Multiple sequence alignment - TraesCS7D01G464600

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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 TraesCS7D01G464600 chr7D 100.000 3203 0 0 1 3203 579101370 579098168 0.000000e+00 5915.0
1 TraesCS7D01G464600 chr7D 89.571 489 41 10 2717 3203 138304565 138304085 2.110000e-171 612.0
2 TraesCS7D01G464600 chr7D 85.166 573 76 9 1640 2208 75948190 75948757 2.140000e-161 579.0
3 TraesCS7D01G464600 chr7D 85.214 514 48 14 2702 3202 15216988 15216490 1.330000e-138 503.0
4 TraesCS7D01G464600 chr7D 76.042 192 46 0 1338 1529 478333588 478333779 2.030000e-17 100.0
5 TraesCS7D01G464600 chr7D 94.118 51 3 0 2497 2547 511662117 511662067 9.530000e-11 78.7
6 TraesCS7D01G464600 chr7B 91.975 2268 138 22 247 2502 643461485 643463720 0.000000e+00 3140.0
7 TraesCS7D01G464600 chr7B 94.881 1387 44 14 1342 2704 643292475 643291092 0.000000e+00 2143.0
8 TraesCS7D01G464600 chr7B 93.150 1197 67 9 353 1548 643297112 643295930 0.000000e+00 1742.0
9 TraesCS7D01G464600 chr7B 91.402 977 67 10 1546 2514 643295825 643294858 0.000000e+00 1323.0
10 TraesCS7D01G464600 chr7B 94.000 200 12 0 1009 1208 643292746 643292547 1.440000e-78 303.0
11 TraesCS7D01G464600 chr7B 88.060 67 5 1 369 435 34829912 34829849 3.430000e-10 76.8
12 TraesCS7D01G464600 chr7B 77.869 122 18 6 2817 2934 11305866 11305982 2.060000e-07 67.6
13 TraesCS7D01G464600 chr7B 91.111 45 4 0 2701 2745 565095756 565095800 9.590000e-06 62.1
14 TraesCS7D01G464600 chr7A 95.211 1211 44 6 1 1208 670948228 670947029 0.000000e+00 1903.0
15 TraesCS7D01G464600 chr7A 90.748 1351 70 27 1342 2674 670946926 670945613 0.000000e+00 1751.0
16 TraesCS7D01G464600 chr7A 85.565 575 70 12 1640 2208 80133504 80134071 9.900000e-165 590.0
17 TraesCS7D01G464600 chr7A 89.352 216 16 3 2305 2516 670945106 670944894 6.810000e-67 265.0
18 TraesCS7D01G464600 chr7A 82.867 286 23 13 2434 2702 670945606 670945330 1.920000e-57 233.0
19 TraesCS7D01G464600 chr7A 77.070 157 25 11 2814 2962 681242134 681242287 2.650000e-11 80.5
20 TraesCS7D01G464600 chr7A 90.741 54 5 0 1478 1531 473884775 473884828 4.430000e-09 73.1
21 TraesCS7D01G464600 chr6A 81.390 1209 172 42 1004 2201 24031427 24030261 0.000000e+00 937.0
22 TraesCS7D01G464600 chr6A 83.058 909 105 29 1311 2201 23896408 23895531 0.000000e+00 780.0
23 TraesCS7D01G464600 chr6A 80.981 999 146 33 1347 2326 24048995 24049968 0.000000e+00 752.0
24 TraesCS7D01G464600 chr6A 84.524 252 36 3 966 1216 24048598 24048847 2.470000e-61 246.0
25 TraesCS7D01G464600 chr6A 83.761 234 36 2 1010 1241 23952356 23952123 1.500000e-53 220.0
26 TraesCS7D01G464600 chr6A 85.075 201 28 2 1009 1208 23896764 23896565 1.510000e-48 204.0
27 TraesCS7D01G464600 chr6A 100.000 35 0 0 2291 2325 24030186 24030152 7.420000e-07 65.8
28 TraesCS7D01G464600 chr3B 95.591 499 18 4 2707 3202 749994326 749993829 0.000000e+00 797.0
29 TraesCS7D01G464600 chr3B 88.060 268 26 5 2915 3181 819707456 819707194 2.400000e-81 313.0
30 TraesCS7D01G464600 chr6B 83.662 863 107 18 1347 2201 42005395 42004559 0.000000e+00 782.0
31 TraesCS7D01G464600 chr6B 81.946 925 130 28 1290 2201 42318490 42317590 0.000000e+00 749.0
32 TraesCS7D01G464600 chr6B 85.774 239 32 2 1004 1241 42318854 42318617 5.300000e-63 252.0
33 TraesCS7D01G464600 chr6B 85.169 236 31 3 1010 1241 42393066 42393301 4.130000e-59 239.0
34 TraesCS7D01G464600 chr6B 82.479 234 39 2 1010 1241 42211963 42211730 1.510000e-48 204.0
35 TraesCS7D01G464600 chr6B 88.636 132 13 2 2570 2700 512252953 512253083 3.310000e-35 159.0
36 TraesCS7D01G464600 chr6D 83.314 863 110 19 1347 2201 25804725 25803889 0.000000e+00 765.0
37 TraesCS7D01G464600 chr6D 78.783 1216 201 38 1010 2217 25852617 25851451 0.000000e+00 763.0
38 TraesCS7D01G464600 chr6D 80.344 1048 160 32 1311 2328 25915301 25916332 0.000000e+00 752.0
39 TraesCS7D01G464600 chr6D 86.722 241 28 3 1004 1241 25880087 25879848 6.810000e-67 265.0
40 TraesCS7D01G464600 chr6D 86.538 208 28 0 1009 1216 25914992 25915199 2.490000e-56 230.0
41 TraesCS7D01G464600 chr6D 81.818 231 42 0 1010 1240 25827580 25827350 9.070000e-46 195.0
42 TraesCS7D01G464600 chr2A 87.247 494 42 12 2701 3181 708522791 708522306 7.810000e-151 544.0
43 TraesCS7D01G464600 chr1D 88.667 450 46 5 2701 3146 86108707 86108259 7.810000e-151 544.0
44 TraesCS7D01G464600 chr5D 90.050 402 30 7 2701 3092 25284724 25284323 2.200000e-141 512.0
45 TraesCS7D01G464600 chr5D 87.121 132 17 0 2570 2701 141425255 141425386 1.990000e-32 150.0
46 TraesCS7D01G464600 chr5D 85.926 135 19 0 2570 2704 495372711 495372577 9.260000e-31 145.0
47 TraesCS7D01G464600 chr5D 90.741 54 4 1 2497 2549 174010676 174010623 1.590000e-08 71.3
48 TraesCS7D01G464600 chr3D 81.423 506 60 17 2701 3203 48536541 48536067 1.800000e-102 383.0
49 TraesCS7D01G464600 chr3D 79.062 320 39 23 2866 3181 36569581 36569876 9.070000e-46 195.0
50 TraesCS7D01G464600 chr3D 86.364 132 16 2 2572 2702 355179475 355179345 3.330000e-30 143.0
51 TraesCS7D01G464600 chr3D 97.297 37 1 0 2513 2549 594581107 594581071 2.670000e-06 63.9
52 TraesCS7D01G464600 chr1A 87.952 166 16 2 275 439 558542949 558543111 3.260000e-45 193.0
53 TraesCS7D01G464600 chr1A 79.310 87 15 3 2704 2789 554886142 554886058 1.240000e-04 58.4
54 TraesCS7D01G464600 chr2D 89.630 135 14 0 2570 2704 518837882 518838016 4.250000e-39 172.0
55 TraesCS7D01G464600 chr2D 74.185 399 64 26 2701 3090 357443963 357444331 2.590000e-26 130.0
56 TraesCS7D01G464600 chrUn 89.474 133 14 0 2572 2704 74563112 74562980 5.500000e-38 169.0
57 TraesCS7D01G464600 chr2B 88.889 135 9 4 307 440 754012266 754012137 9.200000e-36 161.0
58 TraesCS7D01G464600 chr2B 78.981 157 25 5 286 437 99010039 99009886 2.030000e-17 100.0
59 TraesCS7D01G464600 chr3A 89.516 124 12 1 2580 2703 544428201 544428079 4.280000e-34 156.0
60 TraesCS7D01G464600 chr3A 87.879 132 15 1 2572 2703 654060200 654060330 1.540000e-33 154.0
61 TraesCS7D01G464600 chr4B 89.796 98 4 5 344 438 13282363 13282457 1.560000e-23 121.0
62 TraesCS7D01G464600 chr4A 97.778 45 1 0 2505 2549 938151 938195 9.530000e-11 78.7
63 TraesCS7D01G464600 chr5B 90.323 62 1 5 2503 2561 706704844 706704785 3.430000e-10 76.8
64 TraesCS7D01G464600 chr5B 92.308 52 4 0 1478 1529 473638628 473638577 1.230000e-09 75.0
65 TraesCS7D01G464600 chr5B 90.741 54 4 1 2497 2549 184285248 184285301 1.590000e-08 71.3


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 TraesCS7D01G464600 chr7D 579098168 579101370 3202 True 5915.00 5915 100.00000 1 3203 1 chr7D.!!$R4 3202
1 TraesCS7D01G464600 chr7D 75948190 75948757 567 False 579.00 579 85.16600 1640 2208 1 chr7D.!!$F1 568
2 TraesCS7D01G464600 chr7B 643461485 643463720 2235 False 3140.00 3140 91.97500 247 2502 1 chr7B.!!$F3 2255
3 TraesCS7D01G464600 chr7B 643291092 643297112 6020 True 1377.75 2143 93.35825 353 2704 4 chr7B.!!$R2 2351
4 TraesCS7D01G464600 chr7A 670944894 670948228 3334 True 1038.00 1903 89.54450 1 2702 4 chr7A.!!$R1 2701
5 TraesCS7D01G464600 chr7A 80133504 80134071 567 False 590.00 590 85.56500 1640 2208 1 chr7A.!!$F1 568
6 TraesCS7D01G464600 chr6A 24030152 24031427 1275 True 501.40 937 90.69500 1004 2325 2 chr6A.!!$R3 1321
7 TraesCS7D01G464600 chr6A 24048598 24049968 1370 False 499.00 752 82.75250 966 2326 2 chr6A.!!$F1 1360
8 TraesCS7D01G464600 chr6A 23895531 23896764 1233 True 492.00 780 84.06650 1009 2201 2 chr6A.!!$R2 1192
9 TraesCS7D01G464600 chr6B 42004559 42005395 836 True 782.00 782 83.66200 1347 2201 1 chr6B.!!$R1 854
10 TraesCS7D01G464600 chr6B 42317590 42318854 1264 True 500.50 749 83.86000 1004 2201 2 chr6B.!!$R3 1197
11 TraesCS7D01G464600 chr6D 25803889 25804725 836 True 765.00 765 83.31400 1347 2201 1 chr6D.!!$R1 854
12 TraesCS7D01G464600 chr6D 25851451 25852617 1166 True 763.00 763 78.78300 1010 2217 1 chr6D.!!$R3 1207
13 TraesCS7D01G464600 chr6D 25914992 25916332 1340 False 491.00 752 83.44100 1009 2328 2 chr6D.!!$F1 1319

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
86 87 0.099613 ATAGTCTGCGAGCACTGACG 59.900 55.0 10.44 0.0 41.75 4.35 F
1279 1373 0.167470 CAAGCGCAATCAGGTCACAG 59.833 55.0 11.47 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1337 1591 0.321564 GTCACAGCCCTGTACATGCA 60.322 55.0 16.95 0.0 42.83 3.96 R
2878 7198 0.319555 GGAAAAACCGGAAAGCTGGC 60.320 55.0 9.46 0.0 44.98 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 0.980754 TAGGCCGGCCAAGAAGATCA 60.981 55.000 45.13 16.36 38.92 2.92
73 74 8.140112 ACCAAGAAACAATGTCTAGATAGTCT 57.860 34.615 0.00 0.00 0.00 3.24
76 77 6.269315 AGAAACAATGTCTAGATAGTCTGCG 58.731 40.000 0.00 0.00 0.00 5.18
86 87 0.099613 ATAGTCTGCGAGCACTGACG 59.900 55.000 10.44 0.00 41.75 4.35
94 95 3.302347 GAGCACTGACGGGAGGGTG 62.302 68.421 0.00 0.00 34.08 4.61
140 141 2.440247 CCTCGGGCCCAAATGTCC 60.440 66.667 24.92 0.00 0.00 4.02
151 152 3.380142 CCCAAATGTCCGTCAAAACAAG 58.620 45.455 0.00 0.00 0.00 3.16
158 159 3.314080 TGTCCGTCAAAACAAGATGTTCC 59.686 43.478 0.00 0.00 40.14 3.62
159 160 2.882137 TCCGTCAAAACAAGATGTTCCC 59.118 45.455 0.00 0.00 40.14 3.97
219 220 5.244851 ACGGATCAGAGCAGATAACATACAT 59.755 40.000 0.00 0.00 0.00 2.29
234 235 4.645535 ACATACATGTTTGTGAGCTCTGT 58.354 39.130 19.40 11.24 37.90 3.41
266 268 7.483881 TGGGGATAATGTATGTACTCCTATGA 58.516 38.462 0.00 0.00 0.00 2.15
277 279 9.862371 GTATGTACTCCTATGATGACCAATAAG 57.138 37.037 0.00 0.00 0.00 1.73
456 463 0.537188 AGTGACCAGACTTATGCGGG 59.463 55.000 0.00 0.00 0.00 6.13
543 550 1.697432 ACTTCTCCGTTCCAATGTCCA 59.303 47.619 0.00 0.00 0.00 4.02
770 781 1.535462 ACACGAAATGCCACTTGCTAC 59.465 47.619 0.00 0.00 42.00 3.58
771 782 1.806542 CACGAAATGCCACTTGCTACT 59.193 47.619 0.00 0.00 42.00 2.57
772 783 2.226437 CACGAAATGCCACTTGCTACTT 59.774 45.455 0.00 0.00 42.00 2.24
773 784 2.226437 ACGAAATGCCACTTGCTACTTG 59.774 45.455 0.00 0.00 42.00 3.16
774 785 2.599659 GAAATGCCACTTGCTACTTGC 58.400 47.619 0.00 0.00 42.00 4.01
775 786 1.915141 AATGCCACTTGCTACTTGCT 58.085 45.000 0.00 0.00 43.37 3.91
776 787 2.787473 ATGCCACTTGCTACTTGCTA 57.213 45.000 0.00 0.00 43.37 3.49
845 856 2.291465 TCTACGTAGAGTTGTGTTGCGT 59.709 45.455 21.25 0.00 35.29 5.24
862 873 2.948979 TGCGTTTTGTCAACCAGAGAAT 59.051 40.909 0.00 0.00 28.61 2.40
868 879 5.560722 TTTGTCAACCAGAGAATGACCTA 57.439 39.130 3.01 0.00 42.12 3.08
869 880 5.762179 TTGTCAACCAGAGAATGACCTAT 57.238 39.130 3.01 0.00 42.12 2.57
891 902 2.618045 CGGCCTAACTTTGACCATCCTT 60.618 50.000 0.00 0.00 0.00 3.36
901 912 5.012354 ACTTTGACCATCCTTCATGCATTTT 59.988 36.000 0.00 0.00 0.00 1.82
996 1007 8.097078 GATCAATTTGTGAGCTTAGCATATCT 57.903 34.615 7.07 0.00 39.67 1.98
1053 1076 1.684049 CTTCCTCCTGTCCTCCGCT 60.684 63.158 0.00 0.00 0.00 5.52
1229 1266 8.142551 AGTAAGTCAATTATACCCTTAAGCGAG 58.857 37.037 0.00 0.00 0.00 5.03
1249 1342 4.377431 CGAGCATATTTATGTTTCGGGCTC 60.377 45.833 13.81 0.00 41.21 4.70
1255 1348 4.553330 TTTATGTTTCGGGCTCTCTCTT 57.447 40.909 0.00 0.00 0.00 2.85
1279 1373 0.167470 CAAGCGCAATCAGGTCACAG 59.833 55.000 11.47 0.00 0.00 3.66
1298 1504 7.202526 GTCACAGTTGATTTCCTTTCATTTCA 58.797 34.615 0.00 0.00 33.11 2.69
1317 1567 6.573664 TTTCATGGAAGAATGTCACGATTT 57.426 33.333 0.00 0.00 0.00 2.17
1336 1590 7.226523 CACGATTTATGGATGGATTCTGTTACA 59.773 37.037 0.00 0.00 0.00 2.41
1337 1591 7.939039 ACGATTTATGGATGGATTCTGTTACAT 59.061 33.333 0.00 0.00 0.00 2.29
1338 1592 8.232513 CGATTTATGGATGGATTCTGTTACATG 58.767 37.037 0.00 0.00 0.00 3.21
1339 1593 6.882610 TTATGGATGGATTCTGTTACATGC 57.117 37.500 0.00 0.00 33.07 4.06
1590 5577 4.334443 CATGCGTAGTGTCAAAATGCTAC 58.666 43.478 0.00 0.00 0.00 3.58
1594 5581 3.994392 CGTAGTGTCAAAATGCTACTGGT 59.006 43.478 0.00 0.00 33.61 4.00
2539 6592 7.564292 ACTCCCTCCGTAAAGAAATATAAGAGT 59.436 37.037 0.00 0.00 0.00 3.24
2645 6965 0.112412 ACCTCAAACGGGCCTCAAAT 59.888 50.000 0.84 0.00 0.00 2.32
2659 6979 1.753848 CAAATGGCCGGGCTGATCA 60.754 57.895 29.87 8.75 0.00 2.92
2676 6996 1.427809 TCAGCACCCCTCATATCCAG 58.572 55.000 0.00 0.00 0.00 3.86
2678 6998 1.073897 GCACCCCTCATATCCAGCC 59.926 63.158 0.00 0.00 0.00 4.85
2704 7024 4.954118 AGGCGGATATGGGGGCGA 62.954 66.667 0.00 0.00 0.00 5.54
2705 7025 3.948719 GGCGGATATGGGGGCGAA 61.949 66.667 0.00 0.00 0.00 4.70
2707 7027 2.032071 CGGATATGGGGGCGAACC 59.968 66.667 0.00 0.00 39.11 3.62
2719 7039 1.347221 GCGAACCCTATTTGACGCG 59.653 57.895 3.53 3.53 37.06 6.01
2720 7040 1.347221 CGAACCCTATTTGACGCGC 59.653 57.895 5.73 0.00 0.00 6.86
2721 7041 1.347221 GAACCCTATTTGACGCGCG 59.653 57.895 30.96 30.96 0.00 6.86
2722 7042 2.627201 GAACCCTATTTGACGCGCGC 62.627 60.000 32.58 23.91 0.00 6.86
2739 7059 4.415501 CGTGCGTCGAACTGCTGC 62.416 66.667 1.02 0.00 42.86 5.25
2740 7060 3.337889 GTGCGTCGAACTGCTGCA 61.338 61.111 0.88 0.88 0.00 4.41
2742 7062 3.038417 GCGTCGAACTGCTGCACT 61.038 61.111 0.00 0.00 0.00 4.40
2743 7063 2.598632 GCGTCGAACTGCTGCACTT 61.599 57.895 0.00 0.00 0.00 3.16
2744 7064 1.488957 CGTCGAACTGCTGCACTTC 59.511 57.895 0.00 5.07 0.00 3.01
2747 7067 2.558313 GAACTGCTGCACTTCCGC 59.442 61.111 0.00 0.00 0.00 5.54
2748 7068 1.963338 GAACTGCTGCACTTCCGCT 60.963 57.895 0.00 0.00 0.00 5.52
2749 7069 2.180131 GAACTGCTGCACTTCCGCTG 62.180 60.000 0.00 1.05 0.00 5.18
2798 7118 2.749839 GGCCCACTGCATGCGTTA 60.750 61.111 14.09 0.00 43.89 3.18
2799 7119 2.339556 GGCCCACTGCATGCGTTAA 61.340 57.895 14.09 0.00 43.89 2.01
2801 7121 1.021202 GCCCACTGCATGCGTTAATA 58.979 50.000 14.09 0.00 40.77 0.98
2802 7122 1.002468 GCCCACTGCATGCGTTAATAG 60.002 52.381 14.09 6.04 40.77 1.73
2810 7130 3.427309 TGCGTTAATAGCAGTGCGA 57.573 47.368 10.00 4.55 40.01 5.10
2814 7134 1.651987 GTTAATAGCAGTGCGAGGCA 58.348 50.000 10.00 0.00 35.60 4.75
2815 7135 2.006888 GTTAATAGCAGTGCGAGGCAA 58.993 47.619 10.00 0.00 41.47 4.52
2816 7136 2.394930 TAATAGCAGTGCGAGGCAAA 57.605 45.000 10.00 0.00 41.47 3.68
2817 7137 0.804989 AATAGCAGTGCGAGGCAAAC 59.195 50.000 10.00 0.00 41.47 2.93
2819 7139 4.389576 GCAGTGCGAGGCAAACCG 62.390 66.667 0.00 0.00 41.47 4.44
2820 7140 3.726517 CAGTGCGAGGCAAACCGG 61.727 66.667 0.00 0.00 41.47 5.28
2822 7142 3.284449 GTGCGAGGCAAACCGGTT 61.284 61.111 15.86 15.86 41.47 4.44
2823 7143 2.517402 TGCGAGGCAAACCGGTTT 60.517 55.556 26.87 26.87 42.76 3.27
2824 7144 2.122167 TGCGAGGCAAACCGGTTTT 61.122 52.632 29.74 16.21 42.76 2.43
2828 7148 1.075896 AGGCAAACCGGTTTTGGGA 60.076 52.632 29.74 0.00 44.34 4.37
2829 7149 0.688087 AGGCAAACCGGTTTTGGGAA 60.688 50.000 29.74 0.00 44.34 3.97
2830 7150 0.531090 GGCAAACCGGTTTTGGGAAC 60.531 55.000 29.74 14.15 44.34 3.62
2858 7178 3.120796 GGTTCCCTCAACCGGTTTT 57.879 52.632 19.55 0.00 45.58 2.43
2859 7179 1.405872 GGTTCCCTCAACCGGTTTTT 58.594 50.000 19.55 0.00 45.58 1.94
2889 7209 2.507339 TTTCTTTTGCCAGCTTTCCG 57.493 45.000 0.00 0.00 0.00 4.30
2890 7210 0.673437 TTCTTTTGCCAGCTTTCCGG 59.327 50.000 0.00 0.00 0.00 5.14
2891 7211 0.467290 TCTTTTGCCAGCTTTCCGGT 60.467 50.000 0.00 0.00 0.00 5.28
2892 7212 0.389025 CTTTTGCCAGCTTTCCGGTT 59.611 50.000 0.00 0.00 0.00 4.44
2893 7213 0.827368 TTTTGCCAGCTTTCCGGTTT 59.173 45.000 0.00 0.00 0.00 3.27
2894 7214 0.827368 TTTGCCAGCTTTCCGGTTTT 59.173 45.000 0.00 0.00 0.00 2.43
2895 7215 0.827368 TTGCCAGCTTTCCGGTTTTT 59.173 45.000 0.00 0.00 0.00 1.94
2896 7216 0.387565 TGCCAGCTTTCCGGTTTTTC 59.612 50.000 0.00 0.00 0.00 2.29
2897 7217 0.319555 GCCAGCTTTCCGGTTTTTCC 60.320 55.000 0.00 0.00 0.00 3.13
2898 7218 1.328279 CCAGCTTTCCGGTTTTTCCT 58.672 50.000 0.00 0.00 0.00 3.36
2899 7219 1.000274 CCAGCTTTCCGGTTTTTCCTG 60.000 52.381 0.00 2.11 0.00 3.86
2900 7220 1.681264 CAGCTTTCCGGTTTTTCCTGT 59.319 47.619 0.00 0.00 0.00 4.00
2901 7221 2.100749 CAGCTTTCCGGTTTTTCCTGTT 59.899 45.455 0.00 0.00 0.00 3.16
2902 7222 2.764010 AGCTTTCCGGTTTTTCCTGTTT 59.236 40.909 0.00 0.00 0.00 2.83
2903 7223 3.120792 GCTTTCCGGTTTTTCCTGTTTC 58.879 45.455 0.00 0.00 0.00 2.78
2904 7224 3.713288 CTTTCCGGTTTTTCCTGTTTCC 58.287 45.455 0.00 0.00 0.00 3.13
2905 7225 2.740506 TCCGGTTTTTCCTGTTTCCT 57.259 45.000 0.00 0.00 0.00 3.36
2906 7226 3.021177 TCCGGTTTTTCCTGTTTCCTT 57.979 42.857 0.00 0.00 0.00 3.36
2907 7227 3.367321 TCCGGTTTTTCCTGTTTCCTTT 58.633 40.909 0.00 0.00 0.00 3.11
2908 7228 3.770388 TCCGGTTTTTCCTGTTTCCTTTT 59.230 39.130 0.00 0.00 0.00 2.27
2909 7229 4.223255 TCCGGTTTTTCCTGTTTCCTTTTT 59.777 37.500 0.00 0.00 0.00 1.94
2935 7255 9.952030 TTATTTTTGTCCTTTTTCCTCTTTTGT 57.048 25.926 0.00 0.00 0.00 2.83
2936 7256 8.862325 ATTTTTGTCCTTTTTCCTCTTTTGTT 57.138 26.923 0.00 0.00 0.00 2.83
2937 7257 8.684386 TTTTTGTCCTTTTTCCTCTTTTGTTT 57.316 26.923 0.00 0.00 0.00 2.83
2938 7258 7.899178 TTTGTCCTTTTTCCTCTTTTGTTTC 57.101 32.000 0.00 0.00 0.00 2.78
2939 7259 5.646606 TGTCCTTTTTCCTCTTTTGTTTCG 58.353 37.500 0.00 0.00 0.00 3.46
2940 7260 5.041287 GTCCTTTTTCCTCTTTTGTTTCGG 58.959 41.667 0.00 0.00 0.00 4.30
2941 7261 4.707934 TCCTTTTTCCTCTTTTGTTTCGGT 59.292 37.500 0.00 0.00 0.00 4.69
2942 7262 5.186215 TCCTTTTTCCTCTTTTGTTTCGGTT 59.814 36.000 0.00 0.00 0.00 4.44
2943 7263 5.518847 CCTTTTTCCTCTTTTGTTTCGGTTC 59.481 40.000 0.00 0.00 0.00 3.62
2944 7264 4.642445 TTTCCTCTTTTGTTTCGGTTCC 57.358 40.909 0.00 0.00 0.00 3.62
2945 7265 3.570912 TCCTCTTTTGTTTCGGTTCCT 57.429 42.857 0.00 0.00 0.00 3.36
2946 7266 4.693042 TCCTCTTTTGTTTCGGTTCCTA 57.307 40.909 0.00 0.00 0.00 2.94
2947 7267 5.237236 TCCTCTTTTGTTTCGGTTCCTAT 57.763 39.130 0.00 0.00 0.00 2.57
2948 7268 5.627135 TCCTCTTTTGTTTCGGTTCCTATT 58.373 37.500 0.00 0.00 0.00 1.73
2949 7269 6.066032 TCCTCTTTTGTTTCGGTTCCTATTT 58.934 36.000 0.00 0.00 0.00 1.40
2950 7270 6.206048 TCCTCTTTTGTTTCGGTTCCTATTTC 59.794 38.462 0.00 0.00 0.00 2.17
2951 7271 6.206829 CCTCTTTTGTTTCGGTTCCTATTTCT 59.793 38.462 0.00 0.00 0.00 2.52
2952 7272 7.255486 CCTCTTTTGTTTCGGTTCCTATTTCTT 60.255 37.037 0.00 0.00 0.00 2.52
2953 7273 8.002984 TCTTTTGTTTCGGTTCCTATTTCTTT 57.997 30.769 0.00 0.00 0.00 2.52
2954 7274 8.471609 TCTTTTGTTTCGGTTCCTATTTCTTTT 58.528 29.630 0.00 0.00 0.00 2.27
2955 7275 8.637281 TTTTGTTTCGGTTCCTATTTCTTTTC 57.363 30.769 0.00 0.00 0.00 2.29
2956 7276 7.576861 TTGTTTCGGTTCCTATTTCTTTTCT 57.423 32.000 0.00 0.00 0.00 2.52
2957 7277 7.576861 TGTTTCGGTTCCTATTTCTTTTCTT 57.423 32.000 0.00 0.00 0.00 2.52
2958 7278 8.002984 TGTTTCGGTTCCTATTTCTTTTCTTT 57.997 30.769 0.00 0.00 0.00 2.52
2959 7279 8.471609 TGTTTCGGTTCCTATTTCTTTTCTTTT 58.528 29.630 0.00 0.00 0.00 2.27
2960 7280 8.965172 GTTTCGGTTCCTATTTCTTTTCTTTTC 58.035 33.333 0.00 0.00 0.00 2.29
2965 7285 7.016268 GGTTCCTATTTCTTTTCTTTTCCCCTT 59.984 37.037 0.00 0.00 0.00 3.95
2966 7286 8.429641 GTTCCTATTTCTTTTCTTTTCCCCTTT 58.570 33.333 0.00 0.00 0.00 3.11
2971 7291 7.733773 TTTCTTTTCTTTTCCCCTTTCTTCT 57.266 32.000 0.00 0.00 0.00 2.85
2974 7294 6.776116 TCTTTTCTTTTCCCCTTTCTTCTACC 59.224 38.462 0.00 0.00 0.00 3.18
2980 7300 5.924769 TTCCCCTTTCTTCTACCTTTTCT 57.075 39.130 0.00 0.00 0.00 2.52
2981 7301 5.500546 TCCCCTTTCTTCTACCTTTTCTC 57.499 43.478 0.00 0.00 0.00 2.87
2982 7302 4.911522 TCCCCTTTCTTCTACCTTTTCTCA 59.088 41.667 0.00 0.00 0.00 3.27
2984 7304 6.045577 TCCCCTTTCTTCTACCTTTTCTCATT 59.954 38.462 0.00 0.00 0.00 2.57
2985 7305 6.721668 CCCCTTTCTTCTACCTTTTCTCATTT 59.278 38.462 0.00 0.00 0.00 2.32
2986 7306 7.233553 CCCCTTTCTTCTACCTTTTCTCATTTT 59.766 37.037 0.00 0.00 0.00 1.82
3041 7361 8.997621 ATTCCAATTTCTGTTCATGATTTCAG 57.002 30.769 13.42 13.42 0.00 3.02
3042 7362 7.764141 TCCAATTTCTGTTCATGATTTCAGA 57.236 32.000 16.45 16.45 35.54 3.27
3049 7369 9.820725 TTTCTGTTCATGATTTCAGAAATTGTT 57.179 25.926 27.75 0.00 45.57 2.83
3051 7371 8.631797 TCTGTTCATGATTTCAGAAATTGTTCA 58.368 29.630 17.45 4.76 36.09 3.18
3052 7372 8.578308 TGTTCATGATTTCAGAAATTGTTCAC 57.422 30.769 9.84 5.87 36.09 3.18
3053 7373 7.379262 TGTTCATGATTTCAGAAATTGTTCACG 59.621 33.333 9.84 0.00 36.09 4.35
3054 7374 6.380995 TCATGATTTCAGAAATTGTTCACGG 58.619 36.000 9.84 1.75 36.09 4.94
3055 7375 5.766150 TGATTTCAGAAATTGTTCACGGT 57.234 34.783 9.84 0.00 36.09 4.83
3057 7377 7.265647 TGATTTCAGAAATTGTTCACGGTTA 57.734 32.000 9.84 0.00 36.09 2.85
3059 7379 8.020819 TGATTTCAGAAATTGTTCACGGTTATC 58.979 33.333 9.84 0.00 36.09 1.75
3060 7380 6.869315 TTCAGAAATTGTTCACGGTTATCA 57.131 33.333 0.00 0.00 36.09 2.15
3061 7381 6.869315 TCAGAAATTGTTCACGGTTATCAA 57.131 33.333 0.00 0.00 36.09 2.57
3062 7382 7.265647 TCAGAAATTGTTCACGGTTATCAAA 57.734 32.000 0.00 0.00 36.09 2.69
3066 7386 8.576442 AGAAATTGTTCACGGTTATCAAATTCT 58.424 29.630 9.20 9.20 35.11 2.40
3067 7387 8.519492 AAATTGTTCACGGTTATCAAATTCTG 57.481 30.769 0.00 0.00 0.00 3.02
3069 7389 6.627395 TGTTCACGGTTATCAAATTCTGTT 57.373 33.333 0.00 0.00 0.00 3.16
3070 7390 6.664515 TGTTCACGGTTATCAAATTCTGTTC 58.335 36.000 0.00 0.00 0.00 3.18
3071 7391 6.261158 TGTTCACGGTTATCAAATTCTGTTCA 59.739 34.615 0.00 0.00 0.00 3.18
3072 7392 7.040755 TGTTCACGGTTATCAAATTCTGTTCAT 60.041 33.333 0.00 0.00 0.00 2.57
3074 7394 7.881142 TCACGGTTATCAAATTCTGTTCATTT 58.119 30.769 0.00 0.00 0.00 2.32
3076 7396 8.977505 CACGGTTATCAAATTCTGTTCATTTTT 58.022 29.630 0.00 0.00 0.00 1.94
3077 7397 9.191995 ACGGTTATCAAATTCTGTTCATTTTTC 57.808 29.630 0.00 0.00 0.00 2.29
3079 7399 9.405587 GGTTATCAAATTCTGTTCATTTTTCGA 57.594 29.630 0.00 0.00 0.00 3.71
3089 7409 8.694975 TCTGTTCATTTTTCGAAATTTGTTCA 57.305 26.923 12.12 13.04 0.00 3.18
3090 7410 8.591312 TCTGTTCATTTTTCGAAATTTGTTCAC 58.409 29.630 12.12 10.77 0.00 3.18
3091 7411 8.244494 TGTTCATTTTTCGAAATTTGTTCACA 57.756 26.923 12.12 12.71 0.00 3.58
3092 7412 8.712363 TGTTCATTTTTCGAAATTTGTTCACAA 58.288 25.926 12.12 0.00 0.00 3.33
3093 7413 9.701355 GTTCATTTTTCGAAATTTGTTCACAAT 57.299 25.926 12.12 2.27 35.55 2.71
3094 7414 9.699985 TTCATTTTTCGAAATTTGTTCACAATG 57.300 25.926 12.12 14.07 35.55 2.82
3095 7415 7.850003 TCATTTTTCGAAATTTGTTCACAATGC 59.150 29.630 12.12 0.00 35.55 3.56
3097 7417 6.653273 TTTCGAAATTTGTTCACAATGCAA 57.347 29.167 6.47 0.00 35.55 4.08
3098 7418 6.653273 TTCGAAATTTGTTCACAATGCAAA 57.347 29.167 0.00 0.00 35.55 3.68
3100 7420 6.703857 TCGAAATTTGTTCACAATGCAAAAG 58.296 32.000 0.00 0.00 36.00 2.27
3101 7421 6.312426 TCGAAATTTGTTCACAATGCAAAAGT 59.688 30.769 0.00 0.00 36.00 2.66
3102 7422 6.960431 CGAAATTTGTTCACAATGCAAAAGTT 59.040 30.769 0.00 0.00 36.00 2.66
3103 7423 7.045483 CGAAATTTGTTCACAATGCAAAAGTTG 60.045 33.333 0.00 0.00 36.00 3.16
3104 7424 6.740411 ATTTGTTCACAATGCAAAAGTTGT 57.260 29.167 0.00 0.00 39.00 3.32
3105 7425 6.551385 TTTGTTCACAATGCAAAAGTTGTT 57.449 29.167 0.65 0.00 36.48 2.83
3106 7426 5.776519 TGTTCACAATGCAAAAGTTGTTC 57.223 34.783 0.65 0.00 36.48 3.18
3107 7427 5.233225 TGTTCACAATGCAAAAGTTGTTCA 58.767 33.333 0.65 0.01 36.48 3.18
3108 7428 5.348179 TGTTCACAATGCAAAAGTTGTTCAG 59.652 36.000 0.65 0.00 36.48 3.02
3109 7429 3.864583 TCACAATGCAAAAGTTGTTCAGC 59.135 39.130 0.65 0.00 36.48 4.26
3110 7430 2.859538 ACAATGCAAAAGTTGTTCAGCG 59.140 40.909 0.00 0.00 35.13 5.18
3111 7431 2.859538 CAATGCAAAAGTTGTTCAGCGT 59.140 40.909 0.00 0.00 0.00 5.07
3112 7432 3.980646 ATGCAAAAGTTGTTCAGCGTA 57.019 38.095 0.00 0.00 0.00 4.42
3113 7433 3.980646 TGCAAAAGTTGTTCAGCGTAT 57.019 38.095 0.00 0.00 0.00 3.06
3114 7434 5.621197 ATGCAAAAGTTGTTCAGCGTATA 57.379 34.783 0.00 0.00 0.00 1.47
3115 7435 5.621197 TGCAAAAGTTGTTCAGCGTATAT 57.379 34.783 0.00 0.00 0.00 0.86
3116 7436 5.627172 TGCAAAAGTTGTTCAGCGTATATC 58.373 37.500 0.00 0.00 0.00 1.63
3117 7437 5.180304 TGCAAAAGTTGTTCAGCGTATATCA 59.820 36.000 0.00 0.00 0.00 2.15
3118 7438 5.508224 GCAAAAGTTGTTCAGCGTATATCAC 59.492 40.000 0.00 0.00 0.00 3.06
3119 7439 6.598525 CAAAAGTTGTTCAGCGTATATCACA 58.401 36.000 0.00 0.00 0.00 3.58
3120 7440 6.795098 AAAGTTGTTCAGCGTATATCACAA 57.205 33.333 0.00 0.00 0.00 3.33
3121 7441 6.795098 AAGTTGTTCAGCGTATATCACAAA 57.205 33.333 0.00 0.00 0.00 2.83
3123 7443 7.197071 AGTTGTTCAGCGTATATCACAAAAA 57.803 32.000 0.00 0.00 0.00 1.94
3124 7444 7.816640 AGTTGTTCAGCGTATATCACAAAAAT 58.183 30.769 0.00 0.00 0.00 1.82
3125 7445 8.296713 AGTTGTTCAGCGTATATCACAAAAATT 58.703 29.630 0.00 0.00 0.00 1.82
3126 7446 8.365210 GTTGTTCAGCGTATATCACAAAAATTG 58.635 33.333 0.00 0.00 0.00 2.32
3127 7447 7.589395 TGTTCAGCGTATATCACAAAAATTGT 58.411 30.769 0.00 0.00 46.75 2.71
3128 7448 8.079203 TGTTCAGCGTATATCACAAAAATTGTT 58.921 29.630 0.00 0.00 43.23 2.83
3129 7449 8.575454 GTTCAGCGTATATCACAAAAATTGTTC 58.425 33.333 0.00 0.00 43.23 3.18
3171 7491 9.959749 ATTGTTCAACGTACATAAAAGAAATGT 57.040 25.926 0.00 0.00 40.57 2.71
3172 7492 9.790389 TTGTTCAACGTACATAAAAGAAATGTT 57.210 25.926 0.00 0.00 38.49 2.71
3173 7493 9.440784 TGTTCAACGTACATAAAAGAAATGTTC 57.559 29.630 0.00 0.00 38.49 3.18
3174 7494 9.440784 GTTCAACGTACATAAAAGAAATGTTCA 57.559 29.630 0.00 0.00 38.49 3.18
3180 7500 9.393249 CGTACATAAAAGAAATGTTCATTGTGT 57.607 29.630 0.00 11.02 38.49 3.72
3195 7515 9.429359 TGTTCATTGTGTTAAAAATTGTTCAGT 57.571 25.926 0.00 0.00 0.00 3.41
3196 7516 9.687717 GTTCATTGTGTTAAAAATTGTTCAGTG 57.312 29.630 0.00 0.00 0.00 3.66
3197 7517 8.994429 TCATTGTGTTAAAAATTGTTCAGTGT 57.006 26.923 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.773404 GGCCGGCCTACGTACCAA 61.773 66.667 38.76 0.00 42.24 3.67
13 14 0.980754 TGATCTTCTTGGCCGGCCTA 60.981 55.000 43.34 35.88 36.94 3.93
43 44 7.962964 TCTAGACATTGTTTCTTGGTAGTTG 57.037 36.000 0.00 0.00 0.00 3.16
46 47 9.522804 GACTATCTAGACATTGTTTCTTGGTAG 57.477 37.037 0.00 0.00 36.31 3.18
58 59 3.885901 TGCTCGCAGACTATCTAGACATT 59.114 43.478 0.00 0.00 0.00 2.71
59 60 3.252215 GTGCTCGCAGACTATCTAGACAT 59.748 47.826 0.00 0.00 0.00 3.06
73 74 4.056125 CTCCCGTCAGTGCTCGCA 62.056 66.667 2.78 0.00 0.00 5.10
76 77 2.997897 ACCCTCCCGTCAGTGCTC 60.998 66.667 0.00 0.00 0.00 4.26
86 87 4.748144 CTTGCTGGCCACCCTCCC 62.748 72.222 0.00 0.00 0.00 4.30
140 141 3.980646 TGGGAACATCTTGTTTTGACG 57.019 42.857 0.00 0.00 41.28 4.35
174 175 4.507388 CGTTAGTTTTGGTTTCCACGACTA 59.493 41.667 0.00 6.44 33.12 2.59
219 220 3.535280 TGTGTACAGAGCTCACAAACA 57.465 42.857 17.77 11.41 38.80 2.83
224 225 2.350522 CCCATTGTGTACAGAGCTCAC 58.649 52.381 17.77 6.08 0.00 3.51
233 234 8.154856 AGTACATACATTATCCCCATTGTGTAC 58.845 37.037 0.00 0.00 0.00 2.90
234 235 8.270137 AGTACATACATTATCCCCATTGTGTA 57.730 34.615 0.00 0.00 0.00 2.90
241 242 7.483881 TCATAGGAGTACATACATTATCCCCA 58.516 38.462 0.00 0.00 0.00 4.96
266 268 8.537728 TCTAAATTTGCATCCTTATTGGTCAT 57.462 30.769 0.00 0.00 37.07 3.06
277 279 5.643348 CCCAAAAGGTTCTAAATTTGCATCC 59.357 40.000 0.00 0.00 32.73 3.51
456 463 2.332654 CGGGCACACAAAGTAGGGC 61.333 63.158 0.00 0.00 0.00 5.19
770 781 2.096980 CACATGCCATGTCACTAGCAAG 59.903 50.000 7.51 0.00 42.70 4.01
771 782 2.086094 CACATGCCATGTCACTAGCAA 58.914 47.619 7.51 0.00 42.70 3.91
772 783 1.679640 CCACATGCCATGTCACTAGCA 60.680 52.381 7.51 0.00 42.70 3.49
773 784 1.019673 CCACATGCCATGTCACTAGC 58.980 55.000 7.51 0.00 42.70 3.42
774 785 1.671979 CCCACATGCCATGTCACTAG 58.328 55.000 7.51 0.00 42.70 2.57
775 786 0.394216 GCCCACATGCCATGTCACTA 60.394 55.000 7.51 0.00 42.70 2.74
776 787 1.679977 GCCCACATGCCATGTCACT 60.680 57.895 7.51 0.00 42.70 3.41
845 856 4.792068 AGGTCATTCTCTGGTTGACAAAA 58.208 39.130 4.85 0.00 41.17 2.44
868 879 2.421529 GGATGGTCAAAGTTAGGCCGAT 60.422 50.000 0.00 0.00 0.00 4.18
869 880 1.065709 GGATGGTCAAAGTTAGGCCGA 60.066 52.381 0.00 0.00 0.00 5.54
996 1007 1.913951 ATGTCCTGGAAGCCATCGCA 61.914 55.000 0.00 0.00 37.52 5.10
1053 1076 2.501128 GAGAGCTGCCCATACGCA 59.499 61.111 0.00 0.00 37.19 5.24
1229 1266 4.757149 AGAGAGCCCGAAACATAAATATGC 59.243 41.667 0.36 0.00 37.19 3.14
1249 1342 0.870393 TTGCGCTTGCTGAAAGAGAG 59.130 50.000 9.73 0.00 37.87 3.20
1255 1348 0.890542 ACCTGATTGCGCTTGCTGAA 60.891 50.000 9.73 0.00 40.12 3.02
1298 1504 6.356556 TCCATAAATCGTGACATTCTTCCAT 58.643 36.000 0.00 0.00 0.00 3.41
1317 1567 5.939447 TGCATGTAACAGAATCCATCCATA 58.061 37.500 0.00 0.00 0.00 2.74
1336 1590 0.620030 TCACAGCCCTGTACATGCAT 59.380 50.000 16.95 0.00 42.83 3.96
1337 1591 0.321564 GTCACAGCCCTGTACATGCA 60.322 55.000 16.95 0.00 42.83 3.96
1338 1592 1.361668 CGTCACAGCCCTGTACATGC 61.362 60.000 8.98 8.98 42.83 4.06
1339 1593 0.740868 CCGTCACAGCCCTGTACATG 60.741 60.000 0.00 0.00 42.83 3.21
1573 5558 5.689819 CAACCAGTAGCATTTTGACACTAC 58.310 41.667 0.00 0.00 36.16 2.73
1590 5577 7.221452 GTCAGCATTAATTAAATCTGCAACCAG 59.779 37.037 19.34 7.96 40.54 4.00
1594 5581 8.087136 TGTTGTCAGCATTAATTAAATCTGCAA 58.913 29.630 19.34 19.81 0.00 4.08
2539 6592 6.693466 TGGTTGTAGATGTTCGATCTAAACA 58.307 36.000 11.51 11.51 40.63 2.83
2551 6855 0.673644 GTGCGCCTGGTTGTAGATGT 60.674 55.000 4.18 0.00 0.00 3.06
2659 6979 1.422161 GGCTGGATATGAGGGGTGCT 61.422 60.000 0.00 0.00 0.00 4.40
2676 6996 0.685097 TATCCGCCTCATAGTTGGGC 59.315 55.000 0.00 0.00 42.18 5.36
2678 6998 2.355108 CCCATATCCGCCTCATAGTTGG 60.355 54.545 0.00 0.00 0.00 3.77
2704 7024 2.746803 GCGCGCGTCAAATAGGGTT 61.747 57.895 32.35 0.00 0.00 4.11
2705 7025 3.192922 GCGCGCGTCAAATAGGGT 61.193 61.111 32.35 0.00 0.00 4.34
2721 7041 4.415501 CAGCAGTTCGACGCACGC 62.416 66.667 6.41 6.41 42.26 5.34
2722 7042 4.415501 GCAGCAGTTCGACGCACG 62.416 66.667 3.75 0.00 44.09 5.34
2723 7043 3.337889 TGCAGCAGTTCGACGCAC 61.338 61.111 0.00 0.00 0.00 5.34
2724 7044 3.337889 GTGCAGCAGTTCGACGCA 61.338 61.111 0.00 0.00 0.00 5.24
2726 7046 1.488957 GAAGTGCAGCAGTTCGACG 59.511 57.895 24.07 0.00 34.72 5.12
2727 7047 1.862806 GGAAGTGCAGCAGTTCGAC 59.137 57.895 28.86 16.94 42.71 4.20
2728 7048 1.664649 CGGAAGTGCAGCAGTTCGA 60.665 57.895 28.86 0.00 42.71 3.71
2729 7049 2.856032 CGGAAGTGCAGCAGTTCG 59.144 61.111 28.86 21.88 42.71 3.95
2732 7052 2.665008 TTCAGCGGAAGTGCAGCAGT 62.665 55.000 0.00 0.00 40.40 4.40
2733 7053 1.909141 CTTCAGCGGAAGTGCAGCAG 61.909 60.000 17.34 0.00 44.48 4.24
2734 7054 1.962822 CTTCAGCGGAAGTGCAGCA 60.963 57.895 17.34 0.00 44.48 4.41
2735 7055 2.866028 CTTCAGCGGAAGTGCAGC 59.134 61.111 17.34 0.00 44.48 5.25
2755 7075 4.854784 TCACGATGCTCGCTCGCC 62.855 66.667 5.63 0.00 45.12 5.54
2756 7076 2.444624 TTTCACGATGCTCGCTCGC 61.445 57.895 5.63 0.00 45.12 5.03
2757 7077 1.341802 GTTTCACGATGCTCGCTCG 59.658 57.895 5.63 8.47 45.12 5.03
2759 7079 2.094659 CCGTTTCACGATGCTCGCT 61.095 57.895 0.00 0.00 46.05 4.93
2760 7080 2.395690 CCGTTTCACGATGCTCGC 59.604 61.111 0.00 0.00 46.05 5.03
2761 7081 3.081133 CCCGTTTCACGATGCTCG 58.919 61.111 0.00 4.36 46.05 5.03
2762 7082 2.750888 GGCCCGTTTCACGATGCTC 61.751 63.158 0.00 0.00 46.05 4.26
2763 7083 2.746277 GGCCCGTTTCACGATGCT 60.746 61.111 0.00 0.00 46.05 3.79
2764 7084 4.160635 CGGCCCGTTTCACGATGC 62.161 66.667 0.00 0.34 46.05 3.91
2782 7102 1.002468 CTATTAACGCATGCAGTGGGC 60.002 52.381 19.57 3.45 44.09 5.36
2784 7104 1.670295 TGCTATTAACGCATGCAGTGG 59.330 47.619 19.57 3.36 31.40 4.00
2788 7108 1.063912 GCACTGCTATTAACGCATGCA 59.936 47.619 19.57 0.00 39.46 3.96
2789 7109 1.746760 GCACTGCTATTAACGCATGC 58.253 50.000 7.91 7.91 36.70 4.06
2790 7110 1.592543 TCGCACTGCTATTAACGCATG 59.407 47.619 0.00 0.00 36.70 4.06
2791 7111 1.860950 CTCGCACTGCTATTAACGCAT 59.139 47.619 0.00 0.00 36.70 4.73
2792 7112 1.277326 CTCGCACTGCTATTAACGCA 58.723 50.000 0.00 1.81 35.80 5.24
2794 7114 0.577269 GCCTCGCACTGCTATTAACG 59.423 55.000 0.00 0.00 0.00 3.18
2795 7115 1.651987 TGCCTCGCACTGCTATTAAC 58.348 50.000 0.00 0.00 31.71 2.01
2796 7116 2.394930 TTGCCTCGCACTGCTATTAA 57.605 45.000 0.00 0.00 38.71 1.40
2797 7117 2.006888 GTTTGCCTCGCACTGCTATTA 58.993 47.619 0.00 0.00 38.71 0.98
2798 7118 0.804989 GTTTGCCTCGCACTGCTATT 59.195 50.000 0.00 0.00 38.71 1.73
2799 7119 1.026718 GGTTTGCCTCGCACTGCTAT 61.027 55.000 0.00 0.00 38.71 2.97
2801 7121 2.980233 GGTTTGCCTCGCACTGCT 60.980 61.111 0.00 0.00 38.71 4.24
2802 7122 4.389576 CGGTTTGCCTCGCACTGC 62.390 66.667 0.00 0.00 38.71 4.40
2804 7124 3.767630 AACCGGTTTGCCTCGCACT 62.768 57.895 15.86 0.00 38.71 4.40
2805 7125 2.344521 AAAACCGGTTTGCCTCGCAC 62.345 55.000 32.23 0.00 38.71 5.34
2806 7126 2.122167 AAAACCGGTTTGCCTCGCA 61.122 52.632 32.23 0.00 36.47 5.10
2809 7129 1.110518 TCCCAAAACCGGTTTGCCTC 61.111 55.000 32.23 0.00 44.57 4.70
2810 7130 0.688087 TTCCCAAAACCGGTTTGCCT 60.688 50.000 32.23 15.08 44.57 4.75
2814 7134 1.758280 GAAGGTTCCCAAAACCGGTTT 59.242 47.619 26.87 26.87 44.82 3.27
2815 7135 1.405872 GAAGGTTCCCAAAACCGGTT 58.594 50.000 15.86 15.86 44.82 4.44
2816 7136 0.468585 GGAAGGTTCCCAAAACCGGT 60.469 55.000 0.00 0.00 44.82 5.28
2817 7137 1.520600 CGGAAGGTTCCCAAAACCGG 61.521 60.000 0.00 0.00 44.67 5.28
2868 7188 3.194062 CGGAAAGCTGGCAAAAGAAAAA 58.806 40.909 0.00 0.00 0.00 1.94
2869 7189 2.482839 CCGGAAAGCTGGCAAAAGAAAA 60.483 45.455 0.00 0.00 32.79 2.29
2870 7190 1.068434 CCGGAAAGCTGGCAAAAGAAA 59.932 47.619 0.00 0.00 32.79 2.52
2871 7191 0.673437 CCGGAAAGCTGGCAAAAGAA 59.327 50.000 0.00 0.00 32.79 2.52
2872 7192 0.467290 ACCGGAAAGCTGGCAAAAGA 60.467 50.000 9.46 0.00 44.98 2.52
2873 7193 0.389025 AACCGGAAAGCTGGCAAAAG 59.611 50.000 9.46 0.00 44.98 2.27
2874 7194 0.827368 AAACCGGAAAGCTGGCAAAA 59.173 45.000 9.46 0.00 44.98 2.44
2875 7195 0.827368 AAAACCGGAAAGCTGGCAAA 59.173 45.000 9.46 0.00 44.98 3.68
2876 7196 0.827368 AAAAACCGGAAAGCTGGCAA 59.173 45.000 9.46 0.00 44.98 4.52
2877 7197 0.387565 GAAAAACCGGAAAGCTGGCA 59.612 50.000 9.46 0.00 44.98 4.92
2878 7198 0.319555 GGAAAAACCGGAAAGCTGGC 60.320 55.000 9.46 0.00 44.98 4.85
2879 7199 1.000274 CAGGAAAAACCGGAAAGCTGG 60.000 52.381 9.46 0.00 46.62 4.85
2880 7200 1.681264 ACAGGAAAAACCGGAAAGCTG 59.319 47.619 9.46 0.00 44.74 4.24
2881 7201 2.067365 ACAGGAAAAACCGGAAAGCT 57.933 45.000 9.46 0.00 44.74 3.74
2882 7202 2.882927 AACAGGAAAAACCGGAAAGC 57.117 45.000 9.46 0.00 44.74 3.51
2883 7203 3.383505 AGGAAACAGGAAAAACCGGAAAG 59.616 43.478 9.46 0.00 44.74 2.62
2884 7204 3.367321 AGGAAACAGGAAAAACCGGAAA 58.633 40.909 9.46 0.00 44.74 3.13
2885 7205 3.021177 AGGAAACAGGAAAAACCGGAA 57.979 42.857 9.46 0.00 44.74 4.30
2886 7206 2.740506 AGGAAACAGGAAAAACCGGA 57.259 45.000 9.46 0.00 44.74 5.14
2887 7207 3.812156 AAAGGAAACAGGAAAAACCGG 57.188 42.857 0.00 0.00 44.74 5.28
2909 7229 9.952030 ACAAAAGAGGAAAAAGGACAAAAATAA 57.048 25.926 0.00 0.00 0.00 1.40
2910 7230 9.952030 AACAAAAGAGGAAAAAGGACAAAAATA 57.048 25.926 0.00 0.00 0.00 1.40
2911 7231 8.862325 AACAAAAGAGGAAAAAGGACAAAAAT 57.138 26.923 0.00 0.00 0.00 1.82
2912 7232 8.684386 AAACAAAAGAGGAAAAAGGACAAAAA 57.316 26.923 0.00 0.00 0.00 1.94
2913 7233 7.117092 CGAAACAAAAGAGGAAAAAGGACAAAA 59.883 33.333 0.00 0.00 0.00 2.44
2914 7234 6.588373 CGAAACAAAAGAGGAAAAAGGACAAA 59.412 34.615 0.00 0.00 0.00 2.83
2915 7235 6.096695 CGAAACAAAAGAGGAAAAAGGACAA 58.903 36.000 0.00 0.00 0.00 3.18
2916 7236 5.393678 CCGAAACAAAAGAGGAAAAAGGACA 60.394 40.000 0.00 0.00 0.00 4.02
2917 7237 5.041287 CCGAAACAAAAGAGGAAAAAGGAC 58.959 41.667 0.00 0.00 0.00 3.85
2918 7238 4.707934 ACCGAAACAAAAGAGGAAAAAGGA 59.292 37.500 0.00 0.00 0.00 3.36
2919 7239 5.006153 ACCGAAACAAAAGAGGAAAAAGG 57.994 39.130 0.00 0.00 0.00 3.11
2920 7240 5.518847 GGAACCGAAACAAAAGAGGAAAAAG 59.481 40.000 0.00 0.00 0.00 2.27
2921 7241 5.186215 AGGAACCGAAACAAAAGAGGAAAAA 59.814 36.000 0.00 0.00 0.00 1.94
2922 7242 4.707934 AGGAACCGAAACAAAAGAGGAAAA 59.292 37.500 0.00 0.00 0.00 2.29
2923 7243 4.274978 AGGAACCGAAACAAAAGAGGAAA 58.725 39.130 0.00 0.00 0.00 3.13
2924 7244 3.893521 AGGAACCGAAACAAAAGAGGAA 58.106 40.909 0.00 0.00 0.00 3.36
2925 7245 3.570912 AGGAACCGAAACAAAAGAGGA 57.429 42.857 0.00 0.00 0.00 3.71
2926 7246 5.959618 AATAGGAACCGAAACAAAAGAGG 57.040 39.130 0.00 0.00 0.00 3.69
2927 7247 7.203255 AGAAATAGGAACCGAAACAAAAGAG 57.797 36.000 0.00 0.00 0.00 2.85
2928 7248 7.576861 AAGAAATAGGAACCGAAACAAAAGA 57.423 32.000 0.00 0.00 0.00 2.52
2929 7249 8.642908 AAAAGAAATAGGAACCGAAACAAAAG 57.357 30.769 0.00 0.00 0.00 2.27
2930 7250 8.471609 AGAAAAGAAATAGGAACCGAAACAAAA 58.528 29.630 0.00 0.00 0.00 2.44
2931 7251 8.002984 AGAAAAGAAATAGGAACCGAAACAAA 57.997 30.769 0.00 0.00 0.00 2.83
2932 7252 7.576861 AGAAAAGAAATAGGAACCGAAACAA 57.423 32.000 0.00 0.00 0.00 2.83
2933 7253 7.576861 AAGAAAAGAAATAGGAACCGAAACA 57.423 32.000 0.00 0.00 0.00 2.83
2934 7254 8.867112 AAAAGAAAAGAAATAGGAACCGAAAC 57.133 30.769 0.00 0.00 0.00 2.78
2935 7255 8.139350 GGAAAAGAAAAGAAATAGGAACCGAAA 58.861 33.333 0.00 0.00 0.00 3.46
2936 7256 7.255695 GGGAAAAGAAAAGAAATAGGAACCGAA 60.256 37.037 0.00 0.00 0.00 4.30
2937 7257 6.208007 GGGAAAAGAAAAGAAATAGGAACCGA 59.792 38.462 0.00 0.00 0.00 4.69
2938 7258 6.387465 GGGAAAAGAAAAGAAATAGGAACCG 58.613 40.000 0.00 0.00 0.00 4.44
2939 7259 6.497259 AGGGGAAAAGAAAAGAAATAGGAACC 59.503 38.462 0.00 0.00 0.00 3.62
2940 7260 7.540474 AGGGGAAAAGAAAAGAAATAGGAAC 57.460 36.000 0.00 0.00 0.00 3.62
2941 7261 8.561536 AAAGGGGAAAAGAAAAGAAATAGGAA 57.438 30.769 0.00 0.00 0.00 3.36
2942 7262 8.010697 AGAAAGGGGAAAAGAAAAGAAATAGGA 58.989 33.333 0.00 0.00 0.00 2.94
2943 7263 8.195165 AGAAAGGGGAAAAGAAAAGAAATAGG 57.805 34.615 0.00 0.00 0.00 2.57
2944 7264 9.698309 GAAGAAAGGGGAAAAGAAAAGAAATAG 57.302 33.333 0.00 0.00 0.00 1.73
2945 7265 9.434275 AGAAGAAAGGGGAAAAGAAAAGAAATA 57.566 29.630 0.00 0.00 0.00 1.40
2946 7266 8.324191 AGAAGAAAGGGGAAAAGAAAAGAAAT 57.676 30.769 0.00 0.00 0.00 2.17
2947 7267 7.733773 AGAAGAAAGGGGAAAAGAAAAGAAA 57.266 32.000 0.00 0.00 0.00 2.52
2948 7268 7.287005 GGTAGAAGAAAGGGGAAAAGAAAAGAA 59.713 37.037 0.00 0.00 0.00 2.52
2949 7269 6.776116 GGTAGAAGAAAGGGGAAAAGAAAAGA 59.224 38.462 0.00 0.00 0.00 2.52
2950 7270 6.778069 AGGTAGAAGAAAGGGGAAAAGAAAAG 59.222 38.462 0.00 0.00 0.00 2.27
2951 7271 6.679542 AGGTAGAAGAAAGGGGAAAAGAAAA 58.320 36.000 0.00 0.00 0.00 2.29
2952 7272 6.275692 AGGTAGAAGAAAGGGGAAAAGAAA 57.724 37.500 0.00 0.00 0.00 2.52
2953 7273 5.924769 AGGTAGAAGAAAGGGGAAAAGAA 57.075 39.130 0.00 0.00 0.00 2.52
2954 7274 5.924769 AAGGTAGAAGAAAGGGGAAAAGA 57.075 39.130 0.00 0.00 0.00 2.52
2955 7275 6.778069 AGAAAAGGTAGAAGAAAGGGGAAAAG 59.222 38.462 0.00 0.00 0.00 2.27
2956 7276 6.679542 AGAAAAGGTAGAAGAAAGGGGAAAA 58.320 36.000 0.00 0.00 0.00 2.29
2957 7277 6.126303 TGAGAAAAGGTAGAAGAAAGGGGAAA 60.126 38.462 0.00 0.00 0.00 3.13
2958 7278 5.371472 TGAGAAAAGGTAGAAGAAAGGGGAA 59.629 40.000 0.00 0.00 0.00 3.97
2959 7279 4.911522 TGAGAAAAGGTAGAAGAAAGGGGA 59.088 41.667 0.00 0.00 0.00 4.81
2960 7280 5.242795 TGAGAAAAGGTAGAAGAAAGGGG 57.757 43.478 0.00 0.00 0.00 4.79
3015 7335 9.431887 CTGAAATCATGAACAGAAATTGGAATT 57.568 29.630 17.28 0.00 32.90 2.17
3017 7337 8.180706 TCTGAAATCATGAACAGAAATTGGAA 57.819 30.769 20.41 4.09 36.63 3.53
3018 7338 7.764141 TCTGAAATCATGAACAGAAATTGGA 57.236 32.000 20.41 4.80 36.63 3.53
3019 7339 8.821147 TTTCTGAAATCATGAACAGAAATTGG 57.179 30.769 30.01 10.69 46.86 3.16
3025 7345 8.631797 TGAACAATTTCTGAAATCATGAACAGA 58.368 29.630 15.43 19.44 37.56 3.41
3026 7346 8.697067 GTGAACAATTTCTGAAATCATGAACAG 58.303 33.333 15.43 16.53 32.36 3.16
3027 7347 7.379262 CGTGAACAATTTCTGAAATCATGAACA 59.621 33.333 15.43 12.55 32.36 3.18
3033 7353 5.766150 ACCGTGAACAATTTCTGAAATCA 57.234 34.783 15.43 7.90 32.36 2.57
3035 7355 7.881142 TGATAACCGTGAACAATTTCTGAAAT 58.119 30.769 9.76 9.76 32.36 2.17
3038 7358 6.869315 TTGATAACCGTGAACAATTTCTGA 57.131 33.333 0.00 0.00 32.36 3.27
3039 7359 8.519492 AATTTGATAACCGTGAACAATTTCTG 57.481 30.769 0.00 0.00 32.36 3.02
3041 7361 8.638565 CAGAATTTGATAACCGTGAACAATTTC 58.361 33.333 0.00 0.00 34.25 2.17
3042 7362 8.141268 ACAGAATTTGATAACCGTGAACAATTT 58.859 29.630 0.00 0.00 0.00 1.82
3044 7364 7.214467 ACAGAATTTGATAACCGTGAACAAT 57.786 32.000 0.00 0.00 0.00 2.71
3046 7366 6.261158 TGAACAGAATTTGATAACCGTGAACA 59.739 34.615 0.00 0.00 0.00 3.18
3047 7367 6.664515 TGAACAGAATTTGATAACCGTGAAC 58.335 36.000 0.00 0.00 0.00 3.18
3049 7369 7.447374 AATGAACAGAATTTGATAACCGTGA 57.553 32.000 0.00 0.00 0.00 4.35
3051 7371 9.191995 GAAAAATGAACAGAATTTGATAACCGT 57.808 29.630 0.00 0.00 0.00 4.83
3052 7372 8.365210 CGAAAAATGAACAGAATTTGATAACCG 58.635 33.333 0.00 0.00 0.00 4.44
3053 7373 9.405587 TCGAAAAATGAACAGAATTTGATAACC 57.594 29.630 0.00 0.00 0.00 2.85
3066 7386 8.244494 TGTGAACAAATTTCGAAAAATGAACA 57.756 26.923 24.53 20.97 35.27 3.18
3067 7387 9.701355 ATTGTGAACAAATTTCGAAAAATGAAC 57.299 25.926 24.53 19.47 39.55 3.18
3069 7389 7.850003 GCATTGTGAACAAATTTCGAAAAATGA 59.150 29.630 24.53 8.59 39.55 2.57
3070 7390 7.639072 TGCATTGTGAACAAATTTCGAAAAATG 59.361 29.630 15.66 17.77 39.55 2.32
3071 7391 7.692088 TGCATTGTGAACAAATTTCGAAAAAT 58.308 26.923 15.66 4.14 39.55 1.82
3072 7392 7.065216 TGCATTGTGAACAAATTTCGAAAAA 57.935 28.000 15.66 1.42 39.55 1.94
3074 7394 6.653273 TTGCATTGTGAACAAATTTCGAAA 57.347 29.167 13.91 13.91 39.55 3.46
3076 7396 6.312426 ACTTTTGCATTGTGAACAAATTTCGA 59.688 30.769 0.00 0.00 39.55 3.71
3077 7397 6.476896 ACTTTTGCATTGTGAACAAATTTCG 58.523 32.000 0.00 0.00 39.55 3.46
3079 7399 7.592051 ACAACTTTTGCATTGTGAACAAATTT 58.408 26.923 2.68 0.00 37.64 1.82
3080 7400 7.143514 ACAACTTTTGCATTGTGAACAAATT 57.856 28.000 2.68 0.00 37.64 1.82
3081 7401 6.740411 ACAACTTTTGCATTGTGAACAAAT 57.260 29.167 2.68 0.00 37.64 2.32
3082 7402 6.203530 TGAACAACTTTTGCATTGTGAACAAA 59.796 30.769 4.26 0.00 39.00 2.83
3083 7403 5.698089 TGAACAACTTTTGCATTGTGAACAA 59.302 32.000 4.26 0.00 39.00 2.83
3084 7404 5.233225 TGAACAACTTTTGCATTGTGAACA 58.767 33.333 4.26 3.72 39.00 3.18
3087 7407 3.864583 GCTGAACAACTTTTGCATTGTGA 59.135 39.130 4.26 0.00 39.00 3.58
3088 7408 3.301963 CGCTGAACAACTTTTGCATTGTG 60.302 43.478 4.26 0.00 39.00 3.33
3089 7409 2.859538 CGCTGAACAACTTTTGCATTGT 59.140 40.909 0.00 0.00 40.76 2.71
3090 7410 2.859538 ACGCTGAACAACTTTTGCATTG 59.140 40.909 0.00 0.00 0.00 2.82
3091 7411 3.163630 ACGCTGAACAACTTTTGCATT 57.836 38.095 0.00 0.00 0.00 3.56
3092 7412 2.869233 ACGCTGAACAACTTTTGCAT 57.131 40.000 0.00 0.00 0.00 3.96
3093 7413 3.980646 ATACGCTGAACAACTTTTGCA 57.019 38.095 0.00 0.00 0.00 4.08
3094 7414 5.508224 GTGATATACGCTGAACAACTTTTGC 59.492 40.000 0.00 0.00 0.00 3.68
3095 7415 6.598525 TGTGATATACGCTGAACAACTTTTG 58.401 36.000 0.00 0.00 0.00 2.44
3097 7417 6.795098 TTGTGATATACGCTGAACAACTTT 57.205 33.333 0.00 0.00 0.00 2.66
3098 7418 6.795098 TTTGTGATATACGCTGAACAACTT 57.205 33.333 0.00 0.00 0.00 2.66
3100 7420 8.365210 CAATTTTTGTGATATACGCTGAACAAC 58.635 33.333 0.00 0.00 0.00 3.32
3101 7421 8.079203 ACAATTTTTGTGATATACGCTGAACAA 58.921 29.630 0.00 0.00 43.48 2.83
3102 7422 7.589395 ACAATTTTTGTGATATACGCTGAACA 58.411 30.769 0.00 0.00 43.48 3.18
3103 7423 8.447787 AACAATTTTTGTGATATACGCTGAAC 57.552 30.769 0.00 0.00 44.59 3.18
3104 7424 8.293157 TGAACAATTTTTGTGATATACGCTGAA 58.707 29.630 0.00 0.00 44.59 3.02
3105 7425 7.811653 TGAACAATTTTTGTGATATACGCTGA 58.188 30.769 0.00 0.00 44.59 4.26
3106 7426 8.446489 TTGAACAATTTTTGTGATATACGCTG 57.554 30.769 0.00 0.00 44.59 5.18
3107 7427 9.075519 CATTGAACAATTTTTGTGATATACGCT 57.924 29.630 0.00 0.00 44.59 5.07
3108 7428 8.859156 ACATTGAACAATTTTTGTGATATACGC 58.141 29.630 0.00 0.00 44.59 4.42
3145 7465 9.959749 ACATTTCTTTTATGTACGTTGAACAAT 57.040 25.926 0.00 0.00 34.59 2.71
3146 7466 9.790389 AACATTTCTTTTATGTACGTTGAACAA 57.210 25.926 0.00 0.00 35.26 2.83
3147 7467 9.440784 GAACATTTCTTTTATGTACGTTGAACA 57.559 29.630 0.00 0.00 35.26 3.18
3148 7468 9.440784 TGAACATTTCTTTTATGTACGTTGAAC 57.559 29.630 0.00 0.00 35.26 3.18
3152 7472 9.959749 ACAATGAACATTTCTTTTATGTACGTT 57.040 25.926 0.00 0.00 35.26 3.99
3154 7474 9.393249 ACACAATGAACATTTCTTTTATGTACG 57.607 29.630 0.00 0.00 35.26 3.67
3169 7489 9.429359 ACTGAACAATTTTTAACACAATGAACA 57.571 25.926 0.00 0.00 0.00 3.18
3170 7490 9.687717 CACTGAACAATTTTTAACACAATGAAC 57.312 29.630 0.00 0.00 0.00 3.18
3171 7491 9.429359 ACACTGAACAATTTTTAACACAATGAA 57.571 25.926 0.00 0.00 0.00 2.57
3172 7492 8.994429 ACACTGAACAATTTTTAACACAATGA 57.006 26.923 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.