Multiple sequence alignment - TraesCS5D01G284000

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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 TraesCS5D01G284000 chr5D 100.000 5386 0 0 1 5386 384848227 384853612 0.000000e+00 9947
1 TraesCS5D01G284000 chr5A 91.149 5163 274 71 1 5056 485823351 485828437 0.000000e+00 6833
2 TraesCS5D01G284000 chr5A 92.550 349 15 4 5049 5386 485828454 485828802 1.740000e-134 490
3 TraesCS5D01G284000 chr5B 92.887 1195 47 17 1807 2978 462145891 462144712 0.000000e+00 1701
4 TraesCS5D01G284000 chr5B 85.986 1420 81 54 403 1793 462147827 462146497 0.000000e+00 1411
5 TraesCS5D01G284000 chr5B 95.739 704 30 0 3087 3790 462144715 462144012 0.000000e+00 1134
6 TraesCS5D01G284000 chr5B 90.179 560 31 9 3795 4332 462143889 462143332 0.000000e+00 708
7 TraesCS5D01G284000 chr5B 93.536 263 15 2 5112 5372 462142792 462142530 1.820000e-104 390
8 TraesCS5D01G284000 chr5B 90.566 212 11 4 4338 4545 462143289 462143083 6.870000e-69 272
9 TraesCS5D01G284000 chr5B 88.182 110 6 2 5049 5151 462142901 462142792 2.040000e-24 124


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 TraesCS5D01G284000 chr5D 384848227 384853612 5385 False 9947.0 9947 100.000000 1 5386 1 chr5D.!!$F1 5385
1 TraesCS5D01G284000 chr5A 485823351 485828802 5451 False 3661.5 6833 91.849500 1 5386 2 chr5A.!!$F1 5385
2 TraesCS5D01G284000 chr5B 462142530 462147827 5297 True 820.0 1701 91.010714 403 5372 7 chr5B.!!$R1 4969

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
844 849 0.613853 AACAGCCGAGCCCACTAGTA 60.614 55.0 0.00 0.00 0.00 1.82 F
1338 1349 0.039035 TTGCATTACAGGGGTGGGTC 59.961 55.0 0.00 0.00 0.00 4.46 F
1729 1769 0.104304 ACTGTCACGTGACCTTGACC 59.896 55.0 38.12 17.95 44.15 4.02 F
2073 2716 0.252284 TCCCTGTCTCCCAGTCCTTC 60.252 60.0 0.00 0.00 39.74 3.46 F
3252 3914 0.324943 GGACCACTAAGAAGCCAGCA 59.675 55.0 0.00 0.00 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 1769 1.501582 ACCCTAGCTAAGCCCTCAAG 58.498 55.000 0.00 0.00 0.00 3.02 R
2257 2901 1.553690 GCTCCACTCCAGCCTTGGTA 61.554 60.000 0.00 0.00 45.26 3.25 R
3496 4158 2.022195 CACCCTGCCATCTGATTTCTG 58.978 52.381 0.00 0.00 0.00 3.02 R
3813 4593 0.032130 ATTATGTCGTCCTGCGCGAT 59.968 50.000 12.10 0.00 40.59 4.58 R
4823 5669 0.172127 TGCGCTGCTAGTCAGAAGAG 59.828 55.000 9.73 6.66 45.72 2.85 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
49 50 6.607019 ACCCTCTTAATGGTAGTTTCACAAA 58.393 36.000 0.00 0.00 31.61 2.83
96 98 3.136626 CCTCCAAGGTAATCCTACAAGGG 59.863 52.174 0.00 0.00 44.35 3.95
161 163 6.628919 AGTGCGTTTAAATCTACAAGGTTT 57.371 33.333 0.00 0.00 0.00 3.27
163 165 6.261381 AGTGCGTTTAAATCTACAAGGTTTGA 59.739 34.615 0.00 0.00 0.00 2.69
230 232 9.794719 ATTAGTACTATAAGCCTTGGGATTTTC 57.205 33.333 2.79 0.00 31.96 2.29
233 235 8.336987 AGTACTATAAGCCTTGGGATTTTCTTT 58.663 33.333 0.00 0.00 31.96 2.52
235 237 8.067751 ACTATAAGCCTTGGGATTTTCTTTTC 57.932 34.615 0.00 0.00 31.96 2.29
238 242 3.507622 AGCCTTGGGATTTTCTTTTCGAG 59.492 43.478 0.00 0.00 0.00 4.04
250 254 4.801330 TCTTTTCGAGTCCATGAGCTAA 57.199 40.909 0.00 0.00 0.00 3.09
276 280 6.420604 AGAAGCCAAATAAAATGTTTGACACG 59.579 34.615 1.74 0.00 38.51 4.49
338 342 3.181500 GCCCAAGGAACGAAACATGTATC 60.181 47.826 0.00 0.00 0.00 2.24
348 352 5.891451 ACGAAACATGTATCGAATGAGAGA 58.109 37.500 0.00 0.00 41.43 3.10
349 353 6.507900 ACGAAACATGTATCGAATGAGAGAT 58.492 36.000 0.00 0.00 41.43 2.75
350 354 7.649057 ACGAAACATGTATCGAATGAGAGATA 58.351 34.615 0.00 0.00 41.43 1.98
391 396 1.337823 GGTGCTTCGCTTAGAGTTGGA 60.338 52.381 0.00 0.00 0.00 3.53
400 405 2.731976 GCTTAGAGTTGGACAGAACACG 59.268 50.000 0.00 0.00 0.00 4.49
512 517 9.913451 CAACAAAACAAACATAAACAAGTATGG 57.087 29.630 0.00 0.00 36.04 2.74
527 532 5.186409 ACAAGTATGGCTTCAGCAATTTCAT 59.814 36.000 0.30 0.00 44.36 2.57
566 571 7.149202 AGTATCCCATAAATAAGAGTTGGCA 57.851 36.000 0.00 0.00 0.00 4.92
587 592 4.275936 GCAAGGCGTAATTTATCCTCACAT 59.724 41.667 0.00 0.00 0.00 3.21
598 603 1.924731 TCCTCACATCTCACCGTTCT 58.075 50.000 0.00 0.00 0.00 3.01
623 628 2.097728 GCCGAAAAAGCCGTAGCG 59.902 61.111 0.00 0.00 46.67 4.26
652 657 5.583495 TGACAAATAAACCAACCGAAACAG 58.417 37.500 0.00 0.00 0.00 3.16
732 737 6.779115 AACAAAATTAGAAAATGTTCCCGC 57.221 33.333 0.00 0.00 33.92 6.13
733 738 5.848406 ACAAAATTAGAAAATGTTCCCGCA 58.152 33.333 0.00 0.00 33.92 5.69
734 739 6.284459 ACAAAATTAGAAAATGTTCCCGCAA 58.716 32.000 0.00 0.00 33.92 4.85
735 740 6.763610 ACAAAATTAGAAAATGTTCCCGCAAA 59.236 30.769 0.00 0.00 33.92 3.68
736 741 7.281100 ACAAAATTAGAAAATGTTCCCGCAAAA 59.719 29.630 0.00 0.00 33.92 2.44
737 742 7.793927 AAATTAGAAAATGTTCCCGCAAAAA 57.206 28.000 0.00 0.00 33.92 1.94
769 774 5.665360 AGAAAATGGACCCCTCAAAGAAAAA 59.335 36.000 0.00 0.00 0.00 1.94
770 775 6.329986 AGAAAATGGACCCCTCAAAGAAAAAT 59.670 34.615 0.00 0.00 0.00 1.82
771 776 7.512402 AGAAAATGGACCCCTCAAAGAAAAATA 59.488 33.333 0.00 0.00 0.00 1.40
774 779 5.570320 TGGACCCCTCAAAGAAAAATAGAG 58.430 41.667 0.00 0.00 0.00 2.43
843 848 1.481056 AAACAGCCGAGCCCACTAGT 61.481 55.000 0.00 0.00 0.00 2.57
844 849 0.613853 AACAGCCGAGCCCACTAGTA 60.614 55.000 0.00 0.00 0.00 1.82
845 850 1.038130 ACAGCCGAGCCCACTAGTAG 61.038 60.000 0.00 0.00 0.00 2.57
917 922 5.454187 CGGGGCTTAACAGGACAGATAAATA 60.454 44.000 0.00 0.00 0.00 1.40
918 923 6.362248 GGGGCTTAACAGGACAGATAAATAA 58.638 40.000 0.00 0.00 0.00 1.40
919 924 6.831868 GGGGCTTAACAGGACAGATAAATAAA 59.168 38.462 0.00 0.00 0.00 1.40
986 991 1.304464 AGTTAAAGCCCCAGCCAGC 60.304 57.895 0.00 0.00 41.25 4.85
1115 1125 3.077556 TGCTCCTCCGCTTCCTCC 61.078 66.667 0.00 0.00 0.00 4.30
1117 1127 3.532155 CTCCTCCGCTTCCTCCCG 61.532 72.222 0.00 0.00 0.00 5.14
1285 1296 3.039526 CCTCCCCCTCCTCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
1287 1298 3.036959 TCCCCCTCCTCCTCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
1288 1299 4.179599 CCCCCTCCTCCTCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
1289 1300 3.039526 CCCCTCCTCCTCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
1290 1301 1.705450 CCCCTCCTCCTCCTCCCTA 60.705 68.421 0.00 0.00 0.00 3.53
1291 1302 1.304936 CCCCTCCTCCTCCTCCCTAA 61.305 65.000 0.00 0.00 0.00 2.69
1295 1306 1.783979 CTCCTCCTCCTCCCTAAGCTA 59.216 57.143 0.00 0.00 0.00 3.32
1303 1314 2.621998 TCCTCCCTAAGCTATCGTTTCG 59.378 50.000 0.00 0.00 0.00 3.46
1335 1346 0.894835 GGTTTGCATTACAGGGGTGG 59.105 55.000 0.00 0.00 0.00 4.61
1336 1347 0.894835 GTTTGCATTACAGGGGTGGG 59.105 55.000 0.00 0.00 0.00 4.61
1337 1348 0.485099 TTTGCATTACAGGGGTGGGT 59.515 50.000 0.00 0.00 0.00 4.51
1338 1349 0.039035 TTGCATTACAGGGGTGGGTC 59.961 55.000 0.00 0.00 0.00 4.46
1368 1379 1.303282 GAAGGAGATTTGCGGGGGT 59.697 57.895 0.00 0.00 0.00 4.95
1401 1412 1.002033 CCTGCTGTTGTTCTGTTCTGC 60.002 52.381 0.00 0.00 0.00 4.26
1419 1430 2.821969 CTGCTGCCTGATTTTGGTTACT 59.178 45.455 0.00 0.00 0.00 2.24
1449 1471 4.503910 TGATTCTACATCGTTTGGTCCAG 58.496 43.478 0.00 0.00 0.00 3.86
1475 1497 1.989165 GCTAGATGCGACGGATGATTC 59.011 52.381 6.58 0.00 0.00 2.52
1479 1501 0.105593 ATGCGACGGATGATTCTGCT 59.894 50.000 0.00 0.00 0.00 4.24
1494 1516 1.490490 TCTGCTTCTGTGGGTTTGACT 59.510 47.619 0.00 0.00 0.00 3.41
1508 1530 3.433615 GGTTTGACTCATCTGTGCAGTAC 59.566 47.826 0.00 0.00 0.00 2.73
1520 1542 2.288825 TGTGCAGTACTGTGCTTAGGAC 60.289 50.000 23.44 8.13 44.32 3.85
1527 1549 2.054799 ACTGTGCTTAGGACTGGGAAA 58.945 47.619 14.23 0.00 0.00 3.13
1531 1553 4.079253 TGTGCTTAGGACTGGGAAATTTC 58.921 43.478 9.83 9.83 0.00 2.17
1532 1554 4.202567 TGTGCTTAGGACTGGGAAATTTCT 60.203 41.667 17.42 0.00 0.00 2.52
1533 1555 4.156739 GTGCTTAGGACTGGGAAATTTCTG 59.843 45.833 17.42 10.54 0.00 3.02
1535 1557 4.156739 GCTTAGGACTGGGAAATTTCTGTG 59.843 45.833 17.42 9.92 0.00 3.66
1536 1558 3.160679 AGGACTGGGAAATTTCTGTGG 57.839 47.619 17.42 8.35 0.00 4.17
1550 1582 2.676748 TCTGTGGGTTCTTGCCAAAAT 58.323 42.857 0.00 0.00 0.00 1.82
1551 1583 2.627699 TCTGTGGGTTCTTGCCAAAATC 59.372 45.455 0.00 0.00 0.00 2.17
1552 1584 2.629617 CTGTGGGTTCTTGCCAAAATCT 59.370 45.455 0.00 0.00 0.00 2.40
1553 1585 2.627699 TGTGGGTTCTTGCCAAAATCTC 59.372 45.455 0.00 0.00 0.00 2.75
1554 1586 2.627699 GTGGGTTCTTGCCAAAATCTCA 59.372 45.455 0.00 0.00 0.00 3.27
1555 1587 2.892852 TGGGTTCTTGCCAAAATCTCAG 59.107 45.455 0.00 0.00 0.00 3.35
1565 1597 3.428045 GCCAAAATCTCAGACGGATTTGG 60.428 47.826 14.51 14.51 40.95 3.28
1590 1622 1.673920 GCGGTCACCTTGAAAACTCAA 59.326 47.619 0.00 0.00 0.00 3.02
1591 1623 2.540973 GCGGTCACCTTGAAAACTCAAC 60.541 50.000 0.00 0.00 0.00 3.18
1599 1631 8.671028 GTCACCTTGAAAACTCAACTAAAAGTA 58.329 33.333 0.00 0.00 0.00 2.24
1603 1635 8.889717 CCTTGAAAACTCAACTAAAAGTACAGA 58.110 33.333 0.00 0.00 0.00 3.41
1635 1668 7.985634 TTTTCAGAATTTCAGTTTACTGTGC 57.014 32.000 9.53 0.00 44.12 4.57
1636 1669 6.691754 TTCAGAATTTCAGTTTACTGTGCA 57.308 33.333 9.53 0.00 44.12 4.57
1637 1670 6.060028 TCAGAATTTCAGTTTACTGTGCAC 57.940 37.500 10.75 10.75 44.12 4.57
1638 1671 5.822519 TCAGAATTTCAGTTTACTGTGCACT 59.177 36.000 19.41 0.28 44.12 4.40
1639 1672 6.989759 TCAGAATTTCAGTTTACTGTGCACTA 59.010 34.615 19.41 0.00 44.12 2.74
1640 1673 7.661437 TCAGAATTTCAGTTTACTGTGCACTAT 59.339 33.333 19.41 8.54 44.12 2.12
1641 1674 8.935844 CAGAATTTCAGTTTACTGTGCACTATA 58.064 33.333 19.41 7.47 44.12 1.31
1689 1722 2.365617 TGGATCTAAGCTAGGAAAGGCG 59.634 50.000 0.00 0.00 0.00 5.52
1729 1769 0.104304 ACTGTCACGTGACCTTGACC 59.896 55.000 38.12 17.95 44.15 4.02
1756 1796 5.938279 AGGGCTTAGCTAGGGTTTAATAAC 58.062 41.667 3.59 0.00 0.00 1.89
1817 2449 6.040842 TGGGGTCAAAAGAAAAAGAATCAGAG 59.959 38.462 0.00 0.00 0.00 3.35
1834 2466 3.134458 CAGAGACTTGGTTTCTGTGGTC 58.866 50.000 9.21 0.00 39.12 4.02
1839 2471 3.480470 ACTTGGTTTCTGTGGTCATGAG 58.520 45.455 0.00 0.00 0.00 2.90
1871 2509 3.949113 ACTCCTACGAGCTTTTCCTAGAG 59.051 47.826 0.00 0.00 40.03 2.43
1881 2519 3.120025 GCTTTTCCTAGAGAAAGCACAGC 60.120 47.826 25.23 17.59 45.11 4.40
1897 2537 1.915489 ACAGCTTGTGGGGACATATCA 59.085 47.619 0.00 0.00 46.14 2.15
1908 2548 5.009631 TGGGGACATATCAGTCAAAACAAG 58.990 41.667 0.00 0.00 40.29 3.16
1918 2558 6.647334 TCAGTCAAAACAAGCCATCAATTA 57.353 33.333 0.00 0.00 0.00 1.40
1920 2560 7.315142 TCAGTCAAAACAAGCCATCAATTATC 58.685 34.615 0.00 0.00 0.00 1.75
1921 2561 7.177216 TCAGTCAAAACAAGCCATCAATTATCT 59.823 33.333 0.00 0.00 0.00 1.98
1942 2584 7.588497 ATCTAGATAAAAATGCAAGGGGAAC 57.412 36.000 2.53 0.00 0.00 3.62
1943 2585 6.731467 TCTAGATAAAAATGCAAGGGGAACT 58.269 36.000 0.00 0.00 0.00 3.01
2013 2656 2.171840 TGAGCTAGACAGTGAGGGTTC 58.828 52.381 0.00 0.00 0.00 3.62
2073 2716 0.252284 TCCCTGTCTCCCAGTCCTTC 60.252 60.000 0.00 0.00 39.74 3.46
2115 2758 5.391523 GCCGACAAACAAATCAACTGCTATA 60.392 40.000 0.00 0.00 0.00 1.31
2128 2771 9.851686 AATCAACTGCTATATTTAACTGATGGA 57.148 29.630 0.00 0.00 0.00 3.41
2257 2901 6.595326 TGAAGATCGCAGACAATACTGAAATT 59.405 34.615 0.00 0.00 42.51 1.82
2346 2996 9.567848 CCCAAGTAACAATATTATGTGTTCAAC 57.432 33.333 0.43 0.00 38.80 3.18
2382 3041 5.997746 CACATCCACCGATTAATCTGGTTAT 59.002 40.000 21.67 16.87 33.58 1.89
2411 3071 3.603532 TGTGATTTCTGCAGAGGATGAC 58.396 45.455 17.43 18.00 0.00 3.06
2433 3093 4.128643 CCAGTCTAACGGTTTTGTTACCA 58.871 43.478 0.00 0.00 38.12 3.25
2463 3123 2.445525 ACTATTGGCCCCGAATACCATT 59.554 45.455 0.00 0.00 32.39 3.16
2519 3179 6.543831 GCCCTCATGAATGTAGTTGAGTAAAT 59.456 38.462 0.00 0.00 35.01 1.40
2715 3377 2.284190 GCTTCCTGCAGACACCTATTC 58.716 52.381 17.39 0.00 42.31 1.75
2747 3409 2.095059 GTGTTTCACCACATGAGCATCC 60.095 50.000 0.00 0.00 38.99 3.51
2759 3421 5.124936 CACATGAGCATCCAGAGAATTTTCA 59.875 40.000 0.00 0.00 0.00 2.69
2810 3472 3.218453 TCCCACAAATGAACATCAACGT 58.782 40.909 0.00 0.00 0.00 3.99
2817 3479 5.743398 ACAAATGAACATCAACGTTGTCTTG 59.257 36.000 26.47 22.38 29.64 3.02
2844 3506 4.442375 ACTCTGGTGACTCTATTTGTCG 57.558 45.455 0.00 0.00 37.26 4.35
2938 3600 5.204292 TGTCATATCTCTACTGTTCTGCCT 58.796 41.667 0.00 0.00 0.00 4.75
3052 3714 7.876936 ATCACTGTGCTTTCATTTCATAGAT 57.123 32.000 2.12 0.00 0.00 1.98
3053 3715 7.080353 TCACTGTGCTTTCATTTCATAGATG 57.920 36.000 2.12 0.00 0.00 2.90
3056 3718 4.705991 TGTGCTTTCATTTCATAGATGCCA 59.294 37.500 0.00 0.00 0.00 4.92
3059 3721 6.759827 GTGCTTTCATTTCATAGATGCCAATT 59.240 34.615 0.00 0.00 0.00 2.32
3072 3734 9.467258 CATAGATGCCAATTATTGTTACTTTGG 57.533 33.333 4.15 0.00 39.84 3.28
3210 3872 4.023291 ACTTGGATGGTGTTGTCAAAGTT 58.977 39.130 0.00 0.00 35.58 2.66
3252 3914 0.324943 GGACCACTAAGAAGCCAGCA 59.675 55.000 0.00 0.00 0.00 4.41
3255 3917 1.002544 ACCACTAAGAAGCCAGCAGTC 59.997 52.381 0.00 0.00 0.00 3.51
3504 4166 6.992063 CTTAAAGAGCTAAGCCAGAAATCA 57.008 37.500 0.00 0.00 0.00 2.57
3699 4361 4.725790 GCACAAAGGCCTGAATAATCTT 57.274 40.909 5.69 0.00 0.00 2.40
3704 4366 7.362920 GCACAAAGGCCTGAATAATCTTAAGAA 60.363 37.037 5.69 0.00 0.00 2.52
3711 4373 7.366513 GCCTGAATAATCTTAAGAAGGCATTC 58.633 38.462 27.53 21.76 46.55 2.67
3715 4377 7.838696 TGAATAATCTTAAGAAGGCATTCCCAA 59.161 33.333 9.71 1.23 35.94 4.12
3813 4593 9.349713 ACCAGATTTTTAACTTACAATCTGTCA 57.650 29.630 18.55 0.00 46.03 3.58
3817 4597 8.895932 ATTTTTAACTTACAATCTGTCATCGC 57.104 30.769 0.00 0.00 0.00 4.58
3851 4631 1.003233 GCCGGCTGAGAAGAAAGGT 60.003 57.895 22.15 0.00 0.00 3.50
3854 4634 1.674221 CCGGCTGAGAAGAAAGGTGAG 60.674 57.143 0.00 0.00 0.00 3.51
3863 4643 4.709250 AGAAGAAAGGTGAGTTCCTGAAC 58.291 43.478 1.75 1.75 41.45 3.18
4107 4890 1.680522 ATGCTACTGCTAGTGCCGCT 61.681 55.000 0.00 0.00 40.48 5.52
4112 4895 0.457851 ACTGCTAGTGCCGCTTAGAG 59.542 55.000 6.66 4.61 38.71 2.43
4113 4896 0.457851 CTGCTAGTGCCGCTTAGAGT 59.542 55.000 6.66 0.00 38.71 3.24
4125 4908 3.498397 CCGCTTAGAGTGTTTGTTGTCAT 59.502 43.478 0.00 0.00 0.00 3.06
4128 4911 6.128282 CCGCTTAGAGTGTTTGTTGTCATTAT 60.128 38.462 0.00 0.00 0.00 1.28
4262 5056 1.562008 TCTGGGAACAAACACCACAGA 59.438 47.619 0.00 0.00 42.06 3.41
4265 5059 1.676006 GGGAACAAACACCACAGACAG 59.324 52.381 0.00 0.00 0.00 3.51
4267 5061 2.614057 GGAACAAACACCACAGACAGAG 59.386 50.000 0.00 0.00 0.00 3.35
4272 5070 2.847327 ACACCACAGACAGAGGATTG 57.153 50.000 0.00 0.00 0.00 2.67
4293 5091 1.341209 CAGTGTGCTACAGAGTGGACA 59.659 52.381 0.00 0.00 0.00 4.02
4301 5099 3.430098 GCTACAGAGTGGACAATGAGAGG 60.430 52.174 0.00 0.00 0.00 3.69
4363 5205 5.594317 ACCAAGTTGTATGCTTAATCATCCC 59.406 40.000 1.45 0.00 0.00 3.85
4383 5225 3.643320 CCCATATCAGCTCACCAGTTCTA 59.357 47.826 0.00 0.00 0.00 2.10
4450 5293 6.825213 TGATTTCTGTCTAATAGCTGTGCAAT 59.175 34.615 0.00 0.00 0.00 3.56
4458 5301 7.148356 TGTCTAATAGCTGTGCAATTTTCTCTG 60.148 37.037 0.00 0.00 0.00 3.35
4462 5305 3.822735 AGCTGTGCAATTTTCTCTGCTTA 59.177 39.130 0.00 0.00 39.38 3.09
4473 5316 8.909671 CAATTTTCTCTGCTTAATGACACTTTC 58.090 33.333 0.00 0.00 0.00 2.62
4496 5342 8.579850 TTCTGGTCATTATTACTCTTTTGCAT 57.420 30.769 0.00 0.00 0.00 3.96
4554 5400 7.226523 ACAAGAAAAACTAACCCAATTCAATGC 59.773 33.333 0.00 0.00 0.00 3.56
4560 5406 0.614812 ACCCAATTCAATGCCTTGCC 59.385 50.000 0.00 0.00 32.11 4.52
4572 5418 1.222936 CCTTGCCGCCTTCATCTCT 59.777 57.895 0.00 0.00 0.00 3.10
4586 5432 3.625853 TCATCTCTGTCTCCGTCTCATT 58.374 45.455 0.00 0.00 0.00 2.57
4601 5447 0.615331 TCATTTTCTCCTCGCCTGCT 59.385 50.000 0.00 0.00 0.00 4.24
4643 5489 4.819761 GCCACTCATCAGCGGCGA 62.820 66.667 12.98 0.00 38.10 5.54
4678 5524 0.955428 ACACGCACTGGGCTACATTG 60.955 55.000 0.00 0.00 41.67 2.82
4713 5559 4.096984 AGCTTAATGACAATAGTTGCTGGC 59.903 41.667 0.00 0.00 0.00 4.85
4715 5561 5.565592 TTAATGACAATAGTTGCTGGCAG 57.434 39.130 10.94 10.94 33.02 4.85
4734 5580 3.119708 GCAGTTGGAGCTGTTAAATCCAG 60.120 47.826 0.00 0.00 43.71 3.86
4755 5601 3.565905 CAGAATGTGCAAAAGGGACTC 57.434 47.619 0.00 0.00 38.49 3.36
4766 5612 0.912486 AAGGGACTCGGCTTTATGCT 59.088 50.000 0.00 0.00 38.49 3.79
4770 5616 1.859080 GGACTCGGCTTTATGCTTACG 59.141 52.381 0.00 0.00 42.39 3.18
4780 5626 2.749839 TGCTTACGCATGGCACCC 60.750 61.111 0.00 0.00 42.25 4.61
4801 5647 1.476488 GCAACCAGTGGAAACAACTGT 59.524 47.619 18.40 0.00 46.06 3.55
4810 5656 4.461081 AGTGGAAACAACTGTAACTTGCAA 59.539 37.500 0.00 0.00 46.06 4.08
4822 5668 5.473931 TGTAACTTGCAACAAAAGAAAGCA 58.526 33.333 0.00 0.00 0.00 3.91
4823 5669 4.926860 AACTTGCAACAAAAGAAAGCAC 57.073 36.364 0.00 0.00 34.56 4.40
4825 5671 4.176271 ACTTGCAACAAAAGAAAGCACTC 58.824 39.130 0.00 0.00 34.56 3.51
4826 5672 4.082026 ACTTGCAACAAAAGAAAGCACTCT 60.082 37.500 0.00 0.00 34.56 3.24
4830 5676 4.501921 GCAACAAAAGAAAGCACTCTTCTG 59.498 41.667 1.23 1.03 34.49 3.02
4831 5677 5.677091 GCAACAAAAGAAAGCACTCTTCTGA 60.677 40.000 7.82 0.00 34.49 3.27
4833 5679 5.189180 ACAAAAGAAAGCACTCTTCTGACT 58.811 37.500 7.82 0.00 34.49 3.41
4834 5680 6.349300 ACAAAAGAAAGCACTCTTCTGACTA 58.651 36.000 7.82 0.00 34.49 2.59
4835 5681 6.481644 ACAAAAGAAAGCACTCTTCTGACTAG 59.518 38.462 7.82 0.00 34.49 2.57
4836 5682 4.186856 AGAAAGCACTCTTCTGACTAGC 57.813 45.455 0.00 0.00 0.00 3.42
4837 5683 3.576118 AGAAAGCACTCTTCTGACTAGCA 59.424 43.478 0.00 0.00 0.00 3.49
4838 5684 3.591196 AAGCACTCTTCTGACTAGCAG 57.409 47.619 7.59 7.59 46.31 4.24
4839 5685 1.204467 AGCACTCTTCTGACTAGCAGC 59.796 52.381 8.72 0.00 44.52 5.25
4840 5686 1.906757 CACTCTTCTGACTAGCAGCG 58.093 55.000 8.72 4.15 44.52 5.18
4844 5690 1.205655 TCTTCTGACTAGCAGCGCAAT 59.794 47.619 11.47 0.00 44.52 3.56
4892 5738 2.193993 GAGAGCTTAACCCTAACCCCA 58.806 52.381 0.00 0.00 0.00 4.96
4895 5741 4.377134 AGAGCTTAACCCTAACCCCATAA 58.623 43.478 0.00 0.00 0.00 1.90
4899 5745 4.643334 GCTTAACCCTAACCCCATAAAGTG 59.357 45.833 0.00 0.00 0.00 3.16
4905 5751 4.444449 CCCTAACCCCATAAAGTGCTACTC 60.444 50.000 0.00 0.00 0.00 2.59
4911 5757 6.970191 ACCCCATAAAGTGCTACTCTATTTT 58.030 36.000 0.00 0.00 0.00 1.82
4912 5758 6.828785 ACCCCATAAAGTGCTACTCTATTTTG 59.171 38.462 0.00 0.00 0.00 2.44
4913 5759 6.238759 CCCCATAAAGTGCTACTCTATTTTGC 60.239 42.308 0.00 0.00 0.00 3.68
4914 5760 6.318648 CCCATAAAGTGCTACTCTATTTTGCA 59.681 38.462 0.00 0.00 0.00 4.08
4915 5761 7.412853 CCATAAAGTGCTACTCTATTTTGCAG 58.587 38.462 0.00 0.00 34.15 4.41
4937 5793 7.503902 TGCAGACTACAACTGAGTGATATCTAT 59.496 37.037 3.98 0.00 37.54 1.98
4994 5850 4.996788 AAAATGCTGCCCTCTTATTCTG 57.003 40.909 0.00 0.00 0.00 3.02
4995 5851 3.939740 AATGCTGCCCTCTTATTCTGA 57.060 42.857 0.00 0.00 0.00 3.27
4996 5852 3.939740 ATGCTGCCCTCTTATTCTGAA 57.060 42.857 0.00 0.00 0.00 3.02
4998 5854 2.293170 GCTGCCCTCTTATTCTGAACC 58.707 52.381 0.00 0.00 0.00 3.62
4999 5855 2.924421 CTGCCCTCTTATTCTGAACCC 58.076 52.381 0.00 0.00 0.00 4.11
5000 5856 2.239654 CTGCCCTCTTATTCTGAACCCA 59.760 50.000 0.00 0.00 0.00 4.51
5001 5857 2.647299 TGCCCTCTTATTCTGAACCCAA 59.353 45.455 0.00 0.00 0.00 4.12
5002 5858 3.269381 TGCCCTCTTATTCTGAACCCAAT 59.731 43.478 0.00 0.00 0.00 3.16
5003 5859 4.264352 TGCCCTCTTATTCTGAACCCAATT 60.264 41.667 0.00 0.00 0.00 2.32
5004 5860 4.711846 GCCCTCTTATTCTGAACCCAATTT 59.288 41.667 0.00 0.00 0.00 1.82
5054 5952 1.375098 GCTCCAGTTGAGATGCAGCC 61.375 60.000 0.00 0.00 44.42 4.85
5114 6018 2.178890 GCCCTGCTCTTCATCTGCG 61.179 63.158 0.00 0.00 0.00 5.18
5152 6097 2.605257 TGCAGGGGCTAGTTACGATAT 58.395 47.619 0.00 0.00 41.91 1.63
5215 6161 4.269183 CTGTGTATGCAGGGAAATTACCA 58.731 43.478 0.00 0.00 33.11 3.25
5221 6167 0.391927 CAGGGAAATTACCACGGCGA 60.392 55.000 16.62 0.00 0.00 5.54
5365 6311 2.555732 ATGTGGCCATTGGAAGGAAT 57.444 45.000 9.72 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.945285 GGGTTGACAAAGAAAGTGTGAGA 59.055 43.478 0.00 0.00 0.00 3.27
110 112 1.679153 GAGAAAAACCCGTGGCTTCAA 59.321 47.619 0.00 0.00 0.00 2.69
118 120 3.393609 ACTAAGGAAGGAGAAAAACCCGT 59.606 43.478 0.00 0.00 0.00 5.28
123 125 4.081322 ACGCACTAAGGAAGGAGAAAAA 57.919 40.909 0.00 0.00 0.00 1.94
230 232 5.171476 TCTTTAGCTCATGGACTCGAAAAG 58.829 41.667 0.00 0.00 0.00 2.27
233 235 4.748892 CTTCTTTAGCTCATGGACTCGAA 58.251 43.478 0.00 0.00 0.00 3.71
235 237 2.863137 GCTTCTTTAGCTCATGGACTCG 59.137 50.000 0.00 0.00 46.77 4.18
250 254 7.042791 CGTGTCAAACATTTTATTTGGCTTCTT 60.043 33.333 3.98 0.00 41.29 2.52
270 274 5.165676 GTCATACACTTGATAACCGTGTCA 58.834 41.667 0.00 0.00 41.62 3.58
338 342 4.037327 TGGCTTCTCACTATCTCTCATTCG 59.963 45.833 0.00 0.00 0.00 3.34
391 396 2.157834 TAATTGGACGCGTGTTCTGT 57.842 45.000 20.70 0.00 0.00 3.41
400 405 6.797033 GCATGTCTATAACAATAATTGGACGC 59.203 38.462 0.00 0.00 42.37 5.19
487 492 8.608317 GCCATACTTGTTTATGTTTGTTTTGTT 58.392 29.630 0.00 0.00 0.00 2.83
512 517 6.270096 GCTTCATTATGAAATTGCTGAAGC 57.730 37.500 17.65 17.65 46.14 3.86
566 571 5.930135 AGATGTGAGGATAAATTACGCCTT 58.070 37.500 0.00 0.00 0.00 4.35
587 592 0.516001 CGAGTCGAAGAACGGTGAGA 59.484 55.000 6.73 0.00 39.69 3.27
598 603 1.562575 GGCTTTTTCGGCGAGTCGAA 61.563 55.000 18.61 8.54 45.77 3.71
623 628 6.217294 TCGGTTGGTTTATTTGTCATTTTCC 58.783 36.000 0.00 0.00 0.00 3.13
630 635 5.823353 TCTGTTTCGGTTGGTTTATTTGTC 58.177 37.500 0.00 0.00 0.00 3.18
631 636 5.838531 TCTGTTTCGGTTGGTTTATTTGT 57.161 34.783 0.00 0.00 0.00 2.83
652 657 0.110238 TTTGCGTGCGAGCTCAATTC 60.110 50.000 15.40 0.00 38.13 2.17
735 740 9.332713 TGAGGGGTCCATTTTCTATTTATTTTT 57.667 29.630 0.00 0.00 0.00 1.94
736 741 8.909423 TGAGGGGTCCATTTTCTATTTATTTT 57.091 30.769 0.00 0.00 0.00 1.82
737 742 8.909423 TTGAGGGGTCCATTTTCTATTTATTT 57.091 30.769 0.00 0.00 0.00 1.40
738 743 8.909423 TTTGAGGGGTCCATTTTCTATTTATT 57.091 30.769 0.00 0.00 0.00 1.40
739 744 8.343787 TCTTTGAGGGGTCCATTTTCTATTTAT 58.656 33.333 0.00 0.00 0.00 1.40
740 745 7.704727 TCTTTGAGGGGTCCATTTTCTATTTA 58.295 34.615 0.00 0.00 0.00 1.40
743 748 5.796502 TCTTTGAGGGGTCCATTTTCTAT 57.203 39.130 0.00 0.00 0.00 1.98
769 774 2.301296 CCCATCGTGCTCCATTCTCTAT 59.699 50.000 0.00 0.00 0.00 1.98
770 775 1.688735 CCCATCGTGCTCCATTCTCTA 59.311 52.381 0.00 0.00 0.00 2.43
771 776 0.467384 CCCATCGTGCTCCATTCTCT 59.533 55.000 0.00 0.00 0.00 3.10
774 779 1.303309 CTTCCCATCGTGCTCCATTC 58.697 55.000 0.00 0.00 0.00 2.67
843 848 4.037222 TGACAATGGAGATTAGTGGCCTA 58.963 43.478 3.32 0.00 0.00 3.93
844 849 2.846206 TGACAATGGAGATTAGTGGCCT 59.154 45.455 3.32 0.00 0.00 5.19
845 850 3.281727 TGACAATGGAGATTAGTGGCC 57.718 47.619 0.00 0.00 0.00 5.36
917 922 1.134340 TCGCCCGGCACTTGTATATTT 60.134 47.619 10.77 0.00 0.00 1.40
918 923 0.466543 TCGCCCGGCACTTGTATATT 59.533 50.000 10.77 0.00 0.00 1.28
919 924 0.249741 GTCGCCCGGCACTTGTATAT 60.250 55.000 10.77 0.00 0.00 0.86
986 991 1.142748 GACTGGAGATGGAGTGGCG 59.857 63.158 0.00 0.00 0.00 5.69
1279 1290 1.781529 ACGATAGCTTAGGGAGGAGGA 59.218 52.381 0.00 0.00 42.67 3.71
1282 1293 2.621998 CGAAACGATAGCTTAGGGAGGA 59.378 50.000 0.00 0.00 42.67 3.71
1283 1294 2.862921 GCGAAACGATAGCTTAGGGAGG 60.863 54.545 0.00 0.00 42.67 4.30
1285 1296 1.068127 GGCGAAACGATAGCTTAGGGA 59.932 52.381 0.00 0.00 42.67 4.20
1287 1298 1.129326 CGGCGAAACGATAGCTTAGG 58.871 55.000 0.00 0.00 42.67 2.69
1288 1299 0.503117 GCGGCGAAACGATAGCTTAG 59.497 55.000 12.98 0.00 42.67 2.18
1289 1300 0.872881 GGCGGCGAAACGATAGCTTA 60.873 55.000 12.98 0.00 42.67 3.09
1290 1301 2.171725 GGCGGCGAAACGATAGCTT 61.172 57.895 12.98 0.00 42.67 3.74
1291 1302 2.585247 GGCGGCGAAACGATAGCT 60.585 61.111 12.98 0.00 42.67 3.32
1335 1346 4.974399 TCTCCTTCCAGAAAAAGAAGACC 58.026 43.478 1.42 0.00 41.69 3.85
1336 1347 7.366513 CAAATCTCCTTCCAGAAAAAGAAGAC 58.633 38.462 1.42 0.00 41.69 3.01
1337 1348 6.015940 GCAAATCTCCTTCCAGAAAAAGAAGA 60.016 38.462 1.42 0.00 41.69 2.87
1338 1349 6.155136 GCAAATCTCCTTCCAGAAAAAGAAG 58.845 40.000 0.00 0.00 39.38 2.85
1368 1379 4.966787 GCAGGACCCCCAAACGCA 62.967 66.667 0.00 0.00 33.88 5.24
1401 1412 6.375455 AGTGAATAGTAACCAAAATCAGGCAG 59.625 38.462 0.00 0.00 0.00 4.85
1419 1430 7.822334 ACCAAACGATGTAGAATCAAGTGAATA 59.178 33.333 0.00 0.00 0.00 1.75
1434 1445 1.338200 GCTCTCTGGACCAAACGATGT 60.338 52.381 0.00 0.00 0.00 3.06
1475 1497 1.876156 GAGTCAAACCCACAGAAGCAG 59.124 52.381 0.00 0.00 0.00 4.24
1479 1501 3.136443 ACAGATGAGTCAAACCCACAGAA 59.864 43.478 0.00 0.00 0.00 3.02
1494 1516 1.620323 AGCACAGTACTGCACAGATGA 59.380 47.619 22.90 0.00 39.86 2.92
1508 1530 2.859165 TTTCCCAGTCCTAAGCACAG 57.141 50.000 0.00 0.00 0.00 3.66
1520 1542 3.500343 AGAACCCACAGAAATTTCCCAG 58.500 45.455 14.61 7.81 0.00 4.45
1527 1549 2.380064 TGGCAAGAACCCACAGAAAT 57.620 45.000 0.00 0.00 0.00 2.17
1531 1553 2.629617 AGATTTTGGCAAGAACCCACAG 59.370 45.455 0.00 0.00 30.65 3.66
1532 1554 2.627699 GAGATTTTGGCAAGAACCCACA 59.372 45.455 0.00 0.00 30.65 4.17
1533 1555 2.627699 TGAGATTTTGGCAAGAACCCAC 59.372 45.455 0.00 0.00 30.65 4.61
1535 1557 3.057245 GTCTGAGATTTTGGCAAGAACCC 60.057 47.826 0.00 0.00 0.00 4.11
1536 1558 3.365364 CGTCTGAGATTTTGGCAAGAACC 60.365 47.826 0.00 0.00 0.00 3.62
1550 1582 1.067846 CGACACCAAATCCGTCTGAGA 60.068 52.381 0.00 0.00 0.00 3.27
1551 1583 1.350193 CGACACCAAATCCGTCTGAG 58.650 55.000 0.00 0.00 0.00 3.35
1552 1584 0.669318 GCGACACCAAATCCGTCTGA 60.669 55.000 0.00 0.00 0.00 3.27
1553 1585 1.787847 GCGACACCAAATCCGTCTG 59.212 57.895 0.00 0.00 0.00 3.51
1554 1586 1.736645 CGCGACACCAAATCCGTCT 60.737 57.895 0.00 0.00 0.00 4.18
1555 1587 2.736682 CCGCGACACCAAATCCGTC 61.737 63.158 8.23 0.00 0.00 4.79
1565 1597 1.155424 TTTCAAGGTGACCGCGACAC 61.155 55.000 21.63 21.63 37.51 3.67
1618 1651 9.672673 ATCTATAGTGCACAGTAAACTGAAATT 57.327 29.630 21.04 0.00 46.59 1.82
1619 1652 9.102757 CATCTATAGTGCACAGTAAACTGAAAT 57.897 33.333 21.04 4.25 46.59 2.17
1620 1653 7.549134 CCATCTATAGTGCACAGTAAACTGAAA 59.451 37.037 21.04 0.00 46.59 2.69
1621 1654 7.041721 CCATCTATAGTGCACAGTAAACTGAA 58.958 38.462 21.04 0.00 46.59 3.02
1622 1655 6.573434 CCATCTATAGTGCACAGTAAACTGA 58.427 40.000 21.04 6.27 46.59 3.41
1624 1657 5.129485 AGCCATCTATAGTGCACAGTAAACT 59.871 40.000 21.04 0.00 0.00 2.66
1625 1658 5.360591 AGCCATCTATAGTGCACAGTAAAC 58.639 41.667 21.04 0.00 0.00 2.01
1626 1659 5.453339 GGAGCCATCTATAGTGCACAGTAAA 60.453 44.000 21.04 1.33 0.00 2.01
1627 1660 4.039245 GGAGCCATCTATAGTGCACAGTAA 59.961 45.833 21.04 1.29 0.00 2.24
1628 1661 3.574396 GGAGCCATCTATAGTGCACAGTA 59.426 47.826 21.04 10.17 0.00 2.74
1630 1663 2.366590 TGGAGCCATCTATAGTGCACAG 59.633 50.000 21.04 8.06 0.00 3.66
1631 1664 2.397597 TGGAGCCATCTATAGTGCACA 58.602 47.619 21.04 5.47 0.00 4.57
1632 1665 3.475566 TTGGAGCCATCTATAGTGCAC 57.524 47.619 9.40 9.40 0.00 4.57
1633 1666 4.349048 AGATTTGGAGCCATCTATAGTGCA 59.651 41.667 12.04 0.00 0.00 4.57
1634 1667 4.694509 CAGATTTGGAGCCATCTATAGTGC 59.305 45.833 0.00 1.93 0.00 4.40
1635 1668 6.106648 TCAGATTTGGAGCCATCTATAGTG 57.893 41.667 0.00 0.00 0.00 2.74
1636 1669 6.328672 ACTTCAGATTTGGAGCCATCTATAGT 59.671 38.462 0.00 0.00 32.71 2.12
1637 1670 6.649973 CACTTCAGATTTGGAGCCATCTATAG 59.350 42.308 0.00 0.00 32.71 1.31
1638 1671 6.327365 TCACTTCAGATTTGGAGCCATCTATA 59.673 38.462 0.00 0.00 32.71 1.31
1639 1672 5.131642 TCACTTCAGATTTGGAGCCATCTAT 59.868 40.000 0.00 0.00 32.71 1.98
1640 1673 4.471025 TCACTTCAGATTTGGAGCCATCTA 59.529 41.667 0.00 0.00 32.71 1.98
1641 1674 3.265221 TCACTTCAGATTTGGAGCCATCT 59.735 43.478 0.00 0.00 32.71 2.90
1689 1722 2.290916 TCTGACACACAACTCTCGAGAC 59.709 50.000 12.08 0.00 0.00 3.36
1729 1769 1.501582 ACCCTAGCTAAGCCCTCAAG 58.498 55.000 0.00 0.00 0.00 3.02
1756 1796 3.119849 CGTGCTGAAAAACTAGGATTGGG 60.120 47.826 0.00 0.00 0.00 4.12
1817 2449 3.476552 TCATGACCACAGAAACCAAGTC 58.523 45.455 0.00 0.00 0.00 3.01
1881 2519 3.912496 TGACTGATATGTCCCCACAAG 57.088 47.619 0.00 0.00 35.64 3.16
1897 2537 7.472334 AGATAATTGATGGCTTGTTTTGACT 57.528 32.000 0.00 0.00 0.00 3.41
1918 2558 7.357471 AGTTCCCCTTGCATTTTTATCTAGAT 58.643 34.615 10.73 10.73 0.00 1.98
1920 2560 8.519799 TTAGTTCCCCTTGCATTTTTATCTAG 57.480 34.615 0.00 0.00 0.00 2.43
1921 2561 8.887264 TTTAGTTCCCCTTGCATTTTTATCTA 57.113 30.769 0.00 0.00 0.00 1.98
2013 2656 6.522946 AGTGATAGTGATTCATGACATGGAG 58.477 40.000 15.37 0.00 0.00 3.86
2257 2901 1.553690 GCTCCACTCCAGCCTTGGTA 61.554 60.000 0.00 0.00 45.26 3.25
2346 2996 3.303990 CGGTGGATGTGACAGAAAACTTG 60.304 47.826 0.00 0.00 0.00 3.16
2382 3041 5.645067 CCTCTGCAGAAATCACAAGTATGAA 59.355 40.000 18.85 0.00 30.82 2.57
2411 3071 4.737353 GGTAACAAAACCGTTAGACTGG 57.263 45.455 0.00 0.00 32.15 4.00
2433 3093 2.749466 CGGGGCCAATAGTCAATGACAT 60.749 50.000 16.38 4.49 34.60 3.06
2519 3179 8.165239 ACACACAAACATAAGCTGATTTTCTA 57.835 30.769 0.00 0.00 0.00 2.10
2817 3479 5.652994 AATAGAGTCACCAGAGTTGTCTC 57.347 43.478 0.00 0.00 40.70 3.36
3012 3674 6.147581 CACAGTGATTTTGTGGAATTCAGAG 58.852 40.000 7.93 0.00 41.66 3.35
3052 3714 7.014711 TGTTCTCCAAAGTAACAATAATTGGCA 59.985 33.333 0.00 0.00 30.54 4.92
3053 3715 7.375053 TGTTCTCCAAAGTAACAATAATTGGC 58.625 34.615 0.00 0.00 30.54 4.52
3210 3872 6.070251 TCCATTCAGCAGGAAGTTTATCTACA 60.070 38.462 0.00 0.00 39.30 2.74
3252 3914 3.197116 CCCGGTTTGGTACTCTAATGACT 59.803 47.826 0.00 0.00 35.15 3.41
3255 3917 3.055675 TCACCCGGTTTGGTACTCTAATG 60.056 47.826 0.00 0.00 36.67 1.90
3381 4043 7.661040 CAGTTGAATCCAAGTCCTTGTTATTT 58.339 34.615 6.31 0.00 38.85 1.40
3496 4158 2.022195 CACCCTGCCATCTGATTTCTG 58.978 52.381 0.00 0.00 0.00 3.02
3504 4166 2.036256 GCCAACACCCTGCCATCT 59.964 61.111 0.00 0.00 0.00 2.90
3699 4361 4.112634 AGTGTTTGGGAATGCCTTCTTA 57.887 40.909 1.62 0.00 0.00 2.10
3704 4366 4.264172 TGGTATAAGTGTTTGGGAATGCCT 60.264 41.667 0.00 0.00 0.00 4.75
3711 4373 3.426615 TGCCTTGGTATAAGTGTTTGGG 58.573 45.455 0.00 0.00 0.00 4.12
3715 4377 6.540083 AGTTACTTGCCTTGGTATAAGTGTT 58.460 36.000 12.67 0.00 35.26 3.32
3813 4593 0.032130 ATTATGTCGTCCTGCGCGAT 59.968 50.000 12.10 0.00 40.59 4.58
3815 4595 1.559814 CATTATGTCGTCCTGCGCG 59.440 57.895 0.00 0.00 41.07 6.86
3817 4597 1.821241 CGGCATTATGTCGTCCTGCG 61.821 60.000 11.33 0.00 41.12 5.18
3854 4634 2.003301 GAATCGCCAGAGTTCAGGAAC 58.997 52.381 4.00 4.00 41.45 3.62
3863 4643 1.269517 GCTAGGTCTGAATCGCCAGAG 60.270 57.143 0.00 0.00 43.15 3.35
4125 4908 9.547753 GCTCACTCCAGTTCATCTTATTAATAA 57.452 33.333 7.66 7.66 0.00 1.40
4128 4911 7.044181 CAGCTCACTCCAGTTCATCTTATTAA 58.956 38.462 0.00 0.00 0.00 1.40
4132 4915 3.368843 GCAGCTCACTCCAGTTCATCTTA 60.369 47.826 0.00 0.00 0.00 2.10
4135 4918 1.066286 AGCAGCTCACTCCAGTTCATC 60.066 52.381 0.00 0.00 0.00 2.92
4136 4919 0.982704 AGCAGCTCACTCCAGTTCAT 59.017 50.000 0.00 0.00 0.00 2.57
4137 4920 0.761187 AAGCAGCTCACTCCAGTTCA 59.239 50.000 0.00 0.00 0.00 3.18
4138 4921 1.155042 CAAGCAGCTCACTCCAGTTC 58.845 55.000 0.00 0.00 0.00 3.01
4139 4922 0.250640 CCAAGCAGCTCACTCCAGTT 60.251 55.000 0.00 0.00 0.00 3.16
4140 4923 1.374190 CCAAGCAGCTCACTCCAGT 59.626 57.895 0.00 0.00 0.00 4.00
4141 4924 2.039405 GCCAAGCAGCTCACTCCAG 61.039 63.158 0.00 0.00 0.00 3.86
4142 4925 2.033141 GCCAAGCAGCTCACTCCA 59.967 61.111 0.00 0.00 0.00 3.86
4143 4926 2.749441 GGCCAAGCAGCTCACTCC 60.749 66.667 0.00 0.00 0.00 3.85
4144 4927 1.378250 ATGGCCAAGCAGCTCACTC 60.378 57.895 10.96 0.00 0.00 3.51
4219 5013 8.671921 CAGACAACATTCTAATATTGTGCTTCT 58.328 33.333 4.18 0.00 36.26 2.85
4228 5022 8.739972 GTTTGTTCCCAGACAACATTCTAATAT 58.260 33.333 0.00 0.00 39.11 1.28
4232 5026 5.298276 GTGTTTGTTCCCAGACAACATTCTA 59.702 40.000 0.00 0.00 37.43 2.10
4262 5056 2.938354 GCACACTGCAATCCTCTGT 58.062 52.632 0.00 0.00 44.26 3.41
4272 5070 0.318441 TCCACTCTGTAGCACACTGC 59.682 55.000 0.00 0.00 45.46 4.40
4293 5091 1.698532 CCATGCCTAGAGCCTCTCATT 59.301 52.381 0.00 0.00 42.71 2.57
4363 5205 4.202192 TGCTAGAACTGGTGAGCTGATATG 60.202 45.833 0.00 0.00 35.89 1.78
4383 5225 3.151912 ACTTCAGAGCCAATTTCTGCT 57.848 42.857 1.40 0.00 41.41 4.24
4450 5293 7.255242 CCAGAAAGTGTCATTAAGCAGAGAAAA 60.255 37.037 0.00 0.00 0.00 2.29
4473 5316 9.643693 AAAATGCAAAAGAGTAATAATGACCAG 57.356 29.630 0.00 0.00 0.00 4.00
4554 5400 1.094073 CAGAGATGAAGGCGGCAAGG 61.094 60.000 13.08 0.00 0.00 3.61
4560 5406 0.248825 CGGAGACAGAGATGAAGGCG 60.249 60.000 0.00 0.00 0.00 5.52
4572 5418 3.165875 AGGAGAAAATGAGACGGAGACA 58.834 45.455 0.00 0.00 0.00 3.41
4586 5432 1.480212 TTCCAGCAGGCGAGGAGAAA 61.480 55.000 8.18 0.00 32.11 2.52
4678 5524 3.623510 GTCATTAAGCTACTGCAAGGTCC 59.376 47.826 0.00 0.00 42.74 4.46
4713 5559 4.691860 CTGGATTTAACAGCTCCAACTG 57.308 45.455 0.00 0.00 43.59 3.16
4741 5587 1.172812 AAGCCGAGTCCCTTTTGCAC 61.173 55.000 0.00 0.00 0.00 4.57
4742 5588 0.467290 AAAGCCGAGTCCCTTTTGCA 60.467 50.000 0.00 0.00 0.00 4.08
4766 5612 4.706608 TGCGGGTGCCATGCGTAA 62.707 61.111 0.00 0.00 41.78 3.18
4780 5626 0.738389 AGTTGTTTCCACTGGTTGCG 59.262 50.000 0.00 0.00 0.00 4.85
4785 5631 4.733523 GCAAGTTACAGTTGTTTCCACTGG 60.734 45.833 5.14 0.00 35.93 4.00
4797 5643 5.576774 GCTTTCTTTTGTTGCAAGTTACAGT 59.423 36.000 0.00 0.00 0.00 3.55
4801 5647 5.719173 AGTGCTTTCTTTTGTTGCAAGTTA 58.281 33.333 0.00 0.00 35.34 2.24
4810 5656 5.189180 AGTCAGAAGAGTGCTTTCTTTTGT 58.811 37.500 15.62 2.14 39.22 2.83
4822 5668 0.172352 GCGCTGCTAGTCAGAAGAGT 59.828 55.000 15.59 0.00 45.72 3.24
4823 5669 0.172127 TGCGCTGCTAGTCAGAAGAG 59.828 55.000 9.73 6.66 45.72 2.85
4825 5671 1.649664 ATTGCGCTGCTAGTCAGAAG 58.350 50.000 9.73 10.34 45.72 2.85
4826 5672 2.099141 AATTGCGCTGCTAGTCAGAA 57.901 45.000 9.73 4.53 45.72 3.02
4830 5676 2.509870 GAACAAATTGCGCTGCTAGTC 58.490 47.619 9.73 0.00 0.00 2.59
4831 5677 1.200020 GGAACAAATTGCGCTGCTAGT 59.800 47.619 9.73 0.00 0.00 2.57
4833 5679 1.242989 TGGAACAAATTGCGCTGCTA 58.757 45.000 9.73 0.00 31.92 3.49
4834 5680 2.040330 TGGAACAAATTGCGCTGCT 58.960 47.368 9.73 0.00 31.92 4.24
4835 5681 4.651585 TGGAACAAATTGCGCTGC 57.348 50.000 9.73 0.00 31.92 5.25
4873 5719 2.354261 TGGGGTTAGGGTTAAGCTCT 57.646 50.000 4.41 3.05 38.34 4.09
4877 5723 4.643334 GCACTTTATGGGGTTAGGGTTAAG 59.357 45.833 0.00 0.00 0.00 1.85
4892 5738 8.043710 AGTCTGCAAAATAGAGTAGCACTTTAT 58.956 33.333 0.00 0.00 27.96 1.40
4895 5741 5.799213 AGTCTGCAAAATAGAGTAGCACTT 58.201 37.500 0.00 0.00 0.00 3.16
4899 5745 6.814146 AGTTGTAGTCTGCAAAATAGAGTAGC 59.186 38.462 4.81 0.00 32.35 3.58
4905 5751 6.646653 TCACTCAGTTGTAGTCTGCAAAATAG 59.353 38.462 4.81 5.61 33.48 1.73
4911 5757 5.654209 AGATATCACTCAGTTGTAGTCTGCA 59.346 40.000 5.32 0.00 33.48 4.41
4912 5758 6.142818 AGATATCACTCAGTTGTAGTCTGC 57.857 41.667 5.32 0.00 33.48 4.26
4913 5759 9.061435 TGATAGATATCACTCAGTTGTAGTCTG 57.939 37.037 5.32 0.00 37.76 3.51
4914 5760 9.283768 CTGATAGATATCACTCAGTTGTAGTCT 57.716 37.037 19.15 0.00 37.76 3.24
4915 5761 9.062524 ACTGATAGATATCACTCAGTTGTAGTC 57.937 37.037 23.93 2.23 44.39 2.59
4937 5793 1.168407 GCAGGAAGCTTGTGCACTGA 61.168 55.000 19.41 5.85 42.74 3.41
4977 5833 2.356125 GGTTCAGAATAAGAGGGCAGCA 60.356 50.000 0.00 0.00 0.00 4.41
4978 5834 2.293170 GGTTCAGAATAAGAGGGCAGC 58.707 52.381 0.00 0.00 0.00 5.25
4979 5835 2.239654 TGGGTTCAGAATAAGAGGGCAG 59.760 50.000 0.00 0.00 0.00 4.85
4980 5836 2.274542 TGGGTTCAGAATAAGAGGGCA 58.725 47.619 0.00 0.00 0.00 5.36
4981 5837 3.366052 TTGGGTTCAGAATAAGAGGGC 57.634 47.619 0.00 0.00 0.00 5.19
4984 5840 8.462016 CCTGTAAAATTGGGTTCAGAATAAGAG 58.538 37.037 0.00 0.00 0.00 2.85
4985 5841 7.396055 CCCTGTAAAATTGGGTTCAGAATAAGA 59.604 37.037 0.00 0.00 36.32 2.10
4986 5842 7.396055 TCCCTGTAAAATTGGGTTCAGAATAAG 59.604 37.037 0.00 0.00 41.58 1.73
4987 5843 7.177744 GTCCCTGTAAAATTGGGTTCAGAATAA 59.822 37.037 0.00 0.00 41.58 1.40
4989 5845 5.480422 GTCCCTGTAAAATTGGGTTCAGAAT 59.520 40.000 0.00 0.00 41.58 2.40
4991 5847 4.105697 AGTCCCTGTAAAATTGGGTTCAGA 59.894 41.667 0.00 0.00 41.58 3.27
4992 5848 4.218417 CAGTCCCTGTAAAATTGGGTTCAG 59.782 45.833 0.00 0.00 41.58 3.02
4994 5850 3.056821 GCAGTCCCTGTAAAATTGGGTTC 60.057 47.826 0.00 0.00 41.58 3.62
4995 5851 2.897326 GCAGTCCCTGTAAAATTGGGTT 59.103 45.455 0.00 0.00 41.58 4.11
4996 5852 2.110011 AGCAGTCCCTGTAAAATTGGGT 59.890 45.455 0.00 0.00 41.58 4.51
4998 5854 3.690460 AGAGCAGTCCCTGTAAAATTGG 58.310 45.455 0.00 0.00 33.43 3.16
4999 5855 4.142816 CGAAGAGCAGTCCCTGTAAAATTG 60.143 45.833 0.00 0.00 33.43 2.32
5000 5856 4.003648 CGAAGAGCAGTCCCTGTAAAATT 58.996 43.478 0.00 0.00 33.43 1.82
5001 5857 3.600388 CGAAGAGCAGTCCCTGTAAAAT 58.400 45.455 0.00 0.00 33.43 1.82
5002 5858 3.040147 CGAAGAGCAGTCCCTGTAAAA 57.960 47.619 0.00 0.00 33.43 1.52
5003 5859 2.743636 CGAAGAGCAGTCCCTGTAAA 57.256 50.000 0.00 0.00 33.43 2.01
5021 5894 2.498726 GAGCTTCAGAGAGGGGCG 59.501 66.667 0.00 0.00 0.00 6.13
5054 5952 2.072298 CGAGGAGCAACTTTTGGAGAG 58.928 52.381 0.00 0.00 0.00 3.20
5114 6018 1.647346 CATGCATTCCATTGTGTGCC 58.353 50.000 0.00 0.00 36.79 5.01
5163 6108 4.739195 TCCTTGTGTTTCCTTTGTTTTCG 58.261 39.130 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.