Multiple sequence alignment - TraesCS3B01G330300

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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 TraesCS3B01G330300 chr3B 100.000 2928 0 0 1 2928 534193541 534196468 0.000000e+00 5408.0
1 TraesCS3B01G330300 chr3B 86.798 659 46 16 1540 2194 534247433 534248054 0.000000e+00 697.0
2 TraesCS3B01G330300 chr3B 87.678 211 26 0 940 1150 534246860 534247070 2.250000e-61 246.0
3 TraesCS3B01G330300 chr3A 90.542 1660 83 40 924 2536 543176576 543174944 0.000000e+00 2128.0
4 TraesCS3B01G330300 chr3A 82.881 590 45 27 1521 2107 543022382 543021846 2.040000e-131 479.0
5 TraesCS3B01G330300 chr3A 85.474 475 37 13 425 878 543177051 543176588 1.590000e-127 466.0
6 TraesCS3B01G330300 chr3A 89.627 241 22 1 2691 2928 543174951 543174711 1.320000e-78 303.0
7 TraesCS3B01G330300 chr3A 84.564 298 28 9 1 282 543177601 543177306 2.220000e-71 279.0
8 TraesCS3B01G330300 chr3A 97.895 95 2 0 2100 2194 543016209 543016115 6.490000e-37 165.0
9 TraesCS3B01G330300 chr3A 83.721 172 28 0 2746 2917 525244287 525244458 2.330000e-36 163.0
10 TraesCS3B01G330300 chr3A 95.652 46 1 1 446 490 543177138 543177093 4.050000e-09 73.1
11 TraesCS3B01G330300 chr3A 92.857 42 2 1 698 739 543176727 543176687 3.150000e-05 60.2
12 TraesCS3B01G330300 chr3D 90.285 1441 55 21 908 2313 408318678 408320068 0.000000e+00 1807.0
13 TraesCS3B01G330300 chr3D 90.989 910 30 9 1 876 408317791 408318682 0.000000e+00 1179.0
14 TraesCS3B01G330300 chr3D 88.432 389 17 5 2387 2775 408320290 408320650 7.450000e-121 444.0
15 TraesCS3B01G330300 chr3D 86.154 65 6 2 432 494 408318142 408318205 1.880000e-07 67.6
16 TraesCS3B01G330300 chr1D 84.884 172 26 0 2746 2917 202132207 202132036 1.080000e-39 174.0
17 TraesCS3B01G330300 chr5D 86.029 136 17 2 1822 1956 371288620 371288486 8.460000e-31 145.0
18 TraesCS3B01G330300 chr5D 83.784 148 22 1 1809 1956 371036592 371036447 3.930000e-29 139.0
19 TraesCS3B01G330300 chr5B 83.784 148 24 0 1809 1956 441053533 441053386 1.090000e-29 141.0
20 TraesCS3B01G330300 chr5B 81.595 163 30 0 2755 2917 89320360 89320198 5.090000e-28 135.0
21 TraesCS3B01G330300 chr5A 81.111 180 29 2 2740 2917 664995564 664995740 3.930000e-29 139.0
22 TraesCS3B01G330300 chr5A 83.108 148 23 1 1809 1956 474333729 474333584 1.830000e-27 134.0
23 TraesCS3B01G330300 chr5A 82.432 148 24 1 1809 1956 474089529 474089384 8.520000e-26 128.0
24 TraesCS3B01G330300 chr6D 81.325 166 29 2 2753 2917 321664646 321664482 1.830000e-27 134.0
25 TraesCS3B01G330300 chr2A 80.899 178 27 4 2740 2914 481812643 481812816 1.830000e-27 134.0
26 TraesCS3B01G330300 chr7B 80.347 173 34 0 2746 2918 324099562 324099390 6.580000e-27 132.0
27 TraesCS3B01G330300 chr7B 80.420 143 14 8 605 744 597460987 597461118 2.400000e-16 97.1
28 TraesCS3B01G330300 chr1B 79.191 173 34 2 2746 2917 278521051 278521222 5.130000e-23 119.0


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 TraesCS3B01G330300 chr3B 534193541 534196468 2927 False 5408.00 5408 100.000 1 2928 1 chr3B.!!$F1 2927
1 TraesCS3B01G330300 chr3B 534246860 534248054 1194 False 471.50 697 87.238 940 2194 2 chr3B.!!$F2 1254
2 TraesCS3B01G330300 chr3A 543174711 543177601 2890 True 551.55 2128 89.786 1 2928 6 chr3A.!!$R3 2927
3 TraesCS3B01G330300 chr3A 543021846 543022382 536 True 479.00 479 82.881 1521 2107 1 chr3A.!!$R2 586
4 TraesCS3B01G330300 chr3D 408317791 408320650 2859 False 874.40 1807 88.965 1 2775 4 chr3D.!!$F1 2774

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
886 1089 0.172578 CAACCCAGCTGCATCACATG 59.827 55.0 8.66 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2640 3230 0.106769 TTGAGGTGCTGGTGCTTGAA 60.107 50.0 0.0 0.0 40.48 2.69 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
168 201 1.609208 AGTGGTTGACTTGGTGCATC 58.391 50.000 0.00 0.00 0.00 3.91
171 204 1.887854 TGGTTGACTTGGTGCATCATG 59.112 47.619 11.11 11.11 0.00 3.07
172 205 1.888512 GGTTGACTTGGTGCATCATGT 59.111 47.619 17.66 17.66 0.00 3.21
173 206 2.095059 GGTTGACTTGGTGCATCATGTC 60.095 50.000 29.70 29.70 40.24 3.06
174 207 2.816087 GTTGACTTGGTGCATCATGTCT 59.184 45.455 33.34 10.76 40.38 3.41
175 208 2.703416 TGACTTGGTGCATCATGTCTC 58.297 47.619 33.34 18.19 40.38 3.36
176 209 2.303890 TGACTTGGTGCATCATGTCTCT 59.696 45.455 33.34 9.80 40.38 3.10
177 210 2.935201 GACTTGGTGCATCATGTCTCTC 59.065 50.000 29.32 11.40 38.21 3.20
178 211 2.286872 CTTGGTGCATCATGTCTCTCC 58.713 52.381 0.00 0.00 0.00 3.71
179 212 0.176449 TGGTGCATCATGTCTCTCCG 59.824 55.000 0.00 0.00 0.00 4.63
180 213 0.176680 GGTGCATCATGTCTCTCCGT 59.823 55.000 0.00 0.00 0.00 4.69
181 214 1.406069 GGTGCATCATGTCTCTCCGTT 60.406 52.381 0.00 0.00 0.00 4.44
182 215 2.159099 GGTGCATCATGTCTCTCCGTTA 60.159 50.000 0.00 0.00 0.00 3.18
183 216 3.493350 GGTGCATCATGTCTCTCCGTTAT 60.493 47.826 0.00 0.00 0.00 1.89
184 217 4.122776 GTGCATCATGTCTCTCCGTTATT 58.877 43.478 0.00 0.00 0.00 1.40
185 218 4.572389 GTGCATCATGTCTCTCCGTTATTT 59.428 41.667 0.00 0.00 0.00 1.40
186 219 5.065218 GTGCATCATGTCTCTCCGTTATTTT 59.935 40.000 0.00 0.00 0.00 1.82
187 220 6.257849 GTGCATCATGTCTCTCCGTTATTTTA 59.742 38.462 0.00 0.00 0.00 1.52
188 221 6.257849 TGCATCATGTCTCTCCGTTATTTTAC 59.742 38.462 0.00 0.00 0.00 2.01
278 311 2.353889 GGACACTGCTGATGCTGTTATG 59.646 50.000 0.00 0.00 46.76 1.90
375 409 4.981806 AGAGAGCAGATAGATATTCCGC 57.018 45.455 0.00 0.00 0.00 5.54
380 517 6.105333 AGAGCAGATAGATATTCCGCAAATC 58.895 40.000 0.00 0.00 0.00 2.17
395 533 3.483574 CGCAAATCGACCTGTATGTGTTC 60.484 47.826 0.00 0.00 41.67 3.18
539 709 7.744087 AAAGTTCATGTACTCTATGTGCAAA 57.256 32.000 5.37 0.00 44.04 3.68
540 710 6.974932 AGTTCATGTACTCTATGTGCAAAG 57.025 37.500 0.00 0.00 44.04 2.77
600 770 8.137437 GGACAAATCAAAACTTCTCTGAAATCA 58.863 33.333 0.00 0.00 0.00 2.57
753 923 6.481644 AGCTTTGATCCGATTCTGATTCTAAC 59.518 38.462 0.00 0.00 0.00 2.34
760 930 9.314321 GATCCGATTCTGATTCTAACAGTTAAA 57.686 33.333 0.00 0.00 36.81 1.52
879 1082 4.601794 CCACCCAACCCAGCTGCA 62.602 66.667 8.66 0.00 0.00 4.41
880 1083 2.283388 CACCCAACCCAGCTGCAT 60.283 61.111 8.66 0.00 0.00 3.96
882 1085 2.036098 CCCAACCCAGCTGCATCA 59.964 61.111 8.66 0.00 0.00 3.07
883 1086 2.345760 CCCAACCCAGCTGCATCAC 61.346 63.158 8.66 0.00 0.00 3.06
884 1087 1.604308 CCAACCCAGCTGCATCACA 60.604 57.895 8.66 0.00 0.00 3.58
885 1088 0.968901 CCAACCCAGCTGCATCACAT 60.969 55.000 8.66 0.00 0.00 3.21
886 1089 0.172578 CAACCCAGCTGCATCACATG 59.827 55.000 8.66 0.00 0.00 3.21
887 1090 0.968901 AACCCAGCTGCATCACATGG 60.969 55.000 8.66 3.83 0.00 3.66
888 1091 1.379443 CCCAGCTGCATCACATGGT 60.379 57.895 8.66 0.00 0.00 3.55
889 1092 1.663379 CCCAGCTGCATCACATGGTG 61.663 60.000 8.66 0.00 34.45 4.17
891 1094 1.679640 CCAGCTGCATCACATGGTGTA 60.680 52.381 8.66 0.00 34.79 2.90
893 1096 1.019673 GCTGCATCACATGGTGTAGG 58.980 55.000 11.54 0.00 34.79 3.18
894 1097 1.407299 GCTGCATCACATGGTGTAGGA 60.407 52.381 11.54 0.00 34.79 2.94
895 1098 2.747467 GCTGCATCACATGGTGTAGGAT 60.747 50.000 11.54 0.00 34.79 3.24
896 1099 3.548770 CTGCATCACATGGTGTAGGATT 58.451 45.455 2.53 0.00 34.79 3.01
897 1100 3.949754 CTGCATCACATGGTGTAGGATTT 59.050 43.478 2.53 0.00 34.79 2.17
898 1101 4.343231 TGCATCACATGGTGTAGGATTTT 58.657 39.130 0.00 0.00 34.79 1.82
899 1102 4.398988 TGCATCACATGGTGTAGGATTTTC 59.601 41.667 0.00 0.00 34.79 2.29
900 1103 4.496341 GCATCACATGGTGTAGGATTTTCG 60.496 45.833 0.00 0.00 34.79 3.46
901 1104 3.605634 TCACATGGTGTAGGATTTTCGG 58.394 45.455 0.00 0.00 34.79 4.30
902 1105 2.097466 CACATGGTGTAGGATTTTCGGC 59.903 50.000 0.00 0.00 0.00 5.54
903 1106 2.026262 ACATGGTGTAGGATTTTCGGCT 60.026 45.455 0.00 0.00 0.00 5.52
904 1107 2.396590 TGGTGTAGGATTTTCGGCTC 57.603 50.000 0.00 0.00 0.00 4.70
905 1108 1.287425 GGTGTAGGATTTTCGGCTCG 58.713 55.000 0.00 0.00 0.00 5.03
906 1109 1.134907 GGTGTAGGATTTTCGGCTCGA 60.135 52.381 0.00 0.00 0.00 4.04
923 1126 1.887242 GAACAGCGTGCAGACACCA 60.887 57.895 0.00 0.00 44.40 4.17
926 1129 2.433145 AGCGTGCAGACACCATCG 60.433 61.111 0.00 0.00 44.40 3.84
956 1160 1.081556 TCGTTCATTCATCCCGCACG 61.082 55.000 0.00 0.00 0.00 5.34
1011 1218 1.450312 CAGGGCAATGGAGTCCGAC 60.450 63.158 4.30 0.00 0.00 4.79
1228 1603 3.721706 CCACCTCCACTCCTGGCC 61.722 72.222 0.00 0.00 37.49 5.36
1245 1620 4.973055 CCGCCACCCGACGACAAA 62.973 66.667 0.00 0.00 40.02 2.83
1424 1805 1.938814 CGTGCCGCGCATTATTTGG 60.939 57.895 8.75 0.00 41.91 3.28
1452 1833 1.649348 CGATAACGACGACGACGGG 60.649 63.158 22.36 5.68 44.46 5.28
1455 1836 1.709147 ATAACGACGACGACGGGGAG 61.709 60.000 22.36 2.46 44.46 4.30
1476 1860 1.694525 GGGGGAGGAAGAGGAAGGG 60.695 68.421 0.00 0.00 0.00 3.95
1674 2060 3.378399 GACCAAGAGGAGGCTCGCC 62.378 68.421 8.69 0.00 38.69 5.54
1784 2170 5.689383 TCCTGTCAAAATGTTGCTTAGTC 57.311 39.130 0.00 0.00 34.50 2.59
1785 2171 5.376625 TCCTGTCAAAATGTTGCTTAGTCT 58.623 37.500 0.00 0.00 34.50 3.24
1863 2249 1.229428 CAGGCTGATTGTGACAACGT 58.771 50.000 9.42 0.00 0.00 3.99
1987 2374 5.393461 GGTCAGAAAGCTTGGAAATACATGG 60.393 44.000 0.00 0.00 0.00 3.66
1999 2386 5.046014 TGGAAATACATGGGATTTGGTTTGG 60.046 40.000 11.37 0.00 0.00 3.28
2005 2392 4.843516 ACATGGGATTTGGTTTGGTGTATT 59.156 37.500 0.00 0.00 0.00 1.89
2215 2625 5.847304 TGCTAACTGCTGAGAAGTATATGG 58.153 41.667 0.00 0.00 43.37 2.74
2222 2632 6.836527 ACTGCTGAGAAGTATATGGAGTAGTT 59.163 38.462 0.00 0.00 0.00 2.24
2224 2634 7.717568 TGCTGAGAAGTATATGGAGTAGTTTC 58.282 38.462 0.00 0.00 0.00 2.78
2263 2681 2.833794 TGTCTCCTTGTCCTGAAAACG 58.166 47.619 0.00 0.00 0.00 3.60
2277 2695 6.863126 GTCCTGAAAACGAATTCACAAATCAT 59.137 34.615 6.22 0.00 35.55 2.45
2290 2708 2.420022 ACAAATCATAACTGCTGTCCGC 59.580 45.455 0.00 0.00 39.77 5.54
2347 2937 4.683832 GTGATGACACGGCTTAAGATAGT 58.316 43.478 6.67 0.00 37.28 2.12
2348 2938 5.828747 GTGATGACACGGCTTAAGATAGTA 58.171 41.667 6.67 0.00 37.28 1.82
2349 2939 5.686397 GTGATGACACGGCTTAAGATAGTAC 59.314 44.000 6.67 0.00 37.28 2.73
2350 2940 5.358725 TGATGACACGGCTTAAGATAGTACA 59.641 40.000 6.67 6.75 0.00 2.90
2351 2941 4.990257 TGACACGGCTTAAGATAGTACAC 58.010 43.478 6.67 0.00 0.00 2.90
2352 2942 4.460034 TGACACGGCTTAAGATAGTACACA 59.540 41.667 6.67 1.68 0.00 3.72
2353 2943 5.126545 TGACACGGCTTAAGATAGTACACAT 59.873 40.000 6.67 0.00 0.00 3.21
2354 2944 6.319405 TGACACGGCTTAAGATAGTACACATA 59.681 38.462 6.67 0.00 0.00 2.29
2355 2945 7.104043 ACACGGCTTAAGATAGTACACATAA 57.896 36.000 6.67 0.00 0.00 1.90
2427 3017 9.734620 CAGTGTCTTGTTAGAATTGATTTTTCA 57.265 29.630 0.00 0.00 30.65 2.69
2473 3063 4.708576 TGACGATAGATACTCCCTCTGT 57.291 45.455 0.00 0.00 41.38 3.41
2482 3072 6.301169 AGATACTCCCTCTGTAACCTTTTG 57.699 41.667 0.00 0.00 0.00 2.44
2499 3089 6.290605 ACCTTTTGTAAGACGGCTTTTAGTA 58.709 36.000 9.87 0.00 35.56 1.82
2500 3090 6.767423 ACCTTTTGTAAGACGGCTTTTAGTAA 59.233 34.615 9.87 0.00 35.56 2.24
2501 3091 7.282901 ACCTTTTGTAAGACGGCTTTTAGTAAA 59.717 33.333 9.87 1.26 35.56 2.01
2502 3092 8.130469 CCTTTTGTAAGACGGCTTTTAGTAAAA 58.870 33.333 9.87 9.23 35.56 1.52
2503 3093 9.505995 CTTTTGTAAGACGGCTTTTAGTAAAAA 57.494 29.630 9.87 6.89 35.56 1.94
2535 3125 6.965500 CGTCTTATAAAGAAGTTACAGAGCGA 59.035 38.462 0.00 0.00 39.67 4.93
2536 3126 7.644551 CGTCTTATAAAGAAGTTACAGAGCGAT 59.355 37.037 0.00 0.00 39.67 4.58
2537 3127 8.960075 GTCTTATAAAGAAGTTACAGAGCGATC 58.040 37.037 0.00 0.00 39.67 3.69
2538 3128 8.683615 TCTTATAAAGAAGTTACAGAGCGATCA 58.316 33.333 2.38 0.00 33.83 2.92
2539 3129 8.630278 TTATAAAGAAGTTACAGAGCGATCAC 57.370 34.615 2.38 0.00 0.00 3.06
2540 3130 4.521130 AAGAAGTTACAGAGCGATCACA 57.479 40.909 2.38 0.00 0.00 3.58
2541 3131 4.103365 AGAAGTTACAGAGCGATCACAG 57.897 45.455 2.38 0.00 0.00 3.66
2542 3132 3.508012 AGAAGTTACAGAGCGATCACAGT 59.492 43.478 2.38 0.70 0.00 3.55
2543 3133 4.700692 AGAAGTTACAGAGCGATCACAGTA 59.299 41.667 2.38 0.00 0.00 2.74
2544 3134 4.358494 AGTTACAGAGCGATCACAGTAC 57.642 45.455 2.38 0.00 0.00 2.73
2545 3135 4.011023 AGTTACAGAGCGATCACAGTACT 58.989 43.478 2.38 0.00 0.00 2.73
2546 3136 2.929531 ACAGAGCGATCACAGTACTG 57.070 50.000 21.44 21.44 0.00 2.74
2547 3137 2.163509 ACAGAGCGATCACAGTACTGT 58.836 47.619 22.95 22.95 46.17 3.55
2548 3138 2.162608 ACAGAGCGATCACAGTACTGTC 59.837 50.000 25.63 13.96 42.83 3.51
2549 3139 2.162408 CAGAGCGATCACAGTACTGTCA 59.838 50.000 25.63 14.72 42.83 3.58
2550 3140 2.162608 AGAGCGATCACAGTACTGTCAC 59.837 50.000 25.63 17.11 42.83 3.67
2551 3141 1.202582 AGCGATCACAGTACTGTCACC 59.797 52.381 25.63 15.09 42.83 4.02
2552 3142 1.736032 GCGATCACAGTACTGTCACCC 60.736 57.143 25.63 13.45 42.83 4.61
2553 3143 1.819288 CGATCACAGTACTGTCACCCT 59.181 52.381 25.63 8.57 42.83 4.34
2554 3144 2.416027 CGATCACAGTACTGTCACCCTG 60.416 54.545 25.63 13.46 42.83 4.45
2555 3145 2.375014 TCACAGTACTGTCACCCTGA 57.625 50.000 25.63 15.55 42.83 3.86
2556 3146 2.673258 TCACAGTACTGTCACCCTGAA 58.327 47.619 25.63 1.76 42.83 3.02
2557 3147 2.364324 TCACAGTACTGTCACCCTGAAC 59.636 50.000 25.63 0.00 42.83 3.18
2558 3148 2.102420 CACAGTACTGTCACCCTGAACA 59.898 50.000 25.63 0.00 42.83 3.18
2559 3149 2.102588 ACAGTACTGTCACCCTGAACAC 59.897 50.000 22.95 0.00 40.24 3.32
2560 3150 1.692519 AGTACTGTCACCCTGAACACC 59.307 52.381 0.00 0.00 0.00 4.16
2561 3151 1.053424 TACTGTCACCCTGAACACCC 58.947 55.000 0.00 0.00 0.00 4.61
2562 3152 1.073199 CTGTCACCCTGAACACCCC 59.927 63.158 0.00 0.00 0.00 4.95
2563 3153 1.694525 TGTCACCCTGAACACCCCA 60.695 57.895 0.00 0.00 0.00 4.96
2564 3154 1.065410 TGTCACCCTGAACACCCCAT 61.065 55.000 0.00 0.00 0.00 4.00
2565 3155 0.988832 GTCACCCTGAACACCCCATA 59.011 55.000 0.00 0.00 0.00 2.74
2566 3156 1.065418 GTCACCCTGAACACCCCATAG 60.065 57.143 0.00 0.00 0.00 2.23
2567 3157 0.394352 CACCCTGAACACCCCATAGC 60.394 60.000 0.00 0.00 0.00 2.97
2568 3158 0.550147 ACCCTGAACACCCCATAGCT 60.550 55.000 0.00 0.00 0.00 3.32
2569 3159 1.274184 ACCCTGAACACCCCATAGCTA 60.274 52.381 0.00 0.00 0.00 3.32
2570 3160 1.141053 CCCTGAACACCCCATAGCTAC 59.859 57.143 0.00 0.00 0.00 3.58
2571 3161 1.141053 CCTGAACACCCCATAGCTACC 59.859 57.143 0.00 0.00 0.00 3.18
2572 3162 1.837439 CTGAACACCCCATAGCTACCA 59.163 52.381 0.00 0.00 0.00 3.25
2573 3163 1.837439 TGAACACCCCATAGCTACCAG 59.163 52.381 0.00 0.00 0.00 4.00
2574 3164 1.838077 GAACACCCCATAGCTACCAGT 59.162 52.381 0.00 0.00 0.00 4.00
2575 3165 1.497161 ACACCCCATAGCTACCAGTC 58.503 55.000 0.00 0.00 0.00 3.51
2576 3166 1.273609 ACACCCCATAGCTACCAGTCA 60.274 52.381 0.00 0.00 0.00 3.41
2577 3167 1.414181 CACCCCATAGCTACCAGTCAG 59.586 57.143 0.00 0.00 0.00 3.51
2578 3168 1.051812 CCCCATAGCTACCAGTCAGG 58.948 60.000 0.00 0.00 45.67 3.86
2588 3178 4.007644 CAGTCAGGTGCCGCTGGA 62.008 66.667 0.00 0.00 0.00 3.86
2589 3179 3.699894 AGTCAGGTGCCGCTGGAG 61.700 66.667 0.00 0.00 0.00 3.86
2590 3180 4.008933 GTCAGGTGCCGCTGGAGT 62.009 66.667 0.00 0.00 0.00 3.85
2591 3181 2.283604 TCAGGTGCCGCTGGAGTA 60.284 61.111 0.00 0.00 0.00 2.59
2592 3182 1.911269 TCAGGTGCCGCTGGAGTAA 60.911 57.895 0.00 0.00 0.00 2.24
2593 3183 1.221840 CAGGTGCCGCTGGAGTAAT 59.778 57.895 0.00 0.00 0.00 1.89
2594 3184 0.392998 CAGGTGCCGCTGGAGTAATT 60.393 55.000 0.00 0.00 0.00 1.40
2595 3185 1.134521 CAGGTGCCGCTGGAGTAATTA 60.135 52.381 0.00 0.00 0.00 1.40
2596 3186 1.139058 AGGTGCCGCTGGAGTAATTAG 59.861 52.381 0.00 0.00 0.00 1.73
2597 3187 0.938008 GTGCCGCTGGAGTAATTAGC 59.062 55.000 0.00 0.00 0.00 3.09
2598 3188 0.830648 TGCCGCTGGAGTAATTAGCT 59.169 50.000 0.00 0.00 35.36 3.32
2599 3189 1.221414 GCCGCTGGAGTAATTAGCTG 58.779 55.000 0.00 0.00 35.36 4.24
2600 3190 1.871080 CCGCTGGAGTAATTAGCTGG 58.129 55.000 0.00 0.00 35.36 4.85
2601 3191 1.412710 CCGCTGGAGTAATTAGCTGGA 59.587 52.381 0.00 0.00 34.99 3.86
2602 3192 2.158957 CCGCTGGAGTAATTAGCTGGAA 60.159 50.000 0.00 0.00 34.99 3.53
2603 3193 3.126831 CGCTGGAGTAATTAGCTGGAAG 58.873 50.000 0.00 0.00 35.36 3.46
2604 3194 3.430929 CGCTGGAGTAATTAGCTGGAAGT 60.431 47.826 0.00 0.00 35.36 3.01
2605 3195 4.518249 GCTGGAGTAATTAGCTGGAAGTT 58.482 43.478 0.00 0.00 35.30 2.66
2606 3196 4.944317 GCTGGAGTAATTAGCTGGAAGTTT 59.056 41.667 0.00 0.00 35.30 2.66
2607 3197 5.416013 GCTGGAGTAATTAGCTGGAAGTTTT 59.584 40.000 0.00 0.00 35.30 2.43
2608 3198 6.071896 GCTGGAGTAATTAGCTGGAAGTTTTT 60.072 38.462 0.00 0.00 35.30 1.94
2609 3199 7.448748 TGGAGTAATTAGCTGGAAGTTTTTC 57.551 36.000 0.00 0.00 35.30 2.29
2610 3200 7.001674 TGGAGTAATTAGCTGGAAGTTTTTCA 58.998 34.615 0.00 0.00 34.90 2.69
2611 3201 7.040686 TGGAGTAATTAGCTGGAAGTTTTTCAC 60.041 37.037 0.00 0.00 34.90 3.18
2612 3202 7.175119 GGAGTAATTAGCTGGAAGTTTTTCACT 59.825 37.037 0.00 0.00 37.30 3.41
2613 3203 7.875971 AGTAATTAGCTGGAAGTTTTTCACTG 58.124 34.615 0.00 0.00 35.12 3.66
2614 3204 6.959639 AATTAGCTGGAAGTTTTTCACTGA 57.040 33.333 0.00 0.00 35.12 3.41
2615 3205 6.959639 ATTAGCTGGAAGTTTTTCACTGAA 57.040 33.333 0.00 0.00 35.12 3.02
2616 3206 4.907879 AGCTGGAAGTTTTTCACTGAAG 57.092 40.909 0.00 0.00 35.12 3.02
2617 3207 3.067320 AGCTGGAAGTTTTTCACTGAAGC 59.933 43.478 0.00 0.00 36.74 3.86
2618 3208 3.181487 GCTGGAAGTTTTTCACTGAAGCA 60.181 43.478 0.00 0.00 36.60 3.91
2619 3209 4.604976 CTGGAAGTTTTTCACTGAAGCAG 58.395 43.478 0.00 0.00 35.12 4.24
2620 3210 3.181487 TGGAAGTTTTTCACTGAAGCAGC 60.181 43.478 0.00 0.00 35.12 5.25
2621 3211 3.375642 GAAGTTTTTCACTGAAGCAGCC 58.624 45.455 0.00 0.00 35.12 4.85
2622 3212 2.378038 AGTTTTTCACTGAAGCAGCCA 58.622 42.857 0.00 0.00 34.37 4.75
2623 3213 2.961062 AGTTTTTCACTGAAGCAGCCAT 59.039 40.909 0.00 0.00 34.37 4.40
2624 3214 4.144297 AGTTTTTCACTGAAGCAGCCATA 58.856 39.130 0.00 0.00 34.37 2.74
2625 3215 4.584325 AGTTTTTCACTGAAGCAGCCATAA 59.416 37.500 0.00 0.00 34.37 1.90
2626 3216 4.503741 TTTTCACTGAAGCAGCCATAAC 57.496 40.909 0.00 0.00 34.37 1.89
2627 3217 2.113860 TCACTGAAGCAGCCATAACC 57.886 50.000 0.00 0.00 34.37 2.85
2628 3218 1.098050 CACTGAAGCAGCCATAACCC 58.902 55.000 0.00 0.00 34.37 4.11
2629 3219 0.392998 ACTGAAGCAGCCATAACCCG 60.393 55.000 0.00 0.00 34.37 5.28
2630 3220 1.077787 TGAAGCAGCCATAACCCGG 60.078 57.895 0.00 0.00 0.00 5.73
2636 3226 2.912025 GCCATAACCCGGCCATGG 60.912 66.667 18.18 18.18 44.22 3.66
2637 3227 2.923035 CCATAACCCGGCCATGGA 59.077 61.111 18.40 0.00 41.53 3.41
2638 3228 1.460255 CCATAACCCGGCCATGGAT 59.540 57.895 18.40 5.83 41.53 3.41
2639 3229 0.695924 CCATAACCCGGCCATGGATA 59.304 55.000 18.40 7.93 41.53 2.59
2640 3230 1.284785 CCATAACCCGGCCATGGATAT 59.715 52.381 18.40 9.86 41.53 1.63
2641 3231 2.291540 CCATAACCCGGCCATGGATATT 60.292 50.000 18.40 4.18 41.53 1.28
2642 3232 2.871096 TAACCCGGCCATGGATATTC 57.129 50.000 18.40 0.00 0.00 1.75
2643 3233 0.850100 AACCCGGCCATGGATATTCA 59.150 50.000 18.40 0.00 0.00 2.57
2644 3234 0.850100 ACCCGGCCATGGATATTCAA 59.150 50.000 18.40 0.00 0.00 2.69
2645 3235 1.202927 ACCCGGCCATGGATATTCAAG 60.203 52.381 18.40 0.00 0.00 3.02
2646 3236 0.883833 CCGGCCATGGATATTCAAGC 59.116 55.000 18.40 1.51 0.00 4.01
2647 3237 1.608055 CGGCCATGGATATTCAAGCA 58.392 50.000 18.40 0.00 0.00 3.91
2648 3238 1.267806 CGGCCATGGATATTCAAGCAC 59.732 52.381 18.40 0.00 0.00 4.40
2649 3239 1.615392 GGCCATGGATATTCAAGCACC 59.385 52.381 18.40 0.00 0.00 5.01
2650 3240 2.309613 GCCATGGATATTCAAGCACCA 58.690 47.619 18.40 0.00 35.09 4.17
2651 3241 2.295349 GCCATGGATATTCAAGCACCAG 59.705 50.000 18.40 0.00 34.08 4.00
2652 3242 2.295349 CCATGGATATTCAAGCACCAGC 59.705 50.000 5.56 0.00 42.56 4.85
2653 3243 2.804986 TGGATATTCAAGCACCAGCA 57.195 45.000 0.00 0.00 45.49 4.41
2654 3244 2.368439 TGGATATTCAAGCACCAGCAC 58.632 47.619 0.00 0.00 45.49 4.40
2655 3245 1.678101 GGATATTCAAGCACCAGCACC 59.322 52.381 0.00 0.00 45.49 5.01
2656 3246 2.648059 GATATTCAAGCACCAGCACCT 58.352 47.619 0.00 0.00 45.49 4.00
2657 3247 2.113860 TATTCAAGCACCAGCACCTC 57.886 50.000 0.00 0.00 45.49 3.85
2658 3248 0.111061 ATTCAAGCACCAGCACCTCA 59.889 50.000 0.00 0.00 45.49 3.86
2659 3249 0.106769 TTCAAGCACCAGCACCTCAA 60.107 50.000 0.00 0.00 45.49 3.02
2660 3250 0.106769 TCAAGCACCAGCACCTCAAA 60.107 50.000 0.00 0.00 45.49 2.69
2661 3251 0.963962 CAAGCACCAGCACCTCAAAT 59.036 50.000 0.00 0.00 45.49 2.32
2662 3252 0.963962 AAGCACCAGCACCTCAAATG 59.036 50.000 0.00 0.00 45.49 2.32
2663 3253 1.080298 GCACCAGCACCTCAAATGC 60.080 57.895 0.00 0.00 43.74 3.56
2669 3259 1.154150 GCACCTCAAATGCTCGTGC 60.154 57.895 1.71 1.71 42.57 5.34
2670 3260 1.503542 CACCTCAAATGCTCGTGCC 59.496 57.895 7.05 0.00 38.71 5.01
2671 3261 1.073025 ACCTCAAATGCTCGTGCCA 59.927 52.632 7.05 0.00 38.71 4.92
2672 3262 0.322816 ACCTCAAATGCTCGTGCCAT 60.323 50.000 7.05 0.00 38.71 4.40
2673 3263 0.813184 CCTCAAATGCTCGTGCCATT 59.187 50.000 7.05 4.42 38.71 3.16
2674 3264 1.468565 CCTCAAATGCTCGTGCCATTG 60.469 52.381 7.05 11.65 38.71 2.82
2675 3265 1.200716 CTCAAATGCTCGTGCCATTGT 59.799 47.619 17.96 4.89 38.71 2.71
2676 3266 1.068402 TCAAATGCTCGTGCCATTGTG 60.068 47.619 17.96 12.67 38.71 3.33
2677 3267 0.388907 AAATGCTCGTGCCATTGTGC 60.389 50.000 7.05 0.00 38.71 4.57
2678 3268 2.216750 AATGCTCGTGCCATTGTGCC 62.217 55.000 7.05 0.00 38.71 5.01
2679 3269 3.364441 GCTCGTGCCATTGTGCCA 61.364 61.111 0.00 0.00 0.00 4.92
2680 3270 2.918345 GCTCGTGCCATTGTGCCAA 61.918 57.895 0.00 0.00 0.00 4.52
2681 3271 1.081242 CTCGTGCCATTGTGCCAAC 60.081 57.895 0.00 0.00 0.00 3.77
2682 3272 1.518056 CTCGTGCCATTGTGCCAACT 61.518 55.000 0.00 0.00 0.00 3.16
2683 3273 1.106351 TCGTGCCATTGTGCCAACTT 61.106 50.000 0.00 0.00 0.00 2.66
2684 3274 0.595588 CGTGCCATTGTGCCAACTTA 59.404 50.000 0.00 0.00 0.00 2.24
2685 3275 1.202114 CGTGCCATTGTGCCAACTTAT 59.798 47.619 0.00 0.00 0.00 1.73
2686 3276 2.352617 CGTGCCATTGTGCCAACTTATT 60.353 45.455 0.00 0.00 0.00 1.40
2687 3277 3.119673 CGTGCCATTGTGCCAACTTATTA 60.120 43.478 0.00 0.00 0.00 0.98
2688 3278 4.439974 CGTGCCATTGTGCCAACTTATTAT 60.440 41.667 0.00 0.00 0.00 1.28
2689 3279 5.043248 GTGCCATTGTGCCAACTTATTATC 58.957 41.667 0.00 0.00 0.00 1.75
2690 3280 4.955450 TGCCATTGTGCCAACTTATTATCT 59.045 37.500 0.00 0.00 0.00 1.98
2691 3281 6.039270 GTGCCATTGTGCCAACTTATTATCTA 59.961 38.462 0.00 0.00 0.00 1.98
2692 3282 6.262944 TGCCATTGTGCCAACTTATTATCTAG 59.737 38.462 0.00 0.00 0.00 2.43
2693 3283 6.486657 GCCATTGTGCCAACTTATTATCTAGA 59.513 38.462 0.00 0.00 0.00 2.43
2694 3284 7.308229 GCCATTGTGCCAACTTATTATCTAGAG 60.308 40.741 0.00 0.00 0.00 2.43
2695 3285 7.308229 CCATTGTGCCAACTTATTATCTAGAGC 60.308 40.741 0.00 0.00 0.00 4.09
2696 3286 5.611374 TGTGCCAACTTATTATCTAGAGCC 58.389 41.667 0.00 0.00 0.00 4.70
2731 3467 1.827969 GCTGAGTTTCTCTGCCTCCTA 59.172 52.381 14.60 0.00 45.41 2.94
2794 3530 8.200120 TCATTATCACTATCACTAGGCATATGC 58.800 37.037 19.79 19.79 41.14 3.14
2796 3532 6.617782 ATCACTATCACTAGGCATATGCTT 57.382 37.500 26.12 21.74 41.70 3.91
2804 3540 6.637657 TCACTAGGCATATGCTTATCATCAG 58.362 40.000 26.12 14.34 41.70 2.90
2820 3556 4.439968 TCATCAGATTGTGTCTCAGCATC 58.560 43.478 0.00 0.00 34.00 3.91
2821 3557 3.967332 TCAGATTGTGTCTCAGCATCA 57.033 42.857 0.00 0.00 34.00 3.07
2823 3559 3.512724 TCAGATTGTGTCTCAGCATCAGA 59.487 43.478 0.00 0.00 34.00 3.27
2832 3568 6.369890 TGTGTCTCAGCATCAGAAATAGAAAC 59.630 38.462 0.00 0.00 0.00 2.78
2838 3574 8.151141 TCAGCATCAGAAATAGAAACATCATC 57.849 34.615 0.00 0.00 0.00 2.92
2897 3633 7.994425 TCAGGAGTATGCAAAGTTTTATTCA 57.006 32.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 206 8.316956 ACGGAGAGACGTAAAATAACGGAGAG 62.317 46.154 0.00 0.00 46.58 3.20
174 207 6.598614 ACGGAGAGACGTAAAATAACGGAGA 61.599 44.000 0.00 0.00 46.58 3.71
175 208 4.437930 ACGGAGAGACGTAAAATAACGGAG 60.438 45.833 0.00 0.00 46.58 4.63
176 209 3.440173 ACGGAGAGACGTAAAATAACGGA 59.560 43.478 0.00 0.00 46.58 4.69
177 210 3.762779 ACGGAGAGACGTAAAATAACGG 58.237 45.455 0.00 0.00 46.58 4.44
325 359 2.103373 TCGAATCAAGAGCAGCTAGGT 58.897 47.619 0.00 0.00 0.00 3.08
327 361 3.305629 GTGTTCGAATCAAGAGCAGCTAG 59.694 47.826 0.00 0.00 29.74 3.42
329 363 2.072298 GTGTTCGAATCAAGAGCAGCT 58.928 47.619 0.00 0.00 29.74 4.24
370 404 2.276201 CATACAGGTCGATTTGCGGAA 58.724 47.619 0.00 0.00 41.33 4.30
372 406 1.327460 CACATACAGGTCGATTTGCGG 59.673 52.381 0.00 0.00 41.33 5.69
374 408 3.435327 TGAACACATACAGGTCGATTTGC 59.565 43.478 0.00 0.00 0.00 3.68
375 409 5.605564 TTGAACACATACAGGTCGATTTG 57.394 39.130 0.00 0.00 0.00 2.32
380 517 4.513692 TCCTTTTTGAACACATACAGGTCG 59.486 41.667 0.00 0.00 0.00 4.79
710 880 4.804868 AGCTCTGATGATAAGATCGCAT 57.195 40.909 0.00 0.00 0.00 4.73
760 930 8.900781 CAGATCACAGGTCTGAATCATAAAATT 58.099 33.333 4.84 0.00 44.57 1.82
853 1056 2.521708 GTTGGGTGGCTGTGGCTT 60.522 61.111 0.00 0.00 38.73 4.35
878 1081 4.035558 CCGAAAATCCTACACCATGTGATG 59.964 45.833 0.49 0.00 36.96 3.07
879 1082 4.199310 CCGAAAATCCTACACCATGTGAT 58.801 43.478 0.49 0.00 36.96 3.06
880 1083 3.605634 CCGAAAATCCTACACCATGTGA 58.394 45.455 0.49 0.00 36.96 3.58
882 1085 2.026262 AGCCGAAAATCCTACACCATGT 60.026 45.455 0.00 0.00 0.00 3.21
883 1086 2.614057 GAGCCGAAAATCCTACACCATG 59.386 50.000 0.00 0.00 0.00 3.66
884 1087 2.741878 CGAGCCGAAAATCCTACACCAT 60.742 50.000 0.00 0.00 0.00 3.55
885 1088 1.404986 CGAGCCGAAAATCCTACACCA 60.405 52.381 0.00 0.00 0.00 4.17
886 1089 1.134907 TCGAGCCGAAAATCCTACACC 60.135 52.381 0.00 0.00 31.06 4.16
887 1090 2.288961 TCGAGCCGAAAATCCTACAC 57.711 50.000 0.00 0.00 31.06 2.90
897 1100 2.733218 CACGCTGTTCGAGCCGAA 60.733 61.111 5.07 6.01 46.01 4.30
902 1105 1.661509 TGTCTGCACGCTGTTCGAG 60.662 57.895 0.00 0.00 41.67 4.04
903 1106 1.949133 GTGTCTGCACGCTGTTCGA 60.949 57.895 0.00 0.00 41.67 3.71
904 1107 2.546321 GTGTCTGCACGCTGTTCG 59.454 61.111 0.00 0.00 45.38 3.95
905 1108 1.230635 ATGGTGTCTGCACGCTGTTC 61.231 55.000 0.00 0.00 46.13 3.18
906 1109 1.227943 ATGGTGTCTGCACGCTGTT 60.228 52.632 0.00 0.00 46.13 3.16
913 1116 1.987306 TAGCCCGATGGTGTCTGCA 60.987 57.895 0.00 0.00 0.00 4.41
926 1129 0.392060 AATGAACGAACCGGTAGCCC 60.392 55.000 8.00 1.42 0.00 5.19
1228 1603 4.973055 TTTGTCGTCGGGTGGCGG 62.973 66.667 0.00 0.00 0.00 6.13
1416 1797 1.134521 TCGGCGTGCTCTCCAAATAAT 60.135 47.619 6.85 0.00 0.00 1.28
1419 1800 0.464036 TATCGGCGTGCTCTCCAAAT 59.536 50.000 6.85 0.00 0.00 2.32
1424 1805 1.063649 TCGTTATCGGCGTGCTCTC 59.936 57.895 6.85 0.00 37.69 3.20
1452 1833 1.074850 CTCTTCCTCCCCCTCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
1455 1836 0.692756 CTTCCTCTTCCTCCCCCTCC 60.693 65.000 0.00 0.00 0.00 4.30
1476 1860 1.749258 GAAGAACCGGGCCACATCC 60.749 63.158 6.32 0.00 0.00 3.51
1785 2171 8.704668 ATGTGATAGACAATTAGACATGGTACA 58.295 33.333 0.00 0.00 40.34 2.90
1833 2219 2.401583 ATCAGCCTGCATTTCGTACA 57.598 45.000 0.00 0.00 0.00 2.90
1863 2249 1.672363 CAGCTTGATCAATAGCGCCAA 59.328 47.619 8.96 0.00 42.18 4.52
1987 2374 7.039270 GGTTATCAATACACCAAACCAAATCC 58.961 38.462 0.00 0.00 37.05 3.01
1999 2386 5.368145 TGAGCATCCAGGTTATCAATACAC 58.632 41.667 0.00 0.00 0.00 2.90
2005 2392 4.080413 TGACAATGAGCATCCAGGTTATCA 60.080 41.667 0.00 0.00 0.00 2.15
2215 2625 5.049336 GCCTCCTTCACAAAAGAAACTACTC 60.049 44.000 0.00 0.00 0.00 2.59
2222 2632 2.746279 TGGCCTCCTTCACAAAAGAA 57.254 45.000 3.32 0.00 0.00 2.52
2224 2634 2.629617 ACAATGGCCTCCTTCACAAAAG 59.370 45.455 3.32 0.00 0.00 2.27
2228 2638 1.003580 GAGACAATGGCCTCCTTCACA 59.996 52.381 3.32 0.00 0.00 3.58
2229 2639 1.680249 GGAGACAATGGCCTCCTTCAC 60.680 57.143 3.32 0.00 44.23 3.18
2230 2640 0.620556 GGAGACAATGGCCTCCTTCA 59.379 55.000 3.32 0.00 44.23 3.02
2231 2641 3.485764 GGAGACAATGGCCTCCTTC 57.514 57.895 3.32 0.00 44.23 3.46
2252 2670 6.205784 TGATTTGTGAATTCGTTTTCAGGAC 58.794 36.000 0.04 0.00 36.34 3.85
2263 2681 6.749118 GGACAGCAGTTATGATTTGTGAATTC 59.251 38.462 0.00 0.00 0.00 2.17
2345 2935 8.377034 TGGTGGTATGTTTACTTTATGTGTACT 58.623 33.333 0.00 0.00 0.00 2.73
2346 2936 8.445493 GTGGTGGTATGTTTACTTTATGTGTAC 58.555 37.037 0.00 0.00 0.00 2.90
2347 2937 7.607223 GGTGGTGGTATGTTTACTTTATGTGTA 59.393 37.037 0.00 0.00 0.00 2.90
2348 2938 6.431852 GGTGGTGGTATGTTTACTTTATGTGT 59.568 38.462 0.00 0.00 0.00 3.72
2349 2939 6.657541 AGGTGGTGGTATGTTTACTTTATGTG 59.342 38.462 0.00 0.00 0.00 3.21
2350 2940 6.657541 CAGGTGGTGGTATGTTTACTTTATGT 59.342 38.462 0.00 0.00 0.00 2.29
2351 2941 6.882140 TCAGGTGGTGGTATGTTTACTTTATG 59.118 38.462 0.00 0.00 0.00 1.90
2352 2942 7.023171 TCAGGTGGTGGTATGTTTACTTTAT 57.977 36.000 0.00 0.00 0.00 1.40
2353 2943 6.436738 TCAGGTGGTGGTATGTTTACTTTA 57.563 37.500 0.00 0.00 0.00 1.85
2354 2944 5.313280 TCAGGTGGTGGTATGTTTACTTT 57.687 39.130 0.00 0.00 0.00 2.66
2355 2945 4.986054 TCAGGTGGTGGTATGTTTACTT 57.014 40.909 0.00 0.00 0.00 2.24
2456 3046 7.842887 AAAGGTTACAGAGGGAGTATCTATC 57.157 40.000 0.00 0.00 33.73 2.08
2473 3063 6.767423 ACTAAAAGCCGTCTTACAAAAGGTTA 59.233 34.615 0.00 0.00 33.22 2.85
2533 3123 1.819288 AGGGTGACAGTACTGTGATCG 59.181 52.381 32.51 3.46 45.05 3.69
2535 3125 2.889512 TCAGGGTGACAGTACTGTGAT 58.110 47.619 32.51 8.87 45.05 3.06
2536 3126 2.364324 GTTCAGGGTGACAGTACTGTGA 59.636 50.000 32.51 22.50 45.05 3.58
2537 3127 2.102420 TGTTCAGGGTGACAGTACTGTG 59.898 50.000 32.51 16.84 45.05 3.66
2539 3129 2.548067 GGTGTTCAGGGTGACAGTACTG 60.548 54.545 21.44 21.44 0.00 2.74
2540 3130 1.692519 GGTGTTCAGGGTGACAGTACT 59.307 52.381 0.00 0.00 0.00 2.73
2541 3131 1.270678 GGGTGTTCAGGGTGACAGTAC 60.271 57.143 0.00 0.00 0.00 2.73
2542 3132 1.053424 GGGTGTTCAGGGTGACAGTA 58.947 55.000 0.00 0.00 0.00 2.74
2543 3133 1.705997 GGGGTGTTCAGGGTGACAGT 61.706 60.000 0.00 0.00 0.00 3.55
2544 3134 1.073199 GGGGTGTTCAGGGTGACAG 59.927 63.158 0.00 0.00 0.00 3.51
2545 3135 1.065410 ATGGGGTGTTCAGGGTGACA 61.065 55.000 0.00 0.00 0.00 3.58
2546 3136 0.988832 TATGGGGTGTTCAGGGTGAC 59.011 55.000 0.00 0.00 0.00 3.67
2547 3137 1.285280 CTATGGGGTGTTCAGGGTGA 58.715 55.000 0.00 0.00 0.00 4.02
2548 3138 0.394352 GCTATGGGGTGTTCAGGGTG 60.394 60.000 0.00 0.00 0.00 4.61
2549 3139 0.550147 AGCTATGGGGTGTTCAGGGT 60.550 55.000 0.00 0.00 0.00 4.34
2550 3140 1.141053 GTAGCTATGGGGTGTTCAGGG 59.859 57.143 0.00 0.00 0.00 4.45
2551 3141 1.141053 GGTAGCTATGGGGTGTTCAGG 59.859 57.143 0.00 0.00 0.00 3.86
2552 3142 1.837439 TGGTAGCTATGGGGTGTTCAG 59.163 52.381 0.00 0.00 0.00 3.02
2553 3143 1.837439 CTGGTAGCTATGGGGTGTTCA 59.163 52.381 0.00 0.00 0.00 3.18
2554 3144 1.838077 ACTGGTAGCTATGGGGTGTTC 59.162 52.381 0.00 0.00 0.00 3.18
2555 3145 1.838077 GACTGGTAGCTATGGGGTGTT 59.162 52.381 0.00 0.00 0.00 3.32
2556 3146 1.273609 TGACTGGTAGCTATGGGGTGT 60.274 52.381 0.00 0.00 0.00 4.16
2557 3147 1.414181 CTGACTGGTAGCTATGGGGTG 59.586 57.143 0.00 0.00 0.00 4.61
2558 3148 1.692762 CCTGACTGGTAGCTATGGGGT 60.693 57.143 0.00 0.00 0.00 4.95
2559 3149 1.051812 CCTGACTGGTAGCTATGGGG 58.948 60.000 0.00 0.00 0.00 4.96
2571 3161 3.947132 CTCCAGCGGCACCTGACTG 62.947 68.421 1.45 0.00 34.77 3.51
2572 3162 3.699894 CTCCAGCGGCACCTGACT 61.700 66.667 1.45 0.00 34.77 3.41
2573 3163 2.167398 TTACTCCAGCGGCACCTGAC 62.167 60.000 1.45 0.00 34.77 3.51
2574 3164 1.264749 ATTACTCCAGCGGCACCTGA 61.265 55.000 1.45 0.00 34.77 3.86
2575 3165 0.392998 AATTACTCCAGCGGCACCTG 60.393 55.000 1.45 0.00 0.00 4.00
2576 3166 1.139058 CTAATTACTCCAGCGGCACCT 59.861 52.381 1.45 0.00 0.00 4.00
2577 3167 1.583054 CTAATTACTCCAGCGGCACC 58.417 55.000 1.45 0.00 0.00 5.01
2578 3168 0.938008 GCTAATTACTCCAGCGGCAC 59.062 55.000 1.45 0.00 0.00 5.01
2579 3169 0.830648 AGCTAATTACTCCAGCGGCA 59.169 50.000 1.45 0.00 40.29 5.69
2580 3170 1.221414 CAGCTAATTACTCCAGCGGC 58.779 55.000 0.00 0.00 40.29 6.53
2581 3171 1.412710 TCCAGCTAATTACTCCAGCGG 59.587 52.381 0.00 0.00 40.29 5.52
2582 3172 2.890808 TCCAGCTAATTACTCCAGCG 57.109 50.000 0.00 0.00 40.29 5.18
2583 3173 4.143986 ACTTCCAGCTAATTACTCCAGC 57.856 45.455 0.00 0.00 35.49 4.85
2584 3174 7.174946 TGAAAAACTTCCAGCTAATTACTCCAG 59.825 37.037 0.00 0.00 0.00 3.86
2585 3175 7.001674 TGAAAAACTTCCAGCTAATTACTCCA 58.998 34.615 0.00 0.00 0.00 3.86
2586 3176 7.175119 AGTGAAAAACTTCCAGCTAATTACTCC 59.825 37.037 0.00 0.00 34.57 3.85
2587 3177 8.017946 CAGTGAAAAACTTCCAGCTAATTACTC 58.982 37.037 0.00 0.00 36.83 2.59
2588 3178 7.719633 TCAGTGAAAAACTTCCAGCTAATTACT 59.280 33.333 0.00 0.00 36.83 2.24
2589 3179 7.871853 TCAGTGAAAAACTTCCAGCTAATTAC 58.128 34.615 0.00 0.00 36.83 1.89
2590 3180 8.458573 TTCAGTGAAAAACTTCCAGCTAATTA 57.541 30.769 2.20 0.00 36.83 1.40
2591 3181 6.959639 TCAGTGAAAAACTTCCAGCTAATT 57.040 33.333 0.00 0.00 36.83 1.40
2592 3182 6.515696 GCTTCAGTGAAAAACTTCCAGCTAAT 60.516 38.462 7.06 0.00 36.83 1.73
2593 3183 5.221048 GCTTCAGTGAAAAACTTCCAGCTAA 60.221 40.000 7.06 0.00 36.83 3.09
2594 3184 4.275936 GCTTCAGTGAAAAACTTCCAGCTA 59.724 41.667 7.06 0.00 36.83 3.32
2595 3185 3.067320 GCTTCAGTGAAAAACTTCCAGCT 59.933 43.478 7.06 0.00 36.83 4.24
2596 3186 3.181487 TGCTTCAGTGAAAAACTTCCAGC 60.181 43.478 7.06 3.97 36.83 4.85
2597 3187 4.604976 CTGCTTCAGTGAAAAACTTCCAG 58.395 43.478 7.06 2.07 36.83 3.86
2598 3188 3.181487 GCTGCTTCAGTGAAAAACTTCCA 60.181 43.478 7.06 0.00 36.83 3.53
2599 3189 3.375642 GCTGCTTCAGTGAAAAACTTCC 58.624 45.455 7.06 0.00 36.83 3.46
2600 3190 3.181487 TGGCTGCTTCAGTGAAAAACTTC 60.181 43.478 7.06 0.00 36.83 3.01
2601 3191 2.760092 TGGCTGCTTCAGTGAAAAACTT 59.240 40.909 7.06 0.00 36.83 2.66
2602 3192 2.378038 TGGCTGCTTCAGTGAAAAACT 58.622 42.857 7.06 0.00 40.93 2.66
2603 3193 2.869233 TGGCTGCTTCAGTGAAAAAC 57.131 45.000 7.06 0.40 33.43 2.43
2604 3194 4.261994 GGTTATGGCTGCTTCAGTGAAAAA 60.262 41.667 7.06 0.00 33.43 1.94
2605 3195 3.255642 GGTTATGGCTGCTTCAGTGAAAA 59.744 43.478 7.06 0.00 33.43 2.29
2606 3196 2.819608 GGTTATGGCTGCTTCAGTGAAA 59.180 45.455 7.06 0.00 33.43 2.69
2607 3197 2.436417 GGTTATGGCTGCTTCAGTGAA 58.564 47.619 5.25 5.25 33.43 3.18
2608 3198 1.340017 GGGTTATGGCTGCTTCAGTGA 60.340 52.381 0.00 0.00 33.43 3.41
2609 3199 1.098050 GGGTTATGGCTGCTTCAGTG 58.902 55.000 0.00 0.00 33.43 3.66
2610 3200 0.392998 CGGGTTATGGCTGCTTCAGT 60.393 55.000 0.00 0.00 33.43 3.41
2611 3201 1.097547 CCGGGTTATGGCTGCTTCAG 61.098 60.000 0.00 0.00 34.12 3.02
2612 3202 1.077787 CCGGGTTATGGCTGCTTCA 60.078 57.895 0.00 0.00 0.00 3.02
2613 3203 3.827634 CCGGGTTATGGCTGCTTC 58.172 61.111 0.00 0.00 0.00 3.86
2620 3210 0.695924 TATCCATGGCCGGGTTATGG 59.304 55.000 19.48 19.48 42.12 2.74
2621 3211 2.806945 ATATCCATGGCCGGGTTATG 57.193 50.000 6.96 3.21 0.00 1.90
2622 3212 2.647299 TGAATATCCATGGCCGGGTTAT 59.353 45.455 6.96 11.06 0.00 1.89
2623 3213 2.058705 TGAATATCCATGGCCGGGTTA 58.941 47.619 6.96 9.36 0.00 2.85
2624 3214 0.850100 TGAATATCCATGGCCGGGTT 59.150 50.000 6.96 7.49 0.00 4.11
2625 3215 0.850100 TTGAATATCCATGGCCGGGT 59.150 50.000 6.96 0.12 0.00 5.28
2626 3216 1.538047 CTTGAATATCCATGGCCGGG 58.462 55.000 6.96 6.93 0.00 5.73
2627 3217 0.883833 GCTTGAATATCCATGGCCGG 59.116 55.000 6.96 0.00 0.00 6.13
2628 3218 1.267806 GTGCTTGAATATCCATGGCCG 59.732 52.381 6.96 0.00 0.00 6.13
2629 3219 1.615392 GGTGCTTGAATATCCATGGCC 59.385 52.381 6.96 0.00 0.00 5.36
2630 3220 2.295349 CTGGTGCTTGAATATCCATGGC 59.705 50.000 6.96 0.00 0.00 4.40
2631 3221 2.295349 GCTGGTGCTTGAATATCCATGG 59.705 50.000 4.97 4.97 36.03 3.66
2632 3222 2.953648 TGCTGGTGCTTGAATATCCATG 59.046 45.455 0.00 0.00 40.48 3.66
2633 3223 2.954318 GTGCTGGTGCTTGAATATCCAT 59.046 45.455 0.00 0.00 40.48 3.41
2634 3224 2.368439 GTGCTGGTGCTTGAATATCCA 58.632 47.619 0.00 0.00 40.48 3.41
2635 3225 1.678101 GGTGCTGGTGCTTGAATATCC 59.322 52.381 0.00 0.00 40.48 2.59
2636 3226 2.615912 GAGGTGCTGGTGCTTGAATATC 59.384 50.000 0.00 0.00 40.48 1.63
2637 3227 2.025981 TGAGGTGCTGGTGCTTGAATAT 60.026 45.455 0.00 0.00 40.48 1.28
2638 3228 1.350684 TGAGGTGCTGGTGCTTGAATA 59.649 47.619 0.00 0.00 40.48 1.75
2639 3229 0.111061 TGAGGTGCTGGTGCTTGAAT 59.889 50.000 0.00 0.00 40.48 2.57
2640 3230 0.106769 TTGAGGTGCTGGTGCTTGAA 60.107 50.000 0.00 0.00 40.48 2.69
2641 3231 0.106769 TTTGAGGTGCTGGTGCTTGA 60.107 50.000 0.00 0.00 40.48 3.02
2642 3232 0.963962 ATTTGAGGTGCTGGTGCTTG 59.036 50.000 0.00 0.00 40.48 4.01
2643 3233 0.963962 CATTTGAGGTGCTGGTGCTT 59.036 50.000 0.00 0.00 40.48 3.91
2644 3234 1.530013 GCATTTGAGGTGCTGGTGCT 61.530 55.000 0.00 0.00 39.45 4.40
2645 3235 1.080298 GCATTTGAGGTGCTGGTGC 60.080 57.895 0.00 0.00 39.45 5.01
2651 3241 1.154150 GCACGAGCATTTGAGGTGC 60.154 57.895 0.00 0.00 45.82 5.01
2652 3242 1.236616 TGGCACGAGCATTTGAGGTG 61.237 55.000 7.26 0.00 44.61 4.00
2653 3243 0.322816 ATGGCACGAGCATTTGAGGT 60.323 50.000 7.26 0.00 44.61 3.85
2654 3244 0.813184 AATGGCACGAGCATTTGAGG 59.187 50.000 7.26 0.00 44.61 3.86
2655 3245 1.200716 ACAATGGCACGAGCATTTGAG 59.799 47.619 20.05 3.65 44.61 3.02
2656 3246 1.068402 CACAATGGCACGAGCATTTGA 60.068 47.619 20.05 0.00 44.61 2.69
2657 3247 1.342555 CACAATGGCACGAGCATTTG 58.657 50.000 7.26 11.62 44.61 2.32
2658 3248 0.388907 GCACAATGGCACGAGCATTT 60.389 50.000 7.26 0.00 44.61 2.32
2659 3249 1.213537 GCACAATGGCACGAGCATT 59.786 52.632 7.26 2.19 44.61 3.56
2660 3250 2.703798 GGCACAATGGCACGAGCAT 61.704 57.895 7.26 0.00 43.14 3.79
2661 3251 3.364441 GGCACAATGGCACGAGCA 61.364 61.111 7.26 0.00 43.14 4.26
2673 3263 5.130311 TGGCTCTAGATAATAAGTTGGCACA 59.870 40.000 0.00 0.00 0.00 4.57
2674 3264 5.611374 TGGCTCTAGATAATAAGTTGGCAC 58.389 41.667 0.00 0.00 0.00 5.01
2675 3265 5.887214 TGGCTCTAGATAATAAGTTGGCA 57.113 39.130 0.00 0.00 0.00 4.92
2676 3266 5.177696 CGTTGGCTCTAGATAATAAGTTGGC 59.822 44.000 0.00 0.00 0.00 4.52
2677 3267 6.513180 TCGTTGGCTCTAGATAATAAGTTGG 58.487 40.000 0.00 0.00 0.00 3.77
2678 3268 6.144724 GCTCGTTGGCTCTAGATAATAAGTTG 59.855 42.308 0.00 0.00 0.00 3.16
2679 3269 6.041069 AGCTCGTTGGCTCTAGATAATAAGTT 59.959 38.462 0.00 0.00 38.24 2.66
2680 3270 5.536916 AGCTCGTTGGCTCTAGATAATAAGT 59.463 40.000 0.00 0.00 38.24 2.24
2681 3271 6.019779 AGCTCGTTGGCTCTAGATAATAAG 57.980 41.667 0.00 0.00 38.24 1.73
2693 3283 3.077556 ATCCCGAGCTCGTTGGCT 61.078 61.111 32.41 17.44 46.11 4.75
2694 3284 2.892425 CATCCCGAGCTCGTTGGC 60.892 66.667 32.41 0.00 37.74 4.52
2695 3285 2.892425 GCATCCCGAGCTCGTTGG 60.892 66.667 32.41 26.60 37.74 3.77
2696 3286 2.169789 CAGCATCCCGAGCTCGTTG 61.170 63.158 32.41 25.58 41.14 4.10
2731 3467 6.540083 TGATCATGTTGGCTCAATAGATCAT 58.460 36.000 16.41 5.00 35.29 2.45
2777 3513 8.419442 TGATGATAAGCATATGCCTAGTGATAG 58.581 37.037 23.96 0.00 43.38 2.08
2786 3522 6.150641 ACACAATCTGATGATAAGCATATGCC 59.849 38.462 23.96 9.30 37.34 4.40
2794 3530 6.047231 TGCTGAGACACAATCTGATGATAAG 58.953 40.000 0.00 0.00 38.00 1.73
2796 3532 5.603170 TGCTGAGACACAATCTGATGATA 57.397 39.130 0.00 0.00 38.00 2.15
2804 3540 5.814764 ATTTCTGATGCTGAGACACAATC 57.185 39.130 0.00 0.00 0.00 2.67
2861 3597 7.559335 TGCATACTCCTGATGAACCTATTAT 57.441 36.000 0.00 0.00 0.00 1.28
2865 3601 5.189736 ACTTTGCATACTCCTGATGAACCTA 59.810 40.000 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.