Multiple sequence alignment - TraesCS6A01G280400

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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 TraesCS6A01G280400 chr6A 100.000 4176 0 0 1 4176 508845827 508850002 0.000000e+00 7712.0
1 TraesCS6A01G280400 chr6D 95.228 1404 44 7 2469 3870 368302479 368303861 0.000000e+00 2200.0
2 TraesCS6A01G280400 chr6D 94.498 1254 50 7 823 2070 368300912 368302152 0.000000e+00 1916.0
3 TraesCS6A01G280400 chr6D 89.803 608 33 10 814 1410 368212536 368213125 0.000000e+00 752.0
4 TraesCS6A01G280400 chr6D 93.377 302 19 1 2067 2367 368302181 368302482 2.960000e-121 446.0
5 TraesCS6A01G280400 chr6D 94.757 267 12 2 3911 4176 368303862 368304127 8.350000e-112 414.0
6 TraesCS6A01G280400 chr6D 83.333 474 34 16 40 500 135111195 135110754 3.030000e-106 396.0
7 TraesCS6A01G280400 chr6D 91.351 185 15 1 631 815 135110327 135110144 6.930000e-63 252.0
8 TraesCS6A01G280400 chr6D 91.667 132 10 1 2366 2497 112344482 112344352 9.220000e-42 182.0
9 TraesCS6A01G280400 chr6D 91.228 114 9 1 494 606 135110431 135110318 2.010000e-33 154.0
10 TraesCS6A01G280400 chr6B 90.518 1466 83 20 900 2364 553378252 553376842 0.000000e+00 1886.0
11 TraesCS6A01G280400 chr6B 95.186 1101 48 4 2770 3868 553376470 553375373 0.000000e+00 1735.0
12 TraesCS6A01G280400 chr6B 92.000 300 17 4 2469 2761 553376837 553376538 8.350000e-112 414.0
13 TraesCS6A01G280400 chr6B 94.737 266 9 2 3911 4176 553375370 553375110 3.890000e-110 409.0
14 TraesCS6A01G280400 chr6B 97.391 115 2 1 2361 2475 218024960 218024847 1.180000e-45 195.0
15 TraesCS6A01G280400 chr6B 95.726 117 5 0 2356 2472 120355513 120355397 5.510000e-44 189.0
16 TraesCS6A01G280400 chr6B 100.000 40 0 0 1 40 208760285 208760246 1.610000e-09 75.0
17 TraesCS6A01G280400 chr5A 89.677 465 35 7 42 493 53456709 53457173 7.780000e-162 580.0
18 TraesCS6A01G280400 chr5A 93.231 325 18 3 492 814 53457430 53457752 3.780000e-130 475.0
19 TraesCS6A01G280400 chr5A 94.958 119 4 1 2366 2484 522062397 522062281 7.130000e-43 185.0
20 TraesCS6A01G280400 chr2D 90.691 333 19 4 494 815 584231628 584231297 2.310000e-117 433.0
21 TraesCS6A01G280400 chr2D 90.634 331 19 5 494 813 528096144 528095815 2.980000e-116 429.0
22 TraesCS6A01G280400 chr2D 83.991 456 32 17 40 483 584232413 584231987 2.340000e-107 399.0
23 TraesCS6A01G280400 chr2D 86.992 369 24 10 145 500 528096807 528096450 1.090000e-105 394.0
24 TraesCS6A01G280400 chr2D 95.294 85 4 0 40 124 528096884 528096800 7.280000e-28 135.0
25 TraesCS6A01G280400 chr5D 83.544 474 35 10 40 500 137016320 137015877 1.810000e-108 403.0
26 TraesCS6A01G280400 chr5D 90.710 183 15 2 631 813 137015450 137015270 4.170000e-60 243.0
27 TraesCS6A01G280400 chr5D 92.105 114 8 1 494 606 137015554 137015441 4.320000e-35 159.0
28 TraesCS6A01G280400 chr2A 95.652 207 7 1 40 246 171639911 171639707 8.650000e-87 331.0
29 TraesCS6A01G280400 chr2A 89.785 186 16 2 628 813 171625279 171625097 6.980000e-58 235.0
30 TraesCS6A01G280400 chr2A 98.198 111 2 0 2363 2473 722814005 722814115 1.180000e-45 195.0
31 TraesCS6A01G280400 chr2A 96.364 110 4 0 2363 2472 16546936 16547045 9.220000e-42 182.0
32 TraesCS6A01G280400 chr7A 98.182 110 2 0 2363 2472 609519011 609518902 4.260000e-45 193.0
33 TraesCS6A01G280400 chr3A 96.581 117 2 2 2358 2472 308675910 308676026 4.260000e-45 193.0
34 TraesCS6A01G280400 chr5B 97.273 110 3 0 2366 2475 559999857 559999748 1.980000e-43 187.0
35 TraesCS6A01G280400 chr5B 100.000 40 0 0 1 40 303061052 303061091 1.610000e-09 75.0
36 TraesCS6A01G280400 chr1D 100.000 41 0 0 1 41 184151337 184151297 4.480000e-10 76.8
37 TraesCS6A01G280400 chr1D 100.000 40 0 0 1 40 253684833 253684872 1.610000e-09 75.0
38 TraesCS6A01G280400 chr7D 100.000 40 0 0 1 40 516623797 516623758 1.610000e-09 75.0
39 TraesCS6A01G280400 chr2B 100.000 40 0 0 1 40 49780747 49780708 1.610000e-09 75.0
40 TraesCS6A01G280400 chr2B 100.000 40 0 0 1 40 169186459 169186420 1.610000e-09 75.0
41 TraesCS6A01G280400 chr1A 100.000 40 0 0 1 40 318907856 318907895 1.610000e-09 75.0
42 TraesCS6A01G280400 chr1A 100.000 40 0 0 1 40 519129015 519128976 1.610000e-09 75.0
43 TraesCS6A01G280400 chr1B 97.500 40 1 0 504 543 666332220 666332259 7.490000e-08 69.4


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 TraesCS6A01G280400 chr6A 508845827 508850002 4175 False 7712.000000 7712 100.000000 1 4176 1 chr6A.!!$F1 4175
1 TraesCS6A01G280400 chr6D 368300912 368304127 3215 False 1244.000000 2200 94.465000 823 4176 4 chr6D.!!$F2 3353
2 TraesCS6A01G280400 chr6D 368212536 368213125 589 False 752.000000 752 89.803000 814 1410 1 chr6D.!!$F1 596
3 TraesCS6A01G280400 chr6D 135110144 135111195 1051 True 267.333333 396 88.637333 40 815 3 chr6D.!!$R2 775
4 TraesCS6A01G280400 chr6B 553375110 553378252 3142 True 1111.000000 1886 93.110250 900 4176 4 chr6B.!!$R4 3276
5 TraesCS6A01G280400 chr5A 53456709 53457752 1043 False 527.500000 580 91.454000 42 814 2 chr5A.!!$F1 772
6 TraesCS6A01G280400 chr2D 584231297 584232413 1116 True 416.000000 433 87.341000 40 815 2 chr2D.!!$R2 775
7 TraesCS6A01G280400 chr2D 528095815 528096884 1069 True 319.333333 429 90.973333 40 813 3 chr2D.!!$R1 773
8 TraesCS6A01G280400 chr5D 137015270 137016320 1050 True 268.333333 403 88.786333 40 813 3 chr5D.!!$R1 773

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
139 140 0.317269 CGGCCAAATGATCACATCGC 60.317 55.0 2.24 0.00 35.50 4.58 F
1355 1750 0.179127 GGTAGGTTAACTCCGCCGAC 60.179 60.0 5.42 0.00 0.00 4.79 F
1525 1936 0.321564 TGACCTGCGACCTGAAATGG 60.322 55.0 0.00 0.00 0.00 3.16 F
2382 2827 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.0 14.79 0.04 33.41 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 2259 0.259938 AGACCGGGGTATCCTACGTT 59.740 55.000 6.32 0.00 0.00 3.99 R
2373 2818 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44 R
2450 2895 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89 R
3627 4140 0.024746 CTAGTCTCGGTTCGTCGTCG 59.975 60.000 0.00 0.00 38.55 5.12 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
23 24 6.867662 GGATTGACAAATATACACAGGAGG 57.132 41.667 0.00 0.00 0.00 4.30
24 25 5.765182 GGATTGACAAATATACACAGGAGGG 59.235 44.000 0.00 0.00 0.00 4.30
25 26 5.772393 TTGACAAATATACACAGGAGGGT 57.228 39.130 0.00 0.00 0.00 4.34
26 27 5.353394 TGACAAATATACACAGGAGGGTC 57.647 43.478 0.00 0.00 0.00 4.46
27 28 5.030147 TGACAAATATACACAGGAGGGTCT 58.970 41.667 0.00 0.00 0.00 3.85
28 29 5.104941 TGACAAATATACACAGGAGGGTCTG 60.105 44.000 0.00 0.00 40.40 3.51
29 30 4.164221 ACAAATATACACAGGAGGGTCTGG 59.836 45.833 0.00 0.00 38.98 3.86
30 31 3.993658 ATATACACAGGAGGGTCTGGA 57.006 47.619 0.00 0.00 38.98 3.86
31 32 2.642171 ATACACAGGAGGGTCTGGAA 57.358 50.000 0.00 0.00 38.98 3.53
32 33 2.409064 TACACAGGAGGGTCTGGAAA 57.591 50.000 0.00 0.00 38.98 3.13
33 34 1.747444 ACACAGGAGGGTCTGGAAAT 58.253 50.000 0.00 0.00 38.98 2.17
34 35 2.915869 ACACAGGAGGGTCTGGAAATA 58.084 47.619 0.00 0.00 38.98 1.40
35 36 3.256704 ACACAGGAGGGTCTGGAAATAA 58.743 45.455 0.00 0.00 38.98 1.40
36 37 3.852578 ACACAGGAGGGTCTGGAAATAAT 59.147 43.478 0.00 0.00 38.98 1.28
37 38 4.292306 ACACAGGAGGGTCTGGAAATAATT 59.708 41.667 0.00 0.00 38.98 1.40
38 39 5.222337 ACACAGGAGGGTCTGGAAATAATTT 60.222 40.000 0.00 0.00 38.98 1.82
71 72 4.129737 GCAGGAGTACGAGCGGCA 62.130 66.667 1.45 0.00 0.00 5.69
128 129 1.671054 CGATATCCCGCGGCCAAAT 60.671 57.895 22.85 12.49 0.00 2.32
129 130 1.875963 GATATCCCGCGGCCAAATG 59.124 57.895 22.85 4.77 0.00 2.32
139 140 0.317269 CGGCCAAATGATCACATCGC 60.317 55.000 2.24 0.00 35.50 4.58
142 143 1.202177 GCCAAATGATCACATCGCGTT 60.202 47.619 5.77 0.00 35.50 4.84
149 150 2.220615 ATCACATCGCGTTCCCGTCA 62.221 55.000 5.77 0.00 36.15 4.35
294 308 1.141881 CGAAGAGGCAGGCGTACAT 59.858 57.895 0.00 0.00 0.00 2.29
300 314 2.183300 GCAGGCGTACATCCGACA 59.817 61.111 0.00 0.00 38.69 4.35
439 492 2.160853 CGCATCACATCGTGTCGCT 61.161 57.895 8.22 0.00 34.79 4.93
620 1015 1.302511 GTGGCCTTCGACATGGTGT 60.303 57.895 3.32 0.00 0.00 4.16
675 1070 2.979814 AAACAGAAGCAAAACCACCC 57.020 45.000 0.00 0.00 0.00 4.61
701 1096 3.914426 TCTCTCCAAAATCACCTAGGC 57.086 47.619 9.30 0.00 0.00 3.93
758 1153 6.128661 GGAAAATAATCCGGTTTTGAAGTTGC 60.129 38.462 0.00 0.00 0.00 4.17
761 1156 0.464013 TCCGGTTTTGAAGTTGCGGA 60.464 50.000 0.00 0.00 0.00 5.54
985 1380 4.459089 GAGTGGACTGGCCGGAGC 62.459 72.222 21.41 9.74 40.66 4.70
1021 1416 2.989824 AGTGGACGACGGTGGAGG 60.990 66.667 0.00 0.00 0.00 4.30
1351 1746 1.520120 GCCGGTAGGTTAACTCCGC 60.520 63.158 22.07 16.59 38.06 5.54
1355 1750 0.179127 GGTAGGTTAACTCCGCCGAC 60.179 60.000 5.42 0.00 0.00 4.79
1432 1838 4.466015 AGCCGGTAATCAAATTGACCAAAT 59.534 37.500 1.90 0.00 31.89 2.32
1453 1864 6.917217 AATCAGTAGCTATTCTGAAACTGC 57.083 37.500 15.69 8.68 42.67 4.40
1454 1865 5.405935 TCAGTAGCTATTCTGAAACTGCA 57.594 39.130 10.74 0.00 37.69 4.41
1484 1895 1.662517 TGGCATACGCAATTGACGAT 58.337 45.000 22.87 12.36 41.24 3.73
1485 1896 2.013400 TGGCATACGCAATTGACGATT 58.987 42.857 22.87 10.73 41.24 3.34
1486 1897 3.198872 TGGCATACGCAATTGACGATTA 58.801 40.909 22.87 10.54 41.24 1.75
1487 1898 3.623510 TGGCATACGCAATTGACGATTAA 59.376 39.130 22.87 9.91 41.24 1.40
1488 1899 3.966218 GGCATACGCAATTGACGATTAAC 59.034 43.478 22.87 11.31 41.24 2.01
1518 1929 0.534412 CTCATCTTGACCTGCGACCT 59.466 55.000 0.00 0.00 0.00 3.85
1525 1936 0.321564 TGACCTGCGACCTGAAATGG 60.322 55.000 0.00 0.00 0.00 3.16
1541 1952 1.597742 ATGGATAGGTGATGCGTTGC 58.402 50.000 0.00 0.00 0.00 4.17
1714 2126 4.020617 TGCTCGGGGCTGTTGAGG 62.021 66.667 0.00 0.00 42.39 3.86
1725 2137 0.326264 CTGTTGAGGGGCTGCTAAGT 59.674 55.000 0.00 0.00 0.00 2.24
1733 2145 1.682087 GGGGCTGCTAAGTAACCCTTG 60.682 57.143 0.00 0.00 40.64 3.61
1774 2186 7.758076 CAGTGACTGACCTTATCGTATTGTTAA 59.242 37.037 6.79 0.00 32.44 2.01
1837 2249 5.652452 GGTTATCACCACTATTTTTCAGCCT 59.348 40.000 0.00 0.00 43.61 4.58
1845 2257 7.721399 CACCACTATTTTTCAGCCTATCCTTAT 59.279 37.037 0.00 0.00 0.00 1.73
1846 2258 8.282256 ACCACTATTTTTCAGCCTATCCTTATT 58.718 33.333 0.00 0.00 0.00 1.40
1847 2259 9.793259 CCACTATTTTTCAGCCTATCCTTATTA 57.207 33.333 0.00 0.00 0.00 0.98
1861 2273 6.864151 ATCCTTATTAACGTAGGATACCCC 57.136 41.667 13.94 0.00 44.84 4.95
1902 2314 1.530441 CGATGCATCTTCAGTTTGCCG 60.530 52.381 23.73 3.45 35.51 5.69
1931 2343 4.376146 GAGATTCAGTGAGGCCAGTAATC 58.624 47.826 5.01 5.40 0.00 1.75
2019 2431 5.491982 ACAATTAGACACTCATCTTGACCC 58.508 41.667 0.00 0.00 0.00 4.46
2116 2560 9.912634 GAATTTTCCTTCAAATGTACTCATCAA 57.087 29.630 0.00 0.00 32.56 2.57
2125 2569 8.450578 TCAAATGTACTCATCAAACAGTTCTT 57.549 30.769 0.00 0.00 29.80 2.52
2172 2616 6.211584 AGTCCAAAGATCTAACTAACAGCTGA 59.788 38.462 23.35 0.00 0.00 4.26
2191 2636 8.478066 ACAGCTGAGTATTATCACTGAAATGTA 58.522 33.333 23.35 0.00 34.85 2.29
2243 2688 2.376109 CGTAAGACTAAGAGGCTCCCA 58.624 52.381 11.71 0.00 27.04 4.37
2246 2691 2.559381 AGACTAAGAGGCTCCCATGT 57.441 50.000 11.71 5.33 0.00 3.21
2254 2699 0.329596 AGGCTCCCATGTTGACCTTC 59.670 55.000 0.00 0.00 0.00 3.46
2259 2704 1.630369 TCCCATGTTGACCTTCTCCTG 59.370 52.381 0.00 0.00 0.00 3.86
2357 2802 3.810310 ATGCAGGACACTAGACTAAGC 57.190 47.619 0.00 0.00 0.00 3.09
2364 2809 6.734137 CAGGACACTAGACTAAGCAGATTAG 58.266 44.000 3.78 3.78 45.53 1.73
2374 2819 5.715434 CTAAGCAGATTAGTACTCCCTCC 57.285 47.826 0.00 0.00 36.82 4.30
2375 2820 2.588620 AGCAGATTAGTACTCCCTCCG 58.411 52.381 0.00 0.00 0.00 4.63
2376 2821 2.091775 AGCAGATTAGTACTCCCTCCGT 60.092 50.000 0.00 0.00 0.00 4.69
2377 2822 2.694109 GCAGATTAGTACTCCCTCCGTT 59.306 50.000 0.00 0.00 0.00 4.44
2378 2823 3.243468 GCAGATTAGTACTCCCTCCGTTC 60.243 52.174 0.00 0.00 0.00 3.95
2379 2824 3.003482 CAGATTAGTACTCCCTCCGTTCG 59.997 52.174 0.00 0.00 0.00 3.95
2380 2825 1.755179 TTAGTACTCCCTCCGTTCGG 58.245 55.000 0.00 4.74 0.00 4.30
2381 2826 0.911769 TAGTACTCCCTCCGTTCGGA 59.088 55.000 13.34 13.34 0.00 4.55
2382 2827 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
2383 2828 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
2384 2829 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
2385 2830 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2386 2831 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2387 2832 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2388 2833 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2389 2834 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2390 2835 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2391 2836 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2392 2837 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2393 2838 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
2394 2839 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
2395 2840 2.222508 CGTTCGGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
2396 2841 2.991190 GTTCGGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
2397 2842 3.306917 TCGGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
2398 2843 3.655486 TCGGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
2399 2844 4.250464 TCGGAATTACTTGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
2400 2845 5.412640 TCGGAATTACTTGTCGCAGAAATA 58.587 37.500 0.00 0.00 39.69 1.40
2401 2846 5.518847 TCGGAATTACTTGTCGCAGAAATAG 59.481 40.000 0.00 0.00 39.69 1.73
2402 2847 5.518847 CGGAATTACTTGTCGCAGAAATAGA 59.481 40.000 0.00 0.00 39.69 1.98
2403 2848 6.201044 CGGAATTACTTGTCGCAGAAATAGAT 59.799 38.462 0.00 0.00 39.69 1.98
2404 2849 7.348201 GGAATTACTTGTCGCAGAAATAGATG 58.652 38.462 0.00 0.00 39.69 2.90
2405 2850 7.011482 GGAATTACTTGTCGCAGAAATAGATGT 59.989 37.037 0.00 0.00 39.69 3.06
2406 2851 8.942338 AATTACTTGTCGCAGAAATAGATGTA 57.058 30.769 0.00 0.00 39.69 2.29
2407 2852 9.547753 AATTACTTGTCGCAGAAATAGATGTAT 57.452 29.630 0.00 0.00 39.69 2.29
2408 2853 8.575565 TTACTTGTCGCAGAAATAGATGTATC 57.424 34.615 0.00 0.00 39.69 2.24
2409 2854 6.810911 ACTTGTCGCAGAAATAGATGTATCT 58.189 36.000 0.00 0.00 39.69 1.98
2410 2855 6.699204 ACTTGTCGCAGAAATAGATGTATCTG 59.301 38.462 4.67 0.00 39.69 2.90
2411 2856 5.532557 TGTCGCAGAAATAGATGTATCTGG 58.467 41.667 4.67 0.00 39.69 3.86
2412 2857 5.301805 TGTCGCAGAAATAGATGTATCTGGA 59.698 40.000 4.67 0.00 39.69 3.86
2413 2858 6.015095 TGTCGCAGAAATAGATGTATCTGGAT 60.015 38.462 4.67 0.00 39.69 3.41
2414 2859 6.309980 GTCGCAGAAATAGATGTATCTGGATG 59.690 42.308 4.67 0.00 39.69 3.51
2415 2860 6.015095 TCGCAGAAATAGATGTATCTGGATGT 60.015 38.462 4.67 0.00 39.69 3.06
2416 2861 7.176690 TCGCAGAAATAGATGTATCTGGATGTA 59.823 37.037 4.67 0.00 39.69 2.29
2417 2862 7.978414 CGCAGAAATAGATGTATCTGGATGTAT 59.022 37.037 4.67 0.00 39.69 2.29
2418 2863 9.664332 GCAGAAATAGATGTATCTGGATGTATT 57.336 33.333 4.67 0.00 39.69 1.89
2444 2889 9.749340 TTTAGTTCTAGATACATCCATATCCGA 57.251 33.333 0.00 0.00 32.76 4.55
2445 2890 7.873719 AGTTCTAGATACATCCATATCCGAG 57.126 40.000 0.00 0.00 32.76 4.63
2446 2891 7.634718 AGTTCTAGATACATCCATATCCGAGA 58.365 38.462 0.00 0.00 32.76 4.04
2447 2892 7.554835 AGTTCTAGATACATCCATATCCGAGAC 59.445 40.741 0.00 0.00 32.76 3.36
2448 2893 6.958767 TCTAGATACATCCATATCCGAGACA 58.041 40.000 0.00 0.00 32.76 3.41
2449 2894 7.402862 TCTAGATACATCCATATCCGAGACAA 58.597 38.462 0.00 0.00 32.76 3.18
2450 2895 6.522625 AGATACATCCATATCCGAGACAAG 57.477 41.667 0.00 0.00 32.76 3.16
2451 2896 6.013379 AGATACATCCATATCCGAGACAAGT 58.987 40.000 0.00 0.00 32.76 3.16
2452 2897 7.175797 AGATACATCCATATCCGAGACAAGTA 58.824 38.462 0.00 0.00 32.76 2.24
2453 2898 7.670140 AGATACATCCATATCCGAGACAAGTAA 59.330 37.037 0.00 0.00 32.76 2.24
2454 2899 6.672266 ACATCCATATCCGAGACAAGTAAT 57.328 37.500 0.00 0.00 0.00 1.89
2455 2900 7.067496 ACATCCATATCCGAGACAAGTAATT 57.933 36.000 0.00 0.00 0.00 1.40
2456 2901 7.155328 ACATCCATATCCGAGACAAGTAATTC 58.845 38.462 0.00 0.00 0.00 2.17
2457 2902 6.097915 TCCATATCCGAGACAAGTAATTCC 57.902 41.667 0.00 0.00 0.00 3.01
2458 2903 4.923871 CCATATCCGAGACAAGTAATTCCG 59.076 45.833 0.00 0.00 0.00 4.30
2459 2904 5.278808 CCATATCCGAGACAAGTAATTCCGA 60.279 44.000 0.00 0.00 0.00 4.55
2460 2905 4.730949 ATCCGAGACAAGTAATTCCGAA 57.269 40.909 0.00 0.00 0.00 4.30
2461 2906 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
2462 2907 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
2463 2908 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
2464 2909 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
2465 2910 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
2466 2911 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2467 2912 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2495 2940 2.082231 CTCAGAAGCAACCTGGACATG 58.918 52.381 0.00 0.00 32.73 3.21
2528 2973 4.263550 TGCTGTACCTATTTTTGGCCACTA 60.264 41.667 3.88 0.00 0.00 2.74
2701 3153 4.941873 AGCAGTGGCAACTAATTAAGTACC 59.058 41.667 0.00 0.00 44.61 3.34
2738 3190 7.456684 TGTGTTGTTGCACAAAATACAATAC 57.543 32.000 15.55 15.55 45.17 1.89
2878 3389 2.288666 GCGGGATCTGCAGTTGATAAA 58.711 47.619 14.67 0.00 0.00 1.40
2902 3413 3.175133 CCAGGTGGTTGGCTATGTC 57.825 57.895 0.00 0.00 0.00 3.06
3048 3559 1.767289 CAGCTGCAAAACAAGCTCAG 58.233 50.000 0.00 0.00 32.57 3.35
3278 3789 7.356540 TGGTTTGTATTTTCTCGTGTTGTATG 58.643 34.615 0.00 0.00 0.00 2.39
3360 3871 2.680312 TAGACTCAGTGATGCAAGCC 57.320 50.000 0.00 0.00 0.00 4.35
3448 3960 3.111853 TCTACTTGTGAGTGGTTGCTG 57.888 47.619 0.00 0.00 36.60 4.41
3456 3968 1.845809 GAGTGGTTGCTGTCCTTGCG 61.846 60.000 0.00 0.00 0.00 4.85
3539 4051 7.970061 TCTGTCTTTCTGAAATTGTTTGTCAAG 59.030 33.333 2.88 0.00 39.55 3.02
3569 4082 5.798934 GCTTCGTCGTAGGTTATATACATGG 59.201 44.000 0.00 0.00 0.00 3.66
3585 4098 8.783833 ATATACATGGCTGATGTTGATCTTAC 57.216 34.615 7.13 0.00 43.20 2.34
3627 4140 2.034221 GTGGAGGGTGGCCTTCAC 59.966 66.667 3.32 0.00 45.34 3.18
3819 4333 6.310224 CGTTTTCAACTTTCAACAGATTTGGT 59.690 34.615 0.00 0.00 0.00 3.67
3824 4338 4.932146 ACTTTCAACAGATTTGGTTTCGG 58.068 39.130 0.00 0.00 0.00 4.30
3844 4358 3.303049 GGGGGATTTCATCATCAGCTTT 58.697 45.455 0.00 0.00 0.00 3.51
3846 4360 3.069158 GGGGATTTCATCATCAGCTTTGG 59.931 47.826 0.00 0.00 0.00 3.28
3847 4361 3.956199 GGGATTTCATCATCAGCTTTGGA 59.044 43.478 0.00 0.00 0.00 3.53
3858 4372 2.157738 CAGCTTTGGAGAAACCTCTGG 58.842 52.381 0.00 0.00 39.86 3.86
3870 4384 2.286523 CCTCTGGGACGAGCAACCT 61.287 63.158 0.00 0.00 33.58 3.50
3871 4385 1.079543 CTCTGGGACGAGCAACCTG 60.080 63.158 0.00 0.00 0.00 4.00
3872 4386 2.046892 CTGGGACGAGCAACCTGG 60.047 66.667 0.00 0.00 0.00 4.45
3873 4387 2.525629 TGGGACGAGCAACCTGGA 60.526 61.111 0.00 0.00 0.00 3.86
3874 4388 2.266055 GGGACGAGCAACCTGGAG 59.734 66.667 0.00 0.00 0.00 3.86
3875 4389 2.266055 GGACGAGCAACCTGGAGG 59.734 66.667 0.00 0.00 42.17 4.30
3885 4399 3.648694 CCTGGAGGTAGGGGAAGC 58.351 66.667 0.00 0.00 34.06 3.86
3886 4400 1.306997 CCTGGAGGTAGGGGAAGCA 60.307 63.158 0.00 0.00 34.06 3.91
3887 4401 0.695803 CCTGGAGGTAGGGGAAGCAT 60.696 60.000 0.00 0.00 34.06 3.79
3888 4402 0.471617 CTGGAGGTAGGGGAAGCATG 59.528 60.000 0.00 0.00 0.00 4.06
3889 4403 1.149401 GGAGGTAGGGGAAGCATGC 59.851 63.158 10.51 10.51 0.00 4.06
3890 4404 1.635817 GGAGGTAGGGGAAGCATGCA 61.636 60.000 21.98 0.00 0.00 3.96
3891 4405 0.255890 GAGGTAGGGGAAGCATGCAA 59.744 55.000 21.98 0.00 0.00 4.08
3892 4406 0.929244 AGGTAGGGGAAGCATGCAAT 59.071 50.000 21.98 8.26 0.00 3.56
3907 4421 2.865343 GCAATGAGCATTCTGAAGGG 57.135 50.000 4.09 0.00 44.79 3.95
3908 4422 1.407979 GCAATGAGCATTCTGAAGGGG 59.592 52.381 4.09 0.00 44.79 4.79
3909 4423 2.029623 CAATGAGCATTCTGAAGGGGG 58.970 52.381 4.09 0.00 0.00 5.40
3942 4456 5.636543 GGATTTGATTTGAGCTGAAACAAGG 59.363 40.000 0.00 0.00 0.00 3.61
3961 4476 3.871395 GCAGAGGGGGCCTAGCTG 61.871 72.222 0.84 9.49 33.66 4.24
4017 4532 5.189180 GTCTGCACCTAGATCATTTTTCCT 58.811 41.667 0.00 0.00 0.00 3.36
4097 4612 2.381911 GTACGTGGTCCTAATCTCCCA 58.618 52.381 0.00 0.00 0.00 4.37
4141 4656 2.093658 CGTAAACTGTACCCCAGCTGAT 60.094 50.000 17.39 2.50 45.68 2.90
4148 4663 1.340399 TACCCCAGCTGATGCCTCTG 61.340 60.000 17.39 0.00 40.80 3.35
4163 4678 2.113774 CTGGTGCTGCTGGTGGAA 59.886 61.111 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.765182 CCCTCCTGTGTATATTTGTCAATCC 59.235 44.000 0.00 0.00 0.00 3.01
1 2 6.357367 ACCCTCCTGTGTATATTTGTCAATC 58.643 40.000 0.00 0.00 0.00 2.67
2 3 6.158695 AGACCCTCCTGTGTATATTTGTCAAT 59.841 38.462 0.00 0.00 0.00 2.57
3 4 5.487488 AGACCCTCCTGTGTATATTTGTCAA 59.513 40.000 0.00 0.00 0.00 3.18
4 5 5.030147 AGACCCTCCTGTGTATATTTGTCA 58.970 41.667 0.00 0.00 0.00 3.58
5 6 5.360591 CAGACCCTCCTGTGTATATTTGTC 58.639 45.833 0.00 0.00 0.00 3.18
6 7 4.164221 CCAGACCCTCCTGTGTATATTTGT 59.836 45.833 0.00 0.00 32.43 2.83
7 8 4.408921 TCCAGACCCTCCTGTGTATATTTG 59.591 45.833 0.00 0.00 32.43 2.32
8 9 4.631234 TCCAGACCCTCCTGTGTATATTT 58.369 43.478 0.00 0.00 32.43 1.40
9 10 4.280789 TCCAGACCCTCCTGTGTATATT 57.719 45.455 0.00 0.00 32.43 1.28
10 11 3.993658 TCCAGACCCTCCTGTGTATAT 57.006 47.619 0.00 0.00 32.43 0.86
11 12 3.769189 TTCCAGACCCTCCTGTGTATA 57.231 47.619 0.00 0.00 32.43 1.47
12 13 2.642171 TTCCAGACCCTCCTGTGTAT 57.358 50.000 0.00 0.00 32.43 2.29
13 14 2.409064 TTTCCAGACCCTCCTGTGTA 57.591 50.000 0.00 0.00 32.43 2.90
14 15 1.747444 ATTTCCAGACCCTCCTGTGT 58.253 50.000 0.00 0.00 32.43 3.72
15 16 4.510167 ATTATTTCCAGACCCTCCTGTG 57.490 45.455 0.00 0.00 32.43 3.66
16 17 5.510430 GAAATTATTTCCAGACCCTCCTGT 58.490 41.667 6.42 0.00 33.56 4.00
17 18 4.576463 CGAAATTATTTCCAGACCCTCCTG 59.424 45.833 11.53 0.00 36.30 3.86
18 19 4.781934 CGAAATTATTTCCAGACCCTCCT 58.218 43.478 11.53 0.00 36.30 3.69
19 20 3.315470 GCGAAATTATTTCCAGACCCTCC 59.685 47.826 11.53 0.00 36.30 4.30
20 21 3.315470 GGCGAAATTATTTCCAGACCCTC 59.685 47.826 11.53 0.00 36.30 4.30
21 22 3.053619 AGGCGAAATTATTTCCAGACCCT 60.054 43.478 11.53 7.19 36.30 4.34
22 23 3.288092 AGGCGAAATTATTTCCAGACCC 58.712 45.455 11.53 5.37 36.30 4.46
23 24 4.035675 CAGAGGCGAAATTATTTCCAGACC 59.964 45.833 11.53 8.35 36.30 3.85
24 25 4.496507 GCAGAGGCGAAATTATTTCCAGAC 60.497 45.833 11.53 1.76 36.30 3.51
25 26 3.627577 GCAGAGGCGAAATTATTTCCAGA 59.372 43.478 11.53 0.00 36.30 3.86
26 27 3.243201 GGCAGAGGCGAAATTATTTCCAG 60.243 47.826 11.53 0.93 42.47 3.86
27 28 2.687935 GGCAGAGGCGAAATTATTTCCA 59.312 45.455 11.53 0.00 42.47 3.53
28 29 2.952310 AGGCAGAGGCGAAATTATTTCC 59.048 45.455 11.53 5.18 42.47 3.13
29 30 3.793465 GCAGGCAGAGGCGAAATTATTTC 60.793 47.826 7.56 7.56 42.47 2.17
30 31 2.099756 GCAGGCAGAGGCGAAATTATTT 59.900 45.455 0.00 0.00 42.47 1.40
31 32 1.678101 GCAGGCAGAGGCGAAATTATT 59.322 47.619 0.00 0.00 42.47 1.40
32 33 1.312815 GCAGGCAGAGGCGAAATTAT 58.687 50.000 0.00 0.00 42.47 1.28
33 34 2.780595 GCAGGCAGAGGCGAAATTA 58.219 52.632 0.00 0.00 42.47 1.40
34 35 3.595819 GCAGGCAGAGGCGAAATT 58.404 55.556 0.00 0.00 42.47 1.82
128 129 4.513519 GGGAACGCGATGTGATCA 57.486 55.556 15.93 0.00 0.00 2.92
352 366 2.438075 CCTCTGCTTCAGCTGCCC 60.438 66.667 9.47 0.00 42.66 5.36
424 439 1.811266 GCCAGCGACACGATGTGAT 60.811 57.895 3.61 0.00 41.89 3.06
620 1015 2.984562 TCCACATCGGTAGTACGTACA 58.015 47.619 26.55 10.68 35.57 2.90
675 1070 6.541641 CCTAGGTGATTTTGGAGAGAATTGAG 59.458 42.308 0.00 0.00 0.00 3.02
701 1096 7.305474 ACTTTGCAAAACCGTATAAATCTCAG 58.695 34.615 13.84 0.00 0.00 3.35
758 1153 5.865085 TCCTTAATGGATCAATAACCTCCG 58.135 41.667 0.00 0.00 40.56 4.63
761 1156 7.654287 ATCCTCCTTAATGGATCAATAACCT 57.346 36.000 0.00 0.00 45.16 3.50
792 1187 8.661345 ACTGAAGAAGAAAGTATAGTTTTCCCT 58.339 33.333 6.99 2.58 35.62 4.20
889 1284 5.503662 TTCCTTAACTTCGGTTGGTTTTC 57.496 39.130 0.00 0.00 38.76 2.29
923 1318 1.217882 CGATTTGATCTGCCCCGTAC 58.782 55.000 0.00 0.00 0.00 3.67
985 1380 4.227134 CATCCTGCTCCCGTCCGG 62.227 72.222 0.00 0.00 0.00 5.14
1291 1686 4.752879 GCGCGGCTTGAGGGTGTA 62.753 66.667 8.83 0.00 0.00 2.90
1432 1838 5.405935 TGCAGTTTCAGAATAGCTACTGA 57.594 39.130 13.86 10.77 40.66 3.41
1453 1864 3.058085 TGCGTATGCCATTTGCTGATATG 60.058 43.478 4.05 0.00 41.78 1.78
1454 1865 3.148412 TGCGTATGCCATTTGCTGATAT 58.852 40.909 4.05 0.00 41.78 1.63
1484 1895 7.334421 GGTCAAGATGAGTGCTTAATCAGTTAA 59.666 37.037 0.00 0.00 0.00 2.01
1485 1896 6.818644 GGTCAAGATGAGTGCTTAATCAGTTA 59.181 38.462 0.00 0.00 0.00 2.24
1486 1897 5.645497 GGTCAAGATGAGTGCTTAATCAGTT 59.355 40.000 0.00 0.00 0.00 3.16
1487 1898 5.046014 AGGTCAAGATGAGTGCTTAATCAGT 60.046 40.000 0.00 0.00 0.00 3.41
1488 1899 5.293814 CAGGTCAAGATGAGTGCTTAATCAG 59.706 44.000 0.00 0.00 0.00 2.90
1518 1929 3.558931 ACGCATCACCTATCCATTTCA 57.441 42.857 0.00 0.00 0.00 2.69
1525 1936 1.328680 CAGTGCAACGCATCACCTATC 59.671 52.381 0.00 0.00 45.86 2.08
1541 1952 4.084223 GCTTTCAATTCCAATGCAACAGTG 60.084 41.667 0.00 0.00 0.00 3.66
1552 1963 4.405358 AGGTTGTTTGAGCTTTCAATTCCA 59.595 37.500 0.00 0.00 0.00 3.53
1714 2126 1.280998 TCAAGGGTTACTTAGCAGCCC 59.719 52.381 0.00 0.00 37.29 5.19
1725 2137 2.180276 GCCTCTGAGTCTCAAGGGTTA 58.820 52.381 22.25 1.14 30.50 2.85
1733 2145 0.817013 CACTGGAGCCTCTGAGTCTC 59.183 60.000 7.17 7.17 0.00 3.36
1774 2186 0.768221 TGAGAAGACTGGGGTTGCCT 60.768 55.000 0.00 0.00 0.00 4.75
1837 2249 6.603201 CGGGGTATCCTACGTTAATAAGGATA 59.397 42.308 16.64 16.64 46.10 2.59
1845 2257 2.091885 AGACCGGGGTATCCTACGTTAA 60.092 50.000 6.32 0.00 0.00 2.01
1846 2258 1.494721 AGACCGGGGTATCCTACGTTA 59.505 52.381 6.32 0.00 0.00 3.18
1847 2259 0.259938 AGACCGGGGTATCCTACGTT 59.740 55.000 6.32 0.00 0.00 3.99
1890 2302 1.082756 GCGTCACGGCAAACTGAAG 60.083 57.895 0.00 0.00 0.00 3.02
1902 2314 1.263776 CTCACTGAATCTCGCGTCAC 58.736 55.000 5.77 0.00 0.00 3.67
1931 2343 6.507023 AGAGCTACTTGTTTGGTCAATTTTG 58.493 36.000 0.00 0.00 30.73 2.44
2003 2415 1.078759 CGCGGGTCAAGATGAGTGTC 61.079 60.000 0.00 0.00 0.00 3.67
2019 2431 2.046283 TCGCCTATTCATTAGTCGCG 57.954 50.000 0.00 0.00 38.90 5.87
2116 2560 8.837389 GGTCACTGAAATAGTAAAAGAACTGTT 58.163 33.333 0.00 0.00 37.60 3.16
2125 2569 8.098912 GGACTTTAGGGTCACTGAAATAGTAAA 58.901 37.037 0.00 0.00 37.60 2.01
2191 2636 1.350351 ACCTGCTCAACTGCTCTGAAT 59.650 47.619 0.00 0.00 0.00 2.57
2243 2688 5.770162 CCTAAAAACAGGAGAAGGTCAACAT 59.230 40.000 0.00 0.00 38.00 2.71
2246 2691 4.167307 ACCCTAAAAACAGGAGAAGGTCAA 59.833 41.667 0.00 0.00 38.00 3.18
2306 2751 6.884832 TCGGATGAAAAGTAGTGGTAATGAT 58.115 36.000 0.00 0.00 0.00 2.45
2357 2802 3.003482 CGAACGGAGGGAGTACTAATCTG 59.997 52.174 0.00 2.06 0.00 2.90
2364 2809 1.109609 ATTCCGAACGGAGGGAGTAC 58.890 55.000 15.34 0.00 46.06 2.73
2365 2810 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
2366 2811 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
2367 2812 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2368 2813 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2369 2814 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2370 2815 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2371 2816 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
2372 2817 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
2373 2818 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
2374 2819 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
2375 2820 2.991190 TCTGCGACAAGTAATTCCGAAC 59.009 45.455 0.00 0.00 0.00 3.95
2376 2821 3.306917 TCTGCGACAAGTAATTCCGAA 57.693 42.857 0.00 0.00 0.00 4.30
2377 2822 3.306917 TTCTGCGACAAGTAATTCCGA 57.693 42.857 0.00 0.00 0.00 4.55
2378 2823 4.600012 ATTTCTGCGACAAGTAATTCCG 57.400 40.909 0.00 0.00 0.00 4.30
2379 2824 6.903883 TCTATTTCTGCGACAAGTAATTCC 57.096 37.500 0.00 0.00 0.00 3.01
2380 2825 7.910304 ACATCTATTTCTGCGACAAGTAATTC 58.090 34.615 0.00 0.00 0.00 2.17
2381 2826 7.849804 ACATCTATTTCTGCGACAAGTAATT 57.150 32.000 0.00 0.00 0.00 1.40
2382 2827 9.197694 GATACATCTATTTCTGCGACAAGTAAT 57.802 33.333 0.00 0.00 0.00 1.89
2383 2828 8.414003 AGATACATCTATTTCTGCGACAAGTAA 58.586 33.333 0.00 0.00 34.85 2.24
2384 2829 7.862873 CAGATACATCTATTTCTGCGACAAGTA 59.137 37.037 0.00 0.00 34.85 2.24
2385 2830 6.699204 CAGATACATCTATTTCTGCGACAAGT 59.301 38.462 0.00 0.00 34.85 3.16
2386 2831 6.145209 CCAGATACATCTATTTCTGCGACAAG 59.855 42.308 0.00 0.00 35.38 3.16
2387 2832 5.985530 CCAGATACATCTATTTCTGCGACAA 59.014 40.000 0.00 0.00 35.38 3.18
2388 2833 5.301805 TCCAGATACATCTATTTCTGCGACA 59.698 40.000 0.00 0.00 35.38 4.35
2389 2834 5.773575 TCCAGATACATCTATTTCTGCGAC 58.226 41.667 0.00 0.00 35.38 5.19
2390 2835 6.015095 ACATCCAGATACATCTATTTCTGCGA 60.015 38.462 0.00 0.00 35.38 5.10
2391 2836 6.162079 ACATCCAGATACATCTATTTCTGCG 58.838 40.000 0.00 0.00 35.38 5.18
2392 2837 9.664332 AATACATCCAGATACATCTATTTCTGC 57.336 33.333 0.00 0.00 35.38 4.26
2418 2863 9.749340 TCGGATATGGATGTATCTAGAACTAAA 57.251 33.333 0.00 0.00 32.78 1.85
2419 2864 9.397280 CTCGGATATGGATGTATCTAGAACTAA 57.603 37.037 0.00 0.00 32.78 2.24
2420 2865 8.769359 TCTCGGATATGGATGTATCTAGAACTA 58.231 37.037 0.00 0.00 32.78 2.24
2421 2866 7.554835 GTCTCGGATATGGATGTATCTAGAACT 59.445 40.741 0.00 0.00 31.35 3.01
2422 2867 7.337184 TGTCTCGGATATGGATGTATCTAGAAC 59.663 40.741 0.00 0.00 31.35 3.01
2423 2868 7.402862 TGTCTCGGATATGGATGTATCTAGAA 58.597 38.462 0.00 0.00 31.35 2.10
2424 2869 6.958767 TGTCTCGGATATGGATGTATCTAGA 58.041 40.000 0.00 0.00 32.78 2.43
2425 2870 7.338196 ACTTGTCTCGGATATGGATGTATCTAG 59.662 40.741 0.00 0.00 32.78 2.43
2426 2871 7.175797 ACTTGTCTCGGATATGGATGTATCTA 58.824 38.462 0.00 0.00 32.78 1.98
2427 2872 6.013379 ACTTGTCTCGGATATGGATGTATCT 58.987 40.000 0.00 0.00 32.78 1.98
2428 2873 6.274157 ACTTGTCTCGGATATGGATGTATC 57.726 41.667 0.00 0.00 0.00 2.24
2429 2874 7.776618 TTACTTGTCTCGGATATGGATGTAT 57.223 36.000 0.00 0.00 0.00 2.29
2430 2875 7.776618 ATTACTTGTCTCGGATATGGATGTA 57.223 36.000 0.00 0.00 0.00 2.29
2431 2876 6.672266 ATTACTTGTCTCGGATATGGATGT 57.328 37.500 0.00 0.00 0.00 3.06
2432 2877 6.591834 GGAATTACTTGTCTCGGATATGGATG 59.408 42.308 0.00 0.00 0.00 3.51
2433 2878 6.572509 CGGAATTACTTGTCTCGGATATGGAT 60.573 42.308 0.00 0.00 0.00 3.41
2434 2879 5.278808 CGGAATTACTTGTCTCGGATATGGA 60.279 44.000 0.00 0.00 0.00 3.41
2435 2880 4.923871 CGGAATTACTTGTCTCGGATATGG 59.076 45.833 0.00 0.00 0.00 2.74
2436 2881 5.769367 TCGGAATTACTTGTCTCGGATATG 58.231 41.667 0.00 0.00 0.00 1.78
2437 2882 6.214399 GTTCGGAATTACTTGTCTCGGATAT 58.786 40.000 0.00 0.00 0.00 1.63
2438 2883 5.585390 GTTCGGAATTACTTGTCTCGGATA 58.415 41.667 0.00 0.00 0.00 2.59
2439 2884 4.430908 GTTCGGAATTACTTGTCTCGGAT 58.569 43.478 0.00 0.00 0.00 4.18
2440 2885 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
2441 2886 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
2442 2887 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
2443 2888 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
2444 2889 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
2445 2890 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2446 2891 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2447 2892 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2448 2893 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2449 2894 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2450 2895 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2451 2896 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2452 2897 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
2453 2898 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
2454 2899 1.856629 AATACTCCCTCCGTTCGGAA 58.143 50.000 14.79 0.00 33.41 4.30
2455 2900 1.753073 GAAATACTCCCTCCGTTCGGA 59.247 52.381 13.34 13.34 0.00 4.55
2456 2901 1.755380 AGAAATACTCCCTCCGTTCGG 59.245 52.381 4.74 4.74 0.00 4.30
2457 2902 2.426024 TGAGAAATACTCCCTCCGTTCG 59.574 50.000 0.00 0.00 44.34 3.95
2458 2903 3.700038 TCTGAGAAATACTCCCTCCGTTC 59.300 47.826 0.00 0.00 44.34 3.95
2459 2904 3.709587 TCTGAGAAATACTCCCTCCGTT 58.290 45.455 0.00 0.00 44.34 4.44
2460 2905 3.383698 TCTGAGAAATACTCCCTCCGT 57.616 47.619 0.00 0.00 44.34 4.69
2461 2906 3.491792 GCTTCTGAGAAATACTCCCTCCG 60.492 52.174 0.00 0.00 44.34 4.63
2462 2907 3.452627 TGCTTCTGAGAAATACTCCCTCC 59.547 47.826 0.00 0.00 44.34 4.30
2463 2908 4.744795 TGCTTCTGAGAAATACTCCCTC 57.255 45.455 0.00 0.00 44.34 4.30
2464 2909 4.323868 GGTTGCTTCTGAGAAATACTCCCT 60.324 45.833 0.00 0.00 44.34 4.20
2465 2910 3.942115 GGTTGCTTCTGAGAAATACTCCC 59.058 47.826 0.00 0.00 44.34 4.30
2466 2911 4.633565 CAGGTTGCTTCTGAGAAATACTCC 59.366 45.833 0.00 0.00 44.34 3.85
2467 2912 4.633565 CCAGGTTGCTTCTGAGAAATACTC 59.366 45.833 0.00 0.00 45.11 2.59
2701 3153 4.785341 GCAACAACACAAGTTCTCTTACCG 60.785 45.833 0.00 0.00 35.28 4.02
2738 3190 3.740631 TTCGTCATCATCCTGATCCAG 57.259 47.619 0.00 0.00 34.28 3.86
2809 3320 6.665680 ACTAGACTGAGATACATGACCAAACT 59.334 38.462 0.00 0.00 0.00 2.66
3278 3789 2.032680 ACACAACACCCAGTGTACAC 57.967 50.000 18.56 18.56 46.79 2.90
3360 3871 6.415867 GTGATGACAATAAGATTTTCCATGCG 59.584 38.462 0.00 0.00 0.00 4.73
3411 3922 8.818057 CACAAGTAGAAGTATGGCTATACAAAC 58.182 37.037 20.78 12.61 41.33 2.93
3456 3968 4.819630 TGATGTGAGTACAGTTTTTGGACC 59.180 41.667 0.00 0.00 42.01 4.46
3539 4051 0.179179 ACCTACGACGAAGCTAACGC 60.179 55.000 0.00 5.68 0.00 4.84
3569 4082 4.627467 ACAAGACGTAAGATCAACATCAGC 59.373 41.667 0.00 0.00 43.62 4.26
3585 4098 3.303395 GCCTGAAAACAGAGAACAAGACG 60.303 47.826 0.00 0.00 0.00 4.18
3627 4140 0.024746 CTAGTCTCGGTTCGTCGTCG 59.975 60.000 0.00 0.00 38.55 5.12
3819 4333 3.554934 CTGATGATGAAATCCCCCGAAA 58.445 45.455 0.00 0.00 44.73 3.46
3824 4338 3.069158 CCAAAGCTGATGATGAAATCCCC 59.931 47.826 1.45 0.00 44.73 4.81
3844 4358 0.178944 TCGTCCCAGAGGTTTCTCCA 60.179 55.000 0.00 0.00 40.83 3.86
3846 4360 0.108567 GCTCGTCCCAGAGGTTTCTC 60.109 60.000 0.00 0.00 38.63 2.87
3847 4361 0.832135 TGCTCGTCCCAGAGGTTTCT 60.832 55.000 0.00 0.00 38.63 2.52
3858 4372 2.266055 CCTCCAGGTTGCTCGTCC 59.734 66.667 0.00 0.00 0.00 4.79
3870 4384 1.635817 GCATGCTTCCCCTACCTCCA 61.636 60.000 11.37 0.00 0.00 3.86
3871 4385 1.149401 GCATGCTTCCCCTACCTCC 59.851 63.158 11.37 0.00 0.00 4.30
3872 4386 0.255890 TTGCATGCTTCCCCTACCTC 59.744 55.000 20.33 0.00 0.00 3.85
3873 4387 0.929244 ATTGCATGCTTCCCCTACCT 59.071 50.000 20.33 0.00 0.00 3.08
3874 4388 1.035139 CATTGCATGCTTCCCCTACC 58.965 55.000 20.33 0.00 0.00 3.18
3875 4389 1.952296 CTCATTGCATGCTTCCCCTAC 59.048 52.381 20.33 0.00 0.00 3.18
3876 4390 1.751733 GCTCATTGCATGCTTCCCCTA 60.752 52.381 20.33 0.00 42.31 3.53
3877 4391 1.041447 GCTCATTGCATGCTTCCCCT 61.041 55.000 20.33 0.00 42.31 4.79
3878 4392 1.440476 GCTCATTGCATGCTTCCCC 59.560 57.895 20.33 0.00 42.31 4.81
3888 4402 1.407979 CCCCTTCAGAATGCTCATTGC 59.592 52.381 0.00 0.00 43.25 3.56
3889 4403 2.029623 CCCCCTTCAGAATGCTCATTG 58.970 52.381 0.00 0.00 34.76 2.82
3890 4404 1.925255 TCCCCCTTCAGAATGCTCATT 59.075 47.619 0.00 0.00 34.76 2.57
3891 4405 1.600058 TCCCCCTTCAGAATGCTCAT 58.400 50.000 0.00 0.00 34.76 2.90
3892 4406 1.004745 GTTCCCCCTTCAGAATGCTCA 59.995 52.381 0.00 0.00 34.76 4.26
3893 4407 1.756430 GTTCCCCCTTCAGAATGCTC 58.244 55.000 0.00 0.00 34.76 4.26
3894 4408 0.035056 CGTTCCCCCTTCAGAATGCT 60.035 55.000 0.00 0.00 34.76 3.79
3895 4409 0.322546 ACGTTCCCCCTTCAGAATGC 60.323 55.000 0.00 0.00 33.20 3.56
3896 4410 1.271379 ACACGTTCCCCCTTCAGAATG 60.271 52.381 0.00 0.00 35.54 2.67
3897 4411 1.064825 ACACGTTCCCCCTTCAGAAT 58.935 50.000 0.00 0.00 0.00 2.40
3898 4412 0.841289 AACACGTTCCCCCTTCAGAA 59.159 50.000 0.00 0.00 0.00 3.02
3899 4413 0.107831 CAACACGTTCCCCCTTCAGA 59.892 55.000 0.00 0.00 0.00 3.27
3900 4414 0.889186 CCAACACGTTCCCCCTTCAG 60.889 60.000 0.00 0.00 0.00 3.02
3901 4415 1.149627 CCAACACGTTCCCCCTTCA 59.850 57.895 0.00 0.00 0.00 3.02
3902 4416 0.037734 ATCCAACACGTTCCCCCTTC 59.962 55.000 0.00 0.00 0.00 3.46
3903 4417 0.481128 AATCCAACACGTTCCCCCTT 59.519 50.000 0.00 0.00 0.00 3.95
3904 4418 0.481128 AAATCCAACACGTTCCCCCT 59.519 50.000 0.00 0.00 0.00 4.79
3905 4419 0.601057 CAAATCCAACACGTTCCCCC 59.399 55.000 0.00 0.00 0.00 5.40
3906 4420 1.611519 TCAAATCCAACACGTTCCCC 58.388 50.000 0.00 0.00 0.00 4.81
3907 4421 3.934457 AATCAAATCCAACACGTTCCC 57.066 42.857 0.00 0.00 0.00 3.97
3908 4422 4.865776 TCAAATCAAATCCAACACGTTCC 58.134 39.130 0.00 0.00 0.00 3.62
3909 4423 4.382754 GCTCAAATCAAATCCAACACGTTC 59.617 41.667 0.00 0.00 0.00 3.95
3961 4476 0.318762 GATCAGACCTACCGATGCCC 59.681 60.000 0.00 0.00 0.00 5.36
4017 4532 2.912771 TCTGCTGACACGAAAAAGGAA 58.087 42.857 0.00 0.00 0.00 3.36
4061 4576 3.709880 TACGGCCCTTGATGACGCG 62.710 63.158 3.53 3.53 0.00 6.01
4097 4612 4.298332 CTGAGGTTTTGCAAATAAAGCGT 58.702 39.130 13.65 3.33 37.88 5.07
4141 4656 4.340246 CCAGCAGCACCAGAGGCA 62.340 66.667 0.00 0.00 0.00 4.75
4148 4663 3.357079 CGTTCCACCAGCAGCACC 61.357 66.667 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.