Multiple sequence alignment - TraesCS6B01G401700

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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 TraesCS6B01G401700 chr6B 100.000 2725 0 0 1 2725 678173680 678176404 0.000000e+00 5033.0
1 TraesCS6B01G401700 chr6B 83.690 1680 161 47 842 2472 678356770 678358385 0.000000e+00 1480.0
2 TraesCS6B01G401700 chr6B 84.304 1236 111 37 718 1922 678093046 678091863 0.000000e+00 1131.0
3 TraesCS6B01G401700 chr6B 84.947 1136 97 43 943 2046 677045701 677044608 0.000000e+00 1083.0
4 TraesCS6B01G401700 chr6B 82.815 1286 122 48 1073 2315 678542705 678543934 0.000000e+00 1059.0
5 TraesCS6B01G401700 chr6B 80.383 1463 142 71 487 1897 676866361 676864992 0.000000e+00 977.0
6 TraesCS6B01G401700 chr6B 87.288 708 61 18 938 1619 677088413 677087709 0.000000e+00 782.0
7 TraesCS6B01G401700 chr6B 88.397 655 49 15 1925 2565 678091817 678091176 0.000000e+00 763.0
8 TraesCS6B01G401700 chr6B 86.297 686 56 18 1382 2046 677336617 677335949 0.000000e+00 712.0
9 TraesCS6B01G401700 chr6B 88.165 583 52 9 1759 2328 677087688 677087110 0.000000e+00 678.0
10 TraesCS6B01G401700 chr6B 88.686 548 44 12 1794 2328 677777854 677777312 0.000000e+00 652.0
11 TraesCS6B01G401700 chr6B 88.686 548 45 11 1794 2328 677910135 677909592 0.000000e+00 652.0
12 TraesCS6B01G401700 chr6B 89.463 484 36 11 1856 2328 676865074 676864595 5.020000e-167 597.0
13 TraesCS6B01G401700 chr6B 81.304 690 74 24 210 861 677046419 677045747 2.420000e-140 508.0
14 TraesCS6B01G401700 chr6B 78.848 851 87 43 1453 2270 676730383 676729593 3.150000e-134 488.0
15 TraesCS6B01G401700 chr6B 85.280 428 45 13 965 1380 676538363 676537942 2.510000e-115 425.0
16 TraesCS6B01G401700 chr6B 87.539 321 26 10 1062 1378 676492624 676492314 2.580000e-95 359.0
17 TraesCS6B01G401700 chr6B 79.242 501 47 33 717 1188 677337151 677336679 2.050000e-76 296.0
18 TraesCS6B01G401700 chr6B 95.556 180 7 1 2386 2565 677079706 677079528 1.230000e-73 287.0
19 TraesCS6B01G401700 chr6B 95.000 180 8 1 2386 2565 677906750 677906572 5.740000e-72 281.0
20 TraesCS6B01G401700 chr6B 94.444 180 9 1 2386 2565 676859423 676859245 2.670000e-70 276.0
21 TraesCS6B01G401700 chr6B 94.915 177 8 1 2389 2565 677774639 677774464 2.670000e-70 276.0
22 TraesCS6B01G401700 chr6B 89.881 168 13 3 210 377 677778109 677777946 2.130000e-51 213.0
23 TraesCS6B01G401700 chr6B 89.286 168 14 3 210 377 677910390 677910227 9.890000e-50 207.0
24 TraesCS6B01G401700 chr6B 84.404 218 23 6 210 424 678093313 678093104 1.280000e-48 204.0
25 TraesCS6B01G401700 chr6B 92.157 51 4 0 1 51 678093571 678093521 3.760000e-09 73.1
26 TraesCS6B01G401700 chr6A 86.894 1526 115 32 956 2439 593992465 593990983 0.000000e+00 1631.0
27 TraesCS6B01G401700 chr6A 84.945 1541 114 50 955 2438 594254309 594252830 0.000000e+00 1452.0
28 TraesCS6B01G401700 chr6A 81.348 1973 182 83 715 2565 594318903 594320811 0.000000e+00 1434.0
29 TraesCS6B01G401700 chr6A 85.363 895 77 27 938 1801 594365597 594366468 0.000000e+00 878.0
30 TraesCS6B01G401700 chr6A 79.379 805 95 38 1420 2194 593929563 593928800 4.050000e-138 501.0
31 TraesCS6B01G401700 chr6A 83.195 482 48 18 927 1378 593930047 593929569 7.020000e-111 411.0
32 TraesCS6B01G401700 chr6A 81.265 427 49 18 1855 2270 569678358 569677952 1.570000e-82 316.0
33 TraesCS6B01G401700 chr6A 83.285 347 26 11 320 661 594318339 594318658 9.550000e-75 291.0
34 TraesCS6B01G401700 chr6A 97.917 48 1 0 1 48 594318127 594318174 1.740000e-12 84.2
35 TraesCS6B01G401700 chr6D 82.687 1675 156 56 943 2530 447737636 447739263 0.000000e+00 1363.0
36 TraesCS6B01G401700 chr6D 87.896 884 73 11 1661 2533 447278103 447277243 0.000000e+00 1009.0
37 TraesCS6B01G401700 chr6D 87.925 853 54 21 938 1753 447278966 447278126 0.000000e+00 959.0
38 TraesCS6B01G401700 chr6D 82.692 468 54 13 938 1378 447213888 447213421 9.150000e-105 390.0
39 TraesCS6B01G401700 chr6D 87.311 331 32 8 1050 1378 447761128 447761450 1.190000e-98 370.0
40 TraesCS6B01G401700 chr6D 80.360 555 48 26 325 828 447279577 447279033 5.550000e-97 364.0
41 TraesCS6B01G401700 chr6D 78.347 605 78 27 778 1380 447445267 447444714 2.600000e-90 342.0
42 TraesCS6B01G401700 chr6D 83.871 93 7 3 1 85 447737050 447737142 6.250000e-12 82.4
43 TraesCS6B01G401700 chr6D 76.271 177 27 13 331 506 446901362 446901524 2.250000e-11 80.5
44 TraesCS6B01G401700 chr5D 86.709 158 18 2 2567 2723 446132410 446132255 3.610000e-39 172.0
45 TraesCS6B01G401700 chr7D 85.366 164 18 4 2567 2725 613762015 613762177 6.040000e-37 165.0
46 TraesCS6B01G401700 chr7D 87.302 126 10 6 2567 2687 586833189 586833313 3.660000e-29 139.0
47 TraesCS6B01G401700 chr5B 86.806 144 14 3 2567 2705 43803426 43803569 3.630000e-34 156.0
48 TraesCS6B01G401700 chr5B 86.806 144 14 3 2567 2705 43815042 43815185 3.630000e-34 156.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G401700 chr6B 678173680 678176404 2724 False 5033.000000 5033 100.000000 1 2725 1 chr6B.!!$F1 2724
1 TraesCS6B01G401700 chr6B 678356770 678358385 1615 False 1480.000000 1480 83.690000 842 2472 1 chr6B.!!$F2 1630
2 TraesCS6B01G401700 chr6B 678542705 678543934 1229 False 1059.000000 1059 82.815000 1073 2315 1 chr6B.!!$F3 1242
3 TraesCS6B01G401700 chr6B 677044608 677046419 1811 True 795.500000 1083 83.125500 210 2046 2 chr6B.!!$R7 1836
4 TraesCS6B01G401700 chr6B 676864595 676866361 1766 True 787.000000 977 84.923000 487 2328 2 chr6B.!!$R6 1841
5 TraesCS6B01G401700 chr6B 677087110 677088413 1303 True 730.000000 782 87.726500 938 2328 2 chr6B.!!$R8 1390
6 TraesCS6B01G401700 chr6B 678091176 678093571 2395 True 542.775000 1131 87.315500 1 2565 4 chr6B.!!$R12 2564
7 TraesCS6B01G401700 chr6B 677335949 677337151 1202 True 504.000000 712 82.769500 717 2046 2 chr6B.!!$R9 1329
8 TraesCS6B01G401700 chr6B 676729593 676730383 790 True 488.000000 488 78.848000 1453 2270 1 chr6B.!!$R3 817
9 TraesCS6B01G401700 chr6B 677774464 677778109 3645 True 380.333333 652 91.160667 210 2565 3 chr6B.!!$R10 2355
10 TraesCS6B01G401700 chr6B 677906572 677910390 3818 True 380.000000 652 90.990667 210 2565 3 chr6B.!!$R11 2355
11 TraesCS6B01G401700 chr6A 593990983 593992465 1482 True 1631.000000 1631 86.894000 956 2439 1 chr6A.!!$R2 1483
12 TraesCS6B01G401700 chr6A 594252830 594254309 1479 True 1452.000000 1452 84.945000 955 2438 1 chr6A.!!$R3 1483
13 TraesCS6B01G401700 chr6A 594365597 594366468 871 False 878.000000 878 85.363000 938 1801 1 chr6A.!!$F1 863
14 TraesCS6B01G401700 chr6A 594318127 594320811 2684 False 603.066667 1434 87.516667 1 2565 3 chr6A.!!$F2 2564
15 TraesCS6B01G401700 chr6A 593928800 593930047 1247 True 456.000000 501 81.287000 927 2194 2 chr6A.!!$R4 1267
16 TraesCS6B01G401700 chr6D 447277243 447279577 2334 True 777.333333 1009 85.393667 325 2533 3 chr6D.!!$R3 2208
17 TraesCS6B01G401700 chr6D 447737050 447739263 2213 False 722.700000 1363 83.279000 1 2530 2 chr6D.!!$F3 2529
18 TraesCS6B01G401700 chr6D 447444714 447445267 553 True 342.000000 342 78.347000 778 1380 1 chr6D.!!$R2 602

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
401 477 0.106335 ATCCCTGCATCGCTCTGAAG 59.894 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 2583 0.179202 CAGAGACGACGAGCTCACTG 60.179 60.0 15.4 4.49 33.62 3.66 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
43 45 2.190578 GGGCAGGGAATGAGACGG 59.809 66.667 0.00 0.00 0.00 4.79
64 83 0.880278 CACGTTGTGGTGACCCAGAG 60.880 60.000 0.00 0.00 42.94 3.35
110 130 3.836030 CGTAGCAACGGCGATCATATCG 61.836 54.545 16.62 4.97 46.89 2.92
118 138 1.226688 CGATCATATCGCGGCGGAT 60.227 57.895 23.46 16.44 46.55 4.18
121 141 0.458543 ATCATATCGCGGCGGATCAC 60.459 55.000 23.46 0.00 0.00 3.06
153 197 2.504899 CTCGTGTCGTGCGATGCT 60.505 61.111 0.00 0.00 37.74 3.79
154 198 1.226295 CTCGTGTCGTGCGATGCTA 60.226 57.895 0.00 0.00 37.74 3.49
155 199 0.796870 CTCGTGTCGTGCGATGCTAA 60.797 55.000 0.00 0.00 37.74 3.09
158 202 2.158330 TGTCGTGCGATGCTAAGCG 61.158 57.895 0.00 0.00 38.52 4.68
159 203 2.582226 TCGTGCGATGCTAAGCGG 60.582 61.111 0.00 0.00 35.22 5.52
161 205 1.951130 CGTGCGATGCTAAGCGGAT 60.951 57.895 0.00 0.00 38.00 4.18
163 207 1.063806 GTGCGATGCTAAGCGGATAG 58.936 55.000 0.00 0.00 38.00 2.08
164 208 0.673985 TGCGATGCTAAGCGGATAGT 59.326 50.000 0.00 0.00 35.22 2.12
166 210 2.251893 GCGATGCTAAGCGGATAGTAC 58.748 52.381 0.00 0.00 35.22 2.73
167 211 2.351447 GCGATGCTAAGCGGATAGTACA 60.351 50.000 0.00 0.00 35.22 2.90
168 212 3.235195 CGATGCTAAGCGGATAGTACAC 58.765 50.000 0.00 0.00 0.00 2.90
178 222 2.413765 CGGATAGTACACCGGATTAGCG 60.414 54.545 9.46 0.00 44.59 4.26
179 223 2.816087 GGATAGTACACCGGATTAGCGA 59.184 50.000 9.46 0.00 0.00 4.93
180 224 3.254166 GGATAGTACACCGGATTAGCGAA 59.746 47.826 9.46 0.00 0.00 4.70
181 225 4.261741 GGATAGTACACCGGATTAGCGAAA 60.262 45.833 9.46 0.00 0.00 3.46
182 226 3.160777 AGTACACCGGATTAGCGAAAG 57.839 47.619 9.46 0.00 0.00 2.62
195 239 2.753966 CGAAAGCGATGGCACCCTG 61.754 63.158 1.50 0.00 43.41 4.45
207 280 2.204136 ACCCTGGCCACTCCATGA 60.204 61.111 0.00 0.00 45.50 3.07
208 281 1.620589 ACCCTGGCCACTCCATGAT 60.621 57.895 0.00 0.00 45.50 2.45
276 349 0.898326 GAGGTTGGCCGGGTTTCAAT 60.898 55.000 2.18 0.00 40.50 2.57
288 361 0.811281 GTTTCAATCAAGGCGGAGGG 59.189 55.000 0.00 0.00 0.00 4.30
289 362 0.323360 TTTCAATCAAGGCGGAGGGG 60.323 55.000 0.00 0.00 0.00 4.79
290 363 1.497309 TTCAATCAAGGCGGAGGGGT 61.497 55.000 0.00 0.00 0.00 4.95
364 439 1.376543 GTCACGTCGATCAGGTCCTA 58.623 55.000 0.00 0.00 0.00 2.94
378 453 0.815734 GTCCTACTCGTGCCAGCTTA 59.184 55.000 0.00 0.00 0.00 3.09
401 477 0.106335 ATCCCTGCATCGCTCTGAAG 59.894 55.000 0.00 0.00 0.00 3.02
439 518 1.880027 CTTTTCTGGGACCGTCCTTTG 59.120 52.381 17.27 7.87 36.57 2.77
448 527 1.227823 CCGTCCTTTGAGTGTGCCA 60.228 57.895 0.00 0.00 0.00 4.92
510 605 4.426112 CGGCTGCACGCAGAGAGA 62.426 66.667 22.81 0.00 46.30 3.10
693 827 0.871722 ATTTTCTTGTACTGCGCGCA 59.128 45.000 34.12 34.12 0.00 6.09
736 1043 4.281688 AGCACTGGTTTGTAATGCAAGAAT 59.718 37.500 0.00 0.00 38.79 2.40
742 1049 6.577103 TGGTTTGTAATGCAAGAATTTGACA 58.423 32.000 0.00 0.00 38.47 3.58
744 1051 7.010923 TGGTTTGTAATGCAAGAATTTGACAAC 59.989 33.333 0.00 0.00 38.47 3.32
803 1119 0.322456 TGCGCCCTACTTGCTGAATT 60.322 50.000 4.18 0.00 0.00 2.17
867 1202 4.415150 CCCACTGCATCACGCCCT 62.415 66.667 0.00 0.00 41.33 5.19
872 1208 1.153289 CTGCATCACGCCCTTAGCT 60.153 57.895 0.00 0.00 41.33 3.32
885 1221 4.444720 CGCCCTTAGCTCGAGTTTAATTAG 59.555 45.833 15.13 6.46 40.39 1.73
908 1244 7.790782 AGCAATGGTTTTCCTTTCCTTAATA 57.209 32.000 0.00 0.00 41.38 0.98
910 1246 8.825774 AGCAATGGTTTTCCTTTCCTTAATAAT 58.174 29.630 0.00 0.00 41.38 1.28
931 1278 2.472695 AATTTACTCGAGCAGGCACA 57.527 45.000 13.61 0.00 0.00 4.57
934 1281 0.679505 TTACTCGAGCAGGCACAAGT 59.320 50.000 13.61 0.00 0.00 3.16
936 1283 0.882042 ACTCGAGCAGGCACAAGTTG 60.882 55.000 13.61 0.00 0.00 3.16
940 1310 1.267806 CGAGCAGGCACAAGTTGAAAT 59.732 47.619 10.54 0.00 0.00 2.17
950 1321 2.629617 ACAAGTTGAAATTGCCCCTCTG 59.370 45.455 10.54 0.00 0.00 3.35
976 1358 1.073923 CTCCCCGGCCTATAAATTGCT 59.926 52.381 0.00 0.00 0.00 3.91
1070 1521 0.760945 CGCCCCTCCACCTCTCTAAT 60.761 60.000 0.00 0.00 0.00 1.73
1071 1522 1.052617 GCCCCTCCACCTCTCTAATC 58.947 60.000 0.00 0.00 0.00 1.75
1269 1758 1.741401 CGGTCGGTCATGCATGTGT 60.741 57.895 25.43 0.00 0.00 3.72
1275 1764 0.611618 GGTCATGCATGTGTTCCCCA 60.612 55.000 25.43 1.24 0.00 4.96
1278 1767 0.967662 CATGCATGTGTTCCCCAACA 59.032 50.000 18.91 0.00 40.40 3.33
1802 2491 0.255890 TCCTGGCTGGTCAATTAGGC 59.744 55.000 10.44 0.00 39.67 3.93
1864 2583 3.264897 CCGCTCCGCTGCACATAC 61.265 66.667 0.00 0.00 0.00 2.39
2076 2958 2.378806 CGCAACAACTTTCTGCTTCTG 58.621 47.619 0.00 0.00 33.82 3.02
2077 2959 2.223340 CGCAACAACTTTCTGCTTCTGT 60.223 45.455 0.00 0.00 33.82 3.41
2078 2960 3.731867 CGCAACAACTTTCTGCTTCTGTT 60.732 43.478 0.00 0.00 33.82 3.16
2079 2961 4.176271 GCAACAACTTTCTGCTTCTGTTT 58.824 39.130 0.00 0.00 33.20 2.83
2080 2962 4.266265 GCAACAACTTTCTGCTTCTGTTTC 59.734 41.667 0.00 0.00 33.20 2.78
2081 2963 5.644644 CAACAACTTTCTGCTTCTGTTTCT 58.355 37.500 0.00 0.00 0.00 2.52
2082 2964 5.240713 ACAACTTTCTGCTTCTGTTTCTG 57.759 39.130 0.00 0.00 0.00 3.02
2083 2965 4.702131 ACAACTTTCTGCTTCTGTTTCTGT 59.298 37.500 0.00 0.00 0.00 3.41
2084 2966 5.183904 ACAACTTTCTGCTTCTGTTTCTGTT 59.816 36.000 0.00 0.00 0.00 3.16
2085 2967 5.904362 ACTTTCTGCTTCTGTTTCTGTTT 57.096 34.783 0.00 0.00 0.00 2.83
2086 2968 7.094377 ACAACTTTCTGCTTCTGTTTCTGTTTA 60.094 33.333 0.00 0.00 0.00 2.01
2087 2969 7.573968 ACTTTCTGCTTCTGTTTCTGTTTAT 57.426 32.000 0.00 0.00 0.00 1.40
2097 3024 7.873719 TCTGTTTCTGTTTATGTTTCTGGAA 57.126 32.000 0.00 0.00 0.00 3.53
2292 3229 3.982424 CTTCATGACGCGCGCAACC 62.982 63.158 32.58 18.97 0.00 3.77
2424 6159 2.976840 TTTCATGGCGCGCTCAACC 61.977 57.895 32.29 14.61 0.00 3.77
2472 6207 5.975344 TCCTGCTCGTGATATTTTAAGTACG 59.025 40.000 0.00 0.00 0.00 3.67
2522 6257 7.659652 ATTTTACTGTACTTTCAGAGCAGTC 57.340 36.000 0.00 0.00 40.39 3.51
2530 6265 5.238006 ACTTTCAGAGCAGTCGTACTATC 57.762 43.478 0.00 0.00 0.00 2.08
2565 6311 0.322546 GCGGTTGGGATTTCACCTCT 60.323 55.000 0.00 0.00 0.00 3.69
2566 6312 1.065709 GCGGTTGGGATTTCACCTCTA 60.066 52.381 0.00 0.00 0.00 2.43
2567 6313 2.629051 CGGTTGGGATTTCACCTCTAC 58.371 52.381 0.00 0.00 0.00 2.59
2568 6314 2.236395 CGGTTGGGATTTCACCTCTACT 59.764 50.000 0.00 0.00 0.00 2.57
2569 6315 3.307480 CGGTTGGGATTTCACCTCTACTT 60.307 47.826 0.00 0.00 0.00 2.24
2570 6316 4.663334 GGTTGGGATTTCACCTCTACTTT 58.337 43.478 0.00 0.00 0.00 2.66
2571 6317 5.570034 CGGTTGGGATTTCACCTCTACTTTA 60.570 44.000 0.00 0.00 0.00 1.85
2572 6318 5.880887 GGTTGGGATTTCACCTCTACTTTAG 59.119 44.000 0.00 0.00 0.00 1.85
2573 6319 5.099042 TGGGATTTCACCTCTACTTTAGC 57.901 43.478 0.00 0.00 0.00 3.09
2574 6320 4.783227 TGGGATTTCACCTCTACTTTAGCT 59.217 41.667 0.00 0.00 0.00 3.32
2575 6321 5.962031 TGGGATTTCACCTCTACTTTAGCTA 59.038 40.000 0.00 0.00 0.00 3.32
2576 6322 6.127140 TGGGATTTCACCTCTACTTTAGCTAC 60.127 42.308 0.00 0.00 0.00 3.58
2577 6323 6.127140 GGGATTTCACCTCTACTTTAGCTACA 60.127 42.308 0.00 0.00 0.00 2.74
2578 6324 7.419172 GGGATTTCACCTCTACTTTAGCTACAT 60.419 40.741 0.00 0.00 0.00 2.29
2579 6325 7.988028 GGATTTCACCTCTACTTTAGCTACATT 59.012 37.037 0.00 0.00 0.00 2.71
2580 6326 9.384764 GATTTCACCTCTACTTTAGCTACATTT 57.615 33.333 0.00 0.00 0.00 2.32
2581 6327 8.773404 TTTCACCTCTACTTTAGCTACATTTC 57.227 34.615 0.00 0.00 0.00 2.17
2582 6328 7.476540 TCACCTCTACTTTAGCTACATTTCA 57.523 36.000 0.00 0.00 0.00 2.69
2583 6329 7.548097 TCACCTCTACTTTAGCTACATTTCAG 58.452 38.462 0.00 0.00 0.00 3.02
2584 6330 7.178628 TCACCTCTACTTTAGCTACATTTCAGT 59.821 37.037 0.00 0.00 0.00 3.41
2585 6331 7.489757 CACCTCTACTTTAGCTACATTTCAGTC 59.510 40.741 0.00 0.00 0.00 3.51
2586 6332 7.178628 ACCTCTACTTTAGCTACATTTCAGTCA 59.821 37.037 0.00 0.00 0.00 3.41
2587 6333 7.704472 CCTCTACTTTAGCTACATTTCAGTCAG 59.296 40.741 0.00 0.00 0.00 3.51
2588 6334 8.123639 TCTACTTTAGCTACATTTCAGTCAGT 57.876 34.615 0.00 0.00 0.00 3.41
2589 6335 8.585881 TCTACTTTAGCTACATTTCAGTCAGTT 58.414 33.333 0.00 0.00 0.00 3.16
2590 6336 7.426929 ACTTTAGCTACATTTCAGTCAGTTG 57.573 36.000 0.00 0.00 0.00 3.16
2591 6337 7.217200 ACTTTAGCTACATTTCAGTCAGTTGA 58.783 34.615 0.00 0.00 0.00 3.18
2592 6338 7.171678 ACTTTAGCTACATTTCAGTCAGTTGAC 59.828 37.037 4.09 4.09 45.08 3.18
2607 6353 7.209595 GTCAGTTGACTTTTCAATTTGTGTC 57.790 36.000 5.04 2.90 43.72 3.67
2608 6354 6.806249 GTCAGTTGACTTTTCAATTTGTGTCA 59.194 34.615 5.04 5.13 43.72 3.58
2609 6355 7.008628 GTCAGTTGACTTTTCAATTTGTGTCAG 59.991 37.037 5.04 3.46 43.72 3.51
2610 6356 6.808212 CAGTTGACTTTTCAATTTGTGTCAGT 59.192 34.615 12.70 5.69 43.72 3.41
2611 6357 7.008628 CAGTTGACTTTTCAATTTGTGTCAGTC 59.991 37.037 12.70 11.82 43.72 3.51
2612 6358 6.507958 TGACTTTTCAATTTGTGTCAGTCA 57.492 33.333 14.10 14.10 36.82 3.41
2613 6359 6.918626 TGACTTTTCAATTTGTGTCAGTCAA 58.081 32.000 15.01 0.00 36.52 3.18
2614 6360 7.546358 TGACTTTTCAATTTGTGTCAGTCAAT 58.454 30.769 15.01 0.00 36.52 2.57
2615 6361 8.034215 TGACTTTTCAATTTGTGTCAGTCAATT 58.966 29.630 15.01 0.00 36.52 2.32
2616 6362 8.776376 ACTTTTCAATTTGTGTCAGTCAATTT 57.224 26.923 0.00 0.00 0.00 1.82
2617 6363 9.218440 ACTTTTCAATTTGTGTCAGTCAATTTT 57.782 25.926 0.00 0.00 0.00 1.82
2618 6364 9.693157 CTTTTCAATTTGTGTCAGTCAATTTTC 57.307 29.630 0.00 0.00 0.00 2.29
2619 6365 7.769272 TTCAATTTGTGTCAGTCAATTTTCC 57.231 32.000 0.00 0.00 0.00 3.13
2620 6366 5.976534 TCAATTTGTGTCAGTCAATTTTCCG 59.023 36.000 0.00 0.00 0.00 4.30
2621 6367 4.974368 TTTGTGTCAGTCAATTTTCCGT 57.026 36.364 0.00 0.00 0.00 4.69
2622 6368 4.974368 TTGTGTCAGTCAATTTTCCGTT 57.026 36.364 0.00 0.00 0.00 4.44
2623 6369 4.545823 TGTGTCAGTCAATTTTCCGTTC 57.454 40.909 0.00 0.00 0.00 3.95
2624 6370 3.314080 TGTGTCAGTCAATTTTCCGTTCC 59.686 43.478 0.00 0.00 0.00 3.62
2625 6371 3.564225 GTGTCAGTCAATTTTCCGTTCCT 59.436 43.478 0.00 0.00 0.00 3.36
2626 6372 4.036380 GTGTCAGTCAATTTTCCGTTCCTT 59.964 41.667 0.00 0.00 0.00 3.36
2627 6373 4.036262 TGTCAGTCAATTTTCCGTTCCTTG 59.964 41.667 0.00 0.00 0.00 3.61
2628 6374 3.568007 TCAGTCAATTTTCCGTTCCTTGG 59.432 43.478 0.00 0.00 0.00 3.61
2629 6375 3.568007 CAGTCAATTTTCCGTTCCTTGGA 59.432 43.478 0.00 0.00 0.00 3.53
2630 6376 4.218417 CAGTCAATTTTCCGTTCCTTGGAT 59.782 41.667 0.00 0.00 34.91 3.41
2631 6377 4.459337 AGTCAATTTTCCGTTCCTTGGATC 59.541 41.667 0.00 0.00 34.91 3.36
2632 6378 3.438781 TCAATTTTCCGTTCCTTGGATCG 59.561 43.478 11.84 11.84 34.91 3.69
2633 6379 2.554370 TTTTCCGTTCCTTGGATCGT 57.446 45.000 15.98 0.00 34.91 3.73
2634 6380 1.803334 TTTCCGTTCCTTGGATCGTG 58.197 50.000 15.98 9.53 34.91 4.35
2635 6381 0.672401 TTCCGTTCCTTGGATCGTGC 60.672 55.000 15.98 0.00 34.91 5.34
2636 6382 1.079127 CCGTTCCTTGGATCGTGCT 60.079 57.895 15.98 0.00 0.00 4.40
2637 6383 0.673644 CCGTTCCTTGGATCGTGCTT 60.674 55.000 15.98 0.00 0.00 3.91
2638 6384 1.156736 CGTTCCTTGGATCGTGCTTT 58.843 50.000 10.87 0.00 0.00 3.51
2639 6385 1.135972 CGTTCCTTGGATCGTGCTTTG 60.136 52.381 10.87 0.00 0.00 2.77
2640 6386 2.151202 GTTCCTTGGATCGTGCTTTGA 58.849 47.619 0.00 0.00 0.00 2.69
2641 6387 2.099141 TCCTTGGATCGTGCTTTGAG 57.901 50.000 0.00 0.00 0.00 3.02
2642 6388 1.623311 TCCTTGGATCGTGCTTTGAGA 59.377 47.619 0.00 0.00 0.00 3.27
2643 6389 2.237143 TCCTTGGATCGTGCTTTGAGAT 59.763 45.455 0.00 0.00 0.00 2.75
2644 6390 2.611292 CCTTGGATCGTGCTTTGAGATC 59.389 50.000 0.00 0.00 39.84 2.75
2645 6391 3.529533 CTTGGATCGTGCTTTGAGATCT 58.470 45.455 0.00 0.00 40.28 2.75
2646 6392 2.897436 TGGATCGTGCTTTGAGATCTG 58.103 47.619 0.00 0.00 40.28 2.90
2647 6393 2.234661 TGGATCGTGCTTTGAGATCTGT 59.765 45.455 0.00 0.00 40.28 3.41
2648 6394 2.606725 GGATCGTGCTTTGAGATCTGTG 59.393 50.000 0.00 0.00 40.28 3.66
2649 6395 2.820059 TCGTGCTTTGAGATCTGTGT 57.180 45.000 0.00 0.00 0.00 3.72
2650 6396 3.111853 TCGTGCTTTGAGATCTGTGTT 57.888 42.857 0.00 0.00 0.00 3.32
2651 6397 2.802247 TCGTGCTTTGAGATCTGTGTTG 59.198 45.455 0.00 0.00 0.00 3.33
2652 6398 2.545526 CGTGCTTTGAGATCTGTGTTGT 59.454 45.455 0.00 0.00 0.00 3.32
2653 6399 3.002656 CGTGCTTTGAGATCTGTGTTGTT 59.997 43.478 0.00 0.00 0.00 2.83
2654 6400 4.496341 CGTGCTTTGAGATCTGTGTTGTTT 60.496 41.667 0.00 0.00 0.00 2.83
2655 6401 5.343249 GTGCTTTGAGATCTGTGTTGTTTT 58.657 37.500 0.00 0.00 0.00 2.43
2656 6402 5.456822 GTGCTTTGAGATCTGTGTTGTTTTC 59.543 40.000 0.00 0.00 0.00 2.29
2657 6403 5.125257 TGCTTTGAGATCTGTGTTGTTTTCA 59.875 36.000 0.00 0.00 0.00 2.69
2658 6404 6.183360 TGCTTTGAGATCTGTGTTGTTTTCAT 60.183 34.615 0.00 0.00 0.00 2.57
2659 6405 6.698766 GCTTTGAGATCTGTGTTGTTTTCATT 59.301 34.615 0.00 0.00 0.00 2.57
2660 6406 7.223387 GCTTTGAGATCTGTGTTGTTTTCATTT 59.777 33.333 0.00 0.00 0.00 2.32
2661 6407 9.090692 CTTTGAGATCTGTGTTGTTTTCATTTT 57.909 29.630 0.00 0.00 0.00 1.82
2662 6408 9.434420 TTTGAGATCTGTGTTGTTTTCATTTTT 57.566 25.926 0.00 0.00 0.00 1.94
2683 6429 4.751767 TTTTCAATTCTGTTGTTGGGCT 57.248 36.364 0.00 0.00 0.00 5.19
2684 6430 3.731652 TTCAATTCTGTTGTTGGGCTG 57.268 42.857 0.00 0.00 0.00 4.85
2685 6431 1.962807 TCAATTCTGTTGTTGGGCTGG 59.037 47.619 0.00 0.00 0.00 4.85
2686 6432 1.001181 CAATTCTGTTGTTGGGCTGGG 59.999 52.381 0.00 0.00 0.00 4.45
2687 6433 0.188342 ATTCTGTTGTTGGGCTGGGT 59.812 50.000 0.00 0.00 0.00 4.51
2688 6434 0.032615 TTCTGTTGTTGGGCTGGGTT 60.033 50.000 0.00 0.00 0.00 4.11
2689 6435 0.847373 TCTGTTGTTGGGCTGGGTTA 59.153 50.000 0.00 0.00 0.00 2.85
2690 6436 0.958822 CTGTTGTTGGGCTGGGTTAC 59.041 55.000 0.00 0.00 0.00 2.50
2691 6437 0.259065 TGTTGTTGGGCTGGGTTACA 59.741 50.000 0.00 0.00 0.00 2.41
2692 6438 1.342076 TGTTGTTGGGCTGGGTTACAA 60.342 47.619 0.00 0.00 0.00 2.41
2693 6439 1.339929 GTTGTTGGGCTGGGTTACAAG 59.660 52.381 0.00 0.00 30.16 3.16
2694 6440 0.178975 TGTTGGGCTGGGTTACAAGG 60.179 55.000 0.00 0.00 0.00 3.61
2695 6441 0.111639 GTTGGGCTGGGTTACAAGGA 59.888 55.000 0.00 0.00 0.00 3.36
2696 6442 0.854218 TTGGGCTGGGTTACAAGGAA 59.146 50.000 0.00 0.00 0.00 3.36
2697 6443 1.080638 TGGGCTGGGTTACAAGGAAT 58.919 50.000 0.00 0.00 0.00 3.01
2698 6444 1.005450 TGGGCTGGGTTACAAGGAATC 59.995 52.381 0.00 0.00 0.00 2.52
2699 6445 1.379527 GGCTGGGTTACAAGGAATCG 58.620 55.000 0.00 0.00 0.00 3.34
2700 6446 1.065709 GGCTGGGTTACAAGGAATCGA 60.066 52.381 0.00 0.00 0.00 3.59
2701 6447 2.421529 GGCTGGGTTACAAGGAATCGAT 60.422 50.000 0.00 0.00 0.00 3.59
2702 6448 3.279434 GCTGGGTTACAAGGAATCGATT 58.721 45.455 11.20 11.20 0.00 3.34
2703 6449 3.065371 GCTGGGTTACAAGGAATCGATTG 59.935 47.826 16.96 5.04 0.00 2.67
2704 6450 4.513442 CTGGGTTACAAGGAATCGATTGA 58.487 43.478 16.96 0.00 0.00 2.57
2705 6451 4.912586 TGGGTTACAAGGAATCGATTGAA 58.087 39.130 16.96 0.00 0.00 2.69
2706 6452 5.505780 TGGGTTACAAGGAATCGATTGAAT 58.494 37.500 16.96 0.00 0.00 2.57
2707 6453 5.588648 TGGGTTACAAGGAATCGATTGAATC 59.411 40.000 16.96 0.10 0.00 2.52
2722 6468 4.974368 TTGAATCGTTGTTTTGGTCAGT 57.026 36.364 0.00 0.00 0.00 3.41
2723 6469 4.545823 TGAATCGTTGTTTTGGTCAGTC 57.454 40.909 0.00 0.00 0.00 3.51
2724 6470 3.001838 TGAATCGTTGTTTTGGTCAGTCG 59.998 43.478 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 54 1.127567 CCTTGGACTCTGGGTCACCA 61.128 60.000 10.30 0.00 46.16 4.17
56 65 1.271434 GGTTTCCTTGGACTCTGGGTC 60.271 57.143 0.00 0.00 43.79 4.46
57 66 0.771755 GGTTTCCTTGGACTCTGGGT 59.228 55.000 0.00 0.00 0.00 4.51
64 83 1.670083 CGTCCGGGTTTCCTTGGAC 60.670 63.158 0.00 15.44 41.82 4.02
106 126 3.249973 CTCGTGATCCGCCGCGATA 62.250 63.158 15.93 1.81 46.10 2.92
110 130 3.255379 GAACTCGTGATCCGCCGC 61.255 66.667 0.00 0.00 36.19 6.53
111 131 1.413767 CTTGAACTCGTGATCCGCCG 61.414 60.000 0.00 0.00 36.19 6.46
112 132 1.084370 CCTTGAACTCGTGATCCGCC 61.084 60.000 0.00 0.00 36.19 6.13
113 133 1.696832 GCCTTGAACTCGTGATCCGC 61.697 60.000 0.00 0.00 36.19 5.54
114 134 1.413767 CGCCTTGAACTCGTGATCCG 61.414 60.000 0.00 0.00 38.13 4.18
115 135 1.696832 GCGCCTTGAACTCGTGATCC 61.697 60.000 0.00 0.00 0.00 3.36
118 138 2.733218 CGCGCCTTGAACTCGTGA 60.733 61.111 0.00 0.00 35.98 4.35
121 141 3.843240 GAGCGCGCCTTGAACTCG 61.843 66.667 30.33 0.00 0.00 4.18
122 142 3.843240 CGAGCGCGCCTTGAACTC 61.843 66.667 30.33 16.04 0.00 3.01
123 143 4.664677 ACGAGCGCGCCTTGAACT 62.665 61.111 30.33 7.05 42.48 3.01
124 144 4.430423 CACGAGCGCGCCTTGAAC 62.430 66.667 30.33 11.40 42.48 3.18
125 145 4.961511 ACACGAGCGCGCCTTGAA 62.962 61.111 30.33 0.00 42.48 2.69
149 193 2.030185 CGGTGTACTATCCGCTTAGCAT 60.030 50.000 4.70 0.00 40.28 3.79
153 197 2.346766 TCCGGTGTACTATCCGCTTA 57.653 50.000 15.43 4.75 44.63 3.09
154 198 1.700955 ATCCGGTGTACTATCCGCTT 58.299 50.000 15.43 5.86 44.63 4.68
155 199 1.700955 AATCCGGTGTACTATCCGCT 58.299 50.000 15.43 5.99 44.63 5.52
158 202 2.816087 TCGCTAATCCGGTGTACTATCC 59.184 50.000 0.00 0.00 0.00 2.59
159 203 4.494350 TTCGCTAATCCGGTGTACTATC 57.506 45.455 0.00 0.00 0.00 2.08
161 205 3.489738 GCTTTCGCTAATCCGGTGTACTA 60.490 47.826 0.00 0.00 0.00 1.82
163 207 1.591619 GCTTTCGCTAATCCGGTGTAC 59.408 52.381 0.00 0.00 0.00 2.90
164 208 1.799917 CGCTTTCGCTAATCCGGTGTA 60.800 52.381 0.00 0.00 0.00 2.90
166 210 0.804544 TCGCTTTCGCTAATCCGGTG 60.805 55.000 0.00 0.00 35.26 4.94
167 211 0.104304 ATCGCTTTCGCTAATCCGGT 59.896 50.000 0.00 0.00 35.26 5.28
168 212 0.508641 CATCGCTTTCGCTAATCCGG 59.491 55.000 0.00 0.00 35.26 5.14
170 214 0.235926 GCCATCGCTTTCGCTAATCC 59.764 55.000 0.00 0.00 35.26 3.01
172 216 0.657840 GTGCCATCGCTTTCGCTAAT 59.342 50.000 0.00 0.00 35.36 1.73
173 217 1.366111 GGTGCCATCGCTTTCGCTAA 61.366 55.000 0.00 0.00 35.36 3.09
175 219 3.127533 GGTGCCATCGCTTTCGCT 61.128 61.111 0.00 0.00 35.36 4.93
178 222 2.409870 CCAGGGTGCCATCGCTTTC 61.410 63.158 0.00 0.00 35.36 2.62
179 223 2.361610 CCAGGGTGCCATCGCTTT 60.362 61.111 0.00 0.00 35.36 3.51
195 239 1.527844 GGCTGATCATGGAGTGGCC 60.528 63.158 0.00 0.00 37.10 5.36
199 243 2.224378 CCGTAATGGCTGATCATGGAGT 60.224 50.000 0.00 0.00 0.00 3.85
201 245 2.549064 CCGTAATGGCTGATCATGGA 57.451 50.000 0.00 0.00 0.00 3.41
276 349 2.528127 TTCACCCCTCCGCCTTGA 60.528 61.111 0.00 0.00 0.00 3.02
364 439 0.324943 ATGGTTAAGCTGGCACGAGT 59.675 50.000 6.19 0.00 0.00 4.18
378 453 1.153086 GAGCGATGCAGGGATGGTT 60.153 57.895 0.00 0.00 0.00 3.67
448 527 3.381908 TGTTGCTTTCATAAACCGGTTGT 59.618 39.130 23.08 13.50 0.00 3.32
506 601 0.541863 AATGCCGACCCGATTTCTCT 59.458 50.000 0.00 0.00 0.00 3.10
510 605 2.414785 GGCAATGCCGACCCGATTT 61.415 57.895 9.14 0.00 39.62 2.17
663 768 9.779237 CGCAGTACAAGAAAATAGTATTAATCG 57.221 33.333 0.00 0.00 0.00 3.34
674 808 0.871722 TGCGCGCAGTACAAGAAAAT 59.128 45.000 33.09 0.00 0.00 1.82
676 810 1.859398 CTGCGCGCAGTACAAGAAA 59.141 52.632 44.44 16.25 39.10 2.52
736 1043 4.738124 TCAGCGTCAAAATTGTTGTCAAA 58.262 34.783 0.00 0.00 37.11 2.69
742 1049 9.691362 AATACTAATTTCAGCGTCAAAATTGTT 57.309 25.926 11.49 4.27 36.17 2.83
744 1051 9.340695 TGAATACTAATTTCAGCGTCAAAATTG 57.659 29.630 11.49 0.00 36.17 2.32
803 1119 2.264480 CACCCGAATCGGTCTGCA 59.736 61.111 21.12 0.00 46.80 4.41
867 1202 6.821665 ACCATTGCTAATTAAACTCGAGCTAA 59.178 34.615 13.61 11.03 34.19 3.09
872 1208 7.175990 AGGAAAACCATTGCTAATTAAACTCGA 59.824 33.333 0.00 0.00 0.00 4.04
885 1221 9.448438 AATTATTAAGGAAAGGAAAACCATTGC 57.552 29.630 0.00 0.00 0.00 3.56
908 1244 4.941263 TGTGCCTGCTCGAGTAAATTAATT 59.059 37.500 15.13 0.00 0.00 1.40
910 1246 3.932822 TGTGCCTGCTCGAGTAAATTAA 58.067 40.909 15.13 0.00 0.00 1.40
912 1248 2.472695 TGTGCCTGCTCGAGTAAATT 57.527 45.000 15.13 0.00 0.00 1.82
914 1250 1.070134 ACTTGTGCCTGCTCGAGTAAA 59.930 47.619 15.13 0.00 33.81 2.01
916 1252 0.679505 AACTTGTGCCTGCTCGAGTA 59.320 50.000 15.13 8.96 34.28 2.59
922 1269 2.804212 GCAATTTCAACTTGTGCCTGCT 60.804 45.455 0.00 0.00 0.00 4.24
923 1270 1.528161 GCAATTTCAACTTGTGCCTGC 59.472 47.619 0.00 0.00 0.00 4.85
931 1278 2.893489 GACAGAGGGGCAATTTCAACTT 59.107 45.455 0.00 0.00 0.00 2.66
934 1281 2.555227 GGAGACAGAGGGGCAATTTCAA 60.555 50.000 0.00 0.00 0.00 2.69
936 1283 1.683319 GGGAGACAGAGGGGCAATTTC 60.683 57.143 0.00 0.00 0.00 2.17
940 1310 1.613630 GAGGGAGACAGAGGGGCAA 60.614 63.158 0.00 0.00 0.00 4.52
950 1321 2.090377 TATAGGCCGGGGAGGGAGAC 62.090 65.000 2.18 0.00 41.48 3.36
1070 1521 1.943340 CCGTCGACATGATGAGAGAGA 59.057 52.381 17.16 0.00 35.48 3.10
1071 1522 1.599171 GCCGTCGACATGATGAGAGAG 60.599 57.143 17.16 0.00 35.48 3.20
1252 1741 0.447801 GAACACATGCATGACCGACC 59.552 55.000 32.75 12.24 0.00 4.79
1269 1758 1.455959 CGGGTGGTTTGTTGGGGAA 60.456 57.895 0.00 0.00 0.00 3.97
1275 1764 2.203437 GAGCCCGGGTGGTTTGTT 60.203 61.111 24.63 0.00 36.04 2.83
1278 1767 3.837570 GAACGAGCCCGGGTGGTTT 62.838 63.158 24.63 10.90 40.78 3.27
1704 2371 7.009631 CCTTCTATACAGCGATCGGAATTATTG 59.990 40.741 18.30 0.00 0.00 1.90
1766 2453 3.877508 CCAGGAATCGAATTGGGTCTTAC 59.122 47.826 0.00 0.00 0.00 2.34
1824 2543 3.093057 GAGGAAGAAGAGGCTCACTGTA 58.907 50.000 18.26 0.00 0.00 2.74
1825 2544 1.899142 GAGGAAGAAGAGGCTCACTGT 59.101 52.381 18.26 0.00 0.00 3.55
1864 2583 0.179202 CAGAGACGACGAGCTCACTG 60.179 60.000 15.40 4.49 33.62 3.66
1967 2762 8.791675 TGTCTGCATTTTGTCACTCATTAATTA 58.208 29.630 0.00 0.00 0.00 1.40
1968 2763 7.596248 GTGTCTGCATTTTGTCACTCATTAATT 59.404 33.333 0.00 0.00 0.00 1.40
1970 2765 6.437928 GTGTCTGCATTTTGTCACTCATTAA 58.562 36.000 0.00 0.00 0.00 1.40
1971 2766 5.334028 CGTGTCTGCATTTTGTCACTCATTA 60.334 40.000 0.00 0.00 0.00 1.90
2076 2958 7.382218 CCACATTCCAGAAACATAAACAGAAAC 59.618 37.037 0.00 0.00 0.00 2.78
2077 2959 7.432869 CCACATTCCAGAAACATAAACAGAAA 58.567 34.615 0.00 0.00 0.00 2.52
2078 2960 6.015519 CCCACATTCCAGAAACATAAACAGAA 60.016 38.462 0.00 0.00 0.00 3.02
2079 2961 5.476599 CCCACATTCCAGAAACATAAACAGA 59.523 40.000 0.00 0.00 0.00 3.41
2080 2962 5.243730 ACCCACATTCCAGAAACATAAACAG 59.756 40.000 0.00 0.00 0.00 3.16
2081 2963 5.010516 CACCCACATTCCAGAAACATAAACA 59.989 40.000 0.00 0.00 0.00 2.83
2082 2964 5.010617 ACACCCACATTCCAGAAACATAAAC 59.989 40.000 0.00 0.00 0.00 2.01
2083 2965 5.010516 CACACCCACATTCCAGAAACATAAA 59.989 40.000 0.00 0.00 0.00 1.40
2084 2966 4.522405 CACACCCACATTCCAGAAACATAA 59.478 41.667 0.00 0.00 0.00 1.90
2085 2967 4.078537 CACACCCACATTCCAGAAACATA 58.921 43.478 0.00 0.00 0.00 2.29
2086 2968 2.892852 CACACCCACATTCCAGAAACAT 59.107 45.455 0.00 0.00 0.00 2.71
2087 2969 2.305928 CACACCCACATTCCAGAAACA 58.694 47.619 0.00 0.00 0.00 2.83
2097 3024 2.172483 GAGGCGAGACACACCCACAT 62.172 60.000 0.00 0.00 0.00 3.21
2216 3152 1.153066 TGCTTCAAGTTGCGGGACA 60.153 52.632 0.00 0.00 0.00 4.02
2218 3154 2.250939 CGTGCTTCAAGTTGCGGGA 61.251 57.895 0.00 0.00 0.00 5.14
2292 3229 4.631813 AGAAGAAAAATCCTCGGTTCATCG 59.368 41.667 0.00 0.00 0.00 3.84
2424 6159 5.120830 ACGAAGAAAAATCCTCTGTTCATCG 59.879 40.000 7.95 7.95 43.20 3.84
2508 6243 4.944930 AGATAGTACGACTGCTCTGAAAGT 59.055 41.667 0.00 0.00 33.76 2.66
2522 6257 1.001597 GCCGTCCCTCAAGATAGTACG 60.002 57.143 0.00 0.00 0.00 3.67
2530 6265 2.202756 GCTACGCCGTCCCTCAAG 60.203 66.667 0.00 0.00 0.00 3.02
2565 6311 8.364894 TCAACTGACTGAAATGTAGCTAAAGTA 58.635 33.333 0.00 0.00 0.00 2.24
2566 6312 7.171678 GTCAACTGACTGAAATGTAGCTAAAGT 59.828 37.037 0.00 0.00 41.65 2.66
2567 6313 7.513968 GTCAACTGACTGAAATGTAGCTAAAG 58.486 38.462 0.00 0.00 41.65 1.85
2568 6314 7.421530 GTCAACTGACTGAAATGTAGCTAAA 57.578 36.000 0.00 0.00 41.65 1.85
2583 6329 6.806249 TGACACAAATTGAAAAGTCAACTGAC 59.194 34.615 0.00 1.40 46.40 3.51
2584 6330 6.918626 TGACACAAATTGAAAAGTCAACTGA 58.081 32.000 0.00 0.00 46.40 3.41
2585 6331 6.808212 ACTGACACAAATTGAAAAGTCAACTG 59.192 34.615 0.00 0.79 46.40 3.16
2586 6332 6.924111 ACTGACACAAATTGAAAAGTCAACT 58.076 32.000 0.00 0.00 46.40 3.16
2587 6333 6.806249 TGACTGACACAAATTGAAAAGTCAAC 59.194 34.615 16.55 12.72 46.40 3.18
2589 6335 6.507958 TGACTGACACAAATTGAAAAGTCA 57.492 33.333 15.62 15.62 38.72 3.41
2590 6336 7.992180 ATTGACTGACACAAATTGAAAAGTC 57.008 32.000 0.00 7.75 35.15 3.01
2591 6337 8.776376 AAATTGACTGACACAAATTGAAAAGT 57.224 26.923 0.00 0.00 0.00 2.66
2592 6338 9.693157 GAAAATTGACTGACACAAATTGAAAAG 57.307 29.630 0.00 0.00 0.00 2.27
2593 6339 8.663911 GGAAAATTGACTGACACAAATTGAAAA 58.336 29.630 0.00 0.00 0.00 2.29
2594 6340 7.009999 CGGAAAATTGACTGACACAAATTGAAA 59.990 33.333 0.00 0.00 0.00 2.69
2595 6341 6.475076 CGGAAAATTGACTGACACAAATTGAA 59.525 34.615 0.00 0.00 0.00 2.69
2596 6342 5.976534 CGGAAAATTGACTGACACAAATTGA 59.023 36.000 0.00 0.00 0.00 2.57
2597 6343 5.748152 ACGGAAAATTGACTGACACAAATTG 59.252 36.000 0.00 0.00 0.00 2.32
2598 6344 5.901552 ACGGAAAATTGACTGACACAAATT 58.098 33.333 0.00 0.00 0.00 1.82
2599 6345 5.514274 ACGGAAAATTGACTGACACAAAT 57.486 34.783 0.00 0.00 0.00 2.32
2600 6346 4.974368 ACGGAAAATTGACTGACACAAA 57.026 36.364 0.00 0.00 0.00 2.83
2601 6347 4.201970 GGAACGGAAAATTGACTGACACAA 60.202 41.667 0.00 0.00 0.00 3.33
2602 6348 3.314080 GGAACGGAAAATTGACTGACACA 59.686 43.478 0.00 0.00 0.00 3.72
2603 6349 3.564225 AGGAACGGAAAATTGACTGACAC 59.436 43.478 0.00 0.00 0.00 3.67
2604 6350 3.815809 AGGAACGGAAAATTGACTGACA 58.184 40.909 0.00 0.00 0.00 3.58
2605 6351 4.537015 CAAGGAACGGAAAATTGACTGAC 58.463 43.478 0.00 0.00 0.00 3.51
2606 6352 3.568007 CCAAGGAACGGAAAATTGACTGA 59.432 43.478 0.00 0.00 0.00 3.41
2607 6353 3.568007 TCCAAGGAACGGAAAATTGACTG 59.432 43.478 0.00 0.00 0.00 3.51
2608 6354 3.827722 TCCAAGGAACGGAAAATTGACT 58.172 40.909 0.00 0.00 0.00 3.41
2609 6355 4.671766 CGATCCAAGGAACGGAAAATTGAC 60.672 45.833 10.51 0.00 36.89 3.18
2610 6356 3.438781 CGATCCAAGGAACGGAAAATTGA 59.561 43.478 10.51 0.00 36.89 2.57
2611 6357 3.190535 ACGATCCAAGGAACGGAAAATTG 59.809 43.478 20.43 0.00 43.18 2.32
2612 6358 3.190535 CACGATCCAAGGAACGGAAAATT 59.809 43.478 20.43 0.00 43.18 1.82
2613 6359 2.747446 CACGATCCAAGGAACGGAAAAT 59.253 45.455 20.43 0.00 43.18 1.82
2614 6360 2.147958 CACGATCCAAGGAACGGAAAA 58.852 47.619 20.43 0.00 43.18 2.29
2615 6361 1.803334 CACGATCCAAGGAACGGAAA 58.197 50.000 20.43 0.00 43.18 3.13
2616 6362 0.672401 GCACGATCCAAGGAACGGAA 60.672 55.000 20.43 0.00 43.18 4.30
2617 6363 1.079405 GCACGATCCAAGGAACGGA 60.079 57.895 20.43 0.00 43.18 4.69
2618 6364 0.673644 AAGCACGATCCAAGGAACGG 60.674 55.000 20.43 11.68 43.18 4.44
2619 6365 1.135972 CAAAGCACGATCCAAGGAACG 60.136 52.381 15.90 15.90 44.19 3.95
2620 6366 2.151202 TCAAAGCACGATCCAAGGAAC 58.849 47.619 0.00 0.00 0.00 3.62
2621 6367 2.038426 TCTCAAAGCACGATCCAAGGAA 59.962 45.455 0.00 0.00 0.00 3.36
2622 6368 1.623311 TCTCAAAGCACGATCCAAGGA 59.377 47.619 0.00 0.00 0.00 3.36
2623 6369 2.099141 TCTCAAAGCACGATCCAAGG 57.901 50.000 0.00 0.00 0.00 3.61
2624 6370 3.309138 CAGATCTCAAAGCACGATCCAAG 59.691 47.826 0.00 0.00 35.34 3.61
2625 6371 3.264947 CAGATCTCAAAGCACGATCCAA 58.735 45.455 0.00 0.00 35.34 3.53
2626 6372 2.234661 ACAGATCTCAAAGCACGATCCA 59.765 45.455 0.00 0.00 35.34 3.41
2627 6373 2.606725 CACAGATCTCAAAGCACGATCC 59.393 50.000 0.00 0.00 35.34 3.36
2628 6374 3.257393 ACACAGATCTCAAAGCACGATC 58.743 45.455 0.00 0.00 35.06 3.69
2629 6375 3.325293 ACACAGATCTCAAAGCACGAT 57.675 42.857 0.00 0.00 0.00 3.73
2630 6376 2.802247 CAACACAGATCTCAAAGCACGA 59.198 45.455 0.00 0.00 0.00 4.35
2631 6377 2.545526 ACAACACAGATCTCAAAGCACG 59.454 45.455 0.00 0.00 0.00 5.34
2632 6378 4.558538 AACAACACAGATCTCAAAGCAC 57.441 40.909 0.00 0.00 0.00 4.40
2633 6379 5.125257 TGAAAACAACACAGATCTCAAAGCA 59.875 36.000 0.00 0.00 0.00 3.91
2634 6380 5.581605 TGAAAACAACACAGATCTCAAAGC 58.418 37.500 0.00 0.00 0.00 3.51
2635 6381 8.638685 AAATGAAAACAACACAGATCTCAAAG 57.361 30.769 0.00 0.00 0.00 2.77
2636 6382 9.434420 AAAAATGAAAACAACACAGATCTCAAA 57.566 25.926 0.00 0.00 0.00 2.69
2661 6407 4.874966 CAGCCCAACAACAGAATTGAAAAA 59.125 37.500 0.00 0.00 0.00 1.94
2662 6408 4.440880 CAGCCCAACAACAGAATTGAAAA 58.559 39.130 0.00 0.00 0.00 2.29
2663 6409 3.181467 CCAGCCCAACAACAGAATTGAAA 60.181 43.478 0.00 0.00 0.00 2.69
2664 6410 2.364970 CCAGCCCAACAACAGAATTGAA 59.635 45.455 0.00 0.00 0.00 2.69
2665 6411 1.962807 CCAGCCCAACAACAGAATTGA 59.037 47.619 0.00 0.00 0.00 2.57
2666 6412 1.001181 CCCAGCCCAACAACAGAATTG 59.999 52.381 0.00 0.00 0.00 2.32
2667 6413 1.341080 CCCAGCCCAACAACAGAATT 58.659 50.000 0.00 0.00 0.00 2.17
2668 6414 0.188342 ACCCAGCCCAACAACAGAAT 59.812 50.000 0.00 0.00 0.00 2.40
2669 6415 0.032615 AACCCAGCCCAACAACAGAA 60.033 50.000 0.00 0.00 0.00 3.02
2670 6416 0.847373 TAACCCAGCCCAACAACAGA 59.153 50.000 0.00 0.00 0.00 3.41
2671 6417 0.958822 GTAACCCAGCCCAACAACAG 59.041 55.000 0.00 0.00 0.00 3.16
2672 6418 0.259065 TGTAACCCAGCCCAACAACA 59.741 50.000 0.00 0.00 0.00 3.33
2673 6419 1.339929 CTTGTAACCCAGCCCAACAAC 59.660 52.381 0.00 0.00 0.00 3.32
2674 6420 1.698506 CTTGTAACCCAGCCCAACAA 58.301 50.000 0.00 0.00 0.00 2.83
2675 6421 0.178975 CCTTGTAACCCAGCCCAACA 60.179 55.000 0.00 0.00 0.00 3.33
2676 6422 0.111639 TCCTTGTAACCCAGCCCAAC 59.888 55.000 0.00 0.00 0.00 3.77
2677 6423 0.854218 TTCCTTGTAACCCAGCCCAA 59.146 50.000 0.00 0.00 0.00 4.12
2678 6424 1.005450 GATTCCTTGTAACCCAGCCCA 59.995 52.381 0.00 0.00 0.00 5.36
2679 6425 1.763968 GATTCCTTGTAACCCAGCCC 58.236 55.000 0.00 0.00 0.00 5.19
2680 6426 1.065709 TCGATTCCTTGTAACCCAGCC 60.066 52.381 0.00 0.00 0.00 4.85
2681 6427 2.396590 TCGATTCCTTGTAACCCAGC 57.603 50.000 0.00 0.00 0.00 4.85
2682 6428 4.513442 TCAATCGATTCCTTGTAACCCAG 58.487 43.478 7.92 0.00 0.00 4.45
2683 6429 4.561500 TCAATCGATTCCTTGTAACCCA 57.438 40.909 7.92 0.00 0.00 4.51
2684 6430 6.061231 GATTCAATCGATTCCTTGTAACCC 57.939 41.667 7.92 0.00 0.00 4.11
2699 6445 5.519722 ACTGACCAAAACAACGATTCAATC 58.480 37.500 0.00 0.00 0.00 2.67
2700 6446 5.514274 ACTGACCAAAACAACGATTCAAT 57.486 34.783 0.00 0.00 0.00 2.57
2701 6447 4.495019 CGACTGACCAAAACAACGATTCAA 60.495 41.667 0.00 0.00 0.00 2.69
2702 6448 3.001838 CGACTGACCAAAACAACGATTCA 59.998 43.478 0.00 0.00 0.00 2.57
2703 6449 3.541711 CGACTGACCAAAACAACGATTC 58.458 45.455 0.00 0.00 0.00 2.52
2704 6450 3.602390 CGACTGACCAAAACAACGATT 57.398 42.857 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.