Multiple sequence alignment - TraesCS4A01G104200

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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 TraesCS4A01G104200 chr4A 100.000 2466 0 0 1 2466 117699318 117701783 0.000000e+00 4554.0
1 TraesCS4A01G104200 chr4A 85.269 1670 179 36 394 2040 629935512 629937137 0.000000e+00 1659.0
2 TraesCS4A01G104200 chr4A 85.312 497 45 15 154 647 629935137 629935608 2.850000e-134 488.0
3 TraesCS4A01G104200 chr4D 89.760 1914 157 19 441 2321 348041285 348039378 0.000000e+00 2412.0
4 TraesCS4A01G104200 chr4D 87.463 1364 124 23 693 2041 145379903 145378572 0.000000e+00 1528.0
5 TraesCS4A01G104200 chr4D 86.545 550 55 11 37 568 348041625 348041077 2.730000e-164 588.0
6 TraesCS4A01G104200 chr5D 86.349 1912 170 45 154 2043 538686799 538688641 0.000000e+00 2001.0
7 TraesCS4A01G104200 chr5D 84.643 1667 182 38 394 2010 420019256 420020898 0.000000e+00 1592.0
8 TraesCS4A01G104200 chr5D 88.581 289 31 1 1755 2043 560208427 560208713 1.400000e-92 350.0
9 TraesCS4A01G104200 chr5D 89.732 224 18 3 426 647 420019209 420019429 5.190000e-72 281.0
10 TraesCS4A01G104200 chr4B 88.869 1635 144 16 714 2321 428196687 428195064 0.000000e+00 1977.0
11 TraesCS4A01G104200 chr4B 84.126 1682 207 45 394 2040 449518669 449520325 0.000000e+00 1572.0
12 TraesCS4A01G104200 chr4B 88.503 748 55 12 1307 2042 413506962 413506234 0.000000e+00 876.0
13 TraesCS4A01G104200 chr4B 86.551 632 62 14 37 647 428198547 428197918 0.000000e+00 675.0
14 TraesCS4A01G104200 chr4B 88.959 317 32 2 406 719 428197921 428197605 2.970000e-104 388.0
15 TraesCS4A01G104200 chr4B 87.209 258 27 5 394 645 428198016 428197759 3.100000e-74 289.0
16 TraesCS4A01G104200 chr3D 86.142 1638 173 29 426 2042 339817077 339818681 0.000000e+00 1718.0
17 TraesCS4A01G104200 chr2B 85.192 1668 195 25 409 2043 54562881 54561233 0.000000e+00 1664.0
18 TraesCS4A01G104200 chr6A 84.574 1692 195 31 402 2040 571574660 571576338 0.000000e+00 1618.0
19 TraesCS4A01G104200 chr6A 83.990 406 45 7 1654 2043 554477591 554477992 3.000000e-99 372.0
20 TraesCS4A01G104200 chr1A 88.065 1039 104 9 626 1656 80283674 80282648 0.000000e+00 1214.0
21 TraesCS4A01G104200 chr1A 85.124 484 41 18 154 633 80284156 80283700 1.340000e-127 466.0
22 TraesCS4A01G104200 chr1B 85.335 1016 106 20 1060 2043 400360012 400361016 0.000000e+00 1011.0
23 TraesCS4A01G104200 chr3B 85.494 779 73 17 1294 2041 576053728 576052959 0.000000e+00 776.0
24 TraesCS4A01G104200 chr1D 84.190 759 74 24 154 904 80674338 80675058 0.000000e+00 695.0
25 TraesCS4A01G104200 chr5A 86.290 496 40 14 154 647 78449079 78449548 4.700000e-142 514.0
26 TraesCS4A01G104200 chr7A 85.915 497 42 15 154 647 62735855 62736326 2.830000e-139 505.0
27 TraesCS4A01G104200 chr7A 84.507 426 43 8 1636 2043 211154131 211154551 1.370000e-107 399.0
28 TraesCS4A01G104200 chr7A 91.034 290 25 1 1754 2043 519475821 519475533 8.270000e-105 390.0
29 TraesCS4A01G104200 chr7A 89.105 257 25 2 394 647 297784918 297784662 1.420000e-82 316.0
30 TraesCS4A01G104200 chr7A 89.732 224 21 1 426 647 297784965 297784742 4.010000e-73 285.0
31 TraesCS4A01G104200 chr6B 86.947 452 43 6 154 590 672729425 672729875 6.130000e-136 494.0
32 TraesCS4A01G104200 chrUn 74.704 253 42 20 2229 2466 13667219 13666974 2.610000e-15 93.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G104200 chr4A 117699318 117701783 2465 False 4554.00 4554 100.0000 1 2466 1 chr4A.!!$F1 2465
1 TraesCS4A01G104200 chr4A 629935137 629937137 2000 False 1073.50 1659 85.2905 154 2040 2 chr4A.!!$F2 1886
2 TraesCS4A01G104200 chr4D 145378572 145379903 1331 True 1528.00 1528 87.4630 693 2041 1 chr4D.!!$R1 1348
3 TraesCS4A01G104200 chr4D 348039378 348041625 2247 True 1500.00 2412 88.1525 37 2321 2 chr4D.!!$R2 2284
4 TraesCS4A01G104200 chr5D 538686799 538688641 1842 False 2001.00 2001 86.3490 154 2043 1 chr5D.!!$F1 1889
5 TraesCS4A01G104200 chr5D 420019209 420020898 1689 False 936.50 1592 87.1875 394 2010 2 chr5D.!!$F3 1616
6 TraesCS4A01G104200 chr4B 449518669 449520325 1656 False 1572.00 1572 84.1260 394 2040 1 chr4B.!!$F1 1646
7 TraesCS4A01G104200 chr4B 413506234 413506962 728 True 876.00 876 88.5030 1307 2042 1 chr4B.!!$R1 735
8 TraesCS4A01G104200 chr4B 428195064 428198547 3483 True 832.25 1977 87.8970 37 2321 4 chr4B.!!$R2 2284
9 TraesCS4A01G104200 chr3D 339817077 339818681 1604 False 1718.00 1718 86.1420 426 2042 1 chr3D.!!$F1 1616
10 TraesCS4A01G104200 chr2B 54561233 54562881 1648 True 1664.00 1664 85.1920 409 2043 1 chr2B.!!$R1 1634
11 TraesCS4A01G104200 chr6A 571574660 571576338 1678 False 1618.00 1618 84.5740 402 2040 1 chr6A.!!$F2 1638
12 TraesCS4A01G104200 chr1A 80282648 80284156 1508 True 840.00 1214 86.5945 154 1656 2 chr1A.!!$R1 1502
13 TraesCS4A01G104200 chr1B 400360012 400361016 1004 False 1011.00 1011 85.3350 1060 2043 1 chr1B.!!$F1 983
14 TraesCS4A01G104200 chr3B 576052959 576053728 769 True 776.00 776 85.4940 1294 2041 1 chr3B.!!$R1 747
15 TraesCS4A01G104200 chr1D 80674338 80675058 720 False 695.00 695 84.1900 154 904 1 chr1D.!!$F1 750

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
30 31 0.107268 AAGCCGACCTTTTACCACGT 59.893 50.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 3363 0.801067 GAATGGGTCGGTTCGAGTCG 60.801 60.0 6.09 6.09 36.23 4.18 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
27 28 2.500229 CTGAAAGCCGACCTTTTACCA 58.500 47.619 3.17 0.00 43.64 3.25
28 29 2.223745 TGAAAGCCGACCTTTTACCAC 58.776 47.619 3.17 0.00 43.64 4.16
29 30 1.196127 GAAAGCCGACCTTTTACCACG 59.804 52.381 3.17 0.00 43.64 4.94
30 31 0.107268 AAGCCGACCTTTTACCACGT 59.893 50.000 0.00 0.00 0.00 4.49
31 32 0.320160 AGCCGACCTTTTACCACGTC 60.320 55.000 0.00 0.00 0.00 4.34
32 33 1.620413 GCCGACCTTTTACCACGTCG 61.620 60.000 0.00 0.00 45.79 5.12
33 34 1.620413 CCGACCTTTTACCACGTCGC 61.620 60.000 3.06 0.00 45.08 5.19
34 35 1.777199 GACCTTTTACCACGTCGCG 59.223 57.895 0.00 0.00 0.00 5.87
37 38 1.129809 CTTTTACCACGTCGCGCAG 59.870 57.895 8.75 0.00 0.00 5.18
38 39 1.279527 CTTTTACCACGTCGCGCAGA 61.280 55.000 8.75 2.49 0.00 4.26
39 40 0.875040 TTTTACCACGTCGCGCAGAA 60.875 50.000 8.75 0.00 0.00 3.02
41 42 0.668096 TTACCACGTCGCGCAGAATT 60.668 50.000 8.75 0.00 0.00 2.17
69 70 1.353091 AGTCCTTGTCCTCCTTCACC 58.647 55.000 0.00 0.00 0.00 4.02
84 85 1.191489 TCACCTCCGGTCATCAAGCA 61.191 55.000 0.00 0.00 31.02 3.91
85 86 1.021390 CACCTCCGGTCATCAAGCAC 61.021 60.000 0.00 0.00 31.02 4.40
106 107 2.220586 TCCACCATCGGCCTCAACA 61.221 57.895 0.00 0.00 0.00 3.33
107 108 1.303236 CCACCATCGGCCTCAACAA 60.303 57.895 0.00 0.00 0.00 2.83
114 115 0.892755 TCGGCCTCAACAACGACTAT 59.107 50.000 0.00 0.00 0.00 2.12
126 127 6.929049 TCAACAACGACTATCTCTTCACAAAT 59.071 34.615 0.00 0.00 0.00 2.32
138 139 7.979444 TCTCTTCACAAATTCTTATTCGGTT 57.021 32.000 0.00 0.00 0.00 4.44
145 146 7.444183 TCACAAATTCTTATTCGGTTGACTCTT 59.556 33.333 0.00 0.00 0.00 2.85
245 246 0.253044 CCGGAAGTGACATGGACCAT 59.747 55.000 0.00 0.00 0.00 3.55
248 249 1.656652 GAAGTGACATGGACCATCCG 58.343 55.000 3.21 0.00 40.17 4.18
292 294 1.717032 AGCAAGTGACACTAGGGTCA 58.283 50.000 24.06 24.06 45.06 4.02
321 323 1.743772 CGTAGGCTACAAATGGCAGCT 60.744 52.381 23.46 0.00 35.60 4.24
322 324 1.672881 GTAGGCTACAAATGGCAGCTG 59.327 52.381 19.55 10.11 35.60 4.24
332 334 0.901114 ATGGCAGCTGCAAATGTGGA 60.901 50.000 37.63 12.35 44.36 4.02
338 340 3.250744 CAGCTGCAAATGTGGAAAGATG 58.749 45.455 0.00 0.00 0.00 2.90
346 348 5.048083 GCAAATGTGGAAAGATGGACAACTA 60.048 40.000 0.00 0.00 0.00 2.24
414 440 2.638480 TATGGCTGGGCAGATTGTAC 57.362 50.000 2.90 0.00 0.00 2.90
424 450 4.081309 TGGGCAGATTGTACCAGTTACTAC 60.081 45.833 0.00 0.00 0.00 2.73
465 572 9.539825 TTTGTGATGTTTATGCAACTACATTTT 57.460 25.926 10.90 0.00 36.21 1.82
541 891 4.839668 TTGTGGTGTTTATGCAACTACC 57.160 40.909 0.00 0.00 37.21 3.18
549 900 6.806739 GGTGTTTATGCAACTACCTTTGAATC 59.193 38.462 0.00 0.00 35.38 2.52
562 913 8.494433 ACTACCTTTGAATCTATTTGATGGCTA 58.506 33.333 0.00 0.00 35.21 3.93
657 1010 2.555199 GATGGACAGAAATGGACTCCG 58.445 52.381 0.00 0.00 0.00 4.63
658 1085 0.613260 TGGACAGAAATGGACTCCGG 59.387 55.000 0.00 0.00 0.00 5.14
669 1096 0.395312 GGACTCCGGGAGTGTTGAAA 59.605 55.000 33.29 0.00 43.53 2.69
674 1101 1.697432 TCCGGGAGTGTTGAAATCACT 59.303 47.619 0.00 0.00 46.86 3.41
675 1102 2.901192 TCCGGGAGTGTTGAAATCACTA 59.099 45.455 0.00 0.00 44.68 2.74
684 1111 5.237344 AGTGTTGAAATCACTACTGCAAGTC 59.763 40.000 0.00 0.00 39.97 3.01
686 1113 9.972038 AGTGTTGAAATCACTACTGCAAGTCGA 62.972 40.741 0.00 0.00 39.97 4.20
718 2068 3.915073 AGAGCTGGGATCATTGTATGGAT 59.085 43.478 0.00 0.00 0.00 3.41
744 2095 2.562298 TCCATGACCAAAACCATGCTTC 59.438 45.455 0.00 0.00 38.95 3.86
746 2097 0.958091 TGACCAAAACCATGCTTCGG 59.042 50.000 0.00 0.00 0.00 4.30
807 2158 1.098050 GTGGATTCAGGGATGTGCAC 58.902 55.000 10.75 10.75 0.00 4.57
816 2167 3.200605 TCAGGGATGTGCACAATAGACAT 59.799 43.478 25.72 4.84 32.95 3.06
861 2212 0.461548 TCAAGCTAGCTGTCATCGGG 59.538 55.000 20.16 1.09 0.00 5.14
869 2220 1.281867 AGCTGTCATCGGGGATCAAAA 59.718 47.619 0.00 0.00 0.00 2.44
874 2225 2.939103 GTCATCGGGGATCAAAACAGAG 59.061 50.000 0.00 0.00 0.00 3.35
890 2241 6.672266 AAACAGAGACCATCTCAAGAAGTA 57.328 37.500 8.48 0.00 45.73 2.24
973 2330 4.455606 AGATACTTGCACAATTAGGCTCC 58.544 43.478 0.00 0.00 0.00 4.70
1039 2397 7.439056 CACCCACAAATCTAATGCCATTTTATC 59.561 37.037 0.00 0.00 0.00 1.75
1096 2455 1.607178 CCACAAAGCTGATGCCCCA 60.607 57.895 0.00 0.00 40.80 4.96
1109 2468 3.205056 TGATGCCCCATTCTTGAATACCT 59.795 43.478 0.00 0.00 0.00 3.08
1133 2492 7.881751 CCTCAATGGAATACTATCATGTCATGT 59.118 37.037 12.54 3.37 38.35 3.21
1183 2542 0.543749 GGCTGAATGCTAGGTCTGGT 59.456 55.000 0.00 0.00 42.39 4.00
1231 2590 0.250513 GCGAGGAGAATGGTGAGGTT 59.749 55.000 0.00 0.00 0.00 3.50
1237 2596 3.650942 AGGAGAATGGTGAGGTTAACACA 59.349 43.478 8.10 4.36 39.65 3.72
1302 2661 1.534729 AAGAAGGCCAAGGTAAAGCG 58.465 50.000 5.01 0.00 0.00 4.68
1359 2718 0.389025 GGGTTCAAACTTGTGGCTGG 59.611 55.000 0.00 0.00 0.00 4.85
1394 2753 6.593268 AGTCTAGTGGAGATGATGATGATG 57.407 41.667 0.00 0.00 36.29 3.07
1395 2754 6.313324 AGTCTAGTGGAGATGATGATGATGA 58.687 40.000 0.00 0.00 36.29 2.92
1396 2755 6.955267 AGTCTAGTGGAGATGATGATGATGAT 59.045 38.462 0.00 0.00 36.29 2.45
1487 2850 2.936919 TGCTCATCTTGTGGACAACT 57.063 45.000 0.00 0.00 0.00 3.16
1488 2851 3.213206 TGCTCATCTTGTGGACAACTT 57.787 42.857 0.00 0.00 0.00 2.66
1737 3117 6.705381 TGCTTTTGGAAATTTGGTATGTGAAG 59.295 34.615 0.00 0.00 0.00 3.02
1750 3130 7.418337 TGGTATGTGAAGTAGACATGTATGT 57.582 36.000 2.50 0.00 45.16 2.29
1882 3279 8.108551 TCCTGCCAAAATTTTGAATTTTATGG 57.891 30.769 28.44 17.68 40.55 2.74
1911 3308 4.599047 TTTTTCATTCCGTGCTTCCAAT 57.401 36.364 0.00 0.00 0.00 3.16
1988 3386 1.518572 CGAACCGACCCATTCCTCG 60.519 63.158 0.00 0.00 0.00 4.63
2020 3418 6.017211 ACCATTCCATTCCATGATAGTTGA 57.983 37.500 0.00 0.00 0.00 3.18
2052 3450 4.272261 CCAAACACACCCTTTATGTTTTGC 59.728 41.667 0.00 0.00 42.43 3.68
2074 3472 6.973843 TGCGTCTCTAAACTTTTACTACTCA 58.026 36.000 0.00 0.00 0.00 3.41
2151 3549 4.155462 CAGAGTTCACAGTTTGCTATGCAT 59.845 41.667 3.79 3.79 38.76 3.96
2201 3599 9.431887 TCATTACACTACTAGTTTTGATTCCAC 57.568 33.333 0.00 0.00 0.00 4.02
2205 3603 7.833786 ACACTACTAGTTTTGATTCCACGATA 58.166 34.615 0.00 0.00 0.00 2.92
2214 3612 3.864328 TGATTCCACGATATAGGGGGAA 58.136 45.455 11.32 11.32 41.47 3.97
2231 3629 2.993220 GGGAATTCGCCACAATTTCAAC 59.007 45.455 11.31 0.00 0.00 3.18
2239 3637 3.675502 CGCCACAATTTCAACATGCCATA 60.676 43.478 0.00 0.00 0.00 2.74
2329 3727 9.462606 AATGGAATCGAAATCCTTAGTTTTACT 57.537 29.630 18.27 0.00 37.85 2.24
2330 3728 8.857694 TGGAATCGAAATCCTTAGTTTTACTT 57.142 30.769 18.27 0.00 37.85 2.24
2331 3729 8.943002 TGGAATCGAAATCCTTAGTTTTACTTC 58.057 33.333 18.27 0.00 37.85 3.01
2332 3730 8.943002 GGAATCGAAATCCTTAGTTTTACTTCA 58.057 33.333 12.16 0.00 33.98 3.02
2335 3733 8.897872 TCGAAATCCTTAGTTTTACTTCAACT 57.102 30.769 0.00 0.00 38.13 3.16
2336 3734 9.333724 TCGAAATCCTTAGTTTTACTTCAACTT 57.666 29.630 0.00 0.00 35.95 2.66
2337 3735 9.946165 CGAAATCCTTAGTTTTACTTCAACTTT 57.054 29.630 0.00 0.00 35.95 2.66
2347 3745 8.347771 AGTTTTACTTCAACTTTTATTCGTCCC 58.652 33.333 0.00 0.00 29.75 4.46
2348 3746 8.347771 GTTTTACTTCAACTTTTATTCGTCCCT 58.652 33.333 0.00 0.00 0.00 4.20
2349 3747 5.941948 ACTTCAACTTTTATTCGTCCCTG 57.058 39.130 0.00 0.00 0.00 4.45
2350 3748 5.374071 ACTTCAACTTTTATTCGTCCCTGT 58.626 37.500 0.00 0.00 0.00 4.00
2351 3749 5.826208 ACTTCAACTTTTATTCGTCCCTGTT 59.174 36.000 0.00 0.00 0.00 3.16
2352 3750 5.682943 TCAACTTTTATTCGTCCCTGTTG 57.317 39.130 0.00 0.00 36.05 3.33
2353 3751 5.369833 TCAACTTTTATTCGTCCCTGTTGA 58.630 37.500 0.00 0.00 39.73 3.18
2354 3752 5.468746 TCAACTTTTATTCGTCCCTGTTGAG 59.531 40.000 0.00 0.00 37.97 3.02
2355 3753 5.223449 ACTTTTATTCGTCCCTGTTGAGA 57.777 39.130 0.00 0.00 0.00 3.27
2356 3754 4.995487 ACTTTTATTCGTCCCTGTTGAGAC 59.005 41.667 0.00 0.00 0.00 3.36
2357 3755 4.884668 TTTATTCGTCCCTGTTGAGACT 57.115 40.909 0.00 0.00 0.00 3.24
2358 3756 4.884668 TTATTCGTCCCTGTTGAGACTT 57.115 40.909 0.00 0.00 0.00 3.01
2359 3757 3.771577 ATTCGTCCCTGTTGAGACTTT 57.228 42.857 0.00 0.00 0.00 2.66
2360 3758 4.884668 ATTCGTCCCTGTTGAGACTTTA 57.115 40.909 0.00 0.00 0.00 1.85
2361 3759 4.675976 TTCGTCCCTGTTGAGACTTTAA 57.324 40.909 0.00 0.00 0.00 1.52
2362 3760 3.986277 TCGTCCCTGTTGAGACTTTAAC 58.014 45.455 0.00 0.00 0.00 2.01
2363 3761 3.064931 CGTCCCTGTTGAGACTTTAACC 58.935 50.000 0.00 0.00 0.00 2.85
2364 3762 3.493699 CGTCCCTGTTGAGACTTTAACCA 60.494 47.826 0.00 0.00 0.00 3.67
2365 3763 3.813724 GTCCCTGTTGAGACTTTAACCAC 59.186 47.826 0.00 0.00 0.00 4.16
2366 3764 3.714798 TCCCTGTTGAGACTTTAACCACT 59.285 43.478 0.00 0.00 0.00 4.00
2367 3765 4.165372 TCCCTGTTGAGACTTTAACCACTT 59.835 41.667 0.00 0.00 0.00 3.16
2368 3766 4.887655 CCCTGTTGAGACTTTAACCACTTT 59.112 41.667 0.00 0.00 0.00 2.66
2369 3767 5.359860 CCCTGTTGAGACTTTAACCACTTTT 59.640 40.000 0.00 0.00 0.00 2.27
2370 3768 6.544564 CCCTGTTGAGACTTTAACCACTTTTA 59.455 38.462 0.00 0.00 0.00 1.52
2371 3769 7.230712 CCCTGTTGAGACTTTAACCACTTTTAT 59.769 37.037 0.00 0.00 0.00 1.40
2372 3770 8.630037 CCTGTTGAGACTTTAACCACTTTTATT 58.370 33.333 0.00 0.00 0.00 1.40
2373 3771 9.450807 CTGTTGAGACTTTAACCACTTTTATTG 57.549 33.333 0.00 0.00 0.00 1.90
2374 3772 9.179909 TGTTGAGACTTTAACCACTTTTATTGA 57.820 29.630 0.00 0.00 0.00 2.57
2377 3775 9.567776 TGAGACTTTAACCACTTTTATTGATCA 57.432 29.630 0.00 0.00 0.00 2.92
2378 3776 9.827411 GAGACTTTAACCACTTTTATTGATCAC 57.173 33.333 0.00 0.00 0.00 3.06
2379 3777 8.793592 AGACTTTAACCACTTTTATTGATCACC 58.206 33.333 0.00 0.00 0.00 4.02
2380 3778 8.472007 ACTTTAACCACTTTTATTGATCACCA 57.528 30.769 0.00 0.00 0.00 4.17
2381 3779 8.919145 ACTTTAACCACTTTTATTGATCACCAA 58.081 29.630 0.00 0.00 39.41 3.67
2382 3780 9.757227 CTTTAACCACTTTTATTGATCACCAAA 57.243 29.630 0.00 0.00 38.43 3.28
2384 3782 9.757227 TTAACCACTTTTATTGATCACCAAAAG 57.243 29.630 25.50 25.50 41.54 2.27
2385 3783 6.758254 ACCACTTTTATTGATCACCAAAAGG 58.242 36.000 28.07 20.66 40.59 3.11
2386 3784 6.165577 CCACTTTTATTGATCACCAAAAGGG 58.834 40.000 28.07 26.14 40.59 3.95
2387 3785 6.014669 CCACTTTTATTGATCACCAAAAGGGA 60.015 38.462 28.68 3.25 41.70 4.20
2388 3786 7.092716 CACTTTTATTGATCACCAAAAGGGAG 58.907 38.462 28.07 19.64 41.70 4.30
2389 3787 6.782494 ACTTTTATTGATCACCAAAAGGGAGT 59.218 34.615 28.07 15.63 40.59 3.85
2390 3788 6.588719 TTTATTGATCACCAAAAGGGAGTG 57.411 37.500 0.00 0.00 41.15 3.51
2391 3789 3.874383 TTGATCACCAAAAGGGAGTGA 57.126 42.857 0.00 0.00 44.11 3.41
2395 3793 3.593442 TCACCAAAAGGGAGTGATTGT 57.407 42.857 0.00 0.00 41.15 2.71
2396 3794 4.715534 TCACCAAAAGGGAGTGATTGTA 57.284 40.909 0.00 0.00 41.15 2.41
2397 3795 5.055265 TCACCAAAAGGGAGTGATTGTAA 57.945 39.130 0.00 0.00 41.15 2.41
2398 3796 5.070001 TCACCAAAAGGGAGTGATTGTAAG 58.930 41.667 0.00 0.00 41.15 2.34
2399 3797 4.827284 CACCAAAAGGGAGTGATTGTAAGT 59.173 41.667 0.00 0.00 41.15 2.24
2400 3798 4.827284 ACCAAAAGGGAGTGATTGTAAGTG 59.173 41.667 0.00 0.00 41.15 3.16
2401 3799 4.321230 CCAAAAGGGAGTGATTGTAAGTGC 60.321 45.833 0.00 0.00 40.01 4.40
2402 3800 3.788227 AAGGGAGTGATTGTAAGTGCA 57.212 42.857 0.00 0.00 0.00 4.57
2403 3801 4.307032 AAGGGAGTGATTGTAAGTGCAT 57.693 40.909 0.00 0.00 0.00 3.96
2404 3802 5.435686 AAGGGAGTGATTGTAAGTGCATA 57.564 39.130 0.00 0.00 0.00 3.14
2405 3803 5.636903 AGGGAGTGATTGTAAGTGCATAT 57.363 39.130 0.00 0.00 0.00 1.78
2406 3804 6.747414 AGGGAGTGATTGTAAGTGCATATA 57.253 37.500 0.00 0.00 0.00 0.86
2407 3805 6.763355 AGGGAGTGATTGTAAGTGCATATAG 58.237 40.000 0.00 0.00 0.00 1.31
2408 3806 6.327626 AGGGAGTGATTGTAAGTGCATATAGT 59.672 38.462 0.00 0.00 0.00 2.12
2409 3807 6.425114 GGGAGTGATTGTAAGTGCATATAGTG 59.575 42.308 0.00 0.00 0.00 2.74
2429 3827 2.666085 CCCCCTTGTAGGTTTTGCC 58.334 57.895 0.00 0.00 31.93 4.52
2430 3828 1.248101 CCCCCTTGTAGGTTTTGCCG 61.248 60.000 0.00 0.00 43.70 5.69
2431 3829 1.248101 CCCCTTGTAGGTTTTGCCGG 61.248 60.000 0.00 0.00 43.70 6.13
2432 3830 0.250989 CCCTTGTAGGTTTTGCCGGA 60.251 55.000 5.05 0.00 43.70 5.14
2433 3831 1.615919 CCCTTGTAGGTTTTGCCGGAT 60.616 52.381 5.05 0.00 43.70 4.18
2434 3832 2.167662 CCTTGTAGGTTTTGCCGGATT 58.832 47.619 5.05 0.00 43.70 3.01
2435 3833 3.349022 CCTTGTAGGTTTTGCCGGATTA 58.651 45.455 5.05 0.00 43.70 1.75
2436 3834 3.759618 CCTTGTAGGTTTTGCCGGATTAA 59.240 43.478 5.05 0.00 43.70 1.40
2437 3835 4.401202 CCTTGTAGGTTTTGCCGGATTAAT 59.599 41.667 5.05 0.00 43.70 1.40
2438 3836 4.974368 TGTAGGTTTTGCCGGATTAATG 57.026 40.909 5.05 0.00 43.70 1.90
2439 3837 4.590918 TGTAGGTTTTGCCGGATTAATGA 58.409 39.130 5.05 0.00 43.70 2.57
2440 3838 4.396790 TGTAGGTTTTGCCGGATTAATGAC 59.603 41.667 5.05 0.00 43.70 3.06
2441 3839 3.426615 AGGTTTTGCCGGATTAATGACA 58.573 40.909 5.05 0.00 43.70 3.58
2442 3840 3.443681 AGGTTTTGCCGGATTAATGACAG 59.556 43.478 5.05 0.00 43.70 3.51
2443 3841 3.442273 GGTTTTGCCGGATTAATGACAGA 59.558 43.478 5.05 0.00 0.00 3.41
2444 3842 4.082463 GGTTTTGCCGGATTAATGACAGAA 60.082 41.667 5.05 0.00 0.00 3.02
2445 3843 4.963276 TTTGCCGGATTAATGACAGAAG 57.037 40.909 5.05 0.00 0.00 2.85
2446 3844 3.627395 TGCCGGATTAATGACAGAAGT 57.373 42.857 5.05 0.00 0.00 3.01
2447 3845 3.270027 TGCCGGATTAATGACAGAAGTG 58.730 45.455 5.05 0.00 0.00 3.16
2448 3846 2.614057 GCCGGATTAATGACAGAAGTGG 59.386 50.000 5.05 0.00 0.00 4.00
2449 3847 3.873910 CCGGATTAATGACAGAAGTGGT 58.126 45.455 0.00 0.00 0.00 4.16
2450 3848 4.261801 CCGGATTAATGACAGAAGTGGTT 58.738 43.478 0.00 0.00 0.00 3.67
2451 3849 5.424757 CCGGATTAATGACAGAAGTGGTTA 58.575 41.667 0.00 0.00 0.00 2.85
2452 3850 5.878116 CCGGATTAATGACAGAAGTGGTTAA 59.122 40.000 0.00 0.00 0.00 2.01
2453 3851 6.037172 CCGGATTAATGACAGAAGTGGTTAAG 59.963 42.308 0.00 0.00 0.00 1.85
2454 3852 6.037172 CGGATTAATGACAGAAGTGGTTAAGG 59.963 42.308 0.00 0.00 0.00 2.69
2455 3853 7.110155 GGATTAATGACAGAAGTGGTTAAGGA 58.890 38.462 0.00 0.00 0.00 3.36
2456 3854 7.610305 GGATTAATGACAGAAGTGGTTAAGGAA 59.390 37.037 0.00 0.00 0.00 3.36
2457 3855 7.739498 TTAATGACAGAAGTGGTTAAGGAAC 57.261 36.000 0.00 0.00 34.56 3.62
2459 3857 6.681729 ATGACAGAAGTGGTTAAGGAACTA 57.318 37.500 0.00 0.00 38.49 2.24
2460 3858 6.488769 TGACAGAAGTGGTTAAGGAACTAA 57.511 37.500 0.00 0.00 38.49 2.24
2461 3859 7.074653 TGACAGAAGTGGTTAAGGAACTAAT 57.925 36.000 0.00 0.00 38.49 1.73
2462 3860 6.934645 TGACAGAAGTGGTTAAGGAACTAATG 59.065 38.462 0.00 0.00 38.49 1.90
2463 3861 6.838382 ACAGAAGTGGTTAAGGAACTAATGT 58.162 36.000 0.00 0.00 38.49 2.71
2464 3862 6.710744 ACAGAAGTGGTTAAGGAACTAATGTG 59.289 38.462 0.00 0.00 38.49 3.21
2465 3863 6.710744 CAGAAGTGGTTAAGGAACTAATGTGT 59.289 38.462 0.00 0.00 38.49 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.802607 GGTCGGCTTTCAGCTAGACG 60.803 60.000 3.72 3.72 43.84 4.18
3 4 2.100605 AAAGGTCGGCTTTCAGCTAG 57.899 50.000 0.00 0.00 41.99 3.42
8 9 2.223745 GTGGTAAAAGGTCGGCTTTCA 58.776 47.619 0.00 0.00 0.00 2.69
9 10 1.196127 CGTGGTAAAAGGTCGGCTTTC 59.804 52.381 0.00 0.00 0.00 2.62
10 11 1.232119 CGTGGTAAAAGGTCGGCTTT 58.768 50.000 0.00 0.00 0.00 3.51
11 12 0.107268 ACGTGGTAAAAGGTCGGCTT 59.893 50.000 0.00 0.00 0.00 4.35
12 13 0.320160 GACGTGGTAAAAGGTCGGCT 60.320 55.000 0.00 0.00 0.00 5.52
13 14 2.156542 GACGTGGTAAAAGGTCGGC 58.843 57.895 0.00 0.00 0.00 5.54
16 17 1.777199 CGCGACGTGGTAAAAGGTC 59.223 57.895 0.00 0.00 0.00 3.85
17 18 2.312436 GCGCGACGTGGTAAAAGGT 61.312 57.895 12.10 0.00 0.00 3.50
18 19 2.222953 CTGCGCGACGTGGTAAAAGG 62.223 60.000 12.10 0.00 0.00 3.11
19 20 1.129809 CTGCGCGACGTGGTAAAAG 59.870 57.895 12.10 0.00 0.00 2.27
20 21 0.875040 TTCTGCGCGACGTGGTAAAA 60.875 50.000 12.10 0.00 0.00 1.52
22 23 0.668096 AATTCTGCGCGACGTGGTAA 60.668 50.000 12.10 0.00 0.00 2.85
24 25 1.080366 TAATTCTGCGCGACGTGGT 60.080 52.632 12.10 0.00 0.00 4.16
25 26 1.343821 GTAATTCTGCGCGACGTGG 59.656 57.895 12.10 0.00 0.00 4.94
26 27 1.343821 GGTAATTCTGCGCGACGTG 59.656 57.895 12.10 3.50 0.00 4.49
27 28 2.156446 CGGTAATTCTGCGCGACGT 61.156 57.895 12.10 0.00 0.00 4.34
28 29 2.613486 CGGTAATTCTGCGCGACG 59.387 61.111 12.10 0.00 0.00 5.12
29 30 2.320044 GCGGTAATTCTGCGCGAC 59.680 61.111 12.10 0.88 38.74 5.19
37 38 4.473199 GACAAGGACTTTTGCGGTAATTC 58.527 43.478 0.00 0.00 0.00 2.17
38 39 3.254903 GGACAAGGACTTTTGCGGTAATT 59.745 43.478 0.00 0.00 0.00 1.40
39 40 2.817844 GGACAAGGACTTTTGCGGTAAT 59.182 45.455 0.00 0.00 0.00 1.89
41 42 1.418637 AGGACAAGGACTTTTGCGGTA 59.581 47.619 0.00 0.00 0.00 4.02
49 50 1.700186 GGTGAAGGAGGACAAGGACTT 59.300 52.381 0.00 0.00 0.00 3.01
69 70 4.208632 GGTGCTTGATGACCGGAG 57.791 61.111 9.46 0.00 0.00 4.63
106 107 9.877178 ATAAGAATTTGTGAAGAGATAGTCGTT 57.123 29.630 0.00 0.00 0.00 3.85
107 108 9.877178 AATAAGAATTTGTGAAGAGATAGTCGT 57.123 29.630 0.00 0.00 0.00 4.34
114 115 7.659799 TCAACCGAATAAGAATTTGTGAAGAGA 59.340 33.333 0.00 0.00 0.00 3.10
126 127 6.522054 AGAACAAGAGTCAACCGAATAAGAA 58.478 36.000 0.00 0.00 0.00 2.52
138 139 5.084818 TGTCAACTCAAGAACAAGAGTCA 57.915 39.130 0.00 0.00 43.88 3.41
145 146 7.661437 AGCTATAACAATGTCAACTCAAGAACA 59.339 33.333 0.00 0.00 0.00 3.18
248 249 2.487762 TGCCTTGATGTTCGAATTGGTC 59.512 45.455 0.00 0.00 0.00 4.02
272 273 2.884320 TGACCCTAGTGTCACTTGCTA 58.116 47.619 11.54 0.00 40.22 3.49
292 294 0.324923 TGTAGCCTACGGTCCACCAT 60.325 55.000 0.00 0.00 35.14 3.55
297 299 1.949465 CCATTTGTAGCCTACGGTCC 58.051 55.000 0.00 0.00 0.00 4.46
321 323 3.229293 TGTCCATCTTTCCACATTTGCA 58.771 40.909 0.00 0.00 0.00 4.08
322 324 3.940209 TGTCCATCTTTCCACATTTGC 57.060 42.857 0.00 0.00 0.00 3.68
332 334 9.632638 ATTAGCATACATTAGTTGTCCATCTTT 57.367 29.630 0.00 0.00 39.87 2.52
338 340 9.929180 TCATAGATTAGCATACATTAGTTGTCC 57.071 33.333 0.00 0.00 39.87 4.02
346 348 6.652481 GCCACACTCATAGATTAGCATACATT 59.348 38.462 0.00 0.00 0.00 2.71
385 387 1.406539 GCCCAGCCATAAACATCACAG 59.593 52.381 0.00 0.00 0.00 3.66
414 440 6.817765 ACATGGTTCAAATGTAGTAACTGG 57.182 37.500 0.00 0.00 36.50 4.00
424 450 8.537049 AACATCACAAATACATGGTTCAAATG 57.463 30.769 0.00 0.00 0.00 2.32
525 795 7.593825 AGATTCAAAGGTAGTTGCATAAACAC 58.406 34.615 0.00 0.00 41.61 3.32
634 987 3.308402 GGAGTCCATTTCTGTCCATCCAA 60.308 47.826 3.60 0.00 0.00 3.53
638 991 1.210478 CCGGAGTCCATTTCTGTCCAT 59.790 52.381 10.49 0.00 0.00 3.41
657 1010 3.437049 GCAGTAGTGATTTCAACACTCCC 59.563 47.826 0.42 0.00 45.58 4.30
658 1085 4.065088 TGCAGTAGTGATTTCAACACTCC 58.935 43.478 0.42 0.00 45.58 3.85
669 1096 4.631813 GGAATTTCGACTTGCAGTAGTGAT 59.368 41.667 0.42 0.00 0.00 3.06
674 1101 2.343101 CCGGAATTTCGACTTGCAGTA 58.657 47.619 7.98 0.00 0.00 2.74
675 1102 1.156736 CCGGAATTTCGACTTGCAGT 58.843 50.000 7.98 0.00 0.00 4.40
684 1111 0.811616 CCAGCTCTCCCGGAATTTCG 60.812 60.000 0.73 0.00 0.00 3.46
686 1113 0.914417 TCCCAGCTCTCCCGGAATTT 60.914 55.000 0.73 0.00 0.00 1.82
689 1116 1.762460 GATCCCAGCTCTCCCGGAA 60.762 63.158 0.73 0.00 0.00 4.30
718 2068 4.563168 GCATGGTTTTGGTCATGGAATTGA 60.563 41.667 0.00 0.00 40.59 2.57
752 2103 3.076621 CCATCAGCAACAAGACTAGCAA 58.923 45.455 0.00 0.00 0.00 3.91
753 2104 2.616256 CCCATCAGCAACAAGACTAGCA 60.616 50.000 0.00 0.00 0.00 3.49
816 2167 4.202131 TGCTCATTCAAAACAGCATCACAA 60.202 37.500 0.00 0.00 36.96 3.33
861 2212 4.836825 TGAGATGGTCTCTGTTTTGATCC 58.163 43.478 8.30 0.00 43.73 3.36
869 2220 5.575157 TCTACTTCTTGAGATGGTCTCTGT 58.425 41.667 8.30 3.25 43.73 3.41
874 2225 5.654650 TCTTCCTCTACTTCTTGAGATGGTC 59.345 44.000 0.00 0.00 32.44 4.02
890 2241 1.925959 CCCTTCCCCAAATCTTCCTCT 59.074 52.381 0.00 0.00 0.00 3.69
937 2294 6.364706 GTGCAAGTATCTTCATCCGATAGAAG 59.635 42.308 11.42 11.42 39.76 2.85
938 2295 6.183360 TGTGCAAGTATCTTCATCCGATAGAA 60.183 38.462 0.00 0.00 39.76 2.10
944 2301 5.490139 AATTGTGCAAGTATCTTCATCCG 57.510 39.130 0.00 0.00 0.00 4.18
973 2330 1.554891 CCTGCATAGTGCTCATCGCG 61.555 60.000 0.00 0.00 45.31 5.87
1109 2468 8.654094 AGACATGACATGATAGTATTCCATTGA 58.346 33.333 22.19 0.00 0.00 2.57
1202 2561 0.895530 TTCTCCTCGCCTTCGTGATT 59.104 50.000 0.00 0.00 36.96 2.57
1302 2661 3.262420 ACTAGTGGATCATCAACAACGC 58.738 45.455 0.00 0.00 0.00 4.84
1359 2718 1.989165 CACTAGACTTCACAAGCGCTC 59.011 52.381 12.06 0.00 0.00 5.03
1394 2753 3.581332 TCCCAAAGGTCATCGGGTATATC 59.419 47.826 0.00 0.00 39.87 1.63
1395 2754 3.593942 TCCCAAAGGTCATCGGGTATAT 58.406 45.455 0.00 0.00 39.87 0.86
1396 2755 3.049108 TCCCAAAGGTCATCGGGTATA 57.951 47.619 0.00 0.00 39.87 1.47
1465 2824 4.256920 AGTTGTCCACAAGATGAGCATAC 58.743 43.478 0.00 0.00 36.39 2.39
1487 2850 2.645838 AAGGCTCTTGCAGTCTTGAA 57.354 45.000 0.00 0.00 45.96 2.69
1750 3130 3.814625 TCAACAAGGTGCACATAGTTGA 58.185 40.909 29.89 29.89 41.88 3.18
1858 3254 6.807720 GCCATAAAATTCAAAATTTTGGCAGG 59.192 34.615 26.45 17.86 39.61 4.85
1882 3279 3.062504 GCACGGAATGAAAAATGGAATGC 59.937 43.478 0.00 0.00 0.00 3.56
1965 3363 0.801067 GAATGGGTCGGTTCGAGTCG 60.801 60.000 6.09 6.09 36.23 4.18
1994 3392 6.271585 ACTATCATGGAATGGAATGGTTCT 57.728 37.500 0.00 0.00 46.73 3.01
2020 3418 1.419381 GGTGTGTTTGGTTGGGGAAT 58.581 50.000 0.00 0.00 0.00 3.01
2067 3465 8.743085 AACATGCATGAAGAATTATGAGTAGT 57.257 30.769 32.75 0.95 0.00 2.73
2103 3501 9.394767 TGAGTAATGTCAACATGCATATAAGTT 57.605 29.630 0.00 0.00 36.56 2.66
2120 3518 5.237344 GCAAACTGTGAACTCTGAGTAATGT 59.763 40.000 11.30 3.75 0.00 2.71
2125 3523 3.550437 AGCAAACTGTGAACTCTGAGT 57.450 42.857 4.06 4.06 0.00 3.41
2126 3524 4.142945 GCATAGCAAACTGTGAACTCTGAG 60.143 45.833 2.45 2.45 37.20 3.35
2128 3526 3.499537 TGCATAGCAAACTGTGAACTCTG 59.500 43.478 0.00 0.00 37.20 3.35
2185 3583 7.442656 CCCTATATCGTGGAATCAAAACTAGT 58.557 38.462 0.00 0.00 0.00 2.57
2190 3588 4.661240 TCCCCCTATATCGTGGAATCAAAA 59.339 41.667 0.00 0.00 0.00 2.44
2192 3590 3.864328 TCCCCCTATATCGTGGAATCAA 58.136 45.455 0.00 0.00 0.00 2.57
2201 3599 1.553248 TGGCGAATTCCCCCTATATCG 59.447 52.381 6.69 0.00 0.00 2.92
2205 3603 0.923358 TTGTGGCGAATTCCCCCTAT 59.077 50.000 6.69 0.00 0.00 2.57
2214 3612 2.995258 GCATGTTGAAATTGTGGCGAAT 59.005 40.909 0.00 0.00 0.00 3.34
2275 3673 6.707440 AGAGAGAACTCGTCATGAATATGT 57.293 37.500 0.00 0.00 46.64 2.29
2286 3684 8.670135 CGATTCCATTATATAGAGAGAACTCGT 58.330 37.037 0.00 0.00 46.64 4.18
2287 3685 8.884726 TCGATTCCATTATATAGAGAGAACTCG 58.115 37.037 0.00 0.00 46.64 4.18
2321 3719 8.347771 GGGACGAATAAAAGTTGAAGTAAAACT 58.652 33.333 0.00 0.00 39.55 2.66
2322 3720 8.347771 AGGGACGAATAAAAGTTGAAGTAAAAC 58.652 33.333 0.00 0.00 0.00 2.43
2323 3721 8.347035 CAGGGACGAATAAAAGTTGAAGTAAAA 58.653 33.333 0.00 0.00 0.00 1.52
2324 3722 7.499895 ACAGGGACGAATAAAAGTTGAAGTAAA 59.500 33.333 0.00 0.00 0.00 2.01
2325 3723 6.993902 ACAGGGACGAATAAAAGTTGAAGTAA 59.006 34.615 0.00 0.00 0.00 2.24
2326 3724 6.527423 ACAGGGACGAATAAAAGTTGAAGTA 58.473 36.000 0.00 0.00 0.00 2.24
2327 3725 5.374071 ACAGGGACGAATAAAAGTTGAAGT 58.626 37.500 0.00 0.00 0.00 3.01
2328 3726 5.941948 ACAGGGACGAATAAAAGTTGAAG 57.058 39.130 0.00 0.00 0.00 3.02
2329 3727 5.823570 TCAACAGGGACGAATAAAAGTTGAA 59.176 36.000 0.00 0.00 40.50 2.69
2330 3728 5.369833 TCAACAGGGACGAATAAAAGTTGA 58.630 37.500 0.00 0.00 40.98 3.18
2331 3729 5.468746 TCTCAACAGGGACGAATAAAAGTTG 59.531 40.000 0.00 0.00 37.15 3.16
2332 3730 5.469084 GTCTCAACAGGGACGAATAAAAGTT 59.531 40.000 0.00 0.00 0.00 2.66
2333 3731 4.995487 GTCTCAACAGGGACGAATAAAAGT 59.005 41.667 0.00 0.00 0.00 2.66
2334 3732 5.238583 AGTCTCAACAGGGACGAATAAAAG 58.761 41.667 0.00 0.00 37.52 2.27
2335 3733 5.223449 AGTCTCAACAGGGACGAATAAAA 57.777 39.130 0.00 0.00 37.52 1.52
2336 3734 4.884668 AGTCTCAACAGGGACGAATAAA 57.115 40.909 0.00 0.00 37.52 1.40
2337 3735 4.884668 AAGTCTCAACAGGGACGAATAA 57.115 40.909 0.00 0.00 37.52 1.40
2338 3736 4.884668 AAAGTCTCAACAGGGACGAATA 57.115 40.909 0.00 0.00 37.52 1.75
2339 3737 3.771577 AAAGTCTCAACAGGGACGAAT 57.228 42.857 0.00 0.00 37.52 3.34
2340 3738 4.374399 GTTAAAGTCTCAACAGGGACGAA 58.626 43.478 0.00 0.00 37.52 3.85
2341 3739 3.243975 GGTTAAAGTCTCAACAGGGACGA 60.244 47.826 0.00 0.00 37.52 4.20
2342 3740 3.064931 GGTTAAAGTCTCAACAGGGACG 58.935 50.000 0.00 0.00 37.52 4.79
2343 3741 3.813724 GTGGTTAAAGTCTCAACAGGGAC 59.186 47.826 0.00 0.00 0.00 4.46
2344 3742 3.714798 AGTGGTTAAAGTCTCAACAGGGA 59.285 43.478 1.09 0.00 0.00 4.20
2345 3743 4.086706 AGTGGTTAAAGTCTCAACAGGG 57.913 45.455 1.09 0.00 0.00 4.45
2346 3744 6.451064 AAAAGTGGTTAAAGTCTCAACAGG 57.549 37.500 1.09 0.00 0.00 4.00
2347 3745 9.450807 CAATAAAAGTGGTTAAAGTCTCAACAG 57.549 33.333 1.09 0.00 0.00 3.16
2348 3746 9.179909 TCAATAAAAGTGGTTAAAGTCTCAACA 57.820 29.630 1.09 0.00 0.00 3.33
2351 3749 9.567776 TGATCAATAAAAGTGGTTAAAGTCTCA 57.432 29.630 0.00 0.00 0.00 3.27
2352 3750 9.827411 GTGATCAATAAAAGTGGTTAAAGTCTC 57.173 33.333 0.00 0.00 0.00 3.36
2353 3751 8.793592 GGTGATCAATAAAAGTGGTTAAAGTCT 58.206 33.333 0.00 0.00 0.00 3.24
2354 3752 8.573035 TGGTGATCAATAAAAGTGGTTAAAGTC 58.427 33.333 0.00 0.00 0.00 3.01
2355 3753 8.472007 TGGTGATCAATAAAAGTGGTTAAAGT 57.528 30.769 0.00 0.00 0.00 2.66
2356 3754 9.757227 TTTGGTGATCAATAAAAGTGGTTAAAG 57.243 29.630 0.00 0.00 34.98 1.85
2358 3756 9.757227 CTTTTGGTGATCAATAAAAGTGGTTAA 57.243 29.630 24.13 4.60 36.11 2.01
2359 3757 8.364142 CCTTTTGGTGATCAATAAAAGTGGTTA 58.636 33.333 27.09 7.48 38.05 2.85
2360 3758 7.216494 CCTTTTGGTGATCAATAAAAGTGGTT 58.784 34.615 27.09 0.00 38.05 3.67
2361 3759 6.239572 CCCTTTTGGTGATCAATAAAAGTGGT 60.240 38.462 27.09 0.00 38.05 4.16
2362 3760 6.014669 TCCCTTTTGGTGATCAATAAAAGTGG 60.015 38.462 27.09 25.89 38.05 4.00
2363 3761 6.991938 TCCCTTTTGGTGATCAATAAAAGTG 58.008 36.000 27.09 21.70 38.05 3.16
2364 3762 6.782494 ACTCCCTTTTGGTGATCAATAAAAGT 59.218 34.615 27.09 16.45 38.05 2.66
2365 3763 7.039784 TCACTCCCTTTTGGTGATCAATAAAAG 60.040 37.037 24.84 24.84 38.94 2.27
2366 3764 6.780031 TCACTCCCTTTTGGTGATCAATAAAA 59.220 34.615 14.22 14.22 35.44 1.52
2367 3765 6.310941 TCACTCCCTTTTGGTGATCAATAAA 58.689 36.000 0.00 0.00 35.44 1.40
2368 3766 5.886609 TCACTCCCTTTTGGTGATCAATAA 58.113 37.500 0.00 0.00 35.44 1.40
2369 3767 5.512942 TCACTCCCTTTTGGTGATCAATA 57.487 39.130 0.00 0.00 35.44 1.90
2370 3768 4.387026 TCACTCCCTTTTGGTGATCAAT 57.613 40.909 0.00 0.00 35.44 2.57
2371 3769 3.874383 TCACTCCCTTTTGGTGATCAA 57.126 42.857 0.00 0.00 35.44 2.57
2372 3770 4.081406 CAATCACTCCCTTTTGGTGATCA 58.919 43.478 8.01 0.00 46.01 2.92
2373 3771 4.082125 ACAATCACTCCCTTTTGGTGATC 58.918 43.478 8.01 0.00 46.01 2.92
2375 3773 3.593442 ACAATCACTCCCTTTTGGTGA 57.407 42.857 0.00 0.00 42.85 4.02
2376 3774 4.827284 ACTTACAATCACTCCCTTTTGGTG 59.173 41.667 0.00 0.00 38.10 4.17
2377 3775 4.827284 CACTTACAATCACTCCCTTTTGGT 59.173 41.667 0.00 0.00 38.10 3.67
2378 3776 4.321230 GCACTTACAATCACTCCCTTTTGG 60.321 45.833 0.00 0.00 39.97 3.28
2379 3777 4.278170 TGCACTTACAATCACTCCCTTTTG 59.722 41.667 0.00 0.00 0.00 2.44
2380 3778 4.469657 TGCACTTACAATCACTCCCTTTT 58.530 39.130 0.00 0.00 0.00 2.27
2381 3779 4.098914 TGCACTTACAATCACTCCCTTT 57.901 40.909 0.00 0.00 0.00 3.11
2382 3780 3.788227 TGCACTTACAATCACTCCCTT 57.212 42.857 0.00 0.00 0.00 3.95
2383 3781 5.636903 ATATGCACTTACAATCACTCCCT 57.363 39.130 0.00 0.00 0.00 4.20
2384 3782 6.425114 CACTATATGCACTTACAATCACTCCC 59.575 42.308 0.00 0.00 0.00 4.30
2385 3783 7.413475 CACTATATGCACTTACAATCACTCC 57.587 40.000 0.00 0.00 0.00 3.85
2411 3809 1.248101 CGGCAAAACCTACAAGGGGG 61.248 60.000 0.00 0.00 40.58 5.40
2412 3810 1.248101 CCGGCAAAACCTACAAGGGG 61.248 60.000 0.00 0.00 40.58 4.79
2413 3811 0.250989 TCCGGCAAAACCTACAAGGG 60.251 55.000 0.00 0.00 40.58 3.95
2414 3812 1.834188 ATCCGGCAAAACCTACAAGG 58.166 50.000 0.00 0.00 42.49 3.61
2415 3813 5.124776 TCATTAATCCGGCAAAACCTACAAG 59.875 40.000 0.00 0.00 35.61 3.16
2416 3814 5.010933 TCATTAATCCGGCAAAACCTACAA 58.989 37.500 0.00 0.00 35.61 2.41
2417 3815 4.396790 GTCATTAATCCGGCAAAACCTACA 59.603 41.667 0.00 0.00 35.61 2.74
2418 3816 4.396790 TGTCATTAATCCGGCAAAACCTAC 59.603 41.667 0.00 0.00 35.61 3.18
2419 3817 4.590918 TGTCATTAATCCGGCAAAACCTA 58.409 39.130 0.00 0.00 35.61 3.08
2420 3818 3.426615 TGTCATTAATCCGGCAAAACCT 58.573 40.909 0.00 0.00 35.61 3.50
2421 3819 3.442273 TCTGTCATTAATCCGGCAAAACC 59.558 43.478 0.00 0.00 0.00 3.27
2422 3820 4.695217 TCTGTCATTAATCCGGCAAAAC 57.305 40.909 0.00 0.00 0.00 2.43
2423 3821 4.764823 ACTTCTGTCATTAATCCGGCAAAA 59.235 37.500 0.00 0.00 0.00 2.44
2424 3822 4.155826 CACTTCTGTCATTAATCCGGCAAA 59.844 41.667 0.00 0.00 0.00 3.68
2425 3823 3.689161 CACTTCTGTCATTAATCCGGCAA 59.311 43.478 0.00 0.00 0.00 4.52
2426 3824 3.270027 CACTTCTGTCATTAATCCGGCA 58.730 45.455 0.00 0.00 0.00 5.69
2427 3825 2.614057 CCACTTCTGTCATTAATCCGGC 59.386 50.000 0.00 0.00 0.00 6.13
2428 3826 3.873910 ACCACTTCTGTCATTAATCCGG 58.126 45.455 0.00 0.00 0.00 5.14
2429 3827 6.037172 CCTTAACCACTTCTGTCATTAATCCG 59.963 42.308 0.00 0.00 0.00 4.18
2430 3828 7.110155 TCCTTAACCACTTCTGTCATTAATCC 58.890 38.462 0.00 0.00 0.00 3.01
2431 3829 8.451748 GTTCCTTAACCACTTCTGTCATTAATC 58.548 37.037 0.00 0.00 0.00 1.75
2432 3830 8.164070 AGTTCCTTAACCACTTCTGTCATTAAT 58.836 33.333 0.00 0.00 36.15 1.40
2433 3831 7.514721 AGTTCCTTAACCACTTCTGTCATTAA 58.485 34.615 0.00 0.00 36.15 1.40
2434 3832 7.074653 AGTTCCTTAACCACTTCTGTCATTA 57.925 36.000 0.00 0.00 36.15 1.90
2435 3833 5.941788 AGTTCCTTAACCACTTCTGTCATT 58.058 37.500 0.00 0.00 36.15 2.57
2436 3834 5.568620 AGTTCCTTAACCACTTCTGTCAT 57.431 39.130 0.00 0.00 36.15 3.06
2437 3835 6.488769 TTAGTTCCTTAACCACTTCTGTCA 57.511 37.500 0.00 0.00 36.15 3.58
2438 3836 6.935208 ACATTAGTTCCTTAACCACTTCTGTC 59.065 38.462 0.00 0.00 36.15 3.51
2439 3837 6.710744 CACATTAGTTCCTTAACCACTTCTGT 59.289 38.462 0.00 0.00 36.15 3.41
2440 3838 6.710744 ACACATTAGTTCCTTAACCACTTCTG 59.289 38.462 0.00 0.00 36.15 3.02
2441 3839 6.838382 ACACATTAGTTCCTTAACCACTTCT 58.162 36.000 0.00 0.00 36.15 2.85


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

AutoCloner maintained by Alex Coulton.