Multiple sequence alignment - TraesCS4A01G038500

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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 TraesCS4A01G038500 chr4A 100.000 6009 0 0 1 6009 30561602 30555594 0.000000e+00 11097
1 TraesCS4A01G038500 chr4B 92.359 3298 130 49 647 3897 539970206 539966984 0.000000e+00 4582
2 TraesCS4A01G038500 chr4B 89.600 2125 132 39 3934 6004 539966981 539964892 0.000000e+00 2617
3 TraesCS4A01G038500 chr4B 92.402 408 15 3 1 408 539970932 539970541 8.740000e-158 568
4 TraesCS4A01G038500 chr4B 80.068 296 19 19 392 652 539970524 539970234 3.700000e-42 183
5 TraesCS4A01G038500 chr4D 88.919 2599 147 78 1 2550 437520023 437517517 0.000000e+00 3073
6 TraesCS4A01G038500 chr4D 93.289 1356 72 9 3934 5288 437516128 437514791 0.000000e+00 1982
7 TraesCS4A01G038500 chr4D 92.547 1382 53 16 2546 3897 437517492 437516131 0.000000e+00 1936


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 TraesCS4A01G038500 chr4A 30555594 30561602 6008 True 11097.000000 11097 100.00000 1 6009 1 chr4A.!!$R1 6008
1 TraesCS4A01G038500 chr4B 539964892 539970932 6040 True 1987.500000 4582 88.60725 1 6004 4 chr4B.!!$R1 6003
2 TraesCS4A01G038500 chr4D 437514791 437520023 5232 True 2330.333333 3073 91.58500 1 5288 3 chr4D.!!$R1 5287

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
776 885 0.108615 GATACCTCATCGGCCCATCG 60.109 60.0 0.00 0.0 35.61 3.84 F
1750 1872 0.232303 GTTCGTTGTCGTCTGCAAGG 59.768 55.0 0.00 0.0 38.33 3.61 F
2790 2957 0.524862 GCAGTTGGTTGCAGATCCTG 59.475 55.0 6.30 0.0 43.53 3.86 F
3159 3330 0.790814 GTACTCTGAGTTTGGTGCGC 59.209 55.0 16.53 0.0 0.00 6.09 F
4342 4537 0.034616 CCTCGGAGATCTTCATGGGC 59.965 60.0 6.58 0.0 33.89 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 1934 0.744414 ATCCGGGAAAGCATGTCGTG 60.744 55.0 0.00 0.00 0.00 4.35 R
3303 3498 0.108019 AACGACCCTTTGTGGAGTCC 59.892 55.0 0.73 0.73 38.35 3.85 R
4046 4241 0.106708 GCGCAGATAGGTTCATCCCA 59.893 55.0 0.30 0.00 36.75 4.37 R
4363 4558 0.606401 AATCCTCGCAGGTGTTGTGG 60.606 55.0 2.68 0.00 37.88 4.17 R
5339 5535 0.404040 AGTTTTCCGGATCCCAAGCA 59.596 50.0 4.15 0.00 0.00 3.91 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
74 75 0.867753 CTAGAACGCACTAGCCGCTG 60.868 60.000 2.16 0.00 37.52 5.18
264 266 3.640000 GCGTGTTGTGCAGCGAGT 61.640 61.111 0.00 0.00 0.00 4.18
301 303 1.221840 CTCCATGGGGAAGGACGTG 59.778 63.158 5.34 0.00 44.38 4.49
302 304 1.537889 TCCATGGGGAAGGACGTGT 60.538 57.895 13.02 0.00 41.32 4.49
303 305 1.377202 CCATGGGGAAGGACGTGTG 60.377 63.158 2.85 0.00 35.59 3.82
304 306 2.040544 CATGGGGAAGGACGTGTGC 61.041 63.158 0.00 0.00 0.00 4.57
305 307 3.605749 ATGGGGAAGGACGTGTGCG 62.606 63.158 0.00 0.00 44.93 5.34
418 453 2.610859 GCCACTTGGGGAGGAGGA 60.611 66.667 0.00 0.00 37.04 3.71
420 455 2.674220 CCACTTGGGGAGGAGGAGC 61.674 68.421 0.00 0.00 0.00 4.70
421 456 1.614824 CACTTGGGGAGGAGGAGCT 60.615 63.158 0.00 0.00 0.00 4.09
423 458 2.285668 TTGGGGAGGAGGAGCTGG 60.286 66.667 0.00 0.00 0.00 4.85
424 459 3.950861 TTGGGGAGGAGGAGCTGGG 62.951 68.421 0.00 0.00 0.00 4.45
550 600 1.713830 GCGGTTCCTCGGAATTTCG 59.286 57.895 0.00 0.00 36.45 3.46
556 606 3.532542 GTTCCTCGGAATTTCGGAATCT 58.467 45.455 6.24 0.00 37.80 2.40
557 607 4.442472 GGTTCCTCGGAATTTCGGAATCTA 60.442 45.833 6.24 0.00 37.80 1.98
596 658 2.100631 GTGTCCACGGAATCGCTGG 61.101 63.158 0.00 0.00 40.63 4.85
600 662 1.153369 CCACGGAATCGCTGGTGAT 60.153 57.895 0.00 0.00 40.63 3.06
601 663 1.154205 CCACGGAATCGCTGGTGATC 61.154 60.000 0.00 0.00 40.63 2.92
602 664 1.144057 ACGGAATCGCTGGTGATCC 59.856 57.895 0.00 1.22 40.63 3.36
603 665 1.595382 CGGAATCGCTGGTGATCCC 60.595 63.158 0.00 0.00 0.00 3.85
698 803 3.641437 TTTGCGATTTTTGGAGTGGAG 57.359 42.857 0.00 0.00 0.00 3.86
704 809 3.485877 CGATTTTTGGAGTGGAGAATCGC 60.486 47.826 0.00 0.00 39.24 4.58
720 825 1.966451 CGCAACTGTGTTCCTCCCC 60.966 63.158 0.00 0.00 0.00 4.81
721 826 1.456287 GCAACTGTGTTCCTCCCCT 59.544 57.895 0.00 0.00 0.00 4.79
733 838 3.997400 CTCCCCTCGTCCTCGCAGA 62.997 68.421 0.00 0.00 36.96 4.26
775 884 3.842869 GATACCTCATCGGCCCATC 57.157 57.895 0.00 0.00 35.61 3.51
776 885 0.108615 GATACCTCATCGGCCCATCG 60.109 60.000 0.00 0.00 35.61 3.84
777 886 2.172483 ATACCTCATCGGCCCATCGC 62.172 60.000 0.00 0.00 35.61 4.58
824 933 4.033251 TCCCCGACCCCCATTCCT 62.033 66.667 0.00 0.00 0.00 3.36
830 939 1.906105 CGACCCCCATTCCTTTCCGA 61.906 60.000 0.00 0.00 0.00 4.55
834 943 1.688811 CCCATTCCTTTCCGACCCA 59.311 57.895 0.00 0.00 0.00 4.51
907 1024 4.828925 GCACCGGCAGGCTCTCTC 62.829 72.222 0.00 0.00 42.76 3.20
908 1025 4.154347 CACCGGCAGGCTCTCTCC 62.154 72.222 0.00 0.00 42.76 3.71
909 1026 4.390556 ACCGGCAGGCTCTCTCCT 62.391 66.667 0.00 0.00 42.76 3.69
910 1027 3.535962 CCGGCAGGCTCTCTCCTC 61.536 72.222 0.00 0.00 33.25 3.71
911 1028 3.898509 CGGCAGGCTCTCTCCTCG 61.899 72.222 0.00 0.00 33.25 4.63
912 1029 3.535962 GGCAGGCTCTCTCCTCGG 61.536 72.222 0.00 0.00 33.25 4.63
913 1030 4.219999 GCAGGCTCTCTCCTCGGC 62.220 72.222 0.00 0.00 33.25 5.54
914 1031 3.898509 CAGGCTCTCTCCTCGGCG 61.899 72.222 0.00 0.00 33.25 6.46
917 1034 4.264638 GCTCTCTCCTCGGCGCTC 62.265 72.222 7.64 0.00 0.00 5.03
918 1035 3.591835 CTCTCTCCTCGGCGCTCC 61.592 72.222 7.64 0.00 0.00 4.70
1074 1191 0.829990 CTCTTCCTCCCTCCAAGAGC 59.170 60.000 0.00 0.00 37.44 4.09
1087 1204 1.065564 CCAAGAGCCTCCAGGAAAGAG 60.066 57.143 0.00 0.00 37.39 2.85
1107 1224 2.305927 AGAGAGAGGGAGAGATCGATCC 59.694 54.545 21.66 13.02 34.64 3.36
1112 1229 1.080839 GGAGAGATCGATCCTGCGC 60.081 63.158 21.66 12.68 32.51 6.09
1203 1320 1.061570 GGAGTACCGCTACGACACG 59.938 63.158 0.00 0.00 0.00 4.49
1326 1443 1.739196 GTCGGTAACCAACGCTCCC 60.739 63.158 0.00 0.00 0.00 4.30
1329 1446 1.078637 GGTAACCAACGCTCCCCTC 60.079 63.158 0.00 0.00 0.00 4.30
1330 1447 1.078637 GTAACCAACGCTCCCCTCC 60.079 63.158 0.00 0.00 0.00 4.30
1331 1448 1.229400 TAACCAACGCTCCCCTCCT 60.229 57.895 0.00 0.00 0.00 3.69
1332 1449 1.262640 TAACCAACGCTCCCCTCCTC 61.263 60.000 0.00 0.00 0.00 3.71
1333 1450 3.787001 CCAACGCTCCCCTCCTCC 61.787 72.222 0.00 0.00 0.00 4.30
1338 1455 3.773154 GCTCCCCTCCTCCCCTCT 61.773 72.222 0.00 0.00 0.00 3.69
1346 1463 2.015726 TCCTCCCCTCTCCTCCCTC 61.016 68.421 0.00 0.00 0.00 4.30
1372 1489 3.248029 CGCGCAGTGCTTCTCTTT 58.752 55.556 14.33 0.00 43.27 2.52
1373 1490 2.445274 CGCGCAGTGCTTCTCTTTA 58.555 52.632 14.33 0.00 43.27 1.85
1374 1491 1.002366 CGCGCAGTGCTTCTCTTTAT 58.998 50.000 14.33 0.00 43.27 1.40
1375 1492 1.005557 CGCGCAGTGCTTCTCTTTATC 60.006 52.381 14.33 0.00 43.27 1.75
1377 1494 2.675348 GCGCAGTGCTTCTCTTTATCTT 59.325 45.455 14.33 0.00 41.73 2.40
1378 1495 3.242252 GCGCAGTGCTTCTCTTTATCTTC 60.242 47.826 14.33 0.00 41.73 2.87
1379 1496 4.180057 CGCAGTGCTTCTCTTTATCTTCT 58.820 43.478 14.33 0.00 0.00 2.85
1380 1497 4.267452 CGCAGTGCTTCTCTTTATCTTCTC 59.733 45.833 14.33 0.00 0.00 2.87
1415 1535 6.216569 TCTAATCCATTAGATTCTGTCGTGC 58.783 40.000 5.11 0.00 44.34 5.34
1421 1541 2.086054 AGATTCTGTCGTGCCAAGAC 57.914 50.000 3.67 3.67 38.98 3.01
1431 1551 0.946221 GTGCCAAGACCAGTCACTCG 60.946 60.000 0.00 0.00 0.00 4.18
1462 1582 2.354109 TCAGTAACTCAGCGCTTCTG 57.646 50.000 7.50 9.88 44.21 3.02
1480 1600 7.254932 GCGCTTCTGTTAATTATCTCCTGATTT 60.255 37.037 0.00 0.00 34.32 2.17
1481 1601 9.261180 CGCTTCTGTTAATTATCTCCTGATTTA 57.739 33.333 0.00 0.00 34.32 1.40
1625 1745 5.938125 GCCTCTAGTGTTGGATTCTGTTTTA 59.062 40.000 0.00 0.00 0.00 1.52
1652 1772 9.814507 GTTTTCGTTTCTTTTTGGTATTGTTTT 57.185 25.926 0.00 0.00 0.00 2.43
1666 1786 5.473504 GGTATTGTTTTCTTGCCAAGAGAGA 59.526 40.000 7.29 0.00 39.03 3.10
1750 1872 0.232303 GTTCGTTGTCGTCTGCAAGG 59.768 55.000 0.00 0.00 38.33 3.61
1806 1928 3.499918 GGCTATCCGACCAAATTCATCTG 59.500 47.826 0.00 0.00 0.00 2.90
1812 1934 3.485216 CCGACCAAATTCATCTGCGTAAC 60.485 47.826 0.00 0.00 0.00 2.50
1828 1950 1.127951 GTAACACGACATGCTTTCCCG 59.872 52.381 0.00 0.00 0.00 5.14
1941 2063 3.202906 TCAGAACAGGGTTTTTGACTCG 58.797 45.455 0.00 0.00 32.41 4.18
2066 2188 4.642466 TTGTTTGTTTCCCCAGGTTTTT 57.358 36.364 0.00 0.00 0.00 1.94
2098 2220 8.041323 TCCTCTTTGTTTTCATCTACATCTACC 58.959 37.037 0.00 0.00 0.00 3.18
2101 2223 5.925506 TGTTTTCATCTACATCTACCCGA 57.074 39.130 0.00 0.00 0.00 5.14
2103 2225 5.421056 TGTTTTCATCTACATCTACCCGAGT 59.579 40.000 0.00 0.00 0.00 4.18
2104 2226 6.604396 TGTTTTCATCTACATCTACCCGAGTA 59.396 38.462 0.00 0.00 0.00 2.59
2105 2227 6.630444 TTTCATCTACATCTACCCGAGTAC 57.370 41.667 0.00 0.00 0.00 2.73
2107 2229 6.676990 TCATCTACATCTACCCGAGTACTA 57.323 41.667 0.00 0.00 0.00 1.82
2108 2230 6.462500 TCATCTACATCTACCCGAGTACTAC 58.538 44.000 0.00 0.00 0.00 2.73
2109 2231 6.269538 TCATCTACATCTACCCGAGTACTACT 59.730 42.308 0.00 0.00 0.00 2.57
2110 2232 7.452813 TCATCTACATCTACCCGAGTACTACTA 59.547 40.741 0.00 0.00 0.00 1.82
2111 2233 6.987386 TCTACATCTACCCGAGTACTACTAC 58.013 44.000 0.00 0.00 0.00 2.73
2112 2234 5.885449 ACATCTACCCGAGTACTACTACT 57.115 43.478 0.00 0.00 35.77 2.57
2113 2235 6.985653 ACATCTACCCGAGTACTACTACTA 57.014 41.667 0.00 0.00 32.96 1.82
2114 2236 6.991938 ACATCTACCCGAGTACTACTACTAG 58.008 44.000 0.00 0.00 32.96 2.57
2115 2237 6.780031 ACATCTACCCGAGTACTACTACTAGA 59.220 42.308 0.00 0.00 32.96 2.43
2116 2238 6.892658 TCTACCCGAGTACTACTACTAGAG 57.107 45.833 0.00 0.00 32.96 2.43
2124 2246 8.313292 CCGAGTACTACTACTAGAGATATTGGT 58.687 40.741 0.00 0.00 32.96 3.67
2141 2263 8.640651 AGATATTGGTTATTGCAATGCATGTTA 58.359 29.630 22.27 7.62 38.76 2.41
2157 2279 3.211803 TGTTAGCTACGTGCAGTGTAG 57.788 47.619 17.69 17.69 45.94 2.74
2158 2280 2.555325 TGTTAGCTACGTGCAGTGTAGT 59.445 45.455 21.09 13.34 45.94 2.73
2159 2281 3.752747 TGTTAGCTACGTGCAGTGTAGTA 59.247 43.478 21.09 12.63 45.94 1.82
2160 2282 2.915738 AGCTACGTGCAGTGTAGTAC 57.084 50.000 21.09 10.17 45.94 2.73
2161 2283 2.434428 AGCTACGTGCAGTGTAGTACT 58.566 47.619 21.09 0.00 45.94 2.73
2178 2300 2.928801 ACTGTATGTGCCACTTGTCA 57.071 45.000 0.00 0.00 0.00 3.58
2187 2309 2.880890 GTGCCACTTGTCAACAGAAGAT 59.119 45.455 0.00 0.00 0.00 2.40
2244 2366 1.604593 GTGGTGCAGGGTGATGCTT 60.605 57.895 0.00 0.00 46.63 3.91
2332 2454 1.560004 CGCCATCCACATCGATTCCG 61.560 60.000 0.00 0.00 37.07 4.30
2334 2456 1.953559 CCATCCACATCGATTCCGTT 58.046 50.000 0.00 0.00 37.05 4.44
2336 2458 2.549926 CATCCACATCGATTCCGTTGA 58.450 47.619 0.00 0.00 38.48 3.18
2348 2475 8.925700 CATCGATTCCGTTGATATAATCTTGAA 58.074 33.333 0.00 0.00 37.61 2.69
2350 2477 9.489084 TCGATTCCGTTGATATAATCTTGAATT 57.511 29.630 0.00 0.00 37.05 2.17
2381 2512 5.541845 TCTACAACAGTGTCTCATTTGAGG 58.458 41.667 7.68 0.00 42.30 3.86
2389 2520 1.674962 GTCTCATTTGAGGCTGATGGC 59.325 52.381 4.94 0.00 43.13 4.40
2676 2837 6.469782 AAAAATGATGACAGTGAACCACTT 57.530 33.333 0.00 0.00 42.59 3.16
2679 2846 7.581213 AAATGATGACAGTGAACCACTTTTA 57.419 32.000 0.00 0.00 42.59 1.52
2738 2905 3.190327 TCATTGTACCGGTCAAAATGCTG 59.810 43.478 22.68 15.87 0.00 4.41
2779 2946 1.064758 TGTTCCAGACTTGCAGTTGGT 60.065 47.619 7.46 0.00 32.19 3.67
2790 2957 0.524862 GCAGTTGGTTGCAGATCCTG 59.475 55.000 6.30 0.00 43.53 3.86
2792 2959 1.538512 CAGTTGGTTGCAGATCCTGTG 59.461 52.381 6.30 0.00 33.43 3.66
2953 3120 1.221566 CATGGAGTCCATCGTGCCA 59.778 57.895 22.36 0.00 43.15 4.92
3159 3330 0.790814 GTACTCTGAGTTTGGTGCGC 59.209 55.000 16.53 0.00 0.00 6.09
3284 3479 5.957771 TGGACAAATTCTCTATAGCCACT 57.042 39.130 0.00 0.00 0.00 4.00
3302 3497 3.511146 CCACTGGCTTTTGTATGATTGGT 59.489 43.478 0.00 0.00 0.00 3.67
3303 3498 4.487948 CACTGGCTTTTGTATGATTGGTG 58.512 43.478 0.00 0.00 0.00 4.17
3304 3499 3.511146 ACTGGCTTTTGTATGATTGGTGG 59.489 43.478 0.00 0.00 0.00 4.61
3372 3567 8.918202 AGTTACTCATCAAAATGTTACTCCAA 57.082 30.769 0.00 0.00 34.32 3.53
3435 3630 4.698575 TCAACTTTTAAATTTGCGCCCTT 58.301 34.783 4.18 0.00 0.00 3.95
3602 3797 1.529226 ACGAGGCAGAGATATCTCCG 58.471 55.000 25.88 22.63 43.88 4.63
3620 3815 1.665679 CCGTCAACACTGTATGCCATC 59.334 52.381 0.00 0.00 0.00 3.51
3644 3839 2.756400 GTCATGGAGGGTGTGCCA 59.244 61.111 0.00 0.00 38.78 4.92
3709 3904 1.337635 GCTTGCTCTGCTGACTGTACT 60.338 52.381 0.00 0.00 0.00 2.73
3876 4071 3.245229 TGTTGGTGCTGGAATCAAGGTAT 60.245 43.478 0.00 0.00 0.00 2.73
3897 4092 5.695851 ATCAATCAACTGTCAACTGAACC 57.304 39.130 0.00 0.00 0.00 3.62
3899 4094 3.864789 ATCAACTGTCAACTGAACCCT 57.135 42.857 0.00 0.00 0.00 4.34
3900 4095 3.644966 TCAACTGTCAACTGAACCCTT 57.355 42.857 0.00 0.00 0.00 3.95
3901 4096 3.278574 TCAACTGTCAACTGAACCCTTG 58.721 45.455 0.00 0.00 0.00 3.61
3902 4097 3.054728 TCAACTGTCAACTGAACCCTTGA 60.055 43.478 0.00 0.00 0.00 3.02
3903 4098 3.199880 ACTGTCAACTGAACCCTTGAG 57.800 47.619 0.00 0.00 0.00 3.02
3904 4099 2.505819 ACTGTCAACTGAACCCTTGAGT 59.494 45.455 0.00 0.00 0.00 3.41
3905 4100 3.134458 CTGTCAACTGAACCCTTGAGTC 58.866 50.000 0.00 0.00 0.00 3.36
3906 4101 2.771943 TGTCAACTGAACCCTTGAGTCT 59.228 45.455 0.00 0.00 0.00 3.24
3907 4102 3.199946 TGTCAACTGAACCCTTGAGTCTT 59.800 43.478 0.00 0.00 0.00 3.01
3908 4103 3.561725 GTCAACTGAACCCTTGAGTCTTG 59.438 47.826 0.00 0.00 0.00 3.02
3909 4104 3.454447 TCAACTGAACCCTTGAGTCTTGA 59.546 43.478 0.00 0.00 0.00 3.02
3910 4105 3.477210 ACTGAACCCTTGAGTCTTGAC 57.523 47.619 0.00 0.00 0.00 3.18
3911 4106 3.041946 ACTGAACCCTTGAGTCTTGACT 58.958 45.455 2.59 2.59 0.00 3.41
3912 4107 4.223953 ACTGAACCCTTGAGTCTTGACTA 58.776 43.478 3.00 0.00 0.00 2.59
3913 4108 4.039366 ACTGAACCCTTGAGTCTTGACTAC 59.961 45.833 3.00 0.00 0.00 2.73
3914 4109 4.223953 TGAACCCTTGAGTCTTGACTACT 58.776 43.478 3.00 0.00 0.00 2.57
3915 4110 4.281182 TGAACCCTTGAGTCTTGACTACTC 59.719 45.833 3.00 0.00 43.04 2.59
3916 4111 4.120946 ACCCTTGAGTCTTGACTACTCT 57.879 45.455 3.00 0.00 43.13 3.24
3917 4112 4.484912 ACCCTTGAGTCTTGACTACTCTT 58.515 43.478 3.00 0.00 43.13 2.85
3918 4113 4.525100 ACCCTTGAGTCTTGACTACTCTTC 59.475 45.833 3.00 0.00 43.13 2.87
3919 4114 4.524714 CCCTTGAGTCTTGACTACTCTTCA 59.475 45.833 3.00 0.00 43.13 3.02
3920 4115 5.186797 CCCTTGAGTCTTGACTACTCTTCAT 59.813 44.000 3.00 0.00 43.13 2.57
3921 4116 6.098679 CCTTGAGTCTTGACTACTCTTCATG 58.901 44.000 3.00 0.00 43.13 3.07
3922 4117 6.295011 CCTTGAGTCTTGACTACTCTTCATGT 60.295 42.308 3.00 0.00 43.13 3.21
3923 4118 7.094162 CCTTGAGTCTTGACTACTCTTCATGTA 60.094 40.741 3.00 0.00 43.13 2.29
3924 4119 7.147143 TGAGTCTTGACTACTCTTCATGTAC 57.853 40.000 3.00 0.00 43.13 2.90
3925 4120 6.943146 TGAGTCTTGACTACTCTTCATGTACT 59.057 38.462 3.00 0.00 43.13 2.73
3926 4121 7.448777 TGAGTCTTGACTACTCTTCATGTACTT 59.551 37.037 3.00 0.00 43.13 2.24
3927 4122 8.184304 AGTCTTGACTACTCTTCATGTACTTT 57.816 34.615 0.89 0.00 0.00 2.66
3928 4123 9.298250 AGTCTTGACTACTCTTCATGTACTTTA 57.702 33.333 0.89 0.00 0.00 1.85
3976 4171 8.150945 TCTCTGTTATGGAAGCCTAAACATATC 58.849 37.037 0.00 0.00 31.98 1.63
3977 4172 7.801104 TCTGTTATGGAAGCCTAAACATATCA 58.199 34.615 0.00 0.00 31.98 2.15
3978 4173 7.715249 TCTGTTATGGAAGCCTAAACATATCAC 59.285 37.037 0.00 0.00 31.98 3.06
3979 4174 7.342581 TGTTATGGAAGCCTAAACATATCACA 58.657 34.615 0.00 0.00 29.07 3.58
3980 4175 7.831690 TGTTATGGAAGCCTAAACATATCACAA 59.168 33.333 0.00 0.00 29.07 3.33
3981 4176 6.949352 ATGGAAGCCTAAACATATCACAAG 57.051 37.500 0.00 0.00 0.00 3.16
3982 4177 5.815581 TGGAAGCCTAAACATATCACAAGT 58.184 37.500 0.00 0.00 0.00 3.16
3983 4178 6.245408 TGGAAGCCTAAACATATCACAAGTT 58.755 36.000 0.00 0.00 0.00 2.66
3984 4179 6.150976 TGGAAGCCTAAACATATCACAAGTTG 59.849 38.462 0.00 0.00 0.00 3.16
3985 4180 6.151144 GGAAGCCTAAACATATCACAAGTTGT 59.849 38.462 1.64 1.64 0.00 3.32
3986 4181 7.309194 GGAAGCCTAAACATATCACAAGTTGTT 60.309 37.037 5.57 0.00 33.93 2.83
3987 4182 7.524717 AGCCTAAACATATCACAAGTTGTTT 57.475 32.000 5.57 0.00 42.91 2.83
3988 4183 7.370383 AGCCTAAACATATCACAAGTTGTTTG 58.630 34.615 5.57 4.79 41.13 2.93
3989 4184 7.230510 AGCCTAAACATATCACAAGTTGTTTGA 59.769 33.333 5.57 1.91 41.13 2.69
4046 4241 0.991920 ACCATCTGGGGAACAACGAT 59.008 50.000 0.54 0.00 42.91 3.73
4064 4259 2.847327 ATGGGATGAACCTATCTGCG 57.153 50.000 0.00 0.00 34.73 5.18
4154 4349 2.441532 CTCTACGAGCCCGGGGAA 60.442 66.667 25.28 0.00 40.78 3.97
4189 4384 1.200252 CGTCGTGATCAAGGTCTGTCT 59.800 52.381 8.84 0.00 0.00 3.41
4190 4385 2.351835 CGTCGTGATCAAGGTCTGTCTT 60.352 50.000 8.84 0.00 0.00 3.01
4200 4395 4.021632 TCAAGGTCTGTCTTGATCTGTCTG 60.022 45.833 10.43 0.00 45.53 3.51
4220 4415 2.631062 TGTCACCTTCTACGGACACATT 59.369 45.455 0.00 0.00 35.51 2.71
4239 4434 2.663826 TCACTGTTGGTGCAAAAACC 57.336 45.000 9.59 0.00 44.98 3.27
4342 4537 0.034616 CCTCGGAGATCTTCATGGGC 59.965 60.000 6.58 0.00 33.89 5.36
4381 4576 1.003355 CCACAACACCTGCGAGGAT 60.003 57.895 8.91 0.00 37.67 3.24
4479 4674 2.024751 AGGGAGAGGTAAGAGTCTGACC 60.025 54.545 18.23 18.23 0.00 4.02
4507 4702 3.057245 TGTTGCTAGTCTACTCTGCAGTG 60.057 47.826 14.67 14.35 37.07 3.66
4537 4732 0.827507 TTGGGAGCCAAACTGAAGCC 60.828 55.000 0.00 0.00 40.92 4.35
4538 4733 1.228552 GGGAGCCAAACTGAAGCCA 60.229 57.895 0.00 0.00 0.00 4.75
4541 4736 1.615384 GGAGCCAAACTGAAGCCATCT 60.615 52.381 0.00 0.00 0.00 2.90
4544 4739 3.758554 GAGCCAAACTGAAGCCATCTTTA 59.241 43.478 0.00 0.00 31.48 1.85
4639 4834 2.035449 GGCACCCCTTGTAAGAAACAAC 59.965 50.000 0.00 0.00 43.22 3.32
4641 4836 3.243401 GCACCCCTTGTAAGAAACAACTG 60.243 47.826 0.00 0.00 43.22 3.16
4642 4837 2.956333 ACCCCTTGTAAGAAACAACTGC 59.044 45.455 0.00 0.00 43.22 4.40
4650 4845 1.583054 AGAAACAACTGCCGACTGTC 58.417 50.000 0.00 0.00 0.00 3.51
4652 4847 2.364324 AGAAACAACTGCCGACTGTCTA 59.636 45.455 6.21 0.00 0.00 2.59
4657 4852 1.169577 ACTGCCGACTGTCTACTCTG 58.830 55.000 6.21 0.00 0.00 3.35
4659 4854 2.020720 CTGCCGACTGTCTACTCTGAT 58.979 52.381 6.21 0.00 0.00 2.90
4667 4862 6.017770 CCGACTGTCTACTCTGATTAACCTAG 60.018 46.154 6.21 0.00 0.00 3.02
4669 4864 7.280428 CGACTGTCTACTCTGATTAACCTAGAA 59.720 40.741 6.21 0.00 0.00 2.10
4671 4866 8.741841 ACTGTCTACTCTGATTAACCTAGAAAC 58.258 37.037 0.00 0.00 0.00 2.78
4844 5040 1.895798 TGGAGTACAAGTGAGGAGCAG 59.104 52.381 0.00 0.00 0.00 4.24
4964 5160 3.782889 ATTATTTGGCGGCTTGTCTTC 57.217 42.857 11.43 0.00 0.00 2.87
4965 5161 1.083489 TATTTGGCGGCTTGTCTTCG 58.917 50.000 11.43 0.00 0.00 3.79
4983 5179 2.500229 TCGGTTTCCTTTGCGATTCTT 58.500 42.857 0.00 0.00 0.00 2.52
4984 5180 2.882137 TCGGTTTCCTTTGCGATTCTTT 59.118 40.909 0.00 0.00 0.00 2.52
4985 5181 3.058501 TCGGTTTCCTTTGCGATTCTTTC 60.059 43.478 0.00 0.00 0.00 2.62
4988 5184 5.289595 GGTTTCCTTTGCGATTCTTTCTTT 58.710 37.500 0.00 0.00 0.00 2.52
4991 5187 3.506067 TCCTTTGCGATTCTTTCTTTCCC 59.494 43.478 0.00 0.00 0.00 3.97
4994 5190 2.436417 TGCGATTCTTTCTTTCCCTGG 58.564 47.619 0.00 0.00 0.00 4.45
5009 5205 2.645797 TCCCTGGTTAAGTTTACCCTGG 59.354 50.000 8.53 10.07 34.66 4.45
5010 5206 2.377531 CCCTGGTTAAGTTTACCCTGGT 59.622 50.000 8.53 0.00 34.66 4.00
5013 5209 3.818773 CTGGTTAAGTTTACCCTGGTGTG 59.181 47.826 8.53 0.00 34.66 3.82
5058 5254 0.107945 ATTTCGGCTCTCTGTCTGGC 60.108 55.000 0.00 0.00 0.00 4.85
5075 5271 1.605058 GGCCTCTGCGACTTGGTAGA 61.605 60.000 0.00 0.00 38.85 2.59
5148 5344 2.468915 AGCTAAGTTAGTCCACTCCCC 58.531 52.381 11.51 0.00 0.00 4.81
5149 5345 2.044630 AGCTAAGTTAGTCCACTCCCCT 59.955 50.000 11.51 0.00 0.00 4.79
5167 5363 3.368495 CCCTTGTTCGTGTTTTGTAAGC 58.632 45.455 0.00 0.00 0.00 3.09
5256 5452 3.270027 TGCTTTTATCATGTCACCTCCG 58.730 45.455 0.00 0.00 0.00 4.63
5315 5511 3.896122 TGCAAGCGGAAAATCAAGTAAC 58.104 40.909 0.00 0.00 0.00 2.50
5342 5538 7.558604 AGCATAAAATTACCACAATTCATGCT 58.441 30.769 17.42 17.42 40.10 3.79
5346 5542 4.741321 ATTACCACAATTCATGCTTGGG 57.259 40.909 11.14 7.64 31.08 4.12
5400 5598 8.873215 ACTATAGAACCATCACAAATTAGTCG 57.127 34.615 6.78 0.00 0.00 4.18
5402 5600 3.689649 AGAACCATCACAAATTAGTCGGC 59.310 43.478 0.00 0.00 0.00 5.54
5406 5604 3.440173 CCATCACAAATTAGTCGGCTGTT 59.560 43.478 0.00 0.00 0.00 3.16
5442 5640 4.083565 GTGGTGGAATGGCTAGGTTTTAA 58.916 43.478 0.00 0.00 0.00 1.52
5461 5659 7.821846 GGTTTTAATGCCATTTATGACAAGGAA 59.178 33.333 0.00 0.00 0.00 3.36
5470 5668 0.259938 ATGACAAGGAAGGCCCATCC 59.740 55.000 15.88 15.88 37.41 3.51
5475 5673 1.497309 AAGGAAGGCCCATCCGTCAA 61.497 55.000 17.23 0.00 43.98 3.18
5476 5674 1.452108 GGAAGGCCCATCCGTCAAG 60.452 63.158 9.31 0.00 43.98 3.02
5521 5719 2.047179 GCCCGTTCTGACTGGGTC 60.047 66.667 13.36 4.39 39.94 4.46
5522 5720 2.879233 GCCCGTTCTGACTGGGTCA 61.879 63.158 13.36 0.43 40.50 4.02
5523 5721 1.752198 CCCGTTCTGACTGGGTCAA 59.248 57.895 5.42 0.00 42.26 3.18
5524 5722 0.107831 CCCGTTCTGACTGGGTCAAA 59.892 55.000 5.42 0.00 42.26 2.69
5526 5724 2.504367 CCGTTCTGACTGGGTCAAAAT 58.496 47.619 2.04 0.00 42.26 1.82
5527 5725 3.558321 CCCGTTCTGACTGGGTCAAAATA 60.558 47.826 5.42 0.00 42.26 1.40
5566 5786 5.180492 ACTCTCACTAAGTTCTTCTCACTCG 59.820 44.000 0.00 0.00 0.00 4.18
5567 5787 4.456222 TCTCACTAAGTTCTTCTCACTCGG 59.544 45.833 0.00 0.00 0.00 4.63
5580 5800 1.378778 ACTCGGTTCTCCTCTCCCG 60.379 63.158 0.00 0.00 41.75 5.14
5598 5818 1.354040 CGTGCTCTCTCAATGACACC 58.646 55.000 0.00 0.00 0.00 4.16
5620 5840 1.194781 CCACCCCACTGCTAGTCACT 61.195 60.000 0.00 0.00 0.00 3.41
5621 5841 0.036952 CACCCCACTGCTAGTCACTG 60.037 60.000 0.00 0.00 0.00 3.66
5639 5859 3.443045 GTGCCCATGCCTTCGTGG 61.443 66.667 0.00 0.00 46.66 4.94
5657 5902 4.722535 AAGGCGGGGAGGAGAGCA 62.723 66.667 0.00 0.00 0.00 4.26
5665 5910 1.662438 GGGAGGAGAGCACTGACGAG 61.662 65.000 0.00 0.00 0.00 4.18
5670 5915 0.814457 GAGAGCACTGACGAGGACAT 59.186 55.000 0.00 0.00 0.00 3.06
5673 5918 0.969149 AGCACTGACGAGGACATCAA 59.031 50.000 0.00 0.00 0.00 2.57
5680 5925 0.984230 ACGAGGACATCAACATGGGT 59.016 50.000 0.00 0.00 33.82 4.51
5738 5983 9.138596 GTATTCTCTTCTCTGATTAGTTAGGGT 57.861 37.037 0.00 0.00 0.00 4.34
5750 5995 7.808218 TGATTAGTTAGGGTTAGGGTTATTGG 58.192 38.462 0.00 0.00 0.00 3.16
5762 6007 5.485209 AGGGTTATTGGATTCGAGGATAC 57.515 43.478 0.00 0.00 0.00 2.24
5791 6038 8.071122 TGTTTTCAATTTGTTTCATCGATTCC 57.929 30.769 0.00 0.00 0.00 3.01
5809 6056 8.473358 TCGATTCCTTGATCTTGGTACTAATA 57.527 34.615 0.00 0.00 0.00 0.98
5823 6070 7.403837 TGGTACTAATAGATGTAGGAGACCT 57.596 40.000 0.00 0.00 37.71 3.85
5830 6077 1.043673 ATGTAGGAGACCTCGGGCAC 61.044 60.000 0.00 0.00 34.61 5.01
5850 6097 4.676196 GCACCATTTCTGAGCCATTTACTG 60.676 45.833 0.00 0.00 0.00 2.74
5899 6146 1.270550 GCATGTTGCACAAGCTTAGGT 59.729 47.619 0.00 0.00 44.26 3.08
5904 6151 1.795768 TGCACAAGCTTAGGTCGAAG 58.204 50.000 0.00 0.00 42.74 3.79
5917 6164 1.527311 GGTCGAAGAAGTGTGTTGCTC 59.473 52.381 0.00 0.00 39.69 4.26
5924 6171 5.640732 GAAGAAGTGTGTTGCTCTTGAAAA 58.359 37.500 0.00 0.00 31.79 2.29
5976 6225 7.498570 AGAGCACTCTCCTCAATTTTCATTATC 59.501 37.037 0.00 0.00 40.22 1.75
6001 6250 8.356657 TCAGAAACCACATGTATTTTTACAAGG 58.643 33.333 0.00 0.00 33.21 3.61
6002 6251 8.356657 CAGAAACCACATGTATTTTTACAAGGA 58.643 33.333 0.00 0.00 33.21 3.36
6003 6252 8.357402 AGAAACCACATGTATTTTTACAAGGAC 58.643 33.333 0.00 0.00 33.21 3.85
6004 6253 7.833285 AACCACATGTATTTTTACAAGGACT 57.167 32.000 0.00 0.00 33.21 3.85
6005 6254 8.927675 AACCACATGTATTTTTACAAGGACTA 57.072 30.769 0.00 0.00 33.21 2.59
6006 6255 8.927675 ACCACATGTATTTTTACAAGGACTAA 57.072 30.769 0.00 0.00 33.21 2.24
6007 6256 9.357161 ACCACATGTATTTTTACAAGGACTAAA 57.643 29.630 0.00 0.00 33.21 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
279 281 0.466922 GTCCTTCCCCATGGAGCATG 60.467 60.000 15.22 0.00 43.07 4.06
301 303 3.860125 ACACACACGCACACGCAC 61.860 61.111 0.00 0.00 45.53 5.34
302 304 3.858989 CACACACACGCACACGCA 61.859 61.111 0.00 0.00 45.53 5.24
303 305 3.491508 CTCACACACACGCACACGC 62.492 63.158 0.00 0.00 45.53 5.34
305 307 3.014036 CCTCACACACACGCACAC 58.986 61.111 0.00 0.00 0.00 3.82
306 308 2.894879 GCCTCACACACACGCACA 60.895 61.111 0.00 0.00 0.00 4.57
307 309 4.000557 CGCCTCACACACACGCAC 62.001 66.667 0.00 0.00 0.00 5.34
308 310 4.522689 ACGCCTCACACACACGCA 62.523 61.111 0.00 0.00 0.00 5.24
309 311 2.695712 GAAACGCCTCACACACACGC 62.696 60.000 0.00 0.00 0.00 5.34
310 312 1.275657 GAAACGCCTCACACACACG 59.724 57.895 0.00 0.00 0.00 4.49
411 446 3.791586 GTGCCCCAGCTCCTCCTC 61.792 72.222 0.00 0.00 40.80 3.71
534 584 2.103537 TTCCGAAATTCCGAGGAACC 57.896 50.000 6.73 0.00 37.79 3.62
550 600 6.655062 CACGCGAGATAGATAGATAGATTCC 58.345 44.000 15.93 0.00 0.00 3.01
556 606 2.943690 GGGCACGCGAGATAGATAGATA 59.056 50.000 15.93 0.00 0.00 1.98
557 607 1.746220 GGGCACGCGAGATAGATAGAT 59.254 52.381 15.93 0.00 0.00 1.98
617 679 4.624364 TCTGCCGGTGCCACAGTG 62.624 66.667 1.90 0.00 36.33 3.66
698 803 1.464997 GGAGGAACACAGTTGCGATTC 59.535 52.381 0.00 0.00 0.00 2.52
704 809 0.320771 CGAGGGGAGGAACACAGTTG 60.321 60.000 0.00 0.00 0.00 3.16
720 825 1.989165 CTCTTTTTCTGCGAGGACGAG 59.011 52.381 0.00 0.00 42.66 4.18
721 826 1.611977 TCTCTTTTTCTGCGAGGACGA 59.388 47.619 0.00 0.00 42.66 4.20
733 838 4.200092 ACCGCACTTCTTTCTCTCTTTTT 58.800 39.130 0.00 0.00 0.00 1.94
777 886 4.493747 GGAGGAAGGGACGCGACG 62.494 72.222 15.93 0.00 0.00 5.12
778 887 3.066233 GAGGAGGAAGGGACGCGAC 62.066 68.421 15.93 6.56 0.00 5.19
824 933 4.011517 GGAGGCGTGGGTCGGAAA 62.012 66.667 0.00 0.00 40.26 3.13
894 1011 3.898509 CGAGGAGAGAGCCTGCCG 61.899 72.222 0.00 0.00 38.73 5.69
896 1013 4.219999 GCCGAGGAGAGAGCCTGC 62.220 72.222 0.00 0.00 38.73 4.85
897 1014 3.898509 CGCCGAGGAGAGAGCCTG 61.899 72.222 0.00 0.00 38.73 4.85
900 1017 4.264638 GAGCGCCGAGGAGAGAGC 62.265 72.222 2.29 0.00 0.00 4.09
901 1018 3.591835 GGAGCGCCGAGGAGAGAG 61.592 72.222 2.29 0.00 0.00 3.20
959 1076 2.372837 TGGGGGATTTATAGCGGGTTAC 59.627 50.000 0.00 0.00 0.00 2.50
993 1110 2.034879 GTGTGATCTGCGGTGGGTG 61.035 63.158 0.00 0.00 0.00 4.61
1074 1191 2.387757 CCTCTCTCTCTTTCCTGGAGG 58.612 57.143 0.00 0.00 33.98 4.30
1087 1204 2.305927 AGGATCGATCTCTCCCTCTCTC 59.694 54.545 23.96 3.79 31.49 3.20
1107 1224 1.136147 GAACATCTTGGCAGCGCAG 59.864 57.895 11.47 1.31 0.00 5.18
1112 1229 2.864946 CTCTCGATGAACATCTTGGCAG 59.135 50.000 12.05 2.33 35.72 4.85
1203 1320 4.357947 TCGTGCACCAGCTCCGTC 62.358 66.667 12.15 0.00 42.74 4.79
1326 1443 2.612251 GGAGGAGAGGGGAGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
1329 1446 2.612251 GAGGGAGGAGAGGGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
1330 1447 1.673928 ATGGAGGGAGGAGAGGGGAG 61.674 65.000 0.00 0.00 0.00 4.30
1331 1448 0.330532 TATGGAGGGAGGAGAGGGGA 60.331 60.000 0.00 0.00 0.00 4.81
1332 1449 0.178918 GTATGGAGGGAGGAGAGGGG 60.179 65.000 0.00 0.00 0.00 4.79
1333 1450 0.540830 CGTATGGAGGGAGGAGAGGG 60.541 65.000 0.00 0.00 0.00 4.30
1338 1455 3.224324 GCGCGTATGGAGGGAGGA 61.224 66.667 8.43 0.00 0.00 3.71
1392 1512 5.406780 GGCACGACAGAATCTAATGGATTAG 59.593 44.000 0.00 0.58 43.90 1.73
1399 1519 4.184629 GTCTTGGCACGACAGAATCTAAT 58.815 43.478 18.13 0.00 0.00 1.73
1415 1535 2.050269 ACCGAGTGACTGGTCTTGG 58.950 57.895 0.00 0.00 40.16 3.61
1421 1541 4.778415 CCGCGACCGAGTGACTGG 62.778 72.222 8.23 0.00 36.29 4.00
1431 1551 0.509929 GTTACTGAAACACCGCGACC 59.490 55.000 8.23 0.00 38.05 4.79
1486 1606 8.483307 TGACAGGACCGAATTAAATTAACTAC 57.517 34.615 0.00 0.00 0.00 2.73
1563 1683 2.439156 CCTAGCCCCACAAGCAGC 60.439 66.667 0.00 0.00 0.00 5.25
1564 1684 1.078143 GACCTAGCCCCACAAGCAG 60.078 63.158 0.00 0.00 0.00 4.24
1565 1685 2.954684 CGACCTAGCCCCACAAGCA 61.955 63.158 0.00 0.00 0.00 3.91
1566 1686 2.125106 CGACCTAGCCCCACAAGC 60.125 66.667 0.00 0.00 0.00 4.01
1625 1745 8.766000 AACAATACCAAAAAGAAACGAAAACT 57.234 26.923 0.00 0.00 0.00 2.66
1652 1772 4.897509 TGATTCTTCTCTCTTGGCAAGA 57.102 40.909 27.01 27.01 35.87 3.02
1666 1786 2.357569 GGCTCCTGGTCCATTGATTCTT 60.358 50.000 0.00 0.00 0.00 2.52
1750 1872 2.793278 AATCCAAAACCGAACAGCAC 57.207 45.000 0.00 0.00 0.00 4.40
1800 1922 2.258755 CATGTCGTGTTACGCAGATGA 58.741 47.619 0.00 0.00 42.21 2.92
1806 1928 1.463528 GGAAAGCATGTCGTGTTACGC 60.464 52.381 0.00 0.00 42.21 4.42
1812 1934 0.744414 ATCCGGGAAAGCATGTCGTG 60.744 55.000 0.00 0.00 0.00 4.35
1828 1950 4.756502 ACAGGCGAAAAACTAGTAGATCC 58.243 43.478 3.59 0.00 0.00 3.36
1941 2063 6.525629 ACATCTTATTATGCTGTACCAGGTC 58.474 40.000 0.00 0.00 31.21 3.85
2066 2188 9.130661 TGTAGATGAAAACAAAGAGGAAATCAA 57.869 29.630 0.00 0.00 0.00 2.57
2098 2220 8.313292 ACCAATATCTCTAGTAGTAGTACTCGG 58.687 40.741 13.60 8.52 40.23 4.63
2109 2231 9.219603 GCATTGCAATAACCAATATCTCTAGTA 57.780 33.333 12.53 0.00 32.03 1.82
2110 2232 7.720957 TGCATTGCAATAACCAATATCTCTAGT 59.279 33.333 12.53 0.00 34.76 2.57
2111 2233 8.102800 TGCATTGCAATAACCAATATCTCTAG 57.897 34.615 12.53 0.00 34.76 2.43
2112 2234 8.517056 CATGCATTGCAATAACCAATATCTCTA 58.483 33.333 16.46 0.00 43.62 2.43
2113 2235 6.964807 TGCATTGCAATAACCAATATCTCT 57.035 33.333 12.53 0.00 34.76 3.10
2114 2236 7.149973 ACATGCATTGCAATAACCAATATCTC 58.850 34.615 16.46 0.00 43.62 2.75
2115 2237 7.058023 ACATGCATTGCAATAACCAATATCT 57.942 32.000 16.46 0.00 43.62 1.98
2116 2238 7.718272 AACATGCATTGCAATAACCAATATC 57.282 32.000 16.46 0.00 43.62 1.63
2124 2246 5.065859 ACGTAGCTAACATGCATTGCAATAA 59.934 36.000 16.46 3.91 43.62 1.40
2141 2263 2.434428 AGTACTACACTGCACGTAGCT 58.566 47.619 15.40 0.00 45.94 3.32
2157 2279 3.659786 TGACAAGTGGCACATACAGTAC 58.340 45.455 21.41 3.41 44.52 2.73
2158 2280 4.062293 GTTGACAAGTGGCACATACAGTA 58.938 43.478 21.41 0.00 44.52 2.74
2159 2281 2.878406 GTTGACAAGTGGCACATACAGT 59.122 45.455 21.41 10.06 44.52 3.55
2160 2282 2.877786 TGTTGACAAGTGGCACATACAG 59.122 45.455 21.41 6.82 44.52 2.74
2161 2283 2.877786 CTGTTGACAAGTGGCACATACA 59.122 45.455 21.41 8.14 44.52 2.29
2167 2289 2.708216 TCTTCTGTTGACAAGTGGCA 57.292 45.000 0.00 0.00 0.00 4.92
2178 2300 6.435277 ACCACAAATAATCAGCATCTTCTGTT 59.565 34.615 0.00 0.00 35.63 3.16
2187 2309 7.716799 AAAGGATTACCACAAATAATCAGCA 57.283 32.000 6.98 0.00 39.72 4.41
2357 2484 5.991606 CCTCAAATGAGACACTGTTGTAGAA 59.008 40.000 11.94 0.00 44.74 2.10
2364 2491 2.369860 TCAGCCTCAAATGAGACACTGT 59.630 45.455 11.94 0.00 44.74 3.55
2365 2492 3.049708 TCAGCCTCAAATGAGACACTG 57.950 47.619 11.94 14.34 44.74 3.66
2381 2512 4.558538 ATTGATTAAACTCGCCATCAGC 57.441 40.909 0.00 0.00 38.52 4.26
2389 2520 6.998673 AGATCCCCCTAAATTGATTAAACTCG 59.001 38.462 0.00 0.00 0.00 4.18
2662 2823 9.485206 TCTTTACTATAAAAGTGGTTCACTGTC 57.515 33.333 1.01 0.00 44.62 3.51
2738 2905 2.770164 ATACAGTCAACAGAGCCCAC 57.230 50.000 0.00 0.00 0.00 4.61
2779 2946 0.671472 CGTCAGCACAGGATCTGCAA 60.671 55.000 8.02 0.00 37.08 4.08
2790 2957 2.683968 TCATTCTAACACCGTCAGCAC 58.316 47.619 0.00 0.00 0.00 4.40
2792 2959 4.946784 AAATCATTCTAACACCGTCAGC 57.053 40.909 0.00 0.00 0.00 4.26
2953 3120 1.122019 GGTCATAGATGCCGGGGAGT 61.122 60.000 2.18 0.00 0.00 3.85
3137 3308 2.029828 CGCACCAAACTCAGAGTACTCT 60.030 50.000 20.00 20.00 41.37 3.24
3138 3309 2.329379 CGCACCAAACTCAGAGTACTC 58.671 52.381 15.41 15.41 0.00 2.59
3139 3310 1.605712 GCGCACCAAACTCAGAGTACT 60.606 52.381 2.64 0.00 0.00 2.73
3140 3311 0.790814 GCGCACCAAACTCAGAGTAC 59.209 55.000 2.64 0.00 0.00 2.73
3141 3312 0.666274 CGCGCACCAAACTCAGAGTA 60.666 55.000 8.75 0.00 0.00 2.59
3142 3313 1.956170 CGCGCACCAAACTCAGAGT 60.956 57.895 8.75 0.00 0.00 3.24
3159 3330 4.512571 TCCATATTCAATCATGTGTGCTCG 59.487 41.667 0.00 0.00 0.00 5.03
3284 3479 3.509575 GTCCACCAATCATACAAAAGCCA 59.490 43.478 0.00 0.00 0.00 4.75
3302 3497 1.052124 ACGACCCTTTGTGGAGTCCA 61.052 55.000 8.12 8.12 38.35 4.02
3303 3498 0.108019 AACGACCCTTTGTGGAGTCC 59.892 55.000 0.73 0.73 38.35 3.85
3304 3499 1.070289 AGAACGACCCTTTGTGGAGTC 59.930 52.381 0.00 0.00 38.35 3.36
3312 3507 8.631480 ATTTAATTTCAGTAGAACGACCCTTT 57.369 30.769 0.00 0.00 32.39 3.11
3357 3552 7.630513 AACAAGGACTGTTGGAGTAACATTTTG 60.631 37.037 0.00 0.00 46.80 2.44
3372 3567 4.395959 TGTCGAAACTAACAAGGACTGT 57.604 40.909 0.00 0.00 41.27 3.55
3390 3585 5.125100 TGAAGTTTTCAGCATGGAATGTC 57.875 39.130 0.00 0.00 39.91 3.06
3435 3630 9.959721 GAACTCCCTATTTCATTAAGCCATATA 57.040 33.333 0.00 0.00 0.00 0.86
3602 3797 1.062587 GCGATGGCATACAGTGTTGAC 59.937 52.381 0.00 2.59 39.62 3.18
3644 3839 0.181350 GAGGGCTCCCGTTGATGAAT 59.819 55.000 0.00 0.00 41.95 2.57
3709 3904 6.610020 AGCCTGTAACCAGACACTATATACAA 59.390 38.462 0.00 0.00 41.50 2.41
3739 3934 2.887152 AGCCCTGCACAAAAGAAACTAG 59.113 45.455 0.00 0.00 0.00 2.57
3876 4071 3.882888 GGGTTCAGTTGACAGTTGATTGA 59.117 43.478 0.00 0.00 0.00 2.57
3897 4092 5.713792 TGAAGAGTAGTCAAGACTCAAGG 57.286 43.478 5.91 0.00 44.86 3.61
3899 4094 6.656632 ACATGAAGAGTAGTCAAGACTCAA 57.343 37.500 5.91 0.00 44.86 3.02
3900 4095 6.943146 AGTACATGAAGAGTAGTCAAGACTCA 59.057 38.462 5.91 0.00 44.86 3.41
3901 4096 7.385778 AGTACATGAAGAGTAGTCAAGACTC 57.614 40.000 5.91 0.00 43.12 3.36
3902 4097 7.768807 AAGTACATGAAGAGTAGTCAAGACT 57.231 36.000 7.96 7.96 45.02 3.24
3959 4154 5.815581 ACTTGTGATATGTTTAGGCTTCCA 58.184 37.500 0.00 0.00 0.00 3.53
3960 4155 6.151144 ACAACTTGTGATATGTTTAGGCTTCC 59.849 38.462 0.00 0.00 0.00 3.46
3976 4171 7.329226 ACAAGAACAGAAATCAAACAACTTGTG 59.671 33.333 0.00 0.00 41.21 3.33
3977 4172 7.378181 ACAAGAACAGAAATCAAACAACTTGT 58.622 30.769 0.00 0.00 39.10 3.16
3978 4173 7.816945 ACAAGAACAGAAATCAAACAACTTG 57.183 32.000 0.00 0.00 37.56 3.16
3979 4174 7.702348 GCTACAAGAACAGAAATCAAACAACTT 59.298 33.333 0.00 0.00 0.00 2.66
3980 4175 7.196331 GCTACAAGAACAGAAATCAAACAACT 58.804 34.615 0.00 0.00 0.00 3.16
3981 4176 6.417930 GGCTACAAGAACAGAAATCAAACAAC 59.582 38.462 0.00 0.00 0.00 3.32
3982 4177 6.460953 GGGCTACAAGAACAGAAATCAAACAA 60.461 38.462 0.00 0.00 0.00 2.83
3983 4178 5.009610 GGGCTACAAGAACAGAAATCAAACA 59.990 40.000 0.00 0.00 0.00 2.83
3984 4179 5.009610 TGGGCTACAAGAACAGAAATCAAAC 59.990 40.000 0.00 0.00 0.00 2.93
3985 4180 5.009610 GTGGGCTACAAGAACAGAAATCAAA 59.990 40.000 0.00 0.00 0.00 2.69
3986 4181 4.518970 GTGGGCTACAAGAACAGAAATCAA 59.481 41.667 0.00 0.00 0.00 2.57
3987 4182 4.072131 GTGGGCTACAAGAACAGAAATCA 58.928 43.478 0.00 0.00 0.00 2.57
3988 4183 3.440522 GGTGGGCTACAAGAACAGAAATC 59.559 47.826 2.66 0.00 0.00 2.17
3989 4184 3.074538 AGGTGGGCTACAAGAACAGAAAT 59.925 43.478 2.66 0.00 0.00 2.17
4046 4241 0.106708 GCGCAGATAGGTTCATCCCA 59.893 55.000 0.30 0.00 36.75 4.37
4064 4259 2.750888 GGAACGGAATGTCTGCGGC 61.751 63.158 0.00 0.00 44.35 6.53
4100 4295 1.626321 ACCATGTCATCCACCACGTTA 59.374 47.619 0.00 0.00 0.00 3.18
4154 4349 1.585006 GACGACGTGGTCAGGATGT 59.415 57.895 23.70 0.00 36.91 3.06
4189 4384 4.082733 CGTAGAAGGTGACAGACAGATCAA 60.083 45.833 0.00 0.00 0.00 2.57
4190 4385 3.440522 CGTAGAAGGTGACAGACAGATCA 59.559 47.826 0.00 0.00 0.00 2.92
4200 4395 3.251571 GAATGTGTCCGTAGAAGGTGAC 58.748 50.000 0.00 0.00 0.00 3.67
4239 4434 7.116948 CGGTGAAGCTTCAGTATATAATTCCAG 59.883 40.741 29.13 13.80 37.98 3.86
4342 4537 2.434884 ACGATGGTGCTCTTGCCG 60.435 61.111 0.00 0.00 38.71 5.69
4363 4558 0.606401 AATCCTCGCAGGTGTTGTGG 60.606 55.000 2.68 0.00 37.88 4.17
4479 4674 6.148948 GCAGAGTAGACTAGCAACATATCTG 58.851 44.000 0.00 0.00 34.88 2.90
4507 4702 4.706842 TTGGCTCCCAAAGTATATCTCC 57.293 45.455 0.00 0.00 40.92 3.71
4537 4732 6.263344 CACAGATGCAAGTGGAATAAAGATG 58.737 40.000 8.85 0.00 32.24 2.90
4538 4733 6.446781 CACAGATGCAAGTGGAATAAAGAT 57.553 37.500 8.85 0.00 32.24 2.40
4627 4822 2.869801 CAGTCGGCAGTTGTTTCTTACA 59.130 45.455 0.00 0.00 34.12 2.41
4639 4834 1.454201 TCAGAGTAGACAGTCGGCAG 58.546 55.000 0.00 0.00 0.00 4.85
4641 4836 4.352887 GTTAATCAGAGTAGACAGTCGGC 58.647 47.826 0.00 0.00 0.00 5.54
4642 4837 4.641094 AGGTTAATCAGAGTAGACAGTCGG 59.359 45.833 0.00 0.00 0.00 4.79
4667 4862 8.840867 CGTCAGTTAATCTGCTTTATTTGTTTC 58.159 33.333 0.00 0.00 43.32 2.78
4669 4864 7.803189 CACGTCAGTTAATCTGCTTTATTTGTT 59.197 33.333 0.00 0.00 43.32 2.83
4671 4866 6.249260 GCACGTCAGTTAATCTGCTTTATTTG 59.751 38.462 0.00 0.00 43.32 2.32
4680 4875 2.159841 CCGTTGCACGTCAGTTAATCTG 60.160 50.000 7.68 0.00 40.58 2.90
4681 4876 2.066262 CCGTTGCACGTCAGTTAATCT 58.934 47.619 7.68 0.00 40.58 2.40
4700 4895 4.019231 AGGAACCTGTTAACAGAGGAATCC 60.019 45.833 32.50 26.84 46.59 3.01
4862 5058 1.446099 TACGTACGGTCGCTCTCGT 60.446 57.895 21.06 0.00 42.55 4.18
4964 5160 2.989422 AAGAATCGCAAAGGAAACCG 57.011 45.000 0.00 0.00 0.00 4.44
4965 5161 4.505313 AGAAAGAATCGCAAAGGAAACC 57.495 40.909 0.00 0.00 0.00 3.27
4983 5179 5.134850 AGGGTAAACTTAACCAGGGAAAGAA 59.865 40.000 6.33 0.00 43.14 2.52
4984 5180 4.666431 AGGGTAAACTTAACCAGGGAAAGA 59.334 41.667 6.33 0.00 43.14 2.52
4985 5181 4.765339 CAGGGTAAACTTAACCAGGGAAAG 59.235 45.833 6.33 0.00 43.14 2.62
4988 5184 2.645797 CCAGGGTAAACTTAACCAGGGA 59.354 50.000 7.02 0.00 41.93 4.20
4991 5187 3.818773 CACACCAGGGTAAACTTAACCAG 59.181 47.826 6.33 0.00 43.14 4.00
4994 5190 4.514066 CACTCACACCAGGGTAAACTTAAC 59.486 45.833 0.00 0.00 0.00 2.01
5009 5205 1.006832 GGACACACACACACTCACAC 58.993 55.000 0.00 0.00 0.00 3.82
5010 5206 0.901827 AGGACACACACACACTCACA 59.098 50.000 0.00 0.00 0.00 3.58
5013 5209 0.657840 GCAAGGACACACACACACTC 59.342 55.000 0.00 0.00 0.00 3.51
5058 5254 2.428890 AGAATCTACCAAGTCGCAGAGG 59.571 50.000 0.00 0.00 36.95 3.69
5148 5344 7.908193 AATTAGCTTACAAAACACGAACAAG 57.092 32.000 0.00 0.00 0.00 3.16
5149 5345 8.614346 ACTAATTAGCTTACAAAACACGAACAA 58.386 29.630 12.54 0.00 0.00 2.83
5256 5452 4.754667 GCCGTCCCTGAACGACCC 62.755 72.222 0.00 0.00 45.37 4.46
5315 5511 8.971321 GCATGAATTGTGGTAATTTTATGCTAG 58.029 33.333 18.07 0.00 37.43 3.42
5339 5535 0.404040 AGTTTTCCGGATCCCAAGCA 59.596 50.000 4.15 0.00 0.00 3.91
5342 5538 1.986631 TGGTAGTTTTCCGGATCCCAA 59.013 47.619 4.15 0.00 0.00 4.12
5346 5542 4.182339 GAGAAGTGGTAGTTTTCCGGATC 58.818 47.826 4.15 0.00 0.00 3.36
5385 5582 4.685169 AACAGCCGACTAATTTGTGATG 57.315 40.909 0.00 0.00 0.00 3.07
5400 5598 4.546570 CACTAGTGCCTTTTAAAACAGCC 58.453 43.478 10.54 6.98 0.00 4.85
5402 5600 5.507315 CCACCACTAGTGCCTTTTAAAACAG 60.507 44.000 17.86 1.56 45.83 3.16
5406 5604 4.440826 TCCACCACTAGTGCCTTTTAAA 57.559 40.909 17.86 0.00 45.83 1.52
5442 5640 3.385755 GCCTTCCTTGTCATAAATGGCAT 59.614 43.478 0.00 0.00 42.67 4.40
5461 5659 4.115199 GGCTTGACGGATGGGCCT 62.115 66.667 4.53 0.00 39.68 5.19
5470 5668 2.551270 GCTGACGTTGGCTTGACG 59.449 61.111 6.47 7.00 45.46 4.35
5518 5716 0.730840 CGGCTCGGGTTATTTTGACC 59.269 55.000 0.00 0.00 36.41 4.02
5519 5717 0.730840 CCGGCTCGGGTTATTTTGAC 59.269 55.000 5.79 0.00 44.15 3.18
5566 5786 1.950973 GAGCACGGGAGAGGAGAACC 61.951 65.000 0.00 0.00 0.00 3.62
5567 5787 0.968393 AGAGCACGGGAGAGGAGAAC 60.968 60.000 0.00 0.00 0.00 3.01
5580 5800 1.067565 TCGGTGTCATTGAGAGAGCAC 60.068 52.381 0.00 0.00 37.85 4.40
5598 5818 2.227089 GACTAGCAGTGGGGTGGTCG 62.227 65.000 0.00 0.00 43.92 4.79
5639 5859 3.855853 GCTCTCCTCCCCGCCTTC 61.856 72.222 0.00 0.00 0.00 3.46
5643 5863 4.154347 CAGTGCTCTCCTCCCCGC 62.154 72.222 0.00 0.00 0.00 6.13
5648 5893 0.678366 TCCTCGTCAGTGCTCTCCTC 60.678 60.000 0.00 0.00 0.00 3.71
5657 5902 2.354103 CCATGTTGATGTCCTCGTCAGT 60.354 50.000 0.00 0.00 40.16 3.41
5665 5910 1.086696 CGTCACCCATGTTGATGTCC 58.913 55.000 5.86 0.00 0.00 4.02
5670 5915 1.414550 TGAAGTCGTCACCCATGTTGA 59.585 47.619 0.00 0.00 0.00 3.18
5673 5918 1.339055 CCATGAAGTCGTCACCCATGT 60.339 52.381 0.00 0.00 39.72 3.21
5680 5925 1.816224 TCGATGTCCATGAAGTCGTCA 59.184 47.619 0.00 0.00 41.67 4.35
5725 5970 7.628505 TCCAATAACCCTAACCCTAACTAATCA 59.371 37.037 0.00 0.00 0.00 2.57
5726 5971 8.037723 TCCAATAACCCTAACCCTAACTAATC 57.962 38.462 0.00 0.00 0.00 1.75
5738 5983 6.785963 AGTATCCTCGAATCCAATAACCCTAA 59.214 38.462 0.00 0.00 0.00 2.69
5750 5995 9.626045 AATTGAAAACAAAAGTATCCTCGAATC 57.374 29.630 0.00 0.00 0.00 2.52
5762 6007 9.919348 ATCGATGAAACAAATTGAAAACAAAAG 57.081 25.926 0.00 0.00 0.00 2.27
5767 6012 8.298030 AGGAATCGATGAAACAAATTGAAAAC 57.702 30.769 0.00 0.00 0.00 2.43
5768 6013 8.763356 CAAGGAATCGATGAAACAAATTGAAAA 58.237 29.630 0.00 0.00 0.00 2.29
5773 6018 8.059798 AGATCAAGGAATCGATGAAACAAATT 57.940 30.769 0.00 0.00 0.00 1.82
5774 6019 7.636150 AGATCAAGGAATCGATGAAACAAAT 57.364 32.000 0.00 0.00 0.00 2.32
5778 6025 5.355350 ACCAAGATCAAGGAATCGATGAAAC 59.645 40.000 10.11 0.00 0.00 2.78
5781 6028 4.760530 ACCAAGATCAAGGAATCGATGA 57.239 40.909 10.11 0.00 0.00 2.92
5784 6031 6.785337 TTAGTACCAAGATCAAGGAATCGA 57.215 37.500 10.11 0.00 0.00 3.59
5809 6056 0.468400 GCCCGAGGTCTCCTACATCT 60.468 60.000 0.00 0.00 36.74 2.90
5812 6059 1.681327 GTGCCCGAGGTCTCCTACA 60.681 63.158 0.00 0.00 31.76 2.74
5823 6070 1.377202 GCTCAGAAATGGTGCCCGA 60.377 57.895 0.00 0.00 0.00 5.14
5830 6077 3.488047 CGCAGTAAATGGCTCAGAAATGG 60.488 47.826 0.00 0.00 0.00 3.16
5899 6146 2.866156 CAAGAGCAACACACTTCTTCGA 59.134 45.455 0.00 0.00 0.00 3.71
5976 6225 8.356657 TCCTTGTAAAAATACATGTGGTTTCTG 58.643 33.333 9.11 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.