Multiple sequence alignment - TraesCS7D01G337500

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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 TraesCS7D01G337500 chr7D 100.000 2696 0 0 1 2696 430485052 430487747 0.000000e+00 4979.0
1 TraesCS7D01G337500 chr7D 93.210 972 50 9 1 970 536426675 536425718 0.000000e+00 1415.0
2 TraesCS7D01G337500 chr7D 90.642 545 38 6 1715 2257 536425730 536425197 0.000000e+00 712.0
3 TraesCS7D01G337500 chr7D 92.222 90 7 0 2538 2627 50149151 50149062 7.830000e-26 128.0
4 TraesCS7D01G337500 chr7B 94.479 978 52 2 1 976 447998234 447997257 0.000000e+00 1506.0
5 TraesCS7D01G337500 chr7B 92.042 578 26 7 1715 2292 447997276 447996719 0.000000e+00 795.0
6 TraesCS7D01G337500 chr7B 87.980 391 22 12 2306 2696 447998394 447998759 3.190000e-119 438.0
7 TraesCS7D01G337500 chr7B 79.960 499 68 17 1815 2306 74855504 74855031 3.320000e-89 339.0
8 TraesCS7D01G337500 chr7B 91.011 89 8 0 2539 2627 627876480 627876392 1.310000e-23 121.0
9 TraesCS7D01G337500 chr7B 90.000 90 9 0 2538 2627 539442496 539442585 1.700000e-22 117.0
10 TraesCS7D01G337500 chr7B 83.929 112 13 5 2520 2627 115251934 115251824 4.750000e-18 102.0
11 TraesCS7D01G337500 chr7A 93.401 985 45 5 1 976 5681409 5682382 0.000000e+00 1441.0
12 TraesCS7D01G337500 chr7A 92.599 581 34 4 397 976 538510496 538511068 0.000000e+00 826.0
13 TraesCS7D01G337500 chr7A 91.315 403 25 3 1 401 538498722 538499116 2.360000e-150 542.0
14 TraesCS7D01G337500 chr7A 95.070 142 6 1 2165 2306 5682905 5683045 3.490000e-54 222.0
15 TraesCS7D01G337500 chr7A 87.662 154 15 4 2156 2306 167892707 167892555 2.760000e-40 176.0
16 TraesCS7D01G337500 chr7A 83.929 112 16 2 2535 2646 710805012 710805121 3.670000e-19 106.0
17 TraesCS7D01G337500 chr7A 85.567 97 12 2 2523 2618 643964775 643964870 1.710000e-17 100.0
18 TraesCS7D01G337500 chr7A 82.353 102 18 0 2526 2627 132410206 132410307 3.700000e-14 89.8
19 TraesCS7D01G337500 chr3D 95.526 894 40 0 1 894 500190500 500189607 0.000000e+00 1430.0
20 TraesCS7D01G337500 chr3D 92.659 504 32 4 1715 2217 500142813 500142314 0.000000e+00 721.0
21 TraesCS7D01G337500 chr3D 85.957 470 53 5 1812 2280 454267656 454268113 8.670000e-135 490.0
22 TraesCS7D01G337500 chr3D 85.714 455 53 11 1 452 452232671 452232226 1.130000e-128 470.0
23 TraesCS7D01G337500 chr3D 70.822 730 191 21 1005 1722 574728964 574728245 6.010000e-32 148.0
24 TraesCS7D01G337500 chr3D 90.000 90 8 1 2538 2627 391430591 391430503 6.100000e-22 115.0
25 TraesCS7D01G337500 chr3D 80.172 116 20 3 2512 2626 586578909 586579022 1.720000e-12 84.2
26 TraesCS7D01G337500 chr4D 92.627 963 61 8 1 962 495987791 495986838 0.000000e+00 1376.0
27 TraesCS7D01G337500 chr4D 90.404 594 31 11 1714 2306 495986845 495986277 0.000000e+00 758.0
28 TraesCS7D01G337500 chr4D 91.358 81 7 0 2369 2449 468168163 468168243 7.890000e-21 111.0
29 TraesCS7D01G337500 chr2D 91.207 978 67 6 1 976 505637542 505638502 0.000000e+00 1312.0
30 TraesCS7D01G337500 chr1D 90.890 977 77 9 2 976 453044997 453044031 0.000000e+00 1301.0
31 TraesCS7D01G337500 chr1D 96.169 757 25 3 976 1730 362072019 362072773 0.000000e+00 1234.0
32 TraesCS7D01G337500 chr1D 90.000 90 8 1 2539 2628 365323730 365323818 6.100000e-22 115.0
33 TraesCS7D01G337500 chr1B 96.386 747 26 1 976 1721 17726189 17725443 0.000000e+00 1229.0
34 TraesCS7D01G337500 chr1A 91.963 871 59 8 1 870 575603483 575604343 0.000000e+00 1210.0
35 TraesCS7D01G337500 chr1A 92.086 417 30 2 1715 2131 575604594 575605007 3.870000e-163 584.0
36 TraesCS7D01G337500 chr1A 92.857 140 9 1 2167 2305 575605309 575605448 4.550000e-48 202.0
37 TraesCS7D01G337500 chrUn 92.905 592 31 6 1715 2304 280768750 280768168 0.000000e+00 850.0
38 TraesCS7D01G337500 chrUn 92.386 591 32 6 1715 2303 280766781 280767360 0.000000e+00 830.0
39 TraesCS7D01G337500 chrUn 94.958 476 22 2 1 475 280765661 280766135 0.000000e+00 745.0
40 TraesCS7D01G337500 chrUn 94.118 476 26 2 1 475 280769870 280769396 0.000000e+00 723.0
41 TraesCS7D01G337500 chr5B 92.074 593 30 2 1715 2306 23318587 23318011 0.000000e+00 819.0
42 TraesCS7D01G337500 chr5B 90.436 596 37 3 1715 2308 41960723 41960146 0.000000e+00 767.0
43 TraesCS7D01G337500 chr5B 93.474 475 29 2 1 475 41961842 41961370 0.000000e+00 704.0
44 TraesCS7D01G337500 chr5B 93.096 478 29 2 1 475 23319709 23319233 0.000000e+00 697.0
45 TraesCS7D01G337500 chr5B 89.655 87 9 0 2369 2455 412691681 412691595 7.890000e-21 111.0
46 TraesCS7D01G337500 chr2B 95.580 181 8 0 976 1156 11194139 11194319 9.440000e-75 291.0
47 TraesCS7D01G337500 chr2B 90.476 84 8 0 2366 2449 732347395 732347478 7.890000e-21 111.0
48 TraesCS7D01G337500 chr5A 92.222 90 7 0 2538 2627 622387849 622387760 7.830000e-26 128.0
49 TraesCS7D01G337500 chr5A 91.011 89 8 0 2361 2449 29170560 29170648 1.310000e-23 121.0
50 TraesCS7D01G337500 chr5A 88.660 97 9 2 2361 2455 445950127 445950031 1.700000e-22 117.0
51 TraesCS7D01G337500 chr5A 81.308 107 19 1 2522 2627 700366893 700366787 4.780000e-13 86.1
52 TraesCS7D01G337500 chr6D 90.217 92 8 1 2537 2627 245852795 245852704 4.720000e-23 119.0
53 TraesCS7D01G337500 chr4A 91.566 83 7 0 2367 2449 707307320 707307402 6.100000e-22 115.0
54 TraesCS7D01G337500 chr3A 91.566 83 7 0 2367 2449 370232787 370232869 6.100000e-22 115.0
55 TraesCS7D01G337500 chr3A 83.168 101 16 1 2527 2627 302743660 302743561 1.030000e-14 91.6
56 TraesCS7D01G337500 chr6B 89.655 87 9 0 2369 2455 145185769 145185683 7.890000e-21 111.0
57 TraesCS7D01G337500 chr6B 84.404 109 15 2 2519 2627 651986666 651986772 3.670000e-19 106.0
58 TraesCS7D01G337500 chr4B 86.275 102 12 2 2528 2627 120529728 120529829 2.840000e-20 110.0
59 TraesCS7D01G337500 chr4B 100.000 34 0 0 2663 2696 538950466 538950433 2.240000e-06 63.9


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 TraesCS7D01G337500 chr7D 430485052 430487747 2695 False 4979.000000 4979 100.0000 1 2696 1 chr7D.!!$F1 2695
1 TraesCS7D01G337500 chr7D 536425197 536426675 1478 True 1063.500000 1415 91.9260 1 2257 2 chr7D.!!$R2 2256
2 TraesCS7D01G337500 chr7B 447996719 447998234 1515 True 1150.500000 1506 93.2605 1 2292 2 chr7B.!!$R4 2291
3 TraesCS7D01G337500 chr7A 5681409 5683045 1636 False 831.500000 1441 94.2355 1 2306 2 chr7A.!!$F6 2305
4 TraesCS7D01G337500 chr7A 538510496 538511068 572 False 826.000000 826 92.5990 397 976 1 chr7A.!!$F3 579
5 TraesCS7D01G337500 chr3D 500189607 500190500 893 True 1430.000000 1430 95.5260 1 894 1 chr3D.!!$R4 893
6 TraesCS7D01G337500 chr4D 495986277 495987791 1514 True 1067.000000 1376 91.5155 1 2306 2 chr4D.!!$R1 2305
7 TraesCS7D01G337500 chr2D 505637542 505638502 960 False 1312.000000 1312 91.2070 1 976 1 chr2D.!!$F1 975
8 TraesCS7D01G337500 chr1D 453044031 453044997 966 True 1301.000000 1301 90.8900 2 976 1 chr1D.!!$R1 974
9 TraesCS7D01G337500 chr1D 362072019 362072773 754 False 1234.000000 1234 96.1690 976 1730 1 chr1D.!!$F1 754
10 TraesCS7D01G337500 chr1B 17725443 17726189 746 True 1229.000000 1229 96.3860 976 1721 1 chr1B.!!$R1 745
11 TraesCS7D01G337500 chr1A 575603483 575605448 1965 False 665.333333 1210 92.3020 1 2305 3 chr1A.!!$F1 2304
12 TraesCS7D01G337500 chrUn 280765661 280767360 1699 False 787.500000 830 93.6720 1 2303 2 chrUn.!!$F1 2302
13 TraesCS7D01G337500 chrUn 280768168 280769870 1702 True 786.500000 850 93.5115 1 2304 2 chrUn.!!$R1 2303
14 TraesCS7D01G337500 chr5B 23318011 23319709 1698 True 758.000000 819 92.5850 1 2306 2 chr5B.!!$R2 2305
15 TraesCS7D01G337500 chr5B 41960146 41961842 1696 True 735.500000 767 91.9550 1 2308 2 chr5B.!!$R3 2307

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
198 201 0.251121 TTCACCGCCACAATGGACAT 60.251 50.0 0.0 0.0 40.96 3.06 F
853 1035 0.665835 TGGTGCAAGGCAAGTAAACG 59.334 50.0 0.0 0.0 41.47 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1190 1536 2.353208 GCTATCCAATGACTAGGAGCCG 60.353 54.545 0.00 0.0 37.34 5.52 R
2446 3064 0.177604 GCATGTGCTAGCTCTGGTCT 59.822 55.000 17.23 0.0 38.21 3.85 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
188 191 0.537143 ATTGAGTTGCTTCACCGCCA 60.537 50.000 0.00 0.00 0.00 5.69
198 201 0.251121 TTCACCGCCACAATGGACAT 60.251 50.000 0.00 0.00 40.96 3.06
245 250 9.387123 GCGAATGGAAAATAAATCTGAATACTC 57.613 33.333 0.00 0.00 0.00 2.59
341 349 3.374402 CTCTCACCGCCCTCACGT 61.374 66.667 0.00 0.00 0.00 4.49
351 359 2.551912 CCCTCACGTTGGCAACCAC 61.552 63.158 23.68 0.81 30.78 4.16
357 365 4.645921 GTTGGCAACCACCAGCGC 62.646 66.667 19.57 0.00 41.82 5.92
503 675 5.123027 GGAACAACATTTTGCAAAAAGGACA 59.877 36.000 27.10 5.02 36.00 4.02
725 905 8.598041 AGATTAGGAGAAGAGTTATGTGTTGTT 58.402 33.333 0.00 0.00 0.00 2.83
853 1035 0.665835 TGGTGCAAGGCAAGTAAACG 59.334 50.000 0.00 0.00 41.47 3.60
894 1240 7.398047 TGGTCTATCAACCTGTAAAGCTAGTAA 59.602 37.037 0.00 0.00 40.20 2.24
906 1252 7.438564 TGTAAAGCTAGTAATGATATTGCCGA 58.561 34.615 0.00 0.00 0.00 5.54
985 1331 2.642171 AGTACATGGGGAAGTCAGGA 57.358 50.000 0.00 0.00 0.00 3.86
1230 1576 3.171388 CCCCCGCTAGGAATGGCT 61.171 66.667 0.00 0.00 41.02 4.75
1428 1774 4.189639 ACGTTTCAGAGGTCAGGTAATC 57.810 45.455 0.00 0.00 0.00 1.75
1536 1882 4.819088 GTGAAGGAGAAGCTCTCTTTGTTT 59.181 41.667 12.83 2.22 41.96 2.83
1575 1921 6.013842 AGTATTGTAAGCAGGAGCAAAAAC 57.986 37.500 0.00 0.00 45.49 2.43
1844 2190 6.365970 ACTTGGAAATGACAGTGACTCTAT 57.634 37.500 0.00 0.00 0.00 1.98
1851 2197 8.200792 GGAAATGACAGTGACTCTATATGTTCT 58.799 37.037 0.00 0.00 0.00 3.01
2073 2424 7.620491 TGGTATGGTACTTCAGTTCCTTATGTA 59.380 37.037 4.45 0.00 36.57 2.29
2119 2470 7.095270 AGGTTGTAAAACTAATCTGACGTAGG 58.905 38.462 0.00 0.00 46.27 3.18
2138 2489 5.221263 CGTAGGCCTATGTACATATCATCCC 60.221 48.000 22.07 11.25 0.00 3.85
2139 2490 3.706594 AGGCCTATGTACATATCATCCCG 59.293 47.826 15.81 2.92 0.00 5.14
2141 2492 3.451178 GCCTATGTACATATCATCCCGGT 59.549 47.826 15.81 0.00 0.00 5.28
2143 2494 3.981071 ATGTACATATCATCCCGGTGG 57.019 47.619 6.56 0.00 0.00 4.61
2207 2825 2.757314 GGGAAGATTTTGGGAGAGCTTG 59.243 50.000 0.00 0.00 0.00 4.01
2312 2930 4.796231 CTCCGCCCCTGTCGTTCG 62.796 72.222 0.00 0.00 0.00 3.95
2315 2933 3.751246 CGCCCCTGTCGTTCGGTA 61.751 66.667 0.00 0.00 0.00 4.02
2316 2934 2.183555 GCCCCTGTCGTTCGGTAG 59.816 66.667 0.00 0.00 0.00 3.18
2317 2935 2.183555 CCCCTGTCGTTCGGTAGC 59.816 66.667 0.00 0.00 0.00 3.58
2318 2936 2.202570 CCCTGTCGTTCGGTAGCG 60.203 66.667 8.29 8.29 0.00 4.26
2319 2937 2.564975 CCTGTCGTTCGGTAGCGT 59.435 61.111 14.79 0.00 0.00 5.07
2320 2938 1.647545 CCCTGTCGTTCGGTAGCGTA 61.648 60.000 14.79 1.01 0.00 4.42
2321 2939 0.247974 CCTGTCGTTCGGTAGCGTAG 60.248 60.000 14.79 7.11 0.00 3.51
2322 2940 0.445436 CTGTCGTTCGGTAGCGTAGT 59.555 55.000 14.79 0.00 0.00 2.73
2323 2941 1.660607 CTGTCGTTCGGTAGCGTAGTA 59.339 52.381 14.79 0.00 0.00 1.82
2324 2942 2.279741 TGTCGTTCGGTAGCGTAGTAT 58.720 47.619 14.79 0.00 0.00 2.12
2325 2943 3.453424 TGTCGTTCGGTAGCGTAGTATA 58.547 45.455 14.79 0.00 0.00 1.47
2326 2944 4.058124 TGTCGTTCGGTAGCGTAGTATAT 58.942 43.478 14.79 0.00 0.00 0.86
2327 2945 4.084380 TGTCGTTCGGTAGCGTAGTATATG 60.084 45.833 14.79 0.74 0.00 1.78
2328 2946 3.433274 TCGTTCGGTAGCGTAGTATATGG 59.567 47.826 14.79 0.00 0.00 2.74
2329 2947 3.425359 CGTTCGGTAGCGTAGTATATGGG 60.425 52.174 14.79 0.00 0.00 4.00
2330 2948 3.701205 TCGGTAGCGTAGTATATGGGA 57.299 47.619 14.79 0.00 0.00 4.37
2331 2949 4.226427 TCGGTAGCGTAGTATATGGGAT 57.774 45.455 14.79 0.00 0.00 3.85
2332 2950 3.943381 TCGGTAGCGTAGTATATGGGATG 59.057 47.826 14.79 0.00 0.00 3.51
2333 2951 3.066342 CGGTAGCGTAGTATATGGGATGG 59.934 52.174 6.07 0.00 0.00 3.51
2334 2952 3.383825 GGTAGCGTAGTATATGGGATGGG 59.616 52.174 0.00 0.00 0.00 4.00
2335 2953 3.468071 AGCGTAGTATATGGGATGGGA 57.532 47.619 0.00 0.00 0.00 4.37
2336 2954 3.366396 AGCGTAGTATATGGGATGGGAG 58.634 50.000 0.00 0.00 0.00 4.30
2337 2955 3.011369 AGCGTAGTATATGGGATGGGAGA 59.989 47.826 0.00 0.00 0.00 3.71
2338 2956 3.767673 GCGTAGTATATGGGATGGGAGAA 59.232 47.826 0.00 0.00 0.00 2.87
2339 2957 4.222145 GCGTAGTATATGGGATGGGAGAAA 59.778 45.833 0.00 0.00 0.00 2.52
2340 2958 5.279809 GCGTAGTATATGGGATGGGAGAAAA 60.280 44.000 0.00 0.00 0.00 2.29
2341 2959 6.398918 CGTAGTATATGGGATGGGAGAAAAG 58.601 44.000 0.00 0.00 0.00 2.27
2342 2960 5.850046 AGTATATGGGATGGGAGAAAAGG 57.150 43.478 0.00 0.00 0.00 3.11
2343 2961 4.603610 AGTATATGGGATGGGAGAAAAGGG 59.396 45.833 0.00 0.00 0.00 3.95
2344 2962 2.000290 ATGGGATGGGAGAAAAGGGA 58.000 50.000 0.00 0.00 0.00 4.20
2345 2963 0.999712 TGGGATGGGAGAAAAGGGAC 59.000 55.000 0.00 0.00 0.00 4.46
2346 2964 0.999712 GGGATGGGAGAAAAGGGACA 59.000 55.000 0.00 0.00 0.00 4.02
2347 2965 1.357761 GGGATGGGAGAAAAGGGACAA 59.642 52.381 0.00 0.00 0.00 3.18
2348 2966 2.023984 GGGATGGGAGAAAAGGGACAAT 60.024 50.000 0.00 0.00 0.00 2.71
2349 2967 3.026694 GGATGGGAGAAAAGGGACAATG 58.973 50.000 0.00 0.00 0.00 2.82
2350 2968 1.923356 TGGGAGAAAAGGGACAATGC 58.077 50.000 0.00 0.00 0.00 3.56
2351 2969 1.146774 TGGGAGAAAAGGGACAATGCA 59.853 47.619 0.00 0.00 0.00 3.96
2352 2970 1.821136 GGGAGAAAAGGGACAATGCAG 59.179 52.381 0.00 0.00 0.00 4.41
2353 2971 1.203287 GGAGAAAAGGGACAATGCAGC 59.797 52.381 0.00 0.00 0.00 5.25
2354 2972 2.165998 GAGAAAAGGGACAATGCAGCT 58.834 47.619 0.00 0.00 0.00 4.24
2355 2973 3.347216 GAGAAAAGGGACAATGCAGCTA 58.653 45.455 0.00 0.00 0.00 3.32
2356 2974 3.950395 GAGAAAAGGGACAATGCAGCTAT 59.050 43.478 0.00 0.00 0.00 2.97
2357 2975 3.698040 AGAAAAGGGACAATGCAGCTATG 59.302 43.478 0.00 0.00 0.00 2.23
2358 2976 2.814805 AAGGGACAATGCAGCTATGT 57.185 45.000 3.62 3.62 0.00 2.29
2359 2977 3.931907 AAGGGACAATGCAGCTATGTA 57.068 42.857 3.94 0.00 0.00 2.29
2360 2978 4.443978 AAGGGACAATGCAGCTATGTAT 57.556 40.909 3.94 0.00 32.52 2.29
2361 2979 4.443978 AGGGACAATGCAGCTATGTATT 57.556 40.909 3.94 0.00 41.77 1.89
2370 2988 7.880160 AATGCAGCTATGTATTGGTTTTAGA 57.120 32.000 0.00 0.00 39.86 2.10
2371 2989 6.925610 TGCAGCTATGTATTGGTTTTAGAG 57.074 37.500 0.00 0.00 0.00 2.43
2372 2990 5.296780 TGCAGCTATGTATTGGTTTTAGAGC 59.703 40.000 0.00 0.00 0.00 4.09
2373 2991 5.296780 GCAGCTATGTATTGGTTTTAGAGCA 59.703 40.000 0.00 0.00 0.00 4.26
2394 3012 9.979578 AGAGCAAATATAATAGAGTTGAGTCAG 57.020 33.333 0.00 0.00 0.00 3.51
2395 3013 8.600449 AGCAAATATAATAGAGTTGAGTCAGC 57.400 34.615 0.00 0.00 0.00 4.26
2396 3014 8.428063 AGCAAATATAATAGAGTTGAGTCAGCT 58.572 33.333 9.51 9.51 0.00 4.24
2397 3015 9.698309 GCAAATATAATAGAGTTGAGTCAGCTA 57.302 33.333 9.73 5.79 0.00 3.32
2406 3024 9.854668 ATAGAGTTGAGTCAGCTAGTTATAAGA 57.145 33.333 9.73 0.00 0.00 2.10
2407 3025 8.582657 AGAGTTGAGTCAGCTAGTTATAAGAA 57.417 34.615 9.73 0.00 0.00 2.52
2408 3026 9.026121 AGAGTTGAGTCAGCTAGTTATAAGAAA 57.974 33.333 9.73 0.00 0.00 2.52
2409 3027 9.810545 GAGTTGAGTCAGCTAGTTATAAGAAAT 57.189 33.333 9.73 0.00 0.00 2.17
2448 3066 8.974060 TTTGCTTAGTTAGAGGAAAGAAAAGA 57.026 30.769 0.00 0.00 31.94 2.52
2449 3067 7.964604 TGCTTAGTTAGAGGAAAGAAAAGAC 57.035 36.000 0.00 0.00 0.00 3.01
2450 3068 6.935208 TGCTTAGTTAGAGGAAAGAAAAGACC 59.065 38.462 0.00 0.00 0.00 3.85
2451 3069 6.935208 GCTTAGTTAGAGGAAAGAAAAGACCA 59.065 38.462 0.00 0.00 0.00 4.02
2452 3070 7.118535 GCTTAGTTAGAGGAAAGAAAAGACCAG 59.881 40.741 0.00 0.00 0.00 4.00
2453 3071 6.749036 AGTTAGAGGAAAGAAAAGACCAGA 57.251 37.500 0.00 0.00 0.00 3.86
2454 3072 6.764379 AGTTAGAGGAAAGAAAAGACCAGAG 58.236 40.000 0.00 0.00 0.00 3.35
2455 3073 4.014569 AGAGGAAAGAAAAGACCAGAGC 57.985 45.455 0.00 0.00 0.00 4.09
2456 3074 3.650461 AGAGGAAAGAAAAGACCAGAGCT 59.350 43.478 0.00 0.00 0.00 4.09
2457 3075 4.841246 AGAGGAAAGAAAAGACCAGAGCTA 59.159 41.667 0.00 0.00 0.00 3.32
2458 3076 5.046663 AGAGGAAAGAAAAGACCAGAGCTAG 60.047 44.000 0.00 0.00 0.00 3.42
2459 3077 3.687212 GGAAAGAAAAGACCAGAGCTAGC 59.313 47.826 6.62 6.62 0.00 3.42
2460 3078 4.319177 GAAAGAAAAGACCAGAGCTAGCA 58.681 43.478 18.83 0.00 0.00 3.49
2461 3079 3.326836 AGAAAAGACCAGAGCTAGCAC 57.673 47.619 18.83 11.32 0.00 4.40
2462 3080 2.634940 AGAAAAGACCAGAGCTAGCACA 59.365 45.455 18.83 0.00 0.00 4.57
2463 3081 3.262915 AGAAAAGACCAGAGCTAGCACAT 59.737 43.478 18.83 0.00 0.00 3.21
2464 3082 2.687700 AAGACCAGAGCTAGCACATG 57.312 50.000 18.83 11.85 0.00 3.21
2465 3083 0.177604 AGACCAGAGCTAGCACATGC 59.822 55.000 18.83 0.00 42.49 4.06
2480 3098 5.490139 GCACATGCTCATATGTAGTTTGT 57.510 39.130 1.90 4.96 39.17 2.83
2481 3099 5.268544 GCACATGCTCATATGTAGTTTGTG 58.731 41.667 20.00 20.00 39.17 3.33
2482 3100 5.065090 GCACATGCTCATATGTAGTTTGTGA 59.935 40.000 23.73 2.21 39.17 3.58
2483 3101 6.712549 CACATGCTCATATGTAGTTTGTGAG 58.287 40.000 19.84 0.00 39.17 3.51
2484 3102 6.536224 CACATGCTCATATGTAGTTTGTGAGA 59.464 38.462 19.84 0.00 39.17 3.27
2485 3103 6.760298 ACATGCTCATATGTAGTTTGTGAGAG 59.240 38.462 1.90 0.00 39.40 3.20
2486 3104 6.286240 TGCTCATATGTAGTTTGTGAGAGT 57.714 37.500 1.90 0.00 38.81 3.24
2487 3105 6.101997 TGCTCATATGTAGTTTGTGAGAGTG 58.898 40.000 1.90 0.00 38.81 3.51
2488 3106 5.521735 GCTCATATGTAGTTTGTGAGAGTGG 59.478 44.000 1.90 0.00 38.81 4.00
2489 3107 6.628175 GCTCATATGTAGTTTGTGAGAGTGGA 60.628 42.308 1.90 0.00 38.81 4.02
2490 3108 7.239763 TCATATGTAGTTTGTGAGAGTGGAA 57.760 36.000 1.90 0.00 0.00 3.53
2491 3109 7.323420 TCATATGTAGTTTGTGAGAGTGGAAG 58.677 38.462 1.90 0.00 0.00 3.46
2492 3110 5.552870 ATGTAGTTTGTGAGAGTGGAAGT 57.447 39.130 0.00 0.00 0.00 3.01
2493 3111 5.353394 TGTAGTTTGTGAGAGTGGAAGTT 57.647 39.130 0.00 0.00 0.00 2.66
2494 3112 5.116180 TGTAGTTTGTGAGAGTGGAAGTTG 58.884 41.667 0.00 0.00 0.00 3.16
2495 3113 3.545703 AGTTTGTGAGAGTGGAAGTTGG 58.454 45.455 0.00 0.00 0.00 3.77
2496 3114 3.054361 AGTTTGTGAGAGTGGAAGTTGGT 60.054 43.478 0.00 0.00 0.00 3.67
2497 3115 2.910688 TGTGAGAGTGGAAGTTGGTC 57.089 50.000 0.00 0.00 0.00 4.02
2498 3116 2.115427 TGTGAGAGTGGAAGTTGGTCA 58.885 47.619 0.00 0.00 0.00 4.02
2499 3117 2.705658 TGTGAGAGTGGAAGTTGGTCAT 59.294 45.455 0.00 0.00 0.00 3.06
2500 3118 3.901222 TGTGAGAGTGGAAGTTGGTCATA 59.099 43.478 0.00 0.00 0.00 2.15
2501 3119 4.532126 TGTGAGAGTGGAAGTTGGTCATAT 59.468 41.667 0.00 0.00 0.00 1.78
2502 3120 5.719563 TGTGAGAGTGGAAGTTGGTCATATA 59.280 40.000 0.00 0.00 0.00 0.86
2503 3121 6.212589 TGTGAGAGTGGAAGTTGGTCATATAA 59.787 38.462 0.00 0.00 0.00 0.98
2504 3122 7.092891 TGTGAGAGTGGAAGTTGGTCATATAAT 60.093 37.037 0.00 0.00 0.00 1.28
2505 3123 8.421784 GTGAGAGTGGAAGTTGGTCATATAATA 58.578 37.037 0.00 0.00 0.00 0.98
2506 3124 8.988060 TGAGAGTGGAAGTTGGTCATATAATAA 58.012 33.333 0.00 0.00 0.00 1.40
2548 3166 8.712285 TTTAATCAACTATTGTACTCCCTTCG 57.288 34.615 0.00 0.00 0.00 3.79
2549 3167 5.934402 ATCAACTATTGTACTCCCTTCGT 57.066 39.130 0.00 0.00 0.00 3.85
2550 3168 5.733620 TCAACTATTGTACTCCCTTCGTT 57.266 39.130 0.00 0.00 0.00 3.85
2551 3169 6.105397 TCAACTATTGTACTCCCTTCGTTT 57.895 37.500 0.00 0.00 0.00 3.60
2552 3170 6.161381 TCAACTATTGTACTCCCTTCGTTTC 58.839 40.000 0.00 0.00 0.00 2.78
2553 3171 5.997384 ACTATTGTACTCCCTTCGTTTCT 57.003 39.130 0.00 0.00 0.00 2.52
2554 3172 6.356186 ACTATTGTACTCCCTTCGTTTCTT 57.644 37.500 0.00 0.00 0.00 2.52
2555 3173 6.766429 ACTATTGTACTCCCTTCGTTTCTTT 58.234 36.000 0.00 0.00 0.00 2.52
2556 3174 7.222161 ACTATTGTACTCCCTTCGTTTCTTTT 58.778 34.615 0.00 0.00 0.00 2.27
2557 3175 6.954487 ATTGTACTCCCTTCGTTTCTTTTT 57.046 33.333 0.00 0.00 0.00 1.94
2558 3176 9.211485 CTATTGTACTCCCTTCGTTTCTTTTTA 57.789 33.333 0.00 0.00 0.00 1.52
2559 3177 7.486802 TTGTACTCCCTTCGTTTCTTTTTAG 57.513 36.000 0.00 0.00 0.00 1.85
2560 3178 6.585416 TGTACTCCCTTCGTTTCTTTTTAGT 58.415 36.000 0.00 0.00 0.00 2.24
2561 3179 6.703165 TGTACTCCCTTCGTTTCTTTTTAGTC 59.297 38.462 0.00 0.00 0.00 2.59
2562 3180 5.926663 ACTCCCTTCGTTTCTTTTTAGTCT 58.073 37.500 0.00 0.00 0.00 3.24
2563 3181 5.758784 ACTCCCTTCGTTTCTTTTTAGTCTG 59.241 40.000 0.00 0.00 0.00 3.51
2564 3182 4.514066 TCCCTTCGTTTCTTTTTAGTCTGC 59.486 41.667 0.00 0.00 0.00 4.26
2565 3183 4.274950 CCCTTCGTTTCTTTTTAGTCTGCA 59.725 41.667 0.00 0.00 0.00 4.41
2566 3184 5.048713 CCCTTCGTTTCTTTTTAGTCTGCAT 60.049 40.000 0.00 0.00 0.00 3.96
2567 3185 6.148811 CCCTTCGTTTCTTTTTAGTCTGCATA 59.851 38.462 0.00 0.00 0.00 3.14
2568 3186 7.148239 CCCTTCGTTTCTTTTTAGTCTGCATAT 60.148 37.037 0.00 0.00 0.00 1.78
2569 3187 8.879759 CCTTCGTTTCTTTTTAGTCTGCATATA 58.120 33.333 0.00 0.00 0.00 0.86
2572 3190 9.647797 TCGTTTCTTTTTAGTCTGCATATAAGA 57.352 29.630 0.00 0.00 0.00 2.10
2636 3254 9.849166 TGATAGAATAATATATCGCGACAAACA 57.151 29.630 12.93 0.00 33.37 2.83
2640 3258 8.443160 AGAATAATATATCGCGACAAACAATGG 58.557 33.333 12.93 0.00 0.00 3.16
2641 3259 7.667043 ATAATATATCGCGACAAACAATGGT 57.333 32.000 12.93 0.00 0.00 3.55
2642 3260 3.673746 ATATCGCGACAAACAATGGTG 57.326 42.857 12.93 0.00 0.00 4.17
2643 3261 1.518325 ATCGCGACAAACAATGGTGA 58.482 45.000 12.93 0.00 0.00 4.02
2644 3262 1.300481 TCGCGACAAACAATGGTGAA 58.700 45.000 3.71 0.00 0.00 3.18
2645 3263 1.671328 TCGCGACAAACAATGGTGAAA 59.329 42.857 3.71 0.00 0.00 2.69
2646 3264 2.097629 TCGCGACAAACAATGGTGAAAA 59.902 40.909 3.71 0.00 0.00 2.29
2647 3265 2.215363 CGCGACAAACAATGGTGAAAAC 59.785 45.455 0.00 0.00 0.00 2.43
2648 3266 2.215363 GCGACAAACAATGGTGAAAACG 59.785 45.455 0.00 0.00 0.00 3.60
2649 3267 2.786578 CGACAAACAATGGTGAAAACGG 59.213 45.455 0.00 0.00 0.00 4.44
2650 3268 3.487711 CGACAAACAATGGTGAAAACGGA 60.488 43.478 0.00 0.00 0.00 4.69
2651 3269 4.616953 GACAAACAATGGTGAAAACGGAT 58.383 39.130 0.00 0.00 0.00 4.18
2652 3270 4.616953 ACAAACAATGGTGAAAACGGATC 58.383 39.130 0.00 0.00 0.00 3.36
2653 3271 3.552604 AACAATGGTGAAAACGGATCG 57.447 42.857 0.00 0.00 0.00 3.69
2654 3272 2.500229 ACAATGGTGAAAACGGATCGT 58.500 42.857 0.00 0.00 43.97 3.73
2655 3273 2.482721 ACAATGGTGAAAACGGATCGTC 59.517 45.455 0.00 0.00 39.99 4.20
2656 3274 2.465860 ATGGTGAAAACGGATCGTCA 57.534 45.000 0.00 0.00 39.99 4.35
2657 3275 2.242047 TGGTGAAAACGGATCGTCAA 57.758 45.000 0.00 0.00 39.99 3.18
2658 3276 2.773487 TGGTGAAAACGGATCGTCAAT 58.227 42.857 0.00 0.00 39.99 2.57
2659 3277 3.142951 TGGTGAAAACGGATCGTCAATT 58.857 40.909 0.00 0.00 39.99 2.32
2660 3278 4.316645 TGGTGAAAACGGATCGTCAATTA 58.683 39.130 0.00 0.00 39.99 1.40
2661 3279 4.755629 TGGTGAAAACGGATCGTCAATTAA 59.244 37.500 0.00 0.00 39.99 1.40
2662 3280 5.238868 TGGTGAAAACGGATCGTCAATTAAA 59.761 36.000 0.00 0.00 39.99 1.52
2663 3281 5.793457 GGTGAAAACGGATCGTCAATTAAAG 59.207 40.000 0.00 0.00 39.99 1.85
2664 3282 5.793457 GTGAAAACGGATCGTCAATTAAAGG 59.207 40.000 0.00 0.00 39.99 3.11
2665 3283 4.957759 AAACGGATCGTCAATTAAAGGG 57.042 40.909 0.00 0.00 39.99 3.95
2666 3284 3.899052 ACGGATCGTCAATTAAAGGGA 57.101 42.857 0.00 0.00 33.69 4.20
2667 3285 3.528532 ACGGATCGTCAATTAAAGGGAC 58.471 45.455 0.00 0.00 33.69 4.46
2668 3286 3.197116 ACGGATCGTCAATTAAAGGGACT 59.803 43.478 0.00 0.00 35.47 3.85
2669 3287 3.555956 CGGATCGTCAATTAAAGGGACTG 59.444 47.826 0.00 0.00 40.86 3.51
2670 3288 4.679639 CGGATCGTCAATTAAAGGGACTGA 60.680 45.833 0.00 0.00 40.86 3.41
2671 3289 4.571176 GGATCGTCAATTAAAGGGACTGAC 59.429 45.833 0.00 0.00 40.86 3.51
2672 3290 4.884668 TCGTCAATTAAAGGGACTGACT 57.115 40.909 0.00 0.00 40.86 3.41
2673 3291 5.988310 TCGTCAATTAAAGGGACTGACTA 57.012 39.130 0.00 0.00 40.86 2.59
2674 3292 6.540438 TCGTCAATTAAAGGGACTGACTAT 57.460 37.500 0.00 0.00 40.86 2.12
2675 3293 6.338146 TCGTCAATTAAAGGGACTGACTATG 58.662 40.000 0.00 0.00 40.86 2.23
2676 3294 6.070995 TCGTCAATTAAAGGGACTGACTATGT 60.071 38.462 0.00 0.00 40.86 2.29
2677 3295 6.036083 CGTCAATTAAAGGGACTGACTATGTG 59.964 42.308 0.00 0.00 40.86 3.21
2678 3296 6.879458 GTCAATTAAAGGGACTGACTATGTGT 59.121 38.462 0.00 0.00 40.86 3.72
2679 3297 8.038944 GTCAATTAAAGGGACTGACTATGTGTA 58.961 37.037 0.00 0.00 40.86 2.90
2680 3298 8.598916 TCAATTAAAGGGACTGACTATGTGTAA 58.401 33.333 0.00 0.00 40.86 2.41
2681 3299 8.883731 CAATTAAAGGGACTGACTATGTGTAAG 58.116 37.037 0.00 0.00 40.86 2.34
2682 3300 7.549147 TTAAAGGGACTGACTATGTGTAAGT 57.451 36.000 0.00 0.00 42.95 2.24
2683 3301 6.435292 AAAGGGACTGACTATGTGTAAGTT 57.565 37.500 0.00 0.00 40.40 2.66
2684 3302 5.407407 AGGGACTGACTATGTGTAAGTTG 57.593 43.478 0.00 0.00 40.40 3.16
2685 3303 5.084519 AGGGACTGACTATGTGTAAGTTGA 58.915 41.667 0.00 0.00 40.40 3.18
2686 3304 5.047235 AGGGACTGACTATGTGTAAGTTGAC 60.047 44.000 0.00 0.00 40.40 3.18
2687 3305 5.047235 GGGACTGACTATGTGTAAGTTGACT 60.047 44.000 0.00 0.00 40.40 3.41
2688 3306 5.864474 GGACTGACTATGTGTAAGTTGACTG 59.136 44.000 0.00 0.00 40.40 3.51
2689 3307 5.784177 ACTGACTATGTGTAAGTTGACTGG 58.216 41.667 0.00 0.00 37.04 4.00
2690 3308 5.304614 ACTGACTATGTGTAAGTTGACTGGT 59.695 40.000 0.00 0.00 37.04 4.00
2691 3309 6.169557 TGACTATGTGTAAGTTGACTGGTT 57.830 37.500 0.00 0.00 0.00 3.67
2692 3310 6.588204 TGACTATGTGTAAGTTGACTGGTTT 58.412 36.000 0.00 0.00 0.00 3.27
2693 3311 7.051623 TGACTATGTGTAAGTTGACTGGTTTT 58.948 34.615 0.00 0.00 0.00 2.43
2694 3312 7.554835 TGACTATGTGTAAGTTGACTGGTTTTT 59.445 33.333 0.00 0.00 0.00 1.94
2695 3313 7.703328 ACTATGTGTAAGTTGACTGGTTTTTG 58.297 34.615 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
245 250 4.446371 GTGAGGGTGATGAAGGTCATAAG 58.554 47.826 0.00 0.00 37.20 1.73
246 251 3.118775 CGTGAGGGTGATGAAGGTCATAA 60.119 47.826 0.00 0.00 37.20 1.90
248 253 1.208052 CGTGAGGGTGATGAAGGTCAT 59.792 52.381 0.00 0.00 40.34 3.06
250 255 0.741221 GCGTGAGGGTGATGAAGGTC 60.741 60.000 0.00 0.00 0.00 3.85
357 365 1.398390 GAATAGCAGTTGTCGGCTTGG 59.602 52.381 0.00 0.00 41.92 3.61
369 377 9.040543 CGCGTGTAATAATATTTTGAATAGCAG 57.959 33.333 0.00 0.00 0.00 4.24
533 705 1.282157 AGGGTGGCCTTGAAGTACATC 59.718 52.381 3.32 0.00 0.00 3.06
634 806 5.047519 CCCTTCGGGTTAGTCGTAATATGAT 60.048 44.000 0.00 0.00 38.25 2.45
725 905 9.817809 CAGTTTAGTAAGCTCCTCACATTATAA 57.182 33.333 0.00 0.00 0.00 0.98
853 1035 8.933807 GTTGATAGACCAAAGTAAAAGGAGTAC 58.066 37.037 0.00 0.00 0.00 2.73
894 1240 4.665451 TCCATGGAAATCGGCAATATCAT 58.335 39.130 13.46 0.00 0.00 2.45
906 1252 7.558604 CACTGGTCAATTAATTCCATGGAAAT 58.441 34.615 30.28 24.39 37.69 2.17
964 1310 4.030913 CTCCTGACTTCCCCATGTACTAA 58.969 47.826 0.00 0.00 0.00 2.24
965 1311 3.643237 CTCCTGACTTCCCCATGTACTA 58.357 50.000 0.00 0.00 0.00 1.82
966 1312 2.472029 CTCCTGACTTCCCCATGTACT 58.528 52.381 0.00 0.00 0.00 2.73
967 1313 1.134371 GCTCCTGACTTCCCCATGTAC 60.134 57.143 0.00 0.00 0.00 2.90
968 1314 1.204146 GCTCCTGACTTCCCCATGTA 58.796 55.000 0.00 0.00 0.00 2.29
969 1315 0.842030 TGCTCCTGACTTCCCCATGT 60.842 55.000 0.00 0.00 0.00 3.21
970 1316 0.329261 TTGCTCCTGACTTCCCCATG 59.671 55.000 0.00 0.00 0.00 3.66
971 1317 0.622665 CTTGCTCCTGACTTCCCCAT 59.377 55.000 0.00 0.00 0.00 4.00
972 1318 0.473694 TCTTGCTCCTGACTTCCCCA 60.474 55.000 0.00 0.00 0.00 4.96
973 1319 0.915364 ATCTTGCTCCTGACTTCCCC 59.085 55.000 0.00 0.00 0.00 4.81
974 1320 2.797177 AATCTTGCTCCTGACTTCCC 57.203 50.000 0.00 0.00 0.00 3.97
985 1331 5.870978 GCCACATCATTAACAAAATCTTGCT 59.129 36.000 0.00 0.00 35.84 3.91
1171 1517 3.379445 GGGGACTGTCGCTTCCGA 61.379 66.667 21.89 0.00 42.01 4.55
1190 1536 2.353208 GCTATCCAATGACTAGGAGCCG 60.353 54.545 0.00 0.00 37.34 5.52
1230 1576 3.609853 AGCCGCATCAGAATTCAACTTA 58.390 40.909 8.44 0.00 0.00 2.24
1428 1774 2.495270 ACACATGCAGTCAGTCTCTAGG 59.505 50.000 0.00 0.00 0.00 3.02
1929 2280 5.756347 ACGCACAACTTTGTACTTTCATAGA 59.244 36.000 0.00 0.00 39.91 1.98
2054 2405 7.407393 AGGACTACATAAGGAACTGAAGTAC 57.593 40.000 0.00 0.00 40.86 2.73
2057 2408 7.386851 TCAAAGGACTACATAAGGAACTGAAG 58.613 38.462 0.00 0.00 40.86 3.02
2073 2424 5.780793 ACCTCATACTAACACTCAAAGGACT 59.219 40.000 0.00 0.00 0.00 3.85
2114 2465 5.221263 GGGATGATATGTACATAGGCCTACG 60.221 48.000 16.61 10.12 0.00 3.51
2119 2470 3.451178 ACCGGGATGATATGTACATAGGC 59.549 47.826 19.80 14.53 0.00 3.93
2207 2825 3.149981 GAGGGTGCTAATAAATCCAGGC 58.850 50.000 0.00 0.00 0.00 4.85
2243 2861 4.935808 AGGATTTGGACATGAACTAACGAC 59.064 41.667 0.00 0.00 0.00 4.34
2308 2926 3.753272 TCCCATATACTACGCTACCGAAC 59.247 47.826 0.00 0.00 38.29 3.95
2309 2927 4.019792 TCCCATATACTACGCTACCGAA 57.980 45.455 0.00 0.00 38.29 4.30
2310 2928 3.701205 TCCCATATACTACGCTACCGA 57.299 47.619 0.00 0.00 38.29 4.69
2311 2929 3.066342 CCATCCCATATACTACGCTACCG 59.934 52.174 0.00 0.00 41.14 4.02
2312 2930 3.383825 CCCATCCCATATACTACGCTACC 59.616 52.174 0.00 0.00 0.00 3.18
2313 2931 4.275810 TCCCATCCCATATACTACGCTAC 58.724 47.826 0.00 0.00 0.00 3.58
2314 2932 4.228895 TCTCCCATCCCATATACTACGCTA 59.771 45.833 0.00 0.00 0.00 4.26
2315 2933 3.011369 TCTCCCATCCCATATACTACGCT 59.989 47.826 0.00 0.00 0.00 5.07
2316 2934 3.362706 TCTCCCATCCCATATACTACGC 58.637 50.000 0.00 0.00 0.00 4.42
2317 2935 5.995565 TTTCTCCCATCCCATATACTACG 57.004 43.478 0.00 0.00 0.00 3.51
2318 2936 6.296489 CCCTTTTCTCCCATCCCATATACTAC 60.296 46.154 0.00 0.00 0.00 2.73
2319 2937 5.790618 CCCTTTTCTCCCATCCCATATACTA 59.209 44.000 0.00 0.00 0.00 1.82
2320 2938 4.603610 CCCTTTTCTCCCATCCCATATACT 59.396 45.833 0.00 0.00 0.00 2.12
2321 2939 4.601857 TCCCTTTTCTCCCATCCCATATAC 59.398 45.833 0.00 0.00 0.00 1.47
2322 2940 4.601857 GTCCCTTTTCTCCCATCCCATATA 59.398 45.833 0.00 0.00 0.00 0.86
2323 2941 3.399305 GTCCCTTTTCTCCCATCCCATAT 59.601 47.826 0.00 0.00 0.00 1.78
2324 2942 2.783510 GTCCCTTTTCTCCCATCCCATA 59.216 50.000 0.00 0.00 0.00 2.74
2325 2943 1.570979 GTCCCTTTTCTCCCATCCCAT 59.429 52.381 0.00 0.00 0.00 4.00
2326 2944 0.999712 GTCCCTTTTCTCCCATCCCA 59.000 55.000 0.00 0.00 0.00 4.37
2327 2945 0.999712 TGTCCCTTTTCTCCCATCCC 59.000 55.000 0.00 0.00 0.00 3.85
2328 2946 2.899303 TTGTCCCTTTTCTCCCATCC 57.101 50.000 0.00 0.00 0.00 3.51
2329 2947 2.428530 GCATTGTCCCTTTTCTCCCATC 59.571 50.000 0.00 0.00 0.00 3.51
2330 2948 2.225343 TGCATTGTCCCTTTTCTCCCAT 60.225 45.455 0.00 0.00 0.00 4.00
2331 2949 1.146774 TGCATTGTCCCTTTTCTCCCA 59.853 47.619 0.00 0.00 0.00 4.37
2332 2950 1.821136 CTGCATTGTCCCTTTTCTCCC 59.179 52.381 0.00 0.00 0.00 4.30
2333 2951 1.203287 GCTGCATTGTCCCTTTTCTCC 59.797 52.381 0.00 0.00 0.00 3.71
2334 2952 2.165998 AGCTGCATTGTCCCTTTTCTC 58.834 47.619 1.02 0.00 0.00 2.87
2335 2953 2.299326 AGCTGCATTGTCCCTTTTCT 57.701 45.000 1.02 0.00 0.00 2.52
2336 2954 3.445096 ACATAGCTGCATTGTCCCTTTTC 59.555 43.478 1.02 0.00 0.00 2.29
2337 2955 3.434309 ACATAGCTGCATTGTCCCTTTT 58.566 40.909 1.02 0.00 0.00 2.27
2338 2956 3.091633 ACATAGCTGCATTGTCCCTTT 57.908 42.857 1.02 0.00 0.00 3.11
2339 2957 2.814805 ACATAGCTGCATTGTCCCTT 57.185 45.000 1.02 0.00 0.00 3.95
2340 2958 4.139786 CAATACATAGCTGCATTGTCCCT 58.860 43.478 10.20 0.00 33.28 4.20
2341 2959 3.254166 CCAATACATAGCTGCATTGTCCC 59.746 47.826 10.20 0.00 35.27 4.46
2342 2960 3.885297 ACCAATACATAGCTGCATTGTCC 59.115 43.478 10.20 0.00 35.27 4.02
2343 2961 5.505173 AACCAATACATAGCTGCATTGTC 57.495 39.130 10.20 0.00 35.27 3.18
2344 2962 5.920193 AAACCAATACATAGCTGCATTGT 57.080 34.783 1.02 7.55 35.27 2.71
2345 2963 7.706159 TCTAAAACCAATACATAGCTGCATTG 58.294 34.615 1.02 2.52 36.34 2.82
2346 2964 7.469181 GCTCTAAAACCAATACATAGCTGCATT 60.469 37.037 1.02 0.00 0.00 3.56
2347 2965 6.016777 GCTCTAAAACCAATACATAGCTGCAT 60.017 38.462 1.02 0.00 0.00 3.96
2348 2966 5.296780 GCTCTAAAACCAATACATAGCTGCA 59.703 40.000 1.02 0.00 0.00 4.41
2349 2967 5.296780 TGCTCTAAAACCAATACATAGCTGC 59.703 40.000 0.00 0.00 0.00 5.25
2350 2968 6.925610 TGCTCTAAAACCAATACATAGCTG 57.074 37.500 0.00 0.00 0.00 4.24
2351 2969 7.938140 TTTGCTCTAAAACCAATACATAGCT 57.062 32.000 0.00 0.00 0.00 3.32
2368 2986 9.979578 CTGACTCAACTCTATTATATTTGCTCT 57.020 33.333 0.00 0.00 0.00 4.09
2369 2987 8.707839 GCTGACTCAACTCTATTATATTTGCTC 58.292 37.037 0.00 0.00 0.00 4.26
2370 2988 8.428063 AGCTGACTCAACTCTATTATATTTGCT 58.572 33.333 0.00 0.00 0.00 3.91
2371 2989 8.600449 AGCTGACTCAACTCTATTATATTTGC 57.400 34.615 0.00 0.00 0.00 3.68
2380 2998 9.854668 TCTTATAACTAGCTGACTCAACTCTAT 57.145 33.333 0.00 0.00 0.00 1.98
2381 2999 9.682465 TTCTTATAACTAGCTGACTCAACTCTA 57.318 33.333 0.00 0.00 0.00 2.43
2382 3000 8.582657 TTCTTATAACTAGCTGACTCAACTCT 57.417 34.615 0.00 0.00 0.00 3.24
2383 3001 9.810545 ATTTCTTATAACTAGCTGACTCAACTC 57.189 33.333 0.00 0.00 0.00 3.01
2422 3040 9.403583 TCTTTTCTTTCCTCTAACTAAGCAAAA 57.596 29.630 0.00 0.00 0.00 2.44
2423 3041 8.837389 GTCTTTTCTTTCCTCTAACTAAGCAAA 58.163 33.333 0.00 0.00 0.00 3.68
2424 3042 7.444487 GGTCTTTTCTTTCCTCTAACTAAGCAA 59.556 37.037 0.00 0.00 0.00 3.91
2425 3043 6.935208 GGTCTTTTCTTTCCTCTAACTAAGCA 59.065 38.462 0.00 0.00 0.00 3.91
2426 3044 6.935208 TGGTCTTTTCTTTCCTCTAACTAAGC 59.065 38.462 0.00 0.00 0.00 3.09
2427 3045 8.368668 TCTGGTCTTTTCTTTCCTCTAACTAAG 58.631 37.037 0.00 0.00 0.00 2.18
2428 3046 8.258850 TCTGGTCTTTTCTTTCCTCTAACTAA 57.741 34.615 0.00 0.00 0.00 2.24
2429 3047 7.525692 GCTCTGGTCTTTTCTTTCCTCTAACTA 60.526 40.741 0.00 0.00 0.00 2.24
2430 3048 6.742926 GCTCTGGTCTTTTCTTTCCTCTAACT 60.743 42.308 0.00 0.00 0.00 2.24
2431 3049 5.410132 GCTCTGGTCTTTTCTTTCCTCTAAC 59.590 44.000 0.00 0.00 0.00 2.34
2432 3050 5.308237 AGCTCTGGTCTTTTCTTTCCTCTAA 59.692 40.000 0.00 0.00 0.00 2.10
2433 3051 4.841246 AGCTCTGGTCTTTTCTTTCCTCTA 59.159 41.667 0.00 0.00 0.00 2.43
2434 3052 3.650461 AGCTCTGGTCTTTTCTTTCCTCT 59.350 43.478 0.00 0.00 0.00 3.69
2435 3053 4.014569 AGCTCTGGTCTTTTCTTTCCTC 57.985 45.455 0.00 0.00 0.00 3.71
2436 3054 4.564613 GCTAGCTCTGGTCTTTTCTTTCCT 60.565 45.833 7.70 0.00 0.00 3.36
2437 3055 3.687212 GCTAGCTCTGGTCTTTTCTTTCC 59.313 47.826 7.70 0.00 0.00 3.13
2438 3056 4.153296 GTGCTAGCTCTGGTCTTTTCTTTC 59.847 45.833 17.23 0.00 0.00 2.62
2439 3057 4.068599 GTGCTAGCTCTGGTCTTTTCTTT 58.931 43.478 17.23 0.00 0.00 2.52
2440 3058 3.071602 TGTGCTAGCTCTGGTCTTTTCTT 59.928 43.478 17.23 0.00 0.00 2.52
2441 3059 2.634940 TGTGCTAGCTCTGGTCTTTTCT 59.365 45.455 17.23 0.00 0.00 2.52
2442 3060 3.045601 TGTGCTAGCTCTGGTCTTTTC 57.954 47.619 17.23 0.00 0.00 2.29
2443 3061 3.341823 CATGTGCTAGCTCTGGTCTTTT 58.658 45.455 17.23 0.00 0.00 2.27
2444 3062 2.938756 GCATGTGCTAGCTCTGGTCTTT 60.939 50.000 17.23 0.00 38.21 2.52
2445 3063 1.406614 GCATGTGCTAGCTCTGGTCTT 60.407 52.381 17.23 0.00 38.21 3.01
2446 3064 0.177604 GCATGTGCTAGCTCTGGTCT 59.822 55.000 17.23 0.00 38.21 3.85
2447 3065 2.687842 GCATGTGCTAGCTCTGGTC 58.312 57.895 17.23 0.30 38.21 4.02
2448 3066 4.950479 GCATGTGCTAGCTCTGGT 57.050 55.556 17.23 0.41 38.21 4.00
2458 3076 5.065090 TCACAAACTACATATGAGCATGTGC 59.935 40.000 10.38 0.00 39.46 4.57
2459 3077 6.536224 TCTCACAAACTACATATGAGCATGTG 59.464 38.462 10.38 17.43 39.46 3.21
2460 3078 6.643388 TCTCACAAACTACATATGAGCATGT 58.357 36.000 10.38 8.24 41.88 3.21
2461 3079 6.760298 ACTCTCACAAACTACATATGAGCATG 59.240 38.462 10.38 7.69 37.34 4.06
2462 3080 6.760298 CACTCTCACAAACTACATATGAGCAT 59.240 38.462 10.38 0.00 37.34 3.79
2463 3081 6.101997 CACTCTCACAAACTACATATGAGCA 58.898 40.000 10.38 0.00 37.34 4.26
2464 3082 5.521735 CCACTCTCACAAACTACATATGAGC 59.478 44.000 10.38 0.00 37.34 4.26
2465 3083 6.867550 TCCACTCTCACAAACTACATATGAG 58.132 40.000 10.38 5.24 38.51 2.90
2466 3084 6.850752 TCCACTCTCACAAACTACATATGA 57.149 37.500 10.38 0.00 0.00 2.15
2467 3085 7.099764 ACTTCCACTCTCACAAACTACATATG 58.900 38.462 0.00 0.00 0.00 1.78
2468 3086 7.246171 ACTTCCACTCTCACAAACTACATAT 57.754 36.000 0.00 0.00 0.00 1.78
2469 3087 6.665992 ACTTCCACTCTCACAAACTACATA 57.334 37.500 0.00 0.00 0.00 2.29
2470 3088 5.552870 ACTTCCACTCTCACAAACTACAT 57.447 39.130 0.00 0.00 0.00 2.29
2471 3089 5.116180 CAACTTCCACTCTCACAAACTACA 58.884 41.667 0.00 0.00 0.00 2.74
2472 3090 4.511826 CCAACTTCCACTCTCACAAACTAC 59.488 45.833 0.00 0.00 0.00 2.73
2473 3091 4.163458 ACCAACTTCCACTCTCACAAACTA 59.837 41.667 0.00 0.00 0.00 2.24
2474 3092 3.054361 ACCAACTTCCACTCTCACAAACT 60.054 43.478 0.00 0.00 0.00 2.66
2475 3093 3.279434 ACCAACTTCCACTCTCACAAAC 58.721 45.455 0.00 0.00 0.00 2.93
2476 3094 3.054728 TGACCAACTTCCACTCTCACAAA 60.055 43.478 0.00 0.00 0.00 2.83
2477 3095 2.503765 TGACCAACTTCCACTCTCACAA 59.496 45.455 0.00 0.00 0.00 3.33
2478 3096 2.115427 TGACCAACTTCCACTCTCACA 58.885 47.619 0.00 0.00 0.00 3.58
2479 3097 2.910688 TGACCAACTTCCACTCTCAC 57.089 50.000 0.00 0.00 0.00 3.51
2480 3098 6.867519 TTATATGACCAACTTCCACTCTCA 57.132 37.500 0.00 0.00 0.00 3.27
2522 3140 9.158233 CGAAGGGAGTACAATAGTTGATTAAAA 57.842 33.333 0.00 0.00 0.00 1.52
2523 3141 8.316214 ACGAAGGGAGTACAATAGTTGATTAAA 58.684 33.333 0.00 0.00 0.00 1.52
2524 3142 7.844009 ACGAAGGGAGTACAATAGTTGATTAA 58.156 34.615 0.00 0.00 0.00 1.40
2525 3143 7.414222 ACGAAGGGAGTACAATAGTTGATTA 57.586 36.000 0.00 0.00 0.00 1.75
2526 3144 6.295719 ACGAAGGGAGTACAATAGTTGATT 57.704 37.500 0.00 0.00 0.00 2.57
2527 3145 5.934402 ACGAAGGGAGTACAATAGTTGAT 57.066 39.130 0.00 0.00 0.00 2.57
2528 3146 5.733620 AACGAAGGGAGTACAATAGTTGA 57.266 39.130 0.00 0.00 0.00 3.18
2529 3147 6.164176 AGAAACGAAGGGAGTACAATAGTTG 58.836 40.000 0.00 0.00 0.00 3.16
2530 3148 6.356186 AGAAACGAAGGGAGTACAATAGTT 57.644 37.500 0.00 0.00 0.00 2.24
2531 3149 5.997384 AGAAACGAAGGGAGTACAATAGT 57.003 39.130 0.00 0.00 0.00 2.12
2532 3150 7.668525 AAAAGAAACGAAGGGAGTACAATAG 57.331 36.000 0.00 0.00 0.00 1.73
2533 3151 9.211485 CTAAAAAGAAACGAAGGGAGTACAATA 57.789 33.333 0.00 0.00 0.00 1.90
2534 3152 6.954487 AAAAAGAAACGAAGGGAGTACAAT 57.046 33.333 0.00 0.00 0.00 2.71
2535 3153 7.049754 ACTAAAAAGAAACGAAGGGAGTACAA 58.950 34.615 0.00 0.00 0.00 2.41
2536 3154 6.585416 ACTAAAAAGAAACGAAGGGAGTACA 58.415 36.000 0.00 0.00 0.00 2.90
2537 3155 6.927936 AGACTAAAAAGAAACGAAGGGAGTAC 59.072 38.462 0.00 0.00 0.00 2.73
2538 3156 6.927381 CAGACTAAAAAGAAACGAAGGGAGTA 59.073 38.462 0.00 0.00 0.00 2.59
2539 3157 5.758784 CAGACTAAAAAGAAACGAAGGGAGT 59.241 40.000 0.00 0.00 0.00 3.85
2540 3158 5.334182 GCAGACTAAAAAGAAACGAAGGGAG 60.334 44.000 0.00 0.00 0.00 4.30
2541 3159 4.514066 GCAGACTAAAAAGAAACGAAGGGA 59.486 41.667 0.00 0.00 0.00 4.20
2542 3160 4.274950 TGCAGACTAAAAAGAAACGAAGGG 59.725 41.667 0.00 0.00 0.00 3.95
2543 3161 5.418310 TGCAGACTAAAAAGAAACGAAGG 57.582 39.130 0.00 0.00 0.00 3.46
2546 3164 9.647797 TCTTATATGCAGACTAAAAAGAAACGA 57.352 29.630 0.00 0.00 0.00 3.85
2610 3228 9.849166 TGTTTGTCGCGATATATTATTCTATCA 57.151 29.630 14.06 0.00 0.00 2.15
2614 3232 8.443160 CCATTGTTTGTCGCGATATATTATTCT 58.557 33.333 14.06 0.00 0.00 2.40
2615 3233 8.227791 ACCATTGTTTGTCGCGATATATTATTC 58.772 33.333 14.06 0.00 0.00 1.75
2616 3234 8.015087 CACCATTGTTTGTCGCGATATATTATT 58.985 33.333 14.06 0.00 0.00 1.40
2617 3235 7.386573 TCACCATTGTTTGTCGCGATATATTAT 59.613 33.333 14.06 0.00 0.00 1.28
2618 3236 6.702282 TCACCATTGTTTGTCGCGATATATTA 59.298 34.615 14.06 0.00 0.00 0.98
2619 3237 5.525745 TCACCATTGTTTGTCGCGATATATT 59.474 36.000 14.06 0.00 0.00 1.28
2620 3238 5.053811 TCACCATTGTTTGTCGCGATATAT 58.946 37.500 14.06 0.00 0.00 0.86
2621 3239 4.434520 TCACCATTGTTTGTCGCGATATA 58.565 39.130 14.06 0.81 0.00 0.86
2622 3240 3.266636 TCACCATTGTTTGTCGCGATAT 58.733 40.909 14.06 0.00 0.00 1.63
2623 3241 2.689646 TCACCATTGTTTGTCGCGATA 58.310 42.857 14.06 6.83 0.00 2.92
2624 3242 1.518325 TCACCATTGTTTGTCGCGAT 58.482 45.000 14.06 0.00 0.00 4.58
2625 3243 1.300481 TTCACCATTGTTTGTCGCGA 58.700 45.000 3.71 3.71 0.00 5.87
2626 3244 2.112475 TTTCACCATTGTTTGTCGCG 57.888 45.000 0.00 0.00 0.00 5.87
2627 3245 2.215363 CGTTTTCACCATTGTTTGTCGC 59.785 45.455 0.00 0.00 0.00 5.19
2628 3246 2.786578 CCGTTTTCACCATTGTTTGTCG 59.213 45.455 0.00 0.00 0.00 4.35
2629 3247 4.035278 TCCGTTTTCACCATTGTTTGTC 57.965 40.909 0.00 0.00 0.00 3.18
2630 3248 4.616953 GATCCGTTTTCACCATTGTTTGT 58.383 39.130 0.00 0.00 0.00 2.83
2631 3249 3.668191 CGATCCGTTTTCACCATTGTTTG 59.332 43.478 0.00 0.00 0.00 2.93
2632 3250 3.316868 ACGATCCGTTTTCACCATTGTTT 59.683 39.130 0.00 0.00 36.35 2.83
2633 3251 2.882137 ACGATCCGTTTTCACCATTGTT 59.118 40.909 0.00 0.00 36.35 2.83
2634 3252 2.482721 GACGATCCGTTTTCACCATTGT 59.517 45.455 0.00 0.00 41.37 2.71
2635 3253 2.482336 TGACGATCCGTTTTCACCATTG 59.518 45.455 0.00 0.00 41.37 2.82
2636 3254 2.773487 TGACGATCCGTTTTCACCATT 58.227 42.857 0.00 0.00 41.37 3.16
2637 3255 2.465860 TGACGATCCGTTTTCACCAT 57.534 45.000 0.00 0.00 41.37 3.55
2638 3256 2.242047 TTGACGATCCGTTTTCACCA 57.758 45.000 0.00 0.00 41.37 4.17
2639 3257 3.824414 AATTGACGATCCGTTTTCACC 57.176 42.857 0.00 0.00 41.37 4.02
2640 3258 5.793457 CCTTTAATTGACGATCCGTTTTCAC 59.207 40.000 0.00 0.00 41.37 3.18
2641 3259 5.106475 CCCTTTAATTGACGATCCGTTTTCA 60.106 40.000 0.00 0.00 41.37 2.69
2642 3260 5.122711 TCCCTTTAATTGACGATCCGTTTTC 59.877 40.000 0.00 0.00 41.37 2.29
2643 3261 5.005094 TCCCTTTAATTGACGATCCGTTTT 58.995 37.500 0.00 0.00 41.37 2.43
2644 3262 4.393990 GTCCCTTTAATTGACGATCCGTTT 59.606 41.667 0.00 0.00 41.37 3.60
2645 3263 3.937079 GTCCCTTTAATTGACGATCCGTT 59.063 43.478 0.00 0.00 41.37 4.44
2646 3264 3.197116 AGTCCCTTTAATTGACGATCCGT 59.803 43.478 0.00 0.00 45.10 4.69
2647 3265 3.555956 CAGTCCCTTTAATTGACGATCCG 59.444 47.826 0.00 0.00 34.24 4.18
2648 3266 4.571176 GTCAGTCCCTTTAATTGACGATCC 59.429 45.833 0.00 0.00 34.24 3.36
2649 3267 5.420409 AGTCAGTCCCTTTAATTGACGATC 58.580 41.667 0.00 0.00 42.15 3.69
2650 3268 5.422214 AGTCAGTCCCTTTAATTGACGAT 57.578 39.130 0.00 0.00 42.15 3.73
2651 3269 4.884668 AGTCAGTCCCTTTAATTGACGA 57.115 40.909 0.00 0.00 42.15 4.20
2652 3270 6.036083 CACATAGTCAGTCCCTTTAATTGACG 59.964 42.308 0.00 0.00 42.15 4.35
2653 3271 6.879458 ACACATAGTCAGTCCCTTTAATTGAC 59.121 38.462 0.00 0.00 38.68 3.18
2654 3272 7.016153 ACACATAGTCAGTCCCTTTAATTGA 57.984 36.000 0.00 0.00 0.00 2.57
2655 3273 8.786826 TTACACATAGTCAGTCCCTTTAATTG 57.213 34.615 0.00 0.00 0.00 2.32
2656 3274 8.603304 ACTTACACATAGTCAGTCCCTTTAATT 58.397 33.333 0.00 0.00 28.64 1.40
2657 3275 8.147244 ACTTACACATAGTCAGTCCCTTTAAT 57.853 34.615 0.00 0.00 28.64 1.40
2658 3276 7.549147 ACTTACACATAGTCAGTCCCTTTAA 57.451 36.000 0.00 0.00 28.64 1.52
2659 3277 7.233962 TCAACTTACACATAGTCAGTCCCTTTA 59.766 37.037 0.00 0.00 33.66 1.85
2660 3278 6.042781 TCAACTTACACATAGTCAGTCCCTTT 59.957 38.462 0.00 0.00 33.66 3.11
2661 3279 5.542635 TCAACTTACACATAGTCAGTCCCTT 59.457 40.000 0.00 0.00 33.66 3.95
2662 3280 5.047235 GTCAACTTACACATAGTCAGTCCCT 60.047 44.000 0.00 0.00 33.66 4.20
2663 3281 5.047235 AGTCAACTTACACATAGTCAGTCCC 60.047 44.000 0.00 0.00 33.66 4.46
2664 3282 5.864474 CAGTCAACTTACACATAGTCAGTCC 59.136 44.000 0.00 0.00 33.66 3.85
2665 3283 5.864474 CCAGTCAACTTACACATAGTCAGTC 59.136 44.000 0.00 0.00 33.66 3.51
2666 3284 5.304614 ACCAGTCAACTTACACATAGTCAGT 59.695 40.000 0.00 0.00 36.26 3.41
2667 3285 5.784177 ACCAGTCAACTTACACATAGTCAG 58.216 41.667 0.00 0.00 0.00 3.51
2668 3286 5.801531 ACCAGTCAACTTACACATAGTCA 57.198 39.130 0.00 0.00 0.00 3.41
2669 3287 7.492352 AAAACCAGTCAACTTACACATAGTC 57.508 36.000 0.00 0.00 0.00 2.59
2670 3288 7.703328 CAAAAACCAGTCAACTTACACATAGT 58.297 34.615 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.