Multiple sequence alignment - TraesCS2D01G487000

Loading Multiple Alignment...

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 TraesCS2D01G487000 chr2D 100.000 2312 0 0 1 2312 587108444 587106133 0.000000e+00 4270.0
1 TraesCS2D01G487000 chr2D 96.552 290 9 1 1708 1997 499914468 499914756 1.610000e-131 479.0
2 TraesCS2D01G487000 chr2D 89.883 257 20 3 1001 1251 618060727 618060983 2.220000e-85 326.0
3 TraesCS2D01G487000 chr2D 85.870 276 32 4 983 1251 618004094 618004369 1.050000e-73 287.0
4 TraesCS2D01G487000 chr2D 84.706 255 33 5 1003 1251 618074274 618074528 1.370000e-62 250.0
5 TraesCS2D01G487000 chr2D 97.938 97 2 0 2216 2312 586287325 586287421 3.950000e-38 169.0
6 TraesCS2D01G487000 chr2D 90.426 94 6 3 4 94 587005346 587005253 1.120000e-23 121.0
7 TraesCS2D01G487000 chr2D 76.271 177 30 10 638 804 617991792 617991966 1.470000e-12 84.2
8 TraesCS2D01G487000 chr2B 85.880 1296 87 34 4 1251 708827647 708826400 0.000000e+00 1291.0
9 TraesCS2D01G487000 chr2B 86.942 291 29 6 969 1251 754004620 754004909 3.710000e-83 318.0
10 TraesCS2D01G487000 chr2B 85.305 279 32 6 981 1251 754015959 754016236 1.750000e-71 279.0
11 TraesCS2D01G487000 chr2B 85.985 264 31 3 993 1250 754342798 754343061 6.290000e-71 278.0
12 TraesCS2D01G487000 chr2B 88.439 173 10 3 1422 1593 708825999 708825836 1.400000e-47 200.0
13 TraesCS2D01G487000 chr1A 94.859 603 31 0 1710 2312 273509846 273510448 0.000000e+00 942.0
14 TraesCS2D01G487000 chr1A 94.527 603 33 0 1710 2312 273463436 273464038 0.000000e+00 931.0
15 TraesCS2D01G487000 chr1A 95.009 541 27 0 1772 2312 362869740 362870280 0.000000e+00 850.0
16 TraesCS2D01G487000 chr1A 81.188 202 24 12 186 382 418040464 418040656 1.430000e-32 150.0
17 TraesCS2D01G487000 chr5D 95.088 570 28 0 1743 2312 483566368 483565799 0.000000e+00 898.0
18 TraesCS2D01G487000 chr7A 93.046 604 40 2 1709 2312 114462595 114463196 0.000000e+00 881.0
19 TraesCS2D01G487000 chr7A 92.798 486 33 1 1827 2312 651262503 651262020 0.000000e+00 702.0
20 TraesCS2D01G487000 chr7A 88.934 497 50 3 1721 2212 49652065 49652561 1.960000e-170 608.0
21 TraesCS2D01G487000 chr3A 95.228 482 20 1 1814 2295 723318775 723319253 0.000000e+00 760.0
22 TraesCS2D01G487000 chr3A 100.000 28 0 0 195 222 638707376 638707349 4.000000e-03 52.8
23 TraesCS2D01G487000 chr5B 91.071 504 42 2 1714 2217 176236468 176236968 0.000000e+00 678.0
24 TraesCS2D01G487000 chr5B 74.603 189 27 11 272 456 508003402 508003573 1.920000e-06 63.9
25 TraesCS2D01G487000 chr3D 90.909 506 43 3 1715 2219 4316483 4315980 0.000000e+00 676.0
26 TraesCS2D01G487000 chr1B 90.430 512 47 1 1709 2220 46155877 46155368 0.000000e+00 673.0
27 TraesCS2D01G487000 chr2A 93.793 290 15 3 1704 1993 58860318 58860604 1.270000e-117 433.0
28 TraesCS2D01G487000 chr2A 88.716 257 23 2 1001 1251 748558310 748558566 2.230000e-80 309.0
29 TraesCS2D01G487000 chr2A 85.333 300 25 10 962 1251 748698089 748698379 2.250000e-75 292.0
30 TraesCS2D01G487000 chr2A 84.556 259 30 6 1001 1251 748685250 748685506 4.930000e-62 248.0
31 TraesCS2D01G487000 chr2A 74.317 183 27 14 186 358 672400545 672400717 2.480000e-05 60.2
32 TraesCS2D01G487000 chr7D 97.938 97 2 0 2216 2312 612013526 612013622 3.950000e-38 169.0
33 TraesCS2D01G487000 chr7D 94.444 36 2 0 187 222 426185856 426185891 3.210000e-04 56.5
34 TraesCS2D01G487000 chr6A 87.629 97 7 4 188 283 472517073 472516981 8.730000e-20 108.0
35 TraesCS2D01G487000 chr5A 75.521 192 25 13 271 456 535233195 535233370 8.860000e-10 75.0
36 TraesCS2D01G487000 chr5A 92.683 41 1 2 186 226 556387269 556387307 8.920000e-05 58.4
37 TraesCS2D01G487000 chr6D 79.048 105 17 5 353 456 15667473 15667373 1.480000e-07 67.6
38 TraesCS2D01G487000 chr1D 74.038 208 35 16 188 389 425556440 425556634 1.480000e-07 67.6


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 TraesCS2D01G487000 chr2D 587106133 587108444 2311 True 4270.0 4270 100.0000 1 2312 1 chr2D.!!$R2 2311
1 TraesCS2D01G487000 chr2B 708825836 708827647 1811 True 745.5 1291 87.1595 4 1593 2 chr2B.!!$R1 1589
2 TraesCS2D01G487000 chr1A 273509846 273510448 602 False 942.0 942 94.8590 1710 2312 1 chr1A.!!$F2 602
3 TraesCS2D01G487000 chr1A 273463436 273464038 602 False 931.0 931 94.5270 1710 2312 1 chr1A.!!$F1 602
4 TraesCS2D01G487000 chr1A 362869740 362870280 540 False 850.0 850 95.0090 1772 2312 1 chr1A.!!$F3 540
5 TraesCS2D01G487000 chr5D 483565799 483566368 569 True 898.0 898 95.0880 1743 2312 1 chr5D.!!$R1 569
6 TraesCS2D01G487000 chr7A 114462595 114463196 601 False 881.0 881 93.0460 1709 2312 1 chr7A.!!$F2 603
7 TraesCS2D01G487000 chr5B 176236468 176236968 500 False 678.0 678 91.0710 1714 2217 1 chr5B.!!$F1 503
8 TraesCS2D01G487000 chr3D 4315980 4316483 503 True 676.0 676 90.9090 1715 2219 1 chr3D.!!$R1 504
9 TraesCS2D01G487000 chr1B 46155368 46155877 509 True 673.0 673 90.4300 1709 2220 1 chr1B.!!$R1 511

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
997 1033 0.036199 AGCAAGCAGAAGGAGAGCAG 60.036 55.0 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1904 2184 1.816863 GAGCTCCGGACAGTCACCAA 61.817 60.0 0.0 0.0 0.0 3.67 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
25 26 8.638685 AAGGCAATTCATAAAAAGAATCGATG 57.361 30.769 0.00 0.00 34.78 3.84
26 27 7.205297 AGGCAATTCATAAAAAGAATCGATGG 58.795 34.615 0.00 0.00 34.78 3.51
27 28 6.980397 GGCAATTCATAAAAAGAATCGATGGT 59.020 34.615 0.00 0.00 34.78 3.55
82 83 9.712305 ATAGCTTATTCACATATGTGGTAAGTC 57.288 33.333 33.22 28.69 45.65 3.01
83 84 7.796054 AGCTTATTCACATATGTGGTAAGTCT 58.204 34.615 33.22 29.56 45.65 3.24
84 85 8.924303 AGCTTATTCACATATGTGGTAAGTCTA 58.076 33.333 33.22 17.94 45.65 2.59
89 90 9.823647 ATTCACATATGTGGTAAGTCTAAGAAG 57.176 33.333 30.56 4.44 45.65 2.85
90 91 8.362464 TCACATATGTGGTAAGTCTAAGAAGT 57.638 34.615 30.56 0.00 45.65 3.01
91 92 9.470399 TCACATATGTGGTAAGTCTAAGAAGTA 57.530 33.333 30.56 6.88 45.65 2.24
92 93 9.517609 CACATATGTGGTAAGTCTAAGAAGTAC 57.482 37.037 25.41 0.00 42.10 2.73
93 94 9.476928 ACATATGTGGTAAGTCTAAGAAGTACT 57.523 33.333 7.78 0.00 0.00 2.73
97 98 9.696572 ATGTGGTAAGTCTAAGAAGTACTATCA 57.303 33.333 0.00 0.00 0.00 2.15
98 99 9.524496 TGTGGTAAGTCTAAGAAGTACTATCAA 57.476 33.333 0.00 0.00 0.00 2.57
100 101 9.970553 TGGTAAGTCTAAGAAGTACTATCAAGA 57.029 33.333 0.00 1.78 0.00 3.02
144 145 6.606234 TTGTGTTCTTGACGTATGCTTTTA 57.394 33.333 0.00 0.00 0.00 1.52
145 146 6.795098 TGTGTTCTTGACGTATGCTTTTAT 57.205 33.333 0.00 0.00 0.00 1.40
146 147 7.197071 TGTGTTCTTGACGTATGCTTTTATT 57.803 32.000 0.00 0.00 0.00 1.40
147 148 7.644490 TGTGTTCTTGACGTATGCTTTTATTT 58.356 30.769 0.00 0.00 0.00 1.40
148 149 7.801315 TGTGTTCTTGACGTATGCTTTTATTTC 59.199 33.333 0.00 0.00 0.00 2.17
154 155 9.612620 CTTGACGTATGCTTTTATTTCTTTCTT 57.387 29.630 0.00 0.00 0.00 2.52
182 183 9.098355 TGCAGAGAATTGACATATGTTAACTAC 57.902 33.333 14.61 9.35 0.00 2.73
231 232 4.895297 TCCATGGAGCCCTTGAATAAATTC 59.105 41.667 11.44 0.00 37.31 2.17
265 266 9.990360 ATACTTTTATGTTTCCAAAAATTCGGT 57.010 25.926 0.00 0.00 0.00 4.69
369 371 6.092122 ACAAAAAGAAAAACAAGCTTGTAGCC 59.908 34.615 31.31 19.57 43.77 3.93
385 387 1.379527 AGCCTTTTAGCGCATGTACC 58.620 50.000 11.47 0.00 38.01 3.34
386 388 1.091537 GCCTTTTAGCGCATGTACCA 58.908 50.000 11.47 0.00 0.00 3.25
390 392 4.104776 CCTTTTAGCGCATGTACCATTTG 58.895 43.478 11.47 0.00 0.00 2.32
424 426 4.529446 CATGATTTTGTTTTTGTGCAGCC 58.471 39.130 0.00 0.00 0.00 4.85
432 434 3.870419 TGTTTTTGTGCAGCCTGAAATTC 59.130 39.130 0.00 0.00 0.00 2.17
445 447 6.976925 CAGCCTGAAATTCAAGGTATTTCATC 59.023 38.462 10.40 6.90 45.68 2.92
470 475 8.567948 TCGTGAAATTTTTGAGCTCTATTTTCT 58.432 29.630 16.19 0.00 0.00 2.52
471 476 8.633408 CGTGAAATTTTTGAGCTCTATTTTCTG 58.367 33.333 16.19 9.85 0.00 3.02
477 482 7.566760 TTTTGAGCTCTATTTTCTGTGTGAA 57.433 32.000 16.19 0.00 0.00 3.18
478 483 7.566760 TTTGAGCTCTATTTTCTGTGTGAAA 57.433 32.000 16.19 0.00 42.33 2.69
519 524 9.941664 ACATTACATCCTTATATACGCGTATAC 57.058 33.333 34.45 0.00 31.52 1.47
598 605 2.476499 GCCTTGCTCGCGTTTCTC 59.524 61.111 5.77 0.00 0.00 2.87
599 606 2.317609 GCCTTGCTCGCGTTTCTCA 61.318 57.895 5.77 0.00 0.00 3.27
600 607 1.493311 CCTTGCTCGCGTTTCTCAC 59.507 57.895 5.77 0.00 0.00 3.51
602 609 0.162507 CTTGCTCGCGTTTCTCACTG 59.837 55.000 5.77 0.00 0.00 3.66
641 658 2.029844 GCCAACTCAGTCAGGTCGC 61.030 63.158 0.00 0.00 0.00 5.19
712 729 2.126882 TGGGCAGGATAGCAACTGTAT 58.873 47.619 0.00 0.00 37.07 2.29
769 800 0.622136 ACCCGGTATCCTGGAAAACC 59.378 55.000 17.47 17.47 32.04 3.27
771 802 1.004979 CCCGGTATCCTGGAAAACCAA 59.995 52.381 23.65 0.00 28.73 3.67
804 835 2.436824 GGTTTGCTCCGGCTCTCC 60.437 66.667 0.00 0.00 39.59 3.71
806 837 2.927856 TTTGCTCCGGCTCTCCCA 60.928 61.111 0.00 0.00 39.59 4.37
831 863 2.376518 TCCCTCCCGTATATAACCTCGT 59.623 50.000 0.00 0.00 0.00 4.18
839 871 3.190118 CGTATATAACCTCGTCCCACTCC 59.810 52.174 0.00 0.00 0.00 3.85
843 875 2.603473 CCTCGTCCCACTCCCACA 60.603 66.667 0.00 0.00 0.00 4.17
856 888 2.292785 ACTCCCACACTCCTCTCATCAT 60.293 50.000 0.00 0.00 0.00 2.45
880 912 1.613836 AGCAAAGCACCAGGAAGAAG 58.386 50.000 0.00 0.00 0.00 2.85
883 915 1.268899 CAAAGCACCAGGAAGAAGCAG 59.731 52.381 0.00 0.00 0.00 4.24
887 919 1.849823 ACCAGGAAGAAGCAGCCCT 60.850 57.895 0.00 0.00 0.00 5.19
888 920 1.378250 CCAGGAAGAAGCAGCCCTG 60.378 63.158 7.50 7.50 44.29 4.45
900 932 3.210528 GCCCTGCATCAGCTCAGC 61.211 66.667 0.00 0.00 42.74 4.26
902 934 1.524165 CCCTGCATCAGCTCAGCTC 60.524 63.158 0.00 0.00 42.74 4.09
906 938 2.085320 CTGCATCAGCTCAGCTCTTTT 58.915 47.619 0.00 0.00 42.74 2.27
908 940 3.878103 CTGCATCAGCTCAGCTCTTTTAT 59.122 43.478 0.00 0.00 42.74 1.40
950 986 4.581824 AGACACAAGCAATCACAAATCAGT 59.418 37.500 0.00 0.00 0.00 3.41
959 995 5.049198 GCAATCACAAATCAGTCTCAGTTCA 60.049 40.000 0.00 0.00 0.00 3.18
964 1000 5.240183 CACAAATCAGTCTCAGTTCAACCAT 59.760 40.000 0.00 0.00 0.00 3.55
975 1011 2.365293 AGTTCAACCATTTTCCACCAGC 59.635 45.455 0.00 0.00 0.00 4.85
984 1020 4.666253 TCCACCAGCCCAGCAAGC 62.666 66.667 0.00 0.00 0.00 4.01
985 1021 4.980702 CCACCAGCCCAGCAAGCA 62.981 66.667 0.00 0.00 0.00 3.91
987 1023 3.573229 ACCAGCCCAGCAAGCAGA 61.573 61.111 0.00 0.00 0.00 4.26
988 1024 2.282674 CCAGCCCAGCAAGCAGAA 60.283 61.111 0.00 0.00 0.00 3.02
989 1025 2.341101 CCAGCCCAGCAAGCAGAAG 61.341 63.158 0.00 0.00 0.00 2.85
990 1026 2.035312 AGCCCAGCAAGCAGAAGG 59.965 61.111 0.00 0.00 0.00 3.46
991 1027 2.034687 GCCCAGCAAGCAGAAGGA 59.965 61.111 0.00 0.00 0.00 3.36
993 1029 1.681666 CCCAGCAAGCAGAAGGAGA 59.318 57.895 0.00 0.00 0.00 3.71
994 1030 0.392729 CCCAGCAAGCAGAAGGAGAG 60.393 60.000 0.00 0.00 0.00 3.20
995 1031 1.025647 CCAGCAAGCAGAAGGAGAGC 61.026 60.000 0.00 0.00 0.00 4.09
996 1032 0.321387 CAGCAAGCAGAAGGAGAGCA 60.321 55.000 0.00 0.00 0.00 4.26
997 1033 0.036199 AGCAAGCAGAAGGAGAGCAG 60.036 55.000 0.00 0.00 0.00 4.24
998 1034 0.321475 GCAAGCAGAAGGAGAGCAGT 60.321 55.000 0.00 0.00 0.00 4.40
999 1035 1.440708 CAAGCAGAAGGAGAGCAGTG 58.559 55.000 0.00 0.00 0.00 3.66
1000 1036 1.001746 CAAGCAGAAGGAGAGCAGTGA 59.998 52.381 0.00 0.00 0.00 3.41
1001 1037 1.570803 AGCAGAAGGAGAGCAGTGAT 58.429 50.000 0.00 0.00 0.00 3.06
1002 1038 1.207570 AGCAGAAGGAGAGCAGTGATG 59.792 52.381 0.00 0.00 0.00 3.07
1003 1039 1.743091 GCAGAAGGAGAGCAGTGATGG 60.743 57.143 0.00 0.00 0.00 3.51
1004 1040 0.540923 AGAAGGAGAGCAGTGATGGC 59.459 55.000 0.00 0.00 0.00 4.40
1005 1041 0.540923 GAAGGAGAGCAGTGATGGCT 59.459 55.000 0.00 0.00 46.07 4.75
1011 1047 3.807538 GCAGTGATGGCTGGTGCG 61.808 66.667 0.00 0.00 40.82 5.34
1074 1110 3.435186 GCGCTCAAAGACCAGGCC 61.435 66.667 0.00 0.00 0.00 5.19
1077 1113 2.045926 CTCAAAGACCAGGCCGGG 60.046 66.667 21.67 21.67 40.22 5.73
1095 1131 1.144936 GCTCTGCCGCTGGAACTAT 59.855 57.895 0.00 0.00 0.00 2.12
1104 1140 0.179100 GCTGGAACTATGCTCTGCGA 60.179 55.000 0.00 0.00 0.00 5.10
1125 1161 4.740822 ATCCACCGGGCAGCCAAC 62.741 66.667 15.19 0.00 0.00 3.77
1129 1165 4.740822 ACCGGGCAGCCAACATCC 62.741 66.667 15.19 0.00 0.00 3.51
1230 1278 3.775654 GAGGGGCTGAGGACGGTG 61.776 72.222 0.00 0.00 0.00 4.94
1235 1283 1.448540 GGCTGAGGACGGTGATGTG 60.449 63.158 0.00 0.00 0.00 3.21
1317 1549 0.544357 TTCCTGTGGGGTGAGATCGT 60.544 55.000 0.00 0.00 36.25 3.73
1323 1555 0.896479 TGGGGTGAGATCGTTCGTGA 60.896 55.000 0.00 0.00 0.00 4.35
1350 1582 5.644977 TCTGTCTGAATTTCTTCGCTCTA 57.355 39.130 0.00 0.00 33.86 2.43
1354 1586 6.166279 TGTCTGAATTTCTTCGCTCTACAAT 58.834 36.000 0.00 0.00 33.86 2.71
1378 1618 0.874175 TGAACCGACACGCTCAACTG 60.874 55.000 0.00 0.00 0.00 3.16
1387 1627 1.865865 ACGCTCAACTGAACGTGATT 58.134 45.000 7.32 0.00 44.01 2.57
1398 1638 1.002087 GAACGTGATTCAGGTCCAGGT 59.998 52.381 12.05 0.00 37.27 4.00
1411 1651 5.129815 TCAGGTCCAGGTTATACCACATTAC 59.870 44.000 0.00 0.00 41.95 1.89
1413 1653 5.130477 AGGTCCAGGTTATACCACATTACTG 59.870 44.000 0.00 0.00 41.95 2.74
1420 1660 9.095065 CAGGTTATACCACATTACTGAGTTAAC 57.905 37.037 0.00 0.00 41.95 2.01
1432 1710 5.197682 ACTGAGTTAACTAAACGTGAGCT 57.802 39.130 8.42 0.00 43.29 4.09
1447 1725 2.111384 TGAGCTAGTTGGATCCAGGTC 58.889 52.381 15.53 17.67 36.35 3.85
1449 1727 1.204146 GCTAGTTGGATCCAGGTCCA 58.796 55.000 15.53 0.00 46.28 4.02
1463 1741 0.980231 GGTCCAGGCCAGAGTGAGAT 60.980 60.000 5.01 0.00 0.00 2.75
1469 1747 0.029567 GGCCAGAGTGAGATACGTCG 59.970 60.000 0.00 0.00 0.00 5.12
1477 1755 1.132643 GTGAGATACGTCGCAGTTCCT 59.867 52.381 0.00 0.00 34.73 3.36
1533 1811 5.523552 CGTTACTGCATAACTTGGATCATGA 59.476 40.000 0.00 0.00 41.04 3.07
1541 1819 6.017605 GCATAACTTGGATCATGACCTAGTTG 60.018 42.308 30.47 23.65 46.54 3.16
1542 1820 3.878778 ACTTGGATCATGACCTAGTTGC 58.121 45.455 18.41 2.04 39.59 4.17
1543 1821 3.521126 ACTTGGATCATGACCTAGTTGCT 59.479 43.478 18.41 4.38 39.59 3.91
1544 1822 4.018960 ACTTGGATCATGACCTAGTTGCTT 60.019 41.667 18.41 4.13 39.59 3.91
1545 1823 5.189736 ACTTGGATCATGACCTAGTTGCTTA 59.810 40.000 18.41 0.00 39.59 3.09
1546 1824 5.894298 TGGATCATGACCTAGTTGCTTAT 57.106 39.130 0.00 0.00 0.00 1.73
1558 1836 6.126652 ACCTAGTTGCTTATCATTCTGACCAT 60.127 38.462 0.00 0.00 0.00 3.55
1559 1837 7.071196 ACCTAGTTGCTTATCATTCTGACCATA 59.929 37.037 0.00 0.00 0.00 2.74
1560 1838 7.933577 CCTAGTTGCTTATCATTCTGACCATAA 59.066 37.037 0.00 0.00 0.00 1.90
1561 1839 7.798596 AGTTGCTTATCATTCTGACCATAAG 57.201 36.000 0.00 0.00 0.00 1.73
1562 1840 7.568349 AGTTGCTTATCATTCTGACCATAAGA 58.432 34.615 11.13 0.00 0.00 2.10
1563 1841 7.714377 AGTTGCTTATCATTCTGACCATAAGAG 59.286 37.037 11.13 0.00 0.00 2.85
1564 1842 7.129457 TGCTTATCATTCTGACCATAAGAGT 57.871 36.000 11.13 0.00 0.00 3.24
1589 1867 6.969993 AAGAGATATCCCTACACTTCAGAC 57.030 41.667 0.00 0.00 0.00 3.51
1593 1871 5.836358 AGATATCCCTACACTTCAGACTTCC 59.164 44.000 0.00 0.00 0.00 3.46
1594 1872 3.254093 TCCCTACACTTCAGACTTCCA 57.746 47.619 0.00 0.00 0.00 3.53
1595 1873 3.583228 TCCCTACACTTCAGACTTCCAA 58.417 45.455 0.00 0.00 0.00 3.53
1596 1874 3.323979 TCCCTACACTTCAGACTTCCAAC 59.676 47.826 0.00 0.00 0.00 3.77
1597 1875 3.318017 CCTACACTTCAGACTTCCAACG 58.682 50.000 0.00 0.00 0.00 4.10
1598 1876 3.005472 CCTACACTTCAGACTTCCAACGA 59.995 47.826 0.00 0.00 0.00 3.85
1599 1877 2.822764 ACACTTCAGACTTCCAACGAC 58.177 47.619 0.00 0.00 0.00 4.34
1600 1878 2.167693 ACACTTCAGACTTCCAACGACA 59.832 45.455 0.00 0.00 0.00 4.35
1601 1879 2.540101 CACTTCAGACTTCCAACGACAC 59.460 50.000 0.00 0.00 0.00 3.67
1602 1880 2.167693 ACTTCAGACTTCCAACGACACA 59.832 45.455 0.00 0.00 0.00 3.72
1603 1881 2.218953 TCAGACTTCCAACGACACAC 57.781 50.000 0.00 0.00 0.00 3.82
1605 1883 0.742505 AGACTTCCAACGACACACGA 59.257 50.000 0.00 0.00 45.77 4.35
1606 1884 1.129326 GACTTCCAACGACACACGAG 58.871 55.000 0.00 0.00 45.77 4.18
1607 1885 0.742505 ACTTCCAACGACACACGAGA 59.257 50.000 0.00 0.00 45.77 4.04
1608 1886 1.269102 ACTTCCAACGACACACGAGAG 60.269 52.381 0.00 0.00 45.77 3.20
1610 1888 0.742505 TCCAACGACACACGAGAGTT 59.257 50.000 0.00 0.00 46.40 3.01
1611 1889 1.129326 CCAACGACACACGAGAGTTC 58.871 55.000 0.00 0.00 46.40 3.01
1624 1902 4.700596 CGAGAGTTCGCCTGAAATAATC 57.299 45.455 0.00 0.00 40.36 1.75
1625 1903 4.112634 CGAGAGTTCGCCTGAAATAATCA 58.887 43.478 0.00 0.00 40.36 2.57
1626 1904 4.566759 CGAGAGTTCGCCTGAAATAATCAA 59.433 41.667 0.00 0.00 40.36 2.57
1627 1905 5.276584 CGAGAGTTCGCCTGAAATAATCAAG 60.277 44.000 0.00 0.00 40.36 3.02
1628 1906 4.878397 AGAGTTCGCCTGAAATAATCAAGG 59.122 41.667 0.00 0.00 37.67 3.61
1629 1907 4.843728 AGTTCGCCTGAAATAATCAAGGA 58.156 39.130 0.00 0.00 37.67 3.36
1630 1908 4.878397 AGTTCGCCTGAAATAATCAAGGAG 59.122 41.667 0.00 0.00 37.67 3.69
1631 1909 4.753516 TCGCCTGAAATAATCAAGGAGA 57.246 40.909 0.00 0.00 37.67 3.71
1632 1910 5.296151 TCGCCTGAAATAATCAAGGAGAT 57.704 39.130 0.00 0.00 37.67 2.75
1633 1911 5.300752 TCGCCTGAAATAATCAAGGAGATC 58.699 41.667 0.00 0.00 37.67 2.75
1634 1912 4.151335 CGCCTGAAATAATCAAGGAGATCG 59.849 45.833 0.00 0.00 37.67 3.69
1635 1913 5.300752 GCCTGAAATAATCAAGGAGATCGA 58.699 41.667 0.00 0.00 37.67 3.59
1636 1914 5.936956 GCCTGAAATAATCAAGGAGATCGAT 59.063 40.000 0.00 0.00 37.67 3.59
1637 1915 6.091986 GCCTGAAATAATCAAGGAGATCGATC 59.908 42.308 17.91 17.91 37.67 3.69
1638 1916 6.309980 CCTGAAATAATCAAGGAGATCGATCG 59.690 42.308 19.33 9.36 37.67 3.69
1639 1917 6.159293 TGAAATAATCAAGGAGATCGATCGG 58.841 40.000 19.33 8.42 35.39 4.18
1640 1918 5.730296 AATAATCAAGGAGATCGATCGGT 57.270 39.130 19.33 8.34 35.39 4.69
1641 1919 3.377346 AATCAAGGAGATCGATCGGTG 57.623 47.619 19.33 14.97 35.39 4.94
1642 1920 1.032794 TCAAGGAGATCGATCGGTGG 58.967 55.000 19.33 9.73 0.00 4.61
1643 1921 1.032794 CAAGGAGATCGATCGGTGGA 58.967 55.000 19.33 0.00 0.00 4.02
1644 1922 1.033574 AAGGAGATCGATCGGTGGAC 58.966 55.000 19.33 7.65 0.00 4.02
1645 1923 0.183971 AGGAGATCGATCGGTGGACT 59.816 55.000 19.33 0.76 0.00 3.85
1646 1924 1.420514 AGGAGATCGATCGGTGGACTA 59.579 52.381 19.33 0.00 0.00 2.59
1647 1925 1.807742 GGAGATCGATCGGTGGACTAG 59.192 57.143 19.33 0.00 0.00 2.57
1648 1926 2.550423 GGAGATCGATCGGTGGACTAGA 60.550 54.545 19.33 0.00 0.00 2.43
1649 1927 3.139850 GAGATCGATCGGTGGACTAGAA 58.860 50.000 19.33 0.00 0.00 2.10
1650 1928 3.552875 AGATCGATCGGTGGACTAGAAA 58.447 45.455 19.33 0.00 0.00 2.52
1651 1929 3.952323 AGATCGATCGGTGGACTAGAAAA 59.048 43.478 19.33 0.00 0.00 2.29
1652 1930 4.401519 AGATCGATCGGTGGACTAGAAAAA 59.598 41.667 19.33 0.00 0.00 1.94
1653 1931 4.730949 TCGATCGGTGGACTAGAAAAAT 57.269 40.909 16.41 0.00 0.00 1.82
1654 1932 4.679662 TCGATCGGTGGACTAGAAAAATC 58.320 43.478 16.41 0.00 0.00 2.17
1655 1933 4.158949 TCGATCGGTGGACTAGAAAAATCA 59.841 41.667 16.41 0.00 0.00 2.57
1656 1934 4.504461 CGATCGGTGGACTAGAAAAATCAG 59.496 45.833 7.38 0.00 0.00 2.90
1657 1935 5.661458 GATCGGTGGACTAGAAAAATCAGA 58.339 41.667 0.00 0.00 0.00 3.27
1658 1936 5.073311 TCGGTGGACTAGAAAAATCAGAG 57.927 43.478 0.00 0.00 0.00 3.35
1659 1937 4.527038 TCGGTGGACTAGAAAAATCAGAGT 59.473 41.667 0.00 0.00 0.00 3.24
1660 1938 4.865365 CGGTGGACTAGAAAAATCAGAGTC 59.135 45.833 0.00 0.00 36.60 3.36
1661 1939 5.566826 CGGTGGACTAGAAAAATCAGAGTCA 60.567 44.000 0.00 0.00 38.62 3.41
1662 1940 5.639931 GGTGGACTAGAAAAATCAGAGTCAC 59.360 44.000 0.00 0.00 38.62 3.67
1663 1941 6.223852 GTGGACTAGAAAAATCAGAGTCACA 58.776 40.000 0.00 6.00 38.62 3.58
1664 1942 6.876257 GTGGACTAGAAAAATCAGAGTCACAT 59.124 38.462 0.00 0.00 38.62 3.21
1665 1943 7.064016 GTGGACTAGAAAAATCAGAGTCACATC 59.936 40.741 0.00 0.00 38.62 3.06
1666 1944 7.099764 GGACTAGAAAAATCAGAGTCACATCA 58.900 38.462 0.00 0.00 38.62 3.07
1667 1945 7.768120 GGACTAGAAAAATCAGAGTCACATCAT 59.232 37.037 0.00 0.00 38.62 2.45
1668 1946 8.489990 ACTAGAAAAATCAGAGTCACATCATG 57.510 34.615 0.00 0.00 0.00 3.07
1669 1947 6.192234 AGAAAAATCAGAGTCACATCATGC 57.808 37.500 0.00 0.00 0.00 4.06
1670 1948 5.708697 AGAAAAATCAGAGTCACATCATGCA 59.291 36.000 0.00 0.00 0.00 3.96
1671 1949 5.970317 AAAATCAGAGTCACATCATGCAA 57.030 34.783 0.00 0.00 0.00 4.08
1672 1950 5.970317 AAATCAGAGTCACATCATGCAAA 57.030 34.783 0.00 0.00 0.00 3.68
1673 1951 5.970317 AATCAGAGTCACATCATGCAAAA 57.030 34.783 0.00 0.00 0.00 2.44
1674 1952 4.754372 TCAGAGTCACATCATGCAAAAC 57.246 40.909 0.00 0.00 0.00 2.43
1675 1953 4.392047 TCAGAGTCACATCATGCAAAACT 58.608 39.130 0.00 0.00 0.00 2.66
1676 1954 4.453478 TCAGAGTCACATCATGCAAAACTC 59.547 41.667 0.00 0.00 33.53 3.01
1677 1955 4.214758 CAGAGTCACATCATGCAAAACTCA 59.785 41.667 13.71 0.00 35.31 3.41
1678 1956 4.454847 AGAGTCACATCATGCAAAACTCAG 59.545 41.667 13.71 0.00 35.31 3.35
1679 1957 3.504906 AGTCACATCATGCAAAACTCAGG 59.495 43.478 0.00 0.00 0.00 3.86
1680 1958 2.229543 TCACATCATGCAAAACTCAGGC 59.770 45.455 0.00 0.00 0.00 4.85
1681 1959 1.200716 ACATCATGCAAAACTCAGGCG 59.799 47.619 0.00 0.00 0.00 5.52
1682 1960 0.813184 ATCATGCAAAACTCAGGCGG 59.187 50.000 0.00 0.00 0.00 6.13
1683 1961 1.444895 CATGCAAAACTCAGGCGGC 60.445 57.895 0.00 0.00 0.00 6.53
1684 1962 1.604593 ATGCAAAACTCAGGCGGCT 60.605 52.632 5.25 5.25 0.00 5.52
1685 1963 1.870055 ATGCAAAACTCAGGCGGCTG 61.870 55.000 31.58 31.58 0.00 4.85
1686 1964 2.260869 GCAAAACTCAGGCGGCTGA 61.261 57.895 35.79 35.79 0.00 4.26
1693 1971 3.207452 TCAGGCGGCTGAGATAGAA 57.793 52.632 35.14 13.79 0.00 2.10
1694 1972 0.747255 TCAGGCGGCTGAGATAGAAC 59.253 55.000 35.14 0.00 0.00 3.01
1695 1973 0.461548 CAGGCGGCTGAGATAGAACA 59.538 55.000 33.59 0.00 0.00 3.18
1696 1974 0.461961 AGGCGGCTGAGATAGAACAC 59.538 55.000 12.25 0.00 0.00 3.32
1697 1975 0.530870 GGCGGCTGAGATAGAACACC 60.531 60.000 0.00 0.00 0.00 4.16
1698 1976 0.530870 GCGGCTGAGATAGAACACCC 60.531 60.000 0.00 0.00 0.00 4.61
1699 1977 0.249073 CGGCTGAGATAGAACACCCG 60.249 60.000 0.00 0.00 0.00 5.28
1700 1978 0.105039 GGCTGAGATAGAACACCCGG 59.895 60.000 0.00 0.00 0.00 5.73
1701 1979 0.824759 GCTGAGATAGAACACCCGGT 59.175 55.000 0.00 0.00 0.00 5.28
1702 1980 1.207329 GCTGAGATAGAACACCCGGTT 59.793 52.381 0.00 0.00 44.10 4.44
1703 1981 2.893637 CTGAGATAGAACACCCGGTTG 58.106 52.381 0.00 0.00 40.63 3.77
1704 1982 2.496070 CTGAGATAGAACACCCGGTTGA 59.504 50.000 5.78 0.00 40.63 3.18
1705 1983 2.496070 TGAGATAGAACACCCGGTTGAG 59.504 50.000 5.78 0.00 40.63 3.02
1706 1984 2.758979 GAGATAGAACACCCGGTTGAGA 59.241 50.000 5.78 0.00 40.63 3.27
1707 1985 3.375699 AGATAGAACACCCGGTTGAGAT 58.624 45.455 5.78 0.00 40.63 2.75
1904 2184 2.444895 GGGGAGATCTCAGGCGGT 60.445 66.667 23.85 0.00 0.00 5.68
2253 2533 1.443702 CGATCCGTGCACAAGACGA 60.444 57.895 18.64 3.90 39.21 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.707893 CCATCGATTCTTTTTATGAATTGCCTT 59.292 33.333 0.00 0.00 36.03 4.35
1 2 7.147846 ACCATCGATTCTTTTTATGAATTGCCT 60.148 33.333 0.00 0.00 36.03 4.75
2 3 6.980397 ACCATCGATTCTTTTTATGAATTGCC 59.020 34.615 0.00 0.00 36.03 4.52
22 23 7.539712 TCAAAGATAAATCACTCGAACCATC 57.460 36.000 0.00 0.00 0.00 3.51
25 26 7.596749 TCTTCAAAGATAAATCACTCGAACC 57.403 36.000 0.00 0.00 0.00 3.62
26 27 9.319223 GTTTCTTCAAAGATAAATCACTCGAAC 57.681 33.333 0.00 0.00 34.49 3.95
27 28 9.273016 AGTTTCTTCAAAGATAAATCACTCGAA 57.727 29.630 0.00 0.00 34.49 3.71
128 129 9.612620 AAGAAAGAAATAAAAGCATACGTCAAG 57.387 29.630 0.00 0.00 0.00 3.02
144 145 8.199449 TGTCAATTCTCTGCAAAAGAAAGAAAT 58.801 29.630 13.49 0.00 36.41 2.17
145 146 7.546358 TGTCAATTCTCTGCAAAAGAAAGAAA 58.454 30.769 13.49 8.41 36.41 2.52
146 147 7.099266 TGTCAATTCTCTGCAAAAGAAAGAA 57.901 32.000 13.49 5.00 36.41 2.52
147 148 6.698008 TGTCAATTCTCTGCAAAAGAAAGA 57.302 33.333 13.49 11.77 36.41 2.52
148 149 9.073368 CATATGTCAATTCTCTGCAAAAGAAAG 57.927 33.333 13.49 10.12 36.41 2.62
154 155 9.013229 AGTTAACATATGTCAATTCTCTGCAAA 57.987 29.630 9.23 0.00 0.00 3.68
182 183 5.481105 TCAAGCTCCATTTAGCATTTTTGG 58.519 37.500 0.00 0.00 45.30 3.28
340 342 6.873605 ACAAGCTTGTTTTTCTTTTTGTAGCT 59.126 30.769 26.36 0.00 38.47 3.32
341 343 7.060600 ACAAGCTTGTTTTTCTTTTTGTAGC 57.939 32.000 26.36 0.00 38.47 3.58
342 344 8.321005 GCTACAAGCTTGTTTTTCTTTTTGTAG 58.679 33.333 35.20 21.74 44.55 2.74
343 345 7.276878 GGCTACAAGCTTGTTTTTCTTTTTGTA 59.723 33.333 35.20 12.93 41.99 2.41
344 346 6.092122 GGCTACAAGCTTGTTTTTCTTTTTGT 59.908 34.615 35.20 10.62 41.99 2.83
345 347 6.313658 AGGCTACAAGCTTGTTTTTCTTTTTG 59.686 34.615 35.20 10.66 41.99 2.44
346 348 6.406370 AGGCTACAAGCTTGTTTTTCTTTTT 58.594 32.000 35.20 10.54 41.99 1.94
347 349 5.977635 AGGCTACAAGCTTGTTTTTCTTTT 58.022 33.333 35.20 11.28 41.99 2.27
348 350 5.598416 AGGCTACAAGCTTGTTTTTCTTT 57.402 34.783 35.20 12.02 41.99 2.52
349 351 5.598416 AAGGCTACAAGCTTGTTTTTCTT 57.402 34.783 35.20 26.44 41.99 2.52
350 352 5.598416 AAAGGCTACAAGCTTGTTTTTCT 57.402 34.783 35.20 23.03 41.99 2.52
351 353 6.074302 GCTAAAAGGCTACAAGCTTGTTTTTC 60.074 38.462 35.20 21.42 41.99 2.29
352 354 5.753438 GCTAAAAGGCTACAAGCTTGTTTTT 59.247 36.000 35.20 31.31 41.99 1.94
353 355 5.289595 GCTAAAAGGCTACAAGCTTGTTTT 58.710 37.500 35.20 27.93 41.99 2.43
354 356 4.556699 CGCTAAAAGGCTACAAGCTTGTTT 60.557 41.667 35.20 23.70 41.99 2.83
355 357 3.058224 CGCTAAAAGGCTACAAGCTTGTT 60.058 43.478 35.20 18.76 41.99 2.83
356 358 2.484264 CGCTAAAAGGCTACAAGCTTGT 59.516 45.455 32.97 32.97 41.99 3.16
357 359 2.729156 GCGCTAAAAGGCTACAAGCTTG 60.729 50.000 24.84 24.84 41.99 4.01
358 360 1.468914 GCGCTAAAAGGCTACAAGCTT 59.531 47.619 0.00 0.00 41.99 3.74
385 387 8.653338 CAAAATCATGGACTTTTAGAGCAAATG 58.347 33.333 0.00 0.00 0.00 2.32
386 388 8.370182 ACAAAATCATGGACTTTTAGAGCAAAT 58.630 29.630 0.00 0.00 0.00 2.32
390 392 8.593492 AAAACAAAATCATGGACTTTTAGAGC 57.407 30.769 0.00 0.00 0.00 4.09
445 447 8.633408 CAGAAAATAGAGCTCAAAAATTTCACG 58.367 33.333 17.77 9.90 0.00 4.35
452 454 7.566760 TCACACAGAAAATAGAGCTCAAAAA 57.433 32.000 17.77 0.00 0.00 1.94
453 455 7.566760 TTCACACAGAAAATAGAGCTCAAAA 57.433 32.000 17.77 0.65 32.05 2.44
454 456 7.566760 TTTCACACAGAAAATAGAGCTCAAA 57.433 32.000 17.77 3.56 43.00 2.69
555 562 5.774690 TCTCCATGAAGCCTGTTATTGTTTT 59.225 36.000 0.00 0.00 0.00 2.43
559 566 3.310774 CGTCTCCATGAAGCCTGTTATTG 59.689 47.826 0.00 0.00 0.00 1.90
598 605 1.938577 GGCAGTGATGACATAGCAGTG 59.061 52.381 0.00 7.34 46.39 3.66
599 606 1.472201 CGGCAGTGATGACATAGCAGT 60.472 52.381 0.00 0.00 32.86 4.40
600 607 1.215244 CGGCAGTGATGACATAGCAG 58.785 55.000 0.00 0.00 32.86 4.24
602 609 1.825285 CGCGGCAGTGATGACATAGC 61.825 60.000 0.00 0.00 0.00 2.97
626 643 0.597637 CGTTGCGACCTGACTGAGTT 60.598 55.000 0.00 0.00 0.00 3.01
671 688 3.997021 CACCTCAGCTCGTCTTGTTTATT 59.003 43.478 0.00 0.00 0.00 1.40
712 729 1.211969 CTTCTCGCTTTCGTCCCGA 59.788 57.895 0.00 0.00 36.96 5.14
725 742 5.390779 GCTTTCAGATTCACTTCTGCTTCTC 60.391 44.000 0.00 0.00 42.37 2.87
726 743 4.455190 GCTTTCAGATTCACTTCTGCTTCT 59.545 41.667 0.00 0.00 42.37 2.85
728 745 4.023365 GTGCTTTCAGATTCACTTCTGCTT 60.023 41.667 0.00 0.00 42.37 3.91
729 746 3.501445 GTGCTTTCAGATTCACTTCTGCT 59.499 43.478 0.00 0.00 42.37 4.24
731 748 3.190118 GGGTGCTTTCAGATTCACTTCTG 59.810 47.826 0.00 0.00 43.70 3.02
732 749 3.416156 GGGTGCTTTCAGATTCACTTCT 58.584 45.455 0.00 0.00 0.00 2.85
735 752 1.611673 CCGGGTGCTTTCAGATTCACT 60.612 52.381 0.00 0.00 0.00 3.41
736 753 0.804989 CCGGGTGCTTTCAGATTCAC 59.195 55.000 0.00 0.00 0.00 3.18
737 754 0.400213 ACCGGGTGCTTTCAGATTCA 59.600 50.000 6.32 0.00 0.00 2.57
788 819 2.436824 GGGAGAGCCGGAGCAAAC 60.437 66.667 5.05 0.00 43.56 2.93
804 835 0.252284 ATATACGGGAGGGAGGCTGG 60.252 60.000 0.00 0.00 0.00 4.85
806 837 2.559252 GGTTATATACGGGAGGGAGGCT 60.559 54.545 0.00 0.00 0.00 4.58
831 863 1.229209 GAGGAGTGTGGGAGTGGGA 60.229 63.158 0.00 0.00 0.00 4.37
839 871 2.498885 TGTGATGATGAGAGGAGTGTGG 59.501 50.000 0.00 0.00 0.00 4.17
843 875 2.836372 TGCTTGTGATGATGAGAGGAGT 59.164 45.455 0.00 0.00 0.00 3.85
856 888 0.106769 TCCTGGTGCTTTGCTTGTGA 60.107 50.000 0.00 0.00 0.00 3.58
883 915 3.210528 GCTGAGCTGATGCAGGGC 61.211 66.667 0.00 0.00 42.74 5.19
887 919 2.195741 AAAAGAGCTGAGCTGATGCA 57.804 45.000 13.71 0.00 39.88 3.96
888 920 3.875727 TGATAAAAGAGCTGAGCTGATGC 59.124 43.478 13.71 0.00 39.88 3.91
895 927 6.091986 GGACTTTCAGTGATAAAAGAGCTGAG 59.908 42.308 9.53 0.00 37.47 3.35
900 932 8.091449 AGTAGTGGACTTTCAGTGATAAAAGAG 58.909 37.037 9.53 0.00 33.13 2.85
902 934 9.360093 CTAGTAGTGGACTTTCAGTGATAAAAG 57.640 37.037 0.00 0.00 39.81 2.27
906 938 7.120873 GTGTCTAGTAGTGGACTTTCAGTGATA 59.879 40.741 14.39 0.00 39.81 2.15
908 940 5.241064 GTGTCTAGTAGTGGACTTTCAGTGA 59.759 44.000 14.39 0.00 39.81 3.41
922 954 6.785488 TTTGTGATTGCTTGTGTCTAGTAG 57.215 37.500 0.00 0.00 0.00 2.57
928 960 4.863491 ACTGATTTGTGATTGCTTGTGTC 58.137 39.130 0.00 0.00 0.00 3.67
950 986 3.888930 GGTGGAAAATGGTTGAACTGAGA 59.111 43.478 0.00 0.00 0.00 3.27
959 995 0.105246 TGGGCTGGTGGAAAATGGTT 60.105 50.000 0.00 0.00 0.00 3.67
964 1000 1.075674 TTGCTGGGCTGGTGGAAAA 60.076 52.632 0.00 0.00 0.00 2.29
975 1011 0.392729 CTCTCCTTCTGCTTGCTGGG 60.393 60.000 0.00 0.00 0.00 4.45
984 1020 1.743091 GCCATCACTGCTCTCCTTCTG 60.743 57.143 0.00 0.00 0.00 3.02
985 1021 0.540923 GCCATCACTGCTCTCCTTCT 59.459 55.000 0.00 0.00 0.00 2.85
987 1023 0.252479 CAGCCATCACTGCTCTCCTT 59.748 55.000 0.00 0.00 36.81 3.36
988 1024 1.624479 CCAGCCATCACTGCTCTCCT 61.624 60.000 0.00 0.00 36.81 3.69
989 1025 1.153208 CCAGCCATCACTGCTCTCC 60.153 63.158 0.00 0.00 36.81 3.71
990 1026 0.743701 CACCAGCCATCACTGCTCTC 60.744 60.000 0.00 0.00 36.81 3.20
991 1027 1.298993 CACCAGCCATCACTGCTCT 59.701 57.895 0.00 0.00 36.81 4.09
993 1029 2.360852 GCACCAGCCATCACTGCT 60.361 61.111 0.00 0.00 40.41 4.24
994 1030 3.807538 CGCACCAGCCATCACTGC 61.808 66.667 0.00 0.00 36.29 4.40
995 1031 3.129502 CCGCACCAGCCATCACTG 61.130 66.667 0.00 0.00 37.52 3.66
1011 1047 2.203070 ATCCATGACGCCTTCGCC 60.203 61.111 0.00 0.00 39.84 5.54
1023 1059 1.152610 GCTCATGGCCACCATCCAT 60.153 57.895 8.16 0.00 43.15 3.41
1077 1113 1.144936 ATAGTTCCAGCGGCAGAGC 59.855 57.895 1.45 0.43 37.41 4.09
1086 1122 2.402305 GATCGCAGAGCATAGTTCCAG 58.598 52.381 0.00 0.00 45.47 3.86
1104 1140 4.195334 GCTGCCCGGTGGATGGAT 62.195 66.667 0.00 0.00 0.00 3.41
1230 1278 2.113433 CCAGCAGCTGAGGCACATC 61.113 63.158 24.90 0.00 41.70 3.06
1251 1299 2.489329 AGCACAACATGTATTCTGCACC 59.511 45.455 15.39 0.00 0.00 5.01
1252 1300 3.837213 AGCACAACATGTATTCTGCAC 57.163 42.857 15.39 1.50 0.00 4.57
1261 1478 5.472148 CAACCAATTCATAGCACAACATGT 58.528 37.500 0.00 0.00 0.00 3.21
1265 1482 3.911868 TGCAACCAATTCATAGCACAAC 58.088 40.909 0.00 0.00 0.00 3.32
1292 1509 1.151450 CACCCCACAGGAAGCACTT 59.849 57.895 0.00 0.00 39.89 3.16
1293 1510 1.770110 TCACCCCACAGGAAGCACT 60.770 57.895 0.00 0.00 39.89 4.40
1294 1511 1.302832 CTCACCCCACAGGAAGCAC 60.303 63.158 0.00 0.00 39.89 4.40
1295 1512 0.842030 ATCTCACCCCACAGGAAGCA 60.842 55.000 0.00 0.00 39.89 3.91
1296 1513 0.107459 GATCTCACCCCACAGGAAGC 60.107 60.000 0.00 0.00 39.89 3.86
1297 1514 0.176680 CGATCTCACCCCACAGGAAG 59.823 60.000 0.00 0.00 39.89 3.46
1299 1516 0.544357 AACGATCTCACCCCACAGGA 60.544 55.000 0.00 0.00 39.89 3.86
1300 1517 0.108138 GAACGATCTCACCCCACAGG 60.108 60.000 0.00 0.00 43.78 4.00
1317 1549 3.812156 TTCAGACAGAACCTTCACGAA 57.188 42.857 0.00 0.00 0.00 3.85
1323 1555 4.214332 GCGAAGAAATTCAGACAGAACCTT 59.786 41.667 0.00 0.00 39.49 3.50
1350 1582 1.002900 CGTGTCGGTTCAGCAAATTGT 60.003 47.619 0.00 0.00 0.00 2.71
1354 1586 1.495584 GAGCGTGTCGGTTCAGCAAA 61.496 55.000 0.00 0.00 37.83 3.68
1378 1618 1.002087 ACCTGGACCTGAATCACGTTC 59.998 52.381 0.00 0.00 37.35 3.95
1387 1627 3.193395 TGTGGTATAACCTGGACCTGA 57.807 47.619 0.00 0.00 39.58 3.86
1391 1631 6.127140 ACTCAGTAATGTGGTATAACCTGGAC 60.127 42.308 0.00 0.00 39.58 4.02
1411 1651 6.380190 ACTAGCTCACGTTTAGTTAACTCAG 58.620 40.000 12.39 4.82 34.46 3.35
1413 1653 6.089150 CCAACTAGCTCACGTTTAGTTAACTC 59.911 42.308 12.39 0.00 35.93 3.01
1420 1660 4.113354 GGATCCAACTAGCTCACGTTTAG 58.887 47.826 6.95 0.00 0.00 1.85
1447 1725 0.387202 CGTATCTCACTCTGGCCTGG 59.613 60.000 10.07 3.31 0.00 4.45
1449 1727 1.394618 GACGTATCTCACTCTGGCCT 58.605 55.000 3.32 0.00 0.00 5.19
1463 1741 1.068895 TGGAAAAGGAACTGCGACGTA 59.931 47.619 0.00 0.00 40.86 3.57
1469 1747 4.112634 GTGAAAACTGGAAAAGGAACTGC 58.887 43.478 0.00 0.00 40.86 4.40
1477 1755 4.440387 GGCCGTTTAGTGAAAACTGGAAAA 60.440 41.667 12.44 0.00 44.49 2.29
1559 1837 9.138596 GAAGTGTAGGGATATCTCTTAACTCTT 57.861 37.037 17.10 17.10 0.00 2.85
1560 1838 8.282982 TGAAGTGTAGGGATATCTCTTAACTCT 58.717 37.037 11.18 7.30 0.00 3.24
1561 1839 8.466617 TGAAGTGTAGGGATATCTCTTAACTC 57.533 38.462 11.18 5.03 0.00 3.01
1562 1840 8.282982 TCTGAAGTGTAGGGATATCTCTTAACT 58.717 37.037 11.18 11.74 0.00 2.24
1563 1841 8.354426 GTCTGAAGTGTAGGGATATCTCTTAAC 58.646 40.741 11.18 9.60 0.00 2.01
1564 1842 8.282982 AGTCTGAAGTGTAGGGATATCTCTTAA 58.717 37.037 11.18 0.00 0.00 1.85
1589 1867 1.269102 ACTCTCGTGTGTCGTTGGAAG 60.269 52.381 0.00 0.00 40.80 3.46
1593 1871 0.770590 CGAACTCTCGTGTGTCGTTG 59.229 55.000 0.00 0.00 40.33 4.10
1594 1872 3.159446 CGAACTCTCGTGTGTCGTT 57.841 52.632 0.00 0.00 40.33 3.85
1595 1873 4.916412 CGAACTCTCGTGTGTCGT 57.084 55.556 0.00 0.00 40.33 4.34
1601 1879 7.822167 TTGATTATTTCAGGCGAACTCTCGTG 61.822 42.308 0.00 0.00 40.47 4.35
1602 1880 5.853355 TTGATTATTTCAGGCGAACTCTCGT 60.853 40.000 0.00 0.00 40.47 4.18
1603 1881 4.566759 TTGATTATTTCAGGCGAACTCTCG 59.433 41.667 0.00 0.00 40.94 4.04
1604 1882 5.007136 CCTTGATTATTTCAGGCGAACTCTC 59.993 44.000 0.00 0.00 35.27 3.20
1605 1883 4.878397 CCTTGATTATTTCAGGCGAACTCT 59.122 41.667 0.00 0.00 35.27 3.24
1606 1884 4.876107 TCCTTGATTATTTCAGGCGAACTC 59.124 41.667 0.00 0.00 35.27 3.01
1607 1885 4.843728 TCCTTGATTATTTCAGGCGAACT 58.156 39.130 0.00 0.00 35.27 3.01
1608 1886 4.876107 TCTCCTTGATTATTTCAGGCGAAC 59.124 41.667 0.00 0.00 35.27 3.95
1609 1887 5.097742 TCTCCTTGATTATTTCAGGCGAA 57.902 39.130 0.00 0.00 35.27 4.70
1610 1888 4.753516 TCTCCTTGATTATTTCAGGCGA 57.246 40.909 0.00 0.00 35.27 5.54
1611 1889 4.151335 CGATCTCCTTGATTATTTCAGGCG 59.849 45.833 0.00 0.00 35.27 5.52
1612 1890 5.300752 TCGATCTCCTTGATTATTTCAGGC 58.699 41.667 0.00 0.00 35.27 4.85
1613 1891 6.309980 CGATCGATCTCCTTGATTATTTCAGG 59.690 42.308 22.43 0.00 35.27 3.86
1614 1892 6.309980 CCGATCGATCTCCTTGATTATTTCAG 59.690 42.308 22.43 1.44 35.27 3.02
1615 1893 6.159293 CCGATCGATCTCCTTGATTATTTCA 58.841 40.000 22.43 0.00 35.14 2.69
1616 1894 6.090088 CACCGATCGATCTCCTTGATTATTTC 59.910 42.308 22.43 0.00 35.14 2.17
1617 1895 5.928839 CACCGATCGATCTCCTTGATTATTT 59.071 40.000 22.43 0.00 35.14 1.40
1618 1896 5.473931 CACCGATCGATCTCCTTGATTATT 58.526 41.667 22.43 0.00 35.14 1.40
1619 1897 4.081972 CCACCGATCGATCTCCTTGATTAT 60.082 45.833 22.43 0.00 35.14 1.28
1620 1898 3.255888 CCACCGATCGATCTCCTTGATTA 59.744 47.826 22.43 0.00 35.14 1.75
1621 1899 2.036475 CCACCGATCGATCTCCTTGATT 59.964 50.000 22.43 0.00 35.14 2.57
1622 1900 1.615883 CCACCGATCGATCTCCTTGAT 59.384 52.381 22.43 0.00 38.27 2.57
1623 1901 1.032794 CCACCGATCGATCTCCTTGA 58.967 55.000 22.43 0.00 0.00 3.02
1624 1902 1.032794 TCCACCGATCGATCTCCTTG 58.967 55.000 22.43 13.03 0.00 3.61
1625 1903 1.033574 GTCCACCGATCGATCTCCTT 58.966 55.000 22.43 1.81 0.00 3.36
1626 1904 0.183971 AGTCCACCGATCGATCTCCT 59.816 55.000 22.43 3.69 0.00 3.69
1627 1905 1.807742 CTAGTCCACCGATCGATCTCC 59.192 57.143 22.43 1.15 0.00 3.71
1628 1906 2.768698 TCTAGTCCACCGATCGATCTC 58.231 52.381 22.43 0.00 0.00 2.75
1629 1907 2.932855 TCTAGTCCACCGATCGATCT 57.067 50.000 22.43 9.32 0.00 2.75
1630 1908 3.984508 TTTCTAGTCCACCGATCGATC 57.015 47.619 18.66 15.68 0.00 3.69
1631 1909 4.730949 TTTTTCTAGTCCACCGATCGAT 57.269 40.909 18.66 0.00 0.00 3.59
1632 1910 4.158949 TGATTTTTCTAGTCCACCGATCGA 59.841 41.667 18.66 0.00 0.00 3.59
1633 1911 4.430007 TGATTTTTCTAGTCCACCGATCG 58.570 43.478 8.51 8.51 0.00 3.69
1634 1912 5.661458 TCTGATTTTTCTAGTCCACCGATC 58.339 41.667 0.00 0.00 0.00 3.69
1635 1913 5.187967 ACTCTGATTTTTCTAGTCCACCGAT 59.812 40.000 0.00 0.00 0.00 4.18
1636 1914 4.527038 ACTCTGATTTTTCTAGTCCACCGA 59.473 41.667 0.00 0.00 0.00 4.69
1637 1915 4.822026 ACTCTGATTTTTCTAGTCCACCG 58.178 43.478 0.00 0.00 0.00 4.94
1638 1916 5.639931 GTGACTCTGATTTTTCTAGTCCACC 59.360 44.000 0.00 0.00 36.56 4.61
1639 1917 6.223852 TGTGACTCTGATTTTTCTAGTCCAC 58.776 40.000 0.00 0.00 36.56 4.02
1640 1918 6.419484 TGTGACTCTGATTTTTCTAGTCCA 57.581 37.500 0.00 0.00 36.56 4.02
1641 1919 7.099764 TGATGTGACTCTGATTTTTCTAGTCC 58.900 38.462 0.00 0.00 36.56 3.85
1642 1920 8.602328 CATGATGTGACTCTGATTTTTCTAGTC 58.398 37.037 0.00 0.00 37.64 2.59
1643 1921 7.065563 GCATGATGTGACTCTGATTTTTCTAGT 59.934 37.037 0.00 0.00 0.00 2.57
1644 1922 7.065443 TGCATGATGTGACTCTGATTTTTCTAG 59.935 37.037 0.00 0.00 0.00 2.43
1645 1923 6.880529 TGCATGATGTGACTCTGATTTTTCTA 59.119 34.615 0.00 0.00 0.00 2.10
1646 1924 5.708697 TGCATGATGTGACTCTGATTTTTCT 59.291 36.000 0.00 0.00 0.00 2.52
1647 1925 5.946298 TGCATGATGTGACTCTGATTTTTC 58.054 37.500 0.00 0.00 0.00 2.29
1648 1926 5.970317 TGCATGATGTGACTCTGATTTTT 57.030 34.783 0.00 0.00 0.00 1.94
1649 1927 5.970317 TTGCATGATGTGACTCTGATTTT 57.030 34.783 0.00 0.00 0.00 1.82
1650 1928 5.970317 TTTGCATGATGTGACTCTGATTT 57.030 34.783 0.00 0.00 0.00 2.17
1651 1929 5.475909 AGTTTTGCATGATGTGACTCTGATT 59.524 36.000 0.00 0.00 0.00 2.57
1652 1930 5.008331 AGTTTTGCATGATGTGACTCTGAT 58.992 37.500 0.00 0.00 0.00 2.90
1653 1931 4.392047 AGTTTTGCATGATGTGACTCTGA 58.608 39.130 0.00 0.00 0.00 3.27
1654 1932 4.214758 TGAGTTTTGCATGATGTGACTCTG 59.785 41.667 0.00 0.00 34.62 3.35
1655 1933 4.392047 TGAGTTTTGCATGATGTGACTCT 58.608 39.130 0.00 2.80 34.62 3.24
1656 1934 4.379186 CCTGAGTTTTGCATGATGTGACTC 60.379 45.833 0.00 3.46 34.24 3.36
1657 1935 3.504906 CCTGAGTTTTGCATGATGTGACT 59.495 43.478 0.00 0.00 0.00 3.41
1658 1936 3.829948 CCTGAGTTTTGCATGATGTGAC 58.170 45.455 0.00 0.00 0.00 3.67
1659 1937 2.229543 GCCTGAGTTTTGCATGATGTGA 59.770 45.455 0.00 0.00 0.00 3.58
1660 1938 2.602878 GCCTGAGTTTTGCATGATGTG 58.397 47.619 0.00 0.00 0.00 3.21
1661 1939 1.200716 CGCCTGAGTTTTGCATGATGT 59.799 47.619 0.00 0.00 0.00 3.06
1662 1940 1.468565 CCGCCTGAGTTTTGCATGATG 60.469 52.381 0.00 0.00 0.00 3.07
1663 1941 0.813184 CCGCCTGAGTTTTGCATGAT 59.187 50.000 0.00 0.00 0.00 2.45
1664 1942 1.865788 GCCGCCTGAGTTTTGCATGA 61.866 55.000 0.00 0.00 0.00 3.07
1665 1943 1.444895 GCCGCCTGAGTTTTGCATG 60.445 57.895 0.00 0.00 0.00 4.06
1666 1944 1.604593 AGCCGCCTGAGTTTTGCAT 60.605 52.632 0.00 0.00 0.00 3.96
1667 1945 2.203337 AGCCGCCTGAGTTTTGCA 60.203 55.556 0.00 0.00 0.00 4.08
1668 1946 2.256461 CAGCCGCCTGAGTTTTGC 59.744 61.111 0.00 0.00 41.77 3.68
1669 1947 4.063529 TCAGCCGCCTGAGTTTTG 57.936 55.556 0.00 0.00 42.98 2.44
1675 1953 0.747255 GTTCTATCTCAGCCGCCTGA 59.253 55.000 0.00 0.00 45.54 3.86
1676 1954 0.461548 TGTTCTATCTCAGCCGCCTG 59.538 55.000 0.00 0.00 40.54 4.85
1677 1955 0.461961 GTGTTCTATCTCAGCCGCCT 59.538 55.000 0.00 0.00 0.00 5.52
1678 1956 0.530870 GGTGTTCTATCTCAGCCGCC 60.531 60.000 0.00 0.00 0.00 6.13
1679 1957 0.530870 GGGTGTTCTATCTCAGCCGC 60.531 60.000 0.00 0.00 41.26 6.53
1680 1958 3.669354 GGGTGTTCTATCTCAGCCG 57.331 57.895 0.00 0.00 41.26 5.52
1681 1959 0.105039 CCGGGTGTTCTATCTCAGCC 59.895 60.000 0.00 0.00 45.29 4.85
1682 1960 0.824759 ACCGGGTGTTCTATCTCAGC 59.175 55.000 6.32 0.00 0.00 4.26
1683 1961 2.496070 TCAACCGGGTGTTCTATCTCAG 59.504 50.000 21.31 0.00 34.00 3.35
1684 1962 2.496070 CTCAACCGGGTGTTCTATCTCA 59.504 50.000 21.31 0.00 34.00 3.27
1685 1963 2.758979 TCTCAACCGGGTGTTCTATCTC 59.241 50.000 21.31 0.00 34.00 2.75
1686 1964 2.816411 TCTCAACCGGGTGTTCTATCT 58.184 47.619 21.31 0.00 34.00 1.98
1687 1965 3.492829 GGATCTCAACCGGGTGTTCTATC 60.493 52.174 21.31 16.61 34.00 2.08
1688 1966 2.434702 GGATCTCAACCGGGTGTTCTAT 59.565 50.000 21.31 8.81 34.00 1.98
1689 1967 1.829222 GGATCTCAACCGGGTGTTCTA 59.171 52.381 21.31 3.72 34.00 2.10
1690 1968 0.613777 GGATCTCAACCGGGTGTTCT 59.386 55.000 21.31 4.62 34.00 3.01
1691 1969 0.392595 GGGATCTCAACCGGGTGTTC 60.393 60.000 21.31 14.64 34.00 3.18
1692 1970 1.131303 TGGGATCTCAACCGGGTGTT 61.131 55.000 21.31 5.65 37.80 3.32
1693 1971 0.914417 ATGGGATCTCAACCGGGTGT 60.914 55.000 21.31 0.00 0.00 4.16
1694 1972 0.179045 GATGGGATCTCAACCGGGTG 60.179 60.000 15.24 15.24 0.00 4.61
1695 1973 0.326618 AGATGGGATCTCAACCGGGT 60.327 55.000 6.32 0.00 33.42 5.28
1696 1974 0.107456 CAGATGGGATCTCAACCGGG 59.893 60.000 6.32 0.00 37.58 5.73
1697 1975 0.533755 GCAGATGGGATCTCAACCGG 60.534 60.000 0.00 0.00 37.58 5.28
1698 1976 0.533755 GGCAGATGGGATCTCAACCG 60.534 60.000 0.00 0.00 37.58 4.44
1699 1977 0.179006 GGGCAGATGGGATCTCAACC 60.179 60.000 0.00 0.00 37.58 3.77
1700 1978 0.179006 GGGGCAGATGGGATCTCAAC 60.179 60.000 0.00 0.00 37.58 3.18
1701 1979 1.355718 GGGGGCAGATGGGATCTCAA 61.356 60.000 0.00 0.00 37.58 3.02
1702 1980 1.771746 GGGGGCAGATGGGATCTCA 60.772 63.158 0.00 0.00 37.58 3.27
1703 1981 2.888447 CGGGGGCAGATGGGATCTC 61.888 68.421 0.00 0.00 37.58 2.75
1704 1982 2.851102 CGGGGGCAGATGGGATCT 60.851 66.667 0.00 0.00 41.15 2.75
1705 1983 4.650377 GCGGGGGCAGATGGGATC 62.650 72.222 0.00 0.00 0.00 3.36
1904 2184 1.816863 GAGCTCCGGACAGTCACCAA 61.817 60.000 0.00 0.00 0.00 3.67
2227 2507 2.813908 GCACGGATCGTCCACCAC 60.814 66.667 5.15 0.00 38.32 4.16
2253 2533 2.292389 TGTTCCAATGGCCTCCATCAAT 60.292 45.455 3.32 0.00 44.40 2.57


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

AutoCloner maintained by Alex Coulton.