT 57.417 29.630 0.00 0.00 0.00 4.58
287 294 7.581476 TGAATTTTCCTCTACGACAAAATGTC 58.419 34.615 0.39 0.39 43.65 3.06
318 325 8.015185 ACCATTCATGAAATTAAATCTCCTGG 57.985 34.615 13.09 12.74 0.00 4.45
393 406 2.964174 CCGCTGCCAAATGCTTCA 59.036 55.556 0.00 0.00 42.00 3.02
407 420 6.295236 CCAAATGCTTCAGAAATCCCACTAAA 60.295 38.462 0.00 0.00 0.00 1.85
423 436 5.285651 CCACTAAAACGGCTCAAAATTCAA 58.714 37.500 0.00 0.00 0.00 2.69
450 463 2.047061 CCGACAAATATCTCCCCTCCA 58.953 52.381 0.00 0.00 0.00 3.86
474 487 1.959226 GTCAAAGTGCCCGCGAGAA 60.959 57.895 8.23 0.00 0.00 2.87
496 509 1.000163 CGAGATTGCCCACTATAGCGT 60.000 52.381 0.00 0.00 0.00 5.07
546 559 3.493129 CGAAATCATTTCTCCCGCGATTA 59.507 43.478 8.23 0.00 37.52 1.75
588 601 2.095853 CGGCTGATTGTTCGCTTACATT 59.904 45.455 0.00 0.00 0.00 2.71
593 606 3.750652 TGATTGTTCGCTTACATTGCAGA 59.249 39.130 0.00 0.00 0.00 4.26
594 607 3.536158 TTGTTCGCTTACATTGCAGAC 57.464 42.857 0.00 0.00 0.00 3.51
596 609 2.875317 TGTTCGCTTACATTGCAGACAA 59.125 40.909 0.00 0.00 40.87 3.18
612 707 8.994429 TTGCAGACAAGATTTTTGTTTCTTAA 57.006 26.923 0.00 0.00 31.15 1.85
631 726 2.806288 ATTTCGTGAGTTGTATGCGC 57.194 45.000 0.00 0.00 0.00 6.09
658 923 4.946784 AATCATGAGTTTGCGAACCTAC 57.053 40.909 13.41 6.30 36.39 3.18
661 926 0.320073 TGAGTTTGCGAACCTACGGG 60.320 55.000 13.41 0.00 36.39 5.28
676 941 2.420568 CGGGCTACGGCTGAACCTA 61.421 63.158 0.00 0.00 39.42 3.08
685 950 2.028930 ACGGCTGAACCTAGAAGACAAG 60.029 50.000 0.00 0.00 35.61 3.16
689 954 5.394224 CGGCTGAACCTAGAAGACAAGATTA 60.394 44.000 0.00 0.00 35.61 1.75
690 955 6.587273 GGCTGAACCTAGAAGACAAGATTAT 58.413 40.000 0.00 0.00 34.51 1.28
691 956 6.481644 GGCTGAACCTAGAAGACAAGATTATG 59.518 42.308 0.00 0.00 34.51 1.90
692 957 7.044798 GCTGAACCTAGAAGACAAGATTATGT 58.955 38.462 0.00 0.00 35.90 2.29
693 958 7.550906 GCTGAACCTAGAAGACAAGATTATGTT 59.449 37.037 0.00 0.00 32.57 2.71
694 959 9.442047 CTGAACCTAGAAGACAAGATTATGTTT 57.558 33.333 0.00 0.00 32.57 2.83
695 960 9.793259 TGAACCTAGAAGACAAGATTATGTTTT 57.207 29.630 0.00 0.00 32.57 2.43
824 1129 1.600013 CTCATCTTCGTCTCCGATCGT 59.400 52.381 15.09 0.00 43.80 3.73
974 1279 4.326507 AAGCAGCCGCACAGAGCT 62.327 61.111 0.00 0.00 42.61 4.09
981 1286 0.873743 GCCGCACAGAGCTAAGCTAG 60.874 60.000 0.00 0.00 39.88 3.42
983 1288 1.339610 CCGCACAGAGCTAAGCTAGAT 59.660 52.381 0.00 0.00 39.88 1.98
989 1294 2.095263 CAGAGCTAAGCTAGATCGAGCC 60.095 54.545 22.38 8.68 45.41 4.70
1001 1309 3.565307 AGATCGAGCCAGAGAAAGAGAT 58.435 45.455 0.00 0.00 0.00 2.75
1004 1312 1.753649 CGAGCCAGAGAAAGAGATGGA 59.246 52.381 0.00 0.00 34.60 3.41
1008 1316 4.293494 AGCCAGAGAAAGAGATGGACATA 58.707 43.478 0.00 0.00 34.60 2.29
1495 1803 4.689484 TCGACGACCTCGAGTTCT 57.311 55.556 12.31 0.00 46.75 3.01
1574 1891 2.838202 GGTTCTCCATCTACACCTCCAA 59.162 50.000 0.00 0.00 0.00 3.53
1638 1959 8.934697 AGCCAGGTAATCTTGTGACTATATAAA 58.065 33.333 0.00 0.00 0.00 1.40
1639 1960 9.209175 GCCAGGTAATCTTGTGACTATATAAAG 57.791 37.037 0.00 0.00 0.00 1.85
1665 1986 2.418692 ACGGCATCATTGTCACGTTTA 58.581 42.857 0.00 0.00 29.91 2.01
1666 1987 2.158841 ACGGCATCATTGTCACGTTTAC 59.841 45.455 0.00 0.00 29.91 2.01
1667 1988 2.158645 CGGCATCATTGTCACGTTTACA 59.841 45.455 0.00 0.00 0.00 2.41
1856 2214 2.357034 CGGCTACAACTGCACGGT 60.357 61.111 0.00 0.00 0.00 4.83
1995 2356 3.069946 AACGCCCGGGACATCGTA 61.070 61.111 29.31 0.00 34.50 3.43
2417 2793 4.642437 TGCACCAAAGTCAGTTGATTGTTA 59.358 37.500 0.00 0.00 0.00 2.41
2418 2794 5.215160 GCACCAAAGTCAGTTGATTGTTAG 58.785 41.667 0.00 0.00 0.00 2.34
2420 2796 6.430451 CACCAAAGTCAGTTGATTGTTAGTC 58.570 40.000 0.00 0.00 0.00 2.59
2421 2797 6.260936 CACCAAAGTCAGTTGATTGTTAGTCT 59.739 38.462 0.00 0.00 0.00 3.24
2422 2798 6.483640 ACCAAAGTCAGTTGATTGTTAGTCTC 59.516 38.462 0.00 0.00 0.00 3.36
2423 2799 6.708054 CCAAAGTCAGTTGATTGTTAGTCTCT 59.292 38.462 0.00 0.00 0.00 3.10
2424 2800 7.095439 CCAAAGTCAGTTGATTGTTAGTCTCTC 60.095 40.741 0.00 0.00 0.00 3.20
2425 2801 6.031751 AGTCAGTTGATTGTTAGTCTCTCC 57.968 41.667 0.00 0.00 0.00 3.71
2426 2802 5.046950 AGTCAGTTGATTGTTAGTCTCTCCC 60.047 44.000 0.00 0.00 0.00 4.30
2427 2803 4.838423 TCAGTTGATTGTTAGTCTCTCCCA 59.162 41.667 0.00 0.00 0.00 4.37
2428 2804 5.306937 TCAGTTGATTGTTAGTCTCTCCCAA 59.693 40.000 0.00 0.00 0.00 4.12
2429 2805 6.013379 TCAGTTGATTGTTAGTCTCTCCCAAT 60.013 38.462 0.00 0.00 0.00 3.16
2430 2806 7.180229 TCAGTTGATTGTTAGTCTCTCCCAATA 59.820 37.037 0.00 0.00 0.00 1.90
2431 2807 7.989741 CAGTTGATTGTTAGTCTCTCCCAATAT 59.010 37.037 0.00 0.00 0.00 1.28
2432 2808 9.213777 AGTTGATTGTTAGTCTCTCCCAATATA 57.786 33.333 0.00 0.00 0.00 0.86
2433 2809 9.832445 GTTGATTGTTAGTCTCTCCCAATATAA 57.168 33.333 0.00 0.00 0.00 0.98
2435 2811 9.213777 TGATTGTTAGTCTCTCCCAATATAAGT 57.786 33.333 0.00 0.00 0.00 2.24
2436 2812 9.699703 GATTGTTAGTCTCTCCCAATATAAGTC 57.300 37.037 0.00 0.00 0.00 3.01
2437 2813 7.273320 TGTTAGTCTCTCCCAATATAAGTCG 57.727 40.000 0.00 0.00 0.00 4.18
2438 2814 6.832384 TGTTAGTCTCTCCCAATATAAGTCGT 59.168 38.462 0.00 0.00 0.00 4.34
2439 2815 7.341256 TGTTAGTCTCTCCCAATATAAGTCGTT 59.659 37.037 0.00 0.00 0.00 3.85
2440 2816 6.793505 AGTCTCTCCCAATATAAGTCGTTT 57.206 37.500 0.00 0.00 0.00 3.60
2441 2817 7.184067 AGTCTCTCCCAATATAAGTCGTTTT 57.816 36.000 0.00 0.00 0.00 2.43
2442 2818 8.302515 AGTCTCTCCCAATATAAGTCGTTTTA 57.697 34.615 0.00 0.00 0.00 1.52
2443 2819 8.414778 AGTCTCTCCCAATATAAGTCGTTTTAG 58.585 37.037 0.00 0.00 0.00 1.85
2444 2820 7.169476 GTCTCTCCCAATATAAGTCGTTTTAGC 59.831 40.741 0.00 0.00 0.00 3.09
2445 2821 6.880484 TCTCCCAATATAAGTCGTTTTAGCA 58.120 36.000 0.00 0.00 0.00 3.49
2446 2822 7.332557 TCTCCCAATATAAGTCGTTTTAGCAA 58.667 34.615 0.00 0.00 0.00 3.91
2447 2823 7.494625 TCTCCCAATATAAGTCGTTTTAGCAAG 59.505 37.037 0.00 0.00 0.00 4.01
2448 2824 6.037830 TCCCAATATAAGTCGTTTTAGCAAGC 59.962 38.462 0.00 0.00 0.00 4.01
2449 2825 6.038271 CCCAATATAAGTCGTTTTAGCAAGCT 59.962 38.462 0.00 0.00 0.00 3.74
2450 2826 7.225931 CCCAATATAAGTCGTTTTAGCAAGCTA 59.774 37.037 0.00 0.00 0.00 3.32
2451 2827 8.774586 CCAATATAAGTCGTTTTAGCAAGCTAT 58.225 33.333 2.16 0.00 0.00 2.97
2456 2832 9.983804 ATAAGTCGTTTTAGCAAGCTATAAAAC 57.016 29.630 20.97 20.97 43.54 2.43
2461 2837 6.839033 GTTTTAGCAAGCTATAAAACGACCT 58.161 36.000 18.41 0.00 40.22 3.85
2462 2838 7.967178 GTTTTAGCAAGCTATAAAACGACCTA 58.033 34.615 18.41 0.00 40.22 3.08
2463 2839 8.610035 GTTTTAGCAAGCTATAAAACGACCTAT 58.390 33.333 18.41 0.00 40.22 2.57
2464 2840 9.820725 TTTTAGCAAGCTATAAAACGACCTATA 57.179 29.630 2.16 0.00 0.00 1.31
2465 2841 9.991906 TTTAGCAAGCTATAAAACGACCTATAT 57.008 29.630 2.16 0.00 0.00 0.86
2478 2854 8.888579 AAACGACCTATATATTGAAACAGAGG 57.111 34.615 0.00 0.00 0.00 3.69
2479 2855 7.834881 ACGACCTATATATTGAAACAGAGGA 57.165 36.000 0.00 0.00 0.00 3.71
2480 2856 8.246430 ACGACCTATATATTGAAACAGAGGAA 57.754 34.615 0.00 0.00 0.00 3.36
2481 2857 8.361139 ACGACCTATATATTGAAACAGAGGAAG 58.639 37.037 0.00 0.00 0.00 3.46
2482 2858 8.361139 CGACCTATATATTGAAACAGAGGAAGT 58.639 37.037 1.71 0.00 0.00 3.01
2516 2892 8.795513 TGTTTCGTATTCGGGATGTCTATTATA 58.204 33.333 0.00 0.00 37.69 0.98
2550 2926 6.870971 TTTGGAAGCTTCGTAGTAAATTGT 57.129 33.333 19.91 0.00 0.00 2.71
2551 2927 7.966246 TTTGGAAGCTTCGTAGTAAATTGTA 57.034 32.000 19.91 0.00 0.00 2.41
2552 2928 6.956299 TGGAAGCTTCGTAGTAAATTGTAC 57.044 37.500 19.91 1.83 0.00 2.90
2553 2929 6.694447 TGGAAGCTTCGTAGTAAATTGTACT 58.306 36.000 19.91 0.00 0.00 2.73
2554 2930 6.810182 TGGAAGCTTCGTAGTAAATTGTACTC 59.190 38.462 19.91 0.84 0.00 2.59
2555 2931 6.255237 GGAAGCTTCGTAGTAAATTGTACTCC 59.745 42.308 19.91 0.00 0.00 3.85
2556 2932 5.658468 AGCTTCGTAGTAAATTGTACTCCC 58.342 41.667 0.00 0.00 0.00 4.30
2557 2933 5.421374 AGCTTCGTAGTAAATTGTACTCCCT 59.579 40.000 0.00 0.00 0.00 4.20
2558 2934 5.747675 GCTTCGTAGTAAATTGTACTCCCTC 59.252 44.000 0.00 0.00 0.00 4.30
2559 2935 5.841957 TCGTAGTAAATTGTACTCCCTCC 57.158 43.478 0.00 0.00 0.00 4.30
2560 2936 4.336433 TCGTAGTAAATTGTACTCCCTCCG 59.664 45.833 0.00 0.00 0.00 4.63
2561 2937 4.096984 CGTAGTAAATTGTACTCCCTCCGT 59.903 45.833 0.00 0.00 0.00 4.69
2562 2938 4.732672 AGTAAATTGTACTCCCTCCGTC 57.267 45.455 0.00 0.00 0.00 4.79
2563 2939 3.450096 AGTAAATTGTACTCCCTCCGTCC 59.550 47.826 0.00 0.00 0.00 4.79
2564 2940 1.201424 AATTGTACTCCCTCCGTCCC 58.799 55.000 0.00 0.00 0.00 4.46
2565 2941 0.042131 ATTGTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
2566 2942 0.042131 TTGTACTCCCTCCGTCCCAT 59.958 55.000 0.00 0.00 0.00 4.00
2567 2943 0.928505 TGTACTCCCTCCGTCCCATA 59.071 55.000 0.00 0.00 0.00 2.74
2568 2944 1.288633 TGTACTCCCTCCGTCCCATAA 59.711 52.381 0.00 0.00 0.00 1.90
2569 2945 2.090943 TGTACTCCCTCCGTCCCATAAT 60.091 50.000 0.00 0.00 0.00 1.28
2570 2946 3.140707 TGTACTCCCTCCGTCCCATAATA 59.859 47.826 0.00 0.00 0.00 0.98
2571 2947 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2572 2948 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2573 2949 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2574 2950 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2575 2951 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2576 2952 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
2577 2953 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
2578 2954 5.247564 CCCTCCGTCCCATAATATAAGAACA 59.752 44.000 0.00 0.00 0.00 3.18
2579 2955 6.164176 CCTCCGTCCCATAATATAAGAACAC 58.836 44.000 0.00 0.00 0.00 3.32
2580 2956 6.014499 CCTCCGTCCCATAATATAAGAACACT 60.014 42.308 0.00 0.00 0.00 3.55
2581 2957 7.369551 TCCGTCCCATAATATAAGAACACTT 57.630 36.000 0.00 0.00 0.00 3.16
2582 2958 7.798071 TCCGTCCCATAATATAAGAACACTTT 58.202 34.615 0.00 0.00 0.00 2.66
2583 2959 8.269317 TCCGTCCCATAATATAAGAACACTTTT 58.731 33.333 0.00 0.00 0.00 2.27
2584 2960 8.899771 CCGTCCCATAATATAAGAACACTTTTT 58.100 33.333 0.00 0.00 0.00 1.94
2675 3051 5.014228 GGGATTATAGCCCAGGACTTAATGT 59.986 44.000 7.65 0.00 45.31 2.71
2713 3089 8.110860 TCTCAGTGTTTCAAAAGAAAAAGTCT 57.889 30.769 0.00 0.00 38.69 3.24
2740 3116 9.821662 GAGTACTTAATGTGGTAATGTGTTTTC 57.178 33.333 0.00 0.00 0.00 2.29
2744 3120 9.744468 ACTTAATGTGGTAATGTGTTTTCTTTC 57.256 29.630 0.00 0.00 0.00 2.62
2748 3124 7.820044 TGTGGTAATGTGTTTTCTTTCAAAC 57.180 32.000 0.00 0.00 37.20 2.93
2773 3170 9.000486 ACAGTTACTTAAGAAATACTGCCTTTC 58.000 33.333 10.09 0.00 37.18 2.62
2790 3187 9.694137 ACTGCCTTTCTAACTTAATATACGATC 57.306 33.333 0.00 0.00 0.00 3.69
2841 3238 8.849543 AAGTTGTGGAGGGACTACTATTATAA 57.150 34.615 0.00 0.00 42.22 0.98
2914 3319 4.358494 TTTTCGAAACCGAAGCAAAAGA 57.642 36.364 10.79 0.00 45.33 2.52
2915 3320 4.561735 TTTCGAAACCGAAGCAAAAGAT 57.438 36.364 6.47 0.00 45.33 2.40
2916 3321 4.561735 TTCGAAACCGAAGCAAAAGATT 57.438 36.364 0.00 0.00 40.65 2.40
2917 3322 4.561735 TCGAAACCGAAGCAAAAGATTT 57.438 36.364 0.00 0.00 32.51 2.17
2918 3323 4.286910 TCGAAACCGAAGCAAAAGATTTG 58.713 39.130 0.00 0.00 32.51 2.32
2919 3324 3.121362 CGAAACCGAAGCAAAAGATTTGC 60.121 43.478 17.62 17.62 45.22 3.68
2920 3325 2.438868 ACCGAAGCAAAAGATTTGCC 57.561 45.000 20.66 8.56 45.98 4.52
2921 3326 1.963515 ACCGAAGCAAAAGATTTGCCT 59.036 42.857 20.66 10.82 45.98 4.75
2922 3327 2.029918 ACCGAAGCAAAAGATTTGCCTC 60.030 45.455 20.66 17.03 45.98 4.70
2924 3329 3.288809 GAAGCAAAAGATTTGCCTCGT 57.711 42.857 20.66 7.23 45.98 4.18
2925 3330 4.419522 GAAGCAAAAGATTTGCCTCGTA 57.580 40.909 20.66 0.00 45.98 3.43
2926 3331 4.986622 GAAGCAAAAGATTTGCCTCGTAT 58.013 39.130 20.66 2.40 45.98 3.06
2927 3332 6.119144 GAAGCAAAAGATTTGCCTCGTATA 57.881 37.500 20.66 0.00 45.98 1.47
2928 3333 6.699575 AAGCAAAAGATTTGCCTCGTATAT 57.300 33.333 20.66 1.12 45.98 0.86
2929 3334 6.699575 AGCAAAAGATTTGCCTCGTATATT 57.300 33.333 20.66 0.48 45.98 1.28
2930 3335 7.801716 AGCAAAAGATTTGCCTCGTATATTA 57.198 32.000 20.66 0.00 45.98 0.98
2931 3336 8.220755 AGCAAAAGATTTGCCTCGTATATTAA 57.779 30.769 20.66 0.00 45.98 1.40
2932 3337 8.850156 AGCAAAAGATTTGCCTCGTATATTAAT 58.150 29.630 20.66 0.00 45.98 1.40
2933 3338 9.463443 GCAAAAGATTTGCCTCGTATATTAATT 57.537 29.630 15.12 0.00 39.38 1.40
2938 3343 9.449719 AGATTTGCCTCGTATATTAATTAAGGG 57.550 33.333 3.94 0.00 0.00 3.95
2939 3344 9.444600 GATTTGCCTCGTATATTAATTAAGGGA 57.555 33.333 3.94 0.00 0.00 4.20
2940 3345 8.842358 TTTGCCTCGTATATTAATTAAGGGAG 57.158 34.615 3.94 5.68 0.00 4.30
2941 3346 7.786046 TGCCTCGTATATTAATTAAGGGAGA 57.214 36.000 3.94 0.00 0.00 3.71
2942 3347 8.197592 TGCCTCGTATATTAATTAAGGGAGAA 57.802 34.615 3.94 0.00 0.00 2.87
2943 3348 8.822805 TGCCTCGTATATTAATTAAGGGAGAAT 58.177 33.333 3.94 0.00 0.00 2.40
2959 3364 8.794335 AAGGGAGAATAGAGTTTGAAATACAC 57.206 34.615 0.00 0.00 0.00 2.90
2960 3365 7.339482 AGGGAGAATAGAGTTTGAAATACACC 58.661 38.462 0.00 0.00 0.00 4.16
2961 3366 7.182930 AGGGAGAATAGAGTTTGAAATACACCT 59.817 37.037 0.00 0.00 0.00 4.00
2962 3367 7.496263 GGGAGAATAGAGTTTGAAATACACCTC 59.504 40.741 0.00 0.00 0.00 3.85
2963 3368 7.222999 GGAGAATAGAGTTTGAAATACACCTCG 59.777 40.741 0.00 0.00 34.14 4.63
2964 3369 7.612677 AGAATAGAGTTTGAAATACACCTCGT 58.387 34.615 0.00 0.00 34.14 4.18
2965 3370 8.746530 AGAATAGAGTTTGAAATACACCTCGTA 58.253 33.333 0.00 0.00 34.14 3.43
2966 3371 9.362539 GAATAGAGTTTGAAATACACCTCGTAA 57.637 33.333 0.00 0.00 34.14 3.18
2967 3372 8.699283 ATAGAGTTTGAAATACACCTCGTAAC 57.301 34.615 0.00 0.00 34.14 2.50
2968 3373 6.756221 AGAGTTTGAAATACACCTCGTAACT 58.244 36.000 0.00 0.00 34.14 2.24
2969 3374 6.645415 AGAGTTTGAAATACACCTCGTAACTG 59.355 38.462 0.00 0.00 34.14 3.16
2970 3375 6.518493 AGTTTGAAATACACCTCGTAACTGA 58.482 36.000 0.00 0.00 32.59 3.41
2971 3376 6.987992 AGTTTGAAATACACCTCGTAACTGAA 59.012 34.615 0.00 0.00 32.59 3.02
2972 3377 7.496591 AGTTTGAAATACACCTCGTAACTGAAA 59.503 33.333 0.00 0.00 32.59 2.69
2973 3378 7.789273 TTGAAATACACCTCGTAACTGAAAA 57.211 32.000 0.00 0.00 32.59 2.29
2974 3379 7.789273 TGAAATACACCTCGTAACTGAAAAA 57.211 32.000 0.00 0.00 32.59 1.94
3002 3407 3.712091 GAGTGTTACTCTCCCGGTATG 57.288 52.381 0.00 0.00 41.88 2.39
3003 3408 3.285484 GAGTGTTACTCTCCCGGTATGA 58.715 50.000 0.00 0.00 41.88 2.15
3004 3409 3.890147 GAGTGTTACTCTCCCGGTATGAT 59.110 47.826 0.00 0.00 41.88 2.45
3005 3410 3.637229 AGTGTTACTCTCCCGGTATGATG 59.363 47.826 0.00 0.00 0.00 3.07
3006 3411 3.383825 GTGTTACTCTCCCGGTATGATGT 59.616 47.826 0.00 0.00 0.00 3.06
3007 3412 4.028131 TGTTACTCTCCCGGTATGATGTT 58.972 43.478 0.00 0.00 0.00 2.71
3008 3413 4.142026 TGTTACTCTCCCGGTATGATGTTG 60.142 45.833 0.00 0.00 0.00 3.33
3009 3414 1.139058 ACTCTCCCGGTATGATGTTGC 59.861 52.381 0.00 0.00 0.00 4.17
3010 3415 0.468226 TCTCCCGGTATGATGTTGCC 59.532 55.000 0.00 0.00 0.00 4.52
3011 3416 0.535102 CTCCCGGTATGATGTTGCCC 60.535 60.000 0.00 0.00 0.00 5.36
3012 3417 1.225983 CCCGGTATGATGTTGCCCA 59.774 57.895 0.00 0.00 0.00 5.36
3013 3418 0.395036 CCCGGTATGATGTTGCCCAA 60.395 55.000 0.00 0.00 0.00 4.12
3014 3419 1.691196 CCGGTATGATGTTGCCCAAT 58.309 50.000 0.00 0.00 0.00 3.16
3015 3420 2.031120 CCGGTATGATGTTGCCCAATT 58.969 47.619 0.00 0.00 0.00 2.32
3016 3421 2.430332 CCGGTATGATGTTGCCCAATTT 59.570 45.455 0.00 0.00 0.00 1.82
3017 3422 3.118811 CCGGTATGATGTTGCCCAATTTT 60.119 43.478 0.00 0.00 0.00 1.82
3018 3423 4.502962 CGGTATGATGTTGCCCAATTTTT 58.497 39.130 0.00 0.00 0.00 1.94
3039 3444 4.347955 CCCCGGCGGTTACCCAAA 62.348 66.667 26.32 0.00 0.00 3.28
3040 3445 2.748647 CCCGGCGGTTACCCAAAG 60.749 66.667 26.32 1.35 0.00 2.77
3041 3446 2.748647 CCGGCGGTTACCCAAAGG 60.749 66.667 19.97 0.00 40.04 3.11
3042 3447 2.348243 CGGCGGTTACCCAAAGGA 59.652 61.111 0.00 0.00 36.73 3.36
3043 3448 1.078001 CGGCGGTTACCCAAAGGAT 60.078 57.895 0.00 0.00 36.73 3.24
3044 3449 1.373590 CGGCGGTTACCCAAAGGATG 61.374 60.000 0.00 0.00 36.73 3.51
3052 3457 2.830370 CCAAAGGATGGCCTCGGC 60.830 66.667 3.32 0.00 46.28 5.54
3062 3467 3.190878 GCCTCGGCCTTGATGTTG 58.809 61.111 0.00 0.00 34.56 3.33
3063 3468 1.675641 GCCTCGGCCTTGATGTTGT 60.676 57.895 0.00 0.00 34.56 3.32
3064 3469 1.244019 GCCTCGGCCTTGATGTTGTT 61.244 55.000 0.00 0.00 34.56 2.83
3065 3470 0.523072 CCTCGGCCTTGATGTTGTTG 59.477 55.000 0.00 0.00 0.00 3.33
3066 3471 1.522668 CTCGGCCTTGATGTTGTTGA 58.477 50.000 0.00 0.00 0.00 3.18
3067 3472 1.466167 CTCGGCCTTGATGTTGTTGAG 59.534 52.381 0.00 0.00 0.00 3.02
3068 3473 0.109597 CGGCCTTGATGTTGTTGAGC 60.110 55.000 0.00 0.00 0.00 4.26
3069 3474 0.961019 GGCCTTGATGTTGTTGAGCA 59.039 50.000 0.00 0.00 0.00 4.26
3070 3475 1.340889 GGCCTTGATGTTGTTGAGCAA 59.659 47.619 0.00 0.00 34.16 3.91
3071 3476 2.224018 GGCCTTGATGTTGTTGAGCAAA 60.224 45.455 0.00 0.00 39.03 3.68
3072 3477 3.456280 GCCTTGATGTTGTTGAGCAAAA 58.544 40.909 0.00 0.00 39.03 2.44
3073 3478 3.245990 GCCTTGATGTTGTTGAGCAAAAC 59.754 43.478 0.00 0.00 39.03 2.43
3074 3479 4.431809 CCTTGATGTTGTTGAGCAAAACA 58.568 39.130 0.47 0.47 39.03 2.83
3075 3480 4.505191 CCTTGATGTTGTTGAGCAAAACAG 59.495 41.667 4.65 0.00 40.93 3.16
3076 3481 4.717233 TGATGTTGTTGAGCAAAACAGT 57.283 36.364 4.65 0.00 40.93 3.55
3077 3482 5.070770 TGATGTTGTTGAGCAAAACAGTT 57.929 34.783 4.65 0.00 40.93 3.16
3078 3483 4.863689 TGATGTTGTTGAGCAAAACAGTTG 59.136 37.500 4.65 0.00 40.93 3.16
3079 3484 3.583806 TGTTGTTGAGCAAAACAGTTGG 58.416 40.909 4.65 0.00 40.93 3.77
3080 3485 3.256879 TGTTGTTGAGCAAAACAGTTGGA 59.743 39.130 4.65 0.00 40.93 3.53
3081 3486 3.781079 TGTTGAGCAAAACAGTTGGAG 57.219 42.857 0.47 0.00 35.16 3.86
3082 3487 2.426738 TGTTGAGCAAAACAGTTGGAGG 59.573 45.455 0.47 0.00 35.16 4.30
3083 3488 1.032014 TGAGCAAAACAGTTGGAGGC 58.968 50.000 0.00 0.00 0.00 4.70
3084 3489 1.032014 GAGCAAAACAGTTGGAGGCA 58.968 50.000 0.00 0.00 0.00 4.75
3085 3490 1.615392 GAGCAAAACAGTTGGAGGCAT 59.385 47.619 0.00 0.00 0.00 4.40
3086 3491 2.819608 GAGCAAAACAGTTGGAGGCATA 59.180 45.455 0.00 0.00 0.00 3.14
3087 3492 2.558359 AGCAAAACAGTTGGAGGCATAC 59.442 45.455 0.00 0.00 0.00 2.39
3088 3493 2.558359 GCAAAACAGTTGGAGGCATACT 59.442 45.455 0.00 0.00 0.00 2.12
3089 3494 3.366374 GCAAAACAGTTGGAGGCATACTC 60.366 47.826 0.00 0.00 45.84 2.59
3090 3495 4.074970 CAAAACAGTTGGAGGCATACTCT 58.925 43.478 0.00 0.00 45.83 3.24
3091 3496 4.373156 AAACAGTTGGAGGCATACTCTT 57.627 40.909 0.00 0.00 45.83 2.85
3092 3497 4.373156 AACAGTTGGAGGCATACTCTTT 57.627 40.909 0.00 0.00 45.83 2.52
3093 3498 4.373156 ACAGTTGGAGGCATACTCTTTT 57.627 40.909 0.00 0.00 45.83 2.27
3094 3499 4.729868 ACAGTTGGAGGCATACTCTTTTT 58.270 39.130 0.00 0.00 45.83 1.94
3285 3690 7.780008 ATGCATGTCAATACAATTCCATTTG 57.220 32.000 0.00 0.00 39.58 2.32
3299 3704 4.191033 TCCATTTGATTTGACATGCCAC 57.809 40.909 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.949105 ACCATCTCGCAACACCGTTC 60.949 55.000 0.00 0.00 0.00 3.95
18 19 2.183478 ACATTCACCATCTCGCAACA 57.817 45.000 0.00 0.00 0.00 3.33
28 29 5.772393 AGTCAATAGGGTTACATTCACCA 57.228 39.130 0.00 0.00 35.80 4.17
33 34 7.507616 TGAAACCAAAGTCAATAGGGTTACATT 59.492 33.333 0.00 0.00 40.77 2.71
40 41 5.945784 TCAGATGAAACCAAAGTCAATAGGG 59.054 40.000 0.00 0.00 0.00 3.53
46 47 5.436175 TCACTTCAGATGAAACCAAAGTCA 58.564 37.500 0.00 0.00 33.07 3.41
47 48 6.377327 TTCACTTCAGATGAAACCAAAGTC 57.623 37.500 0.00 0.00 33.16 3.01
48 49 6.773976 TTTCACTTCAGATGAAACCAAAGT 57.226 33.333 0.00 0.00 40.32 2.66
49 50 7.428020 TGATTTCACTTCAGATGAAACCAAAG 58.572 34.615 2.47 0.00 46.05 2.77
82 87 9.582648 AGCCTTTATTTTTAACTAAGGAACTCA 57.417 29.630 0.00 0.00 38.49 3.41
259 266 9.410556 CATTTTGTCGTAGAGGAAAATTCAAAT 57.589 29.630 0.00 0.00 37.55 2.32
287 294 8.917088 AGATTTAATTTCATGAATGGTACCCAG 58.083 33.333 9.40 0.00 36.75 4.45
391 404 3.078837 GCCGTTTTAGTGGGATTTCTGA 58.921 45.455 0.00 0.00 0.00 3.27
393 406 3.244770 TGAGCCGTTTTAGTGGGATTTCT 60.245 43.478 0.00 0.00 0.00 2.52
407 420 5.694458 GGTTATTGTTGAATTTTGAGCCGTT 59.306 36.000 0.00 0.00 0.00 4.44
423 436 5.132144 AGGGGAGATATTTGTCGGTTATTGT 59.868 40.000 0.00 0.00 0.00 2.71
450 463 1.315257 GCGGGCACTTTGACATCCAT 61.315 55.000 0.00 0.00 0.00 3.41
474 487 1.344763 GCTATAGTGGGCAATCTCGGT 59.655 52.381 0.84 0.00 0.00 4.69
496 509 3.738281 GCTTCTCTCCGCAGTTATAGCAA 60.738 47.826 0.00 0.00 0.00 3.91
588 601 9.598517 AATTAAGAAACAAAAATCTTGTCTGCA 57.401 25.926 0.00 0.00 36.59 4.41
612 707 2.073056 TGCGCATACAACTCACGAAAT 58.927 42.857 5.66 0.00 0.00 2.17
638 733 2.930040 CGTAGGTTCGCAAACTCATGAT 59.070 45.455 0.00 0.00 35.61 2.45
639 734 2.333926 CGTAGGTTCGCAAACTCATGA 58.666 47.619 0.00 0.00 35.61 3.07
658 923 2.351336 CTAGGTTCAGCCGTAGCCCG 62.351 65.000 0.00 0.00 43.70 6.13
661 926 1.749634 TCTTCTAGGTTCAGCCGTAGC 59.250 52.381 0.00 0.00 43.70 3.58
668 933 9.442047 AAACATAATCTTGTCTTCTAGGTTCAG 57.558 33.333 0.00 0.00 0.00 3.02
700 965 2.520741 ACAAACTTGTGCCGGGGG 60.521 61.111 2.18 0.00 40.49 5.40
712 977 8.629986 CGACATTTCATGATTTCTAACACAAAC 58.370 33.333 0.00 0.00 0.00 2.93
713 978 7.325821 GCGACATTTCATGATTTCTAACACAAA 59.674 33.333 0.00 0.00 0.00 2.83
784 1076 2.796651 CTGGAAAGCCATGCGAGC 59.203 61.111 0.00 0.00 44.91 5.03
865 1170 2.808543 GACATTTCGATATGGGAGCACC 59.191 50.000 18.29 0.00 40.81 5.01
974 1279 3.493767 TCTCTGGCTCGATCTAGCTTA 57.506 47.619 17.77 7.65 42.37 3.09
981 1286 3.552684 CCATCTCTTTCTCTGGCTCGATC 60.553 52.174 0.00 0.00 0.00 3.69
983 1288 1.753649 CCATCTCTTTCTCTGGCTCGA 59.246 52.381 0.00 0.00 0.00 4.04
989 1294 5.242615 TCCGATATGTCCATCTCTTTCTCTG 59.757 44.000 0.00 0.00 0.00 3.35
1001 1309 0.758734 CCCTTGCTCCGATATGTCCA 59.241 55.000 0.00 0.00 0.00 4.02
1004 1312 1.069765 CGCCCTTGCTCCGATATGT 59.930 57.895 0.00 0.00 34.43 2.29
1008 1316 4.181010 ATGCGCCCTTGCTCCGAT 62.181 61.111 4.18 0.00 35.36 4.18
1167 1475 1.947146 CTCGTGGTTGAACGCGTCA 60.947 57.895 14.44 9.96 44.13 4.35
1396 1704 4.096003 CTTCCCCGCATCCGTGGT 62.096 66.667 0.00 0.00 41.61 4.16
1532 1840 3.063704 CACGGTGCACCATGGCAT 61.064 61.111 34.16 10.07 46.92 4.40
1638 1959 3.684788 GTGACAATGATGCCGTTTAGACT 59.315 43.478 0.00 0.00 0.00 3.24
1639 1960 3.483574 CGTGACAATGATGCCGTTTAGAC 60.484 47.826 0.00 0.00 0.00 2.59
1640 1961 2.670905 CGTGACAATGATGCCGTTTAGA 59.329 45.455 0.00 0.00 0.00 2.10
1641 1962 2.415168 ACGTGACAATGATGCCGTTTAG 59.585 45.455 0.00 0.00 0.00 1.85
1643 1964 1.234821 ACGTGACAATGATGCCGTTT 58.765 45.000 0.00 0.00 0.00 3.60
1666 1987 8.728402 GTGAGCTCAACACTGAACAGTATACTG 61.728 44.444 27.66 27.66 40.20 2.74
1667 1988 5.243954 TGAGCTCAACACTGAACAGTATACT 59.756 40.000 15.67 0.00 40.20 2.12
1743 2101 2.755655 CTCCTCGTCCTTGTACATGTCT 59.244 50.000 0.00 0.00 0.00 3.41
1809 2167 1.180456 TGTCGAAGGCGTTCAGGGTA 61.180 55.000 18.45 0.00 38.98 3.69
1872 2230 4.287967 AACGCAAACGCCGTGACG 62.288 61.111 0.00 0.00 45.53 4.35
1917 2275 1.068474 CGTCGAACCGCTTCTTGAAT 58.932 50.000 0.00 0.00 0.00 2.57
2154 2515 3.671411 ACCACGAGCTCGAACGCT 61.671 61.111 40.58 17.00 44.33 5.07
2399 2775 7.095439 GGAGAGACTAACAATCAACTGACTTTG 60.095 40.741 0.00 0.00 0.00 2.77
2404 2780 4.838423 TGGGAGAGACTAACAATCAACTGA 59.162 41.667 0.00 0.00 0.00 3.41
2417 2793 6.793505 AAACGACTTATATTGGGAGAGACT 57.206 37.500 0.00 0.00 0.00 3.24
2418 2794 7.169476 GCTAAAACGACTTATATTGGGAGAGAC 59.831 40.741 0.00 0.00 0.00 3.36
2420 2796 6.984474 TGCTAAAACGACTTATATTGGGAGAG 59.016 38.462 0.00 0.00 0.00 3.20
2421 2797 6.880484 TGCTAAAACGACTTATATTGGGAGA 58.120 36.000 0.00 0.00 0.00 3.71
2422 2798 7.548196 TTGCTAAAACGACTTATATTGGGAG 57.452 36.000 0.00 0.00 0.00 4.30
2423 2799 6.037830 GCTTGCTAAAACGACTTATATTGGGA 59.962 38.462 0.00 0.00 0.00 4.37
2424 2800 6.038271 AGCTTGCTAAAACGACTTATATTGGG 59.962 38.462 0.00 0.00 0.00 4.12
2425 2801 7.016361 AGCTTGCTAAAACGACTTATATTGG 57.984 36.000 0.00 0.00 0.00 3.16
2430 2806 9.983804 GTTTTATAGCTTGCTAAAACGACTTAT 57.016 29.630 16.52 0.00 37.79 1.73
2437 2813 6.839033 AGGTCGTTTTATAGCTTGCTAAAAC 58.161 36.000 19.15 19.15 41.28 2.43
2438 2814 8.726870 ATAGGTCGTTTTATAGCTTGCTAAAA 57.273 30.769 6.42 3.20 0.00 1.52
2439 2815 9.991906 ATATAGGTCGTTTTATAGCTTGCTAAA 57.008 29.630 6.42 0.00 0.00 1.85
2452 2828 9.326413 CCTCTGTTTCAATATATAGGTCGTTTT 57.674 33.333 0.00 0.00 0.00 2.43
2453 2829 8.701895 TCCTCTGTTTCAATATATAGGTCGTTT 58.298 33.333 0.00 0.00 0.00 3.60
2454 2830 8.246430 TCCTCTGTTTCAATATATAGGTCGTT 57.754 34.615 0.00 0.00 0.00 3.85
2455 2831 7.834881 TCCTCTGTTTCAATATATAGGTCGT 57.165 36.000 0.00 0.00 0.00 4.34
2456 2832 8.361139 ACTTCCTCTGTTTCAATATATAGGTCG 58.639 37.037 0.00 0.00 0.00 4.79
2486 2862 5.470777 AGACATCCCGAATACGAAACAAAAA 59.529 36.000 0.00 0.00 42.66 1.94
2487 2863 4.998672 AGACATCCCGAATACGAAACAAAA 59.001 37.500 0.00 0.00 42.66 2.44
2488 2864 4.571919 AGACATCCCGAATACGAAACAAA 58.428 39.130 0.00 0.00 42.66 2.83
2489 2865 4.196626 AGACATCCCGAATACGAAACAA 57.803 40.909 0.00 0.00 42.66 2.83
2490 2866 3.880047 AGACATCCCGAATACGAAACA 57.120 42.857 0.00 0.00 42.66 2.83
2491 2867 9.798994 ATATAATAGACATCCCGAATACGAAAC 57.201 33.333 0.00 0.00 42.66 2.78
2492 2868 9.797556 CATATAATAGACATCCCGAATACGAAA 57.202 33.333 0.00 0.00 42.66 3.46
2493 2869 8.410912 CCATATAATAGACATCCCGAATACGAA 58.589 37.037 0.00 0.00 42.66 3.85
2494 2870 7.776500 TCCATATAATAGACATCCCGAATACGA 59.224 37.037 0.00 0.00 42.66 3.43
2495 2871 7.937649 TCCATATAATAGACATCCCGAATACG 58.062 38.462 0.00 0.00 39.43 3.06
2496 2872 8.915036 ACTCCATATAATAGACATCCCGAATAC 58.085 37.037 0.00 0.00 0.00 1.89
2516 2892 6.357367 ACGAAGCTTCCAAATAATACTCCAT 58.643 36.000 20.62 0.00 0.00 3.41
2550 2926 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2551 2927 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2552 2928 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2553 2929 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
2554 2930 5.247564 TGTTCTTATATTATGGGACGGAGGG 59.752 44.000 0.00 0.00 0.00 4.30
2555 2931 6.014499 AGTGTTCTTATATTATGGGACGGAGG 60.014 42.308 0.00 0.00 0.00 4.30
2556 2932 6.994221 AGTGTTCTTATATTATGGGACGGAG 58.006 40.000 0.00 0.00 0.00 4.63
2557 2933 6.989155 AGTGTTCTTATATTATGGGACGGA 57.011 37.500 0.00 0.00 0.00 4.69
2558 2934 8.446599 AAAAGTGTTCTTATATTATGGGACGG 57.553 34.615 0.00 0.00 33.09 4.79
2601 2977 9.675464 TCTGTCCCATAATATAAGAACGTTTTT 57.325 29.630 9.22 9.22 0.00 1.94
2602 2978 9.326413 CTCTGTCCCATAATATAAGAACGTTTT 57.674 33.333 0.46 0.00 0.00 2.43
2603 2979 7.931948 CCTCTGTCCCATAATATAAGAACGTTT 59.068 37.037 0.46 0.00 0.00 3.60
2604 2980 7.442656 CCTCTGTCCCATAATATAAGAACGTT 58.557 38.462 0.00 0.00 0.00 3.99
2605 2981 6.014499 CCCTCTGTCCCATAATATAAGAACGT 60.014 42.308 0.00 0.00 0.00 3.99
2606 2982 6.210784 TCCCTCTGTCCCATAATATAAGAACG 59.789 42.308 0.00 0.00 0.00 3.95
2607 2983 7.235812 ACTCCCTCTGTCCCATAATATAAGAAC 59.764 40.741 0.00 0.00 0.00 3.01
2608 2984 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
2609 2985 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
2610 2986 8.666129 TTACTCCCTCTGTCCCATAATATAAG 57.334 38.462 0.00 0.00 0.00 1.73
2611 2987 9.629649 AATTACTCCCTCTGTCCCATAATATAA 57.370 33.333 0.00 0.00 0.00 0.98
2613 2989 9.805204 ATAATTACTCCCTCTGTCCCATAATAT 57.195 33.333 0.00 0.00 0.00 1.28
2614 2990 9.046846 CATAATTACTCCCTCTGTCCCATAATA 57.953 37.037 0.00 0.00 0.00 0.98
2615 2991 7.517604 ACATAATTACTCCCTCTGTCCCATAAT 59.482 37.037 0.00 0.00 0.00 1.28
2616 2992 6.849697 ACATAATTACTCCCTCTGTCCCATAA 59.150 38.462 0.00 0.00 0.00 1.90
2617 2993 6.390504 ACATAATTACTCCCTCTGTCCCATA 58.609 40.000 0.00 0.00 0.00 2.74
2618 2994 5.227593 ACATAATTACTCCCTCTGTCCCAT 58.772 41.667 0.00 0.00 0.00 4.00
2619 2995 4.631234 ACATAATTACTCCCTCTGTCCCA 58.369 43.478 0.00 0.00 0.00 4.37
2620 2996 5.632034 AACATAATTACTCCCTCTGTCCC 57.368 43.478 0.00 0.00 0.00 4.46
2621 2997 9.628500 ATTAAAACATAATTACTCCCTCTGTCC 57.372 33.333 0.00 0.00 0.00 4.02
2627 3003 8.977412 CCCACAATTAAAACATAATTACTCCCT 58.023 33.333 0.00 0.00 0.00 4.20
2628 3004 8.973182 TCCCACAATTAAAACATAATTACTCCC 58.027 33.333 0.00 0.00 0.00 4.30
2713 3089 8.911918 AAACACATTACCACATTAAGTACTCA 57.088 30.769 0.00 0.00 0.00 3.41
2744 3120 8.784043 AGGCAGTATTTCTTAAGTAACTGTTTG 58.216 33.333 20.01 8.77 37.31 2.93
2746 3122 8.919777 AAGGCAGTATTTCTTAAGTAACTGTT 57.080 30.769 20.01 0.00 37.31 3.16
2747 3123 8.919777 AAAGGCAGTATTTCTTAAGTAACTGT 57.080 30.769 20.01 7.93 37.31 3.55
2748 3124 9.220767 AGAAAGGCAGTATTTCTTAAGTAACTG 57.779 33.333 17.25 17.25 42.86 3.16
2896 3301 4.286910 CAAATCTTTTGCTTCGGTTTCGA 58.713 39.130 0.00 0.00 44.44 3.71
2897 3302 3.121362 GCAAATCTTTTGCTTCGGTTTCG 60.121 43.478 15.71 0.00 41.87 3.46
2898 3303 3.184379 GGCAAATCTTTTGCTTCGGTTTC 59.816 43.478 20.56 2.45 44.36 2.78
2899 3304 3.130633 GGCAAATCTTTTGCTTCGGTTT 58.869 40.909 20.56 0.00 44.36 3.27
2900 3305 2.365293 AGGCAAATCTTTTGCTTCGGTT 59.635 40.909 20.56 2.43 44.36 4.44
2901 3306 1.963515 AGGCAAATCTTTTGCTTCGGT 59.036 42.857 20.56 2.95 44.36 4.69
2902 3307 2.599659 GAGGCAAATCTTTTGCTTCGG 58.400 47.619 20.56 0.00 44.36 4.30
2904 3309 3.288809 ACGAGGCAAATCTTTTGCTTC 57.711 42.857 20.65 20.65 44.74 3.86
2905 3310 6.699575 ATATACGAGGCAAATCTTTTGCTT 57.300 33.333 20.56 15.26 44.36 3.91
2906 3311 6.699575 AATATACGAGGCAAATCTTTTGCT 57.300 33.333 20.56 9.75 44.36 3.91
2907 3312 9.463443 AATTAATATACGAGGCAAATCTTTTGC 57.537 29.630 14.88 14.88 44.22 3.68
2912 3317 9.449719 CCCTTAATTAATATACGAGGCAAATCT 57.550 33.333 0.00 0.00 0.00 2.40
2913 3318 9.444600 TCCCTTAATTAATATACGAGGCAAATC 57.555 33.333 0.00 0.00 0.00 2.17
2914 3319 9.449719 CTCCCTTAATTAATATACGAGGCAAAT 57.550 33.333 0.00 0.00 0.00 2.32
2915 3320 8.653191 TCTCCCTTAATTAATATACGAGGCAAA 58.347 33.333 0.00 0.00 0.00 3.68
2916 3321 8.197592 TCTCCCTTAATTAATATACGAGGCAA 57.802 34.615 0.00 0.00 0.00 4.52
2917 3322 7.786046 TCTCCCTTAATTAATATACGAGGCA 57.214 36.000 0.00 0.00 0.00 4.75
2933 3338 9.886132 GTGTATTTCAAACTCTATTCTCCCTTA 57.114 33.333 0.00 0.00 0.00 2.69
2934 3339 7.829706 GGTGTATTTCAAACTCTATTCTCCCTT 59.170 37.037 0.00 0.00 0.00 3.95
2935 3340 7.182930 AGGTGTATTTCAAACTCTATTCTCCCT 59.817 37.037 0.00 0.00 0.00 4.20
2936 3341 7.339482 AGGTGTATTTCAAACTCTATTCTCCC 58.661 38.462 0.00 0.00 0.00 4.30
2937 3342 7.222999 CGAGGTGTATTTCAAACTCTATTCTCC 59.777 40.741 0.00 0.00 33.19 3.71
2938 3343 7.760340 ACGAGGTGTATTTCAAACTCTATTCTC 59.240 37.037 0.00 0.00 33.19 2.87
2939 3344 7.612677 ACGAGGTGTATTTCAAACTCTATTCT 58.387 34.615 0.00 0.00 33.19 2.40
2940 3345 7.829378 ACGAGGTGTATTTCAAACTCTATTC 57.171 36.000 0.00 0.00 33.19 1.75
2941 3346 9.148104 GTTACGAGGTGTATTTCAAACTCTATT 57.852 33.333 0.00 0.00 33.19 1.73
2942 3347 8.529476 AGTTACGAGGTGTATTTCAAACTCTAT 58.471 33.333 0.00 0.00 33.19 1.98
2943 3348 7.811236 CAGTTACGAGGTGTATTTCAAACTCTA 59.189 37.037 0.00 0.00 33.19 2.43
2944 3349 6.645415 CAGTTACGAGGTGTATTTCAAACTCT 59.355 38.462 0.00 0.00 33.19 3.24
2945 3350 6.643770 TCAGTTACGAGGTGTATTTCAAACTC 59.356 38.462 0.00 0.00 31.81 3.01
2946 3351 6.518493 TCAGTTACGAGGTGTATTTCAAACT 58.482 36.000 0.00 0.00 31.81 2.66
2947 3352 6.774354 TCAGTTACGAGGTGTATTTCAAAC 57.226 37.500 0.00 0.00 31.81 2.93
2948 3353 7.789273 TTTCAGTTACGAGGTGTATTTCAAA 57.211 32.000 0.00 0.00 31.81 2.69
2949 3354 7.789273 TTTTCAGTTACGAGGTGTATTTCAA 57.211 32.000 0.00 0.00 31.81 2.69
2950 3355 7.789273 TTTTTCAGTTACGAGGTGTATTTCA 57.211 32.000 0.00 0.00 31.81 2.69
2982 3387 3.285484 TCATACCGGGAGAGTAACACTC 58.715 50.000 6.32 0.00 45.38 3.51
2983 3388 3.377253 TCATACCGGGAGAGTAACACT 57.623 47.619 6.32 0.00 0.00 3.55
2984 3389 3.383825 ACATCATACCGGGAGAGTAACAC 59.616 47.826 6.32 0.00 0.00 3.32
2985 3390 3.638860 ACATCATACCGGGAGAGTAACA 58.361 45.455 6.32 0.00 0.00 2.41
2986 3391 4.369182 CAACATCATACCGGGAGAGTAAC 58.631 47.826 6.32 0.00 0.00 2.50
2987 3392 3.181469 GCAACATCATACCGGGAGAGTAA 60.181 47.826 6.32 0.00 0.00 2.24
2988 3393 2.364324 GCAACATCATACCGGGAGAGTA 59.636 50.000 6.32 0.00 0.00 2.59
2989 3394 1.139058 GCAACATCATACCGGGAGAGT 59.861 52.381 6.32 0.00 0.00 3.24
2990 3395 1.541233 GGCAACATCATACCGGGAGAG 60.541 57.143 6.32 0.00 0.00 3.20
2991 3396 0.468226 GGCAACATCATACCGGGAGA 59.532 55.000 6.32 0.00 0.00 3.71
2992 3397 0.535102 GGGCAACATCATACCGGGAG 60.535 60.000 6.32 0.00 39.74 4.30
2993 3398 1.275421 TGGGCAACATCATACCGGGA 61.275 55.000 6.32 0.00 39.74 5.14
2994 3399 0.395036 TTGGGCAACATCATACCGGG 60.395 55.000 6.32 0.00 39.74 5.73
2995 3400 1.691196 ATTGGGCAACATCATACCGG 58.309 50.000 0.00 0.00 39.74 5.28
2996 3401 3.799281 AAATTGGGCAACATCATACCG 57.201 42.857 0.00 0.00 39.74 4.02
3030 3435 1.763968 GAGGCCATCCTTTGGGTAAC 58.236 55.000 5.01 0.00 46.55 2.50
3031 3436 0.254747 CGAGGCCATCCTTTGGGTAA 59.745 55.000 5.01 0.00 46.55 2.85
3032 3437 1.632018 CCGAGGCCATCCTTTGGGTA 61.632 60.000 5.01 0.00 46.55 3.69
3033 3438 2.677228 CGAGGCCATCCTTTGGGT 59.323 61.111 5.01 0.00 46.55 4.51
3034 3439 2.124151 CCGAGGCCATCCTTTGGG 60.124 66.667 5.01 0.00 46.55 4.12
3045 3450 1.244019 AACAACATCAAGGCCGAGGC 61.244 55.000 5.37 5.37 41.06 4.70
3046 3451 0.523072 CAACAACATCAAGGCCGAGG 59.477 55.000 0.00 0.00 0.00 4.63
3047 3452 1.466167 CTCAACAACATCAAGGCCGAG 59.534 52.381 0.00 0.00 0.00 4.63
3048 3453 1.522668 CTCAACAACATCAAGGCCGA 58.477 50.000 0.00 0.00 0.00 5.54
3049 3454 0.109597 GCTCAACAACATCAAGGCCG 60.110 55.000 0.00 0.00 0.00 6.13
3050 3455 0.961019 TGCTCAACAACATCAAGGCC 59.039 50.000 0.00 0.00 0.00 5.19
3051 3456 2.798976 TTGCTCAACAACATCAAGGC 57.201 45.000 0.00 0.00 31.73 4.35
3052 3457 4.431809 TGTTTTGCTCAACAACATCAAGG 58.568 39.130 0.00 0.00 38.23 3.61
3053 3458 5.104374 ACTGTTTTGCTCAACAACATCAAG 58.896 37.500 3.35 0.00 38.23 3.02
3054 3459 5.070770 ACTGTTTTGCTCAACAACATCAA 57.929 34.783 3.35 0.00 38.23 2.57
3055 3460 4.717233 ACTGTTTTGCTCAACAACATCA 57.283 36.364 3.35 0.00 38.23 3.07
3056 3461 4.268405 CCAACTGTTTTGCTCAACAACATC 59.732 41.667 0.00 0.00 38.23 3.06
3057 3462 4.081752 TCCAACTGTTTTGCTCAACAACAT 60.082 37.500 0.00 0.00 38.23 2.71
3058 3463 3.256879 TCCAACTGTTTTGCTCAACAACA 59.743 39.130 0.00 8.74 38.23 3.33
3059 3464 3.843999 TCCAACTGTTTTGCTCAACAAC 58.156 40.909 0.00 0.00 38.23 3.32
3060 3465 3.119173 CCTCCAACTGTTTTGCTCAACAA 60.119 43.478 0.00 0.00 36.22 2.83
3061 3466 2.426738 CCTCCAACTGTTTTGCTCAACA 59.573 45.455 0.00 1.94 35.33 3.33
3062 3467 2.799562 GCCTCCAACTGTTTTGCTCAAC 60.800 50.000 0.00 0.00 0.00 3.18
3063 3468 1.408702 GCCTCCAACTGTTTTGCTCAA 59.591 47.619 0.00 0.00 0.00 3.02
3064 3469 1.032014 GCCTCCAACTGTTTTGCTCA 58.968 50.000 0.00 0.00 0.00 4.26
3065 3470 1.032014 TGCCTCCAACTGTTTTGCTC 58.968 50.000 0.00 0.00 0.00 4.26
3066 3471 1.708341 ATGCCTCCAACTGTTTTGCT 58.292 45.000 0.00 0.00 0.00 3.91
3067 3472 2.558359 AGTATGCCTCCAACTGTTTTGC 59.442 45.455 0.00 0.00 0.00 3.68
3068 3473 4.074970 AGAGTATGCCTCCAACTGTTTTG 58.925 43.478 0.00 0.00 41.47 2.44
3069 3474 4.373156 AGAGTATGCCTCCAACTGTTTT 57.627 40.909 0.00 0.00 41.47 2.43
3070 3475 4.373156 AAGAGTATGCCTCCAACTGTTT 57.627 40.909 0.00 0.00 41.47 2.83
3071 3476 4.373156 AAAGAGTATGCCTCCAACTGTT 57.627 40.909 0.00 0.00 41.47 3.16
3072 3477 4.373156 AAAAGAGTATGCCTCCAACTGT 57.627 40.909 0.00 0.00 41.47 3.55
3073 3478 6.599244 TCATAAAAAGAGTATGCCTCCAACTG 59.401 38.462 0.00 0.00 41.47 3.16
3074 3479 6.721318 TCATAAAAAGAGTATGCCTCCAACT 58.279 36.000 0.00 0.00 41.47 3.16
3075 3480 6.599638 ACTCATAAAAAGAGTATGCCTCCAAC 59.400 38.462 0.00 0.00 44.10 3.77
3076 3481 6.721318 ACTCATAAAAAGAGTATGCCTCCAA 58.279 36.000 0.00 0.00 44.10 3.53
3077 3482 6.313519 ACTCATAAAAAGAGTATGCCTCCA 57.686 37.500 0.00 0.00 44.10 3.86
3108 3513 3.118665 GCCCAATGCACATTTGTCCTATT 60.119 43.478 0.00 0.00 40.77 1.73
3135 3540 2.935955 GTGTTGAACACGGGCTCG 59.064 61.111 13.14 3.27 39.53 5.03
3216 3621 8.124430 TCTAGAACAGGATAAACCCCTAAAGTA 58.876 37.037 0.00 0.00 40.05 2.24
3285 3690 8.986477 AGTTTATAAAAGTGGCATGTCAAATC 57.014 30.769 0.00 0.00 0.00 2.17
3294 3699 9.871238 TGTTTTTACAAGTTTATAAAAGTGGCA 57.129 25.926 0.00 0.00 33.15 4.92


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

AutoCloner maintained by Alex Coulton.