Multiple sequence alignment - TraesCS7B01G390300

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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 TraesCS7B01G390300 chr7B 100.000 2512 0 0 1 2512 656524180 656526691 0.000000e+00 4639.0
1 TraesCS7B01G390300 chr7A 84.951 1236 103 37 1 1199 677705800 677706989 0.000000e+00 1175.0
2 TraesCS7B01G390300 chr7A 89.079 467 39 9 2049 2510 677707875 677708334 1.010000e-158 569.0
3 TraesCS7B01G390300 chr7A 86.828 372 39 6 1231 1599 677707082 677707446 8.370000e-110 407.0
4 TraesCS7B01G390300 chr7A 90.086 232 22 1 1661 1891 677707464 677707695 1.460000e-77 300.0
5 TraesCS7B01G390300 chr7D 85.935 583 44 17 1343 1887 586498388 586498970 2.780000e-164 588.0
6 TraesCS7B01G390300 chr7D 84.272 515 54 16 735 1235 586497721 586498222 6.290000e-131 477.0
7 TraesCS7B01G390300 chr6A 83.740 123 19 1 321 443 520877486 520877365 5.680000e-22 115.0
8 TraesCS7B01G390300 chr4D 83.471 121 19 1 329 448 405467660 405467540 7.350000e-21 111.0
9 TraesCS7B01G390300 chr2B 75.000 200 39 8 326 522 738253904 738254095 5.760000e-12 82.4
10 TraesCS7B01G390300 chr5A 93.333 45 1 1 1184 1226 331809291 331809335 5.800000e-07 65.8
11 TraesCS7B01G390300 chr5A 93.333 45 1 1 1184 1226 331821546 331821590 5.800000e-07 65.8
12 TraesCS7B01G390300 chr5D 97.143 35 0 1 1192 1226 281671143 281671110 9.710000e-05 58.4
13 TraesCS7B01G390300 chr2D 96.875 32 1 0 1195 1226 15014565 15014596 1.000000e-03 54.7


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 TraesCS7B01G390300 chr7B 656524180 656526691 2511 False 4639.00 4639 100.0000 1 2512 1 chr7B.!!$F1 2511
1 TraesCS7B01G390300 chr7A 677705800 677708334 2534 False 612.75 1175 87.7360 1 2510 4 chr7A.!!$F1 2509
2 TraesCS7B01G390300 chr7D 586497721 586498970 1249 False 532.50 588 85.1035 735 1887 2 chr7D.!!$F1 1152

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
27 28 0.170339 GCGTGCATTAGGGTTTGGAC 59.830 55.0 0.0 0.0 0.00 4.02 F
1090 1139 0.035439 CACCCCAGGTATGTGTGTCC 60.035 60.0 0.0 0.0 32.11 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1418 1573 0.179070 TGCACCACTTGTCGCAGTTA 60.179 50.0 0.0 0.0 30.79 2.24 R
2284 2536 0.106318 ATCCAGCCAATCTTCCAGCC 60.106 55.0 0.0 0.0 0.00 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
27 28 0.170339 GCGTGCATTAGGGTTTGGAC 59.830 55.000 0.00 0.00 0.00 4.02
29 30 0.170339 GTGCATTAGGGTTTGGACGC 59.830 55.000 0.00 0.00 38.89 5.19
34 35 2.791501 TTAGGGTTTGGACGCGGCTC 62.792 60.000 13.91 1.82 43.00 4.70
35 36 4.699522 GGGTTTGGACGCGGCTCT 62.700 66.667 13.91 0.00 0.00 4.09
50 51 1.940613 GGCTCTGGTGCGGTTTTATAG 59.059 52.381 0.00 0.00 0.00 1.31
51 52 2.629051 GCTCTGGTGCGGTTTTATAGT 58.371 47.619 0.00 0.00 0.00 2.12
62 63 2.024751 GGTTTTATAGTGGCAGGGGGAA 60.025 50.000 0.00 0.00 0.00 3.97
71 72 1.379044 GCAGGGGGAATGGTCAGTG 60.379 63.158 0.00 0.00 0.00 3.66
72 73 2.078452 CAGGGGGAATGGTCAGTGT 58.922 57.895 0.00 0.00 0.00 3.55
76 77 1.074775 GGGAATGGTCAGTGTGGCA 59.925 57.895 0.00 0.00 0.00 4.92
92 93 2.819595 CAGCACGCTGGCGGTTAT 60.820 61.111 18.99 0.00 44.69 1.89
106 108 6.142818 TGGCGGTTATCCATTATTTTTCAG 57.857 37.500 0.00 0.00 0.00 3.02
107 109 4.982295 GGCGGTTATCCATTATTTTTCAGC 59.018 41.667 0.00 0.00 0.00 4.26
109 111 5.504994 GCGGTTATCCATTATTTTTCAGCGA 60.505 40.000 0.00 0.00 0.00 4.93
116 118 7.630242 TCCATTATTTTTCAGCGAGAGAAAT 57.370 32.000 12.75 12.75 42.02 2.17
117 119 7.697691 TCCATTATTTTTCAGCGAGAGAAATC 58.302 34.615 11.90 0.00 39.49 2.17
136 138 7.065504 AGAAATCAAAGAGGATATTTGGGGAG 58.934 38.462 0.00 0.00 38.04 4.30
144 146 2.899900 GGATATTTGGGGAGAAATGCCC 59.100 50.000 0.00 0.00 45.25 5.36
185 187 5.088141 CAGAACTGCAAACTGTTGAGTAG 57.912 43.478 0.00 2.01 37.99 2.57
186 188 4.572389 CAGAACTGCAAACTGTTGAGTAGT 59.428 41.667 9.89 9.89 37.99 2.73
187 189 5.753438 CAGAACTGCAAACTGTTGAGTAGTA 59.247 40.000 14.10 0.00 37.99 1.82
188 190 6.257849 CAGAACTGCAAACTGTTGAGTAGTAA 59.742 38.462 14.10 0.00 37.99 2.24
189 191 5.986004 ACTGCAAACTGTTGAGTAGTAAC 57.014 39.130 12.76 0.00 36.83 2.50
190 192 5.671493 ACTGCAAACTGTTGAGTAGTAACT 58.329 37.500 12.76 0.00 36.83 2.24
239 241 0.686441 GGGGAATGGTTAGTTGGGGC 60.686 60.000 0.00 0.00 0.00 5.80
265 267 8.380867 CCTAACTCCTTAAAAGGGAAGTTAAGA 58.619 37.037 17.26 5.15 46.47 2.10
279 281 6.071334 GGGAAGTTAAGAAAATTGGAGGGAAG 60.071 42.308 0.00 0.00 0.00 3.46
280 282 6.071334 GGAAGTTAAGAAAATTGGAGGGAAGG 60.071 42.308 0.00 0.00 0.00 3.46
282 284 6.382087 AGTTAAGAAAATTGGAGGGAAGGTT 58.618 36.000 0.00 0.00 0.00 3.50
283 285 6.844388 AGTTAAGAAAATTGGAGGGAAGGTTT 59.156 34.615 0.00 0.00 0.00 3.27
284 286 7.347222 AGTTAAGAAAATTGGAGGGAAGGTTTT 59.653 33.333 0.00 0.00 0.00 2.43
285 287 5.551305 AGAAAATTGGAGGGAAGGTTTTG 57.449 39.130 0.00 0.00 0.00 2.44
286 288 5.215845 AGAAAATTGGAGGGAAGGTTTTGA 58.784 37.500 0.00 0.00 0.00 2.69
287 289 5.305386 AGAAAATTGGAGGGAAGGTTTTGAG 59.695 40.000 0.00 0.00 0.00 3.02
288 290 4.469469 AATTGGAGGGAAGGTTTTGAGA 57.531 40.909 0.00 0.00 0.00 3.27
289 291 4.682021 ATTGGAGGGAAGGTTTTGAGAT 57.318 40.909 0.00 0.00 0.00 2.75
290 292 3.439857 TGGAGGGAAGGTTTTGAGATG 57.560 47.619 0.00 0.00 0.00 2.90
291 293 2.716424 TGGAGGGAAGGTTTTGAGATGT 59.284 45.455 0.00 0.00 0.00 3.06
292 294 3.244911 TGGAGGGAAGGTTTTGAGATGTC 60.245 47.826 0.00 0.00 0.00 3.06
293 295 3.348119 GAGGGAAGGTTTTGAGATGTCC 58.652 50.000 0.00 0.00 0.00 4.02
294 296 2.989571 AGGGAAGGTTTTGAGATGTCCT 59.010 45.455 0.00 0.00 0.00 3.85
302 304 6.352516 AGGTTTTGAGATGTCCTAAGCATAG 58.647 40.000 6.19 0.00 0.00 2.23
314 316 7.777095 TGTCCTAAGCATAGTTGTTTGTTTTT 58.223 30.769 0.00 0.00 0.00 1.94
315 317 7.918562 TGTCCTAAGCATAGTTGTTTGTTTTTC 59.081 33.333 0.00 0.00 0.00 2.29
327 329 4.948621 TGTTTGTTTTTCGGACCCTCTTAA 59.051 37.500 0.00 0.00 0.00 1.85
365 367 3.203716 GGGGAGGATGACATTTACGAAC 58.796 50.000 0.00 0.00 0.00 3.95
376 378 6.310960 TGACATTTACGAACGATTTTCATGG 58.689 36.000 0.14 0.00 0.00 3.66
401 405 9.774742 GGCAATTTTAGTTATAAGAAGTGACAG 57.225 33.333 0.00 0.00 0.00 3.51
409 413 8.522178 AGTTATAAGAAGTGACAGTTTCTTCG 57.478 34.615 14.83 0.00 41.40 3.79
463 467 4.455877 ACAATTTTGTTGAAAAACGGCCAA 59.544 33.333 2.24 0.00 38.47 4.52
522 526 2.226437 AGACGTTTGCCAGTTAGCATTG 59.774 45.455 0.00 0.00 43.64 2.82
575 608 2.095053 TGTGTGTGTGTGTGTGATTTCG 59.905 45.455 0.00 0.00 0.00 3.46
576 609 1.668237 TGTGTGTGTGTGTGATTTCGG 59.332 47.619 0.00 0.00 0.00 4.30
577 610 1.002900 GTGTGTGTGTGTGATTTCGGG 60.003 52.381 0.00 0.00 0.00 5.14
578 611 1.305201 GTGTGTGTGTGATTTCGGGT 58.695 50.000 0.00 0.00 0.00 5.28
579 612 1.673920 GTGTGTGTGTGATTTCGGGTT 59.326 47.619 0.00 0.00 0.00 4.11
580 613 2.098443 GTGTGTGTGTGATTTCGGGTTT 59.902 45.455 0.00 0.00 0.00 3.27
581 614 2.755655 TGTGTGTGTGATTTCGGGTTTT 59.244 40.909 0.00 0.00 0.00 2.43
582 615 3.112580 GTGTGTGTGATTTCGGGTTTTG 58.887 45.455 0.00 0.00 0.00 2.44
598 631 5.641209 CGGGTTTTGGCAATATTTTCATGAA 59.359 36.000 3.38 3.38 0.00 2.57
630 663 6.272324 TGGACAATTCCTTTCGGATCCTATAT 59.728 38.462 10.75 0.00 43.31 0.86
635 668 8.850156 CAATTCCTTTCGGATCCTATATTTTGT 58.150 33.333 10.75 0.00 39.58 2.83
643 676 7.287061 TCGGATCCTATATTTTGTGGACAAAT 58.713 34.615 10.75 0.51 44.30 2.32
653 686 3.816398 TGTGGACAAATATTGGACCCA 57.184 42.857 8.62 6.73 32.80 4.51
694 727 0.961753 CTTTGGAGAGCAACCAACCC 59.038 55.000 8.39 0.00 45.38 4.11
788 826 4.202111 GGCGGCAGTAATCCAATTTTACAT 60.202 41.667 3.07 0.00 33.02 2.29
830 872 8.908786 TCTTCAGTGGATCCAATAAATACATC 57.091 34.615 18.20 0.00 0.00 3.06
856 899 2.982744 GCCGAGCAAAAGGAGTGGC 61.983 63.158 0.00 0.00 0.00 5.01
866 909 5.185056 AGCAAAAGGAGTGGCGTAATTAATT 59.815 36.000 5.89 5.89 0.00 1.40
874 917 6.314400 GGAGTGGCGTAATTAATTAGTTCACA 59.686 38.462 22.72 12.05 0.00 3.58
924 967 6.592994 GTCCTTTAATGCCCGGTCTATATAAC 59.407 42.308 0.00 0.00 0.00 1.89
929 972 2.027561 TGCCCGGTCTATATAACCATGC 60.028 50.000 0.00 12.35 36.53 4.06
979 1023 7.328249 GCATCAGCATATACTAGACTCAAGAAC 59.672 40.741 0.00 0.00 41.58 3.01
984 1028 8.356657 AGCATATACTAGACTCAAGAACACATC 58.643 37.037 0.00 0.00 0.00 3.06
1024 1073 2.096516 GCTGCAACTTTTCTCTCTGTCG 60.097 50.000 0.00 0.00 0.00 4.35
1069 1118 1.450360 AGCCAGTTCTTCCCTCCTTT 58.550 50.000 0.00 0.00 0.00 3.11
1090 1139 0.035439 CACCCCAGGTATGTGTGTCC 60.035 60.000 0.00 0.00 32.11 4.02
1098 1147 2.846206 AGGTATGTGTGTCCATCCATGT 59.154 45.455 0.00 0.00 0.00 3.21
1100 1149 2.425143 ATGTGTGTCCATCCATGTCC 57.575 50.000 0.00 0.00 0.00 4.02
1102 1151 0.394352 GTGTGTCCATCCATGTCCCC 60.394 60.000 0.00 0.00 0.00 4.81
1107 1156 2.127708 GTCCATCCATGTCCCCTTAGT 58.872 52.381 0.00 0.00 0.00 2.24
1115 1164 4.016479 TCCATGTCCCCTTAGTTCTCTACT 60.016 45.833 0.00 0.00 41.04 2.57
1116 1165 4.100189 CCATGTCCCCTTAGTTCTCTACTG 59.900 50.000 0.00 0.00 37.73 2.74
1118 1167 2.431419 GTCCCCTTAGTTCTCTACTGCC 59.569 54.545 0.00 0.00 37.73 4.85
1121 1170 1.763545 CCTTAGTTCTCTACTGCCCCC 59.236 57.143 0.00 0.00 37.73 5.40
1167 1216 5.690464 ATCTAAGATCAGTGCAGGTTCTT 57.310 39.130 13.30 13.30 0.00 2.52
1175 1224 4.944249 GCAGGTTCTTGCGAAACC 57.056 55.556 6.60 6.60 37.57 3.27
1177 1226 1.782028 GCAGGTTCTTGCGAAACCGT 61.782 55.000 8.52 0.00 37.57 4.83
1199 1254 3.969976 TGAGGCCAGATAAATGCTACTCT 59.030 43.478 5.01 0.00 0.00 3.24
1203 1261 4.562552 GGCCAGATAAATGCTACTCTCTCC 60.563 50.000 0.00 0.00 0.00 3.71
1220 1278 5.394738 TCTCTCCGTCCCACAATATAAGAT 58.605 41.667 0.00 0.00 0.00 2.40
1221 1279 5.477291 TCTCTCCGTCCCACAATATAAGATC 59.523 44.000 0.00 0.00 0.00 2.75
1222 1280 4.217767 TCTCCGTCCCACAATATAAGATCG 59.782 45.833 0.00 0.00 0.00 3.69
1249 1366 4.438148 GCAAACTAGGATCTTCCTCTGAC 58.562 47.826 0.00 0.00 45.66 3.51
1264 1381 8.224025 TCTTCCTCTGACTCTACAGATATTGAT 58.776 37.037 0.00 0.00 44.32 2.57
1293 1412 5.543507 TTGTGCAAATTTCCTACACCATT 57.456 34.783 0.00 0.00 0.00 3.16
1302 1421 8.711457 CAAATTTCCTACACCATTTTGTGATTC 58.289 33.333 0.00 0.00 39.57 2.52
1308 1427 6.863126 CCTACACCATTTTGTGATTCAACTTC 59.137 38.462 0.00 0.00 39.57 3.01
1312 1432 6.642131 CACCATTTTGTGATTCAACTTCGAAT 59.358 34.615 0.00 0.00 38.55 3.34
1324 1444 6.000891 TCAACTTCGAATTGAATCAACTGG 57.999 37.500 15.86 0.00 35.63 4.00
1325 1445 5.762711 TCAACTTCGAATTGAATCAACTGGA 59.237 36.000 15.86 0.00 35.63 3.86
1326 1446 5.869753 ACTTCGAATTGAATCAACTGGAG 57.130 39.130 0.00 0.00 35.63 3.86
1327 1447 4.154918 ACTTCGAATTGAATCAACTGGAGC 59.845 41.667 0.00 0.00 35.63 4.70
1328 1448 3.009723 TCGAATTGAATCAACTGGAGCC 58.990 45.455 0.00 0.00 0.00 4.70
1329 1449 3.012518 CGAATTGAATCAACTGGAGCCT 58.987 45.455 0.00 0.00 0.00 4.58
1331 1451 4.635765 CGAATTGAATCAACTGGAGCCTTA 59.364 41.667 0.00 0.00 0.00 2.69
1332 1452 5.297776 CGAATTGAATCAACTGGAGCCTTAT 59.702 40.000 0.00 0.00 0.00 1.73
1334 1454 7.012327 CGAATTGAATCAACTGGAGCCTTATAA 59.988 37.037 0.00 0.00 0.00 0.98
1339 1459 4.708177 TCAACTGGAGCCTTATAATCAGC 58.292 43.478 0.00 0.00 0.00 4.26
1363 1518 6.765989 GCTTAGTAACATTGTGGATATGGACA 59.234 38.462 0.00 0.00 0.00 4.02
1364 1519 7.445402 GCTTAGTAACATTGTGGATATGGACAT 59.555 37.037 0.00 0.00 0.00 3.06
1368 1523 7.884877 AGTAACATTGTGGATATGGACATATGG 59.115 37.037 9.40 0.00 34.36 2.74
1386 1541 1.630126 GGATGCAGGAGAGGGCAAGA 61.630 60.000 0.00 0.00 44.20 3.02
1418 1573 1.747206 GGCAAATGCGAGGACATACCT 60.747 52.381 0.00 0.00 44.65 3.08
1419 1574 2.484770 GGCAAATGCGAGGACATACCTA 60.485 50.000 0.00 0.00 44.56 3.08
1439 1594 1.029408 ACTGCGACAAGTGGTGCAAA 61.029 50.000 0.00 0.00 34.62 3.68
1442 1597 0.593128 GCGACAAGTGGTGCAAATCT 59.407 50.000 0.00 0.00 0.00 2.40
1519 1674 5.447624 TGCTGCATTGAATAATCATCCAG 57.552 39.130 0.00 0.00 34.96 3.86
1520 1675 4.235360 GCTGCATTGAATAATCATCCAGC 58.765 43.478 10.26 10.26 40.62 4.85
1586 1759 5.051240 CGGTAATAAAATGTGAGTCGGTAGC 60.051 44.000 0.00 0.00 0.00 3.58
1617 1799 1.002502 GTGTGGGGGAGGCTGTAAC 60.003 63.158 0.00 0.00 0.00 2.50
1632 1814 7.253905 AGGCTGTAACTAGGTTTCAGATAAA 57.746 36.000 16.97 0.00 41.31 1.40
1766 1950 3.050275 GAAGCACCAGACCACGGC 61.050 66.667 0.00 0.00 0.00 5.68
1829 2019 3.849951 CCCCCATCGTCCAGACCG 61.850 72.222 0.00 0.00 0.00 4.79
1832 2022 2.348104 CCCATCGTCCAGACCGACA 61.348 63.158 0.00 0.00 37.12 4.35
1838 2028 0.447011 CGTCCAGACCGACACTAGAC 59.553 60.000 0.00 0.00 32.74 2.59
1877 2070 1.869574 CGAGCACGATGACACGGAG 60.870 63.158 0.00 0.00 42.66 4.63
1880 2073 0.532573 AGCACGATGACACGGAGATT 59.467 50.000 0.00 0.00 37.61 2.40
1882 2075 1.324736 GCACGATGACACGGAGATTTC 59.675 52.381 0.00 0.00 37.61 2.17
1901 2106 2.652530 CCATTGCTGTGGTGGCAC 59.347 61.111 9.70 9.70 39.55 5.01
1903 2108 2.985282 ATTGCTGTGGTGGCACGG 60.985 61.111 12.17 3.02 39.55 4.94
1904 2109 3.790416 ATTGCTGTGGTGGCACGGT 62.790 57.895 12.17 0.00 39.55 4.83
1915 2120 4.347453 GCACGGTGGCCTTTGCAG 62.347 66.667 10.60 0.00 40.13 4.41
1916 2121 2.906897 CACGGTGGCCTTTGCAGT 60.907 61.111 3.32 0.00 40.13 4.40
1917 2122 1.599518 CACGGTGGCCTTTGCAGTA 60.600 57.895 3.32 0.00 40.13 2.74
1918 2123 1.599797 ACGGTGGCCTTTGCAGTAC 60.600 57.895 3.32 0.00 40.13 2.73
1919 2124 2.332654 CGGTGGCCTTTGCAGTACC 61.333 63.158 3.32 0.00 40.13 3.34
1920 2125 1.074951 GGTGGCCTTTGCAGTACCT 59.925 57.895 3.32 0.00 40.13 3.08
1921 2126 1.244019 GGTGGCCTTTGCAGTACCTG 61.244 60.000 3.32 0.00 40.13 4.00
1922 2127 1.074775 TGGCCTTTGCAGTACCTGG 59.925 57.895 3.32 0.00 40.13 4.45
1923 2128 1.378762 GGCCTTTGCAGTACCTGGA 59.621 57.895 0.00 0.00 40.13 3.86
1924 2129 0.678048 GGCCTTTGCAGTACCTGGAG 60.678 60.000 0.00 0.00 40.13 3.86
1925 2130 0.678048 GCCTTTGCAGTACCTGGAGG 60.678 60.000 0.00 0.00 38.23 4.30
1926 2131 3.338853 GCCTTTGCAGTACCTGGAGGT 62.339 57.143 0.00 3.29 44.19 3.85
1927 2132 4.004226 GCCTTTGCAGTACCTGGAGGTA 62.004 54.545 0.00 1.08 42.73 3.08
1928 2133 5.451590 GCCTTTGCAGTACCTGGAGGTAA 62.452 52.174 7.13 0.00 43.98 2.85
1929 2134 6.861856 GCCTTTGCAGTACCTGGAGGTAAA 62.862 50.000 7.13 0.00 43.98 2.01
1937 2142 2.734755 CCTGGAGGTAAATCATGCCA 57.265 50.000 0.00 0.00 35.99 4.92
1938 2143 2.301346 CCTGGAGGTAAATCATGCCAC 58.699 52.381 0.00 0.00 35.99 5.01
1939 2144 2.092212 CCTGGAGGTAAATCATGCCACT 60.092 50.000 0.00 0.00 35.99 4.00
1940 2145 2.947652 CTGGAGGTAAATCATGCCACTG 59.052 50.000 0.00 0.00 35.99 3.66
1941 2146 2.575735 TGGAGGTAAATCATGCCACTGA 59.424 45.455 0.00 0.00 35.99 3.41
1942 2147 3.209410 GGAGGTAAATCATGCCACTGAG 58.791 50.000 0.00 0.00 35.99 3.35
1943 2148 3.209410 GAGGTAAATCATGCCACTGAGG 58.791 50.000 0.00 0.00 35.99 3.86
1944 2149 2.578021 AGGTAAATCATGCCACTGAGGT 59.422 45.455 0.00 0.00 40.61 3.85
1945 2150 3.780294 AGGTAAATCATGCCACTGAGGTA 59.220 43.478 0.00 0.00 40.61 3.08
1975 2180 8.556213 AGTTTTCACTGACTTGTAAGTTGTAA 57.444 30.769 0.00 0.00 39.88 2.41
1976 2181 8.448615 AGTTTTCACTGACTTGTAAGTTGTAAC 58.551 33.333 0.00 4.22 39.88 2.50
1977 2182 8.448615 GTTTTCACTGACTTGTAAGTTGTAACT 58.551 33.333 0.00 0.00 39.88 2.24
1978 2183 7.534085 TTCACTGACTTGTAAGTTGTAACTG 57.466 36.000 0.00 0.00 39.88 3.16
1979 2184 6.869695 TCACTGACTTGTAAGTTGTAACTGA 58.130 36.000 0.00 0.00 39.88 3.41
1980 2185 7.497595 TCACTGACTTGTAAGTTGTAACTGAT 58.502 34.615 0.00 0.00 39.88 2.90
1981 2186 8.635328 TCACTGACTTGTAAGTTGTAACTGATA 58.365 33.333 0.00 0.00 39.88 2.15
1982 2187 8.916654 CACTGACTTGTAAGTTGTAACTGATAG 58.083 37.037 0.00 0.00 39.88 2.08
1983 2188 8.857098 ACTGACTTGTAAGTTGTAACTGATAGA 58.143 33.333 0.00 0.00 39.88 1.98
1984 2189 9.692749 CTGACTTGTAAGTTGTAACTGATAGAA 57.307 33.333 0.00 0.00 39.88 2.10
2020 2240 1.134226 GCAAGCAATCACACAAGCAC 58.866 50.000 0.00 0.00 0.00 4.40
2026 2246 2.536803 GCAATCACACAAGCACAAACTG 59.463 45.455 0.00 0.00 0.00 3.16
2082 2332 2.046892 GCTCGGACATGCCACTGT 60.047 61.111 0.00 0.00 35.94 3.55
2095 2345 3.276846 ACTGTCCGGCGCACAAAC 61.277 61.111 10.83 1.73 0.00 2.93
2106 2356 2.926838 GGCGCACAAACTTTCAGAAAAA 59.073 40.909 10.83 0.00 0.00 1.94
2112 2362 5.065090 GCACAAACTTTCAGAAAAATGGCTT 59.935 36.000 0.00 0.00 0.00 4.35
2115 2365 7.064966 CACAAACTTTCAGAAAAATGGCTTCTT 59.935 33.333 0.00 0.00 30.58 2.52
2117 2367 6.721704 ACTTTCAGAAAAATGGCTTCTTCT 57.278 33.333 0.00 0.00 30.58 2.85
2118 2368 6.743110 ACTTTCAGAAAAATGGCTTCTTCTC 58.257 36.000 0.00 0.00 30.58 2.87
2119 2369 5.712152 TTCAGAAAAATGGCTTCTTCTCC 57.288 39.130 0.00 0.00 30.58 3.71
2120 2370 3.753272 TCAGAAAAATGGCTTCTTCTCCG 59.247 43.478 0.00 0.00 30.58 4.63
2134 2384 2.961526 TCTCCGTACCAGAAAGATGC 57.038 50.000 0.00 0.00 0.00 3.91
2159 2409 2.378038 GCATTGATCTGCAACCCCTTA 58.622 47.619 2.23 0.00 41.87 2.69
2192 2442 0.745845 GTGCCAGCACGGATCATTCT 60.746 55.000 7.07 0.00 37.19 2.40
2207 2457 5.163478 GGATCATTCTGCTGCAAAATACCTT 60.163 40.000 3.02 0.00 0.00 3.50
2208 2458 5.063180 TCATTCTGCTGCAAAATACCTTG 57.937 39.130 3.02 0.00 0.00 3.61
2214 2464 2.354003 GCTGCAAAATACCTTGGCATGT 60.354 45.455 0.00 0.00 0.00 3.21
2241 2493 6.882140 TCTCTGACAGAAAACTTACCAAAACA 59.118 34.615 6.61 0.00 0.00 2.83
2255 2507 1.002033 CAAAACAGACTGTCAGCCAGC 60.002 52.381 8.93 0.00 45.68 4.85
2281 2533 3.186205 GGACAAATTTGGTTCCAAATGCG 59.814 43.478 24.52 20.47 43.32 4.73
2284 2536 0.389687 ATTTGGTTCCAAATGCGCCG 60.390 50.000 23.59 0.00 42.75 6.46
2285 2537 2.427540 TTTGGTTCCAAATGCGCCGG 62.428 55.000 12.29 0.00 31.88 6.13
2287 2539 3.747976 GTTCCAAATGCGCCGGCT 61.748 61.111 26.68 1.82 40.82 5.52
2318 2570 1.402968 CTGGATGAACATTTCGGGCAG 59.597 52.381 0.00 0.00 0.00 4.85
2319 2571 1.004161 TGGATGAACATTTCGGGCAGA 59.996 47.619 0.00 0.00 0.00 4.26
2333 2585 0.811616 GGCAGACTTATCCTGGTGCG 60.812 60.000 0.00 0.00 32.51 5.34
2335 2587 1.141881 AGACTTATCCTGGTGCGCG 59.858 57.895 0.00 0.00 0.00 6.86
2339 2591 2.852495 CTTATCCTGGTGCGCGTGGT 62.852 60.000 8.43 0.00 0.00 4.16
2354 2606 2.039624 GGTCCTCTCTGCCCTCCA 59.960 66.667 0.00 0.00 0.00 3.86
2364 2616 2.303022 CTCTGCCCTCCACACTTTCTAA 59.697 50.000 0.00 0.00 0.00 2.10
2367 2619 3.686016 TGCCCTCCACACTTTCTAAATC 58.314 45.455 0.00 0.00 0.00 2.17
2383 2637 6.515272 TCTAAATCATTTCTTGCTCAACCC 57.485 37.500 0.00 0.00 0.00 4.11
2387 2641 4.640771 TCATTTCTTGCTCAACCCTAGT 57.359 40.909 0.00 0.00 0.00 2.57
2388 2642 4.579869 TCATTTCTTGCTCAACCCTAGTC 58.420 43.478 0.00 0.00 0.00 2.59
2389 2643 2.743636 TTCTTGCTCAACCCTAGTCG 57.256 50.000 0.00 0.00 0.00 4.18
2391 2645 0.247736 CTTGCTCAACCCTAGTCGCT 59.752 55.000 0.00 0.00 0.00 4.93
2392 2646 1.476891 CTTGCTCAACCCTAGTCGCTA 59.523 52.381 0.00 0.00 0.00 4.26
2393 2647 1.103803 TGCTCAACCCTAGTCGCTAG 58.896 55.000 6.85 6.85 34.16 3.42
2402 2656 1.957177 CCTAGTCGCTAGGCAAGATGA 59.043 52.381 16.56 0.00 45.64 2.92
2403 2657 2.560542 CCTAGTCGCTAGGCAAGATGAT 59.439 50.000 16.56 0.00 45.64 2.45
2404 2658 2.810439 AGTCGCTAGGCAAGATGATC 57.190 50.000 0.00 0.00 0.00 2.92
2405 2659 2.315176 AGTCGCTAGGCAAGATGATCT 58.685 47.619 0.00 0.00 0.00 2.75
2422 2676 2.472695 TCTTGCGAAGTATGCCAAGT 57.527 45.000 0.00 0.00 0.00 3.16
2430 2684 4.380531 CGAAGTATGCCAAGTCCATACAT 58.619 43.478 12.42 2.49 44.62 2.29
2441 2695 6.212955 CCAAGTCCATACATGTTTCGTTTTT 58.787 36.000 2.30 0.00 0.00 1.94
2475 2729 5.909610 GCGTTGTTTGGATTATAAGCTGATC 59.090 40.000 0.02 0.00 0.00 2.92
2488 2742 1.068281 AGCTGATCATCTACACTGCCG 59.932 52.381 0.00 0.00 0.00 5.69
2494 2748 3.165058 TCATCTACACTGCCGATGTTC 57.835 47.619 0.00 0.00 36.72 3.18
2499 2753 0.396435 ACACTGCCGATGTTCTCCAA 59.604 50.000 0.00 0.00 0.00 3.53
2502 2756 1.347707 ACTGCCGATGTTCTCCAAAGA 59.652 47.619 0.00 0.00 0.00 2.52
2504 2758 2.417933 CTGCCGATGTTCTCCAAAGAAG 59.582 50.000 0.00 0.00 42.14 2.85
2507 2761 2.027192 CCGATGTTCTCCAAAGAAGGGA 60.027 50.000 0.00 0.00 42.14 4.20
2508 2762 3.370953 CCGATGTTCTCCAAAGAAGGGAT 60.371 47.826 0.00 0.00 42.14 3.85
2509 2763 3.624861 CGATGTTCTCCAAAGAAGGGATG 59.375 47.826 0.00 0.00 42.14 3.51
2511 2765 2.095461 GTTCTCCAAAGAAGGGATGGC 58.905 52.381 0.00 0.00 42.14 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.024579 ATAAAACCGCACCAGAGCCG 61.025 55.000 0.00 0.00 0.00 5.52
34 35 1.400494 GCCACTATAAAACCGCACCAG 59.600 52.381 0.00 0.00 0.00 4.00
35 36 1.271434 TGCCACTATAAAACCGCACCA 60.271 47.619 0.00 0.00 0.00 4.17
50 51 2.043953 GACCATTCCCCCTGCCAC 60.044 66.667 0.00 0.00 0.00 5.01
51 52 2.534011 TGACCATTCCCCCTGCCA 60.534 61.111 0.00 0.00 0.00 4.92
62 63 1.601759 GTGCTGCCACACTGACCAT 60.602 57.895 0.00 0.00 41.67 3.55
76 77 2.511600 GATAACCGCCAGCGTGCT 60.512 61.111 11.55 0.00 37.81 4.40
86 87 6.018262 TCTCGCTGAAAAATAATGGATAACCG 60.018 38.462 0.00 0.00 39.42 4.44
91 92 7.630242 TTTCTCTCGCTGAAAAATAATGGAT 57.370 32.000 0.00 0.00 31.45 3.41
92 93 7.336679 TGATTTCTCTCGCTGAAAAATAATGGA 59.663 33.333 0.00 0.00 37.05 3.41
106 108 7.351223 CAAATATCCTCTTTGATTTCTCTCGC 58.649 38.462 0.00 0.00 35.99 5.03
107 109 7.041508 CCCAAATATCCTCTTTGATTTCTCTCG 60.042 40.741 0.00 0.00 35.99 4.04
109 111 7.065504 CCCCAAATATCCTCTTTGATTTCTCT 58.934 38.462 0.00 0.00 35.99 3.10
116 118 6.401537 TTTCTCCCCAAATATCCTCTTTGA 57.598 37.500 0.00 0.00 35.99 2.69
117 119 6.462067 GCATTTCTCCCCAAATATCCTCTTTG 60.462 42.308 0.00 0.00 34.17 2.77
136 138 1.252904 TTGAGCAGCCAGGGCATTTC 61.253 55.000 13.63 7.00 44.88 2.17
203 205 8.853912 ACCATTCCCCTATAGCTATAACTACTA 58.146 37.037 14.30 0.38 0.00 1.82
206 208 9.710818 CTAACCATTCCCCTATAGCTATAACTA 57.289 37.037 14.30 0.00 0.00 2.24
216 218 3.984770 CCCCAACTAACCATTCCCCTATA 59.015 47.826 0.00 0.00 0.00 1.31
223 225 3.021695 GTTAGGCCCCAACTAACCATTC 58.978 50.000 0.00 0.00 42.68 2.67
265 267 5.215845 TCTCAAAACCTTCCCTCCAATTTT 58.784 37.500 0.00 0.00 0.00 1.82
279 281 6.116126 ACTATGCTTAGGACATCTCAAAACC 58.884 40.000 11.03 0.00 0.00 3.27
280 282 7.119846 ACAACTATGCTTAGGACATCTCAAAAC 59.880 37.037 11.03 0.00 0.00 2.43
282 284 6.711277 ACAACTATGCTTAGGACATCTCAAA 58.289 36.000 11.03 0.00 0.00 2.69
283 285 6.299805 ACAACTATGCTTAGGACATCTCAA 57.700 37.500 11.03 0.00 0.00 3.02
284 286 5.939764 ACAACTATGCTTAGGACATCTCA 57.060 39.130 11.03 0.00 0.00 3.27
285 287 6.595716 ACAAACAACTATGCTTAGGACATCTC 59.404 38.462 11.03 0.00 0.00 2.75
286 288 6.476378 ACAAACAACTATGCTTAGGACATCT 58.524 36.000 11.03 0.00 0.00 2.90
287 289 6.743575 ACAAACAACTATGCTTAGGACATC 57.256 37.500 11.03 0.00 0.00 3.06
288 290 7.524717 AAACAAACAACTATGCTTAGGACAT 57.475 32.000 11.03 0.00 0.00 3.06
289 291 6.952773 AAACAAACAACTATGCTTAGGACA 57.047 33.333 11.03 0.00 0.00 4.02
290 292 7.112984 CGAAAAACAAACAACTATGCTTAGGAC 59.887 37.037 11.03 0.00 0.00 3.85
291 293 7.136119 CGAAAAACAAACAACTATGCTTAGGA 58.864 34.615 11.03 0.00 0.00 2.94
292 294 6.362283 CCGAAAAACAAACAACTATGCTTAGG 59.638 38.462 11.03 0.00 0.00 2.69
293 295 7.112984 GTCCGAAAAACAAACAACTATGCTTAG 59.887 37.037 5.13 5.13 0.00 2.18
294 296 6.913673 GTCCGAAAAACAAACAACTATGCTTA 59.086 34.615 0.00 0.00 0.00 3.09
302 304 3.129813 AGAGGGTCCGAAAAACAAACAAC 59.870 43.478 0.00 0.00 0.00 3.32
314 316 1.203087 TCACCAGTTAAGAGGGTCCGA 60.203 52.381 0.00 0.00 31.03 4.55
315 317 1.263356 TCACCAGTTAAGAGGGTCCG 58.737 55.000 0.00 0.00 31.03 4.79
327 329 1.099689 CCCAACAAACGTTCACCAGT 58.900 50.000 0.00 0.00 0.00 4.00
399 403 3.307242 GGCATGCTAGTACGAAGAAACTG 59.693 47.826 18.92 0.00 0.00 3.16
401 405 3.259064 TGGCATGCTAGTACGAAGAAAC 58.741 45.455 18.92 0.00 0.00 2.78
409 413 3.565902 GGAAGGAATTGGCATGCTAGTAC 59.434 47.826 18.92 6.28 0.00 2.73
463 467 4.681978 GAACACCCTCGCAGCCGT 62.682 66.667 0.00 0.00 35.54 5.68
474 478 0.250338 AGGAACTCCAAGCGAACACC 60.250 55.000 0.00 0.00 38.89 4.16
475 479 1.531578 GAAGGAACTCCAAGCGAACAC 59.468 52.381 0.00 0.00 38.49 3.32
502 506 2.031157 ACAATGCTAACTGGCAAACGTC 60.031 45.455 0.00 0.00 45.68 4.34
550 554 3.990318 TCACACACACACACACAAAAA 57.010 38.095 0.00 0.00 0.00 1.94
551 555 4.511617 AATCACACACACACACACAAAA 57.488 36.364 0.00 0.00 0.00 2.44
552 556 4.480541 GAAATCACACACACACACACAAA 58.519 39.130 0.00 0.00 0.00 2.83
575 608 7.628769 ATTCATGAAAATATTGCCAAAACCC 57.371 32.000 13.09 0.00 0.00 4.11
576 609 9.911138 AAAATTCATGAAAATATTGCCAAAACC 57.089 25.926 13.09 0.00 0.00 3.27
615 648 6.765989 TGTCCACAAAATATAGGATCCGAAAG 59.234 38.462 5.98 0.00 31.91 2.62
635 668 4.714308 GGAAATGGGTCCAATATTTGTCCA 59.286 41.667 5.42 6.15 37.65 4.02
682 715 0.392461 TGATAGCGGGTTGGTTGCTC 60.392 55.000 0.00 0.00 40.06 4.26
688 721 1.017387 GCTTTCTGATAGCGGGTTGG 58.983 55.000 4.38 0.00 0.00 3.77
694 727 3.114809 CAGACAGAGCTTTCTGATAGCG 58.885 50.000 13.22 3.81 41.65 4.26
713 750 1.464608 CGCCCATGTGTTCTGTAACAG 59.535 52.381 0.00 0.00 46.06 3.16
788 826 3.322541 TGAAGAAGATGTGGACGTGGTTA 59.677 43.478 0.00 0.00 0.00 2.85
830 872 2.094597 TCCTTTTGCTCGGCATCATTTG 60.095 45.455 0.00 0.00 38.76 2.32
845 888 7.933215 ACTAATTAATTACGCCACTCCTTTT 57.067 32.000 3.71 0.00 0.00 2.27
866 909 6.153510 AGCAGTGAGAAGATATGTGTGAACTA 59.846 38.462 0.00 0.00 0.00 2.24
874 917 4.029520 AGGACAGCAGTGAGAAGATATGT 58.970 43.478 0.00 0.00 0.00 2.29
924 967 4.286549 AGGAGGAATCTTATCTCAGCATGG 59.713 45.833 0.00 0.00 36.16 3.66
929 972 3.571828 TCGCAGGAGGAATCTTATCTCAG 59.428 47.826 0.00 0.00 0.00 3.35
979 1023 3.270027 TCTTGCGGAAACTATGGATGTG 58.730 45.455 0.00 0.00 0.00 3.21
984 1028 1.334869 GCCATCTTGCGGAAACTATGG 59.665 52.381 16.35 16.35 37.52 2.74
1024 1073 3.367607 CGATGACGAGGATCTTGAAGAC 58.632 50.000 0.00 0.00 42.66 3.01
1069 1118 1.349688 GACACACATACCTGGGGTGAA 59.650 52.381 18.25 0.00 36.19 3.18
1090 1139 3.713764 AGAGAACTAAGGGGACATGGATG 59.286 47.826 0.00 0.00 0.00 3.51
1098 1147 2.626149 GGGCAGTAGAGAACTAAGGGGA 60.626 54.545 0.00 0.00 35.76 4.81
1100 1149 1.763545 GGGGCAGTAGAGAACTAAGGG 59.236 57.143 0.00 0.00 35.76 3.95
1128 1177 6.484288 TCTTAGATTGGAATTGAAGGCTTCA 58.516 36.000 25.38 25.38 38.04 3.02
1144 1193 5.690464 AGAACCTGCACTGATCTTAGATT 57.310 39.130 0.00 0.00 0.00 2.40
1167 1216 4.243008 TGGCCTCACGGTTTCGCA 62.243 61.111 3.32 0.00 40.63 5.10
1175 1224 1.959042 AGCATTTATCTGGCCTCACG 58.041 50.000 3.32 0.00 0.00 4.35
1177 1226 3.969976 AGAGTAGCATTTATCTGGCCTCA 59.030 43.478 3.32 0.00 0.00 3.86
1181 1230 4.565022 GGAGAGAGTAGCATTTATCTGGC 58.435 47.826 0.00 0.00 0.00 4.85
1199 1254 4.217767 CGATCTTATATTGTGGGACGGAGA 59.782 45.833 0.00 0.00 0.00 3.71
1203 1261 5.107989 CGAAACGATCTTATATTGTGGGACG 60.108 44.000 0.00 0.00 0.00 4.79
1220 1278 3.587797 AGATCCTAGTTTGCGAAACGA 57.412 42.857 0.00 0.00 45.88 3.85
1221 1279 3.062234 GGAAGATCCTAGTTTGCGAAACG 59.938 47.826 0.00 0.00 38.83 3.60
1222 1280 4.601621 GGAAGATCCTAGTTTGCGAAAC 57.398 45.455 0.00 0.00 36.19 2.78
1275 1394 5.988561 TCACAAAATGGTGTAGGAAATTTGC 59.011 36.000 0.68 0.68 39.76 3.68
1276 1395 8.606040 AATCACAAAATGGTGTAGGAAATTTG 57.394 30.769 0.00 0.00 39.76 2.32
1281 1400 6.549364 AGTTGAATCACAAAATGGTGTAGGAA 59.451 34.615 0.00 0.00 40.36 3.36
1289 1408 7.381948 TCAATTCGAAGTTGAATCACAAAATGG 59.618 33.333 15.86 0.00 40.36 3.16
1302 1421 6.000891 TCCAGTTGATTCAATTCGAAGTTG 57.999 37.500 3.35 8.72 36.95 3.16
1308 1427 3.012518 AGGCTCCAGTTGATTCAATTCG 58.987 45.455 1.78 0.00 0.00 3.34
1312 1432 7.345691 TGATTATAAGGCTCCAGTTGATTCAA 58.654 34.615 0.00 0.00 0.00 2.69
1320 1440 5.604650 ACTAAGCTGATTATAAGGCTCCAGT 59.395 40.000 9.69 11.77 33.63 4.00
1321 1441 6.107901 ACTAAGCTGATTATAAGGCTCCAG 57.892 41.667 9.69 11.34 33.63 3.86
1323 1443 7.442656 TGTTACTAAGCTGATTATAAGGCTCC 58.557 38.462 9.69 0.00 33.63 4.70
1324 1444 9.495572 AATGTTACTAAGCTGATTATAAGGCTC 57.504 33.333 9.69 0.00 33.63 4.70
1325 1445 9.277783 CAATGTTACTAAGCTGATTATAAGGCT 57.722 33.333 0.00 5.05 36.53 4.58
1326 1446 9.057089 ACAATGTTACTAAGCTGATTATAAGGC 57.943 33.333 0.00 0.00 0.00 4.35
1334 1454 7.663081 CCATATCCACAATGTTACTAAGCTGAT 59.337 37.037 0.00 0.00 0.00 2.90
1339 1459 8.908786 ATGTCCATATCCACAATGTTACTAAG 57.091 34.615 0.00 0.00 0.00 2.18
1355 1510 5.034878 TCTCCTGCATCCATATGTCCATAT 58.965 41.667 1.24 0.00 35.38 1.78
1363 1518 0.990374 GCCCTCTCCTGCATCCATAT 59.010 55.000 0.00 0.00 0.00 1.78
1364 1519 0.400381 TGCCCTCTCCTGCATCCATA 60.400 55.000 0.00 0.00 31.31 2.74
1368 1523 0.254178 TTCTTGCCCTCTCCTGCATC 59.746 55.000 0.00 0.00 37.33 3.91
1386 1541 0.667993 CATTTGCCCTGACACACGTT 59.332 50.000 0.00 0.00 0.00 3.99
1418 1573 0.179070 TGCACCACTTGTCGCAGTTA 60.179 50.000 0.00 0.00 30.79 2.24
1419 1574 1.029408 TTGCACCACTTGTCGCAGTT 61.029 50.000 0.00 0.00 34.20 3.16
1478 1633 1.153549 GCAGAACTGGTAGAGCGGG 60.154 63.158 3.99 0.00 0.00 6.13
1519 1674 7.007725 CGATTACAAGACATTTGAGAAACATGC 59.992 37.037 0.00 0.00 0.00 4.06
1520 1675 8.017373 ACGATTACAAGACATTTGAGAAACATG 58.983 33.333 0.00 0.00 0.00 3.21
1586 1759 3.073356 TCCCCCACACTTACCTTTAACTG 59.927 47.826 0.00 0.00 0.00 3.16
1617 1799 7.015877 GCGTTCAAGTTTTATCTGAAACCTAG 58.984 38.462 0.00 0.00 39.71 3.02
1632 1814 2.297701 ACATTGACAGGCGTTCAAGTT 58.702 42.857 9.26 0.00 0.00 2.66
1766 1950 2.551887 TCACCGTGATCACCACAAAATG 59.448 45.455 20.03 7.98 45.98 2.32
1829 2019 4.767633 CGAGCACCGTCTAGTGTC 57.232 61.111 0.00 0.00 40.04 3.67
1898 2103 4.347453 CTGCAAAGGCCACCGTGC 62.347 66.667 5.01 9.35 39.02 5.34
1901 2106 2.332654 GGTACTGCAAAGGCCACCG 61.333 63.158 5.01 0.00 40.13 4.94
1903 2108 4.821935 AGGTACTGCAAAGGCCAC 57.178 55.556 5.01 0.00 37.18 5.01
1918 2123 2.092212 AGTGGCATGATTTACCTCCAGG 60.092 50.000 0.00 0.00 42.17 4.45
1919 2124 2.947652 CAGTGGCATGATTTACCTCCAG 59.052 50.000 0.00 0.00 0.00 3.86
1920 2125 2.575735 TCAGTGGCATGATTTACCTCCA 59.424 45.455 0.00 0.00 0.00 3.86
1921 2126 3.209410 CTCAGTGGCATGATTTACCTCC 58.791 50.000 0.00 0.00 0.00 4.30
1922 2127 3.209410 CCTCAGTGGCATGATTTACCTC 58.791 50.000 0.00 0.00 0.00 3.85
1923 2128 2.578021 ACCTCAGTGGCATGATTTACCT 59.422 45.455 0.00 0.00 40.22 3.08
1924 2129 3.004752 ACCTCAGTGGCATGATTTACC 57.995 47.619 0.00 0.00 40.22 2.85
1925 2130 5.449177 GCTTTACCTCAGTGGCATGATTTAC 60.449 44.000 0.00 0.00 40.22 2.01
1926 2131 4.640201 GCTTTACCTCAGTGGCATGATTTA 59.360 41.667 0.00 0.00 40.22 1.40
1927 2132 3.445096 GCTTTACCTCAGTGGCATGATTT 59.555 43.478 0.00 0.00 40.22 2.17
1928 2133 3.019564 GCTTTACCTCAGTGGCATGATT 58.980 45.455 0.00 0.00 40.22 2.57
1929 2134 2.025981 TGCTTTACCTCAGTGGCATGAT 60.026 45.455 0.00 0.00 40.22 2.45
1930 2135 1.350684 TGCTTTACCTCAGTGGCATGA 59.649 47.619 0.00 0.00 40.22 3.07
1931 2136 1.741706 CTGCTTTACCTCAGTGGCATG 59.258 52.381 0.00 0.00 40.22 4.06
1932 2137 1.352352 ACTGCTTTACCTCAGTGGCAT 59.648 47.619 0.00 0.00 41.53 4.40
1933 2138 0.764890 ACTGCTTTACCTCAGTGGCA 59.235 50.000 0.00 0.00 41.53 4.92
1934 2139 1.897560 AACTGCTTTACCTCAGTGGC 58.102 50.000 0.00 0.00 42.19 5.01
1935 2140 3.882888 TGAAAACTGCTTTACCTCAGTGG 59.117 43.478 0.00 0.00 42.19 4.00
1936 2141 4.576463 AGTGAAAACTGCTTTACCTCAGTG 59.424 41.667 0.00 0.00 42.19 3.66
1937 2142 4.576463 CAGTGAAAACTGCTTTACCTCAGT 59.424 41.667 0.00 0.00 44.64 3.41
1938 2143 4.816385 TCAGTGAAAACTGCTTTACCTCAG 59.184 41.667 0.91 0.00 37.63 3.35
1939 2144 4.574828 GTCAGTGAAAACTGCTTTACCTCA 59.425 41.667 0.00 0.00 37.63 3.86
1940 2145 4.816925 AGTCAGTGAAAACTGCTTTACCTC 59.183 41.667 0.00 0.00 37.63 3.85
1941 2146 4.781934 AGTCAGTGAAAACTGCTTTACCT 58.218 39.130 0.00 0.00 37.63 3.08
1942 2147 5.163652 ACAAGTCAGTGAAAACTGCTTTACC 60.164 40.000 0.00 0.00 37.63 2.85
1943 2148 5.880341 ACAAGTCAGTGAAAACTGCTTTAC 58.120 37.500 0.00 1.78 37.63 2.01
1944 2149 7.335924 ACTTACAAGTCAGTGAAAACTGCTTTA 59.664 33.333 0.00 6.73 37.63 1.85
1945 2150 6.151144 ACTTACAAGTCAGTGAAAACTGCTTT 59.849 34.615 0.00 2.52 37.63 3.51
1969 2174 7.172703 CCCCGGATTTATTCTATCAGTTACAAC 59.827 40.741 0.73 0.00 0.00 3.32
1971 2176 6.743208 GCCCCGGATTTATTCTATCAGTTACA 60.743 42.308 0.73 0.00 0.00 2.41
1972 2177 5.642491 GCCCCGGATTTATTCTATCAGTTAC 59.358 44.000 0.73 0.00 0.00 2.50
1975 2180 3.306780 CGCCCCGGATTTATTCTATCAGT 60.307 47.826 0.73 0.00 0.00 3.41
1976 2181 3.262420 CGCCCCGGATTTATTCTATCAG 58.738 50.000 0.73 0.00 0.00 2.90
1977 2182 2.614481 GCGCCCCGGATTTATTCTATCA 60.614 50.000 0.73 0.00 0.00 2.15
1978 2183 2.007608 GCGCCCCGGATTTATTCTATC 58.992 52.381 0.73 0.00 0.00 2.08
1979 2184 1.349688 TGCGCCCCGGATTTATTCTAT 59.650 47.619 0.73 0.00 0.00 1.98
1980 2185 0.759959 TGCGCCCCGGATTTATTCTA 59.240 50.000 0.73 0.00 0.00 2.10
1981 2186 0.818040 GTGCGCCCCGGATTTATTCT 60.818 55.000 0.73 0.00 0.00 2.40
1982 2187 1.652563 GTGCGCCCCGGATTTATTC 59.347 57.895 0.73 0.00 0.00 1.75
1983 2188 2.184167 CGTGCGCCCCGGATTTATT 61.184 57.895 0.73 0.00 0.00 1.40
1984 2189 2.590575 CGTGCGCCCCGGATTTAT 60.591 61.111 0.73 0.00 0.00 1.40
2020 2240 5.809562 TGGTAGAAACAAATGCAACAGTTTG 59.190 36.000 15.52 12.25 40.29 2.93
2026 2246 7.092716 AGAATCATGGTAGAAACAAATGCAAC 58.907 34.615 0.00 0.00 0.00 4.17
2082 2332 1.781025 CTGAAAGTTTGTGCGCCGGA 61.781 55.000 5.05 0.00 0.00 5.14
2095 2345 6.155136 GGAGAAGAAGCCATTTTTCTGAAAG 58.845 40.000 2.75 0.00 35.20 2.62
2106 2356 1.482593 CTGGTACGGAGAAGAAGCCAT 59.517 52.381 0.00 0.00 36.31 4.40
2117 2367 1.134367 CTCGCATCTTTCTGGTACGGA 59.866 52.381 0.00 0.00 45.11 4.69
2118 2368 1.560923 CTCGCATCTTTCTGGTACGG 58.439 55.000 0.00 0.00 0.00 4.02
2119 2369 1.560923 CCTCGCATCTTTCTGGTACG 58.439 55.000 0.00 0.00 0.00 3.67
2120 2370 1.941325 CCCTCGCATCTTTCTGGTAC 58.059 55.000 0.00 0.00 0.00 3.34
2134 2384 0.379669 GTTGCAGATCAATGCCCTCG 59.620 55.000 4.64 0.00 45.91 4.63
2159 2409 4.443266 GCACCCGAGAGCGAGCTT 62.443 66.667 0.00 0.00 40.82 3.74
2181 2431 1.825090 TTTGCAGCAGAATGATCCGT 58.175 45.000 0.00 0.00 39.69 4.69
2186 2436 4.082081 CCAAGGTATTTTGCAGCAGAATGA 60.082 41.667 19.13 3.33 39.69 2.57
2192 2442 1.336131 TGCCAAGGTATTTTGCAGCA 58.664 45.000 0.00 0.00 0.00 4.41
2207 2457 3.490439 TTCTGTCAGAGAAACATGCCA 57.510 42.857 2.12 0.00 37.78 4.92
2214 2464 7.931578 TTTGGTAAGTTTTCTGTCAGAGAAA 57.068 32.000 7.36 6.72 46.93 2.52
2255 2507 4.348863 TTGGAACCAAATTTGTCCATGG 57.651 40.909 23.78 4.97 39.84 3.66
2281 2533 3.521796 GCCAATCTTCCAGCCGGC 61.522 66.667 21.89 21.89 0.00 6.13
2284 2536 0.106318 ATCCAGCCAATCTTCCAGCC 60.106 55.000 0.00 0.00 0.00 4.85
2285 2537 1.030457 CATCCAGCCAATCTTCCAGC 58.970 55.000 0.00 0.00 0.00 4.85
2287 2539 2.041485 TGTTCATCCAGCCAATCTTCCA 59.959 45.455 0.00 0.00 0.00 3.53
2318 2570 1.153628 ACGCGCACCAGGATAAGTC 60.154 57.895 5.73 0.00 0.00 3.01
2319 2571 1.447838 CACGCGCACCAGGATAAGT 60.448 57.895 5.73 0.00 0.00 2.24
2333 2585 4.459089 GGGCAGAGAGGACCACGC 62.459 72.222 0.00 0.00 35.36 5.34
2335 2587 2.363172 GGAGGGCAGAGAGGACCAC 61.363 68.421 0.00 0.00 38.98 4.16
2339 2591 1.610673 GTGTGGAGGGCAGAGAGGA 60.611 63.158 0.00 0.00 0.00 3.71
2354 2606 8.169977 TGAGCAAGAAATGATTTAGAAAGTGT 57.830 30.769 0.00 0.00 0.00 3.55
2364 2616 5.574188 ACTAGGGTTGAGCAAGAAATGATT 58.426 37.500 0.00 0.00 0.00 2.57
2367 2619 3.372206 CGACTAGGGTTGAGCAAGAAATG 59.628 47.826 0.00 0.00 0.00 2.32
2383 2637 3.505680 AGATCATCTTGCCTAGCGACTAG 59.494 47.826 0.00 6.85 34.16 2.57
2387 2641 3.103447 CAAGATCATCTTGCCTAGCGA 57.897 47.619 14.54 0.00 46.03 4.93
2404 2658 1.398390 GGACTTGGCATACTTCGCAAG 59.602 52.381 0.00 0.00 0.00 4.01
2405 2659 1.271108 TGGACTTGGCATACTTCGCAA 60.271 47.619 0.00 0.00 0.00 4.85
2441 2695 0.375454 CAAACAACGCTCACGGACAA 59.625 50.000 0.00 0.00 46.04 3.18
2444 2698 0.250124 ATCCAAACAACGCTCACGGA 60.250 50.000 0.00 0.00 46.04 4.69
2454 2708 8.985315 AGATGATCAGCTTATAATCCAAACAA 57.015 30.769 7.89 0.00 0.00 2.83
2475 2729 3.119291 GAGAACATCGGCAGTGTAGATG 58.881 50.000 20.72 20.72 45.14 2.90
2488 2742 3.950395 CCATCCCTTCTTTGGAGAACATC 59.050 47.826 0.00 0.00 36.99 3.06


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

AutoCloner maintained by Alex Coulton.